*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#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 "force.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 "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.
*/
}
}
}
- 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);
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);
{
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)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff