static void tick_spacing(int n, real axis[], real offset, char axisnm,
real *major, real *minor)
{
real space;
gmx_bool bTryAgain, bFive;
int i, j, t, f = 0, ten;
#define NFACT 4
real major_fact[NFACT] = {5, 4, 2, 1};
real minor_fact[NFACT] = {5, 4, 4, 5};
/* start with interval between 10 matrix points: */
space = max(10*axis[1]-axis[0], axis[min(10, n-1)]-axis[0]);
/* get power of 10 */
ten = (int)ceil(log(space)/log(10))-1;
bTryAgain = TRUE;
for (t = ten+2; t > ten-3 && bTryAgain; t--)
{
for (f = 0; f < NFACT && bTryAgain; f++)
{
space = pow(10, t) * major_fact[f];
/* count how many ticks we would get: */
i = 0;
for (j = 0; j < n; j++)
{
if (bRmod(axis[j], offset, space) )
{
i++;
}
}
/* do we have a reasonable number of ticks ? */
bTryAgain = (i > min(10, n-1)) || (i < 5);
}
}
if (bTryAgain)
{
space = max(10*axis[1]-axis[0], axis[min(10, n-1)]-axis[0]);
fprintf(stderr, "Auto tick spacing failed for %c-axis, guessing %g\n",
axisnm, space);
}
*major = space;
*minor = space / minor_fact[f-1];
fprintf(stderr, "Auto tick spacing for %c-axis: major %g, minor %g\n",
axisnm, *major, *minor);
}
int check_times2(real t,real t0,real tp, real tpp)
{
int r;
real margin;
if (t-tp>0 && tp-tpp>0)
margin = 0.1*min(t-tp,tp-tpp);
else
margin = 0;
r=-1;
if ((((tbegin >= 0.0) && (t >= tbegin)) || ( fabs(tbegin-(-1.0))<GMX_REAL_MIN )) &&
(((tend >= 0.0) && (t <= tend+margin)) || ( fabs(tend-(-1.0))<GMX_REAL_MIN ))) {
if (tdelta > 0 && !bRmod(t-t0,tdelta))
r = -1;
else
r = 0;
}
else if (( fabs(tend -(-1.0)) > GMX_REAL_MIN) && (t>=tend))
r = 1;
if (debug) fprintf(debug,"t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n",
t,t0,tbegin,tend,tdelta,r);
return r;
}
int gmx_trjcat(int argc,char *argv[])
{
static char *desc[] = {
"trjcat 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 -o fixed.trr *.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 xvg file."
"The xvg file should contain something like:[PAR]",
"0 0 1 2 3 4 5[BR]",
"2 1 0 2 3 5 4[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 xvg file then the program",
"tries to be smart. Beware."
};
static bool bVels=TRUE;
static int prec=3;
static bool bCat=FALSE;
static bool bSort=TRUE;
static bool bKeepLast=FALSE;
static bool bSetTime=FALSE;
static bool bDeMux;
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 .xtc and .gro 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" },
{ "-cat", FALSE, etBOOL, {&bCat},
"do not discard double time frames" }
};
#define npargs asize(pa)
int status,ftpin,i,frame,frame_out,step=0,trjout=0;
rvec *x,*v;
real xtcpr,t_corr;
t_trxframe fr,frout;
char **fnms,**fnms_out,*in_file,*out_file;
int n_append;
int trxout=-1;
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;
int isize,j;
atom_id *index=NULL,imax;
char *grpname;
real **val=NULL,*t=NULL,dt_remd;
int n,nset;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffRDMULT },
{ efTRO, "-o", NULL, ffWRMULT },
{ efNDX, "-n", "index", ffOPTRD },
{ efXVG, "-demux", "remd", ffOPTRD }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_BE_NICE|PCA_TIME_UNIT,
NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL);
bIndex = ftp2bSet(efNDX,NFILE,fnm);
bDeMux = ftp2bSet(efXVG,NFILE,fnm);
bSort = bSort && !bDeMux;
imax=NO_ATID;
if (bIndex) {
printf("Select group for output\n");
rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
/* scan index */
imax=index[0];
for(i=1; i<isize; i++)
imax = max(imax, index[i]);
}
if (bDeMux) {
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);
printf("Read %d sets of %d points, dt = %g\n\n",nset,n,dt_remd);
if (debug) {
fprintf(debug,"Dump of replica_index.xvg\n");
for(i=0; (i<n); i++) {
fprintf(debug,"%10g",t[i]);
for(j=0; (j<nset); j++) {
fprintf(debug," %3d",gmx_nint(val[j][i]));
}
fprintf(debug,"\n");
}
}
}
/* prec is in nr of decimal places, xtcprec is a multiplication factor: */
xtcpr=1;
for (i=0; i<prec; i++)
xtcpr*=10;
nfile_in = opt2fns(&fnms,"-f",NFILE,fnm);
if (!nfile_in)
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);
nfile_out = opt2fns(&fnms_out,"-o",NFILE,fnm);
if (!nfile_out)
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");
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);
if (bDeMux) {
if (nfile_out != nset) {
char *buf = strdup(fnms_out[0]);
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);
}
}
do_demux(nfile_in,fnms,fnms_out,n,val,t,dt_remd,isize,index,dt);
}
else {
snew(readtime,nfile_in+1);
snew(timest,nfile_in+1);
scan_trj_files(fnms,nfile_in,readtime,timest,imax);
snew(settime,nfile_in+1);
snew(cont_type,nfile_in+1);
edit_files(fnms,nfile_in,readtime,timest,settime,cont_type,bSetTime,bSort);
/* 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++) {
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",
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);
earliersteps=0;
/* Not checking input format, could be dangerous :-) */
/* Not checking output format, equally dangerous :-) */
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;
if (n_append == -1) {
trxout = open_trx(out_file,"w");
memset(&frout,0,sizeof(frout));
}
else {
/* Read file to find what is the last frame in it */
if (!read_first_frame(&status,out_file,&fr,FLAGS))
gmx_fatal(FARGS,"Reading first frame from %s",out_file);
while (read_next_frame(status,&fr))
;
close_trj(status);
lasttime = fr.time;
bKeepLast = TRUE;
trxout = open_trx(out_file,"a");
frout = fr;
}
/* Lets stitch up some files */
timestep = timest[0];
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 (frame_out >= 0) {
if(cont_type[i]==TIME_CONTINUE) {
begin =frout.time;
begin += 0.5*timestep;
settime[i]=frout.time;
cont_type[i]=TIME_EXPLICIT;
}
else if(cont_type[i]==TIME_LAST) {
begin=frout.time;
begin += 0.5*timestep;
}
/* Or, if the time in the next part should be changed by the
* same amount, start at half a timestep from the last time
* so we dont repeat frames.
*/
/* I don't understand the comment above, but for all the cases
* I tried the code seems to work properly. B. Hess 2008-4-2.
*/
}
/* Or, if time is set explicitly, we check for overlap/gap */
if(cont_type[i]==TIME_EXPLICIT)
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",convert_time(frout.time),time_unit());
}
/* if we don't have a timestep in the current file, use the old one */
if ( timest[i] != 0 )
timestep = timest[i];
read_first_frame(&status,fnms[i],&fr,FLAGS);
if(!fr.bTime) {
fr.time=0;
fprintf(stderr,"\nWARNING: Couldn't find a time in the frame.\n");
}
if(cont_type[i]==TIME_EXPLICIT)
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
* 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;
printf("\n");
if (lasttime != NOTSET)
printf("lasttime %g\n", lasttime);
do {
/* copy the input frame to the output frame */
frout=fr;
/* set the new time by adding the correct calculated above */
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)) {
i=nfile_in;
break;
}
/* determine if we should write this frame (dt is handled elsewhere) */
if (bCat) /* write all frames of all files */
bWrite = TRUE;
else if ( bKeepLast ) /* write till last frame of this traj
and skip first frame(s) of next traj */
bWrite = ( frout.time > lasttime+0.5*timestep );
else /* write till first frame of next traj */
bWrite = ( frout.time < settime[i+1]-0.5*timestep );
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)) {
frame_out++;
last_ok_t=frout.time;
if(bNewFile) {
fprintf(stderr,"\nContinue writing frames from %s t=%g %s, "
"frame=%d \n",
fnms[i],convert_time(frout.time),time_unit(),frame);
bNewFile=FALSE;
}
if (bIndex)
write_trxframe_indexed(trxout,&frout,isize,index);
else
write_trxframe(trxout,&frout);
if ( ((frame % 10) == 0) || (frame < 10) )
fprintf(stderr," -> frame %6d time %8.3f %s \r",
frame_out,convert_time(frout.time),time_unit());
}
}
} while( read_next_frame(status,&fr));
close_trj(status);
earliersteps+=step;
}
if (trxout >= 0)
close_trx(trxout);
fprintf(stderr,"\nLast frame written was %d, time %f %s\n",
frame,convert_time(last_ok_t),time_unit());
}
thanx(stderr);
return 0;
}
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)
{
int i,j,k,natoms,nnn;
int *fp_in,*fp_out;
bool bCont,*bSet;
real t,first_time=0;
t_trxframe *trx;
snew(fp_in,nset);
snew(trx,nset);
snew(bSet,nset);
natoms = -1;
t = -1;
for(i=0; (i<nset); i++) {
nnn = read_first_frame(&(fp_in[i]),fnms[i],&(trx[i]),TRX_NEED_X);
if (natoms == -1) {
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);
if (t == -1)
t = trx[i].time;
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);
}
snew(fp_out,nset);
for(i=0; (i<nset); i++)
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");
do {
while ((k+1 < nval) && ((trx[0].time - time[k+1]) > dt_remd*0.1))
k++;
if (debug)
fprintf(debug,"trx[0].time = %g, time[k] = %g\n",trx[0].time,time[k]);
for(i=0; (i<nset); i++)
bSet[i] = FALSE;
for(i=0; (i<nset); i++) {
j = gmx_nint(value[i][k]);
range_check(j,0,nset);
if (bSet[j])
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 (index)
write_trxframe_indexed(fp_out[j],&trx[i],isize,index);
else
write_trxframe(fp_out[j],&trx[i]);
}
}
bCont = (k < nval);
for(i=0; (i<nset); i++)
bCont = bCont && read_next_frame(fp_in[i],&trx[i]);
} while (bCont);
for(i=0; (i<nset); i++) {
close_trx(fp_in[i]);
close_trx(fp_out[i]);
}
}
static void draw_boxes(t_psdata ps,real x0,real y0,real w,
int nmat,t_matrix mat[],t_psrec *psr)
{
char buf[12];
char *mylab;
real xxx;
char **xtick,**ytick;
real xx,yy,dy,xx00,yy00,offset_x,offset_y;
int i,j,x,y,ntx,nty,strlength;
/* Only necessary when there will be no y-labels */
strlength = 0;
/* Draw the box */
ps_rgb(ps,BLACK);
ps_linewidth(ps,psr->boxlinewidth);
yy00=y0;
for(i=0; (i<nmat); i++) {
dy=box_height(&(mat[i]),psr);
ps_box(ps,x0-1,yy00-1,x0+w+1,yy00+dy+1);
yy00+=dy+box_dh(psr)+box_dh_top(IS_ONCE,psr);
}
/* Draw the ticks on the axes */
ps_linewidth(ps,psr->ticklinewidth);
xx00=x0-1;
yy00=y0-1;
for (i=0; (i<nmat); i++) {
if (mat[i].flags & MAT_SPATIAL_X) {
ntx = mat[i].nx + 1;
offset_x = 0.1;
} else {
ntx = mat[i].nx;
offset_x = 0.6;
}
if (mat[i].flags & MAT_SPATIAL_Y) {
nty = mat[i].ny + 1;
offset_y = 0.1;
} else {
nty = mat[i].ny;
offset_y = 0.6;
}
snew(xtick,ntx);
for(j=0; (j<ntx); j++) {
sprintf(buf,"%g",mat[i].axis_x[j]);
xtick[j]=strdup(buf);
}
ps_strfont(ps,psr->X.tickfont,psr->X.tickfontsize);
for(x=0; (x<ntx); x++) {
xx = xx00 + (x + offset_x)*psr->xboxsize;
if ( ( bRmod(mat[i].axis_x[x], psr->X.offset, psr->X.major) ||
(psr->X.first && (x==0))) &&
( (i == 0) || box_do_all_x_maj_ticks(psr) ) ) {
/* Longer tick marks */
ps_line (ps,xx,yy00,xx,yy00-psr->X.majorticklen);
/* Plot label on lowest graph only */
if (i == 0)
ps_ctext(ps,xx,
yy00-DDD-psr->X.majorticklen-psr->X.tickfontsize*0.8,
xtick[x],eXCenter);
} else if ( bRmod(mat[i].axis_x[x], psr->X.offset, psr->X.minor) &&
( (i == 0) || box_do_all_x_min_ticks(psr) ) ){
/* Shorter tick marks */
ps_line(ps,xx,yy00,xx,yy00-psr->X.minorticklen);
} else if ( bRmod(mat[i].axis_x[x], psr->X.offset, psr->X.major) ) {
/* Even shorter marks, only each X.major */
ps_line(ps,xx,yy00,xx,yy00-(psr->boxspacing/2));
}
}
ps_strfont(ps,psr->Y.tickfont,psr->Y.tickfontsize);
snew(ytick,nty);
for(j=0; (j<nty); j++) {
sprintf(buf,"%g",mat[i].axis_y[j]);
ytick[j]=strdup(buf);
}
for(y=0; (y<nty); y++) {
yy = yy00 + (y + offset_y)*psr->yboxsize;
if ( bRmod(mat[i].axis_y[y], psr->Y.offset, psr->Y.major) ||
(psr->Y.first && (y==0))) {
/* Major ticks */
strlength=max(strlength,(int)strlen(ytick[y]));
ps_line (ps,xx00,yy,xx00-psr->Y.majorticklen,yy);
ps_ctext(ps,xx00-psr->Y.majorticklen-DDD,
yy-psr->Y.tickfontsize/3.0,ytick[y],eXRight);
}
else if ( bRmod(mat[i].axis_y[y], psr->Y.offset, psr->Y.minor) ) {
/* Minor ticks */
ps_line(ps,xx00,yy,xx00-psr->Y.minorticklen,yy);
}
}
sfree(xtick);
sfree(ytick);
/* Label on Y-axis */
if (!psr->bYonce || i==nmat/2) {
if (strlen(psr->Y.label) > 0)
mylab = psr->Y.label;
else
mylab = mat[i].label_y;
if (strlen(mylab) > 0) {
ps_strfont(ps,psr->Y.font,psr->Y.fontsize);
ps_flip(ps,TRUE);
xxx=x0-psr->X.majorticklen-psr->X.tickfontsize*strlength-DDD;
ps_ctext(ps,yy00+box_height(&mat[i],psr)/2.0,612.5-xxx,
mylab,eXCenter);
ps_flip(ps,FALSE);
}
}
yy00+=box_height(&(mat[i]),psr)+box_dh(psr)+box_dh_top(IS_ONCE,psr);
}
/* Label on X-axis */
if (strlen(psr->X.label) > 0)
mylab = psr->X.label;
else
mylab = mat[0].label_x;
if (strlen(mylab) > 0) {
ps_strfont(ps,psr->X.font,psr->X.fontsize);
ps_ctext(ps,x0+w/2,y0-DDD-psr->X.majorticklen-psr->X.tickfontsize*FUDGE-
psr->X.fontsize,mylab,eXCenter);
}
}
int gmx_eneconv(int argc, char *argv[])
{
const char *desc[] = {
"With [IT]multiple files[it] specified for the [TT]-f[tt] option:[PAR]",
"Concatenates several energy files in sorted order.",
"In the 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 the command [TT]gmx eneconv -f *.edr -o fixed.edr[tt] should do",
"the trick. [PAR]",
"With [IT]one file[it] specified for [TT]-f[tt]:[PAR]",
"Reads one energy file and writes another, applying the [TT]-dt[tt],",
"[TT]-offset[tt], [TT]-t0[tt] and [TT]-settime[tt] options and",
"converting to a different format if necessary (indicated by file",
"extentions).[PAR]",
"[TT]-settime[tt] is applied first, then [TT]-dt[tt]/[TT]-offset[tt]",
"followed by [TT]-b[tt] and [TT]-e[tt] to select which frames to write."
};
const char *bugs[] = {
"When combining trajectories the sigma and E^2 (necessary for statistics) are not updated correctly. Only the actual energy is correct. One thus has to compute statistics in another way."
};
ener_file_t in = NULL, out = NULL;
gmx_enxnm_t *enm = NULL;
#if 0
ener_file_t in, out = NULL;
gmx_enxnm_t *enm = NULL;
#endif
t_enxframe *fr, *fro;
gmx_int64_t ee_sum_step = 0, ee_sum_nsteps, ee_sum_nsum;
t_energy *ee_sum;
gmx_int64_t lastfilestep, laststep, startstep_file = 0;
int noutfr;
int nre, nremax, this_nre, nfile, f, i, kkk, nset, *set = NULL;
double last_t;
char **fnms;
real *readtime, *settime, timestep, tadjust;
char buf[22], buf2[22];
int *cont_type;
gmx_bool bNewFile, bFirst, bNewOutput;
gmx_output_env_t *oenv;
gmx_bool warned_about_dh = FALSE;
t_enxblock *blocks = NULL;
int nblocks = 0;
int nblocks_alloc = 0;
t_filenm fnm[] = {
{ efEDR, "-f", NULL, ffRDMULT },
{ efEDR, "-o", "fixed", ffWRITE },
};
#define NFILE asize(fnm)
gmx_bool bWrite;
static real delta_t = 0.0, toffset = 0, scalefac = 1;
static gmx_bool bSetTime = FALSE;
static gmx_bool bSort = TRUE, bError = TRUE;
static real begin = -1;
static real end = -1;
gmx_bool remove_dh = FALSE;
t_pargs pa[] = {
{ "-b", FALSE, etREAL, {&begin},
"First time to use"},
{ "-e", FALSE, etREAL, {&end},
"Last time to use"},
{ "-dt", FALSE, etREAL, {&delta_t},
"Only write out frame when t MOD dt = offset" },
{ "-offset", FALSE, etREAL, {&toffset},
"Time offset for [TT]-dt[tt] option" },
{ "-settime", FALSE, etBOOL, {&bSetTime},
"Change starting time interactively" },
{ "-sort", FALSE, etBOOL, {&bSort},
"Sort energy files (not frames)"},
{ "-rmdh", FALSE, etBOOL, {&remove_dh},
"Remove free energy block data" },
{ "-scalefac", FALSE, etREAL, {&scalefac},
"Multiply energy component by this factor" },
{ "-error", FALSE, etBOOL, {&bError},
"Stop on errors in the file" }
};
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa),
pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
tadjust = 0;
nremax = 0;
nset = 0;
timestep = 0.0;
snew(fnms, argc);
lastfilestep = 0;
laststep = 0;
nfile = opt2fns(&fnms, "-f", NFILE, fnm);
if (!nfile)
{
gmx_fatal(FARGS, "No input files!");
}
snew(settime, nfile+1);
snew(readtime, nfile+1);
snew(cont_type, nfile+1);
nre = scan_ene_files(fnms, nfile, readtime, ×tep, &nremax);
edit_files(fnms, nfile, readtime, settime, cont_type, bSetTime, bSort);
ee_sum_nsteps = 0;
ee_sum_nsum = 0;
snew(ee_sum, nremax);
snew(fr, 1);
snew(fro, 1);
fro->t = -1e20;
fro->nre = nre;
snew(fro->ener, nremax);
noutfr = 0;
bFirst = TRUE;
last_t = fro->t;
for (f = 0; f < nfile; f++)
{
bNewFile = TRUE;
bNewOutput = TRUE;
in = open_enx(fnms[f], "r");
enm = NULL;
do_enxnms(in, &this_nre, &enm);
if (f == 0)
{
if (scalefac != 1)
{
set = select_it(nre, enm, &nset);
}
/* write names to the output file */
out = open_enx(opt2fn("-o", NFILE, fnm), "w");
do_enxnms(out, &nre, &enm);
}
/* start reading from the next file */
while ((fro->t <= (settime[f+1] + GMX_REAL_EPS)) &&
do_enx(in, fr))
{
if (bNewFile)
{
startstep_file = fr->step;
tadjust = settime[f] - fr->t;
if (cont_type[f+1] == TIME_LAST)
{
settime[f+1] = readtime[f+1]-readtime[f]+settime[f];
cont_type[f+1] = TIME_EXPLICIT;
}
bNewFile = FALSE;
}
if (tadjust + fr->t <= last_t)
{
/* Skip this frame, since we already have it / past it */
if (debug)
{
fprintf(debug, "fr->step %s, fr->t %.4f\n",
gmx_step_str(fr->step, buf), fr->t);
fprintf(debug, "tadjust %12.6e + fr->t %12.6e <= t %12.6e\n",
tadjust, fr->t, last_t);
}
continue;
}
fro->step = lastfilestep + fr->step - startstep_file;
fro->t = tadjust + fr->t;
bWrite = ((begin < 0 || (fro->t >= begin-GMX_REAL_EPS)) &&
(end < 0 || (fro->t <= end +GMX_REAL_EPS)) &&
(fro->t <= settime[f+1]+0.5*timestep));
if (debug)
{
fprintf(debug,
"fr->step %s, fr->t %.4f, fro->step %s fro->t %.4f, w %d\n",
gmx_step_str(fr->step, buf), fr->t,
gmx_step_str(fro->step, buf2), fro->t, bWrite);
}
if (bError)
{
if ((end > 0) && (fro->t > end+GMX_REAL_EPS))
{
f = nfile;
break;
}
}
if (fro->t >= begin-GMX_REAL_EPS)
{
if (bFirst)
{
bFirst = FALSE;
}
if (bWrite)
{
update_ee_sum(nre, &ee_sum_step, &ee_sum_nsteps, &ee_sum_nsum, ee_sum,
fr, fro->step);
}
}
/* determine if we should write it */
if (bWrite && (delta_t == 0 || bRmod(fro->t, toffset, delta_t)))
{
laststep = fro->step;
last_t = fro->t;
if (bNewOutput)
{
bNewOutput = FALSE;
fprintf(stderr, "\nContinue writing frames from t=%g, step=%s\n",
fro->t, gmx_step_str(fro->step, buf));
}
/* Copy the energies */
for (i = 0; i < nre; i++)
{
fro->ener[i].e = fr->ener[i].e;
}
fro->nsteps = ee_sum_nsteps;
fro->dt = fr->dt;
if (ee_sum_nsum <= 1)
{
fro->nsum = 0;
}
else
{
fro->nsum = gmx_int64_to_int(ee_sum_nsum,
"energy average summation");
/* Copy the energy sums */
for (i = 0; i < nre; i++)
{
fro->ener[i].esum = ee_sum[i].esum;
fro->ener[i].eav = ee_sum[i].eav;
}
}
/* We wrote the energies, so reset the counts */
ee_sum_nsteps = 0;
ee_sum_nsum = 0;
if (scalefac != 1)
{
for (kkk = 0; kkk < nset; kkk++)
{
fro->ener[set[kkk]].e *= scalefac;
if (fro->nsum > 0)
{
fro->ener[set[kkk]].eav *= scalefac*scalefac;
fro->ener[set[kkk]].esum *= scalefac;
}
}
}
/* Copy restraint stuff */
/*fro->ndisre = fr->ndisre;
fro->disre_rm3tav = fr->disre_rm3tav;
fro->disre_rt = fr->disre_rt;*/
fro->nblock = fr->nblock;
/*fro->nr = fr->nr;*/
fro->block = fr->block;
/* check if we have blocks with delta_h data and are throwing
away data */
if (fro->nblock > 0)
{
if (remove_dh)
{
int i;
if (!blocks || nblocks_alloc < fr->nblock)
{
/* we pre-allocate the blocks */
nblocks_alloc = fr->nblock;
snew(blocks, nblocks_alloc);
}
nblocks = 0; /* number of blocks so far */
for (i = 0; i < fr->nblock; i++)
{
if ( (fr->block[i].id != enxDHCOLL) &&
(fr->block[i].id != enxDH) &&
(fr->block[i].id != enxDHHIST) )
{
/* copy everything verbatim */
blocks[nblocks] = fr->block[i];
nblocks++;
}
}
/* now set the block pointer to the new blocks */
fro->nblock = nblocks;
fro->block = blocks;
}
else if (delta_t > 0)
{
if (!warned_about_dh)
{
for (i = 0; i < fr->nblock; i++)
{
if (fr->block[i].id == enxDH ||
fr->block[i].id == enxDHHIST)
{
int size;
if (fr->block[i].id == enxDH)
{
size = fr->block[i].sub[2].nr;
}
else
{
size = fr->nsteps;
}
if (size > 0)
{
printf("\nWARNING: %s contains delta H blocks or histograms for which\n"
" some data is thrown away on a block-by-block basis, where each block\n"
" contains up to %d samples.\n"
" This is almost certainly not what you want.\n"
" Use the -rmdh option to throw all delta H samples away.\n"
" Use g_energy -odh option to extract these samples.\n",
fnms[f], size);
warned_about_dh = TRUE;
break;
}
}
}
}
}
}
do_enx(out, fro);
if (noutfr % 1000 == 0)
{
fprintf(stderr, "Writing frame time %g ", fro->t);
}
noutfr++;
}
}
if (f == nfile)
{
f--;
}
printf("\nLast step written from %s: t %g, step %s\n",
fnms[f], last_t, gmx_step_str(laststep, buf));
lastfilestep = laststep;
/* set the next time from the last in previous file */
if (cont_type[f+1] == TIME_CONTINUE)
{
settime[f+1] = fro->t;
/* in this case we have already written the last frame of
* previous file, so update begin to avoid doubling it
* with the start of the next file
*/
begin = fro->t+0.5*timestep;
/* cont_type[f+1]==TIME_EXPLICIT; */
}
if ((fro->t < end) && (f < nfile-1) &&
(fro->t < settime[f+1]-1.5*timestep))
{
fprintf(stderr,
"\nWARNING: There might be a gap around t=%g\n", fro->t);
}
/* move energies to lastee */
close_enx(in);
free_enxnms(this_nre, enm);
fprintf(stderr, "\n");
}
if (noutfr == 0)
{
fprintf(stderr, "No frames written.\n");
}
else
{
fprintf(stderr, "Last frame written was at step %s, time %f\n",
gmx_step_str(fro->step, buf), fro->t);
fprintf(stderr, "Wrote %d frames\n", noutfr);
}
return 0;
}
int gmx_trjcat(int argc, char *argv[])
{
const char *desc[] =
{
"[THISMODULE] 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]gmx 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 [REF].xvg[ref] file.",
"The [REF].xvg[ref] file should contain something like::",
"",
" 0 0 1 2 3 4 5",
" 2 1 0 2 3 5 4",
"",
"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 [REF].xvg[ref] file then the program",
"tries to be smart. Beware."
};
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 bDeMux;
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)" },
{ "-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;
t_trxstatus *status, *trxout = NULL;
real t_corr;
t_trxframe fr, frout;
char **fnms, **fnms_out, *out_file;
int n_append;
gmx_bool bNewFile, bIndex, bWrite;
int nfile_in, nfile_out, *cont_type;
real *readtime, *timest, *settime;
real first_time = 0, lasttime, last_ok_t = -1, timestep;
gmx_bool lastTimeSet = FALSE;
real last_frame_time, searchtime;
int isize = 0, j;
int *index = NULL, imax;
char *grpname;
real **val = NULL, *t = NULL, dt_remd;
int n, nset, ftpout = -1, prevEndStep = 0, filetype;
gmx_off_t fpos;
gmx_output_env_t *oenv;
t_filenm fnm[] =
{
{ efTRX, "-f", NULL, ffRDMULT },
{ efTRO, "-o", NULL, ffWRMULT },
{ efNDX, "-n", "index", ffOPTRD },
{ efXVG, "-demux", "remd", ffOPTRD }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_TIME_UNIT, NFILE, fnm,
asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
bIndex = ftp2bSet(efNDX, NFILE, fnm);
bDeMux = ftp2bSet(efXVG, NFILE, fnm);
bSort = bSort && !bDeMux;
imax = -1;
if (bIndex)
{
printf("Select group for output\n");
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
/* scan index */
imax = index[0];
for (i = 1; i < isize; i++)
{
imax = std::max(imax, index[i]);
}
}
if (bDeMux)
{
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);
printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt_remd);
if (debug)
{
fprintf(debug, "Dump of replica_index.xvg\n");
for (i = 0; (i < n); i++)
{
fprintf(debug, "%10g", t[i]);
for (j = 0; (j < nset); j++)
{
fprintf(debug, " %3d", static_cast<int>(std::round(val[j][i])));
}
fprintf(debug, "\n");
}
}
}
nfile_in = opt2fns(&fnms, "-f", NFILE, fnm);
if (!nfile_in)
{
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);
}
ftpin = fn2ftp(fnms[0]);
for (i = 1; i < nfile_in; i++)
{
if (ftpin != fn2ftp(fnms[i]))
{
gmx_fatal(FARGS, "All input files must be of the same format");
}
}
nfile_out = opt2fns(&fnms_out, "-o", NFILE, fnm);
if (!nfile_out)
{
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");
}
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);
}
if (bDeMux)
{
if (nfile_out != nset)
{
char *buf = gmx_strdup(fnms_out[0]);
snew(fnms_out, nset);
for (i = 0; (i < nset); i++)
{
snew(fnms_out[i], std::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);
}
else
{
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,
oenv);
/* Check whether the output file is amongst the input files
* This has to be done after sorting etc.
*/
out_file = fnms_out[0];
ftpout = fn2ftp(out_file);
n_append = -1;
for (i = 0; ((i < nfile_in) && (n_append == -1)); i++)
{
if (std::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",
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);
}
/* Not checking input format, could be dangerous :-) */
/* Not checking output format, equally dangerous :-) */
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;
if (n_append == -1)
{
if (ftpout == efTNG)
{
if (ftpout != ftpin)
{
gmx_fatal(FARGS, "When writing TNG the input file format must also be TNG");
}
if (bIndex)
{
trjtools_gmx_prepare_tng_writing(out_file, 'w', NULL, &trxout,
fnms[0], isize, NULL, index, grpname);
}
else
{
trjtools_gmx_prepare_tng_writing(out_file, 'w', NULL, &trxout,
fnms[0], -1, NULL, NULL, NULL);
}
}
else
{
trxout = open_trx(out_file, "w");
}
std::memset(&frout, 0, sizeof(frout));
}
else
{
t_fileio *stfio;
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);
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");
filetype = gmx_fio_getftp(stfio);
/* Fails if last frame is incomplete
* We can't do anything about it without overwriting
* */
if (filetype == efXTC || filetype == efTNG)
{
lasttime = trx_get_time_of_final_frame(status);
fr.time = lasttime;
}
else
{
while (read_next_frame(oenv, status, &fr))
{
;
}
lasttime = fr.time;
}
lastTimeSet = TRUE;
bKeepLastAppend = TRUE;
close_trj(status);
trxout = open_trx(out_file, "a");
}
else if (bOverwrite)
{
if (gmx_fio_getftp(stfio) != efXTC)
{
gmx_fatal(FARGS, "Overwrite only supported for XTC." );
}
last_frame_time = trx_get_time_of_final_frame(status);
/* 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)
{
/* Jump to one time-frame before the start of next
* trajectory file */
searchtime = settime[1]-timest[0]*1.25;
}
else
{
searchtime = last_frame_time;
}
if (xtc_seek_time(stfio, searchtime, fr.natoms, TRUE))
{
gmx_fatal(FARGS, "Error seeking to append position.");
}
read_next_frame(oenv, status, &fr);
if (std::abs(searchtime - fr.time) > timest[0]*0.5)
{
gmx_fatal(FARGS, "Error seeking: attempted to seek to %f but got %f.",
searchtime, fr.time);
}
lasttime = fr.time;
lastTimeSet = TRUE;
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.");
}
}
if (lastTimeSet)
{
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++)
{
/* Open next file */
/* set the next time from the last frame in previous file */
if (i > 0)
{
/* When writing TNG the step determine which frame to write. Use an
* offset to be able to increase steps properly when changing files. */
if (ftpout == efTNG)
{
prevEndStep = frout.step;
}
if (frame_out >= 0)
{
if (cont_type[i] == TIME_CONTINUE)
{
begin = frout.time;
begin += 0.5*timestep;
settime[i] = frout.time;
cont_type[i] = TIME_EXPLICIT;
}
else if (cont_type[i] == TIME_LAST)
{
begin = frout.time;
begin += 0.5*timestep;
}
/* Or, if the time in the next part should be changed by the
* same amount, start at half a timestep from the last time
* so we dont repeat frames.
*/
/* I don't understand the comment above, but for all the cases
* I tried the code seems to work properly. B. Hess 2008-4-2.
*/
}
/* Or, if time is set explicitly, we check for overlap/gap */
if (cont_type[i] == TIME_EXPLICIT)
{
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),
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)
{
timestep = timest[i];
}
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");
}
if (cont_type[i] == TIME_EXPLICIT)
{
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
* 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;
if (!lastTimeSet)
{
lasttime = 0;
lastTimeSet = true;
}
printf("\n");
printf("lasttime %g\n", lasttime);
do
{
/* copy the input frame to the output frame */
frout = fr;
/* set the new time by adding the correct calculated above */
frout.time += t_corr;
if (ftpout == efTNG)
{
frout.step += prevEndStep;
}
/* quit if we have reached the end of what should be written */
if ((end > 0) && (frout.time > end+GMX_REAL_EPS))
{
i = nfile_in;
break;
}
/* determine if we should write this frame (dt is handled elsewhere) */
if (bCat) /* write all frames of all files */
{
bWrite = TRUE;
}
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 );
}
else /* write till first frame of next traj */
{
bWrite = ( frout.time < settime[i+1]-0.5*timestep );
}
if (bWrite && (frout.time >= begin) )
{
frame++;
if (frame_out == -1)
{
first_time = frout.time;
}
lasttime = frout.time;
lastTimeSet = TRUE;
if (dt == 0 || bRmod(frout.time, first_time, dt))
{
frame_out++;
last_ok_t = frout.time;
if (bNewFile)
{
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),
frame);
bNewFile = FALSE;
}
if (bIndex)
{
write_trxframe_indexed(trxout, &frout, isize, index,
NULL);
}
else
{
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));
fflush(stderr);
}
}
}
}
while (read_next_frame(oenv, status, &fr));
close_trj(status);
}
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));
}
return 0;
}
static void do_demux(int nset, char *fnms[], char *fnms_out[], int nval,
real **value, real *time, real dt_remd, int isize,
int index[], real dt, const gmx_output_env_t *oenv)
{
int i, j, k, natoms, nnn;
t_trxstatus **fp_in, **fp_out;
gmx_bool bCont, *bSet;
real t, first_time = 0;
t_trxframe *trx;
snew(fp_in, nset);
snew(trx, nset);
snew(bSet, nset);
natoms = -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;
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);
}
if (t == -1)
{
t = trx[i].time;
}
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);
}
}
snew(fp_out, nset);
for (i = 0; (i < nset); i++)
{
fp_out[i] = open_trx(fnms_out[i], "w");
}
k = 0;
if (std::round(time[k] - t) != 0)
{
gmx_fatal(FARGS, "First time in demuxing table does not match trajectories");
}
do
{
while ((k+1 < nval) && ((trx[0].time - time[k+1]) > dt_remd*0.1))
{
k++;
}
if (debug)
{
fprintf(debug, "trx[0].time = %g, time[k] = %g\n", trx[0].time, time[k]);
}
for (i = 0; (i < nset); i++)
{
bSet[i] = FALSE;
}
for (i = 0; (i < nset); i++)
{
j = std::round(value[i][k]);
range_check(j, 0, nset);
if (bSet[j])
{
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 (index)
{
write_trxframe_indexed(fp_out[j], &trx[i], isize, index, NULL);
}
else
{
write_trxframe(fp_out[j], &trx[i], NULL);
}
}
}
bCont = (k < nval);
for (i = 0; (i < nset); i++)
{
bCont = bCont && read_next_frame(oenv, fp_in[i], &trx[i]);
}
}
while (bCont);
for (i = 0; (i < nset); i++)
{
close_trx(fp_in[i]);
close_trx(fp_out[i]);
}
}
/* this is the main loop for the correlation type functions
* fx and nx are file pointers to things like read_first_x and
* read_next_x
*/
int corr_loop(t_corr *curr, const char *fn, t_topology *top, int ePBC,
gmx_bool bMol, int gnx[], atom_id *index[],
t_calc_func *calc1, gmx_bool bTen, int *gnx_com, atom_id *index_com[],
real dt, real t_pdb, rvec **x_pdb, matrix box_pdb,
const output_env_t oenv)
{
rvec *x[2]; /* the coordinates to read */
rvec *xa[2]; /* the coordinates to calculate displacements for */
rvec com = {0};
real t, t_prev = 0;
int natoms, i, j, cur = 0, maxframes = 0;
t_trxstatus *status;
#define prev (1-cur)
matrix box;
gmx_bool bFirst;
gmx_rmpbc_t gpbc = NULL;
natoms = read_first_x(oenv, &status, fn, &curr->t0, &(x[cur]), box);
#ifdef DEBUG
fprintf(stderr, "Read %d atoms for first frame\n", natoms);
#endif
if ((gnx_com != NULL) && natoms < top->atoms.nr)
{
fprintf(stderr, "WARNING: The trajectory only contains part of the system (%d of %d atoms) and therefore the COM motion of only this part of the system will be removed\n", natoms, top->atoms.nr);
}
snew(x[prev], natoms);
if (bMol)
{
curr->ncoords = curr->nmol;
snew(xa[0], curr->ncoords);
snew(xa[1], curr->ncoords);
}
else
{
curr->ncoords = natoms;
xa[0] = x[0];
xa[1] = x[1];
}
bFirst = TRUE;
t = curr->t0;
if (x_pdb)
{
*x_pdb = NULL;
}
if (bMol)
{
gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
}
/* the loop over all frames */
do
{
if (x_pdb && ((bFirst && t_pdb < t) ||
(!bFirst &&
t_pdb > t - 0.5*(t - t_prev) &&
t_pdb < t + 0.5*(t - t_prev))))
{
if (*x_pdb == NULL)
{
snew(*x_pdb, natoms);
}
for (i = 0; i < natoms; i++)
{
copy_rvec(x[cur][i], (*x_pdb)[i]);
}
copy_mat(box, box_pdb);
}
/* check whether we've reached a restart point */
if (bRmod(t, curr->t0, dt))
{
curr->nrestart++;
srenew(curr->x0, curr->nrestart);
snew(curr->x0[curr->nrestart-1], curr->ncoords);
srenew(curr->com, curr->nrestart);
srenew(curr->n_offs, curr->nrestart);
srenew(curr->lsq, curr->nrestart);
snew(curr->lsq[curr->nrestart-1], curr->nmol);
for (i = 0; i < curr->nmol; i++)
{
curr->lsq[curr->nrestart-1][i] = gmx_stats_init();
}
if (debug)
{
fprintf(debug, "Extended data structures because of new restart %d\n",
curr->nrestart);
}
}
/* create or extend the frame-based arrays */
if (curr->nframes >= maxframes-1)
{
if (maxframes == 0)
{
for (i = 0; (i < curr->ngrp); i++)
{
curr->ndata[i] = NULL;
curr->data[i] = NULL;
if (bTen)
{
curr->datam[i] = NULL;
}
}
curr->time = NULL;
}
maxframes += 10;
for (i = 0; (i < curr->ngrp); i++)
{
srenew(curr->ndata[i], maxframes);
srenew(curr->data[i], maxframes);
if (bTen)
{
srenew(curr->datam[i], maxframes);
}
for (j = maxframes-10; j < maxframes; j++)
{
curr->ndata[i][j] = 0;
curr->data[i][j] = 0;
if (bTen)
{
clear_mat(curr->datam[i][j]);
}
}
}
srenew(curr->time, maxframes);
}
/* set the time */
curr->time[curr->nframes] = t - curr->t0;
/* for the first frame, the previous frame is a copy of the first frame */
if (bFirst)
{
std::memcpy(xa[prev], xa[cur], curr->ncoords*sizeof(xa[prev][0]));
bFirst = FALSE;
}
/* make the molecules whole */
if (bMol)
{
gmx_rmpbc(gpbc, natoms, box, x[cur]);
}
/* calculate the molecules' centers of masses and put them into xa */
if (bMol)
{
calc_mol_com(gnx[0], index[0], &top->mols, &top->atoms, x[cur], xa[cur]);
}
/* first remove the periodic boundary condition crossings */
for (i = 0; i < curr->ngrp; i++)
{
prep_data(bMol, gnx[i], index[i], xa[cur], xa[prev], box);
}
/* calculate the center of mass */
if (gnx_com)
{
prep_data(bMol, gnx_com[0], index_com[0], xa[cur], xa[prev], box);
calc_com(bMol, gnx_com[0], index_com[0], xa[cur], xa[prev], box,
&top->atoms, com);
}
/* loop over all groups in index file */
for (i = 0; (i < curr->ngrp); i++)
{
/* calculate something useful, like mean square displacements */
calc_corr(curr, i, gnx[i], index[i], xa[cur], (gnx_com != NULL), com,
calc1, bTen);
}
cur = prev;
t_prev = t;
curr->nframes++;
}
while (read_next_x(oenv, status, &t, x[cur], box));
fprintf(stderr, "\nUsed %d restart points spaced %g %s over %g %s\n\n",
curr->nrestart,
output_env_conv_time(oenv, dt), output_env_get_time_unit(oenv),
output_env_conv_time(oenv, curr->time[curr->nframes-1]),
output_env_get_time_unit(oenv) );
if (bMol)
{
gmx_rmpbc_done(gpbc);
}
close_trj(status);
return natoms;
}
static void do_demux(gmx::ArrayRef<const std::string> inFiles,
gmx::ArrayRef<const std::string> outFiles, int nval,
real **value, real *time, real dt_remd, int isize,
int index[], real dt, const gmx_output_env_t *oenv)
{
int k, natoms;
t_trxstatus **fp_in, **fp_out;
gmx_bool bCont, *bSet;
real t, first_time = 0;
t_trxframe *trx;
snew(fp_in, inFiles.size());
snew(trx, inFiles.size());
snew(bSet, inFiles.size());
natoms = -1;
t = -1;
for (gmx::index i = 0; i < inFiles.ssize(); i++)
{
read_first_frame(oenv, &(fp_in[i]), inFiles[i].c_str(), &(trx[i]),
TRX_NEED_X);
if (natoms == -1)
{
natoms = trx[i].natoms;
first_time = trx[i].time;
}
else if (natoms != trx[i].natoms)
{
gmx_fatal(FARGS, "Trajectory file %s has %d atoms while previous trajs had %d atoms", inFiles[i].c_str(), trx[i].natoms, natoms);
}
if (t == -1)
{
t = trx[i].time;
}
else if (t != trx[i].time)
{
gmx_fatal(FARGS, "Trajectory file %s has time %f while previous trajs had time %f", inFiles[i].c_str(), trx[i].time, t);
}
}
snew(fp_out, inFiles.size());
for (gmx::index i = 0; i < inFiles.ssize(); i++)
{
fp_out[i] = open_trx(outFiles[i].c_str(), "w");
}
k = 0;
if (std::round(time[k] - t) != 0)
{
gmx_fatal(FARGS, "First time in demuxing table does not match trajectories");
}
do
{
while ((k+1 < nval) && ((trx[0].time - time[k+1]) > dt_remd*0.1))
{
k++;
}
if (debug)
{
fprintf(debug, "trx[0].time = %g, time[k] = %g\n", trx[0].time, time[k]);
}
for (gmx::index i = 0; i < inFiles.ssize(); i++)
{
bSet[i] = FALSE;
}
for (gmx::index i = 0; i < inFiles.ssize(); i++)
{
int j = gmx::roundToInt(value[i][k]);
range_check(j, 0, inFiles.size());
if (bSet[j])
{
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 (index)
{
write_trxframe_indexed(fp_out[j], &trx[i], isize, index, nullptr);
}
else
{
write_trxframe(fp_out[j], &trx[i], nullptr);
}
}
}
bCont = (k < nval);
for (gmx::index i = 0; i < inFiles.ssize(); i++)
{
bCont = bCont && read_next_frame(oenv, fp_in[i], &trx[i]);
}
}
while (bCont);
for (gmx::index i = 0; i < inFiles.ssize(); i++)
{
close_trx(fp_in[i]);
close_trx(fp_out[i]);
}
}
int gmx_eneconv(int argc,char *argv[])
{
static char *desc[] = {
"With [IT]multiple files[it] specified for the [TT]-f[tt] option:[BR]",
"Concatenates several energy 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 the command [TT]eneconv -o fixed.edr *.edr[tt] should do",
"the trick. [PAR]",
"With [IT]one file[it] specified for [TT]-f[tt]:[BR]",
"Reads one energy file and writes another, applying the [TT]-dt[tt],",
"[TT]-offset[tt], [TT]-t0[tt] and [TT]-settime[tt] options and",
"converting to a different format if necessary (indicated by file",
"extentions).[PAR]",
"[TT]-settime[tt] is applied first, then [TT]-dt[tt]/[TT]-offset[tt]",
"followed by [TT]-b[tt] and [TT]-e[tt] to select which frames to write."
};
static char *bugs[] = {
"When combining trajectories the sigma and E^2 (necessary for statistics) are not updated correctly. Only the actual energy is correct. One thus has to compute statistics in another way."
};
int in,out=0;
t_enxframe *fr,*fro;
t_energy *lastee,*startee;
int laststep,startstep,startstep_file=0,noutfr;
int nre,nremax,this_nre,nfile,i,j,kkk,nset,*set=NULL;
real t=0;
char **fnms;
char **enm=NULL;
real *readtime,*settime,timestep,t1,tadjust;
char inputstring[STRLEN],*chptr;
bool ok;
int *cont_type;
bool bNewFile,bFirst,bNewOutput;
t_filenm fnm[] = {
{ efENX, "-f", NULL, ffRDMULT },
{ efENX, "-o", "fixed", ffWRITE },
};
#define NFILE asize(fnm)
bool bWrite;
static real delta_t=0.0, toffset=0,scalefac=1;
static bool bSetTime=FALSE;
static bool bSort=TRUE,bError=TRUE;
static real begin=-1;
static real end=-1;
t_pargs pa[] = {
{ "-b", FALSE, etREAL, {&begin},
"First time to use"},
{ "-e", FALSE, etREAL, {&end},
"Last time to use"},
{ "-dt", FALSE, etREAL, {&delta_t},
"Only write out frame when t MOD dt = offset" },
{ "-offset", FALSE, etREAL, {&toffset},
"Time offset for -dt option" },
{ "-settime", FALSE, etBOOL, {&bSetTime},
"Change starting time interactively" },
{ "-sort", FALSE, etBOOL, {&bSort},
"Sort energy files (not frames)"},
{ "-scalefac", FALSE, etREAL, {&scalefac},
"Multiply energy component by this factor" },
{ "-error", FALSE, etBOOL, {&bError},
"Stop on errors in the file" }
};
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_BE_NICE ,
NFILE,fnm,asize(pa),pa,asize(desc),desc,asize(bugs),bugs);
tadjust = 0;
nremax = 0;
nset = 0;
timestep = 0.0;
snew(fnms,argc);
nfile=0;
laststep=startstep=0;
nfile = opt2fns(&fnms,"-f",NFILE,fnm);
if (!nfile)
gmx_fatal(FARGS,"No input files!");
snew(settime,nfile+1);
snew(readtime,nfile+1);
snew(cont_type,nfile+1);
nre=scan_ene_files(fnms,nfile,readtime,×tep,&nremax);
edit_files(fnms,nfile,readtime,settime,cont_type,bSetTime,bSort);
snew(fr,1);
snew(fro,1);
fro->t = -1;
fro->nre = nre;
snew(fro->ener,nremax);
if(nfile>1)
snew(lastee,nremax);
else
lastee=NULL;
snew(startee,nremax);
noutfr=0;
bFirst=TRUE;
for(i=0;i<nfile;i++) {
bNewFile=TRUE;
bNewOutput=TRUE;
in=open_enx(fnms[i],"r");
do_enxnms(in,&this_nre,&enm);
if(i==0) {
if (scalefac != 1)
set = select_it(nre,enm,&nset);
/* write names to the output file */
out=open_enx(opt2fn("-o",NFILE,fnm),"w");
do_enxnms(out,&nre,&enm);
}
/* start reading from the next file */
while((t<(settime[i+1]-GMX_REAL_EPS)) &&
do_enx(in,fr)) {
if(bNewFile) {
startstep_file = fr->step;
tadjust = settime[i] - fr->t;
if(cont_type[i+1]==TIME_LAST) {
settime[i+1] = readtime[i+1]-readtime[i]+settime[i];
cont_type[i+1] = TIME_EXPLICIT;
}
bNewFile = FALSE;
}
fro->step = laststep + fr->step - startstep_file;
t = tadjust + fr->t;
/*bWrite = ((begin<0 || (begin>=0 && (t >= begin-GMX_REAL_EPS))) &&
(end <0 || (end >=0 && (t <= end +GMX_REAL_EPS))) &&
(t < settime[i+1]-GMX_REAL_EPS));*/
bWrite = ((begin<0 || (begin>=0 && (t >= begin-GMX_REAL_EPS))) &&
(end <0 || (end >=0 && (t <= end +GMX_REAL_EPS))) &&
(t < settime[i+1]-0.5*timestep));
if (bError)
if ((end > 0) && (t > end+GMX_REAL_EPS)) {
i = nfile;
break;
}
if (t >= begin-GMX_REAL_EPS) {
if (bFirst) {
bFirst = FALSE;
startstep = fr->step;
if (begin > 0)
copy_ee(fr->ener,startee,nre);
}
update_ee(lastee,laststep,startee,startstep,
fr->ener,fro->step,fro->ener,nre);
}
/* determine if we should write it */
if (bWrite && (delta_t==0 || bRmod(t,toffset,delta_t))) {
fro->t = t;
if(bNewOutput) {
bNewOutput=FALSE;
fprintf(stderr,"\nContinue writing frames from t=%g, step=%d\n",
t,fro->step);
}
if (scalefac != 1) {
for(kkk=0; kkk<nset; kkk++) {
fro->ener[set[kkk]].e *= scalefac;
fro->ener[set[kkk]].eav *= scalefac;
fro->ener[set[kkk]].esum *= scalefac;
}
}
/* Copy restraint stuff */
fro->ndisre = fr->ndisre;
fro->disre_rm3tav = fr->disre_rm3tav;
fro->disre_rt = fr->disre_rt;
fro->nblock = fr->nblock;
fro->nr = fr->nr;
fro->block = fr->block;
do_enx(out,fro);
if (noutfr % 1000 == 0)
fprintf(stderr,"Writing frame time %g ",fro->t);
noutfr++;
}
}
/* copy statistics to old */
if (lastee != NULL) {
update_last_ee(lastee,laststep,fr->ener,fro->step,nre);
laststep = fro->step;
/* remove the last frame from statistics since gromacs2.0
* repeats it in the next file
*/
remove_last_eeframe(lastee,laststep,fr->ener,nre);
/* the old part now has (laststep) values, and the new (step+1) */
printf("laststep=%d step=%d\n",laststep,fro->step);
}
/* set the next time from the last in previous file */
if (cont_type[i+1]==TIME_CONTINUE) {
settime[i+1] = fro->t;
/* in this case we have already written the last frame of
* previous file, so update begin to avoid doubling it
* with the start of the next file
*/
begin = fro->t+0.5*timestep;
/* cont_type[i+1]==TIME_EXPLICIT; */
}
if ((fro->t < end) && (i < nfile-1) &&
(fro->t < settime[i+1]-1.5*timestep))
fprintf(stderr,
"\nWARNING: There might be a gap around t=%g\n",t);
/* move energies to lastee */
close_enx(in);
for(kkk=0; kkk<this_nre; kkk++)
sfree(enm[kkk]);
sfree(enm);
enm = NULL;
fprintf(stderr,"\n");
}
if (noutfr == 0)
fprintf(stderr,"No frames written.\n");
else {
fprintf(stderr,"Last frame written was at step %d, time %f\n",
fro->step,fro->t);
fprintf(stderr,"Wrote %d frames\n",noutfr);
}
thanx(stderr);
return 0;
}
