void
write_eigenvectors(char *trnname,int natoms,real mat[],
bool bReverse,int begin,int end,
int WriteXref,rvec *xref,bool bDMR,
rvec xav[], bool bDMA,real eigval[])
{
int trnout;
int ndim,i,j,d,vec;
matrix zerobox;
rvec *x;
ndim = natoms*DIM;
clear_mat(zerobox);
snew(x,natoms);
fprintf (stderr,
"\nWriting %saverage structure & eigenvectors %d--%d to %s\n",
(WriteXref==eWXR_YES) ? "reference, " : "",
begin,end,trnname);
trnout = open_tpx(trnname,"w");
if (WriteXref == eWXR_YES)
{
/* misuse lambda: 0/1 mass weighted fit no/yes */
fwrite_trn(trnout,-1,-1,bDMR ? 1.0 : 0.0,zerobox,natoms,xref,NULL,NULL);
}
else if (WriteXref == eWXR_NOFIT)
{
/* misuse lambda: -1 no fit */
fwrite_trn(trnout,-1,-1,-1.0,zerobox,natoms,x,NULL,NULL);
}
/* misuse lambda: 0/1 mass weighted analysis no/yes */
fwrite_trn(trnout,0,0,bDMA ? 1.0 : 0.0,zerobox,natoms,xav,NULL,NULL);
for(i=0; i<=(end-begin); i++)
{
if (!bReverse)
vec = i;
else
vec = ndim-i-1;
for (j=0; j<natoms; j++)
for(d=0; d<DIM; d++)
x[j][d]=mat[vec*ndim+DIM*j+d];
/* Store the eigenvalue in the time field */
fwrite_trn(trnout,begin+i,eigval[vec],0,zerobox,natoms,x,NULL,NULL);
}
close_trn(trnout);
sfree(x);
}
int write_traj(FILE *log,t_commrec *cr,
char *traj,t_nsborder *nsb,
int step,real t,real lambda,t_nrnb nrnb[],
int natoms,rvec *xx,rvec *vv,rvec *ff,matrix box)
{
static int fp=-1;
if ((fp == -1) && MASTER(cr)) {
#ifdef DEBUG
fprintf(log,"Going to open trajectory file: %s\n",traj);
#endif
fp = open_trn(traj,"w");
}
#define MX(xvf) moveit(log,cr->left,cr->right,#xvf,xvf,nsb)
if (cr->nnodes > 1) {
MX(xx);
MX(vv);
MX(ff);
}
if ((xx || vv || ff) && MASTER(cr)) {
fwrite_trn(fp,step,t,lambda,box,natoms,xx,vv,ff);
gmx_fio_flush(fp);
}
return fp;
}
static void dump_dih_trn(int nframes,int nangles,real **dih,char *fn,real dt)
{
int i,j,k,l,m,na,trn;
rvec *x;
matrix box = {{2,0,0},{0,2,0},{0,0,2}};
na = (nangles*2);
if ((na % 3) != 0)
na = 1+na/3;
else
na = na/3;
printf("There are %d dihedrals. Will fill %d atom positions with cos/sin\n",
nangles,na);
snew(x,na);
trn = open_trn(fn,"w");
for(i=0; (i<nframes); i++) {
k = l = 0;
for(j=0; (j<nangles); j++) {
for(m=0; (m<2); m++) {
x[k][l] = (m == 0) ? cos(dih[j][i]) : sin(dih[j][i]);
l++;
if (l == DIM) {
l = 0;
k++;
}
}
}
fwrite_trn(trn,i,(real)i*dt,0,box,na,x,NULL,NULL);
}
close_trn(trn);
sfree(x);
}
int write_trxframe(t_trxstatus *status,t_trxframe *fr,gmx_conect gc)
{
char title[STRLEN];
real prec;
if (fr->bPrec)
prec = fr->prec;
else
prec = 1000.0;
switch (gmx_fio_getftp(status->fio)) {
case efTRJ:
case efTRR:
break;
default:
if (!fr->bX)
gmx_fatal(FARGS,"Need coordinates to write a %s trajectory",
ftp2ext(gmx_fio_getftp(status->fio)));
break;
}
switch (gmx_fio_getftp(status->fio)) {
case efXTC:
write_xtc(status->fio,fr->natoms,fr->step,fr->time,fr->box,fr->x,prec);
break;
case efTRJ:
case efTRR:
fwrite_trn(status->fio,fr->step,fr->time,fr->lambda,fr->box,fr->natoms,
fr->bX ? fr->x:NULL,fr->bV ? fr->v:NULL ,fr->bF ? fr->f:NULL);
break;
case efGRO:
case efPDB:
case efBRK:
case efENT:
if (!fr->bAtoms)
gmx_fatal(FARGS,"Can not write a %s file without atom names",
ftp2ext(gmx_fio_getftp(status->fio)));
sprintf(title,"frame t= %.3f",fr->time);
if (gmx_fio_getftp(status->fio) == efGRO)
write_hconf_p(gmx_fio_getfp(status->fio),title,fr->atoms,
prec2ndec(prec),fr->x,fr->bV ? fr->v : NULL,fr->box);
else
write_pdbfile(gmx_fio_getfp(status->fio),title,
fr->atoms,fr->x,fr->bPBC ? fr->ePBC : -1,fr->box,
' ',fr->step,gc,TRUE);
break;
case efG87:
write_gms(gmx_fio_getfp(status->fio),fr->natoms,fr->x,fr->box);
break;
case efG96:
write_g96_conf(gmx_fio_getfp(status->fio),fr,-1,NULL);
break;
default:
gmx_fatal(FARGS,"Sorry, write_trxframe can not write %s",
ftp2ext(gmx_fio_getftp(status->fio)));
break;
}
return 0;
}
int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
const atom_id *ind, gmx_conect gc)
{
char title[STRLEN];
rvec *xout = NULL, *vout = NULL, *fout = NULL;
int i, ftp = -1;
real prec;
if (fr->bPrec)
{
prec = fr->prec;
}
else
{
prec = 1000.0;
}
if (status->tng)
{
ftp = efTNG;
}
else if (status->fio)
{
ftp = gmx_fio_getftp(status->fio);
}
else
{
gmx_incons("No input file available");
}
switch (ftp)
{
case efTRR:
case efTNG:
break;
default:
if (!fr->bX)
{
gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
ftp2ext(ftp));
}
break;
}
switch (ftp)
{
case efTRR:
case efTNG:
if (fr->bV)
{
snew(vout, nind);
for (i = 0; i < nind; i++)
{
copy_rvec(fr->v[ind[i]], vout[i]);
}
}
if (fr->bF)
{
snew(fout, nind);
for (i = 0; i < nind; i++)
{
copy_rvec(fr->f[ind[i]], fout[i]);
}
}
/* no break */
case efXTC:
if (fr->bX)
{
snew(xout, nind);
for (i = 0; i < nind; i++)
{
copy_rvec(fr->x[ind[i]], xout[i]);
}
}
break;
default:
break;
}
switch (ftp)
{
case efTNG:
gmx_write_tng_from_trxframe(status->tng, fr, nind);
break;
case efXTC:
write_xtc(status->fio, nind, fr->step, fr->time, fr->box, xout, prec);
break;
case efTRR:
fwrite_trn(status->fio, nframes_read(status),
fr->time, fr->step, fr->box, nind, xout, vout, fout);
break;
case efGRO:
case efPDB:
case efBRK:
case efENT:
if (!fr->bAtoms)
{
gmx_fatal(FARGS, "Can not write a %s file without atom names",
ftp2ext(ftp));
}
sprintf(title, "frame t= %.3f", fr->time);
if (ftp == efGRO)
{
write_hconf_indexed_p(gmx_fio_getfp(status->fio), title, fr->atoms, nind, ind,
prec2ndec(prec),
fr->x, fr->bV ? fr->v : NULL, fr->box);
}
else
{
write_pdbfile_indexed(gmx_fio_getfp(status->fio), title, fr->atoms,
fr->x, -1, fr->box, ' ', fr->step, nind, ind, gc, TRUE);
}
break;
case efG96:
write_g96_conf(gmx_fio_getfp(status->fio), fr, nind, ind);
break;
default:
gmx_fatal(FARGS, "Sorry, write_trxframe_indexed can not write %s",
ftp2ext(ftp));
break;
}
switch (ftp)
{
case efTRR:
case efTNG:
if (vout)
{
sfree(vout);
}
if (fout)
{
sfree(fout);
}
/* no break */
case efXTC:
sfree(xout);
break;
default:
break;
}
return 0;
}
void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
gmx_mdoutf_t of,
int mdof_flags,
gmx_mtop_t *top_global,
gmx_int64_t step, double t,
t_state *state_local, t_state *state_global,
rvec *f_local, rvec *f_global)
{
rvec *local_v;
rvec *global_v;
/* MRS -- defining these variables is to manage the difference
* between half step and full step velocities, but there must be a better way . . . */
local_v = state_local->v;
global_v = state_global->v;
if (DOMAINDECOMP(cr))
{
if (mdof_flags & MDOF_CPT)
{
dd_collect_state(cr->dd, state_local, state_global);
}
else
{
if (mdof_flags & (MDOF_X | MDOF_X_COMPRESSED))
{
dd_collect_vec(cr->dd, state_local, state_local->x,
state_global->x);
}
if (mdof_flags & MDOF_V)
{
dd_collect_vec(cr->dd, state_local, local_v,
global_v);
}
}
if (mdof_flags & MDOF_F)
{
dd_collect_vec(cr->dd, state_local, f_local, f_global);
}
}
else
{
if (mdof_flags & MDOF_CPT)
{
/* All pointers in state_local are equal to state_global,
* but we need to copy the non-pointer entries.
*/
state_global->lambda = state_local->lambda;
state_global->veta = state_local->veta;
state_global->vol0 = state_local->vol0;
copy_mat(state_local->box, state_global->box);
copy_mat(state_local->boxv, state_global->boxv);
copy_mat(state_local->svir_prev, state_global->svir_prev);
copy_mat(state_local->fvir_prev, state_global->fvir_prev);
copy_mat(state_local->pres_prev, state_global->pres_prev);
}
}
if (MASTER(cr))
{
if (mdof_flags & MDOF_CPT)
{
fflush_tng(of->tng);
fflush_tng(of->tng_low_prec);
write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT,
fplog, cr, of->eIntegrator, of->simulation_part,
of->bExpanded, of->elamstats, step, t, state_global);
}
if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
{
if (of->fp_trn)
{
fwrite_trn(of->fp_trn, step, t, state_local->lambda[efptFEP],
state_local->box, top_global->natoms,
(mdof_flags & MDOF_X) ? state_global->x : NULL,
(mdof_flags & MDOF_V) ? global_v : NULL,
(mdof_flags & MDOF_F) ? f_global : NULL);
if (gmx_fio_flush(of->fp_trn) != 0)
{
gmx_file("Cannot write trajectory; maybe you are out of disk space?");
}
}
gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
(const rvec *) state_local->box,
top_global->natoms,
(mdof_flags & MDOF_X) ? (const rvec *) state_global->x : NULL,
(mdof_flags & MDOF_V) ? (const rvec *) global_v : NULL,
(mdof_flags & MDOF_F) ? (const rvec *) f_global : NULL);
}
if (mdof_flags & MDOF_X_COMPRESSED)
{
rvec *xxtc = NULL;
if (of->natoms_x_compressed == of->natoms_global)
{
/* We are writing the positions of all of the atoms to
the compressed output */
xxtc = state_global->x;
}
else
{
/* We are writing the positions of only a subset of
the atoms to the compressed output, so we have to
make a copy of the subset of coordinates. */
int i, j;
snew(xxtc, of->natoms_x_compressed);
for (i = 0, j = 0; (i < of->natoms_x_compressed); i++)
{
if (ggrpnr(of->groups, egcCompressedX, i) == 0)
{
copy_rvec(state_global->x[i], xxtc[j++]);
}
}
}
if (write_xtc(of->fp_xtc, of->natoms_x_compressed, step, t,
state_local->box, xxtc, of->x_compression_precision) == 0)
{
gmx_fatal(FARGS, "XTC error - maybe you are out of disk space?");
}
gmx_fwrite_tng(of->tng_low_prec,
TRUE,
step,
t,
state_local->lambda[efptFEP],
(const rvec *) state_local->box,
of->natoms_x_compressed,
(const rvec *) xxtc,
NULL,
NULL);
if (of->natoms_x_compressed != of->natoms_global)
{
sfree(xxtc);
}
}
}
}
int write_trxframe_indexed(t_trxstatus *status,t_trxframe *fr,int nind,
atom_id *ind, gmx_conect gc)
{
char title[STRLEN];
rvec *xout=NULL,*vout=NULL,*fout=NULL;
int i;
real prec;
if (fr->bPrec)
prec = fr->prec;
else
prec = 1000.0;
switch (gmx_fio_getftp(status->fio)) {
case efTRJ:
case efTRR:
break;
default:
if (!fr->bX)
gmx_fatal(FARGS,"Need coordinates to write a %s trajectory",
ftp2ext(gmx_fio_getftp(status->fio)));
break;
}
switch (gmx_fio_getftp(status->fio)) {
case efTRJ:
case efTRR:
if (fr->bV) {
snew(vout,nind);
for(i=0; i<nind; i++)
copy_rvec(fr->v[ind[i]],vout[i]);
}
if (fr->bF) {
snew(fout,nind);
for(i=0; i<nind; i++)
copy_rvec(fr->f[ind[i]],fout[i]);
}
case efXTC:
case efG87:
if (fr->bX) {
snew(xout,nind);
for(i=0; i<nind; i++)
copy_rvec(fr->x[ind[i]],xout[i]);
}
break;
default:
break;
}
switch (gmx_fio_getftp(status->fio)) {
case efXTC:
write_xtc(status->fio,nind,fr->step,fr->time,fr->box,xout,prec);
break;
case efTRJ:
case efTRR:
fwrite_trn(status->fio,nframes_read(status),
fr->time,fr->step,fr->box,nind,xout,vout,fout);
break;
case efGRO:
case efPDB:
case efBRK:
case efENT:
if (!fr->bAtoms)
gmx_fatal(FARGS,"Can not write a %s file without atom names",
ftp2ext(gmx_fio_getftp(status->fio)));
sprintf(title,"frame t= %.3f",fr->time);
if (gmx_fio_getftp(status->fio) == efGRO)
write_hconf_indexed_p(gmx_fio_getfp(status->fio),title,fr->atoms,nind,ind,
prec2ndec(prec),
fr->x,fr->bV ? fr->v : NULL,fr->box);
else
write_pdbfile_indexed(gmx_fio_getfp(status->fio),title,fr->atoms,
fr->x,-1,fr->box,' ',fr->step,nind,ind,gc,TRUE);
break;
case efG87:
write_gms(gmx_fio_getfp(status->fio),nind,xout,fr->box);
break;
case efG96:
write_g96_conf(gmx_fio_getfp(status->fio),fr,nind,ind);
break;
default:
gmx_fatal(FARGS,"Sorry, write_trxframe_indexed can not write %s",
ftp2ext(gmx_fio_getftp(status->fio)));
break;
}
switch (gmx_fio_getftp(status->fio)) {
case efTRN:
case efTRJ:
case efTRR:
if (vout) sfree(vout);
if (fout) sfree(fout);
case efXTC:
case efG87:
sfree(xout);
break;
default:
break;
}
return 0;
}