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;
}
extern FILE *open_dhdl(const char *filename, const t_inputrec *ir,
const gmx_output_env_t *oenv)
{
FILE *fp;
const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda",
*lambdastate = "\\lambda state";
char title[STRLEN], label_x[STRLEN], label_y[STRLEN];
int i, nps, nsets, nsets_de, nsetsbegin;
int n_lambda_terms = 0;
t_lambda *fep = ir->fepvals; /* for simplicity */
t_expanded *expand = ir->expandedvals;
char **setname;
char buf[STRLEN], lambda_vec_str[STRLEN], lambda_name_str[STRLEN];
int bufplace = 0;
int nsets_dhdl = 0;
int s = 0;
int nsetsextend;
gmx_bool write_pV = FALSE;
/* count the number of different lambda terms */
for (i = 0; i < efptNR; i++)
{
if (fep->separate_dvdl[i])
{
n_lambda_terms++;
}
}
if (fep->n_lambda == 0)
{
sprintf(title, "%s", dhdl);
sprintf(label_x, "Time (ps)");
sprintf(label_y, "%s (%s %s)",
dhdl, unit_energy, "[\\lambda]\\S-1\\N");
}
else
{
sprintf(title, "%s and %s", dhdl, deltag);
sprintf(label_x, "Time (ps)");
sprintf(label_y, "%s and %s (%s %s)",
dhdl, deltag, unit_energy, "[\\8l\\4]\\S-1\\N");
}
fp = gmx_fio_fopen(filename, "w+");
xvgr_header(fp, title, label_x, label_y, exvggtXNY, oenv);
if (!(ir->bSimTemp))
{
bufplace = sprintf(buf, "T = %g (K) ",
ir->opts.ref_t[0]);
}
if ((ir->efep != efepSLOWGROWTH) && (ir->efep != efepEXPANDED))
{
if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
{
/* compatibility output */
sprintf(&(buf[bufplace]), "%s = %.4f", lambda, fep->init_lambda);
}
else
{
print_lambda_vector(fep, fep->init_fep_state, TRUE, FALSE,
lambda_vec_str);
print_lambda_vector(fep, fep->init_fep_state, TRUE, TRUE,
lambda_name_str);
sprintf(&(buf[bufplace]), "%s %d: %s = %s",
lambdastate, fep->init_fep_state,
lambda_name_str, lambda_vec_str);
}
}
xvgr_subtitle(fp, buf, oenv);
nsets_dhdl = 0;
if (fep->dhdl_derivatives == edhdlderivativesYES)
{
nsets_dhdl = n_lambda_terms;
}
/* count the number of delta_g states */
nsets_de = fep->lambda_stop_n - fep->lambda_start_n;
nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
if (fep->n_lambda > 0 && (expand->elmcmove > elmcmoveNO))
{
nsets += 1; /*add fep state for expanded ensemble */
}
if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
nsets += 1; /* add energy to the dhdl as well */
}
nsetsextend = nsets;
if ((ir->epc != epcNO) && (fep->n_lambda > 0) && (fep->init_lambda < 0))
{
nsetsextend += 1; /* for PV term, other terms possible if required for
the reduced potential (only needed with foreign
lambda, and only output when init_lambda is not
set in order to maintain compatibility of the
dhdl.xvg file) */
write_pV = TRUE;
}
snew(setname, nsetsextend);
if (expand->elmcmove > elmcmoveNO)
{
/* state for the fep_vals, if we have alchemical sampling */
sprintf(buf, "%s", "Thermodynamic state");
setname[s] = gmx_strdup(buf);
s += 1;
}
if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
switch (fep->edHdLPrintEnergy)
{
case edHdLPrintEnergyPOTENTIAL:
sprintf(buf, "%s (%s)", "Potential Energy", unit_energy);
break;
case edHdLPrintEnergyTOTAL:
case edHdLPrintEnergyYES:
default:
sprintf(buf, "%s (%s)", "Total Energy", unit_energy);
}
setname[s] = gmx_strdup(buf);
s += 1;
}
if (fep->dhdl_derivatives == edhdlderivativesYES)
{
for (i = 0; i < efptNR; i++)
{
if (fep->separate_dvdl[i])
{
if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
{
/* compatibility output */
sprintf(buf, "%s %s %.4f", dhdl, lambda, fep->init_lambda);
}
else
{
double lam = fep->init_lambda;
if (fep->init_lambda < 0)
{
lam = fep->all_lambda[i][fep->init_fep_state];
}
sprintf(buf, "%s %s = %.4f", dhdl, efpt_singular_names[i],
lam);
}
setname[s] = gmx_strdup(buf);
s += 1;
}
}
}
if (fep->n_lambda > 0)
{
/* g_bar has to determine the lambda values used in this simulation
* from this xvg legend.
*/
if (expand->elmcmove > elmcmoveNO)
{
nsetsbegin = 1; /* for including the expanded ensemble */
}
else
{
nsetsbegin = 0;
}
if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
nsetsbegin += 1;
}
nsetsbegin += nsets_dhdl;
for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
{
print_lambda_vector(fep, i, FALSE, FALSE, lambda_vec_str);
if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
{
/* for compatible dhdl.xvg files */
nps = sprintf(buf, "%s %s %s", deltag, lambda, lambda_vec_str);
}
else
{
nps = sprintf(buf, "%s %s to %s", deltag, lambda, lambda_vec_str);
}
if (ir->bSimTemp)
{
/* print the temperature for this state if doing simulated annealing */
sprintf(&buf[nps], "T = %g (%s)",
ir->simtempvals->temperatures[s-(nsetsbegin)],
unit_temp_K);
}
setname[s] = gmx_strdup(buf);
s++;
}
if (write_pV)
{
sprintf(buf, "pV (%s)", unit_energy);
setname[nsetsextend-1] = gmx_strdup(buf); /* the first entry after
nsets */
}
xvgr_legend(fp, nsetsextend, (const char **)setname, oenv);
for (s = 0; s < nsetsextend; s++)
{
sfree(setname[s]);
}
sfree(setname);
}
return fp;
}
FILE *open_dhdl(const char *filename,const t_inputrec *ir,
const output_env_t oenv)
{
FILE *fp;
const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda";
char title[STRLEN],label_x[STRLEN],label_y[STRLEN];
char **setname;
char buf[STRLEN];
sprintf(label_x,"%s (%s)","Time",unit_time);
if (ir->n_flambda == 0)
{
sprintf(title,"%s",dhdl);
sprintf(label_y,"%s (%s %s)",
dhdl,unit_energy,"[\\lambda]\\S-1\\N");
}
else
{
sprintf(title,"%s, %s",dhdl,deltag);
sprintf(label_y,"(%s)",unit_energy);
}
fp = gmx_fio_fopen(filename,"w+");
xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv);
if (ir->delta_lambda == 0)
{
sprintf(buf,"T = %g (K), %s = %g",
ir->opts.ref_t[0],lambda,ir->init_lambda);
}
else
{
sprintf(buf,"T = %g (K)",
ir->opts.ref_t[0]);
}
xvgr_subtitle(fp,buf,oenv);
if (ir->n_flambda > 0)
{
int nsets,s,nsi=0;
/* g_bar has to determine the lambda values used in this simulation
* from this xvg legend. */
nsets = ( (ir->dhdl_derivatives==dhdlderivativesYES) ? 1 : 0) +
ir->n_flambda;
snew(setname,nsets);
if (ir->dhdl_derivatives == dhdlderivativesYES)
{
sprintf(buf,"%s %s %g",dhdl,lambda,ir->init_lambda);
setname[nsi++] = strdup(buf);
}
for(s=0; s<ir->n_flambda; s++)
{
sprintf(buf,"%s %s %g",deltag,lambda,ir->flambda[s]);
setname[nsi++] = strdup(buf);
}
xvgr_legend(fp,nsets,(const char**)setname,oenv);
for(s=0; s<nsets; s++)
{
sfree(setname[s]);
}
sfree(setname);
}
return fp;
}
static FILE *open_pull_out(const char *fn, t_pull *pull, const output_env_t oenv,
gmx_bool bCoord, unsigned long Flags)
{
FILE *fp;
int nsets, c, m;
char **setname, buf[10];
if (Flags & MD_APPENDFILES)
{
fp = gmx_fio_fopen(fn, "a+");
}
else
{
fp = gmx_fio_fopen(fn, "w+");
if (bCoord)
{
xvgr_header(fp, "Pull COM", "Time (ps)", "Position (nm)",
exvggtXNY, oenv);
}
else
{
xvgr_header(fp, "Pull force", "Time (ps)", "Force (kJ/mol/nm)",
exvggtXNY, oenv);
}
snew(setname, 2*pull->ncoord*DIM);
nsets = 0;
for (c = 0; c < pull->ncoord; c++)
{
if (bCoord)
{
if (pull->bPrintRef)
{
for (m = 0; m < DIM; m++)
{
if (pull->dim[m])
{
sprintf(buf, "%d %s%c", c+1, "c", 'X'+m);
setname[nsets] = strdup(buf);
nsets++;
}
}
}
for (m = 0; m < DIM; m++)
{
if (pull->dim[m])
{
sprintf(buf, "%d %s%c", c+1, "d", 'X'+m);
setname[nsets] = strdup(buf);
nsets++;
}
}
}
else
{
sprintf(buf, "%d", c+1);
setname[nsets] = strdup(buf);
nsets++;
}
}
if (nsets > 1)
{
xvgr_legend(fp, nsets, (const char**)setname, oenv);
}
for (c = 0; c < nsets; c++)
{
sfree(setname[c]);
}
sfree(setname);
}
return fp;
}
static FILE *open_pull_out(const char *fn,t_pull *pull,const output_env_t oenv,
gmx_bool bCoord, unsigned long Flags)
{
FILE *fp;
int nsets,g,m;
char **setname,buf[10];
if(Flags & MD_APPENDFILES)
{
fp = gmx_fio_fopen(fn,"a+");
}
else
{
fp = gmx_fio_fopen(fn,"w+");
if (bCoord)
{
xvgr_header(fp,"Pull COM", "Time (ps)","Position (nm)",
exvggtXNY,oenv);
}
else
{
xvgr_header(fp,"Pull force","Time (ps)","Force (kJ/mol/nm)",
exvggtXNY,oenv);
}
snew(setname,(1+pull->ngrp)*DIM);
nsets = 0;
for(g=0; g<1+pull->ngrp; g++)
{
if (pull->grp[g].nat > 0 &&
(g > 0 || (bCoord && !PULL_CYL(pull))))
{
if (bCoord || pull->eGeom == epullgPOS)
{
if (PULL_CYL(pull))
{
for(m=0; m<DIM; m++)
{
if (pull->dim[m])
{
sprintf(buf,"%d %s%c",g,"c",'X'+m);
setname[nsets] = strdup(buf);
nsets++;
}
}
}
for(m=0; m<DIM; m++)
{
if (pull->dim[m])
{
sprintf(buf,"%d %s%c",
g,(bCoord && g > 0)?"d":"",'X'+m);
setname[nsets] = strdup(buf);
nsets++;
}
}
}
else
{
sprintf(buf,"%d",g);
setname[nsets] = strdup(buf);
nsets++;
}
}
}
if (bCoord || nsets > 1)
{
xvgr_legend(fp,nsets,(const char**)setname,oenv);
}
for(g=0; g<nsets; g++)
{
sfree(setname[g]);
}
sfree(setname);
}
return fp;
}
extern FILE *open_dhdl(const char *filename,const t_inputrec *ir,
const output_env_t oenv)
{
FILE *fp;
const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda",
*lambdastate="\\lambda state",*remain="remaining";
char title[STRLEN],label_x[STRLEN],label_y[STRLEN];
int i,np,nps,nsets,nsets_de,nsetsbegin;
t_lambda *fep;
char **setname;
char buf[STRLEN];
int bufplace=0;
int nsets_dhdl = 0;
int s = 0;
int nsetsextend;
/* for simplicity */
fep = ir->fepvals;
if (fep->n_lambda == 0)
{
sprintf(title,"%s",dhdl);
sprintf(label_x,"Time (ps)");
sprintf(label_y,"%s (%s %s)",
dhdl,unit_energy,"[\\lambda]\\S-1\\N");
}
else
{
sprintf(title,"%s and %s",dhdl,deltag);
sprintf(label_x,"Time (ps)");
sprintf(label_y,"%s and %s (%s %s)",
dhdl,deltag,unit_energy,"[\\8l\\4]\\S-1\\N");
}
fp = gmx_fio_fopen(filename,"w+");
xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv);
if (!(ir->bSimTemp))
{
bufplace = sprintf(buf,"T = %g (K) ",
ir->opts.ref_t[0]);
}
if (ir->efep != efepSLOWGROWTH)
{
if (fep->n_lambda == 0)
{
sprintf(&(buf[bufplace]),"%s = %g",
lambda,fep->init_lambda);
}
else
{
sprintf(&(buf[bufplace]),"%s = %d",
lambdastate,fep->init_fep_state);
}
}
xvgr_subtitle(fp,buf,oenv);
for (i=0;i<efptNR;i++)
{
if (fep->separate_dvdl[i]) {nsets_dhdl++;}
}
/* count the number of delta_g states */
nsets_de = fep->n_lambda;
nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
if (fep->n_lambda>0 && ir->bExpanded)
{
nsets += 1; /*add fep state for expanded ensemble */
}
if (fep->bPrintEnergy)
{
nsets += 1; /* add energy to the dhdl as well */
}
nsetsextend = nsets;
if ((ir->epc!=epcNO) && (fep->n_lambda>0))
{
nsetsextend += 1; /* for PV term, other terms possible if required for the reduced potential (only needed with foreign lambda) */
}
snew(setname,nsetsextend);
if (ir->bExpanded)
{
/* state for the fep_vals, if we have alchemical sampling */
sprintf(buf,"%s","Thermodynamic state");
setname[s] = strdup(buf);
s+=1;
}
if (fep->bPrintEnergy)
{
sprintf(buf,"%s (%s)","Energy",unit_energy);
setname[s] = strdup(buf);
s+=1;
}
for (i=0;i<efptNR;i++)
{
if (fep->separate_dvdl[i]) {
sprintf(buf,"%s (%s)",dhdl,efpt_names[i]);
setname[s] = strdup(buf);
s+=1;
}
}
if (fep->n_lambda > 0)
{
/* g_bar has to determine the lambda values used in this simulation
* from this xvg legend.
*/
if (ir->bExpanded) {
nsetsbegin = 1; /* for including the expanded ensemble */
} else {
nsetsbegin = 0;
}
if (fep->bPrintEnergy)
{
nsetsbegin += 1;
}
nsetsbegin += nsets_dhdl;
for(s=nsetsbegin; s<nsets; s++)
{
nps = sprintf(buf,"%s %s (",deltag,lambda);
for (i=0;i<efptNR;i++)
{
if (fep->separate_dvdl[i])
{
np = sprintf(&buf[nps],"%g,",fep->all_lambda[i][s-(nsetsbegin)]);
nps += np;
}
}
if (ir->bSimTemp)
{
/* print the temperature for this state if doing simulated annealing */
sprintf(&buf[nps],"T = %g (%s))",ir->simtempvals->temperatures[s-(nsetsbegin)],unit_temp_K);
}
else
{
sprintf(&buf[nps-1],")"); /* -1 to overwrite the last comma */
}
setname[s] = strdup(buf);
}
if (ir->epc!=epcNO) {
np = sprintf(buf,"pV (%s)",unit_energy);
setname[nsetsextend-1] = strdup(buf); /* the first entry after nsets */
}
xvgr_legend(fp,nsetsextend,(const char **)setname,oenv);
for(s=0; s<nsetsextend; s++)
{
sfree(setname[s]);
}
sfree(setname);
}
return fp;
}
