*/
#include "gmxpre.h"
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/matio.h"
void print_minimum(FILE *fp, int num, const t_minimum *min)
{
fprintf(fp,
- "Minimum %d at index " "%"GMX_PRId64 " energy %10.3f\n",
+ "Minimum %d at index " "%" GMX_PRId64 " energy %10.3f\n",
num, min->index, min->ener);
}
real **PP, *W, *E, **WW, **EE, *S, **SS, *M, *bE;
rvec xxx;
char *buf;
- double *bfac, efac, bref, Pmax, Wmin, Wmax, Winf, Emin, Emax, Einf, Smin, Smax, Sinf, Mmin, Mmax;
+ double *bfac, efac, bref, Pmax, Wmin, Wmax, Winf, Emin, Emax, Einf, Smin, Smax, Sinf;
real *delta;
- int i, j, k, imin, len, index, d, *nbin, *bindex, bi;
+ int i, j, k, imin, len, index, *nbin, *bindex, bi;
int *nxyz, maxbox;
t_blocka *b;
gmx_bool bOutside;
min_eig[i] = max_eig[i] = eig[i][0];
for (j = 0; (j < n); j++)
{
- min_eig[i] = min(min_eig[i], eig[i][j]);
- max_eig[i] = max(max_eig[i], eig[i][j]);
+ min_eig[i] = std::min(min_eig[i], eig[i][j]);
+ max_eig[i] = std::max(max_eig[i], eig[i][j]);
delta[i] = (max_eig[i]-min_eig[i])/(2.0*ibox[i]);
}
/* Add some extra space, half a bin on each side, unless the
{
bE[j] = (bref - 1/(BOLTZ*enerT[1][j]))*enerT[0][j];
}
- Emin = min(Emin, bE[j]);
+ Emin = std::min(Emin, static_cast<double>(bE[j]));
}
}
else
bOutside = FALSE;
for (i = 0; (i < neig); i++)
{
- nxyz[i] = bfac[i]*(eig[i][j]-min_eig[i]);
+ nxyz[i] = static_cast<int>(bfac[i]*(eig[i][j]-min_eig[i]));
if (nxyz[i] < 0 || nxyz[i] >= ibox[i])
{
bOutside = TRUE;
/* Compute the exponential factor */
if (enerT)
{
- efac = exp(-bE[j]+Emin);
+ efac = std::exp(-bE[j]+Emin);
}
else
{
}
else if (idim[i] == -1)
{
- efac /= sin(DEG2RAD*eig[i][j]);
+ efac /= std::sin(DEG2RAD*eig[i][j]);
}
}
/* Update the probability */
{
if (P[i] != 0)
{
- Pmax = max(P[i], Pmax);
- W[i] = -BOLTZ*Tref*log(P[i]);
+ Pmax = std::max(P[i], Pmax);
+ W[i] = -BOLTZ*Tref*std::log(P[i]);
if (W[i] < Wmin)
{
Wmin = W[i];
imin = i;
}
- Emin = min(E[i], Emin);
- Emax = max(E[i], Emax);
- Wmax = max(W[i], Wmax);
+ Emin = std::min(static_cast<double>(E[i]), Emin);
+ Emax = std::max(static_cast<double>(E[i]), Emax);
+ Wmax = std::max(static_cast<double>(W[i]), Wmax);
}
}
if (pmax > 0)
snew(axis_x, ibox[0]+1);
snew(axis_y, ibox[1]+1);
snew(axis_z, ibox[2]+1);
- maxbox = max(ibox[0], max(ibox[1], ibox[2]));
+ maxbox = std::max(ibox[0], std::max(ibox[1], ibox[2]));
snew(PP, maxbox*maxbox);
snew(WW, maxbox*maxbox);
snew(EE, maxbox*maxbox);
snew(SS, maxbox*maxbox);
- for (i = 0; (i < min(neig, 3)); i++)
+ for (i = 0; (i < std::min(neig, 3)); i++)
{
switch (i)
{
WW[i][j] = W[index3(ibox, i, j, nxyz[ZZ])];
}
}
- snew(buf, strlen(xpm)+4);
+ snew(buf, std::strlen(xpm)+4);
sprintf(buf, "%s", xpm);
- sprintf(&buf[strlen(xpm)-4], "12.xpm");
+ sprintf(&buf[std::strlen(xpm)-4], "12.xpm");
fp = gmx_ffopen(buf, "w");
write_xpm(fp, flags, "Gibbs Energy Landscape", "W (kJ/mol)", "PC1", "PC2",
ibox[0], ibox[1], axis_x, axis_y, WW, 0, gmax, rlo, rhi, &nlevels);
WW[i][j] = W[index3(ibox, i, nxyz[YY], j)];
}
}
- sprintf(&buf[strlen(xpm)-4], "13.xpm");
+ sprintf(&buf[std::strlen(xpm)-4], "13.xpm");
fp = gmx_ffopen(buf, "w");
write_xpm(fp, flags, "SHAM Energy Landscape", "kJ/mol", "PC1", "PC3",
ibox[0], ibox[2], axis_x, axis_z, WW, 0, gmax, rlo, rhi, &nlevels);
WW[i][j] = W[index3(ibox, nxyz[XX], i, j)];
}
}
- sprintf(&buf[strlen(xpm)-4], "23.xpm");
+ sprintf(&buf[std::strlen(xpm)-4], "23.xpm");
fp = gmx_ffopen(buf, "w");
write_xpm(fp, flags, "SHAM Energy Landscape", "kJ/mol", "PC2", "PC3",
ibox[1], ibox[2], axis_y, axis_z, WW, 0, gmax, rlo, rhi, &nlevels);
T[nbin] = enerT[1][j];
nbin++;
}
- bmin = min(enerT[0][j], bmin);
- bmax = max(enerT[0][j], bmax);
+ bmin = std::min(enerT[0][j], bmin);
+ bmax = std::max(enerT[0][j], bmax);
}
bwidth = 1.0;
- blength = (bmax - bmin)/bwidth + 2;
+ blength = static_cast<int>((bmax - bmin)/bwidth + 2);
snew(histo, nbin);
for (i = 0; (i < nbin); i++)
{
}
for (j = 0; (j < n); j++)
{
- k = (enerT[0][j]-bmin)/bwidth;
+ k = static_cast<int>((enerT[0][j]-bmin)/bwidth);
histo[bindex[j]][k]++;
}
fp = xvgropen(fh, "Energy distribution", "E (kJ/mol)", "", oenv);
"is the natural quantity to use, as it will produce bins of the same",
"volume."
};
- static real tb = -1, te = -1, frac = 0.5, filtlen = 0;
- static gmx_bool bHaveT = TRUE, bDer = FALSE, bSubAv = TRUE, bAverCorr = FALSE, bXYdy = FALSE;
- static gmx_bool bEESEF = FALSE, bEENLC = FALSE, bEeFitAc = FALSE, bPower = FALSE;
- static gmx_bool bShamEner = TRUE, bSham = TRUE;
+ static real tb = -1, te = -1;
+ static gmx_bool bHaveT = TRUE, bDer = FALSE;
+ static gmx_bool bSham = TRUE;
static real Tref = 298.15, pmin = 0, ttol = 0, pmax = 0, gmax = 0, emin = 0, emax = 0;
static rvec nrdim = {1, 1, 1};
static rvec nrbox = {32, 32, 32};
static rvec xmin = {0, 0, 0}, xmax = {1, 1, 1};
- static int nsets_in = 1, nb_min = 4, resol = 10, nlevels = 25;
+ static int nsets_in = 1, nlevels = 25;
t_pargs pa[] = {
{ "-time", FALSE, etBOOL, {&bHaveT},
"Expect a time in the input" },
};
#define NPA asize(pa)
- FILE *out;
- int n, e_n, nlast, s, nset, e_nset, d_nset, i, j = 0, *idim, *ibox;
- real **val, **et_val, *t, *e_t, e_dt, d_dt, dt, tot, error;
+ int n, e_n, nset, e_nset = 0, i, *idim, *ibox;
+ real **val, **et_val, *t, *e_t, e_dt, dt;
real *rmin, *rmax;
- double *av, *sig, cum1, cum2, cum3, cum4, db;
const char *fn_ge, *fn_ene;
output_env_t oenv;
gmx_int64_t num_grid_points;
ehisto(opt2fn("-histo", NFILE, fnm), e_n, et_val, oenv);
}
- snew(idim, max(3, nset));
- snew(ibox, max(3, nset));
- snew(rmin, max(3, nset));
- snew(rmax, max(3, nset));
- for (i = 0; (i < min(3, nset)); i++)
+ snew(idim, std::max(3, nset));
+ snew(ibox, std::max(3, nset));
+ snew(rmin, std::max(3, nset));
+ snew(rmax, std::max(3, nset));
+ for (i = 0; (i < std::min(3, nset)); i++)
{
- idim[i] = nrdim[i];
- ibox[i] = nrbox[i];
+ idim[i] = static_cast<int>(nrdim[i]);
+ ibox[i] = static_cast<int>(nrbox[i]);
rmin[i] = xmin[i];
rmax[i] = xmax[i];
}
for (; (i < nset); i++)
{
- idim[i] = nrdim[2];
- ibox[i] = nrbox[2];
+ idim[i] = static_cast<int>(nrdim[2]);
+ ibox[i] = static_cast<int>(nrbox[2]);
rmin[i] = xmin[2];
rmax[i] = xmax[2];
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff