/*
- *
+ *
* 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 forxd
* 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
*/
#define SKIP3 1000
/* Globals for gromos-87 input */
-typedef enum { effXYZ, effXYZBox, effG87, effG87Box, effNR } eFileFormat;
+typedef enum {
+ effXYZ, effXYZBox, effG87, effG87Box, effNR
+} eFileFormat;
struct t_trxstatus
{
- int __frame;
- t_trxframe *xframe;
- int nxframe;
- t_fileio *fio;
- eFileFormat eFF;
- int NATOMS;
- double DT,BOX[3];
+ int __frame;
+ t_trxframe *xframe;
+ int nxframe;
+ t_fileio *fio;
+ eFileFormat eFF;
+ int NATOMS;
+ double DT, BOX[3];
gmx_bool bReadBox;
- char *persistent_line; /* Persistent line for reading g96 trajectories */
+ char *persistent_line; /* Persistent line for reading g96 trajectories */
};
static void initcount(t_trxstatus *status)
{
- status->__frame=-1;
+ status->__frame = -1;
}
static void status_init(t_trxstatus *status)
{
- status->nxframe=0;
- status->xframe=NULL;
- status->fio=NULL;
- status->__frame=-1;
- status->persistent_line=NULL;
+ status->nxframe = 0;
+ status->xframe = NULL;
+ status->fio = NULL;
+ status->__frame = -1;
+ status->persistent_line = NULL;
}
}
static void printcount_(t_trxstatus *status, const output_env_t oenv,
- const char *l,real t)
+ const char *l, real t)
{
- if ((status->__frame < 2*SKIP1 || status->__frame % SKIP1 == 0) &&
- (status->__frame < 2*SKIP2 || status->__frame % SKIP2 == 0) &&
- (status->__frame < 2*SKIP3 || status->__frame % SKIP3 == 0))
- fprintf(stderr,"\r%-14s %6d time %8.3f ",l,status->__frame,
- output_env_conv_time(oenv,t));
+ if ((status->__frame < 2*SKIP1 || status->__frame % SKIP1 == 0) &&
+ (status->__frame < 2*SKIP2 || status->__frame % SKIP2 == 0) &&
+ (status->__frame < 2*SKIP3 || status->__frame % SKIP3 == 0))
+ {
+ fprintf(stderr, "\r%-14s %6d time %8.3f ", l, status->__frame,
+ output_env_conv_time(oenv, t));
+ }
}
-static void printcount(t_trxstatus *status, const output_env_t oenv,real t,
+static void printcount(t_trxstatus *status, const output_env_t oenv, real t,
gmx_bool bSkip)
{
- status->__frame++;
- printcount_(status, oenv,bSkip ? "Skipping frame" : "Reading frame",t);
+ status->__frame++;
+ printcount_(status, oenv, bSkip ? "Skipping frame" : "Reading frame", t);
}
-static void printlast(t_trxstatus *status, const output_env_t oenv,real t)
+static void printlast(t_trxstatus *status, const output_env_t oenv, real t)
{
- printcount_(status, oenv,"Last frame",t);
- fprintf(stderr,"\n");
+ printcount_(status, oenv, "Last frame", t);
+ fprintf(stderr, "\n");
}
static void printincomp(t_trxstatus *status, t_trxframe *fr)
{
- if (fr->not_ok & HEADER_NOT_OK)
- fprintf(stderr,"WARNING: Incomplete header: nr %d time %g\n",
- status->__frame+1,fr->time);
- else if (fr->not_ok)
- fprintf(stderr,"WARNING: Incomplete frame: nr %d time %g\n",
- status->__frame+1,fr->time);
+ if (fr->not_ok & HEADER_NOT_OK)
+ {
+ fprintf(stderr, "WARNING: Incomplete header: nr %d time %g\n",
+ status->__frame+1, fr->time);
+ }
+ else if (fr->not_ok)
+ {
+ fprintf(stderr, "WARNING: Incomplete frame: nr %d time %g\n",
+ status->__frame+1, fr->time);
+ }
}
int prec2ndec(real prec)
{
- if (prec <= 0)
- gmx_fatal(FARGS,"DEATH HORROR prec (%g) <= 0 in prec2ndec",prec);
-
- return (int)(log(prec)/log(10.0)+0.5);
+ if (prec <= 0)
+ {
+ gmx_fatal(FARGS, "DEATH HORROR prec (%g) <= 0 in prec2ndec", prec);
+ }
+
+ return (int)(log(prec)/log(10.0)+0.5);
}
-void clear_trxframe(t_trxframe *fr,gmx_bool bFirst)
+void clear_trxframe(t_trxframe *fr, gmx_bool bFirst)
{
- fr->not_ok = 0;
- fr->bTitle = FALSE;
- fr->bStep = FALSE;
- fr->bTime = FALSE;
- fr->bLambda = FALSE;
- fr->bAtoms = FALSE;
- fr->bPrec = FALSE;
- fr->bX = FALSE;
- fr->bV = FALSE;
- fr->bF = FALSE;
- fr->bBox = FALSE;
- if (bFirst) {
- fr->flags = 0;
- fr->bDouble= FALSE;
- fr->natoms = -1;
- fr->t0 = 0;
- fr->tpf = 0;
- fr->tppf = 0;
- fr->title = NULL;
- fr->step = 0;
- fr->time = 0;
- fr->lambda = 0;
- fr->atoms = NULL;
- fr->prec = 0;
- fr->x = NULL;
- fr->v = NULL;
- fr->f = NULL;
- clear_mat(fr->box);
- fr->bPBC = FALSE;
- fr->ePBC = -1;
- }
+ fr->not_ok = 0;
+ fr->bTitle = FALSE;
+ fr->bStep = FALSE;
+ fr->bTime = FALSE;
+ fr->bLambda = FALSE;
+ fr->bAtoms = FALSE;
+ fr->bPrec = FALSE;
+ fr->bX = FALSE;
+ fr->bV = FALSE;
+ fr->bF = FALSE;
+ fr->bBox = FALSE;
+ if (bFirst)
+ {
+ fr->flags = 0;
+ fr->bDouble = FALSE;
+ fr->natoms = -1;
+ fr->t0 = 0;
+ fr->tpf = 0;
+ fr->tppf = 0;
+ fr->title = NULL;
+ fr->step = 0;
+ fr->time = 0;
+ fr->lambda = 0;
+ fr->atoms = NULL;
+ fr->prec = 0;
+ fr->x = NULL;
+ fr->v = NULL;
+ fr->f = NULL;
+ clear_mat(fr->box);
+ fr->bPBC = FALSE;
+ fr->ePBC = -1;
+ }
}
-void set_trxframe_ePBC(t_trxframe *fr,int ePBC)
+void set_trxframe_ePBC(t_trxframe *fr, int ePBC)
{
- fr->bPBC = (ePBC == -1);
- fr->ePBC = ePBC;
+ fr->bPBC = (ePBC == -1);
+ fr->ePBC = ePBC;
}
-int write_trxframe_indexed(t_trxstatus *status,t_trxframe *fr,int nind,
+int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
const atom_id *ind, gmx_conect gc)
{
- char title[STRLEN];
- rvec *xout=NULL,*vout=NULL,*fout=NULL;
- int i;
- real prec;
-
- if (fr->bPrec)
- prec = fr->prec;
- else
- prec = 1000.0;
-
- switch (gmx_fio_getftp(status->fio)) {
- case efTRJ:
- case efTRR:
- break;
- default:
- if (!fr->bX)
- gmx_fatal(FARGS,"Need coordinates to write a %s trajectory",
- ftp2ext(gmx_fio_getftp(status->fio)));
- break;
- }
-
- switch (gmx_fio_getftp(status->fio)) {
- case efTRJ:
- case efTRR:
- if (fr->bV) {
- snew(vout,nind);
- for(i=0; i<nind; i++)
- copy_rvec(fr->v[ind[i]],vout[i]);
- }
- if (fr->bF) {
- snew(fout,nind);
- for(i=0; i<nind; i++)
- copy_rvec(fr->f[ind[i]],fout[i]);
- }
- /* no break */
- case efXTC:
- case efG87:
- if (fr->bX) {
- snew(xout,nind);
- for(i=0; i<nind; i++)
- copy_rvec(fr->x[ind[i]],xout[i]);
- }
- break;
- default:
- break;
- }
-
- switch (gmx_fio_getftp(status->fio)) {
- case efXTC:
- write_xtc(status->fio,nind,fr->step,fr->time,fr->box,xout,prec);
- break;
- case efTRJ:
- case efTRR:
- fwrite_trn(status->fio,nframes_read(status),
- fr->time,fr->step,fr->box,nind,xout,vout,fout);
- break;
- case efGRO:
- case efPDB:
- case efBRK:
- case efENT:
- if (!fr->bAtoms)
- gmx_fatal(FARGS,"Can not write a %s file without atom names",
- ftp2ext(gmx_fio_getftp(status->fio)));
- sprintf(title,"frame t= %.3f",fr->time);
- if (gmx_fio_getftp(status->fio) == efGRO)
- write_hconf_indexed_p(gmx_fio_getfp(status->fio),title,fr->atoms,nind,ind,
- prec2ndec(prec),
- fr->x,fr->bV ? fr->v : NULL,fr->box);
+ char title[STRLEN];
+ rvec *xout = NULL, *vout = NULL, *fout = NULL;
+ int i;
+ real prec;
+
+ if (fr->bPrec)
+ {
+ prec = fr->prec;
+ }
else
- write_pdbfile_indexed(gmx_fio_getfp(status->fio),title,fr->atoms,
- fr->x,-1,fr->box,' ',fr->step,nind,ind,gc,TRUE);
- break;
- case efG87:
- write_gms(gmx_fio_getfp(status->fio),nind,xout,fr->box);
- break;
- case efG96:
- write_g96_conf(gmx_fio_getfp(status->fio),fr,nind,ind);
- break;
- default:
- gmx_fatal(FARGS,"Sorry, write_trxframe_indexed can not write %s",
- ftp2ext(gmx_fio_getftp(status->fio)));
- break;
- }
-
- switch (gmx_fio_getftp(status->fio)) {
- case efTRN:
- case efTRJ:
- case efTRR:
- if (vout) sfree(vout);
- if (fout) sfree(fout);
- /* no break */
- case efXTC:
- case efG87:
- sfree(xout);
- break;
- default:
- break;
- }
-
- return 0;
+ {
+ prec = 1000.0;
+ }
+
+ switch (gmx_fio_getftp(status->fio))
+ {
+ case efTRJ:
+ case efTRR:
+ break;
+ default:
+ if (!fr->bX)
+ {
+ gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
+ ftp2ext(gmx_fio_getftp(status->fio)));
+ }
+ break;
+ }
+
+ switch (gmx_fio_getftp(status->fio))
+ {
+ case efTRJ:
+ case efTRR:
+ if (fr->bV)
+ {
+ snew(vout, nind);
+ for (i = 0; i < nind; i++)
+ {
+ copy_rvec(fr->v[ind[i]], vout[i]);
+ }
+ }
+ if (fr->bF)
+ {
+ snew(fout, nind);
+ for (i = 0; i < nind; i++)
+ {
+ copy_rvec(fr->f[ind[i]], fout[i]);
+ }
+ }
+ /* no break */
+ case efXTC:
+ case efG87:
+ if (fr->bX)
+ {
+ snew(xout, nind);
+ for (i = 0; i < nind; i++)
+ {
+ copy_rvec(fr->x[ind[i]], xout[i]);
+ }
+ }
+ break;
+ default:
+ break;
+ }
+
+ switch (gmx_fio_getftp(status->fio))
+ {
+ case efXTC:
+ write_xtc(status->fio, nind, fr->step, fr->time, fr->box, xout, prec);
+ break;
+ case efTRJ:
+ case efTRR:
+ fwrite_trn(status->fio, nframes_read(status),
+ fr->time, fr->step, fr->box, nind, xout, vout, fout);
+ break;
+ case efGRO:
+ case efPDB:
+ case efBRK:
+ case efENT:
+ if (!fr->bAtoms)
+ {
+ gmx_fatal(FARGS, "Can not write a %s file without atom names",
+ ftp2ext(gmx_fio_getftp(status->fio)));
+ }
+ sprintf(title, "frame t= %.3f", fr->time);
+ if (gmx_fio_getftp(status->fio) == efGRO)
+ {
+ write_hconf_indexed_p(gmx_fio_getfp(status->fio), title, fr->atoms, nind, ind,
+ prec2ndec(prec),
+ fr->x, fr->bV ? fr->v : NULL, fr->box);
+ }
+ else
+ {
+ write_pdbfile_indexed(gmx_fio_getfp(status->fio), title, fr->atoms,
+ fr->x, -1, fr->box, ' ', fr->step, nind, ind, gc, TRUE);
+ }
+ break;
+ case efG87:
+ write_gms(gmx_fio_getfp(status->fio), nind, xout, fr->box);
+ break;
+ case efG96:
+ write_g96_conf(gmx_fio_getfp(status->fio), fr, nind, ind);
+ break;
+ default:
+ gmx_fatal(FARGS, "Sorry, write_trxframe_indexed can not write %s",
+ ftp2ext(gmx_fio_getftp(status->fio)));
+ break;
+ }
+
+ switch (gmx_fio_getftp(status->fio))
+ {
+ case efTRN:
+ case efTRJ:
+ case efTRR:
+ if (vout)
+ {
+ sfree(vout);
+ }
+ if (fout)
+ {
+ sfree(fout);
+ }
+ /* no break */
+ case efXTC:
+ case efG87:
+ sfree(xout);
+ break;
+ default:
+ break;
+ }
+
+ return 0;
}
-int write_trxframe(t_trxstatus *status,t_trxframe *fr,gmx_conect gc)
+int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc)
{
- char title[STRLEN];
- real prec;
-
- if (fr->bPrec)
- prec = fr->prec;
- else
- prec = 1000.0;
-
- switch (gmx_fio_getftp(status->fio)) {
