#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
-static real minthird = -1.0/3.0, minsixth = -1.0/6.0;
+static real minthird = -1.0 / 3.0, minsixth = -1.0 / 6.0;
static double mypow(double x, double y)
{
}
}
-static real blk_value(t_enxblock *blk, int sub, int index)
+static real blk_value(t_enxblock* blk, int sub, int index)
{
range_check(index, 0, blk->sub[sub].nr);
if (blk->sub[sub].type == xdr_datatype_float)
}
}
-static int *select_it(int nre, char *nm[], int *nset)
+static int* select_it(int nre, char* 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]);
+ fprintf(stderr, " %3d=%14s", k + 1, nm[k]);
}
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 get_orires_parms(const char *topnm, t_inputrec *ir,
- int *nor, int *nex, int **label, real **obs)
+static void get_orires_parms(const char* topnm, t_inputrec* ir, int* nor, int* nex, int** label, real** obs)
{
- gmx_mtop_t mtop;
- t_topology top;
- t_iparams *ip;
- int natoms, i;
- t_iatom *iatom;
- int nb;
- matrix box;
+ gmx_mtop_t mtop;
+ t_topology top;
+ t_iparams* ip;
+ int natoms, i;
+ t_iatom* iatom;
+ int nb;
+ matrix box;
read_tpx(topnm, ir, box, &natoms, nullptr, nullptr, &mtop);
top = gmx_mtop_t_to_t_topology(&mtop, FALSE);
- ip = top.idef.iparams;
- iatom = top.idef.il[F_ORIRES].iatoms;
+ ip = top.idef.iparams;
+ iatom = top.idef.il[F_ORIRES].iatoms;
/* Count how many distance restraint there are... */
nb = top.idef.il[F_ORIRES].nr;
gmx_fatal(FARGS, "No orientation restraints in topology!\n");
}
- *nor = nb/3;
+ *nor = nb / 3;
*nex = 0;
snew(*label, *nor);
snew(*obs, *nor);
for (i = 0; i < nb; i += 3)
{
- (*label)[i/3] = ip[iatom[i]].orires.label;
- (*obs)[i/3] = ip[iatom[i]].orires.obs;
+ (*label)[i / 3] = ip[iatom[i]].orires.label;
+ (*obs)[i / 3] = ip[iatom[i]].orires.obs;
if (ip[iatom[i]].orires.ex >= *nex)
{
- *nex = ip[iatom[i]].orires.ex+1;
+ *nex = ip[iatom[i]].orires.ex + 1;
}
}
- fprintf(stderr, "Found %d orientation restraints with %d experiments",
- *nor, *nex);
+ fprintf(stderr, "Found %d orientation restraints with %d experiments", *nor, *nex);
done_top_mtop(&top, &mtop);
}
-static int get_bounds(real **bounds, int **index, int **dr_pair, int *npairs,
- gmx_localtop_t *top)
+static int get_bounds(real** bounds, int** index, int** dr_pair, int* npairs, gmx_localtop_t* top)
{
- t_functype *functype;
- t_iparams *ip;
- int i, j, k, type, ftype, natom;
- t_ilist *disres;
- t_iatom *iatom;
- real *b;
- int *ind, *pair;
- int nb, label1;
+ t_functype* functype;
+ t_iparams* ip;
+ int i, j, k, type, ftype, natom;
+ t_ilist* disres;
+ t_iatom* iatom;
+ real* b;
+ int * ind, *pair;
+ int nb, label1;
functype = top->idef.functype;
ip = top->idef.iparams;
/* Allocate memory */
snew(b, nb);
snew(ind, nb);
- snew(pair, nb+1);
+ snew(pair, nb + 1);
/* Fill the bound array */
nb = 0;
*bounds = b;
/* Fill the index array */
- label1 = -1;
- disres = &(top->idef.il[F_DISRES]);
- iatom = disres->iatoms;
- for (i = j = k = 0; (i < disres->nr); )
+ label1 = -1;
+ disres = &(top->idef.il[F_DISRES]);
+ iatom = disres->iatoms;
+ for (i = j = k = 0; (i < disres->nr);)
{
type = iatom[i];
ftype = top->idef.functype[type];
- natom = interaction_function[ftype].nratoms+1;
+ natom = interaction_function[ftype].nratoms + 1;
if (label1 != top->idef.iparams[type].disres.label)
{
pair[j] = k;
k++;
i += natom;
}
- pair[j] = k;
- *npairs = k;
+ pair[j] = k;
+ *npairs = k;
if (j != nb)
{
gmx_incons("get_bounds for distance restraints");
return nb;
}
-static void calc_violations(real rt[], real rav3[], int nb, const int index[],
- real bounds[], real *viol, double *st, double *sa)
+static void
+calc_violations(real rt[], real rav3[], int nb, const int index[], real bounds[], real* viol, double* st, double* sa)
{
- const real sixth = 1.0/6.0;
- int i, j;
- double rsum, rav, sumaver, sumt;
+ const real sixth = 1.0 / 6.0;
+ int i, j;
+ double rsum, rav, sumaver, sumt;
sumaver = 0;
sumt = 0;
{
rsum = 0.0;
rav = 0.0;
- for (j = index[i]; (j < index[i+1]); j++)
+ for (j = index[i]; (j < index[i + 1]); j++)
{
if (viol)
{
viol[j] += mypow(rt[j], -3.0);
}
- rav += gmx::square(rav3[j]);
- rsum += mypow(rt[j], -6);
+ rav += gmx::square(rav3[j]);
+ rsum += mypow(rt[j], -6);
}
- rsum = std::max(0.0, mypow(rsum, -sixth)-bounds[i]);
- rav = std::max(0.0, mypow(rav, -sixth)-bounds[i]);
+ rsum = std::max(0.0, mypow(rsum, -sixth) - bounds[i]);
+ rav = std::max(0.0, mypow(rav, -sixth) - bounds[i]);
- sumt += rsum;
+ sumt += rsum;
sumaver += rav;
}
*st = sumt;
*sa = sumaver;
}
-static void analyse_disre(const char *voutfn, int nframes,
- real violaver[], real bounds[], int index[],
- int pair[], int nbounds,
- const gmx_output_env_t *oenv)
+static void analyse_disre(const char* voutfn,
+ int nframes,
+ real violaver[],
+ real bounds[],
+ int index[],
+ int pair[],
+ int nbounds,
+ const gmx_output_env_t* oenv)
{
- FILE *vout;
- double sum, sumt, sumaver;
- int i, j;
+ FILE* vout;
+ double sum, sumt, sumaver;
+ int i, j;
/* Subtract bounds from distances, to calculate violations */
- calc_violations(violaver, violaver,
- nbounds, pair, bounds, nullptr, &sumt, &sumaver);
+ calc_violations(violaver, violaver, nbounds, pair, bounds, nullptr, &sumt, &sumaver);
#ifdef DEBUG
- fprintf(stdout, "\nSum of violations averaged over simulation: %g nm\n",
- sumaver);
- fprintf(stdout, "Largest violation averaged over simulation: %g nm\n\n",
- sumt);
+ fprintf(stdout, "\nSum of violations averaged over simulation: %g nm\n", sumaver);
+ fprintf(stdout, "Largest violation averaged over simulation: %g nm\n\n", sumt);
#endif
- vout = xvgropen(voutfn, "r\\S-3\\N average violations", "DR Index", "nm",
- oenv);
+ vout = xvgropen(voutfn, "r\\S-3\\N average violations", "DR Index", "nm", oenv);
sum = 0.0;
sumt = 0.0;
for (i = 0; (i < nbounds); i++)
{
/* Do ensemble averaging */
sumaver = 0;
- for (j = pair[i]; (j < pair[i+1]); j++)
+ for (j = pair[i]; (j < pair[i + 1]); j++)
{
- sumaver += gmx::square(violaver[j]/real(nframes));
+ sumaver += gmx::square(violaver[j] / real(nframes));
}
- sumaver = std::max(0.0, mypow(sumaver, minsixth)-bounds[i]);
+ sumaver = std::max(0.0, mypow(sumaver, minsixth) - bounds[i]);
- sumt += sumaver;
- sum = std::max(sum, sumaver);
+ sumt += sumaver;
+ sum = std::max(sum, sumaver);
fprintf(vout, "%10d %10.5e\n", index[i], sumaver);
}
#ifdef DEBUG
for (j = 0; (j < dr.ndr); j++)
{
- fprintf(vout, "%10d %10.5e\n", j, mypow(violaver[j]/real(nframes), minthird));
+ fprintf(vout, "%10d %10.5e\n", j, mypow(violaver[j] / real(nframes), minthird));
}
#endif
xvgrclose(vout);
- fprintf(stdout, "\nSum of violations averaged over simulation: %g nm\n",
- sumt);
+ fprintf(stdout, "\nSum of violations averaged over simulation: %g nm\n", sumt);
fprintf(stdout, "Largest violation averaged over simulation: %g nm\n\n", sum);
do_view(oenv, voutfn, "-graphtype bar");
}
-static void print_time(FILE *fp, double t)
+static void print_time(FILE* fp, double t)
{
fprintf(fp, "%12.6f", t);
}
-int gmx_nmr(int argc, char *argv[])
+int gmx_nmr(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"[THISMODULE] extracts distance or orientation restraint",
"data from an energy file. The user is prompted to interactively",
"select the desired terms.[PAR]",
};
- static gmx_bool bPrAll = FALSE;
- static gmx_bool bDp = FALSE, bOrinst = FALSE, bOvec = FALSE;
- static int skip = 0;
- t_pargs pa[] = {
- { "-dp", FALSE, etBOOL, {&bDp},
- "Print energies in high precision" },
- { "-skip", FALSE, etINT, {&skip},
- "Skip number of frames between data points" },
- { "-aver", FALSE, etBOOL, {&bPrAll},
- "Also print the exact average and rmsd stored in the energy frames (only when 1 term is requested)" },
- { "-orinst", FALSE, etBOOL, {&bOrinst},
- "Analyse instantaneous orientation data" },
- { "-ovec", FALSE, etBOOL, {&bOvec},
- "Also plot the eigenvectors with [TT]-oten[tt]" }
- };
- const char * drleg[] = {
- "Running average",
- "Instantaneous"
+ static gmx_bool bPrAll = FALSE;
+ static gmx_bool bDp = FALSE, bOrinst = FALSE, bOvec = FALSE;
+ static int skip = 0;
+ t_pargs pa[] = {
+ { "-dp", FALSE, etBOOL, { &bDp }, "Print energies in high precision" },
+ { "-skip", FALSE, etINT, { &skip }, "Skip number of frames between data points" },
+ { "-aver",
+ FALSE,
+ etBOOL,
+ { &bPrAll },
+ "Also print the exact average and rmsd stored in the energy frames (only when 1 term is "
+ "requested)" },
+ { "-orinst", FALSE, etBOOL, { &bOrinst }, "Analyse instantaneous orientation data" },
+ { "-ovec", FALSE, etBOOL, { &bOvec }, "Also plot the eigenvectors with [TT]-oten[tt]" }
};
-
- FILE /* *out = NULL,*/ *out_disre = nullptr, *fp_pairs = nullptr, *fort = nullptr, *fodt = nullptr, *foten = nullptr;
- ener_file_t fp;
- int timecheck = 0;
- gmx_localtop_t top;
- gmx_enxnm_t *enm = nullptr;
- t_enxframe fr;
- int nre, teller, teller_disre;
- int nor = 0, nex = 0, norfr = 0, enx_i = 0;
- real *bounds = nullptr, *violaver = nullptr, *oobs = nullptr, *orient = nullptr, *odrms = nullptr;
- int *index = nullptr, *pair = nullptr, norsel = 0, *orsel = nullptr, *or_label = nullptr;
- int nbounds = 0, npairs;
- gmx_bool bDisRe, bDRAll, bORA, bORT, bODA, bODR, bODT, bORIRE, bOTEN;
- gmx_bool bCont;
- double sumaver, sumt;
- int *set = nullptr, i, j, k, nset, sss;
- char **pairleg, **odtleg, **otenleg;
- char **leg = nullptr;
- const char *anm_j, *anm_k, *resnm_j, *resnm_k;
- int resnr_j, resnr_k;
- const char *orinst_sub = "@ subtitle \"instantaneous\"\n";
- char buf[256];
- gmx_output_env_t *oenv;
- t_enxblock *blk_disre = nullptr;
+ const char* drleg[] = { "Running average", "Instantaneous" };
+
+ FILE /* *out = NULL,*/ *out_disre = nullptr, *fp_pairs = nullptr, *fort = nullptr,
+ *fodt = nullptr, *foten = nullptr;
+ ener_file_t fp;
+ int timecheck = 0;
+ gmx_localtop_t top;
+ gmx_enxnm_t* enm = nullptr;
+ t_enxframe fr;
+ int nre, teller, teller_disre;
+ int nor = 0, nex = 0, norfr = 0, enx_i = 0;
+ real *bounds = nullptr, *violaver = nullptr, *oobs = nullptr, *orient = nullptr, *odrms = nullptr;
+ int * index = nullptr, *pair = nullptr, norsel = 0, *orsel = nullptr, *or_label = nullptr;
+ int nbounds = 0, npairs;
+ gmx_bool bDisRe, bDRAll, bORA, bORT, bODA, bODR, bODT, bORIRE, bOTEN;
+ gmx_bool bCont;
+ double sumaver, sumt;
+ int * set = nullptr, i, j, k, nset, sss;
+ char ** pairleg, **odtleg, **otenleg;
+ char** leg = nullptr;
+ const char *anm_j, *anm_k, *resnm_j, *resnm_k;
+ int resnr_j, resnr_k;
+ const char* orinst_sub = "@ subtitle \"instantaneous\"\n";
+ char buf[256];
+ gmx_output_env_t* oenv;
+ t_enxblock* blk_disre = nullptr;
int ndisre = 0;
- t_filenm fnm[] = {
- { efEDR, "-f", nullptr, ffREAD },
- { efEDR, "-f2", nullptr, ffOPTRD },
- { efTPR, "-s", nullptr, ffOPTRD },
- // { efXVG, "-o", "energy", ffWRITE },
- { efXVG, "-viol", "violaver", ffOPTWR },
- { efXVG, "-pairs", "pairs", ffOPTWR },
- { efXVG, "-ora", "orienta", ffOPTWR },
- { efXVG, "-ort", "orientt", ffOPTWR },
- { efXVG, "-oda", "orideva", ffOPTWR },
- { efXVG, "-odr", "oridevr", ffOPTWR },
- { efXVG, "-odt", "oridevt", ffOPTWR },
- { efXVG, "-oten", "oriten", ffOPTWR }
- };
+ t_filenm fnm[] = { { efEDR, "-f", nullptr, ffREAD },
+ { efEDR, "-f2", nullptr, ffOPTRD },
+ { efTPR, "-s", nullptr, ffOPTRD },
+ // { efXVG, "-o", "energy", ffWRITE },
+ { efXVG, "-viol", "violaver", ffOPTWR },
+ { efXVG, "-pairs", "pairs", ffOPTWR },
+ { efXVG, "-ora", "orienta", ffOPTWR },
+ { efXVG, "-ort", "orientt", ffOPTWR },
+ { efXVG, "-oda", "orideva", ffOPTWR },
+ { efXVG, "-odr", "oridevr", ffOPTWR },
+ { efXVG, "-odt", "oridevt", ffOPTWR },
+ { efXVG, "-oten", "oriten", ffOPTWR } };
#define NFILE asize(fnm)
- int npargs;
+ int npargs;
npargs = asize(pa);
- if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END,
- NFILE, fnm, npargs, pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END, NFILE, fnm,
+ npargs, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
do_enxnms(fp, &nre, &enm);
free_enxnms(nre, enm);
- t_inputrec irInstance;
- t_inputrec *ir = &irInstance;
+ t_inputrec irInstance;
+ t_inputrec* ir = &irInstance;
init_enxframe(&fr);
gmx::TopologyInformation topInfo;
if (!bDisRe)
{
if (bORIRE || bOTEN)
{
- get_orires_parms(ftp2fn(efTPR, NFILE, fnm), ir,
- &nor, &nex, &or_label, &oobs);
+ get_orires_parms(ftp2fn(efTPR, NFILE, fnm), ir, &nor, &nex, &or_label, &oobs);
}
if (bORIRE)
do
{
j++;
- srenew(orsel, j+1);
+ srenew(orsel, j + 1);
if (1 != scanf("%d", &(orsel[j])))
{
gmx_fatal(FARGS, "Error reading user input");
}
- }
- while (orsel[j] > 0);
+ } while (orsel[j] > 0);
if (orsel[0] == -1)
{
fprintf(stderr, "Selecting all %d orientation restraints\n", nor);
}
if (k == nor)
{
- fprintf(stderr, "Orientation restraint label %d not found\n",
- orsel[i]);
+ fprintf(stderr, "Orientation restraint label %d not found\n", orsel[i]);
}
}
}
}
if (bODT)
{
- fodt = xvgropen(opt2fn("-odt", NFILE, fnm),
- "Orientation restraint deviation",
+ fodt = xvgropen(opt2fn("-odt", NFILE, fnm), "Orientation restraint deviation",
"Time (ps)", "", oenv);
if (bOrinst && output_env_get_print_xvgr_codes(oenv))
{
}
if (bOTEN)
{
- foten = xvgropen(opt2fn("-oten", NFILE, fnm),
- "Order tensor", "Time (ps)", "", oenv);
- snew(otenleg, bOvec ? nex*12 : nex*3);
+ foten = xvgropen(opt2fn("-oten", NFILE, fnm), "Order tensor", "Time (ps)", "", oenv);
+ snew(otenleg, bOvec ? nex * 12 : nex * 3);
for (i = 0; i < nex; i++)
{
for (j = 0; j < 3; j++)
{
- sprintf(buf, "eig%d", j+1);
- otenleg[(bOvec ? 12 : 3)*i+j] = gmx_strdup(buf);
+ sprintf(buf, "eig%d", j + 1);
+ 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] = gmx_strdup(buf);
+ sprintf(buf, "vec%d%s", j / 3 + 1, j % 3 == 0 ? "x" : (j % 3 == 1 ? "y" : "z"));
+ otenleg[12 * i + 3 + j] = gmx_strdup(buf);
}
}
}
- xvgr_legend(foten, bOvec ? nex*12 : nex*3, otenleg, oenv);
+ xvgr_legend(foten, bOvec ? nex * 12 : nex * 3, otenleg, oenv);
for (j = 0; j < 3; j++)
{
sfree(otenleg[j]);
topInfo.fillFromInputFile(ftp2fn(efTPR, NFILE, fnm));
gmx_mtop_generate_local_top(*topInfo.mtop(), &top, ir->efep != efepNO);
}
- nbounds = get_bounds(&bounds, &index, &pair, &npairs,
- &top);
+ nbounds = get_bounds(&bounds, &index, &pair, &npairs, &top);
snew(violaver, npairs);
- out_disre = xvgropen(opt2fn("-o", NFILE, fnm), "Sum of Violations",
- "Time (ps)", "nm", oenv);
+ out_disre = xvgropen(opt2fn("-o", NFILE, fnm), "Sum of Violations", "Time (ps)", "nm", oenv);
xvgr_legend(out_disre, 2, drleg, oenv);
if (bDRAll)
{
- fp_pairs = xvgropen(opt2fn("-pairs", NFILE, fnm), "Pair Distances",
- "Time (ps)", "Distance (nm)", oenv);
+ fp_pairs = xvgropen(opt2fn("-pairs", NFILE, fnm), "Pair Distances", "Time (ps)",
+ "Distance (nm)", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
- fprintf(fp_pairs, "@ subtitle \"averaged (tau=%g) and instantaneous\"\n",
- ir->dr_tau);
+ fprintf(fp_pairs, "@ subtitle \"averaged (tau=%g) and instantaneous\"\n", ir->dr_tau);
}
}
}
{
timecheck = check_times(fr.t);
}
- }
- while (bCont && (timecheck < 0));
+ } while (bCont && (timecheck < 0));
if ((timecheck == 0) && bCont)
{
blk_disre = find_block_id_enxframe(&fr, enxDISRE, nullptr);
if (bDisRe && bDRAll && !leg && blk_disre)
{
- t_iatom *fa;
- t_iparams *ip;
+ t_iatom* fa;
+ t_iparams* ip;
fa = top.idef.il[F_DISRES].iatoms;
ip = top.idef.iparams;
- if (blk_disre->nsub != 2 ||
- (blk_disre->sub[0].nr != blk_disre->sub[1].nr) )
+ if (blk_disre->nsub != 2 || (blk_disre->sub[0].nr != blk_disre->sub[1].nr))
{
gmx_incons("Number of disre sub-blocks not equal to 2");
}
ndisre = blk_disre->sub[0].nr;
- if (ndisre != top.idef.il[F_DISRES].nr/3)
+ if (ndisre != top.idef.il[F_DISRES].nr / 3)
{
- gmx_fatal(FARGS, "Number of disre pairs in the energy file (%d) does not match the number in the run input file (%d)\n",
- ndisre, top.idef.il[F_DISRES].nr/3);
+ gmx_fatal(FARGS,
+ "Number of disre pairs in the energy file (%d) does not match the "
+ "number in the run input file (%d)\n",
+ ndisre, top.idef.il[F_DISRES].nr / 3);
}
snew(pairleg, ndisre);
int molb = 0;
for (i = 0; i < ndisre; i++)
{
snew(pairleg[i], 30);
- j = fa[3*i+1];
- k = fa[3*i+2];
+ j = fa[3 * i + 1];
+ k = fa[3 * i + 2];
mtopGetAtomAndResidueName(topInfo.mtop(), j, &molb, &anm_j, &resnr_j, &resnm_j, nullptr);
mtopGetAtomAndResidueName(topInfo.mtop(), k, &molb, &anm_k, &resnr_k, &resnm_k, nullptr);
- sprintf(pairleg[i], "%d %s %d %s (%d)",
- resnr_j, anm_j, resnr_k, anm_k,
- ip[fa[3*i]].disres.label);
+ sprintf(pairleg[i], "%d %s %d %s (%d)", resnr_j, anm_j, resnr_k, anm_k,
+ ip[fa[3 * i]].disres.label);
}
set = select_it(ndisre, pairleg, &nset);
- snew(leg, 2*nset);
+ snew(leg, 2 * nset);
for (i = 0; (i < nset); i++)
{
- snew(leg[2*i], 32);
- sprintf(leg[2*i], "a %s", pairleg[set[i]]);
- snew(leg[2*i+1], 32);
- sprintf(leg[2*i+1], "i %s", pairleg[set[i]]);
+ snew(leg[2 * i], 32);
+ sprintf(leg[2 * i], "a %s", pairleg[set[i]]);
+ snew(leg[2 * i + 1], 32);
+ sprintf(leg[2 * i + 1], "i %s", pairleg[set[i]]);
}
- xvgr_legend(fp_pairs, 2*nset, leg, oenv);
+ xvgr_legend(fp_pairs, 2 * nset, leg, oenv);
}
/*
*******************************************/
if (ndisre > 0)
{
- GMX_RELEASE_ASSERT(blk_disre != nullptr, "Trying to dereference NULL blk_disre pointer");
- #if !GMX_DOUBLE
- float *disre_rt = blk_disre->sub[0].fval;
- float *disre_rm3tav = blk_disre->sub[1].fval;
- #else
- double *disre_rt = blk_disre->sub[0].dval;
- double *disre_rm3tav = blk_disre->sub[1].dval;
- #endif
+ GMX_RELEASE_ASSERT(blk_disre != nullptr,
+ "Trying to dereference NULL blk_disre pointer");
+#if !GMX_DOUBLE
+ float* disre_rt = blk_disre->sub[0].fval;
+ float* disre_rm3tav = blk_disre->sub[1].fval;
+#else
+ double* disre_rt = blk_disre->sub[0].dval;
+ double* disre_rm3tav = blk_disre->sub[1].dval;
+#endif
print_time(out_disre, fr.t);
if (violaver == nullptr)
}
/* Subtract bounds from distances, to calculate violations */
- calc_violations(disre_rt, disre_rm3tav,
- nbounds, pair, bounds, violaver, &sumt, &sumaver);
+ calc_violations(disre_rt, disre_rm3tav, nbounds, pair, bounds, violaver,
+ &sumt, &sumaver);
fprintf(out_disre, " %8.4f %8.4f\n", sumaver, sumt);
if (bDRAll)
*******************************************/
else
{
- t_enxblock *blk = find_block_id_enxframe(&fr, enx_i, nullptr);
+ t_enxblock* blk = find_block_id_enxframe(&fr, enx_i, nullptr);
if (bORIRE && blk)
{
if (blk->nsub != 1)
if (blk->sub[0].nr != nor)
{
- gmx_fatal(FARGS, "Number of orientation restraints in energy file (%d) does not match with the topology (%d)", blk->sub[0].nr, nor);
+ gmx_fatal(FARGS,
+ "Number of orientation restraints in energy file (%d) does "
+ "not match with the topology (%d)",
+ blk->sub[0].nr, nor);
}
if (bORA || bODA)
{
fprintf(fodt, " %10f", fr.t);
for (i = 0; i < norsel; i++)
{
- fprintf(fodt, " %g", blk_value(blk, 0, orsel[i])-oobs[orsel[i]]);
+ fprintf(fodt, " %g", blk_value(blk, 0, orsel[i]) - oobs[orsel[i]]);
}
fprintf(fodt, "\n");
}
gmx_fatal(FARGS, "Orientational restraints read in incorrectly");
}
- if (blk->sub[0].nr != nex*12)
+ if (blk->sub[0].nr != nex * 12)
{
- gmx_fatal(FARGS, "Number of orientation experiments in energy file (%d) does not match with the topology (%d)",
- blk->sub[0].nr/12, nex);
+ gmx_fatal(FARGS,
+ "Number of orientation experiments in energy file (%d) does "
+ "not match with the topology (%d)",
+ blk->sub[0].nr / 12, nex);
}
fprintf(foten, " %10f", fr.t);
for (i = 0; i < nex; i++)
{
for (j = 0; j < (bOvec ? 12 : 3); j++)
{
- fprintf(foten, " %g", blk_value(blk, 0, i*12+j));
+ fprintf(foten, " %g", blk_value(blk, 0, i * 12 + j));
}
}
fprintf(foten, "\n");
}
teller++;
}
- }
- while (bCont && (timecheck == 0));
+ } while (bCont && (timecheck == 0));
free_enxframe(&fr);
fprintf(stderr, "\n");
}
if (bORA)
{
- FILE *out = xvgropen(opt2fn("-ora", NFILE, fnm),
- "Average calculated orientations",
+ FILE* out = xvgropen(opt2fn("-ora", NFILE, fnm), "Average calculated orientations",
"Restraint label", "", oenv);
if (bOrinst && output_env_get_print_xvgr_codes(oenv))
{
}
for (i = 0; i < nor; i++)
{
- fprintf(out, "%5d %g\n", or_label[i], orient[i]/real(norfr));
+ fprintf(out, "%5d %g\n", or_label[i], orient[i] / real(norfr));
}
xvgrclose(out);
}
if (bODA)
{
- FILE *out = xvgropen(opt2fn("-oda", NFILE, fnm),
- "Average restraint deviation",
+ FILE* out = xvgropen(opt2fn("-oda", NFILE, fnm), "Average restraint deviation",
"Restraint label", "", oenv);
if (bOrinst && output_env_get_print_xvgr_codes(oenv))
{
}
for (i = 0; i < nor; i++)
{
- fprintf(out, "%5d %g\n", or_label[i], orient[i]/real(norfr)-oobs[i]);
+ fprintf(out, "%5d %g\n", or_label[i], orient[i] / real(norfr) - oobs[i]);
}
xvgrclose(out);
}
if (bODR)
{
- FILE *out = xvgropen(opt2fn("-odr", NFILE, fnm),
- "RMS orientation restraint deviations",
+ FILE* out = xvgropen(opt2fn("-odr", NFILE, fnm), "RMS orientation restraint deviations",
"Restraint label", "", oenv);
if (bOrinst && output_env_get_print_xvgr_codes(oenv))
{
}
for (i = 0; i < nor; i++)
{
- fprintf(out, "%5d %g\n", or_label[i], std::sqrt(odrms[i]/real(norfr)));
+ fprintf(out, "%5d %g\n", or_label[i], std::sqrt(odrms[i] / real(norfr)));
}
xvgrclose(out);
}
if (bDisRe)
{
- analyse_disre(opt2fn("-viol", NFILE, fnm),
- teller_disre, violaver, bounds, index, pair, nbounds, oenv);
+ analyse_disre(opt2fn("-viol", NFILE, fnm), teller_disre, violaver, bounds, index, pair,
+ nbounds, oenv);
}
{
- const char *nxy = "-nxy";
+ const char* nxy = "-nxy";
do_view(oenv, opt2fn_null("-ora", NFILE, fnm), nxy);
do_view(oenv, opt2fn_null("-ort", NFILE, fnm), nxy);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff