#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/mdtypes/mdrunoptions.h"
#include "gromacs/mdtypes/state.h"
-#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
gmx_localtop_t* top,
t_nrnb* nrnb,
t_forcerec* fr,
- t_graph** graph,
gmx::MDAtoms* mdAtoms,
gmx_global_stat_t* gstat,
gmx_vsite_t* vsite,
imdSession, pull_work, &ems->s, &ems->f, mdAtoms, top, fr, vsite,
constr, nrnb, nullptr, FALSE);
dd_store_state(cr->dd, &ems->s);
-
- *graph = nullptr;
}
else
{
state_change_natoms(&ems->s, ems->s.natoms);
ems->f.resizeWithPadding(ems->s.natoms);
- mdAlgorithmsSetupAtomData(cr, ir, *top_global, top, fr, graph, mdAtoms, constr, vsite,
+ mdAlgorithmsSetupAtomData(cr, ir, *top_global, top, fr, mdAtoms, constr, vsite,
shellfc ? *shellfc : nullptr);
if (vsite)
gmx::Constraints* constr;
//! Handles strange things.
t_fcdata* fcd;
- //! Molecular graph for SHAKE.
- t_graph* graph;
//! Per-atom data for this domain.
gmx::MDAtoms* mdAtoms;
//! Handles how to calculate the forces.
do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle,
top, ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd, ems->s.lambda,
- graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
+ fr, runScheduleWork, vsite, mu_tot, t, nullptr,
GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY
| (bNS ? GMX_FORCE_NS : 0),
DDBalanceRegionHandler(cr));
gmx_localtop_t top(top_global->ffparams);
gmx_global_stat_t gstat;
- t_graph* graph;
double tmp, minstep;
real stepsize;
real a, b, c, beta = 0.0;
/* Init em and store the local state in s_min */
init_em(fplog, mdlog, CG, cr, inputrec, imdSession, pull_work, state_global, top_global, s_min,
- &top, nrnb, fr, &graph, mdAtoms, &gstat, vsite, constr, nullptr);
+ &top, nrnb, fr, mdAtoms, &gstat, vsite, constr, nullptr);
const bool simulationsShareState = false;
gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
mdModulesNotifier, inputrec, top_global, nullptr, wcycle,
}
EnergyEvaluator energyEvaluator{
- fplog, mdlog, cr, ms, top_global, &top, inputrec,
- imdSession, pull_work, nrnb, wcycle, gstat, vsite, constr,
- fcd, graph, mdAtoms, fr, runScheduleWork, enerd
+ fplog, mdlog, cr, ms, top_global, &top, inputrec, imdSession, pull_work,
+ nrnb, wcycle, gstat, vsite, constr, fcd, mdAtoms, fr, runScheduleWork,
+ enerd
};
/* Call the force routine and some auxiliary (neighboursearching etc.) */
/* do_force always puts the charge groups in the box and shifts again
em_state_t ems;
gmx_localtop_t top(top_global->ffparams);
gmx_global_stat_t gstat;
- t_graph* graph;
int ncorr, nmaxcorr, point, cp, neval, nminstep;
double stepsize, step_taken, gpa, gpb, gpc, tmp, minstep;
real * rho, *alpha, *p, *s, **dx, **dg;
/* Init em */
init_em(fplog, mdlog, LBFGS, cr, inputrec, imdSession, pull_work, state_global, top_global,
- &ems, &top, nrnb, fr, &graph, mdAtoms, &gstat, vsite, constr, nullptr);
+ &ems, &top, nrnb, fr, mdAtoms, &gstat, vsite, constr, nullptr);
const bool simulationsShareState = false;
gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
mdModulesNotifier, inputrec, top_global, nullptr, wcycle,
*/
neval++;
EnergyEvaluator energyEvaluator{
- fplog, mdlog, cr, ms, top_global, &top, inputrec,
- imdSession, pull_work, nrnb, wcycle, gstat, vsite, constr,
- fcd, graph, mdAtoms, fr, runScheduleWork, enerd
+ fplog, mdlog, cr, ms, top_global, &top, inputrec, imdSession, pull_work,
+ nrnb, wcycle, gstat, vsite, constr, fcd, mdAtoms, fr, runScheduleWork,
+ enerd
};
energyEvaluator.run(&ems, mu_tot, vir, pres, -1, TRUE);
const char* SD = "Steepest Descents";
gmx_localtop_t top(top_global->ffparams);
gmx_global_stat_t gstat;
- t_graph* graph;
real stepsize;
real ustep;
gmx_bool bDone, bAbort, do_x, do_f;
/* Init em and store the local state in s_try */
init_em(fplog, mdlog, SD, cr, inputrec, imdSession, pull_work, state_global, top_global, s_try,
- &top, nrnb, fr, &graph, mdAtoms, &gstat, vsite, constr, nullptr);
+ &top, nrnb, fr, mdAtoms, &gstat, vsite, constr, nullptr);
const bool simulationsShareState = false;
gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
mdModulesNotifier, inputrec, top_global, nullptr, wcycle,
sp_header(fplog, SD, inputrec->em_tol, nsteps);
}
EnergyEvaluator energyEvaluator{
- fplog, mdlog, cr, ms, top_global, &top, inputrec,
- imdSession, pull_work, nrnb, wcycle, gstat, vsite, constr,
- fcd, graph, mdAtoms, fr, runScheduleWork, enerd
+ fplog, mdlog, cr, ms, top_global, &top, inputrec, imdSession, pull_work,
+ nrnb, wcycle, gstat, vsite, constr, fcd, mdAtoms, fr, runScheduleWork,
+ enerd
};
/**** HERE STARTS THE LOOP ****
int nnodes;
gmx_localtop_t top(top_global->ffparams);
gmx_global_stat_t gstat;
- t_graph* graph;
tensor vir, pres;
rvec mu_tot = { 0 };
rvec* dfdx;
/* Init em and store the local state in state_minimum */
init_em(fplog, mdlog, NM, cr, inputrec, imdSession, pull_work, state_global, top_global,
- &state_work, &top, nrnb, fr, &graph, mdAtoms, &gstat, vsite, constr, &shellfc);
+ &state_work, &top, nrnb, fr, mdAtoms, &gstat, vsite, constr, &shellfc);
const bool simulationsShareState = false;
gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
mdModulesNotifier, inputrec, top_global, nullptr, wcycle,
/* Make evaluate_energy do a single node force calculation */
cr->nnodes = 1;
EnergyEvaluator energyEvaluator{
- fplog, mdlog, cr, ms, top_global, &top, inputrec,
- imdSession, pull_work, nrnb, wcycle, gstat, vsite, constr,
- fcd, graph, mdAtoms, fr, runScheduleWork, enerd
+ fplog, mdlog, cr, ms, top_global, &top, inputrec, imdSession, pull_work,
+ nrnb, wcycle, gstat, vsite, constr, fcd, mdAtoms, fr, runScheduleWork,
+ enerd
};
energyEvaluator.run(&state_work, mu_tot, vir, pres, -1, TRUE);
cr->nnodes = nnodes;
if (shellfc)
{
/* Now is the time to relax the shells */
- relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, nullptr, step, inputrec,
- imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
- fcd, state_work.s.natoms, state_work.s.x.arrayRefWithPadding(),
- state_work.s.v.arrayRefWithPadding(), state_work.s.box,
- state_work.s.lambda, &state_work.s.hist,
- state_work.f.arrayRefWithPadding(), vir, mdatoms, nrnb,
- wcycle, graph, shellfc, fr, runScheduleWork, t, mu_tot,
- vsite, DDBalanceRegionHandler(nullptr));
+ relax_shell_flexcon(
+ fplog, cr, ms, mdrunOptions.verbose, nullptr, step, inputrec, imdSession,
+ pull_work, bNS, force_flags, &top, constr, enerd, fcd, state_work.s.natoms,
+ state_work.s.x.arrayRefWithPadding(), state_work.s.v.arrayRefWithPadding(),
+ state_work.s.box, state_work.s.lambda, &state_work.s.hist,
+ state_work.f.arrayRefWithPadding(), vir, mdatoms, nrnb, wcycle, shellfc,
+ fr, runScheduleWork, t, mu_tot, vsite, DDBalanceRegionHandler(nullptr));
bNS = false;
step++;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff