* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
/* This file is completely threadsafe - keep it that way! */
#include <stdlib.h>
#include <string.h>
-#include "macros.h"
-#include "names.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
#include "gromacs/utility/futil.h"
#include "filenm.h"
#include "gmxfio.h"
#include "tpxio.h"
-#include "txtdump.h"
+#include "gromacs/legacyheaders/txtdump.h"
#include "confio.h"
-#include "atomprop.h"
-#include "copyrite.h"
-#include "gromacs/topology/mtop_util.h"
+#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/math/vec.h"
+#include "gromacs/topology/atomprop.h"
#include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
tpxv_ComputationalElectrophysiology = 96, /**< support for ion/water position swaps (computational electrophysiology) */
tpxv_Use64BitRandomSeed, /**< change ld_seed from int to gmx_int64_t */
tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, /**< potentials for supporting coarse-grained force fields */
- tpxv_InteractiveMolecularDynamics /**< interactive molecular dynamics (IMD) */
+ tpxv_InteractiveMolecularDynamics, /**< interactive molecular dynamics (IMD) */
+ tpxv_RemoveObsoleteParameters1 /**< remove optimize_fft, dihre_fc, nstcheckpoint */
};
/*! \brief Version number of the file format written to run input
*
* When developing a feature branch that needs to change the run input
* file format, change tpx_tag instead. */
-static const int tpx_version = tpxv_InteractiveMolecularDynamics;
+static const int tpx_version = tpxv_RemoveObsoleteParameters1;
/* This number should only be increased when you edit the TOPOLOGY section
}
if (file_version >= 79)
{
- gmx_fio_do_int(fio, fepvals->bPrintEnergy);
+ gmx_fio_do_int(fio, fepvals->edHdLPrintEnergy);
}
else
{
- fepvals->bPrintEnergy = FALSE;
+ fepvals->edHdLPrintEnergy = edHdLPrintEnergyNO;
}
/* handle lambda_neighbors */
int i, j, k, *tmp, idum = 0;
real rdum, bd_temp;
rvec vdum;
- gmx_bool bSimAnn;
+ gmx_bool bSimAnn, bdum = 0;
real zerotemptime, finish_t, init_temp, finish_temp;
if (file_version != tpx_version)
gmx_fio_do_int(fio, idum);
ir->nsteps = idum;
}
+
if (file_version > 25)
{
if (file_version >= 62)
}
gmx_fio_do_int(fio, ir->ns_type);
gmx_fio_do_int(fio, ir->nstlist);
- gmx_fio_do_int(fio, ir->ndelta);
+ gmx_fio_do_int(fio, idum); /* used to be ndelta; not used anymore */
if (file_version < 41)
{
gmx_fio_do_int(fio, idum);
}
ir->nstcomm = abs(ir->nstcomm);
- if (file_version > 25)
- {
- gmx_fio_do_int(fio, ir->nstcheckpoint);
- }
- else
+ /* ignore nstcheckpoint */
+ if (file_version > 25 && file_version < tpxv_RemoveObsoleteParameters1)
{
- ir->nstcheckpoint = 0;
+ gmx_fio_do_int(fio, idum);
}
gmx_fio_do_int(fio, ir->nstcgsteep);
gmx_fio_do_real(fio, ir->epsilon_surface);
}
- gmx_fio_do_gmx_bool(fio, ir->bOptFFT);
+ /* ignore bOptFFT */
+ if (file_version < tpxv_RemoveObsoleteParameters1)
+ {
+ gmx_fio_do_gmx_bool(fio, bdum);
+ }
if (file_version >= 93)
{
ir->orires_tau = 0;
ir->nstorireout = 0;
}
+
+ /* ignore dihre_fc */
if (file_version >= 26 && file_version < 79)
{
- gmx_fio_do_real(fio, ir->dihre_fc);
+ gmx_fio_do_real(fio, rdum);
if (file_version < 56)
{
gmx_fio_do_real(fio, rdum);
gmx_fio_do_int(fio, idum);
}
}
- else
- {
- ir->dihre_fc = 0;
- }
gmx_fio_do_real(fio, ir->em_stepsize);
gmx_fio_do_real(fio, ir->em_tol);
gmx_fio_ndo_int(fio, block->a, block->nra);
}
+/* This is a primitive routine to make it possible to translate atomic numbers
+ * to element names when reading TPR files, without making the Gromacs library
+ * directory a dependency on mdrun (which is the case if we need elements.dat).
+ */
+static const char *
+atomicnumber_to_element(int atomicnumber)
+{
+ const char * p;
+
+ /* This does not have to be complete, so we only include elements likely
+ * to occur in PDB files.
+ */
+ switch (atomicnumber)
+ {
+ case 1: p = "H"; break;
+ case 5: p = "B"; break;
+ case 6: p = "C"; break;
+ case 7: p = "N"; break;
+ case 8: p = "O"; break;
+ case 9: p = "F"; break;
+ case 11: p = "Na"; break;
+ case 12: p = "Mg"; break;
+ case 15: p = "P"; break;
+ case 16: p = "S"; break;
+ case 17: p = "Cl"; break;
+ case 18: p = "Ar"; break;
+ case 19: p = "K"; break;
+ case 20: p = "Ca"; break;
+ case 25: p = "Mn"; break;
+ case 26: p = "Fe"; break;
+ case 28: p = "Ni"; break;
+ case 29: p = "Cu"; break;
+ case 30: p = "Zn"; break;
+ case 35: p = "Br"; break;
+ case 47: p = "Ag"; break;
+ default: p = ""; break;
+ }
+ return p;
+}
+
+
static void do_atom(t_fileio *fio, t_atom *atom, int ngrp, gmx_bool bRead,
int file_version, gmx_groups_t *groups, int atnr)
{
- int i, myngrp;
+ int i, myngrp;
+ char * p_elem;
gmx_fio_do_real(fio, atom->m);
gmx_fio_do_real(fio, atom->q);
if (file_version >= 52)
{
gmx_fio_do_int(fio, atom->atomnumber);
+ if (bRead)
+ {
+ /* Set element string from atomic number if present.
+ * This routine returns an empty string if the name is not found.
+ */
+ strncpy(atom->elem, atomicnumber_to_element(atom->atomnumber), 4);
+ /* avoid warnings about potentially unterminated string */
+ atom->elem[3] = '\0';
+ }
}
else if (bRead)
{
for (i = 0; (i < nr); i++)
{
gmx_fio_do_string(fio, buf);
- symbuf->buf[i] = strdup(buf);
+ symbuf->buf[i] = gmx_strdup(buf);
}
}
else
static void do_mtop(t_fileio *fio, gmx_mtop_t *mtop, gmx_bool bRead,
int file_version)
{
- int mt, mb, i;
- t_blocka dumb;
+ int mt, mb, i;
+ t_blocka dumb;
if (bRead)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff