/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2006,2007,2008,2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016, 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.
#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,
ild->nr += ils->nr;
}
- }
- }
-
- /* Position restraints need an additional treatment */
- if (dest->il[F_POSRES].nr > 0)
- {
- int n, s, i;
- n = dest->il[F_POSRES].nr/2;
- if (n > dest->iparams_posres_nalloc)
- {
- dest->iparams_posres_nalloc = over_alloc_large(n);
- srenew(dest->iparams_posres, dest->iparams_posres_nalloc);
- }
- /* Set n to the number of original position restraints in dest */
- for (s = 1; s < nsrc; s++)
- {
- n -= src[s].idef.il[F_POSRES].nr/2;
- }
- for (s = 1; s < nsrc; s++)
- {
- for (i = 0; i < src[s].idef.il[F_POSRES].nr/2; i++)
+ /* Position restraints need an additional treatment */
+ if (ftype == F_POSRES || ftype == F_FBPOSRES)
{
- /* Correct the index into iparams_posres */
- dest->il[F_POSRES].iatoms[n*2] = n;
- /* Copy the position restraint force parameters */
- dest->iparams_posres[n] = src[s].idef.iparams_posres[i];
- n++;
+ int nposres = dest->il[ftype].nr/2;
+ if (nposres > dest->iparams_posres_nalloc)
+ {
+ dest->iparams_posres_nalloc = over_alloc_large(nposres);
+ srenew(dest->iparams_posres, dest->iparams_posres_nalloc);
+ }
+ /* Set nposres to the number of original position restraints in dest */
+ for (int s = 1; s < nsrc; s++)
+ {
+ nposres -= src[s].idef.il[ftype].nr/2;
+ }
+ for (int s = 1; s < nsrc; s++)
+ {
+ if (ftype == F_POSRES)
+ {
+ for (int i = 0; i < src[s].idef.il[ftype].nr/2; i++)
+ {
+ /* Correct the index into iparams_posres */
+ dest->il[ftype].iatoms[nposres*2] = nposres;
+ /* Copy the position restraint force parameters */
+ dest->iparams_posres[nposres] = src[s].idef.iparams_posres[i];
+ nposres++;
+ }
+ }
+ else
+ {
+ for (int i = 0; i < src[s].idef.il[ftype].nr/2; i++)
+ {
+ /* Correct the index into iparams_fbposres */
+ dest->il[ftype].iatoms[nposres*2] = nposres;
+ /* Copy the position restraint force parameters */
+ dest->iparams_fbposres[nposres] = src[s].idef.iparams_fbposres[i];
+ nposres++;
+ }
+ }
+ }
}
}
}
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);
--- /dev/null
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
- if (is_bond(nsb, sb, pdba, ai, aj, d[i][j], &index_sb, &bSwap))
++ * Copyright (c) 2013,2014,2015,2016, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version 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.
+ */
+#include "gmxpre.h"
+
+#include "specbond.h"
+
+#include <ctype.h>
+#include <string.h>
+
+#include <cmath>
+
+#include <algorithm>
+
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/strdb.h"
+
+gmx_bool yesno(void)
+{
+ char c;
+
+ do
+ {
+ c = toupper(fgetc(stdin));
+ }
+ while ((c != 'Y') && (c != 'N'));
+
+ return (c == 'Y');
+}
+
+t_specbond *get_specbonds(int *nspecbond)
+{
+ const char *sbfile = "specbond.dat";
+
+ t_specbond *sb = NULL;
+ char r1buf[32], r2buf[32], a1buf[32], a2buf[32], nr1buf[32], nr2buf[32];
+ double length;
+ int nb1, nb2;
+ char **lines;
+ int nlines, i, n;
+
+ nlines = get_lines(sbfile, &lines);
+ if (nlines > 0)
+ {
+ snew(sb, nlines);
+ }
+
+ n = 0;
+ for (i = 0; (i < nlines); i++)
+ {
+ if (sscanf(lines[i], "%s%s%d%s%s%d%lf%s%s",
+ r1buf, a1buf, &nb1, r2buf, a2buf, &nb2, &length, nr1buf, nr2buf) != 9)
+ {
+ fprintf(stderr, "Invalid line '%s' in %s\n", lines[i], sbfile);
+ }
+ else
+ {
+ sb[n].res1 = gmx_strdup(r1buf);
+ sb[n].res2 = gmx_strdup(r2buf);
+ sb[n].newres1 = gmx_strdup(nr1buf);
+ sb[n].newres2 = gmx_strdup(nr2buf);
+ sb[n].atom1 = gmx_strdup(a1buf);
+ sb[n].atom2 = gmx_strdup(a2buf);
+ sb[n].nbond1 = nb1;
+ sb[n].nbond2 = nb2;
+ sb[n].length = length;
+ n++;
+ }
+ sfree(lines[i]);
+ }
+ if (nlines > 0)
+ {
+ sfree(lines);
+ }
+ fprintf(stderr, "%d out of %d lines of %s converted successfully\n",
+ n, nlines, sbfile);
+
+ *nspecbond = n;
+
+ return sb;
+}
+
+void done_specbonds(int nsb, t_specbond sb[])
+{
+ int i;
+
+ for (i = 0; (i < nsb); i++)
+ {
+ sfree(sb[i].res1);
+ sfree(sb[i].res2);
+ sfree(sb[i].atom1);
+ sfree(sb[i].atom2);
+ sfree(sb[i].newres1);
+ sfree(sb[i].newres2);
+ }
+}
+
+static gmx_bool is_special(int nsb, t_specbond sb[], char *res, char *atom)
+{
+ int i;
+
+ for (i = 0; (i < nsb); i++)
+ {
+ if (((strncmp(sb[i].res1, res, 3) == 0) &&
+ (gmx_strcasecmp(sb[i].atom1, atom) == 0)) ||
+ ((strncmp(sb[i].res2, res, 3) == 0) &&
+ (gmx_strcasecmp(sb[i].atom2, atom) == 0)))
+ {
+ return TRUE;
+ }
+ }
+ return FALSE;
+}
+
+static gmx_bool is_bond(int nsb, t_specbond sb[], t_atoms *pdba, int a1, int a2,
+ real d, int *index_sb, gmx_bool *bSwap)
+{
+ int i;
+ char *at1, *at2, *res1, *res2;
+
+ at1 = *pdba->atomname[a1];
+ at2 = *pdba->atomname[a2];
+ res1 = *pdba->resinfo[pdba->atom[a1].resind].name;
+ res2 = *pdba->resinfo[pdba->atom[a2].resind].name;
+
+ if (debug)
+ {
+ fprintf(stderr, "Checking %s-%d %s-%d and %s-%d %s-%d: %g ",
+ res1, pdba->resinfo[pdba->atom[a1].resind].nr, at1, a1+1,
+ res2, pdba->resinfo[pdba->atom[a2].resind].nr, at2, a2+1, d);
+ }
+
+ for (i = 0; (i < nsb); i++)
+ {
+ *index_sb = i;
+ if (((strncmp(sb[i].res1, res1, 3) == 0) &&
+ (gmx_strcasecmp(sb[i].atom1, at1) == 0) &&
+ (strncmp(sb[i].res2, res2, 3) == 0) &&
+ (gmx_strcasecmp(sb[i].atom2, at2) == 0)))
+ {
+ *bSwap = FALSE;
+ if ((0.9*sb[i].length < d) && (1.1*sb[i].length > d))
+ {
+ if (debug)
+ {
+ fprintf(stderr, "%g\n", sb[i].length);
+ }
+ return TRUE;
+ }
+ }
+ if (((strncmp(sb[i].res1, res2, 3) == 0) &&
+ (gmx_strcasecmp(sb[i].atom1, at2) == 0) &&
+ (strncmp(sb[i].res2, res1, 3) == 0) &&
+ (gmx_strcasecmp(sb[i].atom2, at1) == 0)))
+ {
+ *bSwap = TRUE;
+ if ((0.9*sb[i].length < d) && (1.1*sb[i].length > d))
+ {
+ if (debug)
+ {
+ fprintf(stderr, "%g\n", sb[i].length);
+ }
+ return TRUE;
+ }
+ }
+ }
+ if (debug)
+ {
+ fprintf(stderr, "\n");
+ }
+ return FALSE;
+}
+
+static void rename_1res(t_atoms *pdba, int resind, char *newres, gmx_bool bVerbose)
+{
+ if (bVerbose)
+ {
+ printf("Using rtp entry %s for %s %d\n",
+ newres,
+ *pdba->resinfo[resind].name,
+ pdba->resinfo[resind].nr);
+ }
+ /* this used to free *resname, which messes up the symtab! */
+ snew(pdba->resinfo[resind].rtp, 1);
+ *pdba->resinfo[resind].rtp = gmx_strdup(newres);
+}
+
+int mk_specbonds(t_atoms *pdba, rvec x[], gmx_bool bInteractive,
+ t_ssbond **specbonds, gmx_bool bVerbose)
+{
+ t_specbond *sb = NULL;
+ t_ssbond *bonds = NULL;
+ int nsb;
+ int nspec, nbonds;
+ int *specp, *sgp;
+ gmx_bool bDoit, bSwap;
+ int i, j, b, e, e2;
+ int ai, aj, index_sb;
+ real **d;
+ char buf[10];
+
+ nbonds = 0;
+ sb = get_specbonds(&nsb);
+
+ if (nsb > 0)
+ {
+ snew(specp, pdba->nr);
+ snew(sgp, pdba->nr);
+
+ nspec = 0;
+ for (i = 0; (i < pdba->nr); i++)
+ {
+ /* Check if this atom is special and if it is not a double atom
+ * in the input that still needs to be removed.
+ */
+ if (is_special(nsb, sb, *pdba->resinfo[pdba->atom[i].resind].name,
+ *pdba->atomname[i]) &&
+ !(nspec > 0 &&
+ pdba->atom[sgp[nspec-1]].resind == pdba->atom[i].resind &&
+ gmx_strcasecmp(*pdba->atomname[sgp[nspec-1]],
+ *pdba->atomname[i]) == 0))
+ {
+ specp[nspec] = pdba->atom[i].resind;
+ sgp[nspec] = i;
+ nspec++;
+ }
+ }
+ /* distance matrix d[nspec][nspec] */
+ snew(d, nspec);
+ for (i = 0; (i < nspec); i++)
+ {
+ snew(d[i], nspec);
+ }
+
+ for (i = 0; (i < nspec); i++)
+ {
+ ai = sgp[i];
+ for (j = 0; (j < nspec); j++)
+ {
+ aj = sgp[j];
+ d[i][j] = std::sqrt(distance2(x[ai], x[aj]));
+ }
+ }
+ if (nspec > 1)
+ {
+#define MAXCOL 7
+ fprintf(stderr, "Special Atom Distance matrix:\n");
+ for (b = 0; (b < nspec); b += MAXCOL)
+ {
+ /* print resname/number column headings */
+ fprintf(stderr, "%8s%8s", "", "");
+ e = std::min(b+MAXCOL, nspec-1);
+ for (i = b; (i < e); i++)
+ {
+ sprintf(buf, "%s%d", *pdba->resinfo[pdba->atom[sgp[i]].resind].name,
+ pdba->resinfo[specp[i]].nr);
+ fprintf(stderr, "%8s", buf);
+ }
+ fprintf(stderr, "\n");
+ /* print atomname/number column headings */
+ fprintf(stderr, "%8s%8s", "", "");
+ e = std::min(b+MAXCOL, nspec-1);
+ for (i = b; (i < e); i++)
+ {
+ sprintf(buf, "%s%d", *pdba->atomname[sgp[i]], sgp[i]+1);
+ fprintf(stderr, "%8s", buf);
+ }
+ fprintf(stderr, "\n");
+ /* print matrix */
+ e = std::min(b+MAXCOL, nspec);
+ for (i = b+1; (i < nspec); i++)
+ {
+ sprintf(buf, "%s%d", *pdba->resinfo[pdba->atom[sgp[i]].resind].name,
+ pdba->resinfo[specp[i]].nr);
+ fprintf(stderr, "%8s", buf);
+ sprintf(buf, "%s%d", *pdba->atomname[sgp[i]], sgp[i]+1);
+ fprintf(stderr, "%8s", buf);
+ e2 = std::min(i, e);
+ for (j = b; (j < e2); j++)
+ {
+ fprintf(stderr, " %7.3f", d[i][j]);
+ }
+ fprintf(stderr, "\n");
+ }
+ }
+ }
+
+ snew(bonds, nspec);
+
+ for (i = 0; (i < nspec); i++)
+ {
+ ai = sgp[i];
+ for (j = i+1; (j < nspec); j++)
+ {
+ aj = sgp[j];
++ /* Ensure creation of at most nspec special bonds to avoid overflowing bonds[] */
++ if (nbonds < nspec && is_bond(nsb, sb, pdba, ai, aj, d[i][j], &index_sb, &bSwap))
+ {
+ fprintf(stderr, "%s %s-%d %s-%d and %s-%d %s-%d%s",
+ bInteractive ? "Link" : "Linking",
+ *pdba->resinfo[pdba->atom[ai].resind].name,
+ pdba->resinfo[specp[i]].nr,
+ *pdba->atomname[ai], ai+1,
+ *pdba->resinfo[pdba->atom[aj].resind].name,
+ pdba->resinfo[specp[j]].nr,
+ *pdba->atomname[aj], aj+1,
+ bInteractive ? " (y/n) ?" : "...\n");
+ bDoit = bInteractive ? yesno() : TRUE;
+
+ if (bDoit)
+ {
+ /* Store the residue numbers in the bonds array */
+ bonds[nbonds].res1 = specp[i];
+ bonds[nbonds].res2 = specp[j];
+ bonds[nbonds].a1 = gmx_strdup(*pdba->atomname[ai]);
+ bonds[nbonds].a2 = gmx_strdup(*pdba->atomname[aj]);
+ /* rename residues */
+ if (bSwap)
+ {
+ rename_1res(pdba, specp[i], sb[index_sb].newres2, bVerbose);
+ rename_1res(pdba, specp[j], sb[index_sb].newres1, bVerbose);
+ }
+ else
+ {
+ rename_1res(pdba, specp[i], sb[index_sb].newres1, bVerbose);
+ rename_1res(pdba, specp[j], sb[index_sb].newres2, bVerbose);
+ }
+ nbonds++;
+ }
+ }
+ }
+ }
+
+ for (i = 0; (i < nspec); i++)
+ {
+ sfree(d[i]);
+ }
+ sfree(d);
+ sfree(sgp);
+ sfree(specp);
+
+ done_specbonds(nsb, sb);
+ sfree(sb);
+ }
+
+ *specbonds = bonds;
+
+ return nbonds;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff