gmx::ImdSession::Impl Class Reference

Collaboration diagram for gmx::ImdSession::Impl:

Description

Implementation type for the IMD session.

Todo:

Make this class (or one extracted from it) model IForceProvider.

Use RAII for files and allocations

Public Member Functions
	Impl (const MDLogger &mdlog, const MpiComm &mpiComm, const gmx_domdec_t *dd)
	Constructor.
void	prepareMainSocket ()
	Prepare the socket on the MAIN.
void	disconnectClient ()
	Disconnect the client.
void	issueFatalError (const char *msg)
	Prints an error message and disconnects the client. More...
bool	tryConnect ()
	Check whether we got an incoming connection.
void	blockConnect ()
	Wrap imd_tryconnect in order to make it blocking. More...
void	prepareVmdForces ()
	Make sure that our array holding the forces received via IMD is large enough.
void	readVmdForces ()
	Reads forces received via IMD.
void	prepareMDForces ()
	Prepares the MD force arrays.
void	copyToMDForces () const
	Copy IMD forces to MD forces. More...
bool	bForcesChanged () const
	Return true if any of the forces or indices changed.
void	keepOldValues ()
	Update the old_f_ind and old_forces arrays to contain the current values.
void	outputForces (double time)
	Write the applied pull forces to logfile. More...
void	syncNodes (double t)
	Synchronize the nodes.
void	readCommand ()
	Reads header from the client and decides what to do.
void	openOutputFile (const char *fn, int nat_total, const gmx_output_env_t *oenv, StartingBehavior startingBehavior)
	Open IMD output file and write header information. More...
void	prepareMoleculesInImdGroup (const gmx_mtop_t &top_global)
	Creates the molecule start-end position array of molecules in the IMD group.
void	removeMolecularShifts (const matrix box) const
	Removes shifts of molecules diffused outside of the box.
void	prepareForPositionAssembly (gmx::ArrayRef< const gmx::RVec > coords)
	Initialize arrays used to assemble the positions from the other nodes.
bool	run (int64_t step, bool bNS, const matrix box, gmx::ArrayRef< const gmx::RVec > coords, double t)
	Interact with any connected VMD session.

Public Attributes
bool	sessionPossible = false
	True if tpr and mdrun input combine to permit IMD sessions.
FILE *	outf = nullptr
	Output file for IMD data, mainly forces.
int	nat = 0
	Number of atoms that can be pulled via IMD.
int	nat_loc = 0
	Part of the atoms that are local.
int *	ind = nullptr
	Global indices of the IMD atoms.
int *	ind_loc = nullptr
	Local indices of the IMD atoms.
int	nalloc_loc = 0
	Allocation size for ind_loc.
rvec *	xa = nullptr
	Positions for all IMD atoms assembled on the main node.
ivec *	xa_shifts = nullptr
	Shifts for all IMD atoms, to make molecule(s) whole.
ivec *	xa_eshifts = nullptr
	Extra shifts since last DD step.
rvec *	xa_old = nullptr
	Old positions for all IMD atoms on main.
int *	xa_ind = nullptr
	Position of each local atom in the collective array.
int	nstimd = 1
	Global IMD frequency, known to all ranks.
int	nstimd_new = 1
	New frequency from IMD client, main only.
int	defaultNstImd = -1
	Default IMD frequency when disconnected.
int	port = 0
	Port to use for network socket.
IMDSocket *	socket = nullptr
	The IMD socket on the main node.
IMDSocket *	clientsocket = nullptr
	The IMD socket on the client.
int	length = 0
	Length we got with last header.
bool	bWConnect = false
	Shall we block and wait for connection?
bool	bTerminatable = false
	Set if MD can be terminated.
bool	bConnected = false
	Set if connection is present.
bool	bNewForces = false
	Set if we received new forces.
bool	bForceActivated = false
	Set if pulling from VMD is allowed.
IMDEnergyBlock *	energies = nullptr
	Pointer to energies we send back.
int32_t	vmd_nforces = 0
	Number of VMD forces.
int32_t *	vmd_f_ind = nullptr
	VMD forces indices.
float *	vmd_forces = nullptr
	The VMD forces flat in memory.
int	nforces = 0
	Number of actual MD forces; this gets communicated to the clients.
int *	f_ind = nullptr
	Force indices.
rvec *	f = nullptr
	The IMD pulling forces.
char *	coordsendbuf = nullptr
	Buffer for coordinate sending.
char *	energysendbuf = nullptr
	Send buffer for energies.
rvec *	sendxbuf = nullptr
	Buffer to make molecules whole before sending.
t_block	mols
	Molecules block in IMD group.
int	old_nforces = 0
	Old value for nforces.
int *	old_f_ind = nullptr
	Old values for force indices.
rvec *	old_forces = nullptr
	Old values for IMD pulling forces.
const MDLogger &	mdLog_
	Logger.
const MpiComm &	mpiComm_
	Commmunication object.
const gmx_domdec_t *	dd_ = nullptr
	Domain decomposition object.
gmx_wallcycle *	wcycle = nullptr
	Wallcycle counting manager.
gmx_enerdata_t *	enerd = nullptr
	Energy output handler.

Member Function Documentation

void gmx::ImdSession::Impl::blockConnect

(

)

Wrap imd_tryconnect in order to make it blocking.

Used when the simulation should wait for an incoming connection.

void gmx::ImdSession::Impl::copyToMDForces

(

)

const

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.

void gmx::ImdSession::Impl::issueFatalError

(

const char *

msg

)

Prints an error message and disconnects the client.

Does not terminate mdrun!

void gmx::ImdSession::Impl::openOutputFile	(	const char *	fn,
		int	nat_total,
		const gmx_output_env_t *	oenv,
		const gmx::StartingBehavior	startingBehavior
	)

Open IMD output file and write header information.

Call on main only.

void gmx::ImdSession::Impl::outputForces

(

double

time

)

Write the applied pull forces to logfile.

Call on main only!

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The documentation for this class was generated from the following file:

• src/gromacs/imd/imd.cpp