#include "config.h"
-#include <assert.h>
-#include <string.h>
-
+#include <cassert>
#include <cmath>
+#include <cstring>
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/listed-forces/listed-forces.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vecdump.h"
+#include "gromacs/mdlib/force_flags.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/mdlib/rf_util.h"
+#include "gromacs/mdlib/wall.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/forceoutput.h"
+#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-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)
+void ns(FILE *fp,
+ t_forcerec *fr,
+ matrix box,
+ const gmx_groups_t *groups,
+ gmx_localtop_t *top,
+ const t_mdatoms *md,
+ const t_commrec *cr,
+ t_nrnb *nrnb,
+ gmx_bool bFillGrid)
{
int nsearch;
}
}
-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,
+void do_force_lowlevel(t_forcerec *fr,
+ const t_inputrec *ir,
+ const t_idef *idef,
+ const t_commrec *cr,
+ const gmx_multisim_t *ms,
+ t_nrnb *nrnb,
+ gmx_wallcycle_t wcycle,
+ const 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)
+ gmx_enerdata_t *enerd,
+ t_fcdata *fcd,
+ matrix box,
+ t_lambda *fepvals,
+ real *lambda,
+ const t_graph *graph,
+ const t_blocka *excl,
+ rvec mu_tot[],
+ int flags,
+ float *cycles_pme)
{
int i, j;
int donb_flags;
if (ir->nwall)
{
/* foreign lambda component for walls */
- real dvdl_walls = do_walls(ir, fr, box, md, x, forceForUseWithShiftForces, lambda[efptVDW],
+ real dvdl_walls = do_walls(*ir, *fr, box, *md, x,
+ forceWithVirial, 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))
}
}
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
TRUE, box);
}
- do_force_listed(wcycle, box, ir->fepvals, cr,
- idef, (const rvec *) x, hist,
+ do_force_listed(wcycle, box, ir->fepvals, cr, ms,
+ idef, x, hist,
forceForUseWithShiftForces, forceWithVirial,
fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
- DOMAINDECOMP(cr) ? cr->dd->gatindex : nullptr,
+ DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr,
flags);
- where();
*cycles_pme = 0;
md->sqrt_c6A, md->sqrt_c6B,
md->sigmaA, md->sigmaB,
md->sigma3A, md->sigma3B,
- md->nChargePerturbed || md->nTypePerturbed,
+ (md->nChargePerturbed != 0) || (md->nTypePerturbed != 0),
ir->cutoff_scheme != ecutsVERLET,
excl, x, box, mu_tot,
ir->ewald_geometry,
{
real dvdl_rf_excl = 0;
enerd->term[F_RF_EXCL] =
- RF_excl_correction(fr, graph, md, excl, x, forceForUseWithShiftForces,
+ RF_excl_correction(fr, graph, md, excl, DOMAINDECOMP(cr),
+ x, forceForUseWithShiftForces,
fr->fshift, &pbc, lambda[efptCOUL], &dvdl_rf_excl);
enerd->dvdl_lin[efptCOUL] += dvdl_rf_excl;
}
}
- where();
if (debug)
{
}
}
-static real sum_v(int n, real v[])
+static real sum_v(int n, const real v[])
{
real t;
int i;
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
double &enerpart_lambda = enerd->enerpart_lambda[i + 1];
- for (size_t j = 0; j < lambda.size(); j++)
+ for (gmx::index 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];
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff