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Gromacs
2016.5
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All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Macros Groups Pages
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Gromacs
2016.5
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Generic GROMACS namespace.
Declares the integrator for test particle insertion.
Declares the integrators for energy minimization and NMA.
Convenience macro to help us avoid ifdefs each time we use sysconf.
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 | 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 | ConstArrayRef |
| STL-like container for non-mutable interface to a C array (or part of a std::vector). 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 | 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... | |
| 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 | BasicVector |
| C++ class for 3D vectors. More... | |
| class | ArrayRef |
| STL-like container for an interface to a C array (or part of a std::vector). 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 | 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 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 | 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 | IOptionManager |
| Base class for option managers. More... | |
| class | Options |
| Collection of options. More... | |
| class | TimeUnitManager |
| Provides common functionality for time unit conversions. More... | |
| class | TimeUnitBehavior |
| Options behavior to add a time unit option. 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 | 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... | |
| 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 | 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 | TopologyInformation |
| Topology information passed to a trajectory analysis module. More... | |
| class | TrajectoryAnalysisCommandLineRunner |
| Runner for command-line trajectory analysis tools. More... | |
| struct | EmptyArrayRef |
| Tag type to initialize empty array references. More... | |
| class | PrivateImplPointer |
| Helper class to manage a pointer to a private implementation class. 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 | 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 | 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 | NotImplementedError |
| Exception class for use of an unimplemented feature. More... | |
| class | FlagsTemplate |
| Template class for typesafe handling of combination of flags. 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 | 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 | TextLineWrapperSettings |
| Stores settings for line wrapping. More... | |
| class | TextLineWrapper |
| Wraps lines to a predefined length. More... | |
Typedefs | |
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typedef std::shared_ptr < IAnalysisDataModule > | AnalysisDataModulePointer |
| Smart pointer for managing a generic analysis data module. | |
|
typedef ConstArrayRef < AnalysisDataValue > | AnalysisDataValuesRef |
| Shorthand for reference to an array of data values. | |
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typedef std::shared_ptr < AnalysisDataAverageModule > | AnalysisDataAverageModulePointer |
| Smart pointer to manage an AnalysisDataAverageModule object. | |
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typedef std::shared_ptr < AnalysisDataFrameAverageModule > | AnalysisDataFrameAverageModulePointer |
| Smart pointer to manage an AnalysisDataFrameAverageModule object. | |
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typedef std::shared_ptr < AnalysisDataDisplacementModule > | AnalysisDataDisplacementModulePointer |
| Smart pointer to manage an AnalysisDataDisplacementModule object. | |
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typedef std::unique_ptr < AbstractAverageHistogram > | AverageHistogramPointer |
| Smart pointer to manage an AbstractAverageHistogram object. | |
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typedef std::shared_ptr < AnalysisDataSimpleHistogramModule > | AnalysisDataSimpleHistogramModulePointer |
| Smart pointer to manage an AnalysisDataSimpleHistogramModule object. | |
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typedef std::shared_ptr < AnalysisDataWeightedHistogramModule > | AnalysisDataWeightedHistogramModulePointer |
| Smart pointer to manage an AnalysisDataWeightedHistogramModule object. | |
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typedef std::shared_ptr < AnalysisDataBinAverageModule > | AnalysisDataBinAverageModulePointer |
| Smart pointer to manage an AnalysisDataBinAverageModule object. | |
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typedef std::shared_ptr < AnalysisDataLifetimeModule > | AnalysisDataLifetimeModulePointer |
| Smart pointer to manage an AnalysisDataLifetimeModule object. | |
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typedef std::shared_ptr < AnalysisDataPlotModule > | AnalysisDataPlotModulePointer |
| Smart pointer to manage an AnalysisDataPlotModule object. | |
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typedef std::shared_ptr < AnalysisDataVectorPlotModule > | AnalysisDataVectorPlotModulePointer |
| Smart pointer to manage an AnalysisDataVectorPlotModule object. | |
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typedef std::map< std::string, CommandLineModulePointer > | CommandLineModuleMap |
| Container type for mapping module names to module objects. | |
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typedef std::unique_ptr < CommandLineModuleGroupData > | CommandLineModuleGroupDataPointer |
| Smart pointer type for managing a CommandLineModuleGroup. | |
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typedef std::vector < CommandLineModuleGroupDataPointer > | CommandLineModuleGroupList |
| Container type for keeping a list of module groups. | |
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typedef std::unique_ptr < ICommandLineModule > | CommandLineModulePointer |
| Smart pointer type for managing a ICommandLineModule. | |
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typedef std::unique_ptr < ICommandLineOptionsModule > | ICommandLineOptionsModulePointer |
| Smart pointer to manage an ICommandLineOptionsModule. | |
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typedef std::unique_ptr < IExecutableEnvironment > | ExecutableEnvironmentPointer |
| Shorthand for a smart pointer to IExecutableEnvironment. | |
| typedef BasicVector< real > | RVec |
Shorthand for C++ rvec-equivalent type. | |
| typedef double | integrator_t (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t *membed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| Integrator algorithm implementation. More... | |
|
typedef std::array < SimulationSignal, eglsNR > | SimulationSignals |
| Convenience typedef for the group of signals used. | |
|
typedef std::unique_ptr < IHelpTopic > | HelpTopicPointer |
| Smart pointer type to manage a IHelpTopic object. | |
| typedef EnumOption< int > | EnumIntOption |
Shorthand for an enumerated option that stores into an int variable. | |
| 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 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< Selection > | SelectionList |
| 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. | |
|
typedef std::unique_ptr < TrajectoryAnalysisModuleData > | TrajectoryAnalysisModuleDataPointer |
| Smart pointer to manage a TrajectoryAnalysisModuleData object. | |
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typedef std::unique_ptr < TrajectoryAnalysisModule > | TrajectoryAnalysisModulePointer |
| Smart pointer to manage a TrajectoryAnalysisModule. | |
|
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. | |
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typedef ExceptionInfo< struct ExceptionInfoLocation_, ThrowLocation > | ExceptionInfoLocation |
| Stores the location where the exception was thrown. | |
| typedef scoped_cptr< void > | scoped_guard_sfree |
| Simple guard which calls sfree. See scoped_cptr for details. | |
|
typedef std::shared_ptr < TextInputStream > | TextInputStreamPointer |
| Shorthand for a smart pointer to a TextInputStream. | |
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typedef std::shared_ptr < TextOutputStream > | TextOutputStreamPointer |
| Shorthand for a smart pointer to a TextOutputStream. | |
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... | |
| CommandLineProgramContext & | initForCommandLine (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... | |
| bool | cpuIsX86Nehalem (const CpuInfo &cpuInfo) |
| Return true if the CPU is an Intel x86 Nehalem. 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... | |
| 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 > | |
| T | square (T x) |
| calculate x^2 More... | |
| template<typename T > | |
| T | power3 (T x) |
| calculate x^3 More... | |
| template<typename T > | |
| T | power4 (T x) |
| calculate x^4 More... | |
| template<typename T > | |
| T | power5 (T x) |
| calculate x^5 More... | |
| template<typename T > | |
| T | power6 (T x) |
| calculate x^6 More... | |
| template<typename T > | |
| T | power12 (T x) |
| calculate x^12 More... | |
| static real | series_sinhx (real x) |
| Maclaurin series for sinh(x)/x. 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... | |
| 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. | |
| double | do_cg (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t *membed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| Do conjugate gradients minimization. More... | |
| double | do_lbfgs (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t *membed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| Do L-BFGS conjugate gradients minimization. More... | |
| double | do_steep (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t *membed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| Do steepest descents minimization. More... | |
| double | do_nm (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t *membed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| Do normal modes analysis. More... | |
| double | do_tpi (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t *membed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| Do test particle insertion. More... | |
| gmx_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... | |
| static void | simdPrefetch (void *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 | 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, float 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 | 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, double 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, float 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... | |
| static float | log (float x) |
| Float log(x). This is the natural logarithm. More... | |
| static float | exp2 (float x) |
| Float 2^x. More... | |
| 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... | |
| static double | log (double x) |
| Double log(x). This is the natural logarithm. More... | |
| static double | exp2 (double x) |
| Double 2^x. More... | |
| 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 float | reduceIncr4ReturnSum (double *m, double v0, double v1, double v2, double v3) |
| Add each double to four consecutive memory locations, return sum. More... | |
| template<typename T > | |
| void | swap (ArrayRef< T > &a, ArrayRef< T > &b) |
| Simple swap method for ArrayRef objects. More... | |
| template<typename T > | |
| void | swap (ConstArrayRef< T > &a, ConstArrayRef< T > &b) |
| Simple swap method for ConstArrayRef objects. 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... | |
| std::string | bromacs () |
| Return a cool definition for the acronym GROMACS. | |
| std::string | getCoolQuote () |
| Return a string with a cool quote. | |
| 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... | |
| template<class Exception , class Tag , class T > | |
| std::enable_if < std::is_base_of < GromacsException, Exception > ::value, const Exception & > ::type | operator<< (const Exception &ex, const ExceptionInfo< Tag, T > &item) |
| Associates extra information with an exception. More... | |
| const DataFileFinder & | getLibraryFileFinder () |
| 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... | |
| void | init (int *argc, char ***argv) |
| Initializes the GROMACS library. More... | |
| void | finalize () |
| Deinitializes the GROMACS library. More... | |
| const IProgramContext & | getProgramContext () |
| Returns the global IProgramContext instance. More... | |
| void | setProgramContext (const IProgramContext *context) |
| Sets the global IProgramContext instance. More... | |
| template<class T > | |
| void | sfree_wrapper (T *p) |
| sfree wrapper to be used as scoped_cptr deleter | |
| 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::vector< std::string > | splitString (const std::string &str) |
| Splits a string to whitespace separated tokens. 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... | |
| 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... | |
| static const char * | boolToString (bool value) |
| Converts a boolean to a "true"/"false" string. More... | |
| static integrator_t * | my_integrator (unsigned int ei) |
| Return the correct integrator function. | |
| int | mdrunner (gmx_hw_opt_t *hw_opt, FILE *fplog, struct t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, ivec ddxyz, int dd_rank_order, int npme, real rdd, real rconstr, const char *dddlb_opt, real dlb_scale, const char *ddcsx, const char *ddcsy, const char *ddcsz, const char *nbpu_opt, int nstlist_cmdline, gmx_int64_t nsteps_cmdline, int nstepout, int resetstep, int nmultisim, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, real pforce, real cpt_period, real max_hours, int imdport, unsigned long Flags) |
| Driver routine, that calls the different methods. More... | |
Variables | |
| integrator_t | do_steep |
| Steepest descents energy minimization. | |
| integrator_t | do_cg |
| Conjugate gradient energy minimization. | |
| integrator_t | do_lbfgs |
| Conjugate gradient energy minimization using the L-BFGS algorithm. | |
| integrator_t | do_nm |
| Normal mode analysis. | |
| integrator_t | do_tpi |
| Test particle insertion. | |
| integrator_t | do_md |
| MD simulations. | |
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.
| typedef double gmx::integrator_t(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t *membed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
Integrator algorithm implementation.
| [in] | fplog | Log file for output |
| [in] | cr | Communication record |
| [in] | nfile | Number of files |
| [in] | fnm | Filename structure array |
| [in] | oenv | Output information |
| [in] | bVerbose | Verbose output or not |
| [in] | nstglobalcomm | How often global communication is done |
| [in] | vsite | Virtual site information |
| [in] | constr | Constraint information |
| [in] | stepout | How often we writen to the console |
| [in] | inputrec | Input record with mdp options |
| [in] | top_global | Molecular topology for the whole system |
| [in] | fcd | Force and constraint data |
| [in] | state_global | The state (x, v, f, box etc.) of the whole system |
| [in] | mdatoms | Structure containing atom information |
| [in] | nrnb | Accounting for floating point operations |
| [in] | wcycle | Wall cycle timing information |
| [in] | ed | Essential dynamics sampling information |
| [in] | fr | Force record with cut-off information and more |
| [in] | repl_ex_nst | How often we do replica exchange (in steps) |
| [in] | repl_ex_nex | How many replicas we have |
| [in] | repl_ex_seed | The seed for Monte Carlo swaps |
| [in] | membed | Membrane embedding data structure |
| [in] | cpt_period | How often to checkpoint the simulation |
| [in] | max_hours | Maximume length of the simulation (wall time) |
| [in] | imdport | Interactive MD port (socket) |
| [in] | Flags | Flags to control mdrun |
| [in] | walltime_accounting | More timing information |
| 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.
|
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.
|
inlinestatic |
Float Floating-point abs().
| a | any floating point values |
|
inlinestatic |
double doubleing-point abs().
| a | any doubleing point values |
|
inlinestatic |
Float acos.
| x | The argument to evaluate acos for |
|
inlinestatic |
Double acos.
| x | The argument to evaluate acos for |
|
inlinestatic |
Double acos, but with single accuracy.
| x | The argument to evaluate acos for |
|
inlinestatic |
Bitwise andnot for two scalar float variables.
| a | data1 |
| b | data2 |
|
inlinestatic |
Bitwise andnot for two scalar double variables.
| a | data1 |
| b | data2 |
|
inlinestatic |
Bitwise andnot for two scalar integer variables.
| a | data1 |
| b | data2 |
|
inlinestatic |
Returns if the boolean is true.
| a | Logical variable. |
|
inlinestatic |
float asin.
| x | The argument to evaluate asin for |
|
inlinestatic |
Double asin.
| x | The argument to evaluate asin for |
|
inlinestatic |
Double asin, but with single accuracy.
| x | The argument to evaluate asin for |
|
inlinestatic |
Float atan.
| x | The argument to evaluate atan for |
|
inlinestatic |
Double atan.
| x | The argument to evaluate atan for |
|
inlinestatic |
Float atan2(y,x).
| y | Y component of vector, any quartile |
| x | X component of vector, any quartile |
|
inlinestatic |
Double atan2(y,x).
| y | Y component of vector, any quartile |
| x | X component of vector, any quartile |
|
inlinestatic |
Double atan2(y,x), but with single accuracy.
| y | Y component of vector, any quartile |
| x | X component of vector, any quartile |
|
inlinestatic |
Double atan, but with single accuracy.
| x | The argument to evaluate atan for |
|
inlinestatic |
Blend float selection.
| a | First source |
| b | Second source |
| sel | Boolean selector |
|
inlinestatic |
Blend double selection.
| a | First source |
| b | Second source |
| sel | Boolean selector |
|
inlinestatic |
Blend integer selection.
| a | First source |
| b | Second source |
| sel | Boolean selector |
|
inlinestatic |
Composes single value with the magnitude of x and the sign of y.
| x | Value to set sign for |
| y | Value used to set sign |
|
inlinestatic |
Composes double value with the magnitude of x and the sign of y.
| x | Value to set sign for |
| y | Value used to set sign |
|
inlinestatic |
Float cos.
| x | The argument to evaluate cos for |
|
inlinestatic |
Double cos.
| x | The argument to evaluate cos for |
|
inlinestatic |
Double cos, but with single accuracy.
| x | The argument to evaluate cos for |
| bool gmx::cpuIsX86Nehalem | ( | const CpuInfo & | cpuInfo | ) |
Return true if the CPU is an Intel x86 Nehalem.
| cpuInfo | Object with cpu information |
|
inlinestatic |
Just return a boolean (mimicks SIMD real-to-int bool conversions)
| a | boolean |
|
inlinestatic |
Convert double to float (mimicks SIMD conversion)
| a | double |
|
inlinestatic |
Convert float to double (mimicks SIMD conversion)
| a | float |
|
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.
| a | integer |
|
inlinestatic |
Just return a boolean (mimicks SIMD int-to-real bool conversions)
| a | boolean |
|
inlinestatic |
Round single precision floating point to integer.
| a | float |
|
inlinestatic |
Round single precision doubleing point to integer.
| a | double |
|
inlinestatic |
Truncate single precision floating point to integer.
| a | float |
|
inlinestatic |
Truncate single precision doubleing point to integer.
| a | double |
| double gmx::do_cg | ( | FILE * | fplog, |
| t_commrec * | cr, | ||
| int | nfile, | ||
| const t_filenm | fnm[], | ||
| const gmx_output_env_t * | oenv, | ||
| gmx_bool | bVerbose, | ||
| int | nstglobalcomm, | ||
| gmx_vsite_t * | vsite, | ||
| gmx_constr_t | constr, | ||
| int | stepout, | ||
| t_inputrec * | inputrec, | ||
| gmx_mtop_t * | top_global, | ||
| t_fcdata * | fcd, | ||
| t_state * | state_global, | ||
| t_mdatoms * | mdatoms, | ||
| t_nrnb * | nrnb, | ||
| gmx_wallcycle_t | wcycle, | ||
| gmx_edsam_t | ed, | ||
| t_forcerec * | fr, | ||
| int | repl_ex_nst, | ||
| int | repl_ex_nex, | ||
| int | repl_ex_seed, | ||
| gmx_membed_t * | membed, | ||
| real | cpt_period, | ||
| real | max_hours, | ||
| int | imdport, | ||
| unsigned long | Flags, | ||
| gmx_walltime_accounting_t | walltime_accounting | ||
| ) |
Do conjugate gradients minimization.
Integrator algorithm implementation. (FILE *fplog, t_commrec *cr,
| [in] | fplog | Log file for output |
| [in] | cr | Communication record |
| [in] | nfile | Number of files |
| [in] | fnm | Filename structure array |
| [in] | oenv | Output information |
| [in] | bVerbose | Verbose output or not |
| [in] | nstglobalcomm | How often global communication is done |
| [in] | vsite | Virtual site information |
| [in] | constr | Constraint information |
| [in] | stepout | How often we writen to the console |
| [in] | inputrec | Input record with mdp options |
| [in] | top_global | Molecular topology for the whole system |
| [in] | fcd | Force and constraint data |
| [in] | state_global | The state (x, v, f, box etc.) of the whole system |
| [in] | mdatoms | Structure containing atom information |
| [in] | nrnb | Accounting for floating point operations |
| [in] | wcycle | Wall cycle timing information |
| [in] | ed | Essential dynamics sampling information |
| [in] | fr | Force record with cut-off information and more |
| [in] | repl_ex_nst | How often we do replica exchange (in steps) |
| [in] | repl_ex_nex | How many replicas we have |
| [in] | repl_ex_seed | The seed for Monte Carlo swaps |
| [in] | membed | Membrane embedding data structure |
| [in] | cpt_period | How often to checkpoint the simulation |
| [in] | max_hours | Maximume length of the simulation (wall time) |
| [in] | imdport | Interactive MD port (socket) |
| [in] | Flags | Flags to control mdrun |
| [in] | walltime_accounting | More timing information (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t gmx_unused *membed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| double gmx::do_lbfgs | ( | FILE * | fplog, |
| t_commrec * | cr, | ||
| int | nfile, | ||
| const t_filenm | fnm[], | ||
| const gmx_output_env_t * | oenv, | ||
| gmx_bool | bVerbose, | ||
| int | nstglobalcomm, | ||
| gmx_vsite_t * | vsite, | ||
| gmx_constr_t | constr, | ||
| int | stepout, | ||
| t_inputrec * | inputrec, | ||
| gmx_mtop_t * | top_global, | ||
| t_fcdata * | fcd, | ||
| t_state * | state_global, | ||
| t_mdatoms * | mdatoms, | ||
| t_nrnb * | nrnb, | ||
| gmx_wallcycle_t | wcycle, | ||
| gmx_edsam_t | ed, | ||
| t_forcerec * | fr, | ||
| int | repl_ex_nst, | ||
| int | repl_ex_nex, | ||
| int | repl_ex_seed, | ||
| gmx_membed_t * | membed, | ||
| real | cpt_period, | ||
| real | max_hours, | ||
| int | imdport, | ||
| unsigned long | Flags, | ||
| gmx_walltime_accounting_t | walltime_accounting | ||
| ) |
Do L-BFGS conjugate gradients minimization.
Integrator algorithm implementation. (FILE *fplog, t_commrec *cr,
| [in] | fplog | Log file for output |
| [in] | cr | Communication record |
| [in] | nfile | Number of files |
| [in] | fnm | Filename structure array |
| [in] | oenv | Output information |
| [in] | bVerbose | Verbose output or not |
| [in] | nstglobalcomm | How often global communication is done |
| [in] | vsite | Virtual site information |
| [in] | constr | Constraint information |
| [in] | stepout | How often we writen to the console |
| [in] | inputrec | Input record with mdp options |
| [in] | top_global | Molecular topology for the whole system |
| [in] | fcd | Force and constraint data |
| [in] | state_global | The state (x, v, f, box etc.) of the whole system |
| [in] | mdatoms | Structure containing atom information |
| [in] | nrnb | Accounting for floating point operations |
| [in] | wcycle | Wall cycle timing information |
| [in] | ed | Essential dynamics sampling information |
| [in] | fr | Force record with cut-off information and more |
| [in] | repl_ex_nst | How often we do replica exchange (in steps) |
| [in] | repl_ex_nex | How many replicas we have |
| [in] | repl_ex_seed | The seed for Monte Carlo swaps |
| [in] | membed | Membrane embedding data structure |
| [in] | cpt_period | How often to checkpoint the simulation |
| [in] | max_hours | Maximume length of the simulation (wall time) |
| [in] | imdport | Interactive MD port (socket) |
| [in] | Flags | Flags to control mdrun |
| [in] | walltime_accounting | More timing information (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| double gmx::do_nm | ( | FILE * | fplog, |
| t_commrec * | cr, | ||
| int | nfile, | ||
| const t_filenm | fnm[], | ||
| const gmx_output_env_t * | oenv, | ||
| gmx_bool | bVerbose, | ||
| int | nstglobalcomm, | ||
| gmx_vsite_t * | vsite, | ||
| gmx_constr_t | constr, | ||
| int | stepout, | ||
| t_inputrec * | inputrec, | ||
| gmx_mtop_t * | top_global, | ||
| t_fcdata * | fcd, | ||
| t_state * | state_global, | ||
| t_mdatoms * | mdatoms, | ||
| t_nrnb * | nrnb, | ||
| gmx_wallcycle_t | wcycle, | ||
| gmx_edsam_t | ed, | ||
| t_forcerec * | fr, | ||
| int | repl_ex_nst, | ||
| int | repl_ex_nex, | ||
| int | repl_ex_seed, | ||
| gmx_membed_t * | membed, | ||
| real | cpt_period, | ||
| real | max_hours, | ||
| int | imdport, | ||
| unsigned long | Flags, | ||
| gmx_walltime_accounting_t | walltime_accounting | ||
| ) |
Do normal modes analysis.
Integrator algorithm implementation. (FILE *fplog, t_commrec *cr,
| [in] | fplog | Log file for output |
| [in] | cr | Communication record |
| [in] | nfile | Number of files |
| [in] | fnm | Filename structure array |
| [in] | oenv | Output information |
| [in] | bVerbose | Verbose output or not |
| [in] | nstglobalcomm | How often global communication is done |
| [in] | vsite | Virtual site information |
| [in] | constr | Constraint information |
| [in] | stepout | How often we writen to the console |
| [in] | inputrec | Input record with mdp options |
| [in] | top_global | Molecular topology for the whole system |
| [in] | fcd | Force and constraint data |
| [in] | state_global | The state (x, v, f, box etc.) of the whole system |
| [in] | mdatoms | Structure containing atom information |
| [in] | nrnb | Accounting for floating point operations |
| [in] | wcycle | Wall cycle timing information |
| [in] | ed | Essential dynamics sampling information |
| [in] | fr | Force record with cut-off information and more |
| [in] | repl_ex_nst | How often we do replica exchange (in steps) |
| [in] | repl_ex_nex | How many replicas we have |
| [in] | repl_ex_seed | The seed for Monte Carlo swaps |
| [in] | membed | Membrane embedding data structure |
| [in] | cpt_period | How often to checkpoint the simulation |
| [in] | max_hours | Maximume length of the simulation (wall time) |
| [in] | imdport | Interactive MD port (socket) |
| [in] | Flags | Flags to control mdrun |
| [in] | walltime_accounting | More timing information (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| double gmx::do_steep | ( | FILE * | fplog, |
| t_commrec * | cr, | ||
| int | nfile, | ||
| const t_filenm | fnm[], | ||
| const gmx_output_env_t * | oenv, | ||
| gmx_bool | bVerbose, | ||
| int | nstglobalcomm, | ||
| gmx_vsite_t * | vsite, | ||
| gmx_constr_t | constr, | ||
| int | stepout, | ||
| t_inputrec * | inputrec, | ||
| gmx_mtop_t * | top_global, | ||
| t_fcdata * | fcd, | ||
| t_state * | state_global, | ||
| t_mdatoms * | mdatoms, | ||
| t_nrnb * | nrnb, | ||
| gmx_wallcycle_t | wcycle, | ||
| gmx_edsam_t | ed, | ||
| t_forcerec * | fr, | ||
| int | repl_ex_nst, | ||
| int | repl_ex_nex, | ||
| int | repl_ex_seed, | ||
| gmx_membed_t * | membed, | ||
| real | cpt_period, | ||
| real | max_hours, | ||
| int | imdport, | ||
| unsigned long | Flags, | ||
| gmx_walltime_accounting_t | walltime_accounting | ||
| ) |
Do steepest descents minimization.
Integrator algorithm implementation. (FILE *fplog, t_commrec *cr,
| [in] | fplog | Log file for output |
| [in] | cr | Communication record |
| [in] | nfile | Number of files |
| [in] | fnm | Filename structure array |
| [in] | oenv | Output information |
| [in] | bVerbose | Verbose output or not |
| [in] | nstglobalcomm | How often global communication is done |
| [in] | vsite | Virtual site information |
| [in] | constr | Constraint information |
| [in] | stepout | How often we writen to the console |
| [in] | inputrec | Input record with mdp options |
| [in] | top_global | Molecular topology for the whole system |
| [in] | fcd | Force and constraint data |
| [in] | state_global | The state (x, v, f, box etc.) of the whole system |
| [in] | mdatoms | Structure containing atom information |
| [in] | nrnb | Accounting for floating point operations |
| [in] | wcycle | Wall cycle timing information |
| [in] | ed | Essential dynamics sampling information |
| [in] | fr | Force record with cut-off information and more |
| [in] | repl_ex_nst | How often we do replica exchange (in steps) |
| [in] | repl_ex_nex | How many replicas we have |
| [in] | repl_ex_seed | The seed for Monte Carlo swaps |
| [in] | membed | Membrane embedding data structure |
| [in] | cpt_period | How often to checkpoint the simulation |
| [in] | max_hours | Maximume length of the simulation (wall time) |
| [in] | imdport | Interactive MD port (socket) |
| [in] | Flags | Flags to control mdrun |
| [in] | walltime_accounting | More timing information (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| double gmx::do_tpi | ( | FILE * | fplog, |
| t_commrec * | cr, | ||
| int | nfile, | ||
| const t_filenm | fnm[], | ||
| const gmx_output_env_t * | oenv, | ||
| gmx_bool | bVerbose, | ||
| int | nstglobalcomm, | ||
| gmx_vsite_t * | vsite, | ||
| gmx_constr_t | constr, | ||
| int | stepout, | ||
| t_inputrec * | inputrec, | ||
| gmx_mtop_t * | top_global, | ||
| t_fcdata * | fcd, | ||
| t_state * | state_global, | ||
| t_mdatoms * | mdatoms, | ||
| t_nrnb * | nrnb, | ||
| gmx_wallcycle_t | wcycle, | ||
| gmx_edsam_t | ed, | ||
| t_forcerec * | fr, | ||
| int | repl_ex_nst, | ||
| int | repl_ex_nex, | ||
| int | repl_ex_seed, | ||
| gmx_membed_t * | membed, | ||
| real | cpt_period, | ||
| real | max_hours, | ||
| int | imdport, | ||
| unsigned long | Flags, | ||
| gmx_walltime_accounting_t | walltime_accounting | ||
| ) |
Do test particle insertion.
Integrator algorithm implementation. (FILE *fplog, t_commrec *cr,
| [in] | fplog | Log file for output |
| [in] | cr | Communication record |
| [in] | nfile | Number of files |
| [in] | fnm | Filename structure array |
| [in] | oenv | Output information |
| [in] | bVerbose | Verbose output or not |
| [in] | nstglobalcomm | How often global communication is done |
| [in] | vsite | Virtual site information |
| [in] | constr | Constraint information |
| [in] | stepout | How often we writen to the console |
| [in] | inputrec | Input record with mdp options |
| [in] | top_global | Molecular topology for the whole system |
| [in] | fcd | Force and constraint data |
| [in] | state_global | The state (x, v, f, box etc.) of the whole system |
| [in] | mdatoms | Structure containing atom information |
| [in] | nrnb | Accounting for floating point operations |
| [in] | wcycle | Wall cycle timing information |
| [in] | ed | Essential dynamics sampling information |
| [in] | fr | Force record with cut-off information and more |
| [in] | repl_ex_nst | How often we do replica exchange (in steps) |
| [in] | repl_ex_nex | How many replicas we have |
| [in] | repl_ex_seed | The seed for Monte Carlo swaps |
| [in] | membed | Membrane embedding data structure |
| [in] | cpt_period | How often to checkpoint the simulation |
| [in] | max_hours | Maximume length of the simulation (wall time) |
| [in] | imdport | Interactive MD port (socket) |
| [in] | Flags | Flags to control mdrun |
| [in] | walltime_accounting | More timing information (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
|
inlinestatic |
Float erf(x).
| x | Argument. |
|
inlinestatic |
Double erf(x).
| x | Argument. |
|
inlinestatic |
Float erfc(x).
| x | Argument. |
|
inlinestatic |
Double erfc(x).
| x | Argument. |
|
inlinestatic |
Double erfc(x), but with single accuracy.
| x | Argument. |
| double gmx::erfinv | ( | double | x | ) |
Inverse error function, double precision.
| x | Argument, should be in the range -1.0 < x < 1.0 |
| float gmx::erfinv | ( | float | x | ) |
Inverse error function, single precision.
| x | Argument, should be in the range -1.0 < x < 1.0 |
|
inlinestatic |
Double erf(x), but with single accuracy.
| x | Argument. |
|
inlinestatic |
Float exp(x).
| x | Argument. |
|
inlinestatic |
Double exp(x).
| x | Argument. |
|
inlinestatic |
Float 2^x.
| x | Argument. |
|
inlinestatic |
Double 2^x.
| x | Argument. |
|
inlinestatic |
Double 2^x, but with single accuracy.
| x | Argument. |
|
inlinestatic |
Copy single float to three variables.
| scalar | Floating-point input. | |
| [out] | triplets0 | Copy 1. |
| [out] | triplets1 | Copy 2. |
| [out] | triplets2 | Copy 3. |
|
inlinestatic |
Copy single double to three variables.
| scalar | Floating-point input. | |
| [out] | triplets0 | Copy 1. |
| [out] | triplets1 | Copy 2. |
| [out] | triplets2 | Copy 3. |
|
inlinestatic |
Double exp(x), but with single accuracy.
| x | Argument. |
|
inlinestatic |
Float Fused-multiply-add. Result is a*b + c.
| a | factor1 |
| b | factor2 |
| c | term |
|
inlinestatic |
double Fused-multiply-add. Result is a*b + c.
| a | factor1 |
| b | factor2 |
| c | term |
|
inlinestatic |
Float Fused-multiply-subtract. Result is a*b - c.
| a | factor1 |
| b | factor2 |
| c | term |
|
inlinestatic |
double Fused-multiply-subtract. Result is a*b - c.
| a | factor1 |
| b | factor2 |
| c | term |
|
inlinestatic |
Float Fused-negated-multiply-add. Result is -a*b + c.
| a | factor1 |
| b | factor2 |
| c | term |
|
inlinestatic |
double Fused-negated-multiply-add. Result is - a*b + c.
| a | factor1 |
| b | factor2 |
| c | term |
|
inlinestatic |
Float Fused-negated-multiply-subtract. Result is -a*b - c.
| a | factor1 |
| b | factor2 |
| c | term |
|
inlinestatic |
double Fused-negated-multiply-subtract. Result is -a*b - c.
| a | factor1 |
| b | factor2 |
| c | term |
|
inlinestatic |
Load 4 floats from base/offsets and store into variables.
| align | Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points. |
| base | Aligned pointer to the start of the memory. | |
| offset | Integer type with offset to the start of each triplet. | |
| [out] | v0 | First float, base[align*offset[0]]. |
| [out] | v1 | Second float, base[align*offset[0] + 1]. |
| [out] | v2 | Third float, base[align*offset[0] + 2]. |
| [out] | v3 | Fourth float, base[align*offset[0] + 3]. |
|
inlinestatic |
Load 2 floats from base/offsets and store into variables (aligned).
| align | Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points. |
| base | Aligned pointer to the start of the memory. | |
| offset | Integer type with offset to the start of each triplet. | |
| [out] | v0 | First float, base[align*offset[0]]. |
| [out] | v1 | Second float, base[align*offset[0] + 1]. |
|
inlinestatic |
Load 4 doubles from base/offsets and store into variables.
| align | Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points. |
| base | Aligned pointer to the start of the memory. | |
| offset | Integer type with offset to the start of each triplet. | |
| [out] | v0 | First double, base[align*offset[0]]. |
| [out] | v1 | Second double, base[align*offset[0] + 1]. |
| [out] | v2 | Third double, base[align*offset[0] + 2]. |
| [out] | v3 | Fourth double, base[align*offset[0] + 3]. |
|
inlinestatic |
Load 2 doubles from base/offsets and store into variables (aligned).
| align | Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points. |
| base | Aligned pointer to the start of the memory. | |
| offset | Integer type with offset to the start of each triplet. | |
| [out] | v0 | First double, base[align*offset[0]]. |
| [out] | v1 | Second double, base[align*offset[0] + 1]. |
|
inlinestatic |
Load 4 consecutive floats from base/offset into four variables.
| align | Alignment of the memory from which we read. |
| base | Pointer to the start of the memory area | |
| offset | Index to data. | |
| [out] | v0 | 1st float, base[align*offset[0]]. |
| [out] | v1 | 2nd float, base[align*offset[0] + 1]. |
| [out] | v2 | 3rd float, base[align*offset[0] + 2]. |
| [out] | v3 | 4th float, base[align*offset[0] + 3]. |
|
inlinestatic |
Load 2 consecutive floats from base/offset into four variables.
| align | Alignment of the memory from which we read. |
| base | Pointer to the start of the memory area | |
| offset | Index to data. | |
| [out] | v0 | 1st float, base[align*offset[0]]. |
| [out] | v1 | 2nd float, base[align*offset[0] + 1]. |
|
inlinestatic |
Load 4 consecutive doubles from base/offset into four variables.
| align | Alignment of the memory from which we read. |
| base | Pointer to the start of the memory area | |
| offset | Index to data. | |
| [out] | v0 | 1st double, base[align*offset[0]]. |
| [out] | v1 | 2nd double, base[align*offset[0] + 1]. |
| [out] | v2 | 3rd double, base[align*offset[0] + 2]. |
| [out] | v3 | 4th double, base[align*offset[0] + 3]. |
|
inlinestatic |
Load 2 consecutive doubles from base/offset into four variables.
| align | Alignment of the memory from which we read. |
| base | Pointer to the start of the memory area | |
| offset | Index to data. | |
| [out] | v0 | 1st double, base[align*offset[0]]. |
| [out] | v1 | 2nd double, base[align*offset[0] + 1]. |
|
inlinestatic |
Load 2 floats from base/offsets and store into variables (unaligned).
| align | Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points. |
| base | Aligned pointer to the start of the memory. | |
| offset | Integer type with offset to the start of each triplet. | |
| [out] | v0 | First float, base[align*offset[0]]. |
| [out] | v1 | Second float, base[align*offset[0] + 1]. |
|
inlinestatic |
Load 2 doubles from base/offsets and store into variables (unaligned).
| align | Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points. |
| base | Aligned pointer to the start of the memory. | |
| offset | Integer type with offset to the start of each triplet. | |
| [out] | v0 | First double, base[align*offset[0]]. |
| [out] | v1 | Second double, base[align*offset[0] + 1]. |
|
inlinestatic |
Load 3 consecutive floats from base/offsets, store into three vars.
| align | Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points. |
| base | Pointer to the start of the memory area | |
| offset | Offset to the start of data. | |
| [out] | v0 | 1st value, base[align*offset[0]]. |
| [out] | v1 | 2nd value, base[align*offset[0] + 1]. |
| [out] | v2 | 3rd value, base[align*offset[0] + 2]. |
|
inlinestatic |
Load 3 consecutive doubles from base/offsets, store into three vars.
| align | Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points. |
| base | Pointer to the start of the memory area | |
| offset | Offset to the start of data. | |
| [out] | v0 | 1st double, base[align*offset[0]]. |
| [out] | v1 | 2nd double, base[align*offset[0] + 1]. |
| [out] | v2 | 3rd double, base[align*offset[0] + 2]. |
| RealType gmx::generateCanonical | ( | Rng & | g | ) |
Generate a floating-point value with specified number of random bits.
| RealType | Floating-point type to generate |
| Bits | Number of random bits to generate |
| Rng | Random number generator class |
| g | Random 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.
| std::int64_t gmx::greatestCommonDivisor | ( | std::int64_t | p, |
| std::int64_t | q | ||
| ) |
Find greatest common divisor of two numbers.
| p | First number, positive |
| q | Second number, positive |
|
inlinestatic |
Calculate 1/x for float.
| x | Argument that must be nonzero. This routine does not check arguments. |
|
inlinestatic |
Calculate 1/x for double.
| x | Argument that must be nonzero. This routine does not check arguments. |
|
inlinestatic |
Calculate inverse cube root of x in single precision.
| x | Argument |
This routine is typically faster than using std::pow().
|
inlinestatic |
Calculate inverse sixth root of x in double precision.
| x | Argument |
This routine is typically faster than using std::pow().
|
inlinestatic |
Calculate inverse sixth root of integer x in double precision.
| x | Argument |
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.
|
inlinestatic |
Calculate 1/x for double, but with single accuracy.
| x | Argument that must be nonzero. This routine does not check arguments. |
|
inlinestatic |
Calculate inverse sixth root of x in single precision.
| x | Argument, must be greater than zero. |
This routine is typically faster than using std::pow().
|
inlinestatic |
Calculate inverse sixth root of x in double precision.
| x | Argument, must be greater than zero. |
This routine is typically faster than using std::pow().
|
inlinestatic |
Calculate inverse sixth root of integer x in double precision.
| x | Argument, must be greater than zero. |
This routine is typically faster than using std::pow().
|
inlinestatic |
Calculate 1.0/sqrt(x) in single precision.
| x | Positive 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.
|
inlinestatic |
Calculate 1.0/sqrt(x) in double precision, but single range.
| x | Positive 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.
|
inlinestatic |
Calculate 1.0/sqrt(x) for integer x in double precision.
| x | Positive value to calculate inverse square root for. |
|
inlinestatic |
Calculate 1/sqrt(x) for two floats.
| x0 | First argument, x0 must be positive - no argument checking. | |
| x1 | Second argument, x1 must be positive - no argument checking. | |
| [out] | out0 | Result 1/sqrt(x0) |
| [out] | out1 | Result 1/sqrt(x1) |
|
inlinestatic |
Calculate 1/sqrt(x) for two doubles.
| x0 | First argument, x0 must be positive - no argument checking. | |
| x1 | Second argument, x1 must be positive - no argument checking. | |
| [out] | out0 | Result 1/sqrt(x0) |
| [out] | out1 | Result 1/sqrt(x1) |
|
inlinestatic |
Calculate 1/sqrt(x) for two doubles, but with single accuracy.
| x0 | First argument, x0 must be positive - no argument checking. | |
| x1 | Second argument, x1 must be positive - no argument checking. | |
| [out] | out0 | Result 1/sqrt(x0) |
| [out] | out1 | Result 1/sqrt(x1) |
|
inlinestatic |
Calculate 1/sqrt(x) for double, but with single accuracy.
| x | Argument that must be >0. This routine does not check arguments. |
|
inlinestatic |
Float log(x). This is the natural logarithm.
| x | Argument, should be >0. |
|
inlinestatic |
Double log(x). This is the natural logarithm.
| x | Argument, should be >0. |
| unsigned int gmx::log2I | ( | std::uint32_t | x | ) |
Compute floor of logarithm to base 2, 32 bit unsigned argument.
| x | 32-bit unsigned argument |
| unsigned int gmx::log2I | ( | std::uint64_t | x | ) |
Compute floor of logarithm to base 2, 64 bit unsigned argument.
| x | 64-bit unsigned argument |
| unsigned int gmx::log2I | ( | std::int32_t | x | ) |
Compute floor of logarithm to base 2, 32 bit signed argument.
| x | 32-bit signed argument |
| unsigned int gmx::log2I | ( | std::int64_t | x | ) |
Compute floor of logarithm to base 2, 64 bit signed argument.
| x | 64-bit signed argument |
|
inlinestatic |
Double log(x), but with single accuracy. This is the natural logarithm.
| x | Argument, should be >0. |
| gmx_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.
|
inlinestatic |
Add two float variables, masked version.
| a | term1 |
| b | term2 |
| m | mask |
|
inlinestatic |
Add two double variables, masked version.
| a | term1 |
| b | term2 |
| m | mask |
|
inlinestatic |
Float fused multiply-add, masked version.
| a | factor1 |
| b | factor2 |
| c | term |
| m | mask |
|
inlinestatic |
double fused multiply-add, masked version.
| a | factor1 |
| b | factor2 |
| c | term |
| m | mask |
|
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.
| x | Argument that must be nonzero if masked-in. |
| m | Mask |
|
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.
| x | Argument that must be nonzero if masked-in. |
| m | Mask |
|
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.
| x | Argument that must be nonzero if masked-in. |
| m | Mask |
|
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.
| x | Argument that must be >0 if masked-in. |
| m | Mask |
|
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.
| x | Argument that must be >0 if masked-in. |
| m | Mask |
|
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.
| x | Argument that must be >0 if masked-in. |
| m | Mask |
|
inlinestatic |
Multiply two float variables, masked version.
| a | factor1 |
| b | factor2 |
| m | mask |
|
inlinestatic |
Multiply two double variables, masked version.
| a | factor1 |
| b | factor2 |
| m | mask |
|
inlinestatic |
Set each float element to the largest from two variables.
| a | Any floating-point value |
| b | Any floating-point value |
|
inlinestatic |
Set each double element to the largest from two variables.
| a | Any doubleing-point value |
| b | Any doubleing-point value |
| int gmx::mdrunner | ( | gmx_hw_opt_t * | hw_opt, |
| FILE * | fplog, | ||
| struct t_commrec * | cr, | ||
| int | nfile, | ||
| const t_filenm | fnm[], | ||
| const gmx_output_env_t * | oenv, | ||
| gmx_bool | bVerbose, | ||
| int | nstglobalcomm, | ||
| ivec | ddxyz, | ||
| int | dd_rank_order, | ||
| int | npme, | ||
| real | rdd, | ||
| real | rconstr, | ||
| const char * | dddlb_opt, | ||
| real | dlb_scale, | ||
| const char * | ddcsx, | ||
| const char * | ddcsy, | ||
| const char * | ddcsz, | ||
| const char * | nbpu_opt, | ||
| int | nstlist_cmdline, | ||
| gmx_int64_t | nsteps_cmdline, | ||
| int | nstepout, | ||
| int | resetstep, | ||
| int | nmultisim, | ||
| int | repl_ex_nst, | ||
| int | repl_ex_nex, | ||
| int | repl_ex_seed, | ||
| real | pforce, | ||
| real | cpt_period, | ||
| real | max_hours, | ||
| int | imdport, | ||
| unsigned long | Flags | ||
| ) |
Driver routine, that calls the different methods.
| [in] | hw_opt | Hardware detection structure |
| [in] | fplog | File pointer for log file |
| [in] | cr | Communication data |
| [in] | nfile | Number of files |
| [in] | fnm | Array of filenames and file properties |
| [in] | oenv | Output variables for storing xvg files etc. |
| [in] | bVerbose | Verbose output or not |
| [in] | nstglobalcomm | Number of steps between global communication |
| [in] | ddxyz | Division of sub-boxes over processors for use in domain decomposition parallellization |
| [in] | dd_rank_order | Ordering of the PP and PME ranks |
| [in] | npme | The number of separate PME ranks requested, -1 = auto |
| [in] | rdd | The maximum distance for bonded interactions with DD (nm) |
| [in] | rconstr | Maximum distance for P-LINCS (nm) |
| [in] | dddlb_opt | File name for debugging |
| [in] | dlb_scale | File name for debugging |
| [in] | ddcsx | File name for debugging |
| [in] | ddcsy | File name for debugging |
| [in] | ddcsz | File name for debugging |
| [in] | nbpu_opt | Type of nonbonded processing unit |
| [in] | nstlist_cmdline | Override neighbor search frequency |
| [in] | nsteps_cmdline | Override number of simulation steps |
| [in] | nstepout | How often to write to the console |
| [in] | resetstep | Reset the step counter |
| [in] | nmultisim | Number of parallel simulations to run |
| [in] | repl_ex_nst | Number steps between replica exchange attempts |
| [in] | repl_ex_nex | Number of replicas in REMD |
| [in] | repl_ex_seed | The seed for Monte Carlo swaps |
| [in] | pforce | Minimum force for printing (for debugging) |
| [in] | cpt_period | How often to checkpoint the simulation |
| [in] | max_hours | Maximume length of the simulation (wall time) |
| [in] | imdport | Interactive MD port (socket) |
| [in] | Flags | More command line options |
|
inlinestatic |
Set each float element to the smallest from two variables.
| a | Any floating-point value |
| b | Any floating-point value |
|
inlinestatic |
Set each double element to the smallest from two variables.
| a | Any doubleing-point value |
| b | Any doubleing-point value |
|
inlinestatic |
Calculate the force correction due to PME analytically in float.
See the SIMD version of this function for details.
| z2 | input parameter |
|
inlinestatic |
Calculate the force correction due to PME analytically in double.
See the SIMD version of this function for details.
| z2 | input parameter |
|
inlinestatic |
Force correction due to PME in double, but with single accuracy.
See the SIMD version of this function for details.
| z2 | input parameter |
|
inlinestatic |
Calculate the potential correction due to PME analytically in float.
See the SIMD version of this function for details.
| z2 | input parameter |
|
inlinestatic |
Calculate the potential correction due to PME analytically in double.
See the SIMD version of this function for details.
| z2 | input parameter |
|
inlinestatic |
Potential correction due to PME in double, but with single accuracy.
See the SIMD version of this function for details.
| z2 | input parameter |
| T gmx::power12 | ( | T | x | ) |
calculate x^12
| T | Type of argument and return value |
| x | argument |
| T gmx::power3 | ( | T | x | ) |
calculate x^3
| T | Type of argument and return value |
| x | argument |
| T gmx::power4 | ( | T | x | ) |
calculate x^4
| T | Type of argument and return value |
| x | argument |
| T gmx::power5 | ( | T | x | ) |
calculate x^5
| T | Type of argument and return value |
| x | argument |
| T gmx::power6 | ( | T | x | ) |
calculate x^6
| T | Type of argument and return value |
| x | argument |
| void gmx::printBinaryInformation | ( | FILE * | fp, |
| const IProgramContext & | programContext | ||
| ) |
Print basic information about the executable.
| fp | Where to print the information to. | |
| [in] | programContext | Program information object to use. |
| void gmx::printBinaryInformation | ( | FILE * | fp, |
| const IProgramContext & | programContext, | ||
| const BinaryInformationSettings & | settings | ||
| ) |
Print basic information about the executable with custom settings.
Needed to read the members without otherwise unnecessary accessors.
| fp | Where to print the information to. | |
| [in] | programContext | Program information object to use. |
| [in] | settings | Specifies what to print. |
| int gmx::processExceptionAtExitForCommandLine | ( | const std::exception & | ex | ) |
Handles an exception and deinitializes after initForCommandLine.
| [in] | ex | Exception that is the cause for terminating the program. |
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.
|
inlinestatic |
Return sum of all elements in float variable (i.e., the variable itself).
| a | variable to reduce/sum. |
|
inlinestatic |
Return sum of all elements in double variable (i.e., the variable itself).
| a | variable to reduce/sum. |
|
inlinestatic |
Add each float to four consecutive memory locations, return sum.
| m | Pointer to memory where four floats should be incremented |
| v0 | float to be added to m[0] |
| v1 | float to be added to m[1] |
| v2 | float to be added to m[2] |
| v3 | float to be added to m[3] |
|
inlinestatic |
Add each double to four consecutive memory locations, return sum.
| m | Pointer to memory where four floats should be incremented |
| v0 | double to be added to m[0] |
| v1 | double to be added to m[1] |
| v2 | double to be added to m[2] |
| v3 | double to be added to m[3] |
|
inlinestatic |
Float round to nearest integer value (in floating-point format).
| a | Any floating-point value |
|
inlinestatic |
double round to nearest integer value (in doubleing-point format).
| a | Any doubleing-point value |
| int gmx::runCommandLineModule | ( | int | argc, |
| char * | argv[], | ||
| ICommandLineModule * | module | ||
| ) |
Implements a main() method that runs a single module.
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:
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.
| argc | argc passed to main(). | |
| argv | argv passed to main(). | |
| [in] | name | Name for the module. |
| [in] | description | Short description for the module. |
| factory | Factory 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:
Does not throw. All exceptions are caught and handled internally.
|
inlinestatic |
Select from single precision variable where boolean is true.
| a | Floating-point variable to select from |
| mask | Boolean selector |
|
inlinestatic |
Select from double precision variable where boolean is true.
| a | double variable to select from |
| mask | Boolean selector |
|
inlinestatic |
Select from integer variable where boolean is true.
| a | Integer variable to select from |
| mask | Boolean selector |
|
inlinestatic |
Select from single precision variable where boolean is false.
| a | Floating-point variable to select from |
| mask | Boolean selector |
|
inlinestatic |
Select from double precision variable where boolean is false.
| a | double variable to select from |
| mask | Boolean selector |
|
inlinestatic |
Select from integer variable where boolean is false.
| a | Integer variable to select from |
| mask | Boolean selector |
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/.
| [in] | finder | finder 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 gmxlibfn() and libopen().
This method is not thread-safe. See setProgramContext(); the same constraints apply here as well.
Does not throw.
|
static |
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).
| m | Pointer 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). |
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inlinestatic |
Float sin.
| x | The argument to evaluate sin for |
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inlinestatic |
Double sin.
| x | The argument to evaluate sin for |
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inlinestatic |
Float sin & cos.
| x | The argument to evaluate sin/cos for | |
| [out] | sinval | Sin(x) |
| [out] | cosval | Cos(x) |
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inlinestatic |
Double sin & cos.
| x | The argument to evaluate sin/cos for | |
| [out] | sinval | Sin(x) |
| [out] | cosval | Cos(x) |
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inlinestatic |
Double sin & cos, but with single accuracy.
| x | The argument to evaluate sin/cos for | |
| [out] | sinval | Sin(x) |
| [out] | cosval | Cos(x) |
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inlinestatic |
Double sin, but with single accuracy.
| x | The argument to evaluate sin for |
|
inlinestatic |
Calculate sixth root of x in single precision.
| x | Argument, must be greater than or equal to zero. |
This routine is typically faster than using std::pow().
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inlinestatic |
Calculate sixth root of x in double precision.
| x | Argument, must be greater than or equal to zero. |
This routine is typically faster than using std::pow().
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inlinestatic |
Calculate sixth root of integer x, return double.
| x | Argument, must be greater than or equal to zero. |
This routine is typically faster than using std::pow().
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inlinestatic |
Calculate sqrt(x) for double, but with single accuracy.
| x | Argument that must be >=0. |
| T gmx::square | ( | T | x | ) |
calculate x^2
| T | Type of argument and return value |
| x | argument |
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inlinestatic |
Store contents of float variable to aligned memory m.
| [out] | m | Pointer to memory. |
| a | float variable to store |
|
inlinestatic |
Store contents of double variable to aligned memory m.
| [out] | m | Pointer to memory. |
| a | double variable to store |
|
inlinestatic |
Store contents of integer variable to aligned memory m.
| [out] | m | Pointer to memory. |
| a | integer variable to store |
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inlinestatic |
Store contents of float variable to unaligned memory m.
| [out] | m | Pointer to memory, no alignment requirement. |
| a | float variable to store. |
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inlinestatic |
Store contents of double variable to unaligned memory m.
| [out] | m | Pointer to memory, no alignment requirement. |
| a | double variable to store. |
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inlinestatic |
Store contents of integer variable to unaligned memory m.
| [out] | m | Pointer to memory, no alignment requirement. |
| a | integer variable to store. |
|
inlinestatic |
Float tan.
| x | The argument to evaluate tan for |
|
inlinestatic |
Double tan.
| x | The argument to evaluate tan for |
|
inlinestatic |
Double tan, but with single accuracy.
| x | The argument to evaluate tan for |
|
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.
| a | value |
|
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.
| a | value |
|
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.
| a | value |
|
inlinestatic |
Subtract 3 floats from base/offset.
| align | Alignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points. |
| [out] | base | Pointer to the start of the memory area |
| offset | Offset to the start of triplet. | |
| v0 | 1st value, subtracted from base[align*offset[0]]. | |
| v1 | 2nd value, subtracted from base[align*offset[0] + 1]. | |
| v2 | 3rd value, subtracted from base[align*offset[0] + 2]. |
|
inlinestatic |
Subtract 3 doubles from base/offset.
| align | Alignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points. |
| [out] | base | Pointer to the start of the memory area |
| offset | Offset to the start of triplet. | |
| v0 | 1st value, subtracted from base[align*offset[0]]. | |
| v1 | 2nd value, subtracted from base[align*offset[0] + 1]. | |
| v2 | 3rd value, subtracted from base[align*offset[0] + 2]. |
|
inlinestatic |
Add 3 floats to base/offset.
| align | Alignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points. |
| [out] | base | Pointer to the start of the memory area |
| offset | Offset to the start of triplet. | |
| v0 | 1st value, added to base[align*offset[0]]. | |
| v1 | 2nd value, added to base[align*offset[0] + 1]. | |
| v2 | 3rd value, added to base[align*offset[0] + 2]. |
|
inlinestatic |
Add 3 doubles to base/offset.
| align | Alignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points. |
| [out] | base | Pointer to the start of the memory area |
| offset | Offset to the start of triplet. | |
| v0 | 1st value, added to base[align*offset[0]]. | |
| v1 | 2nd value, added to base[align*offset[0] + 1]. | |
| v2 | 3rd value, added to base[align*offset[0] + 2]. |
|
inlinestatic |
Store 3 floats to 3 to base/offset.
| align | Alignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points. |
| [out] | base | Pointer to the start of the memory area |
| offset | Offset to the start of triplet. | |
| v0 | 1st value, written to base[align*offset[0]]. | |
| v1 | 2nd value, written to base[align*offset[0] + 1]. | |
| v2 | 3rd value, written to base[align*offset[0] + 2]. |
|
inlinestatic |
Store 3 doubles to 3 to base/offset.
| align | Alignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points. |
| [out] | base | Pointer to the start of the memory area |
| offset | Offset to the start of triplet. | |
| v0 | 1st value, written to base[align*offset[0]]. | |
| v1 | 2nd value, written to base[align*offset[0] + 1]. | |
| v2 | 3rd value, written to base[align*offset[0] + 2]. |
|
inlinestatic |
Truncate float, i.e. round towards zero - common hardware instruction.
| a | Any floating-point value |
|
inlinestatic |
Truncate double, i.e. round towards zero - common hardware instruction.
| a | Any doubleing-point value |
1.8.5