-/* -*- 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.
*
- *
- * 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.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
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-
- * 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) 2012,2013,2014, 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
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+ * 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 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.
*
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- * GROwing Monsters And Cloning Shrimps
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "typedefs.h"
-#include "mdatoms.h"
-#include "smalloc.h"
-#include "main.h"
-#include "qmmm.h"
-#include "mtop_util.h"
-#include "gmx_omp_nthreads.h"
+#include "gmxpre.h"
+
+#include <math.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
#define ALMOST_ZERO 1e-30
{
md->nChargePerturbed++;
}
+ if (atom->typeB != atom->type)
+ {
+ md->nTypePerturbed++;
+ }
}
tmA += atom->m;
void atoms2md(gmx_mtop_t *mtop, t_inputrec *ir,
int nindex, int *index,
- int start, int homenr,
+ int homenr,
t_mdatoms *md)
{
+ gmx_bool bLJPME;
gmx_mtop_atomlookup_t alook;
int i;
t_grpopts *opts;
gmx_groups_t *groups;
gmx_molblock_t *molblock;
+ bLJPME = EVDW_PME(ir->vdwtype);
+
opts = &ir->opts;
groups = &mtop->groups;
molblock = mtop->molblock;
- /* Index==NULL indicates particle decomposition,
- * unless we have an empty DD node, so also check for homenr and start.
- * This should be signaled properly with an extra parameter or nindex==-1.
+ /* Index==NULL indicates no DD (unless we have a DD node with no
+ * atoms), so also check for homenr. This should be
+ * signaled properly with an extra parameter or nindex==-1.
*/
- if (index == NULL && (homenr > 0 || start > 0))
+ if (index == NULL && (homenr > 0))
{
md->nr = mtop->natoms;
}
srenew(md->massT, md->nalloc);
srenew(md->invmass, md->nalloc);
srenew(md->chargeA, md->nalloc);
+ if (bLJPME)
+ {
+ srenew(md->sqrt_c6A, md->nalloc);
+ srenew(md->sigmaA, md->nalloc);
+ srenew(md->sigma3A, md->nalloc);
+ }
if (md->nPerturbed)
{
srenew(md->chargeB, md->nalloc);
+ if (bLJPME)
+ {
+ srenew(md->sqrt_c6B, md->nalloc);
+ srenew(md->sigmaB, md->nalloc);
+ srenew(md->sigma3B, md->nalloc);
+ }
}
srenew(md->typeA, md->nalloc);
if (md->nPerturbed)
{
int g, ag, molb;
real mA, mB, fac;
+ real c6, c12;
t_atom *atom;
if (index == NULL)
{
md->invmass[i] = 1.0/mA;
}
- md->chargeA[i] = atom->q;
- md->typeA[i] = atom->type;
+ md->chargeA[i] = atom->q;
+ md->typeA[i] = atom->type;
+ if (bLJPME)
+ {
+ c6 = mtop->ffparams.iparams[atom->type*(mtop->ffparams.atnr+1)].lj.c6;
+ c12 = mtop->ffparams.iparams[atom->type*(mtop->ffparams.atnr+1)].lj.c12;
+ md->sqrt_c6A[i] = sqrt(c6);
+ if (c6 == 0.0 || c12 == 0)
+ {
+ md->sigmaA[i] = 1.0;
+ }
+ else
+ {
+ md->sigmaA[i] = pow(c12/c6, 1.0/6.0);
+ }
+ md->sigma3A[i] = 1/(md->sigmaA[i]*md->sigmaA[i]*md->sigmaA[i]);
+ }
if (md->nPerturbed)
{
+ md->bPerturbed[i] = PERTURBED(*atom);
md->chargeB[i] = atom->qB;
md->typeB[i] = atom->typeB;
- md->bPerturbed[i] = PERTURBED(*atom);
+ if (bLJPME)
+ {
+ c6 = mtop->ffparams.iparams[atom->typeB*(mtop->ffparams.atnr+1)].lj.c6;
+ c12 = mtop->ffparams.iparams[atom->typeB*(mtop->ffparams.atnr+1)].lj.c12;
+ md->sqrt_c6B[i] = sqrt(c6);
+ if (c6 == 0.0 || c12 == 0)
+ {
+ md->sigmaB[i] = 1.0;
+ }
+ else
+ {
+ md->sigmaB[i] = pow(c12/c6, 1.0/6.0);
+ }
+ md->sigma3B[i] = 1/(md->sigmaB[i]*md->sigmaB[i]*md->sigmaB[i]);
+ }
}
md->ptype[i] = atom->ptype;
if (md->cTC)
gmx_mtop_atomlookup_destroy(alook);
- md->start = start;
md->homenr = homenr;
md->lambda = 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff