imd.cpp File Reference

#include "gmxpre.h"
#include "imd.h"
#include "config.h"
#include <cerrno>
#include <cstdio>
#include <cstring>
#include <array>
#include <filesystem>
#include <string>
#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/sighandler.h"
#include "gromacs/mdlib/stat.h"
#include "gromacs/mdrunutility/handlerestart.h"
#include "gromacs/mdrunutility/multisim.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/imdmodule.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdrunoptions.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"

Include dependency graph for imd.cpp:

Description

Implements Interactive Molecular Dynamics.

Re-implementation of basic IMD functions to work with VMD, 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	gmx::IMDEnergyBlock
	IMD (interactive molecular dynamics) energy record. More...
struct	gmx::IMDHeader
	IMD (interactive molecular dynamics) communication structure. More...
class	gmx::ImdSession::Impl
	Implementation type for the IMD session. More...
class	gmx::InteractiveMolecularDynamics
	Implement interactive molecular dynamics. More...

Enumerations
enum	gmx::IMDMessageType : int {   gmx::IMDMessageType::Disconnect, gmx::IMDMessageType::Energies, gmx::IMDMessageType::FCoords, gmx::IMDMessageType::Go,   gmx::IMDMessageType::Handshake, gmx::IMDMessageType::Kill, gmx::IMDMessageType::Mdcomm, gmx::IMDMessageType::Pause,   gmx::IMDMessageType::TRate, gmx::IMDMessageType::IOerror, gmx::IMDMessageType::Count }
	Enum for types of IMD messages. More...

Functions
std::unique_ptr< IMDModule >	gmx::createInteractiveMolecularDynamicsModule ()
	Creates a module for interactive molecular dynamics.
static const char *	gmx::enumValueToString (IMDMessageType enumValue)
	Names of the IMDType for error messages.
static void	gmx::fill_header (IMDHeader *header, IMDMessageType type, int32_t length)
	Fills the header with message and the length argument.
static void	gmx::swap_header (IMDHeader *header)
	Swaps the endianess of the header.
static int32_t	gmx::imd_read_multiple (IMDSocket *socket, char *datptr, int32_t toread)
	Reads multiple bytes from socket.
static int32_t	gmx::imd_write_multiple (IMDSocket *socket, const char *datptr, int32_t towrite)
	Writes multiple bytes to socket in analogy to imd_read_multiple.
static int	gmx::imd_handshake (IMDSocket *socket)
	Handshake with IMD client.
static int	gmx::imd_send_energies (IMDSocket *socket, const IMDEnergyBlock *energies, char *buffer)
	Send energies using the energy block and the send buffer.
static IMDMessageType	gmx::imd_recv_header (IMDSocket *socket, int32_t *length)
	Receive IMD header from socket, sets the length and returns the IMD message.
static bool	gmx::imd_recv_mdcomm (IMDSocket *socket, int32_t nforces, int32_t *forcendx, float *forces)
	Receive force indices and forces. More...
void	gmx::write_IMDgroup_to_file (bool bIMD, t_inputrec *ir, const t_state *state, const gmx_mtop_t &sys, int nfile, const t_filenm fnm[])
	Writes out the group of atoms selected for interactive manipulation. More...
static int	gmx::imd_send_rvecs (IMDSocket *socket, int nat, rvec *x, char *buffer)
	Send positions from rvec. More...
static bool	gmx::rvecs_differ (const rvec v1, const rvec v2)
	Returns true if any component of the two rvecs differs.
static void	gmx::shift_positions (const matrix box, rvec x[], const ivec is, int nr)
	Copied and modified from groupcoord.c shift_positions_group().
static void	gmx::imd_check_integrator_parallel (const t_inputrec *ir, const t_commrec *cr)
	Check for non-working integrator / parallel options.
std::unique_ptr< ImdSession >	gmx::makeImdSession (const t_inputrec *ir, const t_commrec *cr, gmx_wallcycle *wcycle, gmx_enerdata_t *enerd, const gmx_multisim_t *ms, const gmx_mtop_t &top_global, const MDLogger &mdlog, gmx::ArrayRef< const gmx::RVec > coords, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const ImdOptions &options, StartingBehavior startingBehavior)
	Makes and returns an initialized IMD session, which may be inactive. More...

Variables
constexpr int	gmx::c_loopWait = 1
	How long shall we wait in seconds until we check for a connection again?
constexpr int	gmx::c_connectWait = 1
	How long shall we check for the IMD_GO?
constexpr int	gmx::c_headerSize = 8
	IMD Header Size.
constexpr int	gmx::c_protocolVersion = 2
	IMD Protocol Version.