std::string Path::getWorkingDirectory()
{
// TODO: Use exceptions instead of gmx_fatal().
char cwd[GMX_PATH_MAX];
gmx_getcwd(cwd, sizeof(cwd));
return cwd;
}
/* Open the file to be processed. The handle variable holds internal
info for the cpp emulator. Return integer status */
int cpp_open_file(const char *filenm, gmx_cpp_t *handle, char **cppopts)
{
gmx_cpp_t cpp;
char *buf, *pdum;
char *ptr, *ptr2;
int i;
unsigned int i1;
/* First process options, they might be necessary for opening files
(especially include statements). */
i = 0;
if (cppopts)
{
while (cppopts[i])
{
if (strstr(cppopts[i], "-I") == cppopts[i])
{
add_include(cppopts[i]+2);
}
if (strstr(cppopts[i], "-D") == cppopts[i])
{
/* If the option contains a =, split it into name and value. */
ptr = strchr(cppopts[i], '=');
if (ptr)
{
buf = gmx_strndup(cppopts[i] + 2, ptr - cppopts[i] - 2);
add_define(buf, ptr + 1);
sfree(buf);
}
else
{
add_define(cppopts[i] + 2, NULL);
}
}
i++;
}
}
if (debug)
{
fprintf(debug, "GMXCPP: added %d command line arguments\n", i);
}
snew(cpp, 1);
*handle = cpp;
cpp->fn = NULL;
/* Find the file. First check whether it is in the current directory. */
if (gmx_fexist(filenm))
{
cpp->fn = gmx_strdup(filenm);
}
else
{
/* If not, check all the paths given with -I. */
for (i = 0; i < nincl; ++i)
{
snew(buf, strlen(incl[i]) + strlen(filenm) + 2);
sprintf(buf, "%s/%s", incl[i], filenm);
if (gmx_fexist(buf))
{
cpp->fn = buf;
break;
}
sfree(buf);
}
/* If still not found, check the Gromacs library search path. */
if (!cpp->fn)
{
cpp->fn = low_gmxlibfn(filenm, FALSE, FALSE);
}
}
if (!cpp->fn)
{
gmx_fatal(FARGS, "Topology include file \"%s\" not found", filenm);
}
if (NULL != debug)
{
fprintf(debug, "GMXCPP: cpp file open %s\n", cpp->fn);
}
/* If the file name has a path component, we need to change to that
* directory. Note that we - just as C - always use UNIX path separators
* internally in include file names.
*/
ptr = strrchr(cpp->fn, '/');
ptr2 = strrchr(cpp->fn, DIR_SEPARATOR);
if (ptr == NULL || (ptr2 != NULL && ptr2 > ptr))
{
ptr = ptr2;
}
if (ptr == NULL)
{
cpp->path = NULL;
cpp->cwd = NULL;
}
else
{
cpp->path = cpp->fn;
*ptr = '\0';
cpp->fn = gmx_strdup(ptr+1);
snew(cpp->cwd, STRLEN);
gmx_getcwd(cpp->cwd, STRLEN);
if (NULL != debug)
{
fprintf(debug, "GMXCPP: cwd %s\n", cpp->cwd);
}
gmx_chdir(cpp->path);
if (NULL != debug)
{
fprintf(debug, "GMXCPP: chdir to %s\n", cpp->path);
}
}
cpp->line_len = 0;
cpp->line = NULL;
cpp->line_nr = 0;
cpp->nifdef = 0;
cpp->ifdefs = NULL;
cpp->child = NULL;
cpp->parent = NULL;
if (cpp->fp == NULL)
{
if (NULL != debug)
{
fprintf(debug, "GMXCPP: opening file %s\n", cpp->fn);
}
cpp->fp = fopen(cpp->fn, "r");
}
if (cpp->fp == NULL)
{
switch (errno)
{
case EINVAL:
default:
return eCPP_UNKNOWN;
}
}
return eCPP_OK;
}
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;
gmx_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;
}
