/*
- *
- * 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) 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
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* of the License, or (at your option) any later version.
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+ * in the README & COPYING files - if they are missing, get the
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+ *
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*/
#ifndef _ns_h
#define _ns_h
#include <stdio.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "pbc.h"
-#include "tgroup.h"
-#include "network.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
#ifdef __cplusplus
extern "C" {
*
****************************************************/
-void init_neighbor_list(FILE *log,t_forcerec *fr,int homenr);
-/*
+void init_neighbor_list(FILE *log, t_forcerec *fr, int homenr);
+/*
* nn is the number of energy terms in the energy matrix
* (ngener*(ngener-1))/2
* start is the first atom on this processor
* homenr is the number of atoms on this processor
*/
-
-int calc_naaj(int icg,int cgtot);
+
+int calc_naaj(int icg, int cgtot);
/* Calculate the number of charge groups to interact with for icg */
/****************************************************
* Calls either ns5_core (when grid selected in .mdp file)
* or ns_simple_core (when simple selected in .mdp file)
*
- * Return total number of pairs searched
+ * Return total number of pairs searched
*
****************************************************/
-void init_ns(FILE *fplog,const t_commrec *cr,
- gmx_ns_t *ns,t_forcerec *fr,
- const gmx_mtop_t *mtop,
- matrix box);
-
-int search_neighbours(FILE *log,t_forcerec *fr,
- rvec x[],matrix box,
- gmx_localtop_t *top,
- gmx_groups_t *groups,
- t_commrec *cr,
- t_nrnb *nrnb,t_mdatoms *md,
- real *lambda,real *dvdlambda,
- gmx_grppairener_t *grppener,
- gmx_bool bFillGrid,
- gmx_bool bDoLongRangeNS,
- gmx_bool bPadListsForKernels);
-
+void init_ns(FILE *fplog, const t_commrec *cr,
+ gmx_ns_t *ns, t_forcerec *fr,
+ const gmx_mtop_t *mtop);
+
+int search_neighbours(FILE *log, t_forcerec *fr, matrix box,
+ gmx_localtop_t *top,
+ gmx_groups_t *groups,
+ t_commrec *cr,
+ t_nrnb *nrnb, t_mdatoms *md,
+ gmx_bool bFillGrid,
+ gmx_bool bDoLongRangeNS);
+
/* Debugging routines from wnblist.c */
-void dump_nblist(FILE *out,t_commrec *cr,t_forcerec *fr,int nDNL);
+void dump_nblist(FILE *out, t_commrec *cr, t_forcerec *fr, int nDNL);
-int read_nblist(FILE *in,FILE *out,int **mat,int natoms,gmx_bool bSymm);
+int read_nblist(FILE *in, FILE *out, int **mat, int natoms, gmx_bool bSymm);
/* Returns total number of neighbors. If bSymm the matrix is symmetrized. */
-int natoms_beyond_ns_buffer(t_inputrec *ir,t_forcerec *fr,t_block *cgs,
- matrix scale_tot,rvec *x);
+int natoms_beyond_ns_buffer(t_inputrec *ir, t_forcerec *fr, t_block *cgs,
+ matrix scale_tot, rvec *x);
/* Returns the number of atoms that moved beyond the ns buffer */
+void reallocate_nblist(t_nblist *nl);
+/* List reallocation, only exported for Verlet scheme use with FEP */
+
#ifdef __cplusplus
}
#endif
-#endif /* _ns_h */
+#endif /* _ns_h */
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