- case efTRJ:
- case efTRR:
- break;
- default:
- if (!fr->bX)
- gmx_fatal(FARGS,"Need coordinates to write a %s trajectory",
- ftp2ext(gmx_fio_getftp(status->fio)));
- break;
- }
-
- switch (gmx_fio_getftp(status->fio)) {
- case efXTC:
- write_xtc(status->fio,fr->natoms,fr->step,fr->time,fr->box,fr->x,prec);
- break;
- case efTRJ:
- case efTRR:
- fwrite_trn(status->fio,fr->step,fr->time,fr->lambda,fr->box,fr->natoms,
- fr->bX ? fr->x:NULL,fr->bV ? fr->v:NULL ,fr->bF ? fr->f:NULL);
- break;
- case efGRO:
- case efPDB:
- case efBRK:
- case efENT:
- if (!fr->bAtoms)
- gmx_fatal(FARGS,"Can not write a %s file without atom names",
- ftp2ext(gmx_fio_getftp(status->fio)));
- sprintf(title,"frame t= %.3f",fr->time);
- if (gmx_fio_getftp(status->fio) == efGRO)
- write_hconf_p(gmx_fio_getfp(status->fio),title,fr->atoms,
- prec2ndec(prec),fr->x,fr->bV ? fr->v : NULL,fr->box);
+ char title[STRLEN];
+ real prec;
+
+ if (fr->bPrec)
+ {
+ prec = fr->prec;
+ }
else
- write_pdbfile(gmx_fio_getfp(status->fio),title,
- fr->atoms,fr->x,fr->bPBC ? fr->ePBC : -1,fr->box,
- ' ',fr->step,gc,TRUE);
- break;
- case efG87:
- write_gms(gmx_fio_getfp(status->fio),fr->natoms,fr->x,fr->box);
- break;
- case efG96:
- write_g96_conf(gmx_fio_getfp(status->fio),fr,-1,NULL);
- break;
- default:
- gmx_fatal(FARGS,"Sorry, write_trxframe can not write %s",
- ftp2ext(gmx_fio_getftp(status->fio)));
- break;
- }
-
- return 0;
+ {
+ prec = 1000.0;
+ }
+
+ switch (gmx_fio_getftp(status->fio))
+ {
+ case efTRJ:
+ case efTRR:
+ break;
+ default:
+ if (!fr->bX)
+ {
+ gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
+ ftp2ext(gmx_fio_getftp(status->fio)));
+ }
+ break;
+ }
+
+ switch (gmx_fio_getftp(status->fio))
+ {
+ case efXTC:
+ write_xtc(status->fio, fr->natoms, fr->step, fr->time, fr->box, fr->x, prec);
+ break;
+ case efTRJ:
+ case efTRR:
+ fwrite_trn(status->fio, fr->step, fr->time, fr->lambda, fr->box, fr->natoms,
+ fr->bX ? fr->x : NULL, fr->bV ? fr->v : NULL, fr->bF ? fr->f : NULL);
+ break;
+ case efGRO:
+ case efPDB:
+ case efBRK:
+ case efENT:
+ if (!fr->bAtoms)
+ {
+ gmx_fatal(FARGS, "Can not write a %s file without atom names",
+ ftp2ext(gmx_fio_getftp(status->fio)));
+ }
+ sprintf(title, "frame t= %.3f", fr->time);
+ if (gmx_fio_getftp(status->fio) == efGRO)
+ {
+ write_hconf_p(gmx_fio_getfp(status->fio), title, fr->atoms,
+ prec2ndec(prec), fr->x, fr->bV ? fr->v : NULL, fr->box);
+ }
+ else
+ {
+ write_pdbfile(gmx_fio_getfp(status->fio), title,
+ fr->atoms, fr->x, fr->bPBC ? fr->ePBC : -1, fr->box,
+ ' ', fr->step, gc, TRUE);
+ }
+ break;
+ case efG87:
+ write_gms(gmx_fio_getfp(status->fio), fr->natoms, fr->x, fr->box);
+ break;
+ case efG96:
+ write_g96_conf(gmx_fio_getfp(status->fio), fr, -1, NULL);
+ break;
+ default:
+ gmx_fatal(FARGS, "Sorry, write_trxframe can not write %s",
+ ftp2ext(gmx_fio_getftp(status->fio)));
+ break;
+ }
+
+ return 0;
}
-int write_trx(t_trxstatus *status,int nind,const atom_id *ind,t_atoms *atoms,
- int step,real time,matrix box,rvec x[],rvec *v,
- gmx_conect gc)
+int write_trx(t_trxstatus *status, int nind, const atom_id *ind, t_atoms *atoms,
+ int step, real time, matrix box, rvec x[], rvec *v,
+ gmx_conect gc)
{
- t_trxframe fr;
-
- clear_trxframe(&fr,TRUE);
- fr.bStep = TRUE;
- fr.step = step;
- fr.bTime = TRUE;
- fr.time = time;
- fr.bAtoms = atoms!=NULL;
- fr.atoms = atoms;
- fr.bX = TRUE;
- fr.x = x;
- fr.bV = v!=NULL;
- fr.v = v;
- fr.bBox = TRUE;
- copy_mat(box,fr.box);
-
- return write_trxframe_indexed(status,&fr,nind,ind,gc);
+ t_trxframe fr;
+
+ clear_trxframe(&fr, TRUE);
+ fr.bStep = TRUE;
+ fr.step = step;
+ fr.bTime = TRUE;
+ fr.time = time;
+ fr.bAtoms = atoms != NULL;
+ fr.atoms = atoms;
+ fr.bX = TRUE;
+ fr.x = x;
+ fr.bV = v != NULL;
+ fr.v = v;
+ fr.bBox = TRUE;
+ copy_mat(box, fr.box);
+
+ return write_trxframe_indexed(status, &fr, nind, ind, gc);
}
void close_trx(t_trxstatus *status)
{
- gmx_fio_close(status->fio);
- sfree(status);
+ gmx_fio_close(status->fio);
+ sfree(status);
}
-t_trxstatus *open_trx(const char *outfile,const char *filemode)
+t_trxstatus *open_trx(const char *outfile, const char *filemode)
{
t_trxstatus *stat;
- if (filemode[0]!='w' && filemode[0]!='a' && filemode[1]!='+')
- gmx_fatal(FARGS,"Sorry, write_trx can only write");
+ if (filemode[0] != 'w' && filemode[0] != 'a' && filemode[1] != '+')
+ {
+ gmx_fatal(FARGS, "Sorry, write_trx can only write");
+ }
- snew(stat,1);
+ snew(stat, 1);
status_init(stat);
- stat->fio=gmx_fio_open(outfile,filemode);
+ stat->fio = gmx_fio_open(outfile, filemode);
return stat;
}
-static gmx_bool gmx_next_frame(t_trxstatus *status,t_trxframe *fr)
+static gmx_bool gmx_next_frame(t_trxstatus *status, t_trxframe *fr)
{
- t_trnheader sh;
- gmx_bool bOK,bRet;
-
- bRet = FALSE;
-
- if (fread_trnheader(status->fio,&sh,&bOK)) {
- fr->bDouble=sh.bDouble;
- fr->natoms=sh.natoms;
- fr->bStep=TRUE;
- fr->step=sh.step;
- fr->bTime=TRUE;
- fr->time=sh.t;
- fr->bLambda = TRUE;
- fr->bFepState = TRUE;
- fr->lambda = sh.lambda;
- fr->bBox = sh.box_size>0;
- if (fr->flags & (TRX_READ_X | TRX_NEED_X)) {
- if (fr->x==NULL)
- snew(fr->x,sh.natoms);
- fr->bX = sh.x_size>0;
- }
- if (fr->flags & (TRX_READ_V | TRX_NEED_V)) {
- if (fr->v==NULL)
- snew(fr->v,sh.natoms);
- fr->bV = sh.v_size>0;
- }
- if (fr->flags & (TRX_READ_F | TRX_NEED_F)) {
- if (fr->f==NULL)
- snew(fr->f,sh.natoms);
- fr->bF = sh.f_size>0;
- }
- if (fread_htrn(status->fio,&sh,fr->box,fr->x,fr->v,fr->f))
- bRet = TRUE;
+ t_trnheader sh;
+ gmx_bool bOK, bRet;
+
+ bRet = FALSE;
+
+ if (fread_trnheader(status->fio, &sh, &bOK))
+ {
+ fr->bDouble = sh.bDouble;
+ fr->natoms = sh.natoms;
+ fr->bStep = TRUE;
+ fr->step = sh.step;
+ fr->bTime = TRUE;
+ fr->time = sh.t;
+ fr->bLambda = TRUE;
+ fr->bFepState = TRUE;
+ fr->lambda = sh.lambda;
+ fr->bBox = sh.box_size > 0;
+ if (fr->flags & (TRX_READ_X | TRX_NEED_X))
+ {
+ if (fr->x == NULL)
+ {
+ snew(fr->x, sh.natoms);
+ }
+ fr->bX = sh.x_size > 0;
+ }
+ if (fr->flags & (TRX_READ_V | TRX_NEED_V))
+ {
+ if (fr->v == NULL)
+ {
+ snew(fr->v, sh.natoms);
+ }
+ fr->bV = sh.v_size > 0;
+ }
+ if (fr->flags & (TRX_READ_F | TRX_NEED_F))
+ {
+ if (fr->f == NULL)
+ {
+ snew(fr->f, sh.natoms);
+ }
+ fr->bF = sh.f_size > 0;
+ }
+ if (fread_htrn(status->fio, &sh, fr->box, fr->x, fr->v, fr->f))
+ {
+ bRet = TRUE;
+ }
+ else
+ {
+ fr->not_ok = DATA_NOT_OK;
+ }
+ }
else
- fr->not_ok = DATA_NOT_OK;
- } else
if (!bOK)
- fr->not_ok = HEADER_NOT_OK;
+ {
+ fr->not_ok = HEADER_NOT_OK;
+ }
- return bRet;
+ return bRet;
}
static void choose_file_format(FILE *fp)
{
- int i,m,c;
- int rc;
- eFileFormat eFF;
- t_trxstatus *stat;
-
- printf("\n\n");
- printf(" Select File Format\n");
- printf("---------------------------\n");
- printf("1. XYZ File\n");
- printf("2. XYZ File with Box\n");
- printf("3. Gromos-87 Ascii Trajectory\n");
- printf("4. Gromos-87 Ascii Trajectory with Box\n");
-
- snew(stat,1);
- status_init(stat);
-
- do {
- printf("\nChoice: ");
- fflush(stdout);
+ int i, m, c;
+ int rc;
+ eFileFormat eFF;
+ t_trxstatus *stat;
+
+ printf("\n\n");
+ printf(" Select File Format\n");
+ printf("---------------------------\n");
+ printf("1. XYZ File\n");
+ printf("2. XYZ File with Box\n");
+ printf("3. Gromos-87 Ascii Trajectory\n");
+ printf("4. Gromos-87 Ascii Trajectory with Box\n");
+
+ snew(stat, 1);
+ status_init(stat);
+
do
{
- rc = scanf("%d",&i);
+ printf("\nChoice: ");
+ fflush(stdout);
+ do
+ {
+ rc = scanf("%d", &i);
+ }
+ while (rc != 1);
+ i--;
}
- while (rc!=1);
- i--;
- } while ((i < 0) || (i >= effNR));
- printf("\n");
-
- stat->eFF = (eFileFormat) i;
+ while ((i < 0) || (i >= effNR));
+ printf("\n");
- for(m=0; (m<DIM); m++) stat->BOX[m]=0;
-
- stat->bReadBox = (stat->eFF == effG87Box) || (stat->eFF == effXYZBox);
-
- switch (stat->eFF) {
- case effXYZ:
- case effXYZBox:
- if( 5 != fscanf(fp,"%d%lf%lf%lf%lf",&stat->NATOMS,&stat->BOX[XX],&stat->BOX[YY],&stat->BOX[ZZ],&stat->DT))
- {
- gmx_fatal(FARGS,"Error reading natoms/box in file");
- }
- break;
- case effG87:
- case effG87Box:
- printf("GROMOS! OH DEAR...\n\n");
- printf("Number of atoms ? ");
- fflush(stdout);
- if (1 != scanf("%d",&stat->NATOMS))
+ stat->eFF = (eFileFormat) i;
+
+ for (m = 0; (m < DIM); m++)
{
- gmx_fatal(FARGS,"Error reading natoms in file");
+ stat->BOX[m] = 0;
}
- printf("Time between timeframes ? ");
- fflush(stdout);
- if( 1 != scanf("%lf",&stat->DT))
+ stat->bReadBox = (stat->eFF == effG87Box) || (stat->eFF == effXYZBox);
+
+ switch (stat->eFF)
{
- gmx_fatal(FARGS,"Error reading dt from file");
- }
+ case effXYZ:
+ case effXYZBox:
+ if (5 != fscanf(fp, "%d%lf%lf%lf%lf", &stat->NATOMS, &stat->BOX[XX], &stat->BOX[YY], &stat->BOX[ZZ], &stat->DT))
+ {
+ gmx_fatal(FARGS, "Error reading natoms/box in file");
+ }
+ break;
+ case effG87:
+ case effG87Box:
+ printf("GROMOS! OH DEAR...\n\n");
+ printf("Number of atoms ? ");
+ fflush(stdout);
+ if (1 != scanf("%d", &stat->NATOMS))
+ {
+ gmx_fatal(FARGS, "Error reading natoms in file");
+ }
+
+ printf("Time between timeframes ? ");
+ fflush(stdout);
+ if (1 != scanf("%lf", &stat->DT))
+ {
+ gmx_fatal(FARGS, "Error reading dt from file");
+ }
- if (stat->eFF == effG87) {
- printf("Box X Y Z ? ");
- fflush(stdout);
- if(3 != scanf("%lf%lf%lf",&stat->BOX[XX],&stat->BOX[YY],&stat->BOX[ZZ]))
- {
- gmx_fatal(FARGS,"Error reading box in file");
- }
+ if (stat->eFF == effG87)
+ {
+ printf("Box X Y Z ? ");
+ fflush(stdout);
+ if (3 != scanf("%lf%lf%lf", &stat->BOX[XX], &stat->BOX[YY], &stat->BOX[ZZ]))
+ {
+ gmx_fatal(FARGS, "Error reading box in file");
+ }
+ }
+ do
+ {
+ c = fgetc(fp);
+ printf("%c", c);
+ }
+ while (c != '\n');
+ printf("\n");
+ fflush(stdout);
+ break;
+ default:
+ printf("Hellow World\n");
}
- do {
- c=fgetc(fp);
- printf("%c",c);
- } while (c != '\n');
- printf("\n");
- fflush(stdout);
- break;
- default:
- printf("Hellow World\n");
- }
}
-static gmx_bool do_read_xyz(t_trxstatus *status, FILE *fp,int natoms,
- rvec x[],matrix box)
+static gmx_bool do_read_xyz(t_trxstatus *status, FILE *fp, int natoms,
+ rvec x[], matrix box)
{
- int i,m;
- double x0;
-
- for(i=0; (i<natoms); i++) {
- for(m=0; (m<DIM); m++) {
- if (fscanf(fp,"%lf",&x0) != 1) {
- if (i || m)
- fprintf(stderr,"error reading statusfile: x[%d][%d]\n",i,m);
- /* else eof! */
- return FALSE;
- }
- x[i][m]=x0;
- }
- }
- if (status->bReadBox) {
- for(m=0; (m<DIM); m++) {
- if (fscanf(fp,"%lf",&x0) != 1)
- return FALSE;
- box[m][m]=x0;
- }
- }
- return TRUE;
+ int i, m;
+ double x0;
+
+ for (i = 0; (i < natoms); i++)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ if (fscanf(fp, "%lf", &x0) != 1)
+ {
+ if (i || m)
+ {
+ fprintf(stderr, "error reading statusfile: x[%d][%d]\n", i, m);
+ }
+ /* else eof! */
+ return FALSE;
+ }
+ x[i][m] = x0;
+ }
+ }
+ if (status->bReadBox)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ if (fscanf(fp, "%lf", &x0) != 1)
+ {
+ return FALSE;
+ }
+ box[m][m] = x0;
+ }
+ }
+ return TRUE;
}
static gmx_bool xyz_next_x(t_trxstatus *status, FILE *fp, const output_env_t oenv,
- real *t, int natoms, rvec x[], matrix box)
- /* Reads until a new x can be found (return TRUE)
- * or eof (return FALSE)
- */
+ real *t, int natoms, rvec x[], matrix box)
+/* Reads until a new x can be found (return TRUE)
+ * or eof (return FALSE)
+ */
{
- real pt;
-
- pt=*t;
- while (!bTimeSet(TBEGIN) || (*t < rTimeValue(TBEGIN))) {
- if (!do_read_xyz(status,fp,natoms,x,box))
- return FALSE;
- printcount(status,oenv,*t,FALSE);
- *t+=status->DT;
- pt=*t;
- }
- if (!bTimeSet(TEND) || (*t <= rTimeValue(TEND))) {
- if (!do_read_xyz(status,fp,natoms,x,box)) {
- printlast(status, oenv,*t);
- return FALSE;
- }
- printcount(status,oenv,*t,FALSE);
- pt=*t;
- *t+=status->DT;
- return TRUE;
- }
- printlast(status,oenv,pt);
- return FALSE;
+ real pt;
+
+ pt = *t;
+ while (!bTimeSet(TBEGIN) || (*t < rTimeValue(TBEGIN)))
+ {
+ if (!do_read_xyz(status, fp, natoms, x, box))
+ {
+ return FALSE;
+ }
+ printcount(status, oenv, *t, FALSE);
+ *t += status->DT;
+ pt = *t;
+ }
+ if (!bTimeSet(TEND) || (*t <= rTimeValue(TEND)))
+ {
+ if (!do_read_xyz(status, fp, natoms, x, box))
+ {
+ printlast(status, oenv, *t);
+ return FALSE;
+ }
+ printcount(status, oenv, *t, FALSE);
+ pt = *t;
+ *t += status->DT;
+ return TRUE;
+ }
+ printlast(status, oenv, pt);
+ return FALSE;
}
-static int xyz_first_x(t_trxstatus *status, FILE *fp, const output_env_t oenv,
+static int xyz_first_x(t_trxstatus *status, FILE *fp, const output_env_t oenv,
real *t, rvec **x, matrix box)
/* Reads fp, mallocs x, and returns x and box
* Returns natoms when successful, FALSE otherwise
*/
{
- int m;
-
- initcount(status);
+ int m;
- clear_mat(box);
- choose_file_format(fp);
+ initcount(status);
- for(m=0; (m<DIM); m++)
- box[m][m]=status->BOX[m];
+ clear_mat(box);
+ choose_file_format(fp);
- snew(*x,status->NATOMS);
- *t=status->DT;
- if (!xyz_next_x(status, fp,oenv,t,status->NATOMS,*x,box))
- return 0;
- *t=0.0;
-
- return status->NATOMS;
+ for (m = 0; (m < DIM); m++)
+ {
+ box[m][m] = status->BOX[m];
+ }
+
+ snew(*x, status->NATOMS);
+ *t = status->DT;
+ if (!xyz_next_x(status, fp, oenv, t, status->NATOMS, *x, box))
+ {
+ return 0;
+ }
+ *t = 0.0;
+
+ return status->NATOMS;
}
-static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp,t_trxframe *fr)
+static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
{
- t_atoms atoms;
- matrix boxpdb;
- int ePBC,model_nr,na;
- char title[STRLEN],*time;
- double dbl;
-
- atoms.nr = fr->natoms;
- atoms.atom=NULL;
- atoms.pdbinfo=NULL;
- /* the other pointers in atoms should not be accessed if these are NULL */
- model_nr=NOTSET;
- na=read_pdbfile(fp,title,&model_nr,&atoms,fr->x,&ePBC,boxpdb,TRUE,NULL);
- set_trxframe_ePBC(fr,ePBC);
- if (nframes_read(status)==0)
- fprintf(stderr," '%s', %d atoms\n",title, fr->natoms);
- fr->bPrec = TRUE;
- fr->prec = 10000;
- fr->bX = TRUE;
- fr->bBox = (boxpdb[XX][XX] != 0.0);
- if (fr->bBox) {
- copy_mat(boxpdb,fr->box);
- }
-
- if (model_nr!=NOTSET) {
- fr->bStep = TRUE;
- fr->step = model_nr;
- }
- time=strstr(title," t= ");
- if (time) {
- fr->bTime = TRUE;
- sscanf(time+4,"%lf",&dbl);
- fr->time=(real)dbl;
- } else {
- fr->bTime = FALSE;
- /* this is a bit dirty, but it will work: if no time is read from
- comment line in pdb file, set time to current frame number */
- if (fr->bStep)
- fr->time=(real)fr->step;
+ t_atoms atoms;
+ matrix boxpdb;
+ int ePBC, model_nr, na;
+ char title[STRLEN], *time;
+ double dbl;
+
+ atoms.nr = fr->natoms;
+ atoms.atom = NULL;
+ atoms.pdbinfo = NULL;
+ /* the other pointers in atoms should not be accessed if these are NULL */
+ model_nr = NOTSET;
+ na = read_pdbfile(fp, title, &model_nr, &atoms, fr->x, &ePBC, boxpdb, TRUE, NULL);
+ set_trxframe_ePBC(fr, ePBC);
+ if (nframes_read(status) == 0)
+ {
+ fprintf(stderr, " '%s', %d atoms\n", title, fr->natoms);
+ }
+ fr->bPrec = TRUE;
+ fr->prec = 10000;
+ fr->bX = TRUE;
+ fr->bBox = (boxpdb[XX][XX] != 0.0);
+ if (fr->bBox)
+ {
+ copy_mat(boxpdb, fr->box);
+ }
+
+ if (model_nr != NOTSET)
+ {
+ fr->bStep = TRUE;
+ fr->step = model_nr;
+ }
+ time = strstr(title, " t= ");
+ if (time)
+ {
+ fr->bTime = TRUE;
+ sscanf(time+4, "%lf", &dbl);
+ fr->time = (real)dbl;
+ }
else
- fr->time=(real)nframes_read(status);
- }
- if (na == 0) {
- return FALSE;
- } else {
- if (na != fr->natoms)
- gmx_fatal(FARGS,"Number of atoms in pdb frame %d is %d instead of %d",
- nframes_read(status),na,fr->natoms);
- return TRUE;
- }
+ {
+ fr->bTime = FALSE;
+ /* this is a bit dirty, but it will work: if no time is read from
+ comment line in pdb file, set time to current frame number */
+ if (fr->bStep)
+ {
+ fr->time = (real)fr->step;
+ }
+ else
+ {
+ fr->time = (real)nframes_read(status);
+ }
+ }
+ if (na == 0)
+ {
+ return FALSE;
+ }
+ else
+ {
+ if (na != fr->natoms)
+ {
+ gmx_fatal(FARGS, "Number of atoms in pdb frame %d is %d instead of %d",
+ nframes_read(status), na, fr->natoms);
+ }
+ return TRUE;
+ }
}
static int pdb_first_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
{
- initcount(status);
-
- fprintf(stderr,"Reading frames from pdb file");
- frewind(fp);
- get_pdb_coordnum(fp, &fr->natoms);
- if (fr->natoms==0)
- gmx_fatal(FARGS,"\nNo coordinates in pdb file\n");
- frewind(fp);
- snew(fr->x,fr->natoms);
- pdb_next_x(status, fp, fr);
-
- return fr->natoms;
+ initcount(status);
+
+ fprintf(stderr, "Reading frames from pdb file");
+ frewind(fp);
+ get_pdb_coordnum(fp, &fr->natoms);
+ if (fr->natoms == 0)
+ {
+ gmx_fatal(FARGS, "\nNo coordinates in pdb file\n");
+ }
+ frewind(fp);
+ snew(fr->x, fr->natoms);
+ pdb_next_x(status, fp, fr);
+
+ return fr->natoms;
}
-gmx_bool read_next_frame(const output_env_t oenv,t_trxstatus *status,t_trxframe *fr)
+gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status, t_trxframe *fr)
{
- real pt;
- int ct;
- gmx_bool bOK,bRet,bMissingData=FALSE,bSkip=FALSE;
- int dummy=0;
-
- bRet = FALSE;
- pt=fr->time;
-
- do {
- clear_trxframe(fr,FALSE);
- fr->tppf = fr->tpf;
- fr->tpf = fr->time;
-
- switch (gmx_fio_getftp(status->fio)) {
- case efTRJ:
- case efTRR:
- bRet = gmx_next_frame(status,fr);
- break;
- case efCPT:
- /* Checkpoint files can not contain mulitple frames */
- break;
- case efG96:
- read_g96_conf(gmx_fio_getfp(status->fio),NULL,fr,
- status->persistent_line);
- bRet = (fr->natoms > 0);
- break;
- case efG87:
- bRet = xyz_next_x(status, gmx_fio_getfp(status->fio),oenv,&fr->time,
- fr->natoms, fr->x,fr->box);
- fr->bTime = bRet;
- fr->bX = bRet;
- fr->bBox = bRet;
- break;
- case efXTC:
- /* B. Hess 2005-4-20
- * Sometimes is off by one frame
- * and sometimes reports frame not present/file not seekable
- */
- /* DvdS 2005-05-31: this has been fixed along with the increased
- * accuracy of the control over -b and -e options.
- */
- if (bTimeSet(TBEGIN) && (fr->time < rTimeValue(TBEGIN))) {
- if (xtc_seek_time(status->fio, rTimeValue(TBEGIN),fr->natoms,TRUE)) {
- gmx_fatal(FARGS,"Specified frame (time %f) doesn't exist or file corrupt/inconsistent.",
- rTimeValue(TBEGIN));
- }
- initcount(status);
- }
- bRet = read_next_xtc(status->fio,fr->natoms,&fr->step,&fr->time,fr->box,
- fr->x,&fr->prec,&bOK);
- fr->bPrec = (bRet && fr->prec > 0);
- fr->bStep = bRet;
- fr->bTime = bRet;
- fr->bX = bRet;
- fr->bBox = bRet;
- if (!bOK) {
- /* Actually the header could also be not ok,
- but from bOK from read_next_xtc this can't be distinguished */
- fr->not_ok = DATA_NOT_OK;
- }
- break;
- case efPDB:
- bRet = pdb_next_x(status, gmx_fio_getfp(status->fio),fr);
- break;
- case efGRO:
- bRet = gro_next_x_or_v(gmx_fio_getfp(status->fio),fr);
- break;
- default:
+ real pt;
+ int ct;
+ gmx_bool bOK, bRet, bMissingData = FALSE, bSkip = FALSE;
+ int dummy = 0;
+
+ bRet = FALSE;
+ pt = fr->time;
+
+ do
+ {
+ clear_trxframe(fr, FALSE);
+ fr->tppf = fr->tpf;
+ fr->tpf = fr->time;
+
+ switch (gmx_fio_getftp(status->fio))
+ {
+ case efTRJ:
+ case efTRR:
+ bRet = gmx_next_frame(status, fr);
+ break;
+ case efCPT:
+ /* Checkpoint files can not contain mulitple frames */
+ break;
+ case efG96:
+ read_g96_conf(gmx_fio_getfp(status->fio), NULL, fr,
+ status->persistent_line);
+ bRet = (fr->natoms > 0);
+ break;
+ case efG87:
+ bRet = xyz_next_x(status, gmx_fio_getfp(status->fio), oenv, &fr->time,
+ fr->natoms, fr->x, fr->box);
+ fr->bTime = bRet;
+ fr->bX = bRet;
+ fr->bBox = bRet;
+ break;
+ case efXTC:
+ /* B. Hess 2005-4-20
+ * Sometimes is off by one frame
+ * and sometimes reports frame not present/file not seekable
+ */
+ /* DvdS 2005-05-31: this has been fixed along with the increased
+ * accuracy of the control over -b and -e options.
+ */
+ if (bTimeSet(TBEGIN) && (fr->time < rTimeValue(TBEGIN)))
+ {
+ if (xtc_seek_time(status->fio, rTimeValue(TBEGIN), fr->natoms, TRUE))
+ {
+ gmx_fatal(FARGS, "Specified frame (time %f) doesn't exist or file corrupt/inconsistent.",
+ rTimeValue(TBEGIN));
+ }
+ initcount(status);
+ }
+ bRet = read_next_xtc(status->fio, fr->natoms, &fr->step, &fr->time, fr->box,
+ fr->x, &fr->prec, &bOK);
+ fr->bPrec = (bRet && fr->prec > 0);
+ fr->bStep = bRet;
+ fr->bTime = bRet;
+ fr->bX = bRet;
+ fr->bBox = bRet;
+ if (!bOK)
+ {
+ /* Actually the header could also be not ok,
+ but from bOK from read_next_xtc this can't be distinguished */
+ fr->not_ok = DATA_NOT_OK;
+ }
+ break;
+ case efPDB:
+ bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr);
+ break;
+ case efGRO:
+ bRet = gro_next_x_or_v(gmx_fio_getfp(status->fio), fr);
+ break;
+ default:
#ifdef GMX_USE_PLUGINS
- bRet = read_next_vmd_frame(dummy,fr);
+ bRet = read_next_vmd_frame(dummy, fr);
#else
- gmx_fatal(FARGS,"DEATH HORROR in read_next_frame ftp=%s,status=%s",
- ftp2ext(gmx_fio_getftp(status->fio)),
- gmx_fio_getname(status->fio));
+ gmx_fatal(FARGS, "DEATH HORROR in read_next_frame ftp=%s,status=%s",
+ ftp2ext(gmx_fio_getftp(status->fio)),
+ gmx_fio_getname(status->fio));
#endif
+ }
+
+ if (bRet)
+ {
+ bMissingData = (((fr->flags & TRX_NEED_X) && !fr->bX) ||
+ ((fr->flags & TRX_NEED_V) && !fr->bV) ||
+ ((fr->flags & TRX_NEED_F) && !fr->bF));
+ bSkip = FALSE;
+ if (!bMissingData)
+ {
+ ct = check_times2(fr->time, fr->t0, fr->tpf, fr->tppf, fr->bDouble);
+ if (ct == 0 || ((fr->flags & TRX_DONT_SKIP) && ct < 0))
+ {
+ printcount(status, oenv, fr->time, FALSE);
+ }
+ else if (ct > 0)
+ {
+ bRet = FALSE;
+ }
+ else
+ {
+ printcount(status, oenv, fr->time, TRUE);
+ bSkip = TRUE;
+ }
+ }
+ }
+
+ }
+ while (bRet && (bMissingData || bSkip));
+
+ if (!bRet)
+ {
+ printlast(status, oenv, pt);
+ if (fr->not_ok)
+ {
+ printincomp(status, fr);
+ }
}
-
- if (bRet) {
- bMissingData = (((fr->flags & TRX_NEED_X) && !fr->bX) ||
- ((fr->flags & TRX_NEED_V) && !fr->bV) ||
- ((fr->flags & TRX_NEED_F) && !fr->bF));
- bSkip = FALSE;
- if (!bMissingData) {
- ct=check_times2(fr->time,fr->t0,fr->tpf,fr->tppf,fr->bDouble);
- if (ct == 0 || ((fr->flags & TRX_DONT_SKIP) && ct<0)) {
- printcount(status, oenv,fr->time,FALSE);
- } else if (ct > 0)
- bRet = FALSE;
- else {
- printcount(status, oenv,fr->time,TRUE);
- bSkip = TRUE;
- }
- }
- }
-
- } while (bRet && (bMissingData || bSkip));
-
- if (!bRet) {
- printlast(status, oenv,pt);
- if (fr->not_ok)
- printincomp(status, fr);
- }
-
- return bRet;
+
+ return bRet;
}
-int read_first_frame(const output_env_t oenv,t_trxstatus **status,
- const char *fn,t_trxframe *fr,int flags)
+int read_first_frame(const output_env_t oenv, t_trxstatus **status,
+ const char *fn, t_trxframe *fr, int flags)
{
- t_fileio *fio;
- gmx_bool bFirst,bOK;
- int dummy=0;
-
- clear_trxframe(fr,TRUE);
- fr->flags = flags;
-
- bFirst = TRUE;
-
- snew((*status), 1);
-
- status_init( *status );
- (*status)->nxframe=1;
- initcount(*status);
-
- fio = (*status)->fio =gmx_fio_open(fn,"r");
- switch (gmx_fio_getftp(fio))
- {
- case efTRJ:
- case efTRR:
- break;
- case efCPT:
- read_checkpoint_trxframe(fio,fr);
- bFirst = FALSE;
- break;
- case efG96:
- /* Can not rewind a compressed file, so open it twice */
- if (!(*status)->persistent_line)
- {
- /* allocate the persistent line */
- snew((*status)->persistent_line, STRLEN+1);
- }
- read_g96_conf(gmx_fio_getfp(fio),fn,fr, (*status)->persistent_line);
- gmx_fio_close(fio);
- clear_trxframe(fr,FALSE);
- if (flags & (TRX_READ_X | TRX_NEED_X))
- snew(fr->x,fr->natoms);
- if (flags & (TRX_READ_V | TRX_NEED_V))
- snew(fr->v,fr->natoms);
- fio = (*status)->fio =gmx_fio_open(fn,"r");
- break;
- case efG87:
- fr->natoms=xyz_first_x(*status, gmx_fio_getfp(fio),oenv,&fr->time,
- &fr->x,fr->box);
- if (fr->natoms) {
- fr->bTime = TRUE;
- fr->bX = TRUE;
- fr->bBox = TRUE;
- printcount(*status,oenv,fr->time,FALSE);
- }
- bFirst = FALSE;
- break;
- case efXTC:
- if (read_first_xtc(fio,&fr->natoms,&fr->step,&fr->time,fr->box,&fr->x,
- &fr->prec,&bOK) == 0) {
- if (bOK) {
- gmx_fatal(FARGS,"No XTC!\n");
- } else {
- fr->not_ok = DATA_NOT_OK;
- }
- }
- if (fr->not_ok) {
- fr->natoms = 0;
- printincomp(*status,fr);
- } else {
- fr->bPrec = (fr->prec > 0);
- fr->bStep = TRUE;
- fr->bTime = TRUE;
- fr->bX = TRUE;
- fr->bBox = TRUE;
- printcount(*status,oenv,fr->time,FALSE);
- }
- bFirst = FALSE;
- break;
- case efPDB:
- pdb_first_x(*status, gmx_fio_getfp(fio),fr);
- if (fr->natoms)
- printcount(*status,oenv,fr->time,FALSE);
- bFirst = FALSE;
- break;
- case efGRO:
- if (gro_first_x_or_v(gmx_fio_getfp(fio),fr))
- printcount(*status,oenv,fr->time,FALSE);
- bFirst = FALSE;
- break;
- default:
+ t_fileio *fio;
+ gmx_bool bFirst, bOK;
+ int dummy = 0;
+
+ clear_trxframe(fr, TRUE);
+ fr->flags = flags;
+
+ bFirst = TRUE;
+
+ snew((*status), 1);
+
+ status_init( *status );
+ (*status)->nxframe = 1;
+ initcount(*status);
+
+ fio = (*status)->fio = gmx_fio_open(fn, "r");
+ switch (gmx_fio_getftp(fio))
+ {
+ case efTRJ:
+ case efTRR:
+ break;
+ case efCPT:
+ read_checkpoint_trxframe(fio, fr);
+ bFirst = FALSE;
+ break;
+ case efG96:
+ /* Can not rewind a compressed file, so open it twice */
+ if (!(*status)->persistent_line)
+ {
+ /* allocate the persistent line */
+ snew((*status)->persistent_line, STRLEN+1);
+ }
+ read_g96_conf(gmx_fio_getfp(fio), fn, fr, (*status)->persistent_line);
+ gmx_fio_close(fio);
+ clear_trxframe(fr, FALSE);
+ if (flags & (TRX_READ_X | TRX_NEED_X))
+ {
+ snew(fr->x, fr->natoms);
+ }
+ if (flags & (TRX_READ_V | TRX_NEED_V))
+ {
+ snew(fr->v, fr->natoms);
+ }
+ fio = (*status)->fio = gmx_fio_open(fn, "r");
+ break;
+ case efG87:
+ fr->natoms = xyz_first_x(*status, gmx_fio_getfp(fio), oenv, &fr->time,
+ &fr->x, fr->box);
+ if (fr->natoms)
+ {
+ fr->bTime = TRUE;
+ fr->bX = TRUE;
+ fr->bBox = TRUE;
+ printcount(*status, oenv, fr->time, FALSE);
+ }
+ bFirst = FALSE;
+ break;
+ case efXTC:
+ if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
+ &fr->prec, &bOK) == 0)
+ {
+ if (bOK)
+ {
+ gmx_fatal(FARGS, "No XTC!\n");
+ }
+ else
+ {
+ fr->not_ok = DATA_NOT_OK;
+ }
+ }
+ if (fr->not_ok)
+ {
+ fr->natoms = 0;
+ printincomp(*status, fr);
+ }
+ else
+ {
+ fr->bPrec = (fr->prec > 0);
+ fr->bStep = TRUE;
+ fr->bTime = TRUE;
+ fr->bX = TRUE;
+ fr->bBox = TRUE;
+ printcount(*status, oenv, fr->time, FALSE);
+ }
+ bFirst = FALSE;
+ break;
+ case efPDB:
+ pdb_first_x(*status, gmx_fio_getfp(fio), fr);
+ if (fr->natoms)
+ {
+ printcount(*status, oenv, fr->time, FALSE);
+ }
+ bFirst = FALSE;
+ break;
+ case efGRO:
+ if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
+ {
+ printcount(*status, oenv, fr->time, FALSE);
+ }
+ bFirst = FALSE;
+ break;
+ default:
#ifdef GMX_USE_PLUGINS
- fprintf(stderr,"The file format of %s is not a known trajectory format to GROMACS.\n"
- "Please make sure that the file is a trajectory!\n"
- "GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
- "This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n",fn);
- gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
- if (!read_first_vmd_frame(&dummy,fn,fr,flags))
- {
- gmx_fatal(FARGS,"Not supported in read_first_frame: %s",fn);
- }
+ fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
+ "Please make sure that the file is a trajectory!\n"
+ "GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
+ "This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
+ gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
+ if (!read_first_vmd_frame(&dummy, fn, fr, flags))
+ {
+ gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
+ }
#else
- gmx_fatal(FARGS,"Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
- "GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
- "Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n",fn);
+ gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
+ "GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
+ "Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
#endif
- break;
- }
+ break;
+ }
+
+ /* Return FALSE if we read a frame that's past the set ending time. */
+ if (!bFirst && (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) > 0))
+ {
+ fr->t0 = fr->time;
+ return FALSE;
+ }
- /* Return FALSE if we read a frame that's past the set ending time. */
- if (!bFirst && (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) > 0)) {
+ if (bFirst ||
+ (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
+ {
+ /* Read a frame when no frame was read or the first was skipped */
+ if (!read_next_frame(oenv, *status, fr))
+ {
+ return FALSE;
+ }
+ }
fr->t0 = fr->time;
- return FALSE;
- }
-
- if (bFirst ||
- (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
- /* Read a frame when no frame was read or the first was skipped */
- if (!read_next_frame(oenv,*status,fr))
- return FALSE;
- fr->t0 = fr->time;
-
- return (fr->natoms > 0);
+
+ return (fr->natoms > 0);
}
/***** C O O R D I N A T E S T U F F *****/
-int read_first_x(const output_env_t oenv,t_trxstatus **status,const char *fn,
- real *t,rvec **x,matrix box)
+int read_first_x(const output_env_t oenv, t_trxstatus **status, const char *fn,
+ real *t, rvec **x, matrix box)
{
- t_trxframe fr;
-
- read_first_frame(oenv,status,fn,&fr,TRX_NEED_X);
-
- snew((*status)->xframe, 1);
- (*status)->nxframe=1;
- (*(*status)->xframe) = fr;
- *t = (*status)->xframe->time;
- *x = (*status)->xframe->x;
- copy_mat((*status)->xframe->box,box);
-
- return (*status)->xframe->natoms;
+ t_trxframe fr;
+
+ read_first_frame(oenv, status, fn, &fr, TRX_NEED_X);
+
+ snew((*status)->xframe, 1);
+ (*status)->nxframe = 1;
+ (*(*status)->xframe) = fr;
+ *t = (*status)->xframe->time;
+ *x = (*status)->xframe->x;
+ copy_mat((*status)->xframe->box, box);
+
+ return (*status)->xframe->natoms;
}
-gmx_bool read_next_x(const output_env_t oenv, t_trxstatus *status,real *t,
- int natoms, rvec x[], matrix box)
+gmx_bool read_next_x(const output_env_t oenv, t_trxstatus *status, real *t,
+ int natoms, rvec x[], matrix box)
{
- gmx_bool bRet;
-
- status->xframe->x= x;
- /*xframe[status].x = x;*/
- bRet = read_next_frame(oenv,status,status->xframe);
- *t = status->xframe->time;
- copy_mat(status->xframe->box,box);
-
- return bRet;
+ gmx_bool bRet;
+
+ status->xframe->x = x;
+ /*xframe[status].x = x;*/
+ bRet = read_next_frame(oenv, status, status->xframe);
+ *t = status->xframe->time;
+ copy_mat(status->xframe->box, box);
+
+ return bRet;
}
void close_trj(t_trxstatus *status)
void rewind_trj(t_trxstatus *status)
{
- initcount(status);
-
- gmx_fio_rewind(status->fio);
+ initcount(status);
+
+ gmx_fio_rewind(status->fio);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff