* 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 <ctype.h>
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "string2.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "names.h"
-#include "symtab.h"
-#include "futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
#include "tpxio.h"
-#include "txtdump.h"
-#include "confio.h"
-#include "atomprop.h"
-#include "copyrite.h"
-#include "vec.h"
-#include "mtop_util.h"
+
+#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.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"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define TPX_TAG_RELEASE "release"
-/* This is the tag string which is stored in the tpx file.
- * Change this if you want to change the tpx format in a feature branch.
- * This ensures that there will not be different tpx formats around which
- * can not be distinguished.
+/*! \brief Tag string for the file format written to run input files
+ * written by this version of the code.
+ *
+ * Change this if you want to change the run input format in a feature
+ * branch. This ensures that there will not be different run input
+ * formats around which cannot be distinguished, while not causing
+ * problems rebasing the feature branch onto upstream changes. When
+ * merging with mainstream GROMACS, set this tag string back to
+ * TPX_TAG_RELEASE, and instead add an element to tpxv and set
+ * tpx_version to that.
*/
static const char *tpx_tag = TPX_TAG_RELEASE;
+/*! \brief Enum of values that describe the contents of a tpr file
+ * whose format matches a version number
+ *
+ * The enum helps the code be more self-documenting and ensure merges
+ * do not silently resolve when two patches make the same bump. When
+ * adding new functionality, add a new element to the end of this
+ * enumeration, change the definition of tpx_version, and write code
+ * below that does the right thing according to the value of
+ * file_version. */
+enum tpxv {
+ 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_RemoveObsoleteParameters1 /**< remove optimize_fft, dihre_fc, nstcheckpoint */
+};
-/* The tpx_version number should be increased whenever the file format changes!
+/*! \brief Version number of the file format written to run input
+ * files by this version of the code.
*
- * The following comment section helps to keep track of which feature has been
- * added in which version.
+ * The tpx_version number should be increased whenever the file format
+ * in the main development branch changes, generally to the highest
+ * value present in tpxv. Backward compatibility for reading old run
+ * input files is maintained by checking this version number against
+ * that of the file and then using the correct code path.
*
- * version feature added
- * 96 support for ion/water position swaps (computational electrophysiology)
- */
-static const int tpx_version = 96;
+ * When developing a feature branch that needs to change the run input
+ * file format, change tpx_tag instead. */
+static const int tpx_version = tpxv_RemoveObsoleteParameters1;
/* This number should only be increased when you edit the TOPOLOGY section
* It first appeared in tpx version 26, when I also moved the inputrecord
* to the end of the tpx file, so we can just skip it if we only
* want the topology.
+ *
+ * In particular, it must be increased when adding new elements to
+ * ftupd, so that old code can read new .tpr files.
*/
-static const int tpx_generation = 25;
+static const int tpx_generation = 26;
/* This number should be the most recent backwards incompatible version
* I.e., if this number is 9, we cannot read tpx version 9 with this code.
{ 43, F_TABBONDS },
{ 43, F_TABBONDSNC },
{ 70, F_RESTRBONDS },
+ { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
{ 76, F_LINEAR_ANGLES },
{ 30, F_CROSS_BOND_BONDS },
{ 30, F_CROSS_BOND_ANGLES },
{ 30, F_UREY_BRADLEY },
{ 34, F_QUARTIC_ANGLES },
{ 43, F_TABANGLES },
+ { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
+ { tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
{ 26, F_FOURDIHS },
{ 26, F_PIDIHS },
{ 43, F_TABDIHS },
/* Needed for backward compatibility */
#define MAXNODES 256
-static void _do_section(t_fileio *fio, int key, gmx_bool bRead, const char *src,
- int line)
-{
- char buf[STRLEN];
- gmx_bool bDbg;
-
- if (gmx_fio_getftp(fio) == efTPA)
- {
- if (!bRead)
- {
- gmx_fio_write_string(fio, itemstr[key]);
- bDbg = gmx_fio_getdebug(fio);
- gmx_fio_setdebug(fio, FALSE);
- gmx_fio_write_string(fio, comment_str[key]);
- gmx_fio_setdebug(fio, bDbg);
- }
- else
- {
- if (gmx_fio_getdebug(fio))
- {
- fprintf(stderr, "Looking for section %s (%s, %d)",
- itemstr[key], src, line);
- }
-
- do
- {
- gmx_fio_do_string(fio, buf);
- }
- while ((gmx_strcasecmp(buf, itemstr[key]) != 0));
-
- if (gmx_strcasecmp(buf, itemstr[key]) != 0)
- {
- gmx_fatal(FARGS, "\nCould not find section heading %s", itemstr[key]);
- }
- else if (gmx_fio_getdebug(fio))
- {
- fprintf(stderr, " and found it\n");
- }
- }
- }
-}
-
-#define do_section(fio, key, bRead) _do_section(fio, key, bRead, __FILE__, __LINE__)
-
/**************************************************************
*
* Now the higer level routines that do io of the structures and arrays
}
}
+static void do_imd(t_fileio *fio, t_IMD *imd, gmx_bool bRead)
+{
+ gmx_fio_do_int(fio, imd->nat);
+ if (bRead)
+ {
+ snew(imd->ind, imd->nat);
+ }
+ gmx_fio_ndo_int(fio, imd->ind, imd->nat);
+}
+
static void do_fepvals(t_fileio *fio, t_lambda *fepvals, gmx_bool bRead, int file_version)
{
/* i is defined in the ndo_double macro; use g to iterate. */
}
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_do_real(fio, bd_temp);
}
gmx_fio_do_real(fio, ir->bd_fric);
- gmx_fio_do_int(fio, ir->ld_seed);
+ if (file_version >= tpxv_Use64BitRandomSeed)
+ {
+ gmx_fio_do_int64(fio, ir->ld_seed);
+ }
+ else
+ {
+ gmx_fio_do_int(fio, idum);
+ ir->ld_seed = idum;
+ }
if (file_version >= 33)
{
for (i = 0; i < DIM; i++)
ir->bRot = FALSE;
}
+ /* Interactive molecular dynamics */
+ if (file_version >= tpxv_InteractiveMolecularDynamics)
+ {
+ gmx_fio_do_int(fio, ir->bIMD);
+ if (TRUE == ir->bIMD)
+ {
+ if (bRead)
+ {
+ snew(ir->imd, 1);
+ }
+ do_imd(fio, ir->imd, bRead);
+ }
+ }
+ else
+ {
+ /* We don't support IMD sessions for old .tpr files */
+ ir->bIMD = FALSE;
+ }
+
/* grpopts stuff */
gmx_fio_do_int(fio, ir->opts.ngtc);
if (file_version >= 69)
}
/* Swap ions */
- if (file_version >= 96)
+ if (file_version >= tpxv_ComputationalElectrophysiology)
{
gmx_fio_do_int(fio, ir->eSwapCoords);
if (ir->eSwapCoords != eswapNO)
iparams->pdihs.cpB = iparams->pdihs.cpA;
}
break;
+ case F_RESTRANGLES:
+ gmx_fio_do_real(fio, iparams->harmonic.rA);
+ gmx_fio_do_real(fio, iparams->harmonic.krA);
+ break;
case F_LINEAR_ANGLES:
gmx_fio_do_real(fio, iparams->linangle.klinA);
gmx_fio_do_real(fio, iparams->linangle.aA);
gmx_fio_do_real(fio, iparams->fene.bm);
gmx_fio_do_real(fio, iparams->fene.kb);
break;
+
case F_RESTRBONDS:
gmx_fio_do_real(fio, iparams->restraint.lowA);
gmx_fio_do_real(fio, iparams->restraint.up1A);
gmx_fio_do_int(fio, iparams->pdihs.mult);
}
break;
+ case F_RESTRDIHS:
+ gmx_fio_do_real(fio, iparams->pdihs.phiA);
+ gmx_fio_do_real(fio, iparams->pdihs.cpA);
+ break;
case F_DISRES:
gmx_fio_do_int(fio, iparams->disres.label);
gmx_fio_do_int(fio, iparams->disres.type);
gmx_fio_do_real(fio, iparams->fbposres.r);
gmx_fio_do_real(fio, iparams->fbposres.k);
break;
+ case F_CBTDIHS:
+ gmx_fio_ndo_real(fio, iparams->cbtdihs.cbtcA, NR_CBTDIHS);
+ break;
case F_RBDIHS:
gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
if (file_version >= 25)
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)
{
gmx_fio_checktype(fio);
gmx_fio_setdebug(fio, bDebugMode());
- /* NEW! XDR tpb file */
+ /* XDR binary topology file */
precision = sizeof(real);
if (bRead)
{
gmx_fio_getname(fio), fver, tpx_version);
}
- do_section(fio, eitemHEADER, bRead);
gmx_fio_do_int(fio, tpx->natoms);
if (fver >= 28)
{
#define do_test(fio, b, p) if (bRead && (p != NULL) && !b) gmx_fatal(FARGS, "No %s in %s",#p, gmx_fio_getname(fio))
do_test(fio, tpx.bBox, state->box);
- do_section(fio, eitemBOX, bRead);
if (tpx.bBox)
{
gmx_fio_ndo_rvec(fio, state->box, DIM);
if (file_version < 26)
{
do_test(fio, tpx.bIr, ir);
- do_section(fio, eitemIR, bRead);
if (tpx.bIr)
{
if (ir)
}
do_test(fio, tpx.bTop, mtop);
- do_section(fio, eitemTOP, bRead);
if (tpx.bTop)
{
if (mtop)
}
}
do_test(fio, tpx.bX, state->x);
- do_section(fio, eitemX, bRead);
if (tpx.bX)
{
if (bRead)
}
do_test(fio, tpx.bV, state->v);
- do_section(fio, eitemV, bRead);
if (tpx.bV)
{
if (bRead)
}
do_test(fio, tpx.bF, f);
- do_section(fio, eitemF, bRead);
if (tpx.bF)
{
gmx_fio_ndo_rvec(fio, f, state->natoms);
if (file_version >= 26)
{
do_test(fio, tpx.bIr, ir);
- do_section(fio, eitemIR, bRead);
if (tpx.bIr)
{
if (file_version >= 53)
gmx_bool fn2bTPX(const char *file)
{
- switch (fn2ftp(file))
- {
- case efTPR:
- case efTPB:
- case efTPA:
- return TRUE;
- default:
- return FALSE;
- }
+ return (efTPR == fn2ftp(file));
}
static void done_gmx_groups_t(gmx_groups_t *g)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff