* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "typedefs.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/fileio/enxio.h"
#include "gromacs/commandline/pargs.h"
-#include "names.h"
-#include "copyrite.h"
-#include "macros.h"
-#include "xvgr.h"
-#include "gstat.h"
-#include "physics.h"
+#include "gromacs/correlationfunctions/autocorr.h"
+#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "viewit.h"
-#include "mtop_util.h"
-#include "gmx_ana.h"
-#include "mdebin.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static real minthird = -1.0/3.0, minsixth = -1.0/6.0;
j = 0;
for (k = 0; k < nre; k++)
{
- newnm[k] = strdup(nm[k].name);
+ newnm[k] = gmx_strdup(nm[k].name);
/* Insert dashes in all the names */
while ((ptr = strchr(newnm[k], ' ')) != NULL)
{
fprintf(vout, "%10d %10.5e\n", j, mypow(violaver[j]/nframes, minthird));
}
#endif
- gmx_ffclose(vout);
+ xvgrclose(vout);
fprintf(stdout, "\nSum of violations averaged over simulation: %g nm\n",
sumt);
}
fprintf(fp1, "\n");
}
- gmx_ffclose(fp0);
- gmx_ffclose(fp1);
+ xvgrclose(fp0);
+ xvgrclose(fp1);
}
typedef struct {
intBulk += 0.5*(eneset[11][i-1] + eneset[11][i])*factor;
fprintf(fp, "%10g %10g %10g\n", (i*Dt), integral, intBulk);
}
- gmx_ffclose(fp);
+ xvgrclose(fp);
for (i = 0; i < 12; i++)
{
}
if (fp)
{
- gmx_ffclose(fp);
+ xvgrclose(fp);
}
sfree(fr);
}
"[BB]Note[bb] that in most cases the energy files contains averages over all",
"MD steps, or over many more points than the number of frames in",
"energy file. This makes the [THISMODULE] statistics output more accurate",
- "than the [TT].xvg[tt] output. When exact averages are not present in the energy",
+ "than the [REF].xvg[ref] output. When exact averages are not present in the energy",
"file, the statistics mentioned above are simply over the single, per-frame",
"energy values.[PAR]",
"Some fluctuation-dependent properties can be calculated provided",
"the correct energy terms are selected, and that the command line option",
"[TT]-fluct_props[tt] is given. The following properties",
- "will be computed:[BR]",
- "Property Energy terms needed[BR]",
- "---------------------------------------------------[BR]",
- "Heat capacity C[SUB]p[sub] (NPT sims): Enthalpy, Temp [BR]",
- "Heat capacity C[SUB]v[sub] (NVT sims): Etot, Temp [BR]",
- "Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp[BR]",
- "Isothermal compressibility: Vol, Temp [BR]",
- "Adiabatic bulk modulus: Vol, Temp [BR]",
- "---------------------------------------------------[BR]",
+ "will be computed:",
+ "",
+ "=============================== ===================",
+ "Property Energy terms needed",
+ "=============================== ===================",
+ "Heat capacity C[SUB]p[sub] (NPT sims): Enthalpy, Temp",
+ "Heat capacity C[SUB]v[sub] (NVT sims): Etot, Temp",
+ "Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp",
+ "Isothermal compressibility: Vol, Temp",
+ "Adiabatic bulk modulus: Vol, Temp",
+ "=============================== ===================",
+ "",
"You always need to set the number of molecules [TT]-nmol[tt].",
"The C[SUB]p[sub]/C[SUB]v[sub] computations do [BB]not[bb] include any corrections",
"for quantum effects. Use the [gmx-dos] program if you need that (and you do).[PAR]"
"from the [TT]ener.edr[tt] file.[PAR]",
"With [TT]-fee[tt] an estimate is calculated for the free-energy",
- "difference with an ideal gas state: [BR]",
- " [GRK]Delta[grk] A = A(N,V,T) - A[SUB]idealgas[sub](N,V,T) = kT [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln][BR]",
- " [GRK]Delta[grk] G = G(N,p,T) - G[SUB]idealgas[sub](N,p,T) = kT [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln][BR]",
+ "difference with an ideal gas state::",
+ "",
+ " [GRK]Delta[grk] A = A(N,V,T) - A[SUB]idealgas[sub](N,V,T) = kT [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln]",
+ " [GRK]Delta[grk] G = G(N,p,T) - G[SUB]idealgas[sub](N,p,T) = kT [LN][CHEVRON][EXP]U[SUB]pot[sub]/kT[exp][chevron][ln]",
+ "",
"where k is Boltzmann's constant, T is set by [TT]-fetemp[tt] and",
"the average is over the ensemble (or time in a trajectory).",
"Note that this is in principle",
"only correct when averaging over the whole (Boltzmann) ensemble",
"and using the potential energy. This also allows for an entropy",
- "estimate using:[BR]",
- " [GRK]Delta[grk] S(N,V,T) = S(N,V,T) - S[SUB]idealgas[sub](N,V,T) = ([CHEVRON]U[SUB]pot[sub][chevron] - [GRK]Delta[grk] A)/T[BR]",
+ "estimate using::",
+ "",
+ " [GRK]Delta[grk] S(N,V,T) = S(N,V,T) - S[SUB]idealgas[sub](N,V,T) = ([CHEVRON]U[SUB]pot[sub][chevron] - [GRK]Delta[grk] A)/T",
" [GRK]Delta[grk] S(N,p,T) = S(N,p,T) - S[SUB]idealgas[sub](N,p,T) = ([CHEVRON]U[SUB]pot[sub][chevron] + pV - [GRK]Delta[grk] G)/T",
- "[PAR]",
+ "",
"When a second energy file is specified ([TT]-f2[tt]), a free energy",
- "difference is calculated [BR] dF = -kT [LN][CHEVRON][EXP]-(E[SUB]B[sub]-E[SUB]A[sub])/kT[exp][chevron][SUB]A[sub][ln] ,",
+ "difference is calculated::",
+ "",
+ " dF = -kT [LN][CHEVRON][EXP]-(E[SUB]B[sub]-E[SUB]A[sub])/kT[exp][chevron][SUB]A[sub][ln] ,",
+ "",
"where E[SUB]A[sub] and E[SUB]B[sub] are the energies from the first and second energy",
"files, and the average is over the ensemble A. The running average",
"of the free energy difference is printed to a file specified by [TT]-ravg[tt].",
t_filenm fnm[] = {
{ efEDR, "-f", NULL, ffREAD },
{ efEDR, "-f2", NULL, ffOPTRD },
- { efTPX, "-s", NULL, ffOPTRD },
+ { efTPR, "-s", NULL, ffOPTRD },
{ efXVG, "-o", "energy", ffWRITE },
{ efXVG, "-viol", "violaver", ffOPTWR },
{ efXVG, "-pairs", "pairs", ffOPTWR },
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_BE_NICE,
+ PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END,
NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
strcat(buf, ")");
}
}
- out = xvgropen(opt2fn("-o", NFILE, fnm), "Gromacs Energies", "Time (ps)", buf,
+ out = xvgropen(opt2fn("-o", NFILE, fnm), "GROMACS Energies", "Time (ps)", buf,
oenv);
snew(leg, nset+1);
}
if (bSum)
{
- leg[nset] = strdup("Sum");
+ leg[nset] = gmx_strdup("Sum");
xvgr_legend(out, nset+1, (const char**)leg, oenv);
}
else
if (bORIRE || bOTEN)
{
- get_orires_parms(ftp2fn(efTPX, NFILE, fnm), &nor, &nex, &or_label, &oobs);
+ get_orires_parms(ftp2fn(efTPR, NFILE, fnm), &nor, &nex, &or_label, &oobs);
}
if (bORIRE)
for (j = 0; j < 3; j++)
{
sprintf(buf, "eig%d", j+1);
- otenleg[(bOvec ? 12 : 3)*i+j] = strdup(buf);
+ otenleg[(bOvec ? 12 : 3)*i+j] = gmx_strdup(buf);
}
if (bOvec)
{
for (j = 0; j < 9; j++)
{
sprintf(buf, "vec%d%s", j/3+1, j%3 == 0 ? "x" : (j%3 == 1 ? "y" : "z"));
- otenleg[12*i+3+j] = strdup(buf);
+ otenleg[12*i+3+j] = gmx_strdup(buf);
}
}
}
}
else if (bDisRe)
{
- nbounds = get_bounds(ftp2fn(efTPX, NFILE, fnm), &bounds, &index, &pair, &npairs,
+ nbounds = get_bounds(ftp2fn(efTPR, NFILE, fnm), &bounds, &index, &pair, &npairs,
&mtop, &top, &ir);
snew(violaver, npairs);
out = xvgropen(opt2fn("-o", NFILE, fnm), "Sum of Violations",
}
else if (bDHDL)
{
- get_dhdl_parms(ftp2fn(efTPX, NFILE, fnm), &ir);
+ get_dhdl_parms(ftp2fn(efTPR, NFILE, fnm), &ir);
}
/* Initiate energies and set them to zero */
close_enx(fp);
if (out)
{
- gmx_ffclose(out);
+ xvgrclose(out);
}
if (bDRAll)
{
- gmx_ffclose(fp_pairs);
+ xvgrclose(fp_pairs);
}
if (bORT)
{
- gmx_ffclose(fort);
+ xvgrclose(fort);
}
if (bODT)
{
- gmx_ffclose(fodt);
+ xvgrclose(fodt);
}
if (bORA)
{
{
fprintf(out, "%5d %g\n", or_label[i], orient[i]/norfr);
}
- gmx_ffclose(out);
+ xvgrclose(out);
}
if (bODA)
{
{
fprintf(out, "%5d %g\n", or_label[i], orient[i]/norfr-oobs[i]);
}
- gmx_ffclose(out);
+ xvgrclose(out);
}
if (bODR)
{
{
fprintf(out, "%5d %g\n", or_label[i], sqrt(odrms[i]/norfr));
}
- gmx_ffclose(out);
+ xvgrclose(out);
}
if (bOTEN)
{
- gmx_ffclose(foten);
+ xvgrclose(foten);
}
if (bDisRe)
{
if (fp_dhdl)
{
- gmx_ffclose(fp_dhdl);
+ gmx_fio_fclose(fp_dhdl);
printf("\n\nWrote %d lambda values with %d samples as ",
dh_lambdas, dh_samples);
if (dh_hists > 0)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff