#include <algorithm>
#include "gromacs/domdec/domdec.h"
-#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/vec.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
return nmin;
}
-void copy_coupling_state(t_state *statea, t_state *stateb,
- gmx_ekindata_t *ekinda, gmx_ekindata_t *ekindb, t_grpopts* opts)
-{
-
- /* MRS note -- might be able to get rid of some of the arguments. Look over it when it's all debugged */
-
- int i, j, nc;
-
- /* Make sure we have enough space for x and v */
- if (statea->nalloc > stateb->nalloc)
- {
- stateb->nalloc = statea->nalloc;
- /* We need to allocate one element extra, since we might use
- * (unaligned) 4-wide SIMD loads to access rvec entries.
- */
- srenew(stateb->x, stateb->nalloc + 1);
- srenew(stateb->v, stateb->nalloc + 1);
- }
-
- stateb->natoms = statea->natoms;
- stateb->ngtc = statea->ngtc;
- stateb->nnhpres = statea->nnhpres;
- stateb->veta = statea->veta;
- if (ekinda)
- {
- copy_mat(ekinda->ekin, ekindb->ekin);
- for (i = 0; i < stateb->ngtc; i++)
- {
- ekindb->tcstat[i].T = ekinda->tcstat[i].T;
- ekindb->tcstat[i].Th = ekinda->tcstat[i].Th;
- copy_mat(ekinda->tcstat[i].ekinh, ekindb->tcstat[i].ekinh);
- copy_mat(ekinda->tcstat[i].ekinf, ekindb->tcstat[i].ekinf);
- ekindb->tcstat[i].ekinscalef_nhc = ekinda->tcstat[i].ekinscalef_nhc;
- ekindb->tcstat[i].ekinscaleh_nhc = ekinda->tcstat[i].ekinscaleh_nhc;
- ekindb->tcstat[i].vscale_nhc = ekinda->tcstat[i].vscale_nhc;
- }
- }
- copy_rvecn(statea->x, stateb->x, 0, stateb->natoms);
- copy_rvecn(statea->v, stateb->v, 0, stateb->natoms);
- copy_mat(statea->box, stateb->box);
- copy_mat(statea->box_rel, stateb->box_rel);
- copy_mat(statea->boxv, stateb->boxv);
-
- for (i = 0; i < stateb->ngtc; i++)
- {
- nc = i*opts->nhchainlength;
- for (j = 0; j < opts->nhchainlength; j++)
- {
- stateb->nosehoover_xi[nc+j] = statea->nosehoover_xi[nc+j];
- stateb->nosehoover_vxi[nc+j] = statea->nosehoover_vxi[nc+j];
- }
- }
- if (stateb->nhpres_xi != NULL)
- {
- for (i = 0; i < stateb->nnhpres; i++)
- {
- nc = i*opts->nhchainlength;
- for (j = 0; j < opts->nhchainlength; j++)
- {
- stateb->nhpres_xi[nc+j] = statea->nhpres_xi[nc+j];
- stateb->nhpres_vxi[nc+j] = statea->nhpres_vxi[nc+j];
- }
- }
- }
-}
-
-real compute_conserved_from_auxiliary(t_inputrec *ir, t_state *state, t_extmass *MassQ)
-{
- real quantity = 0;
- switch (ir->etc)
- {
- case etcNO:
- break;
- case etcBERENDSEN:
- break;
- case etcNOSEHOOVER:
- quantity = NPT_energy(ir, state, MassQ);
- break;
- case etcVRESCALE:
- quantity = vrescale_energy(&(ir->opts), state->therm_integral);
- break;
- default:
- break;
- }
- return quantity;
-}
-
/* TODO Specialize this routine into init-time and loop-time versions?
e.g. bReadEkin is only true when restoring from checkpoint */
void compute_globals(FILE *fplog, gmx_global_stat *gstat, t_commrec *cr, t_inputrec *ir,
if (bStopCM)
{
calc_vcm_grp(0, mdatoms->homenr, mdatoms,
- state->x, state->v, vcm);
+ as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), vcm);
}
if (bTemp || bStopCM || bPres || bEner || bConstrain)
{
wallcycle_start(wcycle, ewcMoveE);
global_stat(gstat, cr, enerd, force_vir, shake_vir, mu_tot,
- ir, ekind, constr, bStopCM ? vcm : NULL,
+ ir, ekind, constr, bStopCM ? vcm : nullptr,
signalBuffer.size(), signalBuffer.data(),
totalNumberOfBondedInteractions,
*bSumEkinhOld, flags);
{
correct_ekin(debug,
0, mdatoms->homenr,
- state->v, vcm->group_p[0],
+ as_rvec_array(state->v.data()), vcm->group_p[0],
mdatoms->massT, mdatoms->tmass, ekind->ekin);
}
{
check_cm_grp(fplog, vcm, ir, 1);
do_stopcm_grp(0, mdatoms->homenr, mdatoms->cVCM,
- state->x, state->v, vcm);
+ as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), vcm);
inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
}
}
}
-void check_nst_param(FILE *fplog, t_commrec *cr,
- const char *desc_nst, int nst,
- const char *desc_p, int *p)
+/* check whether an 'nst'-style parameter p is a multiple of nst, and
+ set it to be one if not, with a warning. */
+static void check_nst_param(const gmx::MDLogger &mdlog,
+ const char *desc_nst, int nst,
+ const char *desc_p, int *p)
{
if (*p > 0 && *p % nst != 0)
{
/* Round up to the next multiple of nst */
*p = ((*p)/nst + 1)*nst;
- md_print_warn(cr, fplog,
- "NOTE: %s changes %s to %d\n", desc_nst, desc_p, *p);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "NOTE: %s changes %s to %d", desc_nst, desc_p, *p);
}
}
return nst;
}
-int check_nstglobalcomm(FILE *fplog, t_commrec *cr,
- int nstglobalcomm, t_inputrec *ir)
+int check_nstglobalcomm(const gmx::MDLogger &mdlog, int nstglobalcomm, t_inputrec *ir)
{
if (!EI_DYNAMICS(ir->eI))
{
nstglobalcomm > ir->nstlist && nstglobalcomm % ir->nstlist != 0)
{
nstglobalcomm = (nstglobalcomm / ir->nstlist)*ir->nstlist;
- md_print_warn(cr, fplog, "WARNING: nstglobalcomm is larger than nstlist, but not a multiple, setting it to %d\n", nstglobalcomm);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "WARNING: nstglobalcomm is larger than nstlist, but not a multiple, setting it to %d",
+ nstglobalcomm);
}
if (ir->nstcalcenergy > 0)
{
- check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ check_nst_param(mdlog, "-gcom", nstglobalcomm,
"nstcalcenergy", &ir->nstcalcenergy);
}
if (ir->etc != etcNO && ir->nsttcouple > 0)
{
- check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ check_nst_param(mdlog, "-gcom", nstglobalcomm,
"nsttcouple", &ir->nsttcouple);
}
if (ir->epc != epcNO && ir->nstpcouple > 0)
{
- check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ check_nst_param(mdlog, "-gcom", nstglobalcomm,
"nstpcouple", &ir->nstpcouple);
}
- check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ check_nst_param(mdlog, "-gcom", nstglobalcomm,
"nstenergy", &ir->nstenergy);
- check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ check_nst_param(mdlog, "-gcom", nstglobalcomm,
"nstlog", &ir->nstlog);
}
if (ir->comm_mode != ecmNO && ir->nstcomm < nstglobalcomm)
{
- md_print_warn(cr, fplog, "WARNING: Changing nstcomm from %d to %d\n",
- ir->nstcomm, nstglobalcomm);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "WARNING: Changing nstcomm from %d to %d",
+ ir->nstcomm, nstglobalcomm);
ir->nstcomm = nstglobalcomm;
}
- if (fplog)
- {
- fprintf(fplog, "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;
}
state->flags |= (1<<estFEPSTATE);
}
state->flags |= (1<<estX);
- if (state->lambda == NULL)
- {
- snew(state->lambda, efptNR);
- }
- if (state->x == NULL)
- {
- /* We need to allocate one element extra, since we might use
- * (unaligned) 4-wide SIMD loads to access rvec entries.
- */
- snew(state->x, state->nalloc + 1);
- }
+ GMX_RELEASE_ASSERT(state->x.size() >= static_cast<unsigned int>(state->natoms), "We should start a run with an initialized state->x");
if (EI_DYNAMICS(ir->eI))
{
state->flags |= (1<<estV);
- if (state->v == NULL)
- {
- snew(state->v, state->nalloc + 1);
- }
+ state->v.resize(state->natoms + 1);
}
if (ir->eI == eiCG)
{
state->flags |= (1<<estCGP);
- if (state->cg_p == NULL)
- {
- /* cg_p is not stored in the tpx file, so we need to allocate it */
- snew(state->cg_p, state->nalloc + 1);
- }
+ /* cg_p is not stored in the tpx file, so we need to allocate it */
+ state->cg_p.resize(state->natoms + 1);
}
state->nnhpres = 0;
if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK))
{
state->flags |= (1<<estBOXV);
+ state->flags |= (1<<estPRES_PREV);
}
- if (ir->epc != epcNO)
+ if (inputrecNptTrotter(ir) || (inputrecNphTrotter(ir)))
{
- 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);
- }
- else
- {
- state->flags |= (1<<estPRES_PREV);
- }
+ 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);
}
}
init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
init_ekinstate(&state->ekinstate, ir);
- snew(state->enerhist, 1);
- init_energyhistory(state->enerhist);
- init_df_history(&state->dfhist, ir->fepvals->n_lambda);
- state->swapstate.eSwapCoords = ir->eSwapCoords;
+
+ if (ir->bExpanded)
+ {
+ snew(state->dfhist, 1);
+ init_df_history(state->dfhist, ir->fepvals->n_lambda);
+ }
+ if (ir->eSwapCoords != eswapNO)
+ {
+ if (state->swapstate == nullptr)
+ {
+ snew(state->swapstate, 1);
+ }
+ state->swapstate->eSwapCoords = ir->eSwapCoords;
+ }
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff