nuphill++;
}
- fprintf(log, "Iter: %d Swapped %4d and %4d (energy: %g prob: %g)\n", i, iswap, jswap,
- enext, prob);
+ fprintf(log, "Iter: %d Swapped %4d and %4d (energy: %g prob: %g)\n", i, iswap, jswap, enext, prob);
if (nullptr != fp)
{
fprintf(fp, "%6d %10g\n", i, enext);
fprintf(log, "Swapped time and frame indices and RMSD to next neighbor:\n");
for (i = 0; (i < m->nn); i++)
{
- fprintf(log, "%10g %5d %10g\n", time[m->m_ind[i]], m->m_ind[i],
+ fprintf(log,
+ "%10g %5d %10g\n",
+ time[m->m_ind[i]],
+ m->m_ind[i],
(i < m->nn - 1) ? m->mat[m->m_ind[i]][m->m_ind[i + 1]] : 0);
}
trans[clust->cl[i] - 1][clust->cl[i - 1] - 1]));
}
}
- ffprintf_dd(stderr, log, buf,
+ ffprintf_dd(stderr,
+ log,
+ buf,
"Counted %d transitions in total, "
"max %d between two specific clusters\n",
- ntranst, maxtrans);
+ ntranst,
+ maxtrans);
if (transfn)
{
fp = gmx_ffopen(transfn, "w");
i = std::min(maxtrans + 1, 80);
- write_xpm(fp, 0, "Cluster Transitions", "# transitions", "from cluster", "to cluster",
- clust->ncl, clust->ncl, axis, axis, trans, 0, maxtrans, rlo, rhi, &i);
+ write_xpm(fp,
+ 0,
+ "Cluster Transitions",
+ "# transitions",
+ "from cluster",
+ "to cluster",
+ clust->ncl,
+ clust->ncl,
+ axis,
+ axis,
+ trans,
+ 0,
+ maxtrans,
+ rlo,
+ rhi,
+ &i);
gmx_ffclose(fp);
}
if (ntransfn)
trxsfn = parse_filename(trxfn, std::max(write_ncl, clust->ncl));
snew(bWrite, nf);
}
- ffprintf_ss(stderr, log, buf, "Writing %s structure for each cluster to %s\n",
- bAverage ? "average" : "middle", trxfn);
+ ffprintf_ss(stderr,
+ log,
+ buf,
+ "Writing %s structure for each cluster to %s\n",
+ bAverage ? "average" : "middle",
+ trxfn);
if (write_ncl)
{
/* find out what we want to tell the user:
}
snew(structure, nf);
- fprintf(log, "\n%3s | %3s %4s | %6s %4s | cluster members\n", "cl.", "#st", "rmsd", "middle",
+ fprintf(log,
+ "\n%3s | %3s %4s | %6s %4s | cluster members\n",
+ "cl.",
+ "#st",
+ "rmsd",
+ "middle",
"rmsd");
for (cl = 1; cl <= clust->ncl; cl++)
{
}
if (bWrite[i])
{
- write_trx(trxsout, iosize, outidx, atoms, i, time[structure[i]],
- boxes[structure[i]], xx[structure[i]], nullptr, nullptr);
+ write_trx(trxsout,
+ iosize,
+ outidx,
+ atoms,
+ i,
+ time[structure[i]],
+ boxes[structure[i]],
+ xx[structure[i]],
+ nullptr,
+ nullptr);
}
}
close_trx(trxsout);
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc,
+ argv,
+ PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
+ NFILE,
+ fnm,
+ asize(pa),
+ pa,
+ asize(desc),
+ desc,
+ 0,
+ nullptr,
+ &oenv))
{
return 0;
}
}
if (bReadMat && output_env_get_time_factor(oenv) != 1)
{
- fprintf(stderr, "\nWarning: assuming the time unit in %s is %s\n",
- opt2fn("-dm", NFILE, fnm), output_env_get_time_unit(oenv).c_str());
+ fprintf(stderr,
+ "\nWarning: assuming the time unit in %s is %s\n",
+ opt2fn("-dm", NFILE, fnm),
+ output_env_get_time_unit(oenv).c_str());
}
if (trx_out_fn && !bReadTraj)
{
gmx_fatal(FARGS,
"Matrix size (%dx%d) does not match the number of "
"frames (%d)",
- readmat[0].nx, readmat[0].ny, nf);
+ readmat[0].nx,
+ readmat[0].ny,
+ nf);
}
nf = readmat[0].nx;
fprintf(stderr,
"WARNING: rmsd cutoff %g is outside range of rmsd values "
"%g to %g\n",
- rmsdcut, rms->minrms, rms->maxrms);
+ rmsdcut,
+ rms->minrms,
+ rms->maxrms);
}
if (bAnalyze && (rmsmin < rms->minrms))
{
eigensolver(eigenvectors, nf, 0, nf, eigenvalues, rms->mat[0]);
sfree(eigenvectors);
- fp = xvgropen(opt2fn("-ev", NFILE, fnm), "RMSD matrix Eigenvalues", "Eigenvector index",
- "Eigenvalues (nm\\S2\\N)", oenv);
+ fp = xvgropen(opt2fn("-ev", NFILE, fnm),
+ "RMSD matrix Eigenvalues",
+ "Eigenvector index",
+ "Eigenvalues (nm\\S2\\N)",
+ oenv);
for (i = 0; (i < nf); i++)
{
fprintf(fp, "%10d %10g\n", i, eigenvalues[i]);
copy_rvec(xtps[index[i]], usextps[i]);
}
useatoms.nr = isize;
- analyze_clusters(nf, &clust, rms->mat, isize, &useatoms, usextps, mass, xx, time, boxes,
- frameindices, ifsize, fitidx, iosize, outidx,
- bReadTraj ? trx_out_fn : nullptr, opt2fn_null("-sz", NFILE, fnm),
- opt2fn_null("-tr", NFILE, fnm), opt2fn_null("-ntr", NFILE, fnm),
- opt2fn_null("-clid", NFILE, fnm), opt2fn_null("-clndx", NFILE, fnm),
- bAverage, write_ncl, write_nst, rmsmin, bFit, log, rlo_bot, rhi_bot, oenv);
+ analyze_clusters(nf,
+ &clust,
+ rms->mat,
+ isize,
+ &useatoms,
+ usextps,
+ mass,
+ xx,
+ time,
+ boxes,
+ frameindices,
+ ifsize,
+ fitidx,
+ iosize,
+ outidx,
+ bReadTraj ? trx_out_fn : nullptr,
+ opt2fn_null("-sz", NFILE, fnm),
+ opt2fn_null("-tr", NFILE, fnm),
+ opt2fn_null("-ntr", NFILE, fnm),
+ opt2fn_null("-clid", NFILE, fnm),
+ opt2fn_null("-clndx", NFILE, fnm),
+ bAverage,
+ write_ncl,
+ write_nst,
+ rmsmin,
+ bFit,
+ log,
+ rlo_bot,
+ rhi_bot,
+ oenv);
sfree(boxes);
sfree(frameindices);
}
fprintf(stderr, "Writing rms distance/clustering matrix ");
if (bReadMat)
{
- write_xpm(fp, 0, readmat[0].title, readmat[0].legend, readmat[0].label_x,
- readmat[0].label_y, nf, nf, readmat[0].axis_x.data(), readmat[0].axis_y.data(),
- rms->mat, 0.0, rms->maxrms, rlo_top, rhi_top, &nlevels);
+ write_xpm(fp,
+ 0,
+ readmat[0].title,
+ readmat[0].legend,
+ readmat[0].label_x,
+ readmat[0].label_y,
+ nf,
+ nf,
+ readmat[0].axis_x.data(),
+ readmat[0].axis_y.data(),
+ rms->mat,
+ 0.0,
+ rms->maxrms,
+ rlo_top,
+ rhi_top,
+ &nlevels);
}
else
{
auto title = gmx::formatString("RMS%sDeviation / Cluster Index", bRMSdist ? " Distance " : " ");
if (minstruct > 1)
{
- write_xpm_split(fp, 0, title, "RMSD (nm)", timeLabel, timeLabel, nf, nf, time, time,
- rms->mat, 0.0, rms->maxrms, &nlevels, rlo_top, rhi_top, 0.0, ncluster,
- &ncluster, TRUE, rlo_bot, rhi_bot);
+ write_xpm_split(fp,
+ 0,
+ title,
+ "RMSD (nm)",
+ timeLabel,
+ timeLabel,
+ nf,
+ nf,
+ time,
+ time,
+ rms->mat,
+ 0.0,
+ rms->maxrms,
+ &nlevels,
+ rlo_top,
+ rhi_top,
+ 0.0,
+ ncluster,
+ &ncluster,
+ TRUE,
+ rlo_bot,
+ rhi_bot);
}
else
{
- write_xpm(fp, 0, title, "RMSD (nm)", timeLabel, timeLabel, nf, nf, time, time, rms->mat,
- 0.0, rms->maxrms, rlo_top, rhi_top, &nlevels);
+ write_xpm(fp,
+ 0,
+ title,
+ "RMSD (nm)",
+ timeLabel,
+ timeLabel,
+ nf,
+ nf,
+ time,
+ time,
+ rms->mat,
+ 0.0,
+ rms->maxrms,
+ rlo_top,
+ rhi_top,
+ &nlevels);
}
}
fprintf(stderr, "\n");
fp = opt2FILE("-om", NFILE, fnm, "w");
auto timeLabel = output_env_get_time_label(oenv);
auto title = gmx::formatString("RMS%sDeviation", bRMSdist ? " Distance " : " ");
- write_xpm(fp, 0, title, "RMSD (nm)", timeLabel, timeLabel, nf, nf, time, time, orig->mat,
- 0.0, orig->maxrms, rlo_top, rhi_top, &nlevels);
+ write_xpm(fp,
+ 0,
+ title,
+ "RMSD (nm)",
+ timeLabel,
+ timeLabel,
+ nf,
+ nf,
+ time,
+ time,
+ orig->mat,
+ 0.0,
+ orig->maxrms,
+ rlo_top,
+ rhi_top,
+ &nlevels);
gmx_ffclose(fp);
done_mat(&orig);
sfree(orig);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff