state.h File Reference

#include <array>
#include <memory>
#include <vector>
#include "gromacs/gpu_utils/hostallocator.h"
#include "gromacs/math/paddedvector.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/real.h"

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Description

This file contains the definition of the microstate of the simulated system.

History of observables that needs to be checkpointed should be stored in ObservablesHistory. The state of the mdrun machinery that needs to be checkpointed is also stored elsewhere.

Author

Berk Hess

Classes
class	gmx::CheckpointData< operation >
	} More...
class	history_t
	History information for NMR distance and orientation restraints. More...
class	ekinstate_t
	Struct used for checkpointing only. More...
struct	df_history_t
	Free-energy sampling history struct. More...
class	t_state
	The microstate of the system. More...

Typedefs
template<class T >
using	PaddedHostVector = gmx::PaddedHostVector< T >
	Convenience alias for until all is moved in the gmx namespace.

Enumerations
enum	StateEntry : int {   Lambda, Box, BoxRel, BoxV,   PressurePrevious, Nhxi, ThermInt, X,   V, SDxNotSupported, Cgp, LDRngNotSupported,   LDRngINotSupported, DisreInitF, DisreRm3Tav, OrireInitF,   OrireDtav, SVirPrev, Nhvxi, Veta,   Vol0, Nhpresxi, Nhpresvxi, FVirPrev,   FepState, MCRngNotSupported, MCRngINotSupported, BarosInt,   PullComPrevStep, Count }
	Enum for all entries in t_state. More...

Functions
const char *	enumValueToString (StateEntry enumValue)
	The names of the state entries, defined in src/gromacs/fileio/checkpoint.cpp.
template<typename Enum >
int	enumValueToBitMask (Enum enumValue)
	Convert enum to bitmask value. More...
void	init_gtc_state (t_state *state, int ngtc, int nnhpres, int nhchainlength)
	Resizes the T- and P-coupling state variables.
void	state_change_natoms (t_state *state, int natoms)
	Change the number of atoms represented by this state, allocating memory as needed.
void	init_dfhist_state (t_state *state, int dfhistNumLambda)
	Allocates memory for free-energy history.
void	comp_state (const t_state *st1, const t_state *st2, bool bRMSD, real ftol, real abstol)
	Compares two states, write the differences to stdout.
rvec *	makeRvecArray (gmx::ArrayRef< const gmx::RVec > v, gmx::index n)
	Allocates an rvec pointer and copy the contents of v to it.
void	set_box_rel (const t_inputrec *ir, t_state *state)
	Determine the relative box components. More...
void	preserve_box_shape (const t_inputrec *ir, matrix box_rel, matrix box)
	Make sure the relative box shape remains the same. More...
static gmx::ArrayRef< const gmx::RVec >	positionsFromStatePointer (const t_state *state)
	Returns an arrayRef to the positions in state when state!=null. More...
void	printLambdaStateToLog (FILE *fplog, gmx::ArrayRef< const real > lambda, bool isInitialOutput)
	Prints the current lambda state to the log file. More...
void	initialize_lambdas (FILE *fplog, FreeEnergyPerturbationType freeEnergyPerturbationType, bool haveSimulatedTempering, const t_lambda &fep, gmx::ArrayRef< const real > simulatedTemperingTemps, gmx::ArrayRef< real > ref_t, bool isMaster, int *fep_state, gmx::ArrayRef< real > lambda)
	Fills fep_state and lambda if needed. More...

Enumeration Type Documentation

enum StateEntry : int

strong

Enum for all entries in t_state.

These enums are used in flags as (1<<est...). The order of these enums should not be changed, since that affects the checkpoint (.cpt) file format.

Function Documentation

template<typename Enum >

int enumValueToBitMask ( Enum  enumValue )

inline

Convert enum to bitmask value.

Used for setting flags in checkpoint header and verifying which flags are set.

void initialize_lambdas	(	FILE *	fplog,
		FreeEnergyPerturbationType	freeEnergyPerturbationType,
		bool	haveSimulatedTempering,
		const t_lambda &	fep,
		gmx::ArrayRef< const real >	simulatedTemperingTemps,
		gmx::ArrayRef< real >	ref_t,
		bool	isMaster,
		int *	fep_state,
		gmx::ArrayRef< real >	lambda
	)

Fills fep_state and lambda if needed.

If FEP or simulated tempering is in use, fills fep_state and lambda on master rank.

Reports the initial lambda state to the log file.

static gmx::ArrayRef<const gmx::RVec> positionsFromStatePointer ( const t_state *  state )

inlinestatic

Returns an arrayRef to the positions in state when state!=null.

When state=nullptr, returns an empty arrayRef.

Note

The size returned is the number of atoms, without padding.

Parameters

[in]

state

The state, can be nullptr

void preserve_box_shape	(	const t_inputrec *	ir,
		matrix	box_rel,
		matrix	box
	)

Make sure the relative box shape remains the same.

This function ensures that the relative box dimensions are preserved, which otherwise might diffuse away due to rounding errors in pressure coupling or the deform option.

Parameters

[in]	ir	Input record
[in]	box_rel	Relative box dimensions
[in,out]	box	The corrected actual box dimensions

void printLambdaStateToLog	(	FILE *	fplog,
		gmx::ArrayRef< const real >	lambda,
		bool	isInitialOutput
	)

Prints the current lambda state to the log file.

Parameters

[in]	fplog	The log file. If fplog == nullptr there will be no output.
[in]	lambda	The array of lambda values.
[in]	isInitialOutput	Whether this output is the initial lambda state or not.

void set_box_rel	(	const t_inputrec *	ir,
		t_state *	state
	)

Determine the relative box components.

Set box_rel e.g. used in mdrun state, used to preserve the box shape

Parameters

[in]	ir	Input record
[in,out]	state	State