/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Green Red Orange Magenta Azure Cyan Skyblue
*/
#include <unistd.h>
#endif
-enum { euSel,euRect, euTric, euCompact, euNR};
+enum {
+ euSel, euRect, euTric, euCompact, euNR
+};
-static void calc_pbc_cluster(int ecenter,int nrefat,t_topology *top,int ePBC,
- rvec x[],atom_id index[],
- rvec clust_com,matrix box, rvec clustercenter)
+static void calc_pbc_cluster(int ecenter, int nrefat, t_topology *top, int ePBC,
+ rvec x[], atom_id index[],
+ rvec clust_com, matrix box, rvec clustercenter)
{
- int m,i,j,j0,j1,jj,ai,aj;
- int imin,jmin;
- real fac,min_dist2;
- rvec dx,xtest,box_center;
- int nmol,imol_center;
- atom_id *molind;
- gmx_bool *bMol,*bTmp;
- rvec *m_com,*m_shift;
- t_pbc pbc;
- real *com_dist2;
- int *cluster;
- int *added;
- int ncluster,nadded;
- real tmp_r2;
-
- calc_box_center(ecenter,box,box_center);
+ int m, i, j, j0, j1, jj, ai, aj;
+ int imin, jmin;
+ real fac, min_dist2;
+ rvec dx, xtest, box_center;
+ int nmol, imol_center;
+ atom_id *molind;
+ gmx_bool *bMol, *bTmp;
+ rvec *m_com, *m_shift;
+ t_pbc pbc;
+ real *com_dist2;
+ int *cluster;
+ int *added;
+ int ncluster, nadded;
+ real tmp_r2;
+
+ calc_box_center(ecenter, box, box_center);
/* Initiate the pbc structure */
- memset(&pbc,0,sizeof(pbc));
- set_pbc(&pbc,ePBC,box);
+ memset(&pbc, 0, sizeof(pbc));
+ set_pbc(&pbc, ePBC, box);
/* Convert atom index to molecular */
nmol = top->mols.nr;
molind = top->mols.index;
- snew(bMol,nmol);
- snew(m_com,nmol);
- snew(m_shift,nmol);
- snew(cluster,nmol);
- snew(added,nmol);
- snew(bTmp,top->atoms.nr);
-
- for(i=0; (i<nrefat); i++) {
+ snew(bMol, nmol);
+ snew(m_com, nmol);
+ snew(m_shift, nmol);
+ snew(cluster, nmol);
+ snew(added, nmol);
+ snew(bTmp, top->atoms.nr);
+
+ for (i = 0; (i < nrefat); i++)
+ {
/* Mark all molecules in the index */
- ai = index[i];
+ ai = index[i];
bTmp[ai] = TRUE;
/* Binary search assuming the molecules are sorted */
- j0=0;
- j1=nmol-1;
- while (j0 < j1) {
- if (ai < molind[j0+1])
+ j0 = 0;
+ j1 = nmol-1;
+ while (j0 < j1)
+ {
+ if (ai < molind[j0+1])
+ {
j1 = j0;
- else if (ai >= molind[j1])
+ }
+ else if (ai >= molind[j1])
+ {
j0 = j1;
- else {
+ }
+ else
+ {
jj = (j0+j1)/2;
- if (ai < molind[jj+1])
+ if (ai < molind[jj+1])
+ {
j1 = jj;
+ }
else
+ {
j0 = jj;
+ }
}
}
bMol[j0] = TRUE;
}
- /* Double check whether all atoms in all molecules that are marked are part
+ /* Double check whether all atoms in all molecules that are marked are part
* of the cluster. Simultaneously compute the center of geometry.
*/
min_dist2 = 10*sqr(trace(box));
imol_center = -1;
ncluster = 0;
- for(i=0; i<nmol; i++)
+ for (i = 0; i < nmol; i++)
{
- for(j=molind[i]; j<molind[i+1]; j++)
+ for (j = molind[i]; j < molind[i+1]; j++)
{
if (bMol[i] && !bTmp[j])
{
- gmx_fatal(FARGS,"Molecule %d marked for clustering but not atom %d in it - check your index!",i+1,j+1);
+ gmx_fatal(FARGS, "Molecule %d marked for clustering but not atom %d in it - check your index!", i+1, j+1);
}
else if (!bMol[i] && bTmp[j])
{
- gmx_fatal(FARGS,"Atom %d marked for clustering but not molecule %d - this is an internal error...",j+1,i+1);
+ gmx_fatal(FARGS, "Atom %d marked for clustering but not molecule %d - this is an internal error...", j+1, i+1);
}
- else if (bMol[i])
+ else if (bMol[i])
{
/* Make molecule whole, move 2nd and higher atom to same periodicity as 1st atom in molecule */
- if(j>molind[i])
+ if (j > molind[i])
{
- pbc_dx(&pbc,x[j],x[j-1],dx);
- rvec_add(x[j-1],dx,x[j]);
+ pbc_dx(&pbc, x[j], x[j-1], dx);
+ rvec_add(x[j-1], dx, x[j]);
}
/* Compute center of geometry of molecule - m_com[i] was zeroed when we did snew() on it! */
- rvec_inc(m_com[i],x[j]);
+ rvec_inc(m_com[i], x[j]);
}
}
- if (bMol[i])
+ if (bMol[i])
{
/* Normalize center of geometry */
fac = 1.0/(molind[i+1]-molind[i]);
- for(m=0; (m<DIM); m++)
+ for (m = 0; (m < DIM); m++)
+ {
m_com[i][m] *= fac;
+ }
/* Determine which molecule is closest to the center of the box */
- pbc_dx(&pbc,box_center,m_com[i],dx);
- tmp_r2=iprod(dx,dx);
-
- if (tmp_r2 < min_dist2)
+ pbc_dx(&pbc, box_center, m_com[i], dx);
+ tmp_r2 = iprod(dx, dx);
+
+ if (tmp_r2 < min_dist2)
{
min_dist2 = tmp_r2;
imol_center = i;
}
- cluster[ncluster++]=i;
+ cluster[ncluster++] = i;
}
}
sfree(bTmp);
- if (ncluster <= 0)
+ if (ncluster <= 0)
{
- fprintf(stderr,"No molecules selected in the cluster\n");
+ fprintf(stderr, "No molecules selected in the cluster\n");
return;
}
- else if (imol_center == -1)
+ else if (imol_center == -1)
{
- fprintf(stderr,"No central molecules could be found\n");
+ fprintf(stderr, "No central molecules could be found\n");
return;
}
-
- nadded = 0;
+
+ nadded = 0;
added[nadded++] = imol_center;
bMol[imol_center] = FALSE;
-
- while (nadded<ncluster)
+
+ while (nadded < ncluster)
{
/* Find min distance between cluster molecules and those remaining to be added */
min_dist2 = 10*sqr(trace(box));
imin = -1;
jmin = -1;
/* Loop over added mols */
- for(i=0;i<nadded;i++)
+ for (i = 0; i < nadded; i++)
{
ai = added[i];
/* Loop over all mols */
- for(j=0;j<ncluster;j++)
+ for (j = 0; j < ncluster; j++)
{
aj = cluster[j];
/* check those remaining to be added */
- if(bMol[aj])
+ if (bMol[aj])
{
- pbc_dx(&pbc,m_com[aj],m_com[ai],dx);
- tmp_r2=iprod(dx,dx);
- if (tmp_r2 < min_dist2)
+ pbc_dx(&pbc, m_com[aj], m_com[ai], dx);
+ tmp_r2 = iprod(dx, dx);
+ if (tmp_r2 < min_dist2)
{
min_dist2 = tmp_r2;
imin = ai;
jmin = aj;
- }
+ }
}
}
}
-
+
/* Add the best molecule */
added[nadded++] = jmin;
bMol[jmin] = FALSE;
/* Calculate the shift from the ai molecule */
- pbc_dx(&pbc,m_com[jmin],m_com[imin],dx);
- rvec_add(m_com[imin],dx,xtest);
- rvec_sub(xtest,m_com[jmin],m_shift[jmin]);
- rvec_inc(m_com[jmin],m_shift[jmin]);
+ pbc_dx(&pbc, m_com[jmin], m_com[imin], dx);
+ rvec_add(m_com[imin], dx, xtest);
+ rvec_sub(xtest, m_com[jmin], m_shift[jmin]);
+ rvec_inc(m_com[jmin], m_shift[jmin]);
- for(j=molind[jmin]; j<molind[jmin+1]; j++)
+ for (j = molind[jmin]; j < molind[jmin+1]; j++)
{
- rvec_inc(x[j],m_shift[jmin]);
+ rvec_inc(x[j], m_shift[jmin]);
}
- fprintf(stdout,"\rClustering iteration %d of %d...",nadded,ncluster);
+ fprintf(stdout, "\rClustering iteration %d of %d...", nadded, ncluster);
fflush(stdout);
}
-
+
sfree(added);
sfree(cluster);
sfree(bMol);
sfree(m_com);
sfree(m_shift);
-
- fprintf(stdout,"\n");
+
+ fprintf(stdout, "\n");
}
-static void put_molecule_com_in_box(int unitcell_enum,int ecenter,
+static void put_molecule_com_in_box(int unitcell_enum, int ecenter,
t_block *mols,
- int natoms,t_atom atom[],
- int ePBC,matrix box,rvec x[])
+ int natoms, t_atom atom[],
+ int ePBC, matrix box, rvec x[])
{
- atom_id i,j;
+ atom_id i, j;
int d;
- rvec com,new_com,shift,dx,box_center;
+ rvec com, new_com, shift, dx, box_center;
real m;
double mtot;
t_pbc pbc;
- calc_box_center(ecenter,box,box_center);
- set_pbc(&pbc,ePBC,box);
- if (mols->nr <= 0)
- gmx_fatal(FARGS,"There are no molecule descriptions. I need a .tpr file for this pbc option.");
- for(i=0; (i<mols->nr); i++) {
+ calc_box_center(ecenter, box, box_center);
+ set_pbc(&pbc, ePBC, box);
+ if (mols->nr <= 0)
+ {
+ gmx_fatal(FARGS, "There are no molecule descriptions. I need a .tpr file for this pbc option.");
+ }
+ for (i = 0; (i < mols->nr); i++)
+ {
/* calc COM */
clear_rvec(com);
mtot = 0;
- for(j=mols->index[i]; (j<mols->index[i+1] && j<natoms); j++) {
+ for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
+ {
m = atom[j].m;
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
+ {
com[d] += m*x[j][d];
+ }
mtot += m;
}
/* calculate final COM */
svmul(1.0/mtot, com, com);
/* check if COM is outside box */
- copy_rvec(com,new_com);
- switch (unitcell_enum) {
- case euRect:
- put_atoms_in_box(ePBC,box,1,&new_com);
- break;
- case euTric:
- put_atoms_in_triclinic_unitcell(ecenter,box,1,&new_com);
- break;
- case euCompact:
- put_atoms_in_compact_unitcell(ePBC,ecenter,box,1,&new_com);
- break;
+ copy_rvec(com, new_com);
+ switch (unitcell_enum)
+ {
+ case euRect:
+ put_atoms_in_box(ePBC, box, 1, &new_com);
+ break;
+ case euTric:
+ put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
+ break;
+ case euCompact:
+ put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
+ break;
}
- rvec_sub(new_com,com,shift);
- if (norm2(shift) > 0) {
+ rvec_sub(new_com, com, shift);
+ if (norm2(shift) > 0)
+ {
if (debug)
- fprintf (debug,"\nShifting position of molecule %d "
+ {
+ fprintf (debug, "\nShifting position of molecule %d "
"by %8.3f %8.3f %8.3f\n", i+1, PR_VEC(shift));
- for(j=mols->index[i]; (j<mols->index[i+1] && j<natoms); j++) {
- rvec_inc(x[j],shift);
+ }
+ for (j = mols->index[i]; (j < mols->index[i+1] && j < natoms); j++)
+ {
+ rvec_inc(x[j], shift);
}
}
}
}
-static void put_residue_com_in_box(int unitcell_enum,int ecenter,
- int natoms,t_atom atom[],
- int ePBC,matrix box,rvec x[])
+static void put_residue_com_in_box(int unitcell_enum, int ecenter,
+ int natoms, t_atom atom[],
+ int ePBC, matrix box, rvec x[])
{
atom_id i, j, res_start, res_end, res_nat;
int d, presnr;
real m;
double mtot;
- rvec box_center,com,new_com,shift;
+ rvec box_center, com, new_com, shift;
- calc_box_center(ecenter,box,box_center);
+ calc_box_center(ecenter, box, box_center);
- presnr = NOTSET;
+ presnr = NOTSET;
res_start = 0;
clear_rvec(com);
mtot = 0;
- for(i=0; i<natoms+1; i++) {
- if (i == natoms || (presnr != atom[i].resind && presnr != NOTSET)) {
+ for (i = 0; i < natoms+1; i++)
+ {
+ if (i == natoms || (presnr != atom[i].resind && presnr != NOTSET))
+ {
/* calculate final COM */
res_end = i;
res_nat = res_end - res_start;
svmul(1.0/mtot, com, com);
/* check if COM is outside box */
- copy_rvec(com,new_com);
- switch (unitcell_enum) {
- case euRect:
- put_atoms_in_box(ePBC,box,1,&new_com);
- break;
- case euTric:
- put_atoms_in_triclinic_unitcell(ecenter,box,1,&new_com);
- break;
- case euCompact:
- put_atoms_in_compact_unitcell(ePBC,ecenter,box,1,&new_com);
- break;
+ copy_rvec(com, new_com);
+ switch (unitcell_enum)
+ {
+ case euRect:
+ put_atoms_in_box(ePBC, box, 1, &new_com);
+ break;
+ case euTric:
+ put_atoms_in_triclinic_unitcell(ecenter, box, 1, &new_com);
+ break;
+ case euCompact:
+ put_atoms_in_compact_unitcell(ePBC, ecenter, box, 1, &new_com);
+ break;
}
- rvec_sub(new_com,com,shift);
- if (norm2(shift)) {
+ rvec_sub(new_com, com, shift);
+ if (norm2(shift))
+ {
if (debug)
- fprintf (debug,"\nShifting position of residue %d (atoms %u-%u) "
- "by %g,%g,%g\n", atom[res_start].resind+1,
+ {
+ fprintf (debug, "\nShifting position of residue %d (atoms %u-%u) "
+ "by %g,%g,%g\n", atom[res_start].resind+1,
res_start+1, res_end+1, PR_VEC(shift));
- for(j=res_start; j<res_end; j++)
- rvec_inc(x[j],shift);
+ }
+ for (j = res_start; j < res_end; j++)
+ {
+ rvec_inc(x[j], shift);
+ }
}
clear_rvec(com);
mtot = 0;
/* remember start of new residue */
res_start = i;
}
- if (i < natoms) {
+ if (i < natoms)
+ {
/* calc COM */
m = atom[i].m;
- for(d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
+ {
com[d] += m*x[i][d];
+ }
mtot += m;
presnr = atom[i].resind;
}
}
-static void center_x(int ecenter,rvec x[],matrix box,int n,int nc,atom_id ci[])
+static void center_x(int ecenter, rvec x[], matrix box, int n, int nc, atom_id ci[])
{
- int i,m,ai;
- rvec cmin,cmax,box_center,dx;
-
- if (nc > 0) {
- copy_rvec(x[ci[0]],cmin);
- copy_rvec(x[ci[0]],cmax);
- for(i=0; i<nc; i++) {
- ai=ci[i];
- for(m=0; m<DIM; m++) {
+ int i, m, ai;
+ rvec cmin, cmax, box_center, dx;
+
+ if (nc > 0)
+ {
+ copy_rvec(x[ci[0]], cmin);
+ copy_rvec(x[ci[0]], cmax);
+ for (i = 0; i < nc; i++)
+ {
+ ai = ci[i];
+ for (m = 0; m < DIM; m++)
+ {
if (x[ai][m] < cmin[m])
- cmin[m]=x[ai][m];
+ {
+ cmin[m] = x[ai][m];
+ }
else if (x[ai][m] > cmax[m])
- cmax[m]=x[ai][m];
+ {
+ cmax[m] = x[ai][m];
+ }
}
}
- calc_box_center(ecenter,box,box_center);
- for(m=0; m<DIM; m++)
+ calc_box_center(ecenter, box, box_center);
+ for (m = 0; m < DIM; m++)
+ {
dx[m] = box_center[m]-(cmin[m]+cmax[m])*0.5;
+ }
- for(i=0; i<n; i++)
- rvec_inc(x[i],dx);
+ for (i = 0; i < n; i++)
+ {
+ rvec_inc(x[i], dx);
+ }
}
}
-static void mk_filenm(char *base,const char *ext,int ndigit,int file_nr,
+static void mk_filenm(char *base, const char *ext, int ndigit, int file_nr,
char out_file[])
{
char nbuf[128];
- int nd=0,fnr;
+ int nd = 0, fnr;
- strcpy(out_file,base);
+ strcpy(out_file, base);
fnr = file_nr;
- do {
+ do
+ {
fnr /= 10;
nd++;
- } while (fnr > 0);
+ }
+ while (fnr > 0);
if (nd < ndigit)
- strncat(out_file,"00000000000",ndigit-nd);
- sprintf(nbuf,"%d.",file_nr);
- strcat(out_file,nbuf);
- strcat(out_file,ext);
+ {
+ strncat(out_file, "00000000000", ndigit-nd);
+ }
+ sprintf(nbuf, "%d.", file_nr);
+ strcat(out_file, nbuf);
+ strcat(out_file, ext);
}
void check_trn(const char *fn)
{
if ((fn2ftp(fn) != efTRJ) && (fn2ftp(fn) != efTRR))
- gmx_fatal(FARGS,"%s is not a trajectory file, exiting\n",fn);
+ {
+ gmx_fatal(FARGS, "%s is not a trajectory file, exiting\n", fn);
+ }
}
#ifndef GMX_NATIVE_WINDOWS
void do_trunc(const char *fn, real t0)
{
- t_fileio *in;
- FILE *fp;
- gmx_bool bStop,bOK;
- t_trnheader sh;
- gmx_off_t fpos;
- char yesno[256];
- int j;
- real t=0;
+ t_fileio *in;
+ FILE *fp;
+ gmx_bool bStop, bOK;
+ t_trnheader sh;
+ gmx_off_t fpos;
+ char yesno[256];
+ int j;
+ real t = 0;
if (t0 == -1)
- gmx_fatal(FARGS,"You forgot to set the truncation time");
+ {
+ gmx_fatal(FARGS, "You forgot to set the truncation time");
+ }
/* Check whether this is a .trj file */
check_trn(fn);
- in = open_trn(fn,"r");
+ in = open_trn(fn, "r");
fp = gmx_fio_getfp(in);
- if (fp == NULL) {
- fprintf(stderr,"Sorry, can not trunc %s, truncation of this filetype is not supported\n",fn);
+ if (fp == NULL)
+ {
+ fprintf(stderr, "Sorry, can not trunc %s, truncation of this filetype is not supported\n", fn);
close_trn(in);
- } else {
- j = 0;
- fpos = gmx_fio_ftell(in);
- bStop= FALSE;
- while (!bStop && fread_trnheader(in,&sh,&bOK)) {
- fread_htrn(in,&sh,NULL,NULL,NULL,NULL);
- fpos=gmx_ftell(fp);
- t=sh.t;
- if (t>=t0) {
+ }
+ else
+ {
+ j = 0;
+ fpos = gmx_fio_ftell(in);
+ bStop = FALSE;
+ while (!bStop && fread_trnheader(in, &sh, &bOK))
+ {
+ fread_htrn(in, &sh, NULL, NULL, NULL, NULL);
+ fpos = gmx_ftell(fp);
+ t = sh.t;
+ if (t >= t0)
+ {
gmx_fseek(fp, fpos, SEEK_SET);
- bStop=TRUE;
+ bStop = TRUE;
}
}
- if (bStop) {
- fprintf(stderr,"Do you REALLY want to truncate this trajectory (%s) at:\n"
+ if (bStop)
+ {
+ fprintf(stderr, "Do you REALLY want to truncate this trajectory (%s) at:\n"
"frame %d, time %g, bytes %ld ??? (type YES if so)\n",
- fn,j,t,(long int)fpos);
- if(1 != scanf("%s",yesno))
- {
- gmx_fatal(FARGS,"Error reading user input");
+ fn, j, t, (long int)fpos);
+ if (1 != scanf("%s", yesno))
+ {
+ gmx_fatal(FARGS, "Error reading user input");
}
- if (strcmp(yesno,"YES") == 0) {
- fprintf(stderr,"Once again, I'm gonna DO this...\n");
+ if (strcmp(yesno, "YES") == 0)
+ {
+ fprintf(stderr, "Once again, I'm gonna DO this...\n");
close_trn(in);
- if(0 != truncate(fn,fpos))
+ if (0 != truncate(fn, fpos))
{
- gmx_fatal(FARGS,"Error truncating file %s",fn);
+ gmx_fatal(FARGS, "Error truncating file %s", fn);
}
}
- else {
- fprintf(stderr,"Ok, I'll forget about it\n");
+ else
+ {
+ fprintf(stderr, "Ok, I'll forget about it\n");
}
}
- else {
- fprintf(stderr,"Already at end of file (t=%g)...\n",t);
+ else
+ {
+ fprintf(stderr, "Already at end of file (t=%g)...\n", t);
close_trn(in);
}
}
}
#endif
-int gmx_trjconv(int argc,char *argv[])
+int gmx_trjconv(int argc, char *argv[])
{
const char *desc[] = {
"[TT]trjconv[tt] can convert trajectory files in many ways:[BR]",
"Option [TT]-pbc[tt] sets the type of periodic boundary condition",
"treatment:[BR]",
"[TT]* mol[tt] puts the center of mass of molecules in the box,",
- "and requires a run input file to be supplied with [TT]-s[tt].[BR]",
+ "and requires a run input file to be supplied with [TT]-s[tt].[BR]",
"[TT]* res[tt] puts the center of mass of residues in the box.[BR]",
"[TT]* atom[tt] puts all the atoms in the box.[BR]",
"[TT]* nojump[tt] checks if atoms jump across the box and then puts",
"All three options give different results for triclinic boxes and",
"identical results for rectangular boxes.",
"[TT]rect[tt] is the ordinary brick shape.",
- "[TT]tric[tt] is the triclinic unit cell.",
+ "[TT]tric[tt] is the triclinic unit cell.",
"[TT]compact[tt] puts all atoms at the closest distance from the center",
"of the box. This can be useful for visualizing e.g. truncated octahedra",
"or rhombic dodecahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
"Use option [TT]-pbc mol[tt] in addition to [TT]-center[tt] when you",
"want all molecules in the box after the centering.[PAR]",
- "It is not always possible to use combinations of [TT]-pbc[tt],",
- "[TT]-fit[tt], [TT]-ur[tt] and [TT]-center[tt] to do exactly what",
- "you want in one call to [TT]trjconv[tt]. Consider using multiple",
- "calls, and check out the GROMACS website for suggestions.[PAR]",
+ "It is not always possible to use combinations of [TT]-pbc[tt],",
+ "[TT]-fit[tt], [TT]-ur[tt] and [TT]-center[tt] to do exactly what",
+ "you want in one call to [TT]trjconv[tt]. Consider using multiple",
+ "calls, and check out the GROMACS website for suggestions.[PAR]",
"With [TT]-dt[tt], it is possible to reduce the number of ",
"frames in the output. This option relies on the accuracy of the times",
"will not be written."
};
- int pbc_enum;
+ int pbc_enum;
enum
{
epSel,
epNR
};
const char *pbc_opt[epNR + 1] =
- { NULL, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
- NULL };
+ {
+ NULL, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
+ NULL
+ };
- int unitcell_enum;
- const char *unitcell_opt[euNR+1] =
- { NULL, "rect", "tric", "compact", NULL };
+ int unitcell_enum;
+ const char *unitcell_opt[euNR+1] =
+ { NULL, "rect", "tric", "compact", NULL };
enum
- { ecSel, ecTric, ecRect, ecZero, ecNR};
- const char *center_opt[ecNR+1] =
- { NULL, "tric", "rect", "zero", NULL };
- int ecenter;
+ {
+ ecSel, ecTric, ecRect, ecZero, ecNR
+ };
+ const char *center_opt[ecNR+1] =
+ { NULL, "tric", "rect", "zero", NULL };
+ int ecenter;
- int fit_enum;
+ int fit_enum;
enum
{
efSel, efNone, efFit, efFitXY, efReset, efResetXY, efPFit, efNR
};
const char *fit[efNR + 1] =
- { NULL, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
- "progressive", NULL };
-
- static gmx_bool bAppend=FALSE,bSeparate=FALSE,bVels=TRUE,bForce=FALSE,bCONECT=FALSE;
- static gmx_bool bCenter=FALSE;
- static int skip_nr=1,ndec=3,nzero=0;
- static real tzero=0,delta_t=0,timestep=0,ttrunc=-1,tdump=-1,split_t=0;
- static rvec newbox = {0,0,0}, shift = {0,0,0}, trans = {0,0,0};
- static char *exec_command=NULL;
- static real dropunder=0,dropover=0;
- static gmx_bool bRound=FALSE;
- static rvec clustercenter = {0,0,0};
-
+ {
+ NULL, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
+ "progressive", NULL
+ };
+
+ static gmx_bool bAppend = FALSE, bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
+ static gmx_bool bCenter = FALSE;
+ static int skip_nr = 1, ndec = 3, nzero = 0;
+ static real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
+ static rvec newbox = {0, 0, 0}, shift = {0, 0, 0}, trans = {0, 0, 0};
+ static char *exec_command = NULL;
+ static real dropunder = 0, dropover = 0;
+ static gmx_bool bRound = FALSE;
+ static rvec clustercenter = {0, 0, 0};
+
t_pargs
pa[] =
- {
- { "-skip", FALSE, etINT,
- { &skip_nr }, "Only write every nr-th frame" },
- { "-dt", FALSE, etTIME,
- { &delta_t },
- "Only write frame when t MOD dt = first time (%t)" },
- { "-round", FALSE, etBOOL,
- { &bRound }, "Round measurements to nearest picosecond"
- },
- { "-dump", FALSE, etTIME,
- { &tdump }, "Dump frame nearest specified time (%t)" },
- { "-t0", FALSE, etTIME,
- { &tzero },
- "Starting time (%t) (default: don't change)" },
- { "-timestep", FALSE, etTIME,
- { ×tep },
- "Change time step between input frames (%t)" },
- { "-pbc", FALSE, etENUM,
- { pbc_opt },
- "PBC treatment (see help text for full description)" },
- { "-ur", FALSE, etENUM,
- { unitcell_opt }, "Unit-cell representation" },
- { "-center", FALSE, etBOOL,
- { &bCenter }, "Center atoms in box" },
- { "-boxcenter", FALSE, etENUM,
- { center_opt }, "Center for -pbc and -center" },
- { "-box", FALSE, etRVEC,
- { newbox },
- "Size for new cubic box (default: read from input)" },
- { "-clustercenter", FALSE, etRVEC,
- { clustercenter },
- "Optional starting point for pbc cluster option" },
- { "-trans", FALSE, etRVEC,
- { trans },
- "All coordinates will be translated by trans. This "
- "can advantageously be combined with -pbc mol -ur "
- "compact." },
- { "-shift", FALSE, etRVEC,
- { shift },
- "All coordinates will be shifted by framenr*shift" },
- { "-fit", FALSE, etENUM,
- { fit },
- "Fit molecule to ref structure in the structure file" },
- { "-ndec", FALSE, etINT,
- { &ndec },
- "Precision for .xtc and .gro writing in number of "
- "decimal places" },
- { "-vel", FALSE, etBOOL,
- { &bVels }, "Read and write velocities if possible" },
- { "-force", FALSE, etBOOL,
- { &bForce }, "Read and write forces if possible" },
+ {
+ { "-skip", FALSE, etINT,
+ { &skip_nr }, "Only write every nr-th frame" },
+ { "-dt", FALSE, etTIME,
+ { &delta_t },
+ "Only write frame when t MOD dt = first time (%t)" },
+ { "-round", FALSE, etBOOL,
+ { &bRound }, "Round measurements to nearest picosecond"},
+ { "-dump", FALSE, etTIME,
+ { &tdump }, "Dump frame nearest specified time (%t)" },
+ { "-t0", FALSE, etTIME,
+ { &tzero },
+ "Starting time (%t) (default: don't change)" },
+ { "-timestep", FALSE, etTIME,
+ { ×tep },
+ "Change time step between input frames (%t)" },
+ { "-pbc", FALSE, etENUM,
+ { pbc_opt },
+ "PBC treatment (see help text for full description)" },
+ { "-ur", FALSE, etENUM,
+ { unitcell_opt }, "Unit-cell representation" },
+ { "-center", FALSE, etBOOL,
+ { &bCenter }, "Center atoms in box" },
+ { "-boxcenter", FALSE, etENUM,
+ { center_opt }, "Center for -pbc and -center" },
+ { "-box", FALSE, etRVEC,
+ { newbox },
+ "Size for new cubic box (default: read from input)" },
+ { "-clustercenter", FALSE, etRVEC,
+ { clustercenter },
+ "Optional starting point for pbc cluster option" },
+ { "-trans", FALSE, etRVEC,
+ { trans },
+ "All coordinates will be translated by trans. This "
+ "can advantageously be combined with -pbc mol -ur "
+ "compact." },
+ { "-shift", FALSE, etRVEC,
+ { shift },
+ "All coordinates will be shifted by framenr*shift" },
+ { "-fit", FALSE, etENUM,
+ { fit },
+ "Fit molecule to ref structure in the structure file" },
+ { "-ndec", FALSE, etINT,
+ { &ndec },
+ "Precision for .xtc and .gro writing in number of "
+ "decimal places" },
+ { "-vel", FALSE, etBOOL,
+ { &bVels }, "Read and write velocities if possible" },
+ { "-force", FALSE, etBOOL,
+ { &bForce }, "Read and write forces if possible" },
#ifndef GMX_NATIVE_WINDOWS
- { "-trunc", FALSE, etTIME,
- { &ttrunc },
- "Truncate input trajectory file after this time (%t)" },
+ { "-trunc", FALSE, etTIME,
+ { &ttrunc },
+ "Truncate input trajectory file after this time (%t)" },
#endif
- { "-exec", FALSE, etSTR,
- { &exec_command },
- "Execute command for every output frame with the "
- "frame number as argument" },
- { "-app", FALSE, etBOOL,
- { &bAppend }, "Append output" },
- { "-split", FALSE, etTIME,
- { &split_t },
- "Start writing new file when t MOD split = first "
- "time (%t)" },
- { "-sep", FALSE, etBOOL,
- { &bSeparate },
- "Write each frame to a separate .gro, .g96 or .pdb "
- "file" },
- { "-nzero", FALSE, etINT,
- { &nzero },
- "If the -sep flag is set, use these many digits "
- "for the file numbers and prepend zeros as needed" },
- { "-dropunder", FALSE, etREAL,
- { &dropunder }, "Drop all frames below this value" },
- { "-dropover", FALSE, etREAL,
- { &dropover }, "Drop all frames above this value" },
- { "-conect", FALSE, etBOOL,
- { &bCONECT },
- "Add conect records when writing [TT].pdb[tt] files. Useful "
- "for visualization of non-standard molecules, e.g. "
- "coarse grained ones" } };
+ { "-exec", FALSE, etSTR,
+ { &exec_command },
+ "Execute command for every output frame with the "
+ "frame number as argument" },
+ { "-app", FALSE, etBOOL,
+ { &bAppend }, "Append output" },
+ { "-split", FALSE, etTIME,
+ { &split_t },
+ "Start writing new file when t MOD split = first "
+ "time (%t)" },
+ { "-sep", FALSE, etBOOL,
+ { &bSeparate },
+ "Write each frame to a separate .gro, .g96 or .pdb "
+ "file" },
+ { "-nzero", FALSE, etINT,
+ { &nzero },
+ "If the -sep flag is set, use these many digits "
+ "for the file numbers and prepend zeros as needed" },
+ { "-dropunder", FALSE, etREAL,
+ { &dropunder }, "Drop all frames below this value" },
+ { "-dropover", FALSE, etREAL,
+ { &dropover }, "Drop all frames above this value" },
+ { "-conect", FALSE, etBOOL,
+ { &bCONECT },
+ "Add conect records when writing [TT].pdb[tt] files. Useful "
+ "for visualization of non-standard molecules, e.g. "
+ "coarse grained ones" }
+ };
#define NPA asize(pa)
- FILE *out=NULL;
- t_trxstatus *trxout=NULL;
- t_trxstatus *status;
- int ftp,ftpin=0,file_nr;
- t_trxframe fr,frout;
- int flags;
- rvec *xmem=NULL,*vmem=NULL,*fmem=NULL;
- rvec *xp=NULL,x_shift,hbox,box_center,dx;
- real xtcpr, lambda,*w_rls=NULL;
- int m,i,d,frame,outframe,natoms,nout,ncent,nre,newstep=0,model_nr;
+ FILE *out = NULL;
+ t_trxstatus *trxout = NULL;
+ t_trxstatus *status;
+ int ftp, ftpin = 0, file_nr;
+ t_trxframe fr, frout;
+ int flags;
+ rvec *xmem = NULL, *vmem = NULL, *fmem = NULL;
+ rvec *xp = NULL, x_shift, hbox, box_center, dx;
+ real xtcpr, lambda, *w_rls = NULL;
+ int m, i, d, frame, outframe, natoms, nout, ncent, nre, newstep = 0, model_nr;
#define SKIP 10
- t_topology top;
- gmx_conect gc=NULL;
- int ePBC=-1;
- t_atoms *atoms=NULL,useatoms;
- matrix top_box;
- atom_id *index,*cindex;
- char *grpnm;
- int *frindex,nrfri;
- char *frname;
- int ifit,irms,my_clust=-1;
- atom_id *ind_fit,*ind_rms;
- char *gn_fit,*gn_rms;
- t_cluster_ndx *clust=NULL;
- t_trxstatus **clust_status=NULL;
- int *clust_status_id=NULL;
- int ntrxopen=0;
- int *nfwritten=NULL;
- int ndrop=0,ncol,drop0=0,drop1=0,dropuse=0;
- double **dropval;
- real tshift=0,t0=-1,dt=0.001,prec;
- gmx_bool bFit,bFitXY,bPFit,bReset;
- int nfitdim;
- gmx_rmpbc_t gpbc=NULL;
- gmx_bool bRmPBC,bPBCWhole,bPBCcomRes,bPBCcomMol,bPBCcomAtom,bPBC,bNoJump,bCluster;
- gmx_bool bCopy,bDoIt,bIndex,bTDump,bSetTime,bTPS=FALSE,bDTset=FALSE;
- gmx_bool bExec,bTimeStep=FALSE,bDumpFrame=FALSE,bSetPrec,bNeedPrec;
- gmx_bool bHaveFirstFrame,bHaveNextFrame,bSetBox,bSetUR,bSplit=FALSE;
- gmx_bool bSubTraj=FALSE,bDropUnder=FALSE,bDropOver=FALSE,bTrans=FALSE;
- gmx_bool bWriteFrame,bSplitHere;
- const char *top_file,*in_file,*out_file=NULL;
- char out_file2[256],*charpt;
- char *outf_base=NULL;
- const char *outf_ext=NULL;
- char top_title[256],title[256],command[256],filemode[5];
- int xdr=0;
- gmx_bool bWarnCompact=FALSE;
- const char *warn;
- output_env_t oenv;
-
- t_filenm fnm[] = {
+ t_topology top;
+ gmx_conect gc = NULL;
+ int ePBC = -1;
+ t_atoms *atoms = NULL, useatoms;
+ matrix top_box;
+ atom_id *index, *cindex;
+ char *grpnm;
+ int *frindex, nrfri;
+ char *frname;
+ int ifit, irms, my_clust = -1;
+ atom_id *ind_fit, *ind_rms;
+ char *gn_fit, *gn_rms;
+ t_cluster_ndx *clust = NULL;
+ t_trxstatus **clust_status = NULL;
+ int *clust_status_id = NULL;
+ int ntrxopen = 0;
+ int *nfwritten = NULL;
+ int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0;
+ double **dropval;
+ real tshift = 0, t0 = -1, dt = 0.001, prec;
+ gmx_bool bFit, bFitXY, bPFit, bReset;
+ int nfitdim;
+ gmx_rmpbc_t gpbc = NULL;
+ gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster;
+ gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE;
+ gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec;
+ gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE;
+ gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE;
+ gmx_bool bWriteFrame, bSplitHere;
+ const char *top_file, *in_file, *out_file = NULL;
+ char out_file2[256], *charpt;
+ char *outf_base = NULL;
+ const char *outf_ext = NULL;
+ char top_title[256], title[256], command[256], filemode[5];
+ int xdr = 0;
+ gmx_bool bWarnCompact = FALSE;
+ const char *warn;
+ output_env_t oenv;
+
+ t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTRO, "-o", NULL, ffWRITE },
{ efTPS, NULL, NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efNDX, "-fr", "frames", ffOPTRD },
{ efNDX, "-sub", "cluster", ffOPTRD },
- { efXVG, "-drop","drop", ffOPTRD }
+ { efXVG, "-drop", "drop", ffOPTRD }
};
#define NFILE asize(fnm)
- parse_common_args(&argc,argv,
- PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
+ parse_common_args(&argc, argv,
+ PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
PCA_TIME_UNIT | PCA_BE_NICE,
- NFILE,fnm,NPA,pa,asize(desc),desc,
- 0,NULL,&oenv);
+ NFILE, fnm, NPA, pa, asize(desc), desc,
+ 0, NULL, &oenv);
- top_file = ftp2fn(efTPS,NFILE,fnm);
+ top_file = ftp2fn(efTPS, NFILE, fnm);
init_top(&top);
/* Check command line */
- in_file=opt2fn("-f",NFILE,fnm);
+ in_file = opt2fn("-f", NFILE, fnm);
- if (ttrunc != -1) {
+ if (ttrunc != -1)
+ {
#ifndef GMX_NATIVE_WINDOWS
- do_trunc(in_file,ttrunc);
+ do_trunc(in_file, ttrunc);
#endif
}
- else {
+ else
+ {
/* mark active cmdline options */
- bSetBox = opt2parg_bSet("-box", NPA, pa);
- bSetTime = opt2parg_bSet("-t0", NPA, pa);
- bSetPrec = opt2parg_bSet("-ndec", NPA, pa);
- bSetUR = opt2parg_bSet("-ur", NPA, pa);
- bExec = opt2parg_bSet("-exec", NPA, pa);
- bTimeStep = opt2parg_bSet("-timestep", NPA, pa);
- bTDump = opt2parg_bSet("-dump", NPA, pa);
- bDropUnder= opt2parg_bSet("-dropunder", NPA, pa);
- bDropOver = opt2parg_bSet("-dropover", NPA, pa);
- bTrans = opt2parg_bSet("-trans",NPA,pa);
- bSplit = (split_t != 0);
-
- /* parse enum options */
- fit_enum = nenum(fit);
- bFit = (fit_enum==efFit || fit_enum==efFitXY);
- bFitXY = fit_enum==efFitXY;
- bReset = (fit_enum==efReset || fit_enum==efResetXY);
- bPFit = fit_enum==efPFit;
- pbc_enum = nenum(pbc_opt);
- bPBCWhole = pbc_enum==epWhole;
- bPBCcomRes = pbc_enum==epComRes;
- bPBCcomMol = pbc_enum==epComMol;
- bPBCcomAtom= pbc_enum==epComAtom;
- bNoJump = pbc_enum==epNojump;
- bCluster = pbc_enum==epCluster;
- bPBC = pbc_enum!=epNone;
+ bSetBox = opt2parg_bSet("-box", NPA, pa);
+ bSetTime = opt2parg_bSet("-t0", NPA, pa);
+ bSetPrec = opt2parg_bSet("-ndec", NPA, pa);
+ bSetUR = opt2parg_bSet("-ur", NPA, pa);
+ bExec = opt2parg_bSet("-exec", NPA, pa);
+ bTimeStep = opt2parg_bSet("-timestep", NPA, pa);
+ bTDump = opt2parg_bSet("-dump", NPA, pa);
+ bDropUnder = opt2parg_bSet("-dropunder", NPA, pa);
+ bDropOver = opt2parg_bSet("-dropover", NPA, pa);
+ bTrans = opt2parg_bSet("-trans", NPA, pa);
+ bSplit = (split_t != 0);
+
+ /* parse enum options */
+ fit_enum = nenum(fit);
+ bFit = (fit_enum == efFit || fit_enum == efFitXY);
+ bFitXY = fit_enum == efFitXY;
+ bReset = (fit_enum == efReset || fit_enum == efResetXY);
+ bPFit = fit_enum == efPFit;
+ pbc_enum = nenum(pbc_opt);
+ bPBCWhole = pbc_enum == epWhole;
+ bPBCcomRes = pbc_enum == epComRes;
+ bPBCcomMol = pbc_enum == epComMol;
+ bPBCcomAtom = pbc_enum == epComAtom;
+ bNoJump = pbc_enum == epNojump;
+ bCluster = pbc_enum == epCluster;
+ bPBC = pbc_enum != epNone;
unitcell_enum = nenum(unitcell_opt);
- ecenter = nenum(center_opt) - ecTric;
+ ecenter = nenum(center_opt) - ecTric;
- /* set and check option dependencies */
- if (bPFit) bFit = TRUE; /* for pfit, fit *must* be set */
- if (bFit) bReset = TRUE; /* for fit, reset *must* be set */
+ /* set and check option dependencies */
+ if (bPFit)
+ {
+ bFit = TRUE; /* for pfit, fit *must* be set */
+ }
+ if (bFit)
+ {
+ bReset = TRUE; /* for fit, reset *must* be set */
+ }
nfitdim = 0;
if (bFit || bReset)
- nfitdim = (fit_enum==efFitXY || fit_enum==efResetXY) ? 2 : 3;
+ {
+ nfitdim = (fit_enum == efFitXY || fit_enum == efResetXY) ? 2 : 3;
+ }
bRmPBC = bFit || bPBCWhole || bPBCcomRes || bPBCcomMol;
-
- if (bSetUR) {
- if (!(bPBCcomRes || bPBCcomMol || bPBCcomAtom)) {
+
+ if (bSetUR)
+ {
+ if (!(bPBCcomRes || bPBCcomMol || bPBCcomAtom))
+ {
fprintf(stderr,
"WARNING: Option for unitcell representation (-ur %s)\n"
" only has effect in combination with -pbc %s, %s or %s.\n"
" Ingoring unitcell representation.\n\n",
- unitcell_opt[0],pbc_opt[2],pbc_opt[3],pbc_opt[4]);
+ unitcell_opt[0], pbc_opt[2], pbc_opt[3], pbc_opt[4]);
bSetUR = FALSE;
}
}
- if (bFit && bPBC) {
- gmx_fatal(FARGS,"PBC condition treatment does not work together with rotational fit.\n"
+ if (bFit && bPBC)
+ {
+ gmx_fatal(FARGS, "PBC condition treatment does not work together with rotational fit.\n"
"Please do the PBC condition treatment first and then run trjconv in a second step\n"
"for the rotational fit.\n"
"First doing the rotational fit and then doing the PBC treatment gives incorrect\n"
- "results!");
- }
+ "results!");
+ }
/* ndec is in nr of decimal places, prec is a multiplication factor: */
prec = 1;
- for (i=0; i<ndec; i++)
+ for (i = 0; i < ndec; i++)
+ {
prec *= 10;
+ }
- bIndex=ftp2bSet(efNDX,NFILE,fnm);
+ bIndex = ftp2bSet(efNDX, NFILE, fnm);
- /* Determine output type */
- out_file=opt2fn("-o",NFILE,fnm);
- ftp=fn2ftp(out_file);
- fprintf(stderr,"Will write %s: %s\n",ftp2ext(ftp),ftp2desc(ftp));
- bNeedPrec = (ftp==efXTC || ftp==efGRO);
- if (bVels) {
+ /* Determine output type */
+ out_file = opt2fn("-o", NFILE, fnm);
+ ftp = fn2ftp(out_file);
+ fprintf(stderr, "Will write %s: %s\n", ftp2ext(ftp), ftp2desc(ftp));
+ bNeedPrec = (ftp == efXTC || ftp == efGRO);
+ if (bVels)
+ {
/* check if velocities are possible in input and output files */
- ftpin=fn2ftp(in_file);
- bVels= (ftp==efTRR || ftp==efTRJ || ftp==efGRO || ftp==efG96)
- && (ftpin==efTRR || ftpin==efTRJ || ftpin==efGRO || ftpin==efG96 ||
- ftpin==efCPT);
+ ftpin = fn2ftp(in_file);
+ bVels = (ftp == efTRR || ftp == efTRJ || ftp == efGRO || ftp == efG96)
+ && (ftpin == efTRR || ftpin == efTRJ || ftpin == efGRO || ftpin == efG96 ||
+ ftpin == efCPT);
}
- if (bSeparate || bSplit) {
- outf_ext = strrchr(out_file,'.');
+ if (bSeparate || bSplit)
+ {
+ outf_ext = strrchr(out_file, '.');
if (outf_ext == NULL)
- gmx_fatal(FARGS,"Output file name '%s' does not contain a '.'",out_file);
+ {
+ gmx_fatal(FARGS, "Output file name '%s' does not contain a '.'", out_file);
+ }
outf_base = strdup(out_file);
outf_base[outf_ext - out_file] = '\0';
}
- bSubTraj = opt2bSet("-sub",NFILE,fnm);
- if (bSubTraj) {
+ bSubTraj = opt2bSet("-sub", NFILE, fnm);
+ if (bSubTraj)
+ {
if ((ftp != efXTC) && (ftp != efTRR))
+ {
/* It seems likely that other trajectory file types
* could work here. */
- gmx_fatal(FARGS,"Can only use the sub option with output file types "
+ gmx_fatal(FARGS, "Can only use the sub option with output file types "
"xtc and trr");
- clust = cluster_index(NULL,opt2fn("-sub",NFILE,fnm));
+ }
+ clust = cluster_index(NULL, opt2fn("-sub", NFILE, fnm));
/* Check for number of files disabled, as FOPEN_MAX is not the correct
* number to check for. In my linux box it is only 16.
*/
if (0 && (clust->clust->nr > FOPEN_MAX-4))
- gmx_fatal(FARGS,"Can not open enough (%d) files to write all the"
+ {
+ gmx_fatal(FARGS, "Can not open enough (%d) files to write all the"
" trajectories.\ntry splitting the index file in %d parts.\n"
"FOPEN_MAX = %d",
- clust->clust->nr,1+clust->clust->nr/FOPEN_MAX,FOPEN_MAX);
- gmx_warning("The -sub option could require as many open output files as there are\n"
- "index groups in the file (%d). If you get I/O errors opening new files,\n"
- "try reducing the number of index groups in the file, and perhaps\n"
- "using trjconv -sub several times on different chunks of your index file.\n",
- clust->clust->nr);
-
- snew(clust_status,clust->clust->nr);
- snew(clust_status_id,clust->clust->nr);
- snew(nfwritten,clust->clust->nr);
- for(i=0; (i<clust->clust->nr); i++)
+ clust->clust->nr, 1+clust->clust->nr/FOPEN_MAX, FOPEN_MAX);
+ }
+ gmx_warning("The -sub option could require as many open output files as there are\n"
+ "index groups in the file (%d). If you get I/O errors opening new files,\n"
+ "try reducing the number of index groups in the file, and perhaps\n"
+ "using trjconv -sub several times on different chunks of your index file.\n",
+ clust->clust->nr);
+
+ snew(clust_status, clust->clust->nr);
+ snew(clust_status_id, clust->clust->nr);
+ snew(nfwritten, clust->clust->nr);
+ for (i = 0; (i < clust->clust->nr); i++)
{
- clust_status[i] = NULL;
+ clust_status[i] = NULL;
clust_status_id[i] = -1;
}
bSeparate = bSplit = FALSE;
}
- /* skipping */
- if (skip_nr <= 0) {
- }
+ /* skipping */
+ if (skip_nr <= 0)
+ {
+ }
/* Determine whether to read a topology */
- bTPS = (ftp2bSet(efTPS,NFILE,fnm) ||
- bRmPBC || bReset || bPBCcomMol || bCluster ||
- (ftp == efGRO) || (ftp == efPDB) || bCONECT);
+ bTPS = (ftp2bSet(efTPS, NFILE, fnm) ||
+ bRmPBC || bReset || bPBCcomMol || bCluster ||
+ (ftp == efGRO) || (ftp == efPDB) || bCONECT);
/* Determine if when can read index groups */
bIndex = (bIndex || bTPS);
- if (bTPS) {
- read_tps_conf(top_file,top_title,&top,&ePBC,&xp,NULL,top_box,
+ if (bTPS)
+ {
+ read_tps_conf(top_file, top_title, &top, &ePBC, &xp, NULL, top_box,
bReset || bPBCcomRes);
- atoms=&top.atoms;
+ atoms = &top.atoms;
if (0 == top.mols.nr && (bCluster || bPBCcomMol))
{
- gmx_fatal(FARGS,"Option -pbc %s requires a .tpr file for the -s option",pbc_opt[pbc_enum]);
+ gmx_fatal(FARGS, "Option -pbc %s requires a .tpr file for the -s option", pbc_opt[pbc_enum]);
}
/* top_title is only used for gro and pdb,
* the header in such a file is top_title t= ...
* to prevent a double t=, remove it from top_title
*/
- if ((charpt=strstr(top_title," t= ")))
- charpt[0]='\0';
+ if ((charpt = strstr(top_title, " t= ")))
+ {
+ charpt[0] = '\0';
+ }
if (bCONECT)
+ {
gc = gmx_conect_generate(&top);
- if (bRmPBC)
- gpbc = gmx_rmpbc_init(&top.idef,ePBC,top.atoms.nr,top_box);
+ }
+ if (bRmPBC)
+ {
+ gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr, top_box);
+ }
}
/* get frame number index */
- frindex=NULL;
- if (opt2bSet("-fr",NFILE,fnm)) {
+ frindex = NULL;
+ if (opt2bSet("-fr", NFILE, fnm))
+ {
printf("Select groups of frame number indices:\n");
- rd_index(opt2fn("-fr",NFILE,fnm),1,&nrfri,(atom_id **)&frindex,&frname);
+ rd_index(opt2fn("-fr", NFILE, fnm), 1, &nrfri, (atom_id **)&frindex, &frname);
if (debug)
- for(i=0; i<nrfri; i++)
- fprintf(debug,"frindex[%4d]=%4d\n",i,frindex[i]);
+ {
+ for (i = 0; i < nrfri; i++)
+ {
+ fprintf(debug, "frindex[%4d]=%4d\n", i, frindex[i]);
+ }
+ }
}
/* get index groups etc. */
- if (bReset) {
+ if (bReset)
+ {
printf("Select group for %s fit\n",
- bFit?"least squares":"translational");
- get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),
- 1,&ifit,&ind_fit,&gn_fit);
+ bFit ? "least squares" : "translational");
+ get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
+ 1, &ifit, &ind_fit, &gn_fit);
- if (bFit) {
- if (ifit < 2)
- gmx_fatal(FARGS,"Need at least 2 atoms to fit!\n");
+ if (bFit)
+ {
+ if (ifit < 2)
+ {
+ gmx_fatal(FARGS, "Need at least 2 atoms to fit!\n");
+ }
else if (ifit == 3)
- fprintf(stderr,"WARNING: fitting with only 2 atoms is not unique\n");
+ {
+ fprintf(stderr, "WARNING: fitting with only 2 atoms is not unique\n");
+ }
}
}
- else if (bCluster) {
+ else if (bCluster)
+ {
printf("Select group for clustering\n");
- get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),
- 1,&ifit,&ind_fit,&gn_fit);
+ get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
+ 1, &ifit, &ind_fit, &gn_fit);
}
- if (bIndex) {
- if (bCenter) {
+ if (bIndex)
+ {
+ if (bCenter)
+ {
printf("Select group for centering\n");
- get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),
- 1,&ncent,&cindex,&grpnm);
+ get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
+ 1, &ncent, &cindex, &grpnm);
}
printf("Select group for output\n");
- get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),
- 1,&nout,&index,&grpnm);
- } else {
+ get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm),
+ 1, &nout, &index, &grpnm);
+ }
+ else
+ {
/* no index file, so read natoms from TRX */
- if (!read_first_frame(oenv,&status,in_file,&fr,TRX_DONT_SKIP))
- gmx_fatal(FARGS,"Could not read a frame from %s",in_file);
+ if (!read_first_frame(oenv, &status, in_file, &fr, TRX_DONT_SKIP))
+ {
+ gmx_fatal(FARGS, "Could not read a frame from %s", in_file);
+ }
natoms = fr.natoms;
close_trj(status);
sfree(fr.x);
- snew(index,natoms);
- for(i=0;i<natoms;i++)
- index[i]=i;
- nout=natoms;
- if (bCenter) {
- ncent = nout;
+ snew(index, natoms);
+ for (i = 0; i < natoms; i++)
+ {
+ index[i] = i;
+ }
+ nout = natoms;
+ if (bCenter)
+ {
+ ncent = nout;
cindex = index;
}
}
- if (bReset) {
- snew(w_rls,atoms->nr);
- for(i=0; (i<ifit); i++)
- w_rls[ind_fit[i]]=atoms->atom[ind_fit[i]].m;
+ if (bReset)
+ {
+ snew(w_rls, atoms->nr);
+ for (i = 0; (i < ifit); i++)
+ {
+ w_rls[ind_fit[i]] = atoms->atom[ind_fit[i]].m;
+ }
- /* Restore reference structure and set to origin,
- store original location (to put structure back) */
+ /* Restore reference structure and set to origin,
+ store original location (to put structure back) */
if (bRmPBC)
- gmx_rmpbc(gpbc,top.atoms.nr,top_box,xp);
- copy_rvec(xp[index[0]],x_shift);
- reset_x_ndim(nfitdim,ifit,ind_fit,atoms->nr,NULL,xp,w_rls);
- rvec_dec(x_shift,xp[index[0]]);
- } else
+ {
+ gmx_rmpbc(gpbc, top.atoms.nr, top_box, xp);
+ }
+ copy_rvec(xp[index[0]], x_shift);
+ reset_x_ndim(nfitdim, ifit, ind_fit, atoms->nr, NULL, xp, w_rls);
+ rvec_dec(x_shift, xp[index[0]]);
+ }
+ else
+ {
clear_rvec(x_shift);
+ }
- if (bDropUnder || bDropOver) {
+ if (bDropUnder || bDropOver)
+ {
/* Read the .xvg file with the drop values */
- fprintf(stderr,"\nReading drop file ...");
- ndrop = read_xvg(opt2fn("-drop",NFILE,fnm),&dropval,&ncol);
- fprintf(stderr," %d time points\n",ndrop);
+ fprintf(stderr, "\nReading drop file ...");
+ ndrop = read_xvg(opt2fn("-drop", NFILE, fnm), &dropval, &ncol);
+ fprintf(stderr, " %d time points\n", ndrop);
if (ndrop == 0 || ncol < 2)
- gmx_fatal(FARGS,"Found no data points in %s",
- opt2fn("-drop",NFILE,fnm));
+ {
+ gmx_fatal(FARGS, "Found no data points in %s",
+ opt2fn("-drop", NFILE, fnm));
+ }
drop0 = 0;
drop1 = 0;
}
/* Make atoms struct for output in GRO or PDB files */
- if ((ftp == efGRO) || ((ftp == efG96) && bTPS) || (ftp == efPDB)) {
+ if ((ftp == efGRO) || ((ftp == efG96) && bTPS) || (ftp == efPDB))
+ {
/* get memory for stuff to go in .pdb file */
- init_t_atoms(&useatoms,atoms->nr,FALSE);
+ init_t_atoms(&useatoms, atoms->nr, FALSE);
sfree(useatoms.resinfo);
useatoms.resinfo = atoms->resinfo;
- for(i=0;(i<nout);i++) {
- useatoms.atomname[i]=atoms->atomname[index[i]];
- useatoms.atom[i]=atoms->atom[index[i]];
- useatoms.nres=max(useatoms.nres,useatoms.atom[i].resind+1);
+ for (i = 0; (i < nout); i++)
+ {
+ useatoms.atomname[i] = atoms->atomname[index[i]];
+ useatoms.atom[i] = atoms->atom[index[i]];
+ useatoms.nres = max(useatoms.nres, useatoms.atom[i].resind+1);
}
- useatoms.nr=nout;
+ useatoms.nr = nout;
}
/* select what to read */
- if (ftp==efTRR || ftp==efTRJ)
- flags = TRX_READ_X;
+ if (ftp == efTRR || ftp == efTRJ)
+ {
+ flags = TRX_READ_X;
+ }
else
+ {
flags = TRX_NEED_X;
+ }
if (bVels)
+ {
flags = flags | TRX_READ_V;
+ }
if (bForce)
+ {
flags = flags | TRX_READ_F;
+ }
/* open trx file for reading */
- bHaveFirstFrame = read_first_frame(oenv,&status,in_file,&fr,flags);
+ bHaveFirstFrame = read_first_frame(oenv, &status, in_file, &fr, flags);
if (fr.bPrec)
- fprintf(stderr,"\nPrecision of %s is %g (nm)\n",in_file,1/fr.prec);
- if (bNeedPrec) {
+ {
+ fprintf(stderr, "\nPrecision of %s is %g (nm)\n", in_file, 1/fr.prec);
+ }
+ if (bNeedPrec)
+ {
if (bSetPrec || !fr.bPrec)
- fprintf(stderr,"\nSetting output precision to %g (nm)\n",1/prec);
+ {
+ fprintf(stderr, "\nSetting output precision to %g (nm)\n", 1/prec);
+ }
else
- fprintf(stderr,"Using output precision of %g (nm)\n",1/prec);
+ {
+ fprintf(stderr, "Using output precision of %g (nm)\n", 1/prec);
+ }
}
- if (bHaveFirstFrame) {
- set_trxframe_ePBC(&fr,ePBC);
+ if (bHaveFirstFrame)
+ {
+ set_trxframe_ePBC(&fr, ePBC);
natoms = fr.natoms;
if (bSetTime)
- tshift=tzero-fr.time;
+ {
+ tshift = tzero-fr.time;
+ }
else
- tzero=fr.time;
+ {
+ tzero = fr.time;
+ }
/* open output for writing */
- if ((bAppend) && (gmx_fexist(out_file))) {
- strcpy(filemode,"a");
- fprintf(stderr,"APPENDING to existing file %s\n",out_file);
- } else
- strcpy(filemode,"w");
- switch (ftp) {
- case efXTC:
- case efG87:
- case efTRR:
- case efTRJ:
- out=NULL;
- if (!bSplit && !bSubTraj)
- trxout = open_trx(out_file,filemode);
- break;
- case efGRO:
- case efG96:
- case efPDB:
- if (( !bSeparate && !bSplit ) && !bSubTraj)
- out=ffopen(out_file,filemode);
- break;
+ if ((bAppend) && (gmx_fexist(out_file)))
+ {
+ strcpy(filemode, "a");
+ fprintf(stderr, "APPENDING to existing file %s\n", out_file);
+ }
+ else
+ {
+ strcpy(filemode, "w");
+ }
+ switch (ftp)
+ {
+ case efXTC:
+ case efG87:
+ case efTRR:
+ case efTRJ:
+ out = NULL;
+ if (!bSplit && !bSubTraj)
+ {
+ trxout = open_trx(out_file, filemode);
+ }
+ break;
+ case efGRO:
+ case efG96:
+ case efPDB:
+ if (( !bSeparate && !bSplit ) && !bSubTraj)
+ {
+ out = ffopen(out_file, filemode);
+ }
+ break;
}
bCopy = FALSE;
if (bIndex)
+ {
/* check if index is meaningful */
- for(i=0; i<nout; i++) {
+ for (i = 0; i < nout; i++)
+ {
if (index[i] >= natoms)
+ {
gmx_fatal(FARGS,
- "Index[%d] %d is larger than the number of atoms in the\n"
- "trajectory file (%d). There is a mismatch in the contents\n"
- "of your -f, -s and/or -n files.",i,index[i]+1,natoms);
+ "Index[%d] %d is larger than the number of atoms in the\n"
+ "trajectory file (%d). There is a mismatch in the contents\n"
+ "of your -f, -s and/or -n files.", i, index[i]+1, natoms);
+ }
bCopy = bCopy || (i != index[i]);
}
- if (bCopy) {
- snew(xmem,nout);
- if (bVels) {
- snew(vmem,nout);
+ }
+ if (bCopy)
+ {
+ snew(xmem, nout);
+ if (bVels)
+ {
+ snew(vmem, nout);
}
- if (bForce) {
- snew(fmem,nout);
+ if (bForce)
+ {
+ snew(fmem, nout);
}
}
if (ftp == efG87)
+ {
fprintf(gmx_fio_getfp(trx_get_fileio(trxout)),
"Generated by %s. #atoms=%d, a BOX is"
- " stored in this file.\n",Program(),nout);
+ " stored in this file.\n", Program(), nout);
+ }
/* Start the big loop over frames */
- file_nr = 0;
+ file_nr = 0;
frame = 0;
outframe = 0;
model_nr = 0;
bDTset = FALSE;
/* Main loop over frames */
- do {
- if (!fr.bStep) {
+ do
+ {
+ if (!fr.bStep)
+ {
/* set the step */
fr.step = newstep;
newstep++;
}
- if (bSubTraj) {
+ if (bSubTraj)
+ {
/*if (frame >= clust->clust->nra)
- gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file\n");*/
+ gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file\n");*/
if (frame > clust->maxframe)
+ {
my_clust = -1;
+ }
else
+ {
my_clust = clust->inv_clust[frame];
- if ((my_clust < 0) || (my_clust >= clust->clust->nr) ||
+ }
+ if ((my_clust < 0) || (my_clust >= clust->clust->nr) ||
(my_clust == NO_ATID))
+ {
my_clust = -1;
+ }
}
- if (bSetBox) {
+ if (bSetBox)
+ {
/* generate new box */
clear_mat(fr.box);
- for (m=0; m<DIM; m++)
+ for (m = 0; m < DIM; m++)
+ {
fr.box[m][m] = newbox[m];
+ }
}
- if (bTrans) {
- for(i=0; i<natoms; i++)
- rvec_inc(fr.x[i],trans);
+ if (bTrans)
+ {
+ for (i = 0; i < natoms; i++)
+ {
+ rvec_inc(fr.x[i], trans);
+ }
}
- if (bTDump) {
+ if (bTDump)
+ {
/* determine timestep */
- if (t0 == -1) {
+ if (t0 == -1)
+ {
t0 = fr.time;
- } else {
- if (!bDTset) {
- dt = fr.time-t0;
+ }
+ else
+ {
+ if (!bDTset)
+ {
+ dt = fr.time-t0;
bDTset = TRUE;
}
}
/* This is not very elegant, as one can not dump a frame after
* a timestep with is more than twice as small as the first one. */
bDumpFrame = (fr.time > tdump-0.5*dt) && (fr.time <= tdump+0.5*dt);
- } else
+ }
+ else
+ {
bDumpFrame = FALSE;
+ }
/* determine if an atom jumped across the box and reset it if so */
- if (bNoJump && (bTPS || frame!=0)) {
- for(d=0; d<DIM; d++)
+ if (bNoJump && (bTPS || frame != 0))
+ {
+ for (d = 0; d < DIM; d++)
+ {
hbox[d] = 0.5*fr.box[d][d];
- for(i=0; i<natoms; i++) {
+ }
+ for (i = 0; i < natoms; i++)
+ {
if (bReset)
- rvec_dec(fr.x[i],x_shift);
- for(m=DIM-1; m>=0; m--)
- if (hbox[m] > 0) {
+ {
+ rvec_dec(fr.x[i], x_shift);
+ }
+ for (m = DIM-1; m >= 0; m--)
+ {
+ if (hbox[m] > 0)
+ {
while (fr.x[i][m]-xp[i][m] <= -hbox[m])
- for(d=0; d<=m; d++)
+ {
+ for (d = 0; d <= m; d++)
+ {
fr.x[i][d] += fr.box[m][d];
+ }
+ }
while (fr.x[i][m]-xp[i][m] > hbox[m])
- for(d=0; d<=m; d++)
+ {
+ for (d = 0; d <= m; d++)
+ {
fr.x[i][d] -= fr.box[m][d];
+ }
+ }
}
+ }
}
}
- else if (bCluster) {
+ else if (bCluster)
+ {
rvec com;
- calc_pbc_cluster(ecenter,ifit,&top,ePBC,fr.x,ind_fit,com,fr.box,clustercenter);
+ calc_pbc_cluster(ecenter, ifit, &top, ePBC, fr.x, ind_fit, com, fr.box, clustercenter);
}
- if (bPFit) {
+ if (bPFit)
+ {
/* Now modify the coords according to the flags,
- for normal fit, this is only done for output frames */
+ for normal fit, this is only done for output frames */
if (bRmPBC)
- gmx_rmpbc_trxfr(gpbc,&fr);
+ {
+ gmx_rmpbc_trxfr(gpbc, &fr);
+ }
- reset_x_ndim(nfitdim,ifit,ind_fit,natoms,NULL,fr.x,w_rls);
- do_fit(natoms,w_rls,xp,fr.x);
+ reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
+ do_fit(natoms, w_rls, xp, fr.x);
}
/* store this set of coordinates for future use */
- if (bPFit || bNoJump) {
+ if (bPFit || bNoJump)
+ {
if (xp == NULL)
- snew(xp,natoms);
- for(i=0; (i<natoms); i++) {
- copy_rvec(fr.x[i],xp[i]);
- rvec_inc(fr.x[i],x_shift);
+ {
+ snew(xp, natoms);
+ }
+ for (i = 0; (i < natoms); i++)
+ {
+ copy_rvec(fr.x[i], xp[i]);
+ rvec_inc(fr.x[i], x_shift);
}
}
- if ( frindex )
+ if (frindex)
+ {
/* see if we have a frame from the frame index group */
- for(i=0; i<nrfri && !bDumpFrame; i++)
+ for (i = 0; i < nrfri && !bDumpFrame; i++)
+ {
bDumpFrame = frame == frindex[i];
+ }
+ }
if (debug && bDumpFrame)
- fprintf(debug,"dumping %d\n",frame);
+ {
+ fprintf(debug, "dumping %d\n", frame);
+ }
bWriteFrame =
( ( !bTDump && !frindex && frame % skip_nr == 0 ) || bDumpFrame );
- if (bWriteFrame && (bDropUnder || bDropOver)) {
- while (dropval[0][drop1]<fr.time && drop1+1<ndrop) {
+ if (bWriteFrame && (bDropUnder || bDropOver))
+ {
+ while (dropval[0][drop1] < fr.time && drop1+1 < ndrop)
+ {
drop0 = drop1;
drop1++;
}
if (fabs(dropval[0][drop0] - fr.time)
- < fabs(dropval[0][drop1] - fr.time)) {
+ < fabs(dropval[0][drop1] - fr.time))
+ {
dropuse = drop0;
- } else {
+ }
+ else
+ {
dropuse = drop1;
}
if ((bDropUnder && dropval[1][dropuse] < dropunder) ||
(bDropOver && dropval[1][dropuse] > dropover))
+ {
bWriteFrame = FALSE;
+ }
}
- if (bWriteFrame) {
+ if (bWriteFrame)
+ {
/* calc new time */
- if (bTimeStep)
+ if (bTimeStep)
+ {
fr.time = tzero+frame*timestep;
+ }
else
- if (bSetTime)
- fr.time += tshift;
+ if (bSetTime)
+ {
+ fr.time += tshift;
+ }
if (bTDump)
- fprintf(stderr,"\nDumping frame at t= %g %s\n",
- output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
+ {
+ fprintf(stderr, "\nDumping frame at t= %g %s\n",
+ output_env_conv_time(oenv, fr.time), output_env_get_time_unit(oenv));
+ }
/* check for writing at each delta_t */
- bDoIt=(delta_t == 0);
+ bDoIt = (delta_t == 0);
if (!bDoIt)
{
if (!bRound)
- bDoIt=bRmod(fr.time,tzero, delta_t);
+ {
+ bDoIt = bRmod(fr.time, tzero, delta_t);
+ }
else
+ {
/* round() is not C89 compatible, so we do this: */
- bDoIt=bRmod(floor(fr.time+0.5),floor(tzero+0.5),
- floor(delta_t+0.5));
+ bDoIt = bRmod(floor(fr.time+0.5), floor(tzero+0.5),
+ floor(delta_t+0.5));
+ }
}
- if (bDoIt || bTDump) {
+ if (bDoIt || bTDump)
+ {
/* print sometimes */
if ( ((outframe % SKIP) == 0) || (outframe < SKIP) )
- fprintf(stderr," -> frame %6d time %8.3f \r",
- outframe,output_env_conv_time(oenv,fr.time));
+ {
+ fprintf(stderr, " -> frame %6d time %8.3f \r",
+ outframe, output_env_conv_time(oenv, fr.time));
+ }
- if (!bPFit) {
+ if (!bPFit)
+ {
/* Now modify the coords according to the flags,
for PFit we did this already! */
if (bRmPBC)
- gmx_rmpbc_trxfr(gpbc,&fr);
+ {
+ gmx_rmpbc_trxfr(gpbc, &fr);
+ }
- if (bReset) {
- reset_x_ndim(nfitdim,ifit,ind_fit,natoms,NULL,fr.x,w_rls);
+ if (bReset)
+ {
+ reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
if (bFit)
- do_fit_ndim(nfitdim,natoms,w_rls,xp,fr.x);
+ {
+ do_fit_ndim(nfitdim, natoms, w_rls, xp, fr.x);
+ }
if (!bCenter)
- for(i=0; i<natoms; i++)
- rvec_inc(fr.x[i],x_shift);
+ {
+ for (i = 0; i < natoms; i++)
+ {
+ rvec_inc(fr.x[i], x_shift);
+ }
+ }
}
if (bCenter)
- center_x(ecenter,fr.x,fr.box,natoms,ncent,cindex);
+ {
+ center_x(ecenter, fr.x, fr.box, natoms, ncent, cindex);
+ }
}
- if (bPBCcomAtom) {
- switch (unitcell_enum) {
- case euRect:
- put_atoms_in_box(ePBC,fr.box,natoms,fr.x);
- break;
- case euTric:
- put_atoms_in_triclinic_unitcell(ecenter,fr.box,natoms,fr.x);
- break;
- case euCompact:
- warn = put_atoms_in_compact_unitcell(ePBC,ecenter,fr.box,
- natoms,fr.x);
- if (warn && !bWarnCompact) {
- fprintf(stderr,"\n%s\n",warn);
- bWarnCompact = TRUE;
- }
- break;
+ if (bPBCcomAtom)
+ {
+ switch (unitcell_enum)
+ {
+ case euRect:
+ put_atoms_in_box(ePBC, fr.box, natoms, fr.x);
+ break;
+ case euTric:
+ put_atoms_in_triclinic_unitcell(ecenter, fr.box, natoms, fr.x);
+ break;
+ case euCompact:
+ warn = put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box,
+ natoms, fr.x);
+ if (warn && !bWarnCompact)
+ {
+ fprintf(stderr, "\n%s\n", warn);
+ bWarnCompact = TRUE;
+ }
+ break;
}
}
- if (bPBCcomRes) {
- put_residue_com_in_box(unitcell_enum,ecenter,
- natoms,atoms->atom,ePBC,fr.box,fr.x);
+ if (bPBCcomRes)
+ {
+ put_residue_com_in_box(unitcell_enum, ecenter,
+ natoms, atoms->atom, ePBC, fr.box, fr.x);
}
- if (bPBCcomMol) {
- put_molecule_com_in_box(unitcell_enum,ecenter,
+ if (bPBCcomMol)
+ {
+ put_molecule_com_in_box(unitcell_enum, ecenter,
&top.mols,
- natoms,atoms->atom,ePBC,fr.box,fr.x);
+ natoms, atoms->atom, ePBC, fr.box, fr.x);
}
/* Copy the input trxframe struct to the output trxframe struct */
- frout = fr;
- frout.bV = (frout.bV && bVels);
- frout.bF = (frout.bF && bForce);
+ frout = fr;
+ frout.bV = (frout.bV && bVels);
+ frout.bF = (frout.bF && bForce);
frout.natoms = nout;
- if (bNeedPrec && (bSetPrec || !fr.bPrec)) {
+ if (bNeedPrec && (bSetPrec || !fr.bPrec))
+ {
frout.bPrec = TRUE;
frout.prec = prec;
}
- if (bCopy) {
+ if (bCopy)
+ {
frout.x = xmem;
- if (frout.bV) {
+ if (frout.bV)
+ {
frout.v = vmem;
}
- if (frout.bF) {
+ if (frout.bF)
+ {
frout.f = fmem;
}
- for(i=0; i<nout; i++) {
- copy_rvec(fr.x[index[i]],frout.x[i]);
- if (frout.bV) {
- copy_rvec(fr.v[index[i]],frout.v[i]);
+ for (i = 0; i < nout; i++)
+ {
+ copy_rvec(fr.x[index[i]], frout.x[i]);
+ if (frout.bV)
+ {
+ copy_rvec(fr.v[index[i]], frout.v[i]);
}
- if (frout.bF) {
- copy_rvec(fr.f[index[i]],frout.f[i]);
+ if (frout.bF)
+ {
+ copy_rvec(fr.f[index[i]], frout.f[i]);
}
}
}
- if (opt2parg_bSet("-shift",NPA,pa))
- for(i=0; i<nout; i++)
- for (d=0; d<DIM; d++)
+ if (opt2parg_bSet("-shift", NPA, pa))
+ {
+ for (i = 0; i < nout; i++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
frout.x[i][d] += outframe*shift[d];
+ }
+ }
+ }
if (!bRound)
- bSplitHere = bSplit && bRmod(fr.time,tzero, split_t);
+ {
+ bSplitHere = bSplit && bRmod(fr.time, tzero, split_t);
+ }
else
{
/* round() is not C89 compatible, so we do this: */
bSplitHere = bSplit && bRmod(floor(fr.time+0.5),
- floor(tzero+0.5),
+ floor(tzero+0.5),
floor(split_t+0.5));
}
- if (bSeparate || bSplitHere)
- mk_filenm(outf_base,ftp2ext(ftp),nzero,file_nr,out_file2);
-
- switch(ftp) {
- case efTRJ:
- case efTRR:
- case efG87:
- case efXTC:
- if ( bSplitHere ) {
- if ( trxout )
- close_trx(trxout);
- trxout = open_trx(out_file2,filemode);
- }
- if (bSubTraj) {
- if (my_clust != -1) {
- char buf[STRLEN];
- if (clust_status_id[my_clust] == -1) {
- sprintf(buf,"%s.%s",clust->grpname[my_clust],ftp2ext(ftp));
- clust_status[my_clust] = open_trx(buf,"w");
- clust_status_id[my_clust] = 1;
- ntrxopen++;
+ if (bSeparate || bSplitHere)
+ {
+ mk_filenm(outf_base, ftp2ext(ftp), nzero, file_nr, out_file2);
+ }
+
+ switch (ftp)
+ {
+ case efTRJ:
+ case efTRR:
+ case efG87:
+ case efXTC:
+ if (bSplitHere)
+ {
+ if (trxout)
+ {
+ close_trx(trxout);
}
- else if (clust_status_id[my_clust] == -2)
- gmx_fatal(FARGS,"File %s.xtc should still be open (%d open .xtc files)\n""in order to write frame %d. my_clust = %d",
- clust->grpname[my_clust],ntrxopen,frame,
- my_clust);
- write_trxframe(clust_status[my_clust],&frout,gc);
- nfwritten[my_clust]++;
- if (nfwritten[my_clust] ==
- (clust->clust->index[my_clust+1]-
- clust->clust->index[my_clust])) {
- close_trx(clust_status[my_clust]);
- clust_status[my_clust] = NULL;
- clust_status_id[my_clust] = -2;
- ntrxopen--;
- if (ntrxopen < 0)
- gmx_fatal(FARGS,"Less than zero open .xtc files!");
+ trxout = open_trx(out_file2, filemode);
+ }
+ if (bSubTraj)
+ {
+ if (my_clust != -1)
+ {
+ char buf[STRLEN];
+ if (clust_status_id[my_clust] == -1)
+ {
+ sprintf(buf, "%s.%s", clust->grpname[my_clust], ftp2ext(ftp));
+ clust_status[my_clust] = open_trx(buf, "w");
+ clust_status_id[my_clust] = 1;
+ ntrxopen++;
+ }
+ else if (clust_status_id[my_clust] == -2)
+ {
+ gmx_fatal(FARGS, "File %s.xtc should still be open (%d open .xtc files)\n" "in order to write frame %d. my_clust = %d",
+ clust->grpname[my_clust], ntrxopen, frame,
+ my_clust);
+ }
+ write_trxframe(clust_status[my_clust], &frout, gc);
+ nfwritten[my_clust]++;
+ if (nfwritten[my_clust] ==
+ (clust->clust->index[my_clust+1]-
+ clust->clust->index[my_clust]))
+ {
+ close_trx(clust_status[my_clust]);
+ clust_status[my_clust] = NULL;
+ clust_status_id[my_clust] = -2;
+ ntrxopen--;
+ if (ntrxopen < 0)
+ {
+ gmx_fatal(FARGS, "Less than zero open .xtc files!");
+ }
+ }
}
}
- }
- else
- write_trxframe(trxout,&frout,gc);
- break;
- case efGRO:
- case efG96:
- case efPDB:
- sprintf(title,"Generated by trjconv : %s t= %9.5f",
- top_title,fr.time);
- if (bSeparate || bSplitHere)
- out=ffopen(out_file2,"w");
- switch(ftp) {
- case efGRO:
- write_hconf_p(out,title,&useatoms,prec2ndec(frout.prec),
- frout.x,frout.bV?frout.v:NULL,frout.box);
- break;
- case efPDB:
- fprintf(out,"REMARK GENERATED BY TRJCONV\n");
- sprintf(title,"%s t= %9.5f",top_title,frout.time);
- /* 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 (ftpin==efPDB && fr.bStep && fr.step > model_nr)
- model_nr = fr.step;
else
- model_nr++;
- write_pdbfile(out,title,&useatoms,frout.x,
- frout.ePBC,frout.box,' ',model_nr,gc,TRUE);
+ {
+ write_trxframe(trxout, &frout, gc);
+ }
break;
+ case efGRO:
case efG96:
- frout.title = title;
- if (bSeparate || bTDump) {
- frout.bTitle = TRUE;
- if (bTPS)
- frout.bAtoms = TRUE;
- frout.atoms = &useatoms;
- frout.bStep = FALSE;
- frout.bTime = FALSE;
- } else {
- frout.bTitle = (outframe == 0);
- frout.bAtoms = FALSE;
- frout.bStep = TRUE;
- frout.bTime = TRUE;
+ case efPDB:
+ sprintf(title, "Generated by trjconv : %s t= %9.5f",
+ top_title, fr.time);
+ if (bSeparate || bSplitHere)
+ {
+ out = ffopen(out_file2, "w");
}
- write_g96_conf(out,&frout,-1,NULL);
- }
- if (bSeparate) {
- ffclose(out);
- out = NULL;
- }
- break;
+ switch (ftp)
+ {
+ case efGRO:
+ write_hconf_p(out, title, &useatoms, prec2ndec(frout.prec),
+ frout.x, frout.bV ? frout.v : NULL, frout.box);
+ break;
+ case efPDB:
+ fprintf(out, "REMARK GENERATED BY TRJCONV\n");
+ sprintf(title, "%s t= %9.5f", top_title, frout.time);
+ /* 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 (ftpin == efPDB && fr.bStep && fr.step > model_nr)
+ {
+ model_nr = fr.step;
+ }
+ else
+ {
+ model_nr++;
+ }
+ write_pdbfile(out, title, &useatoms, frout.x,
+ frout.ePBC, frout.box, ' ', model_nr, gc, TRUE);
+ break;
+ case efG96:
+ frout.title = title;
+ if (bSeparate || bTDump)
+ {
+ frout.bTitle = TRUE;
+ if (bTPS)
+ {
+ frout.bAtoms = TRUE;
+ }
+ frout.atoms = &useatoms;
+ frout.bStep = FALSE;
+ frout.bTime = FALSE;
+ }
+ else
+ {
+ frout.bTitle = (outframe == 0);
+ frout.bAtoms = FALSE;
+ frout.bStep = TRUE;
+ frout.bTime = TRUE;
+ }
+ write_g96_conf(out, &frout, -1, NULL);
+ }
+ if (bSeparate)
+ {
+ ffclose(out);
+ out = NULL;
+ }
+ break;
default:
- gmx_fatal(FARGS,"DHE, ftp=%d\n",ftp);
+ gmx_fatal(FARGS, "DHE, ftp=%d\n", ftp);
}
if (bSeparate || bSplitHere)
+ {
file_nr++;
+ }
/* execute command */
- if (bExec) {
+ if (bExec)
+ {
char c[255];
- sprintf(c,"%s %d",exec_command,file_nr-1);
+ sprintf(c, "%s %d", exec_command, file_nr-1);
/*fprintf(stderr,"Executing '%s'\n",c);*/
#ifdef GMX_NO_SYSTEM
printf("Warning-- No calls to system(3) supported on this platform.");
printf("Warning-- Skipping execution of 'system(\"%s\")'.", c);
#else
- if(0 != system(c))
+ if (0 != system(c))
{
- gmx_fatal(FARGS,"Error executing command: %s",c);
+ gmx_fatal(FARGS, "Error executing command: %s", c);
}
#endif
}
}
}
frame++;
- bHaveNextFrame=read_next_frame(oenv,status,&fr);
- } while (!(bTDump && bDumpFrame) && bHaveNextFrame);
+ bHaveNextFrame = read_next_frame(oenv, status, &fr);
+ }
+ while (!(bTDump && bDumpFrame) && bHaveNextFrame);
}
if (!bHaveFirstFrame || (bTDump && !bDumpFrame))
- fprintf(stderr,"\nWARNING no output, "
- "last frame read at t=%g\n",fr.time);
- fprintf(stderr,"\n");
+ {
+ fprintf(stderr, "\nWARNING no output, "
+ "last frame read at t=%g\n", fr.time);
+ }
+ fprintf(stderr, "\n");
close_trj(status);
sfree(outf_base);
- if (bRmPBC)
- gmx_rmpbc_done(gpbc);
-
+ if (bRmPBC)
+ {
+ gmx_rmpbc_done(gpbc);
+ }
+
if (trxout)
+ {
close_trx(trxout);
+ }
else if (out != NULL)
+ {
ffclose(out);
- if (bSubTraj) {
- for(i=0; (i<clust->clust->nr); i++)
- if (clust_status_id[i] >= 0 )
+ }
+ if (bSubTraj)
+ {
+ for (i = 0; (i < clust->clust->nr); i++)
+ {
+ if (clust_status_id[i] >= 0)
+ {
close_trx(clust_status[i]);
+ }
+ }
}
}
- do_view(oenv,out_file,NULL);
+ do_view(oenv, out_file, NULL);
thanx(stderr);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff