/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <cmath>
+
#include <algorithm>
#include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "types/commrec.h"
-#include "gromacs/utility/smalloc.h"
-#include "vec.h"
-#include "copyrite.h"
#include "gromacs/fileio/tpxio.h"
-#include "readinp.h"
-#include "calcgrid.h"
-#include "checkpoint.h"
-#include "gmx_ana.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/main.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/calculate-ewald-splitting-coefficient.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
#include "gromacs/random/random.h"
-#include "physics.h"
-#include "mdatoms.h"
-#include "coulomb.h"
-#include "mtop_util.h"
-#include "network.h"
-#include "main.h"
-#include "macros.h"
-
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
-/* We use the same defines as in mvdata.c here */
+/* We use the same defines as in broadcaststructs.cpp here */
#define block_bc(cr, d) gmx_bcast( sizeof(d), &(d), (cr))
#define nblock_bc(cr, nr, d) gmx_bcast((nr)*sizeof((d)[0]), (d), (cr))
#define snew_bc(cr, d, nr) { if (!MASTER(cr)) {snew((d), (nr)); }}
{
tmp = m / K + i;
tmp *= 2.0*M_PI;
- nom += pow( tmp, -n );
+ nom += std::pow( tmp, -n );
}
for (i = SUMORDER; i > 0; i--)
{
tmp = m / K + i;
tmp *= 2.0*M_PI;
- nom += pow( tmp, -n );
+ nom += std::pow( tmp, -n );
}
tmp = m / K;
tmp *= 2.0*M_PI;
- denom = pow( tmp, -n )+nom;
+ denom = std::pow( tmp, -n )+nom;
return -nom/denom;
{
tmp = m / K + i;
tmp *= 2.0*M_PI;
- nom += pow( tmp, -2*n );
+ nom += std::pow( tmp, -2*n );
}
for (i = SUMORDER; i > 0; i--)
{
tmp = m / K + i;
tmp *= 2.0*M_PI;
- nom += pow( tmp, -2*n );
+ nom += std::pow( tmp, -2*n );
}
for (i = -SUMORDER; i < SUMORDER+1; i++)
{
tmp = m / K + i;
tmp *= 2.0*M_PI;
- denom += pow( tmp, -n );
+ denom += std::pow( tmp, -n );
}
tmp = eps_poly1(m, K, n);
return nom / denom / denom + tmp*tmp;
{
tmp = m / K + i;
tmp *= 2.0*M_PI;
- nom += i * pow( tmp, -2*n );
+ nom += i * std::pow( tmp, -2*n );
}
for (i = SUMORDER; i > 0; i--)
{
tmp = m / K + i;
tmp *= 2.0*M_PI;
- nom += i * pow( tmp, -2*n );
+ nom += i * std::pow( tmp, -2*n );
}
for (i = -SUMORDER; i < SUMORDER+1; i++)
{
tmp = m / K + i;
tmp *= 2.0*M_PI;
- denom += pow( tmp, -n );
+ denom += std::pow( tmp, -n );
}
return 2.0 * M_PI * nom / denom / denom;
{
tmp = m / K + i;
tmp *= 2.0*M_PI;
- nom += i * i * pow( tmp, -2*n );
+ nom += i * i * std::pow( tmp, -2*n );
}
for (i = SUMORDER; i > 0; i--)
{
tmp = m / K + i;
tmp *= 2.0*M_PI;
- nom += i * i * pow( tmp, -2*n );
+ nom += i * i * std::pow( tmp, -2*n );
}
for (i = -SUMORDER; i < SUMORDER+1; i++)
{
tmp = m / K + i;
tmp *= 2.0*M_PI;
- denom += pow( tmp, -n );
+ denom += std::pow( tmp, -n );
}
return 4.0 * M_PI * M_PI * nom / denom / denom;
for (i = -SUMORDER; i < 0; i++)
{
- tmp = -sin(2.0 * M_PI * i * K * rcoord);
+ tmp = -std::sin(2.0 * M_PI * i * K * rcoord);
tmp1 = 2.0 * M_PI * m / K + 2.0 * M_PI * i;
- tmp2 = pow(tmp1, -n);
+ tmp2 = std::pow(tmp1, -n);
nom += tmp * tmp2 * i;
denom += tmp2;
}
for (i = SUMORDER; i > 0; i--)
{
- tmp = -sin(2.0 * M_PI * i * K * rcoord);
+ tmp = -std::sin(2.0 * M_PI * i * K * rcoord);
tmp1 = 2.0 * M_PI * m / K + 2.0 * M_PI * i;
- tmp2 = pow(tmp1, -n);
+ tmp2 = std::pow(tmp1, -n);
nom += tmp * tmp2 * i;
denom += tmp2;
}
xtot = stopglobal*2+1;
if (PAR(cr))
{
- x_per_core = static_cast<int>(ceil(static_cast<real>(xtot) / cr->nnodes));
+ x_per_core = static_cast<int>(std::ceil(static_cast<real>(xtot) / cr->nnodes));
startlocal = startglobal + x_per_core*cr->nodeid;
stoplocal = startlocal + x_per_core -1;
if (stoplocal > stopglobal)
svmul(nz, info->recipbox[ZZ], tmpvec);
rvec_add(gridpxy, tmpvec, gridp);
tmp = norm2(gridp);
- coeff = exp(-1.0 * M_PI * M_PI * tmp / info->ewald_beta[0] / info->ewald_beta[0] );
+ coeff = std::exp(-1.0 * M_PI * M_PI * tmp / info->ewald_beta[0] / info->ewald_beta[0] );
coeff /= 2.0 * M_PI * info->volume * tmp;
coeff2 = tmp;
/* Here xtot is the number of samples taken for the Monte Carlo calculation
* of the average of term IV of equation 35 in Wang2010. Round up to a
* number of samples that is divisible by the number of nodes */
- x_per_core = static_cast<int>(ceil(info->fracself * nr / cr->nnodes));
+ x_per_core = static_cast<int>(std::ceil(info->fracself * nr / cr->nnodes));
xtot = x_per_core * cr->nnodes;
}
else
{
/* In this case we use all nr particle positions */
xtot = nr;
- x_per_core = static_cast<int>(ceil(static_cast<real>(xtot) / cr->nnodes));
+ x_per_core = static_cast<int>(std::ceil(static_cast<real>(xtot) / cr->nnodes));
}
startlocal = x_per_core * cr->nodeid;
{
for (i = 0; i < xtot; i++)
{
- numbers[i] = static_cast<int>(floor(gmx_rng_uniform_real(rng) * nr));
+ numbers[i] = static_cast<int>(std::floor(gmx_rng_uniform_real(rng) * nr));
}
}
/* Broadcast the random number array to the other nodes */
svmul(nz, info->recipbox[ZZ], tmpvec);
rvec_add(gridpxy, tmpvec, gridp);
tmp = norm2(gridp);
- coeff = exp(-1.0 * M_PI * M_PI * tmp / info->ewald_beta[0] / info->ewald_beta[0] );
+ coeff = std::exp(-1.0 * M_PI * M_PI * tmp / info->ewald_beta[0] / info->ewald_beta[0] );
coeff /= tmp;
e_rec3x += coeff*eps_self(nx, info->nkx[0], info->recipbox[XX], info->pme_order[0], x[ci]);
e_rec3y += coeff*eps_self(ny, info->nky[0], info->recipbox[YY], info->pme_order[0], x[ci]);
e_rec2*= q2_all / M_PI / M_PI / info->volume / info->volume / nr ;
e_rec3/= M_PI * M_PI * info->volume * info->volume * nr ;
*/
- e_rec = sqrt(e_rec1+e_rec2+e_rec3);
+ e_rec = std::sqrt(e_rec1+e_rec2+e_rec3);
return ONE_4PI_EPS0 * e_rec;
edir = info->e_dir[0];
erec = info->e_rec[0];
derr = edir-erec;
- while (fabs(derr/std::min(erec, edir)) > 1e-4)
+ while (std::abs(derr/std::min(erec, edir)) > 1e-4)
{
beta = info->ewald_beta[0];
if (MASTER(cr))
{
i++;
- fprintf(stderr, "difference between real and rec. space error (step %d): %g\n", i, fabs(derr));
+ fprintf(stderr, "difference between real and rec. space error (step %d): %g\n", i, std::abs(derr));
fprintf(stderr, "old beta: %f\n", beta0);
fprintf(stderr, "new beta: %f\n", beta);
}
static t_filenm fnm[] = {
- { efTPX, "-s", NULL, ffREAD },
+ { efTPR, "-s", NULL, ffREAD },
{ efOUT, "-o", "error", ffWRITE },
- { efTPX, "-so", "tuned", ffOPTWR }
+ { efTPR, "-so", "tuned", ffOPTWR }
};
output_env_t oenv = NULL;
t_pargs pa[] = {
{ "-beta", FALSE, etREAL, {&user_beta},
- "If positive, overwrite ewald_beta from [TT].tpr[tt] file with this value" },
+ "If positive, overwrite ewald_beta from [REF].tpr[ref] file with this value" },
{ "-tune", FALSE, etBOOL, {&bTUNE},
"Tune the splitting parameter such that the error is equally distributed between real and reciprocal space" },
{ "-self", FALSE, etREAL, {&fracself},
#define NFILE asize(fnm)
cr = init_commrec();
-#ifdef GMX_LIB_MPI
- MPI_Barrier(MPI_COMM_WORLD);
-#endif
PCA_Flags = PCA_NOEXIT_ON_ARGS;
- PCA_Flags |= (MASTER(cr) ? 0 : PCA_QUIET);
if (!parse_common_args(&argc, argv, PCA_Flags,
NFILE, fnm, asize(pa), pa, asize(desc), desc,
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff