imd.h File Reference

#include "config.h"
#include <cstdio>
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"

Include dependency graph for imd.h:

Description

This file contains datatypes and function declarations necessary for mdrun to interface with VMD via the interactive molecular dynamics protocol.

Author

Martin Hoefling, Carsten Kutzner ckutz.nosp@m.ne@g.nosp@m.wdg.d.nosp@m.e

Functions
void	write_IMDgroup_to_file (gmx_bool bIMD, t_inputrec *ir, t_state *state, gmx_mtop_t *sys, int nfile, const t_filenm fnm[])
	Writes out the group of atoms selected for interactive manipulation. More...
void	dd_make_local_IMD_atoms (gmx_bool bIMD, gmx_domdec_t *dd, t_IMD *imd)
	Make a selection of the home atoms for the IMD group. More...
void	init_IMD (t_inputrec *ir, t_commrec *cr, gmx_mtop_t *top_global, FILE *fplog, int defnstimd, rvec x[], int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions)
	Initializes (or disables) IMD. More...
gmx_bool	do_IMD (gmx_bool bIMD, gmx_int64_t step, t_commrec *cr, gmx_bool bNS, matrix box, rvec x[], t_inputrec *ir, double t, gmx_wallcycle *wcycle)
	IMD required in this time step? Also checks for new IMD connection and syncs the nodes. More...
int	IMD_get_step (t_gmx_IMD *IMDsetup)
	Get the IMD update frequency. More...
void	IMD_apply_forces (gmx_bool bIMD, t_IMD *imd, t_commrec *cr, rvec *f, gmx_wallcycle *wcycle)
	Add external forces from a running interactive molecular dynamics session. More...
void	IMD_fill_energy_record (gmx_bool bIMD, t_IMD *imd, gmx_enerdata_t *enerd, gmx_int64_t step, gmx_bool bHaveNewEnergies)
	Copy energies and convert to float from enerdata to the IMD energy record. More...
void	IMD_send_positions (t_IMD *imd)
	Send positions and energies to the client. More...
void	IMD_prep_energies_send_positions (gmx_bool bIMD, gmx_bool bIMDstep, t_IMD *imd, gmx_enerdata_t *enerd, gmx_int64_t step, gmx_bool bHaveNewEnergies, gmx_wallcycle *wcycle)
	Calls IMD_prepare_energies() and then IMD_send_positions(). More...
void	IMD_finalize (gmx_bool bIMD, t_IMD *imd)
	Finalize IMD and do some cleaning up. More...

Variables
static const char	IMDstr [] = "IMD:"
	Tag output from the IMD module with this string. More...

Function Documentation

void dd_make_local_IMD_atoms	(	gmx_bool	bIMD,
		gmx_domdec_t *	dd,
		t_IMD *	imd
	)

Make a selection of the home atoms for the IMD group.

Should be called at every domain decomposition. Each node checks which of the atoms from "ind" are local and puts its local atom numbers into the "ind_local" array. Furthermore, in "xa_ind" it is stored at which position each local atom belongs in the assembled/collective array, so that on the master node all positions can be merged into the assembled array correctly.

Parameters

bIMD	Only springs into action if bIMD is TRUE. Otherwise returns directly.
dd	Structure containing domain decomposition data.
imd	The IMD group of atoms.

gmx_bool do_IMD	(	gmx_bool	bIMD,
		gmx_int64_t	step,
		t_commrec *	cr,
		gmx_bool	bNS,
		matrix	box,
		rvec	x[],
		t_inputrec *	ir,
		double	t,
		gmx_wallcycle *	wcycle
	)

IMD required in this time step? Also checks for new IMD connection and syncs the nodes.

Parameters

bIMD	Only springs into action if bIMD is TRUE. Otherwise returns directly.
step	The time step.
cr	Information structure for MPI communication.
bNS	Is this a neighbor searching step?
box	The simulation box.
x	The local atomic positions on this node.
ir	The inputrec structure containing the MD input parameters including a pointer to the IMD data structure.
t	The time.
wcycle	Count wallcycles of IMD routines for diagnostic output.

Returns

Whether or not we have to do IMD communication at this step.

void IMD_apply_forces	(	gmx_bool	bIMD,
		t_IMD *	imd,
		t_commrec *	cr,
		rvec *	f,
		gmx_wallcycle *	wcycle
	)

Add external forces from a running interactive molecular dynamics session.

Parameters

bIMD	Returns directly if bIMD is FALSE.
imd	The IMD data structure.
cr	Information structure for MPI communication.
f	The forces.
wcycle	Count wallcycles of IMD routines for diagnostic output.

void IMD_fill_energy_record	(	gmx_bool	bIMD,
		t_IMD *	imd,
		gmx_enerdata_t *	enerd,
		gmx_int64_t	step,
		gmx_bool	bHaveNewEnergies
	)

Copy energies and convert to float from enerdata to the IMD energy record.

We do no conversion, so units in client are SI!

Parameters

bIMD	Only springs into action if bIMD is TRUE. Otherwise returns directly.
imd	The IMD data structure.
enerd	Contains the GROMACS energies for the different interaction types.
step	The time step.
bHaveNewEnergies	Only copy energies if we have done global summing of them before.

void IMD_finalize	(	gmx_bool	bIMD,
		t_IMD *	imd
	)

Finalize IMD and do some cleaning up.

Currently, IMD finalize closes the force output file.

Parameters

bIMD	Returns directly if bIMD is FALSE.
imd	The IMD data structure.

int IMD_get_step

(

t_gmx_IMD *

IMDsetup

)

Get the IMD update frequency.

Parameters

IMDsetup

Opaque pointer to IMD private data.

Returns

The current IMD update/communication frequency

void IMD_prep_energies_send_positions	(	gmx_bool	bIMD,
		gmx_bool	bIMDstep,
		t_IMD *	imd,
		gmx_enerdata_t *	enerd,
		gmx_int64_t	step,
		gmx_bool	bHaveNewEnergies,
		gmx_wallcycle *	wcycle
	)

Calls IMD_prepare_energies() and then IMD_send_positions().

Parameters

bIMD	Returns directly if bIMD is FALSE.
bIMDstep	If true, transfer the positions. Otherwise just update the time step and potentially the energy record.
imd	The IMD data structure.
enerd	Contains the GROMACS energies for the different interaction types.
step	The time step.
bHaveNewEnergies	Only update the energy record if we have done global summing of the energies.
wcycle	Count wallcycles of IMD routines for diagnostic output.

void IMD_send_positions

(

t_IMD *

imd

)

Send positions and energies to the client.

Parameters

imd	The IMD data structure.

void init_IMD	(	t_inputrec *	ir,
		t_commrec *	cr,
		gmx_mtop_t *	top_global,
		FILE *	fplog,
		int	defnstimd,
		rvec	x[],
		int	nfile,
		const t_filenm	fnm[],
		const gmx_output_env_t *	oenv,
		const MdrunOptions &	mdrunOptions
	)

Initializes (or disables) IMD.

This function is called before the main MD loop over time steps, and it must be called prior to any call to dd_partition_system if in parallel.

Parameters

ir	The inputrec structure containing the MD input parameters including a pointer to the IMD data structure.
cr	Information structure for MPI communication.
top_global	The topology of the whole system.
fplog	General output file, normally md.log.
defnstimd	Default IMD update (=communication) frequency.
x	The starting positions of the atoms.
nfile	Number of files.
fnm	Struct containing file names etc.
oenv	Output options.
mdrunOptions	Options for mdrun.

void write_IMDgroup_to_file	(	gmx_bool	bIMD,
		t_inputrec *	ir,
		t_state *	state,
		gmx_mtop_t *	sys,
		int	nfile,
		const t_filenm	fnm[]
	)

Writes out the group of atoms selected for interactive manipulation.

Called by grompp. The resulting file has to be read in by VMD if one wants it to connect to mdrun.

Parameters

bIMD	Only springs into action if bIMD is TRUE. Otherwise returns directly.
ir	Structure containing MD input parameters, among those the IMD data structure.
state	The current state of the MD system.
sys	The global, complete system topology.
nfile	Number of files.
fnm	Filename struct.

Variable Documentation

const char IMDstr[] = "IMD:"

static

Tag output from the IMD module with this string.