#define TIME_EXPLICIT 0
#define TIME_CONTINUE 1
-#define TIME_LAST 2
+#define TIME_LAST 2
#ifndef FLT_MAX
-#define FLT_MAX 1e36
+# define FLT_MAX 1e36
#endif
-static int *select_it(int nre, gmx_enxnm_t *nm, int *nset)
+static int* select_it(int nre, gmx_enxnm_t* nm, int* nset)
{
- gmx_bool *bE;
+ gmx_bool* bE;
int n, k, j, i;
- int *set;
+ int* set;
gmx_bool bVerbose = TRUE;
if ((getenv("GMX_ENER_VERBOSE")) != nullptr)
if (bVerbose)
{
- for (k = 0; (k < nre); )
+ for (k = 0; (k < nre);)
{
for (j = 0; (j < 4) && (k < nre); j++, k++)
{
- fprintf(stderr, " %3d=%14s", k+1, nm[k].name);
+ fprintf(stderr, " %3d=%14s", k + 1, nm[k].name);
}
fprintf(stderr, "\n");
}
}
if ((n > 0) && (n <= nre))
{
- bE[n-1] = TRUE;
+ bE[n - 1] = TRUE;
}
- }
- while (n != 0);
+ } while (n != 0);
snew(set, nre);
for (i = (*nset) = 0; (i < nre); i++)
return set;
}
-static void sort_files(gmx::ArrayRef<std::string> files, real *settime)
+static void sort_files(gmx::ArrayRef<std::string> files, real* settime)
{
for (gmx::index i = 0; i < files.ssize(); i++)
{
}
-static int scan_ene_files(const std::vector<std::string> &files,
- real *readtime, real *timestep, int *nremax)
+static int scan_ene_files(const std::vector<std::string>& files, real* readtime, real* timestep, int* nremax)
{
/* Check number of energy terms and start time of all files */
int nre, nremin = 0, nresav = 0;
ener_file_t in;
real t1, t2;
char inputstring[STRLEN];
- gmx_enxnm_t *enm;
- t_enxframe *fr;
+ gmx_enxnm_t* enm;
+ t_enxframe* fr;
snew(fr, 1);
t1 = fr->t;
do_enx(in, fr);
t2 = fr->t;
- *timestep = t2-t1;
+ *timestep = t2 - t1;
readtime[f] = t1;
close_enx(in);
}
{
fprintf(stderr,
"Energy files don't match, different number of energies:\n"
- " %s: %d\n %s: %d\n", files[f - 1].c_str(), nresav, files[f].c_str(), fr->nre);
+ " %s: %d\n %s: %d\n",
+ files[f - 1].c_str(), nresav, files[f].c_str(), fr->nre);
fprintf(stderr,
"\nContinue conversion using only the first %d terms (n/y)?\n"
- "(you should be sure that the energy terms match)\n", nremin);
- if (nullptr == fgets(inputstring, STRLEN-1, stdin))
+ "(you should be sure that the energy terms match)\n",
+ nremin);
+ if (nullptr == fgets(inputstring, STRLEN - 1, stdin))
{
gmx_fatal(FARGS, "Error reading user input");
}
}
-static void edit_files(gmx::ArrayRef<std::string> files, real *readtime,
- real *settime, int *cont_type, gmx_bool bSetTime, gmx_bool bSort)
+static void edit_files(gmx::ArrayRef<std::string> files,
+ real* readtime,
+ real* settime,
+ int* cont_type,
+ gmx_bool bSetTime,
+ gmx_bool bSort)
{
gmx_bool ok;
char inputstring[STRLEN], *chptr;
}
else
{
- fprintf(stderr, "\n\nEnter the new start time for each file.\n"
+ fprintf(stderr,
+ "\n\nEnter the new start time for each file.\n"
"There are two special options, both disables sorting:\n\n"
"c (continue) - The start time is taken from the end\n"
"of the previous file. Use it when your continuation run\n"
"since this takes possible overlap into account.\n\n");
}
- fprintf(stderr, " File Current start New start\n"
+ fprintf(stderr,
+ " File Current start New start\n"
"---------------------------------------------------------\n");
for (gmx::index i = 0; i < files.ssize(); i++)
ok = FALSE;
do
{
- if (nullptr == fgets(inputstring, STRLEN-1, stdin))
+ if (nullptr == fgets(inputstring, STRLEN - 1, stdin))
{
gmx_fatal(FARGS, "Error reading user input");
}
- inputstring[std::strlen(inputstring)-1] = 0;
+ inputstring[std::strlen(inputstring) - 1] = 0;
if (inputstring[0] == 'c' || inputstring[0] == 'C')
{
ok = TRUE;
settime[i] = FLT_MAX;
}
- else if (inputstring[0] == 'l' ||
- inputstring[0] == 'L')
+ else if (inputstring[0] == 'l' || inputstring[0] == 'L')
{
cont_type[i] = TIME_LAST;
bSort = FALSE;
ok = TRUE;
}
}
- }
- while (!ok);
+ } while (!ok);
}
if (cont_type[0] != TIME_EXPLICIT)
{
/* Write out the new order and start times */
- fprintf(stderr, "\nSummary of files and start times used:\n\n"
+ fprintf(stderr,
+ "\nSummary of files and start times used:\n\n"
" File Start time\n"
"-----------------------------------------\n");
for (gmx::index i = 0; i < files.ssize(); i++)
}
-static void update_ee_sum(int nre,
- int64_t *ee_sum_step,
- int64_t *ee_sum_nsteps,
- int64_t *ee_sum_nsum,
- t_energy *ee_sum,
- t_enxframe *fr, int out_step)
+static void update_ee_sum(int nre,
+ int64_t* ee_sum_step,
+ int64_t* ee_sum_nsteps,
+ int64_t* ee_sum_nsum,
+ t_energy* ee_sum,
+ t_enxframe* fr,
+ int out_step)
{
- int64_t nsteps, nsum, fr_nsum;
- int i;
+ int64_t nsteps, nsum, fr_nsum;
+ int i;
nsteps = *ee_sum_nsteps;
nsum = *ee_sum_nsum;
{
for (i = 0; i < nre; i++)
{
- ee_sum[i].eav +=
- gmx::square(ee_sum[i].esum/nsum
- - (ee_sum[i].esum + fr->ener[i].e)/(nsum + 1))*nsum*(nsum + 1);
+ ee_sum[i].eav += gmx::square(ee_sum[i].esum / nsum
+ - (ee_sum[i].esum + fr->ener[i].e) / (nsum + 1))
+ * nsum * (nsum + 1);
ee_sum[i].esum += fr->ener[i].e;
}
}
{
for (i = 0; i < fr->nre; i++)
{
- ee_sum[i].eav +=
- fr->ener[i].eav +
- gmx::square(ee_sum[i].esum/nsum
- - (ee_sum[i].esum + fr->ener[i].esum)/(nsum + fr->nsum))*
- nsum*(nsum + fr->nsum)/static_cast<double>(fr->nsum);
+ ee_sum[i].eav += fr->ener[i].eav
+ + gmx::square(ee_sum[i].esum / nsum
+ - (ee_sum[i].esum + fr->ener[i].esum) / (nsum + fr->nsum))
+ * nsum * (nsum + fr->nsum) / static_cast<double>(fr->nsum);
ee_sum[i].esum += fr->ener[i].esum;
}
}
nsteps += fr->nsteps;
- nsum += fr_nsum;
+ nsum += fr_nsum;
}
else
{
*ee_sum_nsum = nsum;
}
-int gmx_eneconv(int argc, char *argv[])
+int gmx_eneconv(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"With [IT]multiple files[it] specified for the [TT]-f[tt] option:[PAR]",
"Concatenates several energy files in sorted order.",
"In the case of double time frames, the one",
"[TT]-settime[tt] is applied first, then [TT]-dt[tt]/[TT]-offset[tt]",
"followed by [TT]-b[tt] and [TT]-e[tt] to select which frames to write."
};
- const char *bugs[] = {
- "When combining trajectories the sigma and E^2 (necessary for statistics) are not updated correctly. Only the actual energy is correct. One thus has to compute statistics in another way."
+ const char* bugs[] = {
+ "When combining trajectories the sigma and E^2 (necessary for statistics) are not "
+ "updated correctly. Only the actual energy is correct. One thus has to compute "
+ "statistics in another way."
};
- ener_file_t in = nullptr, out = nullptr;
- gmx_enxnm_t *enm = nullptr;
+ ener_file_t in = nullptr, out = nullptr;
+ gmx_enxnm_t* enm = nullptr;
#if 0
ener_file_t in, out = NULL;
gmx_enxnm_t *enm = NULL;
#endif
- t_enxframe *fr, *fro;
+ t_enxframe * fr, *fro;
int64_t ee_sum_step = 0, ee_sum_nsteps, ee_sum_nsum;
- t_energy *ee_sum;
+ t_energy* ee_sum;
int64_t lastfilestep, laststep, startstep_file = 0;
int noutfr;
int nre, nremax, this_nre, i, kkk, nset, *set = nullptr;
double last_t;
- real *readtime, *settime, timestep, tadjust;
+ real * readtime, *settime, timestep, tadjust;
char buf[22], buf2[22];
- int *cont_type;
+ int* cont_type;
gmx_bool bNewFile, bFirst, bNewOutput;
- gmx_output_env_t *oenv;
+ gmx_output_env_t* oenv;
gmx_bool warned_about_dh = FALSE;
- t_enxblock *blocks = nullptr;
+ t_enxblock* blocks = nullptr;
int nblocks = 0;
int nblocks_alloc = 0;
- t_filenm fnm[] = {
- { efEDR, "-f", nullptr, ffRDMULT },
- { efEDR, "-o", "fixed", ffWRITE },
+ t_filenm fnm[] = {
+ { efEDR, "-f", nullptr, ffRDMULT },
+ { efEDR, "-o", "fixed", ffWRITE },
};
#define NFILE asize(fnm)
- gmx_bool bWrite;
- static real delta_t = 0.0, toffset = 0, scalefac = 1;
- static gmx_bool bSetTime = FALSE;
- static gmx_bool bSort = TRUE, bError = TRUE;
- static real begin = -1;
- static real end = -1;
- gmx_bool remove_dh = FALSE;
-
- t_pargs pa[] = {
- { "-b", FALSE, etREAL, {&begin},
- "First time to use"},
- { "-e", FALSE, etREAL, {&end},
- "Last time to use"},
- { "-dt", FALSE, etREAL, {&delta_t},
- "Only write out frame when t MOD dt = offset" },
- { "-offset", FALSE, etREAL, {&toffset},
- "Time offset for [TT]-dt[tt] option" },
- { "-settime", FALSE, etBOOL, {&bSetTime},
- "Change starting time interactively" },
- { "-sort", FALSE, etBOOL, {&bSort},
- "Sort energy files (not frames)"},
- { "-rmdh", FALSE, etBOOL, {&remove_dh},
- "Remove free energy block data" },
- { "-scalefac", FALSE, etREAL, {&scalefac},
- "Multiply energy component by this factor" },
- { "-error", FALSE, etBOOL, {&bError},
- "Stop on errors in the file" }
+ gmx_bool bWrite;
+ static real delta_t = 0.0, toffset = 0, scalefac = 1;
+ static gmx_bool bSetTime = FALSE;
+ static gmx_bool bSort = TRUE, bError = TRUE;
+ static real begin = -1;
+ static real end = -1;
+ gmx_bool remove_dh = FALSE;
+
+ t_pargs pa[] = {
+ { "-b", FALSE, etREAL, { &begin }, "First time to use" },
+ { "-e", FALSE, etREAL, { &end }, "Last time to use" },
+ { "-dt", FALSE, etREAL, { &delta_t }, "Only write out frame when t MOD dt = offset" },
+ { "-offset", FALSE, etREAL, { &toffset }, "Time offset for [TT]-dt[tt] option" },
+ { "-settime", FALSE, etBOOL, { &bSetTime }, "Change starting time interactively" },
+ { "-sort", FALSE, etBOOL, { &bSort }, "Sort energy files (not frames)" },
+ { "-rmdh", FALSE, etBOOL, { &remove_dh }, "Remove free energy block data" },
+ { "-scalefac", FALSE, etREAL, { &scalefac }, "Multiply energy component by this factor" },
+ { "-error", FALSE, etBOOL, { &bError }, "Stop on errors in the file" }
};
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa),
- pa, asize(desc), desc, asize(bugs), bugs, &oenv))
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc,
+ asize(bugs), bugs, &oenv))
{
return 0;
}
- fprintf(stdout, "Note that major changes are planned in future for "
+ fprintf(stdout,
+ "Note that major changes are planned in future for "
"eneconv, to improve usability and utility.");
tadjust = 0;
}
/* start reading from the next file */
- while ((fro->t <= (settime[f+1] + GMX_REAL_EPS)) &&
- do_enx(in, fr))
+ while ((fro->t <= (settime[f + 1] + GMX_REAL_EPS)) && do_enx(in, fr))
{
if (bNewFile)
{
startstep_file = fr->step;
tadjust = settime[f] - fr->t;
- if (cont_type[f+1] == TIME_LAST)
+ if (cont_type[f + 1] == TIME_LAST)
{
- settime[f+1] = readtime[f+1]-readtime[f]+settime[f];
- cont_type[f+1] = TIME_EXPLICIT;
+ settime[f + 1] = readtime[f + 1] - readtime[f] + settime[f];
+ cont_type[f + 1] = TIME_EXPLICIT;
}
bNewFile = FALSE;
}
/* Skip this frame, since we already have it / past it */
if (debug)
{
- fprintf(debug, "fr->step %s, fr->t %.4f\n",
- gmx_step_str(fr->step, buf), fr->t);
- fprintf(debug, "tadjust %12.6e + fr->t %12.6e <= t %12.6e\n",
- tadjust, fr->t, last_t);
+ fprintf(debug, "fr->step %s, fr->t %.4f\n", gmx_step_str(fr->step, buf), fr->t);
+ fprintf(debug, "tadjust %12.6e + fr->t %12.6e <= t %12.6e\n", tadjust, fr->t, last_t);
}
continue;
}
fro->step = lastfilestep + fr->step - startstep_file;
- fro->t = tadjust + fr->t;
+ fro->t = tadjust + fr->t;
- bWrite = ((begin < 0 || (fro->t >= begin-GMX_REAL_EPS)) &&
- (end < 0 || (fro->t <= end +GMX_REAL_EPS)) &&
- (fro->t <= settime[f+1]+0.5*timestep));
+ bWrite = ((begin < 0 || (fro->t >= begin - GMX_REAL_EPS))
+ && (end < 0 || (fro->t <= end + GMX_REAL_EPS))
+ && (fro->t <= settime[f + 1] + 0.5 * timestep));
if (debug)
{
- fprintf(debug,
- "fr->step %s, fr->t %.4f, fro->step %s fro->t %.4f, w %s\n",
- gmx_step_str(fr->step, buf), fr->t,
- gmx_step_str(fro->step, buf2), fro->t, gmx::boolToString(bWrite));
+ fprintf(debug, "fr->step %s, fr->t %.4f, fro->step %s fro->t %.4f, w %s\n",
+ gmx_step_str(fr->step, buf), fr->t, gmx_step_str(fro->step, buf2), fro->t,
+ gmx::boolToString(bWrite));
}
if (bError)
{
- if ((end > 0) && (fro->t > end+GMX_REAL_EPS))
+ if ((end > 0) && (fro->t > end + GMX_REAL_EPS))
{
f = files.size();
break;
}
}
- if (fro->t >= begin-GMX_REAL_EPS)
+ if (fro->t >= begin - GMX_REAL_EPS)
{
if (bFirst)
{
- bFirst = FALSE;
+ bFirst = FALSE;
}
if (bWrite)
{
- update_ee_sum(nre, &ee_sum_step, &ee_sum_nsteps, &ee_sum_nsum, ee_sum,
- fr, fro->step);
+ update_ee_sum(nre, &ee_sum_step, &ee_sum_nsteps, &ee_sum_nsum, ee_sum, fr, fro->step);
}
}
if (bNewOutput)
{
bNewOutput = FALSE;
- fprintf(stderr, "\nContinue writing frames from t=%g, step=%s\n",
- fro->t, gmx_step_str(fro->step, buf));
+ fprintf(stderr, "\nContinue writing frames from t=%g, step=%s\n", fro->t,
+ gmx_step_str(fro->step, buf));
}
/* Copy the energies */
}
else
{
- fro->nsum = int64_to_int(ee_sum_nsum,
- "energy average summation");
+ fro->nsum = int64_to_int(ee_sum_nsum, "energy average summation");
/* Copy the energy sums */
for (i = 0; i < nre; i++)
{
{
for (kkk = 0; kkk < nset; kkk++)
{
- fro->ener[set[kkk]].e *= scalefac;
+ fro->ener[set[kkk]].e *= scalefac;
if (fro->nsum > 0)
{
- fro->ener[set[kkk]].eav *= scalefac*scalefac;
+ fro->ener[set[kkk]].eav *= scalefac * scalefac;
fro->ener[set[kkk]].esum *= scalefac;
}
}
/*fro->ndisre = fr->ndisre;
fro->disre_rm3tav = fr->disre_rm3tav;
fro->disre_rt = fr->disre_rt;*/
- fro->nblock = fr->nblock;
+ fro->nblock = fr->nblock;
/*fro->nr = fr->nr;*/
- fro->block = fr->block;
+ fro->block = fr->block;
/* check if we have blocks with delta_h data and are throwing
away data */
for (i = 0; i < fr->nblock; i++)
{
- if ( (fr->block[i].id != enxDHCOLL) &&
- (fr->block[i].id != enxDH) &&
- (fr->block[i].id != enxDHHIST) )
+ if ((fr->block[i].id != enxDHCOLL) && (fr->block[i].id != enxDH)
+ && (fr->block[i].id != enxDHHIST))
{
/* copy everything verbatim */
blocks[nblocks] = fr->block[i];
{
for (i = 0; i < fr->nblock; i++)
{
- if (fr->block[i].id == enxDH ||
- fr->block[i].id == enxDHHIST)
+ if (fr->block[i].id == enxDH || fr->block[i].id == enxDHHIST)
{
int size;
if (fr->block[i].id == enxDH)
}
if (size > 0)
{
- printf("\nWARNING: %s contains delta H blocks or histograms for which\n"
- " some data is thrown away on a block-by-block basis, where each block\n"
+ printf("\nWARNING: %s contains delta H blocks or "
+ "histograms for which\n"
+ " some data is thrown away on a "
+ "block-by-block basis, where each block\n"
" contains up to %d samples.\n"
- " This is almost certainly not what you want.\n"
- " Use the -rmdh option to throw all delta H samples away.\n"
- " Use g_energy -odh option to extract these samples.\n",
+ " This is almost certainly not what you "
+ "want.\n"
+ " Use the -rmdh option to throw all delta H "
+ "samples away.\n"
+ " Use g_energy -odh option to extract these "
+ "samples.\n",
files[f].c_str(), size);
warned_about_dh = TRUE;
break;
{
f--;
}
- printf("\nLast step written from %s: t %g, step %s\n",
- files[f].c_str(), last_t, gmx_step_str(laststep, buf));
+ printf("\nLast step written from %s: t %g, step %s\n", files[f].c_str(), last_t,
+ gmx_step_str(laststep, buf));
lastfilestep = laststep;
/* set the next time from the last in previous file */
- if (cont_type[f+1] == TIME_CONTINUE)
+ if (cont_type[f + 1] == TIME_CONTINUE)
{
- settime[f+1] = fro->t;
+ settime[f + 1] = fro->t;
/* in this case we have already written the last frame of
* previous file, so update begin to avoid doubling it
* with the start of the next file
*/
- begin = fro->t+0.5*timestep;
+ begin = fro->t + 0.5 * timestep;
/* cont_type[f+1]==TIME_EXPLICIT; */
}
- if ((fro->t < end) && (f < files.size() - 1) &&
- (fro->t < settime[f+1]-1.5*timestep))
+ if ((fro->t < end) && (f < files.size() - 1) && (fro->t < settime[f + 1] - 1.5 * timestep))
{
- fprintf(stderr,
- "\nWARNING: There might be a gap around t=%g\n", fro->t);
+ fprintf(stderr, "\nWARNING: There might be a gap around t=%g\n", fro->t);
}
/* move energies to lastee */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff