#include <string.h>
#include <algorithm>
+#include <string>
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
-#include "gromacs/legacyheaders/chargegroup.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/domdec/ga2la.h"
+#include "gromacs/gmxlib/chargegroup.h"
+#include "gromacs/gmxlib/network.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/force.h"
+#include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
+#include "gromacs/mdlib/vsite.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topsort.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
#include "domdec_constraints.h"
#include "domdec_internal.h"
} thread_work_t;
/*! \brief Struct for the reverse topology: links bonded interactions to atomsx */
-typedef struct gmx_reverse_top {
+struct gmx_reverse_top_t
+{
//! @cond Doxygen_Suppress
gmx_bool bExclRequired; /**< Do we require all exclusions to be assigned? */
int n_excl_at_max; /**< The maximum number of exclusions one atom can have */
/* Work data structures for multi-threading */
int nthread; /**< The number of threads to be used */
thread_work_t *th_work; /**< Thread work array for local topology generation */
-
- /* Pointers only used for an error message */
- gmx_mtop_t *err_top_global; /**< Pointer to the global top, only used for error reporting */
- gmx_localtop_t *err_top_local; /**< Pointer to the local top, only used for error reporting */
//! @endcond
-} gmx_reverse_top_t;
+};
/*! \brief Returns the number of atom entries for il in gmx_reverse_top_t */
static int nral_rt(int ftype)
}
/*! \brief Print a header on error messages */
-static void print_error_header(FILE *fplog, char *moltypename, int nprint)
+static void print_error_header(FILE *fplog, const char *moltypename, int nprint)
{
fprintf(fplog, "\nMolecule type '%s'\n", moltypename);
fprintf(stderr, "\nMolecule type '%s'\n", moltypename);
/*! \brief Help print error output when interactions are missing */
static void print_missing_interactions_mb(FILE *fplog, t_commrec *cr,
- gmx_reverse_top_t *rt,
- char *moltypename,
- reverse_ilist_t *ril,
+ const gmx_reverse_top_t *rt,
+ const char *moltypename,
+ const reverse_ilist_t *ril,
int a_start, int a_end,
int nat_mol, int nmol,
- t_idef *idef)
+ const t_idef *idef)
{
- int nril_mol, *assigned, *gatindex;
- int ftype, ftype_j, nral, i, j_mol, j, a0, a0_mol, mol, a;
- int nprint;
- t_ilist *il;
- t_iatom *ia;
- gmx_bool bFound;
-
- nril_mol = ril->index[nat_mol];
+ int *assigned;
+ int nril_mol = ril->index[nat_mol];
snew(assigned, nmol*nril_mol);
- gatindex = cr->dd->gatindex;
- for (ftype = 0; ftype < F_NRE; ftype++)
+ int *gatindex = cr->dd->gatindex;
+ for (int ftype = 0; ftype < F_NRE; ftype++)
{
if (dd_check_ftype(ftype, rt->bBCheck, rt->bConstr, rt->bSettle))
{
- nral = NRAL(ftype);
- il = &idef->il[ftype];
- ia = il->iatoms;
- for (i = 0; i < il->nr; i += 1+nral)
+ int nral = NRAL(ftype);
+ const t_ilist *il = &idef->il[ftype];
+ const t_iatom *ia = il->iatoms;
+ for (int i = 0; i < il->nr; i += 1+nral)
{
- a0 = gatindex[ia[1]];
+ int a0 = gatindex[ia[1]];
/* Check if this interaction is in
* the currently checked molblock.
*/
if (a0 >= a_start && a0 < a_end)
{
- mol = (a0 - a_start)/nat_mol;
- a0_mol = (a0 - a_start) - mol*nat_mol;
- j_mol = ril->index[a0_mol];
- bFound = FALSE;
- while (j_mol < ril->index[a0_mol+1] && !bFound)
+ int mol = (a0 - a_start)/nat_mol;
+ int a0_mol = (a0 - a_start) - mol*nat_mol;
+ int j_mol = ril->index[a0_mol];
+ bool found = false;
+ while (j_mol < ril->index[a0_mol+1] && !found)
{
- j = mol*nril_mol + j_mol;
- ftype_j = ril->il[j_mol];
+ int j = mol*nril_mol + j_mol;
+ int ftype_j = ril->il[j_mol];
/* Here we need to check if this interaction has
* not already been assigned, since we could have
* multiply defined interactions.
assigned[j] == 0)
{
/* Check the atoms */
- bFound = TRUE;
- for (a = 0; a < nral; a++)
+ found = true;
+ for (int a = 0; a < nral; a++)
{
if (gatindex[ia[1+a]] !=
a_start + mol*nat_mol + ril->il[j_mol+2+a])
{
- bFound = FALSE;
+ found = false;
}
}
- if (bFound)
+ if (found)
{
assigned[j] = 1;
}
}
j_mol += 2 + nral_rt(ftype_j);
}
- if (!bFound)
+ if (!found)
{
gmx_incons("Some interactions seem to be assigned multiple times");
}
gmx_sumi(nmol*nril_mol, assigned, cr);
- nprint = 10;
- i = 0;
- for (mol = 0; mol < nmol; mol++)
+ int nprint = 10;
+ int i = 0;
+ for (int mol = 0; mol < nmol; mol++)
{
- j_mol = 0;
+ int j_mol = 0;
while (j_mol < nril_mol)
{
- ftype = ril->il[j_mol];
- nral = NRAL(ftype);
- j = mol*nril_mol + j_mol;
+ int ftype = ril->il[j_mol];
+ int nral = NRAL(ftype);
+ int j = mol*nril_mol + j_mol;
if (assigned[j] == 0 &&
!(interaction_function[ftype].flags & IF_VSITE))
{
interaction_function[ftype].longname);
fprintf(stderr, "%20s atoms",
interaction_function[ftype].longname);
+ int a;
for (a = 0; a < nral; a++)
{
fprintf(fplog, "%5d", ril->il[j_mol+2+a]+1);
/*! \brief Help print error output when interactions are missing */
static void print_missing_interactions_atoms(FILE *fplog, t_commrec *cr,
- gmx_mtop_t *mtop, t_idef *idef)
+ const gmx_mtop_t *mtop,
+ const t_idef *idef)
{
- int mb, a_start, a_end;
- gmx_molblock_t *molb;
- gmx_reverse_top_t *rt;
+ int mb, a_start, a_end;
+ const gmx_molblock_t *molb;
+ const gmx_reverse_top_t *rt;
rt = cr->dd->reverse_top;
}
}
-void dd_print_missing_interactions(FILE *fplog, t_commrec *cr, int local_count, gmx_mtop_t *top_global, t_state *state_local)
+void dd_print_missing_interactions(FILE *fplog, t_commrec *cr,
+ int local_count,
+ const gmx_mtop_t *top_global,
+ const gmx_localtop_t *top_local,
+ t_state *state_local)
{
int ndiff_tot, cl[F_NRE], n, ndiff, rest_global, rest_local;
int ftype, nral;
char buf[STRLEN];
gmx_domdec_t *dd;
- gmx_mtop_t *err_top_global;
- gmx_localtop_t *err_top_local;
dd = cr->dd;
- err_top_global = dd->reverse_top->err_top_global;
- err_top_local = dd->reverse_top->err_top_local;
-
if (fplog)
{
fprintf(fplog, "\nNot all bonded interactions have been properly assigned to the domain decomposition cells\n");
for (ftype = 0; ftype < F_NRE; ftype++)
{
nral = NRAL(ftype);
- cl[ftype] = err_top_local->idef.il[ftype].nr/(1+nral);
+ cl[ftype] = top_local->idef.il[ftype].nr/(1+nral);
}
gmx_sumi(F_NRE, cl, cr);
|| (dd->reverse_top->bConstr && ftype == F_CONSTR)
|| (dd->reverse_top->bSettle && ftype == F_SETTLE))
{
- n = gmx_mtop_ftype_count(err_top_global, ftype);
+ n = gmx_mtop_ftype_count(top_global, ftype);
if (ftype == F_CONSTR)
{
- n += gmx_mtop_ftype_count(err_top_global, F_CONSTRNC);
+ n += gmx_mtop_ftype_count(top_global, F_CONSTRNC);
}
ndiff = cl[ftype] - n;
if (ndiff != 0)
}
}
- print_missing_interactions_atoms(fplog, cr, err_top_global,
- &err_top_local->idef);
+ print_missing_interactions_atoms(fplog, cr, top_global, &top_local->idef);
write_dd_pdb("dd_dump_err", 0, "dump", top_global, cr,
-1, state_local->x, state_local->box);
- if (DDMASTER(dd))
+
+ std::string errorMessage;
+
+ if (ndiff_tot > 0)
{
- if (ndiff_tot > 0)
- {
- gmx_incons("One or more interactions were multiple assigned in the domain decompostion");
- }
- else
- {
- gmx_fatal(FARGS, "%d of the %d bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (%g nm) or the two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck", -ndiff_tot, cr->dd->nbonded_global, dd_cutoff_multibody(cr->dd), dd_cutoff_twobody(cr->dd));
- }
+ errorMessage = "One or more interactions were assigned to multiple domains of the domain decompostion. Please report this bug.";
+ }
+ else
+ {
+ errorMessage = gmx::formatString("%d of the %d bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (%g nm) or the two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck", -ndiff_tot, cr->dd->nbonded_global, dd_cutoff_multibody(dd), dd_cutoff_twobody(dd));
}
+ gmx_fatal_collective(FARGS, cr->mpi_comm_mygroup, MASTER(cr), errorMessage.c_str());
}
/*! \brief Return global topology molecule information for global atom index \p i_gl */
}
/*! \brief Run the reverse ilist generation and store it when \p bAssign = TRUE */
-static int low_make_reverse_ilist(const t_ilist *il_mt,
- const t_atom *atom,
- int **vsite_pbc, /* should be const */
+static int low_make_reverse_ilist(const t_ilist *il_mt, const t_atom *atom,
+ const int * const * vsite_pbc,
int *count,
gmx_bool bConstr, gmx_bool bSettle,
gmx_bool bBCheck,
{
int ftype, nral, i, j, nlink, link;
const t_ilist *il;
- t_iatom *ia;
- atom_id a;
+ const t_iatom *ia;
+ int a;
int nint;
gmx_bool bVSite;
/*! \brief Make the reverse ilist: a list of bonded interactions linked to atoms */
static int make_reverse_ilist(const t_ilist *ilist,
const t_atoms *atoms,
- int **vsite_pbc, /* should be const (C issue) */
+ const int * const * vsite_pbc,
gmx_bool bConstr, gmx_bool bSettle,
gmx_bool bBCheck,
gmx_bool bLinkToAllAtoms,
}
/*! \brief Generate the reverse topology */
-static gmx_reverse_top_t *make_reverse_top(gmx_mtop_t *mtop, gmx_bool bFE,
- int ***vsite_pbc_molt,
+static gmx_reverse_top_t *make_reverse_top(const gmx_mtop_t *mtop, gmx_bool bFE,
+ const int * const * const * vsite_pbc_molt,
gmx_bool bConstr, gmx_bool bSettle,
gmx_bool bBCheck, int *nint)
{
}
void dd_make_reverse_top(FILE *fplog,
- gmx_domdec_t *dd, gmx_mtop_t *mtop,
- gmx_vsite_t *vsite,
- t_inputrec *ir, gmx_bool bBCheck)
+ gmx_domdec_t *dd, const gmx_mtop_t *mtop,
+ const gmx_vsite_t *vsite,
+ const t_inputrec *ir, gmx_bool bBCheck)
{
if (fplog)
{
* excluded pair should appear exactly once.
*/
rt->bExclRequired = (ir->cutoff_scheme == ecutsGROUP &&
- IR_EXCL_FORCES(*ir));
+ inputrecExclForces(ir));
int nexcl, mb;
* atom-indexing organization code with the ifunc-adding code, so that
* they can see that nral is the same value. */
static gmx_inline void
-add_ifunc_for_vsites(t_iatom *tiatoms, gmx_ga2la_t ga2la,
+add_ifunc_for_vsites(t_iatom *tiatoms, gmx_ga2la_t *ga2la,
int nral, gmx_bool bHomeA,
int a, int a_gl, int a_mol,
const t_iatom *iatoms,
}
/*! \brief Store a virtual site interaction, complex because of PBC and recursion */
-static void add_vsite(gmx_ga2la_t ga2la, const int *index, const int *rtil,
+static void add_vsite(gmx_ga2la_t *ga2la, const int *index, const int *rtil,
int ftype, int nral,
gmx_bool bHomeA, int a, int a_gl, int a_mol,
const t_iatom *iatoms,
int iz,
int cg_start, int cg_end)
{
- int n_excl_at_max, n, count, jla0, jla1, jla;
- int cg, la0, la1, la, a_gl, mb, mt, mol, a_mol, j, aj_mol;
- const t_blocka *excls;
- gmx_ga2la_t ga2la;
- int cell;
+ int n_excl_at_max, n, count, jla0, jla1, jla;
+ int cg, la0, la1, la, a_gl, mb, mt, mol, a_mol, j, aj_mol;
+ const t_blocka *excls;
+ gmx_ga2la_t *ga2la;
+ int cell;
ga2la = dd->ga2la;
int iz,
int at_start, int at_end)
{
- gmx_ga2la_t ga2la;
- int jla0, jla1;
- int n_excl_at_max, n, at;
+ gmx_ga2la_t *ga2la;
+ int jla0, jla1;
+ int n_excl_at_max, n, at;
ga2la = dd->ga2la;
#pragma omp parallel for num_threads(rt->nthread) schedule(static)
for (thread = 0; thread < rt->nthread; thread++)
{
- int cg0t, cg1t;
- t_idef *idef_t;
- int **vsite_pbc;
- int *vsite_pbc_nalloc;
- t_blocka *excl_t;
-
- cg0t = cg0 + ((cg1 - cg0)* thread )/rt->nthread;
- cg1t = cg0 + ((cg1 - cg0)*(thread+1))/rt->nthread;
-
- if (thread == 0)
+ try
{
- idef_t = idef;
- }
- else
- {
- idef_t = &rt->th_work[thread].idef;
- clear_idef(idef_t);
- }
+ int cg0t, cg1t;
+ t_idef *idef_t;
+ int **vsite_pbc;
+ int *vsite_pbc_nalloc;
+ t_blocka *excl_t;
+
+ cg0t = cg0 + ((cg1 - cg0)* thread )/rt->nthread;
+ cg1t = cg0 + ((cg1 - cg0)*(thread+1))/rt->nthread;
- if (vsite && vsite->bHaveChargeGroups && vsite->n_intercg_vsite > 0)
- {
if (thread == 0)
{
- vsite_pbc = vsite->vsite_pbc_loc;
- vsite_pbc_nalloc = vsite->vsite_pbc_loc_nalloc;
+ idef_t = idef;
}
else
{
- vsite_pbc = rt->th_work[thread].vsite_pbc;
- vsite_pbc_nalloc = rt->th_work[thread].vsite_pbc_nalloc;
+ idef_t = &rt->th_work[thread].idef;
+ clear_idef(idef_t);
}
- }
- else
- {
- vsite_pbc = NULL;
- vsite_pbc_nalloc = NULL;
- }
- rt->th_work[thread].nbonded =
- make_bondeds_zone(dd, zones,
- mtop->molblock,
- bRCheckMB, rcheck, bRCheck2B, rc2,
- la2lc, pbc_null, cg_cm, idef->iparams,
- idef_t,
- vsite_pbc, vsite_pbc_nalloc,
- izone,
- dd->cgindex[cg0t], dd->cgindex[cg1t]);
-
- if (izone < nzone_excl)
- {
- if (thread == 0)
+ if (vsite && vsite->bHaveChargeGroups && vsite->n_intercg_vsite > 0)
{
- excl_t = lexcls;
+ if (thread == 0)
+ {
+ vsite_pbc = vsite->vsite_pbc_loc;
+ vsite_pbc_nalloc = vsite->vsite_pbc_loc_nalloc;
+ }
+ else
+ {
+ vsite_pbc = rt->th_work[thread].vsite_pbc;
+ vsite_pbc_nalloc = rt->th_work[thread].vsite_pbc_nalloc;
+ }
}
else
{
- excl_t = &rt->th_work[thread].excl;
- excl_t->nr = 0;
- excl_t->nra = 0;
+ vsite_pbc = NULL;
+ vsite_pbc_nalloc = NULL;
}
- if (dd->cgindex[dd->ncg_tot] == dd->ncg_tot &&
- !rt->bExclRequired)
- {
- /* No charge groups and no distance check required */
- make_exclusions_zone(dd, zones,
- mtop->moltype, cginfo,
- excl_t,
- izone,
- cg0t, cg1t);
- }
- else
+ rt->th_work[thread].nbonded =
+ make_bondeds_zone(dd, zones,
+ mtop->molblock,
+ bRCheckMB, rcheck, bRCheck2B, rc2,
+ la2lc, pbc_null, cg_cm, idef->iparams,
+ idef_t,
+ vsite_pbc, vsite_pbc_nalloc,
+ izone,
+ dd->cgindex[cg0t], dd->cgindex[cg1t]);
+
+ if (izone < nzone_excl)
{
- rt->th_work[thread].excl_count =
- make_exclusions_zone_cg(dd, zones,
- mtop->moltype, bRCheck2B, rc2,
- la2lc, pbc_null, cg_cm, cginfo,
- excl_t,
- izone,
- cg0t, cg1t);
+ if (thread == 0)
+ {
+ excl_t = lexcls;
+ }
+ else
+ {
+ excl_t = &rt->th_work[thread].excl;
+ excl_t->nr = 0;
+ excl_t->nra = 0;
+ }
+
+ if (dd->cgindex[dd->ncg_tot] == dd->ncg_tot &&
+ !rt->bExclRequired)
+ {
+ /* No charge groups and no distance check required */
+ make_exclusions_zone(dd, zones,
+ mtop->moltype, cginfo,
+ excl_t,
+ izone,
+ cg0t, cg1t);
+ }
+ else
+ {
+ rt->th_work[thread].excl_count =
+ make_exclusions_zone_cg(dd, zones,
+ mtop->moltype, bRCheck2B, rc2,
+ la2lc, pbc_null, cg_cm, cginfo,
+ excl_t,
+ izone,
+ cg0t, cg1t);
+ }
}
}
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
if (rt->nthread > 1)
t_forcerec *fr,
rvec *cgcm_or_x,
gmx_vsite_t *vsite,
- gmx_mtop_t *mtop, gmx_localtop_t *ltop)
+ const gmx_mtop_t *mtop, gmx_localtop_t *ltop)
{
gmx_bool bRCheckMB, bRCheck2B;
real rc = -1;
make_la2lc(dd);
if (fr->bMolPBC)
{
- set_pbc_dd(&pbc, fr->ePBC, dd, TRUE, box);
- pbc_null = &pbc;
+ pbc_null = set_pbc_dd(&pbc, fr->ePBC, dd->nc, TRUE, box);
}
else
{
}
ltop->atomtypes = mtop->atomtypes;
-
- /* For an error message only */
- dd->reverse_top->err_top_global = mtop;
- dd->reverse_top->err_top_local = ltop;
}
-void dd_sort_local_top(gmx_domdec_t *dd, t_mdatoms *mdatoms,
+void dd_sort_local_top(gmx_domdec_t *dd, const t_mdatoms *mdatoms,
gmx_localtop_t *ltop)
{
if (dd->reverse_top->ilsort == ilsortNO_FE)
}
}
-gmx_localtop_t *dd_init_local_top(gmx_mtop_t *top_global)
+gmx_localtop_t *dd_init_local_top(const gmx_mtop_t *top_global)
{
gmx_localtop_t *top;
int i;
return at2cg;
}
-t_blocka *make_charge_group_links(gmx_mtop_t *mtop, gmx_domdec_t *dd,
+t_blocka *make_charge_group_links(const gmx_mtop_t *mtop, gmx_domdec_t *dd,
cginfo_mb_t *cginfo_mb)
{
gmx_bool bExclRequired;
/*! \brief Set the distance, function type and atom indices for the longest atom distance involved in intermolecular interactions for two-body and multi-body bonded interactions */
static void bonded_distance_intermol(const t_ilist *ilists_intermol,
gmx_bool bBCheck,
- rvec *x, int ePBC, matrix box,
+ const rvec *x, int ePBC, matrix box,
bonded_distance_t *bd_2b,
bonded_distance_t *bd_mb)
{
}
//! Compute charge group centers of mass for molecule \p molt
-static void get_cgcm_mol(gmx_moltype_t *molt, gmx_ffparams_t *ffparams,
+static void get_cgcm_mol(const gmx_moltype_t *molt,
+ const gmx_ffparams_t *ffparams,
int ePBC, t_graph *graph, matrix box,
- gmx_vsite_t *vsite,
- rvec *x, rvec *xs, rvec *cg_cm)
+ const gmx_vsite_t *vsite,
+ const rvec *x, rvec *xs, rvec *cg_cm)
{
int n, i;
}
void dd_bonded_cg_distance(FILE *fplog,
- gmx_mtop_t *mtop,
- t_inputrec *ir, rvec *x, matrix box,
+ const gmx_mtop_t *mtop,
+ const t_inputrec *ir,
+ const rvec *x, matrix box,
gmx_bool bBCheck,
real *r_2b, real *r_mb)
{
bonded_distance_t bd_2b = { 0, -1, -1, -1 };
bonded_distance_t bd_mb = { 0, -1, -1, -1 };
- bExclRequired = IR_EXCL_FORCES(*ir);
+ bExclRequired = inputrecExclForces(ir);
vsite = init_vsite(mtop, NULL, TRUE);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff