/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* GROningen Mixture of Alchemy and Childrens' Stories
*/
#include "xdrf.h"
#include "macros.h"
-/* The source code in this file should be thread-safe.
+/* The source code in this file should be thread-safe.
Please keep it that way. */
/* This number should be increased whenever the file format changes! */
static const int enx_version = 5;
-const char *enx_block_id_name[] = {
+const char *enx_block_id_name[] = {
"Averaged orientation restraints",
"Instantaneous orientation restraints",
"Orientation restraint order tensor(s)",
typedef struct {
gmx_bool bOldFileOpen; /* Is this an open old file? */
gmx_bool bReadFirstStep; /* Did we read the first step? */
- int first_step; /* First step in the energy file */
- int step_prev; /* Previous step */
- int nsum_prev; /* Previous step sum length */
- t_energy *ener_prev; /* Previous energy sums */
+ int first_step; /* First step in the energy file */
+ int step_prev; /* Previous step */
+ int nsum_prev; /* Previous step sum length */
+ t_energy *ener_prev; /* Previous energy sums */
} ener_old_t;
struct ener_file
{
ener_old_t eo;
- t_fileio *fio;
- int framenr;
- real frametime;
+ t_fileio *fio;
+ int framenr;
+ real frametime;
};
static void enxsubblock_init(t_enxsubblock *sb)
{
- sb->nr=0;
+ sb->nr = 0;
#ifdef GMX_DOUBLE
- sb->type=xdr_datatype_double;
+ sb->type = xdr_datatype_double;
#else
- sb->type=xdr_datatype_float;
+ sb->type = xdr_datatype_float;
#endif
- sb->fval = NULL;
- sb->dval = NULL;
- sb->ival = NULL;
- sb->lval = NULL;
- sb->cval = NULL;
- sb->sval = NULL;
+ sb->fval = NULL;
+ sb->dval = NULL;
+ sb->ival = NULL;
+ sb->lval = NULL;
+ sb->cval = NULL;
+ sb->sval = NULL;
sb->fval_alloc = 0;
sb->dval_alloc = 0;
sb->ival_alloc = 0;
if (sb->fval_alloc)
{
free(sb->fval);
- sb->fval_alloc=0;
- sb->fval=NULL;
+ sb->fval_alloc = 0;
+ sb->fval = NULL;
}
if (sb->dval_alloc)
{
free(sb->dval);
- sb->dval_alloc=0;
- sb->dval=NULL;
+ sb->dval_alloc = 0;
+ sb->dval = NULL;
}
if (sb->ival_alloc)
{
free(sb->ival);
- sb->ival_alloc=0;
- sb->ival=NULL;
+ sb->ival_alloc = 0;
+ sb->ival = NULL;
}
if (sb->lval_alloc)
{
free(sb->lval);
- sb->lval_alloc=0;
- sb->lval=NULL;
+ sb->lval_alloc = 0;
+ sb->lval = NULL;
}
if (sb->cval_alloc)
{
free(sb->cval);
- sb->cval_alloc=0;
- sb->cval=NULL;
+ sb->cval_alloc = 0;
+ sb->cval = NULL;
}
if (sb->sval_alloc)
{
int i;
- for(i=0;i<sb->sval_alloc;i++)
+ for (i = 0; i < sb->sval_alloc; i++)
{
if (sb->sval[i])
{
}
}
free(sb->sval);
- sb->sval_alloc=0;
- sb->sval=NULL;
+ sb->sval_alloc = 0;
+ sb->sval = NULL;
}
}
static void enxsubblock_alloc(t_enxsubblock *sb)
{
/* allocate the appropriate amount of memory */
- switch(sb->type)
+ switch (sb->type)
{
case xdr_datatype_float:
if (sb->nr > sb->fval_alloc)
{
srenew(sb->fval, sb->nr);
- sb->fval_alloc=sb->nr;
+ sb->fval_alloc = sb->nr;
}
break;
case xdr_datatype_double:
if (sb->nr > sb->dval_alloc)
{
srenew(sb->dval, sb->nr);
- sb->dval_alloc=sb->nr;
+ sb->dval_alloc = sb->nr;
}
break;
case xdr_datatype_int:
if (sb->nr > sb->ival_alloc)
{
srenew(sb->ival, sb->nr);
- sb->ival_alloc=sb->nr;
+ sb->ival_alloc = sb->nr;
}
break;
case xdr_datatype_large_int:
if (sb->nr > sb->lval_alloc)
{
srenew(sb->lval, sb->nr);
- sb->lval_alloc=sb->nr;
+ sb->lval_alloc = sb->nr;
}
break;
case xdr_datatype_char:
if (sb->nr > sb->cval_alloc)
{
srenew(sb->cval, sb->nr);
- sb->cval_alloc=sb->nr;
+ sb->cval_alloc = sb->nr;
}
break;
case xdr_datatype_string:
int i;
srenew(sb->sval, sb->nr);
- for(i=sb->sval_alloc;i<sb->nr;i++)
+ for (i = sb->sval_alloc; i < sb->nr; i++)
{
- sb->sval[i]=NULL;
+ sb->sval[i] = NULL;
}
- sb->sval_alloc=sb->nr;
+ sb->sval_alloc = sb->nr;
}
break;
default:
static void enxblock_init(t_enxblock *eb)
{
- eb->id=enxOR;
- eb->nsub=0;
- eb->sub=NULL;
- eb->nsub_alloc=0;
+ eb->id = enxOR;
+ eb->nsub = 0;
+ eb->sub = NULL;
+ eb->nsub_alloc = 0;
}
static void enxblock_free(t_enxblock *eb)
{
- if (eb->nsub_alloc>0)
+ if (eb->nsub_alloc > 0)
{
int i;
- for(i=0;i<eb->nsub_alloc;i++)
+ for (i = 0; i < eb->nsub_alloc; i++)
{
enxsubblock_free(&(eb->sub[i]));
}
free(eb->sub);
- eb->nsub_alloc=0;
- eb->sub=NULL;
+ eb->nsub_alloc = 0;
+ eb->sub = NULL;
}
}
void init_enxframe(t_enxframe *fr)
{
- fr->e_alloc=0;
- fr->ener=NULL;
+ fr->e_alloc = 0;
+ fr->ener = NULL;
/*fr->d_alloc=0;*/
- fr->ener=NULL;
+ fr->ener = NULL;
/*fr->ndisre=0;*/
- fr->nblock=0;
- fr->nblock_alloc=0;
- fr->block=NULL;
+ fr->nblock = 0;
+ fr->nblock_alloc = 0;
+ fr->block = NULL;
}
void free_enxframe(t_enxframe *fr)
{
- int b;
-
- if (fr->e_alloc)
- {
- sfree(fr->ener);
- }
- for(b=0; b<fr->nblock_alloc; b++)
- {
- enxblock_free(&(fr->block[b]));
- }
- free(fr->block);
+ int b;
+
+ if (fr->e_alloc)
+ {
+ sfree(fr->ener);
+ }
+ for (b = 0; b < fr->nblock_alloc; b++)
+ {
+ enxblock_free(&(fr->block[b]));
+ }
+ free(fr->block);
}
void add_blocks_enxframe(t_enxframe *fr, int n)
{
- fr->nblock=n;
+ fr->nblock = n;
if (n > fr->nblock_alloc)
{
int b;
srenew(fr->block, n);
- for(b=fr->nblock_alloc;b<fr->nblock;b++)
+ for (b = fr->nblock_alloc; b < fr->nblock; b++)
{
enxblock_init(&(fr->block[b]));
}
- fr->nblock_alloc=n;
+ fr->nblock_alloc = n;
}
}
t_enxblock *find_block_id_enxframe(t_enxframe *ef, int id, t_enxblock *prev)
{
- gmx_off_t starti=0;
+ gmx_off_t starti = 0;
gmx_off_t i;
if (prev)
{
- starti=(prev - ef->block) + 1;
+ starti = (prev - ef->block) + 1;
}
- for(i=starti; i<ef->nblock; i++)
+ for (i = starti; i < ef->nblock; i++)
{
if (ef->block[i].id == id)
+ {
return &(ef->block[i]);
+ }
}
return NULL;
}
void add_subblocks_enxblock(t_enxblock *eb, int n)
{
- eb->nsub=n;
+ eb->nsub = n;
if (eb->nsub > eb->nsub_alloc)
{
int b;
srenew(eb->sub, n);
- for(b=eb->nsub_alloc; b<n; b++)
+ for (b = eb->nsub_alloc; b < n; b++)
{
enxsubblock_init(&(eb->sub[b]));
- }
- eb->nsub_alloc=n;
+ }
+ eb->nsub_alloc = n;
}
}
}
else
{
- gmx_fatal(FARGS,"%s\n%s",
+ gmx_fatal(FARGS, "%s\n%s",
msg,
"If you want to use the correct frames before the corrupted frame and avoid this fatal error set the env.var. GMX_ENX_NO_FATAL");
}
}
-static void edr_strings(XDR *xdr,gmx_bool bRead,int file_version,
- int n,gmx_enxnm_t **nms)
+static void edr_strings(XDR *xdr, gmx_bool bRead, int file_version,
+ int n, gmx_enxnm_t **nms)
{
- int i;
+ int i;
gmx_enxnm_t *nm;
if (*nms == NULL)
{
- snew(*nms,n);
+ snew(*nms, n);
}
- for(i=0; i<n; i++)
+ for (i = 0; i < n; i++)
{
nm = &(*nms)[i];
if (bRead)
nm->unit = NULL;
}
}
- if(!xdr_string(xdr,&(nm->name),STRLEN))
+ if (!xdr_string(xdr, &(nm->name), STRLEN))
{
gmx_file("Cannot write energy names to file; maybe you are out of disk space?");
}
if (file_version >= 2)
{
- if(!xdr_string(xdr,&(nm->unit),STRLEN))
+ if (!xdr_string(xdr, &(nm->unit), STRLEN))
{
gmx_file("Cannot write energy names to file; maybe you are out of disk space?");
}
}
}
-void do_enxnms(ener_file_t ef,int *nre,gmx_enxnm_t **nms)
+void do_enxnms(ener_file_t ef, int *nre, gmx_enxnm_t **nms)
{
- int magic=-55555;
- XDR *xdr;
+ int magic = -55555;
+ XDR *xdr;
gmx_bool bRead = gmx_fio_getread(ef->fio);
- int file_version;
- int i;
-
- gmx_fio_checktype(ef->fio);
+ int file_version;
+ int i;
+
+ gmx_fio_checktype(ef->fio);
xdr = gmx_fio_getxdr(ef->fio);
-
- if (!xdr_int(xdr,&magic))
+
+ if (!xdr_int(xdr, &magic))
{
- if(!bRead)
+ if (!bRead)
{
gmx_file("Cannot write energy names to file; maybe you are out of disk space?");
}
- *nre=0;
+ *nre = 0;
return;
}
if (magic > 0)
{
/* Assume this is an old edr format */
- file_version = 1;
- *nre = magic;
- ef->eo.bOldFileOpen = TRUE;
+ file_version = 1;
+ *nre = magic;
+ ef->eo.bOldFileOpen = TRUE;
ef->eo.bReadFirstStep = FALSE;
- srenew(ef->eo.ener_prev,*nre);
+ srenew(ef->eo.ener_prev, *nre);
}
else
{
- ef->eo.bOldFileOpen=FALSE;
+ ef->eo.bOldFileOpen = FALSE;
if (magic != -55555)
{
- gmx_fatal(FARGS,"Energy names magic number mismatch, this is not a GROMACS edr file");
+ gmx_fatal(FARGS, "Energy names magic number mismatch, this is not a GROMACS edr file");
}
file_version = enx_version;
- xdr_int(xdr,&file_version);
+ xdr_int(xdr, &file_version);
if (file_version > enx_version)
{
- gmx_fatal(FARGS,"reading tpx file (%s) version %d with version %d program",gmx_fio_getname(ef->fio),file_version,enx_version);
+ gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program", gmx_fio_getname(ef->fio), file_version, enx_version);
}
- xdr_int(xdr,nre);
+ xdr_int(xdr, nre);
}
if (file_version != enx_version)
{
- fprintf(stderr,"Note: enx file_version %d, software version %d\n",
- file_version,enx_version);
+ fprintf(stderr, "Note: enx file_version %d, software version %d\n",
+ file_version, enx_version);
}
- edr_strings(xdr,bRead,file_version,*nre,nms);
+ edr_strings(xdr, bRead, file_version, *nre, nms);
}
-static gmx_bool do_eheader(ener_file_t ef,int *file_version,t_enxframe *fr,
- int nre_test,gmx_bool *bWrongPrecision,gmx_bool *bOK)
+static gmx_bool do_eheader(ener_file_t ef, int *file_version, t_enxframe *fr,
+ int nre_test, gmx_bool *bWrongPrecision, gmx_bool *bOK)
{
- int magic=-7777777;
- real first_real_to_check;
- int b,i,zero=0,dum=0;
- gmx_bool bRead = gmx_fio_getread(ef->fio);
- int tempfix_nr=0;
- int ndisre=0;
- int startb=0;
+ int magic = -7777777;
+ real first_real_to_check;
+ int b, i, zero = 0, dum = 0;
+ gmx_bool bRead = gmx_fio_getread(ef->fio);
+ int tempfix_nr = 0;
+ int ndisre = 0;
+ int startb = 0;
#ifndef GMX_DOUBLE
- xdr_datatype dtreal=xdr_datatype_float;
+ xdr_datatype dtreal = xdr_datatype_float;
#else
- xdr_datatype dtreal=xdr_datatype_double;
+ xdr_datatype dtreal = xdr_datatype_double;
#endif
-
+
if (bWrongPrecision)
{
*bWrongPrecision = FALSE;
}
- *bOK=TRUE;
+ *bOK = TRUE;
/* The original energy frame started with a real,
* so we have to use a real for compatibility.
* This is VERY DIRTY code, since do_eheader can be called
{
/* Assume we are reading an old format */
*file_version = 1;
- fr->t = first_real_to_check;
- if (!gmx_fio_do_int(ef->fio, dum)) *bOK = FALSE;
+ fr->t = first_real_to_check;
+ if (!gmx_fio_do_int(ef->fio, dum))
+ {
+ *bOK = FALSE;
+ }
fr->step = dum;
}
else
{
- if (!gmx_fio_do_int(ef->fio, magic)) *bOK = FALSE;
+ if (!gmx_fio_do_int(ef->fio, magic))
+ {
+ *bOK = FALSE;
+ }
if (magic != -7777777)
{
enx_warning("Energy header magic number mismatch, this is not a GROMACS edr file");
- *bOK=FALSE;
+ *bOK = FALSE;
return FALSE;
}
*file_version = enx_version;
- if (!gmx_fio_do_int(ef->fio, *file_version)) *bOK = FALSE;
+ if (!gmx_fio_do_int(ef->fio, *file_version))
+ {
+ *bOK = FALSE;
+ }
if (*bOK && *file_version > enx_version)
{
- gmx_fatal(FARGS,"reading tpx file (%s) version %d with version %d program",gmx_fio_getname(ef->fio),file_version,enx_version);
+ gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program", gmx_fio_getname(ef->fio), file_version, enx_version);
}
- if (!gmx_fio_do_double(ef->fio, fr->t)) *bOK = FALSE;
- if (!gmx_fio_do_gmx_large_int(ef->fio, fr->step)) *bOK = FALSE;
- if (!bRead && fr->nsum == 1) {
+ if (!gmx_fio_do_double(ef->fio, fr->t))
+ {
+ *bOK = FALSE;
+ }
+ if (!gmx_fio_do_gmx_large_int(ef->fio, fr->step))
+ {
+ *bOK = FALSE;
+ }
+ if (!bRead && fr->nsum == 1)
+ {
/* Do not store sums of length 1,
* since this does not add information.
*/
- if (!gmx_fio_do_int(ef->fio, zero)) *bOK = FALSE;
- } else {
- if (!gmx_fio_do_int(ef->fio, fr->nsum)) *bOK = FALSE;
+ if (!gmx_fio_do_int(ef->fio, zero))
+ {
+ *bOK = FALSE;
+ }
+ }
+ else
+ {
+ if (!gmx_fio_do_int(ef->fio, fr->nsum))
+ {
+ *bOK = FALSE;
+ }
}
if (*file_version >= 3)
{
- if (!gmx_fio_do_gmx_large_int(ef->fio, fr->nsteps)) *bOK = FALSE;
+ if (!gmx_fio_do_gmx_large_int(ef->fio, fr->nsteps))
+ {
+ *bOK = FALSE;
+ }
}
else
{
- fr->nsteps = max(1,fr->nsum);
+ fr->nsteps = max(1, fr->nsum);
}
if (*file_version >= 5)
{
- if (!gmx_fio_do_double(ef->fio, fr->dt)) *bOK = FALSE;
+ if (!gmx_fio_do_double(ef->fio, fr->dt))
+ {
+ *bOK = FALSE;
+ }
}
else
{
fr->dt = 0;
}
}
- if (!gmx_fio_do_int(ef->fio, fr->nre)) *bOK = FALSE;
+ if (!gmx_fio_do_int(ef->fio, fr->nre))
+ {
+ *bOK = FALSE;
+ }
if (*file_version < 4)
{
- if (!gmx_fio_do_int(ef->fio, ndisre)) *bOK = FALSE;
+ if (!gmx_fio_do_int(ef->fio, ndisre))
+ {
+ *bOK = FALSE;
+ }
}
else
{
/* now reserved for possible future use */
- if (!gmx_fio_do_int(ef->fio, dum)) *bOK = FALSE;
+ if (!gmx_fio_do_int(ef->fio, dum))
+ {
+ *bOK = FALSE;
+ }
}
- if (!gmx_fio_do_int(ef->fio, fr->nblock)) *bOK = FALSE;
- if (fr->nblock < 0) *bOK=FALSE;
+ if (!gmx_fio_do_int(ef->fio, fr->nblock))
+ {
+ *bOK = FALSE;
+ }
+ if (fr->nblock < 0)
+ {
+ *bOK = FALSE;
+ }
- if (ndisre!=0)
+ if (ndisre != 0)
{
if (*file_version >= 4)
{
enx_warning("Distance restraint blocks in old style in new style file");
- *bOK=FALSE;
+ *bOK = FALSE;
return FALSE;
}
- fr->nblock+=1;
+ fr->nblock += 1;
}
/* we now know what these should be, or we've already bailed out because
of wrong precision */
- if ( *file_version==1 && (fr->t < 0 || fr->t > 1e20 || fr->step < 0 ) )
+ if (*file_version == 1 && (fr->t < 0 || fr->t > 1e20 || fr->step < 0 ) )
{
enx_warning("edr file with negative step number or unreasonable time (and without version number).");
- *bOK=FALSE;
+ *bOK = FALSE;
return FALSE;
}
add_blocks_enxframe(fr, fr->nblock);
}
- startb=0;
- if (ndisre>0)
+ startb = 0;
+ if (ndisre > 0)
{
/* sub[0] is the instantaneous data, sub[1] is time averaged */
add_subblocks_enxblock(&(fr->block[0]), 2);
- fr->block[0].id=enxDISRE;
- fr->block[0].sub[0].nr=ndisre;
- fr->block[0].sub[1].nr=ndisre;
- fr->block[0].sub[0].type=dtreal;
- fr->block[0].sub[1].type=dtreal;
+ fr->block[0].id = enxDISRE;
+ fr->block[0].sub[0].nr = ndisre;
+ fr->block[0].sub[1].nr = ndisre;
+ fr->block[0].sub[0].type = dtreal;
+ fr->block[0].sub[1].type = dtreal;
startb++;
}
/* read block header info */
- for(b=startb; b<fr->nblock; b++)
+ for (b = startb; b < fr->nblock; b++)
{
- if (*file_version<4)
+ if (*file_version < 4)
{
- /* blocks in old version files always have 1 subblock that
+ /* blocks in old version files always have 1 subblock that
consists of reals. */
int nrint;
}
}
nrint = fr->block[b].sub[0].nr;
-
+
if (!gmx_fio_do_int(ef->fio, nrint))
{
*bOK = FALSE;
int i;
/* in the new version files, the block header only contains
the ID and the number of subblocks */
- int nsub=fr->block[b].nsub;
+ int nsub = fr->block[b].nsub;
*bOK = *bOK && gmx_fio_do_int(ef->fio, fr->block[b].id);
*bOK = *bOK && gmx_fio_do_int(ef->fio, nsub);
- fr->block[b].nsub=nsub;
+ fr->block[b].nsub = nsub;
if (bRead)
+ {
add_subblocks_enxblock(&(fr->block[b]), nsub);
+ }
/* read/write type & size for each subblock */
- for(i=0;i<nsub;i++)
+ for (i = 0; i < nsub; i++)
{
- t_enxsubblock *sub=&(fr->block[b].sub[i]); /* shortcut */
- int typenr=sub->type;
+ t_enxsubblock *sub = &(fr->block[b].sub[i]); /* shortcut */
+ int typenr = sub->type;
- *bOK=*bOK && gmx_fio_do_int(ef->fio, typenr);
- *bOK=*bOK && gmx_fio_do_int(ef->fio, sub->nr);
+ *bOK = *bOK && gmx_fio_do_int(ef->fio, typenr);
+ *bOK = *bOK && gmx_fio_do_int(ef->fio, sub->nr);
sub->type = (xdr_datatype)typenr;
}
}
}
- if (!gmx_fio_do_int(ef->fio, fr->e_size)) *bOK = FALSE;
+ if (!gmx_fio_do_int(ef->fio, fr->e_size))
+ {
+ *bOK = FALSE;
+ }
/* now reserved for possible future use */
- if (!gmx_fio_do_int(ef->fio, dum)) *bOK = FALSE;
+ if (!gmx_fio_do_int(ef->fio, dum))
+ {
+ *bOK = FALSE;
+ }
/* Do a dummy int to keep the format compatible with the old code */
- if (!gmx_fio_do_int(ef->fio, dum)) *bOK = FALSE;
-
+ if (!gmx_fio_do_int(ef->fio, dum))
+ {
+ *bOK = FALSE;
+ }
+
if (*bOK && *file_version == 1 && nre_test < 0)
{
#if 0
gmx_incons("Problem with reading old format energy files");
}
#endif
-
+
if (!ef->eo.bReadFirstStep)
{
ef->eo.bReadFirstStep = TRUE;
ef->eo.step_prev = fr->step;
ef->eo.nsum_prev = 0;
}
-
+
fr->nsum = fr->step - ef->eo.first_step + 1;
fr->nsteps = fr->step - ef->eo.step_prev;
fr->dt = 0;
}
-
+
return *bOK;
}
-void free_enxnms(int n,gmx_enxnm_t *nms)
+void free_enxnms(int n, gmx_enxnm_t *nms)
{
int i;
- for(i=0; i<n; i++)
+ for (i = 0; i < n; i++)
{
sfree(nms[i].name);
sfree(nms[i].unit);
void close_enx(ener_file_t ef)
{
- if(gmx_fio_close(ef->fio) != 0)
+ if (gmx_fio_close(ef->fio) != 0)
{
gmx_file("Cannot close energy file; it might be corrupt, or maybe you are out of disk space?");
}
static gmx_bool empty_file(const char *fn)
{
- FILE *fp;
- char dum;
- int ret;
+ FILE *fp;
+ char dum;
+ int ret;
gmx_bool bEmpty;
-
- fp = gmx_fio_fopen(fn,"r");
- ret = fread(&dum,sizeof(dum),1,fp);
+
+ fp = gmx_fio_fopen(fn, "r");
+ ret = fread(&dum, sizeof(dum), 1, fp);
bEmpty = feof(fp);
gmx_fio_fclose(fp);
-
+
return bEmpty;
}
-ener_file_t open_enx(const char *fn,const char *mode)
+ener_file_t open_enx(const char *fn, const char *mode)
{
- int nre,i;
- gmx_enxnm_t *nms=NULL;
- int file_version=-1;
- t_enxframe *fr;
- gmx_bool bWrongPrecision,bOK=TRUE;
+ int nre, i;
+ gmx_enxnm_t *nms = NULL;
+ int file_version = -1;
+ t_enxframe *fr;
+ gmx_bool bWrongPrecision, bOK = TRUE;
struct ener_file *ef;
- snew(ef,1);
+ snew(ef, 1);
- if (mode[0]=='r') {
- ef->fio=gmx_fio_open(fn,mode);
+ if (mode[0] == 'r')
+ {
+ ef->fio = gmx_fio_open(fn, mode);
gmx_fio_checktype(ef->fio);
- gmx_fio_setprecision(ef->fio,FALSE);
- do_enxnms(ef,&nre,&nms);
- snew(fr,1);
- do_eheader(ef,&file_version,fr,nre,&bWrongPrecision,&bOK);
- if(!bOK)
+ gmx_fio_setprecision(ef->fio, FALSE);
+ do_enxnms(ef, &nre, &nms);
+ snew(fr, 1);
+ do_eheader(ef, &file_version, fr, nre, &bWrongPrecision, &bOK);
+ if (!bOK)
{
gmx_file("Cannot read energy file header. Corrupt file?");
}
/* Now check whether this file is in single precision */
if (!bWrongPrecision &&
- ((fr->e_size && (fr->nre == nre) &&
+ ((fr->e_size && (fr->nre == nre) &&
(nre*4*(long int)sizeof(float) == fr->e_size)) ) )
{
- fprintf(stderr,"Opened %s as single precision energy file\n",fn);
- free_enxnms(nre,nms);
+ fprintf(stderr, "Opened %s as single precision energy file\n", fn);
+ free_enxnms(nre, nms);
}
else
{
gmx_fio_rewind(ef->fio);
gmx_fio_checktype(ef->fio);
- gmx_fio_setprecision(ef->fio,TRUE);
- do_enxnms(ef,&nre,&nms);
- do_eheader(ef,&file_version,fr,nre,&bWrongPrecision,&bOK);
- if(!bOK)
+ gmx_fio_setprecision(ef->fio, TRUE);
+ do_enxnms(ef, &nre, &nms);
+ do_eheader(ef, &file_version, fr, nre, &bWrongPrecision, &bOK);
+ if (!bOK)
{
gmx_file("Cannot write energy file header; maybe you are out of disk space?");
}
- if (((fr->e_size && (fr->nre == nre) &&
- (nre*4*(long int)sizeof(double) == fr->e_size)) ))
- fprintf(stderr,"Opened %s as double precision energy file\n",
+ if (((fr->e_size && (fr->nre == nre) &&
+ (nre*4*(long int)sizeof(double) == fr->e_size)) ))
+ {
+ fprintf(stderr, "Opened %s as double precision energy file\n",
fn);
- else {
+ }
+ else
+ {
if (empty_file(fn))
- gmx_fatal(FARGS,"File %s is empty",fn);
+ {
+ gmx_fatal(FARGS, "File %s is empty", fn);
+ }
else
- gmx_fatal(FARGS,"Energy file %s not recognized, maybe different CPU?",
+ {
+ gmx_fatal(FARGS, "Energy file %s not recognized, maybe different CPU?",
fn);
+ }
}
- free_enxnms(nre,nms);
+ free_enxnms(nre, nms);
}
free_enxframe(fr);
sfree(fr);
gmx_fio_rewind(ef->fio);
}
- else
- ef->fio = gmx_fio_open(fn,mode);
+ else
+ {
+ ef->fio = gmx_fio_open(fn, mode);
+ }
- ef->framenr=0;
- ef->frametime=0;
+ ef->framenr = 0;
+ ef->frametime = 0;
return ef;
}
return ef->fio;
}
-static void convert_full_sums(ener_old_t *ener_old,t_enxframe *fr)
+static void convert_full_sums(ener_old_t *ener_old, t_enxframe *fr)
{
- int nstep_all;
- int ne,ns,i;
- double esum_all,eav_all;
-
+ int nstep_all;
+ int ne, ns, i;
+ double esum_all, eav_all;
+
if (fr->nsum > 0)
{
ne = 0;
ns = 0;
- for(i=0; i<fr->nre; i++)
+ for (i = 0; i < fr->nre; i++)
{
- if (fr->ener[i].e != 0) ne++;
- if (fr->ener[i].esum != 0) ns++;
+ if (fr->ener[i].e != 0)
+ {
+ ne++;
+ }
+ if (fr->ener[i].esum != 0)
+ {
+ ns++;
+ }
}
if (ne > 0 && ns == 0)
{
fr->nsum = 0;
}
}
-
+
/* Convert old full simulation sums to sums between energy frames */
nstep_all = fr->step - ener_old->first_step + 1;
if (fr->nsum > 1 && fr->nsum == nstep_all && ener_old->nsum_prev > 0)
{
/* Set the new sum length: the frame step difference */
fr->nsum = fr->step - ener_old->step_prev;
- for(i=0; i<fr->nre; i++)
+ for (i = 0; i < fr->nre; i++)
{
- esum_all = fr->ener[i].esum;
- eav_all = fr->ener[i].eav;
+ esum_all = fr->ener[i].esum;
+ eav_all = fr->ener[i].eav;
fr->ener[i].esum = esum_all - ener_old->ener_prev[i].esum;
fr->ener[i].eav = eav_all - ener_old->ener_prev[i].eav
- dsqr(ener_old->ener_prev[i].esum/(nstep_all - fr->nsum)
{
if (fr->nsum != nstep_all)
{
- fprintf(stderr,"\nWARNING: something is wrong with the energy sums, will not use exact averages\n");
+ fprintf(stderr, "\nWARNING: something is wrong with the energy sums, will not use exact averages\n");
ener_old->nsum_prev = 0;
}
else
ener_old->nsum_prev = nstep_all;
}
/* Copy all sums to ener_prev */
- for(i=0; i<fr->nre; i++)
+ for (i = 0; i < fr->nre; i++)
{
ener_old->ener_prev[i].esum = fr->ener[i].esum;
ener_old->ener_prev[i].eav = fr->ener[i].eav;
}
}
-
+
ener_old->step_prev = fr->step;
}
-gmx_bool do_enx(ener_file_t ef,t_enxframe *fr)
+gmx_bool do_enx(ener_file_t ef, t_enxframe *fr)
{
- int file_version=-1;
- int i,b;
- gmx_bool bRead,bOK,bOK1,bSane;
- real tmp1,tmp2,rdum;
- char buf[22];
+ int file_version = -1;
+ int i, b;
+ gmx_bool bRead, bOK, bOK1, bSane;
+ real tmp1, tmp2, rdum;
+ char buf[22];
/*int d_size;*/
-
- bOK = TRUE;
+
+ bOK = TRUE;
bRead = gmx_fio_getread(ef->fio);
if (!bRead)
- {
+ {
fr->e_size = fr->nre*sizeof(fr->ener[0].e)*4;
/*d_size = fr->ndisre*(sizeof(real)*2);*/
}
gmx_fio_checktype(ef->fio);
- if (!do_eheader(ef,&file_version,fr,-1,NULL,&bOK))
+ if (!do_eheader(ef, &file_version, fr, -1, NULL, &bOK))
{
if (bRead)
{
- fprintf(stderr,"\rLast energy frame read %d time %8.3f ",
- ef->framenr-1,ef->frametime);
+ fprintf(stderr, "\rLast energy frame read %d time %8.3f ",
+ ef->framenr-1, ef->frametime);
if (!bOK)
{
fprintf(stderr,
"\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
- ef->framenr,fr->t);
+ ef->framenr, fr->t);
}
}
else
(ef->framenr < 200 || ef->framenr % 100 == 0) &&
(ef->framenr < 2000 || ef->framenr % 1000 == 0))
{
- fprintf(stderr,"\rReading energy frame %6d time %8.3f ",
- ef->framenr,fr->t);
+ fprintf(stderr, "\rReading energy frame %6d time %8.3f ",
+ ef->framenr, fr->t);
}
ef->framenr++;
ef->frametime = fr->t;
}
/* Check sanity of this header */
- bSane = fr->nre > 0 ;
- for(b=0; b<fr->nblock; b++)
+ bSane = fr->nre > 0;
+ for (b = 0; b < fr->nblock; b++)
{
bSane = bSane || (fr->block[b].nsub > 0);
}
if (!((fr->step >= 0) && bSane))
{
- fprintf(stderr,"\nWARNING: there may be something wrong with energy file %s\n",
+ fprintf(stderr, "\nWARNING: there may be something wrong with energy file %s\n",
gmx_fio_getname(ef->fio));
- fprintf(stderr,"Found: step=%s, nre=%d, nblock=%d, time=%g.\n"
+ fprintf(stderr, "Found: step=%s, nre=%d, nblock=%d, time=%g.\n"
"Trying to skip frame expect a crash though\n",
- gmx_step_str(fr->step,buf),fr->nre,fr->nblock,fr->t);
+ gmx_step_str(fr->step, buf), fr->nre, fr->nblock, fr->t);
}
if (bRead && fr->nre > fr->e_alloc)
{
- srenew(fr->ener,fr->nre);
- for(i=fr->e_alloc; (i<fr->nre); i++)
+ srenew(fr->ener, fr->nre);
+ for (i = fr->e_alloc; (i < fr->nre); i++)
{
fr->ener[i].e = 0;
fr->ener[i].eav = 0;
}
fr->e_alloc = fr->nre;
}
-
- for(i=0; i<fr->nre; i++)
+
+ for (i = 0; i < fr->nre; i++)
{
bOK = bOK && gmx_fio_do_real(ef->fio, fr->ener[i].e);
-
+
/* Do not store sums of length 1,
* since this does not add information.
*/
(bRead && fr->nsum > 0) || fr->nsum > 1)
{
tmp1 = fr->ener[i].eav;
- bOK = bOK && gmx_fio_do_real(ef->fio, tmp1);
+ bOK = bOK && gmx_fio_do_real(ef->fio, tmp1);
if (bRead)
+ {
fr->ener[i].eav = tmp1;
-
+ }
+
/* This is to save only in single precision (unless compiled in DP) */
tmp2 = fr->ener[i].esum;
- bOK = bOK && gmx_fio_do_real(ef->fio, tmp2);
+ bOK = bOK && gmx_fio_do_real(ef->fio, tmp2);
if (bRead)
+ {
fr->ener[i].esum = tmp2;
-
+ }
+
if (file_version == 1)
{
/* Old, unused real */
rdum = 0;
- bOK = bOK && gmx_fio_do_real(ef->fio, rdum);
+ bOK = bOK && gmx_fio_do_real(ef->fio, rdum);
}
}
}
-
+
/* Here we can not check for file_version==1, since one could have
* continued an old format simulation with a new one with mdrun -append.
*/
if (bRead && ef->eo.bOldFileOpen)
{
/* Convert old full simulation sums to sums between energy frames */
- convert_full_sums(&(ef->eo),fr);
+ convert_full_sums(&(ef->eo), fr);
}
/* read the blocks */
- for(b=0; b<fr->nblock; b++)
+ for (b = 0; b < fr->nblock; b++)
{
/* now read the subblocks. */
- int nsub=fr->block[b].nsub; /* shortcut */
+ int nsub = fr->block[b].nsub; /* shortcut */
int i;
- for(i=0;i<nsub;i++)
+ for (i = 0; i < nsub; i++)
{
- t_enxsubblock *sub=&(fr->block[b].sub[i]); /* shortcut */
+ t_enxsubblock *sub = &(fr->block[b].sub[i]); /* shortcut */
if (bRead)
{
}
/* read/write data */
- bOK1=TRUE;
+ bOK1 = TRUE;
switch (sub->type)
{
case xdr_datatype_float:
- bOK1=gmx_fio_ndo_float(ef->fio, sub->fval, sub->nr);
+ bOK1 = gmx_fio_ndo_float(ef->fio, sub->fval, sub->nr);
break;
case xdr_datatype_double:
- bOK1=gmx_fio_ndo_double(ef->fio, sub->dval, sub->nr);
+ bOK1 = gmx_fio_ndo_double(ef->fio, sub->dval, sub->nr);
break;
case xdr_datatype_int:
- bOK1=gmx_fio_ndo_int(ef->fio, sub->ival, sub->nr);
+ bOK1 = gmx_fio_ndo_int(ef->fio, sub->ival, sub->nr);
break;
case xdr_datatype_large_int:
- bOK1=gmx_fio_ndo_gmx_large_int(ef->fio, sub->lval, sub->nr);
+ bOK1 = gmx_fio_ndo_gmx_large_int(ef->fio, sub->lval, sub->nr);
break;
case xdr_datatype_char:
- bOK1=gmx_fio_ndo_uchar(ef->fio, sub->cval, sub->nr);
+ bOK1 = gmx_fio_ndo_uchar(ef->fio, sub->cval, sub->nr);
break;
case xdr_datatype_string:
- bOK1=gmx_fio_ndo_string(ef->fio, sub->sval, sub->nr);
+ bOK1 = gmx_fio_ndo_string(ef->fio, sub->sval, sub->nr);
break;
default:
gmx_incons("Reading unknown block data type: this file is corrupted or from the future");
bOK = bOK && bOK1;
}
}
-
- if(!bRead)
+
+ if (!bRead)
{
- if( gmx_fio_flush(ef->fio) != 0)
+ if (gmx_fio_flush(ef->fio) != 0)
{
gmx_file("Cannot write energy file; maybe you are out of disk space?");
}
}
-
+
if (!bOK)
{
if (bRead)
{
- fprintf(stderr,"\nLast energy frame read %d",
+ fprintf(stderr, "\nLast energy frame read %d",
ef->framenr-1);
- fprintf(stderr,"\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
- ef->framenr,fr->t);
+ fprintf(stderr, "\nWARNING: Incomplete energy frame: nr %d time %8.3f\n",
+ ef->framenr, fr->t);
}
else
{
- gmx_fatal(FARGS,"could not write energies");
+ gmx_fatal(FARGS, "could not write energies");
}
- return FALSE;
+ return FALSE;
}
-
+
return TRUE;
}
t_enxframe *fr)
{
int i;
-
- for(i=0; i<nre; i++)
+
+ for (i = 0; i < nre; i++)
{
- if (strcmp(enm[i].name,name) == 0)
+ if (strcmp(enm[i].name, name) == 0)
{
- return fr->ener[i].e;
+ return fr->ener[i].e;
}
}
-
- gmx_fatal(FARGS,"Could not find energy term named '%s'",name);
-
+
+ gmx_fatal(FARGS, "Could not find energy term named '%s'", name);
+
return 0;
}
void get_enx_state(const char *fn, real t, gmx_groups_t *groups, t_inputrec *ir,
t_state *state)
{
- /* Should match the names in mdebin.c */
- static const char *boxvel_nm[] = {
- "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
- "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
- };
-
- static const char *pcouplmu_nm[] = {
- "Pcoupl-Mu-XX", "Pcoupl-Mu-YY", "Pcoupl-Mu-ZZ",
- "Pcoupl-Mu-YX", "Pcoupl-Mu-ZX", "Pcoupl-Mu-ZY"
- };
- static const char *baro_nm[] = {
- "Barostat"
- };
-
-
- int ind0[] = { XX,YY,ZZ,YY,ZZ,ZZ };
- int ind1[] = { XX,YY,ZZ,XX,XX,YY };
- int nre,nfr,i,j,ni,npcoupl;
- char buf[STRLEN];
- const char *bufi;
- gmx_enxnm_t *enm=NULL;
- t_enxframe *fr;
- ener_file_t in;
-
- in = open_enx(fn,"r");
- do_enxnms(in,&nre,&enm);
- snew(fr,1);
- nfr = 0;
- while ((nfr==0 || fr->t != t) && do_enx(in,fr)) {
- nfr++;
- }
- close_enx(in);
- fprintf(stderr,"\n");
-
- if (nfr == 0 || fr->t != t)
- gmx_fatal(FARGS,"Could not find frame with time %f in '%s'",t,fn);
-
- npcoupl = TRICLINIC(ir->compress) ? 6 : 3;
- if (ir->epc == epcPARRINELLORAHMAN) {
- clear_mat(state->boxv);
- for(i=0; i<npcoupl; i++) {
- state->boxv[ind0[i]][ind1[i]] =
- find_energy(boxvel_nm[i],nre,enm,fr);
- }
- fprintf(stderr,"\nREAD %d BOX VELOCITIES FROM %s\n\n",npcoupl,fn);
- }
-
- if (ir->etc == etcNOSEHOOVER)
- {
- char cns[20];
-
- cns[0] = '\0';
-
- for(i=0; i<state->ngtc; i++) {
- ni = groups->grps[egcTC].nm_ind[i];
- bufi = *(groups->grpname[ni]);
- for(j=0; (j<state->nhchainlength); j++)
- {
- if (IR_NVT_TROTTER(ir))
- {
- sprintf(cns,"-%d",j);
- }
- sprintf(buf,"Xi%s-%s",cns,bufi);
- state->nosehoover_xi[i] = find_energy(buf,nre,enm,fr);
- sprintf(buf,"vXi%s-%s",cns,bufi);
- state->nosehoover_vxi[i] = find_energy(buf,nre,enm,fr);
- }
-
- }
- fprintf(stderr,"\nREAD %d NOSE-HOOVER Xi chains FROM %s\n\n",state->ngtc,fn);
-
- if (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir))
- {
- for(i=0; i<state->nnhpres; i++) {
- bufi = baro_nm[0]; /* All barostat DOF's together for now */
- for(j=0; (j<state->nhchainlength); j++)
- {
- sprintf(buf,"Xi-%d-%s",j,bufi);
- state->nhpres_xi[i] = find_energy(buf,nre,enm,fr);
- sprintf(buf,"vXi-%d-%s",j,bufi);
- state->nhpres_vxi[i] = find_energy(buf,nre,enm,fr);
- }
- }
- fprintf(stderr,"\nREAD %d NOSE-HOOVER BAROSTAT Xi chains FROM %s\n\n",state->nnhpres,fn);
- }
- }
-
- free_enxnms(nre,enm);
- free_enxframe(fr);
- sfree(fr);
-}
+ /* Should match the names in mdebin.c */
+ static const char *boxvel_nm[] = {
+ "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
+ "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
+ };
+
+ static const char *pcouplmu_nm[] = {
+ "Pcoupl-Mu-XX", "Pcoupl-Mu-YY", "Pcoupl-Mu-ZZ",
+ "Pcoupl-Mu-YX", "Pcoupl-Mu-ZX", "Pcoupl-Mu-ZY"
+ };
+ static const char *baro_nm[] = {
+ "Barostat"
+ };
+
+
+ int ind0[] = { XX, YY, ZZ, YY, ZZ, ZZ };
+ int ind1[] = { XX, YY, ZZ, XX, XX, YY };
+ int nre, nfr, i, j, ni, npcoupl;
+ char buf[STRLEN];
+ const char *bufi;
+ gmx_enxnm_t *enm = NULL;
+ t_enxframe *fr;
+ ener_file_t in;
+
+ in = open_enx(fn, "r");
+ do_enxnms(in, &nre, &enm);
+ snew(fr, 1);
+ nfr = 0;
+ while ((nfr == 0 || fr->t != t) && do_enx(in, fr))
+ {
+ nfr++;
+ }
+ close_enx(in);
+ fprintf(stderr, "\n");
+
+ if (nfr == 0 || fr->t != t)
+ {
+ gmx_fatal(FARGS, "Could not find frame with time %f in '%s'", t, fn);
+ }
+
+ npcoupl = TRICLINIC(ir->compress) ? 6 : 3;
+ if (ir->epc == epcPARRINELLORAHMAN)
+ {
+ clear_mat(state->boxv);
+ for (i = 0; i < npcoupl; i++)
+ {
+ state->boxv[ind0[i]][ind1[i]] =
+ find_energy(boxvel_nm[i], nre, enm, fr);
+ }
+ fprintf(stderr, "\nREAD %d BOX VELOCITIES FROM %s\n\n", npcoupl, fn);
+ }
+
+ if (ir->etc == etcNOSEHOOVER)
+ {
+ char cns[20];
+
+ cns[0] = '\0';
+ for (i = 0; i < state->ngtc; i++)
+ {
+ ni = groups->grps[egcTC].nm_ind[i];
+ bufi = *(groups->grpname[ni]);
+ for (j = 0; (j < state->nhchainlength); j++)
+ {
+ if (IR_NVT_TROTTER(ir))
+ {
+ sprintf(cns, "-%d", j);
+ }
+ sprintf(buf, "Xi%s-%s", cns, bufi);
+ state->nosehoover_xi[i] = find_energy(buf, nre, enm, fr);
+ sprintf(buf, "vXi%s-%s", cns, bufi);
+ state->nosehoover_vxi[i] = find_energy(buf, nre, enm, fr);
+ }
+
+ }
+ fprintf(stderr, "\nREAD %d NOSE-HOOVER Xi chains FROM %s\n\n", state->ngtc, fn);
+
+ if (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir))
+ {
+ for (i = 0; i < state->nnhpres; i++)
+ {
+ bufi = baro_nm[0]; /* All barostat DOF's together for now */
+ for (j = 0; (j < state->nhchainlength); j++)
+ {
+ sprintf(buf, "Xi-%d-%s", j, bufi);
+ state->nhpres_xi[i] = find_energy(buf, nre, enm, fr);
+ sprintf(buf, "vXi-%d-%s", j, bufi);
+ state->nhpres_vxi[i] = find_energy(buf, nre, enm, fr);
+ }
+ }
+ fprintf(stderr, "\nREAD %d NOSE-HOOVER BAROSTAT Xi chains FROM %s\n\n", state->nnhpres, fn);
+ }
+ }
+
+ free_enxnms(nre, enm);
+ free_enxframe(fr);
+ sfree(fr);
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff