#include <algorithm>
+#include "gromacs/commandline/filenm.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/ewald/ewald.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/pleasecite.h"
}
}
+/*!\brief If there's bonded interactions of type \c ftype1 or \c
+ * ftype2 present in the topology, build an array of the number of
+ * interactions present for each bonded interaction index found in the
+ * topology.
+ *
+ * \c ftype1 or \c ftype2 may be set to -1 to disable seeking for a
+ * valid type with that parameter.
+ *
+ * \c count will be reallocated as necessary to fit the largest bonded
+ * interaction index found, and its current size will be returned in
+ * \c ncount. It will contain zero for every bonded interaction index
+ * for which no interactions are present in the topology.
+ */
static void count_tables(int ftype1, int ftype2, const gmx_mtop_t *mtop,
int *ncount, int **count)
{
const t_ilist *il;
int mt, ftype, stride, i, j, tabnr;
+ // Loop over all moleculetypes
for (mt = 0; mt < mtop->nmoltype; mt++)
{
molt = &mtop->moltype[mt];
+ // Loop over all interaction types
for (ftype = 0; ftype < F_NRE; ftype++)
{
+ // If the current interaction type is one of the types whose tables we're trying to count...
if (ftype == ftype1 || ftype == ftype2)
{
il = &molt->ilist[ftype];
stride = 1 + NRAL(ftype);
+ // ... and there are actually some interactions for this type
for (i = 0; i < il->nr; i += stride)
{
+ // Find out which table index the user wanted
tabnr = mtop->ffparams.iparams[il->iatoms[i]].tab.table;
if (tabnr < 0)
{
gmx_fatal(FARGS, "A bonded table number is smaller than 0: %d\n", tabnr);
}
+ // Make room for this index in the data structure
if (tabnr >= *ncount)
{
srenew(*count, tabnr+1);
}
*ncount = tabnr+1;
}
+ // Record that this table index is used and must have a valid file
(*count)[tabnr]++;
}
}
}
}
+/*!\brief If there's bonded interactions of flavour \c tabext and type
+ * \c ftype1 or \c ftype2 present in the topology, seek them in the
+ * list of filenames passed to mdrun, and make bonded tables from
+ * those files.
+ *
+ * \c ftype1 or \c ftype2 may be set to -1 to disable seeking for a
+ * valid type with that parameter.
+ *
+ * A fatal error occurs if no matching filename is found.
+ */
static bondedtable_t *make_bonded_tables(FILE *fplog,
int ftype1, int ftype2,
const gmx_mtop_t *mtop,
- const char *basefn, const char *tabext)
+ const t_filenm *tabbfnm,
+ const char *tabext)
{
- int i, ncount, *count;
- char tabfn[STRLEN];
+ int ncount, *count;
bondedtable_t *tab;
tab = NULL;
count = NULL;
count_tables(ftype1, ftype2, mtop, &ncount, &count);
+ // Are there any relevant tabulated bond interactions?
if (ncount > 0)
{
snew(tab, ncount);
- for (i = 0; i < ncount; i++)
+ for (int i = 0; i < ncount; i++)
{
+ // Do any interactions exist that requires this table?
if (count[i] > 0)
{
- sprintf(tabfn, "%s", basefn);
- sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1, "_%s%d.%s",
- tabext, i, ftp2ext(efXVG));
- tab[i] = make_bonded_table(fplog, tabfn, NRAL(ftype1)-2);
+ // This pattern enforces the current requirement that
+ // table filenames end in a characteristic sequence
+ // before the file type extension, and avoids table 13
+ // being recognized and used for table 1.
+ std::string patternToFind = gmx::formatString("_%s%d.%s", tabext, i, ftp2ext(efXVG));
+ bool madeTable = false;
+ for (int j = 0; j < tabbfnm->nfiles && !madeTable; ++j)
+ {
+ std::string filename(tabbfnm->fns[j]);
+ if (gmx::endsWith(filename, patternToFind))
+ {
+ // Finally read the table from the file found
+ tab[i] = make_bonded_table(fplog, tabbfnm->fns[j], NRAL(ftype1)-2);
+ madeTable = true;
+ }
+ }
+ if (!madeTable)
+ {
+ bool isPlural = (ftype2 != -1);
+ gmx_fatal(FARGS, "Tabulated interaction of type '%s%s%s' with index %d cannot be used because no table file whose name matched '%s' was passed via the gmx mdrun -tableb command-line option.",
+ interaction_function[ftype1].longname,
+ isPlural ? "' or '" : "",
+ isPlural ? interaction_function[ftype2].longname : "",
+ i,
+ patternToFind.c_str());
+ }
}
}
sfree(count);
matrix box,
const char *tabfn,
const char *tabpfn,
- const char *tabbfn,
+ const t_filenm *tabbfnm,
const char *nbpu_opt,
gmx_bool bNoSolvOpt,
real print_force)
make_wall_tables(fp, ir, tabfn, &mtop->groups, fr);
}
- if (fcd && tabbfn)
+ if (fcd && tabbfnm)
{
- fcd->bondtab = make_bonded_tables(fp,
- F_TABBONDS, F_TABBONDSNC,
- mtop, tabbfn, "b");
- fcd->angletab = make_bonded_tables(fp,
- F_TABANGLES, -1,
- mtop, tabbfn, "a");
- fcd->dihtab = make_bonded_tables(fp,
- F_TABDIHS, -1,
- mtop, tabbfn, "d");
+ // Need to catch std::bad_alloc
+ // TODO Don't need to catch this here, when merging with master branch
+ try
+ {
+ fcd->bondtab = make_bonded_tables(fp,
+ F_TABBONDS, F_TABBONDSNC,
+ mtop, tabbfnm, "b");
+ fcd->angletab = make_bonded_tables(fp,
+ F_TABANGLES, -1,
+ mtop, tabbfnm, "a");
+ fcd->dihtab = make_bonded_tables(fp,
+ F_TABDIHS, -1,
+ mtop, tabbfnm, "d");
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
else
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff