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*
- * This source code is part of
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+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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+ * control is crucial - bugs must be traceable. We will be happy to
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/shellfc.h"
+#include <stdlib.h>
#include <string.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "txtdump.h"
-#include "mdrun.h"
-#include "partdec.h"
-#include "mdatoms.h"
-#include "vsite.h"
-#include "network.h"
-#include "names.h"
-#include "constr.h"
-#include "domdec.h"
-#include "partdec.h"
-#include "physics.h"
-#include "copyrite.h"
-#include "shellfc.h"
-#include "mtop_util.h"
-#include "chargegroup.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
int nnucl;
if (nshell == 0 && nflexcon == 0)
{
+ /* We're not doing shells or flexible constraints */
return NULL;
}
{
fprintf(fplog, "\nNOTE: there all shells that are connected to particles outside thier own charge group, will not predict shells positions during the run\n\n");
}
+ /* Prediction improves performance, so we should implement either:
+ * 1. communication for the atoms needed for prediction
+ * 2. prediction using the velocities of shells; currently the
+ * shell velocities are zeroed, it's a bit tricky to keep
+ * track of the shell displacements and thus the velocity.
+ */
shfc->bPredict = FALSE;
}
}
int a0, a1, *ind, nshell, i;
gmx_domdec_t *dd = NULL;
- if (PAR(cr))
+ if (DOMAINDECOMP(cr))
{
- if (DOMAINDECOMP(cr))
- {
- dd = cr->dd;
- a0 = 0;
- a1 = dd->nat_home;
- }
- else
- {
- pd_at_range(cr, &a0, &a1);
- }
+ dd = cr->dd;
+ a0 = 0;
+ a1 = dd->nat_home;
}
else
{
{
shell[nshell] = shfc->shell_gl[ind[i]];
}
+
/* With inter-cg shells we can no do shell prediction,
* so we do not need the nuclei numbers.
*/
xnew[ZZ] = zo+dz;
}
-static void directional_sd(FILE *log, rvec xold[], rvec xnew[], rvec acc_dir[],
+static void directional_sd(rvec xold[], rvec xnew[], rvec acc_dir[],
int start, int homenr, real step)
{
int i;
}
}
-static void shell_pos_sd(FILE *log, rvec xcur[], rvec xnew[], rvec f[],
+static void shell_pos_sd(rvec xcur[], rvec xnew[], rvec f[],
int ns, t_shell s[], int count)
{
const real step_scale_min = 0.8,
}
}
-static void print_epot(FILE *fp, gmx_large_int_t mdstep, int count, real epot, real df,
+static void print_epot(FILE *fp, gmx_int64_t mdstep, int count, real epot, real df,
int ndir, real sf_dir)
{
char buf[22];
static void init_adir(FILE *log, gmx_shellfc_t shfc,
gmx_constr_t constr, t_idef *idef, t_inputrec *ir,
t_commrec *cr, int dd_ac1,
- gmx_large_int_t step, t_mdatoms *md, int start, int end,
+ gmx_int64_t step, t_mdatoms *md, int start, int end,
rvec *x_old, rvec *x_init, rvec *x,
rvec *f, rvec *acc_dir,
gmx_bool bMolPBC, matrix box,
}
}
}
- constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, md,
+ constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
x, xnold-start, NULL, bMolPBC, box,
lambda[efptBONDED], &(dvdlambda[efptBONDED]),
NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
- constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, md,
+ constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
x, xnew-start, NULL, bMolPBC, box,
lambda[efptBONDED], &(dvdlambda[efptBONDED]),
NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
}
/* Project the acceleration on the old bond directions */
- constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, md,
+ constrain(log, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, 1.0, md,
x_old, xnew-start, acc_dir, bMolPBC, box,
lambda[efptBONDED], &(dvdlambda[efptBONDED]),
NULL, NULL, nrnb, econqDeriv_FlexCon, FALSE, 0, 0);
}
int relax_shell_flexcon(FILE *fplog, t_commrec *cr, gmx_bool bVerbose,
- gmx_large_int_t mdstep, t_inputrec *inputrec,
+ gmx_int64_t mdstep, t_inputrec *inputrec,
gmx_bool bDoNS, int force_flags,
- gmx_bool bStopCM,
gmx_localtop_t *top,
- gmx_mtop_t* mtop,
gmx_constr_t constr,
gmx_enerdata_t *enerd, t_fcdata *fcd,
t_state *state, rvec f[],
t_forcerec *fr,
gmx_bool bBornRadii,
double t, rvec mu_tot,
- int natoms, gmx_bool *bConverged,
+ gmx_bool *bConverged,
gmx_vsite_t *vsite,
FILE *fp_field)
{
char sbuf[22];
gmx_bool bCont, bInit;
int nat, dd_ac0, dd_ac1 = 0, i;
- int start = md->start, homenr = md->homenr, end = start+homenr, cg0, cg1;
+ int start = 0, homenr = md->homenr, end = start+homenr, cg0, cg1;
int nflexcon, g, number_steps, d, Min = 0, count = 0;
#define Try (1-Min) /* At start Try = 1 */
force[i] = shfc->f[i];
}
- /* With particle decomposition this code only works
- * when all particles involved with each shell are in the same cg.
- */
-
if (bDoNS && inputrec->ePBC != epbcNONE && !DOMAINDECOMP(cr))
{
/* This is the only time where the coordinates are used
* before do_force is called, which normally puts all
* charge groups in the box.
*/
- if (PARTDECOMP(cr))
+ if (inputrec->cutoff_scheme == ecutsVERLET)
{
- pd_cg_range(cr, &cg0, &cg1);
+ put_atoms_in_box_omp(fr->ePBC, state->box, md->homenr, state->x);
}
else
{
cg0 = 0;
cg1 = top->cgs.nr;
+ put_charge_groups_in_box(fplog, cg0, cg1, fr->ePBC, state->box,
+ &(top->cgs), state->x, fr->cg_cm);
}
- put_charge_groups_in_box(fplog, cg0, cg1, fr->ePBC, state->box,
- &(top->cgs), state->x, fr->cg_cm);
+
if (graph)
{
mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
}
}
- /* After this all coordinate arrays will contain whole molecules */
+ /* After this all coordinate arrays will contain whole charge groups */
if (graph)
{
shift_self(graph, state->box, state->x);
{
pr_rvecs(debug, 0, "x b4 do_force", state->x + start, homenr);
}
- do_force(fplog, cr, inputrec, mdstep, nrnb, wcycle, top, mtop, groups,
+ do_force(fplog, cr, inputrec, mdstep, nrnb, wcycle, top, groups,
state->box, state->x, &state->hist,
force[Min], force_vir, md, enerd, fcd,
state->lambda, graph,
{
if (vsite)
{
- construct_vsites(fplog, vsite, pos[Min], nrnb, inputrec->delta_t, state->v,
+ construct_vsites(vsite, pos[Min], inputrec->delta_t, state->v,
idef->iparams, idef->il,
- fr->ePBC, fr->bMolPBC, graph, cr, state->box);
+ fr->ePBC, fr->bMolPBC, cr, state->box);
}
if (nflexcon)
x_old-start, state->x, pos[Min], force[Min], acc_dir-start,
fr->bMolPBC, state->box, state->lambda, &dum, nrnb);
- directional_sd(fplog, pos[Min], pos[Try], acc_dir-start, start, end,
+ directional_sd(pos[Min], pos[Try], acc_dir-start, start, end,
fr->fc_stepsize);
}
/* New positions, Steepest descent */
- shell_pos_sd(fplog, pos[Min], pos[Try], force[Min], nshell, shell, count);
+ shell_pos_sd(pos[Min], pos[Try], force[Min], nshell, shell, count);
/* do_force expected the charge groups to be in the box */
if (graph)
}
/* Try the new positions */
do_force(fplog, cr, inputrec, 1, nrnb, wcycle,
- top, mtop, groups, state->box, pos[Try], &state->hist,
+ top, groups, state->box, pos[Try], &state->hist,
force[Try], force_vir,
md, enerd, fcd, state->lambda, graph,
fr, vsite, mu_tot, t, fp_field, NULL, bBornRadii,
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff