-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
+ * Copyright (c) 2012,2013,2014, 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.
*
- * This source code is part of
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
*
- * G R O M A C S
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
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+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
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*
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
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- *
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- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
+ * To help us fund GROMACS development, we humbly ask that you cite
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/pbcutil/ishift.h"
#include "nbnxn_kernel_common.h"
static void
-clear_f_all(const nbnxn_atomdata_t *nbat,real *f)
+clear_f_all(const nbnxn_atomdata_t *nbat, real *f)
{
int i;
- for(i=0; i<nbat->natoms*nbat->fstride; i++)
+ for (i = 0; i < nbat->natoms*nbat->fstride; i++)
{
f[i] = 0;
}
}
static void
-clear_f_flagged(const nbnxn_atomdata_t *nbat,int output_index,real *f)
+clear_f_flagged(const nbnxn_atomdata_t *nbat, int output_index, real *f)
{
const nbnxn_buffer_flags_t *flags;
- unsigned our_flag;
- int g,b,a0,a1,i;
+ unsigned our_flag;
+ int g, b, a0, a1, i;
flags = &nbat->buffer_flags;
our_flag = (1U << output_index);
- for(b=0; b<flags->nflag; b++)
+ for (b = 0; b < flags->nflag; b++)
{
if (flags->flag[b] & our_flag)
{
a0 = b*NBNXN_BUFFERFLAG_SIZE;
a1 = a0 + NBNXN_BUFFERFLAG_SIZE;
- for(i=a0*nbat->fstride; i<a1*nbat->fstride; i++)
+ for (i = a0*nbat->fstride; i < a1*nbat->fstride; i++)
{
f[i] = 0;
}
}
void
-clear_f(const nbnxn_atomdata_t *nbat,int output_index,real *f)
+clear_f(const nbnxn_atomdata_t *nbat, int output_index, real *f)
{
if (nbat->bUseBufferFlags)
{
{
int i;
- for(i=0; i<SHIFTS*DIM; i++)
+ for (i = 0; i < SHIFTS*DIM; i++)
{
fshift[i] = 0;
}
void
reduce_energies_over_lists(const nbnxn_atomdata_t *nbat,
- int nlist,
+ int nlist,
real *Vvdw,
real *Vc)
{
int nb;
- int i,j,ind,indr;
+ int i, j, ind, indr;
- for(nb=0; nb<nlist; nb++)
+ for (nb = 0; nb < nlist; nb++)
{
- for(i=0; i<nbat->nenergrp; i++)
+ for (i = 0; i < nbat->nenergrp; i++)
{
/* Reduce the diagonal terms */
- ind = i*nbat->nenergrp + i;
+ ind = i*nbat->nenergrp + i;
Vvdw[ind] += nbat->out[nb].Vvdw[ind];
Vc[ind] += nbat->out[nb].Vc[ind];
/* Reduce the off-diagonal terms */
- for(j=i+1; j<nbat->nenergrp; j++)
+ for (j = i+1; j < nbat->nenergrp; j++)
{
/* The output should contain only one off-diagonal part */
- ind = i*nbat->nenergrp + j;
- indr = j*nbat->nenergrp + i;
+ ind = i*nbat->nenergrp + j;
+ indr = j*nbat->nenergrp + i;
Vvdw[ind] += nbat->out[nb].Vvdw[ind] + nbat->out[nb].Vvdw[indr];
Vc[ind] += nbat->out[nb].Vc[ind] + nbat->out[nb].Vc[indr];
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff