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37 * Note, that parts of this source code originate from the Simtk release
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39 * https://simtk.org/project/xml/downloads.xml?group_id=161#package_id600
46 #include <types/simple.h>
61 #include "gmx_fatal.h"
66 #include "gpu_utils.h"
67 #include "mtop_util.h"
69 #include "openmm_wrapper.h"
71 using namespace OpenMM;
74 #define MEM_ERR_MSG(str) \
75 "The %s-simulation GPU memory test detected errors. As memory errors would cause incorrect " \
76 "simulation results, gromacs has aborted execution.\n Make sure that your GPU's memory is not " \
77 "overclocked and that the device is properly cooled.\n", (str)
80 #define COMBRULE_CHK_TOL 1e-6
81 #define COMBRULE_SIGMA(sig1, sig2) (((sig1) + (sig2))/2)
82 #define COMBRULE_EPS(eps1, eps2) (sqrt((eps1) * (eps2)))
85 * \brief Convert string to integer type.
86 * \param[in] s String to convert from.
87 * \param[in] f Basefield format flag that takes any of the following I/O
88 * manipulators: dec, hex, oct.
89 * \param[out] t Destination variable to convert to.
92 static gmx_bool from_string(T& t, const string& s, ios_base& (*f)(ios_base&))
95 return !(iss >> f >> t).fail();
99 * \brief Split string around a given delimiter.
100 * \param[in] s String to split.
101 * \param[in] delim Delimiter character.
102 * \returns Vector of strings found in \p s.
104 static vector<string> split(const string &s, char delim)
106 vector<string> elems;
109 while (getline(ss, item, delim))
111 if (item.length() != 0)
112 elems.push_back(item);
118 * \brief Split a string of the form "option=value" into "option" and "value" strings.
119 * This string corresponds to one option and the associated value from the option list
120 * in the mdrun -device argument.
122 * \param[in] s A string containing an "option=value" pair that needs to be split up.
123 * \param[out] opt The name of the option.
124 * \param[out] val Value of the option.
126 static void splitOptionValue(const string &s, string &opt, string &val)
128 size_t eqPos = s.find('=');
129 if (eqPos != string::npos)
131 opt = s.substr(0, eqPos);
132 if (eqPos != s.length()) val = s.substr(eqPos+1);
137 * \brief Compare two strings ignoring case.
138 * This function is in fact a wrapper around the gromacs function gmx_strncasecmp().
139 * \param[in] s1 String.
140 * \param[in] s2 String.
141 * \returns Similarly to the C function strncasecmp(), the return value is an
142 integer less than, equal to, or greater than 0 if \p s1 less than,
143 identical to, or greater than \p s2.
145 static gmx_bool isStringEqNCase(const string& s1, const string& s2)
147 return (gmx_strncasecmp(s1.c_str(), s2.c_str(), max(s1.length(), s2.length())) == 0);
151 * \brief Convert string to upper case.
153 * \param[in] s String to convert to uppercase.
154 * \returns The given string converted to uppercase.
156 static string toUpper(const string &s)
159 std::transform(stmp.begin(), stmp.end(), stmp.begin(), static_cast < int(*)(int) > (toupper));
164 \name Sizes of constant device option arrays GmxOpenMMPlatformOptions#platforms,
165 GmxOpenMMPlatformOptions#memtests, GmxOpenMMPlatformOptions#deviceid,
166 GmxOpenMMPlatformOptions#force_dev. */
168 #define SIZEOF_PLATFORMS 2 // 2
169 #define SIZEOF_MEMTESTS 3
170 #define SIZEOF_DEVICEIDS 1
171 #define SIZEOF_FORCE_DEV 2
173 #define SIZEOF_CHECK_COMBRULE 2
176 /*! Possible platform options in the mdrun -device option. */
177 static const char *devOptStrings[] = { "platform", "deviceid", "memtest", "force-device", "check-combrule" };
179 /*! Enumerated platform options in the mdrun -device option. */
189 * \brief Class to extract and manage the platform options in the mdrun -device option.
192 class GmxOpenMMPlatformOptions
195 GmxOpenMMPlatformOptions(const char *opt);
196 ~GmxOpenMMPlatformOptions() { options.clear(); }
197 string getOptionValue(const string &opt);
198 void remOption(const string &opt);
201 void setOption(const string &opt, const string &val);
203 map<string, string> options; /*!< Data structure to store the option (name, value) pairs. */
205 static const char * const platforms[SIZEOF_PLATFORMS]; /*!< Available OpenMM platforms; size #SIZEOF_PLATFORMS */
206 static const char * const memtests[SIZEOF_MEMTESTS]; /*!< Available types of memory tests, also valid
207 any positive integer >=15; size #SIZEOF_MEMTESTS */
208 static const char * const deviceid[SIZEOF_DEVICEIDS]; /*!< Possible values for deviceid option;
209 also valid any positive integer; size #SIZEOF_DEVICEIDS */
210 static const char * const force_dev[SIZEOF_FORCE_DEV]; /*!< Possible values for for force-device option;
211 size #SIZEOF_FORCE_DEV */
212 static const char * const check_combrule[SIZEOF_CHECK_COMBRULE]; /* XXX temporary debug feature to
213 turn off combination rule check */
216 const char * const GmxOpenMMPlatformOptions::platforms[SIZEOF_PLATFORMS]
217 = {"CUDA", "Reference"};
218 //= { "Reference", "CUDA" /*,"OpenCL"*/ };
219 const char * const GmxOpenMMPlatformOptions::memtests[SIZEOF_MEMTESTS]
220 = { "15", "full", "off" };
221 const char * const GmxOpenMMPlatformOptions::deviceid[SIZEOF_DEVICEIDS]
223 const char * const GmxOpenMMPlatformOptions::force_dev[SIZEOF_FORCE_DEV]
225 const char * const GmxOpenMMPlatformOptions::check_combrule[SIZEOF_CHECK_COMBRULE]
230 * Takes the option list, parses it, checks the options and their values for validity.
231 * When certain options are not provided by the user, as default value the first item
232 * of the respective constant array is taken (GmxOpenMMPlatformOptions#platforms,
233 * GmxOpenMMPlatformOptions#memtests, GmxOpenMMPlatformOptions#deviceid,
234 * GmxOpenMMPlatformOptions#force_dev).
235 * \param[in] optionString Option list part of the mdrun -device parameter.
237 GmxOpenMMPlatformOptions::GmxOpenMMPlatformOptions(const char *optionString)
239 // set default values
240 setOption("platform", platforms[0]);
241 setOption("memtest", memtests[0]);
242 setOption("deviceid", deviceid[0]);
243 setOption("force-device", force_dev[0]);
244 setOption("check-combrule", check_combrule[0]);
246 string opt(optionString);
248 // remove all whitespaces
249 opt.erase(remove_if(opt.begin(), opt.end(), ::isspace), opt.end());
250 // tokenize around ","-s
251 vector<string> tokens = split(opt, ',');
253 for (vector<string>::iterator it = tokens.begin(); it != tokens.end(); ++it)
255 string opt = "", val = "";
256 splitOptionValue(*it, opt, val);
258 if (isStringEqNCase(opt, "platform"))
260 /* no check, this will fail if platform does not exist when we try to set it */
265 if (isStringEqNCase(opt, "memtest"))
267 /* the value has to be an integer >15(s) or "full" OR "off" */
268 if (!isStringEqNCase(val, "full") && !isStringEqNCase(val, "off"))
271 if (!from_string<int>(secs, val, std::dec))
273 gmx_fatal(FARGS, "Invalid value for option memtest option: \"%s\"!", val.c_str());
277 gmx_fatal(FARGS, "Incorrect value for memtest option (%d). "
278 "Memtest needs to run for at least 15s!", secs);
285 if (isStringEqNCase(opt, "deviceid"))
288 if (!from_string<int>(id, val, std::dec) )
290 gmx_fatal(FARGS, "Invalid device id: \"%s\"!", val.c_str());
296 if (isStringEqNCase(opt, "force-device"))
299 if (!isStringEqNCase(val, "yes") && !isStringEqNCase(val, "no"))
301 gmx_fatal(FARGS, "Invalid OpenMM force option: \"%s\"!", val.c_str());
307 if (isStringEqNCase(opt, "check-combrule"))
310 if (!isStringEqNCase(val, "yes") && !isStringEqNCase(val, "no"))
312 gmx_fatal(FARGS, "Invalid OpenMM force option: \"%s\"!", val.c_str());
319 // if we got till here something went wrong
320 gmx_fatal(FARGS, "Invalid OpenMM platform option: \"%s\"!", (*it).c_str());
326 * \brief Getter function.
327 * \param[in] opt Name of the option.
328 * \returns Returns the value associated to an option.
330 string GmxOpenMMPlatformOptions::getOptionValue(const string &opt)
332 map<string, string> :: const_iterator it = options.find(toUpper(opt));
333 if (it != options.end())
344 * \brief Setter function - private, only used from contructor.
345 * \param[in] opt Name of the option.
346 * \param[in] val Value for the option.
348 void GmxOpenMMPlatformOptions::setOption(const string &opt, const string &val)
350 options[toUpper(opt)] = val;
354 * \brief Removes an option with its value from the map structure. If the option
355 * does not exist, returns without any action.
356 * \param[in] opt Name of the option.
358 void GmxOpenMMPlatformOptions::remOption(const string &opt)
360 options.erase(toUpper(opt));
364 * \brief Print option-value pairs to a file (debugging function).
366 void GmxOpenMMPlatformOptions::print()
368 cout << ">> Platform options: " << endl
369 << ">> platform = " << getOptionValue("platform") << endl
370 << ">> deviceID = " << getOptionValue("deviceid") << endl
371 << ">> memtest = " << getOptionValue("memtest") << endl
372 << ">> force-device = " << getOptionValue("force-device") << endl;
376 * \brief Container for OpenMM related data structures that represent the bridge
377 * between the Gromacs data-structures and the OpenMM library and is but it's
378 * only passed through the API functions as void to disable direct access.
383 System* system; /*! The system to simulate. */
384 Context* context; /*! The OpenMM context in which the simulation is carried out. */
385 Integrator* integrator; /*! The integrator used in the simulation. */
386 gmx_bool removeCM; /*! If \true remove venter of motion, false otherwise. */
387 GmxOpenMMPlatformOptions *platformOpt; /*! Platform options. */
391 * \brief Runs memtest on the GPU that has alreaby been initialized by OpenMM.
392 * \param[in] fplog Pointer to gromacs log file.
393 * \param[in] devId Device id of the GPU to run the test on.
394 Note: as OpenMM previously creates the context,for now this is always -1.
395 * \param[in] pre_post Contains either "Pre" or "Post" just to be able to differentiate in
396 * stdout messages/log between memtest carried out before and after simulation.
397 * \param[in] opt Pointer to platform options object.
399 static void runMemtest(FILE* fplog, int devId, const char* pre_post, GmxOpenMMPlatformOptions *opt)
401 char strout_buf[STRLEN];
404 string s = opt->getOptionValue("memtest");
405 const char *test_type = s.c_str();
407 if (!gmx_strcasecmp(test_type, "off"))
413 if (!gmx_strcasecmp(test_type, "full"))
419 from_string<int>(which_test, test_type, std::dec);
425 gmx_fatal(FARGS, "Amount of seconds for memetest is negative (%d). ", which_test);
430 case 0: /* no memtest */
431 sprintf(strout_buf, "%s-simulation GPU memtest skipped. Note, that faulty memory can cause "
432 "incorrect results!", pre_post);
433 fprintf(fplog, "%s\n", strout_buf);
434 gmx_warning(strout_buf);
437 case 1: /* quick memtest */
438 fprintf(fplog, "%s-simulation %s GPU memtest in progress...\n", pre_post, test_type);
439 fprintf(stdout, "\n%s-simulation %s GPU memtest in progress...", pre_post, test_type);
442 res = do_quick_memtest(devId);
445 case 2: /* full memtest */
446 fprintf(fplog, "%s-simulation %s memtest in progress...\n", pre_post, test_type);
447 fprintf(stdout, "\n%s-simulation %s memtest in progress...", pre_post, test_type);
450 res = do_full_memtest(devId);
453 default: /* timed memtest */
454 fprintf(fplog, "%s-simulation ~%ds memtest in progress...\n", pre_post, which_test);
455 fprintf(stdout, "\n%s-simulation ~%ds memtest in progress...", pre_post, which_test);
458 res = do_timed_memtest(devId, which_test);
465 gmx_fatal(FARGS, MEM_ERR_MSG(pre_post));
469 fprintf(fplog, "Memory test completed without errors.\n");
471 fprintf(stdout, "done, no errors detected\n");
478 * \brief Convert Lennard-Jones parameters c12 and c6 to sigma and epsilon.
483 * \param[out] epsilon
485 static void convert_c_12_6(double c12, double c6, double *sigma, double *epsilon)
487 if (c12 == 0 && c6 == 0)
492 else if (c12 > 0 && c6 > 0)
494 *epsilon = (c6*c6)/(4.0*c12);
495 *sigma = pow(c12/c6, 1.0/6.0);
499 gmx_fatal(FARGS,"OpenMM only supports c6 > 0 and c12 > 0 or c6 = c12 = 0.");
504 * \brief Does gromacs option checking.
506 * Checks the gromacs mdp options for features unsupported in OpenMM, case in which
507 * interrupts the execution. It also warns the user about pecularities of OpenMM
509 * \param[in] fplog Gromacs log file pointer.
510 * \param[in] ir Gromacs input parameters, see ::t_inputrec
511 * \param[in] top Gromacs node local topology, \see gmx_localtop_t
512 * \param[in] state Gromacs state structure \see ::t_state
513 * \param[in] mdatoms Gromacs atom parameters, \see ::t_mdatoms
514 * \param[in] fr \see ::t_forcerec
515 * \param[in] state Gromacs systems state, \see ::t_state
517 static void checkGmxOptions(FILE* fplog, GmxOpenMMPlatformOptions *opt,
518 t_inputrec *ir, gmx_localtop_t *top,
519 t_forcerec *fr, t_state *state)
521 char warn_buf[STRLEN];
524 double sigma_ij=0, sigma_ji=0, sigma_ii=0, sigma_jj=0, sigma_comb;
525 double eps_ij=0, eps_ji=0, eps_ii=0, eps_jj=0, eps_comb;
527 /* Abort if unsupported critical options are present */
532 gmx_warning( "OpenMM does not support leap-frog, will use velocity-verlet integrator.");
535 if ( (ir->eI != eiMD) &&
537 (ir->eI != eiVVAK) &&
542 gmx_fatal(FARGS, "OpenMM supports only the following integrators: md/md-vv/md-vv-avek, sd/sd1, and bd.");
546 if ( !(ir->coulombtype == eelPME ||
547 EEL_RF(ir->coulombtype) ||
548 ir->coulombtype == eelRF ||
549 ir->coulombtype == eelEWALD ||
551 (ir->coulombtype == eelCUT && ir->rcoulomb == 0 && ir->rvdw == 0) ||
552 // we could have cut-off combined with GBSA (openmm will use RF)
553 ir->implicit_solvent == eisGBSA) )
555 gmx_fatal(FARGS,"OpenMM supports only the following methods for electrostatics: "
556 "NoCutoff (i.e. rcoulomb = rvdw = 0 ),Reaction-Field, Ewald or PME.");
559 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf != 0)
561 // openmm has epsilon_rf=inf hard-coded
562 gmx_warning("OpenMM will use a Reaction-Field epsilon of infinity instead of %g.",ir->epsilon_rf);
565 if (ir->etc != etcNO &&
570 gmx_warning("OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators.");
573 if (ir->implicit_solvent == eisGBSA &&
574 ir->gb_algorithm != egbOBC )
576 gmx_warning("OpenMM does not support the specified algorithm for Generalized Born, will use OBC instead.");
579 if (ir->opts.ngtc > 1)
580 gmx_fatal(FARGS,"OpenMM does not support multiple temperature coupling groups.");
582 if (ir->epc != epcNO)
583 gmx_warning("OpenMM supports only Monte Carlo barostat for pressure coupling.");
585 if (ir->opts.annealing[0])
586 gmx_fatal(FARGS,"OpenMM does not support simulated annealing.");
588 if (top->idef.il[F_CONSTR].nr > 0 && ir->eConstrAlg != econtSHAKE)
589 gmx_warning("OpenMM provides contraints as a combination "
590 "of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set "
591 "by the \"shake_tol\" option.");
594 gmx_fatal(FARGS,"OpenMM does not support walls.");
596 if (ir->ePull != epullNO)
597 gmx_fatal(FARGS,"OpenMM does not support pulling.");
599 /* check for interaction types */
600 for (i = 0; i < F_EPOT; i++)
602 if (!(i == F_CONSTR ||
606 i == F_UREY_BRADLEY ||
613 i == F_GB12 || /* The GB parameters are hardcoded both in */
614 i == F_GB13 || /* Gromacs and OpenMM */
616 top->idef.il[i].nr > 0)
618 gmx_fatal(FARGS, "OpenMM does not support (some) of the provided interaction "
619 "type(s) (%s) ", interaction_function[i].longname);
623 if (ir->efep != efepNO)
624 gmx_fatal(FARGS,"OpenMM does not support free energy calculations.");
626 if (ir->opts.ngacc > 1)
627 gmx_fatal(FARGS,"OpenMM does not support non-equilibrium MD (accelerated groups).");
629 if (IR_ELEC_FIELD(*ir))
630 gmx_fatal(FARGS,"OpenMM does not support electric fields.");
633 gmx_fatal(FARGS,"OpenMM does not support QMMM calculations.");
635 if (ir->rcoulomb != ir->rvdw)
636 gmx_fatal(FARGS,"OpenMM uses a single cutoff for both Coulomb "
637 "and VdW interactions. Please set rcoulomb equal to rvdw.");
639 if (EEL_FULL(ir->coulombtype))
641 if (ir->ewald_geometry == eewg3DC)
642 gmx_fatal(FARGS,"OpenMM supports only Ewald 3D geometry.");
643 if (ir->epsilon_surface != 0)
644 gmx_fatal(FARGS,"OpenMM does not support dipole correction in Ewald summation.");
647 if (TRICLINIC(state->box))
649 gmx_fatal(FARGS,"OpenMM does not support triclinic unit cells.");
652 /* XXX this is just debugging code to disable the combination rule check */
653 if ( isStringEqNCase(opt->getOptionValue("check-combrule"), "yes") )
655 /* As OpenMM by default uses hardcoded combination rules
656 sigma_ij = (sigma_i + sigma_j)/2, eps_ij = sqrt(eps_i * eps_j)
657 we need to check whether the force field params obey this
658 and if not, we can't use this force field so we exit
659 grace-fatal-fully. */
660 real *nbfp = fr->nbfp;
664 fprintf(debug, ">> Atom parameters: <<\n%10s%5s %5s %5s %5s COMB\n",
665 "", "i-j", "j-i", "i-i", "j-j");
667 /* loop over all i-j atom pairs and verify if
668 sigma_ij = sigma_ji = sigma_comb and eps_ij = eps_ji = eps_comb */
669 for (i = 0; i < natoms; i++)
672 /* nbfp now includes the 6.0/12.0 prefactors to save flops in kernels */
673 c12 = C12(nbfp, natoms, i, i)/12.0;
674 c6 = C6(nbfp, natoms, i, i)/6.0;
675 convert_c_12_6(c12, c6, &sigma_ii, &eps_ii);
677 for (j = 0; j < i; j++)
680 c12 = C12(nbfp, natoms, i, j)/12.0;
681 c6 = C6(nbfp, natoms, i, j)/6.0;
682 convert_c_12_6(c12, c6, &sigma_ij, &eps_ij);
684 c12 = C12(nbfp, natoms, j, i)/12.0;
685 c6 = C6(nbfp, natoms, j, i)/6.0;
686 convert_c_12_6(c12, c6, &sigma_ji, &eps_ji);
688 c12 = C12(nbfp, natoms, j, j)/12.0;
689 c6 = C6(nbfp, natoms, j, j)/6.0;
690 convert_c_12_6(c12, c6, &sigma_jj, &eps_jj);
691 /* OpenMM hardcoded combination rules */
692 sigma_comb = COMBRULE_SIGMA(sigma_ii, sigma_jj);
693 eps_comb = COMBRULE_EPS(eps_ii, eps_jj);
697 fprintf(debug, "i=%-3d j=%-3d", i, j);
698 fprintf(debug, "%-11s", "sigma");
699 fprintf(debug, "%5.3f %5.3f %5.3f %5.3f %5.3f\n",
700 sigma_ij, sigma_ji, sigma_ii, sigma_jj, sigma_comb);
701 fprintf(debug, "%11s%-11s", "", "epsilon");
702 fprintf(debug, "%5.3f %5.3f %5.3f %5.3f %5.3f\n",
703 eps_ij, eps_ji, eps_ii, eps_jj, eps_comb);
706 /* check the values against the rule used by omm */
707 if((fabs(eps_ij) > COMBRULE_CHK_TOL &&
708 fabs(eps_ji) > COMBRULE_CHK_TOL) &&
709 (fabs(sigma_comb - sigma_ij) > COMBRULE_CHK_TOL ||
710 fabs(sigma_comb - sigma_ji) > COMBRULE_CHK_TOL ||
711 fabs(eps_comb - eps_ij) > COMBRULE_CHK_TOL ||
712 fabs(eps_comb - eps_ji) > COMBRULE_CHK_TOL ))
715 "The combination rules of the used force-field do not "
716 "match the one supported by OpenMM: "
717 "sigma_ij = (sigma_i + sigma_j)/2, eps_ij = sqrt(eps_i * eps_j). "
718 "Switch to a force-field that uses these rules in order to "
719 "simulate this system using OpenMM.\n");
723 if (debug) { fprintf(debug, ">><<\n\n"); }
725 /* if we got here, log that everything is fine */
728 fprintf(debug, ">> The combination rule of the used force matches the one used by OpenMM.\n");
730 fprintf(fplog, "The combination rule of the used force field matches the one used by OpenMM.\n");
732 } /* if (are we checking the combination rules) ... */
737 * \brief Initialize OpenMM, run sanity/consistency checks, and return a pointer to
740 * Various gromacs data structures are passed that contain the parameters, state and
741 * other porperties of the system to simulate. These serve as input for initializing
742 * OpenMM. Besides, a set of misc action are taken:
743 * - OpenMM plugins are loaded;
744 * - platform options in \p platformOptStr are parsed and checked;
745 * - Gromacs parameters are checked for OpenMM support and consistency;
746 * - after the OpenMM is initialized memtest executed in the same GPU context.
748 * \param[in] fplog Gromacs log file handler.
749 * \param[in] platformOptStr Platform option string.
750 * \param[in] ir The Gromacs input parameters, see ::t_inputrec
751 * \param[in] top_global Gromacs system toppology, \see ::gmx_mtop_t
752 * \param[in] top Gromacs node local topology, \see gmx_localtop_t
753 * \param[in] mdatoms Gromacs atom parameters, \see ::t_mdatoms
754 * \param[in] fr \see ::t_forcerec
755 * \param[in] state Gromacs systems state, \see ::t_state
756 * \returns Pointer to a
759 void* openmm_init(FILE *fplog, const char *platformOptStr,
761 gmx_mtop_t *top_global, gmx_localtop_t *top,
762 t_mdatoms *mdatoms, t_forcerec *fr, t_state *state)
765 char warn_buf[STRLEN];
766 static gmx_bool hasLoadedPlugins = false;
767 string usedPluginDir;
772 if (!hasLoadedPlugins)
774 vector<string> loadedPlugins;
775 /* Look for OpenMM plugins at various locations (listed in order of priority):
776 - on the path in OPENMM_PLUGIN_DIR environment variable if this is specified
777 - on the path in the OPENMM_PLUGIN_DIR macro that is set by the build script
778 - at the default location assumed by OpenMM
781 char *pluginDir = getenv("OPENMM_PLUGIN_DIR");
783 /* no env var or empty */
784 if (pluginDir != NULL && *pluginDir != '\0')
786 loadedPlugins = Platform::loadPluginsFromDirectory(pluginDir);
787 if (!loadedPlugins.empty())
789 hasLoadedPlugins = true;
790 usedPluginDir = pluginDir;
794 gmx_fatal(FARGS, "The directory provided in the OPENMM_PLUGIN_DIR environment variable "
795 "(%s) does not contain valid OpenMM plugins. Check your OpenMM installation!",
800 /* macro set at build time */
801 #ifdef OPENMM_PLUGIN_DIR
802 if (!hasLoadedPlugins)
804 loadedPlugins = Platform::loadPluginsFromDirectory(OPENMM_PLUGIN_DIR);
805 if (!loadedPlugins.empty())
807 hasLoadedPlugins = true;
808 usedPluginDir = OPENMM_PLUGIN_DIR;
812 /* default loocation */
813 if (!hasLoadedPlugins)
815 loadedPlugins = Platform::loadPluginsFromDirectory(Platform::getDefaultPluginsDirectory());
816 if (!loadedPlugins.empty())
818 hasLoadedPlugins = true;
819 usedPluginDir = Platform::getDefaultPluginsDirectory();
823 /* if there are still no plugins loaded there won't be any */
824 if (!hasLoadedPlugins)
826 gmx_fatal(FARGS, "No OpenMM plugins were found! You can provide the"
827 " plugin directory in the OPENMM_PLUGIN_DIR environment variable.", pluginDir);
830 fprintf(fplog, "\nOpenMM plugins loaded from directory %s:\t", usedPluginDir.c_str());
831 for (int i = 0; i < (int)loadedPlugins.size(); i++)
833 fprintf(fplog, "%s, ", loadedPlugins[i].c_str());
835 fprintf(fplog, "\n");
838 /* parse option string */
839 GmxOpenMMPlatformOptions *opt = new GmxOpenMMPlatformOptions(platformOptStr);
840 devId = atoi(opt->getOptionValue("deviceid").c_str());
847 /* check wheter Gromacs options compatibility with OpenMM */
848 checkGmxOptions(fplog, opt, ir, top, fr, state);
850 /* Create the system. */
851 const t_idef& idef = top->idef;
852 const int numAtoms = top_global->natoms;
853 const int numConstraints = idef.il[F_CONSTR].nr/3;
854 const int numSettle = idef.il[F_SETTLE].nr/2;
855 const int numBonds = idef.il[F_BONDS].nr/3;
856 const int numHarmonic = idef.il[F_HARMONIC].nr/3;
857 const int numUB = idef.il[F_UREY_BRADLEY].nr/4;
858 const int numAngles = idef.il[F_ANGLES].nr/4;
859 const int numPeriodic = idef.il[F_PDIHS].nr/5;
860 const int numPeriodicImproper = idef.il[F_PIDIHS].nr/5;
861 const int numRB = idef.il[F_RBDIHS].nr/5;
862 const int numImproperDih = idef.il[F_IDIHS].nr/5;
863 const int num14 = idef.il[F_LJ14].nr/3;
864 System* sys = new System();
866 sys->addForce(new CMMotionRemover(ir->nstcomm));
868 /* Set bonded force field terms. */
871 * CUDA platform currently doesn't support more than one
872 * instance of a force object, so we pack all forces that
873 * use the same form into one.
876 const int* bondAtoms = (int*) idef.il[F_BONDS].iatoms;
877 HarmonicBondForce* bondForce = new HarmonicBondForce();
878 sys->addForce(bondForce);
880 for (int i = 0; i < numBonds; ++i)
882 int type = bondAtoms[offset++];
883 int atom1 = bondAtoms[offset++];
884 int atom2 = bondAtoms[offset++];
885 bondForce->addBond(atom1, atom2,
886 idef.iparams[type].harmonic.rA, idef.iparams[type].harmonic.krA);
889 const int* harmonicAtoms = (int*) idef.il[F_HARMONIC].iatoms;
891 for (int i = 0; i < numHarmonic; ++i)
893 int type = harmonicAtoms[offset++];
894 int atom1 = harmonicAtoms[offset++];
895 int atom2 = harmonicAtoms[offset++];
896 bondForce->addBond(atom1, atom2,
897 idef.iparams[type].harmonic.rA, idef.iparams[type].harmonic.krA);
900 /* Set the angle force field terms */
901 const int* angleAtoms = (int*) idef.il[F_ANGLES].iatoms;
902 HarmonicAngleForce* angleForce = new HarmonicAngleForce();
903 sys->addForce(angleForce);
905 for (int i = 0; i < numAngles; ++i)
907 int type = angleAtoms[offset++];
908 int atom1 = angleAtoms[offset++];
909 int atom2 = angleAtoms[offset++];
910 int atom3 = angleAtoms[offset++];
911 angleForce->addAngle(atom1, atom2, atom3,
912 idef.iparams[type].harmonic.rA*M_PI/180.0, idef.iparams[type].harmonic.krA);
915 /* Urey-Bradley includes both the angle and bond potential for 1-3 interactions */
916 const int* ubAtoms = (int*) idef.il[F_UREY_BRADLEY].iatoms;
917 /* HarmonicBondForce* ubBondForce = new HarmonicBondForce(); */
918 /* HarmonicAngleForce* ubAngleForce = new HarmonicAngleForce(); */
919 /* sys->addForce(ubBondForce); */
920 /* sys->addForce(ubAngleForce); */
922 for (int i = 0; i < numUB; ++i)
924 int type = ubAtoms[offset++];
925 int atom1 = ubAtoms[offset++];
926 int atom2 = ubAtoms[offset++];
927 int atom3 = ubAtoms[offset++];
928 /* ubBondForce->addBond(atom1, atom3, */
929 bondForce->addBond(atom1, atom3,
930 idef.iparams[type].u_b.r13A, idef.iparams[type].u_b.kUBA);
931 /* ubAngleForce->addAngle(atom1, atom2, atom3, */
932 angleForce->addAngle(atom1, atom2, atom3,
933 idef.iparams[type].u_b.thetaA*M_PI/180.0, idef.iparams[type].u_b.kthetaA);
936 /* Set proper dihedral terms */
937 const int* periodicAtoms = (int*) idef.il[F_PDIHS].iatoms;
938 PeriodicTorsionForce* periodicForce = new PeriodicTorsionForce();
939 sys->addForce(periodicForce);
941 for (int i = 0; i < numPeriodic; ++i)
943 int type = periodicAtoms[offset++];
944 int atom1 = periodicAtoms[offset++];
945 int atom2 = periodicAtoms[offset++];
946 int atom3 = periodicAtoms[offset++];
947 int atom4 = periodicAtoms[offset++];
948 periodicForce->addTorsion(atom1, atom2, atom3, atom4,
949 idef.iparams[type].pdihs.mult,
950 idef.iparams[type].pdihs.phiA*M_PI/180.0,
951 idef.iparams[type].pdihs.cpA);
954 /* Set improper dihedral terms that are represented by a periodic function (as in AMBER FF) */
955 const int* periodicImproperAtoms = (int*) idef.il[F_PIDIHS].iatoms;
956 /* PeriodicTorsionForce* periodicImproperForce = new PeriodicTorsionForce(); */
957 /* sys->addForce(periodicImproperForce); */
959 for (int i = 0; i < numPeriodicImproper; ++i)
961 int type = periodicImproperAtoms[offset++];
962 int atom1 = periodicImproperAtoms[offset++];
963 int atom2 = periodicImproperAtoms[offset++];
964 int atom3 = periodicImproperAtoms[offset++];
965 int atom4 = periodicImproperAtoms[offset++];
966 /* periodicImproperForce->addTorsion(atom1, atom2, atom3, atom4, */
967 periodicForce->addTorsion(atom1, atom2, atom3, atom4,
968 idef.iparams[type].pdihs.mult,
969 idef.iparams[type].pdihs.phiA*M_PI/180.0,
970 idef.iparams[type].pdihs.cpA);
973 /* Ryckaert-Bellemans dihedrals */
974 const int* rbAtoms = (int*) idef.il[F_RBDIHS].iatoms;
975 RBTorsionForce* rbForce = new RBTorsionForce();
976 sys->addForce(rbForce);
978 for (int i = 0; i < numRB; ++i)
980 int type = rbAtoms[offset++];
981 int atom1 = rbAtoms[offset++];
982 int atom2 = rbAtoms[offset++];
983 int atom3 = rbAtoms[offset++];
984 int atom4 = rbAtoms[offset++];
985 rbForce->addTorsion(atom1, atom2, atom3, atom4,
986 idef.iparams[type].rbdihs.rbcA[0], idef.iparams[type].rbdihs.rbcA[1],
987 idef.iparams[type].rbdihs.rbcA[2], idef.iparams[type].rbdihs.rbcA[3],
988 idef.iparams[type].rbdihs.rbcA[4], idef.iparams[type].rbdihs.rbcA[5]);
991 /* Set improper dihedral terms (as in CHARMM FF) */
992 const int* improperDihAtoms = (int*) idef.il[F_IDIHS].iatoms;
993 CustomTorsionForce* improperDihForce = new CustomTorsionForce("2.0*k*asin(sin((theta-theta0)/2))^2");
994 sys->addForce(improperDihForce);
995 improperDihForce->addPerTorsionParameter("k");
996 improperDihForce->addPerTorsionParameter("theta0");
997 vector<double> improperDihParameters(2);
999 for (int i = 0; i < numImproperDih; ++i)
1001 int type = improperDihAtoms[offset++];
1002 int atom1 = improperDihAtoms[offset++];
1003 int atom2 = improperDihAtoms[offset++];
1004 int atom3 = improperDihAtoms[offset++];
1005 int atom4 = improperDihAtoms[offset++];
1006 improperDihParameters[0] = idef.iparams[type].harmonic.krA;
1007 improperDihParameters[1] = idef.iparams[type].harmonic.rA*M_PI/180.0;
1008 improperDihForce->addTorsion(atom1, atom2, atom3, atom4,
1009 improperDihParameters);
1012 /* Set nonbonded parameters and masses. */
1013 int ntypes = fr->ntype;
1014 int* types = mdatoms->typeA;
1015 real* nbfp = fr->nbfp;
1016 real* charges = mdatoms->chargeA;
1017 real* masses = mdatoms->massT;
1018 NonbondedForce* nonbondedForce = new NonbondedForce();
1019 sys->addForce(nonbondedForce);
1024 if (ir->rcoulomb == 0)
1026 nonbondedForce->setNonbondedMethod(NonbondedForce::NoCutoff);
1030 nonbondedForce->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
1034 switch (ir->coulombtype)
1041 nonbondedForce->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
1045 nonbondedForce->setNonbondedMethod(NonbondedForce::Ewald);
1049 nonbondedForce->setNonbondedMethod(NonbondedForce::PME);
1053 gmx_fatal(FARGS,"Internal error: you should not see this message, it means that the"
1054 "electrosatics option check failed. Please report this error!");
1056 sys->setDefaultPeriodicBoxVectors(Vec3(state->box[0][0], 0, 0),
1057 Vec3(0, state->box[1][1], 0), Vec3(0, 0, state->box[2][2]));
1058 nonbondedForce->setCutoffDistance(ir->rcoulomb);
1062 gmx_fatal(FARGS,"OpenMM supports only full periodic boundary conditions "
1063 "(pbc = xyz), or none (pbc = no).");
1067 /* Fix for PME and Ewald error tolerance
1069 * OpenMM uses approximate formulas to calculate the Ewald parameter:
1070 * alpha = (1.0/cutoff)*sqrt(-log(2.0*tolerlance));
1071 * and the grid spacing for PME:
1072 * gridX = ceil(2*alpha*box[0][0]/3*(pow(tol, 0.2)))
1073 * gridY = ceil(2*alpha*box[1][1]/3*(pow(tol, 0.2)));
1074 * gridZ = ceil(2*alpha*box[2][2]/3*(pow(tol, 0.2)));
1077 * If the default ewald_rtol=1e-5 is used we silently adjust the value to the
1078 * OpenMM default of 5e-4 otherwise a warning is issued about the action taken.
1081 double corr_ewald_rtol = 50.0 * ir->ewald_rtol;
1082 if ((ir->ePBC == epbcXYZ) &&
1083 (ir->coulombtype == eelEWALD || ir->coulombtype == eelPME))
1087 fprintf(debug, ">> ewald_rtol = %e (corrected = %e) \n",
1088 ir->ewald_rtol, corr_ewald_rtol);
1091 if (fabs(ir->ewald_rtol - 1e-5) > 1e-10)
1093 gmx_warning("OpenMM uses the ewald_rtol parameter with approximate formulas "
1094 "to calculate the alpha and grid spacing parameters of the Ewald "
1095 "and PME methods. This tolerance need to be corrected in order to get "
1096 "settings close to the ones used in GROMACS. Although the internal correction "
1097 "should work for any reasonable value of ewald_rtol, using values other than "
1098 "the default 1e-5 might cause incorrect behavior.");
1100 if (corr_ewald_rtol > 1)
1102 gmx_fatal(FARGS, "The ewald_rtol accuracy term is >1 after the "
1103 "adjustment for OpenMM (%e)", corr_ewald_rtol);
1106 nonbondedForce->setEwaldErrorTolerance(corr_ewald_rtol);
1109 for (int i = 0; i < numAtoms; ++i)
1111 /* nbfp now includes the 6.0/12.0 derivative prefactors to save flops in kernels*/
1112 double c12 = nbfp[types[i]*2*ntypes+types[i]*2+1]/12.0;
1113 double c6 = nbfp[types[i]*2*ntypes+types[i]*2]/6.0;
1114 double sigma=0.0, epsilon=0.0;
1115 convert_c_12_6(c12, c6, &sigma, &epsilon);
1116 nonbondedForce->addParticle(charges[i], sigma, epsilon);
1117 sys->addParticle(masses[i]);
1120 // Build a table of all exclusions.
1121 vector<set<int> > exclusions(numAtoms);
1122 for (int i = 0; i < numAtoms; i++)
1124 int start = top->excls.index[i];
1125 int end = top->excls.index[i+1];
1126 for (int j = start; j < end; j++)
1127 exclusions[i].insert(top->excls.a[j]);
1130 // Record the 1-4 interactions, and remove them from the list of exclusions.
1131 const int* nb14Atoms = (int*) idef.il[F_LJ14].iatoms;
1133 for (int i = 0; i < num14; ++i)
1135 int type = nb14Atoms[offset++];
1136 int atom1 = nb14Atoms[offset++];
1137 int atom2 = nb14Atoms[offset++];
1138 double sigma=0, epsilon=0;
1139 convert_c_12_6(idef.iparams[type].lj14.c12A,
1140 idef.iparams[type].lj14.c6A,
1142 nonbondedForce->addException(atom1, atom2,
1143 fr->fudgeQQ*charges[atom1]*charges[atom2], sigma, epsilon);
1144 exclusions[atom1].erase(atom2);
1145 exclusions[atom2].erase(atom1);
1148 // Record exclusions.
1149 for (int i = 0; i < numAtoms; i++)
1151 for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
1155 nonbondedForce->addException(i, *iter, 0.0, 1.0, 0.0);
1160 // Add GBSA if needed.
1161 if (ir->implicit_solvent == eisGBSA)
1163 gmx_warning("The OBC scale factors alpha, beta and gamma are hardcoded in OpenMM with the default Gromacs values.");
1164 t_atoms atoms = gmx_mtop_global_atoms(top_global);
1165 GBSAOBCForce* gbsa = new GBSAOBCForce();
1167 sys->addForce(gbsa);
1168 gbsa->setSoluteDielectric(ir->epsilon_r);
1169 gbsa->setSolventDielectric(ir->gb_epsilon_solvent);
1170 gbsa->setCutoffDistance(nonbondedForce->getCutoffDistance());
1171 if (nonbondedForce->getNonbondedMethod() == NonbondedForce::NoCutoff)
1172 gbsa->setNonbondedMethod(GBSAOBCForce::NoCutoff);
1173 else if (nonbondedForce->getNonbondedMethod() == NonbondedForce::CutoffNonPeriodic)
1174 gbsa->setNonbondedMethod(GBSAOBCForce::CutoffNonPeriodic);
1175 else if (nonbondedForce->getNonbondedMethod() == NonbondedForce::CutoffPeriodic)
1176 gbsa->setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
1178 gmx_fatal(FARGS,"OpenMM supports only Reaction-Field electrostatics with OBC/GBSA.");
1180 for (int i = 0; i < numAtoms; ++i)
1182 gbsa->addParticle(charges[i],
1183 top_global->atomtypes.gb_radius[atoms.atom[i].type],
1184 top_global->atomtypes.S_hct[atoms.atom[i].type]);
1186 free_t_atoms(&atoms, FALSE);
1190 const int* constraintAtoms = (int*) idef.il[F_CONSTR].iatoms;
1192 for (int i = 0; i < numConstraints; ++i)
1194 int type = constraintAtoms[offset++];
1195 int atom1 = constraintAtoms[offset++];
1196 int atom2 = constraintAtoms[offset++];
1197 sys->addConstraint(atom1, atom2, idef.iparams[type].constr.dA);
1199 const int* settleAtoms = (int*) idef.il[F_SETTLE].iatoms;
1201 for (int i = 0; i < numSettle; ++i)
1203 int type = settleAtoms[offset++];
1204 int oxygen = settleAtoms[offset++];
1205 sys->addConstraint(oxygen, oxygen+1, idef.iparams[type].settle.doh);
1206 sys->addConstraint(oxygen, oxygen+2, idef.iparams[type].settle.doh);
1207 sys->addConstraint(oxygen+1, oxygen+2, idef.iparams[type].settle.dhh);
1210 // Create an integrator for simulating the system.
1211 double friction = (ir->opts.tau_t[0] == 0.0 ? 0.0 : 1.0/ir->opts.tau_t[0]);
1215 integ = new BrownianIntegrator(ir->opts.ref_t[0], friction, ir->delta_t);
1216 static_cast<BrownianIntegrator*>(integ)->setRandomNumberSeed(ir->ld_seed);
1218 else if (EI_SD(ir->eI))
1220 integ = new LangevinIntegrator(ir->opts.ref_t[0], friction, ir->delta_t);
1221 static_cast<LangevinIntegrator*>(integ)->setRandomNumberSeed(ir->ld_seed);
1225 integ = new VerletIntegrator(ir->delta_t);
1226 if ( ir->etc != etcNO)
1228 AndersenThermostat* thermostat = new AndersenThermostat(ir->opts.ref_t[0], friction);
1229 sys->addForce(thermostat);
1233 // Add pressure coupling
1234 if (ir->epc != epcNO)
1236 // convert gromacs pressure tensor to a scalar
1237 double pressure = (ir->ref_p[0][0] + ir->ref_p[1][1] + ir->ref_p[2][2]) / 3.0;
1238 int frequency = int(ir->tau_p / ir->delta_t); // update frequency in time steps
1239 if (frequency < 1) frequency = 1;
1240 double temperature = ir->opts.ref_t[0]; // in kelvin
1241 sys->addForce(new MonteCarloBarostat(pressure, temperature, frequency));
1244 integ->setConstraintTolerance(ir->shake_tol);
1246 // Create a context and initialize it.
1247 Context* context = NULL;
1250 OpenMM could automatically select the "best" GPU, however we're not't
1251 going to let it do that for now, as the current algorithm is very rudimentary
1252 and we anyway support only CUDA.
1253 if (platformOptStr == NULL || platformOptStr == "")
1255 context = new Context(*sys, *integ);
1260 /* which platform should we use */
1261 for (int i = 0; i < (int)Platform::getNumPlatforms() && context == NULL; i++)
1263 if (isStringEqNCase(opt->getOptionValue("platform"), Platform::getPlatform(i).getName()))
1265 Platform& platform = Platform::getPlatform(i);
1266 // set standard properties
1267 platform.setPropertyDefaultValue("CudaDevice", opt->getOptionValue("deviceid"));
1268 // TODO add extra properties
1269 context = new Context(*sys, *integ, platform);
1272 if (context == NULL)
1274 gmx_fatal(FARGS, "The requested platform \"%s\" could not be found.",
1275 opt->getOptionValue("platform").c_str());
1279 Platform& platform = context->getPlatform();
1280 fprintf(fplog, "Gromacs will use the OpenMM platform: %s\n", platform.getName().c_str());
1282 const vector<string>& properties = platform.getPropertyNames();
1285 for (int i = 0; i < (int)properties.size(); i++)
1287 fprintf(debug, ">> %s: %s\n", properties[i].c_str(),
1288 platform.getPropertyValue(*context, properties[i]).c_str());
1293 if (isStringEqNCase(opt->getOptionValue("platform"), "CUDA"))
1296 if (!from_string<int>(tmp, platform.getPropertyValue(*context, "CudaDevice"), std::dec))
1298 gmx_fatal(FARGS, "Internal error: couldn't determine the device selected by OpenMM");
1302 /* For now this is just to double-check if OpenMM selected the GPU we wanted,
1303 but when we'll let OpenMM select the GPU automatically, it will query the deviceId.
1307 gmx_fatal(FARGS, "Internal error: OpenMM is using device #%d"
1308 "while initialized for device #%d", tmp, devId);
1311 /* check GPU compatibility */
1312 char gpuname[STRLEN];
1313 devId = atoi(opt->getOptionValue("deviceid").c_str());
1314 if (!is_gmx_openmm_supported_gpu(-1, gpuname))
1316 if (!gmx_strcasecmp(opt->getOptionValue("force-device").c_str(), "yes"))
1318 sprintf(warn_buf, "Non-supported GPU selected (#%d, %s), forced continuing."
1319 "Note, that the simulation can be slow or it migth even crash.",
1321 fprintf(fplog, "%s\n", warn_buf);
1322 gmx_warning(warn_buf);
1326 gmx_fatal(FARGS, "The selected GPU (#%d, %s) is not supported by Gromacs! "
1327 "Most probably you have a low-end GPU which would not perform well, "
1328 "or new hardware that has not been tested with the current release. "
1329 "If you still want to try using the device, use the force-device=yes option.",
1335 fprintf(fplog, "Gromacs will run on the GPU #%d (%s).\n", devId, gpuname);
1340 if (isStringEqNCase(opt->getOptionValue("platform"), "CUDA"))
1342 /* pre-simulation memtest */
1343 runMemtest(fplog, -1, "Pre", opt);
1346 vector<Vec3> pos(numAtoms);
1347 vector<Vec3> vel(numAtoms);
1348 for (int i = 0; i < numAtoms; ++i)
1350 pos[i] = Vec3(state->x[i][0], state->x[i][1], state->x[i][2]);
1351 vel[i] = Vec3(state->v[i][0], state->v[i][1], state->v[i][2]);
1353 context->setPositions(pos);
1354 context->setVelocities(vel);
1356 // Return a structure containing the system, integrator, and context.
1357 OpenMMData* data = new OpenMMData();
1359 data->integrator = integ;
1360 data->context = context;
1361 data->removeCM = (ir->nstcomm > 0);
1362 data->platformOpt = opt;
1365 catch (std::exception& e)
1367 gmx_fatal(FARGS, "OpenMM exception caught while initializating: %s", e.what());
1369 return NULL; /* just to avoid warnings */
1373 * \brief Integrate one step.
1375 * \param[in] data OpenMMData object created by openmm_init().
1377 void openmm_take_one_step(void* data)
1379 // static int step = 0; printf("----> taking step #%d\n", step++);
1382 static_cast<OpenMMData*>(data)->integrator->step(1);
1384 catch (std::exception& e)
1386 gmx_fatal(FARGS, "OpenMM exception caught while taking a step: %s", e.what());
1391 * \brief Integrate n steps.
1393 * \param[in] data OpenMMData object created by openmm_init().
1395 void openmm_take_steps(void* data, int nstep)
1399 static_cast<OpenMMData*>(data)->integrator->step(nstep);
1401 catch (std::exception& e)
1403 gmx_fatal(FARGS, "OpenMM exception caught while taking a step: %s", e.what());
1408 * \brief Clean up the data structures cretead for OpenMM.
1410 * \param[in] log Log file pointer.
1411 * \param[in] data OpenMMData object created by openmm_init().
1413 void openmm_cleanup(FILE* fplog, void* data)
1415 OpenMMData* d = static_cast<OpenMMData*>(data);
1417 if (isStringEqNCase(d->platformOpt->getOptionValue("platform"), "CUDA"))
1419 /* post-simulation memtest */
1420 runMemtest(fplog, -1, "Post", d->platformOpt);
1423 delete d->integrator;
1425 delete d->platformOpt;
1430 * \brief Copy the current state information from OpenMM into the Gromacs data structures.
1432 * This function results in the requested proprties to be copied from the
1433 * GPU to host. As this represents a bottleneck, the frequency of pulling data
1434 * should be minimized.
1436 * \param[in] data OpenMMData object created by openmm_init().
1437 * \param[out] time Simulation time for which the state was created.
1438 * \param[out] state State of the system: coordinates and velocities.
1439 * \param[out] f Forces.
1440 * \param[out] enerd Energies.
1441 * \param[in] includePos True if coordinates are requested.
1442 * \param[in] includeVel True if velocities are requested.
1443 * \param[in] includeForce True if forces are requested.
1444 * \param[in] includeEnergy True if energies are requested.
1446 void openmm_copy_state(void *data,
1447 t_state *state, double *time,
1448 rvec f[], gmx_enerdata_t *enerd,
1449 gmx_bool includePos, gmx_bool includeVel, gmx_bool includeForce, gmx_bool includeEnergy)
1453 types += State::Positions;
1455 types += State::Velocities;
1457 types += State::Forces;
1459 types += State::Energy;
1464 State currentState = static_cast<OpenMMData*>(data)->context->getState(types);
1465 int numAtoms = static_cast<OpenMMData*>(data)->system->getNumParticles();
1468 for (int i = 0; i < numAtoms; i++)
1470 Vec3 x = currentState.getPositions()[i];
1471 state->x[i][0] = x[0];
1472 state->x[i][1] = x[1];
1473 state->x[i][2] = x[2];
1478 for (int i = 0; i < numAtoms; i++)
1480 Vec3 v = currentState.getVelocities()[i];
1481 state->v[i][0] = v[0];
1482 state->v[i][1] = v[1];
1483 state->v[i][2] = v[2];
1488 for (int i = 0; i < numAtoms; i++)
1490 Vec3 force = currentState.getForces()[i];
1498 int numConstraints = static_cast<OpenMMData*>(data)->system->getNumConstraints();
1499 int dof = 3*numAtoms-numConstraints;
1500 if (static_cast<OpenMMData*>(data)->removeCM)
1502 enerd->term[F_EPOT] = currentState.getPotentialEnergy();
1503 enerd->term[F_EKIN] = currentState.getKineticEnergy();
1504 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1505 enerd->term[F_TEMP] = 2.0*enerd->term[F_EKIN]/dof/BOLTZ;
1507 *time = currentState.getTime();
1509 catch (std::exception& e)
1511 gmx_fatal(FARGS, "OpenMM exception caught while retrieving state information: %s", e.what());