/*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
* GROMACS is distributed in the hope that it will be useful,
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*
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*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <math.h>
#include <string.h>
#include <assert.h>
#include "sysstuff.h"
#include "typedefs.h"
#include "macros.h"
#include "gromacs/utility/smalloc.h"
#include "macros.h"
#include "physics.h"
#include "force.h"
#include "nonbonded.h"
#include "names.h"
#include "network.h"
#include "pbc.h"
#include "ns.h"
#include "nrnb.h"
#include "bondf.h"
#include "mshift.h"
#include "txtdump.h"
#include "coulomb.h"
#include "pme.h"
#include "mdrun.h"
#include "domdec.h"
#include "qmmm.h"
#include "gmx_omp_nthreads.h"
#include "gromacs/timing/wallcycle.h"
#include "gmx_fatal.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,
gmx_bool bDoLongRangeNS)
{
char *ptr;
int nsearch;
if (!fr->ns.nblist_initialized)
{
init_neighbor_list(fp, fr, md->homenr);
}
if (fr->bTwinRange)
{
fr->nlr = 0;
}
nsearch = search_neighbours(fp, fr, box, top, groups, cr, nrnb, md,
bFillGrid, bDoLongRangeNS);
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 reduce_thread_forces(int n, rvec *f,
tensor vir_q, tensor vir_lj,
real *Vcorr_q, real *Vcorr_lj,
real *dvdl_q, real *dvdl_lj,
int nthreads, f_thread_t *f_t)
{
int t, i;
int nthreads_loop gmx_unused;
/* This reduction can run over any number of threads */
nthreads_loop = gmx_omp_nthreads_get(emntBonded);
#pragma omp parallel for num_threads(nthreads_loop) private(t) schedule(static)
for (i = 0; i < n; i++)
{
for (t = 1; t < nthreads; t++)
{
rvec_inc(f[i], f_t[t].f[i]);
}
}
for (t = 1; t < nthreads; t++)
{
*Vcorr_q += f_t[t].Vcorr_q;
*Vcorr_lj += f_t[t].Vcorr_lj;
*dvdl_q += f_t[t].dvdl[efptCOUL];
*dvdl_lj += f_t[t].dvdl[efptVDW];
m_add(vir_q, f_t[t].vir_q, vir_q);
m_add(vir_lj, f_t[t].vir_lj, vir_lj);
}
}
void gmx_print_sepdvdl(FILE *fplog, const char *s, real v, real dvdlambda)
{
fprintf(fplog, " %-30s V %12.5e dVdl %12.5e\n", s, v, dvdlambda);
}
void do_force_lowlevel(FILE *fplog, gmx_int64_t step,
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 f[],
rvec f_longrange[],
gmx_enerdata_t *enerd,
t_fcdata *fcd,
gmx_localtop_t *top,
gmx_genborn_t *born,
t_atomtypes *atype,
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;
gmx_bool bDoEpot, bSepDVDL, bSB;
int pme_flags;
matrix boxs;
rvec box_size;
t_pbc pbc;
char buf[22];
double clam_i, vlam_i;
real dvdl_dum[efptNR], dvdl_nb[efptNR], lam_i[efptNR];
real dvdl_q, dvdl_lj;
#ifdef GMX_MPI
double t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
#endif
#define PRINT_SEPDVDL(s, v, dvdlambda) if (bSepDVDL) { gmx_print_sepdvdl(fplog, s, v, dvdlambda); }
set_pbc(&pbc, fr->ePBC, box);
/* reset free energy components */
for (i = 0; i < efptNR; i++)
{
dvdl_nb[i] = 0;
dvdl_dum[i] = 0;
}
/* Reset box */
for (i = 0; (i < DIM); i++)
{
box_size[i] = box[i][i];
}
bSepDVDL = (fr->bSepDVDL && do_per_step(step, ir->nstlog));
debug_gmx();
/* do QMMM first if requested */
if (fr->bQMMM)
{
enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr);
}
if (bSepDVDL)
{
fprintf(fplog, "Step %s: non-bonded V and dVdl for rank %d:\n",
gmx_step_str(step, buf), cr->nodeid);
}
/* Call the short range functions all in one go. */
#ifdef 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, f, lambda[efptVDW],
enerd->grpp.ener[egLJSR], nrnb);
PRINT_SEPDVDL("Walls", 0.0, dvdl_walls);
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;
}
if (flags & GMX_FORCE_DO_LR)
{
donb_flags |= GMX_NONBONDED_DO_LR;
}
wallcycle_sub_start(wcycle, ewcsNONBONDED);
do_nonbonded(fr, x, f, f_longrange, 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++)
{
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, f, f_longrange, 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, ewcsBONDED);
calc_gb_forces(cr, md, born, top, x, f, fr, idef,
ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
wallcycle_sub_stop(wcycle, ewcsBONDED);
}
#ifdef 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 (bSepDVDL)
{
real V_short_range = 0;
real dvdl_short_range = 0;
for (i = 0; i < enerd->grpp.nener; i++)
{
V_short_range +=
(fr->bBHAM ?
enerd->grpp.ener[egBHAMSR][i] :
enerd->grpp.ener[egLJSR][i])
+ enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
}
dvdl_short_range = dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
PRINT_SEPDVDL("VdW and Coulomb SR particle-p.",
V_short_range,
dvdl_short_range);
}
debug_gmx();
if (debug)
{
pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
}
/* Shift the coordinates. Must be done before bonded forces and PPPM,
* but is also necessary for SHAKE and update, therefore it can NOT
* go when no bonded forces have to be evaluated.
*/
/* 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 bondeds or correct for exclusions */
if (fr->bMolPBC &&
((flags & GMX_FORCE_BONDED)
|| EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype)))
{
/* 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, cr->dd, TRUE, box);
}
debug_gmx();
if (flags & GMX_FORCE_BONDED)
{
wallcycle_sub_start(wcycle, ewcsBONDED);
calc_bonds(fplog, cr->ms,
idef, x, hist, f, fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL, atype, born,
flags,
fr->bSepDVDL && do_per_step(step, ir->nstlog), step);
/* Check if we have to determine energy differences
* at foreign lambda's.
*/
if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) &&
idef->ilsort != ilsortNO_FE)
{
if (idef->ilsort != ilsortFE_SORTED)
{
gmx_incons("The bonded interactions are not sorted for free energy");
}
for (i = 0; i < enerd->n_lambda; i++)
{
reset_foreign_enerdata(enerd);
for (j = 0; j < efptNR; j++)
{
lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
}
calc_bonds_lambda(fplog, idef, x, fr, &pbc, graph, &(enerd->foreign_grpp), enerd->foreign_term, nrnb, lam_i, md,
fcd, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
}
}
debug_gmx();
wallcycle_sub_stop(wcycle, ewcsBONDED);
}
where();
*cycles_pme = 0;
if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
{
real Vlr = 0, Vcorr = 0;
real dvdl_long_range = 0;
int status = 0;
bSB = (ir->nwall == 2);
if (bSB)
{
copy_mat(box, boxs);
svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
box_size[ZZ] *= ir->wall_ewald_zfac;
}
}
/* Do long-range electrostatics and/or LJ-PME, including related short-range
* corrections.
*/
clear_mat(fr->vir_el_recip);
clear_mat(fr->vir_lj_recip);
if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
{
real Vlr_q = 0, Vlr_lj = 0, Vcorr_q = 0, Vcorr_lj = 0;
real dvdl_long_range_q = 0, dvdl_long_range_lj = 0;
int status = 0;
if (EEL_PME_EWALD(fr->eeltype) || EVDW_PME(fr->vdwtype))
{
real dvdl_long_range_correction_q = 0;
real dvdl_long_range_correction_lj = 0;
/* 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 = gmx_omp_nthreads_get(emntBonded);
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (t = 0; t < nthreads; t++)
{
int s, e, i;
rvec *fnv;
tensor *vir_q, *vir_lj;
real *Vcorrt_q, *Vcorrt_lj, *dvdlt_q, *dvdlt_lj;
if (t == 0)
{
fnv = fr->f_novirsum;
vir_q = &fr->vir_el_recip;
vir_lj = &fr->vir_lj_recip;
Vcorrt_q = &Vcorr_q;
Vcorrt_lj = &Vcorr_lj;
dvdlt_q = &dvdl_long_range_correction_q;
dvdlt_lj = &dvdl_long_range_correction_lj;
}
else
{
fnv = fr->f_t[t].f;
vir_q = &fr->f_t[t].vir_q;
vir_lj = &fr->f_t[t].vir_lj;
Vcorrt_q = &fr->f_t[t].Vcorr_q;
Vcorrt_lj = &fr->f_t[t].Vcorr_lj;
dvdlt_q = &fr->f_t[t].dvdl[efptCOUL];
dvdlt_lj = &fr->f_t[t].dvdl[efptVDW];
for (i = 0; i < fr->natoms_force; i++)
{
clear_rvec(fnv[i]);
}
clear_mat(*vir_q);
clear_mat(*vir_lj);
}
*dvdlt_q = 0;
*dvdlt_lj = 0;
ewald_LRcorrection(fr->excl_load[t], fr->excl_load[t+1],
cr, t, fr,
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, bSB ? boxs : box, mu_tot,
ir->ewald_geometry,
ir->epsilon_surface,
fnv, *vir_q, *vir_lj,
Vcorrt_q, Vcorrt_lj,
lambda[efptCOUL], lambda[efptVDW],
dvdlt_q, dvdlt_lj);
}
if (nthreads > 1)
{
reduce_thread_forces(fr->natoms_force, fr->f_novirsum,
fr->vir_el_recip, fr->vir_lj_recip,
&Vcorr_q, &Vcorr_lj,
&dvdl_long_range_correction_q,
&dvdl_long_range_correction_lj,
nthreads, fr->f_t);
}
wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
}
if (EEL_PME_EWALD(fr->eeltype) && fr->n_tpi == 0)
{
Vcorr_q += ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
&dvdl_long_range_correction_q,
fr->vir_el_recip);
}
PRINT_SEPDVDL("Ewald excl./charge/dip. corr.", Vcorr_q, dvdl_long_range_correction_q);
PRINT_SEPDVDL("Ewald excl. corr. LJ", Vcorr_lj, dvdl_long_range_correction_lj);
enerd->dvdl_lin[efptCOUL] += dvdl_long_range_correction_q;
enerd->dvdl_lin[efptVDW] += dvdl_long_range_correction_lj;
}
if ((EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype)))
{
if (cr->duty & DUTY_PME)
{
/* 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 (EEL_PME(fr->eeltype))
{
pme_flags |= GMX_PME_DO_COULOMB;
}
if (EVDW_PME(fr->vdwtype))
{
pme_flags |= GMX_PME_DO_LJ;
}
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;
}
wallcycle_start(wcycle, ewcPMEMESH);
status = gmx_pme_do(fr->pmedata,
0, md->homenr - fr->n_tpi,
x, fr->f_novirsum,
md->chargeA, md->chargeB,
md->sqrt_c6A, md->sqrt_c6B,
md->sigmaA, md->sigmaB,
bSB ? boxs : box, cr,
DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
nrnb, wcycle,
fr->vir_el_recip, fr->ewaldcoeff_q,
fr->vir_lj_recip, fr->ewaldcoeff_lj,
&Vlr_q, &Vlr_lj,
lambda[efptCOUL], lambda[efptVDW],
&dvdl_long_range_q, &dvdl_long_range_lj, 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);
}
PRINT_SEPDVDL("PME mesh", Vlr_q + Vlr_lj, dvdl_long_range_q+dvdl_long_range_lj);
}
}
if (!EEL_PME(fr->eeltype) && EEL_PME_EWALD(fr->eeltype))
{
Vlr_q = do_ewald(ir, x, fr->f_novirsum,
md->chargeA, md->chargeB,
box_size, cr, md->homenr,
fr->vir_el_recip, fr->ewaldcoeff_q,
lambda[efptCOUL], &dvdl_long_range_q, fr->ewald_table);
PRINT_SEPDVDL("Ewald long-range", Vlr_q, dvdl_long_range_q);
}
/* Note that with separate PME nodes we get the real energies later */
enerd->dvdl_lin[efptCOUL] += dvdl_long_range_q;
enerd->dvdl_lin[efptVDW] += dvdl_long_range_lj;
enerd->term[F_COUL_RECIP] = Vlr_q + Vcorr_q;
enerd->term[F_LJ_RECIP] = Vlr_lj + Vcorr_lj;
if (debug)
{
fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
Vlr_q, Vcorr_q, enerd->term[F_COUL_RECIP]);
pr_rvecs(debug, 0, "vir_el_recip after corr", fr->vir_el_recip, 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, Vcorr_lj, enerd->term[F_LJ_RECIP]);
pr_rvecs(debug, 0, "vir_lj_recip after corr", fr->vir_lj_recip, DIM);
}
}
else
{
/* Is there a reaction-field exclusion correction needed? */
if (EEL_RF(fr->eeltype) && eelRF_NEC != fr->eeltype)
{
/* With the Verlet scheme, exclusion forces are calculated
* in the non-bonded kernel.
*/
if (ir->cutoff_scheme != ecutsVERLET)
{
real dvdl_rf_excl = 0;
enerd->term[F_RF_EXCL] =
RF_excl_correction(fr, graph, md, excl, x, f,
fr->fshift, &pbc, lambda[efptCOUL], &dvdl_rf_excl);
enerd->dvdl_lin[efptCOUL] += dvdl_rf_excl;
PRINT_SEPDVDL("RF exclusion correction",
enerd->term[F_RF_EXCL], dvdl_rf_excl);
}
}
}
where();
debug_gmx();
if (debug)
{
print_nrnb(debug, nrnb);
}
debug_gmx();
#ifdef 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)
{
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]);
epot[F_COUL_LR] = sum_v(grpp->nener, grpp->ener[egCOULLR]);
epot[F_LJ_LR] = sum_v(grpp->nener, grpp->ener[egLJLR]);
/* 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_BHAM_LR] = sum_v(grpp->nener, grpp->ener[egBHAMLR]);
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, real *lambda, t_lambda *fepvals)
{
int i, j, index;
double dlam;
enerd->dvdl_lin[efptVDW] += enerd->term[F_DVDL_VDW]; /* include dispersion correction */
enerd->term[F_DVDL] = 0.0;
for (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]);
}
}
}
/* Notes on the foreign lambda free energy difference evaluation:
* Adding the potential and ekin terms that depend linearly on lambda
* as delta lam * dvdl to the energy differences is exact.
* For the constraints this is not exact, but we have no other option
* without literally changing the lengths and reevaluating the energies at each step.
* (try to remedy this post 4.6 - MRS)
* For the non-bonded LR term we assume that the soft-core (if present)
* no longer affects the energy beyond the short-range cut-off,
* which is a very good approximation (except for exotic settings).
* (investigate how to overcome this post 4.6 - MRS)
*/
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];
}
enerd->term[F_DVDL_CONSTR] = 0;
for (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 */
for (j = 0; j < efptNR; j++)
{
/* Note that this loop is over all dhdl components, not just the separated ones */
dlam = (fepvals->all_lambda[j][i]-lambda[j]);
enerd->enerpart_lambda[i+1] += dlam*enerd->dvdl_lin[j];
if (debug)
{
fprintf(debug, "enerdiff lam %g: (%15s), non-linear %f linear %f*%f\n",
fepvals->all_lambda[j][i], efpt_names[j],
(enerd->enerpart_lambda[i+1] - enerd->enerpart_lambda[0]),
dlam, enerd->dvdl_lin[j]);
}
}
}
}
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(t_forcerec *fr, gmx_bool bNS,
gmx_enerdata_t *enerd,
gmx_bool bMaster)
{
gmx_bool bKeepLR;
int i, j;
/* First reset all energy components, except for the long range terms
* on the master at non neighbor search steps, since the long range
* terms have already been summed at the last neighbor search step.
*/
bKeepLR = (fr->bTwinRange && !bNS);
for (i = 0; (i < egNR); i++)
{
if (!(bKeepLR && bMaster && (i == egCOULLR || i == egLJLR)))
{
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;
}
/* Initialize the dVdlambda term with the long range contribution */
/* Initialize the dvdl term with the long range contribution */
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);
}