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;
}
int gmx_analyze(int argc,char *argv[])
{
static const char *desc[] = {
"g_analyze reads an ascii file and analyzes data sets.",
"A line in the input file may start with a time",
"(see option [TT]-time[tt]) and any number of y values may follow.",
"Multiple sets can also be",
"read when they are seperated by & (option [TT]-n[tt]),",
"in this case only one y value is read from each line.",
"All lines starting with # and @ are skipped.",
"All analyses can also be done for the derivative of a set",
"(option [TT]-d[tt]).[PAR]",
"All options, except for [TT]-av[tt] and [TT]-power[tt] assume that the",
"points are equidistant in time.[PAR]",
"g_analyze always shows the average and standard deviation of each",
"set. For each set it also shows the relative deviation of the third",
"and forth cumulant from those of a Gaussian distribution with the same",
"standard deviation.[PAR]",
"Option [TT]-ac[tt] produces the autocorrelation function(s).[PAR]",
"Option [TT]-cc[tt] plots the resemblance of set i with a cosine of",
"i/2 periods. The formula is:[BR]"
"2 (int0-T y(t) cos(i pi t) dt)^2 / int0-T y(t) y(t) dt[BR]",
"This is useful for principal components obtained from covariance",
"analysis, since the principal components of random diffusion are",
"pure cosines.[PAR]",
"Option [TT]-msd[tt] produces the mean square displacement(s).[PAR]",
"Option [TT]-dist[tt] produces distribution plot(s).[PAR]",
"Option [TT]-av[tt] produces the average over the sets.",
"Error bars can be added with the option [TT]-errbar[tt].",
"The errorbars can represent the standard deviation, the error",
"(assuming the points are independent) or the interval containing",
"90% of the points, by discarding 5% of the points at the top and",
"the bottom.[PAR]",
"Option [TT]-ee[tt] produces error estimates using block averaging.",
"A set is divided in a number of blocks and averages are calculated for",
"each block. The error for the total average is calculated from",
"the variance between averages of the m blocks B_i as follows:",
"error^2 = Sum (B_i - <B>)^2 / (m*(m-1)).",
"These errors are plotted as a function of the block size.",
"Also an analytical block average curve is plotted, assuming",
"that the autocorrelation is a sum of two exponentials.",
"The analytical curve for the block average is:[BR]",
"f(t) = sigma sqrt(2/T ( a (tau1 ((exp(-t/tau1) - 1) tau1/t + 1)) +[BR]",
" (1-a) (tau2 ((exp(-t/tau2) - 1) tau2/t + 1)))),[BR]"
"where T is the total time.",
"a, tau1 and tau2 are obtained by fitting f^2(t) to error^2.",
"When the actual block average is very close to the analytical curve,",
"the error is sigma*sqrt(2/T (a tau1 + (1-a) tau2)).",
"The complete derivation is given in",
"B. Hess, J. Chem. Phys. 116:209-217, 2002.[PAR]",
"Option [TT]-filter[tt] prints the RMS high-frequency fluctuation",
"of each set and over all sets with respect to a filtered average.",
"The filter is proportional to cos(pi t/len) where t goes from -len/2",
"to len/2. len is supplied with the option [TT]-filter[tt].",
"This filter reduces oscillations with period len/2 and len by a factor",
"of 0.79 and 0.33 respectively.[PAR]",
"Option [TT]-g[tt] fits the data to the function given with option",
"[TT]-fitfn[tt].[PAR]",
"Option [TT]-power[tt] fits the data to b t^a, which is accomplished",
"by fitting to a t + b on log-log scale. All points after the first",
"zero or negative value are ignored.[PAR]"
"Option [TT]-luzar[tt] performs a Luzar & Chandler kinetics analysis",
"on output from [TT]g_hbond[tt]. The input file can be taken directly",
"from [TT]g_hbond -ac[tt], and then the same result should be produced."
};
static real tb=-1,te=-1,frac=0.5,filtlen=0,binwidth=0.1,aver_start=0;
static bool bHaveT=TRUE,bDer=FALSE,bSubAv=TRUE,bAverCorr=FALSE,bXYdy=FALSE;
static bool bEESEF=FALSE,bEENLC=FALSE,bEeFitAc=FALSE,bPower=FALSE;
static bool bIntegrate=FALSE,bRegression=FALSE,bLuzar=FALSE,bLuzarError=FALSE;
static int nsets_in=1,d=1,nb_min=4,resol=10;
static real temp=298.15,fit_start=1,smooth_tail_start=-1;
/* must correspond to enum avbar* declared at beginning of file */
static const char *avbar_opt[avbarNR+1] = {
NULL, "none", "stddev", "error", "90", NULL
};
t_pargs pa[] = {
{ "-time", FALSE, etBOOL, {&bHaveT},
"Expect a time in the input" },
{ "-b", FALSE, etREAL, {&tb},
"First time to read from set" },
{ "-e", FALSE, etREAL, {&te},
"Last time to read from set" },
{ "-n", FALSE, etINT, {&nsets_in},
"Read # sets seperated by &" },
{ "-d", FALSE, etBOOL, {&bDer},
"Use the derivative" },
{ "-dp", FALSE, etINT, {&d},
"HIDDENThe derivative is the difference over # points" },
{ "-bw", FALSE, etREAL, {&binwidth},
"Binwidth for the distribution" },
{ "-errbar", FALSE, etENUM, {avbar_opt},
"Error bars for -av" },
{ "-integrate",FALSE,etBOOL, {&bIntegrate},
"Integrate data function(s) numerically using trapezium rule" },
{ "-aver_start",FALSE, etREAL, {&aver_start},
"Start averaging the integral from here" },
{ "-xydy", FALSE, etBOOL, {&bXYdy},
"Interpret second data set as error in the y values for integrating" },
{ "-regression",FALSE,etBOOL,{&bRegression},
"Perform a linear regression analysis on the data" },
{ "-luzar", FALSE, etBOOL, {&bLuzar},
"Do a Luzar and Chandler analysis on a correlation function and related as produced by g_hbond. When in addition the -xydy flag is given the second and fourth column will be interpreted as errors in c(t) and n(t)." },
{ "-temp", FALSE, etREAL, {&temp},
"Temperature for the Luzar hydrogen bonding kinetics analysis" },
{ "-fitstart", FALSE, etREAL, {&fit_start},
"Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation" },
{ "-smooth",FALSE, etREAL, {&smooth_tail_start},
"If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau)" },
{ "-nbmin", FALSE, etINT, {&nb_min},
"HIDDENMinimum number of blocks for block averaging" },
{ "-resol", FALSE, etINT, {&resol},
"HIDDENResolution for the block averaging, block size increases with"
" a factor 2^(1/#)" },
{ "-eeexpfit", FALSE, etBOOL, {&bEESEF},
"HIDDENAlways use a single exponential fit for the error estimate" },
{ "-eenlc", FALSE, etBOOL, {&bEENLC},
"HIDDENAllow a negative long-time correlation" },
{ "-eefitac", FALSE, etBOOL, {&bEeFitAc},
"HIDDENAlso plot analytical block average using a autocorrelation fit" },
{ "-filter", FALSE, etREAL, {&filtlen},
"Print the high-frequency fluctuation after filtering with a cosine filter of length #" },
{ "-power", FALSE, etBOOL, {&bPower},
"Fit data to: b t^a" },
{ "-subav", FALSE, etBOOL, {&bSubAv},
"Subtract the average before autocorrelating" },
{ "-oneacf", FALSE, etBOOL, {&bAverCorr},
"Calculate one ACF over all sets" }
};
#define NPA asize(pa)
FILE *out,*out_fit;
int n,nlast,s,nset,i,j=0;
real **val,*t,dt,tot,error;
double *av,*sig,cum1,cum2,cum3,cum4,db;
char *acfile,*msdfile,*ccfile,*distfile,*avfile,*eefile,*fitfile;
t_filenm fnm[] = {
{ efXVG, "-f", "graph", ffREAD },
{ efXVG, "-ac", "autocorr", ffOPTWR },
{ efXVG, "-msd", "msd", ffOPTWR },
{ efXVG, "-cc", "coscont", ffOPTWR },
{ efXVG, "-dist", "distr", ffOPTWR },
{ efXVG, "-av", "average", ffOPTWR },
{ efXVG, "-ee", "errest", ffOPTWR },
{ efLOG, "-g", "fitlog", ffOPTWR }
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL);
acfile = opt2fn_null("-ac",NFILE,fnm);
msdfile = opt2fn_null("-msd",NFILE,fnm);
ccfile = opt2fn_null("-cc",NFILE,fnm);
distfile = opt2fn_null("-dist",NFILE,fnm);
avfile = opt2fn_null("-av",NFILE,fnm);
eefile = opt2fn_null("-ee",NFILE,fnm);
if (opt2parg_bSet("-fitfn",npargs,ppa))
fitfile = opt2fn("-g",NFILE,fnm);
else
fitfile = opt2fn_null("-g",NFILE,fnm);
val=read_xvg_time(opt2fn("-f",NFILE,fnm),bHaveT,
opt2parg_bSet("-b",npargs,ppa),tb,
opt2parg_bSet("-e",npargs,ppa),te,
nsets_in,&nset,&n,&dt,&t);
printf("Read %d sets of %d points, dt = %g\n\n",nset,n,dt);
if (bDer) {
printf("Calculating the derivative as (f[i+%d]-f[i])/(%d*dt)\n\n",
d,d);
n -= d;
for(s=0; s<nset; s++)
for(i=0; (i<n); i++)
val[s][i] = (val[s][i+d]-val[s][i])/(d*dt);
}
if (bIntegrate) {
real sum,stddev;
printf("Calculating the integral using the trapezium rule\n");
if (bXYdy) {
sum = evaluate_integral(n,t,val[0],val[1],aver_start,&stddev);
printf("Integral %10.3f +/- %10.5f\n",sum,stddev);
}
else {
for(s=0; s<nset; s++) {
sum = evaluate_integral(n,t,val[s],NULL,aver_start,&stddev);
printf("Integral %d %10.5f +/- %10.5f\n",s+1,sum,stddev);
}
}
}
if (fitfile) {
out_fit = ffopen(fitfile,"w");
if (bXYdy && nset>=2) {
do_fit(out_fit,0,TRUE,n,t,val,npargs,ppa);
} else {
for(s=0; s<nset; s++)
do_fit(out_fit,s,FALSE,n,t,val,npargs,ppa);
}
fclose(out_fit);
}
printf(" std. dev. relative deviation of\n");
printf(" standard --------- cumulants from those of\n");
printf("set average deviation sqrt(n-1) a Gaussian distribition\n");
printf(" cum. 3 cum. 4\n");
snew(av,nset);
snew(sig,nset);
for(s=0; (s<nset); s++) {
cum1 = 0;
cum2 = 0;
cum3 = 0;
cum4 = 0;
for(i=0; (i<n); i++)
cum1 += val[s][i];
cum1 /= n;
for(i=0; (i<n); i++) {
db = val[s][i]-cum1;
cum2 += db*db;
cum3 += db*db*db;
cum4 += db*db*db*db;
}
cum2 /= n;
cum3 /= n;
cum4 /= n;
av[s] = cum1;
sig[s] = sqrt(cum2);
if (n > 1)
error = sqrt(cum2/(n-1));
else
error = 0;
printf("SS%d %13.6e %12.6e %12.6e %6.3f %6.3f\n",
s+1,av[s],sig[s],error,
sig[s] ? cum3/(sig[s]*sig[s]*sig[s]*sqrt(8/M_PI)) : 0,
sig[s] ? cum4/(sig[s]*sig[s]*sig[s]*sig[s]*3)-1 : 0);
}
printf("\n");
if (filtlen)
filter(filtlen,n,nset,val,dt);
if (msdfile) {
out=xvgropen(msdfile,"Mean square displacement",
"time","MSD (nm\\S2\\N)");
nlast = (int)(n*frac);
for(s=0; s<nset; s++) {
for(j=0; j<=nlast; j++) {
if (j % 100 == 0)
fprintf(stderr,"\r%d",j);
tot=0;
for(i=0; i<n-j; i++)
tot += sqr(val[s][i]-val[s][i+j]);
tot /= (real)(n-j);
fprintf(out," %g %8g\n",dt*j,tot);
}
if (s<nset-1)
fprintf(out,"&\n");
}
fclose(out);
fprintf(stderr,"\r%d, time=%g\n",j-1,(j-1)*dt);
}
if (ccfile)
plot_coscont(ccfile,n,nset,val);
if (distfile)
histogram(distfile,binwidth,n,nset,val);
if (avfile)
average(avfile,nenum(avbar_opt),n,nset,val,t);
if (eefile)
estimate_error(eefile,nb_min,resol,n,nset,av,sig,val,dt,
bEeFitAc,bEESEF,bEENLC);
if (bPower)
power_fit(n,nset,val,t);
if (acfile) {
if (bSubAv)
for(s=0; s<nset; s++)
for(i=0; i<n; i++)
val[s][i] -= av[s];
do_autocorr(acfile,"Autocorrelation",n,nset,val,dt,
eacNormal,bAverCorr);
}
if (bRegression)
regression_analysis(n,bXYdy,t,val);
if (bLuzar)
luzar_correl(n,t,nset,val,temp,bXYdy,fit_start,smooth_tail_start);
view_all(NFILE, fnm);
thanx(stderr);
return 0;
}
int gmx_analyze(int argc, char *argv[])
{
static const char *desc[] = {
"[TT]g_analyze[tt] reads an ASCII file and analyzes data sets.",
"A line in the input file may start with a time",
"(see option [TT]-time[tt]) and any number of [IT]y[it]-values may follow.",
"Multiple sets can also be",
"read when they are separated by & (option [TT]-n[tt]);",
"in this case only one [IT]y[it]-value is read from each line.",
"All lines starting with # and @ are skipped.",
"All analyses can also be done for the derivative of a set",
"(option [TT]-d[tt]).[PAR]",
"All options, except for [TT]-av[tt] and [TT]-power[tt], assume that the",
"points are equidistant in time.[PAR]",
"[TT]g_analyze[tt] always shows the average and standard deviation of each",
"set, as well as the relative deviation of the third",
"and fourth cumulant from those of a Gaussian distribution with the same",
"standard deviation.[PAR]",
"Option [TT]-ac[tt] produces the autocorrelation function(s).",
"Be sure that the time interval between data points is",
"much shorter than the time scale of the autocorrelation.[PAR]",
"Option [TT]-cc[tt] plots the resemblance of set i with a cosine of",
"i/2 periods. The formula is:[BR]"
"[MATH]2 ([INT][FROM]0[from][TO]T[to][int] y(t) [COS]i [GRK]pi[grk] t[cos] dt)^2 / [INT][FROM]0[from][TO]T[to][int] y^2(t) dt[math][BR]",
"This is useful for principal components obtained from covariance",
"analysis, since the principal components of random diffusion are",
"pure cosines.[PAR]",
"Option [TT]-msd[tt] produces the mean square displacement(s).[PAR]",
"Option [TT]-dist[tt] produces distribution plot(s).[PAR]",
"Option [TT]-av[tt] produces the average over the sets.",
"Error bars can be added with the option [TT]-errbar[tt].",
"The errorbars can represent the standard deviation, the error",
"(assuming the points are independent) or the interval containing",
"90% of the points, by discarding 5% of the points at the top and",
"the bottom.[PAR]",
"Option [TT]-ee[tt] produces error estimates using block averaging.",
"A set is divided in a number of blocks and averages are calculated for",
"each block. The error for the total average is calculated from",
"the variance between averages of the m blocks B[SUB]i[sub] as follows:",
"error^2 = [SUM][sum] (B[SUB]i[sub] - [CHEVRON]B[chevron])^2 / (m*(m-1)).",
"These errors are plotted as a function of the block size.",
"Also an analytical block average curve is plotted, assuming",
"that the autocorrelation is a sum of two exponentials.",
"The analytical curve for the block average is:[BR]",
"[MATH]f(t) = [GRK]sigma[grk][TT]*[tt][SQRT]2/T ( [GRK]alpha[grk] ([GRK]tau[grk][SUB]1[sub] (([EXP]-t/[GRK]tau[grk][SUB]1[sub][exp] - 1) [GRK]tau[grk][SUB]1[sub]/t + 1)) +[BR]",
" (1-[GRK]alpha[grk]) ([GRK]tau[grk][SUB]2[sub] (([EXP]-t/[GRK]tau[grk][SUB]2[sub][exp] - 1) [GRK]tau[grk][SUB]2[sub]/t + 1)))[sqrt][math],[BR]"
"where T is the total time.",
"[GRK]alpha[grk], [GRK]tau[grk][SUB]1[sub] and [GRK]tau[grk][SUB]2[sub] are obtained by fitting f^2(t) to error^2.",
"When the actual block average is very close to the analytical curve,",
"the error is [MATH][GRK]sigma[grk][TT]*[tt][SQRT]2/T (a [GRK]tau[grk][SUB]1[sub] + (1-a) [GRK]tau[grk][SUB]2[sub])[sqrt][math].",
"The complete derivation is given in",
"B. Hess, J. Chem. Phys. 116:209-217, 2002.[PAR]",
"Option [TT]-bal[tt] finds and subtracts the ultrafast \"ballistic\"",
"component from a hydrogen bond autocorrelation function by the fitting",
"of a sum of exponentials, as described in e.g.",
"O. Markovitch, J. Chem. Phys. 129:084505, 2008. The fastest term",
"is the one with the most negative coefficient in the exponential,",
"or with [TT]-d[tt], the one with most negative time derivative at time 0.",
"[TT]-nbalexp[tt] sets the number of exponentials to fit.[PAR]",
"Option [TT]-gem[tt] fits bimolecular rate constants ka and kb",
"(and optionally kD) to the hydrogen bond autocorrelation function",
"according to the reversible geminate recombination model. Removal of",
"the ballistic component first is strongly advised. The model is presented in",
"O. Markovitch, J. Chem. Phys. 129:084505, 2008.[PAR]",
"Option [TT]-filter[tt] prints the RMS high-frequency fluctuation",
"of each set and over all sets with respect to a filtered average.",
"The filter is proportional to cos([GRK]pi[grk] t/len) where t goes from -len/2",
"to len/2. len is supplied with the option [TT]-filter[tt].",
"This filter reduces oscillations with period len/2 and len by a factor",
"of 0.79 and 0.33 respectively.[PAR]",
"Option [TT]-g[tt] fits the data to the function given with option",
"[TT]-fitfn[tt].[PAR]",
"Option [TT]-power[tt] fits the data to [MATH]b t^a[math], which is accomplished",
"by fitting to [MATH]a t + b[math] on log-log scale. All points after the first",
"zero or with a negative value are ignored.[PAR]"
"Option [TT]-luzar[tt] performs a Luzar & Chandler kinetics analysis",
"on output from [TT]g_hbond[tt]. The input file can be taken directly",
"from [TT]g_hbond -ac[tt], and then the same result should be produced."
};
static real tb = -1, te = -1, frac = 0.5, filtlen = 0, binwidth = 0.1, aver_start = 0;
static gmx_bool bHaveT = TRUE, bDer = FALSE, bSubAv = TRUE, bAverCorr = FALSE, bXYdy = FALSE;
static gmx_bool bEESEF = FALSE, bEENLC = FALSE, bEeFitAc = FALSE, bPower = FALSE;
static gmx_bool bIntegrate = FALSE, bRegression = FALSE, bLuzar = FALSE, bLuzarError = FALSE;
static int nsets_in = 1, d = 1, nb_min = 4, resol = 10, nBalExp = 4, nFitPoints = 100;
static real temp = 298.15, fit_start = 1, fit_end = 60, smooth_tail_start = -1, balTime = 0.2, diffusion = 5e-5, rcut = 0.35;
/* must correspond to enum avbar* declared at beginning of file */
static const char *avbar_opt[avbarNR+1] = {
NULL, "none", "stddev", "error", "90", NULL
};
t_pargs pa[] = {
{ "-time", FALSE, etBOOL, {&bHaveT},
"Expect a time in the input" },
{ "-b", FALSE, etREAL, {&tb},
"First time to read from set" },
{ "-e", FALSE, etREAL, {&te},
"Last time to read from set" },
{ "-n", FALSE, etINT, {&nsets_in},
"Read this number of sets separated by &" },
{ "-d", FALSE, etBOOL, {&bDer},
"Use the derivative" },
{ "-dp", FALSE, etINT, {&d},
"HIDDENThe derivative is the difference over this number of points" },
{ "-bw", FALSE, etREAL, {&binwidth},
"Binwidth for the distribution" },
{ "-errbar", FALSE, etENUM, {avbar_opt},
"Error bars for [TT]-av[tt]" },
{ "-integrate", FALSE, etBOOL, {&bIntegrate},
"Integrate data function(s) numerically using trapezium rule" },
{ "-aver_start", FALSE, etREAL, {&aver_start},
"Start averaging the integral from here" },
{ "-xydy", FALSE, etBOOL, {&bXYdy},
"Interpret second data set as error in the y values for integrating" },
{ "-regression", FALSE, etBOOL, {&bRegression},
"Perform a linear regression analysis on the data. If [TT]-xydy[tt] is set a second set will be interpreted as the error bar in the Y value. Otherwise, if multiple data sets are present a multilinear regression will be performed yielding the constant A that minimize [MATH][GRK]chi[grk]^2 = (y - A[SUB]0[sub] x[SUB]0[sub] - A[SUB]1[sub] x[SUB]1[sub] - ... - A[SUB]N[sub] x[SUB]N[sub])^2[math] where now Y is the first data set in the input file and x[SUB]i[sub] the others. Do read the information at the option [TT]-time[tt]." },
{ "-luzar", FALSE, etBOOL, {&bLuzar},
"Do a Luzar and Chandler analysis on a correlation function and related as produced by [TT]g_hbond[tt]. When in addition the [TT]-xydy[tt] flag is given the second and fourth column will be interpreted as errors in c(t) and n(t)." },
{ "-temp", FALSE, etREAL, {&temp},
"Temperature for the Luzar hydrogen bonding kinetics analysis (K)" },
{ "-fitstart", FALSE, etREAL, {&fit_start},
"Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation" },
{ "-fitend", FALSE, etREAL, {&fit_end},
"Time (ps) where to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. Only with [TT]-gem[tt]" },
{ "-smooth", FALSE, etREAL, {&smooth_tail_start},
"If this value is >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: [MATH]y = A [EXP]-x/[GRK]tau[grk][exp][math]" },
{ "-nbmin", FALSE, etINT, {&nb_min},
"HIDDENMinimum number of blocks for block averaging" },
{ "-resol", FALSE, etINT, {&resol},
"HIDDENResolution for the block averaging, block size increases with"
" a factor 2^(1/resol)" },
{ "-eeexpfit", FALSE, etBOOL, {&bEESEF},
"HIDDENAlways use a single exponential fit for the error estimate" },
{ "-eenlc", FALSE, etBOOL, {&bEENLC},
"HIDDENAllow a negative long-time correlation" },
{ "-eefitac", FALSE, etBOOL, {&bEeFitAc},
"HIDDENAlso plot analytical block average using a autocorrelation fit" },
{ "-filter", FALSE, etREAL, {&filtlen},
"Print the high-frequency fluctuation after filtering with a cosine filter of this length" },
{ "-power", FALSE, etBOOL, {&bPower},
"Fit data to: b t^a" },
{ "-subav", FALSE, etBOOL, {&bSubAv},
"Subtract the average before autocorrelating" },
{ "-oneacf", FALSE, etBOOL, {&bAverCorr},
"Calculate one ACF over all sets" },
{ "-nbalexp", FALSE, etINT, {&nBalExp},
"HIDDENNumber of exponentials to fit to the ultrafast component" },
{ "-baltime", FALSE, etREAL, {&balTime},
"HIDDENTime up to which the ballistic component will be fitted" },
/* { "-gemnp", FALSE, etINT, {&nFitPoints}, */
/* "HIDDENNumber of data points taken from the ACF to use for fitting to rev. gem. recomb. model."}, */
/* { "-rcut", FALSE, etREAL, {&rcut}, */
/* "Cut-off for hydrogen bonds in geminate algorithms" }, */
/* { "-gemtype", FALSE, etENUM, {gemType}, */
/* "What type of gminate recombination to use"}, */
/* { "-D", FALSE, etREAL, {&diffusion}, */
/* "The self diffusion coefficient which is used for the reversible geminate recombination model."} */
};
#define NPA asize(pa)
FILE *out, *out_fit;
int n, nlast, s, nset, i, j = 0;
real **val, *t, dt, tot, error;
double *av, *sig, cum1, cum2, cum3, cum4, db;
const char *acfile, *msdfile, *ccfile, *distfile, *avfile, *eefile, *balfile, *gemfile, *fitfile;
output_env_t oenv;
t_filenm fnm[] = {
{ efXVG, "-f", "graph", ffREAD },
{ efXVG, "-ac", "autocorr", ffOPTWR },
{ efXVG, "-msd", "msd", ffOPTWR },
{ efXVG, "-cc", "coscont", ffOPTWR },
{ efXVG, "-dist", "distr", ffOPTWR },
{ efXVG, "-av", "average", ffOPTWR },
{ efXVG, "-ee", "errest", ffOPTWR },
{ efXVG, "-bal", "ballisitc", ffOPTWR },
/* { efXVG, "-gem", "geminate", ffOPTWR }, */
{ efLOG, "-g", "fitlog", ffOPTWR }
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv);
acfile = opt2fn_null("-ac", NFILE, fnm);
msdfile = opt2fn_null("-msd", NFILE, fnm);
ccfile = opt2fn_null("-cc", NFILE, fnm);
distfile = opt2fn_null("-dist", NFILE, fnm);
avfile = opt2fn_null("-av", NFILE, fnm);
eefile = opt2fn_null("-ee", NFILE, fnm);
balfile = opt2fn_null("-bal", NFILE, fnm);
/* gemfile = opt2fn_null("-gem",NFILE,fnm); */
/* When doing autocorrelation we don't want a fitlog for fitting
* the function itself (not the acf) when the user did not ask for it.
*/
if (opt2parg_bSet("-fitfn", npargs, ppa) && acfile == NULL)
{
fitfile = opt2fn("-g", NFILE, fnm);
}
else
{
fitfile = opt2fn_null("-g", NFILE, fnm);
}
val = read_xvg_time(opt2fn("-f", NFILE, fnm), bHaveT,
opt2parg_bSet("-b", npargs, ppa), tb,
opt2parg_bSet("-e", npargs, ppa), te,
nsets_in, &nset, &n, &dt, &t);
printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt);
if (bDer)
{
printf("Calculating the derivative as (f[i+%d]-f[i])/(%d*dt)\n\n",
d, d);
n -= d;
for (s = 0; s < nset; s++)
{
for (i = 0; (i < n); i++)
{
val[s][i] = (val[s][i+d]-val[s][i])/(d*dt);
}
}
}
if (bIntegrate)
{
real sum, stddev;
printf("Calculating the integral using the trapezium rule\n");
if (bXYdy)
{
sum = evaluate_integral(n, t, val[0], val[1], aver_start, &stddev);
printf("Integral %10.3f +/- %10.5f\n", sum, stddev);
}
else
{
for (s = 0; s < nset; s++)
{
sum = evaluate_integral(n, t, val[s], NULL, aver_start, &stddev);
printf("Integral %d %10.5f +/- %10.5f\n", s+1, sum, stddev);
}
}
}
if (fitfile != NULL)
{
out_fit = ffopen(fitfile, "w");
if (bXYdy && nset >= 2)
{
do_fit(out_fit, 0, TRUE, n, t, val, npargs, ppa, oenv);
}
else
{
for (s = 0; s < nset; s++)
{
do_fit(out_fit, s, FALSE, n, t, val, npargs, ppa, oenv);
}
}
ffclose(out_fit);
}
printf(" std. dev. relative deviation of\n");
printf(" standard --------- cumulants from those of\n");
printf("set average deviation sqrt(n-1) a Gaussian distribition\n");
printf(" cum. 3 cum. 4\n");
snew(av, nset);
snew(sig, nset);
for (s = 0; (s < nset); s++)
{
cum1 = 0;
cum2 = 0;
cum3 = 0;
cum4 = 0;
for (i = 0; (i < n); i++)
{
cum1 += val[s][i];
}
cum1 /= n;
for (i = 0; (i < n); i++)
{
db = val[s][i]-cum1;
cum2 += db*db;
cum3 += db*db*db;
cum4 += db*db*db*db;
}
cum2 /= n;
cum3 /= n;
cum4 /= n;
av[s] = cum1;
sig[s] = sqrt(cum2);
if (n > 1)
{
error = sqrt(cum2/(n-1));
}
else
{
error = 0;
}
printf("SS%d %13.6e %12.6e %12.6e %6.3f %6.3f\n",
s+1, av[s], sig[s], error,
sig[s] ? cum3/(sig[s]*sig[s]*sig[s]*sqrt(8/M_PI)) : 0,
sig[s] ? cum4/(sig[s]*sig[s]*sig[s]*sig[s]*3)-1 : 0);
}
printf("\n");
if (filtlen)
{
filter(filtlen, n, nset, val, dt);
}
if (msdfile)
{
out = xvgropen(msdfile, "Mean square displacement",
"time", "MSD (nm\\S2\\N)", oenv);
nlast = (int)(n*frac);
for (s = 0; s < nset; s++)
{
for (j = 0; j <= nlast; j++)
{
if (j % 100 == 0)
{
fprintf(stderr, "\r%d", j);
}
tot = 0;
for (i = 0; i < n-j; i++)
{
tot += sqr(val[s][i]-val[s][i+j]);
}
tot /= (real)(n-j);
fprintf(out, " %g %8g\n", dt*j, tot);
}
if (s < nset-1)
{
fprintf(out, "&\n");
}
}
ffclose(out);
fprintf(stderr, "\r%d, time=%g\n", j-1, (j-1)*dt);
}
if (ccfile)
{
plot_coscont(ccfile, n, nset, val, oenv);
}
if (distfile)
{
histogram(distfile, binwidth, n, nset, val, oenv);
}
if (avfile)
{
average(avfile, nenum(avbar_opt), n, nset, val, t);
}
if (eefile)
{
estimate_error(eefile, nb_min, resol, n, nset, av, sig, val, dt,
bEeFitAc, bEESEF, bEENLC, oenv);
}
if (balfile)
{
do_ballistic(balfile, n, t, val, nset, balTime, nBalExp, oenv);
}
/* if (gemfile) */
/* do_geminate(gemfile,n,t,val,nset,diffusion,rcut,balTime, */
/* nFitPoints, fit_start, fit_end, oenv); */
if (bPower)
{
power_fit(n, nset, val, t);
}
if (acfile != NULL)
{
if (bSubAv)
{
for (s = 0; s < nset; s++)
{
for (i = 0; i < n; i++)
{
val[s][i] -= av[s];
}
}
}
do_autocorr(acfile, oenv, "Autocorrelation", n, nset, val, dt,
eacNormal, bAverCorr);
}
if (bRegression)
{
regression_analysis(n, bXYdy, t, nset, val);
}
if (bLuzar)
{
luzar_correl(n, t, nset, val, temp, bXYdy, fit_start, smooth_tail_start, oenv);
}
view_all(oenv, NFILE, fnm);
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;
}
int gmx_sham(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] makes multi-dimensional free-energy, enthalpy and entropy plots.",
"[THISMODULE] reads one or more [TT].xvg[tt] files and analyzes data sets.",
"The basic purpose of [THISMODULE] is to plot Gibbs free energy landscapes",
"(option [TT]-ls[tt])",
"by Bolzmann inverting multi-dimensional histograms (option [TT]-lp[tt]),",
"but it can also",
"make enthalpy (option [TT]-lsh[tt]) and entropy (option [TT]-lss[tt])",
"plots. The histograms can be made for any quantities the user supplies.",
"A line in the input file may start with a time",
"(see option [TT]-time[tt]) and any number of [IT]y[it]-values may follow.",
"Multiple sets can also be",
"read when they are separated by & (option [TT]-n[tt]),",
"in this case only one [IT]y[it]-value is read from each line.",
"All lines starting with # and @ are skipped.",
"[PAR]",
"Option [TT]-ge[tt] can be used to supply a file with free energies",
"when the ensemble is not a Boltzmann ensemble, but needs to be biased",
"by this free energy. One free energy value is required for each",
"(multi-dimensional) data point in the [TT]-f[tt] input.",
"[PAR]",
"Option [TT]-ene[tt] can be used to supply a file with energies.",
"These energies are used as a weighting function in the single",
"histogram analysis method by Kumar et al. When temperatures",
"are supplied (as a second column in the file), an experimental",
"weighting scheme is applied. In addition the vales",
"are used for making enthalpy and entropy plots.",
"[PAR]",
"With option [TT]-dim[tt], dimensions can be gives for distances.",
"When a distance is 2- or 3-dimensional, the circumference or surface",
"sampled by two particles increases with increasing distance.",
"Depending on what one would like to show, one can choose to correct",
"the histogram and free-energy for this volume effect.",
"The probability is normalized by r and r^2 for dimensions of 2 and 3, ",
"respectively.",
"A value of -1 is used to indicate an angle in degrees between two",
"vectors: a sin(angle) normalization will be applied.",
"[BB]Note[bb] that for angles between vectors the inner-product or cosine",
"is the natural quantity to use, as it will produce bins of the same",
"volume."
};
static real tb = -1, te = -1, frac = 0.5, filtlen = 0;
static gmx_bool bHaveT = TRUE, bDer = FALSE, bSubAv = TRUE, bAverCorr = FALSE, bXYdy = FALSE;
static gmx_bool bEESEF = FALSE, bEENLC = FALSE, bEeFitAc = FALSE, bPower = FALSE;
static gmx_bool bShamEner = TRUE, bSham = TRUE;
static real Tref = 298.15, pmin = 0, ttol = 0, pmax = 0, gmax = 0, emin = 0, emax = 0;
static rvec nrdim = {1, 1, 1};
static rvec nrbox = {32, 32, 32};
static rvec xmin = {0, 0, 0}, xmax = {1, 1, 1};
static int nsets_in = 1, nb_min = 4, resol = 10, nlevels = 25;
t_pargs pa[] = {
{ "-time", FALSE, etBOOL, {&bHaveT},
"Expect a time in the input" },
{ "-b", FALSE, etREAL, {&tb},
"First time to read from set" },
{ "-e", FALSE, etREAL, {&te},
"Last time to read from set" },
{ "-ttol", FALSE, etREAL, {&ttol},
"Tolerance on time in appropriate units (usually ps)" },
{ "-n", FALSE, etINT, {&nsets_in},
"Read this number of sets separated by lines containing only an ampersand" },
{ "-d", FALSE, etBOOL, {&bDer},
"Use the derivative" },
{ "-sham", FALSE, etBOOL, {&bSham},
"Turn off energy weighting even if energies are given" },
{ "-tsham", FALSE, etREAL, {&Tref},
"Temperature for single histogram analysis" },
{ "-pmin", FALSE, etREAL, {&pmin},
"Minimum probability. Anything lower than this will be set to zero" },
{ "-dim", FALSE, etRVEC, {nrdim},
"Dimensions for distances, used for volume correction (max 3 values, dimensions > 3 will get the same value as the last)" },
{ "-ngrid", FALSE, etRVEC, {nrbox},
"Number of bins for energy landscapes (max 3 values, dimensions > 3 will get the same value as the last)" },
{ "-xmin", FALSE, etRVEC, {xmin},
"Minimum for the axes in energy landscape (see above for > 3 dimensions)" },
{ "-xmax", FALSE, etRVEC, {xmax},
"Maximum for the axes in energy landscape (see above for > 3 dimensions)" },
{ "-pmax", FALSE, etREAL, {&pmax},
"Maximum probability in output, default is calculate" },
{ "-gmax", FALSE, etREAL, {&gmax},
"Maximum free energy in output, default is calculate" },
{ "-emin", FALSE, etREAL, {&emin},
"Minimum enthalpy in output, default is calculate" },
{ "-emax", FALSE, etREAL, {&emax},
"Maximum enthalpy in output, default is calculate" },
{ "-nlevels", FALSE, etINT, {&nlevels},
"Number of levels for energy landscape" },
};
#define NPA asize(pa)
FILE *out;
int n, e_n, nlast, s, nset, e_nset, d_nset, i, j = 0, *idim, *ibox;
real **val, **et_val, *t, *e_t, e_dt, d_dt, dt, tot, error;
real *rmin, *rmax;
double *av, *sig, cum1, cum2, cum3, cum4, db;
const char *fn_ge, *fn_ene;
output_env_t oenv;
gmx_int64_t num_grid_points;
t_filenm fnm[] = {
{ efXVG, "-f", "graph", ffREAD },
{ efXVG, "-ge", "gibbs", ffOPTRD },
{ efXVG, "-ene", "esham", ffOPTRD },
{ efXVG, "-dist", "ener", ffOPTWR },
{ efXVG, "-histo", "edist", ffOPTWR },
{ efNDX, "-bin", "bindex", ffOPTWR },
{ efXPM, "-lp", "prob", ffOPTWR },
{ efXPM, "-ls", "gibbs", ffOPTWR },
{ efXPM, "-lsh", "enthalpy", ffOPTWR },
{ efXPM, "-lss", "entropy", ffOPTWR },
{ efPDB, "-ls3", "gibbs3", ffOPTWR },
{ efLOG, "-g", "shamlog", ffOPTWR }
};
#define NFILE asize(fnm)
int npargs;
npargs = asize(pa);
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, npargs, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
val = read_xvg_time(opt2fn("-f", NFILE, fnm), bHaveT,
opt2parg_bSet("-b", npargs, pa), tb-ttol,
opt2parg_bSet("-e", npargs, pa), te+ttol,
nsets_in, &nset, &n, &dt, &t);
printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt);
fn_ge = opt2fn_null("-ge", NFILE, fnm);
fn_ene = opt2fn_null("-ene", NFILE, fnm);
if (fn_ge && fn_ene)
{
gmx_fatal(FARGS, "Can not do free energy and energy corrections at the same time");
}
if (fn_ge || fn_ene)
{
et_val = read_xvg_time(fn_ge ? fn_ge : fn_ene, bHaveT,
opt2parg_bSet("-b", npargs, pa), tb-ttol,
opt2parg_bSet("-e", npargs, pa), te+ttol,
1, &e_nset, &e_n, &e_dt, &e_t);
if (fn_ge)
{
if (e_nset != 1)
{
gmx_fatal(FARGS, "Can only handle one free energy component in %s",
fn_ge);
}
}
else
{
if (e_nset != 1 && e_nset != 2)
{
gmx_fatal(FARGS, "Can only handle one energy component or one energy and one T in %s",
fn_ene);
}
}
if (e_n != n)
{
gmx_fatal(FARGS, "Number of energies (%d) does not match number of entries (%d) in %s", e_n, n, opt2fn("-f", NFILE, fnm));
}
}
else
{
et_val = NULL;
}
if (fn_ene && et_val)
{
ehisto(opt2fn("-histo", NFILE, fnm), e_n, et_val, oenv);
}
snew(idim, max(3, nset));
snew(ibox, max(3, nset));
snew(rmin, max(3, nset));
snew(rmax, max(3, nset));
for (i = 0; (i < min(3, nset)); i++)
{
idim[i] = nrdim[i];
ibox[i] = nrbox[i];
rmin[i] = xmin[i];
rmax[i] = xmax[i];
}
for (; (i < nset); i++)
{
idim[i] = nrdim[2];
ibox[i] = nrbox[2];
rmin[i] = xmin[2];
rmax[i] = xmax[2];
}
/* Check that the grid size is manageable. */
num_grid_points = ibox[0];
for (i = 1; i < nset; i++)
{
gmx_int64_t result;
if (!check_int_multiply_for_overflow(num_grid_points, ibox[i], &result))
{
gmx_fatal(FARGS,
"The number of dimensions and grid points is too large for this tool.\n");
}
num_grid_points = result;
}
/* The number of grid points fits in a gmx_int64_t. */
do_sham(opt2fn("-dist", NFILE, fnm), opt2fn("-bin", NFILE, fnm),
opt2fn("-lp", NFILE, fnm),
opt2fn("-ls", NFILE, fnm), opt2fn("-lsh", NFILE, fnm),
opt2fn("-lss", NFILE, fnm),
opt2fn("-ls3", NFILE, fnm), opt2fn("-g", NFILE, fnm),
n, nset, val, fn_ge != NULL, e_nset, et_val, Tref,
pmax, gmax,
opt2parg_bSet("-emin", NPA, pa) ? &emin : NULL,
opt2parg_bSet("-emax", NPA, pa) ? &emax : NULL,
nlevels, pmin,
idim, ibox,
opt2parg_bSet("-xmin", NPA, pa), rmin,
opt2parg_bSet("-xmax", NPA, pa), rmax);
return 0;
}
int gmx_kinetics(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_kinetics[tt] reads two [TT].xvg[tt] files, each one containing data for N replicas.",
"The first file contains the temperature of each replica at each timestep,",
"and the second contains real values that can be interpreted as",
"an indicator for folding. If the value in the file is larger than",
"the cutoff it is taken to be unfolded and the other way around.[PAR]",
"From these data an estimate of the forward and backward rate constants",
"for folding is made at a reference temperature. In addition,",
"a theoretical melting curve and free energy as a function of temperature",
"are printed in an [TT].xvg[tt] file.[PAR]",
"The user can give a max value to be regarded as intermediate",
"([TT]-ucut[tt]), which, when given will trigger the use of an intermediate state",
"in the algorithm to be defined as those structures that have",
"cutoff < DATA < ucut. Structures with DATA values larger than ucut will",
"not be regarded as potential folders. In this case 8 parameters are optimized.[PAR]",
"The average fraction foled is printed in an [TT].xvg[tt] file together with the fit to it.",
"If an intermediate is used a further file will show the build of the intermediate and the fit to that process.[PAR]",
"The program can also be used with continuous variables (by setting",
"[TT]-nodiscrete[tt]). In this case kinetics of other processes can be",
"studied. This is very much a work in progress and hence the manual",
"(this information) is lagging behind somewhat.[PAR]",
"In order to compile this program you need access to the GNU",
"scientific library."
};
static int nreplica = 1;
static real tref = 298.15;
static real cutoff = 0.2;
static real ucut = 0.0;
static real Euf = 10;
static real Efu = 30;
static real Ei = 10;
static gmx_bool bHaveT = TRUE;
static real t0 = -1;
static real t1 = -1;
static real tb = 0;
static real te = 0;
static real tol = 1e-3;
static int maxiter = 100;
static int skip = 0;
static int nmult = 1;
static gmx_bool bBack = TRUE;
static gmx_bool bSplit = TRUE;
static gmx_bool bSum = TRUE;
static gmx_bool bDiscrete = TRUE;
t_pargs pa[] = {
{ "-time", FALSE, etBOOL, {&bHaveT},
"Expect a time in the input" },
{ "-b", FALSE, etREAL, {&tb},
"First time to read from set" },
{ "-e", FALSE, etREAL, {&te},
"Last time to read from set" },
{ "-bfit", FALSE, etREAL, {&t0},
"Time to start the fit from" },
{ "-efit", FALSE, etREAL, {&t1},
"Time to end the fit" },
{ "-T", FALSE, etREAL, {&tref},
"Reference temperature for computing rate constants" },
{ "-n", FALSE, etINT, {&nreplica},
"Read data for this number of replicas. Only necessary when files are written in xmgrace format using @type and & as delimiters." },
{ "-cut", FALSE, etREAL, {&cutoff},
"Cut-off (max) value for regarding a structure as folded" },
{ "-ucut", FALSE, etREAL, {&ucut},
"Cut-off (max) value for regarding a structure as intermediate (if not folded)" },
{ "-euf", FALSE, etREAL, {&Euf},
"Initial guess for energy of activation for folding (kJ/mol)" },
{ "-efu", FALSE, etREAL, {&Efu},
"Initial guess for energy of activation for unfolding (kJ/mol)" },
{ "-ei", FALSE, etREAL, {&Ei},
"Initial guess for energy of activation for intermediates (kJ/mol)" },
{ "-maxiter", FALSE, etINT, {&maxiter},
"Max number of iterations" },
{ "-back", FALSE, etBOOL, {&bBack},
"Take the back reaction into account" },
{ "-tol", FALSE, etREAL, {&tol},
"Absolute tolerance for convergence of the Nelder and Mead simplex algorithm" },
{ "-skip", FALSE, etINT, {&skip},
"Skip points in the output [TT].xvg[tt] file" },
{ "-split", FALSE, etBOOL, {&bSplit},
"Estimate error by splitting the number of replicas in two and refitting" },
{ "-sum", FALSE, etBOOL, {&bSum},
"Average folding before computing [GRK]chi[grk]^2" },
{ "-discrete", FALSE, etBOOL, {&bDiscrete},
"Use a discrete folding criterion (F <-> U) or a continuous one" },
{ "-mult", FALSE, etINT, {&nmult},
"Factor to multiply the data with before discretization" }
};
#define NPA asize(pa)
FILE *fp;
real dt_t, dt_d, dt_d2;
int nset_t, nset_d, nset_d2, n_t, n_d, n_d2, i;
const char *tfile, *dfile, *dfile2;
t_remd_data remd;
output_env_t oenv;
t_filenm fnm[] = {
{ efXVG, "-f", "temp", ffREAD },
{ efXVG, "-d", "data", ffREAD },
{ efXVG, "-d2", "data2", ffOPTRD },
{ efXVG, "-o", "ft_all", ffWRITE },
{ efXVG, "-o2", "it_all", ffOPTWR },
{ efXVG, "-o3", "ft_repl", ffOPTWR },
{ efXVG, "-ee", "err_est", ffOPTWR },
{ efLOG, "-g", "remd", ffWRITE },
{ efXVG, "-m", "melt", ffWRITE }
};
#define NFILE asize(fnm)
parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_BE_NICE | PCA_TIME_UNIT,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
#ifdef HAVE_LIBGSL
please_cite(stdout, "Spoel2006d");
if (cutoff < 0)
{
gmx_fatal(FARGS, "cutoff should be >= 0 (rather than %f)", cutoff);
}
tfile = opt2fn("-f", NFILE, fnm);
dfile = opt2fn("-d", NFILE, fnm);
dfile2 = opt2fn_null("-d2", NFILE, fnm);
fp = ffopen(opt2fn("-g", NFILE, fnm), "w");
remd.temp = read_xvg_time(tfile, bHaveT,
opt2parg_bSet("-b", NPA, pa), tb,
opt2parg_bSet("-e", NPA, pa), te,
nreplica, &nset_t, &n_t, &dt_t, &remd.time);
printf("Read %d sets of %d points in %s, dt = %g\n\n", nset_t, n_t, tfile, dt_t);
sfree(remd.time);
remd.data = read_xvg_time(dfile, bHaveT,
opt2parg_bSet("-b", NPA, pa), tb,
opt2parg_bSet("-e", NPA, pa), te,
nreplica, &nset_d, &n_d, &dt_d, &remd.time);
printf("Read %d sets of %d points in %s, dt = %g\n\n", nset_d, n_d, dfile, dt_d);
if ((nset_t != nset_d) || (n_t != n_d) || (dt_t != dt_d))
{
gmx_fatal(FARGS, "Files %s and %s are inconsistent. Check log file",
tfile, dfile);
}
if (dfile2)
{
remd.data2 = read_xvg_time(dfile2, bHaveT,
opt2parg_bSet("-b", NPA, pa), tb,
opt2parg_bSet("-e", NPA, pa), te,
nreplica, &nset_d2, &n_d2, &dt_d2, &remd.time);
printf("Read %d sets of %d points in %s, dt = %g\n\n",
nset_d2, n_d2, dfile2, dt_d2);
if ((nset_d2 != nset_d) || (n_d != n_d2) || (dt_d != dt_d2))
{
gmx_fatal(FARGS, "Files %s and %s are inconsistent. Check log file",
dfile, dfile2);
}
}
else
{
remd.data2 = NULL;
}
remd.nreplica = nset_d;
remd.nframe = n_d;
remd.dt = 1;
preprocess_remd(fp, &remd, cutoff, tref, ucut, bBack, Euf, Efu, Ei, t0, t1,
bSum, bDiscrete, nmult);
optimize_remd_parameters(&remd, maxiter, tol);
dump_remd_parameters(fp, &remd, opt2fn("-o", NFILE, fnm),
opt2fn_null("-o2", NFILE, fnm),
opt2fn_null("-o3", NFILE, fnm),
opt2fn_null("-ee", NFILE, fnm),
opt2fn("-m", NFILE, fnm), skip, tref, oenv);
if (bSplit)
{
printf("Splitting set of replicas in two halves\n");
for (i = 0; (i < remd.nreplica); i++)
{
remd.bMask[i] = FALSE;
}
remd.nmask = 0;
for (i = 0; (i < remd.nreplica); i += 2)
{
remd.bMask[i] = TRUE;
remd.nmask++;
}
sum_ft(&remd);
optimize_remd_parameters(&remd, maxiter, tol);
dump_remd_parameters(fp, &remd, "test1.xvg", NULL, NULL, NULL, NULL, skip, tref, oenv);
for (i = 0; (i < remd.nreplica); i++)
{
remd.bMask[i] = !remd.bMask[i];
}
remd.nmask = remd.nreplica - remd.nmask;
sum_ft(&remd);
optimize_remd_parameters(&remd, maxiter, tol);
dump_remd_parameters(fp, &remd, "test2.xvg", NULL, NULL, NULL, NULL, skip, tref, oenv);
for (i = 0; (i < remd.nreplica); i++)
{
remd.bMask[i] = FALSE;
}
remd.nmask = 0;
for (i = 0; (i < remd.nreplica/2); i++)
{
remd.bMask[i] = TRUE;
remd.nmask++;
}
sum_ft(&remd);
optimize_remd_parameters(&remd, maxiter, tol);
dump_remd_parameters(fp, &remd, "test1.xvg", NULL, NULL, NULL, NULL, skip, tref, oenv);
for (i = 0; (i < remd.nreplica); i++)
{
remd.bMask[i] = FALSE;
}
remd.nmask = 0;
for (i = remd.nreplica/2; (i < remd.nreplica); i++)
{
remd.bMask[i] = TRUE;
remd.nmask++;
}
sum_ft(&remd);
optimize_remd_parameters(&remd, maxiter, tol);
dump_remd_parameters(fp, &remd, "test1.xvg", NULL, NULL, NULL, NULL, skip, tref, oenv);
}
ffclose(fp);
view_all(oenv, NFILE, fnm);
#else
fprintf(stderr, "This program should be compiled with the GNU scientific library. Please install the library and reinstall GROMACS.\n");
#endif /*HAVE_LIBGSL*/
return 0;
}
