#include "gromacs/topology/topsort.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
/* for dd_init_local_state */
t_idef *idef)
{
int nril_mol, *assigned, *gatindex;
- int ftype, ftype_j, nral, i, j_mol, j, k, a0, a0_mol, mol, a, a_gl;
+ int ftype, ftype_j, nral, i, j_mol, j, a0, a0_mol, mol, a;
int nprint;
t_ilist *il;
t_iatom *ia;
if (DDMASTER(dd))
{
- fprintf(fplog, "\nA list of missing interactions:\n");
+ if (fplog)
+ {
+ fprintf(fplog, "\nA list of missing interactions:\n");
+ }
fprintf(stderr, "\nA list of missing interactions:\n");
rest_global = dd->nbonded_global;
rest_local = local_count;
|| (dd->reverse_top->bConstr && ftype == F_CONSTR)
|| (dd->reverse_top->bSettle && ftype == F_SETTLE))
{
- nral = NRAL(ftype);
n = gmx_mtop_ftype_count(err_top_global, ftype);
if (ftype == F_CONSTR)
{
{
sprintf(buf, "%20s of %6d missing %6d",
interaction_function[ftype].longname, n, -ndiff);
- fprintf(fplog, "%s\n", buf);
+ if (fplog)
+ {
+ fprintf(fplog, "%s\n", buf);
+ }
fprintf(stderr, "%s\n", buf);
}
rest_global -= n;
{
sprintf(buf, "%20s of %6d missing %6d", "exclusions",
rest_global, -ndiff);
- fprintf(fplog, "%s\n", buf);
+ if (fplog)
+ {
+ fprintf(fplog, "%s\n", buf);
+ }
fprintf(stderr, "%s\n", buf);
}
}
static void global_atomnr_to_moltype_ind(gmx_reverse_top_t *rt, int i_gl,
int *mb, int *mt, int *mol, int *i_mol)
{
- int molb;
-
-
gmx_molblock_ind_t *mbi = rt->mbi;
int start = 0;
int end = rt->nmolblock; /* exclusive */
static int count_excls(t_block *cgs, t_blocka *excls, int *n_intercg_excl)
{
- int n, n_inter, cg, at0, at1, at, excl, atj;
+ int n, cg, at0, at1, at, excl, atj;
n = 0;
*n_intercg_excl = 0;
bVSite = (interaction_function[ftype].flags & IF_VSITE);
nral = NRAL(ftype);
il = &il_mt[ftype];
- ia = il->iatoms;
for (i = 0; i < il->nr; i += 1+nral)
{
ia = il->iatoms + i;
gmx_vsite_t *vsite,
t_inputrec *ir, gmx_bool bBCheck)
{
- int mb, n_recursive_vsite, nexcl, nexcl_icg, a;
+ int mb, nexcl, nexcl_icg;
gmx_molblock_t *molb;
gmx_moltype_t *molt;
}
}
+/* This routine is very similar to add_ifunc, but vsites interactions
+ * have more work to do than other kinds of interactions, and the
+ * complex way nral (and thus vector contents) depends on ftype
+ * confuses static analysis tools unless we fuse the vsite
+ * 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,
+ int nral, gmx_bool bHomeA,
+ int a, int a_gl, int a_mol,
+ const t_iatom *iatoms,
+ t_ilist *il)
+{
+ t_iatom *liatoms;
+
+ if (il->nr+1+nral > il->nalloc)
+ {
+ il->nalloc = over_alloc_large(il->nr+1+nral);
+ srenew(il->iatoms, il->nalloc);
+ }
+ liatoms = il->iatoms + il->nr;
+ il->nr += 1 + nral;
+
+ /* Copy the type */
+ tiatoms[0] = iatoms[0];
+
+ if (bHomeA)
+ {
+ /* We know the local index of the first atom */
+ tiatoms[1] = a;
+ }
+ else
+ {
+ /* Convert later in make_local_vsites */
+ tiatoms[1] = -a_gl - 1;
+ }
+
+ for (int k = 2; k < 1+nral; k++)
+ {
+ int ak_gl = a_gl + iatoms[k] - a_mol;
+ if (!ga2la_get_home(ga2la, ak_gl, &tiatoms[k]))
+ {
+ /* Copy the global index, convert later in make_local_vsites */
+ tiatoms[k] = -(ak_gl + 1);
+ }
+ // Note that ga2la_get_home always sets the third parameter if
+ // it returns TRUE
+ }
+ for (int k = 0; k < 1+nral; k++)
+ {
+ liatoms[k] = tiatoms[k];
+ }
+}
+
static gmx_inline void add_ifunc(int nral, t_iatom *tiatoms, t_ilist *il)
{
t_iatom *liatoms;
t_iatom *iatoms,
t_idef *idef, int **vsite_pbc, int *vsite_pbc_nalloc)
{
- int k, ak_gl, vsi, pbc_a_mol;
- t_iatom tiatoms[1+MAXATOMLIST], *iatoms_r;
+ int k, vsi, pbc_a_mol;
+ t_iatom tiatoms[1+MAXATOMLIST];
int j, ftype_r, nral_r;
- /* Copy the type */
- tiatoms[0] = iatoms[0];
-
- if (bHomeA)
- {
- /* We know the local index of the first atom */
- tiatoms[1] = a;
- }
- else
- {
- /* Convert later in make_local_vsites */
- tiatoms[1] = -a_gl - 1;
- }
-
- for (k = 2; k < 1+nral; k++)
- {
- ak_gl = a_gl + iatoms[k] - a_mol;
- if (!ga2la_get_home(ga2la, ak_gl, &tiatoms[k]))
- {
- /* Copy the global index, convert later in make_local_vsites */
- tiatoms[k] = -(ak_gl + 1);
- }
- }
-
/* Add this interaction to the local topology */
- add_ifunc(nral, tiatoms, &idef->il[ftype]);
+ add_ifunc_for_vsites(tiatoms, ga2la, nral, bHomeA, a, a_gl, a_mol, iatoms, &idef->il[ftype]);
+
if (vsite_pbc)
{
vsi = idef->il[ftype].nr/(1+nral) - 1;
int iz,
int cg_start, int cg_end)
{
- int nizone, n, count, jla0, jla1, jla;
+ int 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 a_loc;
int cell;
ga2la = dd->ga2la;
{
int cg0t, cg1t;
t_idef *idef_t;
- int ftype;
int **vsite_pbc;
int *vsite_pbc_nalloc;
t_blocka *excl_t;
gmx_vsite_t *vsite,
gmx_mtop_t *mtop, gmx_localtop_t *ltop)
{
- gmx_bool bUniqueExcl, bRCheckMB, bRCheck2B, bRCheckExcl;
+ gmx_bool bRCheckMB, bRCheck2B;
real rc = -1;
ivec rcheck;
int d, nexcl;
bRCheckMB = FALSE;
bRCheck2B = FALSE;
- bRCheckExcl = FALSE;
if (dd->reverse_top->bMultiCGmols)
{
d, cellsize_min[d], d, rcheck[d], bRCheck2B);
}
}
- if (dd->reverse_top->bExclRequired)
- {
- bRCheckExcl = bRCheck2B;
- }
- else
- {
- /* If we don't have forces on exclusions,
- * we don't care about exclusions being assigned mulitple times.
- */
- bRCheckExcl = FALSE;
- }
if (bRCheckMB || bRCheck2B)
{
make_la2lc(dd);
static void check_link(t_blocka *link, int cg_gl, int cg_gl_j)
{
- int k, aj;
+ int k;
gmx_bool bFound;
bFound = FALSE;
for (k = link->index[cg_gl]; k < link->index[cg_gl+1]; k++)
{
+ GMX_RELEASE_ASSERT(link->a, "Inconsistent NULL pointer while making charge-group links");
if (link->a[k] == cg_gl_j)
{
bFound = TRUE;
}
if (!bFound)
{
+ GMX_RELEASE_ASSERT(link->a || link->index[cg_gl+1]+1 > link->nalloc_a,
+ "Inconsistent allocation of link");
/* Add this charge group link */
if (link->index[cg_gl+1]+1 > link->nalloc_a)
{
real *r_2b, real *r_mb)
{
gmx_bool bExclRequired;
- int mb, cg_offset, at_offset, *at2cg, mol;
+ int mb, at_offset, *at2cg, mol;
t_graph graph;
gmx_vsite_t *vsite;
gmx_molblock_t *molb;
*r_2b = 0;
*r_mb = 0;
- cg_offset = 0;
at_offset = 0;
for (mb = 0; mb < mtop->nmolblock; mb++)
{
molt = &mtop->moltype[molb->type];
if (molt->cgs.nr == 1 || molb->nmol == 0)
{
- cg_offset += molb->nmol*molt->cgs.nr;
at_offset += molb->nmol*molt->atoms.nr;
}
else
a_mb_2 = at_offset + amol_mb_2;
}
- cg_offset += molt->cgs.nr;
at_offset += molt->atoms.nr;
}
sfree(cg_cm);
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