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/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"

Include dependency graph for state.h:

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	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
typedef struct df_history_t	df_history_t
	Free-energy sampling history struct. More...

Enumerations
enum	{   estLAMBDA, estBOX, estBOX_REL, estBOXV,   estPRES_PREV, estNH_XI, estTHERM_INT, estX,   estV, estSDX_NOTSUPPORTED, estCGP, estLD_RNG_NOTSUPPORTED,   estLD_RNGI_NOTSUPPORTED, estDISRE_INITF, estDISRE_RM3TAV, estORIRE_INITF,   estORIRE_DTAV, estSVIR_PREV, estNH_VXI, estVETA,   estVOL0, estNHPRES_XI, estNHPRES_VXI, estFVIR_PREV,   estFEPSTATE, estMC_RNG_NOTSUPPORTED, estMC_RNGI_NOTSUPPORTED, estBAROS_INT,   estPULLCOMPREVSTEP, estNR }

Functions
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, gmx_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...

Variables
const char *	est_names [estNR]
	The names of the state entries, defined in src/gmxlib/checkpoint.c.

Typedef Documentation

typedef struct df_history_t df_history_t

Free-energy sampling history struct.

Todo:

Split out into microstate and observables history.

Function Documentation

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 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