* 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 "types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "txtdump.h"
-#include "force.h"
-#include "mdrun.h"
-#include "mdatoms.h"
-#include "vsite.h"
-#include "network.h"
-#include "names.h"
-#include "constr.h"
-#include "domdec.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;
}
gmx_shellfc_t init_shell_flexcon(FILE *fplog,
- gmx_bool bCutoffSchemeIsVerlet,
gmx_mtop_t *mtop, int nflexcon,
rvec *x)
{
return NULL;
}
- if (bCutoffSchemeIsVerlet)
- {
- gmx_fatal(FARGS, "The shell code does not work with the Verlet cut-off scheme.\n");
- }
-
snew(shfc, 1);
shfc->nflexcon = nflexcon;
{
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;
}
}
}
}
}
- 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);
force[i] = shfc->f[i];
}
- /* When we had particle decomposition, this code only worked with
- * PD when all particles involved with each shell were in the same
- * charge group. Not sure if this is still relevant. */
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.
*/
- 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);
+ if (inputrec->cutoff_scheme == ecutsVERLET)
+ {
+ 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);
+ }
+
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);