#endif
/* This file is completely threadsafe - keep it that way! */
-#ifdef GMX_THREADS
+#ifdef GMX_THREAD_MPI
#include <thread_mpi.h>
#endif
#include "vec.h"
#include "mtop_util.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.
+ */
+static const char *tpx_tag = TPX_TAG_RELEASE;
+
/* This number should be increased whenever the file format changes! */
-static const int tpx_version = 73;
+static const int tpx_version = 77;
/* This number should only be increased when you edit the TOPOLOGY section
* of the tpx format. This way we can maintain forward compatibility too
{ 43, F_TABBONDS },
{ 43, F_TABBONDSNC },
{ 70, F_RESTRBONDS },
+ { 76, F_LINEAR_ANGLES },
{ 30, F_CROSS_BOND_BONDS },
{ 30, F_CROSS_BOND_ANGLES },
{ 30, F_UREY_BRADLEY },
{ 69, F_VTEMP },
{ 66, F_PDISPCORR },
{ 54, F_DHDL_CON },
+ { 76, F_ANHARM_POL }
};
#define NFTUPD asize(ftupd)
do_pullgrp(fio,&pull->grp[g],bRead,file_version);
}
+
+static void do_rotgrp(t_fileio *fio, t_rotgrp *rotg,gmx_bool bRead, int file_version)
+{
+ gmx_bool bDum=TRUE;
+ int i;
+
+ gmx_fio_do_int(fio,rotg->eType);
+ gmx_fio_do_int(fio,rotg->bMassW);
+ gmx_fio_do_int(fio,rotg->nat);
+ if (bRead)
+ snew(rotg->ind,rotg->nat);
+ gmx_fio_ndo_int(fio,rotg->ind,rotg->nat);
+ if (bRead)
+ snew(rotg->x_ref,rotg->nat);
+ gmx_fio_ndo_rvec(fio,rotg->x_ref,rotg->nat);
+ gmx_fio_do_rvec(fio,rotg->vec);
+ gmx_fio_do_rvec(fio,rotg->pivot);
+ gmx_fio_do_real(fio,rotg->rate);
+ gmx_fio_do_real(fio,rotg->k);
+ gmx_fio_do_real(fio,rotg->slab_dist);
+ gmx_fio_do_real(fio,rotg->min_gaussian);
+ gmx_fio_do_real(fio,rotg->eps);
+ gmx_fio_do_int(fio,rotg->eFittype);
+ gmx_fio_do_int(fio,rotg->PotAngle_nstep);
+ gmx_fio_do_real(fio,rotg->PotAngle_step);
+}
+
+static void do_rot(t_fileio *fio, t_rot *rot,gmx_bool bRead, int file_version)
+{
+ int g;
+
+ gmx_fio_do_int(fio,rot->ngrp);
+ gmx_fio_do_int(fio,rot->nstrout);
+ gmx_fio_do_int(fio,rot->nstsout);
+ if (bRead)
+ snew(rot->grp,rot->ngrp);
+ for(g=0; g<rot->ngrp; g++)
+ do_rotgrp(fio, &rot->grp[g],bRead,file_version);
+}
+
+
static void do_inputrec(t_fileio *fio, t_inputrec *ir,gmx_bool bRead,
int file_version, real *fudgeQQ)
{
if (file_version != tpx_version)
{
/* Give a warning about features that are not accessible */
- fprintf(stderr,"Note: tpx file_version %d, software version %d\n",
+ fprintf(stderr,"Note: file tpx version %d, software tpx version %d\n",
file_version,tpx_version);
}
gmx_fio_do_real(fio,ir->userreal3);
gmx_fio_do_real(fio,ir->userreal4);
+ /* AdResS stuff */
+ if (file_version >= 75) {
+ gmx_fio_do_gmx_bool(fio,ir->bAdress);
+ if(ir->bAdress){
+ if (bRead) snew(ir->adress, 1);
+ gmx_fio_do_int(fio,ir->adress->type);
+ gmx_fio_do_real(fio,ir->adress->const_wf);
+ gmx_fio_do_real(fio,ir->adress->ex_width);
+ gmx_fio_do_real(fio,ir->adress->hy_width);
+ gmx_fio_do_int(fio,ir->adress->icor);
+ gmx_fio_do_int(fio,ir->adress->site);
+ gmx_fio_do_rvec(fio,ir->adress->refs);
+ gmx_fio_do_int(fio,ir->adress->n_tf_grps);
+ gmx_fio_do_real(fio, ir->adress->ex_forcecap);
+ gmx_fio_do_int(fio, ir->adress->n_energy_grps);
+ gmx_fio_do_int(fio,ir->adress->do_hybridpairs);
+
+ if (bRead)snew(ir->adress->tf_table_index,ir->adress->n_tf_grps);
+ if (ir->adress->n_tf_grps > 0) {
+ bDum=gmx_fio_ndo_int(fio,ir->adress->tf_table_index,ir->adress->n_tf_grps);
+ }
+ if (bRead)snew(ir->adress->group_explicit,ir->adress->n_energy_grps);
+ if (ir->adress->n_energy_grps > 0) {
+ bDum=gmx_fio_ndo_int(fio, ir->adress->group_explicit,ir->adress->n_energy_grps);
+ }
+ }
+ } else {
+ ir->bAdress = FALSE;
+ }
+
/* pull stuff */
if (file_version >= 48) {
gmx_fio_do_int(fio,ir->ePull);
ir->ePull = epullNO;
}
+ /* Enforced rotation */
+ if (file_version >= 74) {
+ gmx_fio_do_int(fio,ir->bRot);
+ if (ir->bRot == TRUE) {
+ if (bRead)
+ snew(ir->rot,1);
+ do_rot(fio, ir->rot,bRead,file_version);
+ }
+ } else {
+ ir->bRot = FALSE;
+ }
+
/* grpopts stuff */
gmx_fio_do_int(fio,ir->opts.ngtc);
if (file_version >= 69) {
iparams->pdihs.cpB = iparams->pdihs.cpA;
}
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->linangle.klinB);
+ gmx_fio_do_real(fio,iparams->linangle.aB);
+ break;
case F_FENEBONDS:
gmx_fio_do_real(fio,iparams->fene.bm);
gmx_fio_do_real(fio,iparams->fene.kb);
case F_POLARIZATION:
gmx_fio_do_real(fio,iparams->polarize.alpha);
break;
+ case F_ANHARM_POL:
+ gmx_fio_do_real(fio,iparams->anharm_polarize.alpha);
+ gmx_fio_do_real(fio,iparams->anharm_polarize.drcut);
+ gmx_fio_do_real(fio,iparams->anharm_polarize.khyp);
+ break;
case F_WATER_POL:
if (file_version < 31)
gmx_fatal(FARGS,"Old tpr files with water_polarization not supported. Make a new.");
gmx_bool TopOnlyOK, int *file_version,
int *file_generation)
{
- char buf[STRLEN];
+ char buf[STRLEN];
+ char file_tag[STRLEN];
gmx_bool bDouble;
int precision;
int fver,fgen;
gmx_fio_setprecision(fio,bDouble);
gmx_fio_do_int(fio,precision);
fver = tpx_version;
+ sprintf(file_tag,"%s",tpx_tag);
fgen = tpx_generation;
}
- /* Check versions! */
- gmx_fio_do_int(fio,fver);
+ /* Check versions! */
+ gmx_fio_do_int(fio,fver);
- if(fver>=26)
- gmx_fio_do_int(fio,fgen);
- else
- fgen=0;
+ if (fver >= 77)
+ {
+ gmx_fio_do_string(fio,file_tag);
+ }
+ if (bRead)
+ {
+ if (fver < 77)
+ {
+ /* Versions before 77 don't have the tag, set it to release */
+ sprintf(file_tag,"%s",TPX_TAG_RELEASE);
+ }
+
+ if (strcmp(file_tag,tpx_tag) != 0)
+ {
+ fprintf(stderr,"Note: file tpx tag '%s', software tpx tag '%s'\n",
+ file_tag,tpx_tag);
+
+ /* We only support reading tpx files with the same tag as the code
+ * or tpx files with the release tag and with lower version number.
+ */
+ if (!(strcmp(file_tag,TPX_TAG_RELEASE) == 0 && fver < tpx_version))
+ {
+ gmx_fatal(FARGS,"tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
+ gmx_fio_getname(fio),fver,file_tag,
+ tpx_version,tpx_tag);
+ }
+ }
+ }
+
+ if (fver >= 26)
+ {
+ gmx_fio_do_int(fio,fgen);
+ }
+ else
+ {
+ fgen=0;
+ }
- if(file_version!=NULL)
- *file_version = fver;
- if(file_generation!=NULL)
- *file_generation = fgen;
+ if (file_version != NULL)
+ {
+ *file_version = fver;
+ }
+ if (file_generation != NULL)
+ {
+ *file_generation = fgen;
+ }
if ((fver <= tpx_incompatible_version) ||
{
t_tpxheader header;
int natoms,i,version,generation;
- gmx_bool bTop,bXNULL;
+ gmx_bool bTop,bXNULL=FALSE;
gmx_mtop_t *mtop;
t_topology *topconv;
gmx_atomprop_t aps;
else {
get_stx_coordnum(infile,&natoms);
init_t_atoms(&top->atoms,natoms,(fn2ftp(infile) == efPDB));
- bXNULL = (x == NULL);
+ if (x == NULL)
+ {
+ snew(x,1);
+ bXNULL = TRUE;
+ }
snew(*x,natoms);
if (v)
snew(*v,natoms);
read_stx_conf(infile,title,&top->atoms,*x,(v==NULL) ? NULL : *v,ePBC,box);
- if (bXNULL) {
+ if (bXNULL)
+ {
sfree(*x);
- x = NULL;
+ sfree(x);
}
if (bMass) {
aps = gmx_atomprop_init();
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff