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39 * Implements functions of imd.h.
41 * Re-implementation of basic IMD functions from NAMD/VMD from scratch,
42 * see imdsocket.h for references to the IMD API.
44 * \author Martin Hoefling, Carsten Kutzner <ckutzne@gwdg.de>
56 #ifdef GMX_NATIVE_WINDOWS
63 #include "imdsocket.h"
66 #include "sighandler.h"
67 #include "gmx_ga2la.h"
68 #include "gromacs/mdlib/groupcoord.h"
69 #include "gromacs/fileio/confio.h"
70 #include "gromacs/topology/mtop_util.h"
72 #include "gromacs/timing/wallcycle.h"
74 #include "gromacs/fileio/xvgr.h"
75 #include "gromacs/math/vec.h"
76 #include "gromacs/pbcutil/pbc.h"
77 #include "gromacs/utility/fatalerror.h"
78 #include "gromacs/utility/smalloc.h"
80 /*! \brief How long shall we wait in seconds until we check for a connection again? */
83 /*! \brief How long shall we check for the IMD_GO? */
84 #define IMDCONNECTWAIT 2
86 /*! \brief IMD Header Size. */
88 /*! \brief IMD Protocol Version. */
91 /*! \brief Broadcast d to all nodes */
92 #define block_bc(cr, d) gmx_bcast(sizeof(d), &(d), (cr))
94 /*! \brief Broadcast nr elements of d to all nodes */
95 #define nblock_bc(cr, nr, d) gmx_bcast((nr)*sizeof((d)[0]), (d), (cr))
100 * IMD (interactive molecular dynamics) energy record.
102 * As in the original IMD implementation. Energies in kcal/mol.
103 * NOTE: We return the energies in GROMACS / SI units,
104 * so they also show up as SI in VMD.
109 gmx_int32_t tstep; /**< time step */
110 float T_abs; /**< absolute temperature */
111 float E_tot; /**< total energy */
112 float E_pot; /**< potential energy */
113 float E_vdw; /**< van der Waals energy */
114 float E_coul; /**< Coulomb interaction energy */
115 float E_bond; /**< bonds energy */
116 float E_angle; /**< angles energy */
117 float E_dihe; /**< dihedrals energy */
118 float E_impr; /**< improper dihedrals energy */
123 * \brief IMD (interactive molecular dynamics) communication structure.
125 * This structure defines the IMD communication message header & protocol version.
129 gmx_int32_t type; /**< Type of IMD message, see IMDType_t above */
130 gmx_int32_t length; /**< Length */
135 * \brief IMD (interactive molecular dynamics) main data structure.
137 * Contains private IMD data
139 typedef struct gmx_IMD
141 FILE *outf; /**< Output file for IMD data, mainly forces. */
143 int nat; /**< Number of atoms that can be pulled via IMD. */
144 int nat_loc; /**< Part of the atoms that are local. */
145 atom_id *ind; /**< Global indices of the IMD atoms. */
146 atom_id *ind_loc; /**< Local indices of the IMD atoms. */
147 int nalloc_loc; /**< Allocation size for ind_loc. */
148 rvec *xa; /**< Positions for all IMD atoms assembled on
150 ivec *xa_shifts; /**< Shifts for all IMD atoms, to make
151 molecule(s) whole. */
152 ivec *xa_eshifts; /**< Extra shifts since last DD step. */
153 rvec *xa_old; /**< Old positions for all IMD atoms on master. */
154 int *xa_ind; /**< Position of each local atom in the
157 int nstimd; /**< Global IMD frequency, known to all nodes. */
158 int nstimd_new; /**< New frequency from IMD client, master only. */
159 int nstimd_def; /**< Default IMD frequency when disconnected. */
161 int port; /**< Port to use for network socket. */
162 IMDSocket *socket; /**< The IMD socket on the master node. */
163 IMDSocket *clientsocket; /**< The IMD socket on the client. */
164 int length; /**< Length we got with last header. */
166 gmx_bool bWConnect; /**< Shall we block and wait for connection? */
167 gmx_bool bTerminated; /**< Set if MD is terminated. */
168 gmx_bool bTerminatable; /**< Set if MD can be terminated. */
169 gmx_bool bConnected; /**< Set if connection is present. */
170 gmx_bool bNewForces; /**< Set if we received new forces. */
171 gmx_bool bForceActivated; /**< Set if pulling from VMD is allowed. */
173 IMDEnergyBlock *energies; /**< Pointer to energies we send back. */
175 gmx_int32_t vmd_nforces; /**< Number of VMD forces. */
176 gmx_int32_t *vmd_f_ind; /**< VMD forces indices. */
177 float *vmd_forces; /**< The VMD forces flat in memory. */
178 int nforces; /**< Number of actual MD forces;
179 this gets communicated to the clients. */
180 atom_id *f_ind; /**< Force indices. */
181 rvec *f; /**< The IMD pulling forces. */
183 char *forcesendbuf; /**< Buffer for force sending. */
184 char *coordsendbuf; /**< Buffer for coordinate sending. */
185 char *energysendbuf; /**< Send buffer for energies. */
186 rvec *sendxbuf; /**< Buffer to make molecules whole before
189 t_block mols; /**< Molecules block in IMD group. */
191 /* The next block is used on the master node only to reduce the output
192 * without sacrificing information. If any of these values changes,
193 * we need to write output */
194 int old_nforces; /**< Old value for nforces. */
195 atom_id *old_f_ind; /**< Old values for force indices. */
196 rvec *old_forces; /**< Old values for IMD pulling forces. */
202 * \brief Enum for types of IMD messages.
204 * We use the same records as the NAMD/VMD IMD implementation.
206 typedef enum IMDType_t
208 IMD_DISCONNECT, /**< client disconnect */
209 IMD_ENERGIES, /**< energy data */
210 IMD_FCOORDS, /**< atomic coordinates */
211 IMD_GO, /**< start command for the simulation */
212 IMD_HANDSHAKE, /**< handshake to determine little/big endianness */
213 IMD_KILL, /**< terminates the simulation */
214 IMD_MDCOMM, /**< force data */
215 IMD_PAUSE, /**< pauses the simulation */
216 IMD_TRATE, /**< sets the IMD transmission and processing rate */
217 IMD_IOERROR, /**< I/O error */
218 IMD_NR /**< number of entries */
223 * \brief Names of the IMDType for error messages.
225 const char *eIMDType_names[IMD_NR + 1] = {
242 /*! \brief Fills the header with message and the length argument. */
243 static void fill_header(IMDHeader *header, IMDMessageType type, gmx_int32_t length)
245 /* We (ab-)use htonl network function for the correct endianness */
246 header->type = htonl((gmx_int32_t) type);
247 header->length = htonl(length);
251 /*! \brief Swaps the endianess of the header. */
252 static void swap_header(IMDHeader *header)
254 /* and vice versa... */
255 header->type = ntohl(header->type);
256 header->length = ntohl(header->length);
260 /*! \brief Reads multiple bytes from socket. */
261 static gmx_int32_t imd_read_multiple(IMDSocket *socket, char *datptr, gmx_int32_t toread)
263 gmx_int32_t leftcount, countread;
267 /* Try to read while we haven't reached toread */
268 while (leftcount != 0)
270 if ((countread = imdsock_read(socket, datptr, leftcount)) < 0)
272 /* interrupted function call, try again... */
277 /* this is an unexpected error, return what we got */
280 return toread - leftcount;
283 /* nothing read, finished */
285 else if (countread == 0)
289 leftcount -= countread;
293 /* return nr of bytes read */
294 return toread - leftcount;
298 /*! \brief Writes multiple bytes to socket in analogy to imd_read_multiple. */
299 static gmx_int32_t imd_write_multiple(IMDSocket *socket, const char *datptr, gmx_int32_t towrite)
301 gmx_int32_t leftcount, countwritten;
305 while (leftcount != 0)
307 if ((countwritten = imdsock_write(socket, datptr, leftcount)) <= 0)
315 return towrite - leftcount;
318 leftcount -= countwritten;
319 datptr += countwritten;
322 return towrite - leftcount;
326 /*! \brief Handshake with IMD client. */
327 static int imd_handshake(IMDSocket *socket)
332 fill_header(&header, IMD_HANDSHAKE, 1);
333 header.length = IMDVERSION; /* client wants unswapped version */
335 return (imd_write_multiple(socket, (char *) &header, HEADERSIZE) != HEADERSIZE);
339 /*! \brief Send energies using the energy block and the send buffer. */
340 static int imd_send_energies(IMDSocket *socket, const IMDEnergyBlock *energies, char *buffer)
345 recsize = HEADERSIZE + sizeof(IMDEnergyBlock);
346 fill_header((IMDHeader *) buffer, IMD_ENERGIES, 1);
347 memcpy(buffer + HEADERSIZE, energies, sizeof(IMDEnergyBlock));
349 return (imd_write_multiple(socket, buffer, recsize) != recsize);
353 /*! \brief Receive IMD header from socket, sets the length and returns the IMD message. */
354 static IMDMessageType imd_recv_header(IMDSocket *socket, gmx_int32_t *length)
359 if (imd_read_multiple(socket, (char *) &header, HEADERSIZE) != HEADERSIZE)
363 swap_header(&header);
364 *length = header.length;
366 return (IMDMessageType) header.type;
370 /*! \brief Receive force indices and forces.
372 * The number of forces was previously communicated via the header.
374 static int imd_recv_mdcomm(IMDSocket *socket, gmx_int32_t nforces, gmx_int32_t *forcendx, float *forces)
376 int retsize, retbytes;
379 /* reading indices */
380 retsize = sizeof(gmx_int32_t) * nforces;
381 retbytes = imd_read_multiple(socket, (char *) forcendx, retsize);
382 if (retbytes != retsize)
387 /* reading forces as float array */
388 retsize = 3 * sizeof(float) * nforces;
389 retbytes = imd_read_multiple(socket, (char *) forces, retsize);
390 if (retbytes != retsize)
400 /* GROMACS specific functions for the IMD implementation */
402 extern void write_IMDgroup_to_file(gmx_bool bIMD, t_inputrec *ir, t_state *state,
403 gmx_mtop_t *sys, int nfile, const t_filenm fnm[])
410 IMDatoms = gmx_mtop_global_atoms(sys);
411 write_sto_conf_indexed(opt2fn("-imd", nfile, fnm), "IMDgroup", &IMDatoms,
412 state->x, state->v, ir->ePBC, state->box, ir->imd->nat, ir->imd->ind);
417 extern void dd_make_local_IMD_atoms(gmx_bool bIMD, gmx_domdec_t *dd, t_IMD *imd)
420 t_gmx_IMD_setup *IMDsetup;
425 IMDsetup = imd->setup;
428 dd_make_local_group_indices(
429 ga2la, IMDsetup->nat, IMDsetup->ind, &IMDsetup->nat_loc,
430 &IMDsetup->ind_loc, &IMDsetup->nalloc_loc, IMDsetup->xa_ind);
436 /*! \brief Send positions from rvec.
438 * We need a separate send buffer and conversion to Angstrom.
440 static int imd_send_rvecs(IMDSocket *socket, int nat, rvec *x, char *buffer)
445 int tuplesize = 3 * sizeof(float);
448 /* Required size for the send buffer */
449 size = HEADERSIZE + 3 * sizeof(float) * nat;
452 fill_header((IMDHeader *) buffer, IMD_FCOORDS, (gmx_int32_t) nat);
453 for (i = 0; i < nat; i++)
455 sendx[0] = (float) x[i][0] * NM2A;
456 sendx[1] = (float) x[i][1] * NM2A;
457 sendx[2] = (float) x[i][2] * NM2A;
458 memcpy(buffer + HEADERSIZE + i * tuplesize, sendx, tuplesize);
461 return (imd_write_multiple(socket, buffer, size) != size);
465 /*! \brief Initializes the IMD private data. */
466 static t_gmx_IMD_setup* imd_create(int imdatoms, int nstimddef, int imdport)
468 t_gmx_IMD_setup *IMDsetup = NULL;
472 IMDsetup->nat = imdatoms;
473 IMDsetup->bTerminated = FALSE;
474 IMDsetup->bTerminatable = FALSE;
475 IMDsetup->bWConnect = FALSE;
476 IMDsetup->bConnected = FALSE;
477 IMDsetup->bForceActivated = FALSE;
478 IMDsetup->bNewForces = FALSE;
479 IMDsetup->bForceActivated = FALSE;
480 IMDsetup->nstimd = 1;
481 IMDsetup->nstimd_new = 1;
482 IMDsetup->nstimd_def = nstimddef;
486 fprintf(stderr, "%s You chose a port number < 1. Will automatically assign a free port.\n", IMDstr);
490 IMDsetup->port = imdport;
497 /*! \brief Prepare the socket on the MASTER. */
498 static void imd_prepare_master_socket(t_gmx_IMD_setup *IMDsetup)
503 #ifdef GMX_NATIVE_WINDOWS
504 /* Winsock requires separate initialization */
505 fprintf(stderr, "%s Initializing winsock.\n", IMDstr);
506 #ifdef GMX_HAVE_WINSOCK
507 if (imdsock_winsockinit())
509 gmx_fatal(FARGS, "%s Failed to initialize winsock.\n", IMDstr);
514 /* The rest is identical, first create and bind a socket and set to listen then. */
515 fprintf(stderr, "%s Setting up incoming socket.\n", IMDstr);
516 IMDsetup->socket = imdsock_create();
517 if (!IMDsetup->socket)
519 gmx_fatal(FARGS, "%s Failed to create socket.", IMDstr);
523 ret = imdsock_bind(IMDsetup->socket, IMDsetup->port);
526 gmx_fatal(FARGS, "%s binding socket to port %d failed with error %d.\n", IMDstr, IMDsetup->port, ret);
529 if (imd_sock_listen(IMDsetup->socket))
531 gmx_fatal(FARGS, "%s socket listen failed with error %d.\n", IMDstr, ret);
534 if (imdsock_getport(IMDsetup->socket, &IMDsetup->port))
536 gmx_fatal(FARGS, "%s Could not determine port number.\n", IMDstr, ret);
539 fprintf(stderr, "%s Listening for IMD connection on port %d.\n", IMDstr, IMDsetup->port);
543 /*! \brief Disconnect the client. */
544 static void imd_disconnect(t_gmx_IMD_setup *IMDsetup)
546 /* Write out any buffered pulling data */
547 fflush(IMDsetup->outf);
549 /* we first try to shut down the clientsocket */
550 imdsock_shutdown(IMDsetup->clientsocket);
551 if (!imdsock_destroy(IMDsetup->clientsocket))
553 fprintf(stderr, "%s Failed to destroy socket.\n", IMDstr);
556 /* then we reset the IMD step to its default, and reset the connection boolean */
557 IMDsetup->nstimd_new = IMDsetup->nstimd_def;
558 IMDsetup->clientsocket = NULL;
559 IMDsetup->bConnected = FALSE;
563 /*! \brief Prints an error message and disconnects the client.
565 * Does not terminate mdrun!
567 static void imd_fatal(t_gmx_IMD_setup *IMDsetup, const char *msg)
569 fprintf(stderr, "%s %s", IMDstr, msg);
570 imd_disconnect(IMDsetup);
571 fprintf(stderr, "%s disconnected.\n", IMDstr);
575 /*! \brief Check whether we got an incoming connection. */
576 static gmx_bool imd_tryconnect(t_gmx_IMD_setup *IMDsetup)
578 if (imdsock_tryread(IMDsetup->socket, 0, 0) > 0)
580 /* yes, we got something, accept on clientsocket */
581 IMDsetup->clientsocket = imdsock_accept(IMDsetup->socket);
582 if (!IMDsetup->clientsocket)
584 fprintf(stderr, "%s Accepting the connection on the socket failed.\n", IMDstr);
588 /* handshake with client */
589 if (imd_handshake(IMDsetup->clientsocket))
591 imd_fatal(IMDsetup, "Connection failed.\n");
595 fprintf(stderr, "%s Connection established, checking if I got IMD_GO orders.\n", IMDstr);
597 /* Check if we get the proper "GO" command from client. */
598 if (imdsock_tryread(IMDsetup->clientsocket, IMDCONNECTWAIT, 0) != 1 || imd_recv_header(IMDsetup->clientsocket, &(IMDsetup->length)) != IMD_GO)
600 imd_fatal(IMDsetup, "No IMD_GO order received. IMD connection failed.\n");
604 IMDsetup->bConnected = TRUE;
613 /*! \brief Wrap imd_tryconnect in order to make it blocking.
615 * Used when the simulation should wait for an incoming connection.
617 static void imd_blockconnect(t_gmx_IMD_setup *IMDsetup)
619 /* do not wait for connection, when e.g. ctrl+c is pressed and we will terminate anyways. */
620 if (!(int) gmx_get_stop_condition() == gmx_stop_cond_none)
625 fprintf(stderr, "%s Will wait until I have a connection and IMD_GO orders.\n", IMDstr);
627 /* while we have no clientsocket... 2nd part: we should still react on ctrl+c */
628 while ((!IMDsetup->clientsocket) && ((int) gmx_get_stop_condition() == gmx_stop_cond_none))
630 imd_tryconnect(IMDsetup);
631 #ifdef GMX_NATIVE_WINDOWS
632 /* for whatever reason, it is called Sleep on windows */
641 /*! \brief Make sure that our array holding the forces received via IMD is large enough. */
642 static void imd_prepare_vmd_Forces(t_gmx_IMD_setup *IMDsetup)
644 srenew((IMDsetup->vmd_f_ind), IMDsetup->vmd_nforces);
645 srenew((IMDsetup->vmd_forces), 3*IMDsetup->vmd_nforces);
649 /*! \brief Reads forces received via IMD. */
650 static void imd_read_vmd_Forces(t_gmx_IMD_setup *IMDsetup)
652 /* the length of the previously received header tells us the nr of forces we will receive */
653 IMDsetup->vmd_nforces = IMDsetup->length;
654 /* prepare the arrays */
655 imd_prepare_vmd_Forces(IMDsetup);
656 /* Now we read the forces... */
657 if (!(imd_recv_mdcomm(IMDsetup->clientsocket, IMDsetup->vmd_nforces, IMDsetup->vmd_f_ind, IMDsetup->vmd_forces)))
659 imd_fatal(IMDsetup, "Error while reading forces from remote. Disconnecting\n");
664 /*! \brief Prepares the MD force arrays. */
665 static void imd_prepare_MD_Forces(t_gmx_IMD_setup *IMDsetup)
667 srenew((IMDsetup->f_ind), IMDsetup->nforces);
668 srenew((IMDsetup->f ), IMDsetup->nforces);
672 /*! \brief Copy IMD forces to MD forces.
674 * Do conversion from Cal->Joule and from
675 * Angstrom -> nm and from a pointer array to arrays to 3*N array.
677 static void imd_copyto_MD_Forces(t_gmx_IMD_setup *IMDsetup)
680 real conversion = CAL2JOULE * NM2A;
683 for (i = 0; i < IMDsetup->nforces; i++)
685 /* Copy the indices, a copy is important because we may update the incoming forces
686 * whenever we receive new forces while the MD forces are only communicated upon
687 * IMD communication.*/
688 IMDsetup->f_ind[i] = IMDsetup->vmd_f_ind[i];
690 /* Convert to rvecs and do a proper unit conversion */
691 IMDsetup->f[i][0] = IMDsetup->vmd_forces[3*i ] * conversion;
692 IMDsetup->f[i][1] = IMDsetup->vmd_forces[3*i + 1] * conversion;
693 IMDsetup->f[i][2] = IMDsetup->vmd_forces[3*i + 2] * conversion;
698 /*! \brief Return TRUE if any of the forces or indices changed. */
699 static gmx_bool bForcesChanged(t_gmx_IMD_setup *IMDsetup)
704 /* First, check whether the number of pulled atoms changed */
705 if (IMDsetup->nforces != IMDsetup->old_nforces)
710 /* Second, check whether any of the involved atoms changed */
711 for (i = 0; i < IMDsetup->nforces; i++)
713 if (IMDsetup->f_ind[i] != IMDsetup->old_f_ind[i])
719 /* Third, check whether all forces are the same */
720 for (i = 0; i < IMDsetup->nforces; i++)
722 if (IMDsetup->f[i][XX] != IMDsetup->old_forces[i][XX])
726 if (IMDsetup->f[i][YY] != IMDsetup->old_forces[i][YY])
730 if (IMDsetup->f[i][ZZ] != IMDsetup->old_forces[i][ZZ])
736 /* All old and new forces are identical! */
741 /*! \brief Fill the old_f_ind and old_forces arrays with the new, old values. */
742 static void keep_old_values(t_gmx_IMD_setup *IMDsetup)
747 IMDsetup->old_nforces = IMDsetup->nforces;
749 for (i = 0; i < IMDsetup->nforces; i++)
751 IMDsetup->old_f_ind[i] = IMDsetup->f_ind[i];
752 copy_rvec(IMDsetup->f[i], IMDsetup->old_forces[i]);
757 /*! \brief Returns TRUE if any component of the two rvecs differs. */
758 static gmx_inline gmx_bool rvecs_differ(const rvec v1, const rvec v2)
763 for (i = 0; i < DIM; i++)
775 /*! \brief Write the applied pull forces to logfile.
777 * Call on master only!
779 static void output_imd_forces(t_inputrec *ir, double time)
781 t_gmx_IMD_setup *IMDsetup;
785 IMDsetup = ir->imd->setup;
787 if (bForcesChanged(IMDsetup))
789 /* Write time and total number of applied IMD forces */
790 fprintf(IMDsetup->outf, "%14.6e%6d", time, IMDsetup->nforces);
792 /* Write out the global atom indices of the pulled atoms and the forces itself,
793 * write out a force only if it has changed since the last output */
794 for (i = 0; i < IMDsetup->nforces; i++)
796 if (rvecs_differ(IMDsetup->f[i], IMDsetup->old_forces[i]))
798 fprintf(IMDsetup->outf, "%9d", IMDsetup->ind[IMDsetup->f_ind[i]] + 1);
799 fprintf(IMDsetup->outf, "%12.4e%12.4e%12.4e", IMDsetup->f[i][0], IMDsetup->f[i][1], IMDsetup->f[i][2]);
802 fprintf(IMDsetup->outf, "\n");
804 keep_old_values(IMDsetup);
809 /*! \brief Synchronize the nodes. */
810 static void imd_sync_nodes(t_inputrec *ir, t_commrec *cr, double t)
813 t_gmx_IMD_setup *IMDsetup;
817 IMDsetup = ir->imd->setup;
819 /* Notify the other nodes whether we are still connected. */
822 block_bc(cr, IMDsetup->bConnected);
825 /* ...if not connected, the job is done here. */
826 if (!IMDsetup->bConnected)
831 /* Let the other nodes know whether we got a new IMD synchronization frequency. */
834 block_bc(cr, IMDsetup->nstimd_new);
837 /* Now we all set the (new) nstimd communication time step */
838 IMDsetup->nstimd = IMDsetup->nstimd_new;
840 /* We're done if we don't allow pulling at all */
841 if (!(IMDsetup->bForceActivated))
846 /* OK, let's check if we have received forces which we need to communicate
847 * to the other nodes */
850 if (IMDsetup->bNewForces)
852 new_nforces = IMDsetup->vmd_nforces;
854 /* make the "new_forces" negative, when we did not receive new ones */
857 new_nforces = IMDsetup->vmd_nforces * -1;
861 /* make new_forces known to the clients */
864 block_bc(cr, new_nforces);
867 /* When new_natoms < 0 then we know that these are still the same forces
868 * so we don't communicate them, otherwise... */
869 if (new_nforces >= 0)
871 /* set local VMD and nforces */
872 IMDsetup->vmd_nforces = new_nforces;
873 IMDsetup->nforces = IMDsetup->vmd_nforces;
875 /* now everybody knows the number of forces in f_ind, so we can prepare
876 * the target arrays for indices and forces */
877 imd_prepare_MD_Forces(IMDsetup);
879 /* we first update the MD forces on the master by converting the VMD forces */
882 imd_copyto_MD_Forces(IMDsetup);
883 /* We also write out forces on every update, so that we know which
884 * forces are applied for every step */
887 output_imd_forces(ir, t);
891 /* In parallel mode we communicate the to-be-applied forces to the other nodes */
894 nblock_bc(cr, IMDsetup->nforces, IMDsetup->f_ind);
895 nblock_bc(cr, IMDsetup->nforces, IMDsetup->f );
898 /* done communicating the forces, reset bNewForces */
899 IMDsetup->bNewForces = FALSE;
904 /*! \brief Reads header from the client and decides what to do. */
905 static void imd_readcommand(t_gmx_IMD_setup *IMDsetup)
907 gmx_bool IMDpaused = FALSE;
908 IMDMessageType itype;
911 while (IMDsetup->clientsocket && (imdsock_tryread(IMDsetup->clientsocket, 0, 0) > 0 || IMDpaused))
913 itype = imd_recv_header(IMDsetup->clientsocket, &(IMDsetup->length));
914 /* let's see what we got: */
917 /* IMD asks us to terminate the simulation, check if the user allowed this */
919 if (IMDsetup->bTerminatable)
921 fprintf(stderr, " %s Terminating connection and running simulation (if supported by integrator).\n", IMDstr);
922 IMDsetup->bTerminated = TRUE;
923 IMDsetup->bWConnect = FALSE;
924 gmx_set_stop_condition(gmx_stop_cond_next);
928 fprintf(stderr, " %s Set -imdterm command line switch to allow mdrun termination from within IMD.\n", IMDstr);
933 /* the client doen't want to talk to us anymore */
935 fprintf(stderr, " %s Disconnecting client.\n", IMDstr);
936 imd_disconnect(IMDsetup);
939 /* we got new forces, read them and set bNewForces flag */
941 imd_read_vmd_Forces(IMDsetup);
942 IMDsetup->bNewForces = TRUE;
945 /* the client asks us to (un)pause the simulation. So we toggle the IMDpaused state */
949 fprintf(stderr, " %s Un-pause command received.\n", IMDstr);
954 fprintf(stderr, " %s Pause command received.\n", IMDstr);
960 /* the client sets a new transfer rate, if we get 0, we reset the rate
961 * to the default. VMD filters 0 however */
963 IMDsetup->nstimd_new = (IMDsetup->length > 0) ? IMDsetup->length : IMDsetup->nstimd_def;
964 fprintf(stderr, " %s Update frequency will be set to %d.\n", IMDstr, IMDsetup->nstimd_new);
967 /* Catch all rule for the remaining IMD types which we don't expect */
969 fprintf(stderr, " %s Received unexpected %s.\n", IMDstr, ENUM_NAME((int)itype, IMD_NR, eIMDType_names));
970 imd_fatal(IMDsetup, "Terminating connection\n");
977 /*! \brief Open IMD output file and write header information.
979 * Call on master only.
981 static FILE *open_imd_out(
983 t_gmx_IMD_setup *IMDsetup,
991 /* Open log file of applied IMD forces if requested */
994 /* If we append to an existing file, all the header information is already there */
995 if (Flags & MD_APPENDFILES)
997 fp = gmx_fio_fopen(fn, "a+");
1001 fp = gmx_fio_fopen(fn, "w+");
1002 if (IMDsetup->nat == nat_total)
1004 fprintf(fp, "# Note that you can select an IMD index group in the .mdp file if a subset of the atoms suffices.\n");
1007 xvgr_header(fp, "IMD Pull Forces", "Time (ps)", "# of Forces / Atom IDs / Forces (kJ/mol)", exvggtNONE, oenv);
1009 fprintf(fp, "# Can display and manipulate %d (of a total of %d) atoms via IMD.\n", IMDsetup->nat, nat_total);
1010 fprintf(fp, "# column 1 : time (ps)\n");
1011 fprintf(fp, "# column 2 : total number of atoms feeling an IMD pulling force at that time\n");
1012 fprintf(fp, "# cols. 3.-6 : global atom number of pulled atom, x-force, y-force, z-force (kJ/mol)\n");
1013 fprintf(fp, "# then follow : atom-ID, f[x], f[y], f[z] for more atoms in case the force on multiple atoms is changed simultaneously.\n");
1014 fprintf(fp, "# Note that the force on any atom is always equal to the last value for that atom-ID found in the data.\n");
1018 /* To reduce the output file size we remember the old values and output only
1019 * when something changed */
1020 snew(IMDsetup->old_f_ind, IMDsetup->nat); /* One can never pull on more atoms */
1021 snew(IMDsetup->old_forces, IMDsetup->nat);
1026 fprintf(stdout, "%s For a log of the IMD pull forces explicitly specify '-if' on the command line.\n"
1027 "%s (Not possible with energy minimization.)\n", IMDstr, IMDstr);
1034 extern void IMD_finalize(gmx_bool bIMD, t_IMD *imd)
1038 if (imd->setup->outf)
1040 gmx_fio_fclose(imd->setup->outf);
1047 /*! \brief Creates the molecule start-end position array of molecules in the IMD group. */
1048 static void init_imd_prepare_mols_in_imdgroup(t_gmx_IMD_setup *IMDsetup, gmx_mtop_t *top_global)
1051 int gstart, gend, count;
1052 t_block gmols, lmols;
1056 gmols = top_global->mols;
1057 nat = IMDsetup->nat;
1058 ind = IMDsetup->ind;
1062 /* check whether index is sorted */
1063 for (i = 0; i < nat-1; i++)
1065 if (ind[i] > ind[i+1])
1067 gmx_fatal(FARGS, "%s IMD index is not sorted. This is currently not supported.\n", IMDstr);
1071 snew(lmols.index, gmols.nr+1);
1074 for (i = 0; i < gmols.nr; i++)
1076 gstart = gmols.index[i];
1077 gend = gmols.index[i+1];
1079 for (ii = 0; ii < nat; ii++)
1081 if ((ind[ii] >= gstart) && (ind[ii] < gend))
1088 lmols.index[lmols.nr+1] = lmols.index[lmols.nr]+count;
1092 srenew(lmols.index, lmols.nr+1);
1093 lmols.nalloc_index = lmols.nr+1;
1094 IMDsetup->mols = lmols;
1098 /*! \brief Copied and modified from groupcoord.c shift_positions_group(). */
1099 static void shift_positions(
1101 rvec x[], /* The positions [0..nr] */
1102 ivec is, /* The shift [0..nr] */
1103 int nr) /* The number of positions */
1107 /* Loop over the group's atoms */
1110 for (i = 0; i < nr; i++)
1116 x[i][XX] = x[i][XX]-tx*box[XX][XX]-ty*box[YY][XX]-tz*box[ZZ][XX];
1117 x[i][YY] = x[i][YY]-ty*box[YY][YY]-tz*box[ZZ][YY];
1118 x[i][ZZ] = x[i][ZZ]-tz*box[ZZ][ZZ];
1123 for (i = 0; i < nr; i++)
1129 x[i][XX] = x[i][XX]-tx*box[XX][XX];
1130 x[i][YY] = x[i][YY]-ty*box[YY][YY];
1131 x[i][ZZ] = x[i][ZZ]-tz*box[ZZ][ZZ];
1137 /*! \brief Removes shifts of molecules diffused outside of the box. */
1138 static void imd_remove_molshifts(t_gmx_IMD_setup *IMDsetup, matrix box)
1141 ivec largest, smallest, shift;
1145 mols = IMDsetup->mols;
1147 /* for each molecule also present in IMD group */
1148 for (i = 0; i < mols.nr; i++)
1150 /* first we determine the minimum and maximum shifts for each molecule */
1152 clear_ivec(largest);
1153 clear_ivec(smallest);
1156 copy_ivec(IMDsetup->xa_shifts[mols.index[i]], largest);
1157 copy_ivec(IMDsetup->xa_shifts[mols.index[i]], smallest);
1159 for (ii = mols.index[i]+1; ii < mols.index[i+1]; ii++)
1161 if (IMDsetup->xa_shifts[ii][XX] > largest[XX])
1163 largest[XX] = IMDsetup->xa_shifts[ii][XX];
1165 if (IMDsetup->xa_shifts[ii][XX] < smallest[XX])
1167 smallest[XX] = IMDsetup->xa_shifts[ii][XX];
1170 if (IMDsetup->xa_shifts[ii][YY] > largest[YY])
1172 largest[YY] = IMDsetup->xa_shifts[ii][YY];
1174 if (IMDsetup->xa_shifts[ii][YY] < smallest[YY])
1176 smallest[YY] = IMDsetup->xa_shifts[ii][YY];
1179 if (IMDsetup->xa_shifts[ii][ZZ] > largest[ZZ])
1181 largest[ZZ] = IMDsetup->xa_shifts[ii][ZZ];
1183 if (IMDsetup->xa_shifts[ii][ZZ] < smallest[ZZ])
1185 smallest[ZZ] = IMDsetup->xa_shifts[ii][ZZ];
1190 /* check if we what we can subtract/add to the positions
1191 * to put them back into the central box */
1192 if (smallest[XX] > 0)
1194 shift[XX] = smallest[XX];
1196 if (smallest[YY] > 0)
1198 shift[YY] = smallest[YY];
1200 if (smallest[ZZ] > 0)
1202 shift[ZZ] = smallest[ZZ];
1205 if (largest[XX] < 0)
1207 shift[XX] = largest[XX];
1209 if (largest[YY] < 0)
1211 shift[YY] = largest[YY];
1213 if (largest[ZZ] < 0)
1215 shift[ZZ] = largest[ZZ];
1218 /* is there a shift at all? */
1219 if ((shift[XX]) || (shift[YY]) || (shift[ZZ]))
1221 molsize = mols.index[i+1]-mols.index[i];
1222 /* shift the positions */
1223 shift_positions(box, &(IMDsetup->xa[mols.index[i]]), shift, molsize);
1230 /*! \brief Initialize arrays used to assemble the positions from the other nodes. */
1231 static void init_imd_prepare_for_x_assembly(t_commrec *cr, rvec x[], t_gmx_IMD_setup *IMDsetup)
1236 snew(IMDsetup->xa, IMDsetup->nat);
1237 snew(IMDsetup->xa_ind, IMDsetup->nat);
1238 snew(IMDsetup->xa_shifts, IMDsetup->nat);
1239 snew(IMDsetup->xa_eshifts, IMDsetup->nat);
1240 snew(IMDsetup->xa_old, IMDsetup->nat);
1242 /* Save the original (whole) set of positions such that later the
1243 * molecule can always be made whole again */
1246 for (i = 0; i < IMDsetup->nat; i++)
1248 ii = IMDsetup->ind[i];
1249 copy_rvec(x[ii], IMDsetup->xa_old[i]);
1255 IMDsetup->nat_loc = IMDsetup->nat;
1256 IMDsetup->ind_loc = IMDsetup->ind;
1258 /* xa_ind[i] needs to be set to i for serial runs */
1259 for (i = 0; i < IMDsetup->nat; i++)
1261 IMDsetup->xa_ind[i] = i;
1265 /* Communicate initial coordinates xa_old to all processes */
1269 gmx_bcast(IMDsetup->nat * sizeof(IMDsetup->xa_old[0]), IMDsetup->xa_old, cr);
1276 /*! \brief Check for non-working integrator / parallel options. */
1277 static void imd_check_integrator_parallel(t_inputrec *ir, t_commrec *cr)
1281 if (((ir->eI) == eiSteep) || ((ir->eI) == eiCG) || ((ir->eI) == eiLBFGS) || ((ir->eI) == eiNM))
1283 gmx_fatal(FARGS, "%s Energy minimization via steep, CG, lbfgs and nm in parallel is currently not supported by IMD.\n", IMDstr);
1290 extern void init_IMD(
1293 gmx_mtop_t *top_global,
1298 const t_filenm fnm[],
1301 unsigned long Flags)
1305 t_gmx_IMD_setup *IMDsetup;
1306 gmx_int32_t bufxsize;
1307 gmx_bool bIMD = FALSE;
1310 /* We will allow IMD sessions only if explicitly enabled in the .tpr file */
1311 if (FALSE == ir->bIMD)
1316 /* It seems we have a .tpr file that defines an IMD group and thus allows IMD sessions.
1317 * Check whether we can actually provide the IMD functionality for this setting: */
1320 /* Check whether IMD was enabled by one of the command line switches: */
1321 if ((Flags & MD_IMDWAIT) || (Flags & MD_IMDTERM) || (Flags & MD_IMDPULL))
1323 /* Multiple simulations or replica exchange */
1326 fprintf(stderr, "%s Cannot use IMD for multiple simulations or replica exchange.\n", IMDstr);
1328 /* OK, IMD seems to be allowed and turned on... */
1331 fprintf(stderr, "%s Enabled. This simulation will accept incoming IMD connections.\n", IMDstr);
1337 fprintf(stderr, "%s None of the -imd switches was used.\n"
1338 "%s This run will not accept incoming IMD connections\n", IMDstr, IMDstr);
1340 } /* end master only */
1342 /* Disable IMD if not all the needed functionality is there! */
1343 #if defined(GMX_NATIVE_WINDOWS) && !defined(GMX_HAVE_WINSOCK)
1345 fprintf(stderr, "Disabling IMD because the winsock library was not found at compile time.\n");
1348 /* Let the other nodes know whether we want IMD */
1353 /* ... and update our local inputrec accordingly. */
1356 /*... if not we are done.*/
1363 /* check if we're using a sane integrator / parallel combination */
1364 imd_check_integrator_parallel(ir, cr);
1368 *****************************************************
1369 * From here on we assume that IMD is turned on *
1370 *****************************************************
1374 nat_total = top_global->natoms;
1376 /* Initialize IMD setup structure. If we read in a pre-IMD .tpr file, imd->nat
1377 * will be zero. For those cases we transfer _all_ atomic positions */
1378 ir->imd->setup = imd_create(ir->imd->nat > 0 ? ir->imd->nat : nat_total,
1379 defnstimd, imdport);
1380 IMDsetup = ir->imd->setup;
1382 /* We might need to open an output file for IMD forces data */
1385 IMDsetup->outf = open_imd_out(opt2fn("-if", nfile, fnm), ir->imd->setup, nat_total, oenv, Flags);
1388 /* Make sure that we operate with a valid atom index array for the IMD atoms */
1389 if (ir->imd->nat > 0)
1391 /* Point to the user-supplied array of atom numbers */
1392 IMDsetup->ind = ir->imd->ind;
1396 /* Make a dummy (ind[i] = i) array of all atoms */
1397 snew(IMDsetup->ind, nat_total);
1398 for (i = 0; i < nat_total; i++)
1400 IMDsetup->ind[i] = i;
1404 /* read environment on master and prepare socket for incoming connections */
1407 /* we allocate memory for our IMD energy structure */
1408 gmx_int32_t recsize = HEADERSIZE + sizeof(IMDEnergyBlock);
1409 snew(IMDsetup->energysendbuf, recsize);
1411 /* Shall we wait for a connection? */
1412 if (Flags & MD_IMDWAIT)
1414 IMDsetup->bWConnect = TRUE;
1415 fprintf(stderr, "%s Pausing simulation while no IMD connection present (-imdwait).\n", IMDstr);
1418 /* Will the IMD clients be able to terminate the simulation? */
1419 if (Flags & MD_IMDTERM)
1421 IMDsetup->bTerminatable = TRUE;
1422 fprintf(stderr, "%s Allow termination of the simulation from IMD client (-imdterm).\n", IMDstr);
1425 /* Is pulling from IMD client allowed? */
1426 if (Flags & MD_IMDPULL)
1428 IMDsetup->bForceActivated = TRUE;
1429 fprintf(stderr, "%s Pulling from IMD remote is enabled (-imdpull).\n", IMDstr);
1432 /* Initialize send buffers with constant size */
1433 snew(IMDsetup->sendxbuf, IMDsetup->nat);
1434 snew(IMDsetup->energies, 1);
1435 bufxsize = HEADERSIZE + 3 * sizeof(float) * IMDsetup->nat;
1436 snew(IMDsetup->coordsendbuf, bufxsize);
1439 /* do we allow interactive pulling? If so let the other nodes know. */
1442 block_bc(cr, IMDsetup->bForceActivated);
1445 /* setup the listening socket on master process */
1448 fprintf(fplog, "%s Setting port for connection requests to %d.\n", IMDstr, IMDsetup->port);
1449 fprintf(stderr, "%s Turning on IMD - port for incoming requests is %d.\n", IMDstr, IMDsetup->port);
1450 imd_prepare_master_socket(IMDsetup);
1451 /* Wait until we have a connection if specified before */
1452 if (IMDsetup->bWConnect)
1454 imd_blockconnect(IMDsetup);
1458 fprintf(stderr, "%s -imdwait not set, starting simulation.\n", IMDstr);
1461 /* Let the other nodes know whether we are connected */
1462 imd_sync_nodes(ir, cr, 0);
1464 /* Initialize arrays used to assemble the positions from the other nodes */
1465 init_imd_prepare_for_x_assembly(cr, x, IMDsetup);
1467 /* Initialize molecule blocks to make them whole later...*/
1470 init_imd_prepare_mols_in_imdgroup(IMDsetup, top_global);
1473 gmx_incons("init_IMD: this GROMACS version was not compiled with IMD support!");
1478 extern gmx_bool do_IMD(
1487 gmx_wallcycle_t wcycle)
1489 gmx_bool imdstep = FALSE;
1490 t_gmx_IMD_setup *IMDsetup;
1500 wallcycle_start(wcycle, ewcIMD);
1502 IMDsetup = ir->imd->setup;
1504 /* read command from client and check if new incoming connection */
1507 /* If not already connected, check for new connections */
1508 if (!IMDsetup->clientsocket)
1510 if (IMDsetup->bWConnect)
1512 imd_blockconnect(IMDsetup);
1516 imd_tryconnect(IMDsetup);
1520 /* Let's see if we have new IMD messages for us */
1521 if (IMDsetup->clientsocket)
1523 imd_readcommand(IMDsetup);
1527 /* is this an IMD communication step? */
1528 imdstep = do_per_step(step, IMDsetup->nstimd);
1530 /* OK so this is an IMD step ... */
1533 /* First we sync all nodes to let everybody know whether we are connected to VMD */
1534 imd_sync_nodes(ir, cr, t);
1537 /* If a client is connected, we collect the positions
1538 * and put molecules back into the box before transfer */
1539 if ((imdstep && IMDsetup->bConnected)
1540 || bNS) /* independent of imdstep, we communicate positions at each NS step */
1542 /* Transfer the IMD positions to the master node. Every node contributes
1543 * its local positions x and stores them in the assembled xa array. */
1544 communicate_group_positions(cr, IMDsetup->xa, IMDsetup->xa_shifts, IMDsetup->xa_eshifts,
1545 TRUE, x, IMDsetup->nat, IMDsetup->nat_loc,
1546 IMDsetup->ind_loc, IMDsetup->xa_ind, IMDsetup->xa_old, box);
1548 /* If connected and master -> remove shifts */
1549 if ((imdstep && IMDsetup->bConnected) && MASTER(cr))
1551 imd_remove_molshifts(IMDsetup, box);
1555 wallcycle_stop(wcycle, ewcIMD);
1557 gmx_incons("do_IMD called without IMD support!");
1564 extern void IMD_fill_energy_record(gmx_bool bIMD, t_IMD *imd, gmx_enerdata_t *enerd,
1565 gmx_int64_t step, gmx_bool bHaveNewEnergies)
1567 IMDEnergyBlock *ene;
1574 IMDsetup = imd->setup;
1576 if (IMDsetup->clientsocket)
1578 ene = IMDsetup->energies;
1582 /* In MPI-parallel simulations the energies are not accessible a at every time step.
1583 * We update them if we have new values, otherwise, the energy values from the
1584 * last global communication step are still on display in the viewer. */
1585 if (bHaveNewEnergies)
1587 ene->T_abs = (float) enerd->term[F_TEMP ];
1588 ene->E_pot = (float) enerd->term[F_EPOT ];
1589 ene->E_tot = (float) enerd->term[F_ETOT ];
1590 ene->E_bond = (float) enerd->term[F_BONDS ];
1591 ene->E_angle = (float) enerd->term[F_ANGLES ];
1592 ene->E_dihe = (float) enerd->term[F_PDIHS ];
1593 ene->E_impr = (float) enerd->term[F_IDIHS ];
1594 ene->E_vdw = (float) enerd->term[F_LJ ];
1595 ene->E_coul = (float) (enerd->term[F_COUL_SR] + enerd->term[F_COUL_LR]);
1599 gmx_incons("IMD_fill_energy_record called without IMD support.");
1605 extern void IMD_send_positions(t_IMD *imd)
1611 IMDsetup = imd->setup;
1613 if (IMDsetup->clientsocket)
1616 if (imd_send_energies(IMDsetup->clientsocket, IMDsetup->energies, IMDsetup->energysendbuf))
1618 imd_fatal(IMDsetup, "Error sending updated energies. Disconnecting client.\n");
1621 if (imd_send_rvecs(IMDsetup->clientsocket, IMDsetup->nat, IMDsetup->xa, IMDsetup->coordsendbuf))
1623 imd_fatal(IMDsetup, "Error sending updated positions. Disconnecting client.\n");
1627 gmx_incons("IMD_send_positions called without IMD support.");
1632 extern void IMD_prep_energies_send_positions(gmx_bool bIMD, gmx_bool bIMDstep,
1633 t_IMD *imd, gmx_enerdata_t *enerd,
1634 gmx_int64_t step, gmx_bool bHaveNewEnergies,
1635 gmx_wallcycle_t wcycle)
1640 wallcycle_start(wcycle, ewcIMD);
1642 /* Update time step for IMD and prepare IMD energy record if we have new energies. */
1643 IMD_fill_energy_record(TRUE, imd, enerd, step, bHaveNewEnergies);
1647 /* Send positions and energies to VMD client via IMD */
1648 IMD_send_positions(imd);
1651 wallcycle_stop(wcycle, ewcIMD);
1653 gmx_incons("IMD_prep_energies_send_positions called without IMD support.");
1659 extern int IMD_get_step(t_gmx_IMD IMDsetup)
1661 return IMDsetup->nstimd;
1665 extern void IMD_apply_forces(gmx_bool bIMD, t_IMD *imd, t_commrec *cr, rvec *f,
1666 gmx_wallcycle_t wcycle)
1670 t_gmx_IMD_setup *IMDsetup;
1676 wallcycle_start(wcycle, ewcIMD);
1678 IMDsetup = imd->setup;
1680 /* Are forces allowed at all? If not we're done */
1681 if (!IMDsetup->bForceActivated)
1686 for (i = 0; i < IMDsetup->nforces; i++)
1688 /* j are the indices in the "System group".*/
1689 j = IMDsetup->ind[IMDsetup->f_ind[i]];
1691 /* check if this is a local atom and find out locndx */
1692 if (PAR(cr) && ga2la_get_home(cr->dd->ga2la, j, &locndx))
1697 rvec_inc(f[j], IMDsetup->f[i]);
1700 wallcycle_start(wcycle, ewcIMD);
1702 gmx_incons("IMD_apply_forces called without IMD support.");