void write_sto_conf_indexed(const char *outfile, const char *title,
t_atoms *atoms,
rvec x[], rvec *v, int ePBC, matrix box,
atom_id nindex, atom_id index[])
{
FILE *out;
int ftp;
t_trxframe fr;
ftp = fn2ftp(outfile);
switch (ftp)
{
case efGRO:
out = gmx_fio_fopen(outfile, "w");
write_hconf_indexed_p(out, title, atoms, nindex, index, 3, x, v, box);
gmx_fio_fclose(out);
break;
case efG96:
clear_trxframe(&fr, TRUE);
fr.bTitle = TRUE;
fr.title = title;
fr.natoms = atoms->nr;
fr.bAtoms = TRUE;
fr.atoms = atoms;
fr.bX = TRUE;
fr.x = x;
if (v)
{
fr.bV = TRUE;
fr.v = v;
}
fr.bBox = TRUE;
copy_mat(box, fr.box);
out = gmx_fio_fopen(outfile, "w");
write_g96_conf(out, &fr, nindex, index);
gmx_fio_fclose(out);
break;
case efPDB:
case efBRK:
case efENT:
case efPQR:
out = gmx_fio_fopen(outfile, "w");
write_pdbfile_indexed(out, title, atoms, x, ePBC, box, ' ', -1, nindex, index, NULL, TRUE);
gmx_fio_fclose(out);
break;
case efESP:
out = gmx_fio_fopen(outfile, "w");
write_espresso_conf_indexed(out, title, atoms, nindex, index, x, v, box);
gmx_fio_fclose(out);
break;
case efTPR:
case efTPB:
case efTPA:
gmx_fatal(FARGS, "Sorry, can not write a topology to %s", outfile);
break;
default:
gmx_incons("Not supported in write_sto_conf_indexed");
}
}
//! Helper function to obtain resources
t_trxframe *make_trxframe()
{
t_trxframe *frame;
snew(frame, 1);
clear_trxframe(frame, true);
return frame;
}
gmx_bool read_next_v(const output_env_t oenv,t_trxstatus *status,real *t,
int natoms,rvec v[], matrix box)
{
t_trxframe fr;
gmx_bool bRet;
clear_trxframe(&fr,TRUE);
fr.flags = TRX_NEED_V;
fr.natoms = natoms;
fr.time = *t;
fr.v = v;
bRet = read_next_frame(oenv,status,&fr);
*t = fr.time;
clear_v(&fr);
copy_mat(fr.box,box);
return bRet;
}
int write_trx(t_trxstatus *status, int nind, const int *ind, const t_atoms *atoms,
int step, real time, matrix box, rvec x[], rvec *v,
gmx_conect gc)
{
t_trxframe fr;
clear_trxframe(&fr, TRUE);
fr.bStep = TRUE;
fr.step = step;
fr.bTime = TRUE;
fr.time = time;
fr.bAtoms = atoms != nullptr;
fr.atoms = const_cast<t_atoms *>(atoms);
fr.bX = TRUE;
fr.x = x;
fr.bV = v != nullptr;
fr.v = v;
fr.bBox = TRUE;
copy_mat(box, fr.box);
return write_trxframe_indexed(status, &fr, nind, ind, gc);
}
bool read_first_frame(const gmx_output_env_t *oenv, t_trxstatus **status,
const char *fn, t_trxframe *fr, int flags)
{
t_fileio *fio = nullptr;
gmx_bool bFirst, bOK;
int ftp = fn2ftp(fn);
clear_trxframe(fr, TRUE);
bFirst = TRUE;
snew((*status), 1);
status_init( *status );
initcount(*status);
(*status)->flags = flags;
if (efTNG == ftp)
{
/* Special treatment for TNG files */
gmx_tng_open(fn, 'r', &(*status)->tng);
}
else
{
fio = (*status)->fio = gmx_fio_open(fn, "r");
}
switch (ftp)
{
case efTRR:
break;
case efCPT:
read_checkpoint_trxframe(fio, fr);
bFirst = FALSE;
break;
case efG96:
{
/* Can not rewind a compressed file, so open it twice */
if (!(*status)->persistent_line)
{
/* allocate the persistent line */
snew((*status)->persistent_line, STRLEN+1);
}
t_symtab *symtab = nullptr;
read_g96_conf(gmx_fio_getfp(fio), fn, nullptr, fr, symtab, (*status)->persistent_line);
gmx_fio_close(fio);
clear_trxframe(fr, FALSE);
if (flags & (TRX_READ_X | TRX_NEED_X))
{
snew(fr->x, fr->natoms);
}
if (flags & (TRX_READ_V | TRX_NEED_V))
{
snew(fr->v, fr->natoms);
}
(*status)->fio = gmx_fio_open(fn, "r");
break;
}
case efXTC:
if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
&fr->prec, &bOK) == 0)
{
GMX_RELEASE_ASSERT(!bOK, "Inconsistent results - OK status from read_first_xtc, but 0 atom coords read");
fr->not_ok = DATA_NOT_OK;
}
if (fr->not_ok)
{
fr->natoms = 0;
printincomp(*status, fr);
}
else
{
fr->bPrec = (fr->prec > 0);
fr->bStep = TRUE;
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efTNG:
fr->step = -1;
if (!gmx_read_next_tng_frame((*status)->tng, fr, nullptr, 0))
{
fr->not_ok = DATA_NOT_OK;
fr->natoms = 0;
printincomp(*status, fr);
}
else
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efPDB:
pdb_first_x(*status, gmx_fio_getfp(fio), fr);
if (fr->natoms)
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efGRO:
if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
default:
#if GMX_USE_PLUGINS
fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
"Please make sure that the file is a trajectory!\n"
"GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
"This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
if (!read_first_vmd_frame(fn, &(*status)->vmdplugin, fr))
{
gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
}
#else
gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
"GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
"Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
#endif
break;
}
(*status)->tf = fr->time;
/* Return FALSE if we read a frame that's past the set ending time. */
if (!bFirst && (!(flags & TRX_DONT_SKIP) && check_times(fr->time) > 0))
{
(*status)->t0 = fr->time;
return FALSE;
}
if (bFirst ||
(!(flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
{
/* Read a frame when no frame was read or the first was skipped */
if (!read_next_frame(oenv, *status, fr))
{
return FALSE;
}
}
(*status)->t0 = fr->time;
/* We need the number of atoms for random-access XTC searching, even when
* we don't have access to the actual frame data.
*/
(*status)->natoms = fr->natoms;
return (fr->natoms > 0);
}
bool read_next_frame(const gmx_output_env_t *oenv, t_trxstatus *status, t_trxframe *fr)
{
real pt;
int ct;
gmx_bool bOK, bMissingData = FALSE, bSkip = FALSE;
bool bRet = false;
int ftp;
pt = status->tf;
do
{
clear_trxframe(fr, FALSE);
if (status->tng)
{
/* Special treatment for TNG files */
ftp = efTNG;
}
else
{
ftp = gmx_fio_getftp(status->fio);
}
switch (ftp)
{
case efTRR:
bRet = gmx_next_frame(status, fr);
break;
case efCPT:
/* Checkpoint files can not contain mulitple frames */
break;
case efG96:
{
t_symtab *symtab = nullptr;
read_g96_conf(gmx_fio_getfp(status->fio), nullptr, nullptr, fr,
symtab, status->persistent_line);
bRet = (fr->natoms > 0);
break;
}
case efXTC:
if (bTimeSet(TBEGIN) && (status->tf < rTimeValue(TBEGIN)))
{
if (xtc_seek_time(status->fio, rTimeValue(TBEGIN), fr->natoms, TRUE))
{
gmx_fatal(FARGS, "Specified frame (time %f) doesn't exist or file corrupt/inconsistent.",
rTimeValue(TBEGIN));
}
initcount(status);
}
bRet = read_next_xtc(status->fio, fr->natoms, &fr->step, &fr->time, fr->box,
fr->x, &fr->prec, &bOK);
fr->bPrec = (bRet && fr->prec > 0);
fr->bStep = bRet;
fr->bTime = bRet;
fr->bX = bRet;
fr->bBox = bRet;
if (!bOK)
{
/* Actually the header could also be not ok,
but from bOK from read_next_xtc this can't be distinguished */
fr->not_ok = DATA_NOT_OK;
}
break;
case efTNG:
bRet = gmx_read_next_tng_frame(status->tng, fr, nullptr, 0);
break;
case efPDB:
bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr);
break;
case efGRO:
bRet = gro_next_x_or_v(gmx_fio_getfp(status->fio), fr);
break;
default:
#if GMX_USE_PLUGINS
bRet = read_next_vmd_frame(status->vmdplugin, fr);
#else
gmx_fatal(FARGS, "DEATH HORROR in read_next_frame ftp=%s,status=%s",
ftp2ext(gmx_fio_getftp(status->fio)),
gmx_fio_getname(status->fio));
#endif
}
status->tf = fr->time;
if (bRet)
{
bMissingData = (((status->flags & TRX_NEED_X) && !fr->bX) ||
((status->flags & TRX_NEED_V) && !fr->bV) ||
((status->flags & TRX_NEED_F) && !fr->bF));
bSkip = FALSE;
if (!bMissingData)
{
ct = check_times2(fr->time, status->t0, fr->bDouble);
if (ct == 0 || ((status->flags & TRX_DONT_SKIP) && ct < 0))
{
printcount(status, oenv, fr->time, FALSE);
}
else if (ct > 0)
{
bRet = false;
}
else
{
printcount(status, oenv, fr->time, TRUE);
bSkip = TRUE;
}
}
}
}
while (bRet && (bMissingData || bSkip));
if (!bRet)
{
printlast(status, oenv, pt);
if (fr->not_ok)
{
printincomp(status, fr);
}
}
return bRet;
}
int main (int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_protonate[tt] reads (a) conformation(s) and adds all missing",
"hydrogens as defined in [TT]gmx2.ff/aminoacids.hdb[tt]. If only [TT]-s[tt] is",
"specified, this conformation will be protonated, if also [TT]-f[tt]",
"is specified, the conformation(s) will be read from this file, ",
"which can be either a single conformation or a trajectory.",
"[PAR]",
"If a [TT].pdb[tt] file is supplied, residue names might not correspond to",
"to the GROMACS naming conventions, in which case these residues will",
"probably not be properly protonated.",
"[PAR]",
"If an index file is specified, please note that the atom numbers",
"should correspond to the [BB]protonated[bb] state."
};
char title[STRLEN+1];
const char *infile;
char *grpnm;
t_topology top;
int ePBC;
t_atoms *atoms,*iatoms;
t_protonate protdata;
atom_id *index;
t_trxstatus *status;
t_trxstatus *out;
t_trxframe fr,frout;
rvec *x,*ix;
int nidx,natoms,natoms_out;
matrix box;
int i,frame,resind;
gmx_bool bReadMultiple;
output_env_t oenv;
const char *bugs[] = {
"For the moment, only .pdb files are accepted to the -s flag"
};
t_filenm fnm[] = {
{ efTPS, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efTRO, "-o", "protonated", ffWRITE }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME,
NFILE,fnm,0,NULL,asize(desc),desc,asize(bugs),bugs,&oenv);
infile=opt2fn("-s",NFILE,fnm);
read_tps_conf(infile,title,&top,&ePBC,&x,NULL,box,FALSE);
atoms=&(top.atoms);
printf("Select group to process:\n");
get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidx,&index,&grpnm);
bReadMultiple = opt2bSet("-f",NFILE,fnm);
if (bReadMultiple) {
infile = opt2fn("-f",NFILE,fnm);
if ( !read_first_frame(oenv,&status, infile, &fr, TRX_NEED_X ) ) {
gmx_fatal(FARGS,"cannot read coordinate file %s",infile);
}
natoms = fr.natoms;
} else {
clear_trxframe(&fr,TRUE);
fr.natoms = atoms->nr;
fr.bTitle = TRUE;
fr.title = title;
fr.bX = TRUE;
fr.x = x;
fr.bBox = TRUE;
copy_mat(box, fr.box);
natoms = fr.natoms;
}
/* check input */
if ( natoms == 0 ) {
gmx_fatal(FARGS,"no atoms in coordinate file %s",infile);
}
if ( natoms > atoms->nr ) {
gmx_fatal(FARGS,"topology with %d atoms does not match "
"coordinates with %d atoms",atoms->nr,natoms);
}
for(i=0; i<nidx; i++) {
if (index[i] > natoms) {
gmx_fatal(FARGS,"An atom number in group %s is larger than the number of "
"atoms (%d) in the coordinate file %s",grpnm,natoms,infile);
}
}
/* get indexed copy of atoms */
snew(iatoms,1);
init_t_atoms(iatoms,nidx,FALSE);
snew(iatoms->atom, iatoms->nr);
resind = 0;
for(i=0; i<nidx; i++) {
iatoms->atom[i] = atoms->atom[index[i]];
iatoms->atomname[i] = atoms->atomname[index[i]];
if ( i>0 && (atoms->atom[index[i]].resind!=atoms->atom[index[i-1]].resind) ) {
resind++;
}
iatoms->atom[i].resind = resind;
iatoms->resinfo[resind] = atoms->resinfo[atoms->atom[index[i]].resind];
/* allocate some space for the rtp name and copy from name */
snew(iatoms->resinfo[resind].rtp,1);
*iatoms->resinfo[resind].rtp = gmx_strdup(*atoms->resinfo[resind].name);
iatoms->nres = max(iatoms->nres, iatoms->atom[i].resind+1);
}
init_t_protonate(&protdata);
out = open_trx(opt2fn("-o",NFILE,fnm),"w");
snew(ix, nidx);
frame=0;
do {
if (debug) {
fprintf(debug,"FRAME %d (%d %g)\n",frame,fr.step,fr.time);
}
/* get indexed copy of x */
for(i=0; i<nidx; i++) {
copy_rvec(fr.x[index[i]], ix[i]);
}
/* protonate */
natoms_out = protonate(&iatoms, &ix, &protdata);
/* setup output frame */
frout = fr;
frout.natoms = natoms_out;
frout.bAtoms = TRUE;
frout.atoms = iatoms;
frout.bV = FALSE;
frout.bF = FALSE;
frout.x = ix;
/* write output */
write_trxframe(out,&frout,NULL);
frame++;
} while ( bReadMultiple && read_next_frame(oenv,status, &fr) );
sfree(ix);
sfree(iatoms);
thanx(stderr);
return 0;
}
gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status, t_trxframe *fr)
{
real pt;
int ct;
gmx_bool bOK, bRet, bMissingData = FALSE, bSkip = FALSE;
int dummy = 0;
int ftp;
bRet = FALSE;
pt = fr->tf;
do
{
clear_trxframe(fr, FALSE);
fr->tppf = fr->tpf;
fr->tpf = fr->tf;
if (status->tng)
{
/* Special treatment for TNG files */
ftp = efTNG;
}
else
{
ftp = gmx_fio_getftp(status->fio);
}
switch (ftp)
{
case efTRR:
bRet = gmx_next_frame(status, fr);
break;
case efCPT:
/* Checkpoint files can not contain mulitple frames */
break;
case efG96:
read_g96_conf(gmx_fio_getfp(status->fio), NULL, fr,
status->persistent_line);
bRet = (fr->natoms > 0);
break;
case efXTC:
/* B. Hess 2005-4-20
* Sometimes is off by one frame
* and sometimes reports frame not present/file not seekable
*/
/* DvdS 2005-05-31: this has been fixed along with the increased
* accuracy of the control over -b and -e options.
*/
if (bTimeSet(TBEGIN) && (fr->tf < rTimeValue(TBEGIN)))
{
if (xtc_seek_time(status->fio, rTimeValue(TBEGIN), fr->natoms, TRUE))
{
gmx_fatal(FARGS, "Specified frame (time %f) doesn't exist or file corrupt/inconsistent.",
rTimeValue(TBEGIN));
}
initcount(status);
}
bRet = read_next_xtc(status->fio, fr->natoms, &fr->step, &fr->time, fr->box,
fr->x, &fr->prec, &bOK);
fr->bPrec = (bRet && fr->prec > 0);
fr->bStep = bRet;
fr->bTime = bRet;
fr->bX = bRet;
fr->bBox = bRet;
if (!bOK)
{
/* Actually the header could also be not ok,
but from bOK from read_next_xtc this can't be distinguished */
fr->not_ok = DATA_NOT_OK;
}
break;
case efTNG:
bRet = gmx_read_next_tng_frame(status->tng, fr, NULL, 0);
break;
case efPDB:
bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr);
break;
case efGRO:
bRet = gro_next_x_or_v(gmx_fio_getfp(status->fio), fr);
break;
default:
#ifdef GMX_USE_PLUGINS
bRet = read_next_vmd_frame(fr);
#else
gmx_fatal(FARGS, "DEATH HORROR in read_next_frame ftp=%s,status=%s",
ftp2ext(gmx_fio_getftp(status->fio)),
gmx_fio_getname(status->fio));
#endif
}
fr->tf = fr->time;
if (bRet)
{
bMissingData = (((fr->flags & TRX_NEED_X) && !fr->bX) ||
((fr->flags & TRX_NEED_V) && !fr->bV) ||
((fr->flags & TRX_NEED_F) && !fr->bF));
bSkip = FALSE;
if (!bMissingData)
{
ct = check_times2(fr->time, fr->t0, fr->bDouble);
if (ct == 0 || ((fr->flags & TRX_DONT_SKIP) && ct < 0))
{
printcount(status, oenv, fr->time, FALSE);
}
else if (ct > 0)
{
bRet = FALSE;
}
else
{
printcount(status, oenv, fr->time, TRUE);
bSkip = TRUE;
}
}
}
}
while (bRet && (bMissingData || bSkip));
if (!bRet)
{
printlast(status, oenv, pt);
if (fr->not_ok)
{
printincomp(status, fr);
}
}
return bRet;
}
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;
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, ci, cj, nframe, nclust, n_x, 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 trajectory (%d atoms) do not match!",
tpxh.natoms, natoms);
}
ePBC = read_tpx(tpr, NULL, NULL, &natoms, 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);
}
GMX_RELEASE_ASSERT(mtop != NULL, "Trying to access mtop->mols from NULL mtop pointer");
mols = &(mtop->mols);
/* Make dummy index */
nindex = mols->nr;
snew(index, nindex);
for (i = 0; (i < nindex); i++)
{
index[i] = i;
}
gname = gmx_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)
{
GMX_RELEASE_ASSERT(mols != NULL, "Cannot access index[] from NULL mols pointer");
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 = std::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 [REF].tpr[ref] 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);
xvgrclose(fp);
xvgrclose(gp);
xvgrclose(hp);
xvgrclose(tp);
gmx_mtop_atomlookup_destroy(alook);
if (max_clust_ind >= 0)
{
fp = gmx_ffopen(mcn, "w");
fprintf(fp, "[ max_clust ]\n");
for (i = 0; (i < nindex); i++)
{
if (clust_index[i] == max_clust_ind)
{
if (bMol)
{
GMX_RELEASE_ASSERT(mols != NULL, "Cannot access index[] from NULL mols pointer");
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);
}
}
}
gmx_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 += static_cast<int>((j+1)*nelem/n_x);
}
fprintf(fp, "%5d %8.3f\n", j+1, 0.0);
xvgrclose(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 = std::max(cs_dist[i][j], cmax);
}
}
fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
cmid = 1;
fp = gmx_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);
gmx_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 = std::max(cs_dist[i][j], cmax);
}
}
fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
fp = gmx_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);
gmx_ffclose(fp);
sfree(clust_index);
sfree(clust_size);
sfree(index);
}
int read_first_frame(const output_env_t oenv, t_trxstatus **status,
const char *fn, t_trxframe *fr, int flags)
{
t_fileio *fio;
gmx_bool bFirst, bOK;
int dummy = 0;
clear_trxframe(fr, TRUE);
fr->flags = flags;
bFirst = TRUE;
snew((*status), 1);
status_init( *status );
(*status)->nxframe = 1;
initcount(*status);
fio = (*status)->fio = gmx_fio_open(fn, "r");
switch (gmx_fio_getftp(fio))
{
case efTRJ:
case efTRR:
break;
case efCPT:
read_checkpoint_trxframe(fio, fr);
bFirst = FALSE;
break;
case efG96:
/* Can not rewind a compressed file, so open it twice */
if (!(*status)->persistent_line)
{
/* allocate the persistent line */
snew((*status)->persistent_line, STRLEN+1);
}
read_g96_conf(gmx_fio_getfp(fio), fn, fr, (*status)->persistent_line);
gmx_fio_close(fio);
clear_trxframe(fr, FALSE);
if (flags & (TRX_READ_X | TRX_NEED_X))
{
snew(fr->x, fr->natoms);
}
if (flags & (TRX_READ_V | TRX_NEED_V))
{
snew(fr->v, fr->natoms);
}
fio = (*status)->fio = gmx_fio_open(fn, "r");
break;
case efG87:
fr->natoms = xyz_first_x(*status, gmx_fio_getfp(fio), oenv, &fr->time,
&fr->x, fr->box);
if (fr->natoms)
{
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efXTC:
if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
&fr->prec, &bOK) == 0)
{
if (bOK)
{
gmx_fatal(FARGS, "No XTC!\n");
}
else
{
fr->not_ok = DATA_NOT_OK;
}
}
if (fr->not_ok)
{
fr->natoms = 0;
printincomp(*status, fr);
}
else
{
fr->bPrec = (fr->prec > 0);
fr->bStep = TRUE;
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efPDB:
pdb_first_x(*status, gmx_fio_getfp(fio), fr);
if (fr->natoms)
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
case efGRO:
if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
{
printcount(*status, oenv, fr->time, FALSE);
}
bFirst = FALSE;
break;
default:
#ifdef GMX_USE_PLUGINS
fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
"Please make sure that the file is a trajectory!\n"
"GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
"This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
if (!read_first_vmd_frame(fn, fr))
{
gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
}
#else
gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
"GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
"Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
#endif
break;
}
/* Return FALSE if we read a frame that's past the set ending time. */
if (!bFirst && (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) > 0))
{
fr->t0 = fr->time;
return FALSE;
}
if (bFirst ||
(!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
{
/* Read a frame when no frame was read or the first was skipped */
if (!read_next_frame(oenv, *status, fr))
{
return FALSE;
}
}
fr->t0 = fr->time;
return (fr->natoms > 0);
}
int read_first_frame(const output_env_t oenv,t_trxstatus **status,
const char *fn,t_trxframe *fr,int flags)
{
t_fileio *fio;
gmx_bool bFirst,bOK;
int dummy=0;
clear_trxframe(fr,TRUE);
fr->flags = flags;
bFirst = TRUE;
snew((*status), 1);
status_init( *status );
(*status)->nxframe=1;
initcount(*status);
fio = (*status)->fio =gmx_fio_open(fn,"r");
switch (gmx_fio_getftp(fio))
{
case efTRJ:
case efTRR:
break;
case efCPT:
read_checkpoint_trxframe(fio,fr);
bFirst = FALSE;
break;
case efG96:
/* Can not rewind a compressed file, so open it twice */
read_g96_conf(gmx_fio_getfp(fio),fn,fr);
gmx_fio_close(fio);
clear_trxframe(fr,FALSE);
if (flags & (TRX_READ_X | TRX_NEED_X))
snew(fr->x,fr->natoms);
if (flags & (TRX_READ_V | TRX_NEED_V))
snew(fr->v,fr->natoms);
fio = (*status)->fio =gmx_fio_open(fn,"r");
break;
case efG87:
fr->natoms=xyz_first_x(*status, gmx_fio_getfp(fio),oenv,&fr->time,
&fr->x,fr->box);
if (fr->natoms) {
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status,oenv,fr->time,FALSE);
}
bFirst = FALSE;
break;
case efXTC:
if (read_first_xtc(fio,&fr->natoms,&fr->step,&fr->time,fr->box,&fr->x,
&fr->prec,&bOK) == 0) {
if (bOK) {
gmx_fatal(FARGS,"No XTC!\n");
} else {
fr->not_ok = DATA_NOT_OK;
}
}
if (fr->not_ok) {
fr->natoms = 0;
printincomp(*status,fr);
} else {
fr->bPrec = (fr->prec > 0);
fr->bStep = TRUE;
fr->bTime = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
printcount(*status,oenv,fr->time,FALSE);
}
bFirst = FALSE;
break;
case efPDB:
pdb_first_x(*status, gmx_fio_getfp(fio),fr);
if (fr->natoms)
printcount(*status,oenv,fr->time,FALSE);
bFirst = FALSE;
break;
case efGRO:
if (gro_first_x_or_v(gmx_fio_getfp(fio),fr))
printcount(*status,oenv,fr->time,FALSE);
bFirst = FALSE;
break;
default:
#ifdef GMX_DLOPEN
gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
if (!read_first_vmd_frame(&dummy,fn,fr,flags))
{
gmx_fatal(FARGS,"Not supported in read_first_frame: %s",fn);
}
#else
gmx_fatal(FARGS,"Not supported in read_first_frame: %s",fn);
#endif
break;
}
/* Return FALSE if we read a frame that's past the set ending time. */
if (!bFirst && (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) > 0)) {
fr->t0 = fr->time;
return FALSE;
}
if (bFirst ||
(!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
/* Read a frame when no frame was read or the first was skipped */
if (!read_next_frame(oenv,*status,fr))
return FALSE;
fr->t0 = fr->time;
return (fr->natoms > 0);
}
int read_g96_conf(FILE *fp, const char *infile, t_trxframe *fr, char *line)
{
t_symtab *symtab = NULL;
gmx_bool bAtStart, bTime, bAtoms, bPos, bVel, bBox, bEnd, bFinished;
int natoms, nbp;
double db1, db2, db3, db4, db5, db6, db7, db8, db9;
bAtStart = (ftell(fp) == 0);
clear_trxframe(fr, FALSE);
if (!symtab)
{
snew(symtab, 1);
open_symtab(symtab);
}
natoms = 0;
if (bAtStart)
{
while (!fr->bTitle && fgets2(line, STRLEN, fp))
{
fr->bTitle = (strcmp(line, "TITLE") == 0);
}
if (fr->title == NULL)
{
fgets2(line, STRLEN, fp);
fr->title = gmx_strdup(line);
}
bEnd = FALSE;
while (!bEnd && fgets2(line, STRLEN, fp))
{
bEnd = (strcmp(line, "END") == 0);
}
fgets2(line, STRLEN, fp);
}
/* Do not get a line if we are not at the start of the file, *
* because without a parameter file we don't know what is in *
* the trajectory and we have already read the line in the *
* previous call (VERY DIRTY). */
bFinished = FALSE;
do
{
bTime = (strcmp(line, "TIMESTEP") == 0);
bAtoms = (strcmp(line, "POSITION") == 0);
bPos = (bAtoms || (strcmp(line, "POSITIONRED") == 0));
bVel = (strncmp(line, "VELOCITY", 8) == 0);
bBox = (strcmp(line, "BOX") == 0);
if (bTime)
{
if (!fr->bTime && !fr->bX)
{
fr->bStep = bTime;
fr->bTime = bTime;
do
{
bFinished = (fgets2(line, STRLEN, fp) == NULL);
}
while (!bFinished && (line[0] == '#'));
sscanf(line, "%15d%15lf", &(fr->step), &db1);
fr->time = db1;
}
else
{
bFinished = TRUE;
}
}
if (bPos)
{
if (!fr->bX)
{
fr->bAtoms = bAtoms;
fr->bX = bPos;
natoms = read_g96_pos(line, symtab, fp, infile, fr);
}
else
{
bFinished = TRUE;
}
}
if (fr->v && bVel)
{
fr->bV = bVel;
natoms = read_g96_vel(line, fp, infile, fr);
}
if (bBox)
{
fr->bBox = bBox;
clear_mat(fr->box);
bEnd = FALSE;
while (!bEnd && fgets2(line, STRLEN, fp))
{
bEnd = (strncmp(line, "END", 3) == 0);
if (!bEnd && (line[0] != '#'))
{
nbp = sscanf(line, "%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf%15lf",
&db1, &db2, &db3, &db4, &db5, &db6, &db7, &db8, &db9);
if (nbp < 3)
{
gmx_fatal(FARGS, "Found a BOX line, but no box in %s", infile);
}
fr->box[XX][XX] = db1;
fr->box[YY][YY] = db2;
fr->box[ZZ][ZZ] = db3;
if (nbp == 9)
{
fr->box[XX][YY] = db4;
fr->box[XX][ZZ] = db5;
fr->box[YY][XX] = db6;
fr->box[YY][ZZ] = db7;
fr->box[ZZ][XX] = db8;
fr->box[ZZ][YY] = db9;
}
}
}
bFinished = TRUE;
}
}
while (!bFinished && fgets2(line, STRLEN, fp));
free_symtab(symtab);
fr->natoms = natoms;
return natoms;
}
