/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2012,2014, 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.
+ *
+ * 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.
- *
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
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- * files - if they are missing, get the official version at www.gromacs.org.
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+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
* To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
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*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <stdio.h>
#include <stdlib.h>
-#include "typedefs.h"
-#include "network.h"
-#include "vec.h"
-#include "gmx_fatal.h"
-#include "physics.h"
-#include "main.h"
-#include "calcmu.h"
-void calc_mu(int start,int homenr,rvec x[],real q[],real qB[],
- int nChargePerturbed,
- dvec mu,dvec mu_B)
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+
+void calc_mu(int start, int homenr, rvec x[], real q[], real qB[],
+ int nChargePerturbed,
+ dvec mu, dvec mu_B)
{
- int i,end,m;
-
- end = start + homenr;
-
- clear_dvec(mu);
- for(i=start; (i<end); i++)
- for(m=0; (m<DIM); m++)
- mu[m] += q[i]*x[i][m];
-
- for(m=0; (m<DIM); m++)
- mu[m] *= ENM2DEBYE;
-
- if (nChargePerturbed) {
- clear_dvec(mu_B);
- for(i=start; (i<end); i++)
- for(m=0; (m<DIM); m++)
- mu_B[m] += qB[i]*x[i][m];
-
- for(m=0; (m<DIM); m++)
- mu_B[m] *= ENM2DEBYE;
- } else {
- copy_dvec(mu,mu_B);
- }
+ int i, end, m;
+ double mu_x, mu_y, mu_z;
+
+ end = start + homenr;
+
+ mu_x = mu_y = mu_z = 0.0;
+#pragma omp parallel for reduction(+: mu_x, mu_y, mu_z) schedule(static) \
+ num_threads(gmx_omp_nthreads_get(emntDefault))
+ for (i = start; i < end; i++)
+ {
+ mu_x += q[i]*x[i][XX];
+ mu_y += q[i]*x[i][YY];
+ mu_z += q[i]*x[i][ZZ];
+ }
+ mu[XX] = mu_x;
+ mu[YY] = mu_y;
+ mu[ZZ] = mu_z;
+
+ for (m = 0; (m < DIM); m++)
+ {
+ mu[m] *= ENM2DEBYE;
+ }
+
+ if (nChargePerturbed)
+ {
+ mu_x = mu_y = mu_z = 0.0;
+#pragma omp parallel for reduction(+: mu_x, mu_y, mu_z) schedule(static) \
+ num_threads(gmx_omp_nthreads_get(emntDefault))
+ for (i = start; i < end; i++)
+ {
+ mu_x += qB[i]*x[i][XX];
+ mu_y += qB[i]*x[i][YY];
+ mu_z += qB[i]*x[i][ZZ];
+ }
+ mu_B[XX] = mu_x * ENM2DEBYE;
+ mu_B[YY] = mu_y * ENM2DEBYE;
+ mu_B[ZZ] = mu_z * ENM2DEBYE;
+ }
+ else
+ {
+ copy_dvec(mu, mu_B);
+ }
}
-gmx_bool read_mu(FILE *fp,rvec mu,real *vol)
+gmx_bool read_mu(FILE *fp, rvec mu, real *vol)
{
- /* For backward compatibility */
- real mmm[4];
-
- if (fread(mmm,(size_t)(4*sizeof(real)),1,fp) != 1)
- return FALSE;
-
- copy_rvec(mmm,mu);
- *vol = mmm[3];
-
- return TRUE;
-}
+ /* For backward compatibility */
+ real mmm[4];
+
+ if (fread(mmm, (size_t)(4*sizeof(real)), 1, fp) != 1)
+ {
+ return FALSE;
+ }
+ copy_rvec(mmm, mu);
+ *vol = mmm[3];
+
+ return TRUE;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff