void xvgr_header(FILE *fp, const char *title, const char *xaxis,
const char *yaxis, int exvg_graph_type,
const output_env_t oenv)
{
char pukestr[100], buf[STRLEN];
time_t t;
if (output_env_get_print_xvgr_codes(oenv))
{
time(&t);
gmx_ctime_r(&t, buf, STRLEN);
fprintf(fp, "# This file was created %s", buf);
fprintf(fp, "# by the following command:\n# %s\n#\n", command_line());
fprintf(fp, "# %s is part of G R O M A C S:\n#\n", ShortProgram());
bromacs(pukestr, 99);
fprintf(fp, "# %s\n#\n", pukestr);
fprintf(fp, "@ title \"%s\"\n", xvgrstr(title, oenv, buf, STRLEN));
fprintf(fp, "@ xaxis label \"%s\"\n",
xvgrstr(xaxis, oenv, buf, STRLEN));
fprintf(fp, "@ yaxis label \"%s\"\n",
xvgrstr(yaxis, oenv, buf, STRLEN));
switch (exvg_graph_type)
{
case exvggtXNY:
if (output_env_get_xvg_format(oenv) == exvgXMGR)
{
fprintf(fp, "@TYPE nxy\n");
}
else
{
fprintf(fp, "@TYPE xy\n");
}
break;
case exvggtXYDY:
fprintf(fp, "@TYPE xydy\n");
break;
case exvggtXYDYDY:
fprintf(fp, "@TYPE xydydy\n");
break;
}
}
}
void nice_header (FILE *out,const char *fn)
{
const char *unk = "onbekend";
time_t clock;
char *user=NULL;
int gh;
uid_t uid;
char buf[256];
char timebuf[STRLEN];
#ifdef HAVE_PWD_H
struct passwd *pw;
#endif
/* Print a nice header above the file */
time(&clock);
fprintf (out,"%c\n",COMMENTSIGN);
fprintf (out,"%c\tFile '%s' was generated\n",COMMENTSIGN,fn ? fn : unk);
#ifdef HAVE_PWD_H
uid = getuid();
pw = getpwuid(uid);
gh = gethostname(buf,255);
user= pw->pw_name;
#else
uid = 0;
gh = -1;
#endif
gmx_ctime_r(&clock,timebuf,STRLEN);
fprintf (out,"%c\tBy user: %s (%d)\n",COMMENTSIGN,
user ? user : unk,(int) uid);
fprintf(out,"%c\tOn host: %s\n",COMMENTSIGN,(gh == 0) ? buf : unk);
fprintf (out,"%c\tAt date: %s",COMMENTSIGN,timebuf);
fprintf (out,"%c\n",COMMENTSIGN);
}
void gmx_log_open(const char *lognm, const t_commrec *cr, gmx_bool bMasterOnly,
gmx_bool bAppendFiles, FILE** fplog)
{
int len, pid;
char buf[256], host[256];
time_t t;
char timebuf[STRLEN];
FILE *fp = *fplog;
char *tmpnm;
debug_gmx();
/* Communicate the filename for logfile */
if (cr->nnodes > 1 && !bMasterOnly
#ifdef GMX_THREAD_MPI
/* With thread MPI the non-master log files are opened later
* when the files names are already known on all nodes.
*/
&& FALSE
#endif
)
{
if (MASTER(cr))
{
len = strlen(lognm) + 1;
}
gmx_bcast(sizeof(len), &len, cr);
if (!MASTER(cr))
{
snew(tmpnm, len+8);
}
else
{
tmpnm = gmx_strdup(lognm);
}
gmx_bcast(len*sizeof(*tmpnm), tmpnm, cr);
}
else
{
tmpnm = gmx_strdup(lognm);
}
debug_gmx();
if (!bMasterOnly && !MASTER(cr))
{
/* Since log always ends with '.log' let's use this info */
par_fn(tmpnm, efLOG, cr, FALSE, !bMasterOnly, buf, 255);
fp = gmx_fio_fopen(buf, bAppendFiles ? "a+" : "w+" );
}
else if (!bAppendFiles)
{
fp = gmx_fio_fopen(tmpnm, bAppendFiles ? "a+" : "w+" );
}
sfree(tmpnm);
gmx_fatal_set_log_file(fp);
/* Get some machine parameters */
gmx_gethostname(host, 256);
time(&t);
#ifndef NO_GETPID
# ifdef GMX_NATIVE_WINDOWS
pid = _getpid();
# else
pid = getpid();
# endif
#else
pid = 0;
#endif
if (bAppendFiles)
{
fprintf(fp,
"\n"
"\n"
"-----------------------------------------------------------\n"
"Restarting from checkpoint, appending to previous log file.\n"
"\n"
);
}
gmx_ctime_r(&t, timebuf, STRLEN);
fprintf(fp,
"Log file opened on %s"
"Host: %s pid: %d rank ID: %d number of ranks: %d\n",
timebuf, host, pid, cr->nodeid, cr->nnodes);
try
{
gmx::BinaryInformationSettings settings;
settings.extendedInfo(true);
settings.copyright(!bAppendFiles);
gmx::printBinaryInformation(fp, gmx::getProgramContext(), settings);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
fprintf(fp, "\n\n");
fflush(fp);
debug_gmx();
*fplog = fp;
}
int gmx_covar(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_covar[tt] 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 [TT]g_anaeig[tt].",
"[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 [TT].xpm[tt] file.",
"[PAR]",
"Option [TT]-xpma[tt] writes the atomic covariance matrix to an [TT].xpm[tt] 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;
t_trxstatus *status;
t_trxstatus *trjout;
t_topology top;
int ePBC;
t_atoms *atoms;
rvec *x,*xread,*xref,*xav,*xproj;
matrix box,zerobox;
real *sqrtm,*mat,*eigval,sum,trace,inv_nframes;
real t,tstart,tend,**mat2;
real xj,*w_rls=NULL;
real min,max,*axis;
int ntopatoms,step;
int natoms,nat,count,nframes0,nframes,nlevels;
gmx_large_int_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,*pcwd;
int d,dj,nfit;
atom_id *index,*ifit;
gmx_bool bDiffMass1,bDiffMass2;
time_t now;
char timebuf[STRLEN];
t_rgb rlo,rmi,rhi;
real *tmp;
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)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
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,str,&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]=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;
i=0;
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,box);
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 (sqrt(GMX_LARGE_INT_MAX)<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,nat,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",(int)ndim,(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,nat,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 = 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]);
}
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 = 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);
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 = 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);
ffclose(out);
sfree(axis);
for (i=0; i<ndim/DIM; i++)
sfree(mat2[i]);
sfree(mat2);
}
/* call diagonalization routine */
fprintf(stderr,"\nDiagonalizing ...\n");
fflush(stderr);
snew(eigval,ndim);
snew(tmp,ndim*ndim);
memcpy(tmp,mat,ndim*ndim*sizeof(real));
eigensolver(tmp,ndim,0,ndim,eigval,mat);
sfree(tmp);
/* now write the output */
sum=0;
for(i=0; i<ndim; i++)
sum+=eigval[i];
fprintf(stderr,"\nSum of the eigenvalues: %g (%snm^2)\n",
sum,bM ? "u " : "");
if (fabs(trace-sum)>0.01*trace)
fprintf(stderr,"\nWARNING: eigenvalue sum deviates from the trace of the covariance matrix\n");
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<ndim); i++)
fprintf (out,"%10d %g\n",(int)i+1,eigval[ndim-1-i]);
ffclose(out);
if (end==-1) {
if (nframes-1 < ndim)
end=nframes-1;
else
end=ndim;
}
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,eigval);
out = ffopen(logfile,"w");
time(&now);
gmx_ctime_r(&now,timebuf,STRLEN);
fprintf(out,"Covariance analysis log, written %s\n",timebuf);
fprintf(out,"Program: %s\n",argv[0]);
#if ((defined WIN32 || defined _WIN32 || defined WIN64 || defined _WIN64) && !defined __CYGWIN__ && !defined __CYGWIN32__)
pcwd=_getcwd(str,STRLEN);
#else
pcwd=getcwd(str,STRLEN);
#endif
if(NULL==pcwd)
{
gmx_fatal(FARGS,"Current working directory is undefined");
}
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",(int)ndim,(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",(int)ndim,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);
ffclose(out);
fprintf(stderr,"Wrote the log to %s\n",logfile);
thanx(stderr);
return 0;
}
