/*
- *
+ *
* 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.
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* For more info, check our website at http://www.gromacs.org
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+ *
* And Hey:
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*/
const output_env_t oenv)
{
/* Check start time of all files */
- int i, natoms = 0;
+ int i, natoms = 0;
t_trxstatus *status;
- real t;
- t_trxframe fr;
- gmx_bool ok;
+ real t;
+ t_trxframe fr;
+ gmx_bool ok;
for (i = 0; i < nfiles; i++)
{
ok = read_first_frame(oenv, &status, fnms[i], &fr, FLAGS);
if (!ok)
- gmx_fatal(FARGS,"\nCouldn't read frame from file." );
- if(fr.bTime)
- readtime[i]=fr.time;
+ {
+ gmx_fatal(FARGS, "\nCouldn't read frame from file." );
+ }
+ if (fr.bTime)
+ {
+ readtime[i] = fr.time;
+ }
else
{
- readtime[i]=0;
- fprintf(stderr,"\nWARNING: Couldn't find a time in the frame.\n");
+ readtime[i] = 0;
+ fprintf(stderr, "\nWARNING: Couldn't find a time in the frame.\n");
}
- if(i==0)
+ if (i == 0)
{
- natoms=fr.natoms;
+ natoms = fr.natoms;
}
- else
+ else
{
- if (imax==NO_ATID)
+ if (imax == NO_ATID)
{
- if(natoms!=fr.natoms)
- gmx_fatal(FARGS,"\nDifferent numbers of atoms (%d/%d) in files",
- natoms,fr.natoms);
- }
- else
+ if (natoms != fr.natoms)
+ {
+ gmx_fatal(FARGS, "\nDifferent numbers of atoms (%d/%d) in files",
+ natoms, fr.natoms);
+ }
+ }
+ else
{
- if(fr.natoms <= imax)
+ if (fr.natoms <= imax)
{
- gmx_fatal(FARGS,"\nNot enough atoms (%d) for index group (%d)",
- fr.natoms,imax);
+ gmx_fatal(FARGS, "\nNot enough atoms (%d) for index group (%d)",
+ fr.natoms, imax);
}
}
}
- ok=read_next_frame(oenv,status,&fr);
- if(ok && fr.bTime)
+ ok = read_next_frame(oenv, status, &fr);
+ if (ok && fr.bTime)
{
timestep[i] = fr.time - readtime[i];
- }
- else
+ }
+ else
{
timestep[i] = 0;
}
close_trj(status);
if (fr.bX)
- sfree(fr.x);
+ {
+ sfree(fr.x);
+ }
if (fr.bV)
- sfree(fr.v);
+ {
+ sfree(fr.v);
+ }
if (fr.bF)
- sfree(fr.f);
+ {
+ sfree(fr.f);
+ }
}
- fprintf(stderr,"\n");
+ fprintf(stderr, "\n");
}
static void sort_files(char **fnms, real *settime, int nfile)
{
- int i, j, minidx;
- real timeswap;
+ int i, j, minidx;
+ real timeswap;
char *chptr;
for (i = 0; i < nfile; i++)
}
if (minidx != i)
{
- timeswap = settime[i];
- settime[i] = settime[minidx];
+ timeswap = settime[i];
+ settime[i] = settime[minidx];
settime[minidx] = timeswap;
- chptr = fnms[i];
- fnms[i] = fnms[minidx];
- fnms[minidx] = chptr;
+ chptr = fnms[i];
+ fnms[i] = fnms[minidx];
+ fnms[minidx] = chptr;
}
}
}
real *settime, int *cont_type, gmx_bool bSetTime,
gmx_bool bSort, const output_env_t oenv)
{
- int i;
+ int i;
gmx_bool ok;
- char inputstring[STRLEN], *chptr;
+ char inputstring[STRLEN], *chptr;
if (bSetTime)
{
{
if (NULL == fgets(inputstring, STRLEN - 1, stdin))
{
- gmx_fatal(FARGS,"Error reading user input" );
+ gmx_fatal(FARGS, "Error reading user input" );
}
- inputstring[strlen(inputstring)-1]=0;
+ inputstring[strlen(inputstring)-1] = 0;
- if(inputstring[0]=='c' || inputstring[0]=='C')
+ if (inputstring[0] == 'c' || inputstring[0] == 'C')
{
- cont_type[i]=TIME_CONTINUE;
- bSort=FALSE;
- ok=TRUE;
- settime[i]=FLT_MAX;
+ cont_type[i] = TIME_CONTINUE;
+ bSort = FALSE;
+ ok = TRUE;
+ settime[i] = FLT_MAX;
}
- else if(inputstring[0]=='l' ||
- inputstring[0]=='L')
+ else if (inputstring[0] == 'l' ||
+ inputstring[0] == 'L')
{
- cont_type[i]=TIME_LAST;
- bSort=FALSE;
- ok=TRUE;
- settime[i]=FLT_MAX;
+ cont_type[i] = TIME_LAST;
+ bSort = FALSE;
+ ok = TRUE;
+ settime[i] = FLT_MAX;
}
else
{
- settime[i]=strtod(inputstring,&chptr)*
- output_env_get_time_invfactor(oenv);
- if(chptr==inputstring)
+ settime[i] = strtod(inputstring, &chptr)*
+ output_env_get_time_invfactor(oenv);
+ if (chptr == inputstring)
{
- fprintf(stderr,"'%s' not recognized as a floating point number, 'c' or 'l'. "
- "Try again: ",inputstring);
+ fprintf(stderr, "'%s' not recognized as a floating point number, 'c' or 'l'. "
+ "Try again: ", inputstring);
}
- else {
- cont_type[i]=TIME_EXPLICIT;
- ok=TRUE;
+ else
+ {
+ cont_type[i] = TIME_EXPLICIT;
+ ok = TRUE;
}
}
- } while (!ok);
+ }
+ while (!ok);
}
- if(cont_type[0]!=TIME_EXPLICIT)
+ if (cont_type[0] != TIME_EXPLICIT)
{
- cont_type[0]=TIME_EXPLICIT;
- settime[0]=0;
+ cont_type[0] = TIME_EXPLICIT;
+ settime[0] = 0;
}
}
else
{
- for(i=0;i<nfiles;i++)
+ for (i = 0; i < nfiles; i++)
{
- settime[i]=readtime[i];
+ settime[i] = readtime[i];
}
}
- if(!bSort)
+ if (!bSort)
{
- fprintf(stderr,"Sorting disabled.\n");
+ fprintf(stderr, "Sorting disabled.\n");
}
else
{
- sort_files(fnms,settime,nfiles);
+ sort_files(fnms, settime, nfiles);
}
/* Write out the new order and start times */
- fprintf(stderr,"\nSummary of files and start times used:\n\n"
+ fprintf(stderr, "\nSummary of files and start times used:\n\n"
" File Start time Time step\n"
"---------------------------------------------------------\n");
- for(i=0;i<nfiles;i++)
- switch(cont_type[i])
- {
- case TIME_EXPLICIT:
- fprintf(stderr,"%25s %10.3f %s %10.3f %s",
- fnms[i],
- output_env_conv_time(oenv,settime[i]),output_env_get_time_unit(oenv),
- output_env_conv_time(oenv,timestep[i]),output_env_get_time_unit(oenv));
- if ( i>0 &&
- cont_type[i-1]==TIME_EXPLICIT && settime[i]==settime[i-1] )
- fprintf(stderr," WARNING: same Start time as previous");
- fprintf(stderr,"\n");
- break;
- case TIME_CONTINUE:
- fprintf(stderr,"%25s Continue from last file\n",fnms[i]);
- break;
- case TIME_LAST:
- fprintf(stderr,"%25s Change by same amount as last file\n",
- fnms[i]);
- break;
- }
- fprintf(stderr,"\n");
-
- settime[nfiles]=FLT_MAX;
- cont_type[nfiles]=TIME_EXPLICIT;
- readtime[nfiles]=FLT_MAX;
+ for (i = 0; i < nfiles; i++)
+ {
+ switch (cont_type[i])
+ {
+ case TIME_EXPLICIT:
+ fprintf(stderr, "%25s %10.3f %s %10.3f %s",
+ fnms[i],
+ output_env_conv_time(oenv, settime[i]), output_env_get_time_unit(oenv),
+ output_env_conv_time(oenv, timestep[i]), output_env_get_time_unit(oenv));
+ if (i > 0 &&
+ cont_type[i-1] == TIME_EXPLICIT && settime[i] == settime[i-1])
+ {
+ fprintf(stderr, " WARNING: same Start time as previous");
+ }
+ fprintf(stderr, "\n");
+ break;
+ case TIME_CONTINUE:
+ fprintf(stderr, "%25s Continue from last file\n", fnms[i]);
+ break;
+ case TIME_LAST:
+ fprintf(stderr, "%25s Change by same amount as last file\n",
+ fnms[i]);
+ break;
+ }
+ }
+ fprintf(stderr, "\n");
+
+ settime[nfiles] = FLT_MAX;
+ cont_type[nfiles] = TIME_EXPLICIT;
+ readtime[nfiles] = FLT_MAX;
}
static void do_demux(int nset, char *fnms[], char *fnms_out[], int nval,
real **value, real *time, real dt_remd, int isize,
atom_id index[], real dt, const output_env_t oenv)
{
- int i, j, k, natoms, nnn;
+ int i, j, k, natoms, nnn;
t_trxstatus **fp_in, **fp_out;
- gmx_bool bCont, *bSet;
- real t, first_time = 0;
- t_trxframe *trx;
+ gmx_bool bCont, *bSet;
+ real t, first_time = 0;
+ t_trxframe *trx;
- snew(fp_in,nset);
- snew(trx,nset);
- snew(bSet,nset);
+ snew(fp_in, nset);
+ snew(trx, nset);
+ snew(bSet, nset);
natoms = -1;
- t = -1;
+ t = -1;
for (i = 0; (i < nset); i++)
{
nnn = read_first_frame(oenv, &(fp_in[i]), fnms[i], &(trx[i]),
TRX_NEED_X);
if (natoms == -1)
{
- natoms = nnn;
+ natoms = nnn;
first_time = trx[i].time;
}
else if (natoms != nnn)
{
- gmx_fatal(FARGS,"Trajectory file %s has %d atoms while previous trajs had %d atoms" ,fnms[i],nnn,natoms);
+ gmx_fatal(FARGS, "Trajectory file %s has %d atoms while previous trajs had %d atoms", fnms[i], nnn, natoms);
}
if (t == -1)
{
}
else if (t != trx[i].time)
{
- gmx_fatal(FARGS,"Trajectory file %s has time %f while previous trajs had time %f",fnms[i],trx[i].time,t);
+ gmx_fatal(FARGS, "Trajectory file %s has time %f while previous trajs had time %f", fnms[i], trx[i].time, t);
}
}
- snew(fp_out,nset);
- for(i=0; (i<nset); i++)
+ snew(fp_out, nset);
+ for (i = 0; (i < nset); i++)
{
- fp_out[i] = open_trx(fnms_out[i],"w");
+ fp_out[i] = open_trx(fnms_out[i], "w");
}
k = 0;
if (gmx_nint(time[k] - t) != 0)
{
- gmx_fatal(FARGS,"First time in demuxing table does not match trajectories");
+ gmx_fatal(FARGS, "First time in demuxing table does not match trajectories");
}
do
{
{
k++;
}
- if (debug)
+ if (debug)
{
- fprintf(debug,"trx[0].time = %g, time[k] = %g\n",trx[0].time,time[k]);
+ fprintf(debug, "trx[0].time = %g, time[k] = %g\n", trx[0].time, time[k]);
}
- for(i=0; (i<nset); i++)
+ for (i = 0; (i < nset); i++)
{
bSet[i] = FALSE;
}
- for(i=0; (i<nset); i++)
+ for (i = 0; (i < nset); i++)
{
j = gmx_nint(value[i][k]);
- range_check(j,0,nset);
+ range_check(j, 0, nset);
if (bSet[j])
{
- gmx_fatal(FARGS,"Demuxing the same replica %d twice at time %f",
- j,trx[0].time);
+ gmx_fatal(FARGS, "Demuxing the same replica %d twice at time %f",
+ j, trx[0].time);
}
bSet[j] = TRUE;
- if (dt==0 || bRmod(trx[i].time,first_time,dt))
+ if (dt == 0 || bRmod(trx[i].time, first_time, dt))
{
if (index)
{
- write_trxframe_indexed(fp_out[j],&trx[i],isize,index,NULL);
+ write_trxframe_indexed(fp_out[j], &trx[i], isize, index, NULL);
}
else
{
- write_trxframe(fp_out[j],&trx[i],NULL);
+ write_trxframe(fp_out[j], &trx[i], NULL);
}
}
}
bCont = (k < nval);
- for(i=0; (i<nset); i++)
+ for (i = 0; (i < nset); i++)
{
- bCont = bCont && read_next_frame(oenv,fp_in[i],&trx[i]);
+ bCont = bCont && read_next_frame(oenv, fp_in[i], &trx[i]);
}
- } while (bCont);
+ }
+ while (bCont);
- for(i=0; (i<nset); i++)
+ for (i = 0; (i < nset); i++)
{
close_trx(fp_in[i]);
close_trx(fp_out[i]);
int gmx_trjcat(int argc, char *argv[])
{
const char
- *desc[] =
- {
- "[TT]trjcat[tt] concatenates several input trajectory files in sorted order. ",
- "In case of double time frames the one in the later file is used. ",
- "By specifying [TT]-settime[tt] you will be asked for the start time ",
- "of each file. The input files are taken from the command line, ",
- "such that a command like [TT]trjcat -f *.trr -o fixed.trr[tt] should do ",
- "the trick. Using [TT]-cat[tt], you can simply paste several files ",
- "together without removal of frames with identical time stamps.[PAR]",
- "One important option is inferred when the output file is amongst the",
- "input files. In that case that particular file will be appended to",
- "which implies you do not need to store double the amount of data.",
- "Obviously the file to append to has to be the one with lowest starting",
- "time since one can only append at the end of a file.[PAR]",
- "If the [TT]-demux[tt] option is given, the N trajectories that are",
- "read, are written in another order as specified in the [TT].xvg[tt] file.",
- "The [TT].xvg[tt] file should contain something like:[PAR]",
- "[TT]0 0 1 2 3 4 5[BR]",
- "2 1 0 2 3 5 4[tt][BR]",
- "Where the first number is the time, and subsequent numbers point to",
- "trajectory indices.",
- "The frames corresponding to the numbers present at the first line",
- "are collected into the output trajectory. If the number of frames in",
- "the trajectory does not match that in the [TT].xvg[tt] file then the program",
- "tries to be smart. Beware." };
- static gmx_bool bVels = TRUE;
- static int prec = 3;
- static gmx_bool bCat = FALSE;
- static gmx_bool bSort = TRUE;
- static gmx_bool bKeepLast = FALSE;
+ *desc[] =
+ {
+ "[TT]trjcat[tt] concatenates several input trajectory files in sorted order. ",
+ "In case of double time frames the one in the later file is used. ",
+ "By specifying [TT]-settime[tt] you will be asked for the start time ",
+ "of each file. The input files are taken from the command line, ",
+ "such that a command like [TT]trjcat -f *.trr -o fixed.trr[tt] should do ",
+ "the trick. Using [TT]-cat[tt], you can simply paste several files ",
+ "together without removal of frames with identical time stamps.[PAR]",
+ "One important option is inferred when the output file is amongst the",
+ "input files. In that case that particular file will be appended to",
+ "which implies you do not need to store double the amount of data.",
+ "Obviously the file to append to has to be the one with lowest starting",
+ "time since one can only append at the end of a file.[PAR]",
+ "If the [TT]-demux[tt] option is given, the N trajectories that are",
+ "read, are written in another order as specified in the [TT].xvg[tt] file.",
+ "The [TT].xvg[tt] file should contain something like:[PAR]",
+ "[TT]0 0 1 2 3 4 5[BR]",
+ "2 1 0 2 3 5 4[tt][BR]",
+ "Where the first number is the time, and subsequent numbers point to",
+ "trajectory indices.",
+ "The frames corresponding to the numbers present at the first line",
+ "are collected into the output trajectory. If the number of frames in",
+ "the trajectory does not match that in the [TT].xvg[tt] file then the program",
+ "tries to be smart. Beware."
+ };
+ static gmx_bool bVels = TRUE;
+ static int prec = 3;
+ static gmx_bool bCat = FALSE;
+ static gmx_bool bSort = TRUE;
+ static gmx_bool bKeepLast = FALSE;
static gmx_bool bKeepLastAppend = FALSE;
- static gmx_bool bOverwrite = FALSE;
- static gmx_bool bSetTime = FALSE;
+ static gmx_bool bOverwrite = FALSE;
+ static gmx_bool bSetTime = FALSE;
static gmx_bool bDeMux;
- static real begin = -1;
- static real end = -1;
- static real dt = 0;
+ static real begin = -1;
+ static real end = -1;
+ static real dt = 0;
t_pargs
pa[] =
- {
- { "-b", FALSE, etTIME,
- { &begin }, "First time to use (%t)" },
- { "-e", FALSE, etTIME,
- { &end }, "Last time to use (%t)" },
- { "-dt", FALSE, etTIME,
- { &dt }, "Only write frame when t MOD dt = first time (%t)" },
- { "-prec", FALSE, etINT,
- { &prec }, "Precision for [TT].xtc[tt] and [TT].gro[tt] writing in number of decimal places" },
- { "-vel", FALSE, etBOOL,
- { &bVels }, "Read and write velocities if possible" },
- { "-settime", FALSE, etBOOL,
- { &bSetTime }, "Change starting time interactively" },
- { "-sort", FALSE, etBOOL,
- { &bSort }, "Sort trajectory files (not frames)" },
- { "-keeplast", FALSE, etBOOL,
- { &bKeepLast }, "Keep overlapping frames at end of trajectory" },
- { "-overwrite", FALSE, etBOOL,
- { &bOverwrite }, "Overwrite overlapping frames during appending" },
- { "-cat", FALSE, etBOOL,
- { &bCat }, "Do not discard double time frames" } };
+ {
+ { "-b", FALSE, etTIME,
+ { &begin }, "First time to use (%t)" },
+ { "-e", FALSE, etTIME,
+ { &end }, "Last time to use (%t)" },
+ { "-dt", FALSE, etTIME,
+ { &dt }, "Only write frame when t MOD dt = first time (%t)" },
+ { "-prec", FALSE, etINT,
+ { &prec }, "Precision for [TT].xtc[tt] and [TT].gro[tt] writing in number of decimal places" },
+ { "-vel", FALSE, etBOOL,
+ { &bVels }, "Read and write velocities if possible" },
+ { "-settime", FALSE, etBOOL,
+ { &bSetTime }, "Change starting time interactively" },
+ { "-sort", FALSE, etBOOL,
+ { &bSort }, "Sort trajectory files (not frames)" },
+ { "-keeplast", FALSE, etBOOL,
+ { &bKeepLast }, "Keep overlapping frames at end of trajectory" },
+ { "-overwrite", FALSE, etBOOL,
+ { &bOverwrite }, "Overwrite overlapping frames during appending" },
+ { "-cat", FALSE, etBOOL,
+ { &bCat }, "Do not discard double time frames" }
+ };
#define npargs asize(pa)
- int ftpin, i, frame, frame_out, step = 0, trjout = 0;
+ int ftpin, i, frame, frame_out, step = 0, trjout = 0;
t_trxstatus *status;
- rvec *x, *v;
- real xtcpr, t_corr;
- t_trxframe fr, frout;
- char **fnms, **fnms_out, *in_file, *out_file;
- int n_append;
+ rvec *x, *v;
+ real xtcpr, t_corr;
+ t_trxframe fr, frout;
+ char **fnms, **fnms_out, *in_file, *out_file;
+ int n_append;
t_trxstatus *trxout = NULL;
- gmx_bool bNewFile, bIndex, bWrite;
- int earliersteps, nfile_in, nfile_out, *cont_type, last_ok_step;
- real *readtime, *timest, *settime;
- real first_time = 0, lasttime = NOTSET, last_ok_t = -1, timestep;
- real last_frame_time, searchtime;
- int isize, j;
- atom_id *index = NULL, imax;
- char *grpname;
- real **val = NULL, *t = NULL, dt_remd;
- int n, nset;
- gmx_bool bOK;
- gmx_off_t fpos;
+ gmx_bool bNewFile, bIndex, bWrite;
+ int earliersteps, nfile_in, nfile_out, *cont_type, last_ok_step;
+ real *readtime, *timest, *settime;
+ real first_time = 0, lasttime = NOTSET, last_ok_t = -1, timestep;
+ real last_frame_time, searchtime;
+ int isize, j;
+ atom_id *index = NULL, imax;
+ char *grpname;
+ real **val = NULL, *t = NULL, dt_remd;
+ int n, nset;
+ gmx_bool bOK;
+ gmx_off_t fpos;
output_env_t oenv;
- t_filenm fnm[] =
- {
- { efTRX, "-f", NULL, ffRDMULT },
- { efTRO, "-o", NULL, ffWRMULT },
- { efNDX, "-n", "index", ffOPTRD },
- { efXVG, "-demux", "remd", ffOPTRD } };
+ t_filenm fnm[] =
+ {
+ { efTRX, "-f", NULL, ffRDMULT },
+ { efTRO, "-o", NULL, ffWRMULT },
+ { efNDX, "-n", "index", ffOPTRD },
+ { efXVG, "-demux", "remd", ffOPTRD }
+ };
#define NFILE asize(fnm)
bIndex = ftp2bSet(efNDX, NFILE, fnm);
bDeMux = ftp2bSet(efXVG, NFILE, fnm);
- bSort = bSort && !bDeMux;
+ bSort = bSort && !bDeMux;
imax = NO_ATID;
if (bIndex)
}
if (bDeMux)
{
- nset = 0;
+ nset = 0;
dt_remd = 0;
- val = read_xvg_time(opt2fn("-demux", NFILE, fnm), TRUE,
- opt2parg_bSet("-b", npargs, pa), begin,
- opt2parg_bSet("-e", npargs, pa), end, 1, &nset, &n,
- &dt_remd, &t);
+ val = read_xvg_time(opt2fn("-demux", NFILE, fnm), TRUE,
+ opt2parg_bSet("-b", npargs, pa), begin,
+ opt2parg_bSet("-e", npargs, pa), end, 1, &nset, &n,
+ &dt_remd, &t);
printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt_remd);
if (debug)
{
{
xtcpr *= 10;
}
-
+
nfile_in = opt2fns(&fnms, "-f", NFILE, fnm);
if (!nfile_in)
{
- gmx_fatal(FARGS,"No input files!" );
+ gmx_fatal(FARGS, "No input files!" );
}
-
+
if (bDeMux && (nfile_in != nset))
{
- gmx_fatal(FARGS,"You have specified %d files and %d entries in the demux table",nfile_in,nset);
+ gmx_fatal(FARGS, "You have specified %d files and %d entries in the demux table", nfile_in, nset);
}
-
- nfile_out = opt2fns(&fnms_out,"-o",NFILE,fnm);
+
+ nfile_out = opt2fns(&fnms_out, "-o", NFILE, fnm);
if (!nfile_out)
{
- gmx_fatal(FARGS,"No output files!");
+ gmx_fatal(FARGS, "No output files!");
}
if ((nfile_out > 1) && !bDeMux)
{
- gmx_fatal(FARGS,"Don't know what to do with more than 1 output file if not demultiplexing");
+ gmx_fatal(FARGS, "Don't know what to do with more than 1 output file if not demultiplexing");
}
else if (bDeMux && (nfile_out != nset) && (nfile_out != 1))
{
- gmx_fatal(FARGS,"Number of output files should be 1 or %d (#input files), not %d",nset,nfile_out);
+ gmx_fatal(FARGS, "Number of output files should be 1 or %d (#input files), not %d", nset, nfile_out);
}
- if (bDeMux)
+ if (bDeMux)
{
- if (nfile_out != nset)
+ if (nfile_out != nset)
{
char *buf = strdup(fnms_out[0]);
- snew(fnms_out,nset);
- for(i=0; (i<nset); i++)
+ snew(fnms_out, nset);
+ for (i = 0; (i < nset); i++)
{
- snew(fnms_out[i],strlen(buf)+32);
- sprintf(fnms_out[i],"%d_%s",i,buf);
+ snew(fnms_out[i], strlen(buf)+32);
+ sprintf(fnms_out[i], "%d_%s", i, buf);
}
sfree(buf);
}
- do_demux(nfile_in,fnms,fnms_out,n,val,t,dt_remd,isize,index,dt,oenv);
+ do_demux(nfile_in, fnms, fnms_out, n, val, t, dt_remd, isize, index, dt, oenv);
}
- else
+ else
{
- snew(readtime,nfile_in+1);
- snew(timest,nfile_in+1);
- scan_trj_files(fnms,nfile_in,readtime,timest,imax,oenv);
+ snew(readtime, nfile_in+1);
+ snew(timest, nfile_in+1);
+ scan_trj_files(fnms, nfile_in, readtime, timest, imax, oenv);
- snew(settime,nfile_in+1);
- snew(cont_type,nfile_in+1);
- edit_files(fnms,nfile_in,readtime,timest,settime,cont_type,bSetTime,bSort,
+ snew(settime, nfile_in+1);
+ snew(cont_type, nfile_in+1);
+ edit_files(fnms, nfile_in, readtime, timest, settime, cont_type, bSetTime, bSort,
oenv);
- /* Check whether the output file is amongst the input files
+ /* Check whether the output file is amongst the input files
* This has to be done after sorting etc.
*/
out_file = fnms_out[0];
n_append = -1;
- for(i=0; ((i<nfile_in) && (n_append==-1)); i++)
+ for (i = 0; ((i < nfile_in) && (n_append == -1)); i++)
{
- if (strcmp(fnms[i],out_file) == 0)
+ if (strcmp(fnms[i], out_file) == 0)
{
n_append = i;
}
}
- if (n_append == 0) {
- fprintf(stderr,"Will append to %s rather than creating a new file\n",
+ if (n_append == 0)
+ {
+ fprintf(stderr, "Will append to %s rather than creating a new file\n",
out_file);
}
else if (n_append != -1)
{
- gmx_fatal(FARGS,"Can only append to the first file which is %s (not %s)",
- fnms[0],out_file);
+ gmx_fatal(FARGS, "Can only append to the first file which is %s (not %s)",
+ fnms[0], out_file);
}
- earliersteps=0;
+ earliersteps = 0;
/* Not checking input format, could be dangerous :-) */
/* Not checking output format, equally dangerous :-) */
- frame=-1;
- frame_out=-1;
+ frame = -1;
+ frame_out = -1;
/* the default is not to change the time at all,
* but this is overridden by the edit_files routine
*/
- t_corr=0;
+ t_corr = 0;
- if (n_append == -1)
+ if (n_append == -1)
{
- trxout = open_trx(out_file,"w");
- memset(&frout,0,sizeof(frout));
+ trxout = open_trx(out_file, "w");
+ memset(&frout, 0, sizeof(frout));
}
- else
+ else
{
t_fileio *stfio;
- if (!read_first_frame(oenv,&status,out_file,&fr,FLAGS))
- gmx_fatal(FARGS,"Reading first frame from %s",out_file);
+ if (!read_first_frame(oenv, &status, out_file, &fr, FLAGS))
+ {
+ gmx_fatal(FARGS, "Reading first frame from %s", out_file);
+ }
- stfio=trx_get_fileio(status);
+ stfio = trx_get_fileio(status);
if (!bKeepLast && !bOverwrite)
{
fprintf(stderr, "\n\nWARNING: Appending without -overwrite implies -keeplast "
- "between the first two files. \n"
- "If the trajectories have an overlap and have not been written binary \n"
- "reproducible this will produce an incorrect trajectory!\n\n");
-
+ "between the first two files. \n"
+ "If the trajectories have an overlap and have not been written binary \n"
+ "reproducible this will produce an incorrect trajectory!\n\n");
+
/* Fails if last frame is incomplete
* We can't do anything about it without overwriting
* */
- if (gmx_fio_getftp(stfio) == efXTC)
+ if (gmx_fio_getftp(stfio) == efXTC)
{
- lasttime =
- xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
- gmx_fio_getxdr(stfio),
- fr.natoms,&bOK);
+ lasttime =
+ xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
+ gmx_fio_getxdr(stfio),
+ fr.natoms, &bOK);
fr.time = lasttime;
if (!bOK)
{
- gmx_fatal(FARGS,"Error reading last frame. Maybe seek not supported." );
- }
+ gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
+ }
}
- else
+ else
{
- while (read_next_frame(oenv,status,&fr))
+ while (read_next_frame(oenv, status, &fr))
+ {
;
- lasttime = fr.time;
+ }
+ lasttime = fr.time;
}
bKeepLastAppend = TRUE;
close_trj(status);
- trxout = open_trx(out_file,"a");
+ trxout = open_trx(out_file, "a");
}
else if (bOverwrite)
{
- if (gmx_fio_getftp(stfio) != efXTC) {
- gmx_fatal(FARGS,"Overwrite only supported for XTC." );
+ if (gmx_fio_getftp(stfio) != efXTC)
+ {
+ gmx_fatal(FARGS, "Overwrite only supported for XTC." );
}
- last_frame_time =
- xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
- gmx_fio_getxdr(stfio),
- fr.natoms,&bOK);
+ last_frame_time =
+ xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
+ gmx_fio_getxdr(stfio),
+ fr.natoms, &bOK);
if (!bOK)
{
- gmx_fatal(FARGS,"Error reading last frame. Maybe seek not supported." );
+ gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
}
- /* xtc_seek_time broken for trajectories containing only 1 or 2 frames
+ /* xtc_seek_time broken for trajectories containing only 1 or 2 frames
* or when seek time = 0 */
- if (nfile_in>1 && settime[1]<last_frame_time+timest[0]*0.5)
+ if (nfile_in > 1 && settime[1] < last_frame_time+timest[0]*0.5)
{
/* Jump to one time-frame before the start of next
* trajectory file */
searchtime = settime[1]-timest[0]*1.25;
- }
- else
+ }
+ else
{
searchtime = last_frame_time;
}
- if (xtc_seek_time(stfio,searchtime,fr.natoms,TRUE))
+ if (xtc_seek_time(stfio, searchtime, fr.natoms, TRUE))
{
- gmx_fatal(FARGS,"Error seeking to append position.");
+ gmx_fatal(FARGS, "Error seeking to append position.");
}
- read_next_frame(oenv,status,&fr);
+ read_next_frame(oenv, status, &fr);
if (fabs(searchtime - fr.time) > timest[0]*0.5)
{
- gmx_fatal(FARGS,"Error seeking: attempted to seek to %f but got %f.",
- searchtime,fr.time);
+ gmx_fatal(FARGS, "Error seeking: attempted to seek to %f but got %f.",
+ searchtime, fr.time);
}
- lasttime = fr.time;
- fpos = gmx_fio_ftell(stfio);
+ lasttime = fr.time;
+ fpos = gmx_fio_ftell(stfio);
close_trj(status);
- trxout = open_trx(out_file,"r+");
- if (gmx_fio_seek(trx_get_fileio(trxout),fpos)) {
- gmx_fatal(FARGS,"Error seeking to append position.");
+ trxout = open_trx(out_file, "r+");
+ if (gmx_fio_seek(trx_get_fileio(trxout), fpos))
+ {
+ gmx_fatal(FARGS, "Error seeking to append position.");
}
}
- printf("\n Will append after %f \n",lasttime);
+ printf("\n Will append after %f \n", lasttime);
frout = fr;
}
/* Lets stitch up some files */
timestep = timest[0];
- for(i=n_append+1; (i<nfile_in); i++)
+ for (i = n_append+1; (i < nfile_in); i++)
{
/* Open next file */
/* set the next time from the last frame in previous file */
- if (i > 0)
+ if (i > 0)
{
- if (frame_out >= 0)
+ if (frame_out >= 0)
{
- if(cont_type[i]==TIME_CONTINUE)
+ if (cont_type[i] == TIME_CONTINUE)
{
- begin =frout.time;
- begin += 0.5*timestep;
- settime[i]=frout.time;
- cont_type[i]=TIME_EXPLICIT;
+ begin = frout.time;
+ begin += 0.5*timestep;
+ settime[i] = frout.time;
+ cont_type[i] = TIME_EXPLICIT;
}
- else if(cont_type[i]==TIME_LAST)
+ else if (cont_type[i] == TIME_LAST)
{
- begin=frout.time;
+ begin = frout.time;
begin += 0.5*timestep;
}
/* Or, if the time in the next part should be changed by the
*/
}
/* Or, if time is set explicitly, we check for overlap/gap */
- if(cont_type[i]==TIME_EXPLICIT)
+ if (cont_type[i] == TIME_EXPLICIT)
{
- if( ( i < nfile_in ) &&
- ( frout.time < settime[i]-1.5*timestep ) )
+ if ( ( i < nfile_in ) &&
+ ( frout.time < settime[i]-1.5*timestep ) )
{
fprintf(stderr, "WARNING: Frames around t=%f %s have a different "
"spacing than the rest,\n"
"might be a gap or overlap that couldn't be corrected "
- "automatically.\n",output_env_conv_time(oenv,frout.time),
+ "automatically.\n", output_env_conv_time(oenv, frout.time),
output_env_get_time_unit(oenv));
}
}
}
/* if we don't have a timestep in the current file, use the old one */
- if ( timest[i] != 0 )
+ if (timest[i] != 0)
{
timestep = timest[i];
}
- read_first_frame(oenv,&status,fnms[i],&fr,FLAGS);
- if(!fr.bTime)
+ read_first_frame(oenv, &status, fnms[i], &fr, FLAGS);
+ if (!fr.bTime)
{
- fr.time=0;
- fprintf(stderr,"\nWARNING: Couldn't find a time in the frame.\n");
+ fr.time = 0;
+ fprintf(stderr, "\nWARNING: Couldn't find a time in the frame.\n");
}
- if(cont_type[i]==TIME_EXPLICIT)
+ if (cont_type[i] == TIME_EXPLICIT)
{
- t_corr=settime[i]-fr.time;
+ t_corr = settime[i]-fr.time;
}
/* t_corr is the amount we want to change the time.
* If the user has chosen not to change the time for
- * this part of the trajectory t_corr remains at
+ * this part of the trajectory t_corr remains at
* the value it had in the last part, changing this
* by the same amount.
* If no value was given for the first trajectory part
* we let the time start at zero, see the edit_files routine.
*/
- bNewFile=TRUE;
+ bNewFile = TRUE;
printf("\n");
if (lasttime != NOTSET)
printf("lasttime %g\n", lasttime);
}
- do
+ do
{
/* copy the input frame to the output frame */
- frout=fr;
+ frout = fr;
/* set the new time by adding the correct calculated above */
- frout.time += t_corr;
+ frout.time += t_corr;
/* quit if we have reached the end of what should be written */
- if((end > 0) && (frout.time > end+GMX_REAL_EPS))
+ if ((end > 0) && (frout.time > end+GMX_REAL_EPS))
{
- i=nfile_in;
+ i = nfile_in;
break;
}
{
bWrite = TRUE;
}
- else if ( bKeepLast || (bKeepLastAppend && i==1))
- /* write till last frame of this traj
- and skip first frame(s) of next traj */
+ else if (bKeepLast || (bKeepLastAppend && i == 1))
+ /* write till last frame of this traj
+ and skip first frame(s) of next traj */
{
bWrite = ( frout.time > lasttime+0.5*timestep );
}
bWrite = ( frout.time < settime[i+1]-0.5*timestep );
}
- if( bWrite && (frout.time >= begin) )
+ if (bWrite && (frout.time >= begin) )
{
frame++;
if (frame_out == -1)
+ {
first_time = frout.time;
+ }
lasttime = frout.time;
- if (dt==0 || bRmod(frout.time,first_time,dt))
+ if (dt == 0 || bRmod(frout.time, first_time, dt))
{
frame_out++;
- last_ok_t=frout.time;
- if(bNewFile)
+ last_ok_t = frout.time;
+ if (bNewFile)
{
- fprintf(stderr,"\nContinue writing frames from %s t=%g %s, "
+ fprintf(stderr, "\nContinue writing frames from %s t=%g %s, "
"frame=%d \n",
- fnms[i],output_env_conv_time(oenv,frout.time),output_env_get_time_unit(oenv),
+ fnms[i], output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv),
frame);
- bNewFile=FALSE;
+ bNewFile = FALSE;
}
if (bIndex)
{
- write_trxframe_indexed(trxout,&frout,isize,index,
+ write_trxframe_indexed(trxout, &frout, isize, index,
NULL);
}
else
{
- write_trxframe(trxout,&frout,NULL);
+ write_trxframe(trxout, &frout, NULL);
}
if ( ((frame % 10) == 0) || (frame < 10) )
{
- fprintf(stderr," -> frame %6d time %8.3f %s \r",
- frame_out,output_env_conv_time(oenv,frout.time),output_env_get_time_unit(oenv));
+ fprintf(stderr, " -> frame %6d time %8.3f %s \r",
+ frame_out, output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv));
}
}
}
- } while( read_next_frame(oenv,status,&fr));
+ }
+ while (read_next_frame(oenv, status, &fr));
close_trj(status);
- earliersteps+=step;
- }
+ earliersteps += step;
+ }
if (trxout)
{
close_trx(trxout);
}
- fprintf(stderr,"\nLast frame written was %d, time %f %s\n",
- frame,output_env_conv_time(oenv,last_ok_t),output_env_get_time_unit(oenv));
+ fprintf(stderr, "\nLast frame written was %d, time %f %s\n",
+ frame, output_env_conv_time(oenv, last_ok_t), output_env_get_time_unit(oenv));
}
thanx(stderr);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff