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Merge branch 'master' into pygromacs
[alexxy/gromacs.git]
/
src
/
gromacs
/
gmxana
/
gmx_dipoles.cpp
diff --git
a/src/gromacs/gmxana/gmx_dipoles.cpp
b/src/gromacs/gmxana/gmx_dipoles.cpp
index a173e8291d9f833f5a40b56d5bf3b165b1bfad96..3b5f3b4356ce15db08d16d7c30fc028177c11905 100644
(file)
--- a/
src/gromacs/gmxana/gmx_dipoles.cpp
+++ b/
src/gromacs/gmxana/gmx_dipoles.cpp
@@
-36,8
+36,8
@@
*/
#include "gmxpre.h"
*/
#include "gmxpre.h"
-#include <
math.
h>
-#include <
string.h
>
+#include <
cmat
h>
+#include <
cstring
>
#include <algorithm>
#include <algorithm>
@@
-145,7
+145,7
@@
static void add2gkr(t_gkrbin *gb, real r, real cosa, real phi)
}
if (index < gb->nx)
{
}
if (index < gb->nx)
{
- alpha = acos(cosa);
+ alpha =
std::
acos(cosa);
if (gb->bPhi)
{
cy = static_cast<int>((M_PI+phi)*gb->ny/(2*M_PI));
if (gb->bPhi)
{
cy = static_cast<int>((M_PI+phi)*gb->ny/(2*M_PI));
@@
-166,9
+166,9
@@
static void add2gkr(t_gkrbin *gb, real r, real cosa, real phi)
static void rvec2sprvec(rvec dipcart, rvec dipsp)
{
clear_rvec(dipsp);
static void rvec2sprvec(rvec dipcart, rvec dipsp)
{
clear_rvec(dipsp);
- dipsp[0] = s
qrt(dipcart[XX]*dipcart[XX]+dipcart[YY]*dipcart[YY]+dipcart[ZZ]*dipcart[ZZ]);
/* R */
- dipsp[1] =
atan2(dipcart[YY], dipcart[XX]);
/* Theta */
- dipsp[2] =
atan2(sqrt(dipcart[XX]*dipcart[XX]+dipcart[YY]*dipcart[YY]), dipcart[ZZ]);
/* Phi */
+ dipsp[0] = s
td::sqrt(dipcart[XX]*dipcart[XX]+dipcart[YY]*dipcart[YY]+dipcart[ZZ]*dipcart[ZZ]);
/* R */
+ dipsp[1] =
std::atan2(dipcart[YY], dipcart[XX]);
/* Theta */
+ dipsp[2] =
std::atan2(std::sqrt(dipcart[XX]*dipcart[XX]+dipcart[YY]*dipcart[YY]), dipcart[ZZ]);
/* Phi */
}
}
@@
-206,7
+206,7
@@
void do_gkr(t_gkrbin *gb, int ncos, int *ngrp, int *molindex[],
qtot = 0;
for (j = j0; j < j1; j++)
{
qtot = 0;
for (j = j0; j < j1; j++)
{
- q =
f
abs(atom[j].q);
+ q =
std::
abs(atom[j].q);
qtot += q;
for (k = 0; k < DIM; k++)
{
qtot += q;
for (k = 0; k < DIM; k++)
{
@@
-247,7
+247,7
@@
void do_gkr(t_gkrbin *gb, int ncos, int *ngrp, int *molindex[],
phi = dih_angle(xi, xj, xk, xl, &pbc,
r_ij, r_kj, r_kl, mm, nn, /* out */
&sign, &t1, &t2, &t3);
phi = dih_angle(xi, xj, xk, xl, &pbc,
r_ij, r_kj, r_kl, mm, nn, /* out */
&sign, &t1, &t2, &t3);
- cosa = cos(phi);
+ cosa =
std::
cos(phi);
}
else
{
}
else
{
@@
-370,7
+370,7
@@
static void print_gkrbin(const char *fn, t_gkrbin *gb,
* Multiply by 2 because we only take half the matrix of interactions
* into account.
*/
* Multiply by 2 because we only take half the matrix of interactions
* into account.
*/
- fac = 2.0/(
(double) ngrp * (double)
nframes);
+ fac = 2.0/(
ngrp *
nframes);
x0 = 0;
for (i = 0; i < last; i++)
x0 = 0;
for (i = 0; i < last; i++)
@@
-457,7
+457,7
@@
static void neutralize_mols(int n, int *index, t_block *mols, t_atom *atom)
qtot += atom[a].q;
}
/* This check is only for the count print */
qtot += atom[a].q;
}
/* This check is only for the count print */
- if (
f
abs(qtot) > 0.01)
+ if (
std::
abs(qtot) > 0.01)
{
ncharged++;
}
{
ncharged++;
}
@@
-655,7
+655,7
@@
static void update_slab_dipoles(int k0, int k1, rvec x[], rvec mu,
xdim += x[k][idim];
}
xdim /= (k1-k0);
xdim += x[k][idim];
}
xdim /= (k1-k0);
- k = (
(int)
(xdim*nslice/box[idim][idim] + nslice)) % nslice;
+ k = (
static_cast<int>
(xdim*nslice/box[idim][idim] + nslice)) % nslice;
rvec_inc(slab_dipole[k], mu);
}
rvec_inc(slab_dipole[k], mu);
}
@@
-704,15
+704,15
@@
static void compute_avercos(int n, rvec dip[], real *dd, rvec axis, gmx_bool bPa
ddc1 = ddc2 = ddc3 = 0;
for (i = k = 0; (i < n); i++)
{
ddc1 = ddc2 = ddc3 = 0;
for (i = k = 0; (i < n); i++)
{
- ddc1 +=
f
abs(cos_angle(dip[i], xxx));
- ddc2 +=
f
abs(cos_angle(dip[i], yyy));
- ddc3 +=
f
abs(cos_angle(dip[i], zzz));
+ ddc1 +=
std::
abs(cos_angle(dip[i], xxx));
+ ddc2 +=
std::
abs(cos_angle(dip[i], yyy));
+ ddc3 +=
std::
abs(cos_angle(dip[i], zzz));
if (bPairs)
{
for (j = i+1; (j < n); j++, k++)
{
dc = cos_angle(dip[i], dip[j]);
if (bPairs)
{
for (j = i+1; (j < n); j++, k++)
{
dc = cos_angle(dip[i], dip[j]);
- d +=
f
abs(dc);
+ d +=
std::
abs(dc);
}
}
}
}
}
}
@@
-825,19
+825,19
@@
static void do_dip(t_topology *top, int ePBC, real volume,
/* Determine the indexes of the energy grps we need */
for (i = 0; (i < nre); i++)
{
/* Determine the indexes of the energy grps we need */
for (i = 0; (i < nre); i++)
{
- if (strstr(enm[i].name, "Volume"))
+ if (st
d::st
rstr(enm[i].name, "Volume"))
{
iVol = i;
}
{
iVol = i;
}
- else if (strstr(enm[i].name, "Mu-X"))
+ else if (st
d::st
rstr(enm[i].name, "Mu-X"))
{
iMu[XX] = i;
}
{
iMu[XX] = i;
}
- else if (strstr(enm[i].name, "Mu-Y"))
+ else if (st
d::st
rstr(enm[i].name, "Mu-Y"))
{
iMu[YY] = i;
}
{
iMu[YY] = i;
}
- else if (strstr(enm[i].name, "Mu-Z"))
+ else if (st
d::st
rstr(enm[i].name, "Mu-Z"))
{
iMu[ZZ] = i;
}
{
iMu[ZZ] = i;
}
@@
-1020,7
+1020,7
@@
static void do_dip(t_topology *top, int ePBC, real volume,
{
/* Use 0.7 iso 0.5 to account for pressure scaling */
/* rcut = 0.7*sqrt(max_cutoff2(box)); */
{
/* Use 0.7 iso 0.5 to account for pressure scaling */
/* rcut = 0.7*sqrt(max_cutoff2(box)); */
- rcut = 0.7*sqrt(sqr(box[XX][XX])+sqr(box[YY][YY])+sqr(box[ZZ][ZZ]));
+ rcut = 0.7*s
td::s
qrt(sqr(box[XX][XX])+sqr(box[YY][YY])+sqr(box[ZZ][ZZ]));
gkrbin = mk_gkrbin(rcut, rcmax, bPhi, ndegrees);
}
gkrbin = mk_gkrbin(rcut, rcmax, bPhi, ndegrees);
}
@@
-1113,12
+1113,12
@@
static void do_dip(t_topology *top, int ePBC, real volume,
M_av[m] += dipole[i][m]; /* M per frame */
mu_mol += dipole[i][m]*dipole[i][m]; /* calc. mu for distribution */
}
M_av[m] += dipole[i][m]; /* M per frame */
mu_mol += dipole[i][m]*dipole[i][m]; /* calc. mu for distribution */
}
- mu_mol = sqrt(mu_mol);
+ mu_mol = s
td::s
qrt(mu_mol);
mu_ave += mu_mol; /* calc. the average mu */
/* Update the dipole distribution */
mu_ave += mu_mol; /* calc. the average mu */
/* Update the dipole distribution */
- ibin =
(int)
(ndipbin*mu_mol/mu_max + 0.5);
+ ibin =
static_cast<int>
(ndipbin*mu_mol/mu_max + 0.5);
if (ibin < ndipbin)
{
dipole_bin[ibin]++;
if (ibin < ndipbin)
{
dipole_bin[ibin]++;
@@
-1207,9
+1207,9
@@
static void do_dip(t_topology *top, int ePBC, real volume,
if (cosaver)
{
compute_avercos(gnx_tot, dipole, &dd, dipaxis, bPairs);
if (cosaver)
{
compute_avercos(gnx_tot, dipole, &dd, dipaxis, bPairs);
- rms_cos = sqrt(sqr(dipaxis[XX]-0.5)+
- sqr(dipaxis[YY]-0.5)+
- sqr(dipaxis[ZZ]-0.5));
+ rms_cos = s
td::s
qrt(sqr(dipaxis[XX]-0.5)+
+
sqr(dipaxis[YY]-0.5)+
+
sqr(dipaxis[ZZ]-0.5));
if (bPairs)
{
fprintf(caver, "%10.3e %10.3e %10.3e %10.3e %10.3e %10.3e\n",
if (bPairs)
{
fprintf(caver, "%10.3e %10.3e %10.3e %10.3e %10.3e %10.3e\n",
@@
-1243,7
+1243,7
@@
static void do_dip(t_topology *top, int ePBC, real volume,
{
fprintf(outmtot, "%10g %12.8e %12.8e %12.8e %12.8e\n",
t, M_av[XX], M_av[YY], M_av[ZZ],
{
fprintf(outmtot, "%10g %12.8e %12.8e %12.8e %12.8e\n",
t, M_av[XX], M_av[YY], M_av[ZZ],
- sqrt(M_av2[XX]+M_av2[YY]+M_av2[ZZ]));
+ s
td::s
qrt(M_av2[XX]+M_av2[YY]+M_av2[ZZ]));
}
for (m = 0; (m < DIM); m++)
}
for (m = 0; (m < DIM); m++)
@@
-1398,7
+1398,7
@@
static void do_dip(t_topology *top, int ePBC, real volume,
{
do_autocorr(corf, oenv, "Dipole Autocorrelation Function",
teller, gnx_tot, muall, dt,
{
do_autocorr(corf, oenv, "Dipole Autocorrelation Function",
teller, gnx_tot, muall, dt,
- mode, strcmp(corrtype, "molsep"));
+ mode, st
d::st
rcmp(corrtype, "molsep"));
}
}
}
}
}
}
@@
-1456,7
+1456,7
@@
static void do_dip(t_topology *top, int ePBC, real volume,
for (i = 0; (i < ndipbin); i++)
{
fprintf(outdd, "%10g %10f\n",
for (i = 0; (i < ndipbin); i++)
{
fprintf(outdd, "%10g %10f\n",
- (i*mu_max)/ndipbin,
dipole_bin[i]/(double)
teller);
+ (i*mu_max)/ndipbin,
static_cast<real>(dipole_bin[i])/
teller);
}
xvgrclose(outdd);
sfree(dipole_bin);
}
xvgrclose(outdd);
sfree(dipole_bin);