*/
#include "gmxpre.h"
-#include "gromacs/legacyheaders/constr.h"
+#include "constr.h"
#include <assert.h>
#include <stdlib.h>
#include <algorithm>
#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/pdbio.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/splitter.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
+#include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/splitter.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/invblock.h"
#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/txtdump.h"
typedef struct gmx_constr {
int ncon_tot; /* The total number of constraints */
tensor *vir_r_m_dr_th; /* Thread local working data */
int *settle_error; /* Thread local working data */
- gmx_mtop_t *warn_mtop; /* Only used for printing warnings */
+ const gmx_mtop_t *warn_mtop; /* Only used for printing warnings */
} t_gmx_constr;
typedef struct {
- atom_id iatom[3];
- atom_id blocknr;
+ int iatom[3];
+ int blocknr;
} t_sortblock;
static int pcomp(const void *p1, const void *p2)
{
int db;
- atom_id min1, min2, max1, max2;
+ int min1, min2, max1, max2;
t_sortblock *a1 = (t_sortblock *)p1;
t_sortblock *a2 = (t_sortblock *)p2;
}
static void write_constr_pdb(const char *fn, const char *title,
- gmx_mtop_t *mtop,
+ const gmx_mtop_t *mtop,
int start, int homenr, t_commrec *cr,
rvec x[], matrix box)
{
gmx_fio_fclose(out);
}
-static void dump_confs(FILE *fplog, gmx_int64_t step, gmx_mtop_t *mtop,
+static void dump_confs(FILE *fplog, gmx_int64_t step, const gmx_mtop_t *mtop,
int start, int homenr, t_commrec *cr,
rvec x[], rvec xprime[], matrix box)
{
* by the constraint coordinate communication routine,
* so that here we can use normal pbc.
*/
- pbc_null = set_pbc_dd(&pbc, ir->ePBC, cr->dd, FALSE, box);
+ pbc_null = set_pbc_dd(&pbc, ir->ePBC,
+ DOMAINDECOMP(cr) ? cr->dd->nc : nullptr,
+ FALSE, box);
}
else
{
#pragma omp parallel for num_threads(nth) schedule(static)
for (th = 0; th < nth; th++)
{
- int start_th, end_th;
-
- if (th > 0)
+ try
{
- clear_mat(constr->vir_r_m_dr_th[th]);
+ int start_th, end_th;
- constr->settle_error[th] = -1;
- }
+ if (th > 0)
+ {
+ clear_mat(constr->vir_r_m_dr_th[th]);
- start_th = (nsettle* th )/nth;
- end_th = (nsettle*(th+1))/nth;
- if (start_th >= 0 && end_th - start_th > 0)
- {
- csettle(constr->settled,
- end_th-start_th,
- settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
- pbc_null,
- x[0], xprime[0],
- invdt, v ? v[0] : NULL, calcvir_atom_end,
- th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
- th == 0 ? &settle_error : &constr->settle_error[th]);
+ constr->settle_error[th] = -1;
+ }
+
+ start_th = (nsettle* th )/nth;
+ end_th = (nsettle*(th+1))/nth;
+ if (start_th >= 0 && end_th - start_th > 0)
+ {
+ csettle(constr->settled,
+ end_th-start_th,
+ settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
+ pbc_null,
+ x[0], xprime[0],
+ invdt, v ? v[0] : NULL, calcvir_atom_end,
+ th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
+ th == 0 ? &settle_error : &constr->settle_error[th]);
+ }
}
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
inc_nrnb(nrnb, eNR_SETTLE, nsettle);
if (v != NULL)
#pragma omp parallel for num_threads(nth) schedule(static)
for (th = 0; th < nth; th++)
{
- int start_th, end_th;
-
- if (th > 0)
+ try
{
- clear_mat(constr->vir_r_m_dr_th[th]);
- }
-
- start_th = (nsettle* th )/nth;
- end_th = (nsettle*(th+1))/nth;
-
- if (start_th >= 0 && end_th - start_th > 0)
- {
- settle_proj(constr->settled, econq,
- end_th-start_th,
- settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
- pbc_null,
- x,
- xprime, min_proj, calcvir_atom_end,
- th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th]);
+ int start_th, end_th;
+
+ if (th > 0)
+ {
+ clear_mat(constr->vir_r_m_dr_th[th]);
+ }
+
+ start_th = (nsettle* th )/nth;
+ end_th = (nsettle*(th+1))/nth;
+
+ if (start_th >= 0 && end_th - start_th > 0)
+ {
+ settle_proj(constr->settled, econq,
+ end_th-start_th,
+ settle->iatoms+start_th*(1+NRAL(F_SETTLE)),
+ pbc_null,
+ x,
+ xprime, min_proj, calcvir_atom_end,
+ th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th]);
+ }
}
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
/* This is an overestimate */
inc_nrnb(nrnb, eNR_SETTLE, nsettle);
}
}
-real constr_rmsd(struct gmx_constr *constr, gmx_bool bSD2)
+real constr_rmsd(struct gmx_constr *constr)
{
if (constr->lincsd)
{
- return lincs_rmsd(constr->lincsd, bSD2);
+ return lincs_rmsd(constr->lincsd);
}
else
{
}
static void make_shake_sblock_serial(struct gmx_constr *constr,
- t_idef *idef, t_mdatoms *md)
+ t_idef *idef, const t_mdatoms *md)
{
int i, j, m, ncons;
int bstart, bnr;
t_blocka sblocks;
t_sortblock *sb;
t_iatom *iatom;
- atom_id *inv_sblock;
+ int *inv_sblock;
/* Since we are processing the local topology,
* the F_CONSTRNC ilist has been concatenated to the F_CONSTR ilist.
}
static void make_shake_sblock_dd(struct gmx_constr *constr,
- t_ilist *ilcon, t_block *cgs,
- gmx_domdec_t *dd)
+ const t_ilist *ilcon, const t_block *cgs,
+ const gmx_domdec_t *dd)
{
int ncons, c, cg;
t_iatom *iatom;
}
t_blocka make_at2con(int start, int natoms,
- t_ilist *ilist, t_iparams *iparams,
+ const t_ilist *ilist, const t_iparams *iparams,
gmx_bool bDynamics, int *nflexiblecons)
{
int *count, ncon, con, con_tot, nflexcon, ftype, i, a;
}
void set_constraints(struct gmx_constr *constr,
- gmx_localtop_t *top, t_inputrec *ir,
- t_mdatoms *md, t_commrec *cr)
+ gmx_localtop_t *top, const t_inputrec *ir,
+ const t_mdatoms *md, t_commrec *cr)
{
- t_idef *idef;
- int ncons;
- t_ilist *settle;
- int iO, iH;
+ t_idef *idef;
+ int ncons;
+ const t_ilist *settle;
+ int iO, iH;
idef = &top->idef;
}
}
-static void constr_recur(t_blocka *at2con,
- t_ilist *ilist, t_iparams *iparams, gmx_bool bTopB,
+static void constr_recur(const t_blocka *at2con,
+ const t_ilist *ilist, const t_iparams *iparams,
+ gmx_bool bTopB,
int at, int depth, int nc, int *path,
real r0, real r1, real *r2max,
int *count)
}
}
-static real constr_r_max_moltype(gmx_moltype_t *molt, t_iparams *iparams,
- t_inputrec *ir)
+static real constr_r_max_moltype(const gmx_moltype_t *molt,
+ const t_iparams *iparams,
+ const t_inputrec *ir)
{
int natoms, nflexcon, *path, at, count;
return rmax;
}
-real constr_r_max(FILE *fplog, gmx_mtop_t *mtop, t_inputrec *ir)
+real constr_r_max(FILE *fplog, const gmx_mtop_t *mtop, const t_inputrec *ir)
{
int mt;
real rmax;
}
gmx_constr_t init_constraints(FILE *fplog,
- gmx_mtop_t *mtop, t_inputrec *ir,
+ const gmx_mtop_t *mtop, const t_inputrec *ir,
gmx_edsam_t ed, t_state *state,
t_commrec *cr)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff