/*!
* \brief Convert string to integer type.
- * \param[in] s String to convert from.
- * \param[in] ios_base Basefield format flag that takes any of the following I/O
- * manipulators: dec, hex, oct.
- * \param[out] Destination variable to convert to.
+ * \param[in] s String to convert from.
+ * \param[in] f Basefield format flag that takes any of the following I/O
+ * manipulators: dec, hex, oct.
+ * \param[out] t Destination variable to convert to.
*/
template <class T>
static bool from_string(T& t, const string& s, ios_base& (*f)(ios_base&))
/*!
* \brief Split string around a given delimiter.
* \param[in] s String to split.
- * \param[in] delim Delimiter character that defines the boundaries of substring in \p s.
+ * \param[in] delim Delimiter character.
* \returns Vector of strings found in \p s.
*/
static vector<string> split(const string &s, char delim)
GmxOpenMMPlatformOptions#memtests, GmxOpenMMPlatformOptions#deviceid,
GmxOpenMMPlatformOptions#force_dev. */
/* {@ */
-#define SIZEOF_PLATFORMS 1
+#define SIZEOF_PLATFORMS 1 // 2
#define SIZEOF_MEMTESTS 3
#define SIZEOF_DEVICEIDS 1
#define SIZEOF_FORCE_DEV 2
size #SIZEOF_FORCE_DEV */
};
-const char * const GmxOpenMMPlatformOptions::platforms[SIZEOF_PLATFORMS] = { "Cuda" /*,"OpenCL"*/ };
-const char * const GmxOpenMMPlatformOptions::memtests[SIZEOF_MEMTESTS] = { "15", "full", "off" };
-const char * const GmxOpenMMPlatformOptions::deviceid[SIZEOF_DEVICEIDS] = { "0" };
-const char * const GmxOpenMMPlatformOptions::force_dev[SIZEOF_FORCE_DEV] = { "no", "yes" };
+const char * const GmxOpenMMPlatformOptions::platforms[SIZEOF_PLATFORMS]
+ = {"CUDA"};
+ //= { "Reference", "CUDA" /*,"OpenCL"*/ };
+const char * const GmxOpenMMPlatformOptions::memtests[SIZEOF_MEMTESTS]
+ = { "15", "full", "off" };
+const char * const GmxOpenMMPlatformOptions::deviceid[SIZEOF_DEVICEIDS]
+ = { "0" };
+const char * const GmxOpenMMPlatformOptions::force_dev[SIZEOF_FORCE_DEV]
+ = { "no", "yes" };
/*!
* \brief Contructor.
if (isStringEqNCase(opt, "platform"))
{
+ /* no check, this will fail if platform does not exist when we try to set it */
setOption(opt, val);
continue;
}
if (isStringEqNCase(opt, "memtest"))
{
- if (!isStringEqNCase(val, "full") && !isStringEqNCase(val, "off")) /* the value has to be an integer >15 */
+ /* the value has to be an integer >15(s) or "full" OR "off" */
+ if (!isStringEqNCase(val, "full") && !isStringEqNCase(val, "off"))
{
int secs;
if (!from_string<int>(secs, val, std::dec))
{
- gmx_fatal(FARGS, "Invalid value for option memtestoption: \"%s\"!\n", val.c_str());
+ gmx_fatal(FARGS, "Invalid value for option memtest option: \"%s\"!", val.c_str());
}
if (secs < 15)
{
gmx_fatal(FARGS, "Incorrect value for memtest option (%d). "
- "Memtest needs to run for at least 15s!\n", secs);
+ "Memtest needs to run for at least 15s!", secs);
}
}
setOption(opt, val);
int id;
if (!from_string<int>(id, val, std::dec) )
{
- gmx_fatal(FARGS, "Invalid device id: \"%s\"!\n", val.c_str());
+ gmx_fatal(FARGS, "Invalid device id: \"%s\"!", val.c_str());
}
setOption(opt, val);
continue;
if (isStringEqNCase(opt, "force-device"))
{
+ /* */
if (!isStringEqNCase(val, "yes") && !isStringEqNCase(val, "no"))
{
- gmx_fatal(FARGS, "Invalid OpenMM force option: \"%s\"!\n", val.c_str());
+ gmx_fatal(FARGS, "Invalid OpenMM force option: \"%s\"!", val.c_str());
}
setOption(opt, val);
continue;
}
// if we got till here something went wrong
- gmx_fatal(FARGS, "Invalid OpenMM platform option: \"%s\"!\n", (*it).c_str());
+ gmx_fatal(FARGS, "Invalid OpenMM platform option: \"%s\"!", (*it).c_str());
}
}
* stdout messages/log between memtest carried out before and after simulation.
* \param[in] opt Pointer to platform options object.
*/
-void runMemtest(FILE* fplog, int devId, const char* pre_post, GmxOpenMMPlatformOptions *opt)
+static void runMemtest(FILE* fplog, int devId, const char* pre_post, GmxOpenMMPlatformOptions *opt)
{
char warn_buf[STRLEN];
{
case 0: /* no memtest */
sprintf(warn_buf, "%s-simulation GPU memtest skipped. Note, that faulty memory can cause "
- "incorrect results!\n", pre_post);
- fprintf(fplog, "%s", warn_buf);
+ "incorrect results!", pre_post);
+ fprintf(fplog, "%s\n", warn_buf);
gmx_warning(warn_buf);
break; /* case 0 */
* interrupts the execution. It also warns the user about pecularities of OpenMM
* implementations.
* \param[in] ir Gromacs structure for input options, \see ::t_inputrec
- * \param[in] top Gromacs topology, \see ::gmx_localtop_t
+ * \param[in] top Gromacs local topology, \see ::gmx_localtop_t
+ * \param[in] state Gromacs state structure \see ::t_state
*/
-void checkGmxOptions(t_inputrec *ir, gmx_localtop_t *top)
+static void checkGmxOptions(t_inputrec *ir, gmx_localtop_t *top, t_state *state)
{
-
char warn_buf[STRLEN];
- // Abort if unsupported critical options are present
+ /* Abort if unsupported critical options are present */
/* Integrator */
if (ir->eI == eiMD)
- gmx_warning( "OpenMM does not support leap-frog, will use velocity-verlet integrator.\n");
+ {
+ gmx_warning( "OpenMM does not support leap-frog, will use velocity-verlet integrator.");
+ }
if ( (ir->eI != eiMD) &&
(ir->eI != eiVV) &&
(ir->eI != eiSD2) &&
(ir->eI != eiBD) )
{
- gmx_fatal(FARGS, "OpenMM supports only the following integrators: md/md-vv/md-vv-avek, sd/sd1, and bd.\n");
+ gmx_fatal(FARGS, "OpenMM supports only the following integrators: md/md-vv/md-vv-avek, sd/sd1, and bd.");
}
/* Electroctstics */
( !(ir->coulombtype == eelCUT && ir->rcoulomb == 0 && ir->rvdw == 0)) )
{
gmx_fatal(FARGS,"OpenMM supports only the following methods for electrostatics: "
- "NoCutoff (i.e. rcoulomb = rvdw = 0 ),Reaction-Field, Ewald or PME.\n");
+ "NoCutoff (i.e. rcoulomb = rvdw = 0 ),Reaction-Field, Ewald or PME.");
}
- if ( (ir->etc != etcNO) &&
- (ir->eI != eiSD1) &&
- (ir->eI != eiSD2) &&
- (ir->eI != eiBD) )
+ if (ir->etc != etcNO &&
+ ir->eI != eiSD1 &&
+ ir->eI != eiSD2 &&
+ ir->eI != eiBD )
{
- gmx_warning("OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators.\n");
+ gmx_warning("OpenMM supports only Andersen thermostat with the md/md-vv/md-vv-avek integrators.");
}
if (ir->opts.ngtc > 1)
- gmx_fatal(FARGS,"OpenMM does not support multiple temperature coupling groups.\n");
+ gmx_fatal(FARGS,"OpenMM does not support multiple temperature coupling groups.");
if (ir->epc != etcNO)
- gmx_fatal(FARGS,"OpenMM does not support pressure coupling.\n");
+ gmx_fatal(FARGS,"OpenMM does not support pressure coupling.");
if (ir->opts.annealing[0])
- gmx_fatal(FARGS,"OpenMM does not support simulated annealing.\n");
+ gmx_fatal(FARGS,"OpenMM does not support simulated annealing.");
if (ir->eConstrAlg != econtSHAKE)
- gmx_warning("Constraints in OpenMM are done by a combination "
+ gmx_warning("OpenMM provides contraints as a combination "
"of SHAKE, SETTLE and CCMA. Accuracy is based on the SHAKE tolerance set "
- "by the \"shake_tol\" option.\n");
+ "by the \"shake_tol\" option.");
if (ir->nwall != 0)
- gmx_fatal(FARGS,"OpenMM does not support walls.\n");
+ gmx_fatal(FARGS,"OpenMM does not support walls.");
if (ir->ePull != epullNO)
- gmx_fatal(FARGS,"OpenMM does not support pulling.\n");
+ gmx_fatal(FARGS,"OpenMM does not support pulling.");
- if (top->idef.il[F_DISRES].nr > 0)
- gmx_fatal(FARGS,"OpenMM does not support distant restraints.\n");
-
- if (top->idef.il[F_ORIRES].nr > 0)
- gmx_fatal(FARGS,"OpenMM does not support orientation restraints.\n");
-
- if (top->idef.il[F_ANGRES].nr > 0)
- gmx_fatal(FARGS,"OpenMM does not support angle restraints.\n");
-
- if (top->idef.il[F_DIHRES].nr > 0)
- gmx_fatal(FARGS,"OpenMM does not support dihedral restraints.\n");
+ /* check for restraints */
+ int i;
+ for (i = 0; i < F_EPOT; i++)
+ {
+ if (i != F_CONSTR &&
+ i != F_SETTLE &&
+ i != F_BONDS &&
+ i != F_ANGLES &&
+ i != F_PDIHS &&
+ i != F_RBDIHS &&
+ i != F_LJ14 &&
+ top->idef.il[i].nr > 0)
+ {
+ /* TODO fix the message */
+ gmx_fatal(FARGS, "OpenMM does not support (some) of the provided restaint(s).");
+ }
+ }
if (ir->efep != efepNO)
- gmx_fatal(FARGS,"OpenMM does not support free energy calculations.\n");
+ gmx_fatal(FARGS,"OpenMM does not support free energy calculations.");
if (ir->opts.ngacc > 1)
- gmx_fatal(FARGS,"OpenMM does not support non-equilibrium MD (accelerated groups).\n");
+ gmx_fatal(FARGS,"OpenMM does not support non-equilibrium MD (accelerated groups).");
if (IR_ELEC_FIELD(*ir))
- gmx_fatal(FARGS,"OpenMM does not support electric fields.\n");
+ gmx_fatal(FARGS,"OpenMM does not support electric fields.");
if (ir->bQMMM)
- gmx_fatal(FARGS,"OpenMM does not support QMMM calculations.\n");
+ gmx_fatal(FARGS,"OpenMM does not support QMMM calculations.");
if (ir->rcoulomb != ir->rvdw)
gmx_fatal(FARGS,"OpenMM uses a single cutoff for both Coulomb "
- "and VdW interactions. Please set rcoulomb equal to rvdw.\n");
+ "and VdW interactions. Please set rcoulomb equal to rvdw.");
+
+ if (EEL_FULL(ir->coulombtype))
+ {
+ if (ir->ewald_geometry == eewg3DC)
+ gmx_fatal(FARGS,"OpenMM supports only Ewald 3D geometry.");
+ if (ir->epsilon_surface != 0)
+ gmx_fatal(FARGS,"OpenMM does not support dipole correction in Ewald summation.");
+ }
+ if (TRICLINIC(state->box))
+ {
+ gmx_fatal(FARGS,"OpenMM does not support triclinic unit cells.");
+ }
+
+}
+
+
+/*!
+ * \brief Convert Lennard-Jones parameters c12 and c6 to sigma and epsilon.
+ *
+ * \param[in] c12
+ * \param[in] c6
+ * \param[out] sigma
+ * \param[out] epsilon
+ */
+static void* convert_c_12_6(double c12, double c6, double *sigma, double *epsilon)
+{
+ if (c12 == 0 && c6 == 0)
+ {
+ *epsilon = 0.0;
+ *sigma = 1.0;
+ }
+ else if (c12 > 0 && c6 > 0)
+ {
+ *epsilon = (c6*c6)/(4.0*c12);
+ *sigma = pow(c12/c6, 1.0/6.0);
+ }
+ else
+ {
+ gmx_fatal(FARGS,"OpenMM does only supports c6 > 0 and c12 > 0 or both 0.");
+ }
}
/*!
*
* \param[in] fplog Gromacs log file handler.
* \param[in] platformOptStr Platform option string.
- * \param[in] cr TODO remove!
- * \param[in] ir The Gromacs input parameters.
- * \param[in] top_global TODO
- * \param[in] top TODO
- * \param[in] mdatoms TODO
- * \param[in] fr TODO
- * \param[in] state TODO
+ * \param[in] ir The Gromacs input parameters, see ::t_inputrec
+ * \param[in] top_global TODO Gromacs whole system toppology, \see ::gmx_mtop_t
+ * \param[in] top TODO Gromacs node local topology, \see gmx_localtop_t
+ * \param[in] mdatoms TODO \see ::t_mdatoms
+ * \param[in] fr TODO \see ::t_forcerec
+ * \param[in] state TODO \see ::t_state
*
*/
void* openmm_init(FILE *fplog, const char *platformOptStr,
- t_commrec *cr,t_inputrec *ir,
+ t_inputrec *ir,
gmx_mtop_t *top_global, gmx_localtop_t *top,
- t_mdatoms *mdatoms, t_forcerec *fr,t_state *state)
+ t_mdatoms *mdatoms, t_forcerec *fr, t_state *state)
{
char warn_buf[STRLEN];
GmxOpenMMPlatformOptions *opt = new GmxOpenMMPlatformOptions(platformOptStr);
/* check wheter Gromacs options compatibility with OpenMM */
- checkGmxOptions(ir, top);
+ checkGmxOptions(ir, top, state);
// Create the system.
const t_idef& idef = top->idef;
real* masses = mdatoms->massT;
NonbondedForce* nonbondedForce = new NonbondedForce();
sys->addForce(nonbondedForce);
-
- if (ir->rcoulomb == 0)
- {
- nonbondedForce->setNonbondedMethod(NonbondedForce::NoCutoff);
- }
- else
+
+ switch (ir->ePBC)
{
+ case epbcNONE:
+ if (ir->rcoulomb == 0)
+ {
+ nonbondedForce->setNonbondedMethod(NonbondedForce::NoCutoff);
+ }
+ else
+ {
+ nonbondedForce->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
+ }
+ break;
+ case epbcXYZ:
switch (ir->coulombtype)
{
- case eelRF: // TODO what is the correct condition?
- if (ir->ePBC == epbcXYZ)
- {
- nonbondedForce->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
- sys->setPeriodicBoxVectors(Vec3(state->box[0][0], 0, 0),
- Vec3(0, state->box[1][1], 0), Vec3(0, 0, state->box[2][2]));
- }
- else if (ir->ePBC == epbcNONE)
- nonbondedForce->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
- else
- gmx_fatal(FARGS,"OpenMM supports only full periodic boundary conditions "
- "(pbc = xyz), or none (pbc = no).\n");
- nonbondedForce->setCutoffDistance(ir->rcoulomb);
+ case eelRF:
+ nonbondedForce->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
break;
case eelEWALD:
- if (ir->ewald_geometry == eewg3DC)
- gmx_fatal(FARGS,"OpenMM supports only Ewald 3D geometry.\n");
- if (ir->epsilon_surface != 0)
- gmx_fatal(FARGS,"OpenMM does not support dipole correction in Ewald summation.\n");
nonbondedForce->setNonbondedMethod(NonbondedForce::Ewald);
- nonbondedForce->setCutoffDistance(ir->rcoulomb);
- sys->setPeriodicBoxVectors(Vec3(state->box[0][0], 0, 0),
- Vec3(0, state->box[1][1], 0), Vec3(0, 0, state->box[2][2]));
break;
case eelPME:
nonbondedForce->setNonbondedMethod(NonbondedForce::PME);
- nonbondedForce->setCutoffDistance(ir->rcoulomb);
- sys->setPeriodicBoxVectors(Vec3(state->box[0][0], 0, 0),
- Vec3(0, state->box[1][1], 0), Vec3(0, 0, state->box[2][2]));
break;
default:
gmx_fatal(FARGS,"Internal error: you should not see this message, it that the"
"electrosatics option check failed. Please report this error!");
- }
+ }
+ sys->setPeriodicBoxVectors(Vec3(state->box[0][0], 0, 0),
+ Vec3(0, state->box[1][1], 0), Vec3(0, 0, state->box[2][2]));
+ nonbondedForce->setCutoffDistance(ir->rcoulomb);
+
+ break;
+ default:
+ gmx_fatal(FARGS,"OpenMM supports only full periodic boundary conditions "
+ "(pbc = xyz), or none (pbc = no).");
}
for (int i = 0; i < numAtoms; ++i)
{
- real c6 = nbfp[types[i]*2*ntypes+types[i]*2];
- real c12 = nbfp[types[i]*2*ntypes+types[i]*2+1];
- if (c12 <= 0)
- nonbondedForce->addParticle(charges[i], 1.0, 0.0);
- else
- nonbondedForce->addParticle(charges[i], pow(c12/c6, (real) (1.0/6.0)), c6*c6/(4.0*c12));
+ double c12 = nbfp[types[i]*2*ntypes+types[i]*2+1];
+ double c6 = nbfp[types[i]*2*ntypes+types[i]*2];
+ double sigma, epsilon;
+ convert_c_12_6(c12, c6, &sigma, &epsilon);
+ nonbondedForce->addParticle(charges[i], sigma, epsilon);
sys->addParticle(masses[i]);
}
int type = nb14Atoms[offset++];
int atom1 = nb14Atoms[offset++];
int atom2 = nb14Atoms[offset++];
- real c6 = idef.iparams[type].lj14.c6A;
- real c12 = idef.iparams[type].lj14.c12A;
- real sigma, epsilon;
- if (c12 <= 0)
- {
- epsilon = (real) 0.0;
- sigma = (real) 1.0;
- }
- else
- {
- epsilon = (real) ((c6*c6)/(4.0*c12));
- sigma = (real) pow(c12/c6, (real) (1.0/6.0));
- }
+ double sigma, epsilon;
+ convert_c_12_6(idef.iparams[type].lj14.c12A,
+ idef.iparams[type].lj14.c6A,
+ &sigma, &epsilon);
nonbondedForce->addException(atom1, atom2,
fr->fudgeQQ*charges[atom1]*charges[atom2], sigma, epsilon);
exclusions[atom1].erase(atom2);
for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
{
if (i < *iter)
+ {
nonbondedForce->addException(i, *iter, 0.0, 1.0, 0.0);
+ }
}
}
// Add GBSA if needed.
- t_atoms atoms;
- atoms = gmx_mtop_global_atoms(top_global);
-
if (ir->implicit_solvent == eisGBSA)
{
- GBSAOBCForce* gbsa = new GBSAOBCForce();
+ t_atoms atoms = gmx_mtop_global_atoms(top_global);
+ GBSAOBCForce* gbsa = new GBSAOBCForce();
+
sys->addForce(gbsa);
gbsa->setSoluteDielectric(ir->epsilon_r);
gbsa->setSolventDielectric(ir->gb_epsilon_solvent);
else if (nonbondedForce->getNonbondedMethod() == NonbondedForce::CutoffPeriodic)
gbsa->setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
else
- gmx_fatal(FARGS,"OpenMM supports only Reaction-Field electrostatics with OBC/GBSA.\n");
+ gmx_fatal(FARGS,"OpenMM supports only Reaction-Field electrostatics with OBC/GBSA.");
for (int i = 0; i < numAtoms; ++i)
+ {
gbsa->addParticle(charges[i],
top_global->atomtypes.gb_radius[atoms.atom[i].type],
top_global->atomtypes.S_hct[atoms.atom[i].type]);
+ }
+ free_t_atoms(&atoms, FALSE);
}
// Set constraints.
}
// Create an integrator for simulating the system.
- real friction = (ir->opts.tau_t[0] == 0.0 ? 0.0 : 1.0/ir->opts.tau_t[0]);
+ double friction = (ir->opts.tau_t[0] == 0.0 ? 0.0 : 1.0/ir->opts.tau_t[0]);
Integrator* integ;
- if (ir->eI == eiMD || ir->eI == eiVV || ir->eI == eiVVAK)
- {
- integ = new VerletIntegrator(ir->delta_t);
- if ( ir->etc != etcNO)
- {
- real collisionFreq = ir->opts.tau_t[0] / 1000; /* tau_t (ps) / 1000 = collisionFreq (fs^-1) */
- AndersenThermostat* thermostat = new AndersenThermostat(ir->opts.ref_t[0], friction);
- sys->addForce(thermostat);
- }
- }
- else if (ir->eI == eiBD)
+ if (ir->eI == eiBD)
{
integ = new BrownianIntegrator(ir->opts.ref_t[0], friction, ir->delta_t);
static_cast<BrownianIntegrator*>(integ)->setRandomNumberSeed(ir->ld_seed);
integ = new LangevinIntegrator(ir->opts.ref_t[0], friction, ir->delta_t);
static_cast<LangevinIntegrator*>(integ)->setRandomNumberSeed(ir->ld_seed);
}
+ else
+ {
+ integ = new VerletIntegrator(ir->delta_t);
+ if ( ir->etc != etcNO)
+ {
+ real collisionFreq = ir->opts.tau_t[0] / 1000; /* tau_t (ps) / 1000 = collisionFreq (fs^-1) */
+ AndersenThermostat* thermostat = new AndersenThermostat(ir->opts.ref_t[0], friction);
+ sys->addForce(thermostat);
+ }
+ }
integ->setConstraintTolerance(ir->shake_tol);
// Create a context and initialize it.
}
if (context == NULL)
{
- gmx_fatal(FARGS, "The requested platform \"%s\" could not be found.\n",
+ gmx_fatal(FARGS, "The requested platform \"%s\" could not be found.",
opt->getOptionValue("platform").c_str());
}
}
}
}
- /* For now this is just to double-check if OpenMM selected the GPU we wanted,
- but when we'll let OpenMM select the GPU automatically it will query the devideId.
- */
- int tmp;
- if (!from_string<int>(tmp, platform.getPropertyValue(*context, "CudaDevice"), std::dec))
+ /* only for CUDA */
+ if (isStringEqNCase(opt->getOptionValue("platform"), "CUDA"))
{
- gmx_fatal(FARGS, "Internal error: couldn't determine the device selected by OpenMM");
- if (tmp != devId)
+ /* For now this is just to double-check if OpenMM selected the GPU we wanted,
+ but when we'll let OpenMM select the GPU automatically, it will query the devideId.
+ */
+ int tmp;
+ if (!from_string<int>(tmp, platform.getPropertyValue(*context, "CudaDevice"), std::dec))
{
- gmx_fatal(FARGS, "Internal error: OpenMM is using device #%d while initialized for device #%d",
- tmp, devId);
+ gmx_fatal(FARGS, "Internal error: couldn't determine the device selected by OpenMM");
+ if (tmp != devId)
+ {
+ gmx_fatal(FARGS, "Internal error: OpenMM is using device #%d"
+ "while initialized for device #%d", tmp, devId);
+ }
}
- }
-
- /* check GPU compatibility */
- char gpuname[STRLEN];
- devId = atoi(opt->getOptionValue("deviceid").c_str());
- if (!is_supported_cuda_gpu(-1, gpuname))
- {
- if (!gmx_strcasecmp(opt->getOptionValue("force-device").c_str(), "yes"))
+
+ /* check GPU compatibility */
+ char gpuname[STRLEN];
+ devId = atoi(opt->getOptionValue("deviceid").c_str());
+ if (!is_supported_cuda_gpu(-1, gpuname))
{
- sprintf(warn_buf, "Non-supported GPU selected (#%d, %s), forced continuing.\n"
- "Note, that the simulation can be slow or it migth even crash.",
- devId, gpuname);
- fprintf(fplog, "%s", warn_buf);
- gmx_warning(warn_buf);
+ if (!gmx_strcasecmp(opt->getOptionValue("force-device").c_str(), "yes"))
+ {
+ sprintf(warn_buf, "Non-supported GPU selected (#%d, %s), forced continuing."
+ "Note, that the simulation can be slow or it migth even crash.",
+ devId, gpuname);
+ fprintf(fplog, "%s\n", warn_buf);
+ gmx_warning(warn_buf);
+ }
+ else
+ {
+ gmx_fatal(FARGS, "The selected GPU (#%d, %s) is not supported by Gromacs! "
+ "Most probably you have a low-end GPU which would not perform well, "
+ "or new hardware that has not been tested yet with Gromacs-OpenMM. "
+ "If you still want to try using the device, use the force=on option.",
+ devId, gpuname);
+ }
}
else
{
- gmx_fatal(FARGS, "The selected GPU (#%d, %s) is not supported by Gromacs! "
- "Most probably you have a low-end GPU which would not perform well, "
- "or new hardware that has not been tested yet with Gromacs-OpenMM. "
- "If you still want to try using the device, use the force=on option.",
- devId, gpuname);
+ fprintf(fplog, "Gromacs will run on the GPU #%d (%s).\n", devId, gpuname);
}
}
- else
+
+ /* only for CUDA */
+ if (isStringEqNCase(opt->getOptionValue("platform"), "CUDA"))
{
- fprintf(fplog, "Gromacs will run on the GPU #%d (%s).\n", devId, gpuname);
+ /* pre-simulation memtest */
+ runMemtest(fplog, -1, "Pre", opt);
}
- /* do the pre-simulation memtest */
- runMemtest(fplog, -1, "Pre", opt);
-
vector<Vec3> pos(numAtoms);
vector<Vec3> vel(numAtoms);
for (int i = 0; i < numAtoms; ++i)
}
catch (std::exception& e)
{
- gmx_fatal(FARGS, "OpenMM exception caught while initializating: %s\n", e.what());
+ gmx_fatal(FARGS, "OpenMM exception caught while initializating: %s", e.what());
}
}
}
catch (std::exception& e)
{
- gmx_fatal(FARGS, "OpenMM exception caught while taking a step: %s\n", e.what());
+ gmx_fatal(FARGS, "OpenMM exception caught while taking a step: %s", e.what());
}
}
}
catch (std::exception& e)
{
- gmx_fatal(FARGS, "OpenMM exception caught while taking a step: %s\n", e.what());
+ gmx_fatal(FARGS, "OpenMM exception caught while taking a step: %s", e.what());
}
}
void openmm_cleanup(FILE* fplog, void* data)
{
OpenMMData* d = static_cast<OpenMMData*>(data);
- runMemtest(fplog, -1, "Post", d->platformOpt);
+ /* only for CUDA */
+ if (isStringEqNCase(d->platformOpt->getOptionValue("platform"), "CUDA"))
+ {
+ /* post-simulation memtest */
+ runMemtest(fplog, -1, "Post", d->platformOpt);
+ }
delete d->system;
delete d->integrator;
delete d->context;
* should be minimized.
*
* \param[in] data OpenMMData object created by openmm_init().
- * \param[out] time
+ * \param[out] time Simulation time for which the state was created.
* \param[out] state State of the system: coordinates and velocities.
* \param[out] f Forces.
* \param[out] enerd Energies.
}
catch (std::exception& e)
{
- gmx_fatal(FARGS, "OpenMM exception caught while retrieving state information: %s\n", e.what());
+ gmx_fatal(FARGS, "OpenMM exception caught while retrieving state information: %s", e.what());
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff