Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 1234]

gmx	Generic GROMACS namespace
compat	Compatibility aliases for standard library features
not_null	Restricts a pointer or smart pointer to only hold non-null values
detail
PaddingTraits	Traits classes for handling padding for types used with PaddedVector
internal
SimdTraits	Simd traits
test	Testing utilities namespace
AnalysisDataTestInputPointSet	Represents a single set of points in AnalysisDataTestInputFrame structure
AnalysisDataTestInputFrame	Represents a single frame in AnalysisDataTestInput structure
AnalysisDataTestInput	Represents static input data for AbstractAnalysisData tests
AnalysisDataTestFixture	Test fixture for AbstractAnalysisData testing
AllocatorTest	Templated test fixture
CommandLine	Helper class for tests that need to construct command lines
CommandLineTestHelper	Helper class for tests that construct command lines that need to reference existing files
CommandLineTestBase	Test fixture for tests that call a single command-line program with input/output files
ConfMatch	Match the contents as an gro file
IFileMatcher	Represents a file matcher, matching file contents against reference (or other) data
IFileMatcherSettings	Represents a factory for creating a file matcher
TextFileMatch	Use a ITextBlockMatcher for matching the contents
NoContentsMatch	Do not check the contents of the file
InteractiveTestHelper	Helper class for testing interactive sessions
LoggerTestHelper	Helper class for tests to check output written to a logger
TestReferenceChecker	Handles comparison to test reference data
TestReferenceData	Handles creation of and comparison to test reference data
StdioTestHelper	Helper class for tests where code reads directly from stdin
StringTestBase	Test fixture for tests that check string formatting
FloatingPointDifference	Computes and represents a floating-point difference value
FloatingPointTolerance	Specifies a floating-point comparison tolerance and checks whether a difference is within the tolerance
TestException	Exception class for reporting errors in tests
TestFileManager	Helper for tests that need input and output files
TestFileInputRedirector	In-memory implementation for IFileInputRedirector for tests
TestFileOutputRedirector	In-memory implementation of IFileOutputRedirector for tests
TestOptionsProvider	Provides additional options for the test executable
ITextBlockMatcher	Represents a text matcher, matching text stream contents against reference data
ITextBlockMatcherSettings	Represents a factory for creating a text matcher
ExactTextMatch	Use an exact text match (the contents should be exactly equal)
NoTextMatch	Do not match the text (the contents are ignored)
FilteringExactTextMatch	Use an exact text match after scrubbing lines of the text that match the supplied regular expressions
XvgMatch	Match the contents as an xvg file
AbstractAnalysisData	Abstract base class for all objects that provide data
AnalysisData	Parallelizable data container for raw data
AnalysisDataHandle	Handle for inserting data into AnalysisData
AbstractAnalysisArrayData	Abstract base class for data objects that present in-memory data
AnalysisArrayData	Simple in-memory data array
AnalysisDataValue	Value type for representing a single value in analysis data objects
AnalysisDataFrameHeader	Value type for storing frame-level information for analysis data
AnalysisDataPointSetRef	Value type wrapper for non-mutable access to a set of data column values
AnalysisDataFrameRef	Value type wrapper for non-mutable access to a data frame
IAnalysisDataModule	Interface for a module that gets notified whenever data is added
AnalysisDataModuleSerial	Convenience base class for serial analysis data modules
AnalysisDataModuleParallel	Convenience base class for parallel analysis data modules
AnalysisDataModuleManager	Encapsulates handling of data modules attached to AbstractAnalysisData
AnalysisDataStorageFrame	Allows assigning values for a data frame in AnalysisDataStorage
AnalysisDataStorage	Helper class that implements storage of data
AnalysisDataAverageModule	Data module for independently averaging each column in input data
AnalysisDataFrameAverageModule	Data module for averaging of columns for each frame
AnalysisDataDisplacementModule	Data module for calculating displacements
AnalysisHistogramSettingsInitializer	Provides "named parameter" idiom for constructing histograms
AnalysisHistogramSettings	Contains parameters that specify histogram bin locations
AbstractAverageHistogram	Base class for representing histograms averaged over frames
AnalysisDataSimpleHistogramModule	Data module for per-frame histograms
AnalysisDataWeightedHistogramModule	Data module for per-frame weighted histograms
AnalysisDataBinAverageModule	Data module for bin averages
AnalysisDataLifetimeModule	Data module for computing lifetime histograms for columns in input data
AnalysisDataPlotSettings	Common settings for data plots
AbstractPlotModule	Abstract data module for writing data into a file
AnalysisDataPlotModule	Plotting module for straightforward plotting of data
AnalysisDataVectorPlotModule	Plotting module specifically for data consisting of vectors
AnalysisDataParallelOptions	Parallelization options for analysis data objects
Awh	Coupling of the accelerated weight histogram method (AWH) with the system
CommandLineHelpContext	Context information for writing out command-line help
GlobalCommandLineHelpContext	Helper for passing CommandLineHelpContext into parse_common_args()
ArrayRef	STL-like interface to a C array of T (or part of a std container of T)
CommandLineHelpWriter	Writes help information for Options
CommandLineModuleSettings	Settings to pass information between a module and the general runner
ICommandLineModule	Module that can be run from command line using CommandLineModuleManager
CommandLineModuleManager	Implements a wrapper command-line interface for multiple modules
CommandLineModuleGroup	Handle to add content to a group added with CommandLineModuleManager::addModuleGroup()
ICommandLineOptionsModuleSettings	Settings to pass information between a CommandLineOptionsModule and generic code that runs it
ICommandLineOptionsModule	Module that can be run from a command line and uses gmx::Options for argument processing
CommandLineParser	Implements command-line parsing for Options objects
IExecutableEnvironment	Allows customization of the way various directories are found by CommandLineProgramContext
CommandLineProgramContext	Program context implementation for command line programs
HashedMap	Unordered key to value mapping
LocalAtomSet	A local atom set collects local, global and collective indices of the home atoms on a rank. The indices of the home atoms are automatically updated during domain decomposition, thus gmx::LocalAtomSet::localIndex enables iteration over local atoms properties like coordinates or forces. TODO: add a LocalAtomSet iterator
LocalAtomSetManager	Hands out handles to local atom set indices and triggers index recalculation for all sets upon domain decomposition if run in parallel
ClfftInitializer	Handle clFFT library init and tear down in RAII style
HostAllocationPolicy	Policy class for configuring gmx::Allocator, to manage allocations of memory that may be needed for e.g. GPU transfers
OpenClTraits	Stub for OpenCL type traits
OpenClTraitsBase	Implements common trait infrastructure for OpenCL types
OpenClTraits< cl_context >	Implements traits for cl_context
OpenClTraits< cl_command_queue >	Implements traits for cl_command_queue
OpenClTraits< cl_program >	Implements traits for cl_program
OpenClTraits< cl_kernel >	Implements traits for cl_kernel
ClHandle	Wrapper of OpenCL type cl_type to implement RAII
CpuInfo	Detect CPU capabilities and basic logical processor info
LogicalProcessor	Entry with basic information for a single logical processor
HardwareTopology	Information about sockets, cores, threads, numa, caches
Cache	Information about a single cache level
Core	Information about a single core in a socket
Device	Information about a single PCI device
HWThread	Information about a single hardware thread in a core
LogicalProcessor	Information about socket, core and hwthread for a logical processor
Machine	Hardware topology information about the entire machine
Numa	Information about a single numa node
NumaNode	Information about each numa node in system
Socket	Information about a single socket in the system
ArrayRefWithPadding	Interface to a C array of T (or part of a std container of T), that includes padding that is suitable for the kinds of SIMD operations GROMACS uses
StaticLog2	Evaluate log2(n) for integer n statically at compile time
StaticLog2< 1 >	Specialization of StaticLog2<n> for n==1
StaticLog2< 0 >	Specialization of StaticLog2<n> for n==0
PaddedVector	PaddedVector is a container of elements in contiguous storage that allocates extra memory for safe SIMD-style loads for operations used in GROMACS
BasicVector	C++ class for 3D vectors
CheckpointHandler	Class handling the checkpoint signal
Constraints	Handles constraints
MDAtoms	Contains a C-style t_mdatoms while managing some of its memory with C++ vectors with allocators
PpForceWorkload	Manage what force calculation work is required each step
ResetHandler	Class handling the reset of counters
SimulationSignal	POD-style object used by mdrun ranks to set and receive signals within and between simulations
SimulationSignaller	Object used by mdrun ranks to signal to each other at this step
StopHandler	Class handling the stop signal
StopConditionSignal	Class setting the stop signal based on gmx_get_stop_condition()
StopConditionTime	Class setting the stop signal based on maximal run time
StopHandlerBuilder	Class preparing the creation of a StopHandler
UpdateGroupsCog	Class for managing and computing centers of geometry of update groups
LegacyMdrunOptions	This class provides the same command-line option functionality to both CLI and API sessions
Mdrunner	Runner object for supporting setup and execution of mdrun
MdrunnerBuilder	Build a gmx::Mdrunner
SimulationContext	Simulation environment and configuration
MDModules	Manages the collection of all modules used for mdrun
ForceWithVirial	Container for force and virial for algorithms that provide their own virial tensor contribution
ForceProviderInput	Helper struct that bundles data for passing it over to the force providers
ForceProviderOutput	Helper struct bundling the output data of a force provider
IForceProvider	Interface for a component that provides forces during MD
IMDModule	Extension module for GROMACS simulations
IMDOutputProvider	Interface for handling additional output files during a simulation
IMdpOptionProvider	Interface for handling mdp/tpr input to a mdrun module
TextTableFormatter	Formats rows of a table for text output
HelpManager	Helper for providing interactive online help
AbstractSimpleHelpTopic	Abstract base class for help topics that have simple text and no subtopics
AbstractCompositeHelpTopic	Abstract base class for help topics that have simple text and subtopics
SimpleHelpTopic	Template for simple implementation of AbstractSimpleHelpTopic
CompositeHelpTopic	Template for simple implementation of AbstractCompositeHelpTopic
HelpLinks	Hyperlink data for writing out help
HelpWriterContext	Context information for writing out help
IHelpTopic	Provides a single online help topic
OptionStorageTemplate	Templated base class for constructing option value storage classes
AbstractOption	Abstract base class for specifying option properties
OptionTemplate	Templated base class for constructing concrete option settings classes
OptionInfo	Gives information and allows modifications to an option after creation
AbstractOptionStorage	Abstract base class for converting, validating, and storing option values
AbstractOptionSection	Base class for specifying option section properties
AbstractOptionSectionHandle	Base class for handles to option sections
BooleanOption	Specifies an option that provides boolean values
IntegerOption	Specifies an option that provides integer values
Int64Option	Specifies an option that provides 64-bit integer values
DoubleOption	Specifies an option that provides floating-point (double) values
FloatOption	Specifies an option that provides floating-point (float) values
StringOption	Specifies an option that provides string values
EnumOption	Specifies an option that accepts enumerated string values and writes the selected index into an enum variable
BooleanOptionInfo	Wrapper class for accessing boolean option information
IntegerOptionInfo	Wrapper class for accessing integer option information
Int64OptionInfo	Wrapper class for accessing 64-bit integer option information
DoubleOptionInfo	Wrapper class for accessing floating-point option information
FloatOptionInfo	Wrapper class for accessing floating-point option information
StringOptionInfo	Wrapper class for accessing string option information
EnumOptionInfo	Wrapper class for accessing enum option information
OptionsBehaviorCollection	Container for IOptionsBehavior objects
FileNameOption	Specifies an option that provides file names
FileNameOptionInfo	Wrapper class for accessing file name option information
FileNameOptionManager	Handles interaction of file name options with global options
IOptionsBehavior	Interface to provide extension points for options parsing
IOptionsContainer	Interface for adding input options
IOptionsContainerWithSections	Interface for adding input options with sections
OptionManagerContainer	Container to keep managers added with Options::addManager() and pass them to options
IOptionManager	Base class for option managers
Options	Collection of options
OptionsAssigner	Decorator class for assigning values to Options
OptionSection	Declares a simple option section
OptionSectionHandle	Allows adding options to an OptionSection
OptionStorageTemplateSimple	Simplified option storage template for options that have one-to-one value conversion
OptionsVisitor	Pure interface for visiting options in a Options object
OptionsTypeVisitor	Abstract base class for visiting options of a particular type
OptionsIterator	Decorator class for visiting options in a Options object
OptionsModifyingVisitor	Pure interface for visiting options in a Options object, allowing modifications
OptionsModifyingTypeVisitor	Abstract base class for visiting options of a particular type, allowing modifications
OptionsModifyingIterator	Decorator class for visiting options in a Options object, allowing changes
RepeatingOptionSectionHandle	Allows adding options to an RepeatingOptionSection
RepeatingOptionSection	Declares an option section that creates a structure for each instance
TimeUnitManager	Provides common functionality for time unit conversions
TimeUnitBehavior	Options behavior to add a time unit option
OptionValueConverterSimple	Helper for converting from Variant to a given type
ExponentialDistribution	Exponential distribution
param_type	Exponential distribution parameters
GammaDistribution	Gamma distribution
param_type	Gamma distribution parameters
NormalDistribution	Normal distribution
param_type	Normal distribution parameters
TabulatedNormalDistribution	Tabulated normal random distribution
param_type	Normal distribution parameter class (mean and stddev)
ThreeFry2x64General	General implementation class for ThreeFry counter-based random engines
ThreeFry2x64	ThreeFry2x64 random engine with 20 iteractions
ThreeFry2x64Fast	ThreeFry2x64 random engine with 13 iteractions
UniformIntDistribution	Uniform integer distribution
param_type	Uniform int distribution parameters
UniformRealDistribution	Uniform real distribution
param_type	Uniform real distribution parameters
RestraintManager	Manage the Restraint potentials available for Molecular Dynamics
Site	Abstraction for a restraint interaction site
RestraintMDModule	MDModule wrapper for Restraint implementations
PotentialPointData	Structure to hold the results of IRestraintPotential::evaluate()
IRestraintPotential	Interface for Restraint potentials
AnalysisNeighborhoodPositions	Input positions for neighborhood searching
AnalysisNeighborhood	Neighborhood searching for analysis tools
AnalysisNeighborhoodPair	Value type to represent a pair of positions found in neighborhood searching
AnalysisNeighborhoodSearch	Initialized neighborhood search with a fixed set of reference positions
AnalysisNeighborhoodPairSearch	Initialized neighborhood pair search with a fixed set of positions
Selection	Provides access to a single selection
SelectionPosition	Provides access to information about a single selected position
SelectionCollection	Collection of selections
SelectionTopologyProperties	Describes topology properties required for selection evaluation
SelectionFileOption	Specifies a special option that provides selections from a file
SelectionFileOptionInfo	Wrapper class for accessing and modifying selection file option information
SelectionOption	Specifies an option that provides selection(s)
SelectionOptionInfo	Wrapper class for accessing and modifying selection option information
ITopologyProvider	Provides topology information to SelectionOptionBehavior
SelectionOptionBehavior	Options behavior to allow using SelectionOptions
SelectionOptionManager	Handles interaction of selection options with other options and user input
Simd4Double	SIMD4 double type
Simd4DBool	SIMD4 variable type to use for logical comparisons on doubles
Simd4Float	SIMD4 float type
Simd4FBool	SIMD4 variable type to use for logical comparisons on floats
SimdDouble	Double SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1
SimdDInt32	Integer SIMD variable type to use for conversions to/from double
SimdDBool	Boolean type for double SIMD data
SimdDIBool	Boolean type for integer datatypes corresponding to double SIMD
SimdFloat	Float SIMD variable. Available if GMX_SIMD_HAVE_FLOAT is 1
SimdFInt32	Integer SIMD variable type to use for conversions to/from float
SimdFBool	Boolean type for float SIMD data
SimdFIBool	Boolean type for integer datatypes corresponding to float SIMD
SimdFloatTag	Tag type to select to load SimdFloat with simdLoad(U)
SimdDoubleTag	Tag type to select to load SimdDouble with simdLoad(U)
SimdFInt32Tag	Tag type to select to load SimdFInt32 with simdLoad(U)
SimdDInt32Tag	Tag type to select to load SimdDInt32 with simdLoad(U)
AlignedArray< float, N >	Identical to std::array with GMX_SIMD_FLOAT_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual)
AlignedArray< double, N >	Identical to std::array with GMX_SIMD_DOUBLE_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual)
SimdSetZeroProxy	Proxy object to enable setZero() for SIMD and real types
CubicSplineTable	Cubic spline interpolation table
QuadraticSplineTable	Quadratic spline interpolation table
AnalyticalSplineTableInput	Specification for analytical table function (name, function, derivative)
NumericalSplineTableInput	Specification for vector table function (name, function, derivative, spacing)
GpuTaskMapping	Specifies the GPU deviceID_ available for task_ to use
RangePartitioning	Division of a range of indices into consecutive blocks
Block	Struct for returning the range of a block
iterator	An iterator that loops over integers
TrajectoryAnalysisModuleData	Base class for thread-local data storage during trajectory analysis
TrajectoryAnalysisModule	Base class for trajectory analysis modules
TrajectoryAnalysisSettings	Trajectory analysis module configuration object
TrajectoryAnalysisCommandLineRunner	Runner for command-line trajectory analysis tools
UnionFinder	Union-find data structure for keeping track of disjoint sets
MappedUnionFinder	Extension of UnionFind that supports non-consecutive integer indices as items
TopologyInformation	Topology information available to a trajectory analysis module
AlignedAllocationPolicy	Policy class for configuring gmx::Allocator, to manage allocations of aligned memory for SIMD code
PageAlignedAllocationPolicy	Policy class for configuring gmx::Allocator, to manage allocations of page-aligned memory that can be locked for asynchronous transfer to GPU devices
Allocator	Policy-based memory allocator
EmptyArrayRef	Tag type to initialize empty array references
BinaryInformationSettings	Settings for printBinaryInformation()
PrivateImplPointer	Helper class to manage a pointer to a private implementation class
DataFileOptions	Search parameters for DataFileFinder
DataFileInfo	Information about a data file found by DataFileFinder::enumerateFiles()
DataFileFinder	Searches data files from a set of paths
DirectoryEnumerator	Lists files in a directory
ExceptionInfo	Stores additional context information for exceptions
ExceptionInitializer	Provides information for Gromacs exception constructors
GromacsException	Base class for all exception objects in Gromacs
FileIOError	Exception class for file I/O errors
UserInputError	Exception class for user input errors
InvalidInputError	Exception class for situations where user input cannot be parsed/understood
InconsistentInputError	Exception class for situations where user input is inconsistent
ToleranceError	Exception class when a specified tolerance cannot be achieved
SimulationInstabilityError	Exception class for simulation instabilities
InternalError	Exception class for internal errors
APIError	Exception class for incorrect use of an API
RangeError	Exception class for out-of-range values or indices
NotImplementedError	Exception class for use of an unimplemented feature
IFileInputRedirector	Allows overriding file existence checks from code that supports it
IFileOutputRedirector	Allows capturing stdout and file output from code that supports it
StandardInputStream	Text input stream implementation for reading from stdin
TextInputFile	Text input stream implementation for reading from a file
TextOutputFile	Text output stream implementation for writing to a file
FlagsTemplate	Template class for typesafe handling of combination of flags
Regex	Represents a regular expression
ISerializer	Interface for types that convert standard data types into a form suitable for storage or transfer
KeyValueTreePath	Identifies an entry in a key-value tree
KeyValueTreeBuilder	Root builder for creating trees that have an object at the root
KeyValueTreeValueBuilder	Builder for KeyValueTreeValue objects
KeyValueTreeUniformArrayBuilder	Builder for KeyValueTreeArray objects where all elements are of type T
KeyValueTreeObjectArrayBuilder	Builder for KeyValueTreeArray objects where all elements are KeyValueTreeObject objects
KeyValueTreeObjectBuilder	Builder for KeyValueTreeObject objects
IKeyValueTreeTransformRules	Interface to declare rules for transforming key-value trees
KeyValueTreeTransformRulesScoped	Helper object returned from IKeyValueTreeTransformRules::scopedTransform()
KeyValueTreeTransformRuleBuilder	Provides methods to specify one transformation rule
AfterFrom	Properties that can be specified after from()
ToObject	Properties that can be specified after from().toObject()
ToValue	Properties that can be specified after from().to()
ILogTarget	Target where log output can be written
LogEntryWriter	Helper class for creating log entries with GMX_LOG
LogLevelHelper	Represents a single logging level
MDLogger	Declares a logging interface
LoggerBuilder	Initializes loggers
LoggerOwner	Manages memory for a logger built with LoggerBuilder
MessageStringCollector	Helper class for collecting message strings, optionally with context
MessageStringContext	Convenience class for creating a message context
no_delete	Deleter for std::shared_ptr that does nothing
PhysicalNodeCommunicator	Holds a communicator for the physical node of this rank
InstallationPrefixInfo	Provides information about installation prefix (see IProgramContext::installationPrefix())
IProgramContext	Provides context information about the program that is calling the library
StringCompare	Compare object for std::string STL containers and algorithms that supports run-time decision on how to compare
StringOutputStream	Text output stream implementation for writing to an in-memory string
StringInputStream	Helper class to convert static string data to a stream
StringFormatter	Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms
IdentityFormatter	Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further
TextLineWrapperSettings	Stores settings for line wrapping
TextLineWrapper	Wraps lines to a predefined length
TextReader	Reads text from a TextInputStream
TextInputStream	Interface for reading text
TextOutputStream	Interface for writing text
TextWriter	Writes text into a TextOutputStream
isIntegralConstant	Is true if type is a std::integral_constant
Variant	Represents a dynamically typed value of an arbitrary type
df_history_t	Free-energy sampling history struct
DomdecOptions	Structure containing all (command line) options for the domain decomposition
ekinstate_t	Struct used for checkpointing only
EwaldBoxZScaler	Class to handle box scaling for Ewald and PME
ForceProviders	Evaluates forces from a collection of gmx::IForceProvider
gmx_ana_index_t	Stores a single index group
gmx_ana_indexmap_t	Data structure for calculating index group mappings
gmx_ana_pos_t	Stores a set of positions together with their origins
gmx_ffparams_t	Struct that holds all force field parameters for the simulated system
gmx_ga2la_t	Global to local atom mapping
Entry	Structure for the local atom info
gmx_molblock_t	Block of molecules of the same type, used in gmx_mtop_t
gmx_moltype_t	Molecules type data: atoms, interactions and exclusions
gmx_sparsematrix	Sparse matrix storage format
GpuEventSynchronizer	A class which allows for CPU thread to mark and wait for certain GPU stream execution point. The event can be put into the stream with markEvent() and then later waited on with waitForEvent(). This can be repeated as necessary, but the current implementation does not allow waiting on completed event more than once, expecting only exact pairs of markEvent(stream); waitForEvent(). The class generally attempts to track the correctness of its state transitions, but please note that calling waitForEvent() right after the construction will fail with OpenCL but succeed with CUDA
GpuRegionTimerImpl	The OpenCL implementation of the GPU code region timing. With OpenCL, one has to use cl_event handle for each API call that has to be timed, and accumulate the timing afterwards. As we would like to avoid overhead on API calls, we only query and accumulate cl_event timing at the end of time steps, not after the API calls. Thus, this implementation does not reuse a single cl_event for multiple calls, but instead maintains an array of cl_events to be used within any single code region. The array size is fixed at a small but sufficiently large value for the number of cl_events that might contribute to a timer region, currently 10
GpuRegionTimerWrapper	This is a GPU region timing wrapper class. It allows for host-side tracking of the accumulated execution timespans in GPU code (measuring kernel or transfers duration). It also partially tracks the correctness of the timer state transitions, as far as current implementation allows (see TODO in getLastRangeTime() for a disabled check). Internally it uses GpuRegionTimerImpl for measuring regions
history_t	History information for NMR distance and orientation restraints
InteractionListHandle	Type for returning a list of InteractionList references
MoleculeBlockIndices	Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents
nonbonded_verlet_group_t	Non-bonded interaction group data structure
nonbonded_verlet_t	Top-level non-bonded data structure for the Verlet-type cut-off scheme
NumPmeDomains	Struct for passing around the number of PME domains
ObservablesHistory	Observables history, for writing/reading to/from checkpoint file
ReplicaExchangeParameters	The parameters for the replica exchange algorithm
t_filenm	File name option definition for C code
t_mdatoms	Declares mdatom data structure
t_pargs	Command-line argument definition for C code
t_pbc	Structure containing info on periodic boundary conditions
t_state	The microstate of the system
TypedClMemory	A minimal cl_mem wrapper that remembers its allocation type. The only point is making template type deduction possible