int get_tpr_version(const char *infile)
{
char buf[STRLEN];
gmx_bool bDouble;
int precision,fver;
t_fileio *fio;
fio = open_tpx(infile,"r");
gmx_fio_checktype(fio);
precision = sizeof(real);
gmx_fio_do_string(fio,buf);
if (strncmp(buf,"VERSION",7))
gmx_fatal(FARGS,"Can not read file %s,\n"
" this file is from a Gromacs version which is older than 2.0\n"
" Make a new one with grompp or use a gro or pdb file, if possible",
gmx_fio_getname(fio));
gmx_fio_do_int(fio,precision);
bDouble = (precision == sizeof(double));
if ((precision != sizeof(float)) && !bDouble)
gmx_fatal(FARGS,"Unknown precision in file %s: real is %d bytes "
"instead of %d or %d",
gmx_fio_getname(fio),precision,sizeof(float),sizeof(double));
gmx_fio_setprecision(fio,bDouble);
fprintf(stderr,"Reading file %s, %s (%s precision)\n",
gmx_fio_getname(fio),buf,bDouble ? "double" : "single");
gmx_fio_do_int(fio,fver);
close_tpx(fio);
return fver;
}
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);
}
static void list_trn(char *fn)
{
int fpread,fpwrite,nframe,indent;
char buf[256];
rvec *x,*v,*f;
matrix box;
t_trnheader trn;
bool bOK;
fpread = open_trn(fn,"r");
fpwrite = open_tpx(NULL,"w");
gmx_fio_setdebug(fpwrite,TRUE);
nframe = 0;
while (fread_trnheader(fpread,&trn,&bOK)) {
snew(x,trn.natoms);
snew(v,trn.natoms);
snew(f,trn.natoms);
if (fread_htrn(fpread,&trn,
trn.box_size ? box : NULL,
trn.x_size ? x : NULL,
trn.v_size ? v : NULL,
trn.f_size ? f : NULL)) {
sprintf(buf,"%s frame %d",fn,nframe);
indent=0;
indent=pr_title(stdout,indent,buf);
pr_indent(stdout,indent);
fprintf(stdout,"natoms=%10d step=%10d time=%12.7e lambda=%10g\n",
trn.natoms,trn.step,trn.t,trn.lambda);
if (trn.box_size)
pr_rvecs(stdout,indent,"box",box,DIM);
if (trn.x_size)
pr_rvecs(stdout,indent,"x",x,trn.natoms);
if (trn.v_size)
pr_rvecs(stdout,indent,"v",v,trn.natoms);
if (trn.f_size)
pr_rvecs(stdout,indent,"f",f,trn.natoms);
}
else
fprintf(stderr,"\nWARNING: Incomplete frame: nr %d, t=%g\n",
nframe,trn.t);
sfree(x);
sfree(v);
sfree(f);
nframe++;
}
if (!bOK)
fprintf(stderr,"\nWARNING: Incomplete frame header: nr %d, t=%g\n",
nframe,trn.t);
close_tpx(fpwrite);
close_trn(fpread);
}
static void list_trn(char *fn)
{
static real mass[5] = { 15.9994, 1.008, 1.008, 0.0, 0.0 };
int i,j=0,m,fpread,fpwrite,nframe;
rvec *x,*v,*f,fmol[2],xcm[2],torque[j],dx;
real mmm,len;
matrix box;
t_trnheader trn;
gmx_bool bOK;
printf("Going to open %s\n",fn);
fpread = open_trn(fn,"r");
fpwrite = open_tpx(NULL,"w");
gmx_fio_setdebug(fpwrite,TRUE);
mmm=mass[0]+2*mass[1];
for(i=0; (i<5); i++)
mass[i] /= mmm;
nframe = 0;
while (fread_trnheader(fpread,&trn,&bOK)) {
snew(x,trn.natoms);
snew(v,trn.natoms);
snew(f,trn.natoms);
if (fread_htrn(fpread,&trn,
trn.box_size ? box : NULL,
trn.x_size ? x : NULL,
trn.v_size ? v : NULL,
trn.f_size ? f : NULL)) {
if (trn.x_size && trn.f_size) {
printf("There are %d atoms\n",trn.natoms);
for(j=0; (j<2); j++) {
clear_rvec(xcm[j]);
clear_rvec(fmol[j]);
clear_rvec(torque[j]);
for(i=5*j; (i<5*j+5); i++) {
rvec_inc(fmol[j],f[i]);
for(m=0; (m<DIM); m++)
xcm[j][m] += mass[i%5]*x[i][m];
}
for(i=5*j; (i<5*j+5); i++) {
rvec_dec(x[i],xcm[j]);
cprod(x[i],f[i],dx);
rvec_inc(torque[j],dx);
rvec_inc(x[i],xcm[j]);
}
}
pr_rvecs(stdout,0,"FMOL ",fmol,2);
pr_rvecs(stdout,0,"TORQUE",torque,2);
printf("Distance matrix Water1-Water2\n%5s","");
for(j=0; (j<5); j++)
printf(" %10s",nm[j]);
printf("\n");
for(j=0; (j<5); j++) {
printf("%5s",nm[j]);
for(i=5; (i<10); i++) {
rvec_sub(x[i],x[j],dx);
len = sqrt(iprod(dx,dx));
printf(" %10.7f",len);
}
printf("\n");
}
}
}
sfree(x);
sfree(v);
sfree(f);
nframe++;
}
if (!bOK)
fprintf(stderr,"\nWARNING: Incomplete frame header: nr %d, t=%g\n",
nframe,trn.t);
close_tpx(fpwrite);
close_trn(fpread);
}
