-/* -*- 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) 2006,2007,2008,2009,2010,2011,2012,2013,2014, 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 file is part of Gromacs Copyright (c) 1991-2008
- * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
- *
- * 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
+ * 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.
*
- * To help us fund GROMACS development, we humbly ask that you cite
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+ * Lesser General Public License for more details.
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*
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+ * 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
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+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <string.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "domdec.h"
-#include "domdec_network.h"
-#include "names.h"
-#include "network.h"
-#include "vec.h"
-#include "pbc.h"
-#include "chargegroup.h"
-#include "gmx_random.h"
-#include "topsort.h"
-#include "mtop_util.h"
-#include "mshift.h"
-#include "vsite.h"
-#include "gmx_ga2la.h"
-#include "force.h"
-#include "gmx_omp_nthreads.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/domdec_network.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topsort.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* for dd_init_local_state */
#define NITEM_DD_INIT_LOCAL_STATE 5
void dd_make_reverse_top(FILE *fplog,
gmx_domdec_t *dd, gmx_mtop_t *mtop,
- gmx_vsite_t *vsite, gmx_constr_t constr,
+ gmx_vsite_t *vsite,
t_inputrec *ir, gmx_bool bBCheck)
{
int mb, n_recursive_vsite, nexcl, nexcl_icg, a;
if (dd->bInterCGcons || dd->bInterCGsettles)
{
- init_domdec_constraints(dd, mtop, constr);
+ init_domdec_constraints(dd, mtop);
}
if (fplog)
{
}
}
-static inline void add_ifunc(int nral, t_iatom *tiatoms, t_ilist *il)
+static gmx_inline void add_ifunc(int nral, t_iatom *tiatoms, t_ilist *il)
{
t_iatom *liatoms;
int k;
real rc2,
int *la2lc, t_pbc *pbc_null, rvec *cg_cm,
const t_iparams *ip_in,
- t_idef *idef, gmx_vsite_t *vsite,
+ t_idef *idef,
int **vsite_pbc,
int *vsite_pbc_nalloc,
int iz, int nzone,
bRCheckMB, rcheck, bRCheck2B, rc2,
la2lc, pbc_null, cg_cm, idef->iparams,
idef_t,
- vsite, vsite_pbc, vsite_pbc_nalloc,
+ vsite_pbc, vsite_pbc_nalloc,
iz, zones->n,
dd->cgindex[cg0t], dd->cgindex[cg1t]);
lcgs->index = dd->cgindex;
}
-void dd_make_local_top(FILE *fplog,
- gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
+void dd_make_local_top(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
int npbcdim, matrix box,
rvec cellsize_min, ivec npulse,
t_forcerec *fr,
{
dd->nbonded_local += nexcl;
- forcerec_set_excl_load(fr, ltop, NULL);
+ forcerec_set_excl_load(fr, ltop);
}
ltop->atomtypes = mtop->atomtypes;
init_state(state_local, 0, buf[1], buf[2], buf[3], buf[4]);
state_local->flags = buf[0];
-
- /* With Langevin Dynamics we need to make proper storage space
- * in the global and local state for the random numbers.
- */
- if (state_local->flags & (1<<estLD_RNG))
- {
- if (DDMASTER(dd) && state_global->nrngi > 1)
- {
- state_global->nrng = dd->nnodes*gmx_rng_n();
- srenew(state_global->ld_rng, state_global->nrng);
- }
- state_local->nrng = gmx_rng_n();
- snew(state_local->ld_rng, state_local->nrng);
- }
- if (state_local->flags & (1<<estLD_RNGI))
- {
- if (DDMASTER(dd) && state_global->nrngi > 1)
- {
- state_global->nrngi = dd->nnodes;
- srenew(state_global->ld_rngi, state_global->nrngi);
- }
- snew(state_local->ld_rngi, 1);
- }
}
static void check_link(t_blocka *link, int cg_gl, int cg_gl_j)
if (vsite)
{
- construct_vsites(NULL, vsite, xs, NULL, 0.0, NULL,
+ construct_vsites(vsite, xs, 0.0, NULL,
ffparams->iparams, molt->ilist,
- epbcNONE, TRUE, NULL, NULL, NULL);
+ epbcNONE, TRUE, NULL, NULL);
}
calc_cgcm(NULL, 0, molt->cgs.nr, &molt->cgs, xs, cg_cm);
}
void dd_bonded_cg_distance(FILE *fplog,
- gmx_domdec_t *dd, gmx_mtop_t *mtop,
+ gmx_mtop_t *mtop,
t_inputrec *ir, rvec *x, matrix box,
gmx_bool bBCheck,
real *r_2b, real *r_mb)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff