void done_mdoutf(gmx_mdoutf_t of)
{
if (of->fp_ene != NULL)
{
close_enx(of->fp_ene);
}
if (of->fp_xtc)
{
close_xtc(of->fp_xtc);
}
if (of->fp_trn)
{
gmx_trr_close(of->fp_trn);
}
if (of->fp_dhdl != NULL)
{
gmx_fio_fclose(of->fp_dhdl);
}
if (of->fp_field != NULL)
{
/* This is opened sometimes with xvgropen, sometimes with
* gmx_fio_fopen, so we use the least common denominator for closing.
*/
gmx_fio_fclose(of->fp_field);
}
gmx_tng_close(&of->tng);
gmx_tng_close(&of->tng_low_prec);
sfree(of);
}
void done_mdoutf(gmx_mdoutf_t of)
{
if (of->fp_ene != NULL)
{
close_enx(of->fp_ene);
}
if (of->fp_xtc)
{
close_xtc(of->fp_xtc);
}
if (of->fp_trn)
{
close_trn(of->fp_trn);
}
if (of->fp_dhdl != NULL)
{
gmx_fio_fclose(of->fp_dhdl);
}
if (of->fp_field != NULL)
{
gmx_fio_fclose(of->fp_field);
}
gmx_tng_close(&of->tng);
gmx_tng_close(&of->tng_low_prec);
sfree(of);
}
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");
}
}
void finish_pull(FILE *fplog,t_pull *pull)
{
if (pull->out_x)
{
gmx_fio_fclose(pull->out_x);
}
if (pull->out_f)
{
gmx_fio_fclose(pull->out_f);
}
}
void finish_pull(t_pull *pull)
{
if (pull->out_x)
{
gmx_fio_fclose(pull->out_x);
}
if (pull->out_f)
{
gmx_fio_fclose(pull->out_f);
}
}
void get_stx_coordnum(const char *infile, int *natoms)
{
FILE *in;
int ftp, tpxver, tpxgen;
t_trxframe fr;
char g96_line[STRLEN+1];
ftp = fn2ftp(infile);
range_check(ftp, 0, efNR);
switch (ftp)
{
case efGRO:
get_coordnum(infile, natoms);
break;
case efG96:
in = gmx_fio_fopen(infile, "r");
fr.title = NULL;
fr.natoms = -1;
fr.atoms = NULL;
fr.x = NULL;
fr.v = NULL;
fr.f = NULL;
*natoms = read_g96_conf(in, infile, &fr, g96_line);
gmx_fio_fclose(in);
break;
case efPDB:
case efBRK:
case efENT:
in = gmx_fio_fopen(infile, "r");
get_pdb_coordnum(in, natoms);
gmx_fio_fclose(in);
break;
case efESP:
*natoms = get_espresso_coordnum(infile);
break;
case efTPA:
case efTPB:
case efTPR:
{
t_tpxheader tpx;
read_tpxheader(infile, &tpx, TRUE, &tpxver, &tpxgen);
*natoms = tpx.natoms;
break;
}
default:
gmx_fatal(FARGS, "File type %s not supported in get_stx_coordnum",
ftp2ext(ftp));
}
}
static void print_rtp(const char *filenm, const char *title, t_atoms *atoms,
t_params plist[], gpp_atomtype_t atype, int cgnr[])
{
FILE *fp;
int i, tp;
char *tpnm;
fp = gmx_fio_fopen(filenm, "w");
fprintf(fp, "; %s\n", title);
fprintf(fp, "\n");
fprintf(fp, "[ %s ]\n", *atoms->resinfo[0].name);
fprintf(fp, "\n");
fprintf(fp, "[ atoms ]\n");
for (i = 0; (i < atoms->nr); i++)
{
tp = atoms->atom[i].type;
if ((tpnm = get_atomtype_name(tp, atype)) == NULL)
{
gmx_fatal(FARGS, "tp = %d, i = %d in print_rtp", tp, i);
}
fprintf(fp, "%-8s %12s %8.4f %5d\n",
*atoms->atomname[i], tpnm,
atoms->atom[i].q, cgnr[i]);
}
print_pl(fp, plist, F_BONDS, "bonds", atoms->atomname);
print_pl(fp, plist, F_ANGLES, "angles", atoms->atomname);
print_pl(fp, plist, F_PDIHS, "dihedrals", atoms->atomname);
print_pl(fp, plist, F_IDIHS, "impropers", atoms->atomname);
gmx_fio_fclose(fp);
}
void write_inpfile(const char *fn,int ninp,t_inpfile inp[],gmx_bool bHaltOnUnknown,
warninp_t wi)
{
FILE *out;
int i;
char warn_buf[STRLEN];
sort_inp(ninp,inp);
out=gmx_fio_fopen(fn,"w");
nice_header(out,fn);
for(i=0; (i<ninp); i++) {
if (inp[i].bSet) {
if(inp[i].name[0]==';' || (strlen(inp[i].name)>2 && inp[i].name[1]==';'))
fprintf(out,"%-24s\n",inp[i].name);
else
fprintf(out,"%-24s = %s\n",inp[i].name,inp[i].value ? inp[i].value : "");
} else if (!inp[i].bObsolete) {
sprintf(warn_buf,"Unknown left-hand '%s' in parameter file\n",
inp[i].name);
if (bHaltOnUnknown) {
warning_error(wi,warn_buf);
} else {
warning(wi,warn_buf);
}
}
}
gmx_fio_fclose(out);
check_warning_error(wi,FARGS);
}
void gmx_log_close(FILE *fp)
{
if (fp) {
gmx_fatal_set_log_file(NULL);
gmx_fio_fclose(fp);
}
}
void write_sto_conf_mtop(const char *outfile, const char *title,
gmx_mtop_t *mtop,
rvec x[], rvec *v, int ePBC, matrix box)
{
int ftp;
FILE *out;
t_atoms atoms;
ftp = fn2ftp(outfile);
switch (ftp)
{
case efGRO:
out = gmx_fio_fopen(outfile, "w");
write_hconf_mtop(out, title, mtop, 3, x, v, box);
gmx_fio_fclose(out);
break;
default:
/* This is a brute force approach which requires a lot of memory.
* We should implement mtop versions of all writing routines.
*/
atoms = gmx_mtop_global_atoms(mtop);
write_sto_conf(outfile, title, &atoms, x, v, ePBC, box);
done_atom(&atoms);
break;
}
}
void print_rgrid_pdb(char *fn,int nx,int ny,int nz,real ***grid)
{
FILE *fp;
int ix,iy,iz,n,ig;
real x,y,z,g;
n=1;
fp=gmx_fio_fopen(fn,"w");
for(ix=0; (ix<nx); ix++) {
for(iy=0; (iy<ny); iy++) {
for(iz=0; (iz<nz); iz++) {
g=grid[ix][iy][iz];
ig=g;
if ((ig != 0) || (1)) {
x = 4*ix;
y = 4*iy;
z = 4*iz;
fprintf(fp,"ATOM %5d Na Na 1 %8.3f%8.3f%8.3f%6.2f%6.2f\n",
n++,x,y,z,0.0,g);
}
}
}
}
gmx_fio_fclose(fp);
}
int main(int argc,char *argv[])
{
FILE *fp;
int nnn[] = { 8, 10, 12, 15, 16, 18, 20, 24, 25, 27, 30, 32, 36, 40,
45, 48, 50, 54, 60, 64, 72, 75, 80, 81, 90, 100 };
#define NNN asize(nnn)
int *niter;
int i,j,n,nit,ntot,n3;
double t,nflop;
double *rt,*ct;
t_complex ***g;
real ***h;
snew(rt,NNN);
snew(ct,NNN);
snew(niter,NNN);
for(i=0; (i<NNN); i++) {
n = nnn[i];
fprintf(stderr,"\rReal %d ",n);
if (n < 16)
niter[i] = 100;
else if (n < 26)
niter[i] = 50;
else if (n < 51)
niter[i] = 10;
else
niter[i] = 5;
nit = niter[i];
h = mk_rgrid(n+2,n,n);
start_time();
for(j=0; (j<nit); j++) {
testrft(stdout,h,n,n,n,(j==0));
}
update_time();
rt[i] = node_time();
free_rgrid(h,n,n);
fprintf(stderr,"\rComplex %d ",n);
g = mk_cgrid(n,n,n);
start_time();
for(j=0; (j<nit); j++) {
testfft(stdout,g,n,n,n,(j==0));
}
update_time();
ct[i] = node_time();
free_cgrid(g,n,n);
}
fprintf(stderr,"\n");
fp=xvgropen("timing.xvg","FFT timings per grid point","n","t (s)");
for(i=0; (i<NNN); i++) {
n3 = 2*niter[i]*nnn[i]*nnn[i]*nnn[i];
fprintf(fp,"%10d %10g %10g\n",nnn[i],rt[i]/n3,ct[i]/n3);
}
gmx_fio_fclose(fp);
return 0;
}
void ps_close(t_psdata ps)
{
fprintf(ps->fp, "%%showpage\n");
fprintf(ps->fp, "%%%%EOF\n");
gmx_fio_fclose(ps->fp);
sfree(ps->rgb);
sfree(ps);
}
void writecmap(char *fn,int n,t_mapping map[])
{
FILE *out;
out=gmx_fio_fopen(fn,"w");
printcmap(out,n,map);
gmx_fio_fclose(out);
}
static void write_constr_pdb(const char *fn, const char *title,
gmx_mtop_t *mtop,
int start, int homenr, t_commrec *cr,
rvec x[], matrix box)
{
char fname[STRLEN], format[STRLEN];
FILE *out;
int dd_ac0 = 0, dd_ac1 = 0, i, ii, resnr;
gmx_domdec_t *dd;
char *anm, *resnm;
dd = NULL;
if (DOMAINDECOMP(cr))
{
dd = cr->dd;
dd_get_constraint_range(dd, &dd_ac0, &dd_ac1);
start = 0;
homenr = dd_ac1;
}
if (PAR(cr))
{
sprintf(fname, "%s_n%d.pdb", fn, cr->sim_nodeid);
}
else
{
sprintf(fname, "%s.pdb", fn);
}
sprintf(format, "%s\n", get_pdbformat());
out = gmx_fio_fopen(fname, "w");
fprintf(out, "TITLE %s\n", title);
gmx_write_pdb_box(out, -1, box);
for (i = start; i < start+homenr; i++)
{
if (dd != NULL)
{
if (i >= dd->nat_home && i < dd_ac0)
{
continue;
}
ii = dd->gatindex[i];
}
else
{
ii = i;
}
gmx_mtop_atominfo_global(mtop, ii, &anm, &resnr, &resnm);
fprintf(out, format, "ATOM", (ii+1)%100000,
anm, resnm, ' ', resnr%10000, ' ',
10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ]);
}
fprintf(out, "TER\n");
gmx_fio_fclose(out);
}
void gmx_pdb_read_conf(const char *infile,
t_topology *top, rvec x[], int *ePBC, matrix box)
{
FILE *in = gmx_fio_fopen(infile, "r");
char title[STRLEN];
read_pdbfile(in, title, NULL, &top->atoms, &top->symtab, x, ePBC, box, TRUE, NULL);
top->name = put_symtab(&top->symtab, title);
gmx_fio_fclose(in);
}
static void get_coordnum (const char *infile, int *natoms)
{
FILE *in;
char title[STRLEN];
in = gmx_fio_fopen(infile, "r");
get_coordnum_fp(in, title, natoms);
gmx_fio_fclose (in);
}
void gmx_pdb_read_conf(const char *infile,
t_symtab *symtab, char ***name, t_atoms *atoms,
rvec x[], int *ePBC, matrix box)
{
FILE *in = gmx_fio_fopen(infile, "r");
char title[STRLEN];
read_pdbfile(in, title, NULL, atoms, symtab, x, ePBC, box, TRUE, NULL);
*name = put_symtab(symtab, title);
gmx_fio_fclose(in);
}
void write_conf_p(char *outfile, char *title, t_atoms *atoms, int pr,
rvec *x, rvec *v,matrix box)
{
FILE *out;
out=gmx_fio_fopen(outfile,"w");
write_hconf_p(out,title,atoms,pr,x,v,box);
gmx_fio_fclose (out);
}
void pr_f(char *fn,int natoms,rvec f[])
{
FILE *fp;
int i;
fp=gmx_fio_fopen(fn,"w");
for(i=0; (i<natoms); i++)
fprintf(fp," %12.5e\n %12.5e\n %12.5e\n",f[i][XX],f[i][YY],f[i][ZZ]);
gmx_fio_fclose(fp);
}
static void get_stx_coordnum(const char *infile, int *natoms)
{
FILE *in;
int ftp;
t_trxframe fr;
char g96_line[STRLEN+1];
ftp = fn2ftp(infile);
range_check(ftp, 0, efNR);
switch (ftp)
{
case efGRO:
get_coordnum(infile, natoms);
break;
case efG96:
{
in = gmx_fio_fopen(infile, "r");
fr.title = NULL;
fr.natoms = -1;
fr.atoms = NULL;
fr.x = NULL;
fr.v = NULL;
fr.f = NULL;
*natoms = read_g96_conf(in, infile, &fr, NULL, g96_line);
sfree(const_cast<char *>(fr.title));
gmx_fio_fclose(in);
break;
}
case efPDB:
case efBRK:
case efENT:
in = gmx_fio_fopen(infile, "r");
get_pdb_coordnum(in, natoms);
gmx_fio_fclose(in);
break;
case efESP:
*natoms = get_espresso_coordnum(infile);
break;
default:
gmx_fatal(FARGS, "File type %s not supported in get_stx_coordnum",
ftp2ext(ftp));
}
}
void print_phi(char *fn,int natoms,rvec x[],real phi[])
{
FILE *fp;
int i;
fp=gmx_fio_fopen(fn,"w");
for(i=0; (i<natoms); i++)
fprintf(fp,"%10d %12.5e\n",i,phi[i]);
gmx_fio_fclose(fp);
}
void read_pdb_conf(char *infile,char *title,
t_atoms *atoms,rvec x[],int *ePBC,matrix box,bool bChange,
gmx_conect conect)
{
FILE *in;
in = gmx_fio_fopen(infile,"r");
read_pdbfile(in,title,NULL,atoms,x,ePBC,box,bChange,conect);
gmx_fio_fclose(in);
}
static void read_stx_conf(const char *infile, t_topology *top,
rvec x[], rvec *v, int *ePBC, matrix box)
{
FILE *in;
t_trxframe fr;
int ftp;
char g96_line[STRLEN+1];
if (top->atoms.nr == 0)
{
fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
}
else if (top->atoms.atom == NULL)
{
gmx_mem("Uninitialized array atom");
}
if (ePBC)
{
*ePBC = -1;
}
ftp = fn2ftp(infile);
switch (ftp)
{
case efGRO:
gmx_gro_read_conf(infile, top, x, v, box);
break;
case efG96:
fr.title = NULL;
fr.natoms = top->atoms.nr;
fr.atoms = &top->atoms;
fr.x = x;
fr.v = v;
fr.f = NULL;
in = gmx_fio_fopen(infile, "r");
read_g96_conf(in, infile, &fr, &top->symtab, g96_line);
gmx_fio_fclose(in);
copy_mat(fr.box, box);
top->name = put_symtab(&top->symtab, fr.title);
sfree(const_cast<char *>(fr.title));
break;
case efPDB:
case efBRK:
case efENT:
gmx_pdb_read_conf(infile, top, x, ePBC, box);
break;
case efESP:
gmx_espresso_read_conf(infile, top, x, v, box);
break;
default:
gmx_incons("Not supported in read_stx_conf");
}
}
int readcmap(char *fn,t_mapping **map)
{
FILE *in;
int n;
in=libopen(fn);
n=getcmap(in,fn,map);
gmx_fio_fclose(in);
return n;
}
int get_espresso_coordnum(const char *infile)
{
FILE *fp;
char word[STRLEN];
int natoms, level, r;
gmx_bool bFoundParticles;
natoms = 0;
fp = gmx_fio_fopen(infile, "r");
bFoundParticles = FALSE;
level = 0;
while ((r = get_espresso_word(fp, word)) && !bFoundParticles)
{
if (level == 1 && strcmp(word, "particles") == 0 && !bFoundParticles)
{
bFoundParticles = TRUE;
level += check_open_parenthesis(fp, r, infile, "particles");
while (level > 0 && (r = get_espresso_word(fp, word)))
{
if (r == 2)
{
level++;
if (level == 2)
{
natoms++;
}
}
else if (r == 3)
{
level--;
}
}
}
else if (r == 2)
{
level++;
}
else if (r == 3)
{
level--;
}
}
if (!bFoundParticles)
{
fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n",
infile);
}
gmx_fio_fclose(fp);
return natoms;
}
static void read_whole_conf(char *infile, char *title,
t_atoms *atoms, rvec x[],rvec *v, matrix box)
{
FILE *in;
int ndec;
/* open file */
in=gmx_fio_fopen(infile,"r");
get_w_conf(in, infile, title, atoms, &ndec, x, v, box);
gmx_fio_fclose(in);
}
static void tpx2methods(const char *tpx, const char *tex)
{
FILE *fp;
t_inputrec ir;
t_state state;
gmx_mtop_t mtop;
read_tpx_state(tpx, &ir, &state, &mtop);
fp = gmx_fio_fopen(tex, "w");
fprintf(fp, "\\section{Methods}\n");
tpx2system(fp, &mtop);
tpx2params(fp, &ir);
gmx_fio_fclose(fp);
}
void write_inpfile(const char *fn, int ninp, t_inpfile inp[], gmx_bool bHaltOnUnknown,
warninp_t wi)
{
FILE *out;
int i;
char warn_buf[STRLEN];
sort_inp(ninp, inp);
out = gmx_fio_fopen(fn, "w");
nice_header(out, fn);
try
{
gmx::BinaryInformationSettings settings;
settings.generatedByHeader(true);
settings.linePrefix(";\t");
gmx::printBinaryInformation(out, gmx::getProgramContext(), settings);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
for (i = 0; (i < ninp); i++)
{
if (inp[i].bSet)
{
if (inp[i].name[0] == ';' || (strlen(inp[i].name) > 2 && inp[i].name[1] == ';'))
{
fprintf(out, "%-24s\n", inp[i].name);
}
else
{
fprintf(out, "%-24s = %s\n", inp[i].name, inp[i].value ? inp[i].value : "");
}
}
else if (!inp[i].bObsolete)
{
sprintf(warn_buf, "Unknown left-hand '%s' in parameter file\n",
inp[i].name);
if (bHaltOnUnknown)
{
warning_error(wi, warn_buf);
}
else
{
warning(wi, warn_buf);
}
}
}
gmx_fio_fclose(out);
check_warning_error(wi, FARGS);
}
static gmx_bool empty_file(const char *fn)
{
FILE *fp;
char dum;
int ret;
gmx_bool bEmpty;
fp = gmx_fio_fopen(fn,"r");
ret = fread(&dum,sizeof(dum),1,fp);
bEmpty = feof(fp);
gmx_fio_fclose(fp);
return bEmpty;
}