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*
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*/
#include "gmxpre.h"
#include "force.h"
#include "config.h"
#include <assert.h>
#include <string.h>
#include <cmath>
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/ewald/ewald.h"
#include "gromacs/ewald/long-range-correction.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
#include "gromacs/listed-forces/listed-forces.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/forcerec-threading.h"
#include "gromacs/mdlib/genborn.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/ns.h"
#include "gromacs/mdlib/qmmm.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/forceoutput.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
/* PLUMED */
#include "../../../Plumed.h"
int plumedswitch=0;
plumed plumedmain;
void(*plumedcmd)(plumed,const char*,const void*)=NULL;
/* END PLUMED */
void ns(FILE *fp,
t_forcerec *fr,
matrix box,
gmx_groups_t *groups,
gmx_localtop_t *top,
t_mdatoms *md,
t_commrec *cr,
t_nrnb *nrnb,
gmx_bool bFillGrid)
{
int nsearch;
if (!fr->ns->nblist_initialized)
{
init_neighbor_list(fp, fr, md->homenr);
}
nsearch = search_neighbours(fp, fr, box, top, groups, cr, nrnb, md,
bFillGrid);
if (debug)
{
fprintf(debug, "nsearch = %d\n", nsearch);
}
/* Check whether we have to do dynamic load balancing */
/*if ((nsb->nstDlb > 0) && (mod(step,nsb->nstDlb) == 0))
count_nb(cr,nsb,&(top->blocks[ebCGS]),nns,fr->nlr,
&(top->idef),opts->ngener);
*/
if (fr->ns->dump_nl > 0)
{
dump_nblist(fp, cr, fr, fr->ns->dump_nl);
}
}
static void clearEwaldThreadOutput(ewald_corr_thread_t *ewc_t)
{
ewc_t->Vcorr_q = 0;
ewc_t->Vcorr_lj = 0;
ewc_t->dvdl[efptCOUL] = 0;
ewc_t->dvdl[efptVDW] = 0;
clear_mat(ewc_t->vir_q);
clear_mat(ewc_t->vir_lj);
}
static void reduceEwaldThreadOuput(int nthreads, ewald_corr_thread_t *ewc_t)
{
ewald_corr_thread_t &dest = ewc_t[0];
for (int t = 1; t < nthreads; t++)
{
dest.Vcorr_q += ewc_t[t].Vcorr_q;
dest.Vcorr_lj += ewc_t[t].Vcorr_lj;
dest.dvdl[efptCOUL] += ewc_t[t].dvdl[efptCOUL];
dest.dvdl[efptVDW] += ewc_t[t].dvdl[efptVDW];
m_add(dest.vir_q, ewc_t[t].vir_q, dest.vir_q);
m_add(dest.vir_lj, ewc_t[t].vir_lj, dest.vir_lj);
}
}
void do_force_lowlevel(t_forcerec *fr, t_inputrec *ir,
t_idef *idef, t_commrec *cr,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
t_mdatoms *md,
rvec x[], history_t *hist,
rvec *forceForUseWithShiftForces,
gmx::ForceWithVirial *forceWithVirial,
gmx_enerdata_t *enerd,
t_fcdata *fcd,
gmx_localtop_t *top,
gmx_genborn_t *born,
gmx_bool bBornRadii,
matrix box,
t_lambda *fepvals,
real *lambda,
t_graph *graph,
t_blocka *excl,
rvec mu_tot[],
int flags,
float *cycles_pme)
{
int i, j;
int donb_flags;
int pme_flags;
t_pbc pbc;
real dvdl_dum[efptNR], dvdl_nb[efptNR];
#if GMX_MPI
double t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
#endif
set_pbc(&pbc, fr->ePBC, box);
/* reset free energy components */
for (i = 0; i < efptNR; i++)
{
dvdl_nb[i] = 0;
dvdl_dum[i] = 0;
}
/* do QMMM first if requested */
if (fr->bQMMM)
{
enerd->term[F_EQM] = calculate_QMMM(cr, forceForUseWithShiftForces, fr);
}
/* Call the short range functions all in one go. */
#if GMX_MPI
/*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
#define TAKETIME FALSE
if (TAKETIME)
{
MPI_Barrier(cr->mpi_comm_mygroup);
t0 = MPI_Wtime();
}
#endif
if (ir->nwall)
{
/* foreign lambda component for walls */
real dvdl_walls = do_walls(ir, fr, box, md, x, forceForUseWithShiftForces, lambda[efptVDW],
enerd->grpp.ener[egLJSR], nrnb);
enerd->dvdl_lin[efptVDW] += dvdl_walls;
}
/* If doing GB, reset dvda and calculate the Born radii */
if (ir->implicit_solvent)
{
wallcycle_sub_start(wcycle, ewcsNONBONDED);
for (i = 0; i < born->nr; i++)
{
fr->dvda[i] = 0;
}
if (bBornRadii)
{
calc_gb_rad(cr, fr, ir, top, x, fr->gblist, born, md, nrnb);
}
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
}
where();
/* We only do non-bonded calculation with group scheme here, the verlet
* calls are done from do_force_cutsVERLET(). */
if (fr->cutoff_scheme == ecutsGROUP && (flags & GMX_FORCE_NONBONDED))
{
donb_flags = 0;
/* Add short-range interactions */
donb_flags |= GMX_NONBONDED_DO_SR;
/* Currently all group scheme kernels always calculate (shift-)forces */
if (flags & GMX_FORCE_FORCES)
{
donb_flags |= GMX_NONBONDED_DO_FORCE;
}
if (flags & GMX_FORCE_VIRIAL)
{
donb_flags |= GMX_NONBONDED_DO_SHIFTFORCE;
}
if (flags & GMX_FORCE_ENERGY)
{
donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
}
wallcycle_sub_start(wcycle, ewcsNONBONDED);
do_nonbonded(fr, x, forceForUseWithShiftForces, md, excl,
&enerd->grpp, nrnb,
lambda, dvdl_nb, -1, -1, donb_flags);
/* If we do foreign lambda and we have soft-core interactions
* we have to recalculate the (non-linear) energies contributions.
*/
if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) && fepvals->sc_alpha != 0)
{
for (i = 0; i < enerd->n_lambda; i++)
{
real lam_i[efptNR];
for (j = 0; j < efptNR; j++)
{
lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
}
reset_foreign_enerdata(enerd);
do_nonbonded(fr, x, forceForUseWithShiftForces, md, excl,
&(enerd->foreign_grpp), nrnb,
lam_i, dvdl_dum, -1, -1,
(donb_flags & ~GMX_NONBONDED_DO_FORCE) | GMX_NONBONDED_DO_FOREIGNLAMBDA);
sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
}
}
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
where();
}
/* If we are doing GB, calculate bonded forces and apply corrections
* to the solvation forces */
/* MRS: Eventually, many need to include free energy contribution here! */
if (ir->implicit_solvent)
{
wallcycle_sub_start(wcycle, ewcsLISTED);
calc_gb_forces(cr, md, born, top, x, forceForUseWithShiftForces, fr, idef,
ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
wallcycle_sub_stop(wcycle, ewcsLISTED);
}
#if GMX_MPI
if (TAKETIME)
{
t1 = MPI_Wtime();
fr->t_fnbf += t1-t0;
}
#endif
if (fepvals->sc_alpha != 0)
{
enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
}
else
{
enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
}
if (fepvals->sc_alpha != 0)
/* even though coulomb part is linear, we already added it, beacuse we
need to go through the vdw calculation anyway */
{
enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
}
else
{
enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
}
if (debug)
{
pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
}
/* Shift the coordinates. Must be done before listed forces and PPPM,
* but is also necessary for SHAKE and update, therefore it can NOT
* go when no listed forces have to be evaluated.
*
* The shifting and PBC code is deliberately not timed, since with
* the Verlet scheme it only takes non-zero time with triclinic
* boxes, and even then the time is around a factor of 100 less
* than the next smallest counter.
*/
/* Here sometimes we would not need to shift with NBFonly,
* but we do so anyhow for consistency of the returned coordinates.
*/
if (graph)
{
shift_self(graph, box, x);
if (TRICLINIC(box))
{
inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
}
else
{
inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
}
}
/* Check whether we need to do listed interactions or correct for exclusions */
if (fr->bMolPBC &&
((flags & GMX_FORCE_LISTED)
|| EEL_RF(fr->ic->eeltype) || EEL_FULL(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype)))
{
/* TODO There are no electrostatics methods that require this
transformation, when using the Verlet scheme, so update the
above conditional. */
/* Since all atoms are in the rectangular or triclinic unit-cell,
* only single box vector shifts (2 in x) are required.
*/
set_pbc_dd(&pbc, fr->ePBC, DOMAINDECOMP(cr) ? cr->dd->nc : nullptr,
TRUE, box);
}
do_force_listed(wcycle, box, ir->fepvals, cr,
idef, (const rvec *) x, hist,
forceForUseWithShiftForces, forceWithVirial,
fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
DOMAINDECOMP(cr) ? cr->dd->gatindex : nullptr,
flags);
where();
*cycles_pme = 0;
/* Do long-range electrostatics and/or LJ-PME, including related short-range
* corrections.
*/
if (EEL_FULL(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
{
int status = 0;
real Vlr_q = 0, Vlr_lj = 0;
/* We reduce all virial, dV/dlambda and energy contributions, except
* for the reciprocal energies (Vlr_q, Vlr_lj) into the same struct.
*/
ewald_corr_thread_t &ewaldOutput = fr->ewc_t[0];
clearEwaldThreadOutput(&ewaldOutput);
if (EEL_PME_EWALD(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
{
/* With the Verlet scheme exclusion forces are calculated
* in the non-bonded kernel.
*/
/* The TPI molecule does not have exclusions with the rest
* of the system and no intra-molecular PME grid
* contributions will be calculated in
* gmx_pme_calc_energy.
*/
if ((ir->cutoff_scheme == ecutsGROUP && fr->n_tpi == 0) ||
ir->ewald_geometry != eewg3D ||
ir->epsilon_surface != 0)
{
int nthreads, t;
wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
if (fr->n_tpi > 0)
{
gmx_fatal(FARGS, "TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
}
nthreads = fr->nthread_ewc;
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (t = 0; t < nthreads; t++)
{
try
{
ewald_corr_thread_t &ewc_t = fr->ewc_t[t];
if (t > 0)
{
clearEwaldThreadOutput(&ewc_t);
}
/* Threading is only supported with the Verlet cut-off
* scheme and then only single particle forces (no
* exclusion forces) are calculated, so we can store
* the forces in the normal, single forceWithVirial->force_ array.
*/
ewald_LRcorrection(md->homenr, cr, nthreads, t, fr, ir,
md->chargeA, md->chargeB,
md->sqrt_c6A, md->sqrt_c6B,
md->sigmaA, md->sigmaB,
md->sigma3A, md->sigma3B,
md->nChargePerturbed || md->nTypePerturbed,
ir->cutoff_scheme != ecutsVERLET,
excl, x, box, mu_tot,
ir->ewald_geometry,
ir->epsilon_surface,
as_rvec_array(forceWithVirial->force_.data()),
ewc_t.vir_q, ewc_t.vir_lj,
&ewc_t.Vcorr_q, &ewc_t.Vcorr_lj,
lambda[efptCOUL], lambda[efptVDW],
&ewc_t.dvdl[efptCOUL], &ewc_t.dvdl[efptVDW]);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
if (nthreads > 1)
{
reduceEwaldThreadOuput(nthreads, fr->ewc_t);
}
wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
}
if (EEL_PME_EWALD(fr->ic->eeltype) && fr->n_tpi == 0)
{
/* This is not in a subcounter because it takes a
negligible and constant-sized amount of time */
ewaldOutput.Vcorr_q +=
ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
&ewaldOutput.dvdl[efptCOUL],
ewaldOutput.vir_q);
}
if ((EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype)) &&
thisRankHasDuty(cr, DUTY_PME) && (pme_run_mode(fr->pmedata) == PmeRunMode::CPU))
{
/* Do reciprocal PME for Coulomb and/or LJ. */
assert(fr->n_tpi >= 0);
if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
{
pme_flags = GMX_PME_SPREAD | GMX_PME_SOLVE;
if (flags & GMX_FORCE_FORCES)
{
pme_flags |= GMX_PME_CALC_F;
}
if (flags & GMX_FORCE_VIRIAL)
{
pme_flags |= GMX_PME_CALC_ENER_VIR;
}
if (fr->n_tpi > 0)
{
/* We don't calculate f, but we do want the potential */
pme_flags |= GMX_PME_CALC_POT;
}
/* With domain decomposition we close the CPU side load
* balancing region here, because PME does global
* communication that acts as a global barrier.
*/
if (DOMAINDECOMP(cr))
{
ddCloseBalanceRegionCpu(cr->dd);
}
wallcycle_start(wcycle, ewcPMEMESH);
status = gmx_pme_do(fr->pmedata,
0, md->homenr - fr->n_tpi,
x,
as_rvec_array(forceWithVirial->force_.data()),
md->chargeA, md->chargeB,
md->sqrt_c6A, md->sqrt_c6B,
md->sigmaA, md->sigmaB,
box, cr,
DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
nrnb, wcycle,
ewaldOutput.vir_q, ewaldOutput.vir_lj,
&Vlr_q, &Vlr_lj,
lambda[efptCOUL], lambda[efptVDW],
&ewaldOutput.dvdl[efptCOUL],
&ewaldOutput.dvdl[efptVDW],
pme_flags);
*cycles_pme = wallcycle_stop(wcycle, ewcPMEMESH);
if (status != 0)
{
gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
}
/* We should try to do as little computation after
* this as possible, because parallel PME synchronizes
* the nodes, so we want all load imbalance of the
* rest of the force calculation to be before the PME
* call. DD load balancing is done on the whole time
* of the force call (without PME).
*/
}
if (fr->n_tpi > 0)
{
if (EVDW_PME(ir->vdwtype))
{
gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
}
/* Determine the PME grid energy of the test molecule
* with the PME grid potential of the other charges.
*/
gmx_pme_calc_energy(fr->pmedata, fr->n_tpi,
x + md->homenr - fr->n_tpi,
md->chargeA + md->homenr - fr->n_tpi,
&Vlr_q);
}
}
}
if (!EEL_PME(fr->ic->eeltype) && EEL_PME_EWALD(fr->ic->eeltype))
{
Vlr_q = do_ewald(ir, x, as_rvec_array(forceWithVirial->force_.data()),
md->chargeA, md->chargeB,
box, cr, md->homenr,
ewaldOutput.vir_q, fr->ic->ewaldcoeff_q,
lambda[efptCOUL], &ewaldOutput.dvdl[efptCOUL],
fr->ewald_table);
}
/* Note that with separate PME nodes we get the real energies later */
forceWithVirial->addVirialContribution(ewaldOutput.vir_q);
forceWithVirial->addVirialContribution(ewaldOutput.vir_lj);
enerd->dvdl_lin[efptCOUL] += ewaldOutput.dvdl[efptCOUL];
enerd->dvdl_lin[efptVDW] += ewaldOutput.dvdl[efptVDW];
enerd->term[F_COUL_RECIP] = Vlr_q + ewaldOutput.Vcorr_q;
enerd->term[F_LJ_RECIP] = Vlr_lj + ewaldOutput.Vcorr_lj;
if (debug)
{
fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
Vlr_q, ewaldOutput.Vcorr_q, enerd->term[F_COUL_RECIP]);
pr_rvecs(debug, 0, "vir_el_recip after corr", ewaldOutput.vir_q, DIM);
pr_rvecs(debug, 0, "fshift after LR Corrections", fr->fshift, SHIFTS);
fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n",
Vlr_lj, ewaldOutput.Vcorr_lj, enerd->term[F_LJ_RECIP]);
pr_rvecs(debug, 0, "vir_lj_recip after corr", ewaldOutput.vir_lj, DIM);
}
}
else
{
/* Is there a reaction-field exclusion correction needed?
* With the Verlet scheme, exclusion forces are calculated
* in the non-bonded kernel.
*/
if (ir->cutoff_scheme != ecutsVERLET && EEL_RF(fr->ic->eeltype))
{
real dvdl_rf_excl = 0;
enerd->term[F_RF_EXCL] =
RF_excl_correction(fr, graph, md, excl, x, forceForUseWithShiftForces,
fr->fshift, &pbc, lambda[efptCOUL], &dvdl_rf_excl);
enerd->dvdl_lin[efptCOUL] += dvdl_rf_excl;
}
}
where();
if (debug)
{
print_nrnb(debug, nrnb);
}
#if GMX_MPI
if (TAKETIME)
{
t2 = MPI_Wtime();
MPI_Barrier(cr->mpi_comm_mygroup);
t3 = MPI_Wtime();
fr->t_wait += t3-t2;
if (fr->timesteps == 11)
{
char buf[22];
fprintf(stderr, "* PP load balancing info: rank %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
cr->nodeid, gmx_step_str(fr->timesteps, buf),
100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
(fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
}
fr->timesteps++;
}
#endif
if (debug)
{
pr_rvecs(debug, 0, "fshift after bondeds", fr->fshift, SHIFTS);
}
/* PLUMED */
if(plumedswitch){
int plumedNeedsEnergy;
(*plumedcmd)(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
if(!plumedNeedsEnergy) (*plumedcmd)(plumedmain,"performCalc",NULL);
}
/* END PLUMED */
}
void init_enerdata(int ngener, int n_lambda, gmx_enerdata_t *enerd)
{
int i, n2;
for (i = 0; i < F_NRE; i++)
{
enerd->term[i] = 0;
enerd->foreign_term[i] = 0;
}
for (i = 0; i < efptNR; i++)
{
enerd->dvdl_lin[i] = 0;
enerd->dvdl_nonlin[i] = 0;
}
n2 = ngener*ngener;
if (debug)
{
fprintf(debug, "Creating %d sized group matrix for energies\n", n2);
}
enerd->grpp.nener = n2;
enerd->foreign_grpp.nener = n2;
for (i = 0; (i < egNR); i++)
{
snew(enerd->grpp.ener[i], n2);
snew(enerd->foreign_grpp.ener[i], n2);
}
if (n_lambda)
{
enerd->n_lambda = 1 + n_lambda;
snew(enerd->enerpart_lambda, enerd->n_lambda);
}
else
{
enerd->n_lambda = 0;
}
}
void destroy_enerdata(gmx_enerdata_t *enerd)
{
int i;
for (i = 0; (i < egNR); i++)
{
sfree(enerd->grpp.ener[i]);
}
for (i = 0; (i < egNR); i++)
{
sfree(enerd->foreign_grpp.ener[i]);
}
if (enerd->n_lambda)
{
sfree(enerd->enerpart_lambda);
}
}
static real sum_v(int n, real v[])
{
real t;
int i;
t = 0.0;
for (i = 0; (i < n); i++)
{
t = t + v[i];
}
return t;
}
void sum_epot(gmx_grppairener_t *grpp, real *epot)
{
int i;
/* Accumulate energies */
epot[F_COUL_SR] = sum_v(grpp->nener, grpp->ener[egCOULSR]);
epot[F_LJ] = sum_v(grpp->nener, grpp->ener[egLJSR]);
epot[F_LJ14] = sum_v(grpp->nener, grpp->ener[egLJ14]);
epot[F_COUL14] = sum_v(grpp->nener, grpp->ener[egCOUL14]);
/* We have already added 1-2,1-3, and 1-4 terms to F_GBPOL */
epot[F_GBPOL] += sum_v(grpp->nener, grpp->ener[egGB]);
/* lattice part of LR doesnt belong to any group
* and has been added earlier
*/
epot[F_BHAM] = sum_v(grpp->nener, grpp->ener[egBHAMSR]);
epot[F_EPOT] = 0;
for (i = 0; (i < F_EPOT); i++)
{
if (i != F_DISRESVIOL && i != F_ORIRESDEV)
{
epot[F_EPOT] += epot[i];
}
}
}
void sum_dhdl(gmx_enerdata_t *enerd, gmx::ArrayRef<const real> lambda, t_lambda *fepvals)
{
int index;
enerd->dvdl_lin[efptVDW] += enerd->term[F_DVDL_VDW]; /* include dispersion correction */
enerd->term[F_DVDL] = 0.0;
for (int i = 0; i < efptNR; i++)
{
if (fepvals->separate_dvdl[i])
{
/* could this be done more readably/compactly? */
switch (i)
{
case (efptMASS):
index = F_DKDL;
break;
case (efptCOUL):
index = F_DVDL_COUL;
break;
case (efptVDW):
index = F_DVDL_VDW;
break;
case (efptBONDED):
index = F_DVDL_BONDED;
break;
case (efptRESTRAINT):
index = F_DVDL_RESTRAINT;
break;
default:
index = F_DVDL;
break;
}
enerd->term[index] = enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
if (debug)
{
fprintf(debug, "dvdl-%s[%2d]: %f: non-linear %f + linear %f\n",
efpt_names[i], i, enerd->term[index], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
}
}
else
{
enerd->term[F_DVDL] += enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
if (debug)
{
fprintf(debug, "dvd-%sl[%2d]: %f: non-linear %f + linear %f\n",
efpt_names[0], i, enerd->term[F_DVDL], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
}
}
}
if (fepvals->separate_dvdl[efptBONDED])
{
enerd->term[F_DVDL_BONDED] += enerd->term[F_DVDL_CONSTR];
}
else
{
enerd->term[F_DVDL] += enerd->term[F_DVDL_CONSTR];
}
for (int i = 0; i < fepvals->n_lambda; i++)
{
/* note we are iterating over fepvals here!
For the current lam, dlam = 0 automatically,
so we don't need to add anything to the
enerd->enerpart_lambda[0] */
/* we don't need to worry about dvdl_lin contributions to dE at
current lambda, because the contributions to the current
lambda are automatically zeroed */
double &enerpart_lambda = enerd->enerpart_lambda[i + 1];
for (size_t j = 0; j < lambda.size(); j++)
{
/* Note that this loop is over all dhdl components, not just the separated ones */
const double dlam = fepvals->all_lambda[j][i] - lambda[j];
enerpart_lambda += dlam*enerd->dvdl_lin[j];
/* Constraints can not be evaluated at foreign lambdas, so we add
* a linear extrapolation. This is an approximation, but usually
* quite accurate since constraints change little between lambdas.
*/
if ((j == efptBONDED && fepvals->separate_dvdl[efptBONDED]) ||
(j == efptFEP && !fepvals->separate_dvdl[efptBONDED]))
{
enerpart_lambda += dlam*enerd->term[F_DVDL_CONSTR];
}
if (j == efptMASS && !fepvals->separate_dvdl[j])
{
enerpart_lambda += dlam*enerd->term[F_DKDL];
}
if (debug)
{
fprintf(debug, "enerdiff lam %g: (%15s), non-linear %f linear %f*%f\n",
fepvals->all_lambda[j][i], efpt_names[j],
enerpart_lambda - enerd->enerpart_lambda[0],
dlam, enerd->dvdl_lin[j]);
}
}
}
/* The constrain contribution is now included in other terms, so clear it */
enerd->term[F_DVDL_CONSTR] = 0;
}
void reset_foreign_enerdata(gmx_enerdata_t *enerd)
{
int i, j;
/* First reset all foreign energy components. Foreign energies always called on
neighbor search steps */
for (i = 0; (i < egNR); i++)
{
for (j = 0; (j < enerd->grpp.nener); j++)
{
enerd->foreign_grpp.ener[i][j] = 0.0;
}
}
/* potential energy components */
for (i = 0; (i <= F_EPOT); i++)
{
enerd->foreign_term[i] = 0.0;
}
}
void reset_enerdata(gmx_enerdata_t *enerd)
{
int i, j;
/* First reset all energy components. */
for (i = 0; (i < egNR); i++)
{
for (j = 0; (j < enerd->grpp.nener); j++)
{
enerd->grpp.ener[i][j] = 0.0;
}
}
for (i = 0; i < efptNR; i++)
{
enerd->dvdl_lin[i] = 0.0;
enerd->dvdl_nonlin[i] = 0.0;
}
/* Normal potential energy components */
for (i = 0; (i <= F_EPOT); i++)
{
enerd->term[i] = 0.0;
}
enerd->term[F_DVDL] = 0.0;
enerd->term[F_DVDL_COUL] = 0.0;
enerd->term[F_DVDL_VDW] = 0.0;
enerd->term[F_DVDL_BONDED] = 0.0;
enerd->term[F_DVDL_RESTRAINT] = 0.0;
enerd->term[F_DKDL] = 0.0;
if (enerd->n_lambda > 0)
{
for (i = 0; i < enerd->n_lambda; i++)
{
enerd->enerpart_lambda[i] = 0.0;
}
}
/* reset foreign energy data - separate function since we also call it elsewhere */
reset_foreign_enerdata(enerd);
}