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Description

Generic GROMACS namespace.

Functionality for testing whether calls to mdrun produce the same energy and force quantities when they should do so.

Declares the integrators for energy minimization and NMA.

Convenience macro to help us avoid ifdefs each time we use sysconf.

Author
David van der Spoel david.nosp@m..van.nosp@m.dersp.nosp@m.oel@.nosp@m.icm.u.nosp@m.u.se

Namespaces

 compat
 Compatibility aliases for standard library features.
 
 test
 Testing utilities namespace.
 

Classes

class  AbstractAnalysisData
 Abstract base class for all objects that provide data. More...
 
class  AnalysisData
 Parallelizable data container for raw data. More...
 
class  AnalysisDataHandle
 Handle for inserting data into AnalysisData. More...
 
class  AbstractAnalysisArrayData
 Abstract base class for data objects that present in-memory data. More...
 
class  AnalysisArrayData
 Simple in-memory data array. More...
 
class  AnalysisDataValue
 Value type for representing a single value in analysis data objects. More...
 
class  AnalysisDataFrameHeader
 Value type for storing frame-level information for analysis data. More...
 
class  AnalysisDataPointSetRef
 Value type wrapper for non-mutable access to a set of data column values. More...
 
class  AnalysisDataFrameRef
 Value type wrapper for non-mutable access to a data frame. More...
 
class  IAnalysisDataModule
 Interface for a module that gets notified whenever data is added. More...
 
class  AnalysisDataModuleSerial
 Convenience base class for serial analysis data modules. More...
 
class  AnalysisDataModuleParallel
 Convenience base class for parallel analysis data modules. More...
 
class  AnalysisDataModuleManager
 Encapsulates handling of data modules attached to AbstractAnalysisData. More...
 
class  AnalysisDataStorageFrame
 Allows assigning values for a data frame in AnalysisDataStorage. More...
 
class  AnalysisDataStorage
 Helper class that implements storage of data. More...
 
class  ArrayRef
 STL-like interface to a C array of T (or part of a std container of T). More...
 
class  AnalysisDataAverageModule
 Data module for independently averaging each column in input data. More...
 
class  AnalysisDataFrameAverageModule
 Data module for averaging of columns for each frame. More...
 
class  AnalysisDataDisplacementModule
 Data module for calculating displacements. More...
 
class  AnalysisHistogramSettingsInitializer
 Provides "named parameter" idiom for constructing histograms. More...
 
class  AnalysisHistogramSettings
 Contains parameters that specify histogram bin locations. More...
 
class  AbstractAverageHistogram
 Base class for representing histograms averaged over frames. More...
 
class  AnalysisDataSimpleHistogramModule
 Data module for per-frame histograms. More...
 
class  AnalysisDataWeightedHistogramModule
 Data module for per-frame weighted histograms. More...
 
class  AnalysisDataBinAverageModule
 Data module for bin averages. More...
 
class  AnalysisDataLifetimeModule
 Data module for computing lifetime histograms for columns in input data. More...
 
class  AnalysisDataPlotSettings
 Common settings for data plots. More...
 
class  AbstractPlotModule
 Abstract data module for writing data into a file. More...
 
class  AnalysisDataPlotModule
 Plotting module for straightforward plotting of data. More...
 
class  AnalysisDataVectorPlotModule
 Plotting module specifically for data consisting of vectors. More...
 
class  AnalysisDataParallelOptions
 Parallelization options for analysis data objects. More...
 
class  Awh
 Coupling of the accelerated weight histogram method (AWH) with the system. More...
 
struct  DensityFittingModuleInfo
 Information about the density fitting module. More...
 
class  CommandLineHelpContext
 Context information for writing out command-line help. More...
 
class  GlobalCommandLineHelpContext
 Helper for passing CommandLineHelpContext into parse_common_args(). More...
 
class  CommandLineHelpWriter
 Writes help information for Options. More...
 
class  CommandLineModuleSettings
 Settings to pass information between a module and the general runner. More...
 
class  ICommandLineModule
 Module that can be run from command line using CommandLineModuleManager. More...
 
class  CommandLineModuleManager
 Implements a wrapper command-line interface for multiple modules. More...
 
class  CommandLineModuleGroup
 Handle to add content to a group added with CommandLineModuleManager::addModuleGroup(). More...
 
class  ICommandLineOptionsModuleSettings
 Settings to pass information between a CommandLineOptionsModule and generic code that runs it. More...
 
class  ICommandLineOptionsModule
 Module that can be run from a command line and uses gmx::Options for argument processing. More...
 
class  CommandLineParser
 Implements command-line parsing for Options objects. More...
 
class  IExecutableEnvironment
 Allows customization of the way various directories are found by CommandLineProgramContext. More...
 
class  CommandLineProgramContext
 Program context implementation for command line programs. More...
 
class  TrajectoryFileOpener
 Low level method to take care of only file opening and closing. More...
 
class  TrajectoryFrameWriter
 Writes coordinate frames to a sink, e.g. a trajectory file. More...
 
class  IOutputAdapter
 OutputAdapter class for handling trajectory file flag setting and processing. More...
 
class  OutputAdapterContainer
 Storage for output adapters that modify the state of a t_trxframe object. More...
 
class  OutputSelector
 OutputSelector class controls setting which coordinates are actually written. More...
 
class  SetAtoms
 SetAtoms class controls availability of atoms data. More...
 
class  SetBox
 Allows changing box information when writing a coordinate file. More...
 
class  SetForces
 SetForces class allows changing writing of forces to file. More...
 
class  SetPrecision
 SetPrecision class allows changing file writing precision. More...
 
class  SetStartTime
 SetStartTime class allows changing trajectory time information. More...
 
class  SetTimeStep
 SetTimeStep class allows changing trajectory time information. More...
 
class  SetVelocities
 SetVelocities class allows changing writing of velocities to file. More...
 
class  OutputRequirementOptionDirector
 Container for the user input values that will be used by the builder to determine which OutputAdapters should/could/will be registered to the coordinate file writer. More...
 
struct  OutputRequirements
 Finalized version of requirements after processing. More...
 
class  DomainDecompositionBuilder
 Builds a domain decomposition management object. More...
 
class  FixedCapacityVector
 Vector that behaves likes std::vector but has fixed capacity. More...
 
class  HashedMap
 Unordered key to value mapping. More...
 
class  GpuHaloExchange
 Manages GPU Halo Exchange object. More...
 
class  LocalAtomSet
 A local atom set collects local, global and collective indices of the home atoms on a rank. The indices of the home atoms are automatically updated during domain decomposition, thus gmx::LocalAtomSet::localIndex enables iteration over local atoms properties like coordinates or forces. TODO: add a LocalAtomSet iterator. More...
 
class  LocalAtomSetManager
 Hands out handles to local atom set indices and triggers index recalculation for all sets upon domain decomposition if run in parallel. More...
 
class  LocalTopologyChecker
 Has responsibility for checking that the local topology distributed across domains describes a total number of bonded interactions that matches the system topology. More...
 
struct  DomdecOptions
 Structure containing all (command line) options for the domain decomposition. More...
 
class  SeparatePmeRanksPermitted
 Class for managing usage of separate PME-only ranks. More...
 
class  PmeForceSenderGpu
 Manages sending forces from PME-only ranks to their PP ranks. More...
 
class  PmePpCommGpu
 Manages communication related to GPU buffers between this PME rank and its PP rank. More...
 
struct  MDModulesCheckpointReadingDataOnMaster
 Provides the MDModules with the checkpointed data on the master rank. More...
 
struct  MDModulesCheckpointReadingBroadcast
 Provides the MDModules with the communication record to broadcast. More...
 
struct  MDModulesWriteCheckpointData
 Writing the MDModules data to a checkpoint file. More...
 
class  MrcDensityMapOfFloatReader
 Read an mrc/ccp4 file that contains float values. More...
 
class  MrcDensityMapOfFloatFromFileReader
 Read an mrc density map from a given file. More...
 
class  MrcDensityMapOfFloatWriter
 Write an mrc/ccp4 file that contains float values. More...
 
struct  MrcDataStatistics
 Statistics about mrc data arrays. More...
 
struct  MrcDensitySkewData
 Skew matrix and translation. As named in "EMDB Map Distribution Format Description Version 1.01 (c) emdatabank.org 2014". More...
 
struct  CrystallographicLabels
 Crystallographic labels for mrc data. More...
 
struct  MrcDensityMapHeader
 A container for the data in mrc density map file formats. More...
 
class  ArrayRefWithPadding
 Interface to a C array of T (or part of a std container of T), that includes padding that is suitable for the kinds of SIMD operations GROMACS uses. More...
 
class  ListOfLists
 A list of lists, optimized for performance. More...
 
class  ClfftInitializer
 Handle clFFT library init and tear down in RAII style also with mutual exclusion. More...
 
class  DeviceStreamManager
 Device stream and context manager. More...
 
class  HostAllocationPolicy
 Policy class for configuring gmx::Allocator, to manage allocations of memory that may be needed for e.g. GPU transfers. More...
 
struct  OpenClTraits
 Stub for OpenCL type traits. More...
 
struct  OpenClTraitsBase
 Implements common trait infrastructure for OpenCL types. More...
 
struct  OpenClTraits< cl_context >
 Implements traits for cl_context. More...
 
struct  OpenClTraits< cl_command_queue >
 Implements traits for cl_command_queue. More...
 
struct  OpenClTraits< cl_program >
 Implements traits for cl_program. More...
 
struct  OpenClTraits< cl_kernel >
 Implements traits for cl_kernel. More...
 
class  ClHandle
 Wrapper of OpenCL type cl_type to implement RAII. More...
 
class  CpuInfo
 Detect CPU capabilities and basic logical processor info. More...
 
class  HardwareTopology
 Information about sockets, cores, threads, numa, caches. More...
 
struct  EnumerationArray
 Wrapper for a C-style array with size and indexing defined by an enum. Useful for declaring arrays of enum names for debug or other printing. An ArrayRef<DataType> may be constructed from an object of this type. More...
 
class  TranslateAndScale
 Transform coordinates in three dimensions by first translating, then scaling them. More...
 
class  AffineTransformation
 Affine transformation of three-dimensional coordinates. More...
 
class  DensitySimilarityMeasure
 Measure similarity and gradient between densities. More...
 
class  DensityFittingForce
 Manages evaluation of density-fitting forces for particles that were spread with a kernel. More...
 
struct  ExponentialMovingAverageState
 Store the state of exponential moving averages. More...
 
class  ExponentialMovingAverage
 Evaluate the exponential moving average with bias correction. More...
 
struct  GaussianSpreadKernelParameters
 Parameters for density spreading kernels. More...
 
class  GaussTransform3D
 Sums Gaussian values at three dimensional lattice coordinates. The Gaussian is defined as $A \frac{1}{\sigma^3 \sqrt(2^3\pi^3)} * \exp(-\frac{(x-x0)^2}{2 \sigma^2})$. More...
 
class  MultiDimArray
 Multidimensional array that manages its own memory. More...
 
class  PaddedVector
 PaddedVector is a container of elements in contiguous storage that allocates extra memory for safe SIMD-style loads for operations used in GROMACS. More...
 
class  CheckpointHandler
 Class handling the checkpoint signal. More...
 
class  Constraints
 Handles constraints. More...
 
class  MDAtoms
 Contains a C-style t_mdatoms while managing some of its memory with C++ vectors with allocators. More...
 
class  ResetHandler
 Class handling the reset of counters. More...
 
class  SettleData
 Data for executing SETTLE constraining. More...
 
struct  shakedata
 Working data for the SHAKE algorithm. More...
 
class  SimulationSignal
 POD-style object used by mdrun ranks to set and receive signals within and between simulations. More...
 
class  SimulationSignaller
 Object used by mdrun ranks to signal to each other at this step. More...
 
class  StopHandler
 Class handling the stop signal. More...
 
class  StopConditionSignal
 Class setting the stop signal based on gmx_get_stop_condition() More...
 
class  StopConditionTime
 Class setting the stop signal based on maximal run time. More...
 
class  StopHandlerBuilder
 Class preparing the creation of a StopHandler. More...
 
class  Update
 Contains data for update phase. More...
 
class  UpdateGroups
 Owns the update grouping and related data. More...
 
class  UpdateGroupsCog
 Class for managing and computing centers of geometry of update groups. More...
 
class  VirtualSitesHandler
 Class that handles construction of vsites and spreading of vsite forces. More...
 
class  WholeMoleculeTransform
 This class manages a coordinate buffer with molecules not split over periodic boundary conditions for use in force calculations which require whole molecules. More...
 
class  LegacyMdrunOptions
 This class provides the same command-line option functionality to both CLI and API sessions. More...
 
class  MDModules
 Manages the collection of all modules used for mdrun. More...
 
class  MembedHolder
 Membed SimulatorBuilder parameter type. More...
 
class  Mdrunner
 Runner object for supporting setup and execution of mdrun. More...
 
class  MdrunnerBuilder
 Build a gmx::Mdrunner. More...
 
class  SimulationContext
 Simulation environment and configuration. More...
 
struct  SimulatorConfig
 Simulation configuation settings. More...
 
struct  SimulatorStateData
 Data for a specific simulation state. More...
 
class  SimulatorEnv
 Collection of environmental information for a simulation. More...
 
class  Profiling
 Collection of profiling information. More...
 
class  ConstraintsParam
 Collection of constraint parameters. More...
 
class  LegacyInput
 Collection of legacy input information. More...
 
class  InteractiveMD
 SimulatorBuilder parameter type for InteractiveMD. More...
 
class  IonSwapping
 Parameter type for IonSwapping SimulatorBuilder component. More...
 
class  TopologyData
 Collection of handles to topology information. More...
 
class  BoxDeformationHandle
 Handle to information about the box. More...
 
class  SimulatorBuilder
 Class preparing the creation of Simulator objects. More...
 
class  accessor_basic
 The most basic memory access model for mdspan. More...
 
class  extents
 Multidimensional extents with static and dynamic dimensions. More...
 
class  layout_right
 Right-aligned array layout indexer. Carries the mapping class performing the translation from multidimensional index to one-dimensional number. More...
 
class  basic_mdspan
 Multidimensional array indexing and memory access with flexible mapping and access model. More...
 
class  CheckpointData
 } More...
 
struct  IsSerializableEnum
 { More...
 
class  ReadCheckpointDataHolder
 Holder for read checkpoint data. More...
 
class  WriteCheckpointDataHolder
 Holder for write checkpoint data. More...
 
class  ForceBuffersView
 A view of the force buffer. More...
 
class  ForceBuffers
 Object that holds the force buffers. More...
 
class  ForceWithShiftForces
 Container for force and virial for algorithms that compute shift forces for virial calculation. More...
 
class  ForceWithVirial
 Container for force and virial for algorithms that provide their own virial tensor contribution. More...
 
class  ForceOutputs
 Force and virial output buffers for use in force computation. More...
 
class  ForceProviderInput
 Helper struct that bundles data for passing it over to the force providers. More...
 
class  ForceProviderOutput
 Helper struct bundling the output data of a force provider. More...
 
class  IForceProvider
 Interface for a component that provides forces during MD. More...
 
class  ForceProviders
 Evaluates forces from a collection of gmx::IForceProvider. More...
 
class  IMDModule
 Extension module for GROMACS simulations. More...
 
class  IMDOutputProvider
 Interface for handling additional output files during a simulation. More...
 
class  IMdpOptionProvider
 Interface for handling mdp/tpr input to a mdrun module. More...
 
struct  MtsLevel
 Setting for a single level for multiple time step integration. More...
 
struct  GromppMtsOpts
 Struct for passing the MTS mdp options to setupMtsLevels() More...
 
class  ObservablesReducerBuilder
 Builder for ObservablesReducer. More...
 
class  ObservablesReducer
 Manage reduction of observables for registered subscribers. More...
 
class  StepWorkload
 Describes work done on this domain by the current rank that may change per-step. More...
 
class  DomainLifetimeWorkload
 Describes work done on this domain on every step of its lifetime, but which might change after the next domain paritioning. More...
 
class  SimulationWorkload
 Manage what computation is required during the simulation. More...
 
class  ModularSimulator
 The modular simulator. More...
 
class  ElementNotFoundError
 Exception class signalling that a requested element was not found. More...
 
class  MissingElementConnectionError
 Exception class signalling that elements were not connected properly. More...
 
class  SimulationAlgorithmSetupError
 Exception class signalling that the ModularSimulatorAlgorithm was set up in an incompatible way. More...
 
class  CheckpointError
 Exception class signalling an error in reading or writing modular checkpoints. More...
 
struct  BenchmarkSystem
 Description of the system used for benchmarking. More...
 
class  Range
 Defines a range of integer numbers and accompanying operations. More...
 
class  TextTableFormatter
 Formats rows of a table for text output. More...
 
class  HelpManager
 Helper for providing interactive online help. More...
 
class  AbstractSimpleHelpTopic
 Abstract base class for help topics that have simple text and no subtopics. More...
 
class  AbstractCompositeHelpTopic
 Abstract base class for help topics that have simple text and subtopics. More...
 
class  SimpleHelpTopic
 Template for simple implementation of AbstractSimpleHelpTopic. More...
 
class  CompositeHelpTopic
 Template for simple implementation of AbstractCompositeHelpTopic. More...
 
class  HelpLinks
 Hyperlink data for writing out help. More...
 
class  HelpWriterContext
 Context information for writing out help. More...
 
class  IHelpTopic
 Provides a single online help topic. More...
 
class  OptionStorageTemplate
 Templated base class for constructing option value storage classes. More...
 
class  AbstractOption
 Abstract base class for specifying option properties. More...
 
class  OptionTemplate
 Templated base class for constructing concrete option settings classes. More...
 
class  OptionInfo
 Gives information and allows modifications to an option after creation. More...
 
class  AbstractOptionStorage
 Abstract base class for converting, validating, and storing option values. More...
 
class  AbstractOptionSection
 Base class for specifying option section properties. More...
 
class  AbstractOptionSectionHandle
 Base class for handles to option sections. More...
 
class  BooleanOption
 Specifies an option that provides boolean values. More...
 
class  IntegerOption
 Specifies an option that provides integer values. More...
 
class  Int64Option
 Specifies an option that provides 64-bit integer values. More...
 
class  DoubleOption
 Specifies an option that provides floating-point (double) values. More...
 
class  FloatOption
 Specifies an option that provides floating-point (float) values. More...
 
class  StringOption
 Specifies an option that provides string values. More...
 
class  EnumOption
 Specifies an option that accepts an EnumerationArray of string values and writes the selected index into an enum variable. More...
 
class  LegacyEnumOption
 Specifies an option that accepts enumerated string values and writes the selected index into an enum variable. More...
 
class  BooleanOptionInfo
 Wrapper class for accessing boolean option information. More...
 
class  IntegerOptionInfo
 Wrapper class for accessing integer option information. More...
 
class  Int64OptionInfo
 Wrapper class for accessing 64-bit integer option information. More...
 
class  DoubleOptionInfo
 Wrapper class for accessing floating-point option information. More...
 
class  FloatOptionInfo
 Wrapper class for accessing floating-point option information. More...
 
class  StringOptionInfo
 Wrapper class for accessing string option information. More...
 
class  EnumOptionInfo
 Wrapper class for accessing enum option information. More...
 
class  OptionsBehaviorCollection
 Container for IOptionsBehavior objects. More...
 
class  FileNameOption
 Specifies an option that provides file names. More...
 
class  FileNameOptionInfo
 Wrapper class for accessing file name option information. More...
 
class  FileNameOptionManager
 Handles interaction of file name options with global options. More...
 
class  IOptionsBehavior
 Interface to provide extension points for options parsing. More...
 
class  IOptionsContainer
 Interface for adding input options. More...
 
class  IOptionsContainerWithSections
 Interface for adding input options with sections. More...
 
class  OptionManagerContainer
 Container to keep managers added with Options::addManager() and pass them to options. More...
 
class  IOptionManager
 Base class for option managers. More...
 
class  Options
 Collection of options. More...
 
class  OptionsAssigner
 Decorator class for assigning values to Options. More...
 
class  OptionSection
 Declares a simple option section. More...
 
class  OptionSectionHandle
 Allows adding options to an OptionSection. More...
 
class  OptionStorageTemplateSimple
 Simplified option storage template for options that have one-to-one value conversion. More...
 
class  OptionsVisitor
 Pure interface for visiting options in a Options object. More...
 
class  OptionsTypeVisitor
 Abstract base class for visiting options of a particular type. More...
 
class  OptionsIterator
 Decorator class for visiting options in a Options object. More...
 
class  OptionsModifyingVisitor
 Pure interface for visiting options in a Options object, allowing modifications. More...
 
class  OptionsModifyingTypeVisitor
 Abstract base class for visiting options of a particular type, allowing modifications. More...
 
class  OptionsModifyingIterator
 Decorator class for visiting options in a Options object, allowing changes. More...
 
class  RepeatingOptionSectionHandle
 Allows adding options to an RepeatingOptionSection. More...
 
class  RepeatingOptionSection
 Declares an option section that creates a structure for each instance. More...
 
class  TimeUnitManager
 Provides common functionality for time unit conversions. More...
 
class  TimeUnitBehavior
 Options behavior to add a time unit option. More...
 
class  OptionValueConverterSimple
 Helper for converting from Any to a given type. More...
 
class  PullCoordExpressionParser
 Class with a mathematical expression and parser. More...
 
class  ExponentialDistribution
 Exponential distribution. More...
 
class  GammaDistribution
 Gamma distribution. More...
 
class  NormalDistribution
 Normal distribution. More...
 
class  TabulatedNormalDistribution
 Tabulated normal random distribution. More...
 
class  ThreeFry2x64General
 General implementation class for ThreeFry counter-based random engines. More...
 
class  ThreeFry2x64
 ThreeFry2x64 random engine with 20 iteractions. More...
 
class  ThreeFry2x64Fast
 ThreeFry2x64 random engine with 13 iteractions. More...
 
class  UniformIntDistribution
 Uniform integer distribution. More...
 
class  UniformRealDistribution
 Uniform real distribution. More...
 
class  RestraintManager
 Manage the Restraint potentials available for Molecular Dynamics. More...
 
class  RestraintMDModule
 MDModule wrapper for Restraint implementations. More...
 
class  Site
 Abstraction for a restraint interaction site. More...
 
class  AnalysisNeighborhoodPositions
 Input positions for neighborhood searching. More...
 
class  AnalysisNeighborhood
 Neighborhood searching for analysis tools. More...
 
class  AnalysisNeighborhoodPair
 Value type to represent a pair of positions found in neighborhood searching. More...
 
class  AnalysisNeighborhoodSearch
 Initialized neighborhood search with a fixed set of reference positions. More...
 
class  AnalysisNeighborhoodPairSearch
 Initialized neighborhood pair search with a fixed set of positions. More...
 
class  Selection
 Provides access to a single selection. More...
 
class  SelectionPosition
 Provides access to information about a single selected position. More...
 
class  SelectionCollection
 Collection of selections. More...
 
struct  SelectionTopologyProperties
 Describes topology properties required for selection evaluation. More...
 
class  SelectionFileOption
 Specifies a special option that provides selections from a file. More...
 
class  SelectionFileOptionInfo
 Wrapper class for accessing and modifying selection file option information. More...
 
class  SelectionOption
 Specifies an option that provides selection(s). More...
 
class  SelectionOptionInfo
 Wrapper class for accessing and modifying selection option information. More...
 
class  ITopologyProvider
 Provides topology information to SelectionOptionBehavior. More...
 
class  SelectionOptionBehavior
 Options behavior to allow using SelectionOptions. More...
 
class  SelectionOptionManager
 Handles interaction of selection options with other options and user input. More...
 
class  Simd4Double
 SIMD4 double type. More...
 
class  Simd4DBool
 SIMD4 variable type to use for logical comparisons on doubles. More...
 
class  Simd4Float
 SIMD4 float type. More...
 
class  Simd4FBool
 SIMD4 variable type to use for logical comparisons on floats. More...
 
class  SimdDouble
 Double SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1. More...
 
class  SimdDInt32
 Integer SIMD variable type to use for conversions to/from double. More...
 
class  SimdDBool
 Boolean type for double SIMD data. More...
 
class  SimdDIBool
 Boolean type for integer datatypes corresponding to double SIMD. More...
 
class  SimdFloat
 Float SIMD variable. Available if GMX_SIMD_HAVE_FLOAT is 1. More...
 
class  SimdFInt32
 Integer SIMD variable type to use for conversions to/from float. More...
 
class  SimdFBool
 Boolean type for float SIMD data. More...
 
class  SimdFIBool
 Boolean type for integer datatypes corresponding to float SIMD. More...
 
struct  SimdFloatTag
 Tag type to select to load SimdFloat with simdLoad(U) More...
 
struct  SimdDoubleTag
 Tag type to select to load SimdDouble with simdLoad(U) More...
 
struct  SimdFInt32Tag
 Tag type to select to load SimdFInt32 with simdLoad(U) More...
 
struct  SimdDInt32Tag
 Tag type to select to load SimdDInt32 with simdLoad(U) More...
 
struct  AlignedArray< float, N >
 Identical to std::array with GMX_SIMD_FLOAT_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual). More...
 
struct  AlignedArray< double, N >
 Identical to std::array with GMX_SIMD_DOUBLE_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual). More...
 
class  SimdSetZeroProxy
 Proxy object to enable setZero() for SIMD and real types. More...
 
class  CubicSplineTable
 Cubic spline interpolation table. More...
 
class  QuadraticSplineTable
 Quadratic spline interpolation table. More...
 
struct  AnalyticalSplineTableInput
 Specification for analytical table function (name, function, derivative) More...
 
struct  NumericalSplineTableInput
 Specification for vector table function (name, function, derivative, spacing) More...
 
struct  DevelopmentFeatureFlags
 Structure that holds boolean flags corresponding to the development features present enabled through environment variables. More...
 
struct  GpuTaskMapping
 Specifies the GPU deviceID_ available for task_ to use. More...
 
class  GpuTaskAssignmentsBuilder
 Builder for the GpuTaskAssignments for all ranks on this node. More...
 
class  GpuTaskAssignments
 Contains the GPU task assignment for all ranks on this physical node. More...
 
class  ConvertTprInfo
 Declares gmx convert-tpr. More...
 
class  RangePartitioning
 Division of a range of indices into consecutive blocks. More...
 
struct  ExclusionBlock
 Describes exclusions for a single atom. More...
 
class  TrajectoryAnalysisModuleData
 Base class for thread-local data storage during trajectory analysis. More...
 
class  TrajectoryAnalysisModule
 Base class for trajectory analysis modules. More...
 
class  TrajectoryAnalysisSettings
 Trajectory analysis module configuration object. More...
 
class  TrajectoryAnalysisCommandLineRunner
 Runner for command-line trajectory analysis tools. More...
 
class  UnionFinder
 Union-find data structure for keeping track of disjoint sets. More...
 
class  MappedUnionFinder
 Extension of UnionFind that supports non-consecutive integer indices as items. More...
 
class  TopologyInformation
 Topology information available to a trajectory analysis module. More...
 
class  AlignedAllocationPolicy
 Policy class for configuring gmx::Allocator, to manage allocations of aligned memory for SIMD code. More...
 
class  PageAlignedAllocationPolicy
 Policy class for configuring gmx::Allocator, to manage allocations of page-aligned memory that can be locked for asynchronous transfer to GPU devices. More...
 
class  Allocator
 Policy-based memory allocator. More...
 
class  Any
 Represents a dynamically typed value of an arbitrary type - deprecated. More...
 
class  BinaryInformationSettings
 Settings for printBinaryInformation(). More...
 
class  DataFileOptions
 Search parameters for DataFileFinder. More...
 
struct  DataFileInfo
 Information about a data file found by DataFileFinder::enumerateFiles(). More...
 
class  DataFileFinder
 Searches data files from a set of paths. More...
 
class  DefaultInitializationAllocator
 Allocator adaptor that interposes construct() calls to convert value initialization into default initialization. More...
 
class  DirectoryEnumerator
 Lists files in a directory. More...
 
class  EnumerationIterator
 Allows iterating sequential enumerators. More...
 
class  EnumerationWrapper
 Allows constructing iterators for looping over sequential enumerators. More...
 
class  IFileInputRedirector
 Allows overriding file existence checks from code that supports it. More...
 
class  IFileOutputRedirector
 Allows capturing stdout and file output from code that supports it. More...
 
class  StandardInputStream
 Text input stream implementation for reading from stdin. More...
 
class  TextInputFile
 Text input stream implementation for reading from a file. More...
 
class  TextOutputFile
 Text output stream implementation for writing to a file. More...
 
class  FlagsTemplate
 Template class for typesafe handling of combination of flags. More...
 
class  ISerializer
 Interface for types that convert standard data types into a form suitable for storage or transfer. More...
 
class  KeyValueTreePath
 Identifies an entry in a key-value tree. More...
 
class  KeyValueTreeBuilder
 Root builder for creating trees that have an object at the root. More...
 
class  KeyValueTreeValueBuilder
 Builder for KeyValueTreeValue objects. More...
 
class  KeyValueTreeUniformArrayBuilder
 Builder for KeyValueTreeArray objects where all elements are of type T. More...
 
class  KeyValueTreeObjectArrayBuilder
 Builder for KeyValueTreeArray objects where all elements are KeyValueTreeObject objects. More...
 
class  KeyValueTreeObjectBuilder
 Builder for KeyValueTreeObject objects. More...
 
class  IKeyValueTreeTransformRules
 Interface to declare rules for transforming key-value trees. More...
 
class  KeyValueTreeTransformRulesScoped
 Helper object returned from IKeyValueTreeTransformRules::scopedTransform(). More...
 
class  KeyValueTreeTransformRuleBuilder
 Provides methods to specify one transformation rule. More...
 
class  ILogTarget
 Target where log output can be written. More...
 
class  LogEntryWriter
 Helper class for creating log entries with GMX_LOG. More...
 
class  LogLevelHelper
 Represents a single logging level. More...
 
class  MDLogger
 Declares a logging interface. More...
 
class  LoggerBuilder
 Initializes loggers. More...
 
class  LoggerOwner
 Manages memory for a logger built with LoggerBuilder. More...
 
class  MDModulesNotifier
 Organizes notifications about an event of interest to modules. More...
 
struct  BuildMDModulesNotifier< CurrentCallParameter, CallParameter...>
 Template specialization to assemble MDModulesNotifier. More...
 
struct  MDModulesEnergyOutputToDensityFittingRequestChecker
 Check if module outputs energy to a specific field. More...
 
struct  MDModulesEnergyOutputToQMMMRequestChecker
 Check if QMMM module outputs energy to a specific field. More...
 
class  EnergyCalculationFrequencyErrors
 Collect errors for the energy calculation frequency. More...
 
struct  SimulationTimeStep
 Provides the simulation time step in ps. More...
 
struct  CoordinatesAndBoxPreprocessed
 Provides coordinates and simulation box. More...
 
struct  MdRunInputFilename
 Mdrun input filename. More...
 
struct  QMInputFileName
 Notification for QM program input filename provided by user as command-line argument for grompp. More...
 
struct  MDModulesNotifiers
 Group of notifers to organize that MDModules can receive callbacks they subscribe to. More...
 
class  MessageStringCollector
 Helper class for collecting message strings, optionally with context. More...
 
class  MessageStringContext
 Convenience class for creating a message context. More...
 
struct  no_delete
 Deleter for std::shared_ptr that does nothing. More...
 
class  PhysicalNodeCommunicator
 Holds a communicator for the physical node of this rank. More...
 
struct  InstallationPrefixInfo
 Provides information about installation prefix (see IProgramContext::installationPrefix()). More...
 
class  IProgramContext
 Provides context information about the program that is calling the library. More...
 
class  StringCompare
 Compare object for std::string STL containers and algorithms that supports run-time decision on how to compare. More...
 
class  StringOutputStream
 Text output stream implementation for writing to an in-memory string. More...
 
class  StringInputStream
 Helper class to convert static string data to a stream. More...
 
class  StringToEnumValueConverter
 A class to convert a string to an enum value of type EnumType. More...
 
class  StringFormatter
 Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms. More...
 
class  IdentityFormatter
 Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further. More...
 
class  EqualCaseInsensitive
 Function object for comparisons with equalCaseInsensitive. More...
 
class  TextLineWrapperSettings
 Stores settings for line wrapping. More...
 
class  TextLineWrapper
 Wraps lines to a predefined length. More...
 
class  TextReader
 Reads text from a TextInputStream. More...
 
class  TextInputStream
 Interface for reading text. More...
 
class  TextOutputStream
 Interface for writing text. More...
 
class  TextWriter
 Writes text into a TextOutputStream. More...
 
struct  isIntegralConstant
 Is true if type is a std::integral_constant. More...
 
class  NonbondedBenchmarkInfo
 Declares gmx nonbonded-bench. More...
 
class  BasicVector
 C++ class for 3D vectors. More...
 
struct  StaticLog2
 Evaluate log2(n) for integer n statically at compile time. More...
 
struct  StaticLog2< 1 >
 Specialization of StaticLog2<n> for n==1. More...
 
struct  StaticLog2< 0 >
 Specialization of StaticLog2<n> for n==0. More...
 
class  PotentialPointData
 Structure to hold the results of IRestraintPotential::evaluate(). More...
 
class  IRestraintPotential
 Interface for Restraint potentials. More...
 
class  ExceptionInfo
 Stores additional context information for exceptions. More...
 
class  ExceptionInitializer
 Provides information for Gromacs exception constructors. More...
 
class  GromacsException
 Base class for all exception objects in Gromacs. More...
 
class  FileIOError
 Exception class for file I/O errors. More...
 
class  UserInputError
 Exception class for user input errors. More...
 
class  InvalidInputError
 Exception class for situations where user input cannot be parsed/understood. More...
 
class  InconsistentInputError
 Exception class for situations where user input is inconsistent. More...
 
class  ToleranceError
 Exception class when a specified tolerance cannot be achieved. More...
 
class  SimulationInstabilityError
 Exception class for simulation instabilities. More...
 
class  InternalError
 Exception class for internal errors. More...
 
class  APIError
 Exception class for incorrect use of an API. More...
 
class  RangeError
 Exception class for out-of-range values or indices. More...
 
class  NotImplementedError
 Exception class for use of an unimplemented feature. More...
 
class  ParallelConsistencyError
 Exception class for use when ensuring that MPI ranks to throw in a coordinated fashion. More...
 
class  ModularSimulatorError
 Exception class for modular simulator. More...
 

Typedefs

typedef std::shared_ptr
< IAnalysisDataModule
AnalysisDataModulePointer
 Smart pointer for managing a generic analysis data module.
 
typedef ArrayRef< const
AnalysisDataValue
AnalysisDataValuesRef
 Shorthand for reference to an array of data values.
 
typedef std::shared_ptr
< AnalysisDataAverageModule
AnalysisDataAverageModulePointer
 Smart pointer to manage an AnalysisDataAverageModule object.
 
typedef std::shared_ptr
< AnalysisDataFrameAverageModule
AnalysisDataFrameAverageModulePointer
 Smart pointer to manage an AnalysisDataFrameAverageModule object.
 
typedef std::shared_ptr
< AnalysisDataDisplacementModule
AnalysisDataDisplacementModulePointer
 Smart pointer to manage an AnalysisDataDisplacementModule object.
 
typedef std::unique_ptr
< AbstractAverageHistogram
AverageHistogramPointer
 Smart pointer to manage an AbstractAverageHistogram object.
 
typedef std::shared_ptr
< AnalysisDataSimpleHistogramModule
AnalysisDataSimpleHistogramModulePointer
 Smart pointer to manage an AnalysisDataSimpleHistogramModule object.
 
typedef std::shared_ptr
< AnalysisDataWeightedHistogramModule
AnalysisDataWeightedHistogramModulePointer
 Smart pointer to manage an AnalysisDataWeightedHistogramModule object.
 
typedef std::shared_ptr
< AnalysisDataBinAverageModule
AnalysisDataBinAverageModulePointer
 Smart pointer to manage an AnalysisDataBinAverageModule object.
 
typedef std::shared_ptr
< AnalysisDataLifetimeModule
AnalysisDataLifetimeModulePointer
 Smart pointer to manage an AnalysisDataLifetimeModule object.
 
typedef std::shared_ptr
< AnalysisDataPlotModule
AnalysisDataPlotModulePointer
 Smart pointer to manage an AnalysisDataPlotModule object.
 
typedef std::shared_ptr
< AnalysisDataVectorPlotModule
AnalysisDataVectorPlotModulePointer
 Smart pointer to manage an AnalysisDataVectorPlotModule object.
 
typedef double awh_dvec [c_biasMaxNumDim]
 A real vector in AWH coordinate space.
 
typedef int awh_ivec [c_biasMaxNumDim]
 An integer vector in AWH coordinate space.
 
typedef int force_env_t
 Type for CP2K force environment handle.
 
typedef std::unique_ptr
< ICommandLineModule
CommandLineModulePointer
 Smart pointer type for managing a ICommandLineModule.
 
typedef std::map< std::string,
CommandLineModulePointer
CommandLineModuleMap
 Container type for mapping module names to module objects.
 
typedef std::unique_ptr
< CommandLineModuleGroupData > 
CommandLineModuleGroupDataPointer
 Smart pointer type for managing a CommandLineModuleGroup.
 
typedef std::vector
< CommandLineModuleGroupDataPointer
CommandLineModuleGroupList
 Container type for keeping a list of module groups.
 
typedef std::unique_ptr
< ICommandLineOptionsModule
ICommandLineOptionsModulePointer
 Smart pointer to manage an ICommandLineOptionsModule.
 
typedef std::unique_ptr
< IExecutableEnvironment
ExecutableEnvironmentPointer
 Shorthand for a smart pointer to IExecutableEnvironment.
 
using TrajectoryFrameWriterPointer = std::unique_ptr< TrajectoryFrameWriter >
 Smart pointer to manage the TrajectoryFrameWriter object.
 
using OutputAdapterPointer = std::unique_ptr< IOutputAdapter >
 Smart pointer to manage the frame adapter object.
 
using OutputSelectorPointer = std::unique_ptr< OutputSelector >
 Smart pointer to manage the object.
 
using SetAtomsPointer = std::unique_ptr< SetAtoms >
 Smart pointer to manage the object.
 
using SetBoxPointer = std::unique_ptr< SetBox >
 Smart pointer to manage the object.
 
using SetForcesPointer = std::unique_ptr< SetForces >
 Smart pointer to manage the object.
 
using SetPrecisionPointer = std::unique_ptr< SetPrecision >
 Smart pointer to manage the outputselector object.
 
using SetStartTimePointer = std::unique_ptr< SetStartTime >
 Smart pointer to manage the object.
 
using SetTimeStepPointer = std::unique_ptr< SetTimeStep >
 Smart pointer to manage the object.
 
using SetVelocitiesPointer = std::unique_ptr< SetVelocities >
 Smart pointer to manage the object.
 
typedef struct
gmx::CacheLineAlignedFlag 
CacheLineAlignedFlag
 
template<class T >
using HostAllocator = Allocator< T, HostAllocationPolicy >
 Memory allocator that uses HostAllocationPolicy. More...
 
template<class T >
using HostVector = std::vector< T, HostAllocator< T >>
 Convenience alias for std::vector that uses HostAllocator.
 
template<class T >
using PaddedHostVector = PaddedVector< T, HostAllocator< T >>
 Convenience alias for PaddedVector that uses HostAllocator.
 
template<class ElementType >
using BasicMatrix3x3 = MultiDimArray< std::array< ElementType, 3 *3 >, extents< 3, 3 >>
 Three-by-three matrix of ElementType. More...
 
using Matrix3x3 = BasicMatrix3x3< real >
 Three-by-three real number matrix. More...
 
using Matrix3x3Span = Matrix3x3::view_type
 Convenience alias for a matrix view.
 
using Matrix3x3ConstSpan = Matrix3x3::const_view_type
 Convenience alias for a const matrix view.
 
using mode = sycl::access_mode
 
typedef std::array
< SimulationSignal, eglsNR > 
SimulationSignals
 Convenience typedef for the group of signals used.
 
using VirialHandling = VirtualSitesHandler::VirialHandling
 VirialHandling is often used outside VirtualSitesHandler class members.
 
typedef std::array
< std::vector< int >
, c_ftypeVsiteEnd-c_ftypeVsiteStart
VsitePbc
 Type for storing PBC atom information for all vsite types in the system.
 
using SimulatorFunctionType ) = void(
 Function type for simulator code.
 
using LogFilePtr = std::unique_ptr< t_fileio, functor_wrapper< t_fileio, closeLogFile >>
 Simple guard pointer See unique_cptr for details.
 
using dynamicExtents2D = extents< dynamic_extent, dynamic_extent >
 Convenience type for often-used two dimensional extents.
 
using dynamicExtents3D = extents< dynamic_extent, dynamic_extent, dynamic_extent >
 Convenience type for often-used three dimensional extents.
 
template<class T , ptrdiff_t... Indices>
using mdspan = basic_mdspan< T, extents< Indices...>, layout_right, accessor_basic< T >>
 basic_mdspan with wrapped indices, basic_accessor policiy and right-aligned memory layout.
 
using ReadCheckpointData = CheckpointData< CheckpointDataOperation::Read >
 Convenience shortcut for reading checkpoint data.
 
using WriteCheckpointData = CheckpointData< CheckpointDataOperation::Write >
 Convenience shortcut for writing checkpoint data.
 
using Step = int64_t
 Step number.
 
typedef std::function< void()> CheckBondedInteractionsCallback
 The function type allowing to request a check of the number of bonded interactions.
 
using EnergyContribution = std::function< real(Step, Time)>
 Function type for elements contributing energy.
 
using Time = double
 Simulation time.
 
typedef std::function< void()> SimulatorRunFunction
 The function type that can be scheduled to be run during the simulator run.
 
typedef std::function< void(SimulatorRunFunction)> RegisterRunFunction
 The function type that allows to register run functions.
 
typedef std::function< void(Step,
Time, const
RegisterRunFunction &)> 
SchedulingFunction
 The function type scheduling run functions for a step / time using a RegisterRunFunction reference.
 
typedef std::function< void(Step,
Time)> 
SignallerCallback
 The function type that can be registered to signallers for callback.
 
typedef std::function< void(gmx_mdoutf
*, Step, Time, bool, bool)> 
ITrajectoryWriterCallback
 Function type for trajectory writing clients.
 
typedef std::function< void(Step)> PropagatorCallback
 Generic callback to the propagator.
 
typedef std::function< void()> DomDecCallback
 Callback used by the DomDecHelper object to inform clients about system re-partitioning.
 
using ReferenceTemperatureCallback = std::function< void(ArrayRef< const real >, ReferenceTemperatureChangeAlgorithm algorithm)>
 Callback updating the reference temperature.
 
typedef std::unique_ptr
< AbstractCompositeHelpTopic
CompositeHelpTopicPointer
 Smart pointer type to manage a AbstractCompositeHelpTopic object.
 
typedef std::unique_ptr
< IHelpTopic
HelpTopicPointer
 Smart pointer type to manage a IHelpTopic object.
 
typedef FloatOption RealOption
 Typedef for either DoubleOption or FloatOption, depending on precision. More...
 
typedef FloatOptionInfo RealOptionInfo
 Typedef for either DoubleOptionInfo or FloatOptionInfo, depending on precision. More...
 
typedef std::shared_ptr
< IOptionsBehavior
OptionsBehaviorPointer
 Smart pointer for behaviors stored in OptionsBehaviorCollection.
 
typedef FlagsTemplate< OptionFlagOptionFlags
 Holds a combination of OptionFlag values.
 
typedef std::random_device RandomDevice
 Random device. More...
 
typedef ThreeFry2x64Fast DefaultRandomEngine
 Default fast and accurate random engine in Gromacs. More...
 
typedef std::list
< SelectionParserValue > 
SelectionParserValueList
 Container for a list of SelectionParserValue objects.
 
typedef std::unique_ptr
< SelectionParserValueList
SelectionParserValueListPointer
 Smart pointer type for managing a SelectionParserValueList.
 
typedef std::list
< SelectionParserParameter > 
SelectionParserParameterList
 Container for a list of SelectionParserParameter objects.
 
typedef std::unique_ptr
< SelectionParserParameterList
SelectionParserParameterListPointer
 Smart pointer type for managing a SelectionParserParameterList.
 
typedef std::vector< SelectionSelectionList
 Container of selections used in public selection interfaces.
 
typedef std::unique_ptr
< internal::SelectionData > 
SelectionDataPointer
 Smart pointer for managing an internal selection data object.
 
typedef std::vector
< SelectionDataPointer
SelectionDataList
 Container for storing a list of selections internally.
 
typedef std::shared_ptr
< SelectionTreeElement > 
SelectionTreeElementPointer
 Smart pointer type for selection tree element pointers.
 
using GpuTasksOnRanks = std::vector< std::vector< GpuTask >>
 Container of compute tasks suitable to run on a GPU e.g. on each rank of a node.
 
using GpuTaskAssignment = std::vector< GpuTaskMapping >
 Container of GPU tasks on a rank, specifying the task type and GPU device ID, e.g. potentially ready for consumption by the modules on that rank.
 
using BoxMatrix = std::array< std::array< real, DIM >, DIM >
 A 3x3 matrix data type useful for simulation boxes. More...
 
typedef std::unique_ptr
< TrajectoryAnalysisModuleData
TrajectoryAnalysisModuleDataPointer
 Smart pointer to manage a TrajectoryAnalysisModuleData object.
 
typedef std::unique_ptr
< TrajectoryAnalysisModule
TrajectoryAnalysisModulePointer
 Smart pointer to manage a TrajectoryAnalysisModule.
 
template<class T >
using AlignedAllocator = Allocator< T, AlignedAllocationPolicy >
 Aligned memory allocator. More...
 
template<class T >
using PageAlignedAllocator = Allocator< T, PageAlignedAllocationPolicy >
 PageAligned memory allocator. More...
 
using FilePtr = std::unique_ptr< FILE, functor_wrapper< FILE, fclose_wrapper >>
 Simple guard pointer which calls fclose. See unique_cptr for details.
 
using MPI_Comm_ptr = gmx::unique_cptr< MPI_Comm, MPI_Comm_free_wrapper >
 Make a smart pointer for MPI communicators.
 
typedef std::shared_ptr
< TextInputStream
TextInputStreamPointer
 Shorthand for a smart pointer to a TextInputStream.
 
typedef std::shared_ptr
< TextOutputStream
TextOutputStreamPointer
 Shorthand for a smart pointer to a TextOutputStream.
 
template<typename T , void D = sfree_wrapper>
using unique_cptr = std::unique_ptr< T, functor_wrapper< T, D >>
 unique_ptr which takes function pointer (has to return void) as template argument
 
typedef unique_cptr< void > sfree_guard
 Simple guard which calls sfree. See unique_cptr for details.
 
typedef BasicVector< realRVec
 Shorthand for C++ rvec-equivalent type.
 
typedef BasicVector< double > DVec
 Shorthand for C++ dvec-equivalent type.
 
typedef BasicVector< int > IVec
 Shorthand for C++ ivec-equivalent type.
 
using Vector = ::gmx::RVec
 Provide a vector type name with a more stable interface than RVec and a more stable implementation than vec3<>.
 
using index = std::ptrdiff_t
 Integer type for indexing into arrays or vectors. More...
 
typedef ExceptionInfo< struct
ExceptionInfoErrno_, int > 
ExceptionInfoErrno
 Stores errno value that triggered the exception.
 
typedef ExceptionInfo< struct
ExceptionInfoApiFunc_, const
char * > 
ExceptionInfoApiFunction
 Stores the function name that returned the errno in ExceptionInfoErrno.
 
typedef ExceptionInfo< struct
ExceptionInfoLocation_,
ThrowLocation > 
ExceptionInfoLocation
 Stores the location where the exception was thrown.
 
using ClContext = ClHandle< cl_context >
 Convenience declarations.
 
using ClCommandQueue = ClHandle< cl_command_queue >
 
using ClProgram = ClHandle< cl_program >
 
using ClKernel = ClHandle< cl_kernel >
 

Enumerations

enum  AwhOutputEntryType {
  AwhOutputEntryType::MetaData, AwhOutputEntryType::CoordValue, AwhOutputEntryType::Pmf, AwhOutputEntryType::Bias,
  AwhOutputEntryType::Visits, AwhOutputEntryType::Weights, AwhOutputEntryType::Target, AwhOutputEntryType::ForceCorrelationVolume,
  AwhOutputEntryType::FrictionTensor
}
 Enum with the AWH variables to write. More...
 
enum  AwhOutputMetaData { AwhOutputMetaData::NumBlock, AwhOutputMetaData::TargetError, AwhOutputMetaData::ScaledSampleWeight, AwhOutputMetaData::Count }
 Enum with the types of metadata to write. More...
 
enum  Normalization { Normalization::None, Normalization::Coordinate, Normalization::FreeEnergy, Normalization::Distribution }
 Enum with different ways of normalizing the output. More...
 
enum  DensityFittingAmplitudeMethod : int { DensityFittingAmplitudeMethod::Unity, DensityFittingAmplitudeMethod::Mass, DensityFittingAmplitudeMethod::Charge, Count }
 The methods that determine how amplitudes are spread on a grid in density guided simulations. More...
 
enum  QMMMQMMethod { QMMMQMMethod::PBE, QMMMQMMethod::BLYP, QMMMQMMethod::INPUT, Count }
 Enumerator for supported QM methods Also could be INPUT which means external input file provided with the name determined by QMMMParameters::qminputfilename_. More...
 
enum  CoordinateFileFlags : unsigned long {
  CoordinateFileFlags::Base = 1 << 0, CoordinateFileFlags::RequireForceOutput = 1 << 1, CoordinateFileFlags::RequireVelocityOutput = 1 << 2, CoordinateFileFlags::RequireAtomConnections = 1 << 3,
  CoordinateFileFlags::RequireAtomInformation = 1 << 4, CoordinateFileFlags::RequireChangedOutputPrecision = 1 << 5, CoordinateFileFlags::RequireNewFrameStartTime = 1 << 6, CoordinateFileFlags::RequireNewFrameTimeStep = 1 << 7,
  CoordinateFileFlags::RequireNewBox = 1 << 8, CoordinateFileFlags::RequireCoordinateSelection = 1 << 9, CoordinateFileFlags::Count
}
 The enums here define the flags specifying the requirements of different outputadapter modules. More...
 
enum  ChangeSettingType : int { PreservedIfPresent, Always, Never, Count }
 Enum class for setting basic flags in a t_trxframe.
 
enum  ChangeAtomsType {
  PreservedIfPresent, AlwaysFromStructure, Never, Always,
  Count
}
 Enum class for t_atoms settings.
 
enum  ChangeFrameInfoType { PreservedIfPresent, Always, Count }
 Enum class for setting fields new or not.
 
enum  ChangeFrameTimeType {
  PreservedIfPresent, StartTime, TimeStep, Both,
  Count
}
 Enum class for setting frame time from user input.
 
enum  DdRankOrder {
  DdRankOrder::select, DdRankOrder::interleave, DdRankOrder::pp_pme, DdRankOrder::cartesian,
  DdRankOrder::Count
}
 The options for the domain decomposition MPI task ordering. More...
 
enum  DlbOption {
  DlbOption::select, DlbOption::turnOnWhenUseful, DlbOption::no, DlbOption::yes,
  DlbOption::Count
}
 The options for the dynamic load balancing. More...
 
enum  DDBondedChecking : bool { DDBondedChecking::ExcludeZeroLimit = false, DDBondedChecking::All = true }
 Options for checking bonded interactions. More...
 
enum  FftBackend {
  Cufft, Ocl, HeFFTe_CUDA, SyclMkl,
  SyclRocfft, Sycl, Count
}
 
enum  SpaceGroup : int32_t { SpaceGroup::P1 = 1 }
 Space group in three dimensions. More...
 
enum  MrcDataMode : int32_t {
  MrcDataMode::uInt8 = 0, MrcDataMode::int16 = 1, MrcDataMode::float32 = 2, MrcDataMode::complexInt32 = 3,
  MrcDataMode::complexFloat64 = 4
}
 The type of density data stored in an mrc file. As named in "EMDB Map Distribution Format Description Version 1.01 (c) emdatabank.org 2014" Modes 0-4 are defined by the standard. NOTE only mode 2 is currently implemented and used. More...
 
enum  DeviceStreamType : int {
  DeviceStreamType::NonBondedLocal, DeviceStreamType::NonBondedNonLocal, DeviceStreamType::Pme, DeviceStreamType::PmePpTransfer,
  DeviceStreamType::UpdateAndConstraints, DeviceStreamType::Count
}
 Class enum to describe the different logical streams used for GPU work. More...
 
enum  PinningPolicy : int { CannotBePinned, PinnedIfSupported }
 Helper enum for pinning policy of the allocation of HostAllocationPolicy. More...
 
enum  Architecture { Unknown, Architecture::X86, Architecture::Arm, Architecture::PowerPC }
 Enum for GROMACS CPU hardware detection support. More...
 
enum  IMDMessageType : int {
  IMDMessageType::Disconnect, IMDMessageType::Energies, IMDMessageType::FCoords, IMDMessageType::Go,
  IMDMessageType::Handshake, IMDMessageType::Kill, IMDMessageType::Mdcomm, IMDMessageType::Pause,
  IMDMessageType::TRate, IMDMessageType::IOerror, IMDMessageType::Count
}
 Enum for types of IMD messages. More...
 
enum  DensitySimilarityMeasureMethod : int { DensitySimilarityMeasureMethod::innerProduct, DensitySimilarityMeasureMethod::relativeEntropy, DensitySimilarityMeasureMethod::crossCorrelation, Count }
 The methods that determine how two densities are compared to one another. More...
 
enum  CheckpointSignal { noSignal = 0, doCheckpoint = 1 }
 Checkpoint signals. More...
 
enum  ConstraintVariable : int {
  Positions, Velocities, Derivative, Deriv_FlexCon,
  Force, ForceDispl
}
 Describes supported flavours of constrained updates.
 
enum  FlexibleConstraintTreatment { FlexibleConstraintTreatment::Include, FlexibleConstraintTreatment::Exclude }
 Tells make_at2con how to treat flexible constraints. More...
 
enum  NumTempScaleValues { NumTempScaleValues::None = 0, NumTempScaleValues::Single = 1, NumTempScaleValues::Multiple = 2, NumTempScaleValues::Count = 3 }
 Sets the number of different temperature coupling values. More...
 
enum  VelocityScalingType { VelocityScalingType::None = 0, VelocityScalingType::Diagonal = 1, VelocityScalingType::Count = 2 }
 Different variants of the Parrinello-Rahman velocity scaling. More...
 
enum  ResetSignal { noSignal = 0, doResetCounters = 1 }
 Reset signals. More...
 
enum  StopSignal : int { noSignal = 0, stopAtNextNSStep = 1, stopImmediately = -1 }
 Stop signals. More...
 
enum  VSiteCalculatePosition { Yes, No }
 Whether we're calculating the virtual site position.
 
enum  VSiteCalculateVelocity { Yes, No }
 Whether we're calculating the virtual site velocity.
 
enum  PbcMode { PbcMode::all, PbcMode::none }
 PBC modes for vsite construction and spreading. More...
 
enum  VSiteOperation { VSiteOperation::Positions, VSiteOperation::Velocities, VSiteOperation::PositionsAndVelocities, VSiteOperation::Count }
 Whether we calculate vsite positions, velocities, or both. More...
 
enum  VirtualSiteVirialHandling : int { VirtualSiteVirialHandling::None, VirtualSiteVirialHandling::Pbc, VirtualSiteVirialHandling::NonLinear }
 Tells how to handle virial contributions due to virtual sites. More...
 
enum  StartingBehavior : int { StartingBehavior::RestartWithAppending, StartingBehavior::RestartWithoutAppending, StartingBehavior::NewSimulation, StartingBehavior::Count }
 Enumeration for describing how mdrun is (re)starting. More...
 
enum  : std::ptrdiff_t { dynamic_extent = -1 }
 Define constant that signals dynamic extent.
 
enum  AwhTargetType : int {
  Constant, Cutoff, Boltzmann, LocalBoltzmann,
  Count, Default = Constant
}
 Target distribution enum.
 
enum  AwhHistogramGrowthType : int { ExponentialLinear, Linear, Count, Default = ExponentialLinear }
 Weight histogram growth enum.
 
enum  AwhPotentialType : int { Convolved, Umbrella, Count, Default = Convolved }
 AWH potential type enum.
 
enum  AwhCoordinateProviderType : int { Pull, FreeEnergyLambda, Count, Default = Pull }
 AWH bias reaction coordinate provider.
 
enum  CheckpointDataOperation { Read, Write, Count }
 The operations on CheckpointData. More...
 
enum  AtomLocality : int { AtomLocality::Local = 0, AtomLocality::NonLocal = 1, AtomLocality::All = 2, AtomLocality::Count = 3 }
 Atom locality indicator: local, non-local, all. More...
 
enum  InteractionLocality : int { InteractionLocality::Local = 0, InteractionLocality::NonLocal = 1, InteractionLocality::Count = 2 }
 Interaction locality indicator: local, non-local, all. More...
 
enum  AppendingBehavior { AppendingBehavior::Auto, AppendingBehavior::Appending, AppendingBehavior::NoAppending }
 Enumeration for mdrun appending behavior. More...
 
enum  MtsForceGroups : int {
  MtsForceGroups::LongrangeNonbonded, MtsForceGroups::Nonbonded, MtsForceGroups::Pair, MtsForceGroups::Dihedral,
  MtsForceGroups::Angle, MtsForceGroups::Pull, MtsForceGroups::Awh, MtsForceGroups::Count
}
 Force group available for selection for multiple time step integration. More...
 
enum  ReductionRequirement : int { ReductionRequirement::Soon, ReductionRequirement::Eventually }
 Control whether reduction is required soon. More...
 
enum  ObservablesReducerStatus : int { ObservablesReducerStatus::ReadyToReduce, ObservablesReducerStatus::AlreadyReducedThisStep }
 Report whether the reduction has happened this step. More...
 
enum  ComputeGlobalsAlgorithm { LeapFrog, VelocityVerlet }
 The different global reduction schemes we know about.
 
enum  EnergySignallerEvent { EnergyCalculationStep, VirialCalculationStep, FreeEnergyCalculationStep }
 The energy events signalled by the EnergySignaller.
 
enum  TrajectoryEvent { StateWritingStep, EnergyWritingStep }
 The trajectory writing events.
 
enum  ModularSimulatorBuilderState { AcceptingClientRegistrations, NotAcceptingClientRegistrations }
 Enum allowing builders to store whether they can accept client registrations.
 
enum  ReportPreviousStepConservedEnergy { Yes, No, Count }
 Enum describing whether an element is reporting conserved energy from the previous step.
 
enum  ScheduleOnInitStep { ScheduleOnInitStep::Yes, ScheduleOnInitStep::No, ScheduleOnInitStep::Count }
 Whether the element does schedule on the initial step. More...
 
enum  NhcUsage { NhcUsage::System, NhcUsage::Barostat, NhcUsage::Count }
 The usages of Nose-Hoover chains. More...
 
enum  ScaleVelocities { PreStepOnly, PreStepAndPostStep }
 Which velocities the thermostat scales.
 
enum  IntegrationStage {
  IntegrationStage::PositionsOnly, IntegrationStage::VelocitiesOnly, IntegrationStage::LeapFrog, IntegrationStage::VelocityVerletPositionsAndVelocities,
  IntegrationStage::ScaleVelocities, IntegrationStage::ScalePositions, IntegrationStage::Count
}
 The different integration types we know about. More...
 
enum  NumPositionScalingValues { NumPositionScalingValues::None, NumPositionScalingValues::Single, NumPositionScalingValues::Multiple, NumPositionScalingValues::Count }
 Sets the number of different position scaling values. More...
 
enum  NumVelocityScalingValues { NumVelocityScalingValues::None, NumVelocityScalingValues::Single, NumVelocityScalingValues::Multiple, Count }
 Sets the number of different velocity scaling values. More...
 
enum  ParrinelloRahmanVelocityScaling { ParrinelloRahmanVelocityScaling::No, ParrinelloRahmanVelocityScaling::Diagonal, ParrinelloRahmanVelocityScaling::Full, Count }
 Sets the type of Parrinello-Rahman pressure scaling. More...
 
enum  ReferenceTemperatureChangeAlgorithm
 
enum  EnergySignallerVirialMode { EnergySignallerVirialMode::Off, EnergySignallerVirialMode::OnStep, EnergySignallerVirialMode::OnStepAndNext, EnergySignallerVirialMode::Count }
 When we calculate virial. More...
 
enum  UseFullStepKE { Yes, No, Count }
 Enum describing whether the thermostat is using full or half step kinetic energy.
 
enum  HelpOutputFormat { eHelpOutputFormat_Console, eHelpOutputFormat_Rst, eHelpOutputFormat_Other, eHelpOutputFormat_NR }
 Output format for help writing. More...
 
enum  OptionFileType : int {
  Topology, RunInput, Trajectory, Energy,
  PDB, Index, Plot, GenericData,
  Csv, QMInput, Count
}
 Purpose of file(s) provided through an option.
 
enum  OptionFlag : uint64_t {
  efOption_Set = 1 << 0, efOption_HasDefaultValue = 1 << 1, efOption_ExplicitDefaultValue = 1 << 2, efOption_ClearOnNextSet = 1 << 3,
  efOption_Required = 1 << 4, efOption_MultipleTimes = 1 << 5, efOption_Hidden = 1 << 6, efOption_Vector = 1 << 8,
  efOption_DefaultValueIfSetExists = 1 << 11, efOption_NoDefaultValue = 1 << 9, efOption_DontCheckMinimumCount = 1 << 10
}
 Flags for options. More...
 
enum  COMShiftType : int { Residue, Molecule, Count }
 How COM shifting should be applied.
 
enum  CenteringType : int { Triclinic, Rectangular, Zero, Count }
 Helper enum class to define centering types.
 
enum  UnitCellType : int { Triclinic, Rectangular, Compact, Count }
 Helper enum class to define Unit cell representation types.
 
enum  RandomDomain {
  RandomDomain::Other = 0x00000000, RandomDomain::MaxwellVelocities = 0x00001000, RandomDomain::TestParticleInsertion = 0x00002000, RandomDomain::UpdateCoordinates = 0x00003000,
  RandomDomain::UpdateConstraints = 0x00004000, RandomDomain::Thermostat = 0x00005000, RandomDomain::Barostat = 0x00006000, RandomDomain::ReplicaExchange = 0x00007000,
  RandomDomain::ExpandedEnsemble = 0x00008000, RandomDomain::AwhBiasing = 0x00009000
}
 Enumerated values for fixed part of random seed (domain) More...
 
enum  SimdType {
  SimdType::None, SimdType::Reference, SimdType::Generic, SimdType::X86_Sse2,
  SimdType::X86_Sse4_1, SimdType::X86_Avx128Fma, SimdType::X86_Avx, SimdType::X86_Avx2,
  SimdType::X86_Avx2_128, SimdType::X86_Avx512, SimdType::X86_Avx512Knl, SimdType::Arm_NeonAsimd,
  SimdType::Arm_Sve, SimdType::Ibm_Vsx
}
 Enumerated options for SIMD architectures. More...
 
enum  TaskTarget : int { Auto, Cpu, Gpu }
 Record where a compute task is targetted.
 
enum  EmulateGpuNonbonded : bool { EmulateGpuNonbonded::No, EmulateGpuNonbonded::Yes }
 Help pass GPU-emulation parameters with type safety. More...
 
enum  GpuTask : int { GpuTask::Nonbonded, GpuTask::Pme, GpuTask::Count }
 Types of compute tasks that can be run on a GPU. More...
 
enum  ErrorCode {
  eeOK, eeOutOfMemory, eeFileNotFound, eeFileIO,
  eeInvalidInput, eeInconsistentInput, eeTolerance, eeInstability,
  eeNotImplemented, eeInvalidValue, eeInvalidCall, eeInternalError,
  eeAPIError, eeRange, eeParallelConsistency, eeModularSimulator,
  eeUnknownError
}
 Possible error return codes from Gromacs functions. More...
 
enum  EndianSwapBehavior : int {
  EndianSwapBehavior::DoNotSwap, EndianSwapBehavior::Swap, EndianSwapBehavior::SwapIfHostIsBigEndian, EndianSwapBehavior::SwapIfHostIsLittleEndian,
  EndianSwapBehavior::Count
}
 Specify endian swapping behavoir. More...
 
enum  CudaAwareMpiStatus : int { CudaAwareMpiStatus::Supported, CudaAwareMpiStatus::NotSupported, CudaAwareMpiStatus::NotKnown }
 Enum describing CUDA-aware support in underlying MPI library. More...
 
enum  StringCompareType { StringCompareType::Exact, StringCompareType::CaseInsensitive, StringCompareType::CaseAndDashInsensitive }
 Specifies how strings should be compared in various contexts. More...
 
enum  StripStrings : int { StripStrings::No, StripStrings::Yes }
 Enum class for whether StringToEnumValueConverter will strip strings of leading and trailing whitespace before comparison. More...
 
enum  TimeUnit : int {
  Femtoseconds, Picoseconds, Nanoseconds, Microseconds,
  Milliseconds, Seconds, Count, Default = Picoseconds
}
 Time values for TimeUnitManager and legacy oenv module.
 

Functions

AnalysisHistogramSettingsInitializer histogramFromRange (real min, real max)
 Initializes a histogram using a range and a bin width. More...
 
AnalysisHistogramSettingsInitializer histogramFromBins (real start, int nbins, real binwidth)
 Initializes a histogram using bin width and the number of bins. More...
 
static bool anyDimUsesProvider (const AwhBiasParams &awhBiasParams, const AwhCoordinateProviderType awhCoordProvider)
 Checks whether any dimension uses the given coordinate provider type. More...
 
static bool anyDimUsesProvider (const AwhParams &awhParams, const AwhCoordinateProviderType awhCoordProvider)
 Checks whether any dimension uses the given coordinate provider type. More...
 
static bool anyDimUsesPull (const ArrayRef< BiasCoupledToSystem > biasCoupledToSystem)
 Checks whether any dimension uses pulling as a coordinate provider. More...
 
std::unique_ptr< AwhprepareAwhModule (FILE *fplog, const t_inputrec &inputRecord, t_state *stateGlobal, const t_commrec *commRecord, const gmx_multisim_t *multiSimRecord, bool startingFromCheckpoint, bool usingShellParticles, const std::string &biasInitFilename, pull_t *pull_work)
 Makes an Awh and prepares to use it if the user input requests that. More...
 
static int64_t countSamples (ArrayRef< const PointState > pointState)
 Count the total number of samples / sample weight over all grid points. More...
 
static void ensureStateAndRunConsistency (const BiasParams &params, const BiasState &state)
 Check if the state (loaded from checkpoint) and the run are consistent. More...
 
double getDeviationFromPointAlongGridAxis (const BiasGrid &grid, int dimIndex, int pointIndex, double value)
 Get the deviation along one dimension from the given value to a point in the grid. More...
 
double getDeviationFromPointAlongGridAxis (const BiasGrid &grid, int dimIndex, int pointIndex1, int pointIndex2)
 Get the deviation from one point to another along one dimension in the grid. More...
 
bool pointsAlongLambdaAxis (const BiasGrid &grid, int pointIndex1, int pointIndex2)
 Checks whether two points are along a free energy lambda state axis. More...
 
bool pointsHaveDifferentLambda (const BiasGrid &grid, int pointIndex1, int pointIndex2)
 Checks whether two points are different in the free energy lambda state dimension (if any). More...
 
void linearArrayIndexToMultiDim (int indexLinear, int ndim, const awh_ivec numPointsDim, awh_ivec indexMulti)
 Convert a linear array index to a multidimensional one. More...
 
void linearGridindexToMultiDim (const BiasGrid &grid, int indexLinear, awh_ivec indexMulti)
 Convert a linear grid point index to a multidimensional one. More...
 
int multiDimArrayIndexToLinear (const awh_ivec indexMulti, int numDim, const awh_ivec numPointsDim)
 Convert multidimensional array index to a linear one. More...
 
int multiDimGridIndexToLinear (const BiasGrid &grid, const awh_ivec indexMulti)
 Convert a multidimensional grid point index to a linear one. More...
 
bool advancePointInSubgrid (const BiasGrid &grid, const awh_ivec subgridOrigin, const awh_ivec subgridNpoints, int *gridPointIndex)
 Find the next grid point in the sub-part of the grid given a starting point. More...
 
static int pointDistanceAlongAxis (const GridAxis &axis, double x, double x0)
 Returns the point distance between from value x to value x0 along the given axis. More...
 
static bool valueIsInGrid (const awh_dvec value, ArrayRef< const GridAxis > axis)
 Query if a value is in range of the grid. More...
 
static int getNearestIndexInGrid (const awh_dvec value, ArrayRef< const GridAxis > axis)
 Map a value to the nearest point in the grid. More...
 
void mapGridToDataGrid (std::vector< int > *gridpointToDatapoint, const double *const *data, int numDataPoints, const std::string &dataFilename, const BiasGrid &grid, const std::string &correctFormatMessage)
 Maps each point in the grid to a point in the data grid. More...
 
template<typename T >
void sumOverSimulations (ArrayRef< T > data, MPI_Comm multiSimComm, const bool broadcastWithinSimulation, const t_commrec &commRecord)
 Sum an array over all simulations on master ranks or all ranks of each simulation. More...
 
bool haveBiasSharingWithinSimulation (const AwhParams &awhParams)
 Returns if any bias is sharing within a simulation. More...
 
void biasesAreCompatibleForSharingBetweenSimulations (const AwhParams &awhParams, ArrayRef< const size_t > pointSize, const BiasSharing &biasSharing)
 Checks whether biases are compatible for sharing between simulations, throws when not. More...
 
static void normalizeFreeEnergyAndPmfSum (std::vector< PointState > *pointState)
 Normalizes the free energy and PMF sum. More...
 
static int countTrailingZeroRows (const double *const *data, int numRows, int numColumns)
 Count trailing data rows containing only zeros. More...
 
static void readUserPmfAndTargetDistribution (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, const std::string &filename, int numBias, int biasIndex, std::vector< PointState > *pointState)
 Initializes the PMF and target with data read from an input table. More...
 
static void normalizeBlock (AwhEnergyBlock *block, const Bias &bias)
 Normalizes block data for output. More...
 
void initCorrelationGridHistory (CorrelationGridHistory *correlationGridHistory, int numCorrelationTensors, int tensorSize, int blockDataListSize)
 Initialize correlation grid history, sets all sizes. More...
 
CorrelationGridHistory initCorrelationGridHistoryFromState (const CorrelationGrid &corrGrid)
 Allocate a correlation grid history with the same structure as the given correlation grid. More...
 
void updateCorrelationGridHistory (CorrelationGridHistory *corrGridHist, const CorrelationGrid &corrGrid)
 Update the correlation grid history for checkpointing. More...
 
void restoreCorrelationGridStateFromHistory (const CorrelationGridHistory &corrGridHist, CorrelationGrid *corrGrid)
 Restores the correlation grid state from the correlation grid history. More...
 
const char * enumValueToString (AwhTargetType enumValue)
 String for target distribution.
 
const char * enumValueToString (AwhHistogramGrowthType enumValue)
 String for weight histogram growth.
 
const char * enumValueToString (AwhPotentialType enumValue)
 String for AWH potential type.
 
const char * enumValueToString (AwhCoordinateProviderType enumValue)
 String for AWH bias reaction coordinate provider.
 
static double get_pull_coord_period (const t_pull_coord &pullCoordParams, const t_pbc &pbc, const real intervalLength)
 Gets the period of a pull coordinate. More...
 
static bool intervalIsInPeriodicInterval (double origin, double end, double period)
 Checks if the given interval is defined in the correct periodic interval. More...
 
static bool valueIsInInterval (double origin, double end, double period, double value)
 Checks if a value is within an interval. More...
 
static void checkInputConsistencyInterval (const AwhParams &awhParams, warninp_t wi)
 Check if the starting configuration is consistent with the given interval. More...
 
static void setStateDependentAwhPullDimParams (AwhDimParams *dimParams, const int biasIndex, const int dimIndex, const pull_params_t &pull_params, pull_t *pull_work, const t_pbc &pbc, const tensor &compressibility, warninp_t wi)
 Sets AWH parameters, for one AWH pull dimension. More...
 
void setStateDependentAwhParams (AwhParams *awhParams, const pull_params_t &pull_params, pull_t *pull_work, const matrix box, PbcType pbcType, const tensor &compressibility, const t_grpopts *inputrecGroupOptions, real initLambda, const gmx_mtop_t &mtop, warninp_t wi)
 Sets AWH parameters that need state parameters such as the box vectors. More...
 
void checkAwhParams (const AwhParams &awhParams, const t_inputrec &inputrec, warninp_t wi)
 Check the AWH parameters. More...
 
bool awhHasFepLambdaDimension (const AwhParams &awhParams)
 Returns true when AWH has a bias with a free energy lambda state dimension.
 
bool operator== (const DensityFittingParameters &lhs, const DensityFittingParameters &rhs)
 Check if two structs holding density fitting parameters are equal. More...
 
bool operator!= (const DensityFittingParameters &lhs, const DensityFittingParameters &rhs)
 Check if two structs holding density fitting parameters are not equal. More...
 
std::unique_ptr< IMDModulecreateElectricFieldModule ()
 Creates a module for an external electric field. More...
 
RVec computeQMBoxVec (const RVec &a, const RVec &b, const RVec &c, real h, real minNorm, real maxNorm)
 Transforms vector a such as distance from it to the plane defined by vectors b and c will be h minimum length will be milL and maximum length maxL. More...
 
CommandLineProgramContextinitForCommandLine (int *argc, char ***argv)
 Initializes the GROMACS library for command-line use. More...
 
void finalizeForCommandLine ()
 Deinitializes the GROMACS library after initForCommandLine(). More...
 
int processExceptionAtExitForCommandLine (const std::exception &ex)
 Handles an exception and deinitializes after initForCommandLine. More...
 
int runCommandLineModule (int argc, char *argv[], ICommandLineModule *module)
 Implements a main() method that runs a single module. More...
 
int runCommandLineModule (int argc, char *argv[], const char *name, const char *description, std::function< std::unique_ptr< ICommandLineOptionsModule >()> factory)
 Implements a main() method that runs a single module. More...
 
void writeCommandLineHelpCMain (const CommandLineHelpContext &context, const char *name, int(*mainFunction)(int argc, char *argv[]))
 Helper to implement ICommandLineModule::writeHelp() with a C-like main() function that calls parse_common_args(). More...
 
static int getFileType (const std::string &filename)
 Get the internal file type from the filename. More...
 
static unsigned long getSupportedOutputAdapters (int filetype)
 Get the flag representing the requirements for a given file output. More...
 
static OutputAdapterContainer addOutputAdapters (const OutputRequirements &requirements, AtomsDataPtr atoms, const Selection &sel, unsigned long abilities)
 Creates a new container object with the user requested IOutputAdapter derived methods attached to it. More...
 
std::unique_ptr
< TrajectoryFrameWriter
createTrajectoryFrameWriter (const gmx_mtop_t *top, const Selection &sel, const std::string &filename, AtomsDataPtr atoms, OutputRequirements requirements)
 Factory function for TrajectoryFrameWriter. More...
 
static void deepCopy_t_trxframe (const t_trxframe &input, t_trxframe *copy, RVec *xvec, RVec *vvec, RVec *fvec, int *indexvec)
 Create a deep copy of a t_trxframe input into copy. More...
 
static t_trxstatus * openTNG (const std::string &name, const Selection &sel, const gmx_mtop_t *mtop)
 Method to open TNG file. More...
 
unsigned long convertFlag (CoordinateFileFlags flag)
 Conversion of flag to its corresponding unsigned long value.
 
static void adjustAtomInformation (t_atoms *atoms, t_atoms *selectionAtoms, const Selection &sel)
 Modify atoms information in coordinate frame to fit output selection. More...
 
static void flagInteractionsForType (const int ftype, const InteractionList &il, const reverse_ilist_t &ril, const Range< int > &atomRange, const int numAtomsPerMolecule, ArrayRef< const int > globalAtomIndices, ArrayRef< int > isAssigned)
 Checks whether interactions have been assigned for one function type. More...
 
static std::string printMissingInteractionsMolblock (const t_commrec *cr, const gmx_reverse_top_t &rt, const char *moltypename, const reverse_ilist_t &ril, const Range< int > &atomRange, const int numAtomsPerMolecule, const int numMolecules, const InteractionDefinitions &idef)
 Help print error output when interactions are missing in a molblock. More...
 
static void printMissingInteractionsAtoms (const MDLogger &mdlog, const t_commrec *cr, const gmx_mtop_t &mtop, const InteractionDefinitions &idef)
 Help print error output when interactions are missing.
 
static void dd_print_missing_interactions (const MDLogger &mdlog, const t_commrec *cr, const int numBondedInteractionsOverAllDomains, const int expectedNumGlobalBondedInteractions, const gmx_mtop_t &top_global, const gmx_localtop_t &top_local, ArrayRef< const RVec > x, const matrix box)
 Print error output when interactions are missing.
 
static int computeExpectedNumGlobalBondedInteractions (const gmx_mtop_t &mtop, const bool useUpdateGroups)
 Compute the total bonded interaction count. More...
 
void mdAlgorithmsSetupAtomData (const t_commrec *cr, const t_inputrec &inputrec, const gmx_mtop_t &top_global, gmx_localtop_t *top, t_forcerec *fr, ForceBuffers *force, MDAtoms *mdAtoms, Constraints *constr, VirtualSitesHandler *vsite, gmx_shellfc_t *shellfc)
 Sets atom data for several MD algorithms. More...
 
void make_local_shells (const t_commrec *cr, const t_mdatoms &md, gmx_shellfc_t *shfc)
 Gets the local shell with domain decomposition. More...
 
bool check_grid_jump (int64_t step, const gmx_domdec_t *dd, real cutoff, const gmx_ddbox_t *ddbox, bool bFatal)
 Check whether the DD grid has moved too far for correctness.
 
void print_dd_statistics (const t_commrec *cr, const t_inputrec &inputrec, FILE *fplog)
 Print statistics for domain decomposition communication.
 
void dd_partition_system (FILE *fplog, const gmx::MDLogger &mdlog, int64_t step, const t_commrec *cr, bool bMasterState, int nstglobalcomm, t_state *state_global, const gmx_mtop_t &top_global, const t_inputrec &inputrec, gmx::ImdSession *imdSession, pull_t *pull_work, t_state *state_local, gmx::ForceBuffers *f, gmx::MDAtoms *mdAtoms, gmx_localtop_t *top_local, t_forcerec *fr, gmx::VirtualSitesHandler *vsite, gmx::Constraints *constr, t_nrnb *nrnb, gmx_wallcycle *wcycle, bool bVerbose)
 TODO Remove fplog when group scheme and charge groups are gone. More...
 
static void handleClfftError (clfftStatus status, const char *msg)
 Throws the exception on clFFT error.
 
 makePlan ("complex-to-real", rocfft_transform_type_real_inverse, PlanSetupData{rocfft_array_type_hermitian_interleaved, makeComplexStrides(complexGridSizePadded), computeTotalSize(complexGridSizePadded)}, PlanSetupData{rocfft_array_type_real, makeRealStrides(realGridSizePadded), computeTotalSize(realGridSizePadded)}, std::vector< size_t >{size_t(realGridSize[ZZ]), size_t(realGridSize[YY]), size_t(realGridSize[XX])}, pmeStream)
 
realGrid_ * realGrid ()), complexGrid_(*complexGrid->buffer_.get()),{GMX_RELEASE_ASSERT(performOutOfPlaceFFT,"Only out-of-place FFT is implemented in hipSYCL"
 
 GMX_RELEASE_ASSERT (allocateGrids==false,"Grids need to be pre-allocated")
 
 GMX_RELEASE_ASSERT (gridSizesInXForEachRank.size()==1 &&gridSizesInYForEachRank.size()==1,"FFT decomposition not implemented with SYCL backend")
 
template<typename ValueType >
void readKvtCheckpointValue (compat::not_null< ValueType * > value, const std::string &name, const std::string &identifier, const KeyValueTreeObject &kvt)
 Read to a key-value-tree value used for checkpointing. More...
 
template void readKvtCheckpointValue (compat::not_null< std::int64_t * > value, const std::string &name, const std::string &identifier, const KeyValueTreeObject &kvt)
 Read to a key-value-tree value used for checkpointing. More...
 
template void readKvtCheckpointValue (compat::not_null< real * > value, const std::string &name, const std::string &identifier, const KeyValueTreeObject &kvt)
 Read to a key-value-tree value used for checkpointing. More...
 
template<typename ValueType >
void writeKvtCheckpointValue (const ValueType &value, const std::string &name, const std::string &identifier, KeyValueTreeObjectBuilder kvtBuilder)
 Write to a key-value-tree used for checkpointing. More...
 
template void writeKvtCheckpointValue (const std::int64_t &value, const std::string &name, const std::string &identifier, KeyValueTreeObjectBuilder kvtBuilder)
 Write to a key-value-tree used for checkpointing. More...
 
template void writeKvtCheckpointValue (const real &value, const std::string &name, const std::string &identifier, KeyValueTreeObjectBuilder kvtBuilder)
 Write to a key-value-tree used for checkpointing. More...
 
size_t numberOfExpectedDataItems (const MrcDensityMapHeader &header)
 Return the number of density data items that are expected to follow this header. More...
 
TranslateAndScale getCoordinateTransformationToLattice (const MrcDensityMapHeader &header)
 Extract the transformation into lattice coordinates. More...
 
dynamicExtents3D getDynamicExtents3D (const MrcDensityMapHeader &header)
 Extract the extents of the density data. More...
 
bool mrcHeaderIsSane (const MrcDensityMapHeader &header)
 Checks if the values in the header are sane. More...
 
void serializeMrcDensityMapHeader (ISerializer *serializer, const MrcDensityMapHeader &mrcHeader)
 Serializes an MrcDensityMapHeader from a given serializer. More...
 
MrcDensityMapHeader deserializeMrcDensityMapHeader (ISerializer *serializer)
 Deserializes an MrcDensityMapHeader from a given serializer. More...
 
template<typename T >
static Float3asGenericFloat3Pointer (T *in)
 Reinterpret-cast any pointer in to Float3, checking the type compatibility.
 
template<typename T >
static const Float3asGenericFloat3Pointer (const T *in)
 Reinterpret-cast any const pointer in to Float3, checking the type compatibility.
 
template<typename C >
static Float3asGenericFloat3Pointer (C &in)
 Reinterpret-cast any container in to Float3, checking the type compatibility.
 
template<typename C >
static const Float3asGenericFloat3Pointer (const C &in)
 Reinterpret-cast any const container in to Float3, checking the type compatibility.
 
template<class T1 , class T2 >
bool operator== (const Allocator< T1, HostAllocationPolicy > &a, const Allocator< T2, HostAllocationPolicy > &b)
 Return true if two allocators are identical. More...
 
template<typename PinnableVector >
void changePinningPolicy (PinnableVector *v, PinningPolicy pinningPolicy)
 Helper function for changing the pinning policy of a pinnable vector. More...
 
void pinBuffer (void *pointer, std::size_t numBytes) noexcept
 Pin the allocation to physical memory. More...
 
void unpinBuffer (void *pointer) noexcept
 Unpin the allocation. More...
 
void doDeviceTransfers (const DeviceInformation &deviceInfo, ArrayRef< const char > input, ArrayRef< char > output)
 Helper function for GPU test code to be platform agnostic. More...
 
bool cpuIsX86Nehalem (const CpuInfo &cpuInfo)
 Return true if the CPU is an Intel x86 Nehalem. More...
 
bool cpuIsAmdZen1 (const CpuInfo &cpuInfo)
 Return true if the CPU is a first generation AMD Zen (produced by AMD or Hygon) More...
 
static DeviceDetectionResult detectAllDeviceInformation (const PhysicalNodeCommunicator &physicalNodeComm)
 Detect GPUs when that makes sense to attempt. More...
 
static void gmx_collect_hardware_mpi (const gmx::CpuInfo &cpuInfo, const PhysicalNodeCommunicator &physicalNodeComm, gmx_hw_info_t *hardwareInfo)
 Reduce the locally collected hardwareInfo over MPI ranks.
 
void hardwareTopologyDoubleCheckDetection (const gmx::MDLogger gmx_unused &mdlog, const gmx::HardwareTopology gmx_unused &hardwareTopology)
 
std::unique_ptr< gmx_hw_info_t > gmx_detect_hardware (const PhysicalNodeCommunicator &physicalNodeComm)
 Run detection and make correct and consistent hardware information available on all ranks. More...
 
void logHardwareDetectionWarnings (const gmx::MDLogger &mdlog, const gmx_hw_info_t &hardwareInformation)
 Issue warnings to mdlog that were decided during detection. More...
 
void hardwareTopologyDoubleCheckDetection (const gmx::MDLogger &mdlog, const gmx::HardwareTopology &hardwareTopology)
 Sanity check hardware topology and print some notes to log. More...
 
static bool runningOnCompatibleOSForAmd ()
 Return true if executing on compatible OS for AMD OpenCL. More...
 
static bool runningOnCompatibleHWForNvidia (const DeviceInformation &deviceInfo)
 Return true if executing on compatible GPU for NVIDIA OpenCL. More...
 
static DeviceStatus isDeviceFunctional (const DeviceInformation &deviceInfo)
 Checks that device deviceInfo is compatible with GROMACS. More...
 
std::string makeOpenClInternalErrorString (const char *message, cl_int status)
 Make an error string following an OpenCL API call. More...
 
static bool isDeviceFunctional (const DeviceInformation &deviceInfo, std::string *errorMessage)
 Checks that device deviceInfo is sane (ie can run a kernel). More...
 
static DeviceStatus checkGpu (size_t deviceId, const DeviceInformation &deviceInfo)
 Check whether the ocl_gpu_device is suitable for use by mdrun. More...
 
int identifyAvx512FmaUnits ()
 Test whether machine has dual AVX512 FMA units. More...
 
std::unique_ptr< IMDModulecreateInteractiveMolecularDynamicsModule ()
 Creates a module for interactive molecular dynamics.
 
static const char * enumValueToString (IMDMessageType enumValue)
 Names of the IMDType for error messages.
 
static void fill_header (IMDHeader *header, IMDMessageType type, int32_t length)
 Fills the header with message and the length argument.
 
static void swap_header (IMDHeader *header)
 Swaps the endianess of the header.
 
static int32_t imd_read_multiple (IMDSocket *socket, char *datptr, int32_t toread)
 Reads multiple bytes from socket.
 
static int32_t imd_write_multiple (IMDSocket *socket, const char *datptr, int32_t towrite)
 Writes multiple bytes to socket in analogy to imd_read_multiple.
 
static int imd_handshake (IMDSocket *socket)
 Handshake with IMD client.
 
static int imd_send_energies (IMDSocket *socket, const IMDEnergyBlock *energies, char *buffer)
 Send energies using the energy block and the send buffer.
 
static IMDMessageType imd_recv_header (IMDSocket *socket, int32_t *length)
 Receive IMD header from socket, sets the length and returns the IMD message.
 
static bool imd_recv_mdcomm (IMDSocket *socket, int32_t nforces, int32_t *forcendx, float *forces)
 Receive force indices and forces. More...
 
void write_IMDgroup_to_file (bool bIMD, t_inputrec *ir, const t_state *state, const gmx_mtop_t &sys, int nfile, const t_filenm fnm[])
 Writes out the group of atoms selected for interactive manipulation. More...
 
static int imd_send_rvecs (IMDSocket *socket, int nat, rvec *x, char *buffer)
 Send positions from rvec. More...
 
static bool rvecs_differ (const rvec v1, const rvec v2)
 Returns true if any component of the two rvecs differs.
 
static void shift_positions (const matrix box, rvec x[], const ivec is, int nr)
 Copied and modified from groupcoord.c shift_positions_group().
 
static void imd_check_integrator_parallel (const t_inputrec *ir, const t_commrec *cr)
 Check for non-working integrator / parallel options.
 
std::unique_ptr< ImdSession > makeImdSession (const t_inputrec *ir, const t_commrec *cr, gmx_wallcycle *wcycle, gmx_enerdata_t *enerd, const gmx_multisim_t *ms, const gmx_mtop_t &top_global, const MDLogger &mdlog, gmx::ArrayRef< const gmx::RVec > coords, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const ImdOptions &options, StartingBehavior startingBehavior)
 Makes and returns an initialized IMD session, which may be inactive. More...
 
int imdsock_winsockinit ()
 Define a function to initialize winsock.
 
static void print_IMD_error (const char *file, int line, char *msg)
 Print a nice error message on UNIX systems, using errno.h.
 
IMDSocket * imdsock_create ()
 Create an IMD master socket. More...
 
void imd_sleep (unsigned int seconds)
 Portability wrapper around sleep function.
 
int imdsock_bind (IMDSocket *sock, int port)
 Bind the IMD socket to address and port. More...
 
int imd_sock_listen (IMDSocket *sock)
 Set socket to listening state. More...
 
IMDSocket * imdsock_accept (IMDSocket *sock)
 Accept incoming connection and redirect to client socket. More...
 
int imdsock_getport (IMDSocket *sock, int *port)
 Get the port number used for IMD connection. More...
 
int imd_htonl (int src)
 Portability wrapper around system htonl function.
 
int imd_ntohl (int src)
 Portability wrapper around system ntohl function.
 
int imdsock_write (IMDSocket *sock, const char *buffer, int length)
 Write to socket. More...
 
int imdsock_read (IMDSocket *sock, char *buffer, int length)
 Read from socket. More...
 
void imdsock_shutdown (IMDSocket *sock)
 Shutdown the socket. More...
 
int imdsock_destroy (IMDSocket *sock)
 Close the socket and free the sock struct memory. More...
 
int imdsock_tryread (IMDSocket *sock, int timeoutsec, int timeoutusec)
 Try to read from the socket. More...
 
bool buildSupportsListedForcesGpu (std::string *error)
 Checks whether the GROMACS build allows to compute bonded interactions on a GPU. More...
 
bool inputSupportsListedForcesGpu (const t_inputrec &ir, const gmx_mtop_t &mtop, std::string *error)
 Checks whether the input system allows to compute bonded interactions on a GPU. More...
 
static bool someInteractionsCanRunOnGpu (const InteractionLists &ilists)
 Returns whether there are any interactions in ilists suitable for a GPU.
 
static bool bondedInteractionsCanRunOnGpu (const gmx_mtop_t &mtop)
 Returns whether there are any bonded interactions in the global topology suitable for a GPU.
 
static void PrintTo (const RVec &value, std::ostream *os)
 Print an RVec to os.
 
static void PrintTo (const PaddedVector< RVec > &vector, std::ostream *os)
 Print a padded vector of RVec to os.
 
void exponentialMovingAverageStateAsKeyValueTree (KeyValueTreeObjectBuilder builder, const ExponentialMovingAverageState &state)
 Convert the exponential moving average state as key-value-tree object.
 
ExponentialMovingAverageState exponentialMovingAverageStateFromKeyValueTree (const KeyValueTreeObject &object)
 Sets the exponential moving average state from a key-value-tree object. More...
 
unsigned int log2I (std::uint32_t x)
 Compute floor of logarithm to base 2, 32 bit unsigned argument. More...
 
unsigned int log2I (std::uint64_t x)
 Compute floor of logarithm to base 2, 64 bit unsigned argument. More...
 
unsigned int log2I (std::int32_t x)
 Compute floor of logarithm to base 2, 32 bit signed argument. More...
 
unsigned int log2I (std::int64_t x)
 Compute floor of logarithm to base 2, 64 bit signed argument. More...
 
std::int64_t greatestCommonDivisor (std::int64_t p, std::int64_t q)
 Find greatest common divisor of two numbers. More...
 
double erfinv (double x)
 Inverse error function, double precision. More...
 
float erfinv (float x)
 Inverse error function, single precision. More...
 
IntegerBox spreadRangeWithinLattice (const IVec &center, dynamicExtents3D extent, IVec range)
 Construct a box that holds all indices that are not more than a given range remote from center coordinates and still within a given lattice extent. More...
 
void invertBoxMatrix (const matrix src, matrix dest)
 Invert a simulation-box matrix in src, return in dest. More...
 
void invertMatrix (const matrix src, matrix dest)
 Invert a general 3x3 matrix in src, return in dest. More...
 
Matrix3x3 transpose (Matrix3x3ConstSpan matrixView)
 Calculate the transpose of a 3x3 matrix, from its view.
 
void matrixVectorMultiply (Matrix3x3ConstSpan matrix, RVec *v)
 Multiply matrix with vector.
 
constexpr real determinant (Matrix3x3ConstSpan matrix)
 Determinant of a 3x3 matrix.
 
constexpr real trace (Matrix3x3ConstSpan matrixView)
 Calculates the trace of a 3x3 matrix view.
 
template<typename ElementType , int N, int M = N>
MultiDimArray< std::array
< ElementType, N *M >, extents
< N, M > > 
identityMatrix ()
 Create an identity matrix of ElementType with N * M elements. More...
 
static Matrix3x3 createMatrix3x3FromLegacyMatrix (const matrix legacyMatrix)
 Create new matrix type from legacy type.
 
static void fillLegacyMatrix (Matrix3x3ConstSpan newMatrix, matrix legacyMatrix)
 Fill legacy matrix from new matrix type.
 
template<class TContainer , class Extents >
constexpr MultiDimArray
< TContainer, Extents >
::const_iterator 
begin (const MultiDimArray< TContainer, Extents > &multiDimArray)
 Free MultiDimArray begin function addressing its contiguous memory.
 
template<class TContainer , class Extents >
constexpr MultiDimArray
< TContainer, Extents >
::iterator 
begin (MultiDimArray< TContainer, Extents > &multiDimArray)
 Free MultiDimArray begin function addressing its contiguous memory.
 
template<class TContainer , class Extents >
constexpr MultiDimArray
< TContainer, Extents >
::const_iterator 
end (const MultiDimArray< TContainer, Extents > &multiDimArray)
 Free MultiDimArray end function addressing its contiguous memory.
 
template<class TContainer , class Extents >
constexpr MultiDimArray
< TContainer, Extents >
::iterator 
end (MultiDimArray< TContainer, Extents > &multiDimArray)
 Free MultiDimArray end function addressing its contiguous memory.
 
template<class TContainer , class Extents >
void swap (MultiDimArray< TContainer, Extents > &a, MultiDimArray< TContainer, Extents > &b) noexcept
 Swap function.
 
OptimisationResult nelderMead (const std::function< real(ArrayRef< const real >)> &functionToMinimize, ArrayRef< const real > initialGuess, real minimumRelativeSimplexLength=1e-8, int maxSteps=10'000)
 Derivative-free downhill simplex optimisation. More...
 
std::unique_ptr< BoxDeformation > prepareBoxDeformation (const matrix &initialBox, DDRole ddRole, NumRanks numRanks, MPI_Comm communicator, const t_inputrec &inputrec)
 Factory function for box deformation module. More...
 
static CheckpointSignal convertToCheckpointSignal (signed char sig)
 Convert signed char (as used by SimulationSignal) to CheckpointSignal enum. More...
 
static void clear_constraint_quantity_nonlocal (const gmx_domdec_t &dd, ArrayRef< RVec > q)
 Clears constraint quantities for atoms in nonlocal region.
 
void too_many_constraint_warnings (ConstraintAlgorithm eConstrAlg, int warncount)
 Generate a fatal error because of too many LINCS/SETTLE warnings.
 
static void write_constr_pdb (const char *fn, const char *title, const gmx_mtop_t &mtop, int start, int homenr, const t_commrec *cr, ArrayRef< const RVec > x, const matrix box)
 Writes out coordinates.
 
static void dump_confs (FILE *log, int64_t step, const gmx_mtop_t &mtop, int start, int homenr, const t_commrec *cr, ArrayRef< const RVec > x, ArrayRef< const RVec > xprime, const matrix box)
 Writes out domain contents to help diagnose crashes.
 
FlexibleConstraintTreatment flexibleConstraintTreatment (bool haveDynamicsIntegrator)
 Returns the flexible constraint treatment depending on whether the integrator is dynamic.
 
static ListOfLists< int > makeAtomsToConstraintsList (int numAtoms, ArrayRef< const InteractionList > ilists, ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
 Returns a block struct to go from atoms to constraints. More...
 
ListOfLists< int > make_at2con (int numAtoms, ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
 Returns a ListOfLists object to go from atoms to constraints. More...
 
ListOfLists< int > make_at2con (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
 Returns a ListOfLists object to go from atoms to constraints. More...
 
int countFlexibleConstraints (ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > iparams)
 Return the number of flexible constraints in the ilist and iparams.
 
static std::vector< int > make_at2settle (int natoms, const InteractionList &ilist)
 Returns the index of the settle to which each atom belongs.
 
static std::vector
< ListOfLists< int > > 
makeAtomToConstraintMappings (const gmx_mtop_t &mtop, FlexibleConstraintTreatment flexibleConstraintTreatment)
 Makes a per-moleculetype container of mappings from atom indices to constraint indices. More...
 
void do_constrain_first (FILE *log, gmx::Constraints *constr, const t_inputrec *inputrec, int numAtoms, int numHomeAtoms, ArrayRefWithPadding< RVec > x, ArrayRefWithPadding< RVec > v, const matrix box, real lambda)
 Constrain the initial coordinates and velocities.
 
void constrain_velocities (gmx::Constraints *constr, bool do_log, bool do_ene, int64_t step, t_state *state, real *dvdlambda, bool computeVirial, tensor constraintsVirial)
 Constrain velocities only. More...
 
void constrain_coordinates (gmx::Constraints *constr, bool do_log, bool do_ene, int64_t step, t_state *state, ArrayRefWithPadding< RVec > xp, real *dvdlambda, bool computeVirial, tensor constraintsVirial)
 Constraint coordinates. More...
 
static bool isConstraintFlexible (ArrayRef< const t_iparams > iparams, int iparamsIndex)
 Returns whether constraint with parameter iparamsIndex is a flexible constraint.
 
const int * constr_iatomptr (gmx::ArrayRef< const int > iatom_constr, gmx::ArrayRef< const int > iatom_constrnc, int con)
 Returns the constraint iatoms for a constraint number con which comes from a list where F_CONSTR and F_CONSTRNC constraints are concatenated.
 
bool inter_charge_group_constraints (const gmx_mtop_t &mtop)
 Returns whether there are inter charge group constraints.
 
bool inter_charge_group_settles (const gmx_mtop_t &mtop)
 Returns whether there are inter charge group settles.
 
static void constr_recur (const ListOfLists< int > &at2con, const InteractionLists &ilist, gmx::ArrayRef< const t_iparams > iparams, gmx_bool bTopB, int at, int depth, int nc, ArrayRef< int > path, real r0, real r1, real *r2max, int *count)
 Recursing function to help find all adjacent constraints.
 
static real constr_r_max_moltype (const gmx_moltype_t *molt, gmx::ArrayRef< const t_iparams > iparams, const t_inputrec *ir)
 Find the interaction radius needed for constraints for this molecule type.
 
real constr_r_max (const MDLogger &mdlog, const gmx_mtop_t *mtop, const t_inputrec *ir)
 Returns an estimate of the maximum distance between atoms required for LINCS.
 
real calculateAcceptanceWeight (LambdaWeightCalculation calculationMode, real lambdaEnergyDifference)
 Calculates the acceptance weight for a lambda state transition. More...
 
gmx::EnumerationArray
< FreeEnergyPerturbationCouplingType,
real
currentLambdas (int64_t step, const t_lambda &fepvals, int currentLambdaState)
 Evaluate the current lambdas. More...
 
void launchForceReductionKernel (int numAtoms, int atomStart, bool addRvecForce, bool accumulate, DeviceBuffer< Float3 > d_nbnxmForceToAdd, DeviceBuffer< Float3 > d_rvecForceToAdd, DeviceBuffer< Float3 > d_baseForce, DeviceBuffer< int > d_cell, const DeviceStream &deviceStream)
 Backend-specific function to launch GPU Force Reduction kernel. More...
 
template<bool addRvecForce, bool accumulateForce>
static auto reduceKernel (sycl::handler &cgh, DeviceAccessor< Float3, mode::read > a_nbnxmForce, OptionalAccessor< Float3, mode::read, addRvecForce > a_rvecForceToAdd, DeviceAccessor< Float3, accumulateForce?mode::read_write:mode::write > a_forceTotal, DeviceAccessor< int, mode::read > a_cell, const int atomStart)
 Function returning the force reduction kernel lambda.
 
template<bool addRvecForce, bool accumulateForce>
static void launchReductionKernel_ (const int numAtoms, const int atomStart, const DeviceBuffer< Float3 > &b_nbnxmForce, const DeviceBuffer< Float3 > &b_rvecForceToAdd, DeviceBuffer< Float3 > &b_forceTotal, const DeviceBuffer< int > &b_cell, const DeviceStream &deviceStream)
 Force reduction SYCL kernel launch code.
 
void launchLeapFrogKernel (int numAtoms, DeviceBuffer< Float3 > d_x, DeviceBuffer< Float3 > d_xp, DeviceBuffer< Float3 > d_v, DeviceBuffer< Float3 > d_f, DeviceBuffer< float > d_inverseMasses, float dt, bool doTemperatureScaling, int numTempScaleValues, DeviceBuffer< unsigned short > d_tempScaleGroups, DeviceBuffer< float > d_lambdas, VelocityScalingType prVelocityScalingType, Float3 prVelocityScalingMatrixDiagonal, const DeviceStream &deviceStream)
 Backend-specific function to launch GPU Leap Frog kernel. More...
 
template<NumTempScaleValues numTempScaleValues, VelocityScalingType velocityScaling>
auto leapFrogKernel (sycl::handler &cgh, DeviceAccessor< Float3, mode::read_write > a_x, DeviceAccessor< Float3, mode::discard_write > a_xp, DeviceAccessor< Float3, mode::read_write > a_v, DeviceAccessor< Float3, mode::read > a_f, DeviceAccessor< float, mode::read > a_inverseMasses, float dt, OptionalAccessor< float, mode::read, numTempScaleValues!=NumTempScaleValues::None > a_lambdas, OptionalAccessor< unsigned short, mode::read, numTempScaleValues==NumTempScaleValues::Multiple > a_tempScaleGroups, Float3 prVelocityScalingMatrixDiagonal)
 Main kernel for the Leap-Frog integrator. More...
 
template<NumTempScaleValues numTempScaleValues, VelocityScalingType velocityScaling, class... Args>
static sycl::event launchLeapFrogKernel (const DeviceStream &deviceStream, int numAtoms, Args &&...args)
 Leap Frog SYCL kernel launch code.
 
static NumTempScaleValues getTempScalingType (bool doTemperatureScaling, int numTempScaleValues)
 Convert doTemperatureScaling and numTempScaleValues to NumTempScaleValues.
 
template<class... Args>
static sycl::event launchLeapFrogKernel (NumTempScaleValues tempScalingType, VelocityScalingType prVelocityScalingType, Args &&...args)
 Select templated kernel and launch it.
 
real lincs_rmsd (const Lincs *lincsd)
 Return the RMSD of the constraint.
 
static void lincs_matrix_expand (const Lincs &lincsd, const Task &li_task, gmx::ArrayRef< const real > blcc, gmx::ArrayRef< real > rhs1, gmx::ArrayRef< real > rhs2, gmx::ArrayRef< real > sol)
 Do a set of nrec LINCS matrix multiplications. More...
 
static void lincs_update_atoms_noind (int ncons, gmx::ArrayRef< const AtomPair > atoms, real preFactor, gmx::ArrayRef< const real > fac, gmx::ArrayRef< const gmx::RVec > r, gmx::ArrayRef< const real > invmass, rvec *x)
 Update atomic coordinates when an index is not required.
 
static void lincs_update_atoms_ind (gmx::ArrayRef< const int > ind, gmx::ArrayRef< const AtomPair > atoms, real preFactor, gmx::ArrayRef< const real > fac, gmx::ArrayRef< const gmx::RVec > r, gmx::ArrayRef< const real > invmass, rvec *x)
 Update atomic coordinates when an index is required.
 
static void lincs_update_atoms (Lincs *li, int th, real preFactor, gmx::ArrayRef< const real > fac, gmx::ArrayRef< const gmx::RVec > r, gmx::ArrayRef< const real > invmass, rvec *x)
 Update coordinates for atoms.
 
template<int align>
static void gmx_simdcall gatherLoadUTransposeTSANSafe (const real *base, const std::int32_t *offset, SimdReal *v0, SimdReal *v1, SimdReal *v2)
 Helper function so that we can run TSAN with SIMD support (where implemented).
 
static void gmx_simdcall calc_dr_x_f_simd (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec *gmx_restrict x, const rvec *gmx_restrict f, const real *gmx_restrict blc, const real *pbc_simd, rvec *gmx_restrict r, real *gmx_restrict rhs, real *gmx_restrict sol)
 Calculate the constraint distance vectors r to project on from x. More...
 
static void do_lincsp (ArrayRefWithPadding< const RVec > xPadded, ArrayRefWithPadding< RVec > fPadded, ArrayRef< RVec > fp, t_pbc *pbc, Lincs *lincsd, int th, ArrayRef< const real > invmass, ConstraintVariable econq, bool bCalcDHDL, bool bCalcVir, tensor rmdf)
 LINCS projection, works on derivatives of the coordinates.
 
static void gmx_simdcall calc_dr_x_xp_simd (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec *gmx_restrict x, const rvec *gmx_restrict xp, const real *gmx_restrict bllen, const real *gmx_restrict blc, const real *pbc_simd, rvec *gmx_restrict r, real *gmx_restrict rhs, real *gmx_restrict sol)
 Calculate the constraint distance vectors r to project on from x. More...
 
static gmx_unused void calc_dist_iter (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec *gmx_restrict xp, const real *gmx_restrict bllen, const real *gmx_restrict blc, const t_pbc *pbc, real wfac, real *gmx_restrict rhs, real *gmx_restrict sol, bool *bWarn)
 Determine the distances and right-hand side for the next iteration.
 
static void gmx_simdcall calc_dist_iter_simd (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec *gmx_restrict x, const real *gmx_restrict bllen, const real *gmx_restrict blc, const real *pbc_simd, real wfac, real *gmx_restrict rhs, real *gmx_restrict sol, bool *bWarn)
 As calc_dist_iter(), but using SIMD intrinsics.
 
static void do_lincs (ArrayRefWithPadding< const RVec > xPadded, ArrayRefWithPadding< RVec > xpPadded, const matrix box, t_pbc *pbc, Lincs *lincsd, int th, ArrayRef< const real > invmass, const t_commrec *cr, bool bCalcDHDL, real wangle, bool *bWarn, real invdt, ArrayRef< RVec > vRef, bool bCalcVir, tensor vir_r_m_dr)
 Implements LINCS constraining.
 
static void set_lincs_matrix_task (Lincs *li, Task *li_task, ArrayRef< const real > invmass, int *ncc_triangle, int *nCrossTaskTriangles)
 Sets the elements in the LINCS matrix for task task.
 
static void set_lincs_matrix (Lincs *li, ArrayRef< const real > invmass, real lambda)
 Sets the elements in the LINCS matrix.
 
static int count_triangle_constraints (const InteractionLists &ilist, const ListOfLists< int > &at2con)
 Finds all triangles of atoms that share constraints to a central atom.
 
static bool more_than_two_sequential_constraints (const InteractionLists &ilist, const ListOfLists< int > &at2con)
 Finds sequences of sequential constraints.
 
Lincs * init_lincs (FILE *fplog, const gmx_mtop_t &mtop, int nflexcon_global, ArrayRef< const ListOfLists< int >> atomsToConstraintsPerMolType, bool bPLINCS, int nIter, int nProjOrder, ObservablesReducerBuilder *observablesReducerBuilder)
 Initializes and returns the lincs data struct.
 
void done_lincs (Lincs *li)
 Destructs the lincs object when it is not nullptr.
 
static void lincs_thread_setup (Lincs *li, int natoms)
 Sets up the work division over the threads.
 
static void assign_constraint (Lincs *li, int constraint_index, int a1, int a2, real lenA, real lenB, const ListOfLists< int > &at2con)
 Assign a constraint.
 
static void check_assign_connected (Lincs *li, gmx::ArrayRef< const int > iatom, const InteractionDefinitions &idef, bool bDynamics, int a1, int a2, const ListOfLists< int > &at2con)
 Check if constraint with topology index constraint_index is connected to other constraints, and if so add those connected constraints to our task.
 
static void check_assign_triangle (Lincs *li, gmx::ArrayRef< const int > iatom, const InteractionDefinitions &idef, bool bDynamics, int constraint_index, int a1, int a2, const ListOfLists< int > &at2con)
 Check if constraint with topology index constraint_index is involved in a constraint triangle, and if so add the other two constraints in the triangle to our task.
 
static void set_matrix_indices (Lincs *li, const Task &li_task, const ListOfLists< int > &at2con, bool bSortMatrix)
 Sets matrix indices.
 
void set_lincs (const InteractionDefinitions &idef, int numAtoms, ArrayRef< const real > invmass, real lambda, bool bDynamics, const t_commrec *cr, Lincs *li)
 Initialize lincs stuff.
 
static void lincs_warning (gmx_domdec_t *dd, ArrayRef< const RVec > x, ArrayRef< const RVec > xprime, t_pbc *pbc, int ncons, gmx::ArrayRef< const AtomPair > atoms, gmx::ArrayRef< const real > bllen, real wangle, int maxwarn, int *warncount)
 Issues a warning when LINCS constraints cannot be satisfied.
 
static LincsDeviations makeLincsDeviations (const Lincs &lincsd, ArrayRef< const RVec > x, const t_pbc *pbc)
 Determine how well the constraints have been satisfied.
 
bool constrain_lincs (bool computeRmsd, const t_inputrec &ir, int64_t step, Lincs *lincsd, ArrayRef< const real > invmass, const t_commrec *cr, const gmx_multisim_t *ms, ArrayRefWithPadding< const RVec > x, ArrayRefWithPadding< RVec > xprime, ArrayRef< RVec > min_proj, const matrix box, t_pbc *pbc, bool hasMassPerturbed, real lambda, real *dvdlambda, real invdt, ArrayRef< RVec > v, bool bCalcVir, tensor vir_r_m_dr, ConstraintVariable econq, t_nrnb *nrnb, int maxwarn, int *warncount)
 Applies LINCS constraints. More...
 
ArrayRef< reallincs_rmsdData (Lincs *lincsd)
 Return the data for determining constraint RMS relative deviations.
 
static std::vector
< std::vector
< AtomsAdjacencyListElement > > 
constructAtomsAdjacencyList (const int numAtoms, ArrayRef< const int > iatoms)
 Constructs and returns an atom constraint adjacency list.
 
int countCoupled (int a, ArrayRef< int > numCoupledConstraints, ArrayRef< const std::vector< AtomsAdjacencyListElement >> atomsAdjacencyList)
 Helper function to go through constraints recursively. More...
 
void addWithCoupled (ArrayRef< const int > iatoms, const int stride, ArrayRef< const std::vector< AtomsAdjacencyListElement >> atomsAdjacencyList, ArrayRef< int > splitMap, const int c, int *currentMapIndex)
 Add constraint to splitMap with all constraints coupled to it. More...
 
static std::vector< int > countNumCoupledConstraints (ArrayRef< const int > iatoms, ArrayRef< const std::vector< AtomsAdjacencyListElement >> atomsAdjacencyList)
 Computes and returns how many constraints are coupled to each constraint. More...
 
void launchLincsGpuKernel (LincsGpuKernelParameters *kernelParams, const DeviceBuffer< Float3 > &d_x, DeviceBuffer< Float3 > d_xp, bool updateVelocities, DeviceBuffer< Float3 > d_v, real invdt, bool computeVirial, const DeviceStream &deviceStream)
 Backend-specific function to launch LINCS kernel. More...
 
template<bool updateVelocities, bool computeVirial, bool haveCoupledConstraints>
auto lincsKernel (sycl::handler &cgh, const int numConstraintsThreads, DeviceAccessor< AtomPair, mode::read > a_constraints, DeviceAccessor< float, mode::read > a_constraintsTargetLengths, OptionalAccessor< int, mode::read, haveCoupledConstraints > a_coupledConstraintsCounts, OptionalAccessor< int, mode::read, haveCoupledConstraints > a_coupledConstraintsIndices, OptionalAccessor< float, mode::read, haveCoupledConstraints > a_massFactors, OptionalAccessor< float, mode::read_write, haveCoupledConstraints > a_matrixA, DeviceAccessor< float, mode::read > a_inverseMasses, const int numIterations, const int expansionOrder, DeviceAccessor< Float3, mode::read > a_x, DeviceAccessor< Float3, mode::read_write > a_xp, const float invdt, OptionalAccessor< Float3, mode::read_write, updateVelocities > a_v, OptionalAccessor< float, mode::read_write, computeVirial > a_virialScaled, PbcAiuc pbcAiuc)
 Main kernel for LINCS constraints. More...
 
template<bool updateVelocities, bool computeVirial, bool haveCoupledConstraints, class... Args>
static sycl::event launchLincsKernel (const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&...args)
 
template<class... Args>
static sycl::event launchLincsKernel (bool updateVelocities, bool computeVirial, bool haveCoupledConstraints, Args &&...args)
 Select templated kernel and launch it.
 
template<typename... Args>
std::unique_ptr< ConstraintsmakeConstraints (const gmx_mtop_t &mtop, const t_inputrec &ir, pull_t *pull_work, bool doEssentialDynamics, Args &&...args)
 Factory function for Constraints. More...
 
std::unique_ptr< MDAtomsmakeMDAtoms (FILE *fp, const gmx_mtop_t &mtop, const t_inputrec &ir, bool useGpuForPme)
 Builder function for MdAtomsWrapper. More...
 
static ResetSignal convertToResetSignal (signed char sig)
 Convert signed char (as used by SimulationSignal) to ResetSignal enum. More...
 
static void initializeProjectionMatrix (const real invmO, const real invmH, const real dOH, const real dHH, matrix inverseCouplingMatrix)
 Initializes a projection matrix. More...
 
SettleParameters settleParameters (real mO, real mH, real dOH, real invmO, real invmH, real dHH)
 Computes and returns settle parameters. More...
 
void settle_proj (const SettleData &settled, ConstraintVariable econq, int nsettle, const int iatoms[], const t_pbc *pbc,ArrayRef< const RVec > x, ArrayRef< RVec > der, ArrayRef< RVec > derp, int CalcVirAtomEnd, tensor vir_r_m_dder)
 Analytical algorithm to subtract the components of derivatives of coordinates working on settle type constraint.
 
template<typename T , typename TypeBool , int packSize, typename TypePbc , bool bCorrectVelocity, bool bCalcVirial>
static void settleTemplate (const SettleData &settled, int settleStart, int settleEnd, const TypePbc pbc, const real *x, real *xprime, real invdt, real *gmx_restrict v, tensor vir_r_m_dr, bool *bErrorHasOccurred)
 The actual settle code, templated for real/SimdReal and for optimization.
 
template<typename T , typename TypeBool , int packSize, typename TypePbc >
static void settleTemplateWrapper (const SettleData &settled, int nthread, int thread, TypePbc pbc, const real x[], real xprime[], real invdt, real *v, bool bCalcVirial, tensor vir_r_m_dr, bool *bErrorHasOccurred)
 Wrapper template function that divides the settles over threads and instantiates the core template with instantiated booleans.
 
void csettle (const SettleData &settled,int nthread,int thread,const t_pbc *pbc,ArrayRefWithPadding< const RVec > x,ArrayRefWithPadding< RVec > xprime,real invdt,ArrayRefWithPadding< RVec > v,bool bCalcVirial,tensor vir_r_m_dr,bool *bErrorHasOccurred)
 Constrain coordinates using SETTLE. Can be called on any number of threads.
 
void launchSettleGpuKernel (int numSettles, const DeviceBuffer< WaterMolecule > &d_atomIds, const SettleParameters &settleParameters, const DeviceBuffer< Float3 > &d_x, DeviceBuffer< Float3 > d_xp, bool updateVelocities, DeviceBuffer< Float3 > d_v, real invdt, bool computeVirial, DeviceBuffer< float > virialScaled, const PbcAiuc &pbcAiuc, const DeviceStream &deviceStream)
 Apply SETTLE. More...
 
template<bool updateVelocities, bool computeVirial>
auto settleKernel (sycl::handler &cgh, const int numSettles, DeviceAccessor< WaterMolecule, mode::read > a_settles, SettleParameters pars, DeviceAccessor< Float3, mode::read > a_x, DeviceAccessor< Float3, mode::read_write > a_xp, float invdt, OptionalAccessor< Float3, mode::read_write, updateVelocities > a_v, OptionalAccessor< float, mode::read_write, computeVirial > a_virialScaled, PbcAiuc pbcAiuc)
 Function returning the SETTLE kernel lambda.
 
template<bool updateVelocities, bool computeVirial, class... Args>
static sycl::event launchSettleKernel (const DeviceStream &deviceStream, int numSettles, Args &&...args)
 SETTLE SYCL kernel launch code.
 
template<class... Args>
static sycl::event launchSettleKernel (bool updateVelocities, bool computeVirial, Args &&...args)
 Select templated kernel and launch it.
 
static int pcomp (const void *p1, const void *p2)
 Compares sort blocks.
 
static void pr_sortblock (FILE *fp, const char *title, int nsb, t_sortblock sb[])
 Prints sortblocks.
 
static void resizeLagrangianData (shakedata *shaked, int ncons)
 Reallocates a vector.
 
void make_shake_sblock_serial (shakedata *shaked, InteractionDefinitions *idef, int numAtoms)
 Make SHAKE blocks when not using DD.
 
void make_shake_sblock_dd (shakedata *shaked, const InteractionList &ilcon)
 Make SHAKE blocks when using DD.
 
void cshake (const int iatom[], int ncon, int *nnit, int maxnit, ArrayRef< const real > constraint_distance_squared, ArrayRef< RVec > positions, const t_pbc *pbc, ArrayRef< const RVec > initial_displacements, ArrayRef< const real > half_of_reduced_mass, real omega, ArrayRef< const real > invmass, ArrayRef< const real > distance_squared_tolerance, ArrayRef< real > scaled_lagrange_multiplier, int *nerror)
 Inner kernel for SHAKE constraints. More...
 
static void crattle (const int iatom[], int ncon, int *nnit, int maxnit, ArrayRef< const real > constraint_distance_squared, ArrayRef< RVec > vp, ArrayRef< const RVec > rij, ArrayRef< const real > m2, real omega, ArrayRef< const real > invmass, ArrayRef< const real > distance_squared_tolerance, ArrayRef< real > scaled_lagrange_multiplier, int *nerror, real invdt)
 Implements RATTLE (ie. SHAKE for velocity verlet integrators)
 
static int vec_shakef (FILE *fplog, shakedata *shaked, ArrayRef< const real > invmass, int ncon, ArrayRef< const t_iparams > ip, const int *iatom, real tol, ArrayRef< const RVec > x, ArrayRef< RVec > prime, const t_pbc *pbc, real omega, bool bFEP, real lambda, ArrayRef< real > scaled_lagrange_multiplier, real invdt, ArrayRef< RVec > v, bool bCalcVir, tensor vir_r_m_dr, ConstraintVariable econq)
 Applies SHAKE.
 
static void check_cons (FILE *log, int nc, ArrayRef< const RVec > x, ArrayRef< const RVec > prime, ArrayRef< const RVec > v, const t_pbc *pbc, ArrayRef< const t_iparams > ip, const int *iatom, ArrayRef< const real > invmass, ConstraintVariable econq)
 Check that constraints are satisfied.
 
static bool bshakef (FILE *log, shakedata *shaked, ArrayRef< const real > invmass, const InteractionDefinitions &idef, const t_inputrec &ir, ArrayRef< const RVec > x_s, ArrayRef< RVec > prime, const t_pbc *pbc, t_nrnb *nrnb, real lambda, real *dvdlambda, real invdt, ArrayRef< RVec > v, bool bCalcVir, tensor vir_r_m_dr, bool bDumpOnError, ConstraintVariable econq)
 Applies SHAKE.
 
bool constrain_shake (FILE *log,shakedata *shaked,gmx::ArrayRef< const real > invmass,const InteractionDefinitions &idef,const t_inputrec &ir,ArrayRef< const RVec > x_s,ArrayRef< RVec > xprime,ArrayRef< RVec > vprime,const t_pbc *pbc,t_nrnb *nrnb,real lambda,real *dvdlambda,real invdt,ArrayRef< RVec > v,bool bCalcVir,tensor vir_r_m_dr,bool bDumpOnError,ConstraintVariable econq)
 Shake all the atoms blockwise. It is assumed that all the constraints in the idef->shakes field are sorted, to ascending block nr. The sblock array points into the idef->shakes.iatoms field, with block 0 starting at sblock[0] and running to ( < ) sblock[1], block n running from sblock[n] to sblock[n+1]. Array sblock should be large enough. Return TRUE when OK, FALSE when shake-error.
 
static StopSignal convertToStopSignal (signed char sig)
 Convert signed char (as used by SimulationSignal) to StopSignal enum. More...
 
void launchScaleCoordinatesKernel (int numAtoms, DeviceBuffer< Float3 > d_coordinates, const ScalingMatrix &mu, const DeviceStream &deviceStream)
 Launches positions of velocities scaling kernel. More...
 
static auto scaleKernel (sycl::handler &cgh, DeviceAccessor< Float3, sycl::access_mode::read_write > a_x, const ScalingMatrix scalingMatrix)
 Function returning the scaling kernel lambda.
 
static bool hasFlexibleConstraints (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)
 Returns whether moltype contains flexible constraints.
 
static bool hasIncompatibleVsites (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)
 Returns whether moltype has incompatible vsites. More...
 
static InteractionList jointConstraintList (const gmx_moltype_t &moltype)
 Returns a merged list with constraints of all types.
 
static AtomIndexExtremes vsiteConstructRange (int a, const gmx_moltype_t &moltype)
 Returns the range of constructing atom for vsite with atom index a.
 
static AtomIndexExtremes constraintAtomRange (int a, const ListOfLists< int > &at2con, const InteractionList &ilistConstraints)
 Returns the range of atoms constrained to atom a (including a itself)
 
static std::vector< bool > buildIsParticleVsite (const gmx_moltype_t &moltype)
 Returns a list that tells whether atoms in moltype are vsites.
 
static int detectGroup (int firstAtom, const gmx_moltype_t &moltype, const ListOfLists< int > &at2con, const InteractionList &ilistConstraints)
 Returns the size of the update group starting at firstAtom or 0 when criteria (see updategroups.h) are not met.
 
static RangePartitioning makeUpdateGroupingsPerMoleculeType (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)
 Returns a list of update groups for moltype.
 
std::vector< RangePartitioningmakeUpdateGroupingsPerMoleculeType (const gmx_mtop_t &mtop)
 Returns a vector with update groups for each moleculetype in mtop or an empty vector when the criteria (see below) are not satisfied. More...
 
static std::unordered_multimap
< int, int > 
getAngleIndices (const gmx_moltype_t &moltype)
 Returns a map of angles ilist.iatoms indices with the middle atom as key.
 
template<int numPartnerAtoms>
static real constraintGroupRadius (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams, const int centralAtom, const ListOfLists< int > &at2con, const std::unordered_multimap< int, int > &angleIndices, const real constraintLength, const real temperature)
 When possible, computes the maximum radius of constrained atom in an update group. More...
 
static real computeMaxUpdateGroupRadius (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams, const RangePartitioning &updateGrouping, real temperature)
 Returns the maximum update group radius for moltype.
 
real computeMaxUpdateGroupRadius (const gmx_mtop_t &mtop, ArrayRef< const RangePartitioning > updateGroupingPerMoleculeType, real temperature)
 Returns the maximum update group radius. More...
 
real computeCutoffMargin (PbcType pbcType, matrix box, real rlist)
 Return the margin required for successful domain decomposition. More...
 
bool systemHasConstraintsOrVsites (const gmx_mtop_t &mtop)
 Returns whether mtop contains any constraints and/or vsites. More...
 
UpdateGroups makeUpdateGroups (const gmx::MDLogger &mdlog, std::vector< RangePartitioning > &&updateGroupingPerMoleculeType, real maxUpdateGroupRadius, bool useDomainDecomposition, bool systemHasConstraintsOrVsites, real cutoffMargin)
 Builder for update groups. More...
 
static int vsiteIlistNrCount (ArrayRef< const InteractionList > ilist)
 Returns the sum of the vsite ilist sizes over all vsite types. More...
 
static int pbc_rvec_sub (const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
 Computes the distance between xi and xj, pbc is used when pbc!=nullptr.
 
static real inverseNorm (const rvec x)
 Returns the 1/norm(x)
 
static PbcMode getPbcMode (const t_pbc *pbcPtr)
 Returns the PBC mode based on the system PBC and vsite properties. More...
 
template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void construct_vsites_thread (ArrayRef< RVec > x, ArrayRef< RVec > v, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist, const t_pbc *pbc_null)
 Executes the vsite construction task for a single thread. More...
 
template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void construct_vsites (const ThreadingInfo *threadingInfo, ArrayRef< RVec > x, ArrayRef< RVec > v, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist, const DomainInfo &domainInfo, const matrix box)
 Dispatch the vsite construction tasks for all threads. More...
 
void constructVirtualSites (ArrayRef< RVec > x, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist)
 Create positions of vsite atoms based for the local system. More...
 
static int vsite_count (ArrayRef< const InteractionList > ilist, int ftype)
 Returns the number of virtual sites in the interaction list, for VSITEN the number of atoms.
 
template<VirialHandling virialHandling>
static void spreadForceForThread (ArrayRef< const RVec > x, ArrayRef< RVec > f, ArrayRef< RVec > fshift, matrix dxdf, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist, const t_pbc *pbc_null)
 Executes the force spreading task for a single thread.
 
static void spreadForceWrapper (ArrayRef< const RVec > x, ArrayRef< RVec > f, const VirialHandling virialHandling, ArrayRef< RVec > fshift, matrix dxdf, const bool clearDxdf, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist, const t_pbc *pbc_null)
 Wrapper function for calling the templated thread-local spread function.
 
static void clearTaskForceBufferUsedElements (InterdependentTask *idTask)
 Clears the task force buffer elements that are written by task idTask.
 
static std::vector< int > makeAtomToGroupMapping (const gmx::RangePartitioning &grouping)
 Returns the an array with group indices for each atom. More...
 
int countNonlinearVsites (const gmx_mtop_t &mtop)
 Return the number of non-linear virtual site constructions in the system.
 
int countInterUpdategroupVsites (const gmx_mtop_t &mtop, ArrayRef< const RangePartitioning > updateGroupingsPerMoleculeType)
 Return the number of virtual sites that cross update groups. More...
 
std::unique_ptr
< VirtualSitesHandler
makeVirtualSitesHandler (const gmx_mtop_t &mtop, const t_commrec *cr, PbcType pbcType, ArrayRef< const RangePartitioning > updateGroupingPerMoleculeType)
 Create the virtual site handler. More...
 
 iparams_ (mtop.ffparams.iparams)
 
static void flagAtom (InterdependentTask *idTask, const int atom, const int numThreads, const int numAtomsPerThread)
 Flag that atom atom which is home in another task, if it has not already been added before.
 
static void assignVsitesToThread (VsiteThread *tData, int thread, int nthread, int natperthread, gmx::ArrayRef< int > taskIndex, ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > ip, ArrayRef< const ParticleType > ptype)
 Here we try to assign all vsites that are in our local range. More...
 
static void assignVsitesToSingleTask (VsiteThread *tData, int task, gmx::ArrayRef< const int > taskIndex, ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > ip)
 Assign all vsites with taskIndex[]==task to task tData.
 
void constructVirtualSitesGlobal (const gmx_mtop_t &mtop, ArrayRef< RVec > x)
 Create positions of vsite atoms for the whole system assuming all molecules are wholex. More...
 
static bool is_multisim_option_set (int argc, const char *const argv[])
 Return whether the command-line parameter that will trigger a multi-simulation is set.
 
static DevelopmentFeatureFlags manageDevelopmentFeatures (const gmx::MDLogger &mdlog, const bool useGpuForNonbonded, const PmeRunMode pmeRunMode, const int numRanksPerSimulation, const int numPmeRanksPerSimulation)
 Manage any development feature flag variables encountered. More...
 
static void threadMpiMdrunnerAccessBarrier ()
 Barrier for safe simultaneous thread access to mdrunner data. More...
 
static void mdrunner_start_fn (const void *arg)
 The callback used for running on spawned threads. More...
 
static bool gpuAccelerationOfNonbondedIsUseful (const MDLogger &mdlog, const t_inputrec &ir, const bool issueWarning, const bool doRerun)
 Return whether GPU acceleration of nonbondeds is supported with the given settings. More...
 
static gmx::LoggerOwner buildLogger (FILE *fplog, const bool isSimulationMasterRank)
 Initializes the logger for mdrun.
 
static TaskTarget findTaskTarget (const char *optionString)
 Make a TaskTarget from an mdrun argument string.
 
static void finish_run (FILE *fplog, const gmx::MDLogger &mdlog, const t_commrec *cr, const t_inputrec &inputrec, t_nrnb nrnb[], gmx_wallcycle *wcycle, gmx_walltime_accounting_t walltime_accounting, nonbonded_verlet_t *nbv, const gmx_pme_t *pme, gmx_bool bWriteStat)
 Finish run, aggregate data to print performance info.
 
void applyLocalState (const SimulationInput &simulationInput, t_fileio *logfio, const t_commrec *cr, int *dd_nc, t_inputrec *ir, t_state *state, ObservablesHistory *observablesHistory, bool reproducibilityRequested, const MDModulesNotifiers &notifiers, gmx::ReadCheckpointDataHolder *modularSimulatorCheckpointData, bool useModularSimulator)
 Initialize local stateful simulation data. More...
 
SimulationInputHandle makeSimulationInput (const LegacyMdrunOptions &options)
 
int computeFepPeriod (const t_inputrec &inputrec, const ReplicaExchangeParameters &replExParams)
 Compute the period at which FEP calculation is performed. More...
 
std::tuple< StartingBehavior,
LogFilePtr
handleRestart (bool isSimulationMaster, MPI_Comm communicator, const gmx_multisim_t *ms, AppendingBehavior appendingBehavior, int nfile, t_filenm fnm[])
 Handle startup of mdrun, particularly regarding -cpi and -append. More...
 
static void prepareLogFile (BinaryInformationSettings settings, FILE *fplog)
 Implements aspects of logfile handling common to opening either for writing or appending.
 
LogFilePtr openLogFile (const char *lognm, bool appendFiles)
 Open the log file for writing/appending. More...
 
void prepareLogAppending (FILE *fplog)
 Prepare to use the open log file when appending. More...
 
void closeLogFile (t_fileio *logfio)
 Close the log file.
 
template<class BasicMdspan >
constexpr std::enable_if_t
< BasicMdspan::is_always_contiguous(),
typename BasicMdspan::pointer > 
begin (const BasicMdspan &basicMdspan)
 Free begin function addressing memory of a contiguously laid out basic_mdspan. More...
 
template<class BasicMdspan >
constexpr std::enable_if_t
< BasicMdspan::is_always_contiguous(),
typename BasicMdspan::pointer > 
end (const BasicMdspan &basicMdspan)
 Free end function addressing memory of a contiguously laid out basic_mdspan. More...
 
template<class BasicMdspan >
constexpr BasicMdspan addElementwise (const BasicMdspan &span1, const BasicMdspan &span2)
 Elementwise addition.
 
template<class BasicMdspan >
constexpr BasicMdspan subtractElementwise (const BasicMdspan &span1, const BasicMdspan &span2)
 Elementwise subtraction - left minus right.
 
template<class BasicMdspan >
constexpr BasicMdspan multiplyElementwise (const BasicMdspan &span1, const BasicMdspan &span2)
 Elementwise multiplication.
 
template<class BasicMdspan >
constexpr BasicMdspan divideElementwise (const BasicMdspan &span1, const BasicMdspan &span2)
 Elementwise division - left / right.
 
template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>
constexpr bool operator== (const extents< LHS...> &lhs, const extents< RHS...> &rhs) noexcept
 Comparison operator. More...
 
template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>
constexpr bool operator!= (const extents< LHS...> &lhs, const extents< RHS...> &rhs) noexcept
 Check for non-equality. More...
 
template<CheckpointDataOperation operation, typename T >
ArrayRef< std::conditional_t
< operation==CheckpointDataOperation::Write||std::is_const
< T >::value, const typename
T::value_type, typename
T::value_type > > 
makeCheckpointArrayRef (T &container)
 
template<CheckpointDataOperation operation, typename T >
ArrayRef< std::conditional_t
< operation==CheckpointDataOperation::Write||std::is_const
< T >::value, const T, T > > 
makeCheckpointArrayRefFromArray (T *begin, size_t size)
 
template<typename VersionEnum >
VersionEnum checkpointVersion (const ReadCheckpointData *checkpointData, const std::string &key, const VersionEnum programVersion)
 Read a checkpoint version enum variable. More...
 
template<typename VersionEnum >
VersionEnum checkpointVersion (WriteCheckpointData *checkpointData, const std::string &key, const VersionEnum programVersion)
 Write the current code checkpoint version enum variable. More...
 
 forceMtsCombined_ ({})
 
 view_ ({},{}, false)
 
 useForceMtsCombined_ (false)
 
template<class T >
T & makeRefFromPointer (T *ptr)
 Take pointer, check if valid, return reference.
 
static const char * enumValueToString (AtomLocality enumValue)
 Get the human-friendly name for atom localities. More...
 
static const char * enumValueToString (InteractionLocality enumValue)
 Get the human-friendly name for interaction localities. More...
 
static InteractionLocality atomToInteractionLocality (const AtomLocality atomLocality)
 Convert atom locality to interaction locality. More...
 
int nonbondedMtsFactor (const t_inputrec &ir)
 Returns the interval in steps at which the non-bonded pair forces are calculated. More...
 
std::vector< MtsLevelsetupMtsLevels (const GromppMtsOpts &mtsOpts, std::vector< std::string > *errorMessages)
 Sets up and returns the MTS levels and checks requirements of MTS. More...
 
bool haveValidMtsSetup (const t_inputrec &ir)
 Returns whether we use MTS and the MTS setup is internally valid. More...
 
std::vector< std::string > checkMtsRequirements (const t_inputrec &ir)
 Checks whether the MTS requirements on other algorithms and output frequencies are met. More...
 
static int forceGroupMtsLevel (ArrayRef< const MtsLevel > mtsLevels, const MtsForceGroups mtsForceGroup)
 Returns the MTS level at which a force group is to be computed. More...
 
bool needStateGpu (SimulationWorkload simulationWorkload)
 If StatePropagatorDataGpu object is needed. More...
 
 conservedEnergyContribution_ (0)
 
 previousStepConservedEnergyContribution_ (0)
 
 conservedEnergyContributionStep_ (-1)
 
 reportPreviousStepConservedEnergy_ (reportPreviousStepConservedEnergy)
 
 statePropagatorData_ (statePropagatorData)
 
 energyData_ (energyData)
 
 fplog_ (fplog)
 
 inputrec_ (inputrec)
 
 mdAtoms_ (mdAtoms)
 
 nrnb_ (nrnb)
 
 identifier_ ("FirstOrderPressureCoupling-"+std::string(enumValueToString(pressureCouplingType_)))
 
template<typename... Ts>
auto checkUseModularSimulator (Ts &&...args) -> decltype(ModularSimulator::isInputCompatible(std::forward< Ts >(args)...))
 Whether or not to use the ModularSimulator. More...
 
 numDegreesOfFreedom_ (numDegreesOfFreedom)
 
 simulationTimeStep_ (simulationTimeStep)
 
 referenceTemperature_ (referenceTemperature)
 
 mttkPropagatorConnection_ (mttkPropagatorConnection)
 
 nextEnergyCalculationStep_ (-1)
 
template<NumVelocityScalingValues numStartVelocityScalingValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, NumVelocityScalingValues numEndVelocityScalingValues>
static void updateVelocities (int a, real dt, real lambdaStart, real lambdaEnd, const rvec *gmx_restrict invMassPerDim, rvec *gmx_restrict v, const rvec *gmx_restrict f, const rvec diagPR, const matrix matrixPR)
 Update velocities.
 
static void updatePositions (int a, real dt, const rvec *gmx_restrict x, rvec *gmx_restrict xprime, const rvec *gmx_restrict v)
 Update positions.
 
template<NumVelocityScalingValues numStartVelocityScalingValues>
static void scaleVelocities (int a, real lambda, rvec *gmx_restrict v)
 Scale velocities.
 
template<NumPositionScalingValues numPositionScalingValues>
static void scalePositions (int a, real lambda, rvec *gmx_restrict x)
 Scale positions.
 
template<ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
static bool diagonalizePRMatrix (matrix matrixPR, rvec diagPR)
 Helper function diagonalizing the PR matrix if possible.
 
 scalingStepPR_ (-1)
 
 wcycle_ (wcycle)
 
template<IntegrationStage integrationStage>
constexpr bool hasStartVelocityScaling ()
 
template<IntegrationStage integrationStage>
constexpr bool hasEndVelocityScaling ()
 
template<IntegrationStage integrationStage>
constexpr bool hasPositionScaling ()
 
template<IntegrationStage integrationStage>
constexpr bool hasParrinelloRahmanScaling ()
 
template<IntegrationStage integrationStage>
static PropagatorConnection getConnection (Propagator< integrationStage > gmx_unused *propagator, const PropagatorTag &propagatorTag)
 
template<CheckpointDataOperation operation>
static void doCheckpointData (CheckpointData< operation > *checkpointData, ArrayRef< double > previousStepCom)
 
static void runAllCallbacks (const std::vector< SignallerCallback > &callbacks, Step step, Time time)
 Helper function to call all callbacks in a list.
 
template<typename Element , typename... Args>
ISimulatorElement * getElementPointer (LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer, Args &&...args)
 
template<typename Base , typename Element >
static std::enable_if_t
< std::is_base_of< Base,
Element >::value, Base * > 
castOrNull (Element *element)
 Returns a pointer casted to type Base if the Element is derived from Base.
 
template<typename Base , typename Element >
static std::enable_if_t
<!std::is_base_of< Base,
Element >::value, Base * > 
castOrNull (Element gmx_unused *element)
 Returns a nullptr of type Base if Element is not derived from Base.
 
 ddpCount_ (0)
 
 element_ (std::make_unique< Element >(this, fplog, cr, inputrec->nstxout, inputrec->nstvout, inputrec->nstfout, inputrec->nstxout_compressed, canMoleculesBeDistributedOverPBC, writeFinalConfiguration, finalConfigurationFilename, inputrec, globalTop))
 
 referenceTemperatureHelper_ (std::make_unique< ReferenceTemperatureHelper >(inputrec, this, mdatoms))
 
 vvResetVelocities_ (false)
 
 isRegularSimulationEnd_ (false)
 
 lastStep_ (-1)
 
 globalState_ (globalState)
 
static void updateGlobalState (t_state *globalState, const PaddedHostVector< RVec > &x, const PaddedHostVector< RVec > &v, const tensor box, int ddpCount, int ddpCountCgGl, const std::vector< int > &cgGl)
 Update the legacy global state. More...
 
bool timesClose (Time time, Time referenceTime)
 Check whether two times are nearly equal. More...
 
static void generateCoordinates (int multiplicationFactor, std::vector< gmx::RVec > *coordinates, matrix box)
 Generates coordinates and a box for the base system scaled by multiplicationFactor.
 
void assignOptionsFromKeyValueTree (Options *options, const KeyValueTreeObject &tree, IKeyValueTreeErrorHandler *errorHandler)
 Assigns option values from a given KeyValueTreeObject. More...
 
void checkForUnknownOptionsInKeyValueTree (const KeyValueTreeObject &tree, const Options &options)
 Checks that a given KeyValueTreeObject can be assigned to given Options. More...
 
KeyValueTreeObject adjustKeyValueTreeFromOptions (const KeyValueTreeObject &tree, const Options &options)
 Adjusts a KeyValueTreeObject to the structure of given Options. More...
 
bool boxesAreEqual (const matrix box1, const matrix box2)
 Returns whether two boxes are of equal size and shape (within reasonable tolerance).
 
bool boxIsZero (const matrix box)
 Returns whether a box is only initialised to zero or not.
 
void shiftAtoms (const RVec &shift, ArrayRef< RVec > x)
 Shift all coordinates. More...
 
void placeCoordinatesWithCOMInBox (const PbcType &pbcType, UnitCellType unitCellType, CenteringType centerType, const matrix box, ArrayRef< RVec > x, const gmx_mtop_t &mtop, COMShiftType comShiftType)
 Moves collection of atoms along the center of mass into a box. More...
 
static int xyzToShiftIndex (int x, int y, int z)
 Convert grid coordinates to shift index.
 
static int ivecToShiftIndex (ivec iv)
 Convert grid coordinates to shift index.
 
static int shiftIndexToXDim (int iv)
 Return the shift in the X dimension of grid space corresponding to iv.
 
const char * centerTypeNames (CenteringType type)
 Get names for the different centering types. More...
 
const char * unitCellTypeNames (UnitCellType type)
 Get names for the different unit cell representation types. More...
 
double getTransformationPullCoordinateValue (pull_coord_work_t *coord, ArrayRef< const pull_coord_work_t > variableCoords)
 Calculates pull->coord[coord_ind].spatialData.value for a transformation pull coordinate. More...
 
static double computeDerivativeForTransformationPullCoord (pull_coord_work_t *coord, const int variablePcrdIndex)
 Calculates and returns the derivative of a transformation pull coordinate from a dependent coordinate. More...
 
static void distributeTransformationPullCoordForce (pull_coord_work_t *pcrd, gmx::ArrayRef< pull_coord_work_t > variableCoords, const double transformationCoordForce)
 Distributes the force from a transformation pull coordiante to the dependent pull coordinates by computing the inner derivatives. More...
 
void applyTransformationPullCoordForce (pull_coord_work_t *pcrd, gmx::ArrayRef< pull_coord_work_t > variableCoords, double transformationCoordForce)
 Applies a force of a transformation pull coordinate and distributes it to pull coordinates of lower rank. More...
 
static bool checkIfRandomDeviceIsFunctional ()
 Check if the RDRAND random device functioning correctly. More...
 
template<typename GeneratorType >
static uint64_t makeRandomSeedInternal (GeneratorType &gen)
 Get the next pure or pseudo-random number. More...
 
uint64_t makeRandomSeed ()
 Return 64 random bits from the random device, suitable as seed. More...
 
template<class RealType = real, unsigned int Bits, class Rng >
RealType generateCanonical (Rng &g)
 Generate a floating-point value with specified number of random bits. More...
 
void compileSelection (SelectionCollection *coll)
 
void swap (SelectionCollection &lhs, SelectionCollection &rhs)
 
HelpTopicPointer createSelectionHelpTopic ()
 */ More...
 
static void gmx_unused simdPrefetch (void gmx_unused *m)
 Prefetch memory at address m. More...
 
static void store (float *m, float a)
 Store contents of float variable to aligned memory m. More...
 
static void storeU (float *m, float a)
 Store contents of float variable to unaligned memory m. More...
 
static float fma (float a, float b, float c)
 Float Fused-multiply-add. Result is a*b + c. More...
 
static float fms (float a, float b, float c)
 Float Fused-multiply-subtract. Result is a*b - c. More...
 
static float fnma (float a, float b, float c)
 Float Fused-negated-multiply-add. Result is -a*b + c. More...
 
static float fnms (float a, float b, float c)
 Float Fused-negated-multiply-subtract. Result is -a*b - c. More...
 
static float maskAdd (float a, float b, float m)
 Add two float variables, masked version. More...
 
static float maskzMul (float a, float b, float m)
 Multiply two float variables, masked version. More...
 
static float maskzFma (float a, float b, float c, float m)
 Float fused multiply-add, masked version. More...
 
static float gmx_simdcall maskzRcp (float x, float m)
 Float 1.0/x, masked version. More...
 
static float abs (float a)
 Float Floating-point abs(). More...
 
static float max (float a, float b)
 Set each float element to the largest from two variables. More...
 
static float min (float a, float b)
 Set each float element to the smallest from two variables. More...
 
static float round (float a)
 Float round to nearest integer value (in floating-point format). More...
 
static float trunc (float a)
 Truncate float, i.e. round towards zero - common hardware instruction. More...
 
static float reduce (float a)
 Return sum of all elements in float variable (i.e., the variable itself). More...
 
static float andNot (float a, float b)
 Bitwise andnot for two scalar float variables. More...
 
static bool testBits (float a)
 Return true if any bits are set in the float variable. More...
 
static bool anyTrue (bool a)
 Returns if the boolean is true. More...
 
static float selectByMask (float a, bool mask)
 Select from single precision variable where boolean is true. More...
 
static float selectByNotMask (float a, bool mask)
 Select from single precision variable where boolean is false. More...
 
static float blend (float a, float b, bool sel)
 Blend float selection. More...
 
static std::int32_t cvtR2I (float a)
 Round single precision floating point to integer. More...
 
static std::int32_t cvttR2I (float a)
 Truncate single precision floating point to integer. More...
 
static std::int32_t cvtI2R (std::int32_t a)
 Return integer. More...
 
static void store (double *m, double a)
 Store contents of double variable to aligned memory m. More...
 
static void storeU (double *m, double a)
 Store contents of double variable to unaligned memory m. More...
 
static double fma (double a, double b, double c)
 double Fused-multiply-add. Result is a*b + c. More...
 
static double fms (double a, double b, double c)
 double Fused-multiply-subtract. Result is a*b - c. More...
 
static double fnma (double a, double b, double c)
 double Fused-negated-multiply-add. Result is - a*b + c. More...
 
static double fnms (double a, double b, double c)
 double Fused-negated-multiply-subtract. Result is -a*b - c. More...
 
static double maskAdd (double a, double b, double m)
 Add two double variables, masked version. More...
 
static double maskzMul (double a, double b, double m)
 Multiply two double variables, masked version. More...
 
static double maskzFma (double a, double b, double c, double m)
 double fused multiply-add, masked version. More...
 
static double gmx_simdcall maskzRcp (double x, double m)
 Double 1.0/x, masked version. More...
 
static double abs (double a)
 double doubleing-point abs(). More...
 
static double max (double a, double b)
 Set each double element to the largest from two variables. More...
 
static double min (double a, double b)
 Set each double element to the smallest from two variables. More...
 
static double round (double a)
 double round to nearest integer value (in doubleing-point format). More...
 
static double trunc (double a)
 Truncate double, i.e. round towards zero - common hardware instruction. More...
 
static double reduce (double a)
 Return sum of all elements in double variable (i.e., the variable itself). More...
 
static double andNot (double a, double b)
 Bitwise andnot for two scalar double variables. More...
 
static bool testBits (double a)
 Return true if any bits are set in the double variable. More...
 
static double selectByMask (double a, bool mask)
 Select from double precision variable where boolean is true. More...
 
static double selectByNotMask (double a, bool mask)
 Select from double precision variable where boolean is false. More...
 
static double blend (double a, double b, bool sel)
 Blend double selection. More...
 
static std::int32_t cvtR2I (double a)
 Round single precision doubleing point to integer. More...
 
static std::int32_t cvttR2I (double a)
 Truncate single precision doubleing point to integer. More...
 
static double cvtF2D (float a)
 Convert float to double (mimicks SIMD conversion) More...
 
static float cvtD2F (double a)
 Convert double to float (mimicks SIMD conversion) More...
 
static void store (std::int32_t *m, std::int32_t a)
 Store contents of integer variable to aligned memory m. More...
 
static void storeU (std::int32_t *m, std::int32_t a)
 Store contents of integer variable to unaligned memory m. More...
 
static std::int32_t andNot (std::int32_t a, std::int32_t b)
 Bitwise andnot for two scalar integer variables. More...
 
static bool testBits (std::int32_t a)
 Return true if any bits are set in the integer variable. More...
 
static std::int32_t selectByMask (std::int32_t a, bool mask)
 Select from integer variable where boolean is true. More...
 
static std::int32_t selectByNotMask (std::int32_t a, bool mask)
 Select from integer variable where boolean is false. More...
 
static std::int32_t blend (std::int32_t a, std::int32_t b, bool sel)
 Blend integer selection. More...
 
static bool cvtB2IB (bool a)
 Just return a boolean (mimicks SIMD real-to-int bool conversions) More...
 
static bool cvtIB2B (bool a)
 Just return a boolean (mimicks SIMD int-to-real bool conversions) More...
 
static float copysign (float x, float y)
 Composes single value with the magnitude of x and the sign of y. More...
 
static void invsqrtPair (float x0, float x1, float *out0, float *out1)
 Calculate 1/sqrt(x) for two floats. More...
 
static float inv (float x)
 Calculate 1/x for float. More...
 
static float maskzInvsqrt (float x, bool m)
 Calculate 1/sqrt(x) for masked entry of float. More...
 
static float maskzInv (float x, bool m)
 Calculate 1/x for masked entry of float. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static float sqrt (float x)
 Float sqrt(x). This is the square root. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static float cbrt (float x)
 Float cbrt(x). This is the cubic root. More...
 
static float log (float x)
 Float log(x). This is the natural logarithm. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static float exp2 (float x)
 Float 2^x. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static float exp (float x)
 Float exp(x). More...
 
static float erf (float x)
 Float erf(x). More...
 
static float erfc (float x)
 Float erfc(x). More...
 
static void sincos (float x, float *sinval, float *cosval)
 Float sin & cos. More...
 
static float sin (float x)
 Float sin. More...
 
static float cos (float x)
 Float cos. More...
 
static float tan (float x)
 Float tan. More...
 
static float asin (float x)
 float asin. More...
 
static float acos (float x)
 Float acos. More...
 
static float atan (float x)
 Float atan. More...
 
static float atan2 (float y, float x)
 Float atan2(y,x). More...
 
static float pmeForceCorrection (float z2)
 Calculate the force correction due to PME analytically in float. More...
 
static float pmePotentialCorrection (float z2)
 Calculate the potential correction due to PME analytically in float. More...
 
static double copysign (double x, double y)
 Composes double value with the magnitude of x and the sign of y. More...
 
static void invsqrtPair (double x0, double x1, double *out0, double *out1)
 Calculate 1/sqrt(x) for two doubles. More...
 
static double inv (double x)
 Calculate 1/x for double. More...
 
static double maskzInvsqrt (double x, bool m)
 Calculate 1/sqrt(x) for masked entry of double. More...
 
static double maskzInv (double x, bool m)
 Calculate 1/x for masked entry of double. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static double sqrt (double x)
 Double sqrt(x). This is the square root. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static double cbrt (double x)
 Double cbrt(x). This is the cubic root. More...
 
static double log (double x)
 Double log(x). This is the natural logarithm. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static double exp2 (double x)
 Double 2^x. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static double exp (double x)
 Double exp(x). More...
 
static double erf (double x)
 Double erf(x). More...
 
static double erfc (double x)
 Double erfc(x). More...
 
static void sincos (double x, double *sinval, double *cosval)
 Double sin & cos. More...
 
static double sin (double x)
 Double sin. More...
 
static double cos (double x)
 Double cos. More...
 
static double tan (double x)
 Double tan. More...
 
static double asin (double x)
 Double asin. More...
 
static double acos (double x)
 Double acos. More...
 
static double atan (double x)
 Double atan. More...
 
static double atan2 (double y, double x)
 Double atan2(y,x). More...
 
static double pmeForceCorrection (double z2)
 Calculate the force correction due to PME analytically in double. More...
 
static double pmePotentialCorrection (double z2)
 Calculate the potential correction due to PME analytically in double. More...
 
static double invsqrtSingleAccuracy (double x)
 Calculate 1/sqrt(x) for double, but with single accuracy. More...
 
static void invsqrtPairSingleAccuracy (double x0, double x1, double *out0, double *out1)
 Calculate 1/sqrt(x) for two doubles, but with single accuracy. More...
 
static double invSingleAccuracy (double x)
 Calculate 1/x for double, but with single accuracy. More...
 
static double maskzInvsqrtSingleAccuracy (double x, bool m)
 Calculate 1/sqrt(x) for masked entry of double, but with single accuracy. More...
 
static double maskzInvSingleAccuracy (double x, bool m)
 Calculate 1/x for masked entry of double, but with single accuracy. More...
 
static double sqrtSingleAccuracy (double x)
 Calculate sqrt(x) for double, but with single accuracy. More...
 
static double logSingleAccuracy (double x)
 Double log(x), but with single accuracy. This is the natural logarithm. More...
 
static double exp2SingleAccuracy (double x)
 Double 2^x, but with single accuracy. More...
 
static double expSingleAccuracy (double x)
 Double exp(x), but with single accuracy. More...
 
static double erfSingleAccuracy (double x)
 Double erf(x), but with single accuracy. More...
 
static double erfcSingleAccuracy (double x)
 Double erfc(x), but with single accuracy. More...
 
static void sincosSingleAccuracy (double x, double *sinval, double *cosval)
 Double sin & cos, but with single accuracy. More...
 
static double sinSingleAccuracy (double x)
 Double sin, but with single accuracy. More...
 
static double cosSingleAccuracy (double x)
 Double cos, but with single accuracy. More...
 
static double tanSingleAccuracy (double x)
 Double tan, but with single accuracy. More...
 
static double asinSingleAccuracy (double x)
 Double asin, but with single accuracy. More...
 
static double acosSingleAccuracy (double x)
 Double acos, but with single accuracy. More...
 
static double atanSingleAccuracy (double x)
 Double atan, but with single accuracy. More...
 
static double atan2SingleAccuracy (double y, double x)
 Double atan2(y,x), but with single accuracy. More...
 
static double pmeForceCorrectionSingleAccuracy (double z2)
 Force correction due to PME in double, but with single accuracy. More...
 
static double pmePotentialCorrectionSingleAccuracy (double z2)
 Potential correction due to PME in double, but with single accuracy. More...
 
template<int align>
static void gatherLoadTranspose (const float *base, const std::int32_t offset[], float *v0, float *v1, float *v2, float *v3)
 Load 4 consecutive floats from base/offset into four variables. More...
 
template<int align>
static void gatherLoadTranspose (const float *base, const std::int32_t offset[], float *v0, float *v1)
 Load 2 consecutive floats from base/offset into four variables. More...
 
template<int align>
static void gatherLoadUTranspose (const float *base, const std::int32_t offset[], float *v0, float *v1, float *v2)
 Load 3 consecutive floats from base/offsets, store into three vars. More...
 
template<int align>
static void transposeScatterStoreU (float *base, const std::int32_t offset[], float v0, float v1, float v2)
 Store 3 floats to 3 to base/offset. More...
 
template<int align>
static void transposeScatterIncrU (float *base, const std::int32_t offset[], float v0, float v1, float v2)
 Add 3 floats to base/offset. More...
 
template<int align>
static void transposeScatterDecrU (float *base, const std::int32_t offset[], float v0, float v1, float v2)
 Subtract 3 floats from base/offset. More...
 
static void expandScalarsToTriplets (float scalar, float *triplets0, float *triplets1, float *triplets2)
 Copy single float to three variables. More...
 
template<int align>
static void gatherLoadBySimdIntTranspose (const float *base, std::int32_t offset, float *v0, float *v1, float *v2, float *v3)
 Load 4 floats from base/offsets and store into variables. More...
 
template<int align>
static void gatherLoadUBySimdIntTranspose (const float *base, std::int32_t offset, float *v0, float *v1)
 Load 2 floats from base/offsets and store into variables (unaligned). More...
 
template<int align>
static void gatherLoadBySimdIntTranspose (const float *base, std::int32_t offset, float *v0, float *v1)
 Load 2 floats from base/offsets and store into variables (aligned). More...
 
static float reduceIncr4ReturnSum (float *m, float v0, float v1, float v2, float v3)
 Add each float to four consecutive memory locations, return sum. More...
 
template<int align>
static void gatherLoadTranspose (const double *base, const std::int32_t offset[], double *v0, double *v1, double *v2, double *v3)
 Load 4 consecutive doubles from base/offset into four variables. More...
 
template<int align>
static void gatherLoadTranspose (const double *base, const std::int32_t offset[], double *v0, double *v1)
 Load 2 consecutive doubles from base/offset into four variables. More...
 
template<int align>
static void gatherLoadUTranspose (const double *base, const std::int32_t offset[], double *v0, double *v1, double *v2)
 Load 3 consecutive doubles from base/offsets, store into three vars. More...
 
template<int align>
static void transposeScatterStoreU (double *base, const std::int32_t offset[], double v0, double v1, double v2)
 Store 3 doubles to 3 to base/offset. More...
 
template<int align>
static void transposeScatterIncrU (double *base, const std::int32_t offset[], double v0, double v1, double v2)
 Add 3 doubles to base/offset. More...
 
template<int align>
static void transposeScatterDecrU (double *base, const std::int32_t offset[], double v0, double v1, double v2)
 Subtract 3 doubles from base/offset. More...
 
static void expandScalarsToTriplets (double scalar, double *triplets0, double *triplets1, double *triplets2)
 Copy single double to three variables. More...
 
template<int align>
static void gatherLoadBySimdIntTranspose (const double *base, std::int32_t offset, double *v0, double *v1, double *v2, double *v3)
 Load 4 doubles from base/offsets and store into variables. More...
 
template<int align>
static void gatherLoadUBySimdIntTranspose (const double *base, std::int32_t offset, double *v0, double *v1)
 Load 2 doubles from base/offsets and store into variables (unaligned). More...
 
template<int align>
static void gatherLoadBySimdIntTranspose (const double *base, std::int32_t offset, double *v0, double *v1)
 Load 2 doubles from base/offsets and store into variables (aligned). More...
 
static double reduceIncr4ReturnSum (double *m, double v0, double v1, double v2, double v3)
 Add each double to four consecutive memory locations, return sum. More...
 
static SimdFloat gmx_simdcall invsqrtSingleAccuracy (SimdFloat x)
 Calculate 1/sqrt(x) for SIMD float, only targeting single accuracy. More...
 
static SimdFloat maskzInvsqrtSingleAccuracy (SimdFloat x, SimdFBool m)
 Calculate 1/sqrt(x) for masked SIMD floats, only targeting single accuracy. More...
 
static void gmx_simdcall invsqrtPairSingleAccuracy (SimdFloat x0, SimdFloat x1, SimdFloat *out0, SimdFloat *out1)
 Calculate 1/sqrt(x) for two SIMD floats, only targeting single accuracy. More...
 
static SimdFloat gmx_simdcall invSingleAccuracy (SimdFloat x)
 Calculate 1/x for SIMD float, only targeting single accuracy. More...
 
static SimdFloat maskzInvSingleAccuracy (SimdFloat x, SimdFBool m)
 Calculate 1/x for masked SIMD floats, only targeting single accuracy. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall sqrtSingleAccuracy (SimdFloat x)
 Calculate sqrt(x) for SIMD float, always targeting single accuracy. More...
 
static SimdFloat gmx_simdcall cbrtSingleAccuracy (SimdFloat x)
 Calculate cbrt(x) for SIMD float, always targeting single accuracy. More...
 
static SimdFloat gmx_simdcall invcbrtSingleAccuracy (SimdFloat x)
 Calculate 1/cbrt(x) for SIMD float, always targeting single accuracy. More...
 
static SimdFloat gmx_simdcall log2SingleAccuracy (SimdFloat x)
 SIMD float log2(x), only targeting single accuracy. This is the base-2 logarithm. More...
 
static SimdFloat gmx_simdcall logSingleAccuracy (SimdFloat x)
 SIMD float log(x), only targeting single accuracy. This is the natural logarithm. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall exp2SingleAccuracy (SimdFloat x)
 SIMD float 2^x, only targeting single accuracy. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall expSingleAccuracy (SimdFloat x)
 SIMD float e^x, only targeting single accuracy. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall powSingleAccuracy (SimdFloat x, SimdFloat y)
 SIMD pow(x,y), only targeting single accuracy. More...
 
static SimdFloat gmx_simdcall erfSingleAccuracy (SimdFloat x)
 SIMD float erf(x), only targeting single accuracy. More...
 
static SimdFloat gmx_simdcall erfcSingleAccuracy (SimdFloat x)
 SIMD float erfc(x), only targeting single accuracy. More...
 
static void gmx_simdcall sinCosSingleAccuracy (SimdFloat x, SimdFloat *sinval, SimdFloat *cosval)
 SIMD float sin & cos, only targeting single accuracy. More...
 
static SimdFloat gmx_simdcall sinSingleAccuracy (SimdFloat x)
 SIMD float sin(x), only targeting single accuracy. More...
 
static SimdFloat gmx_simdcall cosSingleAccuracy (SimdFloat x)
 SIMD float cos(x), only targeting single accuracy. More...
 
static SimdFloat gmx_simdcall tanSingleAccuracy (SimdFloat x)
 SIMD float tan(x), only targeting single accuracy. More...
 
static SimdFloat gmx_simdcall asinSingleAccuracy (SimdFloat x)
 SIMD float asin(x), only targeting single accuracy. More...
 
static SimdFloat gmx_simdcall acosSingleAccuracy (SimdFloat x)
 SIMD float acos(x), only targeting single accuracy. More...
 
static SimdFloat gmx_simdcall atanSingleAccuracy (SimdFloat x)
 SIMD float atan(x), only targeting single accuracy. More...
 
static SimdFloat gmx_simdcall atan2SingleAccuracy (SimdFloat y, SimdFloat x)
 SIMD float atan2(y,x), only targeting single accuracy. More...
 
static SimdFloat gmx_simdcall pmeForceCorrectionSingleAccuracy (SimdFloat z2)
 SIMD Analytic PME force correction, only targeting single accuracy. More...
 
static SimdFloat gmx_simdcall pmePotentialCorrectionSingleAccuracy (SimdFloat z2)
 SIMD Analytic PME potential correction, only targeting single accuracy. More...
 
static Simd4Float gmx_simdcall invsqrtSingleAccuracy (Simd4Float x)
 Calculate 1/sqrt(x) for SIMD4 float, only targeting single accuracy. More...
 
const std::string & simdString (SimdType s)
 Return a string with the name of a SIMD type. More...
 
SimdType simdSuggested (const CpuInfo &c)
 Return the SIMD type that would fit this hardware best.
 
SimdType simdCompiled ()
 Return the SIMD type the library was compiled with.
 
bool simdCheck (SimdType s, FILE *log, bool warnToStdErr)
 Check if binary was compiled with the provided SIMD type. More...
 
static SimdFloat gmx_simdcall iprod (SimdFloat ax, SimdFloat ay, SimdFloat az, SimdFloat bx, SimdFloat by, SimdFloat bz)
 SIMD float inner product of multiple float vectors. More...
 
static SimdFloat gmx_simdcall norm2 (SimdFloat ax, SimdFloat ay, SimdFloat az)
 SIMD float norm squared of multiple vectors. More...
 
static void gmx_simdcall cprod (SimdFloat ax, SimdFloat ay, SimdFloat az, SimdFloat bx, SimdFloat by, SimdFloat bz, SimdFloat *cx, SimdFloat *cy, SimdFloat *cz)
 SIMD float cross-product of multiple vectors. More...
 
static SimdDouble gmx_simdcall iprod (SimdDouble ax, SimdDouble ay, SimdDouble az, SimdDouble bx, SimdDouble by, SimdDouble bz)
 SIMD double inner product of multiple double vectors. More...
 
static SimdDouble gmx_simdcall norm2 (SimdDouble ax, SimdDouble ay, SimdDouble az)
 SIMD double norm squared of multiple vectors. More...
 
static void gmx_simdcall cprod (SimdDouble ax, SimdDouble ay, SimdDouble az, SimdDouble bx, SimdDouble by, SimdDouble bz, SimdDouble *cx, SimdDouble *cy, SimdDouble *cz)
 SIMD double cross-product of multiple vectors. More...
 
static Simd4Float gmx_simdcall norm2 (Simd4Float ax, Simd4Float ay, Simd4Float az)
 SIMD4 float norm squared of multiple vectors. More...
 
static Simd4Double gmx_simdcall norm2 (Simd4Double ax, Simd4Double ay, Simd4Double az)
 SIMD4 double norm squared of multiple vectors. More...
 
std::unique_ptr< IMDModulecreateSwapCoordinatesModule ()
 Creates a module for Computational Electrophysiology swapping.
 
bool decideWhetherToUseGpusForNonbondedWithThreadMpi (TaskTarget nonbondedTarget, bool haveAvailableDevices, const std::vector< int > &userGpuTaskAssignment, EmulateGpuNonbonded emulateGpuNonbonded, bool buildSupportsNonbondedOnGpu, bool nonbondedOnGpuIsUseful, int numRanksPerSimulation)
 Decide whether this thread-MPI simulation will run nonbonded tasks on GPUs. More...
 
static bool decideWhetherToUseGpusForPmeFft (const TaskTarget pmeFftTarget)
 
static bool canUseGpusForPme (const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const gmx_hw_info_t &hardwareInfo, const t_inputrec &inputrec, std::string *errorMessage)
 
bool decideWhetherToUseGpusForPmeWithThreadMpi (bool useGpuForNonbonded, TaskTarget pmeTarget, TaskTarget pmeFftTarget, int numDevicesToUse, const std::vector< int > &userGpuTaskAssignment, const gmx_hw_info_t &hardwareInfo, const t_inputrec &inputrec, int numRanksPerSimulation, int numPmeRanksPerSimulation)
 Decide whether this thread-MPI simulation will run PME tasks on GPUs. More...
 
bool decideWhetherToUseGpusForNonbonded (TaskTarget nonbondedTarget, const std::vector< int > &userGpuTaskAssignment, EmulateGpuNonbonded emulateGpuNonbonded, bool buildSupportsNonbondedOnGpu, bool nonbondedOnGpuIsUseful, bool gpusWereDetected)
 Decide whether the simulation will try to run nonbonded tasks on GPUs. More...
 
bool decideWhetherToUseGpusForPme (bool useGpuForNonbonded, TaskTarget pmeTarget, TaskTarget pmeFftTarget, const std::vector< int > &userGpuTaskAssignment, const gmx_hw_info_t &hardwareInfo, const t_inputrec &inputrec, int numRanksPerSimulation, int numPmeRanksPerSimulation, bool gpusWereDetected)
 Decide whether the simulation will try to run tasks of different types on GPUs. More...
 
PmeRunMode determinePmeRunMode (bool useGpuForPme, const TaskTarget &pmeFftTarget, const t_inputrec &inputrec)
 Determine PME run mode. More...
 
bool decideWhetherToUseGpusForBonded (bool useGpuForNonbonded, bool useGpuForPme, TaskTarget bondedTarget, const t_inputrec &inputrec, const gmx_mtop_t &mtop, int numPmeRanksPerSimulation, bool gpusWereDetected)
 Decide whether the simulation will try to run bonded tasks on GPUs. More...
 
bool decideWhetherToUseGpuForUpdate (bool isDomainDecomposition, bool useUpdateGroups, PmeRunMode pmeRunMode, bool havePmeOnlyRank, bool useGpuForNonbonded, TaskTarget updateTarget, bool gpusWereDetected, const t_inputrec &inputrec, const gmx_mtop_t &mtop, bool useEssentialDynamics, bool doOrientationRestraints, bool haveFrozenAtoms, bool doRerun, const DevelopmentFeatureFlags &devFlags, const gmx::MDLogger &mdlog)
 Decide whether to use GPU for update. More...
 
bool decideWhetherDirectGpuCommunicationCanBeUsed (const DevelopmentFeatureFlags &devFlags, const gmx::MDLogger &mdlog)
 Decide whether direct GPU communication can be used. More...
 
bool decideWhetherToUseGpuForHalo (bool havePPDomainDecomposition, bool useGpuForNonbonded, bool canUseDirectGpuComm, bool useModularSimulator, bool doRerun, bool haveEnergyMinimization)
 Decide whether to use GPU for halo exchange. More...
 
SimulationWorkload createSimulationWorkload (const t_inputrec &inputrec, bool disableNonbondedCalculation, const DevelopmentFeatureFlags &devFlags, bool havePpDomainDecomposition, bool haveSeparatePmeRank, bool useGpuForNonbonded, PmeRunMode pmeRunMode, bool useGpuForBonded, bool useGpuForUpdate, bool useGpuDirectHalo, bool canUseDirectGpuComm, bool useGpuPmeDecomposition)
 Build datastructure that contains decisions whether to run different workload task on GPUs. More...
 
std::vector< GpuTaskfindGpuTasksOnThisRank (bool haveGpusOnThisPhysicalNode, TaskTarget nonbondedTarget, TaskTarget pmeTarget, TaskTarget bondedTarget, TaskTarget updateTarget, bool useGpuForNonbonded, bool useGpuForPme, bool rankHasPpTask, bool rankHasPmeTask)
 Returns container of all tasks on this rank that are eligible for GPU execution. More...
 
GpuTasksOnRanks findAllGpuTasksOnThisNode (ArrayRef< const GpuTask > gpuTasksOnThisRank, const PhysicalNodeCommunicator &physicalNodeComm)
 Returns container of all tasks on all ranks of this node that are eligible for GPU execution. More...
 
void reportGpuUsage (const MDLogger &mdlog, ArrayRef< const GpuTaskAssignment > gpuTaskAssignmentOnRanksOfThisNode, size_t numGpuTasksOnThisNode, size_t numPpRanks, bool printHostName, PmeRunMode pmeRunMode, const SimulationWorkload &simulationWork)
 Log a report on how GPUs are being used on the ranks of the physical node of rank 0 of the simulation. More...
 
void checkHardwareOversubscription (int numThreadsOnThisRank, int rank, const HardwareTopology &hwTop, const PhysicalNodeCommunicator &comm, const MDLogger &mdlog)
 Warns for oversubscribing the hardware threads, when that is the case.
 
template<GpuTask TaskType>
static bool hasTaskType (const GpuTaskMapping &mapping)
 Function for whether the task of mapping has value TaskType. More...
 
static bool hasPmeOrNonbondedTask (const GpuTaskMapping &mapping)
 Function for whether the mapping has the GPU PME or Nonbonded task. More...
 
static std::vector< int > parseGpuDeviceIdentifierList (const std::string &gpuIdString)
 Parse a GPU ID specifier string into a container. More...
 
std::vector< int > parseUserGpuIdString (const std::string &gpuIdString)
 Parse a GPU ID specifier string into a container describing device IDs exposed to the run. More...
 
std::vector< int > makeListOfAvailableDevices (gmx::ArrayRef< const std::unique_ptr< DeviceInformation >> deviceInfoList, const std::string &devicesSelectedByUserString)
 Implement GPU ID selection by returning the available GPU IDs on this physical node that are compatible. More...
 
std::vector< int > parseUserTaskAssignmentString (const std::string &gpuIdString)
 Parse a GPU ID specifier string into a container describing device ID to task mapping. More...
 
std::vector< int > makeGpuIds (ArrayRef< const int > compatibleGpus, size_t numGpuTasks)
 Make a vector containing numGpuTasks IDs of the IDs found in compatibleGpus. More...
 
std::string makeGpuIdString (const std::vector< int > &gpuIds, int totalNumberOfTasks)
 Convert a container of GPU deviced IDs to a string that can be used by gmx tune_pme as input to mdrun -gputasks. More...
 
void checkUserGpuIds (ArrayRef< const std::unique_ptr< DeviceInformation >> deviceInfoList, ArrayRef< const int > compatibleGpus, ArrayRef< const int > gpuIds)
 Check that all user-selected GPUs are compatible. More...
 
void writeHeader (TextWriter *writer, const std::string &text, const std::string &section, bool writeFormattedText)
 Write appropiate Header to output stream. More...
 
void writeSystemInformation (TextWriter *writer, const gmx_mtop_t &top, bool writeFormattedText)
 Write information about the molecules in the system. More...
 
void writeParameterInformation (TextWriter *writer, const t_inputrec &ir, bool writeFormattedText)
 Write information about system parameters. More...
 
void writeInformation (TextOutputFile *outputStream, const t_inputrec &ir, const gmx_mtop_t &top, bool writeFormattedText, bool notStdout)
 Wrapper for writing out information. More...
 
void blockaToExclusionBlocks (const t_blocka *b, gmx::ArrayRef< ExclusionBlock > b2)
 Convert the exclusions. More...
 
void exclusionBlocksToBlocka (gmx::ArrayRef< const ExclusionBlock > b2, t_blocka *b)
 Convert the exclusions expressed in b into t_blocka form.
 
void mergeExclusions (ListOfLists< int > *excl, gmx::ArrayRef< ExclusionBlock > b2)
 Merge the contents of b2 into excl. More...
 
void registerTrajectoryAnalysisModules (CommandLineModuleManager *manager)
 Registers all trajectory analysis command-line modules. More...
 
gmx_rmpbc_t gmx_rmpbc_init (const gmx::TopologyInformation &topInfo)
 Convenience overload useful for implementing legacy tools.
 
static std::size_t getPageSize ()
 Return a page size, from a sysconf/WinAPI query if available, or a default guess (4096 bytes). More...
 
std::size_t pageSize ()
 Return the memory page size on this system. More...
 
std::string simpleValueToString (const Any &value)
 Converts a Any value to a string. More...
 
void printBinaryInformation (FILE *fp, const IProgramContext &programContext)
 Print basic information about the executable. More...
 
void printBinaryInformation (FILE *fp, const IProgramContext &programContext, const BinaryInformationSettings &settings)
 Print basic information about the executable with custom settings. More...
 
void printBinaryInformation (TextWriter *writer, const IProgramContext &programContext, const BinaryInformationSettings &settings)
 Print basic information about the executable with custom settings. More...
 
std::string bromacs ()
 Return a cool definition for the acronym GROMACS.
 
std::string getCoolQuote ()
 Return a string with a cool quote.
 
std::string getCudaDriverVersionString ()
 Returns a string of the CUDA driver version.
 
std::string getCudaRuntimeVersionString ()
 Returns a string of the CUDA runtime version.
 
template<typename EnumerationArrayType >
EnumerationArrayType::EnumerationWrapperType keysOf (const EnumerationArrayType &)
 Returns an object that provides iterators over the keys associated with EnumerationArrayType. More...
 
const char * getErrorCodeString (int errorcode)
 Returns a short string description of an error code. More...
 
void printFatalErrorMessage (FILE *fp, const std::exception &ex)
 Formats a standard fatal error message for reporting an exception. More...
 
std::string formatExceptionMessageToString (const std::exception &ex)
 Formats an error message for reporting an exception. More...
 
void formatExceptionMessageToFile (FILE *fp, const std::exception &ex)
 Formats an error message for reporting an exception. More...
 
void formatExceptionMessageToWriter (TextWriter *writer, const std::exception &ex)
 Formats an error message for reporting an exception. More...
 
int processExceptionAtExit (const std::exception &ex)
 Handles an exception that is causing the program to terminate. More...
 
void processExceptionAsFatalError (const std::exception &ex)
 Helper function for terminating the program on an exception. More...
 
void fclose_wrapper (FILE *fp)
 fclose wrapper to be used as unique_ptr deleter
 
IFileInputRedirectordefaultFileInputRedirector ()
 Returns default implementation for IFileInputRedirector. More...
 
IFileOutputRedirectordefaultFileOutputRedirector ()
 Returns default implementation for IFileOutputRedirector. More...
 
const DataFileFindergetLibraryFileFinder ()
 Gets a finder for locating data files from share/top/. More...
 
void setLibraryFileFinder (const DataFileFinder *finder)
 Sets a finder for location data files from share/top/. More...
 
std::string findLibraryFile (const std::string &filename, bool bAddCWD=true, bool bFatal=true)
 Finds full path for a library file. More...
 
std::string findLibraryFile (const char *filename, bool bAddCWD=true, bool bFatal=true)
 Finds full path for a library file. More...
 
FilePtr openLibraryFile (const std::string &filename, bool bAddCWD=true, bool bFatal=true)
 Opens a library file for reading in an RAII-style FILE handle. More...
 
FilePtr openLibraryFile (const char *filename, bool bAddCWD=true, bool bFatal=true)
 Opens a library file for reading in an RAII-style FILE handle. More...
 
IKeyValueTreeErrorHandler * defaultKeyValueTreeErrorHandler ()
 Returns a default IKeyValueTreeErrorHandler that throws on first exception.
 
void init (int *argc, char ***argv)
 Initializes the GROMACS library. More...
 
void finalize ()
 Deinitializes the GROMACS library. More...
 
void dumpKeyValueTree (TextWriter *writer, const KeyValueTreeObject &tree)
 Writes a human-readable representation of the tree with given writer. More...
 
void compareKeyValueTrees (TextWriter *writer, const KeyValueTreeObject &tree1, const KeyValueTreeObject &tree2, real ftol, real abstol)
 Compares two KeyValueTrees and prints any differences.
 
KeyValueTreePath operator+ (const KeyValueTreePath &a, const KeyValueTreePath &b)
 Combines two paths as with KeyValueTreePath::append().
 
KeyValueTreePath operator+ (const KeyValueTreePath &a, const std::string &b)
 Combines an element to a path as with KeyValueTreePath::append().
 
static std::string simpleValueToString (const KeyValueTreeValue &value)
 Helper function to format a simple KeyValueTreeValue.
 
void writeKeyValueTreeAsMdp (TextWriter *writer, const KeyValueTreeObject &tree)
 Write a flat key-value tree to writer in mdp style. More...
 
void serializeKeyValueTree (const KeyValueTreeObject &root, ISerializer *serializer)
 Serializes a KeyValueTreeObject with given serializer.
 
KeyValueTreeObject deserializeKeyValueTree (ISerializer *serializer)
 Deserializes a KeyValueTreeObject from a given serializer.
 
CudaAwareMpiStatus checkMpiCudaAwareSupport ()
 Wrapper on top of MPIX_Query_cuda_support() For MPI implementations which don't support this function, it returns NotKnown Even when an MPI implementation does support this function, MPI library might not be robust enough to detect CUDA-aware support at runtime correcly e.g. when UCX PML is used or CUDA is disabled at runtime. More...
 
void niceHeader (TextWriter *writer, const char *fn, char commentChar)
 Prints creation time stamp and user information into a string as comments, and returns it. More...
 
void MPI_Comm_free_wrapper (MPI_Comm *comm)
 Wrapper function for RAII-style cleanup. More...
 
const IProgramContextgetProgramContext ()
 Returns the global IProgramContext instance. More...
 
void setProgramContext (const IProgramContext *context)
 Sets the global IProgramContext instance. More...
 
bool boolFromString (const char *str)
 Parses a boolean from a string. More...
 
int intFromString (const char *str)
 Parses an integer from a string. More...
 
int64_t int64FromString (const char *str)
 Parses a 64-bit integer from a string. More...
 
float floatFromString (const char *str)
 Parses a float value from a string. More...
 
double doubleFromString (const char *str)
 Parses a double value from a string. More...
 
template<typename T >
static T fromString (const char *str)
 Parses a value from a string to a given type. More...
 
template<typename T >
static T fromString (const std::string &str)
 Parses a value from a string to a given type. More...
 
template<typename T >
static T fromStdString (const std::string &str)
 Parses a value from a string to a given type. More...
 
template<>
bool fromString< bool > (const char *str)
 Implementation for boolean values.
 
template<>
int fromString< int > (const char *str)
 Implementation for integer values.
 
template<>
int64_t fromString< int64_t > (const char *str)
 Implementation for 64-bit integer values.
 
template<>
float fromString< float > (const char *str)
 Implementation for float values.
 
template<>
double fromString< double > (const char *str)
 Implementation for double values.
 
static const char * boolToString (bool value)
 Converts a boolean to a "true"/"false" string. More...
 
static std::string intToString (int t)
 Returns a string containing the value of t. More...
 
static std::string int64ToString (int64_t t)
 Returns a string containing the value of t. More...
 
static std::string doubleToString (double t)
 Returns a string containing the value of t. More...
 
template<typename ValueType , int NumExpectedValues>
static std::optional
< std::array< ValueType,
NumExpectedValues > > 
parsedArrayFromInputString (const std::string &str)
 Convert a string into an array of values. More...
 
template<typename ValueType , int NumExpectedValues>
static std::string stringIdentityTransformWithArrayCheck (const std::string &toConvert, const std::string &errorContextMessage)
 Returns the input string, throwing an excpetion if the demanded conversion to an array will not succeed. More...
 
std::size_t countWords (const char *s)
 Returns number of space-separated words in zero-terminated char ptr. More...
 
std::size_t countWords (const std::string &str)
 Returns the number of space-separated words in a string object. More...
 
bool endsWith (const char *str, const char *suffix)
 Tests whether a string ends with another string. More...
 
std::string stripSuffixIfPresent (const std::string &str, const char *suffix)
 Removes a suffix from a string. More...
 
std::string stripString (const std::string &str)
 Removes leading and trailing whitespace from a string. More...
 
std::string formatString (const char *fmt,...)
 Formats a string (snprintf() wrapper). More...
 
std::string formatStringV (const char *fmt, va_list ap)
 Formats a string (vsnprintf() wrapper). More...
 
std::vector< std::string > splitString (const std::string &str)
 Splits a string to whitespace separated tokens. More...
 
std::vector< std::string > splitDelimitedString (const std::string &str, char delim)
 Splits a string to tokens separated by a given delimiter. More...
 
std::vector< std::string > splitAndTrimDelimitedString (const std::string &str, char delim)
 Splits str to tokens separated by delimiter delim. Removes leading and trailing whitespace from those strings with std::isspace. More...
 
std::string replaceAll (const std::string &input, const char *from, const char *to)
 Replace all occurrences of a string with another string. More...
 
std::string replaceAll (const std::string &input, const std::string &from, const std::string &to)
 Replace all occurrences of a string with another string. More...
 
std::string replaceAllWords (const std::string &input, const char *from, const char *to)
 Replace whole words with others. More...
 
std::string replaceAllWords (const std::string &input, const std::string &from, const std::string &to)
 Replace whole words with others. More...
 
bool equalCaseInsensitive (const std::string &source, const std::string &target)
 Return whether two strings are equal, ignoring case. More...
 
bool equalCaseInsensitive (const std::string &source, const std::string &target, size_t maxLengthOfComparison)
 Checks if at most maxLengthOfComparison characters of two strings match case insensitive. More...
 
std::string toUpperCase (const std::string &text)
 Makes the string uppercase. More...
 
std::string toLowerCase (const std::string &text)
 Makes the string lowercase. More...
 
static bool isNullOrEmpty (const char *str)
 Tests whether a string is null or empty. More...
 
static bool startsWith (const std::string &str, const std::string &prefix)
 Tests whether a string starts with another string. More...
 
static bool startsWith (const char *str, const char *prefix)
 Tests whether a string starts with another string. More...
 
static bool endsWith (const std::string &str, const char *suffix)
 Tests whether a string ends with another string. More...
 
static bool contains (const std::string &str, const char *substr)
 Tests whether a string contains another as a substring. More...
 
static bool contains (const std::string &str, const std::string &substr)
 Tests whether a string contains another as a substring. More...
 
static bool endsWith (const std::string &str, const std::string &suffix)
 Tests whether a string ends with another string. More...
 
template<typename InputIterator , typename FormatterType >
std::string formatAndJoin (InputIterator begin, InputIterator end, const char *separator, const FormatterType &formatter)
 Formats all the range as strings, and then joins them with a separator in between. More...
 
template<typename ContainerType , typename FormatterType >
std::string formatAndJoin (const ContainerType &container, const char *separator, const FormatterType &formatter)
 Formats all elements of the container as strings, and then joins them with a separator in between. More...
 
template<typename InputIterator >
std::string joinStrings (InputIterator begin, InputIterator end, const char *separator)
 Joins strings from a range with a separator in between. More...
 
template<typename ContainerType >
std::string joinStrings (const ContainerType &container, const char *separator)
 Joins strings from a container with a separator in between. More...
 
template<size_t count>
std::string joinStrings (const char *const (&array)[count], const char *separator)
 Joins strings from an array with a separator in between. More...
 
std::string getSyclCompilerVersion ()
 Returns an internal version strings of the Intel DPC++ and hipSYCL compiler.
 
template<class Function >
auto dispatchTemplatedFunction (Function &&f)
 
template<class T >
void free_wrapper (T *p)
 Wrapper of standard library free(), to be used as unique_cptr deleter for memory allocated by malloc, e.g. by an external library such as TNG.
 
template<class T >
void sfree_wrapper (T *p)
 sfree wrapper to be used as unique_cptr deleter
 
template<typename T , typename D >
std::unique_ptr< T, D > create_unique_with_deleter (T *t, D d)
 Create unique_ptr with any deleter function or lambda.
 
int gmx_mdrun (int argc, char *argv[])
 Implements C-style main function for mdrun. More...
 
int gmx_mdrun (MPI_Comm communicator, const gmx_hw_info_t &hwinfo, int argc, char *argv[])
 Implements C-style main function for mdrun. More...
 
static float invsqrt (float x)
 Calculate 1.0/sqrt(x) in single precision. More...
 
static double invsqrt (double x)
 Calculate 1.0/sqrt(x) in double precision, but single range. More...
 
static double invsqrt (int x)
 Calculate 1.0/sqrt(x) for integer x in double precision. More...
 
static float invcbrt (float x)
 Calculate inverse cube root of x in single precision. More...
 
static double invcbrt (double x)
 Calculate inverse sixth root of x in double precision. More...
 
static double invcbrt (int x)
 Calculate inverse sixth root of integer x in double precision. More...
 
static float sixthroot (float x)
 Calculate sixth root of x in single precision. More...
 
static double sixthroot (double x)
 Calculate sixth root of x in double precision. More...
 
static double sixthroot (int x)
 Calculate sixth root of integer x, return double. More...
 
static float invsixthroot (float x)
 Calculate inverse sixth root of x in single precision. More...
 
static double invsixthroot (double x)
 Calculate inverse sixth root of x in double precision. More...
 
static double invsixthroot (int x)
 Calculate inverse sixth root of integer x in double precision. More...
 
template<typename T >
square (T x)
 calculate x^2 More...
 
template<typename T >
power3 (T x)
 calculate x^3 More...
 
template<typename T >
power4 (T x)
 calculate x^4 More...
 
template<typename T >
power5 (T x)
 calculate x^5 More...
 
template<typename T >
power6 (T x)
 calculate x^6 More...
 
template<typename T >
power12 (T x)
 calculate x^12 More...
 
static real series_sinhx (real x)
 Maclaurin series for sinh(x)/x. More...
 
constexpr int32_t exactDiv (int32_t a, int32_t b)
 Exact integer division, 32bit. More...
 
constexpr int64_t exactDiv (int64_t a, int64_t b)
 Exact integer division, 64bit.
 
static int roundToInt (float x)
 Round float to int. More...
 
static int roundToInt (double x)
 Round double to int.
 
static int64_t roundToInt64 (float x)
 Round float to int64_t.
 
static int64_t roundToInt64 (double x)
 Round double to int64_t.
 
template<typename T , typename = std::enable_if_t<std::is_integral<T>::value>>
static constexpr bool isPowerOfTwo (const T v)
 Check whether v is an integer power of 2.
 
template<typename ValueType >
BasicVector< ValueType > operator* (const BasicVector< ValueType > &basicVector, const ValueType &scalar)
 Allow vector scalar multiplication.
 
template<typename ValueType >
BasicVector< ValueType > operator* (const ValueType &scalar, const BasicVector< ValueType > &basicVector)
 Allow scalar vector multiplication.
 
template<typename VectorType >
static VectorType unitVector (const VectorType &v)
 unitv for gmx::BasicVector
 
template<typename ValueType >
static ValueType norm (BasicVector< ValueType > v)
 norm for gmx::BasicVector
 
template<typename ValueType >
static ValueType norm2 (BasicVector< ValueType > v)
 Square of the vector norm for gmx::BasicVector.
 
template<typename VectorType >
static VectorType cross (const VectorType &a, const VectorType &b)
 cross product for gmx::BasicVector
 
template<typename ValueType >
static ValueType dot (BasicVector< ValueType > a, BasicVector< ValueType > b)
 dot product for gmx::BasicVector
 
template<typename VectorType >
static VectorType scaleByVector (const VectorType &a, const VectorType &b)
 Multiply two vectors element by element and return the result.
 
template<typename VectorType >
static VectorType elementWiseMin (const VectorType &a, const VectorType &b)
 Return the element-wise minimum of two vectors.
 
template<typename VectorType >
static VectorType elementWiseMax (const VectorType &a, const VectorType &b)
 Return the element-wise maximum of two vectors.
 
template<typename ValueType >
static BasicVector< ValueType >
::RawArray * 
as_vec_array (BasicVector< ValueType > *x)
 Casts a gmx::BasicVector array into an equivalent raw C array.
 
template<typename ValueType >
static const BasicVector
< ValueType >::RawArray * 
as_vec_array (const BasicVector< ValueType > *x)
 Casts a gmx::BasicVector array into an equivalent raw C array.
 
static rvec * as_rvec_array (RVec *x)
 Casts a gmx::RVec array into an rvec array.
 
static const rvec * as_rvec_array (const RVec *x)
 Casts a gmx::RVec array into an rvec array.
 
static dvec * as_dvec_array (DVec *x)
 Casts a gmx::DVec array into an Dvec array.
 
static ivec * as_ivec_array (IVec *x)
 Casts a gmx::IVec array into an ivec array.
 
static const dvec * as_dvec_array (const DVec *x)
 Casts a gmx::DVec array into an dvec array.
 
static const ivec * as_ivec_array (const IVec *x)
 Casts a gmx::IVec array into an ivec array.
 
template<typename T >
ArrayRef< std::conditional_t
< std::is_const< T >::value,
const typename T::value_type,
typename T::value_type > > 
makeArrayRef (T &c)
 Create ArrayRef from container with type deduction. More...
 
template<typename T >
ArrayRef< const typename
T::value_type > 
makeConstArrayRef (const T &c)
 Create ArrayRef to const T from container with type deduction. More...
 
template<typename T >
void swap (ArrayRef< T > &a, ArrayRef< T > &b)
 Simple swap method for ArrayRef objects. More...
 
template<typename T >
std::vector< T > copyOf (const ArrayRef< const T > &arrayRef)
 Return a vector that is a copy of an ArrayRef. More...
 
template<typename T >
index ssize (const T &t)
 Return signed size of container.
 
template<class Exception , class Tag , class T >
std::enable_if_t
< std::is_base_of
< GromacsException, Exception >
::value, Exception > 
operator<< (Exception ex, const ExceptionInfo< Tag, T > &item)
 Associates extra information with an exception. More...
 
void applyGlobalSimulationState (const SimulationInput &simulationInput, PartialDeserializedTprFile *partialDeserializedTpr, t_state *globalState, t_inputrec *inputrec, gmx_mtop_t *globalTopology)
 Get the global simulation input. More...
 
std::unique_ptr< t_stateglobalSimulationState (const SimulationInput &)
 
void applyGlobalInputRecord (const SimulationInput &, t_inputrec *)
 
void applyGlobalTopology (const SimulationInput &, gmx_mtop_t *)
 
Constant width-4 double precision SIMD types and instructions
static Simd4Double gmx_simdcall load4 (const double *m)
 Load 4 double values from aligned memory into SIMD4 variable. More...
 
static void gmx_simdcall store4 (double *m, Simd4Double a)
 Store the contents of SIMD4 double to aligned memory m. More...
 
static Simd4Double gmx_simdcall load4U (const double *m)
 Load SIMD4 double from unaligned memory. More...
 
static void gmx_simdcall store4U (double *m, Simd4Double a)
 Store SIMD4 double to unaligned memory. More...
 
static Simd4Double gmx_simdcall simd4SetZeroD ()
 Set all SIMD4 double elements to 0. More...
 
static Simd4Double gmx_simdcall operator& (Simd4Double a, Simd4Double b)
 Bitwise and for two SIMD4 double variables. More...
 
static Simd4Double gmx_simdcall andNot (Simd4Double a, Simd4Double b)
 Bitwise andnot for two SIMD4 double variables. c=(~a) & b. More...
 
static Simd4Double gmx_simdcall operator| (Simd4Double a, Simd4Double b)
 Bitwise or for two SIMD4 doubles. More...
 
static Simd4Double gmx_simdcall operator^ (Simd4Double a, Simd4Double b)
 Bitwise xor for two SIMD4 double variables. More...
 
static Simd4Double gmx_simdcall operator+ (Simd4Double a, Simd4Double b)
 Add two double SIMD4 variables. More...
 
static Simd4Double gmx_simdcall operator- (Simd4Double a, Simd4Double b)
 Subtract two SIMD4 variables. More...
 
static Simd4Double gmx_simdcall operator- (Simd4Double a)
 SIMD4 floating-point negate. More...
 
static Simd4Double gmx_simdcall operator* (Simd4Double a, Simd4Double b)
 Multiply two SIMD4 variables. More...
 
static Simd4Double gmx_simdcall fma (Simd4Double a, Simd4Double b, Simd4Double c)
 SIMD4 Fused-multiply-add. Result is a*b+c. More...
 
static Simd4Double gmx_simdcall fms (Simd4Double a, Simd4Double b, Simd4Double c)
 SIMD4 Fused-multiply-subtract. Result is a*b-c. More...
 
static Simd4Double gmx_simdcall fnma (Simd4Double a, Simd4Double b, Simd4Double c)
 SIMD4 Fused-negated-multiply-add. Result is -a*b+c. More...
 
static Simd4Double gmx_simdcall fnms (Simd4Double a, Simd4Double b, Simd4Double c)
 SIMD4 Fused-negated-multiply-subtract. Result is -a*b-c. More...
 
static Simd4Double gmx_simdcall rsqrt (Simd4Double x)
 SIMD4 1.0/sqrt(x) lookup. More...
 
static Simd4Double gmx_simdcall abs (Simd4Double a)
 SIMD4 Floating-point abs(). More...
 
static Simd4Double gmx_simdcall max (Simd4Double a, Simd4Double b)
 Set each SIMD4 element to the largest from two variables. More...
 
static Simd4Double gmx_simdcall min (Simd4Double a, Simd4Double b)
 Set each SIMD4 element to the largest from two variables. More...
 
static Simd4Double gmx_simdcall round (Simd4Double a)
 SIMD4 Round to nearest integer value (in floating-point format). More...
 
static Simd4Double gmx_simdcall trunc (Simd4Double a)
 Truncate SIMD4, i.e. round towards zero - common hardware instruction. More...
 
static double gmx_simdcall dotProduct (Simd4Double a, Simd4Double b)
 Return dot product of two double precision SIMD4 variables. More...
 
static void gmx_simdcall transpose (Simd4Double *v0, Simd4Double *v1, Simd4Double *v2, Simd4Double *v3)
 SIMD4 double transpose. More...
 
static Simd4DBool gmx_simdcall operator== (Simd4Double a, Simd4Double b)
 a==b for SIMD4 double More...
 
static Simd4DBool gmx_simdcall operator!= (Simd4Double a, Simd4Double b)
 a!=b for SIMD4 double More...
 
static Simd4DBool gmx_simdcall operator< (Simd4Double a, Simd4Double b)
 a<b for SIMD4 double More...
 
static Simd4DBool gmx_simdcall operator<= (Simd4Double a, Simd4Double b)
 a<=b for SIMD4 double. More...
 
static Simd4DBool gmx_simdcall operator&& (Simd4DBool a, Simd4DBool b)
 Logical and on single precision SIMD4 booleans. More...
 
static Simd4DBool gmx_simdcall operator|| (Simd4DBool a, Simd4DBool b)
 Logical or on single precision SIMD4 booleans. More...
 
static bool gmx_simdcall anyTrue (Simd4DBool a)
 Returns non-zero if any of the boolean in SIMD4 a is True, otherwise 0. More...
 
static Simd4Double gmx_simdcall selectByMask (Simd4Double a, Simd4DBool mask)
 Select from single precision SIMD4 variable where boolean is true. More...
 
static Simd4Double gmx_simdcall selectByNotMask (Simd4Double a, Simd4DBool mask)
 Select from single precision SIMD4 variable where boolean is false. More...
 
static Simd4Double gmx_simdcall blend (Simd4Double a, Simd4Double b, Simd4DBool sel)
 Vector-blend SIMD4 selection. More...
 
static double gmx_simdcall reduce (Simd4Double a)
 Return sum of all elements in SIMD4 double variable. More...
 
Constant width-4 single precision SIMD types and instructions
static Simd4Float gmx_simdcall load4 (const float *m)
 Load 4 float values from aligned memory into SIMD4 variable. More...
 
static void gmx_simdcall store4 (float *m, Simd4Float a)
 Store the contents of SIMD4 float to aligned memory m. More...
 
static Simd4Float gmx_simdcall load4U (const float *m)
 Load SIMD4 float from unaligned memory. More...
 
static void gmx_simdcall store4U (float *m, Simd4Float a)
 Store SIMD4 float to unaligned memory. More...
 
static Simd4Float gmx_simdcall simd4SetZeroF ()
 Set all SIMD4 float elements to 0. More...
 
static Simd4Float gmx_simdcall operator& (Simd4Float a, Simd4Float b)
 Bitwise and for two SIMD4 float variables. More...
 
static Simd4Float gmx_simdcall andNot (Simd4Float a, Simd4Float b)
 Bitwise andnot for two SIMD4 float variables. c=(~a) & b. More...
 
static Simd4Float gmx_simdcall operator| (Simd4Float a, Simd4Float b)
 Bitwise or for two SIMD4 floats. More...
 
static Simd4Float gmx_simdcall operator^ (Simd4Float a, Simd4Float b)
 Bitwise xor for two SIMD4 float variables. More...
 
static Simd4Float gmx_simdcall operator+ (Simd4Float a, Simd4Float b)
 Add two float SIMD4 variables. More...
 
static Simd4Float gmx_simdcall operator- (Simd4Float a, Simd4Float b)
 Subtract two SIMD4 variables. More...
 
static Simd4Float gmx_simdcall operator- (Simd4Float a)
 SIMD4 floating-point negate. More...
 
static Simd4Float gmx_simdcall operator* (Simd4Float a, Simd4Float b)
 Multiply two SIMD4 variables. More...
 
static Simd4Float gmx_simdcall fma (Simd4Float a, Simd4Float b, Simd4Float c)
 SIMD4 Fused-multiply-add. Result is a*b+c. More...
 
static Simd4Float gmx_simdcall fms (Simd4Float a, Simd4Float b, Simd4Float c)
 SIMD4 Fused-multiply-subtract. Result is a*b-c. More...
 
static Simd4Float gmx_simdcall fnma (Simd4Float a, Simd4Float b, Simd4Float c)
 SIMD4 Fused-negated-multiply-add. Result is -a*b+c. More...
 
static Simd4Float gmx_simdcall fnms (Simd4Float a, Simd4Float b, Simd4Float c)
 SIMD4 Fused-negated-multiply-subtract. Result is -a*b-c. More...
 
static Simd4Float gmx_simdcall rsqrt (Simd4Float x)
 SIMD4 1.0/sqrt(x) lookup. More...
 
static Simd4Float gmx_simdcall abs (Simd4Float a)
 SIMD4 Floating-point fabs(). More...
 
static Simd4Float gmx_simdcall max (Simd4Float a, Simd4Float b)
 Set each SIMD4 element to the largest from two variables. More...
 
static Simd4Float gmx_simdcall min (Simd4Float a, Simd4Float b)
 Set each SIMD4 element to the largest from two variables. More...
 
static Simd4Float gmx_simdcall round (Simd4Float a)
 SIMD4 Round to nearest integer value (in floating-point format). More...
 
static Simd4Float gmx_simdcall trunc (Simd4Float a)
 Truncate SIMD4, i.e. round towards zero - common hardware instruction. More...
 
static float gmx_simdcall dotProduct (Simd4Float a, Simd4Float b)
 Return dot product of two single precision SIMD4 variables. More...
 
static void gmx_simdcall transpose (Simd4Float *v0, Simd4Float *v1, Simd4Float *v2, Simd4Float *v3)
 SIMD4 float transpose. More...
 
static Simd4FBool gmx_simdcall operator== (Simd4Float a, Simd4Float b)
 a==b for SIMD4 float More...
 
static Simd4FBool gmx_simdcall operator!= (Simd4Float a, Simd4Float b)
 a!=b for SIMD4 float More...
 
static Simd4FBool gmx_simdcall operator< (Simd4Float a, Simd4Float b)
 a<b for SIMD4 float More...
 
static Simd4FBool gmx_simdcall operator<= (Simd4Float a, Simd4Float b)
 a<=b for SIMD4 float. More...
 
static Simd4FBool gmx_simdcall operator&& (Simd4FBool a, Simd4FBool b)
 Logical and on single precision SIMD4 booleans. More...
 
static Simd4FBool gmx_simdcall operator|| (Simd4FBool a, Simd4FBool b)
 Logical or on single precision SIMD4 booleans. More...
 
static bool gmx_simdcall anyTrue (Simd4FBool a)
 Returns non-zero if any of the boolean in SIMD4 a is True, otherwise 0. More...
 
static Simd4Float gmx_simdcall selectByMask (Simd4Float a, Simd4FBool mask)
 Select from single precision SIMD4 variable where boolean is true. More...
 
static Simd4Float gmx_simdcall selectByNotMask (Simd4Float a, Simd4FBool mask)
 Select from single precision SIMD4 variable where boolean is false. More...
 
static Simd4Float gmx_simdcall blend (Simd4Float a, Simd4Float b, Simd4FBool sel)
 Vector-blend SIMD4 selection. More...
 
static float gmx_simdcall reduce (Simd4Float a)
 Return sum of all elements in SIMD4 float variable. More...
 
SIMD implementation load/store operations for double precision floating point
static SimdDouble gmx_simdcall simdLoad (const double *m, SimdDoubleTag={})
 Load GMX_SIMD_DOUBLE_WIDTH numbers from aligned memory. More...
 
static void gmx_simdcall store (double *m, SimdDouble a)
 Store the contents of SIMD double variable to aligned memory m. More...
 
static SimdDouble gmx_simdcall simdLoadU (const double *m, SimdDoubleTag={})
 Load SIMD double from unaligned memory. More...
 
static void gmx_simdcall storeU (double *m, SimdDouble a)
 Store SIMD double to unaligned memory. More...
 
static SimdDouble gmx_simdcall setZeroD ()
 Set all SIMD double variable elements to 0.0. More...
 
SIMD implementation load/store operations for integers (corresponding to double)
static SimdDInt32 gmx_simdcall simdLoad (const std::int32_t *m, SimdDInt32Tag)
 Load aligned SIMD integer data, width corresponds to gmx::SimdDouble. More...
 
static void gmx_simdcall store (std::int32_t *m, SimdDInt32 a)
 Store aligned SIMD integer data, width corresponds to gmx::SimdDouble. More...
 
static SimdDInt32 gmx_simdcall simdLoadU (const std::int32_t *m, SimdDInt32Tag)
 Load unaligned integer SIMD data, width corresponds to gmx::SimdDouble. More...
 
static void gmx_simdcall storeU (std::int32_t *m, SimdDInt32 a)
 Store unaligned SIMD integer data, width corresponds to gmx::SimdDouble. More...
 
static SimdDInt32 gmx_simdcall setZeroDI ()
 Set all SIMD (double) integer variable elements to 0. More...
 
template<int index>
static std::int32_t gmx_simdcall extract (SimdDInt32 a)
 Extract element with index i from gmx::SimdDInt32. More...
 
SIMD implementation double precision floating-point bitwise logical operations
static SimdDouble gmx_simdcall operator& (SimdDouble a, SimdDouble b)
 Bitwise and for two SIMD double variables. More...
 
static SimdDouble gmx_simdcall andNot (SimdDouble a, SimdDouble b)
 Bitwise andnot for SIMD double. More...
 
static SimdDouble gmx_simdcall operator| (SimdDouble a, SimdDouble b)
 Bitwise or for SIMD double. More...
 
static SimdDouble gmx_simdcall operator^ (SimdDouble a, SimdDouble b)
 Bitwise xor for SIMD double. More...
 
SIMD implementation double precision floating-point arithmetics
static SimdDouble gmx_simdcall operator+ (SimdDouble a, SimdDouble b)
 Add two double SIMD variables. More...
 
static SimdDouble gmx_simdcall operator- (SimdDouble a, SimdDouble b)
 Subtract two double SIMD variables. More...
 
static SimdDouble gmx_simdcall operator- (SimdDouble a)
 SIMD double precision negate. More...
 
static SimdDouble gmx_simdcall operator* (SimdDouble a, SimdDouble b)
 Multiply two double SIMD variables. More...
 
static SimdDouble gmx_simdcall fma (SimdDouble a, SimdDouble b, SimdDouble c)
 SIMD double Fused-multiply-add. Result is a*b+c. More...
 
static SimdDouble gmx_simdcall fms (SimdDouble a, SimdDouble b, SimdDouble c)
 SIMD double Fused-multiply-subtract. Result is a*b-c. More...
 
static SimdDouble gmx_simdcall fnma (SimdDouble a, SimdDouble b, SimdDouble c)
 SIMD double Fused-negated-multiply-add. Result is -a*b+c. More...
 
static SimdDouble gmx_simdcall fnms (SimdDouble a, SimdDouble b, SimdDouble c)
 SIMD double Fused-negated-multiply-subtract. Result is -a*b-c. More...
 
static SimdDouble gmx_simdcall rsqrt (SimdDouble x)
 double SIMD 1.0/sqrt(x) lookup. More...
 
static SimdDouble gmx_simdcall rcp (SimdDouble x)
 SIMD double 1.0/x lookup. More...
 
static SimdDouble gmx_simdcall maskAdd (SimdDouble a, SimdDouble b, SimdDBool m)
 Add two double SIMD variables, masked version. More...
 
static SimdDouble gmx_simdcall maskzMul (SimdDouble a, SimdDouble b, SimdDBool m)
 Multiply two double SIMD variables, masked version. More...
 
static SimdDouble gmx_simdcall maskzFma (SimdDouble a, SimdDouble b, SimdDouble c, SimdDBool m)
 SIMD double fused multiply-add, masked version. More...
 
static SimdDouble gmx_simdcall maskzRsqrt (SimdDouble x, SimdDBool m)
 SIMD double 1.0/sqrt(x) lookup, masked version. More...
 
static SimdDouble gmx_simdcall maskzRcp (SimdDouble x, SimdDBool m)
 SIMD double 1.0/x lookup, masked version. More...
 
static SimdDouble gmx_simdcall abs (SimdDouble a)
 SIMD double floating-point fabs(). More...
 
static SimdDouble gmx_simdcall max (SimdDouble a, SimdDouble b)
 Set each SIMD double element to the largest from two variables. More...
 
static SimdDouble gmx_simdcall min (SimdDouble a, SimdDouble b)
 Set each SIMD double element to the smallest from two variables. More...
 
static SimdDouble gmx_simdcall round (SimdDouble a)
 SIMD double round to nearest integer value (in floating-point format). More...
 
static SimdDouble gmx_simdcall trunc (SimdDouble a)
 Truncate SIMD double, i.e. round towards zero - common hardware instruction. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall frexp (SimdDouble value, SimdDInt32 *exponent)
 Extract (integer) exponent and fraction from double precision SIMD. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall ldexp (SimdDouble value, SimdDInt32 exponent)
 Multiply a SIMD double value by the number 2 raised to an exp power. More...
 
static double gmx_simdcall reduce (SimdDouble a)
 Return sum of all elements in SIMD double variable. More...
 
SIMD implementation double precision floating-point comparison, boolean, selection.
static SimdDBool gmx_simdcall operator== (SimdDouble a, SimdDouble b)
 SIMD a==b for double SIMD. More...
 
static SimdDBool gmx_simdcall operator!= (SimdDouble a, SimdDouble b)
 SIMD a!=b for double SIMD. More...
 
static SimdDBool gmx_simdcall operator< (SimdDouble a, SimdDouble b)
 SIMD a<b for double SIMD. More...
 
static SimdDBool gmx_simdcall operator<= (SimdDouble a, SimdDouble b)
 SIMD a<=b for double SIMD. More...
 
static SimdDBool gmx_simdcall testBits (SimdDouble a)
 Return true if any bits are set in the single precision SIMD. More...
 
static SimdDBool gmx_simdcall operator&& (SimdDBool a, SimdDBool b)
 Logical and on double precision SIMD booleans. More...
 
static SimdDBool gmx_simdcall operator|| (SimdDBool a, SimdDBool b)
 Logical or on double precision SIMD booleans. More...
 
static bool gmx_simdcall anyTrue (SimdDBool a)
 Returns non-zero if any of the boolean in SIMD a is True, otherwise 0. More...
 
static SimdDouble gmx_simdcall selectByMask (SimdDouble a, SimdDBool mask)
 Select from double precision SIMD variable where boolean is true. More...
 
static SimdDouble gmx_simdcall selectByNotMask (SimdDouble a, SimdDBool mask)
 Select from double precision SIMD variable where boolean is false. More...
 
static SimdDouble gmx_simdcall blend (SimdDouble a, SimdDouble b, SimdDBool sel)
 Vector-blend SIMD double selection. More...
 
SIMD implementation integer (corresponding to double) bitwise logical operations
static SimdDInt32 gmx_simdcall operator& (SimdDInt32 a, SimdDInt32 b)
 Integer SIMD bitwise and. More...
 
static SimdDInt32 gmx_simdcall andNot (SimdDInt32 a, SimdDInt32 b)
 Integer SIMD bitwise not/complement. More...
 
static SimdDInt32 gmx_simdcall operator| (SimdDInt32 a, SimdDInt32 b)
 Integer SIMD bitwise or. More...
 
static SimdDInt32 gmx_simdcall operator^ (SimdDInt32 a, SimdDInt32 b)
 Integer SIMD bitwise xor. More...
 
SIMD implementation integer (corresponding to double) arithmetics
static SimdDInt32 gmx_simdcall operator+ (SimdDInt32 a, SimdDInt32 b)
 Add SIMD integers. More...
 
static SimdDInt32 gmx_simdcall operator- (SimdDInt32 a, SimdDInt32 b)
 Subtract SIMD integers. More...
 
static SimdDInt32 gmx_simdcall operator* (SimdDInt32 a, SimdDInt32 b)
 Multiply SIMD integers. More...
 
SIMD implementation integer (corresponding to double) comparisons, boolean selection
static SimdDIBool gmx_simdcall operator== (SimdDInt32 a, SimdDInt32 b)
 Equality comparison of two integers corresponding to double values. More...
 
static SimdDIBool gmx_simdcall operator< (SimdDInt32 a, SimdDInt32 b)
 Less-than comparison of two SIMD integers corresponding to double values. More...
 
static SimdDIBool gmx_simdcall testBits (SimdDInt32 a)
 Check if any bit is set in each element. More...
 
static SimdDIBool gmx_simdcall operator&& (SimdDIBool a, SimdDIBool b)
 Logical AND on SimdDIBool. More...
 
static SimdDIBool gmx_simdcall operator|| (SimdDIBool a, SimdDIBool b)
 Logical OR on SimdDIBool. More...
 
static bool gmx_simdcall anyTrue (SimdDIBool a)
 Returns true if any of the boolean in x is True, otherwise 0. More...
 
static SimdDInt32 gmx_simdcall selectByMask (SimdDInt32 a, SimdDIBool mask)
 Select from gmx::SimdDInt32 variable where boolean is true. More...
 
static SimdDInt32 gmx_simdcall selectByNotMask (SimdDInt32 a, SimdDIBool mask)
 Select from gmx::SimdDInt32 variable where boolean is false. More...
 
static SimdDInt32 gmx_simdcall blend (SimdDInt32 a, SimdDInt32 b, SimdDIBool sel)
 Vector-blend SIMD integer selection. More...
 
SIMD implementation conversion operations
static SimdDInt32 gmx_simdcall cvtR2I (SimdDouble a)
 Round double precision floating point to integer. More...
 
static SimdDInt32 gmx_simdcall cvttR2I (SimdDouble a)
 Truncate double precision floating point to integer. More...
 
static SimdDouble gmx_simdcall cvtI2R (SimdDInt32 a)
 Convert integer to double precision floating point. More...
 
static SimdDIBool gmx_simdcall cvtB2IB (SimdDBool a)
 Convert from double precision boolean to corresponding integer boolean. More...
 
static SimdDBool gmx_simdcall cvtIB2B (SimdDIBool a)
 Convert from integer boolean to corresponding double precision boolean. More...
 
static SimdDouble gmx_simdcall cvtF2D (SimdFloat gmx_unused f)
 Convert SIMD float to double. More...
 
static SimdFloat gmx_simdcall cvtD2F (SimdDouble gmx_unused d)
 Convert SIMD double to float. More...
 
static void gmx_simdcall cvtF2DD (SimdFloat gmx_unused f, SimdDouble gmx_unused *d0, SimdDouble gmx_unused *d1)
 Convert SIMD float to double. More...
 
static SimdFloat gmx_simdcall cvtDD2F (SimdDouble gmx_unused d0, SimdDouble gmx_unused d1)
 Convert SIMD double to float. More...
 
static SimdFInt32 gmx_simdcall cvtR2I (SimdFloat a)
 Round single precision floating point to integer. More...
 
static SimdFInt32 gmx_simdcall cvttR2I (SimdFloat a)
 Truncate single precision floating point to integer. More...
 
static SimdFloat gmx_simdcall cvtI2R (SimdFInt32 a)
 Convert integer to single precision floating point. More...
 
static SimdFIBool gmx_simdcall cvtB2IB (SimdFBool a)
 Convert from single precision boolean to corresponding integer boolean. More...
 
static SimdFBool gmx_simdcall cvtIB2B (SimdFIBool a)
 Convert from integer boolean to corresponding single precision boolean. More...
 
SIMD implementation load/store operations for single precision floating point
static SimdFloat gmx_simdcall simdLoad (const float *m, SimdFloatTag={})
 Load GMX_SIMD_FLOAT_WIDTH float numbers from aligned memory. More...
 
static void gmx_simdcall store (float *m, SimdFloat a)
 Store the contents of SIMD float variable to aligned memory m. More...
 
static SimdFloat gmx_simdcall simdLoadU (const float *m, SimdFloatTag={})
 Load SIMD float from unaligned memory. More...
 
static void gmx_simdcall storeU (float *m, SimdFloat a)
 Store SIMD float to unaligned memory. More...
 
static SimdFloat gmx_simdcall setZeroF ()
 Set all SIMD float variable elements to 0.0. More...
 
SIMD implementation load/store operations for integers (corresponding to float)
static SimdFInt32 gmx_simdcall simdLoad (const std::int32_t *m, SimdFInt32Tag)
 Load aligned SIMD integer data, width corresponds to gmx::SimdFloat. More...
 
static void gmx_simdcall store (std::int32_t *m, SimdFInt32 a)
 Store aligned SIMD integer data, width corresponds to gmx::SimdFloat. More...
 
static SimdFInt32 gmx_simdcall simdLoadU (const std::int32_t *m, SimdFInt32Tag)
 Load unaligned integer SIMD data, width corresponds to gmx::SimdFloat. More...
 
static void gmx_simdcall storeU (std::int32_t *m, SimdFInt32 a)
 Store unaligned SIMD integer data, width corresponds to gmx::SimdFloat. More...
 
static SimdFInt32 gmx_simdcall setZeroFI ()
 Set all SIMD (float) integer variable elements to 0. More...
 
template<int index>
static std::int32_t gmx_simdcall extract (SimdFInt32 a)
 Extract element with index i from gmx::SimdFInt32. More...
 
SIMD implementation single precision floating-point bitwise logical operations
static SimdFloat gmx_simdcall operator& (SimdFloat a, SimdFloat b)
 Bitwise and for two SIMD float variables. More...
 
static SimdFloat gmx_simdcall andNot (SimdFloat a, SimdFloat b)
 Bitwise andnot for SIMD float. More...
 
static SimdFloat gmx_simdcall operator| (SimdFloat a, SimdFloat b)
 Bitwise or for SIMD float. More...
 
static SimdFloat gmx_simdcall operator^ (SimdFloat a, SimdFloat b)
 Bitwise xor for SIMD float. More...
 
SIMD implementation single precision floating-point arithmetics
static SimdFloat gmx_simdcall operator+ (SimdFloat a, SimdFloat b)
 Add two float SIMD variables. More...
 
static SimdFloat gmx_simdcall operator- (SimdFloat a, SimdFloat b)
 Subtract two float SIMD variables. More...
 
static SimdFloat gmx_simdcall operator- (SimdFloat a)
 SIMD single precision negate. More...
 
static SimdFloat gmx_simdcall operator* (SimdFloat a, SimdFloat b)
 Multiply two float SIMD variables. More...
 
static SimdFloat gmx_simdcall fma (SimdFloat a, SimdFloat b, SimdFloat c)
 SIMD float Fused-multiply-add. Result is a*b+c. More...
 
static SimdFloat gmx_simdcall fms (SimdFloat a, SimdFloat b, SimdFloat c)
 SIMD float Fused-multiply-subtract. Result is a*b-c. More...
 
static SimdFloat gmx_simdcall fnma (SimdFloat a, SimdFloat b, SimdFloat c)
 SIMD float Fused-negated-multiply-add. Result is -a*b+c. More...
 
static SimdFloat gmx_simdcall fnms (SimdFloat a, SimdFloat b, SimdFloat c)
 SIMD float Fused-negated-multiply-subtract. Result is -a*b-c. More...
 
static SimdFloat gmx_simdcall rsqrt (SimdFloat x)
 SIMD float 1.0/sqrt(x) lookup. More...
 
static SimdFloat gmx_simdcall rcp (SimdFloat x)
 SIMD float 1.0/x lookup. More...
 
static SimdFloat gmx_simdcall maskAdd (SimdFloat a, SimdFloat b, SimdFBool m)
 Add two float SIMD variables, masked version. More...
 
static SimdFloat gmx_simdcall maskzMul (SimdFloat a, SimdFloat b, SimdFBool m)
 Multiply two float SIMD variables, masked version. More...
 
static SimdFloat gmx_simdcall maskzFma (SimdFloat a, SimdFloat b, SimdFloat c, SimdFBool m)
 SIMD float fused multiply-add, masked version. More...
 
static SimdFloat gmx_simdcall maskzRsqrt (SimdFloat x, SimdFBool m)
 SIMD float 1.0/sqrt(x) lookup, masked version. More...
 
static SimdFloat gmx_simdcall maskzRcp (SimdFloat x, SimdFBool m)
 SIMD float 1.0/x lookup, masked version. More...
 
static SimdFloat gmx_simdcall abs (SimdFloat a)
 SIMD float Floating-point abs(). More...
 
static SimdFloat gmx_simdcall max (SimdFloat a, SimdFloat b)
 Set each SIMD float element to the largest from two variables. More...
 
static SimdFloat gmx_simdcall min (SimdFloat a, SimdFloat b)
 Set each SIMD float element to the smallest from two variables. More...
 
static SimdFloat gmx_simdcall round (SimdFloat a)
 SIMD float round to nearest integer value (in floating-point format). More...
 
static SimdFloat gmx_simdcall trunc (SimdFloat a)
 Truncate SIMD float, i.e. round towards zero - common hardware instruction. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall frexp (SimdFloat value, SimdFInt32 *exponent)
 Extract (integer) exponent and fraction from single precision SIMD. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall ldexp (SimdFloat value, SimdFInt32 exponent)
 Multiply a SIMD float value by the number 2 raised to an exp power. More...
 
static float gmx_simdcall reduce (SimdFloat a)
 Return sum of all elements in SIMD float variable. More...
 
SIMD implementation single precision floating-point comparisons, boolean, selection.
static SimdFBool gmx_simdcall operator== (SimdFloat a, SimdFloat b)
 SIMD a==b for single SIMD. More...
 
static SimdFBool gmx_simdcall operator!= (SimdFloat a, SimdFloat b)
 SIMD a!=b for single SIMD. More...
 
static SimdFBool gmx_simdcall operator< (SimdFloat a, SimdFloat b)
 SIMD a<b for single SIMD. More...
 
static SimdFBool gmx_simdcall operator<= (SimdFloat a, SimdFloat b)
 SIMD a<=b for single SIMD. More...
 
static SimdFBool gmx_simdcall testBits (SimdFloat a)
 Return true if any bits are set in the single precision SIMD. More...
 
static SimdFBool gmx_simdcall operator&& (SimdFBool a, SimdFBool b)
 Logical and on single precision SIMD booleans. More...
 
static SimdFBool gmx_simdcall operator|| (SimdFBool a, SimdFBool b)
 Logical or on single precision SIMD booleans. More...
 
static bool gmx_simdcall anyTrue (SimdFBool a)
 Returns non-zero if any of the boolean in SIMD a is True, otherwise 0. More...
 
static SimdFloat gmx_simdcall selectByMask (SimdFloat a, SimdFBool mask)
 Select from single precision SIMD variable where boolean is true. More...
 
static SimdFloat gmx_simdcall selectByNotMask (SimdFloat a, SimdFBool mask)
 Select from single precision SIMD variable where boolean is false. More...
 
static SimdFloat gmx_simdcall blend (SimdFloat a, SimdFloat b, SimdFBool sel)
 Vector-blend SIMD float selection. More...
 
SIMD implementation integer (corresponding to float) bitwise logical operations
static SimdFInt32 gmx_simdcall operator& (SimdFInt32 a, SimdFInt32 b)
 Integer SIMD bitwise and. More...
 
static SimdFInt32 gmx_simdcall andNot (SimdFInt32 a, SimdFInt32 b)
 Integer SIMD bitwise not/complement. More...
 
static SimdFInt32 gmx_simdcall operator| (SimdFInt32 a, SimdFInt32 b)
 Integer SIMD bitwise or. More...
 
static SimdFInt32 gmx_simdcall operator^ (SimdFInt32 a, SimdFInt32 b)
 Integer SIMD bitwise xor. More...
 
SIMD implementation integer (corresponding to float) arithmetics
static SimdFInt32 gmx_simdcall operator+ (SimdFInt32 a, SimdFInt32 b)
 Add SIMD integers. More...
 
static SimdFInt32 gmx_simdcall operator- (SimdFInt32 a, SimdFInt32 b)
 Subtract SIMD integers. More...
 
static SimdFInt32 gmx_simdcall operator* (SimdFInt32 a, SimdFInt32 b)
 Multiply SIMD integers. More...
 
SIMD implementation integer (corresponding to float) comparisons, boolean, selection
static SimdFIBool gmx_simdcall operator== (SimdFInt32 a, SimdFInt32 b)
 Equality comparison of two integers corresponding to float values. More...
 
static SimdFIBool gmx_simdcall operator< (SimdFInt32 a, SimdFInt32 b)
 Less-than comparison of two SIMD integers corresponding to float values. More...
 
static SimdFIBool gmx_simdcall testBits (SimdFInt32 a)
 Check if any bit is set in each element. More...
 
static SimdFIBool gmx_simdcall operator&& (SimdFIBool a, SimdFIBool b)
 Logical AND on SimdFIBool. More...
 
static SimdFIBool gmx_simdcall operator|| (SimdFIBool a, SimdFIBool b)
 Logical OR on SimdFIBool. More...
 
static bool gmx_simdcall anyTrue (SimdFIBool a)
 Returns true if any of the boolean in x is True, otherwise 0. More...
 
static SimdFInt32 gmx_simdcall selectByMask (SimdFInt32 a, SimdFIBool mask)
 Select from gmx::SimdFInt32 variable where boolean is true. More...
 
static SimdFInt32 gmx_simdcall selectByNotMask (SimdFInt32 a, SimdFIBool mask)
 Select from gmx::SimdFInt32 variable where boolean is false. More...
 
static SimdFInt32 gmx_simdcall blend (SimdFInt32 a, SimdFInt32 b, SimdFIBool sel)
 Vector-blend SIMD integer selection. More...
 
Higher-level SIMD utilities accessing partial (half-width) SIMD doubles.

See the single-precision versions for documentation. Since double precision is typically half the width of single, this double version is likely only useful with 512-bit and larger implementations.

static SimdDouble gmx_simdcall loadDualHsimd (const double *m0, const double *m1)
 Load low & high parts of SIMD double from different locations. More...
 
static SimdDouble gmx_simdcall loadDuplicateHsimd (const double *m)
 Load half-SIMD-width double data, spread to both halves. More...
 
static SimdDouble gmx_simdcall loadU1DualHsimd (const double *m)
 Load two doubles, spread 1st in low half, 2nd in high half. More...
 
static void gmx_simdcall storeDualHsimd (double *m0, double *m1, SimdDouble a)
 Store low & high parts of SIMD double to different locations. More...
 
static void gmx_simdcall incrDualHsimd (double *m0, double *m1, SimdDouble a)
 Add each half of SIMD variable to separate memory adresses. More...
 
static void gmx_simdcall decr3Hsimd (double *m, SimdDouble a0, SimdDouble a1, SimdDouble a2)
 Add the two halves of three SIMD doubles, subtract the sum from three half-SIMD-width consecutive doubles in memory. More...
 
template<int align>
static void gmx_simdcall gatherLoadTransposeHsimd (const double *base0, const double *base1, std::int32_t offset[], SimdDouble *v0, SimdDouble *v1)
 Load 2 consecutive doubles from each of GMX_SIMD_DOUBLE_WIDTH/2 offsets, transpose into SIMD double (low half from base0, high from base1). More...
 
static double gmx_simdcall reduceIncr4ReturnSumHsimd (double *m, SimdDouble v0, SimdDouble v1)
 Reduce the 4 half-SIMD-with doubles in 2 SIMD variables (sum halves), increment four consecutive doubles in memory, return sum. More...
 
static SimdDouble gmx_simdcall loadUNDuplicate4 (const double *m)
 Load N doubles and duplicate them 4 times each. More...
 
static SimdDouble gmx_simdcall load4DuplicateN (const double *m)
 Load 4 doubles and duplicate them N times each. More...
 
static SimdDouble gmx_simdcall loadU4NOffset (const double *m, int offset)
 Load doubles in blocks of 4 at fixed offsets. More...
 
Higher-level SIMD utilities accessing partial (half-width) SIMD floats.

These functions are optional. The are only useful for SIMD implementation where the width is 8 or larger, and where it would be inefficient to process 4*8, 8*8, or more, interactions in parallel.

Currently, only Intel provides very wide SIMD implementations, but these also come with excellent support for loading, storing, accessing and shuffling parts of the register in so-called 'lanes' of 4 bytes each. We can use this to load separate parts into the low/high halves of the register in the inner loop of the nonbonded kernel, which e.g. makes it possible to process 4*4 nonbonded interactions as a pattern of 2*8. We can also use implementations with width 16 or greater.

To make this more generic, when GMX_SIMD_HAVE_HSIMD_UTIL_REAL is 1, the SIMD implementation provides seven special routines that:

  • Load the low/high parts of a SIMD variable from different pointers
  • Load half the SIMD width from one pointer, and duplicate in low/high parts
  • Load two reals, put 1st one in all low elements, and 2nd in all high ones.
  • Store the low/high parts of a SIMD variable to different pointers
  • Subtract both SIMD halves from a single half-SIMD-width memory location.
  • Load aligned pairs (LJ parameters) from two base pointers, with a common offset list, and put these in the low/high SIMD halves.
  • Reduce each half of two SIMD registers (i.e., 4 parts in total), increment four adjacent memory positions, and return the total sum.

Remember: this is ONLY used when the native SIMD width is large. You will just waste time if you implement it for normal 16-byte SIMD architectures.

This is part of the new C++ SIMD interface, so these functions are only available when using C++. Since some Gromacs code reliying on the SIMD module is still C (not C++), we have kept the C-style naming for now - this will change once we are entirely C++.

static SimdFloat gmx_simdcall loadDualHsimd (const float *m0, const float *m1)
 Load low & high parts of SIMD float from different locations. More...
 
static SimdFloat gmx_simdcall loadDuplicateHsimd (const float *m)
 Load half-SIMD-width float data, spread to both halves. More...
 
static SimdFloat gmx_simdcall loadU1DualHsimd (const float *m)
 Load two floats, spread 1st in low half, 2nd in high half. More...
 
static void gmx_simdcall storeDualHsimd (float *m0, float *m1, SimdFloat a)
 Store low & high parts of SIMD float to different locations. More...
 
static void gmx_simdcall incrDualHsimd (float *m0, float *m1, SimdFloat a)
 Add each half of SIMD variable to separate memory adresses. More...
 
static void gmx_simdcall decr3Hsimd (float *m, SimdFloat a0, SimdFloat a1, SimdFloat a2)
 Add the two halves of three SIMD floats, subtract the sum from three half-SIMD-width consecutive floats in memory. More...
 
template<int align>
static void gmx_simdcall gatherLoadTransposeHsimd (const float *base0, const float *base1, const std::int32_t offset[], SimdFloat *v0, SimdFloat *v1)
 Load 2 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH/2 offsets, transpose into SIMD float (low half from base0, high from base1). More...
 
static float gmx_simdcall reduceIncr4ReturnSumHsimd (float *m, SimdFloat v0, SimdFloat v1)
 Reduce the 4 half-SIMD-with floats in 2 SIMD variables (sum halves), increment four consecutive floats in memory, return sum. More...
 
static SimdFloat gmx_simdcall loadUNDuplicate4 (const float *m)
 Load N floats and duplicate them 4 times each. More...
 
static SimdFloat gmx_simdcall load4DuplicateN (const float *m)
 Load 4 floats and duplicate them N times each. More...
 
static SimdFloat gmx_simdcall loadU4NOffset (const float *m, int offset)
 Load floats in blocks of 4 at fixed offsets. More...
 
Single precision SIMD math functions
Note
In most cases you should use the real-precision functions instead.
static SimdFloat gmx_simdcall copysign (SimdFloat x, SimdFloat y)
 Composes floating point value with the magnitude of x and the sign of y. More...
 
static SimdFloat gmx_simdcall rsqrtIter (SimdFloat lu, SimdFloat x)
 Perform one Newton-Raphson iteration to improve 1/sqrt(x) for SIMD float. More...
 
static SimdFloat gmx_simdcall invsqrt (SimdFloat x)
 Calculate 1/sqrt(x) for SIMD float. More...
 
static void gmx_simdcall invsqrtPair (SimdFloat x0, SimdFloat x1, SimdFloat *out0, SimdFloat *out1)
 Calculate 1/sqrt(x) for two SIMD floats. More...
 
static SimdFloat gmx_simdcall rcpIter (SimdFloat lu, SimdFloat x)
 Perform one Newton-Raphson iteration to improve 1/x for SIMD float. More...
 
static SimdFloat gmx_simdcall inv (SimdFloat x)
 Calculate 1/x for SIMD float. More...
 
static SimdFloat gmx_simdcall operator/ (SimdFloat nom, SimdFloat denom)
 Division for SIMD floats. More...
 
static SimdFloat maskzInvsqrt (SimdFloat x, SimdFBool m)
 Calculate 1/sqrt(x) for masked entries of SIMD float. More...
 
static SimdFloat gmx_simdcall maskzInv (SimdFloat x, SimdFBool m)
 Calculate 1/x for SIMD float, masked version. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall sqrt (SimdFloat x)
 Calculate sqrt(x) for SIMD floats. More...
 
static SimdFloat gmx_simdcall cbrt (SimdFloat x)
 Cube root for SIMD floats. More...
 
static SimdFloat gmx_simdcall invcbrt (SimdFloat x)
 Inverse cube root for SIMD floats. More...
 
static SimdFloat gmx_simdcall log2 (SimdFloat x)
 SIMD float log2(x). This is the base-2 logarithm. More...
 
static SimdFloat gmx_simdcall log (SimdFloat x)
 SIMD float log(x). This is the natural logarithm. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall exp2 (SimdFloat x)
 SIMD float 2^x. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall exp (SimdFloat x)
 SIMD float exp(x). More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall pow (SimdFloat x, SimdFloat y)
 SIMD float pow(x,y) More...
 
static SimdFloat gmx_simdcall erf (SimdFloat x)
 SIMD float erf(x). More...
 
static SimdFloat gmx_simdcall erfc (SimdFloat x)
 SIMD float erfc(x). More...
 
static void gmx_simdcall sincos (SimdFloat x, SimdFloat *sinval, SimdFloat *cosval)
 SIMD float sin & cos. More...
 
static SimdFloat gmx_simdcall sin (SimdFloat x)
 SIMD float sin(x). More...
 
static SimdFloat gmx_simdcall cos (SimdFloat x)
 SIMD float cos(x). More...
 
static SimdFloat gmx_simdcall tan (SimdFloat x)
 SIMD float tan(x). More...
 
static SimdFloat gmx_simdcall asin (SimdFloat x)
 SIMD float asin(x). More...
 
static SimdFloat gmx_simdcall acos (SimdFloat x)
 SIMD float acos(x). More...
 
static SimdFloat gmx_simdcall atan (SimdFloat x)
 SIMD float asin(x). More...
 
static SimdFloat gmx_simdcall atan2 (SimdFloat y, SimdFloat x)
 SIMD float atan2(y,x). More...
 
static SimdFloat gmx_simdcall pmeForceCorrection (SimdFloat z2)
 Calculate the force correction due to PME analytically in SIMD float. More...
 
static SimdFloat gmx_simdcall pmePotentialCorrection (SimdFloat z2)
 Calculate the potential correction due to PME analytically in SIMD float. More...
 
Double precision SIMD math functions
Note
In most cases you should use the real-precision functions instead.
static SimdDouble gmx_simdcall copysign (SimdDouble x, SimdDouble y)
 Composes floating point value with the magnitude of x and the sign of y. More...
 
static SimdDouble gmx_simdcall rsqrtIter (SimdDouble lu, SimdDouble x)
 Perform one Newton-Raphson iteration to improve 1/sqrt(x) for SIMD double. More...
 
static SimdDouble gmx_simdcall invsqrt (SimdDouble x)
 Calculate 1/sqrt(x) for SIMD double. More...
 
static void gmx_simdcall invsqrtPair (SimdDouble x0, SimdDouble x1, SimdDouble *out0, SimdDouble *out1)
 Calculate 1/sqrt(x) for two SIMD doubles. More...
 
static SimdDouble gmx_simdcall rcpIter (SimdDouble lu, SimdDouble x)
 Perform one Newton-Raphson iteration to improve 1/x for SIMD double. More...
 
static SimdDouble gmx_simdcall inv (SimdDouble x)
 Calculate 1/x for SIMD double. More...
 
static SimdDouble gmx_simdcall operator/ (SimdDouble nom, SimdDouble denom)
 Division for SIMD doubles. More...
 
static SimdDouble maskzInvsqrt (SimdDouble x, SimdDBool m)
 Calculate 1/sqrt(x) for masked entries of SIMD double. More...
 
static SimdDouble gmx_simdcall maskzInv (SimdDouble x, SimdDBool m)
 Calculate 1/x for SIMD double, masked version. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall sqrt (SimdDouble x)
 Calculate sqrt(x) for SIMD doubles. More...
 
static SimdDouble gmx_simdcall cbrt (SimdDouble x)
 Cube root for SIMD doubles. More...
 
static SimdDouble gmx_simdcall invcbrt (SimdDouble x)
 Inverse cube root for SIMD doubles. More...
 
static SimdDouble gmx_simdcall log2 (SimdDouble x)
 SIMD double log2(x). This is the base-2 logarithm. More...
 
static SimdDouble gmx_simdcall log (SimdDouble x)
 SIMD double log(x). This is the natural logarithm. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall exp2 (SimdDouble x)
 SIMD double 2^x. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall exp (SimdDouble x)
 SIMD double exp(x). More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall pow (SimdDouble x, SimdDouble y)
 SIMD double pow(x,y) More...
 
static SimdDouble gmx_simdcall erf (SimdDouble x)
 SIMD double erf(x). More...
 
static SimdDouble gmx_simdcall erfc (SimdDouble x)
 SIMD double erfc(x). More...
 
static void gmx_simdcall sincos (SimdDouble x, SimdDouble *sinval, SimdDouble *cosval)
 SIMD double sin & cos. More...
 
static SimdDouble gmx_simdcall sin (SimdDouble x)
 SIMD double sin(x). More...
 
static SimdDouble gmx_simdcall cos (SimdDouble x)
 SIMD double cos(x). More...
 
static SimdDouble gmx_simdcall tan (SimdDouble x)
 SIMD double tan(x). More...
 
static SimdDouble gmx_simdcall asin (SimdDouble x)
 SIMD double asin(x). More...
 
static SimdDouble gmx_simdcall acos (SimdDouble x)
 SIMD double acos(x). More...
 
static SimdDouble gmx_simdcall atan (SimdDouble x)
 SIMD double asin(x). More...
 
static SimdDouble gmx_simdcall atan2 (SimdDouble y, SimdDouble x)
 SIMD double atan2(y,x). More...
 
static SimdDouble gmx_simdcall pmeForceCorrection (SimdDouble z2)
 Calculate the force correction due to PME analytically in SIMD double. More...
 
static SimdDouble gmx_simdcall pmePotentialCorrection (SimdDouble z2)
 Calculate the potential correction due to PME analytically in SIMD double. More...
 
SIMD math functions for double prec. data, single prec. accuracy
Note
In some cases we do not need full double accuracy of individual SIMD math functions, although the data is stored in double precision SIMD registers. This might be the case for special algorithms, or if the architecture does not support single precision. Since the full double precision evaluation of math functions typically require much more expensive polynomial approximations these functions implement the algorithms used in the single precision SIMD math functions, but they operate on double precision SIMD variables.
static SimdDouble gmx_simdcall invsqrtSingleAccuracy (SimdDouble x)
 Calculate 1/sqrt(x) for SIMD double, but in single accuracy. More...
 
static SimdDouble maskzInvsqrtSingleAccuracy (SimdDouble x, SimdDBool m)
 1/sqrt(x) for masked-in entries of SIMD double, but in single accuracy. More...
 
static void gmx_simdcall invsqrtPairSingleAccuracy (SimdDouble x0, SimdDouble x1, SimdDouble *out0, SimdDouble *out1)
 Calculate 1/sqrt(x) for two SIMD doubles, but single accuracy. More...
 
static SimdDouble gmx_simdcall invSingleAccuracy (SimdDouble x)
 Calculate 1/x for SIMD double, but in single accuracy. More...
 
static SimdDouble gmx_simdcall maskzInvSingleAccuracy (SimdDouble x, SimdDBool m)
 1/x for masked entries of SIMD double, single accuracy. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall sqrtSingleAccuracy (SimdDouble x)
 Calculate sqrt(x) (correct for 0.0) for SIMD double, with single accuracy. More...
 
static SimdDouble gmx_simdcall cbrtSingleAccuracy (SimdDouble x)
 Cube root for SIMD doubles, single accuracy. More...
 
static SimdDouble gmx_simdcall invcbrtSingleAccuracy (SimdDouble x)
 Inverse cube root for SIMD doubles, single accuracy. More...
 
static SimdDouble gmx_simdcall log2SingleAccuracy (SimdDouble x)
 SIMD log2(x). Double precision SIMD data, single accuracy. More...
 
static SimdDouble gmx_simdcall logSingleAccuracy (SimdDouble x)
 SIMD log(x). Double precision SIMD data, single accuracy. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall exp2SingleAccuracy (SimdDouble x)
 SIMD 2^x. Double precision SIMD, single accuracy. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall expSingleAccuracy (SimdDouble x)
 SIMD exp(x). Double precision SIMD, single accuracy. More...
 
template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall powSingleAccuracy (SimdDouble x, SimdDouble y)
 SIMD pow(x,y). Double precision SIMD data, single accuracy. More...
 
static SimdDouble gmx_simdcall erfSingleAccuracy (SimdDouble x)
 SIMD erf(x). Double precision SIMD data, single accuracy. More...
 
static SimdDouble gmx_simdcall erfcSingleAccuracy (SimdDouble x)
 SIMD erfc(x). Double precision SIMD data, single accuracy. More...
 
static void gmx_simdcall sinCosSingleAccuracy (SimdDouble x, SimdDouble *sinval, SimdDouble *cosval)
 SIMD sin & cos. Double precision SIMD data, single accuracy. More...
 
static SimdDouble gmx_simdcall sinSingleAccuracy (SimdDouble x)
 SIMD sin(x). Double precision SIMD data, single accuracy. More...
 
static SimdDouble gmx_simdcall cosSingleAccuracy (SimdDouble x)
 SIMD cos(x). Double precision SIMD data, single accuracy. More...
 
static SimdDouble gmx_simdcall tanSingleAccuracy (SimdDouble x)
 SIMD tan(x). Double precision SIMD data, single accuracy. More...
 
static SimdDouble gmx_simdcall asinSingleAccuracy (SimdDouble x)
 SIMD asin(x). Double precision SIMD data, single accuracy. More...
 
static SimdDouble gmx_simdcall acosSingleAccuracy (SimdDouble x)
 SIMD acos(x). Double precision SIMD data, single accuracy. More...
 
static SimdDouble gmx_simdcall atanSingleAccuracy (SimdDouble x)
 SIMD asin(x). Double precision SIMD data, single accuracy. More...
 
static SimdDouble gmx_simdcall atan2SingleAccuracy (SimdDouble y, SimdDouble x)
 SIMD atan2(y,x). Double precision SIMD data, single accuracy. More...
 
static SimdDouble gmx_simdcall pmeForceCorrectionSingleAccuracy (SimdDouble z2)
 Analytical PME force correction, double SIMD data, single accuracy. More...
 
static SimdDouble gmx_simdcall pmePotentialCorrectionSingleAccuracy (SimdDouble z2)
 Analytical PME potential correction, double SIMD data, single accuracy. More...
 
SIMD4 math functions
Note
Only a subset of the math functions are implemented for SIMD4.
static Simd4Float gmx_simdcall rsqrtIter (Simd4Float lu, Simd4Float x)
 Perform one Newton-Raphson iteration to improve 1/sqrt(x) for SIMD4 float. More...
 
static Simd4Float gmx_simdcall invsqrt (Simd4Float x)
 Calculate 1/sqrt(x) for SIMD4 float. More...
 
static Simd4Double gmx_simdcall rsqrtIter (Simd4Double lu, Simd4Double x)
 Perform one Newton-Raphson iteration to improve 1/sqrt(x) for SIMD4 double. More...
 
static Simd4Double gmx_simdcall invsqrt (Simd4Double x)
 Calculate 1/sqrt(x) for SIMD4 double. More...
 
static Simd4Double gmx_simdcall invsqrtSingleAccuracy (Simd4Double x)
 Calculate 1/sqrt(x) for SIMD4 double, but in single accuracy. More...
 

Overloads for converting a value of a given type to a string.

Exceptions
std::bad_allocif out of memory.
static std::string toString (bool t)
 
static std::string toString (int t)
 
static std::string toString (int64_t t)
 
static std::string toString (float t)
 
static std::string toString (double t)
 
static std::string toString (std::string t)
 
template<typename T >
std::remove_const_t< T > norm (T *v)
 Forward operations on C Array style vectors to C implementations. More...
 
template<typename T >
std::remove_const_t< T > norm2 (T *v)
 

Variables

const gmx::EnumerationArray
< XvgFormat, const char * > 
c_xvgFormatNames
 Names for XvgFormat. More...
 
static const int c_linewidth = 80 - 2
 Linewidth used for warning output.
 
static const int c_indent = 0
 Indent used for warning output.
 
static const int c_biasMaxNumDim = 4
 The maximum dimensionality of the AWH coordinate.
 
static const EnumerationArray
< DensitySimilarityMeasureMethod,
const char * > 
c_densitySimilarityMeasureMethodNames
 Name the methods that may be used to evaluate similarity between densities. More...
 
static const EnumerationArray
< DensityFittingAmplitudeMethod,
const char * > 
c_densityFittingAmplitudeMethodNames
 The names of the methods to determine the amplitude of the atoms to be spread on a grid. More...
 
static const std::string c_qmmmCP2KModuleName = "qmmm-cp2k"
 Tag with name of the QMMM with CP2K MDModule.
 
static const EnumerationArray
< QMMMQMMethod, const char * > 
c_qmmmQMMethodNames
 The names of the supported QM methods. More...
 
const std::vector< std::string > periodic_system
 symbols of the elements in periodic table More...
 
static const EnumerationArray
< ChangeSettingType, const
char * > 
c_changeSettingTypeNames
 Mapping for enums from ChangeSettingType. More...
 
static const EnumerationArray
< ChangeAtomsType, const char * > 
c_changeAtomsTypeNames
 Mapping for enums from ChangeAtomsType. More...
 
 pmeStream
 
static constexpr Architecture c_architecture
 Constant that tells what the architecture is. More...
 
constexpr int c_loopWait = 1
 How long shall we wait in seconds until we check for a connection again?
 
constexpr int c_connectWait = 1
 How long shall we check for the IMD_GO?
 
constexpr int c_headerSize = 8
 IMD Header Size.
 
constexpr int c_protocolVersion = 2
 IMD Protocol Version.
 
static const char IMDstr [] = "IMD:"
 Tag output from the IMD module with this string. More...
 
constexpr int c_maxConnections = 1
 Currently only 1 client connection is supported.
 
static constexpr int numFTypesOnGpu = 8
 The number on bonded function types supported on GPUs.
 
constexpr std::array< int,
numFTypesOnGpu
fTypesOnGpu
 List of all bonded function types supported on GPUs. More...
 
static const int simd_width = 4
 Define simd_width for memory allocation used for SIMD code.
 
static constexpr int c_threadsPerBlock = 256
 Number of threads in a GPU block.
 
static constexpr int sc_workGroupSize = 256
 Number of work-items in a work-group.
 
static constexpr int c_ftypeVsiteStart = F_VSITE1
 The start value of the vsite indices in the ftype enum. More...
 
static constexpr int c_ftypeVsiteEnd = F_VSITEN + 1
 The start and end value of the vsite indices in the ftype enum.
 
constexpr bool BUGFREE_NOEXCEPT_STRING = std::is_nothrow_move_assignable<std::string>::value
 Work-around for GCC bug 58265 still present in CentOS 7 devtoolset-7.
 
static constexpr int64_t sc_atomInfo_EnergyGroupIdMask = 0b11111111
 The first 8 bits are reserved for energy-group ID.
 
static const
gmx::EnumerationArray
< MtsForceGroups, std::string > 
mtsForceGroupNames
 Names for the MTS force groups. More...
 
const std::array< RVec, 2 > c_forces = { { { 0.5, 0.1, 1.2 }, { -2.1, 0.2, 0.3 } } }
 
static constexpr int s_maxNumThreadsForReduction = 256
 The max thread number is arbitrary, we used a fixed number to avoid memory management. Using more than 16 threads is probably never useful performance wise.
 
 boxRel_ { { 0 } }
 
static constexpr
EnumerationArray< NhcUsage,
const char * > 
nhcUsageNames = { "System", "Barostat" }
 
 boxVelocity_ { { 0 } }
 
 previousBox_ { { 0 } }
 
constexpr int c_centralShiftIndex = detail::c_numIvecs / 2
 
constexpr int c_numShiftVectors = detail::c_numIvecs
 
constexpr double c_angstrom = 1e-10
 
constexpr double c_kilo = 1e3
 
constexpr double c_nano = 1e-9
 
constexpr double c_pico = 1e-12
 
constexpr double c_nm2A = c_nano / c_angstrom
 
constexpr double c_cal2Joule = 4.184
 
constexpr double c_electronCharge = 1.602176634e-19
 
constexpr double c_amu = 1.66053906660e-27
 
constexpr double c_boltzmann = 1.380649e-23
 
constexpr double c_avogadro = 6.02214076e23
 
constexpr double c_universalGasConstant = c_boltzmann * c_avogadro
 
constexpr double c_boltz = c_universalGasConstant / c_kilo
 
constexpr double c_faraday = c_electronCharge * c_avogadro
 
constexpr double c_planck1 = 6.62607015e-34
 
constexpr double c_planck = (c_planck1 * c_avogadro / (c_pico * c_kilo))
 
constexpr double c_epsilon0Si = 8.8541878128e-12
 
constexpr double c_epsilon0
 
constexpr double c_speedOfLight
 
constexpr double c_rydberg = 1.0973731568160e-02
 
constexpr double c_one4PiEps0 = (1.0 / (4.0 * 3.14159265358979323846 * c_epsilon0))
 
constexpr double c_barMdunits = (1e5 * c_nano * c_pico * c_pico / c_amu)
 
constexpr double c_presfac = 1.0 / c_barMdunits
 
constexpr double c_debye2Enm = (1e-15 / (c_speedOfLight * c_electronCharge))
 
constexpr double c_enm2Debye = 1.0 / c_debye2Enm
 
constexpr double c_fieldfac = c_faraday / c_kilo
 
constexpr double c_hartree2Kj = ((2.0 * c_rydberg * c_planck * c_speedOfLight) / c_avogadro)
 
constexpr double c_bohr2Nm = 0.0529177210903
 
constexpr double c_hartreeBohr2Md = (c_hartree2Kj * c_avogadro / c_bohr2Nm)
 
constexpr double c_rad2Deg = 180.0 / 3.14159265358979323846
 
constexpr double c_deg2Rad = 3.14159265358979323846 / 180.0
 
static constexpr int64_t sc_atomInfo_FreeEnergyPerturbation = 1 << 15
 Constants whose bit describes a property of an atom in AtomInfoWithinMoleculeBlock.atomInfo. More...
 
static constexpr int64_t sc_atomInfo_HasPerturbedChargeIn14Interaction = 1 << 16
 
static constexpr int64_t sc_atomInfo_Exclusion = 1 << 17
 
static constexpr int64_t sc_atomInfo_Constraint = 1 << 20
 
static constexpr int64_t sc_atomInfo_Settle = 1 << 21
 
static constexpr int64_t sc_atomInfo_BondCommunication = 1 << 22
 
static constexpr int64_t sc_atomInfo_HasVdw = 1 << 23
 
static constexpr int64_t sc_atomInfo_HasCharge = 1 << 24
 
constexpr int c_dBoxZ = 1
 Maximum dimensions of grid expressing shifts across PBC.
 
constexpr int c_dBoxY = 1
 
constexpr int c_dBoxX = 2
 

Higher-level SIMD utility functions, double precision.

These include generic functions to work with triplets of data, typically coordinates, and a few utility functions to load and update data in the nonbonded kernels. These functions should be available on all implementations.

static const int c_simdBestPairAlignmentDouble = 2
 Best alignment to use for aligned pairs of double data. More...
 
template<int align>
static void gmx_simdcall gatherLoadTranspose (const double *base, const std::int32_t offset[], SimdDouble *v0, SimdDouble *v1, SimdDouble *v2, SimdDouble *v3)
 Load 4 consecutive double from each of GMX_SIMD_DOUBLE_WIDTH offsets, and transpose into 4 SIMD double variables. More...
 
template<int align>
static void gmx_simdcall gatherLoadTranspose (const double *base, const std::int32_t offset[], SimdDouble *v0, SimdDouble *v1)
 Load 2 consecutive double from each of GMX_SIMD_DOUBLE_WIDTH offsets, and transpose into 2 SIMD double variables. More...
 
template<int align>
static void gmx_simdcall gatherLoadUTranspose (const double *base, const std::int32_t offset[], SimdDouble *v0, SimdDouble *v1, SimdDouble *v2)
 Load 3 consecutive doubles from each of GMX_SIMD_DOUBLE_WIDTH offsets, and transpose into 3 SIMD double variables. More...
 
template<int align>
static void gmx_simdcall transposeScatterStoreU (double *base, const std::int32_t offset[], SimdDouble v0, SimdDouble v1, SimdDouble v2)
 Transpose and store 3 SIMD doubles to 3 consecutive addresses at GMX_SIMD_DOUBLE_WIDTH offsets. More...
 
template<int align>
static void gmx_simdcall transposeScatterIncrU (double *base, const std::int32_t offset[], SimdDouble v0, SimdDouble v1, SimdDouble v2)
 Transpose and add 3 SIMD doubles to 3 consecutive addresses at GMX_SIMD_DOUBLE_WIDTH offsets. More...
 
template<int align>
static void gmx_simdcall transposeScatterDecrU (double *base, const std::int32_t offset[], SimdDouble v0, SimdDouble v1, SimdDouble v2)
 Transpose and subtract 3 SIMD doubles to 3 consecutive addresses at GMX_SIMD_DOUBLE_WIDTH offsets. More...
 
static void gmx_simdcall expandScalarsToTriplets (SimdDouble scalar, SimdDouble *triplets0, SimdDouble *triplets1, SimdDouble *triplets2)
 Expand each element of double SIMD variable into three identical consecutive elements in three SIMD outputs. More...
 
template<int align>
static void gmx_simdcall gatherLoadBySimdIntTranspose (const double *base, SimdDInt32 offset, SimdDouble *v0, SimdDouble *v1, SimdDouble *v2, SimdDouble *v3)
 Load 4 consecutive doubles from each of GMX_SIMD_DOUBLE_WIDTH offsets specified by a SIMD integer, transpose into 4 SIMD double variables. More...
 
template<int align>
static void gmx_simdcall gatherLoadUBySimdIntTranspose (const double *base, SimdDInt32 offset, SimdDouble *v0, SimdDouble *v1)
 Load 2 consecutive doubles from each of GMX_SIMD_DOUBLE_WIDTH offsets (unaligned) specified by SIMD integer, transpose into 2 SIMD doubles. More...
 
template<int align>
static void gmx_simdcall gatherLoadBySimdIntTranspose (const double *base, SimdDInt32 offset, SimdDouble *v0, SimdDouble *v1)
 Load 2 consecutive doubles from each of GMX_SIMD_DOUBLE_WIDTH offsets specified by a SIMD integer, transpose into 2 SIMD double variables. More...
 
static double gmx_simdcall reduceIncr4ReturnSum (double *m, SimdDouble v0, SimdDouble v1, SimdDouble v2, SimdDouble v3)
 Reduce each of four SIMD doubles, add those values to four consecutive doubles in memory, return sum. More...
 

Higher-level SIMD utility functions, single precision.

These include generic functions to work with triplets of data, typically coordinates, and a few utility functions to load and update data in the nonbonded kernels. These functions should be available on all implementations, although some wide SIMD implementations (width>=8) also provide special optional versions to work with half or quarter registers to improve the performance in the nonbonded kernels.

static const int c_simdBestPairAlignmentFloat = 2
 Best alignment to use for aligned pairs of float data. More...
 
template<int align>
static void gmx_simdcall gatherLoadTranspose (const float *base, const std::int32_t offset[], SimdFloat *v0, SimdFloat *v1, SimdFloat *v2, SimdFloat *v3)
 Load 4 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH offsets, and transpose into 4 SIMD float variables. More...
 
template<int align>
static void gmx_simdcall gatherLoadTranspose (const float *base, const std::int32_t offset[], SimdFloat *v0, SimdFloat *v1)
 Load 2 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH offsets, and transpose into 2 SIMD float variables. More...
 
template<int align>
static void gmx_simdcall gatherLoadUTranspose (const float *base, const std::int32_t offset[], SimdFloat *v0, SimdFloat *v1, SimdFloat *v2)
 Load 3 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH offsets, and transpose into 3 SIMD float variables. More...
 
template<int align>
static void gmx_simdcall transposeScatterStoreU (float *base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
 Transpose and store 3 SIMD floats to 3 consecutive addresses at GMX_SIMD_FLOAT_WIDTH offsets. More...
 
template<int align>
static void gmx_simdcall transposeScatterIncrU (float *base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
 Transpose and add 3 SIMD floats to 3 consecutive addresses at GMX_SIMD_FLOAT_WIDTH offsets. More...
 
template<int align>
static void gmx_simdcall transposeScatterDecrU (float *base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
 Transpose and subtract 3 SIMD floats to 3 consecutive addresses at GMX_SIMD_FLOAT_WIDTH offsets. More...
 
static void gmx_simdcall expandScalarsToTriplets (SimdFloat scalar, SimdFloat *triplets0, SimdFloat *triplets1, SimdFloat *triplets2)
 Expand each element of float SIMD variable into three identical consecutive elements in three SIMD outputs. More...
 
template<int align>
static void gmx_simdcall gatherLoadBySimdIntTranspose (const float *base, SimdFInt32 offset, SimdFloat *v0, SimdFloat *v1, SimdFloat *v2, SimdFloat *v3)
 Load 4 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH offsets specified by a SIMD integer, transpose into 4 SIMD float variables. More...
 
template<int align>
static void gmx_simdcall gatherLoadUBySimdIntTranspose (const float *base, SimdFInt32 offset, SimdFloat *v0, SimdFloat *v1)
 Load 2 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH offsets (unaligned) specified by SIMD integer, transpose into 2 SIMD floats. More...
 
template<int align>
static void gmx_simdcall gatherLoadBySimdIntTranspose (const float *base, SimdFInt32 offset, SimdFloat *v0, SimdFloat *v1)
 Load 2 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH offsets specified by a SIMD integer, transpose into 2 SIMD float variables. More...
 
static float gmx_simdcall reduceIncr4ReturnSum (float *m, SimdFloat v0, SimdFloat v1, SimdFloat v2, SimdFloat v3)
 Reduce each of four SIMD floats, add those values to four consecutive floats in memory, return sum. More...
 

SIMD data types

The actual storage of these types is implementation dependent. The documentation is generated from the reference implementation, but for normal usage this will likely not be what you are using.

typedef SimdFloat SimdReal
 Real precision floating-point SIMD datatype. More...
 
typedef SimdFBool SimdBool
 Boolean SIMD type for usage with SimdReal. More...
 
typedef SimdFInt32 SimdInt32
 32-bit integer SIMD type. More...
 
typedef SimdFIBool SimdIBool
 Boolean SIMD type for usage with SimdInt32. More...
 
typedef Simd4Float Simd4Real
 Real precision floating-point SIMD4 datatype. More...
 
typedef Simd4FBool Simd4Bool
 Boolean SIMD4 type for usage with SimdReal. More...
 
const int c_simdBestPairAlignment = c_simdBestPairAlignmentFloat
 

High-level SIMD proxy objects to disambiguate load/set operations

using Simd4NFloat = SimdFloat
 
using Simd4NDouble = SimdDouble
 
using Simd4NReal = Simd4NFloat
 
template<typename T >
static std::remove_const_t< T > load (const internal::SimdTraitsT< T > *m)
 Load function that returns SIMD or scalar. More...
 
template<typename T >
static T load (const std::enable_if_t< std::is_arithmetic_v< T >, T > *m)
 
template<typename T , size_t N>
static T gmx_simdcall load (const AlignedArray< internal::SimdTraitsT< T >, N > &m)
 
template<typename T >
static T loadU (const internal::SimdTraitsT< T > *m)
 Load function that returns SIMD or scalar based on template argument. More...
 
template<typename T >
static T loadU (const std::enable_if_t< std::is_arithmetic_v< T >, T > *m)
 
template<typename T , size_t N>
static T gmx_simdcall loadU (const AlignedArray< internal::SimdTraitsT< T >, N > &m)
 
static SimdSetZeroProxy
gmx_simdcall 
setZero ()
 Helper function to set any SIMD or scalar variable to zero. More...
 
template<typename T >
load (const internal::Simd4TraitsT< T > *m)
 
template<typename T >
loadU (const internal::Simd4TraitsT< T > *m)
 
static Simd4NFloat gmx_simdcall loadUNDuplicate4 (const float *f)
 
static Simd4NFloat gmx_simdcall load4DuplicateN (const float *f)
 
static Simd4NFloat gmx_simdcall loadU4NOffset (const float *f, int)
 
static Simd4NDouble gmx_simdcall loadUNDuplicate4 (const double *f)
 
static Simd4NDouble gmx_simdcall load4DuplicateN (const double *f)
 
static Simd4NDouble gmx_simdcall loadU4NOffset (const double *f, int)
 

Typedef Documentation

template<class T >
using gmx::AlignedAllocator = typedef Allocator<T, AlignedAllocationPolicy>

Aligned memory allocator.

Template Parameters
TType of objects to allocate

This convenience partial specialization can be used for the optional allocator template parameter in standard library containers, which is necessary e.g. to use SIMD aligned load and store operations on data in those containers. The memory will always be aligned according to the behavior of AlignedAllocationPolicy.

template<class ElementType >
using gmx::BasicMatrix3x3 = typedef MultiDimArray<std::array<ElementType, 3 * 3>, extents<3, 3>>

Three-by-three matrix of ElementType.

Template Parameters
ElementTypetype of element to be stored in matrix
using gmx::BoxMatrix = typedef std::array<std::array<real, DIM>, DIM>

A 3x3 matrix data type useful for simulation boxes.

Todo:
Implement a full replacement for C-style real[DIM][DIM]

Default fast and accurate random engine in Gromacs.

This engine will return 2*2^64 random results using the default gmx::RandomDomain::Other stream, and can be initialized with a single seed argument without having to remember empty template angle brackets.

template<class T >
using gmx::HostAllocator = typedef Allocator<T, HostAllocationPolicy>

Memory allocator that uses HostAllocationPolicy.

Template Parameters
TType of objects to allocate

This convenience partial specialization can be used for the optional allocator template parameter in standard library containers whose memory may be used for e.g. GPU transfers. The memory will always be allocated according to the behavior of HostAllocationPolicy.

using gmx::index = typedef std::ptrdiff_t

Integer type for indexing into arrays or vectors.

Same as ptrdiff_t.

Three-by-three real number matrix.

Note
will replace the C-style real[3][3] "matrix"
template<class T >
using gmx::PageAlignedAllocator = typedef Allocator<T, PageAlignedAllocationPolicy>

PageAligned memory allocator.

Template Parameters
TType of objects to allocate

This convenience partial specialization can be used for the optional allocator template parameter in standard library containers, which is necessary for locking memory pages for asynchronous transfer between a GPU device and the host. The memory will always be aligned according to the behavior of PageAlignedAllocationPolicy.

typedef std::random_device gmx::RandomDevice

Random device.

For now this is identical to the standard library, but since we use the GROMACS random module for all other random engines and distributions it is convenient to have this too in the same module.

Boolean SIMD4 type for usage with SimdReal.

This type is only available if GMX_SIMD4_HAVE_REAL is 1.

If GMX_DOUBLE is 1, this will be set to Simd4DBool internally, otherwise Simd4FBool. This is necessary since some SIMD implementations use bitpatterns for marking truth, so single- vs. double precision booleans are not necessarily exchangable. As long as you just use this type you will not have to worry about precision.

Note
This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack structures too.

Real precision floating-point SIMD4 datatype.

This type is only available if GMX_SIMD4_HAVE_REAL is 1.

Simd4Double if GMX_DOUBLE is 1, otherwise Simd4Float.

Note
This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack structures too.

Boolean SIMD type for usage with SimdReal.

This type is only available if GMX_SIMD_HAVE_REAL is 1.

If GMX_DOUBLE is 1, this will be set to SimdDBool internally, otherwise SimdFBool. This is necessary since some SIMD implementations use bitpatterns for marking truth, so single- vs. double precision booleans are not necessarily exchangable. As long as you just use this type you will not have to worry about precision.

See SimdIBool for an explanation of real vs. integer booleans.

Note
This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack structures too.

Boolean SIMD type for usage with SimdInt32.

This type is only available if GMX_SIMD_HAVE_INT32_ARITHMETICS is 1.

If GMX_DOUBLE is 1, this will be set to SimdDIBool internally, otherwise SimdFIBool. This is necessary since some SIMD implementations use bitpatterns for marking truth, so single- vs. double precision booleans are not necessarily exchangable, and while a double-precision boolean might be represented with a 64-bit mask, the corresponding integer might only use a 32-bit mask.

We provide conversion routines for these cases, so the only thing you need to keep in mind is to use SimdBool when working with SimdReal while you pick SimdIBool when working with SimdInt32 .

To convert between them, use cvtB2IB and cvtIB2B.

Note
This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack structures too.

32-bit integer SIMD type.

If GMX_DOUBLE is 1, this will be set to SimdDInt32 internally, otherwise SimdFInt32. This might seem a strange implementation detail, but it is because some SIMD implementations use different types/widths of integers registers when converting from double vs. single precision floating point. As long as you just use this type you will not have to worry about precision.

Note
This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack structures too.

Real precision floating-point SIMD datatype.

This type is only available if GMX_SIMD_HAVE_REAL is 1.

SimdDouble if GMX_DOUBLE is 1, otherwise SimdFloat.

Note
This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack structures too.

Enumeration Type Documentation

Enumeration for mdrun appending behavior.

Enumerator
Auto 

Append only if user command-line and file input is correct.

Appending 

Must append.

NoAppending 

Must not append.

enum gmx::Architecture
strong

Enum for GROMACS CPU hardware detection support.

Enumerator
X86 

Not one of the cases below.

Arm 

X86.

PowerPC 

ARM.

IBM PowerPC

enum gmx::AtomLocality : int
strong

Atom locality indicator: local, non-local, all.

Used for calls to: gridding, force calculation, x/f buffer operations

Enumerator
Local 

Local atoms.

NonLocal 

Non-local atoms.

All 

Both local and non-local atoms.

Count 

The number of atom locality types.

Enum with the AWH variables to write.

Enumerator
MetaData 

Meta data.

CoordValue 

Coordinate value.

Pmf 

The pmf.

Bias 

The bias.

Visits 

The number of visits.

Weights 

The weights.

Target 

The target distribition.

ForceCorrelationVolume 

The volume of the force correlation tensor.

FrictionTensor 

The full friction tensor.

Enum with the types of metadata to write.

Enumerator
NumBlock 

The number of blocks.

TargetError 

The target error.

ScaledSampleWeight 

The logarithm of the sample weight relative to a sample weight of 1 at the initial time.

Count 

The number of enum values, not including Count.

enum gmx::CheckpointSignal
strong

Checkpoint signals.

Signals set and read by CheckpointHandler. Possible signals include

  • nothing to signal
  • do checkpoint (at next NS step)
enum gmx::CudaAwareMpiStatus : int
strong

Enum describing CUDA-aware support in underlying MPI library.

Enumerator
Supported 

CUDA-aware support available.

NotSupported 

CUDA-aware support NOT available.

NotKnown 

CUDA-aware support status not known.

enum gmx::DDBondedChecking : bool
strong

Options for checking bonded interactions.

These values must match the bool false and true used for mdrun -ddcheck

Enumerator
ExcludeZeroLimit 

Do not check bonded interactions that go to 0 for large distances.

All 

Check all bonded interactions.

enum gmx::DdRankOrder
strong

The options for the domain decomposition MPI task ordering.

Enumerator
select 

First value (needed to cope with command-line parsing)

interleave 

Interleave the PP and PME ranks.

pp_pme 

First all PP ranks, all PME rank at the end.

cartesian 

Use Cartesian communicators for PP, PME and PP-PME.

Count 

The number of options.

The methods that determine how amplitudes are spread on a grid in density guided simulations.

Enumerator
Unity 

same spread amplitude, unity, for all atoms

Mass 

atom mass is the spread amplitude

Charge 

partial charge determines the spread amplitude

The methods that determine how two densities are compared to one another.

Enumerator
innerProduct 

Measure similarity between densities as normalized inner product of their voxel values.

\[ \mathrm{Similarity}(\rho_{\mathrm{r}},\rho_{\mathrm{c}}) = \frac{1}{N_\mathrm{voxel}}/\sum_{v=1}^{N_\mathrm{voxel}} \rho^v_{\mathrm{r}} \rho^v_{\mathrm{c}} \]

relativeEntropy 

Measure similarity between densities by negative relative entropy.

Note
Voxels with negative values are ignored.

\[ \mathrm{Similarity}(\rho_{\mathrm{r}},\rho_{\mathrm{c}}) = \sum_{v=1}^{N_\mathrm{voxel}} \rho^v_{\mathrm{r}} (\log(\rho^v_{\mathrm{c}}) - \log(\rho^v_{\mathrm{r}})) \]

crossCorrelation 

Measure similarity between densities by cross correlation.

\[ \mathrm{Similarity}(\rho_{\mathrm{r}},\rho_{\mathrm{c}}) = \frac{\sum_{v}\left((\rho_{\mathrm{r}} - \bar{\rho}_{\mathrm{r}})(\rho_{\mathrm{c}} - \bar{\rho}_{\mathrm{c}})\right)} {\sqrt{\sum_v(\rho_{\mathrm{r}} - \bar{\rho}_{\mathrm{r}})^2 \sum_v (\rho_{\mathrm{c}} - \bar{\rho}_{\mathrm{c}})^2}} \]

enum gmx::DeviceStreamType : int
strong

Class enum to describe the different logical streams used for GPU work.

Whether the actual streams differ is an implementation detail of the manager class.

Enumerator
NonBondedLocal 

Stream primarily for short-ranged local nonbonded work.

NonBondedNonLocal 

Stream primarily for short-ranged nonlocal nonbonded work.

Pme 

Stream primarily for PME work.

PmePpTransfer 

Stream primarily for data exchange between PME and PP ranks.

UpdateAndConstraints 

Stream primarily for update and constraints.

Count 

Conventional termination of the enumeration.

enum gmx::DlbOption
strong

The options for the dynamic load balancing.

Enumerator
select 

First value (needed to cope with command-line parsing)

turnOnWhenUseful 

Turn on DLB when we think it would improve performance.

no 

Never turn on DLB.

yes 

Turn on DLB from the start and keep it on.

Count 

The number of options.

enum gmx::EmulateGpuNonbonded : bool
strong

Help pass GPU-emulation parameters with type safety.

Enumerator
No 

Do not emulate GPUs.

Yes 

Do emulate GPUs.

enum gmx::EndianSwapBehavior : int
strong

Specify endian swapping behavoir.

Enumerator
DoNotSwap 

Don't touch anything.

Swap 

User-enforced swapping.

SwapIfHostIsBigEndian 

Only swap if machine we execute on is big-endian.

SwapIfHostIsLittleEndian 

Only swap if machine we execute on is little-endian.

Count 

Number of possible behaviors.

When we calculate virial.

Enumerator
Off 

No specific virial calculation - calculate when energy is calculated.

OnStep 

Calculate on virial frequency steps.

OnStepAndNext 

Calculate on virial frequency steps and on step after.

Count 

The number of entries.

Tells make_at2con how to treat flexible constraints.

Enumerator
Include 

Include all flexible constraints.

Exclude 

Exclude all flexible constraints.

enum gmx::GpuTask : int
strong

Types of compute tasks that can be run on a GPU.

These names refer to existing practice in GROMACS, which is not strictly accurate.

Enumerator
Nonbonded 

Short-ranged interactions.

Pme 

Long-ranged interactions.

Count 

Number of possible tasks.

Output format for help writing.

Enumerator
eHelpOutputFormat_Console 

Plain text directly on the console.

eHelpOutputFormat_Rst 

reStructuredText for online manual and man pages.

eHelpOutputFormat_Other 

Used for extensions in other modules.

eHelpOutputFormat_NR 

Used for the number of output formats.

enum gmx::IMDMessageType : int
strong

Enum for types of IMD messages.

We use the same records as the NAMD/VMD IMD implementation.

Enumerator
Disconnect 

client disconnect

Energies 

energy data

FCoords 

atomic coordinates

Go 

start command for the simulation

Handshake 

handshake to determine little/big endianness

Kill 

terminates the simulation

Mdcomm 

force data

Pause 

pauses the simulation

TRate 

sets the IMD transmission and processing rate

IOerror 

I/O error.

Count 

number of entries

enum gmx::InteractionLocality : int
strong

Interaction locality indicator: local, non-local, all.

Used for calls to: pair-search, force calculation, x/f buffer operations

Enumerator
Local 

Interactions between local atoms only.

NonLocal 

Interactions between non-local and (non-)local atoms.

Count 

The number of interaction locality types.

enum gmx::MrcDataMode : int32_t
strong

The type of density data stored in an mrc file. As named in "EMDB Map Distribution Format Description Version 1.01 (c) emdatabank.org 2014" Modes 0-4 are defined by the standard. NOTE only mode 2 is currently implemented and used.

Enumerator
uInt8 

compressed data mode, 8 bits, signed byte (range -128 to 127, ISO/IEC 10967)

int16 

16 bits, signed integer (range -32768 to 32767, ISO/IEC 10967)

float32 

32 bits, floating point number (IEEE 754)

complexInt32 

32 bits, complex signed integers (ISO/IEC 10967)

complexFloat64 

64 bits, complex floating point numbers (IEEE 754)

enum gmx::MtsForceGroups : int
strong

Force group available for selection for multiple time step integration.

Enumerator
LongrangeNonbonded 

PME-mesh or Ewald for electrostatics and/or LJ.

Nonbonded 

Non-bonded pair interactions.

Pair 

Bonded pair interactions.

Dihedral 

Dihedrals, including cmap (not restraints)

Angle 

Bonded angle potentials (not restraints)

Pull 

COM pulling.

Awh 

Accelerated weight histogram method.

Count 

The number of groups above.

enum gmx::NhcUsage
strong

The usages of Nose-Hoover chains.

Enumerator
System 

Couple system to temperature bath.

Barostat 

Couple barostat to temperature bath.

Count 

Number of enum entries.

enum gmx::Normalization
strong

Enum with different ways of normalizing the output.

Enumerator
None 

No normalization.

Coordinate 

Scale using the internal/user input coordinate scaling factor.

FreeEnergy 

Normalize free energy values by subtracting the minimum value.

Distribution 

Normalize the distribution to 1.

Sets the number of different temperature coupling values.

This is needed to template the kernel

Todo:
Unify with similar enum in CPU update module
Enumerator
None 

No temperature coupling.

Single 

Single T-scaling value (one group)

Multiple 

Multiple T-scaling values, need to use T-group indices.

Count 

Number of valid values.

enum gmx::ObservablesReducerStatus : int
strong

Report whether the reduction has happened this step.

Enumerator
ReadyToReduce 

Reduction has not yet happened this step.

AlreadyReducedThisStep 

Reduction has happened this step.

enum gmx::OptionFlag : uint64_t

Flags for options.

These flags are not part of the public interface, even though they are in an installed header. They are needed in a few template class implementations.

Todo:
The flags related to default values are confusing, consider reorganizing them.
Enumerator
efOption_Set 

Option has been set.

efOption_HasDefaultValue 

The current value of the option is a programmatic default value.

efOption_ExplicitDefaultValue 

An explicit default value has been provided for the option.

efOption_ClearOnNextSet 

Next assignment to the option clears old values.

This flag is set when a new option source starts, such that values from the new source will overwrite old ones.

efOption_Required 

Option is required to be set.

efOption_MultipleTimes 

Option can be specified multiple times.

efOption_Hidden 

Option is hidden from standard help.

efOption_Vector 

Option value is a vector, but a single value is also accepted.

See Also
AbstractOption::setVector()
efOption_DefaultValueIfSetExists 

Option has a defaultValueIfSet() specified.

efOption_NoDefaultValue 

Option does not support default values.

efOption_DontCheckMinimumCount 

Storage object does its custom checking for minimum value count.

If this flag is set, the class derived from OptionStorageTemplate should implement processSetValues(), processAll(), and possible other functions it provides such that it always fails if not enough values are provided. This is useful to override the default check, which is done in OptionStorageTemplate::processSet().

enum gmx::PbcMode
strong

PBC modes for vsite construction and spreading.

Enumerator
all 

Apply normal, simple PBC for all vsites.

none 

No PBC treatment needed.

enum gmx::PinningPolicy : int
strong

Helper enum for pinning policy of the allocation of HostAllocationPolicy.

For an efficient non-blocking transfer (e.g. to a GPU), the memory pages for a buffer need to be pinned to a physical page. Aligning such buffers to a physical page should miminize the number of pages that need to be pinned. However, some buffers that may be used for such transfers may also be used in either GROMACS builds or run paths that cannot use such a device, so the policy can be configured so that the resource consumption is no higher than required for correct, efficient operation in all cases.

enum gmx::QMMMQMMethod
strong

Enumerator for supported QM methods Also could be INPUT which means external input file provided with the name determined by QMMMParameters::qminputfilename_.

Enumerator
PBE 

DFT with PBE functional.

BLYP 

DFT with BLYP functional.

INPUT 

User provides suitable input file for QM package.

enum gmx::RandomDomain
strong

Enumerated values for fixed part of random seed (domain)

Random numbers are used in many places in GROMACS, and to avoid identical streams the random seeds should be different. Instead of keeping track of several different user-provided seeds, it is better to use the fact that generators like ThreeFry take two 64-bit keys, and combine a general user-provided 64-bit random seed with a second constant value from this list to make each stream guaranteed unique.

Note
There is no reason to go overboard with adding options; we only need to guarantee different streams for cases that might be present simultaneously in a single simulation. As an example, two different integrators (or thermostats) can reuse the same domain.
When you do add options, leave some space between the values so you can group new options with old ones without changing old values.
Enumerator
Other 

Generic - stream uniqueness is not important.

MaxwellVelocities 

Veolcity assignment from Maxwell distribution.

TestParticleInsertion 

Test particle insertion.

UpdateCoordinates 

Particle integrators.

UpdateConstraints 

Second integrator step for constraints.

Thermostat 

Stochastic temperature coupling.

Barostat 

Stochastic pressure coupling.

ReplicaExchange 

Replica exchange metropolis moves.

ExpandedEnsemble 

Expanded ensemble lambda moves.

AwhBiasing 

AWH biasing reference value moves.

enum gmx::ReductionRequirement : int
strong

Control whether reduction is required soon.

Enumerator
Soon 

Reduce whenever the runner next checks with the ObservablesReducer.

Eventually 

Reduce whenever the runner next checks with the ObservablesReducer after some module requires reduction Soon.

enum gmx::ResetSignal
strong

Reset signals.

Signals set and read by ResetHandler. Possible signals include

  • nothing to signal
  • reset counters (as soon as signal is received)

Whether the element does schedule on the initial step.

Enumerator
Yes 

Schedule on first step.

No 

Do not schedule on first step.

Count 

Number of enum entries.

enum gmx::SimdType
strong

Enumerated options for SIMD architectures.

Enumerator
None 

Disable all SIMD support.

Reference 

Gromacs reference software SIMD.

Generic 

Placeholder for future support for gcc generic SIMD.

X86_Sse2 

SSE2.

X86_Sse4_1 

SSE4.1.

X86_Avx128Fma 

128-bit Avx with FMA (Amd)

X86_Avx 

256-bit Avx

X86_Avx2 

AVX2.

X86_Avx2_128 

128-bit AVX2, better than 256-bit for AMD Ryzen

X86_Avx512 

AVX_512.

X86_Avx512Knl 

AVX_512_KNL.

Arm_NeonAsimd 

64-bit ARM AArch64 Advanced SIMD

Arm_Sve 

ARM Scalable Vector Extensions.

Ibm_Vsx 

IBM VSX SIMD (Power7 and later)

enum gmx::SpaceGroup : int32_t
strong

Space group in three dimensions.

Currently only "no symmetry" is supported, the complete enum class would hold 230 symbols.

Table 12.3.4.1 Standard space-group symbols, pages 824-831, International Tables for Crystallography, Volume A, fifth edition

Enumerator
P1 

no symmetry

enum gmx::StartingBehavior : int
strong

Enumeration for describing how mdrun is (re)starting.

Enumerator
RestartWithAppending 

Restarting with appending, if a checkpoint is supplied and other conditions are met.

RestartWithoutAppending 

Restarting without appending, when a checkpoint is supplied.

NewSimulation 

Not restarting.

Count 

Mark the end of the enumeration.

enum gmx::StopSignal : int
strong

Stop signals.

Signals that stop conditions can send to all ranks. Possible signals include

  • nothing to signal
  • stop at the next neighbor-searching step
  • stop as soon as signal is received
enum gmx::StripStrings : int
strong

Enum class for whether StringToEnumValueConverter will strip strings of leading and trailing whitespace before comparison.

Enumerator
No 

Do not strip strings.

Yes 

Strip strings.

Different variants of the Parrinello-Rahman velocity scaling.

This is needed to template the kernel

Todo:
Unify with similar enum in CPU update module
Enumerator
None 

Do not apply velocity scaling (not a PR-coupling run or step)

Diagonal 

Apply velocity scaling using a diagonal matrix.

Count 

Number of valid values.

enum gmx::VirtualSiteVirialHandling : int
strong

Tells how to handle virial contributions due to virtual sites.

Enumerator
None 

Do not compute virial contributions.

Pbc 

Add contributions working over PBC to shift forces.

NonLinear 

Compute contributions due to non-linear virtual sites.

enum gmx::VSiteOperation
strong

Whether we calculate vsite positions, velocities, or both.

Enumerator
Positions 

Calculate only positions.

Velocities 

Calculate only velocities.

PositionsAndVelocities 

Calculate both positions and velocities.

Count 

The number of entries.

Function Documentation

static float gmx::abs ( float  a)
inlinestatic

Float Floating-point abs().

Parameters
aany floating point values
Returns
abs(a) for each element.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::abs ( double  a)
inlinestatic

double doubleing-point abs().

Parameters
aany doubleing point values
Returns
abs(a) for each element.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::acos ( float  x)
inlinestatic

Float acos.

Parameters
xThe argument to evaluate acos for
Returns
Acos(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::acos ( double  x)
inlinestatic

Double acos.

Parameters
xThe argument to evaluate acos for
Returns
Acos(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::acosSingleAccuracy ( double  x)
inlinestatic

Double acos, but with single accuracy.

Parameters
xThe argument to evaluate acos for
Returns
Acos(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static OutputAdapterContainer gmx::addOutputAdapters ( const OutputRequirements &  requirements,
AtomsDataPtr  atoms,
const Selection &  sel,
unsigned long  abilities 
)
static

Creates a new container object with the user requested IOutputAdapter derived methods attached to it.

Parameters
[in]requirementsSpecifications for modules to add.
[in]atomsLocal copy of atom information to use.
[in]selSelection to use for choosing atoms to write out.
[in]abilitiesSpecifications for what the output method can do.
Returns
New container for IoutputAdapter derived methods.
void gmx::addWithCoupled ( ArrayRef< const int >  iatoms,
const int  stride,
ArrayRef< const std::vector< AtomsAdjacencyListElement >>  atomsAdjacencyList,
ArrayRef< int >  splitMap,
const int  c,
int *  currentMapIndex 
)
inline

Add constraint to splitMap with all constraints coupled to it.

Adds the constraint c from the constrain list iatoms to the map splitMap if it was not yet added. Then goes through all the constraints coupled to c and calls itself recursively. This ensures that all the coupled constraints will be added to neighboring locations in the final data structures on the device, hence mapping all coupled constraints to the same thread block. A value of -1 in the splitMap is used to flag that constraint was not yet added to the splitMap.

Parameters
[in]iatomsThe list of constraints.
[in]strideNumber of elements per constraint in iatoms.
[in]atomsAdjacencyListInformation about connections between atoms.
[out]splitMapMap of sequential constraint indexes to indexes to be on the device
[in]cSequential index for constraint to consider adding.
[in,out]currentMapIndexThe rolling index for the constraints mapping.
static void gmx::adjustAtomInformation ( t_atoms *  atoms,
t_atoms *  selectionAtoms,
const Selection &  sel 
)
static

Modify atoms information in coordinate frame to fit output selection.

Changes the information contained in the coordinate frame t_atoms struct to match the selection provided to the module.

Parameters
[in]atomsPointer to original t_atoms.
[in]selectionAtomsPointer to local atoms.
[in]selReference to selection.
bool gmx::advancePointInSubgrid ( const BiasGrid &  grid,
const awh_ivec  subgridOrigin,
const awh_ivec  subgridNpoints,
int *  gridPointIndex 
)

Find the next grid point in the sub-part of the grid given a starting point.

The given grid point index is updated to the next valid grid point index by traversing the sub-part of the grid, here termed the subgrid. Since the subgrid range might extend beyond the actual size of the grid, the subgrid is traversed until a point both in the subgrid and grid is found. If no point is found, the function returns false and the index is not modified. The starting point needs to be inside of the subgrid. However, if this index is not given, meaning < 0, then the search is initialized at the subgrid origin, i.e. in this case the "next" grid point index is defined to be the first common grid/subgrid point.

Parameters
[in]gridThe grid.
[in]subgridOriginVector locating the subgrid origin relative to the grid origin.
[in]subgridNpointsNumber of points along each subgrid dimension.
[in,out]gridPointIndexPointer to the starting/next grid point index.
Returns
true if the grid point was updated.
static float gmx::andNot ( float  a,
float  b 
)
inlinestatic

Bitwise andnot for two scalar float variables.

Parameters
adata1
bdata2
Returns
(~data1) & data2
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::andNot ( double  a,
double  b 
)
inlinestatic

Bitwise andnot for two scalar double variables.

Parameters
adata1
bdata2
Returns
(~data1) & data2
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static std::int32_t gmx::andNot ( std::int32_t  a,
std::int32_t  b 
)
inlinestatic

Bitwise andnot for two scalar integer variables.

Parameters
adata1
bdata2
Returns
(~data1) & data2
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static bool gmx::anyDimUsesProvider ( const AwhBiasParams &  awhBiasParams,
const AwhCoordinateProviderType  awhCoordProvider 
)
static

Checks whether any dimension uses the given coordinate provider type.

Parameters
[in]awhBiasParamsThe bias params to check.
[in]awhCoordProviderThe type of coordinate provider
Returns
true if any dimension of the bias is linked to the given provider
static bool gmx::anyDimUsesProvider ( const AwhParams &  awhParams,
const AwhCoordinateProviderType  awhCoordProvider 
)
static

Checks whether any dimension uses the given coordinate provider type.

Parameters
[in]awhParamsThe AWH params to check.
[in]awhCoordProviderThe type of coordinate provider
Returns
true if any dimension of awh is linked to the given provider type.
static bool gmx::anyDimUsesPull ( const ArrayRef< BiasCoupledToSystem >  biasCoupledToSystem)
static

Checks whether any dimension uses pulling as a coordinate provider.

Parameters
[in]biasCoupledToSystemThe AWH biases to check.
Returns
true if any dimension of the provided biases is linked to pulling.
static bool gmx::anyTrue ( bool  a)
inlinestatic

Returns if the boolean is true.

Parameters
aLogical variable.
Returns
true if a is true, otherwise false.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
void gmx::applyGlobalSimulationState ( const SimulationInput &  simulationInput,
PartialDeserializedTprFile partialDeserializedTpr,
t_state globalState,
t_inputrec *  inputrec,
gmx_mtop_t *  globalTopology 
)

Get the global simulation input.

Acquire global simulation data structures from the SimulationInput handle. Note that global data is returned in the calling thread. In parallel computing contexts, the client is responsible for calling only where needed.

Example: if (SIMMASTER(cr)) { // Only the master rank has the global state globalState = globalSimulationState(simulationInput);

// Read (nearly) all data required for the simulation applyGlobalInputRecord(simulationInput, inputrec); applyGlobalTopology(simulationInput, &mtop); }

Todo:
Factor the logic for global/local and master-rank-checks. The SimulationInput utilities should behave properly for the various distributed data scenarios. Consider supplying data directly to the consumers rather than exposing the implementation details of the legacy aggregate types.
void gmx::applyLocalState ( const SimulationInput &  simulationInput,
t_fileio *  logfio,
const t_commrec *  cr,
int *  dd_nc,
t_inputrec *  ir,
t_state state,
ObservablesHistory observablesHistory,
bool  reproducibilityRequested,
const MDModulesNotifiers &  notifiers,
gmx::ReadCheckpointDataHolder modularSimulatorCheckpointData,
bool  useModularSimulator 
)

Initialize local stateful simulation data.

Establish an invariant for the simulator at a trajectory point. Call on all ranks (after domain decomposition and task assignments).

After this call, the simulator has all of the information it will receive in order to advance a trajectory from the current step. Checkpoint information has been applied, if applicable, and stateful data has been (re)initialized.

Warning
Mdrunner instances do not clearly distinguish between global and local versions of t_state.
Todo:
Factor the distributed data aspects of simulation input data into the SimulationInput implementation.
Todo:
Consider refactoring to decouple the checkpoint facility from its consumers (state, observablesHistory, mdModulesNotifiers, and parts of ir).
Warning
It is the caller’s responsibility to make sure that preconditions are satisfied for the parameter objects.
See Also
globalSimulationState()
applyGlobalInputRecord()
applyGlobalTopology()
void gmx::applyTransformationPullCoordForce ( pull_coord_work_t *  pcrd,
gmx::ArrayRef< pull_coord_work_t >  variableCoords,
double  transformationCoordForce 
)

Applies a force of a transformation pull coordinate and distributes it to pull coordinates of lower rank.

Parameters
[in,out]pcrdThe transformation pull coordinate to act on
[in,out]variableCoordsList of variable coords up to the coord index of pcrd
[in]transformationCoordForceThe force working on coord pcrd
static float gmx::asin ( float  x)
inlinestatic

float asin.

Parameters
xThe argument to evaluate asin for
Returns
Asin(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::asin ( double  x)
inlinestatic

Double asin.

Parameters
xThe argument to evaluate asin for
Returns
Asin(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::asinSingleAccuracy ( double  x)
inlinestatic

Double asin, but with single accuracy.

Parameters
xThe argument to evaluate asin for
Returns
Asin(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::assignVsitesToThread ( VsiteThread *  tData,
int  thread,
int  nthread,
int  natperthread,
gmx::ArrayRef< int >  taskIndex,
ArrayRef< const InteractionList >  ilist,
ArrayRef< const t_iparams >  ip,
ArrayRef< const ParticleType >  ptype 
)
static

Here we try to assign all vsites that are in our local range.

Our task local atom range is tData->rangeStart - tData->rangeEnd. Vsites that depend only on local atoms, as indicated by taskIndex[]==thread, are assigned to task tData->ilist. Vsites that depend on non-local atoms but not on other vsites are assigned to task tData->id_task.ilist. taskIndex[] is set for all vsites in our range, either to our local tasks or to the single last task as taskIndex[]=2*nthreads.

static float gmx::atan ( float  x)
inlinestatic

Float atan.

Parameters
xThe argument to evaluate atan for
Returns
Atan(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::atan ( double  x)
inlinestatic

Double atan.

Parameters
xThe argument to evaluate atan for
Returns
Atan(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::atan2 ( float  y,
float  x 
)
inlinestatic

Float atan2(y,x).

Parameters
yY component of vector, any quartile
xX component of vector, any quartile
Returns
Atan(y,x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::atan2 ( double  y,
double  x 
)
inlinestatic

Double atan2(y,x).

Parameters
yY component of vector, any quartile
xX component of vector, any quartile
Returns
Atan(y,x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::atan2SingleAccuracy ( double  y,
double  x 
)
inlinestatic

Double atan2(y,x), but with single accuracy.

Parameters
yY component of vector, any quartile
xX component of vector, any quartile
Returns
Atan(y,x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::atanSingleAccuracy ( double  x)
inlinestatic

Double atan, but with single accuracy.

Parameters
xThe argument to evaluate atan for
Returns
Atan(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static InteractionLocality gmx::atomToInteractionLocality ( const AtomLocality  atomLocality)
inlinestatic

Convert atom locality to interaction locality.

In the current implementation the this is straightforward conversion: local to local, non-local to non-local.

Parameters
[in]atomLocalityAtom locality specifier
Returns
Interaction locality corresponding to the atom locality passed.
template<class BasicMdspan >
constexpr std::enable_if_t<BasicMdspan::is_always_contiguous(), typename BasicMdspan::pointer> gmx::begin ( const BasicMdspan &  basicMdspan)

Free begin function addressing memory of a contiguously laid out basic_mdspan.

Note
Changing the elements that basic_mdspan views does not change the view itself, so a single begin that takes a const view suffices.
void gmx::biasesAreCompatibleForSharingBetweenSimulations ( const AwhParams &  awhParams,
ArrayRef< const size_t >  pointSize,
const BiasSharing &  biasSharing 
)

Checks whether biases are compatible for sharing between simulations, throws when not.

Should be called simultaneously on the master rank of every simulation. Note that this only checks for technical compatibility. It is up to the user to check that the sharing physically makes sense. Throws an exception when shared biases are not compatible.

Parameters
[in]awhParamsThe AWH parameters.
[in]pointSizeVector of grid-point sizes for each bias.
[in]biasSharingObject for communication for sharing bias data over simulations.
static float gmx::blend ( float  a,
float  b,
bool  sel 
)
inlinestatic

Blend float selection.

Parameters
aFirst source
bSecond source
selBoolean selector
Returns
Select b if sel is true, a otherwise.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::blend ( double  a,
double  b,
bool  sel 
)
inlinestatic

Blend double selection.

Parameters
aFirst source
bSecond source
selBoolean selector
Returns
Select b if sel is true, a otherwise.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static std::int32_t gmx::blend ( std::int32_t  a,
std::int32_t  b,
bool  sel 
)
inlinestatic

Blend integer selection.

Parameters
aFirst source
bSecond source
selBoolean selector
Returns
Select b if sel is true, a otherwise.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
void gmx::blockaToExclusionBlocks ( const t_blocka *  b,
gmx::ArrayRef< ExclusionBlock >  b2 
)

Convert the exclusions.

Convert t_blocka exclusions in b into ExclusionBlock form and include them in b2.

Parameters
[in]bExclusions in t_blocka form.
[in,out]b2ExclusionBlocks to populate with t_blocka exclusions.
bool gmx::buildSupportsListedForcesGpu ( std::string *  error)

Checks whether the GROMACS build allows to compute bonded interactions on a GPU.

Parameters
[out]errorIf non-null, the diagnostic message when bondeds cannot run on a GPU.
Returns
true when this build can run bonded interactions on a GPU, false otherwise.
Exceptions
std::bad_allocwhen out of memory.
static void gmx_simdcall gmx::calc_dr_x_f_simd ( int  b0,
int  b1,
gmx::ArrayRef< const AtomPair >  atoms,
const rvec *gmx_restrict  x,
const rvec *gmx_restrict  f,
const real *gmx_restrict  blc,
const real pbc_simd,
rvec *gmx_restrict  r,
real *gmx_restrict  rhs,
real *gmx_restrict  sol 
)
static

Calculate the constraint distance vectors r to project on from x.

Determine the right-hand side of the matrix equation using quantity f. This function only differs from calc_dr_x_xp_simd below in that no constraint length is subtracted and no PBC is used for f.

static void gmx_simdcall gmx::calc_dr_x_xp_simd ( int  b0,
int  b1,
gmx::ArrayRef< const AtomPair >  atoms,
const rvec *gmx_restrict  x,
const rvec *gmx_restrict  xp,
const real *gmx_restrict  bllen,
const real *gmx_restrict  blc,
const real pbc_simd,
rvec *gmx_restrict  r,
real *gmx_restrict  rhs,
real *gmx_restrict  sol 
)
static

Calculate the constraint distance vectors r to project on from x.

Determine the right-hand side of the matrix equation using coordinates xp.

real gmx::calculateAcceptanceWeight ( LambdaWeightCalculation  calculationMode,
real  lambdaEnergyDifference 
)

Calculates the acceptance weight for a lambda state transition.

Parameters
[in]calculationModeHow the lambda weights are calculated
[in]lambdaEnergyDifferenceThe difference in energy between the two states
Returns
The acceptance weight
template<MathOptimization opt = MathOptimization::Safe>
static float gmx::cbrt ( float  x)
inlinestatic

Float cbrt(x). This is the cubic root.

Parameters
xArgument, should be >= 0.
Returns
The cubic root of x. Undefined if argument is invalid.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<MathOptimization opt = MathOptimization::Safe>
static double gmx::cbrt ( double  x)
inlinestatic

Double cbrt(x). This is the cubic root.

Parameters
xArgument, should be >= 0.
Returns
The cubic root of x. Undefined if argument is invalid.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
const char * gmx::centerTypeNames ( CenteringType  type)

Get names for the different centering types.

Parameters
[in]typeWhat name needs to be provided.
template<typename PinnableVector >
void gmx::changePinningPolicy ( PinnableVector *  v,
PinningPolicy  pinningPolicy 
)

Helper function for changing the pinning policy of a pinnable vector.

If the vector has contents, then a full reallocation and buffer copy are needed if the policy change requires tighter restrictions, and desirable even if the policy change requires looser restrictions. That cost is OK, because GROMACS will do this operation very rarely (e.g. when auto-tuning and deciding to switch whether a task will run on a GPU, or not).

void gmx::checkAwhParams ( const AwhParams &  awhParams,
const t_inputrec &  inputrec,
warninp_t  wi 
)

Check the AWH parameters.

Parameters
[in]awhParamsThe AWH parameters.
[in]inputrecInput parameter struct.
[in,out]wiStruct for bookeeping warnings.
static DeviceStatus gmx::checkGpu ( size_t  deviceId,
const DeviceInformation deviceInfo 
)
static

Check whether the ocl_gpu_device is suitable for use by mdrun.

Runs sanity checks: checking that the runtime can compile a dummy kernel and this can be executed; Runs compatibility checks verifying the device OpenCL version requirement and vendor/OS support.

Parameters
[in]deviceIdThe runtime-reported numeric ID of the device.
[in]deviceInfoThe device info pointer.
Returns
A DeviceStatus to indicate if the GPU device is supported and if it was able to run basic functionality checks.
static bool gmx::checkIfRandomDeviceIsFunctional ( )
static

Check if the RDRAND random device functioning correctly.

Due to a bug in AMD Ryzen microcode, RDRAND may always return -1 (0xFFFFFFFF). To avoid that, fall back to using PRNG instead of RDRAND if this happens.

Returns
The result of the checks.
static void gmx::checkInputConsistencyInterval ( const AwhParams &  awhParams,
warninp_t  wi 
)
static

Check if the starting configuration is consistent with the given interval.

Parameters
[in]awhParamsAWH parameters.
[in,out]wiStruct for bookeeping warnings.
CudaAwareMpiStatus gmx::checkMpiCudaAwareSupport ( )

Wrapper on top of MPIX_Query_cuda_support() For MPI implementations which don't support this function, it returns NotKnown Even when an MPI implementation does support this function, MPI library might not be robust enough to detect CUDA-aware support at runtime correcly e.g. when UCX PML is used or CUDA is disabled at runtime.

Returns
CUDA-aware status in MPI implementation
std::vector< std::string > gmx::checkMtsRequirements ( const t_inputrec &  ir)

Checks whether the MTS requirements on other algorithms and output frequencies are met.

Note: exits with an assertion failure when ir.useMts == true && haveValidMtsSetup(ir) == false

Parameters
[in]irComplete input record
Returns
list of error messages, empty when all MTS requirements are met
template<typename VersionEnum >
VersionEnum gmx::checkpointVersion ( const ReadCheckpointData *  checkpointData,
const std::string &  key,
const VersionEnum  programVersion 
)

Read a checkpoint version enum variable.

This reads the checkpoint version from file. The read version is returned.

If the read version is more recent than the code version, this throws an error, since we cannot know what has changed in the meantime. Using newer checkpoint files with old code is not a functionality we can offer. Note, however, that since the checkpoint version is saved by module, older checkpoint files of all simulations that don't use that specific module can still be used.

Allowing backwards compatibility of files (i.e., reading an older checkpoint file with a newer version of the code) is in the responsibility of the caller module. They can use the returned file checkpoint version to do that:

const auto fileVersion = checkpointVersion(checkpointData, "version", c_currentVersion);
if (fileVersion >= CheckpointVersion::AddedX)
{
    checkpointData->scalar("x", &x_));
}
Template Parameters
VersionEnumThe type of the checkpoint version enum
Parameters
checkpointDataA reading checkpoint data object
keyThe key under which the version is saved - also used for error output
programVersionThe checkpoint version of the current code
Returns
The checkpoint version read from file
template<typename VersionEnum >
VersionEnum gmx::checkpointVersion ( WriteCheckpointData *  checkpointData,
const std::string &  key,
const VersionEnum  programVersion 
)

Write the current code checkpoint version enum variable.

Write the current program checkpoint version to the checkpoint data object. Returns the written checkpoint version to mirror the signature of the reading version.

Template Parameters
VersionEnumThe type of the checkpoint version enum
Parameters
checkpointDataA writing checkpoint data object
keyThe key under which the version is saved
programVersionThe checkpoint version of the current code
Returns
The checkpoint version written to file
void gmx::checkUserGpuIds ( ArrayRef< const std::unique_ptr< DeviceInformation >>  deviceInfoList,
ArrayRef< const int >  compatibleGpus,
ArrayRef< const int >  gpuIds 
)

Check that all user-selected GPUs are compatible.

Given the gpuIds and hardwareInfo, throw if any selected GPUs is not compatible.

The error is given with a suitable descriptive message, which will have context if this check is done after the hardware detection results have been reported to the user. However, note that only the GPUs detected on the master rank are reported, because of the existing limitations of that reporting.

Todo:
Note that the selected GPUs can be different on each rank, and the IDs of compatible GPUs can be different on each node, so this routine ought to do communication to determine whether all ranks are able to proceed. Currently this relies on the MPI runtime to kill the other processes because GROMACS lacks the appropriate infrastructure to do a good job of coordinating error messages and behaviour across MPMD ranks and multiple simulations.
Parameters
[in]deviceInfoListInformation on the GPUs on this physical node.
[in]compatibleGpusVector of GPUs that are compatible
[in]gpuIdsThe GPU IDs selected by the user.
Exceptions
std::bad_allocIf out of memory InconsistentInputError If the assigned GPUs are not valid
real gmx::computeCutoffMargin ( PbcType  pbcType,
matrix  box,
real  rlist 
)

Return the margin required for successful domain decomposition.

Parameters
[in]pbcTypeThe PBC type in use
[in]boxThe box in use
[in]rlistThe list size in use
static double gmx::computeDerivativeForTransformationPullCoord ( pull_coord_work_t *  coord,
const int  variablePcrdIndex 
)
static

Calculates and returns the derivative of a transformation pull coordinate from a dependent coordinate.

Note #1: this requires that getTransformationPullCoordinateValue() has been called before with the current coordinates.

Note #2: this method will not compute inner derivates. That is taken care of in the regular pull code

Parameters
[in]coordThe (transformation) coordinate to compute the value for
[in]variablePcrdIndexPull coordinate index of a variable.
static int gmx::computeExpectedNumGlobalBondedInteractions ( const gmx_mtop_t &  mtop,
const bool  useUpdateGroups 
)
static

Compute the total bonded interaction count.

Parameters
[in]mtopThe global system topology
[in]useUpdateGroupsWhether update groups are in use

When using domain decomposition without update groups, constraint-type interactions can be split across domains, and so we do not consider them in this correctness check. Otherwise, we include them.

int gmx::computeFepPeriod ( const t_inputrec &  inputrec,
const ReplicaExchangeParameters replExParams 
)

Compute the period at which FEP calculation is performed.

This harmonizes the free energy calculation period specified by nstdhdl with the periods specified by expanded ensemble, replica exchange, and AWH.

Parameters
inputrecThe input record
replExParamsThe replica exchange parameters
Returns
The period required by the involved algorithms
real gmx::computeMaxUpdateGroupRadius ( const gmx_mtop_t &  mtop,
ArrayRef< const RangePartitioning >  updateGroupingPerMoleculeType,
real  temperature 
)

Returns the maximum update group radius.

Note
When updateGroups is empty, 0 is returned.
Parameters
[in]mtopThe system topology
[in]updateGroupingPerMoleculeTypeList of update group, size should match the number of moltypes in mtop or be 0
[in]temperatureThe maximum reference temperature, pass -1 when unknown or not applicable
RVec gmx::computeQMBoxVec ( const RVec &  a,
const RVec &  b,
const RVec &  c,
real  h,
real  minNorm,
real  maxNorm 
)

Transforms vector a such as distance from it to the plane defined by vectors b and c will be h minimum length will be milL and maximum length maxL.

Parameters
[in]aVector which should be scaled
[in]bFirst vector that forms the plane
[in]cSecond vector that forms the plane
[in]hDistance from the end of a to the plane of (b,c)
[in]minNormMinimum norm of vector
[in]maxNormMaximum norm of vector
void gmx::constrain_coordinates ( gmx::Constraints constr,
bool  do_log,
bool  do_ene,
int64_t  step,
t_state state,
ArrayRefWithPadding< RVec >  xp,
real dvdlambda,
bool  computeVirial,
tensor  constraintsVirial 
)

Constraint coordinates.

The dvdlambda contribution has to be added to the bonded interactions

bool gmx::constrain_lincs ( bool  computeRmsd,
const t_inputrec &  ir,
int64_t  step,
Lincs *  lincsd,
ArrayRef< const real invmass,
const t_commrec *  cr,
const gmx_multisim_t ms,
ArrayRefWithPadding< const RVec >  x,
ArrayRefWithPadding< RVec >  xprime,
ArrayRef< RVec >  min_proj,
const matrix  box,
t_pbc pbc,
bool  hasMassPerturbed,
real  lambda,
real dvdlambda,
real  invdt,
ArrayRef< RVec >  v,
bool  bCalcVir,
tensor  vir_r_m_dr,
ConstraintVariable  econq,
t_nrnb *  nrnb,
int  maxwarn,
int *  warncount 
)

Applies LINCS constraints.

Returns
true if the constraining succeeded.
void gmx::constrain_velocities ( gmx::Constraints constr,
bool  do_log,
bool  do_ene,
int64_t  step,
t_state state,
real dvdlambda,
bool  computeVirial,
tensor  constraintsVirial 
)

Constrain velocities only.

The dvdlambda contribution has to be added to the bonded interactions

template<int numPartnerAtoms>
static real gmx::constraintGroupRadius ( const gmx_moltype_t moltype,
gmx::ArrayRef< const t_iparams >  iparams,
const int  centralAtom,
const ListOfLists< int > &  at2con,
const std::unordered_multimap< int, int > &  angleIndices,
const real  constraintLength,
const real  temperature 
)
static

When possible, computes the maximum radius of constrained atom in an update group.

Supports groups with 2 or 3 atoms where all partner atoms are connected to each other by angle potentials. The temperature is used to compute a radius that is not exceeded with a chance of 10^-9. Note that this computation assumes there are no other strong forces working on these angular degrees of freedom. The return value is -1 when all partners are not connected to each other by one angle potential, when a potential is perturbed or when an angle could reach more than 180 degrees.

template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void gmx::construct_vsites ( const ThreadingInfo *  threadingInfo,
ArrayRef< RVec >  x,
ArrayRef< RVec >  v,
ArrayRef< const t_iparams >  ip,
ArrayRef< const InteractionList >  ilist,
const DomainInfo &  domainInfo,
const matrix  box 
)
static

Dispatch the vsite construction tasks for all threads.

Parameters
[in]threadingInfoUsed to divide work over threads when != nullptr
[in,out]xCoordinates to construct vsites for
[in,out]vWhen not empty, velocities are generated for virtual sites
[in]ipInteraction parameters for all interaction, only vsite parameters are used
[in]ilistThe interaction lists, only vsites are usesd
[in]domainInfoInformation about PBC and DD
[in]boxUsed for PBC when PBC is set in domainInfo
template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void gmx::construct_vsites_thread ( ArrayRef< RVec >  x,
ArrayRef< RVec >  v,
ArrayRef< const t_iparams >  ip,
ArrayRef< const InteractionList >  ilist,
const t_pbc pbc_null 
)
static

Executes the vsite construction task for a single thread.

Template Parameters
operationWhether we are calculating positions, velocities, or both
Parameters
[in,out]xCoordinates to construct vsites for
[in,out]vVelocities are generated for virtual sites if operation requires it
[in]ipInteraction parameters for all interaction, only vsite parameters are used
[in]ilistThe interaction lists, only vsites are usesd
[in]pbc_nullPBC struct, used for PBC distance calculations when !=nullptr
void gmx::constructVirtualSites ( ArrayRef< RVec >  x,
ArrayRef< const t_iparams >  ip,
ArrayRef< const InteractionList >  ilist 
)

Create positions of vsite atoms based for the local system.

Parameters
[in,out]xThe coordinates
[in]ipInteraction parameters
[in]ilistThe interaction list
void gmx::constructVirtualSitesGlobal ( const gmx_mtop_t &  mtop,
ArrayRef< RVec >  x 
)

Create positions of vsite atoms for the whole system assuming all molecules are wholex.

Parameters
[in]mtopThe global topology
[in,out]xThe global coordinates
static CheckpointSignal gmx::convertToCheckpointSignal ( signed char  sig)
inlinestatic

Convert signed char (as used by SimulationSignal) to CheckpointSignal enum.

Expected values are sig == 0 – no signal sig >= 1 – signal received

static ResetSignal gmx::convertToResetSignal ( signed char  sig)
inlinestatic

Convert signed char (as used by SimulationSignal) to ResetSignal enum.

Expected values are sig == 0 – no signal sig >= 1 – signal received

static StopSignal gmx::convertToStopSignal ( signed char  sig)
inlinestatic

Convert signed char (as used by SimulationSignal) to StopSignal enum.

  • Expected values are sig == 0 – no signal sig >= 1 – stop at next NS sig <= -1 – stop asap
static float gmx::copysign ( float  x,
float  y 
)
inlinestatic

Composes single value with the magnitude of x and the sign of y.

Parameters
xValue to set sign for
yValue used to set sign
Returns
Magnitude of x, sign of y
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::copysign ( double  x,
double  y 
)
inlinestatic

Composes double value with the magnitude of x and the sign of y.

Parameters
xValue to set sign for
yValue used to set sign
Returns
Magnitude of x, sign of y
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::cos ( float  x)
inlinestatic

Float cos.

Parameters
xThe argument to evaluate cos for
Returns
Cos(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::cos ( double  x)
inlinestatic

Double cos.

Parameters
xThe argument to evaluate cos for
Returns
Cos(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::cosSingleAccuracy ( double  x)
inlinestatic

Double cos, but with single accuracy.

Parameters
xThe argument to evaluate cos for
Returns
Cos(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
int gmx::countCoupled ( int  a,
ArrayRef< int >  numCoupledConstraints,
ArrayRef< const std::vector< AtomsAdjacencyListElement >>  atomsAdjacencyList 
)
inline

Helper function to go through constraints recursively.

For each constraint, counts the number of coupled constraints and stores the value in numCoupledConstraints array. This information is used to split the array of constraints between thread blocks on a GPU so there is no coupling between constraints from different thread blocks. After the numCoupledConstraints array is filled, the value numCoupledConstraints[c] should be equal to the number of constraints that are coupled to c and located after it in the constraints array.

Parameters
[in]aAtom index.
[in,out]numCoupledConstraintsIndicates if the constraint was already counted and stores the number of constraints (i) connected to it and (ii) located after it in memory. This array is filled by this recursive function. For a set of coupled constraints, only for the first one in this list the number of consecutive coupled constraints is needed: if there is not enough space for this set of constraints in the thread block, the group has to be moved to the next one.
[in]atomsAdjacencyListStores information about connections between atoms.
int gmx::countInterUpdategroupVsites ( const gmx_mtop_t &  mtop,
ArrayRef< const RangePartitioning >  updateGroupingsPerMoleculeType 
)

Return the number of virtual sites that cross update groups.

Parameters
[in]mtopThe global topology
[in]updateGroupingsPerMoleculeTypeUpdate grouping per molecule type, pass empty when not using update groups
static std::vector<int> gmx::countNumCoupledConstraints ( ArrayRef< const int >  iatoms,
ArrayRef< const std::vector< AtomsAdjacencyListElement >>  atomsAdjacencyList 
)
static

Computes and returns how many constraints are coupled to each constraint.

Needed to introduce splits in data so that all coupled constraints will be computed in a single GPU block. The position c of the vector numCoupledConstraints should have the number of constraints that are coupled to a constraint c and are after c in the vector. Only first index of the connected group of the constraints is needed later in the code, hence the numCoupledConstraints vector is also used to keep track if the constrain was already counted.

static int64_t gmx::countSamples ( ArrayRef< const PointState >  pointState)
static

Count the total number of samples / sample weight over all grid points.

Parameters
[in]pointStateThe state of the points in a bias.
Returns
the total sample count.
static int gmx::countTrailingZeroRows ( const double *const *  data,
int  numRows,
int  numColumns 
)
static

Count trailing data rows containing only zeros.

Parameters
[in]data2D data array.
[in]numRowsNumber of rows in array.
[in]numColumnsNumber of cols in array.
Returns
the number of trailing zero rows.
bool gmx::cpuIsAmdZen1 ( const CpuInfo &  cpuInfo)

Return true if the CPU is a first generation AMD Zen (produced by AMD or Hygon)

Parameters
cpuInfoObject with cpu information
Returns
True if running on a first generation AMD Zen
bool gmx::cpuIsX86Nehalem ( const CpuInfo &  cpuInfo)

Return true if the CPU is an Intel x86 Nehalem.

Parameters
cpuInfoObject with cpu information
Returns
True if running on Nehalem CPU
std::unique_ptr< IMDModule > gmx::createElectricFieldModule ( )

Creates a module for an external electric field.

The returned class describes the time dependent electric field that can be applied to all charges in a simulation. The field is described by the following: E(t) = A cos(omega*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(sigma))); If sigma = 0 there is no pulse and we have instead E(t) = A cos(omega*t)

force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e

WARNING: There can be problems with the virial. Since the field is not self-consistent this is unavoidable. For neutral molecules the virial is correct within this approximation. For neutral systems with many charged molecules the error is small. But for systems with a net charge or a few charged molecules the error can be significant when the field is high. Solution: implement a self-consistent electric field into PME.

SimulationWorkload gmx::createSimulationWorkload ( const t_inputrec &  inputrec,
bool  disableNonbondedCalculation,
const DevelopmentFeatureFlags &  devFlags,
bool  havePpDomainDecomposition,
bool  haveSeparatePmeRank,
bool  useGpuForNonbonded,
PmeRunMode  pmeRunMode,
bool  useGpuForBonded,
bool  useGpuForUpdate,
bool  useGpuDirectHalo,
bool  canUseDirectGpuComm,
bool  useGpuPmeDecomposition 
)

Build datastructure that contains decisions whether to run different workload task on GPUs.

Parameters
[in]inputrecThe input record
[in]disableNonbondedCalculationDisable calculation of nonbonded forces
[in]devFlagsThe development feature flags
[in]havePpDomainDecompositionWhether PP domain decomposition is used in this run.
[in]haveSeparatePmeRankWhether separate PME rank(s) are used in this run.
[in]useGpuForNonbondedWhether we have short-range nonbonded interactions calculations on GPU(s).
[in]pmeRunModeRun mode indicating what resource is PME execured on.
[in]useGpuForBondedWhether bonded interactions are calculated on GPU(s).
[in]useGpuForUpdateWhether coordinate update and constraint solving is performed on GPU(s).
[in]useGpuDirectHaloWhether halo exchange is performed directly between GPUs.
[in]canUseDirectGpuCommWhether direct GPU communication can be used in this run.
[in]useGpuPmeDecompositionGPU based PME decomposition used.
Returns
Simulation lifetime constant workload description.
std::unique_ptr< TrajectoryFrameWriter > gmx::createTrajectoryFrameWriter ( const gmx_mtop_t *  top,
const Selection &  sel,
const std::string &  filename,
AtomsDataPtr  atoms,
OutputRequirements  requirements 
)

Factory function for TrajectoryFrameWriter.

Used to initialize a new instance of TrajectoryFrameWriter with the user supplied information for writing trajectory data to disk. Information needed is the file type, file name corresponding to the type, if available topology information and selection information.

If supplied, the modules contained within adapters are registered on the TrajectoryFrameWriter if possible.

The factory function is responsible for the initial santity checks concerning file types and availability of topology information, with the registration of modules being the second part.

Parameters
[in]topPointer to full topology or null.
[in]selReference to global selection used to construct the object.
[in]filenameName of new output file, used to deduce file type.
[in]atomsSmart Pointer to atoms data or null.
[in]requirementsContainer for settings obtained to specify which OutputAdapters should be registered.
Exceptions
InconsistentInputErrorWhen user input and requirements don't match.
void gmx::cshake ( const int  iatom[],
int  ncon,
int *  nnit,
int  maxnit,
ArrayRef< const real constraint_distance_squared,
ArrayRef< RVec >  positions,
const t_pbc pbc,
ArrayRef< const RVec >  initial_displacements,
ArrayRef< const real half_of_reduced_mass,
real  omega,
ArrayRef< const real invmass,
ArrayRef< const real distance_squared_tolerance,
ArrayRef< real scaled_lagrange_multiplier,
int *  nerror 
)

Inner kernel for SHAKE constraints.

Regular iterative shake.

Original implementation from R.C. van Schaik and W.F. van Gunsteren (ETH Zuerich, June 1992), adapted for GROMACS by David van der Spoel November 1992.

The algorithm here is based section five of Ryckaert, Ciccotti and Berendsen, J Comp Phys, 23, 327, 1977.

Parameters
[in]iatomMini-topology of triplets of constraint type (unused in this function) and indices of two atoms involved
[in]nconNumber of constraints
[out]nnitNumber of iterations performed
[in]maxnitMaximum number of iterations permitted
[in]constraint_distance_squaredThe objective value for each constraint
[in,out]positionsThe initial (and final) values of the positions of all atoms
[in]pbcPBC information
[in]initial_displacementsThe initial displacements of each constraint
[in]half_of_reduced_massHalf of the reduced mass for each constraint
[in]omegaSHAKE over-relaxation factor (set non-1.0 by using shake-sor=yes in the .mdp, but there is no documentation anywhere)
[in]invmassInverse mass of each atom
[in]distance_squared_toleranceMultiplicative tolerance on the difference in the square of the constrained distance (see code)
[out]scaled_lagrange_multiplierScaled Lagrange multiplier for each constraint (-2 * eta from p. 336 of the paper, divided by the constraint distance)
[out]nerrorZero upon success, returns one more than the index of the problematic constraint if the input was malformed
Todo:
Make SHAKE use better data structures, in particular for iatom.
gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, real > gmx::currentLambdas ( int64_t  step,
const t_lambda &  fepvals,
int  currentLambdaState 
)

Evaluate the current lambdas.

Parameters
[in]stepthe current simulation step
[in]fepvalsdescribing the lambda setup
[in]currentLambdaStatethe lambda state to use to set the lambdas, -1 if not set
Returns
the current lambda-value array
static bool gmx::cvtB2IB ( bool  a)
inlinestatic

Just return a boolean (mimicks SIMD real-to-int bool conversions)

Parameters
aboolean
Returns
same boolean
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::cvtD2F ( double  a)
inlinestatic

Convert double to float (mimicks SIMD conversion)

Parameters
adouble
Returns
a, as float
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::cvtF2D ( float  a)
inlinestatic

Convert float to double (mimicks SIMD conversion)

Parameters
afloat
Returns
a, as double double
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static std::int32_t gmx::cvtI2R ( std::int32_t  a)
inlinestatic

Return integer.

This function mimicks the SIMD integer-to-real conversion routines. By simply returning an integer, we let the compiler sort out whether the conversion should be to float or double rather than using proxy objects.

Parameters
ainteger
Returns
same value (a)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static bool gmx::cvtIB2B ( bool  a)
inlinestatic

Just return a boolean (mimicks SIMD int-to-real bool conversions)

Parameters
aboolean
Returns
same boolean
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static std::int32_t gmx::cvtR2I ( float  a)
inlinestatic

Round single precision floating point to integer.

Parameters
afloat
Returns
Integer format, a rounded to nearest integer.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static std::int32_t gmx::cvtR2I ( double  a)
inlinestatic

Round single precision doubleing point to integer.

Parameters
adouble
Returns
Integer format, a rounded to nearest integer.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static std::int32_t gmx::cvttR2I ( float  a)
inlinestatic

Truncate single precision floating point to integer.

Parameters
afloat
Returns
Integer format, a truncated to integer.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static std::int32_t gmx::cvttR2I ( double  a)
inlinestatic

Truncate single precision doubleing point to integer.

Parameters
adouble
Returns
Integer format, a truncated to integer.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
void gmx::dd_partition_system ( FILE *  fplog,
const gmx::MDLogger mdlog,
int64_t  step,
const t_commrec *  cr,
bool  bMasterState,
int  nstglobalcomm,
t_state state_global,
const gmx_mtop_t &  top_global,
const t_inputrec &  inputrec,
gmx::ImdSession *  imdSession,
pull_t *  pull_work,
t_state state_local,
gmx::ForceBuffers f,
gmx::MDAtoms mdAtoms,
gmx_localtop_t top_local,
t_forcerec *  fr,
gmx::VirtualSitesHandler vsite,
gmx::Constraints constr,
t_nrnb *  nrnb,
gmx_wallcycle *  wcycle,
bool  bVerbose 
)

TODO Remove fplog when group scheme and charge groups are gone.

Partition the system over the nodes.

step is only used for printing error messages. If bMasterState==TRUE then state_global from the master node is used, else state_local is redistributed between the nodes. When f!=NULL, *f will be reallocated to the size of state_local.

Parameters
[in]fplogPointer to the log file
[in]mdlogMD file logger
[in]stepCurrent step
[in]crCommunication record
[in]bMasterStateIs it a master state
[in]nstglobalcommWill globals be computed on this step
[in]state_globalGlobal state
[in]top_globalGlobal topology
[in]inputrecInput record
[in]imdSessionIMD handle
[in]pull_workPulling data
[in]state_localLocal state
[in]fForce buffer
[in]mdAtomsMD atoms
[in]top_localLocal topology
[in]frForce record
[in]vsiteVirtual sites handler
[in]constrConstraints
[in]nrnbCycle counters
[in]wcycleTimers
[in]bVerboseBe verbose
bool gmx::decideWhetherDirectGpuCommunicationCanBeUsed ( const DevelopmentFeatureFlags &  devFlags,
const gmx::MDLogger mdlog 
)

Decide whether direct GPU communication can be used.

Takes into account the build type which determines feature support as well as GPU development feature flags, determines whether this run can use direct GPU communication. The final decision whether the run will use direct communication for either of the features which rely on it is made during task assignment / simulationWorkload initialization.

Parameters
[in]devFlagsGPU development / experimental feature flags.
[in]mdlogMD logger.
Returns
Whether the MPI-parallel runs can use direct GPU communication.
bool gmx::decideWhetherToUseGpuForHalo ( bool  havePPDomainDecomposition,
bool  useGpuForNonbonded,
bool  canUseDirectGpuComm,
bool  useModularSimulator,
bool  doRerun,
bool  haveEnergyMinimization 
)

Decide whether to use GPU for halo exchange.

Parameters
[in]havePPDomainDecompositionWhether PP domain decomposition is in use.
[in]useGpuForNonbondedWhether GPUs will be used for nonbonded interactions.
[in]canUseDirectGpuCommWhether direct GPU communication can be used.
[in]useModularSimulatorWhether modularsimulator is in use.
[in]doRerunWhether this is a rerun.
[in]haveEnergyMinimizationWhether energy minimization is in use.
Returns
Whether halo exchange can be run on GPU.
bool gmx::decideWhetherToUseGpuForUpdate ( bool  isDomainDecomposition,
bool  useUpdateGroups,
PmeRunMode  pmeRunMode,
bool  havePmeOnlyRank,
bool  useGpuForNonbonded,
TaskTarget  updateTarget,
bool  gpusWereDetected,
const t_inputrec &  inputrec,
const gmx_mtop_t &  mtop,
bool  useEssentialDynamics,
bool  doOrientationRestraints,
bool  haveFrozenAtoms,
bool  doRerun,
const DevelopmentFeatureFlags &  devFlags,
const gmx::MDLogger mdlog 
)

Decide whether to use GPU for update.

Parameters
[in]isDomainDecompositionWhether there more than one domain.
[in]useUpdateGroupsIf the constraints can be split across domains.
[in]pmeRunModePME running mode: CPU, GPU or mixed.
[in]havePmeOnlyRankIf there is a PME-only rank in the simulation.
[in]useGpuForNonbondedWhether GPUs will be used for nonbonded interactions.
[in]updateTargetUser choice for running simulation on GPU.
[in]gpusWereDetectedWhether compatible GPUs were detected on any node.
[in]inputrecThe user input.
[in]mtopThe global topology.
[in]useEssentialDynamicsIf essential dynamics is active.
[in]doOrientationRestraintsIf orientation restraints are enabled.
[in]haveFrozenAtomsIf this simulation has frozen atoms (see Issue #3920).
[in]doRerunIt this is a rerun.
[in]devFlagsGPU development / experimental feature flags.
[in]mdlogMD logger.
Returns
Whether complete simulation can be run on GPU.
Exceptions
std::bad_allocIf out of memory InconsistentInputError If the user requirements are inconsistent.
bool gmx::decideWhetherToUseGpusForBonded ( bool  useGpuForNonbonded,
bool  useGpuForPme,
TaskTarget  bondedTarget,
const t_inputrec &  inputrec,
const gmx_mtop_t &  mtop,
int  numPmeRanksPerSimulation,
bool  gpusWereDetected 
)

Decide whether the simulation will try to run bonded tasks on GPUs.

Parameters
[in]useGpuForNonbondedWhether GPUs will be used for nonbonded interactions.
[in]useGpuForPmeWhether GPUs will be used for PME interactions.
[in]bondedTargetThe user's choice for mdrun -bonded for where to assign tasks.
[in]inputrecThe user input.
[in]mtopThe global topology.
[in]numPmeRanksPerSimulationThe number of PME ranks in each simulation, can be -1 for auto.
[in]gpusWereDetectedWhether compatible GPUs were detected on any node.
Returns
Whether the simulation will run bondeded tasks on GPUs.
Exceptions
std::bad_allocIf out of memory InconsistentInputError If the user requirements are inconsistent.
bool gmx::decideWhetherToUseGpusForNonbonded ( TaskTarget  nonbondedTarget,
const std::vector< int > &  userGpuTaskAssignment,
EmulateGpuNonbonded  emulateGpuNonbonded,
bool  buildSupportsNonbondedOnGpu,
bool  nonbondedOnGpuIsUseful,
bool  gpusWereDetected 
)

Decide whether the simulation will try to run nonbonded tasks on GPUs.

The final decision cannot be made until after the duty of the rank is known. But we need to know if nonbonded will run on GPUs for setting up DD (particularly rlist) and determining duty. If the user requires GPUs for the tasks of that duty, then it will be an error when none are found.

With thread-MPI, calls have been made to decideWhetherToUseGpusForNonbondedWithThreadMpi() and decideWhetherToUseGpusForPmeWithThreadMpi() to help determine the number of ranks and run some checks, but the final decision is made in this routine, along with many more consistency checks.

Parameters
[in]nonbondedTargetThe user's choice for mdrun -nb for where to assign short-ranged nonbonded interaction tasks.
[in]userGpuTaskAssignmentThe user-specified assignment of GPU tasks to device IDs.
[in]emulateGpuNonbondedWhether we will emulate GPU calculation of nonbonded interactions.
[in]buildSupportsNonbondedOnGpuWhether GROMACS was build with GPU support.
[in]nonbondedOnGpuIsUsefulWhether computing nonbonded interactions on a GPU is useful for this calculation.
[in]gpusWereDetectedWhether compatible GPUs were detected on any node.
Returns
Whether the simulation will run nonbonded and PME tasks, respectively, on GPUs.
Exceptions
std::bad_allocIf out of memory InconsistentInputError If the user requirements are inconsistent.
bool gmx::decideWhetherToUseGpusForNonbondedWithThreadMpi ( TaskTarget  nonbondedTarget,
bool  haveAvailableDevices,
const std::vector< int > &  userGpuTaskAssignment,
EmulateGpuNonbonded  emulateGpuNonbonded,
bool  buildSupportsNonbondedOnGpu,
bool  nonbondedOnGpuIsUseful,
int  numRanksPerSimulation 
)

Decide whether this thread-MPI simulation will run nonbonded tasks on GPUs.

The number of GPU tasks and devices influences both the choice of the number of ranks, and checks upon any such choice made by the user. So we need to consider this before any automated choice of the number of thread-MPI ranks.

Parameters
[in]nonbondedTargetThe user's choice for mdrun -nb for where to assign short-ranged nonbonded interaction tasks.
[in]haveAvailableDevicesWhether there are available devices.
[in]userGpuTaskAssignmentThe user-specified assignment of GPU tasks to device IDs.
[in]emulateGpuNonbondedWhether we will emulate GPU calculation of nonbonded interactions.
[in]buildSupportsNonbondedOnGpuWhether GROMACS was built with GPU support.
[in]nonbondedOnGpuIsUsefulWhether computing nonbonded interactions on a GPU is useful for this calculation.
[in]numRanksPerSimulationThe number of ranks in each simulation.
Returns
Whether the simulation will run nonbonded tasks on GPUs.
Exceptions
std::bad_allocIf out of memory InconsistentInputError If the user requirements are inconsistent.
bool gmx::decideWhetherToUseGpusForPme ( bool  useGpuForNonbonded,
TaskTarget  pmeTarget,
TaskTarget  pmeFftTarget,
const std::vector< int > &  userGpuTaskAssignment,
const gmx_hw_info_t &  hardwareInfo,
const t_inputrec &  inputrec,
int  numRanksPerSimulation,
int  numPmeRanksPerSimulation,
bool  gpusWereDetected 
)

Decide whether the simulation will try to run tasks of different types on GPUs.

The final decision cannot be made until after the duty of the rank is known. But we need to know if nonbonded will run on GPUs for setting up DD (particularly rlist) and determining duty. If the user requires GPUs for the tasks of that duty, then it will be an error when none are found.

With thread-MPI, calls have been made to decideWhetherToUseGpusForNonbondedWithThreadMpi() and decideWhetherToUseGpusForPmeWithThreadMpi() to help determine the number of ranks and run some checks, but the final decision is made in this routine, along with many more consistency checks.

Parameters
[in]useGpuForNonbondedWhether GPUs will be used for nonbonded interactions.
[in]pmeTargetThe user's choice for mdrun -pme for where to assign long-ranged PME nonbonded interaction tasks.
[in]pmeFftTargetThe user's choice for mdrun -pmefft for where to do FFT for PME.
[in]userGpuTaskAssignmentThe user-specified assignment of GPU tasks to device IDs.
[in]hardwareInfoHardware information
[in]inputrecThe user input
[in]numRanksPerSimulationThe number of ranks in each simulation.
[in]numPmeRanksPerSimulationThe number of PME ranks in each simulation.
[in]gpusWereDetectedWhether compatible GPUs were detected on any node.
Returns
Whether the simulation will run nonbonded and PME tasks, respectively, on GPUs.
Exceptions
std::bad_allocIf out of memory InconsistentInputError If the user requirements are inconsistent.
bool gmx::decideWhetherToUseGpusForPmeWithThreadMpi ( bool  useGpuForNonbonded,
TaskTarget  pmeTarget,
TaskTarget  pmeFftTarget,
int  numDevicesToUse,
const std::vector< int > &  userGpuTaskAssignment,
const gmx_hw_info_t &  hardwareInfo,
const t_inputrec &  inputrec,
int  numRanksPerSimulation,
int  numPmeRanksPerSimulation 
)

Decide whether this thread-MPI simulation will run PME tasks on GPUs.

The number of GPU tasks and devices influences both the choice of the number of ranks, and checks upon any such choice made by the user. So we need to consider this before any automated choice of the number of thread-MPI ranks.

Parameters
[in]useGpuForNonbondedWhether GPUs will be used for nonbonded interactions.
[in]pmeTargetThe user's choice for mdrun -pme for where to assign long-ranged PME nonbonded interaction tasks.
[in]pmeFftTargetThe user's choice for mdrun -pmefft for where to run FFT.
[in]numDevicesToUseThe number of compatible GPUs that the user permitted us to use.
[in]userGpuTaskAssignmentThe user-specified assignment of GPU tasks to device IDs.
[in]hardwareInfoHardware information
[in]inputrecThe user input
[in]numRanksPerSimulationThe number of ranks in each simulation.
[in]numPmeRanksPerSimulationThe number of PME ranks in each simulation.
Returns
Whether the simulation will run PME tasks on GPUs.
Exceptions
std::bad_allocIf out of memory InconsistentInputError If the user requirements are inconsistent.
static void gmx::deepCopy_t_trxframe ( const t_trxframe &  input,
t_trxframe *  copy,
RVec *  xvec,
RVec *  vvec,
RVec *  fvec,
int *  indexvec 
)
static

Create a deep copy of a t_trxframe input into copy.

When running the analysis tools and changing values with the outputadapters, a deep copy of the input coordinate frame has to be created first to ensure that the data is not changed if it is needed for other tools following with analysis later. Therefore, the data is passed to copy by performing a deep copy first.

The method allocates new storage for coordinates of the x, v, and f arrays in the new coordinate frame. This means that those arrays need to be free'd after the frame has been processed and been written to disk.

Parameters
[in]inputReference input coordinate frame.
[in,out]copyPointer to new output frame that will receive the deep copy.
[in]xvecPointer to local coordinate storage vector.
[in]vvecPointer to local velocity storage vector.
[in]fvecPointer to local force storage vector.
[in]indexvecPointer to local index storage vector.
MrcDensityMapHeader gmx::deserializeMrcDensityMapHeader ( ISerializer *  serializer)

Deserializes an MrcDensityMapHeader from a given serializer.

Parameters
[in]serializerthe serializer
Returns
mrc density map header
static DeviceDetectionResult gmx::detectAllDeviceInformation ( const PhysicalNodeCommunicator &  physicalNodeComm)
static

Detect GPUs when that makes sense to attempt.

Parameters
[in]physicalNodeCommThe communicator across this physical node
Returns
The result of the detection, perhaps including diagnostic messages to issue later.
Todo:
Coordinating the efficient detection of devices across multiple ranks per node should be separated from the lower-level hardware detection. See https://gitlab.com/gromacs/gromacs/-/issues/3650.
PmeRunMode gmx::determinePmeRunMode ( bool  useGpuForPme,
const TaskTarget &  pmeFftTarget,
const t_inputrec &  inputrec 
)

Determine PME run mode.

Given the PME task assignment in useGpuForPme and the user-provided FFT task target in pmeFftTarget, returns a PME run mode for the current run. It also checks the compatibility of the two.

Note
Aborts the run upon incompatible values of useGpuForPme and pmeFftTarget.
Parameters
[in]useGpuForPmePME task assignment, true if PME task is mapped to the GPU.
[in]pmeFftTargetThe user's choice for -pmefft for where to assign the FFT work of the PME task.
[in]inputrecThe user input record
static void gmx::distributeTransformationPullCoordForce ( pull_coord_work_t *  pcrd,
gmx::ArrayRef< pull_coord_work_t >  variableCoords,
const double  transformationCoordForce 
)
static

Distributes the force from a transformation pull coordiante to the dependent pull coordinates by computing the inner derivatives.

Parameters
pcrdThe transformation pull coord
variableCoordsThe dependent pull coordinates
transformationCoordForceThe force to distribute
void gmx::doDeviceTransfers ( const DeviceInformation deviceInfo,
ArrayRef< const char >  input,
ArrayRef< char >  output 
)

Helper function for GPU test code to be platform agnostic.

Transfers input to device 0, if present, and transfers it back into output. Both sizes must match. If no devices are present, do a simple host-side buffer copy instead.

Exceptions
InternalErrorUpon any GPU API error condition.
template<class BasicMdspan >
constexpr std::enable_if_t<BasicMdspan::is_always_contiguous(), typename BasicMdspan::pointer> gmx::end ( const BasicMdspan &  basicMdspan)

Free end function addressing memory of a contiguously laid out basic_mdspan.

Note
Changing the elements that basic_mdspan views does not change the view itself, so a single end that takes a const view suffices.
static void gmx::ensureStateAndRunConsistency ( const BiasParams &  params,
const BiasState &  state 
)
static

Check if the state (loaded from checkpoint) and the run are consistent.

When the state and the run setup are inconsistent, an exception is thrown.

Parameters
[in]paramsThe parameters of the bias.
[in]stateThe state of the bias.
static const char* gmx::enumValueToString ( AtomLocality  enumValue)
static

Get the human-friendly name for atom localities.

Parameters
[in]enumValueThe enum value to get the name for.
static const char* gmx::enumValueToString ( InteractionLocality  enumValue)
static

Get the human-friendly name for interaction localities.

Parameters
[in]enumValueThe enum value to get the name for.
static float gmx::erf ( float  x)
inlinestatic

Float erf(x).

Parameters
xArgument.
Returns
erf(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::erf ( double  x)
inlinestatic

Double erf(x).

Parameters
xArgument.
Returns
erf(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::erfc ( float  x)
inlinestatic

Float erfc(x).

Parameters
xArgument.
Returns
erfc(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::erfc ( double  x)
inlinestatic

Double erfc(x).

Parameters
xArgument.
Returns
erfc(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::erfcSingleAccuracy ( double  x)
inlinestatic

Double erfc(x), but with single accuracy.

Parameters
xArgument.
Returns
erfc(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
double gmx::erfinv ( double  x)

Inverse error function, double precision.

Parameters
xArgument, should be in the range -1.0 < x < 1.0
Returns
The inverse of the error function if the argument is inside the range, +/- infinity if it is exactly 1.0 or -1.0, and NaN otherwise.
float gmx::erfinv ( float  x)

Inverse error function, single precision.

Parameters
xArgument, should be in the range -1.0 < x < 1.0
Returns
The inverse of the error function if the argument is inside the range, +/- infinity if it is exactly 1.0 or -1.0, and NaN otherwise.
static double gmx::erfSingleAccuracy ( double  x)
inlinestatic

Double erf(x), but with single accuracy.

Parameters
xArgument.
Returns
erf(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
constexpr int32_t gmx::exactDiv ( int32_t  a,
int32_t  b 
)

Exact integer division, 32bit.

Parameters
adividend. Function asserts that it is a multiple of divisor
bdivisor
Returns
quotient of division
template<MathOptimization opt = MathOptimization::Safe>
static float gmx::exp ( float  x)
inlinestatic

Float exp(x).

Parameters
xArgument.
Returns
exp(x). Undefined if input argument caused overflow.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<MathOptimization opt = MathOptimization::Safe>
static double gmx::exp ( double  x)
inlinestatic

Double exp(x).

Parameters
xArgument.
Returns
exp(x). Undefined if input argument caused overflow.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<MathOptimization opt = MathOptimization::Safe>
static float gmx::exp2 ( float  x)
inlinestatic

Float 2^x.

Parameters
xArgument.
Returns
2^x. Undefined if input argument caused overflow.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<MathOptimization opt = MathOptimization::Safe>
static double gmx::exp2 ( double  x)
inlinestatic

Double 2^x.

Parameters
xArgument.
Returns
2^x. Undefined if input argument caused overflow.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::exp2SingleAccuracy ( double  x)
inlinestatic

Double 2^x, but with single accuracy.

Parameters
xArgument.
Returns
2^x. Undefined if input argument caused overflow.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::expandScalarsToTriplets ( float  scalar,
float *  triplets0,
float *  triplets1,
float *  triplets2 
)
inlinestatic

Copy single float to three variables.

Parameters
scalarFloating-point input.
[out]triplets0Copy 1.
[out]triplets1Copy 2.
[out]triplets2Copy 3.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::expandScalarsToTriplets ( double  scalar,
double *  triplets0,
double *  triplets1,
double *  triplets2 
)
inlinestatic

Copy single double to three variables.

Parameters
scalarFloating-point input.
[out]triplets0Copy 1.
[out]triplets1Copy 2.
[out]triplets2Copy 3.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
ExponentialMovingAverageState gmx::exponentialMovingAverageStateFromKeyValueTree ( const KeyValueTreeObject &  object)

Sets the exponential moving average state from a key-value-tree object.

Sets the expoential moving average state from a key-value-tree object.

static double gmx::expSingleAccuracy ( double  x)
inlinestatic

Double exp(x), but with single accuracy.

Parameters
xArgument.
Returns
exp(x). Undefined if input argument caused overflow.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
GpuTasksOnRanks gmx::findAllGpuTasksOnThisNode ( ArrayRef< const GpuTask >  gpuTasksOnThisRank,
const PhysicalNodeCommunicator &  physicalNodeComm 
)

Returns container of all tasks on all ranks of this node that are eligible for GPU execution.

Perform all necessary communication for preparing for task assignment. Separating this aspect makes it possible to unit test the logic of task assignment.

std::vector< GpuTask > gmx::findGpuTasksOnThisRank ( bool  haveGpusOnThisPhysicalNode,
TaskTarget  nonbondedTarget,
TaskTarget  pmeTarget,
TaskTarget  bondedTarget,
TaskTarget  updateTarget,
bool  useGpuForNonbonded,
bool  useGpuForPme,
bool  rankHasPpTask,
bool  rankHasPmeTask 
)

Returns container of all tasks on this rank that are eligible for GPU execution.

Parameters
[in]haveGpusOnThisPhysicalNodeWhether there are any GPUs on this physical node.
[in]nonbondedTargetThe user's choice for mdrun -nb for where to assign short-ranged nonbonded interaction tasks.
[in]pmeTargetThe user's choice for mdrun -pme for where to assign long-ranged PME nonbonded interaction tasks.
[in]bondedTargetThe user's choice for mdrun -bonded for where to assign tasks.
[in]updateTargetThe user's choice for mdrun -update for where to assign tasks.
[in]useGpuForNonbondedWhether GPUs will be used for nonbonded interactions.
[in]useGpuForPmeWhether GPUs will be used for PME interactions.
[in]rankHasPpTaskWhether this rank has a PP task
[in]rankHasPmeTaskWhether this rank has a PME task
std::string gmx::findLibraryFile ( const std::string &  filename,
bool  bAddCWD = true,
bool  bFatal = true 
)

Finds full path for a library file.

Searches in the configured library directories for filename. If bAddCWD is true, searches first in the current directory. Fatal error results if the file is not found in any location and bFatal is true.

std::string gmx::findLibraryFile ( const char *  filename,
bool  bAddCWD = true,
bool  bFatal = true 
)

Finds full path for a library file.

Searches in the configured library directories for filename. If bAddCWD is true, searches first in the current directory. Fatal error results if the file is not found in any location and bFatal is true.

static void gmx::flagInteractionsForType ( const int  ftype,
const InteractionList &  il,
const reverse_ilist_t &  ril,
const Range< int > &  atomRange,
const int  numAtomsPerMolecule,
ArrayRef< const int >  globalAtomIndices,
ArrayRef< int >  isAssigned 
)
static

Checks whether interactions have been assigned for one function type.

Loops over a list of interactions in the local topology of one function type and flags each of the interactions as assigned in the global isAssigned list. Exits with an inconsistency error when an interaction is assigned more than once.

static float gmx::fma ( float  a,
float  b,
float  c 
)
inlinestatic

Float Fused-multiply-add. Result is a*b + c.

Parameters
afactor1
bfactor2
cterm
Returns
a*b + c
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::fma ( double  a,
double  b,
double  c 
)
inlinestatic

double Fused-multiply-add. Result is a*b + c.

Parameters
afactor1
bfactor2
cterm
Returns
a*b + c
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::fms ( float  a,
float  b,
float  c 
)
inlinestatic

Float Fused-multiply-subtract. Result is a*b - c.

Parameters
afactor1
bfactor2
cterm
Returns
a*b - c
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::fms ( double  a,
double  b,
double  c 
)
inlinestatic

double Fused-multiply-subtract. Result is a*b - c.

Parameters
afactor1
bfactor2
cterm
Returns
a*b - c
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::fnma ( float  a,
float  b,
float  c 
)
inlinestatic

Float Fused-negated-multiply-add. Result is -a*b + c.

Parameters
afactor1
bfactor2
cterm
Returns
-a*b + c
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::fnma ( double  a,
double  b,
double  c 
)
inlinestatic

double Fused-negated-multiply-add. Result is - a*b + c.

Parameters
afactor1
bfactor2
cterm
Returns
-a*b + c
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::fnms ( float  a,
float  b,
float  c 
)
inlinestatic

Float Fused-negated-multiply-subtract. Result is -a*b - c.

Parameters
afactor1
bfactor2
cterm
Returns
-a*b - c
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::fnms ( double  a,
double  b,
double  c 
)
inlinestatic

double Fused-negated-multiply-subtract. Result is -a*b - c.

Parameters
afactor1
bfactor2
cterm
Returns
-a*b - c
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static int gmx::forceGroupMtsLevel ( ArrayRef< const MtsLevel >  mtsLevels,
const MtsForceGroups  mtsForceGroup 
)
inlinestatic

Returns the MTS level at which a force group is to be computed.

Parameters
[in]mtsLevelsList of force groups for each MTS level, can be empty without MTS
[in]mtsForceGroupThe force group to query the MTS level for
template<int align>
static void gmx::gatherLoadBySimdIntTranspose ( const float *  base,
std::int32_t  offset,
float *  v0,
float *  v1,
float *  v2,
float *  v3 
)
inlinestatic

Load 4 floats from base/offsets and store into variables.

Template Parameters
alignAlignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.
Parameters
baseAligned pointer to the start of the memory.
offsetInteger type with offset to the start of each triplet.
[out]v0First float, base[align*offset[0]].
[out]v1Second float, base[align*offset[0] + 1].
[out]v2Third float, base[align*offset[0] + 2].
[out]v3Fourth float, base[align*offset[0] + 3].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::gatherLoadBySimdIntTranspose ( const float *  base,
std::int32_t  offset,
float *  v0,
float *  v1 
)
inlinestatic

Load 2 floats from base/offsets and store into variables (aligned).

Template Parameters
alignAlignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.
Parameters
baseAligned pointer to the start of the memory.
offsetInteger type with offset to the start of each triplet.
[out]v0First float, base[align*offset[0]].
[out]v1Second float, base[align*offset[0] + 1].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::gatherLoadBySimdIntTranspose ( const double *  base,
std::int32_t  offset,
double *  v0,
double *  v1,
double *  v2,
double *  v3 
)
inlinestatic

Load 4 doubles from base/offsets and store into variables.

Template Parameters
alignAlignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.
Parameters
baseAligned pointer to the start of the memory.
offsetInteger type with offset to the start of each triplet.
[out]v0First double, base[align*offset[0]].
[out]v1Second double, base[align*offset[0] + 1].
[out]v2Third double, base[align*offset[0] + 2].
[out]v3Fourth double, base[align*offset[0] + 3].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::gatherLoadBySimdIntTranspose ( const double *  base,
std::int32_t  offset,
double *  v0,
double *  v1 
)
inlinestatic

Load 2 doubles from base/offsets and store into variables (aligned).

Template Parameters
alignAlignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.
Parameters
baseAligned pointer to the start of the memory.
offsetInteger type with offset to the start of each triplet.
[out]v0First double, base[align*offset[0]].
[out]v1Second double, base[align*offset[0] + 1].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::gatherLoadTranspose ( const float *  base,
const std::int32_t  offset[],
float *  v0,
float *  v1,
float *  v2,
float *  v3 
)
inlinestatic

Load 4 consecutive floats from base/offset into four variables.

Template Parameters
alignAlignment of the memory from which we read.
Parameters
basePointer to the start of the memory area
offsetIndex to data.
[out]v01st float, base[align*offset[0]].
[out]v12nd float, base[align*offset[0] + 1].
[out]v23rd float, base[align*offset[0] + 2].
[out]v34th float, base[align*offset[0] + 3].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::gatherLoadTranspose ( const float *  base,
const std::int32_t  offset[],
float *  v0,
float *  v1 
)
inlinestatic

Load 2 consecutive floats from base/offset into four variables.

Template Parameters
alignAlignment of the memory from which we read.
Parameters
basePointer to the start of the memory area
offsetIndex to data.
[out]v01st float, base[align*offset[0]].
[out]v12nd float, base[align*offset[0] + 1].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::gatherLoadTranspose ( const double *  base,
const std::int32_t  offset[],
double *  v0,
double *  v1,
double *  v2,
double *  v3 
)
inlinestatic

Load 4 consecutive doubles from base/offset into four variables.

Template Parameters
alignAlignment of the memory from which we read.
Parameters
basePointer to the start of the memory area
offsetIndex to data.
[out]v01st double, base[align*offset[0]].
[out]v12nd double, base[align*offset[0] + 1].
[out]v23rd double, base[align*offset[0] + 2].
[out]v34th double, base[align*offset[0] + 3].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::gatherLoadTranspose ( const double *  base,
const std::int32_t  offset[],
double *  v0,
double *  v1 
)
inlinestatic

Load 2 consecutive doubles from base/offset into four variables.

Template Parameters
alignAlignment of the memory from which we read.
Parameters
basePointer to the start of the memory area
offsetIndex to data.
[out]v01st double, base[align*offset[0]].
[out]v12nd double, base[align*offset[0] + 1].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::gatherLoadUBySimdIntTranspose ( const float *  base,
std::int32_t  offset,
float *  v0,
float *  v1 
)
inlinestatic

Load 2 floats from base/offsets and store into variables (unaligned).

Template Parameters
alignAlignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.
Parameters
baseAligned pointer to the start of the memory.
offsetInteger type with offset to the start of each triplet.
[out]v0First float, base[align*offset[0]].
[out]v1Second float, base[align*offset[0] + 1].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::gatherLoadUBySimdIntTranspose ( const double *  base,
std::int32_t  offset,
double *  v0,
double *  v1 
)
inlinestatic

Load 2 doubles from base/offsets and store into variables (unaligned).

Template Parameters
alignAlignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.
Parameters
baseAligned pointer to the start of the memory.
offsetInteger type with offset to the start of each triplet.
[out]v0First double, base[align*offset[0]].
[out]v1Second double, base[align*offset[0] + 1].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::gatherLoadUTranspose ( const float *  base,
const std::int32_t  offset[],
float *  v0,
float *  v1,
float *  v2 
)
inlinestatic

Load 3 consecutive floats from base/offsets, store into three vars.

Template Parameters
alignAlignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.
Parameters
basePointer to the start of the memory area
offsetOffset to the start of data.
[out]v01st value, base[align*offset[0]].
[out]v12nd value, base[align*offset[0] + 1].
[out]v23rd value, base[align*offset[0] + 2].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::gatherLoadUTranspose ( const double *  base,
const std::int32_t  offset[],
double *  v0,
double *  v1,
double *  v2 
)
inlinestatic

Load 3 consecutive doubles from base/offsets, store into three vars.

Template Parameters
alignAlignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.
Parameters
basePointer to the start of the memory area
offsetOffset to the start of data.
[out]v01st double, base[align*offset[0]].
[out]v12nd double, base[align*offset[0] + 1].
[out]v23rd double, base[align*offset[0] + 2].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<class RealType = real, unsigned int Bits, class Rng >
RealType gmx::generateCanonical ( Rng &  g)

Generate a floating-point value with specified number of random bits.

Template Parameters
RealTypeFloating-point type to generate
BitsNumber of random bits to generate
RngRandom number generator class
Parameters
gRandom number generator to use

This implementation avoids the bug in libc++ and stdlibc++ (which is due to the C++ standard being unclear) where 1.0 can be returned occasionally.

static double gmx::get_pull_coord_period ( const t_pull_coord &  pullCoordParams,
const t_pbc pbc,
const real  intervalLength 
)
static

Gets the period of a pull coordinate.

Parameters
[in]pullCoordParamsThe parameters for the pull coordinate.
[in]pbcThe PBC setup
[in]intervalLengthThe length of the AWH interval for this pull coordinate
Returns
the period (or 0 if not periodic).
TranslateAndScale gmx::getCoordinateTransformationToLattice ( const MrcDensityMapHeader &  header)

Extract the transformation into lattice coordinates.

Note
Transformation into lattice coordinates is not treated uniformly in different implementations for the mrc format,e.g., vmd, pymol and chimera have different conventions. Following the vmd implementation here.

In determining the density origin coordinates, explicit ORIGIN records (also called origin2k) in the user defined floats 13 - 15, corresponding to words 50,51 and 52 in the mrc header, precedence over ColumnRowSectionStart. Only if above values are zero, using the column, row and section start to determine the translation vector.

Parameters
[in]headerfrom which the coordinate transformation is to be extracted
Returns
a functor that transforms real space coordinates into the lattice
double gmx::getDeviationFromPointAlongGridAxis ( const BiasGrid &  grid,
int  dimIndex,
int  pointIndex,
double  value 
)

Get the deviation along one dimension from the given value to a point in the grid.

Parameters
[in]gridThe grid.
[in]dimIndexDimensional index in [0, ndim -1].
[in]pointIndexBiasGrid point index.
[in]valueValue along the given dimension.
Returns
the deviation of the given value to the given point.
double gmx::getDeviationFromPointAlongGridAxis ( const BiasGrid &  grid,
int  dimIndex,
int  pointIndex1,
int  pointIndex2 
)

Get the deviation from one point to another along one dimension in the grid.

Parameters
[in]gridThe grid.
[in]dimIndexDimensional index in [0, ndim -1].
[in]pointIndex1Grid point index of the first point.
[in]pointIndex2Grid point index of the second point.
Returns
the deviation of the two points along the given axis.
dynamicExtents3D gmx::getDynamicExtents3D ( const MrcDensityMapHeader &  header)

Extract the extents of the density data.

Parameters
[in]headerfrom which the extents are to be extracted
Returns
density data extents in three dimensions.
static int gmx::getFileType ( const std::string &  filename)
static

Get the internal file type from the filename.

Parameters
[in]filenameFilename of output file.
Exceptions
InvalidInputErrorWhen unable to work on an emoty file name.
Returns
integer value of file type.
static int gmx::getNearestIndexInGrid ( const awh_dvec  value,
ArrayRef< const GridAxis >  axis 
)
static

Map a value to the nearest point in the grid.

Parameters
[in]valueValue.
[in]axisThe grid axes.
Returns
the point index nearest to the value.
static std::size_t gmx::getPageSize ( )
static

Return a page size, from a sysconf/WinAPI query if available, or a default guess (4096 bytes).

Todo:
Move this function into sysinfo.cpp where other OS-specific code/includes live
static PbcMode gmx::getPbcMode ( const t_pbc pbcPtr)
static

Returns the PBC mode based on the system PBC and vsite properties.

Parameters
[in]pbcPtrA pointer to a PBC struct or nullptr when no PBC treatment is required
static unsigned long gmx::getSupportedOutputAdapters ( int  filetype)
static

Get the flag representing the requirements for a given file output.

Also checks if the supplied topology is sufficient through the pointer to mtop.

Parameters
[in]filetypeInternal file type used to check requirements.
Exceptions
InvalidInputErrorWhen encountering an invalid file type.
Returns
Requirements represent by the bitmask in the return type.
double gmx::getTransformationPullCoordinateValue ( pull_coord_work_t *  coord,
ArrayRef< const pull_coord_work_t >  variableCoords 
)

Calculates pull->coord[coord_ind].spatialData.value for a transformation pull coordinate.

This requires the values of the pull coordinates of lower indices to be set

Parameters
[in]coordThe (transformation) coordinate to compute the value for
[in]variableCoordsPull coordinates used as variables, entries 0 to coord->coordIndex will be used
Returns
Transformation value for pull coordinate.
std::unique_ptr< gmx_hw_info_t > gmx::gmx_detect_hardware ( const PhysicalNodeCommunicator &  physicalNodeComm)

Run detection and make correct and consistent hardware information available on all ranks.

May do communication on MPI_COMM_WORLD when compiled with real MPI.

This routine is designed to be called once on each process. In a thread-MPI configuration, it may only be called before the threads are spawned. With real MPI, communication is needed to coordinate the results. In all cases, any thread within a process may use the returned handle.

Todo:
Replace the use of MPI_COMM_WORLD e.g. by using a libraryCommWorld argument. See https://gitlab.com/gromacs/gromacs/-/issues/3650
int gmx::gmx_mdrun ( int  argc,
char *  argv[] 
)

Implements C-style main function for mdrun.

This implementation detects hardware itself, as suits the gmx wrapper binary.

Parameters
[in]argcNumber of C-style command-line arguments
[in]argvC-style command-line argument strings
int gmx::gmx_mdrun ( MPI_Comm  communicator,
const gmx_hw_info_t &  hwinfo,
int  argc,
char *  argv[] 
)

Implements C-style main function for mdrun.

This implementation facilitates reuse of infrastructure. This includes the information about the hardware detected across the given communicator. That suits e.g. efficient implementation of test fixtures.

Parameters
[in]communicatorThe communicator to use for the simulation
[in]hwinfoDescribes the hardware detected on the physical nodes of the communicator
[in]argcNumber of C-style command-line arguments
[in]argvC-style command-line argument strings
Todo:
Progress on https://gitlab.com/gromacs/gromacs/-/issues/3774 will remove the need of test binaries to call gmx_mdrun in a way that is different from the command-line and gmxapi.
static bool gmx::gpuAccelerationOfNonbondedIsUseful ( const MDLogger &  mdlog,
const t_inputrec &  ir,
const bool  issueWarning,
const bool  doRerun 
)
static

Return whether GPU acceleration of nonbondeds is supported with the given settings.

If not, and if a warning may be issued, logs a warning about falling back to CPU code. With thread-MPI, only the first call to this function should have issueWarning true.

std::int64_t gmx::greatestCommonDivisor ( std::int64_t  p,
std::int64_t  q 
)

Find greatest common divisor of two numbers.

Parameters
pFirst number, positive
qSecond number, positive
Returns
Greatest common divisor of p and q
std::tuple< StartingBehavior, LogFilePtr > gmx::handleRestart ( bool  isSimulationMaster,
MPI_Comm  communicator,
const gmx_multisim_t ms,
AppendingBehavior  appendingBehavior,
int  nfile,
t_filenm  fnm[] 
)

Handle startup of mdrun, particularly regarding -cpi and -append.

If there is a checkpoint file, then prepare to start from that state. If possible/required, do so with appending. If some files are not found when appending should be done, we will instead issue a fatal error to avoid unintentional problems.

If there is no checkpoint file, we return a value to indicate a new simulation is starting.

On return, fnm is updated with suffix strings for part numbers if we are doing a restart from checkpoint and are not appending.

The routine also does communication to coordinate behaviour between all simulations, including for error conditions.

Exceptions
FileIOErrorWhen the filesystem behavior prevents the user's choices being implemented.
InconsistentInputErrorWhen the users's choices cannot be implemented.
GromacsExceptionOn ranks upon which the error condition was not detected.
Parameters
[in]isSimulationMasterWhether this rank is the master rank of a simulation
[in]communicatorMPI communicator
[in]msHandles multi-simulations.
[in]appendingBehaviorUser choice for appending
[in]nfileSize of fnm struct
[in,out]fnmFilename parameters to mdrun
Returns
Description of how mdrun is starting
void gmx::hardwareTopologyDoubleCheckDetection ( const gmx::MDLogger mdlog,
const gmx::HardwareTopology hardwareTopology 
)

Sanity check hardware topology and print some notes to log.

Parameters
mdlogLogger.
hardwareTopologyReference to hardwareTopology object.
static bool gmx::hasIncompatibleVsites ( const gmx_moltype_t moltype,
gmx::ArrayRef< const t_iparams >  iparams 
)
static

Returns whether moltype has incompatible vsites.

For simplicity the only compatible vsites are linear 2 or 3 atom sites that are constructed in between the 2 or 3 contructing atoms,

static bool gmx::hasPmeOrNonbondedTask ( const GpuTaskMapping &  mapping)
static

Function for whether the mapping has the GPU PME or Nonbonded task.

Parameters
[in]mappingCurrent GPU task mapping.
Returns
If PME on Nonbonded GPU task was assigned to this mapping.
template<GpuTask TaskType>
static bool gmx::hasTaskType ( const GpuTaskMapping &  mapping)
static

Function for whether the task of mapping has value TaskType.

Parameters
[in]mappingCurrent GPU task mapping.
Returns
If TaskType task was assigned to the mapping.
bool gmx::haveBiasSharingWithinSimulation ( const AwhParams &  awhParams)

Returns if any bias is sharing within a simulation.

Parameters
[in]awhParamsThe AWH parameters.
bool gmx::haveValidMtsSetup ( const t_inputrec &  ir)

Returns whether we use MTS and the MTS setup is internally valid.

Note that setupMtsLevels would have returned at least one error message when this function returns false

int gmx::identifyAvx512FmaUnits ( )

Test whether machine has dual AVX512 FMA units.

Returns
1 or 2 for the number of AVX512 FMA units if AVX512 support is present, 0 if we know the hardware does not have AVX512 support, or -1 if the test cannot run because the compiler lacked AVX512 support.
template<typename ElementType , int N, int M = N>
MultiDimArray<std::array<ElementType, N * M>, extents<N, M> > gmx::identityMatrix ( )

Create an identity matrix of ElementType with N * M elements.

Template Parameters
ElementTypetype of matrix elements
Nnumber of rows
Mnumber of columns, defaults to number of rows if not set
Returns
a matrix with values one where row equals column index and null where row does not equal column index
static bool gmx::imd_recv_mdcomm ( IMDSocket *  socket,
int32_t  nforces,
int32_t *  forcendx,
float *  forces 
)
static

Receive force indices and forces.

The number of forces was previously communicated via the header.

static int gmx::imd_send_rvecs ( IMDSocket *  socket,
int  nat,
rvec *  x,
char *  buffer 
)
static

Send positions from rvec.

We need a separate send buffer and conversion to Angstrom.

int gmx::imd_sock_listen ( IMDSocket *  sock)

Set socket to listening state.

Prints out an error message if unsuccessful.

Parameters
sockThe IMD socket.
Returns
0 if successful.
IMDSocket * gmx::imdsock_accept ( IMDSocket *  sock)

Accept incoming connection and redirect to client socket.

Prints out an error message if unsuccessful.

Parameters
sockThe IMD socket.
Returns
IMD socket if successful, NULL otherwise.
int gmx::imdsock_bind ( IMDSocket *  sock,
int  port 
)

Bind the IMD socket to address and port.

Prints out an error message if unsuccessful. If port == 0, bind() assigns a free port automatically.

Parameters
sockThe IMD socket.
portThe port to bind to.
Returns
0 if successful.
IMDSocket * gmx::imdsock_create ( )

Create an IMD master socket.

Returns
The IMD socket if successful. Otherwise prints an error message and returns NULL.
int gmx::imdsock_destroy ( IMDSocket *  sock)

Close the socket and free the sock struct memory.

Writes an error message if unsuccessful.

Parameters
sockThe IMD socket.
Returns
1 on success, or 0 if unsuccessful.
int gmx::imdsock_getport ( IMDSocket *  sock,
int *  port 
)

Get the port number used for IMD connection.

Prints out an error message if unsuccessful.

Parameters
sockThe IMD socket.
portThe assigned port number.
Returns
0 if successful, an error code otherwise.
int gmx::imdsock_read ( IMDSocket *  sock,
char *  buffer,
int  length 
)

Read from socket.

Parameters
sockThe IMD socket.
bufferBuffer to put the read data.
lengthNumber of bytes to read.
Returns
The number of bytes read, or -1 for errors.
void gmx::imdsock_shutdown ( IMDSocket *  sock)

Shutdown the socket.

Parameters
sockThe IMD socket.
int gmx::imdsock_tryread ( IMDSocket *  sock,
int  timeoutsec,
int  timeoutusec 
)

Try to read from the socket.

Time out after waiting the interval specified. Print an error message if unsuccessful.

Parameters
sockThe IMD socket.
timeoutsecTime out seconds
timeoutusecTime out microseconds
int gmx::imdsock_write ( IMDSocket *  sock,
const char *  buffer,
int  length 
)

Write to socket.

Parameters
sockThe IMD socket.
bufferThe data to write.
lengthNumber of bytes to write.
Returns
The number of bytes written, or -1.
void gmx::initCorrelationGridHistory ( CorrelationGridHistory *  correlationGridHistory,
int  numCorrelationTensors,
int  tensorSize,
int  blockDataListSize 
)

Initialize correlation grid history, sets all sizes.

Parameters
[in,out]correlationGridHistoryCorrelation grid history for master rank.
[in]numCorrelationTensorsNumber of correlation tensors in the grid.
[in]tensorSizeNumber of correlation elements in each tensor.
[in]blockDataListSizeThe number of blocks in the list of each tensor element.
CorrelationGridHistory gmx::initCorrelationGridHistoryFromState ( const CorrelationGrid &  corrGrid)

Allocate a correlation grid history with the same structure as the given correlation grid.

This function would be called at the start of a new simulation. Note that only sizes and memory are initialized here. History data is set by updateCorrelationGridHistory.

Parameters
[in,out]corrGridCorrelation grid state to initialize with.
Returns
the correlation grid history struct.
static void gmx::initializeProjectionMatrix ( const real  invmO,
const real  invmH,
const real  dOH,
const real  dHH,
matrix  inverseCouplingMatrix 
)
static

Initializes a projection matrix.

Parameters
[in]invmOReciprocal oxygen mass
[in]invmHReciprocal hydrogen mass
[in]dOHTarget O-H bond length
[in]dHHTarget H-H bond length
[out]inverseCouplingMatrixInverse bond coupling matrix for the projection version of SETTLE
bool gmx::inputSupportsListedForcesGpu ( const t_inputrec &  ir,
const gmx_mtop_t &  mtop,
std::string *  error 
)

Checks whether the input system allows to compute bonded interactions on a GPU.

Parameters
[in]irInput system.
[in]mtopComplete system topology to search for supported interactions.
[out]errorIf non-null, the error message if the input is not supported on GPU.
Returns
true if PME can run on GPU with this input, false otherwise.
static bool gmx::intervalIsInPeriodicInterval ( double  origin,
double  end,
double  period 
)
static

Checks if the given interval is defined in the correct periodic interval.

Parameters
[in]originStart value of interval.
[in]endEnd value of interval.
[in]periodPeriod (or 0 if not periodic).
Returns
true if the end point values are in the correct periodic interval.
static float gmx::inv ( float  x)
inlinestatic

Calculate 1/x for float.

Parameters
xArgument that must be nonzero. This routine does not check arguments.
Returns
1/x. Result is undefined if your argument was invalid.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::inv ( double  x)
inlinestatic

Calculate 1/x for double.

Parameters
xArgument that must be nonzero. This routine does not check arguments.
Returns
1/x. Result is undefined if your argument was invalid.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::invcbrt ( float  x)
inlinestatic

Calculate inverse cube root of x in single precision.

Parameters
xArgument
Returns
x^(-1/3)

This routine is typically faster than using std::pow().

static double gmx::invcbrt ( double  x)
inlinestatic

Calculate inverse sixth root of x in double precision.

Parameters
xArgument
Returns
x^(-1/3)

This routine is typically faster than using std::pow().

static double gmx::invcbrt ( int  x)
inlinestatic

Calculate inverse sixth root of integer x in double precision.

Parameters
xArgument
Returns
x^(-1/3)

This routine is typically faster than using std::pow().

void gmx::invertBoxMatrix ( const matrix  src,
matrix  dest 
)

Invert a simulation-box matrix in src, return in dest.

This routine assumes that src is a simulation-box matrix, i.e. has zeroes in the upper-right triangle. A fatal error occurs if the product of the leading diagonal is too small. The inversion can be done "in place", i.e src and dest can be the same matrix.

void gmx::invertMatrix ( const matrix  src,
matrix  dest 
)

Invert a general 3x3 matrix in src, return in dest.

A fatal error occurs if the determinant is too small. src and dest cannot be the same matrix.

static double gmx::invSingleAccuracy ( double  x)
inlinestatic

Calculate 1/x for double, but with single accuracy.

Parameters
xArgument that must be nonzero. This routine does not check arguments.
Returns
1/x. Result is undefined if your argument was invalid.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::invsixthroot ( float  x)
inlinestatic

Calculate inverse sixth root of x in single precision.

Parameters
xArgument, must be greater than zero.
Returns
x^(-1/6)

This routine is typically faster than using std::pow().

static double gmx::invsixthroot ( double  x)
inlinestatic

Calculate inverse sixth root of x in double precision.

Parameters
xArgument, must be greater than zero.
Returns
x^(-1/6)

This routine is typically faster than using std::pow().

static double gmx::invsixthroot ( int  x)
inlinestatic

Calculate inverse sixth root of integer x in double precision.

Parameters
xArgument, must be greater than zero.
Returns
x^(-1/6)

This routine is typically faster than using std::pow().

static float gmx::invsqrt ( float  x)
inlinestatic

Calculate 1.0/sqrt(x) in single precision.

Parameters
xPositive value to calculate inverse square root for

For now this is implemented with std::sqrt(x) since gcc seems to do a decent job optimizing it. However, we might decide to use instrinsics or compiler-specific functions in the future.

Returns
1.0/sqrt(x)
static double gmx::invsqrt ( double  x)
inlinestatic

Calculate 1.0/sqrt(x) in double precision, but single range.

Parameters
xPositive value to calculate inverse square root for, must be in the input domain valid for single precision.

For now this is implemented with std::sqrt(x). However, we might decide to use instrinsics or compiler-specific functions in the future, and then we want to have the freedom to do the first step in single precision.

Returns
1.0/sqrt(x)
static double gmx::invsqrt ( int  x)
inlinestatic

Calculate 1.0/sqrt(x) for integer x in double precision.

Parameters
xPositive value to calculate inverse square root for.
Returns
1.0/sqrt(x)
static void gmx::invsqrtPair ( float  x0,
float  x1,
float *  out0,
float *  out1 
)
inlinestatic

Calculate 1/sqrt(x) for two floats.

Parameters
x0First argument, x0 must be positive - no argument checking.
x1Second argument, x1 must be positive - no argument checking.
[out]out0Result 1/sqrt(x0)
[out]out1Result 1/sqrt(x1)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::invsqrtPair ( double  x0,
double  x1,
double *  out0,
double *  out1 
)
inlinestatic

Calculate 1/sqrt(x) for two doubles.

Parameters
x0First argument, x0 must be positive - no argument checking.
x1Second argument, x1 must be positive - no argument checking.
[out]out0Result 1/sqrt(x0)
[out]out1Result 1/sqrt(x1)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::invsqrtPairSingleAccuracy ( double  x0,
double  x1,
double *  out0,
double *  out1 
)
inlinestatic

Calculate 1/sqrt(x) for two doubles, but with single accuracy.

Parameters
x0First argument, x0 must be positive - no argument checking.
x1Second argument, x1 must be positive - no argument checking.
[out]out0Result 1/sqrt(x0)
[out]out1Result 1/sqrt(x1)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::invsqrtSingleAccuracy ( double  x)
inlinestatic

Calculate 1/sqrt(x) for double, but with single accuracy.

Parameters
xArgument that must be >0. This routine does not check arguments.
Returns
1/sqrt(x). Result is undefined if your argument was invalid.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static DeviceStatus gmx::isDeviceFunctional ( const DeviceInformation deviceInfo)
static

Checks that device deviceInfo is compatible with GROMACS.

Vendor and OpenCL version support checks are executed an the result of these returned.

Parameters
[in]deviceInfoThe device info pointer.
Returns
The status enumeration value for the checked device:
static bool gmx::isDeviceFunctional ( const DeviceInformation deviceInfo,
std::string *  errorMessage 
)
static

Checks that device deviceInfo is sane (ie can run a kernel).

Compiles and runs a dummy kernel to determine whether the given OpenCL device functions properly.

Parameters
[in]deviceInfoThe device info pointer.
[out]errorMessageAn error message related to a failing OpenCL API call.
Exceptions
std::bad_allocWhen out of memory.
Returns
Whether the device passed sanity checks
template<typename EnumerationArrayType >
EnumerationArrayType::EnumerationWrapperType gmx::keysOf ( const EnumerationArrayType &  )

Returns an object that provides iterators over the keys associated with EnumerationArrayType.

This helper function is useful in contexts where there is an object of an EnumerationArray, and we want to use a range-based for loop over the keys associated with it, and it would be inconvenient to use the very word EnumerationArray<...> type, nor introduce a using statement for this purpose. It is legal in C++ to call a static member function (such as keys()) via an object rather than the type, but clang-tidy warns about that. So instead we make available a free function that calls that static method.

void gmx::launchForceReductionKernel ( int  numAtoms,
int  atomStart,
bool  addRvecForce,
bool  accumulate,
DeviceBuffer< Float3 d_nbnxmForceToAdd,
DeviceBuffer< Float3 d_rvecForceToAdd,
DeviceBuffer< Float3 d_baseForce,
DeviceBuffer< int >  d_cell,
const DeviceStream deviceStream 
)

Backend-specific function to launch GPU Force Reduction kernel.

Select templated Force reduction kernel and launch it.

In pseudocode:

* for (int i = 0; i < numAtoms; i++) {
* totalForce = d_nbnxmForceToAdd[d_cell[i]]
* if (accumulate)
* totalForce += d_baseForce[atomStart + i]
* if (addRvecForce)
* totalForce += d_rvecForceToAdd[atomStart + i]
* d_baseForce[atomStart + i] = totalForce[i]
* }
*
Parameters
numAtomsNumber of atoms subject to reduction.
atomStartFirst atom index (for d_rvecForceToAdd and d_baseForce).
addRvecForceWhen false, d_rvecForceToAdd is ignored.
accumulateWhen false, the previous values of d_baseForce are discarded.
d_nbnxmForceToAddBuffer containing Nbnxm forces in Nbnxm layout.
d_rvecForceToAddOptional buffer containing arbitrary forces in linear layout.
d_baseForceDestination buffer for forces in linear layout.
d_cellAtom index to Nbnxm cell index.
deviceStreamDevice stream for kernel submission.
void gmx::launchLeapFrogKernel ( int  numAtoms,
DeviceBuffer< Float3 d_x,
DeviceBuffer< Float3 d_xp,
DeviceBuffer< Float3 d_v,
DeviceBuffer< Float3 d_f,
DeviceBuffer< float >  d_inverseMasses,
float  dt,
bool  doTemperatureScaling,
int  numTempScaleValues,
DeviceBuffer< unsigned short >  d_tempScaleGroups,
DeviceBuffer< float >  d_lambdas,
VelocityScalingType  prVelocityScalingType,
Float3  prVelocityScalingMatrixDiagonal,
const DeviceStream deviceStream 
)

Backend-specific function to launch GPU Leap Frog kernel.

Parameters
numAtomsTotal number of atoms.
[in,out]d_xBuffer containing initial coordinates, and where the updated ones will be written.
[out]d_xpBuffer where a copy of the initial coordinates will be written.
[in,out]d_vBuffer containing initial velocities, and where the updated ones will be written.
[in]d_fBuffer containing forces.
[in]d_inverseMassesBuffer containing atoms' reciprocal masses.
dtTimestep.
doTemperatureScalingWhether temperature scaling is needed.
numTempScaleValuesNumber of different T-couple values.
d_tempScaleGroupsMapping of atoms into temperature scaling groups.
d_lambdasTemperature scaling factors (one per group).
prVelocityScalingTypeType of Parrinello-Rahman velocity rescaling.
prVelocityScalingMatrixDiagonalDiagonal elements of Parrinello-Rahman velocity scaling matrix.
deviceStreamDevice stream for kernel launch.
void gmx::launchLincsGpuKernel ( LincsGpuKernelParameters *  kernelParams,
const DeviceBuffer< Float3 > &  d_x,
DeviceBuffer< Float3 d_xp,
bool  updateVelocities,
DeviceBuffer< Float3 d_v,
real  invdt,
bool  computeVirial,
const DeviceStream deviceStream 
)

Backend-specific function to launch LINCS kernel.

Parameters
kernelParamsLINCS parameters.
d_xInitial coordinates before the integration.
d_xpCoordinates after the integration which will be updated.
updateVelocitiesWhether to also update velocities.
d_vVelocities to update (ignored if updateVelocities is false).
invdtReciprocal of timestep.
computeVirialWhether to compute the virial.
deviceStreamDevice stream for kernel launch.
void gmx::launchScaleCoordinatesKernel ( int  numAtoms,
DeviceBuffer< Float3 d_coordinates,
const ScalingMatrix &  mu,
const DeviceStream deviceStream 
)

Launches positions of velocities scaling kernel.

Parameters
[in]numAtomsNumber of atoms in the system.
[in]d_coordinatesDevice buffer with position or velocities to be scaled.
[in]muScaling matrix.
[in]deviceStreamStream to launch kernel in.
void gmx::launchSettleGpuKernel ( int  numSettles,
const DeviceBuffer< WaterMolecule > &  d_atomIds,
const SettleParameters &  settleParameters,
const DeviceBuffer< Float3 > &  d_x,
DeviceBuffer< Float3 d_xp,
bool  updateVelocities,
DeviceBuffer< Float3 d_v,
real  invdt,
bool  computeVirial,
DeviceBuffer< float >  virialScaled,
const PbcAiuc pbcAiuc,
const DeviceStream deviceStream 
)

Apply SETTLE.

Applies SETTLE to coordinates and velocities, stored on GPU. Data at pointers d_xp and d_v change in the GPU memory. The results are not automatically copied back to the CPU memory. Method uses this class data structures which should be updated when needed using update method.

Parameters
[in]numSettlesNumber of SETTLE constraints.
[in]d_atomIdsDevice buffer with indices of atoms to be SETTLEd.
[in]settleParametersParameters for SETTLE constraints.
[in]d_xCoordinates before timestep (in GPU memory)
[in,out]d_xpCoordinates after timestep (in GPU memory). The resulting constrained coordinates will be saved here.
[in]updateVelocitiesIf the velocities should be updated.
[in,out]d_vVelocities to update (in GPU memory, can be nullptr if not updated)
[in]invdtReciprocal timestep (to scale Lagrange multipliers when velocities are updated)
[in]computeVirialIf virial should be updated.
[in,out]virialScaledScaled virial tensor to be updated.
[in]pbcAiucPBC data.
[in]deviceStreamDevice stream to launch kernel in.
template<NumTempScaleValues numTempScaleValues, VelocityScalingType velocityScaling>
auto gmx::leapFrogKernel ( sycl::handler &  cgh,
DeviceAccessor< Float3, mode::read_write >  a_x,
DeviceAccessor< Float3, mode::discard_write >  a_xp,
DeviceAccessor< Float3, mode::read_write >  a_v,
DeviceAccessor< Float3, mode::read >  a_f,
DeviceAccessor< float, mode::read >  a_inverseMasses,
float  dt,
OptionalAccessor< float, mode::read, numTempScaleValues!=NumTempScaleValues::None a_lambdas,
OptionalAccessor< unsigned short, mode::read, numTempScaleValues==NumTempScaleValues::Multiple >  a_tempScaleGroups,
Float3  prVelocityScalingMatrixDiagonal 
)

Main kernel for the Leap-Frog integrator.

The coordinates and velocities are updated on the GPU. Also saves the intermediate values of the coordinates for further use in constraints.

Each GPU thread works with a single particle.

Template Parameters
numTempScaleValuesThe number of different T-couple values.
velocityScalingType of the Parrinello-Rahman velocity rescaling.
Parameters
cghSYCL's command group handler.
[in,out]a_xCoordinates to update upon integration.
[out]a_xpA copy of the coordinates before the integration (for constraints).
[in,out]a_vVelocities to update.
[in]a_fAtomic forces.
[in]a_inverseMassesReciprocal masses.
[in]dtTimestep.
[in]a_lambdasTemperature scaling factors (one per group).
[in]a_tempScaleGroupsMapping of atoms into groups.
[in]prVelocityScalingMatrixDiagonalDiagonal elements of Parrinello-Rahman velocity scaling matrix.
static void gmx::lincs_matrix_expand ( const Lincs &  lincsd,
const Task &  li_task,
gmx::ArrayRef< const real blcc,
gmx::ArrayRef< real rhs1,
gmx::ArrayRef< real rhs2,
gmx::ArrayRef< real sol 
)
static

Do a set of nrec LINCS matrix multiplications.

This function will return with up to date thread-local constraint data, without an OpenMP barrier.

template<bool updateVelocities, bool computeVirial, bool haveCoupledConstraints>
auto gmx::lincsKernel ( sycl::handler &  cgh,
const int  numConstraintsThreads,
DeviceAccessor< AtomPair, mode::read >  a_constraints,
DeviceAccessor< float, mode::read >  a_constraintsTargetLengths,
OptionalAccessor< int, mode::read, haveCoupledConstraints >  a_coupledConstraintsCounts,
OptionalAccessor< int, mode::read, haveCoupledConstraints >  a_coupledConstraintsIndices,
OptionalAccessor< float, mode::read, haveCoupledConstraints >  a_massFactors,
OptionalAccessor< float, mode::read_write, haveCoupledConstraints >  a_matrixA,
DeviceAccessor< float, mode::read >  a_inverseMasses,
const int  numIterations,
const int  expansionOrder,
DeviceAccessor< Float3, mode::read >  a_x,
DeviceAccessor< Float3, mode::read_write >  a_xp,
const float  invdt,
OptionalAccessor< Float3, mode::read_write, updateVelocities >  a_v,
OptionalAccessor< float, mode::read_write, computeVirial a_virialScaled,
PbcAiuc  pbcAiuc 
)

Main kernel for LINCS constraints.

See Hess et al., J. Comput. Chem. 18: 1463-1472 (1997) for the description of the algorithm.

In GPU version, one thread is responsible for all computations for one constraint. The blocks are filled in a way that no constraint is coupled to the constraint from the next block. This is achieved by moving active threads to the next block, if the correspondent group of coupled constraints is to big to fit the current thread block. This may leave some 'dummy' threads in the end of the thread block, i.e. threads that are not required to do actual work. Since constraints from different blocks are not coupled, there is no need to synchronize across the device. However, extensive communication in a thread block are still needed.

Todo:

Reduce synchronization overhead. Some ideas are:

  1. Consider going to warp-level synchronization for the coupled constraints.
  2. Move more data to local/shared memory and try to get rid of atomic operations (at least on the device level).
  3. Use analytical solution for matrix A inversion.
  4. Introduce mapping of thread id to both single constraint and single atom, thus designating Nth threads to deal with Nat <= Nth coupled atoms and Nc <= Nth coupled constraints. See Issue #2885 for details (https://gitlab.com/gromacs/gromacs/-/issues/2885)

The use of restrict for gm_xp and gm_v causes failure, probably because of the atomic operations. Investigate this issue further.

Template Parameters
updateVelocitiesWhether velocities should be updated this step.
computeVirialWhether virial tensor should be computed this step.
haveCoupledConstraintsIf there are coupled constraints (i.e. LINCS iterations are needed).
Parameters
[in]cghSYCL handler.
[in]numConstraintsThreadsTotal number of threads.
[in]a_constraintsList of constrained atoms.
[in]a_constraintsTargetLengthsEquilibrium distances for the constraints.
[in]a_coupledConstraintsCountsNumber of constraints, coupled with the current one.
[in]a_coupledConstraintsIndicesList of coupled with the current one.
[in]a_massFactorsMass factors.
[in]a_matrixAElements of the coupling matrix.
[in]a_inverseMasses1/mass for all atoms.
[in]numIterationsNumber of iterations used to correct the projection.
[in]expansionOrderOrder of expansion when inverting the matrix.
[in]a_xUnconstrained positions.
[in,out]a_xpPositions at the previous step, will be updated.
[in]invdtInverse timestep (needed to update velocities).
[in,out]a_vVelocities of atoms, will be updated if updateVelocities.
[in,out]a_virialScaledScaled virial tensor (6 floats: [XX, XY, XZ, YY, YZ, ZZ]. Will be updated if updateVirial.
[in]pbcAiucPeriodic boundary data.
void gmx::linearArrayIndexToMultiDim ( int  indexLinear,
int  ndim,
const awh_ivec  numPointsDim,
awh_ivec  indexMulti 
)

Convert a linear array index to a multidimensional one.

Parameters
[in]indexLinearLinear array index
[in]ndimNumber of dimensions of the array.
[in]numPointsDimNumber of points for each dimension.
[out]indexMultiThe multidimensional index.
void gmx::linearGridindexToMultiDim ( const BiasGrid &  grid,
int  indexLinear,
awh_ivec  indexMulti 
)

Convert a linear grid point index to a multidimensional one.

Parameters
[in]gridThe grid.
[in]indexLinearLinear grid point index to convert to a multidimensional one.
[out]indexMultiThe multidimensional index.
template<typename T >
static std::remove_const_t<T> gmx::load ( const internal::SimdTraitsT< T > *  m)
inlinestatic

Load function that returns SIMD or scalar.

Note that a load of T* where T is const returns a value, which is a copy, and the caller cannot be constrained to not change it, so the return type uses std::remove_const_t.

Template Parameters
TType to load (type is always mandatory)
Parameters
mPointer to aligned memory
Returns
Loaded value
template<typename T >
static T gmx::loadU ( const internal::SimdTraitsT< T > *  m)
inlinestatic

Load function that returns SIMD or scalar based on template argument.

Template Parameters
TType to load (type is always mandatory)
Parameters
mPointer to unaligned memory
Returns
Loaded SimdFloat/Double/Int or basic scalar type
static float gmx::log ( float  x)
inlinestatic

Float log(x). This is the natural logarithm.

Parameters
xArgument, should be >0.
Returns
The natural logarithm of x. Undefined if argument is invalid.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::log ( double  x)
inlinestatic

Double log(x). This is the natural logarithm.

Parameters
xArgument, should be >0.
Returns
The natural logarithm of x. Undefined if argument is invalid.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
unsigned int gmx::log2I ( std::uint32_t  x)

Compute floor of logarithm to base 2, 32 bit unsigned argument.

Parameters
x32-bit unsigned argument
Returns
log2(x)
Note
This version of the overloaded function uses unsigned arguments to be able to handle arguments using all 32 bits.
unsigned int gmx::log2I ( std::uint64_t  x)

Compute floor of logarithm to base 2, 64 bit unsigned argument.

Parameters
x64-bit unsigned argument
Returns
log2(x)
Note
This version of the overloaded function uses unsigned arguments to be able to handle arguments using all 64 bits.
unsigned int gmx::log2I ( std::int32_t  x)

Compute floor of logarithm to base 2, 32 bit signed argument.

Parameters
x32-bit signed argument
Returns
log2(x)
Note
This version of the overloaded function will assert that x is not negative.
unsigned int gmx::log2I ( std::int64_t  x)

Compute floor of logarithm to base 2, 64 bit signed argument.

Parameters
x64-bit signed argument
Returns
log2(x)
Note
This version of the overloaded function will assert that x is not negative.
void gmx::logHardwareDetectionWarnings ( const gmx::MDLogger mdlog,
const gmx_hw_info_t &  hardwareInformation 
)

Issue warnings to mdlog that were decided during detection.

Parameters
[in]mdlogLogger
[in]hardwareInformationThe hardwareInformation
static double gmx::logSingleAccuracy ( double  x)
inlinestatic

Double log(x), but with single accuracy. This is the natural logarithm.

Parameters
xArgument, should be >0.
Returns
The natural logarithm of x. Undefined if argument is invalid.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
ListOfLists< int > gmx::make_at2con ( int  numAtoms,
ArrayRef< const InteractionList >  ilist,
ArrayRef< const t_iparams >  iparams,
FlexibleConstraintTreatment  flexibleConstraintTreatment 
)

Returns a ListOfLists object to go from atoms to constraints.

The object will contain constraint indices with lower indices directly matching the order in F_CONSTR and higher indices matching the order in F_CONSTRNC offset by the number of constraints in F_CONSTR.

Parameters
[in]numAtomsThe number of atoms to construct the list for
[in]ilistInteraction list, size F_NRE
[in]iparamsInteraction parameters, can be null when flexibleConstraintTreatment==Include
[in]flexibleConstraintTreatmentThe flexible constraint treatment, see enum above
Returns
a ListOfLists object with all constraints for each atom
ListOfLists< int > gmx::make_at2con ( const gmx_moltype_t moltype,
gmx::ArrayRef< const t_iparams >  iparams,
FlexibleConstraintTreatment  flexibleConstraintTreatment 
)

Returns a ListOfLists object to go from atoms to constraints.

The object will contain constraint indices with lower indices directly matching the order in F_CONSTR and higher indices matching the order in F_CONSTRNC offset by the number of constraints in F_CONSTR.

Parameters
[in]moltypeThe molecule data
[in]iparamsInteraction parameters, can be null when flexibleConstraintTreatment==Include
[in]flexibleConstraintTreatmentThe flexible constraint treatment, see enum above
Returns
a ListOfLists object with all constraints for each atom
void gmx::make_local_shells ( const t_commrec *  cr,
const t_mdatoms md,
gmx_shellfc_t *  shfc 
)

Gets the local shell with domain decomposition.

Parameters
[in]crCommunication record
[in]mdThe MD atom data
[in,out]shfcThe shell/flexible-constraint data
template<typename T >
ArrayRef<std::conditional_t<std::is_const<T>::value, const typename T::value_type, typename T::value_type> > gmx::makeArrayRef ( T &  c)

Create ArrayRef from container with type deduction.

See Also
ArrayRef
Todo:
Use std::is_const_v when CUDA 11 is a requirement.
static ListOfLists<int> gmx::makeAtomsToConstraintsList ( int  numAtoms,
ArrayRef< const InteractionList >  ilists,
ArrayRef< const t_iparams >  iparams,
FlexibleConstraintTreatment  flexibleConstraintTreatment 
)
static

Returns a block struct to go from atoms to constraints.

The block struct will contain constraint indices with lower indices directly matching the order in F_CONSTR and higher indices matching the order in F_CONSTRNC offset by the number of constraints in F_CONSTR.

Parameters
[in]numAtomsThe number of atoms to construct the list for
[in]ilistsThe interaction lists, size F_NRE
[in]iparamsInteraction parameters, can be null when flexibleConstraintTreatment==Include
[in]flexibleConstraintTreatmentThe flexible constraint treatment, see enum above
Returns
a block struct with all constraints for each atom
static std::vector<ListOfLists<int> > gmx::makeAtomToConstraintMappings ( const gmx_mtop_t &  mtop,
FlexibleConstraintTreatment  flexibleConstraintTreatment 
)
static

Makes a per-moleculetype container of mappings from atom indices to constraint indices.

Note that flexible constraints are only enabled with a dynamical integrator.

static std::vector<int> gmx::makeAtomToGroupMapping ( const gmx::RangePartitioning grouping)
static

Returns the an array with group indices for each atom.

Parameters
[in]groupingThe paritioning of the atom range into atom groups
template<typename T >
ArrayRef<const typename T::value_type> gmx::makeConstArrayRef ( const T &  c)

Create ArrayRef to const T from container with type deduction.

See Also
ArrayRef
template<typename... Args>
std::unique_ptr<Constraints> gmx::makeConstraints ( const gmx_mtop_t &  mtop,
const t_inputrec &  ir,
pull_t *  pull_work,
bool  doEssentialDynamics,
Args &&...  args 
)

Factory function for Constraints.

We only want an object to manage computing constraints when the simulation requires one. Checking for whether the object was made adds overhead to simulations that use constraints, while avoiding overhead on those that do not, so is a design trade-off we might reconsider some time.

Using a private constructor and a factory function ensures that we can only make a Constraints object when the prerequisites are satisfied, ie. that something needs them and if necessary has already been initialized.

Using the parameter pack insulates the factory function from changes to the type signature of the constructor that don't affect the logic here.

std::vector< int > gmx::makeGpuIds ( ArrayRef< const int >  compatibleGpus,
size_t  numGpuTasks 
)

Make a vector containing numGpuTasks IDs of the IDs found in compatibleGpus.

Exceptions
std::bad_allocIf out of memory
Returns
A sorted vector of IDs of compatible vectors, whose length matches that of the number of GPU tasks required.
std::string gmx::makeGpuIdString ( const std::vector< int > &  gpuIds,
int  totalNumberOfTasks 
)

Convert a container of GPU deviced IDs to a string that can be used by gmx tune_pme as input to mdrun -gputasks.

Produce a valid input for mdrun -gputasks that refers to the device IDs in gpuIds but produces a mapping for totalNumberOfTasks tasks. Note that gmx tune_pme does not currently support filling mdrun -gputasks.

Parameters
[in]gpuIdsContainer of device IDs
[in]totalNumberOfTasksTotal number of tasks for the output mapping produced by the returned string.
Returns
A string that is suitable to pass to mdrun -gputasks.
Exceptions
std::bad_allocIf out of memory.
std::unique_ptr< ImdSession > gmx::makeImdSession ( const t_inputrec *  ir,
const t_commrec *  cr,
gmx_wallcycle *  wcycle,
gmx_enerdata_t enerd,
const gmx_multisim_t ms,
const gmx_mtop_t &  top_global,
const MDLogger &  mdlog,
gmx::ArrayRef< const gmx::RVec coords,
int  nfile,
const t_filenm  fnm[],
const gmx_output_env_t *  oenv,
const ImdOptions &  options,
StartingBehavior  startingBehavior 
)

Makes and returns an initialized IMD session, which may be inactive.

This function is called before the main MD loop over time steps.

Parameters
irThe inputrec structure containing the MD input parameters
crInformation structure for MPI communication.
wcycleCount wallcycles of IMD routines for diagnostic output.
enerdContains the GROMACS energies for the different interaction types.
msHandler for multi-simulations.
top_globalThe topology of the whole system.
mdlogLogger
coordsThe starting positions of the atoms.
nfileNumber of files.
fnmStruct containing file names etc.
oenvOutput options.
optionsOptions for interactive MD.
startingBehaviorDescribes whether this is a restart appending to output files
std::vector< int > gmx::makeListOfAvailableDevices ( gmx::ArrayRef< const std::unique_ptr< DeviceInformation >>  deviceInfoList,
const std::string &  devicesSelectedByUserString 
)

Implement GPU ID selection by returning the available GPU IDs on this physical node that are compatible.

If the string supplied by the user is empty, then return the IDs of all compatible GPUs on this physical node. Otherwise, check the user specified compatible GPUs and return their IDs.

Parameters
[in]deviceInfoListInformation on the GPUs on this physical node.
[in]devicesSelectedByUserStringString like "013" or "0,1,3" typically supplied by the user to mdrun -gpu_id. Must contain only unique decimal digits, or only decimal digits separated by comma delimiters. A terminal comma is accceptable (and required to specify a single ID that is larger than 9).
Returns
A vector of unique compatible GPU IDs on this physical node.
Exceptions
std::bad_allocIf out of memory. InvalidInputError If an invalid character is found (ie not a digit or ',') or if identifiers are duplicated in the specifier list. InvalidInputError If devicesSelectedByUserString specifies IDs of the devices that are not compatible.
std::unique_ptr< MDAtoms > gmx::makeMDAtoms ( FILE *  fp,
const gmx_mtop_t &  mtop,
const t_inputrec &  ir,
const bool  rankHasPmeGpuTask 
)

Builder function for MdAtomsWrapper.

Builder function.

std::string gmx::makeOpenClInternalErrorString ( const char *  message,
cl_int  status 
)
inline

Make an error string following an OpenCL API call.

It is meant to be called with status != CL_SUCCESS, but it will work correctly even if it is called with no OpenCL failure.

Todo:
Make use of this function more.
Parameters
[in]messageSupplies context, e.g. the name of the API call that returned the error.
[in]statusOpenCL API status code
Returns
A string describing the OpenCL error.
uint64_t gmx::makeRandomSeed ( )

Return 64 random bits from the random device, suitable as seed.

If the internal random device output is smaller than 64 bits, this routine will use multiple calls internally until we have 64 bits of random data.

Returns
64-bit unsigned integer with random bits.
template<typename GeneratorType >
static uint64_t gmx::makeRandomSeedInternal ( GeneratorType &  gen)
static

Get the next pure or pseudo-random number.

Returns the next random number taken from the hardware generator or from PRNG.

Parameters
[in]genPseudo-random/random numbers generator/device to use.
Returns
Random or pseudo-random number.
std::vector< RangePartitioning > gmx::makeUpdateGroupingsPerMoleculeType ( const gmx_mtop_t &  mtop)

Returns a vector with update groups for each moleculetype in mtop or an empty vector when the criteria (see below) are not satisfied.

An empty vector is returned when at least one moleculetype does not obey the restrictions of update groups, e.g. more than two constraints in a row.

Currently valid update groups are:

  • a single atom which is not a virtual site and does not have constraints;
  • or a group of atoms where all virtual sites are constructed from atoms within the group and at least one non-vsite atom is constrained to all other non-vsite atoms.

To have update groups, all virtual sites should be linear 2 or 3 atom constructions with coefficients >= 0 and sum of coefficients <= 1.

This vector is generally consumed in constructing an UpdateGroups object.

Parameters
[in]mtopThe system topology
UpdateGroups gmx::makeUpdateGroups ( const gmx::MDLogger mdlog,
std::vector< RangePartitioning > &&  updateGroupingPerMoleculeType,
real  maxUpdateGroupRadius,
bool  useDomainDecomposition,
bool  systemHasConstraintsOrVsites,
real  cutoffMargin 
)

Builder for update groups.

Checks the conditions for using update groups, and logs a message if they cannot be used, along with the reason why not.

If PP domain decomposition is not in use, there is no reason to use update groups.

All molecule types in the system topology must be conform to the requirements, such that makeUpdateGroupingsPerMoleculeType() returns a non-empty vector.

When we have constraints and/or vsites, it is beneficial to use update groups (when possible) to allow independent update of groups. But if there are no constraints or vsites, then there is no need to use update groups at all.

To use update groups, the large domain-to-domain cutoff distance should be compatible with the box size.

std::unique_ptr< VirtualSitesHandler > gmx::makeVirtualSitesHandler ( const gmx_mtop_t &  mtop,
const t_commrec *  cr,
PbcType  pbcType,
ArrayRef< const RangePartitioning >  updateGroupingPerMoleculeType 
)

Create the virtual site handler.

Parameters
[in]mtopThe global topology
[in]crThe communication record
[in]pbcTypeThe type of PBC
[in]updateGroupingPerMoleculeTypeUpdate grouping per molecule type, pass empty when not using update groups
Returns
A valid vsite handler object or nullptr when there are no virtual sites
static DevelopmentFeatureFlags gmx::manageDevelopmentFeatures ( const gmx::MDLogger mdlog,
const bool  useGpuForNonbonded,
const PmeRunMode  pmeRunMode,
const int  numRanksPerSimulation,
const int  numPmeRanksPerSimulation 
)
static

Manage any development feature flag variables encountered.

The use of dev features indicated by environment variables is logged in order to ensure that runs with such features enabled can be identified from their log and standard output. Any cross dependencies are also checked, and if unsatisfied, a fatal error issued.

Note that some development features overrides are applied already here: the GPU communication flags are set to false in non-tMPI and non-CUDA builds.

Parameters
[in]mdlogLogger object.
[in]useGpuForNonbondedTrue if the nonbonded task is offloaded in this run.
[in]pmeRunModeRun mode indicating what resource is PME execured on.
[in]numRanksPerSimulationThe number of ranks in each simulation.
[in]numPmeRanksPerSimulationThe number of PME ranks in each simulation, can be -1
Returns
The object populated with development feature flags.
void gmx::mapGridToDataGrid ( std::vector< int > *  gridpointToDatapoint,
const double *const *  data,
int  numDataPoints,
const std::string &  dataFilename,
const BiasGrid &  grid,
const std::string &  correctFormatMessage 
)

Maps each point in the grid to a point in the data grid.

This functions maps an AWH bias grid to a user provided input data grid. The value of data grid point i along dimension d is given by data[d][i]. The number of dimensions of the data should equal that of the grid. A fatal error is thrown if extracting the data fails or the data does not cover the whole grid.

Parameters
[out]gridpointToDatapointArray mapping each grid point to a data point index.
[in]data2D array in format ndim x ndatapoints with data grid point values.
[in]numDataPointsNumber of data points.
[in]dataFilenameThe data filename.
[in]gridThe grid.
[in]correctFormatMessageString to include in error message if extracting the data fails.
static float gmx::maskAdd ( float  a,
float  b,
float  m 
)
inlinestatic

Add two float variables, masked version.

Parameters
aterm1
bterm2
mmask
Returns
a+b where mask is true, a otherwise.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::maskAdd ( double  a,
double  b,
double  m 
)
inlinestatic

Add two double variables, masked version.

Parameters
aterm1
bterm2
mmask
Returns
a+b where mask is true, a otherwise.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::maskzFma ( float  a,
float  b,
float  c,
float  m 
)
inlinestatic

Float fused multiply-add, masked version.

Parameters
afactor1
bfactor2
cterm
mmask
Returns
a*b+c where mask is true, 0.0 otherwise.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::maskzFma ( double  a,
double  b,
double  c,
double  m 
)
inlinestatic

double fused multiply-add, masked version.

Parameters
afactor1
bfactor2
cterm
mmask
Returns
a*b+c where mask is true, 0.0 otherwise.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::maskzInv ( float  x,
bool  m 
)
inlinestatic

Calculate 1/x for masked entry of float.

This routine only evaluates 1/x if mask is true. Illegal values for a masked-out float will not lead to floating-point exceptions.

Parameters
xArgument that must be nonzero if masked-in.
mMask
Returns
1/x. Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::maskzInv ( double  x,
bool  m 
)
inlinestatic

Calculate 1/x for masked entry of double.

This routine only evaluates 1/x if mask is true. Illegal values for a masked-out double will not lead to floating-point exceptions.

Parameters
xArgument that must be nonzero if masked-in.
mMask
Returns
1/x. Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::maskzInvSingleAccuracy ( double  x,
bool  m 
)
inlinestatic

Calculate 1/x for masked entry of double, but with single accuracy.

This routine only evaluates 1/x if mask is true. Illegal values for a masked-out double will not lead to floating-point exceptions.

Parameters
xArgument that must be nonzero if masked-in.
mMask
Returns
1/x. Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::maskzInvsqrt ( float  x,
bool  m 
)
inlinestatic

Calculate 1/sqrt(x) for masked entry of float.

This routine only evaluates 1/sqrt(x) if mask is true. Illegal values for a masked-out float will not lead to floating-point exceptions.

Parameters
xArgument that must be >0 if masked-in.
mMask
Returns
1/sqrt(x). Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::maskzInvsqrt ( double  x,
bool  m 
)
inlinestatic

Calculate 1/sqrt(x) for masked entry of double.

This routine only evaluates 1/sqrt(x) if mask is true. Illegal values for a masked-out double will not lead to floating-point exceptions.

Parameters
xArgument that must be >0 if masked-in.
mMask
Returns
1/sqrt(x). Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::maskzInvsqrtSingleAccuracy ( double  x,
bool  m 
)
inlinestatic

Calculate 1/sqrt(x) for masked entry of double, but with single accuracy.

This routine only evaluates 1/sqrt(x) if mask is true. Illegal values for a masked-out double will not lead to floating-point exceptions.

Parameters
xArgument that must be >0 if masked-in.
mMask
Returns
1/sqrt(x). Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::maskzMul ( float  a,
float  b,
float  m 
)
inlinestatic

Multiply two float variables, masked version.

Parameters
afactor1
bfactor2
mmask
Returns
a*b where mask is true, 0.0 otherwise.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::maskzMul ( double  a,
double  b,
double  m 
)
inlinestatic

Multiply two double variables, masked version.

Parameters
afactor1
bfactor2
mmask
Returns
a*b where mask is true, 0.0 otherwise.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx_simdcall gmx::maskzRcp ( float  x,
float  m 
)
inlinestatic

Float 1.0/x, masked version.

Parameters
xArgument, x>0 for entries where mask is true.
mMask
Returns
1/x. The result for masked-out entries will be 0.0.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx_simdcall gmx::maskzRcp ( double  x,
double  m 
)
inlinestatic

Double 1.0/x, masked version.

Parameters
xArgument, x>0 for entries where mask is true.
mMask
Returns
Approximation of 1/x. The result for masked-out entries will be 0.0.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::max ( float  a,
float  b 
)
inlinestatic

Set each float element to the largest from two variables.

Parameters
aAny floating-point value
bAny floating-point value
Returns
max(a,b) for each element.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::max ( double  a,
double  b 
)
inlinestatic

Set each double element to the largest from two variables.

Parameters
aAny doubleing-point value
bAny doubleing-point value
Returns
max(a,b) for each element.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
void gmx::mdAlgorithmsSetupAtomData ( const t_commrec *  cr,
const t_inputrec &  inputrec,
const gmx_mtop_t &  top_global,
gmx_localtop_t top,
t_forcerec *  fr,
ForceBuffers *  force,
MDAtoms *  mdAtoms,
Constraints *  constr,
VirtualSitesHandler *  vsite,
gmx_shellfc_t *  shellfc 
)

Sets atom data for several MD algorithms.

Most MD algorithms require two different setup calls: one for initialization and parameter setting and one for atom data setup. This routine sets the atom data for the (locally available) atoms. This is called at the start of serial runs and during domain decomposition.

Parameters
[in]crCommunication record
[in]inputrecInput parameter record
[in]top_globalThe global topology
[in,out]topThe local topology
[in,out]frThe force calculation parameter/data record
[out]forceThe force buffer
[out]mdAtomsThe MD atom data
[in,out]constrThe constraints handler, can be NULL
[in,out]vsiteThe virtual site data, can be NULL
[in,out]shellfcThe shell/flexible-constraint data, can be NULL
static void gmx::mdrunner_start_fn ( const void *  arg)
static

The callback used for running on spawned threads.

Obtains the pointer to the master mdrunner object from the one argument permitted to the thread-launch API call, copies it to make a new runner for this thread, reinitializes necessary data, and proceeds to the simulation.

void gmx::mergeExclusions ( ListOfLists< int > *  excl,
gmx::ArrayRef< ExclusionBlock >  b2 
)

Merge the contents of b2 into excl.

Requires that b2 and excl describe the same number of particles, if b2 describes a non-zero number.

static float gmx::min ( float  a,
float  b 
)
inlinestatic

Set each float element to the smallest from two variables.

Parameters
aAny floating-point value
bAny floating-point value
Returns
min(a,b) for each element.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::min ( double  a,
double  b 
)
inlinestatic

Set each double element to the smallest from two variables.

Parameters
aAny doubleing-point value
bAny doubleing-point value
Returns
min(a,b) for each element.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
void gmx::MPI_Comm_free_wrapper ( MPI_Comm *  comm)

Wrapper function for RAII-style cleanup.

This is needed to discard the return value so it can be used as a deleter by a smart pointer.

bool gmx::mrcHeaderIsSane ( const MrcDensityMapHeader &  header)

Checks if the values in the header are sane.

Checks extents and numbers of columns, rows and sections, as well as unit cell angles for positivity and to be within bounds.

Bounds are set generously not to hamper future creative uses of mrc files.

Returns
true if all header values are within resonable albeit generous bounds
int gmx::multiDimArrayIndexToLinear ( const awh_ivec  indexMulti,
int  numDim,
const awh_ivec  numPointsDim 
)

Convert multidimensional array index to a linear one.

Parameters
[in]indexMultiMultidimensional index to convert to a linear one.
[in]numDimNumber of dimensions of the array.
[in]numPointsDimNumber of points of the array.
Returns
the linear index.
Note
This function can be used without having an initialized grid.
int gmx::multiDimGridIndexToLinear ( const BiasGrid &  grid,
const awh_ivec  indexMulti 
)

Convert a multidimensional grid point index to a linear one.

Parameters
[in]gridThe grid.
[in]indexMultiMultidimensional grid point index to convert to a linear one.
Returns
the linear index.
bool gmx::needStateGpu ( SimulationWorkload  simulationWorkload)
inline

If StatePropagatorDataGpu object is needed.

Parameters
[in]simulationWorkloadSimulation workload flags.
Returns
Whether the StatePropagatorDataGpu object is needed/was created for this run.
OptimisationResult gmx::nelderMead ( const std::function< real(ArrayRef< const real >)> &  functionToMinimize,
ArrayRef< const real initialGuess,
real  minimumRelativeSimplexLength = 1e-8,
int  maxSteps = 10'000 
)

Derivative-free downhill simplex optimisation.

Find a local minimum of an N-dimensional mapping $\mathbb{R}^N\to\mathbb{R}$ using the downhill simplex algorithm by Nelder and Mead as described in

  Saša Singer and John Nelder (2009), Scholarpedia, 4(7):2928.
  doi:10.4249/scholarpedia.2928

Stops when the oriented simplex length is less than a constant factor times the initial lengths or when a maximum step size is reached.

For best performance pre-condition problem magnitudes to 1.

The following algorithm is implemented in this function 1 Define the N+1 vertices of the initial simplex The inital simplex is constructed from the initial guess and N additional vertices by adding 0.05 to the initial guess (or 0.0025 if the initial guess is the null vector) from the initial vertex (in line with usual implementations).

1a Sort vertices according to function value with the lowest function value first in order to minimize the function.

2 Calculate the centroid of the simplex as arithmetic mean of all vertices except the worst, $ x_c = \frac1n \sum_{i=1}{N} x_i$.

3 Reflect the worst simplex vertex (the one with the highest function value) at the centroid to obtain a reflection point $ x_r = x_c + \alpha (x_c - x_{N+1}) $ which lies outside the vertex.

3a Replace worst point with reflection point if reflection point function value is better than second worst point, but not better than best and go to 1a.

4 If the reflection point is better than all other points so far, attempt an expansion by calculating the expansion point at $ x_e = x_c + \gamma (x_r - x_c) $. Swap out the worst point in the vertex with the expansion point if better than reflection point, otherwise use the reflection point and go to 1a.

5 Attempt contraction, because reflection was not successful; $ x_t = x_c + \rho (x_{N+1} - x_c) $. If the contraction point is better than the worst point, swap out worst point with contracted point and go to 1a.

6 Shrink the vertex. Replace all points except the best one with $ x_i = x_1 + \sigma (x_i - x_1) $ and go to 1a.

Parameters
[in]functionToMinimizefunction to be minimized
[in]initialGuessof coordinates
[in]minimumRelativeSimplexLengthminimal oriented simplex length with respect to initial simplex
[in]maxStepsto run algorithm for
Returns
the lowest found function value and corresponding coordinates.
void gmx::niceHeader ( TextWriter *  writer,
const char *  fn,
char  commentChar 
)

Prints creation time stamp and user information into a string as comments, and returns it.

Parameters
[out]writerWhere to print the information.
[in]fnName of the file being written; if nullptr, described as "unknown".
[in]commentCharCharacter to use as the starting delimiter for comments.
Exceptions
std::bad_allocif out of memory.
int gmx::nonbondedMtsFactor ( const t_inputrec &  ir)

Returns the interval in steps at which the non-bonded pair forces are calculated.

Note: returns 1 when multiple time-stepping is not activated.

template<typename T >
std::remove_const_t<T> gmx::norm ( T *  v)

Forward operations on C Array style vectors to C implementations.

Since vec.h and vectypes.h independently declare norm and norm2 in different namespaces, code that includes both headers but does not specify the namespace from which to use norm and norm2 cannot properly resolve overloads without the following helper templates.

Template Parameters
Tarray element type (e.g. real, int, etc.)
Parameters
vaddress of first vector element
Returns
magnitude or squared magnitude of vector
static void gmx::normalizeBlock ( AwhEnergyBlock *  block,
const Bias &  bias 
)
static

Normalizes block data for output.

Parameters
[in,out]blockThe block to normalize.
[in]biasThe AWH bias.
static void gmx::normalizeFreeEnergyAndPmfSum ( std::vector< PointState > *  pointState)
static

Normalizes the free energy and PMF sum.

Parameters
[in]pointStateThe state of the points.
size_t gmx::numberOfExpectedDataItems ( const MrcDensityMapHeader &  header)

Return the number of density data items that are expected to follow this header.

Exceptions
InternalErrorif the number of data items cannot be determined
Returns
the number of voxels
FilePtr gmx::openLibraryFile ( const std::string &  filename,
bool  bAddCWD = true,
bool  bFatal = true 
)

Opens a library file for reading in an RAII-style FILE handle.

Works as findLibraryFile(), except that it opens the file and returns a file handle.

FilePtr gmx::openLibraryFile ( const char *  filename,
bool  bAddCWD = true,
bool  bFatal = true 
)

Opens a library file for reading in an RAII-style FILE handle.

Works as findLibraryFile(), except that it opens the file and returns a file handle.

LogFilePtr gmx::openLogFile ( const char *  lognm,
bool  appendFiles 
)

Open the log file for writing/appending.

Exceptions
FileIOErrorwhen the log file cannot be opened.
static t_trxstatus* gmx::openTNG ( const std::string &  name,
const Selection &  sel,
const gmx_mtop_t *  mtop 
)
static

Method to open TNG file.

Only need extra method to open this kind of file as it may need access to a Selection sel, if it is valid. Otherwise atom indices will be taken from the topology mtop.

Parameters
[in]nameName of the output file.
[in]selReference to selection.
[in]mtopPointer to topology, tested before that it is valid.
Todo:
Those should be methods in a replacement for t_trxstatus instead.
bool gmx::operator!= ( const DensityFittingParameters &  lhs,
const DensityFittingParameters &  rhs 
)

Check if two structs holding density fitting parameters are not equal.

Parameters
[in]lhsleft hand side to be compared
[in]rhsright hand side to be compared
Returns
true if lhs is not equal rhs
template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>
constexpr bool gmx::operator!= ( const extents< LHS...> &  lhs,
const extents< RHS...> &  rhs 
)
noexcept

Check for non-equality.

Returns
true if extents are unequal
bool gmx::operator== ( const DensityFittingParameters &  lhs,
const DensityFittingParameters &  rhs 
)

Check if two structs holding density fitting parameters are equal.

Parameters
[in]lhsleft hand side to be compared
[in]rhsright hand side to be compared
Returns
true if all elements in DensityFittingParameters are equal, else false
template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>
constexpr bool gmx::operator== ( const extents< LHS...> &  lhs,
const extents< RHS...> &  rhs 
)
noexcept

Comparison operator.

Returns
true if extents are equal
template<class T1 , class T2 >
bool gmx::operator== ( const Allocator< T1, HostAllocationPolicy > &  a,
const Allocator< T2, HostAllocationPolicy > &  b 
)

Return true if two allocators are identical.

True if pinning policy is the same.

std::size_t gmx::pageSize ( )

Return the memory page size on this system.

Implements the "construct on first use" idiom to avoid the static initialization order fiasco where a possible static page-aligned container would be initialized before the alignment variable was.

Note that thread-safety is guaranteed by the C++11 language standard.

template<typename ValueType , int NumExpectedValues>
static std::optional<std::array<ValueType, NumExpectedValues> > gmx::parsedArrayFromInputString ( const std::string &  str)
inlinestatic

Convert a string into an array of values.

Template Parameters
ValueTypearray element type to convert into
NumExpectedValuesnumber of values of the array
Returns
an array containing the converted string, optionally null if the white-space stripped string is empty
Exceptions
InvalidInputErrorif splitting the string at whitespaces does not result in NumExpectedValues or zero substrings
InvalidInputErrorif conversion of any of the NumExpectedValues substrings of the splitted input string fails

Converts a string into an array of type ValueType with exactly NumExpectedValues.

No result is returned if the string is empty or contains only whitespace .

static std::vector<int> gmx::parseGpuDeviceIdentifierList ( const std::string &  gpuIdString)
static

Parse a GPU ID specifier string into a container.

Parameters
[in]gpuIdStringString like "013" or "0,1,3" typically supplied by the user. Must contain only unique decimal digits, or only decimal digits separated by comma delimiters. A terminal comma is accceptable (and required to specify a single ID that is larger than 9).
Returns
A vector of numeric IDs extracted from gpuIdString.
Exceptions
std::bad_allocIf out of memory. InvalidInputError If an invalid character is found (ie not a digit or ',').
std::vector< int > gmx::parseUserGpuIdString ( const std::string &  gpuIdString)

Parse a GPU ID specifier string into a container describing device IDs exposed to the run.

Parameters
[in]gpuIdStringString like "013" or "0,1,3" typically supplied by the user to mdrun -gpu_id. Must contain only unique decimal digits, or only decimal digits separated by comma delimiters. A terminal comma is accceptable (and required to specify a single ID that is larger than 9).
Returns
A vector of unique GPU IDs.
Exceptions
std::bad_allocIf out of memory. InvalidInputError If an invalid character is found (ie not a digit or ',') or if identifiers are duplicated in the specifier list.
std::vector< int > gmx::parseUserTaskAssignmentString ( const std::string &  gpuIdString)

Parse a GPU ID specifier string into a container describing device ID to task mapping.

Parameters
[in]gpuIdStringString like "0011" or "0,0,1,1" typically supplied by the user to mdrun -gputasks. Must contain only decimal digits, or only decimal digits separated by comma delimiters. A terminal comma is accceptable (and required to specify a single ID that is larger than 9).
Returns
A vector of GPU IDs.
Exceptions
std::bad_allocIf out of memory. InvalidInputError If an invalid character is found (ie not a digit or ',').
void gmx::pinBuffer ( void *  pointer,
std::size_t  numBytes 
)
noexcept

Pin the allocation to physical memory.

Requires that pointer is not nullptr.

Does not throw.

void gmx::placeCoordinatesWithCOMInBox ( const PbcType pbcType,
UnitCellType  unitCellType,
CenteringType  centerType,
const matrix  box,
ArrayRef< RVec >  x,
const gmx_mtop_t &  mtop,
COMShiftType  comShiftType 
)

Moves collection of atoms along the center of mass into a box.

This ensures that the centre of mass (COM) of a molecule is placed within a predefined coordinate space (usually a simulation box).

Parameters
[in]pbcTypeWhat kind of PBC are we handling today.
[in]unitCellTypeKind of unitcell used for the box.
[in]centerTypeHow atoms should be centered.
[in]boxThe currently available box to place things into.
[in,out]xView in coordinates to shift.
[in]mtopTopology with residue and molecule information.
[in]comShiftTypeWhether residues or molecules are shifted.
static float gmx::pmeForceCorrection ( float  z2)
inlinestatic

Calculate the force correction due to PME analytically in float.

See the SIMD version of this function for details.

Parameters
z2input parameter
Returns
Correction to use on force
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::pmeForceCorrection ( double  z2)
inlinestatic

Calculate the force correction due to PME analytically in double.

See the SIMD version of this function for details.

Parameters
z2input parameter
Returns
Correction to use on force
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::pmeForceCorrectionSingleAccuracy ( double  z2)
inlinestatic

Force correction due to PME in double, but with single accuracy.

See the SIMD version of this function for details.

Parameters
z2input parameter
Returns
Correction to use on force
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::pmePotentialCorrection ( float  z2)
inlinestatic

Calculate the potential correction due to PME analytically in float.

See the SIMD version of this function for details.

Parameters
z2input parameter
Returns
Correction to use on potential.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::pmePotentialCorrection ( double  z2)
inlinestatic

Calculate the potential correction due to PME analytically in double.

See the SIMD version of this function for details.

Parameters
z2input parameter
Returns
Correction to use on potential.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::pmePotentialCorrectionSingleAccuracy ( double  z2)
inlinestatic

Potential correction due to PME in double, but with single accuracy.

See the SIMD version of this function for details.

Parameters
z2input parameter
Returns
Correction to use on potential.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static int gmx::pointDistanceAlongAxis ( const GridAxis &  axis,
double  x,
double  x0 
)
static

Returns the point distance between from value x to value x0 along the given axis.

Note that the returned distance may be negative or larger than the number of points in the axis. For a periodic axis, the distance is chosen to be in [0, period), i.e. always positive but not the shortest one.

Parameters
[in]axisBiasGrid axis.
[in]xFrom value.
[in]x0To value.
Returns
(x - x0) in number of points.
bool gmx::pointsAlongLambdaAxis ( const BiasGrid &  grid,
int  pointIndex1,
int  pointIndex2 
)

Checks whether two points are along a free energy lambda state axis.

Parameters
[in]gridThe grid.
[in]pointIndex1Grid point index of the first point.
[in]pointIndex2Grid point index of the second point.
Returns
true if the two points are along a free energy lambda state axis.
bool gmx::pointsHaveDifferentLambda ( const BiasGrid &  grid,
int  pointIndex1,
int  pointIndex2 
)

Checks whether two points are different in the free energy lambda state dimension (if any).

Parameters
[in]gridThe grid.
[in]pointIndex1Grid point index of the first point.
[in]pointIndex2Grid point index of the second point.
Returns
true if the two points have different lambda values.
template<typename T >
T gmx::power12 ( x)

calculate x^12

Template Parameters
TType of argument and return value
Parameters
xargument
Returns
x^12
template<typename T >
T gmx::power3 ( x)

calculate x^3

Template Parameters
TType of argument and return value
Parameters
xargument
Returns
x^3
template<typename T >
T gmx::power4 ( x)

calculate x^4

Template Parameters
TType of argument and return value
Parameters
xargument
Returns
x^4
template<typename T >
T gmx::power5 ( x)

calculate x^5

Template Parameters
TType of argument and return value
Parameters
xargument
Returns
x^5
template<typename T >
T gmx::power6 ( x)

calculate x^6

Template Parameters
TType of argument and return value
Parameters
xargument
Returns
x^6
std::unique_ptr< Awh > gmx::prepareAwhModule ( FILE *  fplog,
const t_inputrec &  inputRecord,
t_state stateGlobal,
const t_commrec *  commRecord,
const gmx_multisim_t multiSimRecord,
bool  startingFromCheckpoint,
bool  usingShellParticles,
const std::string &  biasInitFilename,
pull_t *  pull_work 
)

Makes an Awh and prepares to use it if the user input requests that.

Restores state from history in checkpoint if needed.

Parameters
[in,out]fplogGeneral output file, normally md.log, can be nullptr.
[in]inputRecordGeneral input parameters (as set up by grompp).
[in]stateGlobalA pointer to the global state structure.
[in]commRecordStruct for communication, can be nullptr.
[in]multiSimRecordMulti-sim handler
[in]startingFromCheckpointWhether the simulation is starting from a checkpoint
[in]usingShellParticlesWhether the user requested shell particles (which is unsupported)
[in]biasInitFilenameName of file to read PMF and target from.
[in,out]pull_workPointer to a pull struct which AWH will couple to, has to be initialized, is assumed not to change during the lifetime of the Awh object.
Returns
An initialized Awh module, or nullptr if none was requested.
Exceptions
InvalidInputErrorIf another active module is not supported.
std::unique_ptr< BoxDeformation > gmx::prepareBoxDeformation ( const matrix &  initialBox,
DDRole  ddRole,
NumRanks  numRanks,
MPI_Comm  communicator,
const t_inputrec &  inputrec 
)

Factory function for box deformation module.

If the inputrec specifies the use of box deformation during the update phase, communicates the initialBox from SIMMASTER to other ranks, and constructs and returns an object to manage that update.

Exceptions
NotImplementedErrorif the inputrec specifies an unsupported combination.
void gmx::prepareLogAppending ( FILE *  fplog)

Prepare to use the open log file when appending.

Does not throw.

void gmx::printBinaryInformation ( FILE *  fp,
const IProgramContext &  programContext 
)

Print basic information about the executable.

Parameters
fpWhere to print the information to.
[in]programContextProgram information object to use.
void gmx::printBinaryInformation ( FILE *  fp,
const IProgramContext &  programContext,
const BinaryInformationSettings &  settings 
)

Print basic information about the executable with custom settings.

Parameters
fpWhere to print the information to.
[in]programContextProgram information object to use.
[in]settingsSpecifies what to print.
See Also
BinaryInformationSettings
void gmx::printBinaryInformation ( TextWriter *  writer,
const IProgramContext &  programContext,
const BinaryInformationSettings &  settings 
)

Print basic information about the executable with custom settings.

Needed to read the members without otherwise unnecessary accessors.

Parameters
[out]writerWhere to print the information.
[in]programContextProgram information object to use.
[in]settingsSpecifies what to print.
Exceptions
std::bad_allocif out of memory.
See Also
BinaryInformationSettings
static std::string gmx::printMissingInteractionsMolblock ( const t_commrec *  cr,
const gmx_reverse_top_t &  rt,
const char *  moltypename,
const reverse_ilist_t &  ril,
const Range< int > &  atomRange,
const int  numAtomsPerMolecule,
const int  numMolecules,
const InteractionDefinitions &  idef 
)
static

Help print error output when interactions are missing in a molblock.

Note
This function needs to be called on all ranks (contains a global summation)
int gmx::processExceptionAtExitForCommandLine ( const std::exception &  ex)

Handles an exception and deinitializes after initForCommandLine.

Parameters
[in]exException that is the cause for terminating the program.
Returns
Return code to return from main().

This method should be called as the last thing before terminating the program because of an exception. See processExceptionAtExit() for details. Additionally this method undoes the work done by initForCommandLine.

Does not throw.

template<typename ValueType >
void gmx::readKvtCheckpointValue ( compat::not_null< ValueType * >  value,
const std::string &  name,
const std::string &  identifier,
const KeyValueTreeObject &  kvt 
)

Read to a key-value-tree value used for checkpointing.

Template Parameters
ValueType
Parameters
[in]valuethe value to be checkpointed
[in]namename of the value to be checkpointed
[in]identifieruniquely identifies the module that is checkpointing typically the module name
[in]kvtthe key value tree to read from
Exceptions
InternalErrorif kvt does not contain requested value.
Note
Triggers assertion if value type is not correct.
template void gmx::readKvtCheckpointValue ( compat::not_null< std::int64_t * >  value,
const std::string &  name,
const std::string &  identifier,
const KeyValueTreeObject &  kvt 
)

Read to a key-value-tree value used for checkpointing.

Template Parameters
ValueType
Parameters
[in]valuethe value to be checkpointed
[in]namename of the value to be checkpointed
[in]identifieruniquely identifies the module that is checkpointing typically the module name
[in]kvtthe key value tree to read from
Exceptions
InternalErrorif kvt does not contain requested value.
Note
Triggers assertion if value type is not correct.
template void gmx::readKvtCheckpointValue ( compat::not_null< real * >  value,
const std::string &  name,
const std::string &  identifier,
const KeyValueTreeObject &  kvt 
)

Read to a key-value-tree value used for checkpointing.

Template Parameters
ValueType
Parameters
[in]valuethe value to be checkpointed
[in]namename of the value to be checkpointed
[in]identifieruniquely identifies the module that is checkpointing typically the module name
[in]kvtthe key value tree to read from
Exceptions
InternalErrorif kvt does not contain requested value.
Note
Triggers assertion if value type is not correct.
static void gmx::readUserPmfAndTargetDistribution ( ArrayRef< const DimParams >  dimParams,
const BiasGrid &  grid,
const std::string &  filename,
int  numBias,
int  biasIndex,
std::vector< PointState > *  pointState 
)
static

Initializes the PMF and target with data read from an input table.

Parameters
[in]dimParamsThe dimension parameters.
[in]gridThe grid.
[in]filenameThe filename to read PMF and target from.
[in]numBiasNumber of biases.
[in]biasIndexThe index of the bias.
[in,out]pointStateThe state of the points in this bias.
static float gmx::reduce ( float  a)
inlinestatic

Return sum of all elements in float variable (i.e., the variable itself).

Parameters
avariable to reduce/sum.
Returns
The argument variable itself.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::reduce ( double  a)
inlinestatic

Return sum of all elements in double variable (i.e., the variable itself).

Parameters
avariable to reduce/sum.
Returns
The argument variable itself.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::reduceIncr4ReturnSum ( float *  m,
float  v0,
float  v1,
float  v2,
float  v3 
)
inlinestatic

Add each float to four consecutive memory locations, return sum.

Parameters
mPointer to memory where four floats should be incremented
v0float to be added to m[0]
v1float to be added to m[1]
v2float to be added to m[2]
v3float to be added to m[3]
Returns
v0+v1+v2+v3.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::reduceIncr4ReturnSum ( double *  m,
double  v0,
double  v1,
double  v2,
double  v3 
)
inlinestatic

Add each double to four consecutive memory locations, return sum.

Parameters
mPointer to memory where four floats should be incremented
v0double to be added to m[0]
v1double to be added to m[1]
v2double to be added to m[2]
v3double to be added to m[3]
Returns
v0+v1+v2+v3.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
void gmx::reportGpuUsage ( const MDLogger &  mdlog,
ArrayRef< const GpuTaskAssignment >  gpuTaskAssignmentOnRanksOfThisNode,
size_t  numGpuTasksOnThisNode,
size_t  numPpRanks,
bool  printHostName,
PmeRunMode  pmeRunMode,
const SimulationWorkload &  simulationWork 
)

Log a report on how GPUs are being used on the ranks of the physical node of rank 0 of the simulation.

Todo:
It could be useful to report also whether any nodes differed, and in what way.
Parameters
[in]mdlogLogging object.
[in]gpuTaskAssignmentOnRanksOfThisNodeThe selected GPU IDs.
[in]numGpuTasksOnThisNodeThe number of GPU tasks on this node.
[in]numPpRanksNumber of PP ranks on this node
[in]printHostNamePrint the hostname in the usage information
[in]pmeRunModeDescribes the execution of PME tasks
[in]simulationWorkSimulation workload descriptor
Exceptions
std::bad_allocif out of memory
void gmx::restoreCorrelationGridStateFromHistory ( const CorrelationGridHistory &  corrGridHist,
CorrelationGrid *  corrGrid 
)

Restores the correlation grid state from the correlation grid history.

Parameters
[in]corrGridHistCorrelation grid history to read.
[in,out]corrGridCorrelation grid state to set.
static float gmx::round ( float  a)
inlinestatic

Float round to nearest integer value (in floating-point format).

Parameters
aAny floating-point value
Returns
The nearest integer, represented in floating-point format.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::round ( double  a)
inlinestatic

double round to nearest integer value (in doubleing-point format).

Parameters
aAny doubleing-point value
Returns
The nearest integer, represented in doubleing-point format.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static int gmx::roundToInt ( float  x)
inlinestatic

Round float to int.

Rounding behavior is round to nearest. Rounding of halfway cases is implementation defined (either halfway to even or halfway away from zero).

int gmx::runCommandLineModule ( int  argc,
char *  argv[],
ICommandLineModule *  module 
)

Implements a main() method that runs a single module.

Parameters
argcargc passed to main().
argvargv passed to main().
moduleModule to run.

This method allows for uniform behavior for binaries that only contain a single module without duplicating any of the implementation from CommandLineModuleManager (startup headers, common options etc.).

The signature assumes that module construction does not throw (because otherwise the caller would need to duplicate all the exception handling code). It is possible to move the construction inside the try/catch in this method using an indirection similar to TrajectoryAnalysisCommandLineRunner::runAsMain(), but until that is necessary, the current approach leads to simpler code.

Usage:

int main(int argc, char *argv[])
{
CustomCommandLineModule module;
return gmx::runCommandLineModule(argc, argv, &module);
}

Does not throw. All exceptions are caught and handled internally.

int gmx::runCommandLineModule ( int  argc,
char *  argv[],
const char *  name,
const char *  description,
std::function< std::unique_ptr< ICommandLineOptionsModule >()>  factory 
)

Implements a main() method that runs a single module.

Parameters
argcargc passed to main().
argvargv passed to main().
[in]nameName for the module.
[in]descriptionShort description for the module.
factoryFactory method that creates the module to run.

This method allows for uniform behavior for binaries that only contain a single module without duplicating any of the implementation from CommandLineModuleManager (startup headers, common options etc.).

Usage:

class CustomCommandLineOptionsModule : public ICommandLineOptionsModule
{
// <...>
};
static ICommandLineOptionsModule *create()
{
return new CustomCommandLineOptionsModule();
}
int main(int argc, char *argv[])
{
argc, argv, "mymodule", "short description", &create);
}

Does not throw. All exceptions are caught and handled internally.

static bool gmx::runningOnCompatibleHWForNvidia ( const DeviceInformation deviceInfo)
static

Return true if executing on compatible GPU for NVIDIA OpenCL.

There are known issues with OpenCL when running on NVIDIA Volta or newer (CC 7+). As a workaround, we recommend using CUDA on such hardware.

This function relies on cl_nv_device_attribute_query. In case it's not functioning properly, we trust the user and mark the device as compatible.

Returns
true if running on Pascal (CC 6.x) or older, or if we can not determine device generation.
static bool gmx::runningOnCompatibleOSForAmd ( )
static

Return true if executing on compatible OS for AMD OpenCL.

This is assumed to be true for OS X version of at least 10.10.4 and all other OS flavors.

Uses the BSD sysctl() interfaces to extract the kernel version.

Returns
true if version is 14.4 or later (= OS X version 10.10.4), or OS is not Darwin.
static float gmx::selectByMask ( float  a,
bool  mask 
)
inlinestatic

Select from single precision variable where boolean is true.

Parameters
aFloating-point variable to select from
maskBoolean selector
Returns
a is selected for true, 0 for false.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::selectByMask ( double  a,
bool  mask 
)
inlinestatic

Select from double precision variable where boolean is true.

Parameters
adouble variable to select from
maskBoolean selector
Returns
a is selected for true, 0 for false.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static std::int32_t gmx::selectByMask ( std::int32_t  a,
bool  mask 
)
inlinestatic

Select from integer variable where boolean is true.

Parameters
aInteger variable to select from
maskBoolean selector
Returns
a is selected for true, 0 for false.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::selectByNotMask ( float  a,
bool  mask 
)
inlinestatic

Select from single precision variable where boolean is false.

Parameters
aFloating-point variable to select from
maskBoolean selector
Returns
a is selected for false, 0 for true.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::selectByNotMask ( double  a,
bool  mask 
)
inlinestatic

Select from double precision variable where boolean is false.

Parameters
adouble variable to select from
maskBoolean selector
Returns
a is selected for false, 0 for true.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static std::int32_t gmx::selectByNotMask ( std::int32_t  a,
bool  mask 
)
inlinestatic

Select from integer variable where boolean is false.

Parameters
aInteger variable to select from
maskBoolean selector
Returns
a is selected for false, 0 for true.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
void gmx::serializeMrcDensityMapHeader ( ISerializer *  serializer,
const MrcDensityMapHeader &  mrcHeader 
)

Serializes an MrcDensityMapHeader from a given serializer.

Parameters
[in]serializerthe serializer
[in]mrcHeaderfile header to be serialized
static real gmx::series_sinhx ( real  x)
inlinestatic

Maclaurin series for sinh(x)/x.

Used for NH chains and MTTK pressure control. Here, we compute it to 10th order, which might be an overkill. 8th is probably enough, but it's not very much more expensive.

void gmx::setLibraryFileFinder ( const DataFileFinder *  finder)

Sets a finder for location data files from share/top/.

Parameters
[in]finderfinder to set (can be NULL to restore the default finder).

The library does not take ownership of finder. The provided object must remain valid until the global instance is changed by another call to setLibraryFileFinder().

The global instance is used by findLibraryFile() and openLibraryFile().

This method is not thread-safe. See setProgramContext(); the same constraints apply here as well.

Does not throw.

void gmx::setStateDependentAwhParams ( AwhParams *  awhParams,
const pull_params_t &  pull_params,
pull_t *  pull_work,
const matrix  box,
PbcType  pbcType,
const tensor &  compressibility,
const t_grpopts *  inputrecGroupOptions,
real  initLambda,
const gmx_mtop_t &  mtop,
warninp_t  wi 
)

Sets AWH parameters that need state parameters such as the box vectors.

Parameters
[in,out]awhParamsAWH parameters.
[in]pull_paramsPull parameters.
[in,out]pull_workPull working struct to register AWH bias in.
[in]boxBox vectors.
[in]pbcTypePeriodic boundary conditions enum.
[in]compressibilityCompressibility matrix for pressure coupling, pass all 0 without pressure coupling
[in]inputrecGroupOptionsParameters for atom groups.
[in]initLambdaThe starting lambda, to allow using free energy lambda as reaction coordinate provider in any dimension.
[in]mtopThe system topology.
[in,out]wiStruct for bookeeping warnings.
Note
This function currently relies on the function set_pull_init to have been called.
static void gmx::setStateDependentAwhPullDimParams ( AwhDimParams *  dimParams,
const int  biasIndex,
const int  dimIndex,
const pull_params_t &  pull_params,
pull_t *  pull_work,
const t_pbc pbc,
const tensor &  compressibility,
warninp_t  wi 
)
static

Sets AWH parameters, for one AWH pull dimension.

Parameters
[in,out]dimParamsAWH dimension parameters.
[in]biasIndexThe index of the bias containing this AWH pull dimension.
[in]dimIndexThe index of this AWH pull dimension.
[in]pull_paramsPull parameters.
[in,out]pull_workPull working struct to register AWH bias in.
[in]pbcA pbc information structure.
[in]compressibilityCompressibility matrix for pressure coupling, pass all 0 without pressure coupling.
[in,out]wiStruct for bookeeping warnings.
SettleParameters gmx::settleParameters ( real  mO,
real  mH,
real  dOH,
real  invmO,
real  invmH,
real  dHH 
)

Computes and returns settle parameters.

Parameters
[in]mOMass of oxygen atom
[in]mHMass of hydrogen atom
[in]invmOReciprocal mass of oxygen atom
[in]invmHReciprocal mass of hydrogen atom
[in]dOHTarget O-H bond length
[in]dHHTarget H-H bond length
std::vector< MtsLevel > gmx::setupMtsLevels ( const GromppMtsOpts &  mtsOpts,
std::vector< std::string > *  errorMessages 
)

Sets up and returns the MTS levels and checks requirements of MTS.

Appends errors about allowed input values ir to errorMessages, when not nullptr.

Parameters
[in]mtsOptsOptions for setting the MTS levels
[in,out]errorMessagesList of error messages, can be nullptr
static SimdSetZeroProxy gmx_simdcall gmx::setZero ( )
inlinestatic

Helper function to set any SIMD or scalar variable to zero.

Returns
Proxy object that will call the actual function to set a SIMD/scalar variable to zero based on the conversion function called when you assign the result.
void gmx::shiftAtoms ( const RVec &  shift,
ArrayRef< RVec >  x 
)

Shift all coordinates.

Shift coordinates by a previously calculated value.

Can be used to e.g. place particles in a box.

Parameters
[in]shiftTranslation that should be applied.
[in]xCoordinates to translate.
bool gmx::simdCheck ( SimdType  s,
FILE *  log,
bool  warnToStdErr 
)

Check if binary was compiled with the provided SIMD type.

Parameters
sSIMD type to query. If this matches the suggested type for this cpu, the routine returns quietly.
logIf not nullptr, statistics will be printed to the file. If we do not have a match there will also be a warning.
warnToStdErrIf true, warnings will also be printed to stderr.
static void gmx_unused gmx::simdPrefetch ( void gmx_unused m)
inlinestatic

Prefetch memory at address m.

This typically prefetches one cache line of memory from address m, usually 64bytes or more, but the exact amount will depend on the implementation. On many platforms this is simply a no-op. Technically it might not be part of the SIMD instruction set, but since it is a hardware-specific function that is normally only used in tight loops where we also apply SIMD, it fits well here.

There are no guarantees about the level of cache or temporality, but usually we expect stuff to end up in level 2, and be used in a few hundred clock cycles, after which it stays in cache until evicted (normal caching).

Parameters
mPointer to location prefetch. There are no alignment requirements, but if the pointer is not aligned the prefetch might start at the lower cache line boundary (meaning fewer bytes are prefetched).
const std::string & gmx::simdString ( SimdType  s)

Return a string with the name of a SIMD type.

Parameters
sSIMD type to turn into string
static float gmx::sin ( float  x)
inlinestatic

Float sin.

Parameters
xThe argument to evaluate sin for
Returns
Sin(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::sin ( double  x)
inlinestatic

Double sin.

Parameters
xThe argument to evaluate sin for
Returns
Sin(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::sincos ( float  x,
float *  sinval,
float *  cosval 
)
inlinestatic

Float sin & cos.

Parameters
xThe argument to evaluate sin/cos for
[out]sinvalSin(x)
[out]cosvalCos(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::sincos ( double  x,
double *  sinval,
double *  cosval 
)
inlinestatic

Double sin & cos.

Parameters
xThe argument to evaluate sin/cos for
[out]sinvalSin(x)
[out]cosvalCos(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::sincosSingleAccuracy ( double  x,
double *  sinval,
double *  cosval 
)
inlinestatic

Double sin & cos, but with single accuracy.

Parameters
xThe argument to evaluate sin/cos for
[out]sinvalSin(x)
[out]cosvalCos(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::sinSingleAccuracy ( double  x)
inlinestatic

Double sin, but with single accuracy.

Parameters
xThe argument to evaluate sin for
Returns
Sin(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::sixthroot ( float  x)
inlinestatic

Calculate sixth root of x in single precision.

Parameters
xArgument, must be greater than or equal to zero.
Returns
x^(1/6)

This routine is typically faster than using std::pow().

static double gmx::sixthroot ( double  x)
inlinestatic

Calculate sixth root of x in double precision.

Parameters
xArgument, must be greater than or equal to zero.
Returns
x^(1/6)

This routine is typically faster than using std::pow().

static double gmx::sixthroot ( int  x)
inlinestatic

Calculate sixth root of integer x, return double.

Parameters
xArgument, must be greater than or equal to zero.
Returns
x^(1/6)

This routine is typically faster than using std::pow().

IntegerBox gmx::spreadRangeWithinLattice ( const IVec &  center,
dynamicExtents3D  extent,
IVec  range 
)

Construct a box that holds all indices that are not more than a given range remote from center coordinates and still within a given lattice extent.

Parameters
[in]centerthe coordinates of the center of the spread range
[in]extentthe end of the lattice, number of lattice points in each dimension
[in]rangethe distance from the center
Returns
box describing the range of indices
template<MathOptimization opt = MathOptimization::Safe>
static float gmx::sqrt ( float  x)
inlinestatic

Float sqrt(x). This is the square root.

Parameters
xArgument, should be >= 0.
Returns
The square root of x. Undefined if argument is invalid.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<MathOptimization opt = MathOptimization::Safe>
static double gmx::sqrt ( double  x)
inlinestatic

Double sqrt(x). This is the square root.

Parameters
xArgument, should be >= 0.
Returns
The square root of x. Undefined if argument is invalid.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::sqrtSingleAccuracy ( double  x)
inlinestatic

Calculate sqrt(x) for double, but with single accuracy.

Parameters
xArgument that must be >=0.
Returns
sqrt(x).
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<typename T >
T gmx::square ( x)

calculate x^2

Template Parameters
TType of argument and return value
Parameters
xargument
Returns
x^2
static void gmx::store ( float *  m,
float  a 
)
inlinestatic

Store contents of float variable to aligned memory m.

Parameters
[out]mPointer to memory.
afloat variable to store
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::store ( double *  m,
double  a 
)
inlinestatic

Store contents of double variable to aligned memory m.

Parameters
[out]mPointer to memory.
adouble variable to store
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::store ( std::int32_t *  m,
std::int32_t  a 
)
inlinestatic

Store contents of integer variable to aligned memory m.

Parameters
[out]mPointer to memory.
ainteger variable to store
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::storeU ( float *  m,
float  a 
)
inlinestatic

Store contents of float variable to unaligned memory m.

Parameters
[out]mPointer to memory, no alignment requirement.
afloat variable to store.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::storeU ( double *  m,
double  a 
)
inlinestatic

Store contents of double variable to unaligned memory m.

Parameters
[out]mPointer to memory, no alignment requirement.
adouble variable to store.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::storeU ( std::int32_t *  m,
std::int32_t  a 
)
inlinestatic

Store contents of integer variable to unaligned memory m.

Parameters
[out]mPointer to memory, no alignment requirement.
ainteger variable to store.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<typename ValueType , int NumExpectedValues>
static std::string gmx::stringIdentityTransformWithArrayCheck ( const std::string &  toConvert,
const std::string &  errorContextMessage 
)
inlinestatic

Returns the input string, throwing an excpetion if the demanded conversion to an array will not succeed.

Template Parameters
ValueTypearray element type to convert into
NumExpectedValuesnumber of values of the array
Parameters
[in]toConvertthe string to convert
[in]errorContextMessagethe message to add to the thrown exceptions if conversion of the string is bound to fail at some point
Returns
the input string
Exceptions
InvalidInputErrorif splitting the string at whitespaces does not result in NumExpectedValues or zero substrings
InvalidInputErrorif conversion of any of the NumExpectedValues substrings of the splitted input string fails

A typical use of this function would be in .mdp string option parsing where information in the .mdp file is transformed into the data that is stored in the .tpr file.

template<typename T >
void gmx::sumOverSimulations ( ArrayRef< T >  data,
MPI_Comm  multiSimComm,
const bool  broadcastWithinSimulation,
const t_commrec &  commRecord 
)

Sum an array over all simulations on master ranks or all ranks of each simulation.

This assumes the data is identical on all ranks within each simulation.

Parameters
[in,out]dataThe data to sum.
[in]multiSimCommCommunicator for the master ranks of sharing simulations.
[in]broadcastWithinSimulationBroadcast the result to all ranks within the simulation
[in]commRecordStruct for intra-simulation communication.
bool gmx::systemHasConstraintsOrVsites ( const gmx_mtop_t &  mtop)

Returns whether mtop contains any constraints and/or vsites.

When we have constraints and/or vsites, it is beneficial to use update groups (when possible) to allow independent update of groups.

static float gmx::tan ( float  x)
inlinestatic

Float tan.

Parameters
xThe argument to evaluate tan for
Returns
Tan(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::tan ( double  x)
inlinestatic

Double tan.

Parameters
xThe argument to evaluate tan for
Returns
Tan(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::tanSingleAccuracy ( double  x)
inlinestatic

Double tan, but with single accuracy.

Parameters
xThe argument to evaluate tan for
Returns
Tan(x)
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static bool gmx::testBits ( float  a)
inlinestatic

Return true if any bits are set in the float variable.

This function is used to handle bitmasks, mainly for exclusions in the inner kernels. Note that it will return true even for -0.0f (sign bit set), so it is not identical to not-equal.

Parameters
avalue
Returns
True if any bit in a is nonzero.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static bool gmx::testBits ( double  a)
inlinestatic

Return true if any bits are set in the double variable.

This function is used to handle bitmasks, mainly for exclusions in the inner kernels. Note that it will return true even for -0.0 (sign bit set), so it is not identical to not-equal.

Parameters
avalue
Returns
True if any bit in a is nonzero.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static bool gmx::testBits ( std::int32_t  a)
inlinestatic

Return true if any bits are set in the integer variable.

This function is used to handle bitmasks, mainly for exclusions in the inner kernels.

Parameters
avalue
Returns
True if any bit in a is nonzero.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static void gmx::threadMpiMdrunnerAccessBarrier ( )
static

Barrier for safe simultaneous thread access to mdrunner data.

Used to ensure that the master thread does not modify mdrunner during copy on the spawned threads.

bool gmx::timesClose ( Time  time,
Time  referenceTime 
)
inline

Check whether two times are nearly equal.

Times are considered close if their absolute difference is smaller than c_timePrecision.

Parameters
timeThe test time
referenceTimeThe reference time
Returns
bool Whether the absolute difference is < c_timePrecision
template<int align>
static void gmx::transposeScatterDecrU ( float *  base,
const std::int32_t  offset[],
float  v0,
float  v1,
float  v2 
)
inlinestatic

Subtract 3 floats from base/offset.

Template Parameters
alignAlignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points.
Parameters
[out]basePointer to the start of the memory area
offsetOffset to the start of triplet.
v01st value, subtracted from base[align*offset[0]].
v12nd value, subtracted from base[align*offset[0] + 1].
v23rd value, subtracted from base[align*offset[0] + 2].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::transposeScatterDecrU ( double *  base,
const std::int32_t  offset[],
double  v0,
double  v1,
double  v2 
)
inlinestatic

Subtract 3 doubles from base/offset.

Template Parameters
alignAlignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points.
Parameters
[out]basePointer to the start of the memory area
offsetOffset to the start of triplet.
v01st value, subtracted from base[align*offset[0]].
v12nd value, subtracted from base[align*offset[0] + 1].
v23rd value, subtracted from base[align*offset[0] + 2].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::transposeScatterIncrU ( float *  base,
const std::int32_t  offset[],
float  v0,
float  v1,
float  v2 
)
inlinestatic

Add 3 floats to base/offset.

Template Parameters
alignAlignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points.
Parameters
[out]basePointer to the start of the memory area
offsetOffset to the start of triplet.
v01st value, added to base[align*offset[0]].
v12nd value, added to base[align*offset[0] + 1].
v23rd value, added to base[align*offset[0] + 2].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::transposeScatterIncrU ( double *  base,
const std::int32_t  offset[],
double  v0,
double  v1,
double  v2 
)
inlinestatic

Add 3 doubles to base/offset.

Template Parameters
alignAlignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points.
Parameters
[out]basePointer to the start of the memory area
offsetOffset to the start of triplet.
v01st value, added to base[align*offset[0]].
v12nd value, added to base[align*offset[0] + 1].
v23rd value, added to base[align*offset[0] + 2].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::transposeScatterStoreU ( float *  base,
const std::int32_t  offset[],
float  v0,
float  v1,
float  v2 
)
inlinestatic

Store 3 floats to 3 to base/offset.

Template Parameters
alignAlignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points.
Parameters
[out]basePointer to the start of the memory area
offsetOffset to the start of triplet.
v01st value, written to base[align*offset[0]].
v12nd value, written to base[align*offset[0] + 1].
v23rd value, written to base[align*offset[0] + 2].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
template<int align>
static void gmx::transposeScatterStoreU ( double *  base,
const std::int32_t  offset[],
double  v0,
double  v1,
double  v2 
)
inlinestatic

Store 3 doubles to 3 to base/offset.

Template Parameters
alignAlignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points.
Parameters
[out]basePointer to the start of the memory area
offsetOffset to the start of triplet.
v01st value, written to base[align*offset[0]].
v12nd value, written to base[align*offset[0] + 1].
v23rd value, written to base[align*offset[0] + 2].
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static float gmx::trunc ( float  a)
inlinestatic

Truncate float, i.e. round towards zero - common hardware instruction.

Parameters
aAny floating-point value
Returns
Integer rounded towards zero, represented in floating-point format.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
static double gmx::trunc ( double  a)
inlinestatic

Truncate double, i.e. round towards zero - common hardware instruction.

Parameters
aAny doubleing-point value
Returns
Integer rounded towards zero, represented in doubleing-point format.
Note
This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.
const char * gmx::unitCellTypeNames ( UnitCellType  type)

Get names for the different unit cell representation types.

Parameters
[in]typeWhat name needs to be provided.
void gmx::unpinBuffer ( void *  pointer)
noexcept

Unpin the allocation.

Requries that pointer is not nullptr and was previously pinned with pinBuffer().

Does not throw.

void gmx::updateCorrelationGridHistory ( CorrelationGridHistory *  corrGridHist,
const CorrelationGrid &  corrGrid 
)

Update the correlation grid history for checkpointing.

Parameters
[in,out]corrGridHistCorrelation grid history to set.
[in]corrGridCorrelation grid state to read.
static void gmx::updateGlobalState ( t_state globalState,
const PaddedHostVector< RVec > &  x,
const PaddedHostVector< RVec > &  v,
const tensor  box,
int  ddpCount,
int  ddpCountCgGl,
const std::vector< int > &  cgGl 
)
static

Update the legacy global state.

When restoring from checkpoint, data will be distributed during domain decomposition at setup stage. Domain decomposition still uses the legacy global t_state object so make sure it's up-to-date.

static bool gmx::valueIsInGrid ( const awh_dvec  value,
ArrayRef< const GridAxis >  axis 
)
static

Query if a value is in range of the grid.

Parameters
[in]valueValue to check.
[in]axisThe grid axes.
Returns
true if the value is in the grid.
static bool gmx::valueIsInInterval ( double  origin,
double  end,
double  period,
double  value 
)
static

Checks if a value is within an interval.

Parameters
[in]originStart value of interval.
[in]endEnd value of interval.
[in]periodPeriod (or 0 if not periodic).
[in]valueValue to check.
Returns
true if the value is within the interval.
static int gmx::vsiteIlistNrCount ( ArrayRef< const InteractionList >  ilist)
static

Returns the sum of the vsite ilist sizes over all vsite types.

Parameters
[in]ilistThe interaction list
void gmx::write_IMDgroup_to_file ( bool  bIMD,
t_inputrec *  ir,
const t_state state,
const gmx_mtop_t &  sys,
int  nfile,
const t_filenm  fnm[] 
)

Writes out the group of atoms selected for interactive manipulation.

Called by grompp. The resulting file has to be read in by VMD if one wants it to connect to mdrun.

Parameters
bIMDOnly springs into action if bIMD is TRUE. Otherwise returns directly.
irStructure containing MD input parameters, among those the IMD data structure.
stateThe current state of the MD system.
sysThe global, complete system topology.
nfileNumber of files.
fnmFilename struct.
void gmx::writeHeader ( TextWriter *  writer,
const std::string &  text,
const std::string &  section,
bool  writeFormattedText 
)

Write appropiate Header to output stream.

Parameters
[in]writerTextWriter object for writing information.
[in]textString with the header before writing.
[in]sectionString with section text for header.
[in]writeFormattedTextIf we need to format the text for LaTeX output or not
void gmx::writeInformation ( TextOutputFile *  outputStream,
const t_inputrec &  ir,
const gmx_mtop_t &  top,
bool  writeFormattedText,
bool  notStdout 
)

Wrapper for writing out information.

This function is actual called from within the run method to write the information to the terminal or to file. New write out methods should be added to it instead of adding them in run.

Parameters
[in]outputStreamThe filestream used to write the information to.
[in]irReference to inputrec of the run input.
[in]topLocal topology used to derive the information to write out.
[in]writeFormattedTextDecide if we want formatted text output or not.
[in]notStdoutBool to see if we can close the file after writing or not in case of stdout.
void gmx::writeKeyValueTreeAsMdp ( TextWriter *  writer,
const KeyValueTreeObject &  tree 
)

Write a flat key-value tree to writer in mdp style.

Sub-objects will output nothing, so they can be used to contain a special key-value pair to create a comment, as well as the normal key and value. The comment pair will have a key of "comment", and the value will be used as a comment (if non-empty).

template<typename ValueType >
void gmx::writeKvtCheckpointValue ( const ValueType &  value,
const std::string &  name,
const std::string &  identifier,
KeyValueTreeObjectBuilder  kvtBuilder 
)

Write to a key-value-tree used for checkpointing.

Template Parameters
ValueType
Parameters
[in]valuename of the value to be checkpointed
[in]namethe value to be checkpointed
[in]identifieruniquely identifies the module that is checkpointing typically the module name
[in]kvtBuilderthe key-value-tree builder used to store the checkpoint values
template void gmx::writeKvtCheckpointValue ( const std::int64_t &  value,
const std::string &  name,
const std::string &  identifier,
KeyValueTreeObjectBuilder  kvtBuilder 
)

Write to a key-value-tree used for checkpointing.

Template Parameters
ValueType
Parameters
[in]valuename of the value to be checkpointed
[in]namethe value to be checkpointed
[in]identifieruniquely identifies the module that is checkpointing typically the module name
[in]kvtBuilderthe key-value-tree builder used to store the checkpoint values
template void gmx::writeKvtCheckpointValue ( const real value,
const std::string &  name,
const std::string &  identifier,
KeyValueTreeObjectBuilder  kvtBuilder 
)

Write to a key-value-tree used for checkpointing.

Template Parameters
ValueType
Parameters
[in]valuename of the value to be checkpointed
[in]namethe value to be checkpointed
[in]identifieruniquely identifies the module that is checkpointing typically the module name
[in]kvtBuilderthe key-value-tree builder used to store the checkpoint values
void gmx::writeParameterInformation ( TextWriter *  writer,
const t_inputrec &  ir,
bool  writeFormattedText 
)

Write information about system parameters.

This method writes the basic information for the system parameters and simulation settings as reported in the ir.

Parameters
[in]writerTextWriter object for writing information.
[in]irReference to inputrec of the run input.
[in]writeFormattedTextDecide if we want formatted text output or not.
void gmx::writeSystemInformation ( TextWriter *  writer,
const gmx_mtop_t &  top,
bool  writeFormattedText 
)

Write information about the molecules in the system.

This method should write all possible information about the molecular composition of the system.

Parameters
[in]writerTextWriter object for writing information.
[in]topLocal topology used to derive the information to write out.
[in]writeFormattedTextDecide if we want formatted text output or not.

Variable Documentation

constexpr Architecture gmx::c_architecture
static
Initial value:
=
Architecture::Unknown

Constant that tells what the architecture is.

const EnumerationArray<ChangeAtomsType, const char*> gmx::c_changeAtomsTypeNames
static
Initial value:
= {
{ "preserved-if-present", "always-from-structure", "never", "always" }
}

Mapping for enums from ChangeAtomsType.

const EnumerationArray<ChangeSettingType, const char*> gmx::c_changeSettingTypeNames
static
Initial value:
= {
{ "preserved-if-present", "always", "never" }
}

Mapping for enums from ChangeSettingType.

const EnumerationArray<DensityFittingAmplitudeMethod, const char*> gmx::c_densityFittingAmplitudeMethodNames
static
Initial value:
= {
{ "unity", "mass", "charge" }
}

The names of the methods to determine the amplitude of the atoms to be spread on a grid.

const EnumerationArray<DensitySimilarityMeasureMethod, const char*> gmx::c_densitySimilarityMeasureMethodNames
static
Initial value:
= {
{ "inner-product", "relative-entropy", "cross-correlation" }
}

Name the methods that may be used to evaluate similarity between densities.

constexpr double gmx::c_epsilon0
Initial value:
=
((c_epsilon0Si * c_nano * c_kilo) / (c_electronCharge * c_electronCharge * c_avogadro))
constexpr int gmx::c_ftypeVsiteStart = F_VSITE1
static

The start value of the vsite indices in the ftype enum.

The validity of the start and end values is checked in makeVirtualSitesHandler(). This is used to avoid loops over all ftypes just to get the vsite entries. (We should replace the fixed ilist array by only the used entries.)

const EnumerationArray<QMMMQMMethod, const char*> gmx::c_qmmmQMMethodNames
static
Initial value:
= {
{ "PBE", "BLYP", "INPUT" }
}

The names of the supported QM methods.

constexpr double gmx::c_speedOfLight
Initial value:
=
2.99792458e05
const gmx::EnumerationArray<XvgFormat, const char*> gmx::c_xvgFormatNames
Initial value:
= {
{ "xmgrace", "xmgr", "none" }
}

Names for XvgFormat.

Technically this duplicates a definition in pargs.cpp for legacy support code, but as the latter will go away and the alternatives are ugly, the duplication is acceptable.

constexpr std::array<int, numFTypesOnGpu> gmx::fTypesOnGpu
Initial value:
= { F_BONDS, F_ANGLES, F_UREY_BRADLEY,
F_PDIHS, F_RBDIHS, F_IDIHS,
F_PIDIHS, F_LJ14 }

List of all bonded function types supported on GPUs.

Note
This list should be in sync with the actual GPU code.
Perturbed interactions are not supported on GPUs.
The function types in the list are ordered on increasing value.
Currently bonded are only supported with CUDA, not with OpenCL.
const char gmx::IMDstr[] = "IMD:"
static

Tag output from the IMD module with this string.

const gmx::EnumerationArray<MtsForceGroups, std::string> gmx::mtsForceGroupNames
static
Initial value:
= {
"longrange-nonbonded", "nonbonded", "pair", "dihedral", "angle", "pull", "awh"
}

Names for the MTS force groups.

const std::vector<std::string> gmx::periodic_system
Initial value:
= {
"X ", "H ", "He ", "Li ", "Be ", "B ", "C ", "N ", "O ", "F ", "Ne ", "Na ",
"Mg ", "Al ", "Si ", "P ", "S ", "Cl ", "Ar ", "K ", "Ca ", "Sc ", "Ti ", "V ",
"Cr ", "Mn ", "Fe ", "Co ", "Ni ", "Cu ", "Zn ", "Ga ", "Ge ", "As ", "Se ", "Br ",
"Kr ", "Rb ", "Sr ", "Y ", "Zr ", "Nb ", "Mo ", "Tc ", "Ru ", "Rh ", "Pd ", "Ag ",
"Cd ", "In ", "Sn ", "Sb ", "Te ", "I ", "Xe ", "Cs ", "Ba ", "La ", "Ce ", "Pr ",
"Nd ", "Pm ", "Sm ", "Eu ", "Gd ", "Tb ", "Dy ", "Ho ", "Er ", "Tm ", "Yb ", "Lu ",
"Hf ", "Ta ", "W ", "Re ", "Os ", "Ir ", "Pt ", "Au ", "Hg ", "Tl ", "Pb ", "Bi ",
"Po ", "At ", "Rn ", "Fr ", "Ra ", "Ac ", "Th ", "Pa ", "U ", "Np ", "Pu ", "Am ",
"Cm ", "Bk ", "Cf ", "Es ", "Fm ", "Md ", "No ", "Lr ", "Rf ", "Db ", "Sg ", "Bh ",
"Hs ", "Mt ", "Ds ", "Rg ", "Cn ", "Nh ", "Fl ", "Mc ", "Lv ", "Ts ", "Og "
}

symbols of the elements in periodic table

constexpr int64_t gmx::sc_atomInfo_FreeEnergyPerturbation = 1 << 15
static

Constants whose bit describes a property of an atom in AtomInfoWithinMoleculeBlock.atomInfo.

No bit should exceed 1 << 63, so that it fits into a 64-bit integer.

Since the tpx format support max 256 energy groups, we do the same here, reserving bits 0-7 for the energy-group ID.