#include "gmxpre.h"
#include "imd.h"
#include "config.h"
#include <errno.h>
#include <string.h>
#include <unistd.h>
#include "gromacs/commandline/filenm.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/ga2la.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/imd/imdsocket.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/broadcaststructs.h"
#include "gromacs/mdlib/groupcoord.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/sighandler.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"

Include dependency graph for imd.cpp:

Description

Implements functions of imd.h.

Re-implementation of basic IMD functions from NAMD/VMD from scratch, see imdsocket.h for references to the IMD API.

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

Classes
struct	IMDEnergyBlock
	IMD (interactive molecular dynamics) energy record. More...

struct	IMDHeader
	IMD (interactive molecular dynamics) communication structure. More...

struct	t_gmx_IMD
	IMD (interactive molecular dynamics) main data structure. More...

Macros
#define	IMDLOOPWAIT 1
	How long shall we wait in seconds until we check for a connection again?

#define	IMDCONNECTWAIT 2
	How long shall we check for the IMD_GO?

#define	HEADERSIZE 8
	IMD Header Size.

#define	IMDVERSION 2
	IMD Protocol Version.

Typedefs
typedef struct t_gmx_IMD	t_gmx_IMD_setup
	IMD (interactive molecular dynamics) main data structure. More...

typedef enum IMDType_t	IMDMessageType
	Enum for types of IMD messages. More...

Enumerations
enum	IMDType_t { IMD_DISCONNECT, IMD_ENERGIES, IMD_FCOORDS, IMD_GO, IMD_HANDSHAKE, IMD_KILL, IMD_MDCOMM, IMD_PAUSE, IMD_TRATE, IMD_IOERROR, IMD_NR }
	Enum for types of IMD messages. More...

Functions
static void	fill_header (IMDHeader *header, IMDMessageType type, gmx_int32_t length)
	Fills the header with message and the length argument.

static void	swap_header (IMDHeader *header)
	Swaps the endianess of the header.

static gmx_int32_t	imd_read_multiple (IMDSocket socket, char datptr, gmx_int32_t toread)
	Reads multiple bytes from socket.

static gmx_int32_t	imd_write_multiple (IMDSocket socket, const char datptr, gmx_int32_t towrite)
	Writes multiple bytes to socket in analogy to imd_read_multiple.

static int	imd_handshake (IMDSocket *socket)
	Handshake with IMD client.

static int	imd_send_energies (IMDSocket socket, const IMDEnergyBlock energies, char *buffer)
	Send energies using the energy block and the send buffer.

static IMDMessageType	imd_recv_header (IMDSocket socket, gmx_int32_t length)
	Receive IMD header from socket, sets the length and returns the IMD message.

static int	imd_recv_mdcomm (IMDSocket socket, gmx_int32_t nforces, gmx_int32_t forcendx, float *forces)
	Receive force indices and forces. More...

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...

static int	imd_send_rvecs (IMDSocket socket, int nat, rvec x, char *buffer)
	Send positions from rvec. More...

static t_gmx_IMD_setup *	imd_create (int imdatoms, int nstimddef, int imdport)
	Initializes the IMD private data.

static void	imd_prepare_master_socket (t_gmx_IMD_setup *IMDsetup)
	Prepare the socket on the MASTER.

static void	imd_disconnect (t_gmx_IMD_setup *IMDsetup)
	Disconnect the client.

static void	imd_fatal (t_gmx_IMD_setup IMDsetup, const char msg)
	Prints an error message and disconnects the client. More...

static gmx_bool	imd_tryconnect (t_gmx_IMD_setup *IMDsetup)
	Check whether we got an incoming connection.

static void	imd_blockconnect (t_gmx_IMD_setup *IMDsetup)
	Wrap imd_tryconnect in order to make it blocking. More...

static void	imd_prepare_vmd_Forces (t_gmx_IMD_setup *IMDsetup)
	Make sure that our array holding the forces received via IMD is large enough.

static void	imd_read_vmd_Forces (t_gmx_IMD_setup *IMDsetup)
	Reads forces received via IMD.

static void	imd_prepare_MD_Forces (t_gmx_IMD_setup *IMDsetup)
	Prepares the MD force arrays.

static void	imd_copyto_MD_Forces (t_gmx_IMD_setup *IMDsetup)
	Copy IMD forces to MD forces. More...

static gmx_bool	bForcesChanged (t_gmx_IMD_setup *IMDsetup)
	Return TRUE if any of the forces or indices changed.

static void	keep_old_values (t_gmx_IMD_setup *IMDsetup)
	Fill the old_f_ind and old_forces arrays with the new, old values.

static gmx_bool	rvecs_differ (const rvec v1, const rvec v2)
	Returns TRUE if any component of the two rvecs differs.

static void	output_imd_forces (t_inputrec *ir, double time)
	Write the applied pull forces to logfile. More...

static void	imd_sync_nodes (t_inputrec ir, t_commrec cr, double t)
	Synchronize the nodes.

static void	imd_readcommand (t_gmx_IMD_setup *IMDsetup)
	Reads header from the client and decides what to do.

static FILE *	open_imd_out (const char fn, t_gmx_IMD_setup IMDsetup, int nat_total, const gmx_output_env_t *oenv, const ContinuationOptions &continuationOptions)
	Open IMD output file and write header information. More...

void	IMD_finalize (gmx_bool bIMD, t_IMD *imd)
	Finalize IMD and do some cleaning up. More...

static void	init_imd_prepare_mols_in_imdgroup (t_gmx_IMD_setup IMDsetup, gmx_mtop_t top_global)
	Creates the molecule start-end position array of molecules in the IMD group.

static void	shift_positions (matrix box, rvec x[], ivec is, int nr)
	Copied and modified from groupcoord.c shift_positions_group().

static void	imd_remove_molshifts (t_gmx_IMD_setup *IMDsetup, matrix box)
	Removes shifts of molecules diffused outside of the box.

static void	init_imd_prepare_for_x_assembly (t_commrec cr, rvec x[], t_gmx_IMD_setup IMDsetup)
	Initialize arrays used to assemble the positions from the other nodes.

static void	imd_check_integrator_parallel (t_inputrec ir, t_commrec cr)
	Check for non-working integrator / parallel options.

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...

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...

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...

Variables
const char *	eIMDType_names [IMD_NR+1]
	Names of the IMDType for error messages. More...

Typedef Documentation

typedef enum IMDType_t IMDMessageType

Enum for types of IMD messages.

We use the same records as the NAMD/VMD IMD implementation.

typedef struct t_gmx_IMD t_gmx_IMD_setup

IMD (interactive molecular dynamics) main data structure.

Contains private IMD data

Enumeration Type Documentation

enum IMDType_t

Enum for types of IMD messages.

We use the same records as the NAMD/VMD IMD implementation.

Enumerator
IMD_DISCONNECT	client disconnect
IMD_ENERGIES	energy data
IMD_FCOORDS	atomic coordinates
IMD_GO	start command for the simulation
IMD_HANDSHAKE	handshake to determine little/big endianness
IMD_KILL	terminates the simulation
IMD_MDCOMM	force data
IMD_PAUSE	pauses the simulation
IMD_TRATE	sets the IMD transmission and processing rate
IMD_IOERROR	I/O error.
IMD_NR	number of entries

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.

static void imd_blockconnect ( t_gmx_IMD_setup * IMDsetup )

static

Wrap imd_tryconnect in order to make it blocking.

Used when the simulation should wait for an incoming connection.

static void imd_copyto_MD_Forces ( t_gmx_IMD_setup * IMDsetup )

static

Copy IMD forces to MD forces.

Do conversion from Cal->Joule and from Angstrom -> nm and from a pointer array to arrays to 3*N array.

static void imd_fatal	(	t_gmx_IMD_setup *	IMDsetup,
		const char *	msg
	)

static

Prints an error message and disconnects the client.

Does not terminate mdrun!

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.

static int imd_recv_mdcomm	(	IMDSocket *	socket,
		gmx_int32_t	nforces,
		gmx_int32_t *	forcendx,
		float *	forces
	)

static

Receive force indices and forces.

The number of forces was previously communicated via the header.

void IMD_send_positions ( t_IMD * imd )

Send positions and energies to the client.

Parameters

imd	The IMD data structure.

static int imd_send_rvecs	(	IMDSocket *	socket,
		int	nat,
		rvec *	x,
		char *	buffer
	)

static

Send positions from rvec.

We need a separate send buffer and conversion to Angstrom.

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.

static FILE* open_imd_out	(	const char *	fn,
		t_gmx_IMD_setup *	IMDsetup,
		int	nat_total,
		const gmx_output_env_t *	oenv,
		const ContinuationOptions &	continuationOptions
	)

static

Open IMD output file and write header information.

Call on master only.

static void output_imd_forces	(	t_inputrec *	ir,
		double	time
	)

static

Write the applied pull forces to logfile.

Call on master only!

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* eIMDType_names[IMD_NR+1]

Initial value:

= {
    "IMD_DISCONNECT",
    "IMD_ENERGIES",
    "IMD_FCOORDS",
    "IMD_GO",
    "IMD_HANDSHAKE",
    "IMD_KILL",
    "IMD_MDCOMM",
    "IMD_PAUSE",
    "IMD_TRATE",
    "IMD_IOERROR",
    nullptr
}

Names of the IMDType for error messages.

Description

Classes

Macros

Typedefs

Enumerations

Functions

Variables

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation