#include "gromacs/utility/snprintf.h"
// TODO move this to multi-sim module
-bool multisim_int_all_are_equal(const gmx_multisim_t *ms,
- int64_t value)
+bool multisim_int_all_are_equal(const gmx_multisim_t* ms, int64_t value)
{
- bool allValuesAreEqual = true;
- int64_t *buf;
+ bool allValuesAreEqual = true;
+ int64_t* buf;
GMX_RELEASE_ASSERT(ms, "Invalid use of multi-simulation pointer");
return allValuesAreEqual;
}
-int multisim_min(const gmx_multisim_t *ms, int nmin, int n)
+int multisim_min(const gmx_multisim_t* ms, int nmin, int n)
{
- int *buf;
+ int* buf;
gmx_bool bPos, bEqual;
int s, d;
bEqual = TRUE;
for (s = 0; s < ms->nsim; s++)
{
- bPos = bPos && (buf[s] > 0);
+ bPos = bPos && (buf[s] > 0);
bEqual = bEqual && (buf[s] == buf[0]);
}
if (bPos)
/* TODO Specialize this routine into init-time and loop-time versions?
e.g. bReadEkin is only true when restoring from checkpoint */
-void compute_globals(gmx_global_stat *gstat, t_commrec *cr, const t_inputrec *ir,
- t_forcerec *fr, gmx_ekindata_t *ekind,
- const rvec *x, const rvec *v, const matrix box,
- real vdwLambda, const t_mdatoms *mdatoms,
- t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
- gmx_enerdata_t *enerd, tensor force_vir, tensor shake_vir, tensor total_vir,
- tensor pres, rvec mu_tot, gmx::Constraints *constr,
- gmx::SimulationSignaller *signalCoordinator,
- const matrix lastbox, int *totalNumberOfBondedInteractions,
- gmx_bool *bSumEkinhOld, const int flags)
+void compute_globals(gmx_global_stat* gstat,
+ t_commrec* cr,
+ const t_inputrec* ir,
+ t_forcerec* fr,
+ gmx_ekindata_t* ekind,
+ const rvec* x,
+ const rvec* v,
+ const matrix box,
+ real vdwLambda,
+ const t_mdatoms* mdatoms,
+ t_nrnb* nrnb,
+ t_vcm* vcm,
+ gmx_wallcycle_t wcycle,
+ gmx_enerdata_t* enerd,
+ tensor force_vir,
+ tensor shake_vir,
+ tensor total_vir,
+ tensor pres,
+ rvec mu_tot,
+ gmx::Constraints* constr,
+ gmx::SimulationSignaller* signalCoordinator,
+ const matrix lastbox,
+ int* totalNumberOfBondedInteractions,
+ gmx_bool* bSumEkinhOld,
+ const int flags)
{
gmx_bool bEner, bPres, bTemp;
- gmx_bool bStopCM, bGStat,
- bReadEkin, bEkinAveVel, bScaleEkin, bConstrain;
+ gmx_bool bStopCM, bGStat, bReadEkin, bEkinAveVel, bScaleEkin, bConstrain;
gmx_bool bCheckNumberOfBondedInteractions;
real dvdl_ekin;
}
if (!bReadEkin)
{
- calc_ke_part(
- x, v, box,
- &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel);
+ calc_ke_part(x, v, box, &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel);
}
}
* so signal that we still have to do it.
*/
*bSumEkinhOld = TRUE;
-
}
else
{
if (PAR(cr))
{
wallcycle_start(wcycle, ewcMoveE);
- global_stat(gstat, cr, enerd, force_vir, shake_vir, mu_tot,
- ir, ekind, constr, bStopCM ? vcm : nullptr,
- signalBuffer.size(), signalBuffer.data(),
- totalNumberOfBondedInteractions,
- *bSumEkinhOld, flags);
+ global_stat(gstat, cr, enerd, force_vir, shake_vir, mu_tot, ir, ekind, constr,
+ bStopCM ? vcm : nullptr, signalBuffer.size(), signalBuffer.data(),
+ totalNumberOfBondedInteractions, *bSumEkinhOld, flags);
wallcycle_stop(wcycle, ewcMoveE);
}
signalCoordinator->finalizeSignals();
if (bEner)
{
/* Calculate the amplitude of the cosine velocity profile */
- ekind->cosacc.vcos = ekind->cosacc.mvcos/mdatoms->tmass;
+ ekind->cosacc.vcos = ekind->cosacc.mvcos / mdatoms->tmass;
}
if (bTemp)
bEkinAveVel: If TRUE, we simply multiply ekin by ekinscale to get a full step kinetic energy.
If FALSE, we average ekinh_old and ekinh*ekinscale_nhc to get an averaged half step kinetic energy.
*/
- enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, &dvdl_ekin,
- bEkinAveVel, bScaleEkin);
+ enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, &dvdl_ekin, bEkinAveVel, bScaleEkin);
enerd->dvdl_lin[efptMASS] = static_cast<double>(dvdl_ekin);
enerd->term[F_EKIN] = trace(ekind->ekin);
total_vir and pres tensors */
const DispersionCorrection::Correction correction =
- fr->dispersionCorrection->calculate(lastbox, vdwLambda);
+ fr->dispersionCorrection->calculate(lastbox, vdwLambda);
if (bEner)
{
- enerd->term[F_DISPCORR] = correction.energy;
- enerd->term[F_EPOT] += correction.energy;
+ enerd->term[F_DISPCORR] = correction.energy;
+ enerd->term[F_EPOT] += correction.energy;
enerd->term[F_DVDL_VDW] += correction.dvdl;
}
if (bPres)
correction.correctVirial(total_vir);
correction.correctPressure(pres);
enerd->term[F_PDISPCORR] = correction.pressure;
- enerd->term[F_PRES] += correction.pressure;
+ enerd->term[F_PRES] += correction.pressure;
}
}
}
-void setCurrentLambdasRerun(int64_t step, const t_lambda *fepvals,
- const t_trxframe *rerun_fr, const double *lam0,
- t_state *globalState)
+void setCurrentLambdasRerun(int64_t step,
+ const t_lambda* fepvals,
+ const t_trxframe* rerun_fr,
+ const double* lam0,
+ t_state* globalState)
{
- GMX_RELEASE_ASSERT(globalState != nullptr, "setCurrentLambdasGlobalRerun should be called with a valid state object");
+ GMX_RELEASE_ASSERT(globalState != nullptr,
+ "setCurrentLambdasGlobalRerun should be called with a valid state object");
if (rerun_fr->bLambda)
{
else
{
/* find out between which two value of lambda we should be */
- real frac = step*fepvals->delta_lambda;
- int fep_state = static_cast<int>(std::floor(frac*fepvals->n_lambda));
+ real frac = step * fepvals->delta_lambda;
+ int fep_state = static_cast<int>(std::floor(frac * fepvals->n_lambda));
/* interpolate between this state and the next */
/* this assumes that the initial lambda corresponds to lambda==0, which is verified in grompp */
- frac = frac*fepvals->n_lambda - fep_state;
+ frac = frac * fepvals->n_lambda - fep_state;
for (int i = 0; i < efptNR; i++)
{
- globalState->lambda[i] = lam0[i] + (fepvals->all_lambda[i][fep_state]) +
- frac*(fepvals->all_lambda[i][fep_state+1] - fepvals->all_lambda[i][fep_state]);
+ globalState->lambda[i] =
+ lam0[i] + (fepvals->all_lambda[i][fep_state])
+ + frac * (fepvals->all_lambda[i][fep_state + 1] - fepvals->all_lambda[i][fep_state]);
}
}
}
}
}
-void setCurrentLambdasLocal(const int64_t step, const t_lambda *fepvals,
- const double *lam0, gmx::ArrayRef<real> lambda,
- const int currentFEPState)
+void setCurrentLambdasLocal(const int64_t step,
+ const t_lambda* fepvals,
+ const double* lam0,
+ gmx::ArrayRef<real> lambda,
+ const int currentFEPState)
/* find the current lambdas. If rerunning, we either read in a state, or a lambda value,
requiring different logic. */
{
if (fepvals->delta_lambda != 0)
{
/* find out between which two value of lambda we should be */
- real frac = step*fepvals->delta_lambda;
+ real frac = step * fepvals->delta_lambda;
if (fepvals->n_lambda > 0)
{
- int fep_state = static_cast<int>(std::floor(frac*fepvals->n_lambda));
+ int fep_state = static_cast<int>(std::floor(frac * fepvals->n_lambda));
/* interpolate between this state and the next */
/* this assumes that the initial lambda corresponds to lambda==0, which is verified in grompp */
- frac = frac*fepvals->n_lambda - fep_state;
+ frac = frac * fepvals->n_lambda - fep_state;
for (int i = 0; i < efptNR; i++)
{
- lambda[i] = lam0[i] + (fepvals->all_lambda[i][fep_state]) +
- frac*(fepvals->all_lambda[i][fep_state + 1] - fepvals->all_lambda[i][fep_state]);
+ lambda[i] = lam0[i] + (fepvals->all_lambda[i][fep_state])
+ + frac * (fepvals->all_lambda[i][fep_state + 1] - fepvals->all_lambda[i][fep_state]);
}
}
else
}
}
-static void min_zero(int *n, int i)
+static void min_zero(int* n, int i)
{
if (i > 0 && (*n == 0 || i < *n))
{
gmx_incons("All 4 inputs for determining nstglobalcomm are <= 0");
}
- while (nst > 1 && ((i1 > 0 && i1 % nst != 0) ||
- (i2 > 0 && i2 % nst != 0) ||
- (i3 > 0 && i3 % nst != 0) ||
- (i4 > 0 && i4 % nst != 0)))
+ while (nst > 1
+ && ((i1 > 0 && i1 % nst != 0) || (i2 > 0 && i2 % nst != 0) || (i3 > 0 && i3 % nst != 0)
+ || (i4 > 0 && i4 % nst != 0)))
{
nst--;
}
return nst;
}
-int computeGlobalCommunicationPeriod(const gmx::MDLogger &mdlog,
- t_inputrec *ir,
- const t_commrec *cr)
+int computeGlobalCommunicationPeriod(const gmx::MDLogger& mdlog, t_inputrec* ir, const t_commrec* cr)
{
int nstglobalcomm;
{
// Set up the default behaviour
- if (!(ir->nstcalcenergy > 0 ||
- ir->nstlist > 0 ||
- ir->etc != etcNO ||
- ir->epc != epcNO))
+ if (!(ir->nstcalcenergy > 0 || ir->nstlist > 0 || ir->etc != etcNO || ir->epc != epcNO))
{
/* The user didn't choose the period for anything
important, so we just make sure we can send signals and
* here a leftover of the twin-range scheme? Can we remove
* nstlist when we remove the group scheme?
*/
- nstglobalcomm = lcd4(ir->nstcalcenergy,
- ir->nstlist,
- ir->etc != etcNO ? ir->nsttcouple : 0,
+ nstglobalcomm = lcd4(ir->nstcalcenergy, ir->nstlist, ir->etc != etcNO ? ir->nsttcouple : 0,
ir->epc != epcNO ? ir->nstpcouple : 0);
}
}
// a (performance) note and mdrun should not change ir.
if (ir->comm_mode != ecmNO && ir->nstcomm < nstglobalcomm)
{
- GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
- "WARNING: Changing nstcomm from %d to %d",
- ir->nstcomm, nstglobalcomm);
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendTextFormatted("WARNING: Changing nstcomm from %d to %d", ir->nstcomm, nstglobalcomm);
ir->nstcomm = nstglobalcomm;
}
if (cr->nnodes > 1)
{
- GMX_LOG(mdlog.info).appendTextFormatted(
- "Intra-simulation communication will occur every %d steps.\n", nstglobalcomm);
+ GMX_LOG(mdlog.info)
+ .appendTextFormatted("Intra-simulation communication will occur every %d steps.\n",
+ nstglobalcomm);
}
return nstglobalcomm;
-
}
-void rerun_parallel_comm(t_commrec *cr, t_trxframe *fr,
- gmx_bool *bLastStep)
+void rerun_parallel_comm(t_commrec* cr, t_trxframe* fr, gmx_bool* bLastStep)
{
- rvec *xp, *vp;
+ rvec *xp, *vp;
if (MASTER(cr) && *bLastStep)
{
fr->v = vp;
*bLastStep = (fr->natoms < 0);
-
}
// TODO Most of this logic seems to belong in the respective modules
-void set_state_entries(t_state *state, const t_inputrec *ir)
+void set_state_entries(t_state* state, const t_inputrec* ir)
{
/* The entries in the state in the tpx file might not correspond
* with what is needed, so we correct this here.
state->flags = 0;
if (ir->efep != efepNO || ir->bExpanded)
{
- state->flags |= (1<<estLAMBDA);
- state->flags |= (1<<estFEPSTATE);
+ state->flags |= (1 << estLAMBDA);
+ state->flags |= (1 << estFEPSTATE);
}
- state->flags |= (1<<estX);
- GMX_RELEASE_ASSERT(state->x.size() == state->natoms, "We should start a run with an initialized state->x");
+ state->flags |= (1 << estX);
+ GMX_RELEASE_ASSERT(state->x.size() == state->natoms,
+ "We should start a run with an initialized state->x");
if (EI_DYNAMICS(ir->eI))
{
- state->flags |= (1<<estV);
+ state->flags |= (1 << estV);
}
state->nnhpres = 0;
if (ir->ePBC != epbcNONE)
{
- state->flags |= (1<<estBOX);
+ state->flags |= (1 << estBOX);
if (inputrecPreserveShape(ir))
{
- state->flags |= (1<<estBOX_REL);
+ state->flags |= (1 << estBOX_REL);
}
if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK))
{
- state->flags |= (1<<estBOXV);
- state->flags |= (1<<estPRES_PREV);
+ state->flags |= (1 << estBOXV);
+ state->flags |= (1 << estPRES_PREV);
}
if (inputrecNptTrotter(ir) || (inputrecNphTrotter(ir)))
{
state->nnhpres = 1;
- state->flags |= (1<<estNHPRES_XI);
- state->flags |= (1<<estNHPRES_VXI);
- state->flags |= (1<<estSVIR_PREV);
- state->flags |= (1<<estFVIR_PREV);
- state->flags |= (1<<estVETA);
- state->flags |= (1<<estVOL0);
+ state->flags |= (1 << estNHPRES_XI);
+ state->flags |= (1 << estNHPRES_VXI);
+ state->flags |= (1 << estSVIR_PREV);
+ state->flags |= (1 << estFVIR_PREV);
+ state->flags |= (1 << estVETA);
+ state->flags |= (1 << estVOL0);
}
if (ir->epc == epcBERENDSEN)
{
- state->flags |= (1<<estBAROS_INT);
+ state->flags |= (1 << estBAROS_INT);
}
}
if (ir->etc == etcNOSEHOOVER)
{
- state->flags |= (1<<estNH_XI);
- state->flags |= (1<<estNH_VXI);
+ state->flags |= (1 << estNH_XI);
+ state->flags |= (1 << estNH_VXI);
}
if (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)
{
- state->flags |= (1<<estTHERM_INT);
+ state->flags |= (1 << estTHERM_INT);
}
- init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
+ init_gtc_state(state, state->ngtc, state->nnhpres,
+ ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
init_ekinstate(&state->ekinstate, ir);
if (ir->bExpanded)
if (ir->pull && ir->pull->bSetPbcRefToPrevStepCOM)
{
- state->flags |= (1<<estPULLCOMPREVSTEP);
+ state->flags |= (1 << estPULLCOMPREVSTEP);
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff