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40 * Implements Interactive Molecular Dynamics
42 * Re-implementation of basic IMD functions to work with VMD,
43 * see imdsocket.h for references to the IMD API.
45 * \author Martin Hoefling, Carsten Kutzner <ckutzne@gwdg.de>
58 #include "gromacs/commandline/filenm.h"
59 #include "gromacs/domdec/domdec_struct.h"
60 #include "gromacs/domdec/ga2la.h"
61 #include "gromacs/fileio/confio.h"
62 #include "gromacs/fileio/gmxfio.h"
63 #include "gromacs/fileio/xvgr.h"
64 #include "gromacs/gmxlib/network.h"
65 #include "gromacs/imd/imdsocket.h"
66 #include "gromacs/math/units.h"
67 #include "gromacs/math/vec.h"
68 #include "gromacs/mdlib/broadcaststructs.h"
69 #include "gromacs/mdlib/groupcoord.h"
70 #include "gromacs/mdlib/sighandler.h"
71 #include "gromacs/mdlib/stat.h"
72 #include "gromacs/mdrunutility/handlerestart.h"
73 #include "gromacs/mdrunutility/multisim.h"
74 #include "gromacs/mdtypes/enerdata.h"
75 #include "gromacs/mdtypes/imdmodule.h"
76 #include "gromacs/mdtypes/inputrec.h"
77 #include "gromacs/mdtypes/md_enums.h"
78 #include "gromacs/mdtypes/mdrunoptions.h"
79 #include "gromacs/mdtypes/state.h"
80 #include "gromacs/pbcutil/pbc.h"
81 #include "gromacs/timing/wallcycle.h"
82 #include "gromacs/topology/mtop_util.h"
83 #include "gromacs/topology/topology.h"
84 #include "gromacs/utility/fatalerror.h"
85 #include "gromacs/utility/logger.h"
86 #include "gromacs/utility/smalloc.h"
87 #include "gromacs/utility/stringutil.h"
92 /*! \brief How long shall we wait in seconds until we check for a connection again? */
93 constexpr int c_loopWait = 1;
95 /*! \brief How long shall we check for the IMD_GO? */
96 constexpr int c_connectWait = 1;
98 /*! \brief IMD Header Size. */
99 constexpr int c_headerSize = 8;
101 /*! \brief IMD Protocol Version. */
102 constexpr int c_protocolVersion = 2;
106 * IMD (interactive molecular dynamics) energy record.
108 * As in the original IMD implementation. Energies in kcal/mol.
109 * NOTE: We return the energies in GROMACS / SI units,
110 * so they also show up as SI in VMD.
115 int32_t tstep; /**< time step */
116 float T_abs; /**< absolute temperature */
117 float E_tot; /**< total energy */
118 float E_pot; /**< potential energy */
119 float E_vdw; /**< van der Waals energy */
120 float E_coul; /**< Coulomb interaction energy */
121 float E_bond; /**< bonds energy */
122 float E_angle; /**< angles energy */
123 float E_dihe; /**< dihedrals energy */
124 float E_impr; /**< improper dihedrals energy */
129 * \brief IMD (interactive molecular dynamics) communication structure.
131 * This structure defines the IMD communication message header & protocol version.
135 int32_t type; /**< Type of IMD message, see IMDType_t above */
136 int32_t length; /**< Length */
141 * \brief Implementation type for the IMD session
143 * \todo Make this class (or one extracted from it) model
145 * \todo Use RAII for files and allocations
147 class ImdSession::Impl
151 Impl(const MDLogger& mdlog);
154 /*! \brief Prepare the socket on the MASTER. */
155 void prepareMasterSocket();
156 /*! \brief Disconnect the client. */
157 void disconnectClient();
158 /*! \brief Prints an error message and disconnects the client.
160 * Does not terminate mdrun!
162 void issueFatalError(const char* msg);
163 /*! \brief Check whether we got an incoming connection. */
165 /*! \brief Wrap imd_tryconnect in order to make it blocking.
167 * Used when the simulation should wait for an incoming connection.
170 /*! \brief Make sure that our array holding the forces received via IMD is large enough. */
171 void prepareVmdForces();
172 /*! \brief Reads forces received via IMD. */
173 void readVmdForces();
174 /*! \brief Prepares the MD force arrays. */
175 void prepareMDForces();
176 /*! \brief Copy IMD forces to MD forces.
178 * Do conversion from Cal->Joule and from
179 * Angstrom -> nm and from a pointer array to arrays to 3*N array.
181 void copyToMDForces();
182 /*! \brief Return true if any of the forces or indices changed. */
183 bool bForcesChanged() const;
184 /*! \brief Update the old_f_ind and old_forces arrays to contain the current values. */
185 void keepOldValues();
186 /*! \brief Write the applied pull forces to logfile.
188 * Call on master only!
190 void outputForces(double time);
191 /*! \brief Synchronize the nodes. */
192 void syncNodes(const t_commrec* cr, double t);
193 /*! \brief Reads header from the client and decides what to do. */
195 /*! \brief Open IMD output file and write header information.
197 * Call on master only.
199 void openOutputFile(const char* fn, int nat_total, const gmx_output_env_t* oenv, StartingBehavior startingBehavior);
200 /*! \brief Creates the molecule start-end position array of molecules in the IMD group. */
201 void prepareMoleculesInImdGroup(const gmx_mtop_t* top_global);
202 /*! \brief Removes shifts of molecules diffused outside of the box. */
203 void removeMolecularShifts(const matrix box);
204 /*! \brief Initialize arrays used to assemble the positions from the other nodes. */
205 void prepareForPositionAssembly(const t_commrec* cr, const rvec x[]);
206 /*! \brief Interact with any connected VMD session */
207 bool run(int64_t step, bool bNS, const matrix box, const rvec x[], double t);
209 // TODO rename all the data members to have underscore suffixes
211 //! True if tpr and mdrun input combine to permit IMD sessions
212 bool sessionPossible = false;
213 //! Output file for IMD data, mainly forces.
214 FILE* outf = nullptr;
216 //! Number of atoms that can be pulled via IMD.
218 //! Part of the atoms that are local.
220 //! Global indices of the IMD atoms.
222 //! Local indices of the IMD atoms.
223 int* ind_loc = nullptr;
224 //! Allocation size for ind_loc.
226 //! Positions for all IMD atoms assembled on the master node.
228 //! Shifts for all IMD atoms, to make molecule(s) whole.
229 ivec* xa_shifts = nullptr;
230 //! Extra shifts since last DD step.
231 ivec* xa_eshifts = nullptr;
232 //! Old positions for all IMD atoms on master.
233 rvec* xa_old = nullptr;
234 //! Position of each local atom in the collective array.
235 int* xa_ind = nullptr;
237 //! Global IMD frequency, known to all ranks.
239 //! New frequency from IMD client, master only.
241 //! Default IMD frequency when disconnected.
242 int defaultNstImd = -1;
244 //! Port to use for network socket.
246 //! The IMD socket on the master node.
247 IMDSocket* socket = nullptr;
248 //! The IMD socket on the client.
249 IMDSocket* clientsocket = nullptr;
250 //! Length we got with last header.
253 //! Shall we block and wait for connection?
254 bool bWConnect = false;
255 //! Set if MD is terminated.
256 bool bTerminated = false;
257 //! Set if MD can be terminated.
258 bool bTerminatable = false;
259 //! Set if connection is present.
260 bool bConnected = false;
261 //! Set if we received new forces.
262 bool bNewForces = false;
263 //! Set if pulling from VMD is allowed.
264 bool bForceActivated = false;
266 //! Pointer to energies we send back.
267 IMDEnergyBlock* energies = nullptr;
269 //! Number of VMD forces.
270 int32_t vmd_nforces = 0;
271 //! VMD forces indices.
272 int32_t* vmd_f_ind = nullptr;
273 //! The VMD forces flat in memory.
274 float* vmd_forces = nullptr;
275 //! Number of actual MD forces; this gets communicated to the clients.
278 int* f_ind = nullptr;
279 //! The IMD pulling forces.
282 //! Buffer for force sending.
283 char* forcesendbuf = nullptr;
284 //! Buffer for coordinate sending.
285 char* coordsendbuf = nullptr;
286 //! Send buffer for energies.
287 char* energysendbuf = nullptr;
288 //! Buffer to make molecules whole before sending.
289 rvec* sendxbuf = nullptr;
291 //! Molecules block in IMD group.
294 /* The next block is used on the master node only to reduce the output
295 * without sacrificing information. If any of these values changes,
296 * we need to write output */
297 //! Old value for nforces.
299 //! Old values for force indices.
300 int* old_f_ind = nullptr;
301 //! Old values for IMD pulling forces.
302 rvec* old_forces = nullptr;
305 const MDLogger& mdlog;
306 //! Commmunication object
307 const t_commrec* cr = nullptr;
308 //! Wallcycle counting manager.
309 gmx_wallcycle* wcycle = nullptr;
310 //! Energy output handler
311 gmx_enerdata_t* enerd = nullptr;
315 * \brief Implement interactive molecular dynamics.
317 * \todo Some aspects of this module provides forces (when the user
318 * pulls on things in VMD), so in future it should have a class that
319 * models IForceProvider and is contributed to the collection of such
322 class InteractiveMolecularDynamics final : public IMDModule
325 IMdpOptionProvider* mdpOptionProvider() override { return nullptr; }
326 IMDOutputProvider* outputProvider() override { return nullptr; }
327 void initForceProviders(ForceProviders* /* forceProviders */) override {}
330 std::unique_ptr<IMDModule> createInteractiveMolecularDynamicsModule()
332 return std::make_unique<InteractiveMolecularDynamics>();
335 /*! \brief Enum for types of IMD messages.
337 * We use the same records as the NAMD/VMD IMD implementation.
339 typedef enum IMDType_t
341 IMD_DISCONNECT, /**< client disconnect */
342 IMD_ENERGIES, /**< energy data */
343 IMD_FCOORDS, /**< atomic coordinates */
344 IMD_GO, /**< start command for the simulation */
345 IMD_HANDSHAKE, /**< handshake to determine little/big endianness */
346 IMD_KILL, /**< terminates the simulation */
347 IMD_MDCOMM, /**< force data */
348 IMD_PAUSE, /**< pauses the simulation */
349 IMD_TRATE, /**< sets the IMD transmission and processing rate */
350 IMD_IOERROR, /**< I/O error */
351 IMD_NR /**< number of entries */
355 /*! \brief Names of the IMDType for error messages.
357 static const char* eIMDType_names[IMD_NR + 1] = { "IMD_DISCONNECT", "IMD_ENERGIES", "IMD_FCOORDS",
358 "IMD_GO", "IMD_HANDSHAKE", "IMD_KILL",
359 "IMD_MDCOMM", "IMD_PAUSE", "IMD_TRATE",
360 "IMD_IOERROR", nullptr };
363 /*! \brief Fills the header with message and the length argument. */
364 static void fill_header(IMDHeader* header, IMDMessageType type, int32_t length)
366 /* We (ab-)use htonl network function for the correct endianness */
367 header->type = imd_htonl(static_cast<int32_t>(type));
368 header->length = imd_htonl(length);
372 /*! \brief Swaps the endianess of the header. */
373 static void swap_header(IMDHeader* header)
375 /* and vice versa... */
376 header->type = imd_ntohl(header->type);
377 header->length = imd_ntohl(header->length);
381 /*! \brief Reads multiple bytes from socket. */
382 static int32_t imd_read_multiple(IMDSocket* socket, char* datptr, int32_t toread)
384 int32_t leftcount, countread;
388 /* Try to read while we haven't reached toread */
389 while (leftcount != 0)
391 if ((countread = imdsock_read(socket, datptr, leftcount)) < 0)
393 /* interrupted function call, try again... */
398 /* this is an unexpected error, return what we got */
401 return toread - leftcount;
404 /* nothing read, finished */
406 else if (countread == 0)
410 leftcount -= countread;
414 /* return nr of bytes read */
415 return toread - leftcount;
419 /*! \brief Writes multiple bytes to socket in analogy to imd_read_multiple. */
420 static int32_t imd_write_multiple(IMDSocket* socket, const char* datptr, int32_t towrite)
422 int32_t leftcount, countwritten;
426 while (leftcount != 0)
428 if ((countwritten = imdsock_write(socket, datptr, leftcount)) <= 0)
436 return towrite - leftcount;
439 leftcount -= countwritten;
440 datptr += countwritten;
443 return towrite - leftcount;
447 /*! \brief Handshake with IMD client. */
448 static int imd_handshake(IMDSocket* socket)
453 fill_header(&header, IMD_HANDSHAKE, 1);
454 header.length = c_protocolVersion; /* client wants unswapped version */
456 return static_cast<int>(imd_write_multiple(socket, reinterpret_cast<char*>(&header), c_headerSize)
461 /*! \brief Send energies using the energy block and the send buffer. */
462 static int imd_send_energies(IMDSocket* socket, const IMDEnergyBlock* energies, char* buffer)
467 recsize = c_headerSize + sizeof(IMDEnergyBlock);
468 fill_header(reinterpret_cast<IMDHeader*>(buffer), IMD_ENERGIES, 1);
469 memcpy(buffer + c_headerSize, energies, sizeof(IMDEnergyBlock));
471 return static_cast<int>(imd_write_multiple(socket, buffer, recsize) != recsize);
475 /*! \brief Receive IMD header from socket, sets the length and returns the IMD message. */
476 static IMDMessageType imd_recv_header(IMDSocket* socket, int32_t* length)
481 if (imd_read_multiple(socket, reinterpret_cast<char*>(&header), c_headerSize) != c_headerSize)
485 swap_header(&header);
486 *length = header.length;
488 return static_cast<IMDMessageType>(header.type);
492 /*! \brief Receive force indices and forces.
494 * The number of forces was previously communicated via the header.
496 static bool imd_recv_mdcomm(IMDSocket* socket, int32_t nforces, int32_t* forcendx, float* forces)
498 /* reading indices */
499 int retsize = sizeof(int32_t) * nforces;
500 int retbytes = imd_read_multiple(socket, reinterpret_cast<char*>(forcendx), retsize);
501 if (retbytes != retsize)
506 /* reading forces as float array */
507 retsize = 3 * sizeof(float) * nforces;
508 retbytes = imd_read_multiple(socket, reinterpret_cast<char*>(forces), retsize);
509 return (retbytes == retsize);
512 /* GROMACS specific functions for the IMD implementation */
513 void write_IMDgroup_to_file(bool bIMD,
515 const t_state* state,
516 const gmx_mtop_t* sys,
518 const t_filenm fnm[])
525 IMDatoms = gmx_mtop_global_atoms(sys);
526 write_sto_conf_indexed(opt2fn("-imd", nfile, fnm), "IMDgroup", &IMDatoms, state->x.rvec_array(),
527 state->v.rvec_array(), ir->ePBC, state->box, ir->imd->nat, ir->imd->ind);
532 void ImdSession::dd_make_local_IMD_atoms(const gmx_domdec_t* dd)
534 if (!impl_->sessionPossible)
539 dd_make_local_group_indices(dd->ga2la, impl_->nat, impl_->ind, &impl_->nat_loc, &impl_->ind_loc,
540 &impl_->nalloc_loc, impl_->xa_ind);
544 /*! \brief Send positions from rvec.
546 * We need a separate send buffer and conversion to Angstrom.
548 static int imd_send_rvecs(IMDSocket* socket, int nat, rvec* x, char* buffer)
553 int tuplesize = 3 * sizeof(float);
556 /* Required size for the send buffer */
557 size = c_headerSize + 3 * sizeof(float) * nat;
560 fill_header(reinterpret_cast<IMDHeader*>(buffer), IMD_FCOORDS, static_cast<int32_t>(nat));
561 for (i = 0; i < nat; i++)
563 sendx[0] = static_cast<float>(x[i][0]) * NM2A;
564 sendx[1] = static_cast<float>(x[i][1]) * NM2A;
565 sendx[2] = static_cast<float>(x[i][2]) * NM2A;
566 memcpy(buffer + c_headerSize + i * tuplesize, sendx, tuplesize);
569 return static_cast<int>(imd_write_multiple(socket, buffer, size) != size);
573 void ImdSession::Impl::prepareMasterSocket()
575 if (imdsock_winsockinit() == -1)
577 gmx_fatal(FARGS, "%s Failed to initialize winsock.\n", IMDstr);
580 /* The rest is identical, first create and bind a socket and set to listen then. */
581 GMX_LOG(mdlog.warning).appendTextFormatted("%s Setting up incoming socket.", IMDstr);
582 socket = imdsock_create();
585 gmx_fatal(FARGS, "%s Failed to create socket.", IMDstr);
589 int ret = imdsock_bind(socket, port);
592 gmx_fatal(FARGS, "%s binding socket to port %d failed with error %d.\n", IMDstr, port, ret);
595 if (imd_sock_listen(socket))
597 gmx_fatal(FARGS, "%s socket listen failed with error %d.\n", IMDstr, ret);
600 if (imdsock_getport(socket, &port))
602 gmx_fatal(FARGS, "%s Could not determine port number.\n", IMDstr);
605 GMX_LOG(mdlog.warning).appendTextFormatted("%s Listening for IMD connection on port %d.", IMDstr, port);
609 void ImdSession::Impl::disconnectClient()
611 /* Write out any buffered pulling data */
614 /* we first try to shut down the clientsocket */
615 imdsock_shutdown(clientsocket);
616 if (!imdsock_destroy(clientsocket))
618 GMX_LOG(mdlog.warning).appendTextFormatted("%s Failed to destroy socket.", IMDstr);
621 /* then we reset the IMD step to its default, and reset the connection boolean */
622 nstimd_new = defaultNstImd;
623 clientsocket = nullptr;
628 void ImdSession::Impl::issueFatalError(const char* msg)
630 GMX_LOG(mdlog.warning).appendTextFormatted("%s %s", IMDstr, msg);
632 GMX_LOG(mdlog.warning).appendTextFormatted("%s disconnected.", IMDstr);
636 bool ImdSession::Impl::tryConnect()
638 if (imdsock_tryread(socket, 0, 0) > 0)
640 /* yes, we got something, accept on clientsocket */
641 clientsocket = imdsock_accept(socket);
644 GMX_LOG(mdlog.warning)
645 .appendTextFormatted("%s Accepting the connection on the socket failed.", IMDstr);
649 /* handshake with client */
650 if (imd_handshake(clientsocket))
652 issueFatalError("Connection failed.");
656 GMX_LOG(mdlog.warning)
657 .appendTextFormatted("%s Connection established, checking if I got IMD_GO orders.", IMDstr);
659 /* Check if we get the proper "GO" command from client. */
660 if (imdsock_tryread(clientsocket, c_connectWait, 0) != 1
661 || imd_recv_header(clientsocket, &(length)) != IMD_GO)
663 issueFatalError("No IMD_GO order received. IMD connection failed.");
676 void ImdSession::Impl::blockConnect()
678 /* do not wait for connection, when e.g. ctrl+c is pressed and we will terminate anyways. */
679 if (!(static_cast<int>(gmx_get_stop_condition()) == gmx_stop_cond_none))
684 GMX_LOG(mdlog.warning)
685 .appendTextFormatted("%s Will wait until I have a connection and IMD_GO orders.", IMDstr);
687 /* while we have no clientsocket... 2nd part: we should still react on ctrl+c */
688 while ((!clientsocket) && (static_cast<int>(gmx_get_stop_condition()) == gmx_stop_cond_none))
691 imd_sleep(c_loopWait);
696 void ImdSession::Impl::prepareVmdForces()
698 srenew((vmd_f_ind), vmd_nforces);
699 srenew((vmd_forces), 3 * vmd_nforces);
703 void ImdSession::Impl::readVmdForces()
705 /* the length of the previously received header tells us the nr of forces we will receive */
706 vmd_nforces = length;
707 /* prepare the arrays */
709 /* Now we read the forces... */
710 if (!(imd_recv_mdcomm(clientsocket, vmd_nforces, vmd_f_ind, vmd_forces)))
712 issueFatalError("Error while reading forces from remote. Disconnecting");
717 void ImdSession::Impl::prepareMDForces()
719 srenew((f_ind), nforces);
720 srenew((f), nforces);
724 void ImdSession::Impl::copyToMDForces()
727 real conversion = CAL2JOULE * NM2A;
730 for (i = 0; i < nforces; i++)
732 /* Copy the indices, a copy is important because we may update the incoming forces
733 * whenever we receive new forces while the MD forces are only communicated upon
734 * IMD communication.*/
735 f_ind[i] = vmd_f_ind[i];
737 /* Convert to rvecs and do a proper unit conversion */
738 f[i][0] = vmd_forces[3 * i] * conversion;
739 f[i][1] = vmd_forces[3 * i + 1] * conversion;
740 f[i][2] = vmd_forces[3 * i + 2] * conversion;
745 /*! \brief Returns true if any component of the two rvecs differs. */
746 static inline bool rvecs_differ(const rvec v1, const rvec v2)
748 for (int i = 0; i < DIM; i++)
759 bool ImdSession::Impl::bForcesChanged() const
761 /* First, check whether the number of pulled atoms changed */
762 if (nforces != old_nforces)
767 /* Second, check whether any of the involved atoms changed */
768 for (int i = 0; i < nforces; i++)
770 if (f_ind[i] != old_f_ind[i])
776 /* Third, check whether all forces are the same */
777 for (int i = 0; i < nforces; i++)
779 if (rvecs_differ(f[i], old_forces[i]))
785 /* All old and new forces are identical! */
790 void ImdSession::Impl::keepOldValues()
792 old_nforces = nforces;
794 for (int i = 0; i < nforces; i++)
796 old_f_ind[i] = f_ind[i];
797 copy_rvec(f[i], old_forces[i]);
802 void ImdSession::Impl::outputForces(double time)
804 if (!bForcesChanged())
809 /* Write time and total number of applied IMD forces */
810 fprintf(outf, "%14.6e%6d", time, nforces);
812 /* Write out the global atom indices of the pulled atoms and the forces itself,
813 * write out a force only if it has changed since the last output */
814 for (int i = 0; i < nforces; i++)
816 if (rvecs_differ(f[i], old_forces[i]))
818 fprintf(outf, "%9d", ind[f_ind[i]] + 1);
819 fprintf(outf, "%12.4e%12.4e%12.4e", f[i][0], f[i][1], f[i][2]);
828 void ImdSession::Impl::syncNodes(const t_commrec* cr, double t)
830 /* Notify the other nodes whether we are still connected. */
833 block_bc(cr, bConnected);
836 /* ...if not connected, the job is done here. */
842 /* Let the other nodes know whether we got a new IMD synchronization frequency. */
845 block_bc(cr, nstimd_new);
848 /* Now we all set the (new) nstimd communication time step */
851 /* We're done if we don't allow pulling at all */
852 if (!(bForceActivated))
857 /* OK, let's check if we have received forces which we need to communicate
858 * to the other nodes */
864 new_nforces = vmd_nforces;
866 /* make the "new_forces" negative, when we did not receive new ones */
869 new_nforces = vmd_nforces * -1;
873 /* make new_forces known to the clients */
876 block_bc(cr, new_nforces);
879 /* When new_natoms < 0 then we know that these are still the same forces
880 * so we don't communicate them, otherwise... */
886 /* set local VMD and nforces */
887 vmd_nforces = new_nforces;
888 nforces = vmd_nforces;
890 /* now everybody knows the number of forces in f_ind, so we can prepare
891 * the target arrays for indices and forces */
894 /* we first update the MD forces on the master by converting the VMD forces */
898 /* We also write out forces on every update, so that we know which
899 * forces are applied for every step */
906 /* In parallel mode we communicate the to-be-applied forces to the other nodes */
909 nblock_bc(cr, nforces, f_ind);
910 nblock_bc(cr, nforces, f);
913 /* done communicating the forces, reset bNewForces */
918 void ImdSession::Impl::readCommand()
920 bool IMDpaused = false;
922 while (clientsocket && (imdsock_tryread(clientsocket, 0, 0) > 0 || IMDpaused))
924 IMDMessageType itype = imd_recv_header(clientsocket, &(length));
925 /* let's see what we got: */
928 /* IMD asks us to terminate the simulation, check if the user allowed this */
932 GMX_LOG(mdlog.warning)
933 .appendTextFormatted(
934 " %s Terminating connection and running simulation (if "
935 "supported by integrator).",
939 gmx_set_stop_condition(gmx_stop_cond_next);
943 GMX_LOG(mdlog.warning)
944 .appendTextFormatted(
945 " %s Set -imdterm command line switch to allow mdrun "
946 "termination from within IMD.",
952 /* the client doen't want to talk to us anymore */
954 GMX_LOG(mdlog.warning).appendTextFormatted(" %s Disconnecting client.", IMDstr);
958 /* we got new forces, read them and set bNewForces flag */
964 /* the client asks us to (un)pause the simulation. So we toggle the IMDpaused state */
968 GMX_LOG(mdlog.warning).appendTextFormatted(" %s Un-pause command received.", IMDstr);
973 GMX_LOG(mdlog.warning).appendTextFormatted(" %s Pause command received.", IMDstr);
979 /* the client sets a new transfer rate, if we get 0, we reset the rate
980 * to the default. VMD filters 0 however */
982 nstimd_new = (length > 0) ? length : defaultNstImd;
983 GMX_LOG(mdlog.warning)
984 .appendTextFormatted(" %s Update frequency will be set to %d.", IMDstr, nstimd_new);
987 /* Catch all rule for the remaining IMD types which we don't expect */
989 GMX_LOG(mdlog.warning)
990 .appendTextFormatted(" %s Received unexpected %s.", IMDstr,
991 enum_name(static_cast<int>(itype), IMD_NR, eIMDType_names));
992 issueFatalError("Terminating connection");
999 void ImdSession::Impl::openOutputFile(const char* fn,
1001 const gmx_output_env_t* oenv,
1002 const gmx::StartingBehavior startingBehavior)
1004 /* Open log file of applied IMD forces if requested */
1008 "%s For a log of the IMD pull forces explicitly specify '-if' on the command "
1010 "%s (Not possible with energy minimization.)\n",
1015 /* If we append to an existing file, all the header information is already there */
1016 if (startingBehavior == StartingBehavior::RestartWithAppending)
1018 outf = gmx_fio_fopen(fn, "a+");
1022 outf = gmx_fio_fopen(fn, "w+");
1023 if (nat == nat_total)
1026 "# Note that you can select an IMD index group in the .mdp file if a subset of "
1027 "the atoms suffices.\n");
1030 xvgr_header(outf, "IMD Pull Forces", "Time (ps)",
1031 "# of Forces / Atom IDs / Forces (kJ/mol)", exvggtNONE, oenv);
1033 fprintf(outf, "# Can display and manipulate %d (of a total of %d) atoms via IMD.\n", nat, nat_total);
1034 fprintf(outf, "# column 1 : time (ps)\n");
1036 "# column 2 : total number of atoms feeling an IMD pulling force at that "
1039 "# cols. 3.-6 : global atom number of pulled atom, x-force, y-force, z-force "
1042 "# then follow : atom-ID, f[x], f[y], f[z] for more atoms in case the force on "
1043 "multiple atoms is changed simultaneously.\n");
1045 "# Note that the force on any atom is always equal to the last value for that "
1046 "atom-ID found in the data.\n");
1050 /* To reduce the output file size we remember the old values and output only
1051 * when something changed */
1052 snew(old_f_ind, nat); /* One can never pull on more atoms */
1053 snew(old_forces, nat);
1057 ImdSession::Impl::Impl(const MDLogger& mdlog) : mdlog(mdlog)
1062 ImdSession::Impl::~Impl()
1066 gmx_fio_fclose(outf);
1072 void ImdSession::Impl::prepareMoleculesInImdGroup(const gmx_mtop_t* top_global)
1074 /* check whether index is sorted */
1075 for (int i = 0; i < nat - 1; i++)
1077 if (ind[i] > ind[i + 1])
1079 gmx_fatal(FARGS, "%s IMD index is not sorted. This is currently not supported.\n", IMDstr);
1083 RangePartitioning gmols = gmx_mtop_molecules(*top_global);
1086 snew(lmols.index, gmols.numBlocks() + 1);
1089 for (int i = 0; i < gmols.numBlocks(); i++)
1091 auto mol = gmols.block(i);
1093 for (int ii = 0; ii < nat; ii++)
1095 if (mol.isInRange(ind[ii]))
1102 lmols.index[lmols.nr + 1] = lmols.index[lmols.nr] + count;
1106 srenew(lmols.index, lmols.nr + 1);
1107 lmols.nalloc_index = lmols.nr + 1;
1112 /*! \brief Copied and modified from groupcoord.c shift_positions_group(). */
1113 static void shift_positions(const matrix box,
1114 rvec x[], /* The positions [0..nr] */
1115 const ivec is, /* The shift [0..nr] */
1116 int nr) /* The number of positions */
1120 /* Loop over the group's atoms */
1123 for (i = 0; i < nr; i++)
1129 x[i][XX] = x[i][XX] - tx * box[XX][XX] - ty * box[YY][XX] - tz * box[ZZ][XX];
1130 x[i][YY] = x[i][YY] - ty * box[YY][YY] - tz * box[ZZ][YY];
1131 x[i][ZZ] = x[i][ZZ] - tz * box[ZZ][ZZ];
1136 for (i = 0; i < nr; i++)
1142 x[i][XX] = x[i][XX] - tx * box[XX][XX];
1143 x[i][YY] = x[i][YY] - ty * box[YY][YY];
1144 x[i][ZZ] = x[i][ZZ] - tz * box[ZZ][ZZ];
1150 void ImdSession::Impl::removeMolecularShifts(const matrix box)
1152 /* for each molecule also present in IMD group */
1153 for (int i = 0; i < mols.nr; i++)
1155 /* first we determine the minimum and maximum shifts for each molecule */
1157 ivec largest, smallest, shift;
1158 clear_ivec(largest);
1159 clear_ivec(smallest);
1162 copy_ivec(xa_shifts[mols.index[i]], largest);
1163 copy_ivec(xa_shifts[mols.index[i]], smallest);
1165 for (int ii = mols.index[i] + 1; ii < mols.index[i + 1]; ii++)
1167 if (xa_shifts[ii][XX] > largest[XX])
1169 largest[XX] = xa_shifts[ii][XX];
1171 if (xa_shifts[ii][XX] < smallest[XX])
1173 smallest[XX] = xa_shifts[ii][XX];
1176 if (xa_shifts[ii][YY] > largest[YY])
1178 largest[YY] = xa_shifts[ii][YY];
1180 if (xa_shifts[ii][YY] < smallest[YY])
1182 smallest[YY] = xa_shifts[ii][YY];
1185 if (xa_shifts[ii][ZZ] > largest[ZZ])
1187 largest[ZZ] = xa_shifts[ii][ZZ];
1189 if (xa_shifts[ii][ZZ] < smallest[ZZ])
1191 smallest[ZZ] = xa_shifts[ii][ZZ];
1195 /* check if we what we can subtract/add to the positions
1196 * to put them back into the central box */
1197 if (smallest[XX] > 0)
1199 shift[XX] = smallest[XX];
1201 if (smallest[YY] > 0)
1203 shift[YY] = smallest[YY];
1205 if (smallest[ZZ] > 0)
1207 shift[ZZ] = smallest[ZZ];
1210 if (largest[XX] < 0)
1212 shift[XX] = largest[XX];
1214 if (largest[YY] < 0)
1216 shift[YY] = largest[YY];
1218 if (largest[ZZ] < 0)
1220 shift[ZZ] = largest[ZZ];
1223 /* is there a shift at all? */
1224 if ((shift[XX]) || (shift[YY]) || (shift[ZZ]))
1226 int molsize = mols.index[i + 1] - mols.index[i];
1227 /* shift the positions */
1228 shift_positions(box, &(xa[mols.index[i]]), shift, molsize);
1234 void ImdSession::Impl::prepareForPositionAssembly(const t_commrec* cr, const rvec x[])
1238 snew(xa_shifts, nat);
1239 snew(xa_eshifts, nat);
1242 /* Save the original (whole) set of positions such that later the
1243 * molecule can always be made whole again */
1246 for (int i = 0; i < nat; i++)
1249 copy_rvec(x[ii], xa_old[i]);
1258 /* xa_ind[i] needs to be set to i for serial runs */
1259 for (int i = 0; i < nat; i++)
1265 /* Communicate initial coordinates xa_old to all processes */
1268 gmx_bcast(nat * sizeof(xa_old[0]), xa_old, cr);
1273 /*! \brief Check for non-working integrator / parallel options. */
1274 static void imd_check_integrator_parallel(const t_inputrec* ir, const t_commrec* cr)
1278 if (((ir->eI) == eiSteep) || ((ir->eI) == eiCG) || ((ir->eI) == eiLBFGS) || ((ir->eI) == eiNM))
1281 "%s Energy minimization via steep, CG, lbfgs and nm in parallel is currently "
1282 "not supported by IMD.\n",
1288 std::unique_ptr<ImdSession> makeImdSession(const t_inputrec* ir,
1289 const t_commrec* cr,
1290 gmx_wallcycle* wcycle,
1291 gmx_enerdata_t* enerd,
1292 const gmx_multisim_t* ms,
1293 const gmx_mtop_t* top_global,
1294 const MDLogger& mdlog,
1297 const t_filenm fnm[],
1298 const gmx_output_env_t* oenv,
1299 const ImdOptions& options,
1300 const gmx::StartingBehavior startingBehavior)
1302 std::unique_ptr<ImdSession> session(new ImdSession(mdlog));
1303 auto impl = session->impl_.get();
1305 /* We will allow IMD sessions only if supported by the binary and
1306 explicitly enabled in the .tpr file */
1307 if (!GMX_IMD || !ir->bIMD)
1312 // TODO As IMD is intended for interactivity, and the .tpr file
1313 // opted in for that, it is acceptable to write more terminal
1314 // output than in a typical simulation. However, all the GMX_LOG
1315 // statements below should go to both the log file and to the
1316 // terminal. This is probably be implemented by adding a logging
1317 // stream named like ImdInfo, to separate it from warning and to
1318 // send it to both destinations.
1320 if (EI_DYNAMICS(ir->eI))
1322 impl->defaultNstImd = ir->nstcalcenergy;
1324 else if (EI_ENERGY_MINIMIZATION(ir->eI))
1326 impl->defaultNstImd = 1;
1330 GMX_LOG(mdlog.warning)
1331 .appendTextFormatted(
1332 "%s Integrator '%s' is not supported for Interactive Molecular Dynamics, "
1333 "running normally instead",
1334 IMDstr, ei_names[ir->eI]);
1339 GMX_LOG(mdlog.warning)
1340 .appendTextFormatted(
1341 "%s Cannot use IMD for multiple simulations or replica exchange, running "
1347 bool createSession = false;
1348 /* It seems we have a .tpr file that defines an IMD group and thus allows IMD connections.
1349 * Check whether we can actually provide the IMD functionality for this setting: */
1352 /* Check whether IMD was enabled by one of the command line switches: */
1353 if (options.wait || options.terminatable || options.pull)
1355 GMX_LOG(mdlog.warning)
1356 .appendTextFormatted(
1357 "%s Enabled. This simulation will accept incoming IMD connections.", IMDstr);
1358 createSession = true;
1362 GMX_LOG(mdlog.warning)
1363 .appendTextFormatted(
1364 "%s None of the -imd switches was used.\n"
1365 "%s This run will not accept incoming IMD connections",
1368 } /* end master only */
1370 /* Let the other nodes know whether we want IMD */
1373 block_bc(cr, createSession);
1376 /*... if not we are done.*/
1383 /* check if we're using a sane integrator / parallel combination */
1384 imd_check_integrator_parallel(ir, cr);
1388 *****************************************************
1389 * From here on we assume that IMD is turned on *
1390 *****************************************************
1393 int nat_total = top_global->natoms;
1395 /* Initialize IMD session. If we read in a pre-IMD .tpr file, ir->imd->nat
1396 * will be zero. For those cases we transfer _all_ atomic positions */
1397 impl->sessionPossible = true;
1398 impl->nat = ir->imd->nat > 0 ? ir->imd->nat : nat_total;
1399 if (options.port >= 1)
1401 impl->port = options.port;
1404 impl->wcycle = wcycle;
1405 impl->enerd = enerd;
1407 /* We might need to open an output file for IMD forces data */
1410 impl->openOutputFile(opt2fn("-if", nfile, fnm), nat_total, oenv, startingBehavior);
1413 /* Make sure that we operate with a valid atom index array for the IMD atoms */
1414 if (ir->imd->nat > 0)
1416 /* Point to the user-supplied array of atom numbers */
1417 impl->ind = ir->imd->ind;
1421 /* Make a dummy (ind[i] = i) array of all atoms */
1422 snew(impl->ind, nat_total);
1423 for (int i = 0; i < nat_total; i++)
1429 /* read environment on master and prepare socket for incoming connections */
1432 /* we allocate memory for our IMD energy structure */
1433 int32_t recsize = c_headerSize + sizeof(IMDEnergyBlock);
1434 snew(impl->energysendbuf, recsize);
1436 /* Shall we wait for a connection? */
1439 impl->bWConnect = true;
1440 GMX_LOG(mdlog.warning)
1441 .appendTextFormatted(
1442 "%s Pausing simulation while no IMD connection present (-imdwait).", IMDstr);
1445 /* Will the IMD clients be able to terminate the simulation? */
1446 if (options.terminatable)
1448 impl->bTerminatable = true;
1449 GMX_LOG(mdlog.warning)
1450 .appendTextFormatted(
1451 "%s Allow termination of the simulation from IMD client (-imdterm).", IMDstr);
1454 /* Is pulling from IMD client allowed? */
1457 impl->bForceActivated = true;
1458 GMX_LOG(mdlog.warning)
1459 .appendTextFormatted("%s Pulling from IMD remote is enabled (-imdpull).", IMDstr);
1462 /* Initialize send buffers with constant size */
1463 snew(impl->sendxbuf, impl->nat);
1464 snew(impl->energies, 1);
1465 int32_t bufxsize = c_headerSize + 3 * sizeof(float) * impl->nat;
1466 snew(impl->coordsendbuf, bufxsize);
1469 /* do we allow interactive pulling? If so let the other nodes know. */
1472 block_bc(cr, impl->bForceActivated);
1475 /* setup the listening socket on master process */
1478 GMX_LOG(mdlog.warning).appendTextFormatted("%s Setting port for connection requests to %d.", IMDstr, impl->port);
1479 impl->prepareMasterSocket();
1480 /* Wait until we have a connection if specified before */
1481 if (impl->bWConnect)
1483 impl->blockConnect();
1487 GMX_LOG(mdlog.warning).appendTextFormatted("%s -imdwait not set, starting simulation.", IMDstr);
1490 /* Let the other nodes know whether we are connected */
1491 impl->syncNodes(cr, 0);
1493 /* Initialize arrays used to assemble the positions from the other nodes */
1494 impl->prepareForPositionAssembly(cr, x);
1496 /* Initialize molecule blocks to make them whole later...*/
1499 impl->prepareMoleculesInImdGroup(top_global);
1506 bool ImdSession::Impl::run(int64_t step, bool bNS, const matrix box, const rvec x[], double t)
1509 if (!sessionPossible)
1514 wallcycle_start(wcycle, ewcIMD);
1516 /* read command from client and check if new incoming connection */
1519 /* If not already connected, check for new connections */
1532 /* Let's see if we have new IMD messages for us */
1539 /* is this an IMD communication step? */
1540 bool imdstep = do_per_step(step, nstimd);
1542 /* OK so this is an IMD step ... */
1545 /* First we sync all nodes to let everybody know whether we are connected to VMD */
1549 /* If a client is connected, we collect the positions
1550 * and put molecules back into the box before transfer */
1551 if ((imdstep && bConnected) || bNS) /* independent of imdstep, we communicate positions at each NS step */
1553 /* Transfer the IMD positions to the master node. Every node contributes
1554 * its local positions x and stores them in the assembled xa array. */
1555 communicate_group_positions(cr, xa, xa_shifts, xa_eshifts, true, x, nat, nat_loc, ind_loc,
1556 xa_ind, xa_old, box);
1558 /* If connected and master -> remove shifts */
1559 if ((imdstep && bConnected) && MASTER(cr))
1561 removeMolecularShifts(box);
1565 wallcycle_stop(wcycle, ewcIMD);
1570 bool ImdSession::run(int64_t step, bool bNS, const matrix box, const rvec x[], double t)
1572 return impl_->run(step, bNS, box, x, t);
1575 void ImdSession::fillEnergyRecord(int64_t step, bool bHaveNewEnergies)
1577 if (!impl_->sessionPossible || !impl_->clientsocket)
1582 IMDEnergyBlock* ene = impl_->energies;
1586 /* In MPI-parallel simulations the energies are not accessible a at every time step.
1587 * We update them if we have new values, otherwise, the energy values from the
1588 * last global communication step are still on display in the viewer. */
1589 if (bHaveNewEnergies)
1591 ene->T_abs = static_cast<float>(impl_->enerd->term[F_TEMP]);
1592 ene->E_pot = static_cast<float>(impl_->enerd->term[F_EPOT]);
1593 ene->E_tot = static_cast<float>(impl_->enerd->term[F_ETOT]);
1594 ene->E_bond = static_cast<float>(impl_->enerd->term[F_BONDS]);
1595 ene->E_angle = static_cast<float>(impl_->enerd->term[F_ANGLES]);
1596 ene->E_dihe = static_cast<float>(impl_->enerd->term[F_PDIHS]);
1597 ene->E_impr = static_cast<float>(impl_->enerd->term[F_IDIHS]);
1598 ene->E_vdw = static_cast<float>(impl_->enerd->term[F_LJ]);
1599 ene->E_coul = static_cast<float>(impl_->enerd->term[F_COUL_SR]);
1604 void ImdSession::sendPositionsAndEnergies()
1606 if (!impl_->sessionPossible || !impl_->clientsocket)
1611 if (imd_send_energies(impl_->clientsocket, impl_->energies, impl_->energysendbuf))
1613 impl_->issueFatalError("Error sending updated energies. Disconnecting client.");
1616 if (imd_send_rvecs(impl_->clientsocket, impl_->nat, impl_->xa, impl_->coordsendbuf))
1618 impl_->issueFatalError("Error sending updated positions. Disconnecting client.");
1623 void ImdSession::updateEnergyRecordAndSendPositionsAndEnergies(bool bIMDstep, int64_t step, bool bHaveNewEnergies)
1625 if (!impl_->sessionPossible)
1630 wallcycle_start(impl_->wcycle, ewcIMD);
1632 /* Update time step for IMD and prepare IMD energy record if we have new energies. */
1633 fillEnergyRecord(step, bHaveNewEnergies);
1637 /* Send positions and energies to VMD client via IMD */
1638 sendPositionsAndEnergies();
1641 wallcycle_stop(impl_->wcycle, ewcIMD);
1644 void ImdSession::applyForces(rvec* f)
1646 if (!impl_->sessionPossible || !impl_->bForceActivated)
1651 wallcycle_start(impl_->wcycle, ewcIMD);
1653 for (int i = 0; i < impl_->nforces; i++)
1655 /* j are the indices in the "System group".*/
1656 int j = impl_->ind[impl_->f_ind[i]];
1658 /* check if this is a local atom and find out locndx */
1660 const t_commrec* cr = impl_->cr;
1661 if (PAR(cr) && (locndx = cr->dd->ga2la->findHome(j)))
1666 rvec_inc(f[j], impl_->f[i]);
1669 wallcycle_stop(impl_->wcycle, ewcIMD);
1672 ImdSession::ImdSession(const MDLogger& mdlog) : impl_(new Impl(mdlog)) {}
1674 ImdSession::~ImdSession() = default;