static void edit_files(gmx::ArrayRef<std::string> files,
real *readtime, real *timestep,
real *settime, int *cont_type, gmx_bool bSetTime,
gmx_bool bSort, const gmx_output_env_t *oenv)
{
gmx_bool ok;
char inputstring[STRLEN], *chptr;
auto timeUnit = output_env_get_time_unit(oenv);
if (bSetTime)
{
fprintf(stderr, "\n\nEnter the new start time (%s) for each file.\n"
"There are two special options, both disable sorting:\n\n"
"c (continue) - The start time is taken from the end\n"
"of the previous file. Use it when your continuation run\n"
"restarts with t=0.\n\n"
"l (last) - The time in this file will be changed the\n"
"same amount as in the previous. Use it when the time in the\n"
"new run continues from the end of the previous one,\n"
"since this takes possible overlap into account.\n\n",
timeUnit.c_str());
fprintf(
stderr,
" File Current start (%s) New start (%s)\n"
"---------------------------------------------------------\n",
timeUnit.c_str(), timeUnit.c_str());
for (gmx::index i = 0; i < files.ssize(); i++)
{
fprintf(stderr, "%25s %10.3f %s ", files[i].c_str(),
output_env_conv_time(oenv, readtime[i]), timeUnit.c_str());
ok = FALSE;
do
{
if (nullptr == fgets(inputstring, STRLEN - 1, stdin))
{
gmx_fatal(FARGS, "Error reading user input" );
}
inputstring[std::strlen(inputstring)-1] = 0;
if (inputstring[0] == 'c' || inputstring[0] == 'C')
{
cont_type[i] = TIME_CONTINUE;
bSort = FALSE;
ok = TRUE;
settime[i] = FLT_MAX;
}
else if (inputstring[0] == 'l' ||
inputstring[0] == 'L')
{
cont_type[i] = TIME_LAST;
bSort = FALSE;
ok = TRUE;
settime[i] = FLT_MAX;
}
else
{
settime[i] = strtod(inputstring, &chptr)*
output_env_get_time_invfactor(oenv);
if (chptr == inputstring)
{
fprintf(stderr, "'%s' not recognized as a floating point number, 'c' or 'l'. "
"Try again: ", inputstring);
}
else
{
cont_type[i] = TIME_EXPLICIT;
ok = TRUE;
}
}
}
while (!ok);
}
if (cont_type[0] != TIME_EXPLICIT)
{
cont_type[0] = TIME_EXPLICIT;
settime[0] = 0;
}
}
else
{
for (gmx::index i = 0; i < files.ssize(); i++)
{
settime[i] = readtime[i];
}
}
if (!bSort)
{
fprintf(stderr, "Sorting disabled.\n");
}
else
{
sort_files(files, settime);
}
/* Write out the new order and start times */
fprintf(stderr, "\nSummary of files and start times used:\n\n"
" File Start time Time step\n"
"---------------------------------------------------------\n");
for (gmx::index i = 0; i < files.ssize(); i++)
{
switch (cont_type[i])
{
case TIME_EXPLICIT:
fprintf(stderr, "%25s %10.3f %s %10.3f %s",
files[i].c_str(),
output_env_conv_time(oenv, settime[i]), timeUnit.c_str(),
output_env_conv_time(oenv, timestep[i]), timeUnit.c_str());
if (i > 0 &&
cont_type[i-1] == TIME_EXPLICIT && settime[i] == settime[i-1])
{
fprintf(stderr, " WARNING: same Start time as previous");
}
fprintf(stderr, "\n");
break;
case TIME_CONTINUE:
fprintf(stderr, "%25s Continue from last file\n", files[i].c_str());
break;
case TIME_LAST:
fprintf(stderr, "%25s Change by same amount as last file\n",
files[i].c_str());
break;
}
}
fprintf(stderr, "\n");
settime[files.size()] = FLT_MAX;
cont_type[files.size()] = TIME_EXPLICIT;
readtime[files.size()] = FLT_MAX;
}
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 = nullptr;
real t_corr;
t_trxframe fr, frout;
int n_append;
gmx_bool bNewFile, bIndex, bWrite;
int *cont_type;
real *readtime, *timest, *settime;
real first_time = 0, lasttime = 0, last_ok_t = -1, timestep;
gmx_bool lastTimeSet = FALSE;
real last_frame_time, searchtime;
int isize = 0, j;
int *index = nullptr, imax;
char *grpname;
real **val = nullptr, *t = nullptr, dt_remd;
int n, nset, ftpout = -1, prevEndStep = 0, filetype;
gmx_off_t fpos;
gmx_output_env_t *oenv;
t_filenm fnm[] =
{
{ efTRX, "-f", nullptr, ffRDMULT },
{ efTRO, "-o", nullptr, 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, nullptr, &oenv))
{
return 0;
}
fprintf(stdout, "Note that major changes are planned in future for "
"trjcat, to improve usability and utility.");
auto timeUnit = output_env_get_time_unit(oenv);
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");
}
}
}
gmx::ArrayRef<const std::string> inFiles = opt2fns("-f", NFILE, fnm);
if (inFiles.empty())
{
gmx_fatal(FARGS, "No input files!" );
}
if (bDeMux && ssize(inFiles) != nset)
{
gmx_fatal(FARGS, "You have specified %td files and %d entries in the demux table", inFiles.ssize(), nset);
}
ftpin = fn2ftp(inFiles[0].c_str());
if (ftpin != efTRR && ftpin != efXTC && ftpin != efTNG)
{
gmx_fatal(FARGS, "gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)");
}
for (const std::string &inFile : inFiles)
{
if (ftpin != fn2ftp(inFile.c_str()))
{
gmx_fatal(FARGS, "All input files must be of the same (trr, xtc or tng) format");
}
}
gmx::ArrayRef<const std::string> outFiles = opt2fns("-o", NFILE, fnm);
if (outFiles.empty())
{
gmx_fatal(FARGS, "No output files!");
}
if ((outFiles.size() > 1) && !bDeMux)
{
gmx_fatal(FARGS, "Don't know what to do with more than 1 output file if not demultiplexing");
}
else if (bDeMux && ssize(outFiles) != nset && outFiles.size() != 1)
{
gmx_fatal(FARGS, "Number of output files should be 1 or %d (#input files), not %td", nset, outFiles.ssize());
}
if (bDeMux)
{
auto outFilesDemux = gmx::copyOf(outFiles);
if (gmx::ssize(outFilesDemux) != nset)
{
std::string name = outFilesDemux[0];
outFilesDemux.resize(nset);
for (i = 0; (i < nset); i++)
{
outFilesDemux[0] = gmx::formatString("%d_%s", i, name.c_str());
}
}
do_demux(inFiles, outFilesDemux, n, val, t, dt_remd, isize, index, dt, oenv);
}
else
{
snew(readtime, inFiles.size() + 1);
snew(timest, inFiles.size() + 1);
scan_trj_files(inFiles, readtime, timest, imax, oenv);
snew(settime, inFiles.size() + 1);
snew(cont_type, inFiles.size() + 1);
auto inFilesEdited = gmx::copyOf(inFiles);
edit_files(inFilesEdited, 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.
*/
const char *out_file = outFiles[0].c_str();
ftpout = fn2ftp(out_file);
n_append = -1;
for (size_t i = 0; i < inFilesEdited.size() && n_append == -1; i++)
{
if (std::strcmp(inFilesEdited[i].c_str(), 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)",
inFilesEdited[0].c_str(), 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)
{
trxout = trjtools_gmx_prepare_tng_writing(out_file, 'w', nullptr,
inFilesEdited[0].c_str(), isize, nullptr, gmx::arrayRefFromArray(index, isize), grpname);
}
else
{
trxout = trjtools_gmx_prepare_tng_writing(out_file, 'w', nullptr,
inFilesEdited[0].c_str(), -1, nullptr, {}, nullptr);
}
}
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_trx(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 (inFilesEdited.size() > 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_trx(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 (size_t i = n_append + 1; i < inFilesEdited.size(); 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 < inFilesEdited.size() &&
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),
timeUnit.c_str());
}
}
}
/* 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, inFilesEdited[i].c_str(), &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 = inFilesEdited.size();
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",
inFilesEdited[i].c_str(),
output_env_conv_time(oenv, frout.time), timeUnit.c_str(),
frame);
bNewFile = FALSE;
}
if (bIndex)
{
write_trxframe_indexed(trxout, &frout, isize, index,
nullptr);
}
else
{
write_trxframe(trxout, &frout, nullptr);
}
if ( ((frame % 10) == 0) || (frame < 10) )
{
fprintf(stderr, " -> frame %6d time %8.3f %s \r",
frame_out, output_env_conv_time(oenv, frout.time), timeUnit.c_str());
fflush(stderr);
}
}
}
}
while (read_next_frame(oenv, status, &fr));
close_trx(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), timeUnit.c_str());
}
return 0;
}
void do_corr(const char *trx_file, const char *ndx_file, const char *msd_file,
const char *mol_file, const char *pdb_file, real t_pdb,
int nrgrp, t_topology *top, int ePBC,
gmx_bool bTen, gmx_bool bMW, gmx_bool bRmCOMM,
int type, real dim_factor, int axis,
real dt, real beginfit, real endfit, const output_env_t oenv)
{
t_corr *msd;
int *gnx; /* the selected groups' sizes */
atom_id **index; /* selected groups' indices */
char **grpname;
int i, i0, i1, j, N, nat_trx;
real *DD, *SigmaD, a, a2, b, r, chi2;
rvec *x;
matrix box;
int *gnx_com = NULL; /* the COM removal group size */
atom_id **index_com = NULL; /* the COM removal group atom indices */
char **grpname_com = NULL; /* the COM removal group name */
snew(gnx, nrgrp);
snew(index, nrgrp);
snew(grpname, nrgrp);
fprintf(stderr, "\nSelect a group to calculate mean squared displacement for:\n");
get_index(&top->atoms, ndx_file, nrgrp, gnx, index, grpname);
if (bRmCOMM)
{
snew(gnx_com, 1);
snew(index_com, 1);
snew(grpname_com, 1);
fprintf(stderr, "\nNow select a group for center of mass removal:\n");
get_index(&top->atoms, ndx_file, 1, gnx_com, index_com, grpname_com);
}
if (mol_file)
{
index_atom2mol(&gnx[0], index[0], &top->mols);
}
msd = init_corr(nrgrp, type, axis, dim_factor,
mol_file == NULL ? 0 : gnx[0], bTen, bMW, dt, top,
beginfit, endfit);
nat_trx =
corr_loop(msd, trx_file, top, ePBC, mol_file ? gnx[0] : 0, gnx, index,
(mol_file != NULL) ? calc1_mol : (bMW ? calc1_mw : calc1_norm),
bTen, gnx_com, index_com, dt, t_pdb,
pdb_file ? &x : NULL, box, oenv);
/* Correct for the number of points */
for (j = 0; (j < msd->ngrp); j++)
{
for (i = 0; (i < msd->nframes); i++)
{
msd->data[j][i] /= msd->ndata[j][i];
if (bTen)
{
msmul(msd->datam[j][i], 1.0/msd->ndata[j][i], msd->datam[j][i]);
}
}
}
if (mol_file)
{
if (pdb_file && x == NULL)
{
fprintf(stderr, "\nNo frame found need time tpdb = %g ps\n"
"Can not write %s\n\n", t_pdb, pdb_file);
}
i = top->atoms.nr;
top->atoms.nr = nat_trx;
printmol(msd, mol_file, pdb_file, index[0], top, x, ePBC, box, oenv);
top->atoms.nr = i;
}
DD = NULL;
SigmaD = NULL;
if (beginfit == -1)
{
i0 = static_cast<int>(0.1*(msd->nframes - 1) + 0.5);
beginfit = msd->time[i0];
}
else
{
for (i0 = 0; i0 < msd->nframes && msd->time[i0] < beginfit; i0++)
{
;
}
}
if (endfit == -1)
{
i1 = static_cast<int>(0.9*(msd->nframes - 1) + 0.5) + 1;
endfit = msd->time[i1-1];
}
else
{
for (i1 = i0; i1 < msd->nframes && msd->time[i1] <= endfit; i1++)
{
;
}
}
fprintf(stdout, "Fitting from %g to %g %s\n\n", beginfit, endfit,
output_env_get_time_unit(oenv));
N = i1-i0;
if (N <= 2)
{
fprintf(stdout, "Not enough points for fitting (%d).\n"
"Can not determine the diffusion constant.\n", N);
}
else
{
snew(DD, msd->ngrp);
snew(SigmaD, msd->ngrp);
for (j = 0; j < msd->ngrp; j++)
{
if (N >= 4)
{
lsq_y_ax_b(N/2, &(msd->time[i0]), &(msd->data[j][i0]), &a, &b, &r, &chi2);
lsq_y_ax_b(N/2, &(msd->time[i0+N/2]), &(msd->data[j][i0+N/2]), &a2, &b, &r, &chi2);
SigmaD[j] = std::abs(a-a2);
}
else
{
SigmaD[j] = 0;
}
lsq_y_ax_b(N, &(msd->time[i0]), &(msd->data[j][i0]), &(DD[j]), &b, &r, &chi2);
DD[j] *= FACTOR/msd->dim_factor;
SigmaD[j] *= FACTOR/msd->dim_factor;
if (DD[j] > 0.01 && DD[j] < 1e4)
{
fprintf(stdout, "D[%10s] %.4f (+/- %.4f) 1e-5 cm^2/s\n",
grpname[j], DD[j], SigmaD[j]);
}
else
{
fprintf(stdout, "D[%10s] %.4g (+/- %.4g) 1e-5 cm^2/s\n",
grpname[j], DD[j], SigmaD[j]);
}
}
}
/* Print mean square displacement */
corr_print(msd, bTen, msd_file,
"Mean Square Displacement",
"MSD (nm\\S2\\N)",
msd->time[msd->nframes-1], beginfit, endfit, DD, SigmaD, grpname, oenv);
}
static void clust_size(const char *ndx, const char *trx, const char *xpm,
const char *xpmw, const char *ncl, const char *acl,
const char *mcl, const char *histo, const char *tempf,
const char *mcn, gmx_bool bMol, gmx_bool bPBC, const char *tpr,
real cut, int nskip, int nlevels,
t_rgb rmid, t_rgb rhi, int ndf,
const output_env_t oenv)
{
FILE *fp, *gp, *hp, *tp;
atom_id *index = NULL;
int nindex, natoms;
t_trxstatus *status;
rvec *x = NULL, *v = NULL, dx;
t_pbc pbc;
char *gname;
char timebuf[32];
gmx_bool bSame, bTPRwarn = TRUE;
/* Topology stuff */
t_trxframe fr;
t_tpxheader tpxh;
gmx_mtop_t *mtop = NULL;
int ePBC = -1;
t_block *mols = NULL;
gmx_mtop_atomlookup_t alook;
t_atom *atom;
int version, generation, ii, jj, nsame;
real temp, tfac;
/* Cluster size distribution (matrix) */
real **cs_dist = NULL;
real tf, dx2, cut2, *t_x = NULL, *t_y, cmid, cmax, cav, ekin;
int i, j, k, ai, aj, ak, ci, cj, nframe, nclust, n_x, n_y, max_size = 0;
int *clust_index, *clust_size, max_clust_size, max_clust_ind, nav, nhisto;
t_rgb rlo = { 1.0, 1.0, 1.0 };
clear_trxframe(&fr, TRUE);
sprintf(timebuf, "Time (%s)", output_env_get_time_unit(oenv));
tf = output_env_get_time_factor(oenv);
fp = xvgropen(ncl, "Number of clusters", timebuf, "N", oenv);
gp = xvgropen(acl, "Average cluster size", timebuf, "#molecules", oenv);
hp = xvgropen(mcl, "Max cluster size", timebuf, "#molecules", oenv);
tp = xvgropen(tempf, "Temperature of largest cluster", timebuf, "T (K)",
oenv);
if (!read_first_frame(oenv, &status, trx, &fr, TRX_NEED_X | TRX_READ_V))
{
gmx_file(trx);
}
natoms = fr.natoms;
x = fr.x;
if (tpr)
{
snew(mtop, 1);
read_tpxheader(tpr, &tpxh, TRUE, &version, &generation);
if (tpxh.natoms != natoms)
{
gmx_fatal(FARGS, "tpr (%d atoms) and xtc (%d atoms) do not match!",
tpxh.natoms, natoms);
}
ePBC = read_tpx(tpr, NULL, NULL, &natoms, NULL, NULL, NULL, mtop);
}
if (ndf <= -1)
{
tfac = 1;
}
else
{
tfac = ndf/(3.0*natoms);
}
if (bMol)
{
if (ndx)
{
printf("Using molecules rather than atoms. Not reading index file %s\n",
ndx);
}
mols = &(mtop->mols);
/* Make dummy index */
nindex = mols->nr;
snew(index, nindex);
for (i = 0; (i < nindex); i++)
{
index[i] = i;
}
gname = strdup("mols");
}
else
{
rd_index(ndx, 1, &nindex, &index, &gname);
}
alook = gmx_mtop_atomlookup_init(mtop);
snew(clust_index, nindex);
snew(clust_size, nindex);
cut2 = cut*cut;
nframe = 0;
n_x = 0;
snew(t_y, nindex);
for (i = 0; (i < nindex); i++)
{
t_y[i] = i+1;
}
max_clust_size = 1;
max_clust_ind = -1;
do
{
if ((nskip == 0) || ((nskip > 0) && ((nframe % nskip) == 0)))
{
if (bPBC)
{
set_pbc(&pbc, ePBC, fr.box);
}
max_clust_size = 1;
max_clust_ind = -1;
/* Put all atoms/molecules in their own cluster, with size 1 */
for (i = 0; (i < nindex); i++)
{
/* Cluster index is indexed with atom index number */
clust_index[i] = i;
/* Cluster size is indexed with cluster number */
clust_size[i] = 1;
}
/* Loop over atoms */
for (i = 0; (i < nindex); i++)
{
ai = index[i];
ci = clust_index[i];
/* Loop over atoms (only half a matrix) */
for (j = i+1; (j < nindex); j++)
{
cj = clust_index[j];
/* If they are not in the same cluster already */
if (ci != cj)
{
aj = index[j];
/* Compute distance */
if (bMol)
{
bSame = FALSE;
for (ii = mols->index[ai]; !bSame && (ii < mols->index[ai+1]); ii++)
{
for (jj = mols->index[aj]; !bSame && (jj < mols->index[aj+1]); jj++)
{
if (bPBC)
{
pbc_dx(&pbc, x[ii], x[jj], dx);
}
else
{
rvec_sub(x[ii], x[jj], dx);
}
dx2 = iprod(dx, dx);
bSame = (dx2 < cut2);
}
}
}
else
{
if (bPBC)
{
pbc_dx(&pbc, x[ai], x[aj], dx);
}
else
{
rvec_sub(x[ai], x[aj], dx);
}
dx2 = iprod(dx, dx);
bSame = (dx2 < cut2);
}
/* If distance less than cut-off */
if (bSame)
{
/* Merge clusters: check for all atoms whether they are in
* cluster cj and if so, put them in ci
*/
for (k = 0; (k < nindex); k++)
{
if (clust_index[k] == cj)
{
if (clust_size[cj] <= 0)
{
gmx_fatal(FARGS, "negative cluster size %d for element %d",
clust_size[cj], cj);
}
clust_size[cj]--;
clust_index[k] = ci;
clust_size[ci]++;
}
}
}
}
}
}
n_x++;
srenew(t_x, n_x);
t_x[n_x-1] = fr.time*tf;
srenew(cs_dist, n_x);
snew(cs_dist[n_x-1], nindex);
nclust = 0;
cav = 0;
nav = 0;
for (i = 0; (i < nindex); i++)
{
ci = clust_size[i];
if (ci > max_clust_size)
{
max_clust_size = ci;
max_clust_ind = i;
}
if (ci > 0)
{
nclust++;
cs_dist[n_x-1][ci-1] += 1.0;
max_size = max(max_size, ci);
if (ci > 1)
{
cav += ci;
nav++;
}
}
}
fprintf(fp, "%14.6e %10d\n", fr.time, nclust);
if (nav > 0)
{
fprintf(gp, "%14.6e %10.3f\n", fr.time, cav/nav);
}
fprintf(hp, "%14.6e %10d\n", fr.time, max_clust_size);
}
/* Analyse velocities, if present */
if (fr.bV)
{
if (!tpr)
{
if (bTPRwarn)
{
printf("You need a [TT].tpr[tt] file to analyse temperatures\n");
bTPRwarn = FALSE;
}
}
else
{
v = fr.v;
/* Loop over clusters and for each cluster compute 1/2 m v^2 */
if (max_clust_ind >= 0)
{
ekin = 0;
for (i = 0; (i < nindex); i++)
{
if (clust_index[i] == max_clust_ind)
{
ai = index[i];
gmx_mtop_atomnr_to_atom(alook, ai, &atom);
ekin += 0.5*atom->m*iprod(v[ai], v[ai]);
}
}
temp = (ekin*2.0)/(3.0*tfac*max_clust_size*BOLTZ);
fprintf(tp, "%10.3f %10.3f\n", fr.time, temp);
}
}
}
nframe++;
}
while (read_next_frame(oenv, status, &fr));
close_trx(status);
ffclose(fp);
ffclose(gp);
ffclose(hp);
ffclose(tp);
gmx_mtop_atomlookup_destroy(alook);
if (max_clust_ind >= 0)
{
fp = ffopen(mcn, "w");
fprintf(fp, "[ max_clust ]\n");
for (i = 0; (i < nindex); i++)
{
if (clust_index[i] == max_clust_ind)
{
if (bMol)
{
for (j = mols->index[i]; (j < mols->index[i+1]); j++)
{
fprintf(fp, "%d\n", j+1);
}
}
else
{
fprintf(fp, "%d\n", index[i]+1);
}
}
}
ffclose(fp);
}
/* Print the real distribution cluster-size/numer, averaged over the trajectory. */
fp = xvgropen(histo, "Cluster size distribution", "Cluster size", "()", oenv);
nhisto = 0;
fprintf(fp, "%5d %8.3f\n", 0, 0.0);
for (j = 0; (j < max_size); j++)
{
real nelem = 0;
for (i = 0; (i < n_x); i++)
{
nelem += cs_dist[i][j];
}
fprintf(fp, "%5d %8.3f\n", j+1, nelem/n_x);
nhisto += (int)((j+1)*nelem/n_x);
}
fprintf(fp, "%5d %8.3f\n", j+1, 0.0);
ffclose(fp);
fprintf(stderr, "Total number of atoms in clusters = %d\n", nhisto);
/* Look for the smallest entry that is not zero
* This will make that zero is white, and not zero is coloured.
*/
cmid = 100.0;
cmax = 0.0;
for (i = 0; (i < n_x); i++)
{
for (j = 0; (j < max_size); j++)
{
if ((cs_dist[i][j] > 0) && (cs_dist[i][j] < cmid))
{
cmid = cs_dist[i][j];
}
cmax = max(cs_dist[i][j], cmax);
}
}
fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
cmid = 1;
fp = ffopen(xpm, "w");
write_xpm3(fp, 0, "Cluster size distribution", "# clusters", timebuf, "Size",
n_x, max_size, t_x, t_y, cs_dist, 0, cmid, cmax,
rlo, rmid, rhi, &nlevels);
ffclose(fp);
cmid = 100.0;
cmax = 0.0;
for (i = 0; (i < n_x); i++)
{
for (j = 0; (j < max_size); j++)
{
cs_dist[i][j] *= (j+1);
if ((cs_dist[i][j] > 0) && (cs_dist[i][j] < cmid))
{
cmid = cs_dist[i][j];
}
cmax = max(cs_dist[i][j], cmax);
}
}
fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
fp = ffopen(xpmw, "w");
write_xpm3(fp, 0, "Weighted cluster size distribution", "Fraction", timebuf,
"Size", n_x, max_size, t_x, t_y, cs_dist, 0, cmid, cmax,
rlo, rmid, rhi, &nlevels);
ffclose(fp);
sfree(clust_index);
sfree(clust_size);
sfree(index);
}
/* 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;
}
int main(int argc,char *argv[])
{
const char *desc[] = {
"[TT]do_multiprot[tt] ",
"reads a trajectory file and aligns it to a reference structure ",
"each time frame",
"calling the multiprot program. This allows you to use a reference",
"structure whose sequence is different than that of the protein in the ",
"trajectory, since the alignment is based on the geometry, not sequence.",
"The output of [TT]do_multiprot[tt] includes the rmsd and the number of residues",
"on which it was calculated.",
"[PAR]",
"An aligned trajectory file is generated with the [TT]-ox[tt] option.[PAR]",
"With the [TT]-cr[tt] option, the number of hits in the alignment is given",
"per residue. This number can be between 0 and the number of frames, and",
"indicates the structural conservation of this residue.[PAR]",
"If you do not have the [TT]multiprot[tt] program, get it. [TT]do_multiprot[tt] assumes",
"that the [TT]multiprot[tt] executable is [TT]/usr/local/bin/multiprot[tt]. If this is ",
"not the case, then you should set an environment variable [BB]MULTIPROT[bb]",
"pointing to the [TT]multiprot[tt] executable, e.g.: [PAR]",
"[TT]setenv MULTIPROT /usr/MultiProtInstall/multiprot.Linux[tt][PAR]",
"Note that at the current implementation only binary alignment (your",
"molecule to a reference) is supported. In addition, note that the ",
"by default [TT]multiprot[tt] aligns the two proteins on their C-alpha carbons.",
"and that this depends on the [TT]multiprot[tt] parameters which are not dealt ",
"with here. Thus, the C-alpha carbons is expected to give the same "
"results as choosing the whole protein and will be slightly faster.[PAR]",
"For information about [TT]multiprot[tt], see:",
"http://bioinfo3d.cs.tau.ac.il/MultiProt/.[PAR]"
};
static bool bVerbose;
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"HIDDENGenerate miles of useless information" }
};
const char *bugs[] = {
"The program is very slow, since multiprot is run externally"
};
t_trxstatus *status;
t_trxstatus *trxout=NULL;
FILE *tapein,*fo,*frc,*tmpf,*out=NULL,*fres=NULL;
const char *fnRef;
const char *fn="2_sol.res";
t_topology top;
int ePBC;
t_atoms *atoms,ratoms,useatoms;
t_trxframe fr;
t_pdbinfo p;
int nres,nres2,nr0;
real t;
int i,j,natoms,nratoms,nframe=0,model_nr=-1;
int cur_res,prev_res;
int nout;
t_countres *countres=NULL;
matrix box,rbox;
int gnx;
char *grpnm,*ss_str;
atom_id *index;
rvec *xp,*x,*xr;
char pdbfile[32],refpdb[256],title[256],rtitle[256],filemode[5];
char out_title[256];
char multiprot[256],*mptr;
int ftp;
int outftp=-1;
real rmsd;
bool bTrjout,bCountres;
const char *TrjoutFile=NULL;
output_env_t oenv;
static rvec translation={0,0,0},rotangles={0,0,0};
gmx_rmpbc_t gpbc=NULL;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTX, "-r", NULL , ffREAD },
{ efXVG, "-o", "rmss", ffWRITE },
{ efXVG, "-rc", "rescount", ffWRITE},
{ efXVG, "-cr", "countres", ffOPTWR},
{ efTRX, "-ox", "aligned", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE ,
NFILE,fnm, asize(pa),pa, asize(desc),desc,
asize(bugs),bugs,&oenv
);
fnRef=opt2fn("-r",NFILE,fnm);
bTrjout = opt2bSet("-ox",NFILE,fnm);
bCountres= opt2bSet("-cr",NFILE,fnm);
if (bTrjout) {
TrjoutFile = opt2fn_null("-ox",NFILE,fnm);
}
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xp,NULL,box,FALSE);
gpbc = gmx_rmpbc_init(&top.idef,ePBC,top.atoms.nr,box);
atoms=&(top.atoms);
ftp=fn2ftp(fnRef);
get_stx_coordnum(fnRef,&nratoms);
init_t_atoms(&ratoms,nratoms,TRUE);
snew(xr,nratoms);
read_stx_conf(fnRef,rtitle,&ratoms,xr,NULL,&ePBC,rbox);
if (bVerbose) {
fprintf(stderr,"Read %d atoms\n",atoms->nr);
fprintf(stderr,"Read %d reference atoms\n",ratoms.nr);
}
if (bCountres) {
snew(countres,ratoms.nres);
j=0;
cur_res=0;
for (i=0;i<ratoms.nr;i++) {
prev_res=cur_res;
cur_res=ratoms.atom[i].resind;
if (cur_res != prev_res) {
countres[j].resnr=cur_res;
countres[j].count=0;
j++;
}
}
}
get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpnm);
nres=0;
nr0=-1;
for(i=0; (i<gnx); i++) {
if (atoms->atom[index[i]].resind != nr0) {
nr0=atoms->atom[index[i]].resind;
nres++;
}
}
fprintf(stderr,"There are %d residues in your selected group\n",nres);
strcpy(pdbfile,"ddXXXXXX");
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile,"w")) == NULL) {
sprintf(pdbfile,"%ctmp%cfilterXXXXXX",DIR_SEPARATOR,DIR_SEPARATOR);
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile,"w")) == NULL) {
gmx_fatal(FARGS,"Can not open tmp file %s",pdbfile);
}
}
else {
gmx_ffclose(tmpf);
}
if (ftp != efPDB) {
strcpy(refpdb,"ddXXXXXX");
gmx_tmpnam(refpdb);
strcat(refpdb,".pdb");
write_sto_conf(refpdb,rtitle,&ratoms,xr,NULL,ePBC,rbox);
}
else {
strcpy(refpdb,fnRef);
}
if ((mptr=getenv("MULTIPROT")) == NULL) {
mptr="/usr/local/bin/multiprot";
}
if (!gmx_fexist(mptr)) {
gmx_fatal(FARGS,"MULTIPROT executable (%s) does not exist (use setenv MULTIPROT)",
mptr);
}
sprintf (multiprot,"%s %s %s > /dev/null %s",
mptr, refpdb, pdbfile, "2> /dev/null");
if (bVerbose)
fprintf(stderr,"multiprot cmd='%s'\n",multiprot);
if (!read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,TRX_READ_X))
gmx_fatal(FARGS,"Could not read a frame from %s",ftp2fn(efTRX,NFILE,fnm));
natoms = fr.natoms;
if (bTrjout) {
nout=natoms;
/* open file now */
outftp=fn2ftp(TrjoutFile);
if (bVerbose)
fprintf(stderr,"Will write %s: %s\n",ftp2ext(ftp),ftp2desc(outftp));
strcpy(filemode,"w");
switch (outftp) {
case efXTC:
case efG87:
case efTRR:
case efTRJ:
out=NULL;
trxout = open_trx(TrjoutFile,filemode);
break;
case efGRO:
case efG96:
case efPDB:
/* Make atoms struct for output in GRO or PDB files */
/* get memory for stuff to go in pdb file */
init_t_atoms(&useatoms,nout,FALSE);
sfree(useatoms.resinfo);
useatoms.resinfo=atoms->resinfo;
for(i=0;(i<nout);i++) {
useatoms.atomname[i]=atoms->atomname[i];
useatoms.atom[i]=atoms->atom[i];
useatoms.nres=max(useatoms.nres,useatoms.atom[i].resind+1);
}
useatoms.nr=nout;
out=gmx_ffopen(TrjoutFile,filemode);
break;
}
if (outftp == efG87)
fprintf(gmx_fio_getfp(trx_get_fileio(trxout)),"Generated by %s. #atoms=%d, a BOX is"
" stored in this file.\n",ShortProgram(),nout);
}
if (natoms > atoms->nr) {
gmx_fatal(FARGS,"\nTrajectory does not match topology!");
}
if (gnx > natoms) {
gmx_fatal(FARGS,"\nTrajectory does not match selected group!");
}
fo = xvgropen(opt2fn("-o",NFILE,fnm),"RMSD","Time (ps)","RMSD (nm)",oenv);
frc = xvgropen(opt2fn("-rc",NFILE,fnm),"Number of Residues in the alignment","Time (ps)","Residues",oenv);
do {
t = output_env_conv_time(oenv,fr.time);
gmx_rmpbc(gpbc,natoms,fr.box,fr.x);
tapein=gmx_ffopen(pdbfile,"w");
write_pdbfile_indexed(tapein,NULL,atoms,fr.x,ePBC,fr.box,' ',-1,gnx,index,NULL,TRUE);
gmx_ffclose(tapein);
system(multiprot);
remove(pdbfile);
process_multiprot_output(fn, &rmsd, &nres2,rotangles,translation,bCountres,countres);
fprintf(fo,"%12.7f",t);
fprintf(fo," %12.7f\n",rmsd);
fprintf(frc,"%12.7f",t);
fprintf(frc,"%12d\n",nres2);
if (bTrjout) {
rotate_conf(natoms,fr.x,NULL,rotangles[XX],rotangles[YY],rotangles[ZZ]);
for(i=0; i<natoms; i++) {
rvec_inc(fr.x[i],translation);
}
switch(outftp) {
case efTRJ:
case efTRR:
case efG87:
case efXTC:
write_trxframe(trxout,&fr,NULL);
break;
case efGRO:
case efG96:
case efPDB:
sprintf(out_title,"Generated by do_multiprot : %s t= %g %s",
title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
switch(outftp) {
case efGRO:
write_hconf_p(out,out_title,&useatoms,prec2ndec(fr.prec),
fr.x,NULL,fr.box);
break;
case efPDB:
fprintf(out,"REMARK GENERATED BY DO_MULTIPROT\n");
sprintf(out_title,"%s t= %g %s",title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
/* if reading from pdb, we want to keep the original
model numbering else we write the output frame
number plus one, because model 0 is not allowed in pdb */
if (ftp==efPDB && fr.step > model_nr) {
model_nr = fr.step;
}
else {
model_nr++;
}
write_pdbfile(out,out_title,&useatoms,fr.x,ePBC,fr.box,' ',model_nr,NULL,TRUE);
break;
case efG96:
fr.title = out_title;
fr.bTitle = (nframe == 0);
fr.bAtoms = FALSE;
fr.bStep = TRUE;
fr.bTime = TRUE;
write_g96_conf(out,&fr,-1,NULL);
}
break;
}
}
nframe++;
} while(read_next_frame(oenv,status,&fr));
if (bCountres) {
fres= xvgropen(opt2fn("-cr",NFILE,fnm),"Number of frames in which the residues are aligned to","Residue","Number",oenv);
for (i=0;i<ratoms.nres;i++) {
fprintf(fres,"%10d %12d\n",countres[i].resnr,countres[i].count);
}
gmx_ffclose(fres);
}
gmx_ffclose(fo);
gmx_ffclose(frc);
fprintf(stderr,"\n");
close_trj(status);
if (trxout != NULL) {
close_trx(trxout);
}
else if (out != NULL) {
gmx_ffclose(out);
}
view_all(oenv,NFILE, fnm);
sfree(xr);
if (bCountres) {
sfree(countres);
}
free_t_atoms(&ratoms,TRUE);
if (bTrjout) {
if (outftp==efPDB || outftp==efGRO || outftp==efG96) {
free_t_atoms(&useatoms,TRUE);
}
}
gmx_thanx(stderr);
return 0;
}
static void periodic_mindist_plot(const char *trxfn, const char *outfn,
t_topology *top, int ePBC,
int n, atom_id index[], gmx_bool bSplit,
const output_env_t oenv)
{
FILE *out;
const char *leg[5] = { "min per.", "max int.", "box1", "box2", "box3" };
t_trxstatus *status;
real t;
rvec *x;
matrix box;
int natoms, ind_min[2] = {0, 0}, ind_mini = 0, ind_minj = 0;
real r, rmin, rmax, rmint, tmint;
gmx_bool bFirst;
gmx_rmpbc_t gpbc = NULL;
natoms = read_first_x(oenv, &status, trxfn, &t, &x, box);
check_index(NULL, n, index, NULL, natoms);
out = xvgropen(outfn, "Minimum distance to periodic image",
output_env_get_time_label(oenv), "Distance (nm)", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(out, "@ subtitle \"and maximum internal distance\"\n");
}
xvgr_legend(out, 5, leg, oenv);
rmint = box[XX][XX];
tmint = 0;
if (NULL != top)
{
gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
}
bFirst = TRUE;
do
{
if (NULL != top)
{
gmx_rmpbc(gpbc, natoms, box, x);
}
periodic_dist(box, x, n, index, &rmin, &rmax, ind_min);
if (rmin < rmint)
{
rmint = rmin;
tmint = t;
ind_mini = ind_min[0];
ind_minj = ind_min[1];
}
if (bSplit && !bFirst && abs(t/output_env_get_time_factor(oenv)) < 1e-5)
{
fprintf(out, "&\n");
}
fprintf(out, "\t%g\t%6.3f %6.3f %6.3f %6.3f %6.3f\n",
output_env_conv_time(oenv, t), rmin, rmax, norm(box[0]), norm(box[1]), norm(box[2]));
bFirst = FALSE;
}
while (read_next_x(oenv, status, &t, x, box));
if (NULL != top)
{
gmx_rmpbc_done(gpbc);
}
ffclose(out);
fprintf(stdout,
"\nThe shortest periodic distance is %g (nm) at time %g (%s),\n"
"between atoms %d and %d\n",
rmint, output_env_conv_time(oenv, tmint), output_env_get_time_unit(oenv),
index[ind_mini]+1, index[ind_minj]+1);
}
void parse_common_args(int *argc,char *argv[],unsigned long Flags,
int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
int ndesc,const char **desc,
int nbugs,const char **bugs,
output_env_t *oenv)
{
gmx_bool bHelp=FALSE,bHidden=FALSE,bQuiet=FALSE,bVersion=FALSE;
const char *manstr[] = { NULL, "no", "html", "tex", "nroff", "ascii",
"completion", "py", "xml", "wiki", NULL };
/* This array should match the order of the enum in oenv.h */
const char *xvg_format[] = { NULL, "xmgrace", "xmgr", "none", NULL };
/* This array should match the order of the enum in oenv.h */
const char *time_units[] = { NULL, "fs", "ps", "ns", "us", "ms", "s",
NULL };
int nicelevel=0,mantp=0,npri=0,debug_level=0,verbose_level=0;
char *deffnm=NULL;
real tbegin=0,tend=0,tdelta=0;
gmx_bool bView=FALSE;
t_pargs *all_pa=NULL;
t_pargs npri_pa = { "-npri", FALSE, etINT, {&npri},
"HIDDEN Set non blocking priority (try 128)" };
t_pargs nice_pa = { "-nice", FALSE, etINT, {&nicelevel},
"Set the nicelevel" };
t_pargs deffnm_pa = { "-deffnm", FALSE, etSTR, {&deffnm},
"Set the default filename for all file options" };
t_pargs begin_pa = { "-b", FALSE, etTIME, {&tbegin},
"First frame (%t) to read from trajectory" };
t_pargs end_pa = { "-e", FALSE, etTIME, {&tend},
"Last frame (%t) to read from trajectory" };
t_pargs dt_pa = { "-dt", FALSE, etTIME, {&tdelta},
"Only use frame when t MOD dt = first time (%t)" };
t_pargs view_pa = { "-w", FALSE, etBOOL, {&bView},
"View output xvg, xpm, eps and pdb files" };
t_pargs xvg_pa = { "-xvg", FALSE, etENUM, {xvg_format},
"xvg plot formatting" };
t_pargs time_pa = { "-tu", FALSE, etENUM, {time_units},
"Time unit" };
/* Maximum number of extra arguments */
#define EXTRA_PA 16
t_pargs pca_pa[] = {
{ "-h", FALSE, etBOOL, {&bHelp},
"Print help info and quit" },
{ "-version", FALSE, etBOOL, {&bVersion},
"Print version info and quit" },
{ "-verb", FALSE, etINT, {&verbose_level},
"HIDDENLevel of verbosity for this program" },
{ "-hidden", FALSE, etBOOL, {&bHidden},
"HIDDENPrint hidden options" },
{ "-quiet",FALSE, etBOOL, {&bQuiet},
"HIDDENDo not print help info" },
{ "-man", FALSE, etENUM, {manstr},
"HIDDENWrite manual and quit" },
{ "-debug",FALSE, etINT, {&debug_level},
"HIDDENWrite file with debug information, 1: short, 2: also x and f" },
};
#define NPCA_PA asize(pca_pa)
FILE *fp;
gmx_bool bPrint,bExit,bXvgr;
int i,j,k,npall,max_pa,cmdlength;
char *ptr,*newdesc;
const char *envstr;
#define FF(arg) ((Flags & arg)==arg)
snew(*oenv, 1);
cmdlength = strlen(argv[0]);
/* Check for double arguments */
for (i=1; (i<*argc); i++)
{
cmdlength += strlen(argv[i]);
if (argv[i] && (strlen(argv[i]) > 1) && (!isdigit(argv[i][1])))
{
for (j=i+1; (j<*argc); j++)
{
if ( (argv[i][0]=='-') && (argv[j][0]=='-') &&
(strcmp(argv[i],argv[j])==0) )
{
if (FF(PCA_NOEXIT_ON_ARGS))
fprintf(stderr,"Double command line argument %s\n",
argv[i]);
else
gmx_fatal(FARGS,"Double command line argument %s\n",
argv[i]);
}
}
}
}
debug_gmx();
set_program_name(argv[0]);
set_command_line(*argc, argv);
/* Handle the flags argument, which is a bit field
* The FF macro returns whether or not the bit is set
*/
bPrint = !FF(PCA_SILENT);
/* Check ALL the flags ... */
max_pa = NPCA_PA + EXTRA_PA + npargs+1;
snew(all_pa,max_pa);
for(i=npall=0; (i<NPCA_PA); i++)
npall = add_parg(npall,all_pa,&(pca_pa[i]));
#ifdef __sgi
envstr = getenv("GMXNPRIALL");
if (envstr)
npri=strtol(envstr,NULL,10);
if (FF(PCA_BE_NICE)) {
envstr = getenv("GMXNPRI");
if (envstr)
npri=strtol(envstr,NULL,10);
}
npall = add_parg(npall,all_pa,&npri_pa);
#endif
if (FF(PCA_BE_NICE))
nicelevel=19;
npall = add_parg(npall,all_pa,&nice_pa);
if (FF(PCA_CAN_SET_DEFFNM))
npall = add_parg(npall,all_pa,&deffnm_pa);
if (FF(PCA_CAN_BEGIN))
npall = add_parg(npall,all_pa,&begin_pa);
if (FF(PCA_CAN_END))
npall = add_parg(npall,all_pa,&end_pa);
if (FF(PCA_CAN_DT))
{
npall = add_parg(npall,all_pa,&dt_pa);
}
if (FF(PCA_TIME_UNIT)) {
npall = add_parg(npall,all_pa,&time_pa);
}
if (FF(PCA_CAN_VIEW))
npall = add_parg(npall,all_pa,&view_pa);
bXvgr = FALSE;
for(i=0; (i<nfile); i++)
{
bXvgr = bXvgr || (fnm[i].ftp == efXVG);
}
if (bXvgr)
{
npall = add_parg(npall,all_pa,&xvg_pa);
}
/* Now append the program specific arguments */
for(i=0; (i<npargs); i++)
npall = add_parg(npall,all_pa,&(pa[i]));
/* set etENUM options to default */
for(i=0; (i<npall); i++)
{
if (all_pa[i].type==etENUM)
{
all_pa[i].u.c[0]=all_pa[i].u.c[1];
}
}
set_default_time_unit(time_units,FF(PCA_TIME_UNIT));
set_default_xvg_format(xvg_format);
/* Now parse all the command-line options */
get_pargs(argc,argv,npall,all_pa,FF(PCA_KEEP_ARGS));
/* set program name, command line, and default values for output options */
output_env_init(*oenv, *argc, argv, (time_unit_t)nenum(time_units), bView,
(xvg_format_t)nenum(xvg_format), verbose_level, debug_level);
if (bVersion) {
printf("Program: %s\n",output_env_get_program_name(*oenv));
gmx_print_version_info(stdout);
exit(0);
}
if (FF(PCA_CAN_SET_DEFFNM) && (deffnm!=NULL))
set_default_file_name(deffnm);
/* Parse the file args */
parse_file_args(argc,argv,nfile,fnm,FF(PCA_KEEP_ARGS),!FF(PCA_NOT_READ_NODE));
/* Open the debug file */
if (debug_level > 0) {
char buf[256];
if (gmx_mpi_initialized())
sprintf(buf,"%s%d.debug",output_env_get_short_program_name(*oenv),
gmx_node_rank());
else
sprintf(buf,"%s.debug",output_env_get_short_program_name(*oenv));
init_debug(debug_level,buf);
fprintf(stderr,"Opening debug file %s (src code file %s, line %d)\n",
buf,__FILE__,__LINE__);
}
/* Now copy the results back... */
for(i=0,k=npall-npargs; (i<npargs); i++,k++)
memcpy(&(pa[i]),&(all_pa[k]),(size_t)sizeof(pa[i]));
for(i=0; (i<npall); i++)
all_pa[i].desc = mk_desc(&(all_pa[i]), output_env_get_time_unit(*oenv));
bExit = bHelp || (strcmp(manstr[0],"no") != 0);
#if (defined __sgi && USE_SGI_FPE)
doexceptions();
#endif
/* Set the nice level */
#ifdef __sgi
if (npri != 0 && !bExit) {
schedctl(MPTS_RTPRI,0,npri);
}
#endif
#ifdef HAVE_UNISTD_H
#ifndef GMX_NO_NICE
/* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
if (nicelevel != 0 && !bExit)
{
#ifdef GMX_THREADS
static gmx_bool nice_set=FALSE; /* only set it once */
tMPI_Thread_mutex_lock(&init_mutex);
if (!nice_set)
{
#endif
i=nice(nicelevel); /* assign ret value to avoid warnings */
#ifdef GMX_THREADS
nice_set=TRUE;
}
tMPI_Thread_mutex_unlock(&init_mutex);
#endif
}
#endif
#endif
/* Update oenv for parsed command line options settings. */
(*oenv)->xvg_format = (xvg_format_t)nenum(xvg_format);
(*oenv)->time_unit = (time_unit_t)nenum(time_units);
if (!(FF(PCA_QUIET) || bQuiet )) {
if (bHelp)
write_man(stderr,"help",output_env_get_program_name(*oenv),
ndesc,desc,nfile, fnm,npall,all_pa, nbugs,bugs,bHidden);
else if (bPrint) {
pr_fns(stderr,nfile,fnm);
print_pargs(stderr,npall,all_pa,FALSE);
}
}
if (strcmp(manstr[0],"no") != 0) {
if(!strcmp(manstr[0],"completion")) {
/* one file each for csh, bash and zsh if we do completions */
fp=man_file(*oenv,"completion-zsh");
write_man(fp,"completion-zsh",output_env_get_program_name(*oenv),
ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
fp=man_file(*oenv,"completion-bash");
write_man(fp,"completion-bash",output_env_get_program_name(*oenv),
ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
fp=man_file(*oenv,"completion-csh");
write_man(fp,"completion-csh",output_env_get_program_name(*oenv),
ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
} else {
fp=man_file(*oenv,manstr[0]);
write_man(fp,manstr[0],output_env_get_program_name(*oenv),
ndesc,desc,nfile,fnm, npall, all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
}
}
/* convert time options, must be done after printing! */
for(i=0; i<npall; i++) {
if ((all_pa[i].type == etTIME) && (*all_pa[i].u.r >= 0)) {
*all_pa[i].u.r *= output_env_get_time_invfactor(*oenv);
}
}
/* Extract Time info from arguments */
if (FF(PCA_CAN_BEGIN) && opt2parg_bSet("-b",npall,all_pa))
setTimeValue(TBEGIN,opt2parg_real("-b",npall,all_pa));
if (FF(PCA_CAN_END) && opt2parg_bSet("-e",npall,all_pa))
setTimeValue(TEND,opt2parg_real("-e",npall,all_pa));
if (FF(PCA_CAN_DT) && opt2parg_bSet("-dt",npall,all_pa))
setTimeValue(TDELTA,opt2parg_real("-dt",npall,all_pa));
/* clear memory */
for (i = 0; i < npall; ++i)
sfree((void *)all_pa[i].desc);
sfree(all_pa);
if (!FF(PCA_NOEXIT_ON_ARGS)) {
if (*argc > 1) {
gmx_cmd(argv[1]);
}
}
if (bExit) {
if (gmx_parallel_env_initialized())
/*gmx_abort(gmx_node_rank(),gmx_node_num(),0);*/
gmx_finalize();
exit(0);
}
#undef FF
}
int gmx_covar(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] calculates and diagonalizes the (mass-weighted)",
"covariance matrix.",
"All structures are fitted to the structure in the structure file.",
"When this is not a run input file periodicity will not be taken into",
"account. When the fit and analysis groups are identical and the analysis",
"is non mass-weighted, the fit will also be non mass-weighted.",
"[PAR]",
"The eigenvectors are written to a trajectory file ([TT]-v[tt]).",
"When the same atoms are used for the fit and the covariance analysis,",
"the reference structure for the fit is written first with t=-1.",
"The average (or reference when [TT]-ref[tt] is used) structure is",
"written with t=0, the eigenvectors",
"are written as frames with the eigenvector number as timestamp.",
"[PAR]",
"The eigenvectors can be analyzed with [gmx-anaeig].",
"[PAR]",
"Option [TT]-ascii[tt] writes the whole covariance matrix to",
"an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ...",
"[PAR]",
"Option [TT]-xpm[tt] writes the whole covariance matrix to an [REF].xpm[ref] file.",
"[PAR]",
"Option [TT]-xpma[tt] writes the atomic covariance matrix to an [REF].xpm[ref] file,",
"i.e. for each atom pair the sum of the xx, yy and zz covariances is",
"written.",
"[PAR]",
"Note that the diagonalization of a matrix requires memory and time",
"that will increase at least as fast as than the square of the number",
"of atoms involved. It is easy to run out of memory, in which",
"case this tool will probably exit with a 'Segmentation fault'. You",
"should consider carefully whether a reduced set of atoms will meet",
"your needs for lower costs."
};
static gmx_bool bFit = TRUE, bRef = FALSE, bM = FALSE, bPBC = TRUE;
static int end = -1;
t_pargs pa[] = {
{ "-fit", FALSE, etBOOL, {&bFit},
"Fit to a reference structure"},
{ "-ref", FALSE, etBOOL, {&bRef},
"Use the deviation from the conformation in the structure file instead of from the average" },
{ "-mwa", FALSE, etBOOL, {&bM},
"Mass-weighted covariance analysis"},
{ "-last", FALSE, etINT, {&end},
"Last eigenvector to write away (-1 is till the last)" },
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Apply corrections for periodic boundary conditions" }
};
FILE *out = NULL; /* initialization makes all compilers happy */
t_trxstatus *status;
t_topology top;
int ePBC;
t_atoms *atoms;
rvec *x, *xread, *xref, *xav, *xproj;
matrix box, zerobox;
real *sqrtm, *mat, *eigenvalues, sum, trace, inv_nframes;
real t, tstart, tend, **mat2;
real xj, *w_rls = NULL;
real min, max, *axis;
int natoms, nat, nframes0, nframes, nlevels;
gmx_int64_t ndim, i, j, k, l;
int WriteXref;
const char *fitfile, *trxfile, *ndxfile;
const char *eigvalfile, *eigvecfile, *averfile, *logfile;
const char *asciifile, *xpmfile, *xpmafile;
char str[STRLEN], *fitname, *ananame;
int d, dj, nfit;
atom_id *index, *ifit;
gmx_bool bDiffMass1, bDiffMass2;
char timebuf[STRLEN];
t_rgb rlo, rmi, rhi;
real *eigenvectors;
output_env_t oenv;
gmx_rmpbc_t gpbc = NULL;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "eigenval", ffWRITE },
{ efTRN, "-v", "eigenvec", ffWRITE },
{ efSTO, "-av", "average.pdb", ffWRITE },
{ efLOG, NULL, "covar", ffWRITE },
{ efDAT, "-ascii", "covar", ffOPTWR },
{ efXPM, "-xpm", "covar", ffOPTWR },
{ efXPM, "-xpma", "covara", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
clear_mat(zerobox);
fitfile = ftp2fn(efTPS, NFILE, fnm);
trxfile = ftp2fn(efTRX, NFILE, fnm);
ndxfile = ftp2fn_null(efNDX, NFILE, fnm);
eigvalfile = ftp2fn(efXVG, NFILE, fnm);
eigvecfile = ftp2fn(efTRN, NFILE, fnm);
averfile = ftp2fn(efSTO, NFILE, fnm);
logfile = ftp2fn(efLOG, NFILE, fnm);
asciifile = opt2fn_null("-ascii", NFILE, fnm);
xpmfile = opt2fn_null("-xpm", NFILE, fnm);
xpmafile = opt2fn_null("-xpma", NFILE, fnm);
read_tps_conf(fitfile, &top, &ePBC, &xref, NULL, box, TRUE);
atoms = &top.atoms;
if (bFit)
{
printf("\nChoose a group for the least squares fit\n");
get_index(atoms, ndxfile, 1, &nfit, &ifit, &fitname);
if (nfit < 3)
{
gmx_fatal(FARGS, "Need >= 3 points to fit!\n");
}
}
else
{
nfit = 0;
}
printf("\nChoose a group for the covariance analysis\n");
get_index(atoms, ndxfile, 1, &natoms, &index, &ananame);
bDiffMass1 = FALSE;
if (bFit)
{
snew(w_rls, atoms->nr);
for (i = 0; (i < nfit); i++)
{
w_rls[ifit[i]] = atoms->atom[ifit[i]].m;
if (i)
{
bDiffMass1 = bDiffMass1 || (w_rls[ifit[i]] != w_rls[ifit[i-1]]);
}
}
}
bDiffMass2 = FALSE;
snew(sqrtm, natoms);
for (i = 0; (i < natoms); i++)
{
if (bM)
{
sqrtm[i] = std::sqrt(atoms->atom[index[i]].m);
if (i)
{
bDiffMass2 = bDiffMass2 || (sqrtm[i] != sqrtm[i-1]);
}
}
else
{
sqrtm[i] = 1.0;
}
}
if (bFit && bDiffMass1 && !bDiffMass2)
{
bDiffMass1 = natoms != nfit;
for (i = 0; (i < natoms) && !bDiffMass1; i++)
{
bDiffMass1 = index[i] != ifit[i];
}
if (!bDiffMass1)
{
fprintf(stderr, "\n"
"Note: the fit and analysis group are identical,\n"
" while the fit is mass weighted and the analysis is not.\n"
" Making the fit non mass weighted.\n\n");
for (i = 0; (i < nfit); i++)
{
w_rls[ifit[i]] = 1.0;
}
}
}
/* Prepare reference frame */
if (bPBC)
{
gpbc = gmx_rmpbc_init(&top.idef, ePBC, atoms->nr);
gmx_rmpbc(gpbc, atoms->nr, box, xref);
}
if (bFit)
{
reset_x(nfit, ifit, atoms->nr, NULL, xref, w_rls);
}
snew(x, natoms);
snew(xav, natoms);
ndim = natoms*DIM;
if (std::sqrt(static_cast<real>(GMX_INT64_MAX)) < static_cast<real>(ndim))
{
gmx_fatal(FARGS, "Number of degrees of freedoms to large for matrix.\n");
}
snew(mat, ndim*ndim);
fprintf(stderr, "Calculating the average structure ...\n");
nframes0 = 0;
nat = read_first_x(oenv, &status, trxfile, &t, &xread, box);
if (nat != atoms->nr)
{
fprintf(stderr, "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n", natoms, nat);
}
do
{
nframes0++;
/* calculate x: a fitted struture of the selected atoms */
if (bPBC)
{
gmx_rmpbc(gpbc, nat, box, xread);
}
if (bFit)
{
reset_x(nfit, ifit, nat, NULL, xread, w_rls);
do_fit(nat, w_rls, xref, xread);
}
for (i = 0; i < natoms; i++)
{
rvec_inc(xav[i], xread[index[i]]);
}
}
while (read_next_x(oenv, status, &t, xread, box));
close_trj(status);
inv_nframes = 1.0/nframes0;
for (i = 0; i < natoms; i++)
{
for (d = 0; d < DIM; d++)
{
xav[i][d] *= inv_nframes;
xread[index[i]][d] = xav[i][d];
}
}
write_sto_conf_indexed(opt2fn("-av", NFILE, fnm), "Average structure",
atoms, xread, NULL, epbcNONE, zerobox, natoms, index);
sfree(xread);
fprintf(stderr, "Constructing covariance matrix (%dx%d) ...\n", static_cast<int>(ndim), static_cast<int>(ndim));
nframes = 0;
nat = read_first_x(oenv, &status, trxfile, &t, &xread, box);
tstart = t;
do
{
nframes++;
tend = t;
/* calculate x: a (fitted) structure of the selected atoms */
if (bPBC)
{
gmx_rmpbc(gpbc, nat, box, xread);
}
if (bFit)
{
reset_x(nfit, ifit, nat, NULL, xread, w_rls);
do_fit(nat, w_rls, xref, xread);
}
if (bRef)
{
for (i = 0; i < natoms; i++)
{
rvec_sub(xread[index[i]], xref[index[i]], x[i]);
}
}
else
{
for (i = 0; i < natoms; i++)
{
rvec_sub(xread[index[i]], xav[i], x[i]);
}
}
for (j = 0; j < natoms; j++)
{
for (dj = 0; dj < DIM; dj++)
{
k = ndim*(DIM*j+dj);
xj = x[j][dj];
for (i = j; i < natoms; i++)
{
l = k+DIM*i;
for (d = 0; d < DIM; d++)
{
mat[l+d] += x[i][d]*xj;
}
}
}
}
}
while (read_next_x(oenv, status, &t, xread, box) &&
(bRef || nframes < nframes0));
close_trj(status);
gmx_rmpbc_done(gpbc);
fprintf(stderr, "Read %d frames\n", nframes);
if (bRef)
{
/* copy the reference structure to the ouput array x */
snew(xproj, natoms);
for (i = 0; i < natoms; i++)
{
copy_rvec(xref[index[i]], xproj[i]);
}
}
else
{
xproj = xav;
}
/* correct the covariance matrix for the mass */
inv_nframes = 1.0/nframes;
for (j = 0; j < natoms; j++)
{
for (dj = 0; dj < DIM; dj++)
{
for (i = j; i < natoms; i++)
{
k = ndim*(DIM*j+dj)+DIM*i;
for (d = 0; d < DIM; d++)
{
mat[k+d] = mat[k+d]*inv_nframes*sqrtm[i]*sqrtm[j];
}
}
}
}
/* symmetrize the matrix */
for (j = 0; j < ndim; j++)
{
for (i = j; i < ndim; i++)
{
mat[ndim*i+j] = mat[ndim*j+i];
}
}
trace = 0;
for (i = 0; i < ndim; i++)
{
trace += mat[i*ndim+i];
}
fprintf(stderr, "\nTrace of the covariance matrix: %g (%snm^2)\n",
trace, bM ? "u " : "");
if (asciifile)
{
out = gmx_ffopen(asciifile, "w");
for (j = 0; j < ndim; j++)
{
for (i = 0; i < ndim; i += 3)
{
fprintf(out, "%g %g %g\n",
mat[ndim*j+i], mat[ndim*j+i+1], mat[ndim*j+i+2]);
}
}
gmx_ffclose(out);
}
if (xpmfile)
{
min = 0;
max = 0;
snew(mat2, ndim);
for (j = 0; j < ndim; j++)
{
mat2[j] = &(mat[ndim*j]);
for (i = 0; i <= j; i++)
{
if (mat2[j][i] < min)
{
min = mat2[j][i];
}
if (mat2[j][j] > max)
{
max = mat2[j][i];
}
}
}
snew(axis, ndim);
for (i = 0; i < ndim; i++)
{
axis[i] = i+1;
}
rlo.r = 0; rlo.g = 0; rlo.b = 1;
rmi.r = 1; rmi.g = 1; rmi.b = 1;
rhi.r = 1; rhi.g = 0; rhi.b = 0;
out = gmx_ffopen(xpmfile, "w");
nlevels = 80;
write_xpm3(out, 0, "Covariance", bM ? "u nm^2" : "nm^2",
"dim", "dim", ndim, ndim, axis, axis,
mat2, min, 0.0, max, rlo, rmi, rhi, &nlevels);
gmx_ffclose(out);
sfree(axis);
sfree(mat2);
}
if (xpmafile)
{
min = 0;
max = 0;
snew(mat2, ndim/DIM);
for (i = 0; i < ndim/DIM; i++)
{
snew(mat2[i], ndim/DIM);
}
for (j = 0; j < ndim/DIM; j++)
{
for (i = 0; i <= j; i++)
{
mat2[j][i] = 0;
for (d = 0; d < DIM; d++)
{
mat2[j][i] += mat[ndim*(DIM*j+d)+DIM*i+d];
}
if (mat2[j][i] < min)
{
min = mat2[j][i];
}
if (mat2[j][j] > max)
{
max = mat2[j][i];
}
mat2[i][j] = mat2[j][i];
}
}
snew(axis, ndim/DIM);
for (i = 0; i < ndim/DIM; i++)
{
axis[i] = i+1;
}
rlo.r = 0; rlo.g = 0; rlo.b = 1;
rmi.r = 1; rmi.g = 1; rmi.b = 1;
rhi.r = 1; rhi.g = 0; rhi.b = 0;
out = gmx_ffopen(xpmafile, "w");
nlevels = 80;
write_xpm3(out, 0, "Covariance", bM ? "u nm^2" : "nm^2",
"atom", "atom", ndim/DIM, ndim/DIM, axis, axis,
mat2, min, 0.0, max, rlo, rmi, rhi, &nlevels);
gmx_ffclose(out);
sfree(axis);
for (i = 0; i < ndim/DIM; i++)
{
sfree(mat2[i]);
}
sfree(mat2);
}
/* call diagonalization routine */
snew(eigenvalues, ndim);
snew(eigenvectors, ndim*ndim);
std::memcpy(eigenvectors, mat, ndim*ndim*sizeof(real));
fprintf(stderr, "\nDiagonalizing ...\n");
fflush(stderr);
eigensolver(eigenvectors, ndim, 0, ndim, eigenvalues, mat);
sfree(eigenvectors);
/* now write the output */
sum = 0;
for (i = 0; i < ndim; i++)
{
sum += eigenvalues[i];
}
fprintf(stderr, "\nSum of the eigenvalues: %g (%snm^2)\n",
sum, bM ? "u " : "");
if (std::abs(trace-sum) > 0.01*trace)
{
fprintf(stderr, "\nWARNING: eigenvalue sum deviates from the trace of the covariance matrix\n");
}
/* Set 'end', the maximum eigenvector and -value index used for output */
if (end == -1)
{
if (nframes-1 < ndim)
{
end = nframes-1;
fprintf(stderr, "\nWARNING: there are fewer frames in your trajectory than there are\n");
fprintf(stderr, "degrees of freedom in your system. Only generating the first\n");
fprintf(stderr, "%d out of %d eigenvectors and eigenvalues.\n", end, static_cast<int>(ndim));
}
else
{
end = ndim;
}
}
fprintf(stderr, "\nWriting eigenvalues to %s\n", eigvalfile);
sprintf(str, "(%snm\\S2\\N)", bM ? "u " : "");
out = xvgropen(eigvalfile,
"Eigenvalues of the covariance matrix",
"Eigenvector index", str, oenv);
for (i = 0; (i < end); i++)
{
fprintf (out, "%10d %g\n", static_cast<int>(i+1), eigenvalues[ndim-1-i]);
}
xvgrclose(out);
if (bFit)
{
/* misuse lambda: 0/1 mass weighted analysis no/yes */
if (nfit == natoms)
{
WriteXref = eWXR_YES;
for (i = 0; i < nfit; i++)
{
copy_rvec(xref[ifit[i]], x[i]);
}
}
else
{
WriteXref = eWXR_NO;
}
}
else
{
/* misuse lambda: -1 for no fit */
WriteXref = eWXR_NOFIT;
}
write_eigenvectors(eigvecfile, natoms, mat, TRUE, 1, end,
WriteXref, x, bDiffMass1, xproj, bM, eigenvalues);
out = gmx_ffopen(logfile, "w");
gmx_format_current_time(timebuf, STRLEN);
fprintf(out, "Covariance analysis log, written %s\n", timebuf);
fprintf(out, "Program: %s\n", argv[0]);
gmx_getcwd(str, STRLEN);
fprintf(out, "Working directory: %s\n\n", str);
fprintf(out, "Read %d frames from %s (time %g to %g %s)\n", nframes, trxfile,
output_env_conv_time(oenv, tstart), output_env_conv_time(oenv, tend), output_env_get_time_unit(oenv));
if (bFit)
{
fprintf(out, "Read reference structure for fit from %s\n", fitfile);
}
if (ndxfile)
{
fprintf(out, "Read index groups from %s\n", ndxfile);
}
fprintf(out, "\n");
fprintf(out, "Analysis group is '%s' (%d atoms)\n", ananame, natoms);
if (bFit)
{
fprintf(out, "Fit group is '%s' (%d atoms)\n", fitname, nfit);
}
else
{
fprintf(out, "No fit was used\n");
}
fprintf(out, "Analysis is %smass weighted\n", bDiffMass2 ? "" : "non-");
if (bFit)
{
fprintf(out, "Fit is %smass weighted\n", bDiffMass1 ? "" : "non-");
}
fprintf(out, "Diagonalized the %dx%d covariance matrix\n", static_cast<int>(ndim), static_cast<int>(ndim));
fprintf(out, "Trace of the covariance matrix before diagonalizing: %g\n",
trace);
fprintf(out, "Trace of the covariance matrix after diagonalizing: %g\n\n",
sum);
fprintf(out, "Wrote %d eigenvalues to %s\n", static_cast<int>(end), eigvalfile);
if (WriteXref == eWXR_YES)
{
fprintf(out, "Wrote reference structure to %s\n", eigvecfile);
}
fprintf(out, "Wrote average structure to %s and %s\n", averfile, eigvecfile);
fprintf(out, "Wrote eigenvectors %d to %d to %s\n", 1, end, eigvecfile);
gmx_ffclose(out);
fprintf(stderr, "Wrote the log to %s\n", logfile);
return 0;
}
