* 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 "grompp.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "grompp.h"
-#include <sys/types.h>
-#include <math.h>
-#include <string.h>
+#include <assert.h>
#include <errno.h>
#include <limits.h>
-#include <assert.h>
+#include <math.h>
+#include <string.h>
+
+#include <sys/types.h>
-#include "macros.h"
-#include "readir.h"
-#include "toputil.h"
-#include "topio.h"
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
-#include "readir.h"
-#include "names.h"
-#include "grompp-impl.h"
-#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "splitter.h"
-#include "gromacs/gmxpreprocess/sortwater.h"
-#include "convparm.h"
-#include "warninp.h"
+#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
#include "gromacs/fileio/trxio.h"
-#include "vsite_parm.h"
-#include "txtdump.h"
-#include "calcgrid.h"
-#include "add_par.h"
-#include "gromacs/fileio/enxio.h"
-#include "perf_est.h"
-#include "compute_io.h"
-#include "gpp_atomtype.h"
-#include "gromacs/topology/mtop_util.h"
-#include "genborn.h"
-#include "calc_verletbuf.h"
-#include "tomorse.h"
+#include "gromacs/gmxpreprocess/add_par.h"
+#include "gromacs/gmxpreprocess/calc_verletbuf.h"
+#include "gromacs/gmxpreprocess/compute_io.h"
+#include "gromacs/gmxpreprocess/convparm.h"
+#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/gmxpreprocess/sortwater.h"
+#include "gromacs/gmxpreprocess/tomorse.h"
+#include "gromacs/gmxpreprocess/topio.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/gmxpreprocess/vsite_parm.h"
#include "gromacs/imd/imd.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/perf_est.h"
+#include "gromacs/legacyheaders/splitter.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/random/random.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
}
}
+static void check_shells_inputrec(gmx_mtop_t *mtop,
+ t_inputrec *ir,
+ warninp_t wi)
+{
+ gmx_mtop_atomloop_all_t aloop;
+ t_atom *atom;
+ int a, nshells = 0;
+ char warn_buf[STRLEN];
+
+ aloop = gmx_mtop_atomloop_all_init(mtop);
+ while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
+ {
+ if (atom->ptype == eptShell ||
+ atom->ptype == eptBond)
+ {
+ nshells++;
+ }
+ }
+ if (IR_TWINRANGE(*ir) && (nshells > 0))
+ {
+ snprintf(warn_buf, STRLEN,
+ "The combination of using shells and a twin-range cut-off is not supported");
+ warning_error(wi, warn_buf);
+ }
+ if ((nshells > 0) && (ir->nstcalcenergy != 1))
+ {
+ set_warning_line(wi, "unknown", -1);
+ snprintf(warn_buf, STRLEN,
+ "There are %d shells, changing nstcalcenergy from %d to 1",
+ nshells, ir->nstcalcenergy);
+ ir->nstcalcenergy = 1;
+ warning(wi, warn_buf);
+ }
+}
+
static gmx_bool nint_ftype(gmx_mtop_t *mtop, t_molinfo *mi, int ftype)
{
int nint, mb;
int i, j;
read_posres (mtop, mi, FALSE, fnA, rc_scaling, ePBC, com, wi);
- if (strcmp(fnA, fnB) != 0)
- {
- read_posres(mtop, mi, TRUE, fnB, rc_scaling, ePBC, comB, wi);
- }
+ /* It is safer to simply read the b-state posres rather than trying
+ * to be smart and copy the positions.
+ */
+ read_posres(mtop, mi, TRUE, fnB, rc_scaling, ePBC, comB, wi);
}
static void set_wall_atomtype(gpp_atomtype_t at, t_gromppopts *opts,
{ efNDX, NULL, NULL, ffOPTRD },
{ efTOP, NULL, NULL, ffREAD },
{ efTOP, "-pp", "processed", ffOPTWR },
- { efTPX, "-o", NULL, ffWRITE },
+ { efTPR, "-o", NULL, ffWRITE },
{ efTRN, "-t", NULL, ffOPTRD },
{ efEDR, "-e", NULL, ffOPTRD },
/* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
}
/* If we are using CMAP, setup the pre-interpolation grid */
- if (plist->ncmap > 0)
+ if (plist[F_CMAP].ncmap > 0)
{
- init_cmap_grid(&sys->ffparams.cmap_grid, plist->nc, plist->grid_spacing);
- setup_cmap(plist->grid_spacing, plist->nc, plist->cmap, &sys->ffparams.cmap_grid);
+ init_cmap_grid(&sys->ffparams.cmap_grid, plist[F_CMAP].nc, plist[F_CMAP].grid_spacing);
+ setup_cmap(plist[F_CMAP].grid_spacing, plist[F_CMAP].nc, plist[F_CMAP].cmap, &sys->ffparams.cmap_grid);
}
set_wall_atomtype(atype, opts, ir, wi);
check_vel(sys, state.v);
}
+ /* check for shells and inpurecs */
+ check_shells_inputrec(sys, ir, wi);
+
/* check masses */
check_mol(sys, wi);
}
done_warning(wi, FARGS);
- write_tpx_state(ftp2fn(efTPX, NFILE, fnm), ir, &state, sys);
+ write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, sys);
/* Output IMD group, if bIMD is TRUE */
write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE, fnm);