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 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));
}
}
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 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;
}
}
t_psdata ps_open(const char *fn, real x1, real y1, real x2, real y2)
{
t_psdata ps;
snew(ps, 1);
ps->fp = gmx_fio_fopen(fn, "w");
fprintf(ps->fp, "%%!PS-Adobe-2.0 EPSF-1.2\n");
fprintf(ps->fp, "%%%%Creator: GROMACS\n");
fprintf(ps->fp, "%%%%Title: %s\n", fn);
fprintf(ps->fp, "%%%%BoundingBox: %g %g %g %g\n", x1, y1, x2, y2);
fprintf(ps->fp, "%%%%EndComments\n");
fprintf(ps->fp, "/m {moveto} bind def\n");
fprintf(ps->fp, "/l {lineto} bind def\n");
fprintf(ps->fp, "/rm {rmoveto} bind def\n");
fprintf(ps->fp, "/r {rlineto} bind def\n");
fprintf(ps->fp, "/f {fill} bind def\n");
fprintf(ps->fp, "/s {stroke} bind def\n");
ps->nrgb = 0;
ps->maxrgb = 0;
ps->rgb = NULL;
ps->gen_ybox = 0;
ps->ostack = 0;
return ps;
}
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 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);
}
void init_debug (const int dbglevel,const char *dbgfile)
{
no_buffers();
debug=gmx_fio_fopen(dbgfile,"w");
bDebug = TRUE;
if (dbglevel >= 2)
gmx_debug_at = TRUE;
}
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 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);
}
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);
}
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);
}
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 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 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);
}
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_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");
}
}
FILE *xvgropen_type(const char *fn, const char *title, const char *xaxis,
const char *yaxis, int exvg_graph_type,
const gmx_output_env_t *oenv)
{
FILE *fp;
fp = gmx_fio_fopen(fn, "w");
xvgr_header(fp, title, xaxis, yaxis, exvg_graph_type, oenv);
return fp;
}
void gmx_log_open(const char *lognm, const t_commrec *cr,
gmx_bool bAppendFiles, FILE** fplog)
{
int pid;
char host[256];
char timebuf[STRLEN];
FILE *fp = *fplog;
debug_gmx();
if (!bAppendFiles)
{
fp = gmx_fio_fopen(lognm, bAppendFiles ? "a+" : "w+" );
}
gmx_fatal_set_log_file(fp);
/* Get some machine parameters */
gmx_gethostname(host, 256);
pid = gmx_getpid();
gmx_format_current_time(timebuf, STRLEN);
if (bAppendFiles)
{
fprintf(fp,
"\n"
"\n"
"-----------------------------------------------------------\n"
"Restarting from checkpoint, appending to previous log file.\n"
"\n"
);
}
fprintf(fp,
"Log file opened on %s"
"Host: %s pid: %d rank ID: %d number of ranks: %d\n",
timebuf, host, pid, cr->nodeid, cr->nnodes);
try
{
gmx::BinaryInformationSettings settings;
settings.extendedInfo(true);
settings.copyright(!bAppendFiles);
gmx::printBinaryInformation(fp, gmx::getProgramContext(), settings);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
fprintf(fp, "\n");
fflush(fp);
debug_gmx();
*fplog = fp;
}
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 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;
}
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 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);
}
static FILE *man_file(const output_env_t oenv,const char *mantp)
{
FILE *fp;
char buf[256];
const char *pr = output_env_get_short_program_name(oenv);
if (strcmp(mantp,"ascii") != 0)
sprintf(buf,"%s.%s",pr,mantp);
else
sprintf(buf,"%s.txt",pr);
fp = gmx_fio_fopen(buf,"w");
return fp;
}
void write_grid_pqr(char *fn,int nx,int ny,int nz,real ***phi)
{
FILE *fp;
int i,j,k,rnr=0;
real fac=4.0;
fp=gmx_fio_fopen(fn,"w");
for(i=0; (i<nx); i++)
for(j=0; (j<ny); j++)
for(k=0; (k<nz); k++,rnr++)
fprintf(fp,"%-6s%5d %-4.4s%3.3s %c%4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
"ATOM",(i+1),"C","C",' ',
1+((rnr+1) % 10000),fac*i,fac*j,fac*k,0.0,phi[i][j][k]);
gmx_fio_fclose(fp);
}
void write_pqr(char *fn,t_atoms *atoms,rvec x[],real phi[],real dx)
{
FILE *fp;
int i,rnr;
fp=gmx_fio_fopen(fn,"w");
for(i=0; (i<atoms->nr); i++) {
rnr=atoms->atom[i].resnr;
fprintf(fp,"%-6s%5d %-4.4s%3.3s %c%4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
"ATOM",(i+1),*atoms->atomname[i],*atoms->resname[rnr],' ',
(rnr+1) % 10000,
10*(dx+x[i][XX]),10*x[i][YY],10*(x[i][ZZ]),0.0,phi[i]);
}
gmx_fio_fclose(fp);
}
void
AbstractPlotModule::dataStarted(AbstractAnalysisData * /* data */)
{
if (!impl_->filename_.empty())
{
if (impl_->bPlain_)
{
impl_->fp_ = gmx_fio_fopen(impl_->filename_.c_str(), "w");
}
else
{
time_unit_t time_unit
= static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
xvg_format_t xvg_format
= (impl_->settings_.plotFormat() > 0
? static_cast<xvg_format_t>(impl_->settings_.plotFormat())
: exvgNONE);
output_env_t oenv;
output_env_init(&oenv, getProgramContext(), time_unit, FALSE, xvg_format, 0);
boost::shared_ptr<output_env> oenvGuard(oenv, &output_env_done);
impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(),
impl_->xlabel_.c_str(), impl_->ylabel_.c_str(),
oenv);
const SelectionCollection *selections
= impl_->settings_.selectionCollection();
if (selections != NULL)
{
selections->printXvgrInfo(impl_->fp_, oenv);
}
if (!impl_->subtitle_.empty())
{
xvgr_subtitle(impl_->fp_, impl_->subtitle_.c_str(), oenv);
}
if (output_env_get_print_xvgr_codes(oenv)
&& !impl_->legend_.empty())
{
std::vector<const char *> legend;
legend.reserve(impl_->legend_.size());
for (size_t i = 0; i < impl_->legend_.size(); ++i)
{
legend.push_back(impl_->legend_[i].c_str());
}
xvgr_legend(impl_->fp_, legend.size(), &legend[0], oenv);
}
}
}
}
