*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014, 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.
#include <string.h>
#include "typedefs.h"
#include "smalloc.h"
-#include "grompp.h"
+#include "grompp-impl.h"
#include "macros.h"
#include "toputil.h"
#include "hackblock.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _add_par_h
-#define _add_par_h
+#ifndef GMX_GMXPREPROCESS_ADD_PAR_H
+#define GMX_GMXPREPROCESS_ADD_PAR_H
#include "typedefs.h"
#include "pdb2top.h"
{
#endif
-extern void add_param(t_params *ps, int ai, int aj, real *c, char *s);
+void add_param(t_params *ps, int ai, int aj, real *c, char *s);
-extern void add_imp_param(t_params *ps, int ai, int aj, int ak, int al,
- real c0, real c1, char *s);
+void add_imp_param(t_params *ps, int ai, int aj, int ak, int al,
+ real c0, real c1, char *s);
-extern void add_dih_param(t_params *ps, int ai, int aj, int ak, int al,
- real c0, real c1, real c2, char *s);
+void add_dih_param(t_params *ps, int ai, int aj, int ak, int al,
+ real c0, real c1, real c2, char *s);
-extern void add_cmap_param(t_params *ps, int ai, int aj, int ak, int al, int am,
- char *s);
+void add_cmap_param(t_params *ps, int ai, int aj, int ak, int al, int am,
+ char *s);
-extern void add_vsite2_atoms(t_params *ps, int ai, int aj, int ak);
+void add_vsite2_atoms(t_params *ps, int ai, int aj, int ak);
-extern void add_vsite3_atoms(t_params *ps, int ai, int aj, int ak, int al,
- gmx_bool bSwapParity);
+void add_vsite3_atoms(t_params *ps, int ai, int aj, int ak, int al,
+ gmx_bool bSwapParity);
-extern void add_vsite2_param(t_params *ps, int ai, int aj, int ak, real c0);
+void add_vsite2_param(t_params *ps, int ai, int aj, int ak, real c0);
-extern void add_vsite3_param(t_params *ps, int ai, int aj, int ak, int al,
- real c0, real c1);
+void add_vsite3_param(t_params *ps, int ai, int aj, int ak, int al,
+ real c0, real c1);
-extern void add_vsite4_atoms(t_params *ps, int ai, int aj, int ak, int al,
- int am);
+void add_vsite4_atoms(t_params *ps, int ai, int aj, int ak, int al,
+ int am);
-extern int search_jtype(t_restp *rp, char *name, gmx_bool bFirstRes);
+int search_jtype(t_restp *rp, char *name, gmx_bool bFirstRes);
#ifdef __cplusplus
}
#endif
-#endif /* _add_par_h */
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _calc_verletbuf_h
-#define _calc_verletbuf_h
+#ifndef GMX_GMXPREPROCESS_CALC_VERLETBUF_H
+#define GMX_GMXPREPROCESS_CALC_VERLETBUF_H
#include "typedefs.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
typedef struct
{
int cluster_size_i; /* Cluster pair-list i-cluster size atom count */
int *n_nonlin_vsite,
real *rlist);
-#endif /* _calc_verletbuf_h */
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014, 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _compute_io_h
-#define _compute_io_h
+#ifndef GMX_GMXPREPROCESS_COMPUTE_IO_H
+#define GMX_GMXPREPROCESS_COMPUTE_IO_H
#include "typedefs.h"
-extern double compute_io(t_inputrec *ir, int natoms, gmx_groups_t *groups,
- int nrener, int nrepl);
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+double compute_io(t_inputrec *ir, int natoms, gmx_groups_t *groups,
+ int nrener, int nrepl);
/* Return total output to be written from this simulation. */
-#endif /* _compute_io_h */
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _convparm_h
-#define _convparm_h
+#ifndef GMX_GMXPREPROCESS_CONVPARM_H
+#define GMX_GMXPREPROCESS_CONVPARM_H
#include "typedefs.h"
-extern void convert_params(int atnr, t_params nbtypes[],
- t_molinfo *mi, int comb, double reppow, real fudgeQQ,
- gmx_mtop_t *mtop);
+#ifdef __cplusplus
+extern "C" {
+#endif
-#endif /* _convparm_h */
+void convert_params(int atnr, t_params nbtypes[],
+ t_molinfo *mi, int comb, double reppow, real fudgeQQ,
+ gmx_mtop_t *mtop);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _fflibutil_h
-#define _fflibutil_h
+#ifndef GMX_GMXPREPROCESS_FFLIBUTIL_H
+#define GMX_GMXPREPROCESS_FFLIBUTIL_H
#ifdef HAVE_CONFIG_H
#include <config.h>
extern "C" {
#endif
-extern const char *fflib_forcefield_dir_ext();
+const char *fflib_forcefield_dir_ext();
/* Returns the name of the force field directory extension */
-extern const char *fflib_forcefield_itp();
+const char *fflib_forcefield_itp();
/* Returns the name of the main forcefield itp file */
-extern const char *fflib_forcefield_doc();
+const char *fflib_forcefield_doc();
/* Returns the name of the forcefield documentation file */
-extern void fflib_filename_base(const char *filename, char *filebase, int maxlen);
+void fflib_filename_base(const char *filename, char *filebase, int maxlen);
/* Return the base file name of filename in base,
* i.e. remove path and extension, if present.
* base should be at least of size maxlen.
*/
-extern int fflib_search_file_end(const char *ffdir,
- const char *file_end,
- gmx_bool bFatalError,
- char ***filenames);
+int fflib_search_file_end(const char *ffdir,
+ const char *file_end,
+ gmx_bool bFatalError,
+ char ***filenames);
/* Search for files ending on file_end in the force field directory fflib.
* fflib should be in the GROMACS lib.path.
* Return the number of files and the file names in filenames.
*/
-extern int fflib_search_file_in_dirend(const char *filename, const char *dirend,
- char ***dirnames);
+int fflib_search_file_in_dirend(const char *filename, const char *dirend,
+ char ***dirnames);
/* Search for files with name filename in subdirectories with names
* ending on dirend.
* Return the number of files and the directory names in dirnames.
*/
-extern gmx_bool fflib_fexist(const char *file);
+gmx_bool fflib_fexist(const char *file);
/* Check if a file exists in the force field library */
-extern FILE *fflib_open(const char *file);
+FILE *fflib_open(const char *file);
/* Open force field library file "file" for reading.
* "file" should contain the whole path to the force field library,
* either absolute or relative to the current dir.
}
#endif
-#endif /* _fflibutil_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _gen_ad_h
-#define _gen_ad_h
+#ifndef GMX_GMXPREPROCESS_GEN_AD_H
+#define GMX_GMXPREPROCESS_GEN_AD_H
#include "typedefs.h"
#include "toputil.h"
}
#endif
-#endif /* _gen_ad_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _gen_vsite_h
-#define _gen_vsite_h
+#ifndef GMX_GMXPREPROCESS_GEN_VSITE_H
+#define GMX_GMXPREPROCESS_GEN_VSITE_H
#include "typedefs.h"
-#include "grompp.h"
+#include "grompp-impl.h"
#include "gpp_atomtype.h"
#include "hackblock.h"
/* stuff for pdb2gmx */
-extern void do_vsites(int nrtp, t_restp rtp[], gpp_atomtype_t atype,
- t_atoms *at, t_symtab *symtab, rvec *x[],
- t_params plist[], int *dummy_type[], int *cgnr[],
- real mHmult, gmx_bool bVSiteAromatics,
- const char *ffdir);
+void do_vsites(int nrtp, t_restp rtp[], gpp_atomtype_t atype,
+ t_atoms *at, t_symtab *symtab, rvec *x[],
+ t_params plist[], int *dummy_type[], int *cgnr[],
+ real mHmult, gmx_bool bVSiteAromatics,
+ const char *ffdir);
-extern void do_h_mass(t_params *psb, int vsite_type[], t_atoms *at, real mHmult,
- gmx_bool bDeuterate);
+void do_h_mass(t_params *psb, int vsite_type[], t_atoms *at, real mHmult,
+ gmx_bool bDeuterate);
#ifdef __cplusplus
}
#endif
-#endif /* _gen_vsite_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _genhydro_h
-#define _genhydro_h
+#ifndef GMX_GMXPREPROCESS_GENHYDRO_H
+#define GMX_GMXPREPROCESS_GENHYDRO_H
#include "gromacs/fileio/pdbio.h"
#include "hackblock.h"
-extern int add_h(t_atoms **pdbaptr, rvec *xptr[],
- int nah, t_hackblock ah[],
- int nterpairs,
- t_hackblock **ntdb, t_hackblock **ctdb,
- int *rN, int *rC, gmx_bool bMissing,
- int **nabptr, t_hack ***abptr,
- gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba);
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+int add_h(t_atoms **pdbaptr, rvec *xptr[],
+ int nah, t_hackblock ah[],
+ int nterpairs,
+ t_hackblock **ntdb, t_hackblock **ctdb,
+ int *rN, int *rC, gmx_bool bMissing,
+ int **nabptr, t_hack ***abptr,
+ gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba);
/* Generate hydrogen atoms and N and C terminal patches.
* int nterpairs is the number of termini pairs in the molecule
* ntdb[i] and ctdb[i] may be NULL, no replacement will be done then.
* return the New total number of atoms
*/
-extern int protonate(t_atoms **atoms, rvec **x, t_protonate *protdata);
+int protonate(t_atoms **atoms, rvec **x, t_protonate *protdata);
/* Protonate molecule according to gmx2.ff/aminoacids.hdb
* when called the first time, new atoms are added to atoms,
* second time only coordinates are generated
* return the new total number of atoms
*/
-extern void deprotonate(t_atoms *atoms, rvec *x);
+void deprotonate(t_atoms *atoms, rvec *x);
/* Deprotonate any molecule: all atoms whose name begins with H will be
* removed
*/
+#ifdef __cplusplus
+}
+#endif
+
#endif
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _gmxcpp_h
-#define _gmxcpp_h
+#ifndef GMX_GMXPREPROCESS_GMXCPP_H
+#define GMX_GMXPREPROCESS_GMXCPP_H
typedef struct gmx_cpp *gmx_cpp_t;
/* The possible return codes for these functions */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014, 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _gpp_atomtype_h
-#define _gpp_atomtype_h
+#ifndef GMX_GMXPREPROCESS_GPP_ATOMTYPE_H
+#define GMX_GMXPREPROCESS_GPP_ATOMTYPE_H
#include <stdio.h>
#include "typedefs.h"
-#include "grompp.h"
+#include "grompp-impl.h"
#ifdef __cplusplus
extern "C" {
}
#endif
-#endif /* _gpp_atomtype_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014, 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _gpp_bondatomtype_h
-#define _gpp_bondatomtype_h
+#ifndef GMX_GMXPREPROCESS_GPP_BONDATOMTYPE_H
+#define GMX_GMXPREPROCESS_GPP_BONDATOMTYPE_H
#ifdef HAVE_CONFIG_H
#include <config.h>
#include <stdio.h>
#include "typedefs.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
typedef struct gpp_bondatomtype *t_bond_atomtype;
-extern int get_bond_atomtype_type(char *str, t_bond_atomtype at);
+int get_bond_atomtype_type(char *str, t_bond_atomtype at);
/* Return atomtype corresponding to case-insensitive str
or NOTSET if not found */
-extern char *get_bond_atomtype_name(int nt, t_bond_atomtype at);
+char *get_bond_atomtype_name(int nt, t_bond_atomtype at);
/* Return name corresponding to atomtype nt, or NULL if not found */
-extern t_bond_atomtype init_bond_atomtype(void);
+t_bond_atomtype init_bond_atomtype(void);
/* Return a new atomtype structure */
-extern void done_bond_atomtype(t_bond_atomtype *at);
+void done_bond_atomtype(t_bond_atomtype *at);
/* Free the memory in the structure */
-extern void add_bond_atomtype(t_bond_atomtype at, t_symtab *tab,
- char *name);
+void add_bond_atomtype(t_bond_atomtype at, t_symtab *tab,
+ char *name);
/* Add a complete new atom type to an existing atomtype structure */
-#endif /* _gpp_bond_atomtype_h */
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _gpp_nextnb_h
-#define _gpp_nextnb_h
+#ifndef GMX_GMXPREPROCESS_GPP_NEXTNB_H
+#define GMX_GMXPREPROCESS_GPP_NEXTNB_H
-#include "grompp.h"
+#include "grompp-impl.h"
#ifdef __cplusplus
extern "C" {
}
#endif
-#endif /* _gpp_nextnb_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _grompp_h
-#define _grompp_h
+#ifndef GMX_GMXPREPROCESS_GROMPP_IMPL_H
+#define GMX_GMXPREPROCESS_GROMPP_IMPL_H
-#include <stdio.h>
#include "typedefs.h"
#ifdef __cplusplus
}
#endif
-#endif /* _grompp_h */
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "grompp.h"
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include "readir.h"
#include "symtab.h"
#include "names.h"
-#include "grompp.h"
+#include "grompp-impl.h"
#include "random.h"
#include "vec.h"
#include "gromacs/fileio/futil.h"
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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.
+ *
+ * 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.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 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 research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_GMXPREPROCESS_GROMPP_H
+#define GMX_GMXPREPROCESS_GROMPP_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+#if 0
+}
+#endif
+
+int gmx_grompp(int argc, char *argv[]);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
#include "gmx_fatal.h"
#include "macros.h"
-/* There are 11 types of adding hydrogens, numbered from
- * 1 thru 11. Each of these has a specific number of
- * control atoms, that determine how the hydrogens are added.
- * Here these number are given. Because arrays start at 0 an
- * extra dummy for index 0 is added
+/* Number of control atoms for each 'add' type.
+ *
+ * There are 11 types of adding hydrogens, numbered from 1 thru
+ * 11. Each of these has a specific number of control atoms, that
+ * determine how the hydrogens are added. Here these number are
+ * given. Because arrays start at 0, an extra dummy for index 0 is
+ * added.
*/
const int ncontrol[] = { -1, 3, 3, 3, 3, 4, 3, 1, 3, 3, 1, 1 };
#define maxcontrol asize(ncontrol)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014, 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _h_db_h
-#define _h_db_h
+#ifndef GMX_GMXPREPROCESS_H_DB_H
+#define GMX_GMXPREPROCESS_H_DB_H
#include "sysstuff.h"
#include "hackblock.h"
-/* number of control atoms for each 'add' type */
-extern const int ncontrol[];
+#ifdef __cplusplus
+extern "C" {
+#endif
/* functions for the h-database */
-extern void read_ab(char *line, const char *fn, t_hack *ab);
+void read_ab(char *line, const char *fn, t_hack *ab);
/* Read one add block */
-extern int read_h_db(const char *ffdir, t_hackblock **ah);
+int read_h_db(const char *ffdir, t_hackblock **ah);
/* Read the database from hdb file(s) in ffdir or current dir */
-extern void print_ab(FILE *out, t_hack *ab, char *nname);
+void print_ab(FILE *out, t_hack *ab, char *nname);
/* print one add block */
-extern void print_h_db(FILE *out, int nh, t_hackblock ah[]);
+void print_h_db(FILE *out, int nh, t_hackblock ah[]);
/* Print the database to file */
-extern int compaddh(const void *a, const void *b);
+int compaddh(const void *a, const void *b);
-extern t_hackblock *search_h_db(int nh, t_hackblock ah[], char *key);
+t_hackblock *search_h_db(int nh, t_hackblock ah[], char *key);
/* Search for an entry in the database */
+#ifdef __cplusplus
+}
+#endif
-
-#endif /* _h_db_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _hackblock_h
-#define _hackblock_h
+#ifndef GMX_GMXPREPROCESS_HACKBLOCK_H
+#define GMX_GMXPREPROCESS_HACKBLOCK_H
#include "typedefs.h"
#include "../fileio/pdbio.h"
-#include "grompp.h"
+#include "grompp-impl.h"
#include "gpp_atomtype.h"
#ifdef __cplusplus
}
#endif
-#endif /* _hackblock_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _hizzie_h
-#define _hizzie_h
+#ifndef GMX_GMXPREPROCESS_HIZZIE_H
+#define GMX_GMXPREPROCESS_HIZZIE_H
-extern void set_histp(t_atoms *pdba, rvec *x, real angle, real distance);
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+void set_histp(t_atoms *pdba, rvec *x, real angle, real distance);
/* calculate HIStidine protonation state */
-#endif /* _pdb2gmx_h */
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
#include <stdio.h>
+#ifdef __cplusplus
+extern "C" {
+#endif
+
typedef struct {
char *elem, *type;
double q, m;
double *blen;
} t_nm2type;
-extern t_nm2type *rd_nm2type(const char *ffdir, int *nnm);
+t_nm2type *rd_nm2type(const char *ffdir, int *nnm);
/* Read the name 2 type database. nnm is the number of entries
* ff is the force field.
*/
-extern void dump_nm2type(FILE *fp, int nnm, t_nm2type nm2t[]);
+void dump_nm2type(FILE *fp, int nnm, t_nm2type nm2t[]);
/* Dump the database for debugging. Can be reread by the program */
-extern int nm2type(int nnm, t_nm2type nm2t[], t_symtab *tab, t_atoms *atoms,
- gpp_atomtype_t atype, int *nbonds, t_params *bond);
+int nm2type(int nnm, t_nm2type nm2t[], t_symtab *tab, t_atoms *atoms,
+ gpp_atomtype_t atype, int *nbonds, t_params *bond);
/* Try to determine the atomtype (force field dependent) for the atoms
* with help of the bond list
*/
+#ifdef __cplusplus
+}
+#endif
+
#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "pdb2gmx.h"
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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.
+ *
+ * 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.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 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 research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_GMXPREPROCESS_PDB2GMX_H
+#define GMX_GMXPREPROCESS_PDB2GMX_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+#if 0
+}
+#endif
+
+int gmx_pdb2gmx(int argc, char *argv[]);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _pdb2top_h
-#define _pdb2top_h
+#ifndef GMX_GMXPREPROCESS_PDB2TOP_H
+#define GMX_GMXPREPROCESS_PDB2TOP_H
#include "typedefs.h"
-#include "grompp.h"
+#include "grompp-impl.h"
#include "gpp_atomtype.h"
#include "toputil.h"
#include "hackblock.h"
}
#endif
-#endif /* _pdb2top_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _pgutil_h
-#define _pgutil_h
+#ifndef GMX_GMXPREPROCESS_PGUTIL_H
+#define GMX_GMXPREPROCESS_PGUTIL_H
#include "typedefs.h"
{
#endif
-extern atom_id search_atom(const char *type, int start,
- t_atoms *atoms,
- const char *bondtype, gmx_bool bAllowMissing);
+atom_id search_atom(const char *type, int start,
+ t_atoms *atoms,
+ const char *bondtype, gmx_bool bAllowMissing);
/* Search an atom in array of pointers to strings, starting from start
* if type starts with '-' then searches backwards from start.
* bondtype is only used for printing the error/warning string,
* When bAllowMissing=FALSE an fatal error is issued, otherwise a warning.
*/
-extern void set_at(t_atom *at, real m, real q, int type, int resind);
+void set_at(t_atom *at, real m, real q, int type, int resind);
#ifdef __cplusplus
}
#endif
-#endif /* _pgutil_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "protonate.h"
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 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.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \internal \brief Declares C-style main functions as used in
- * remaining 4.x-style GROMACS tools
- *
- * \author Mark Abraham <mark.j.abraham@gmail.com>
- */
+#ifndef GMX_GMXPREPROCESS_PROTONATE_H
+#define GMX_GMXPREPROCESS_PROTONATE_H
-#ifndef GMX_LEGACYCMAINFUNCTIONS_H
-#define GMX_LEGACYCMAINFUNCTIONS_H
-
-extern "C"
-{
+#ifdef __cplusplus
+extern "C" {
+#endif
+#if 0
+}
+#endif
-int gmx_grompp(int argc, char *argv[]);
-int gmx_pdb2gmx(int argc, char *argv[]);
int gmx_protonate(int argc, char *argv[]);
-int gmx_x2top(int argc, char *argv[]);
+#ifdef __cplusplus
}
+#endif
#endif
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _readir_h
-#define _readir_h
+#ifndef GMX_GMXPREPROCESS_READIR_H
+#define GMX_GMXPREPROCESS_READIR_H
#include "typedefs.h"
#include "string2.h"
#include "readinp.h"
-#include "grompp.h"
+#include "grompp-impl.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
enum {
eshNONE, eshHBONDS, eshALLBONDS, eshHANGLES, eshALLANGLES, eshNR
} t_gromppopts;
/*! \brief Initialise object to hold strings parsed from an .mdp file */
-extern void init_inputrec_strings();
+void init_inputrec_strings();
/*! \brief Clean up object that holds strings parsed from an .mdp file */
void done_inputrec_strings();
-extern void init_ir(t_inputrec *ir, t_gromppopts *opts);
+void init_ir(t_inputrec *ir, t_gromppopts *opts);
/* Initiate stuff */
-extern void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
- warninp_t wi);
+void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
+ warninp_t wi);
/* Validate inputrec data.
* Fatal errors will be added to nerror.
*/
-extern int search_string(const char *s, int ng, char *gn[]);
+int search_string(const char *s, int ng, char *gn[]);
/* Returns the index of string s in the index groups */
-extern void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr,
- warninp_t wi);
+void double_check(t_inputrec *ir, matrix box, gmx_bool bConstr,
+ warninp_t wi);
/* Do more checks */
-extern void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
- warninp_t wi);
+void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
+ warninp_t wi);
/* Do even more checks */
-extern void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
- rvec *x,
- warninp_t wi);
+void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
+ rvec *x,
+ warninp_t wi);
/* Even more checks, charge group radii vs. cut-off's only. */
-extern void get_ir(const char *mdparin, const char *mdparout,
- t_inputrec *ir, t_gromppopts *opts,
- warninp_t wi);
+void get_ir(const char *mdparin, const char *mdparout,
+ t_inputrec *ir, t_gromppopts *opts,
+ warninp_t wi);
/* Read the input file, and retrieve data for inputrec.
* More data are read, but the are only evaluated when the next
* function is called. Also prints the input file back to mdparout.
*/
-extern void do_index(const char* mdparin,
- const char *ndx,
- gmx_mtop_t *mtop,
- gmx_bool bVerbose,
- t_inputrec *ir,
- rvec *v,
- warninp_t wi);
+void do_index(const char* mdparin,
+ const char *ndx,
+ gmx_mtop_t *mtop,
+ gmx_bool bVerbose,
+ t_inputrec *ir,
+ rvec *v,
+ warninp_t wi);
/* Read the index file and assign grp numbers to atoms.
* If v is not NULL, the velocities will be scaled to the correct number
* of degrees of freedom.
/* Routines In readpull.c */
-extern char **read_pullparams(int *ninp_p, t_inpfile **inp,
- t_pull *pull, gmx_bool *bStart,
- warninp_t wi);
+char **read_pullparams(int *ninp_p, t_inpfile **inp,
+ t_pull *pull, gmx_bool *bStart,
+ warninp_t wi);
/* Reads the pull parameters, returns a list of the pull group names */
-extern void make_pull_groups(t_pull *pull,
- char **pgnames,
- const t_blocka *grps, char **gnames);
+void make_pull_groups(t_pull *pull,
+ char **pgnames,
+ const t_blocka *grps, char **gnames);
/* Process the pull group parameters after reading the index groups */
-extern void make_pull_coords(t_pull *pull);
+void make_pull_coords(t_pull *pull);
/* Process the pull coordinates after reading the pull groups */
-extern void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
- const output_env_t oenv, gmx_bool bStart);
+void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
+ const output_env_t oenv, gmx_bool bStart);
/* Prints the initial pull group distances in x.
* If bStart adds the distance to the initial reference location.
*/
-extern int str_nelem(const char *str, int maxptr, char *ptr[]);
+int str_nelem(const char *str, int maxptr, char *ptr[]);
/* helper function from readir.c to convert strings */
-extern void read_adressparams(int *ninp_p, t_inpfile **inp_p, t_adress *adress, warninp_t wi);
+void read_adressparams(int *ninp_p, t_inpfile **inp_p, t_adress *adress, warninp_t wi);
/* Reads in AdResS related parameters */
-extern void do_adress_index(t_adress *adress, gmx_groups_t *groups, char **gnames, t_grpopts *opts, warninp_t wi);
+void do_adress_index(t_adress *adress, gmx_groups_t *groups, char **gnames, t_grpopts *opts, warninp_t wi);
/* Generate adress groups */
-extern char **read_rotparams(int *ninp_p, t_inpfile **inp, t_rot *rot, warninp_t wi);
+char **read_rotparams(int *ninp_p, t_inpfile **inp, t_rot *rot, warninp_t wi);
/* Reads enforced rotation parameters, returns a list of the rot group names */
-extern void make_rotation_groups(t_rot *rot, char **rotgnames,
- t_blocka *grps, char **gnames);
+void make_rotation_groups(t_rot *rot, char **rotgnames,
+ t_blocka *grps, char **gnames);
/* Process the rotation parameters after reading the index groups */
-extern void set_reference_positions(t_rot *rot, rvec *x, matrix box,
- const char *fn, gmx_bool bSet, warninp_t wi);
+void set_reference_positions(t_rot *rot, rvec *x, matrix box,
+ const char *fn, gmx_bool bSet, warninp_t wi);
+
+#ifdef __cplusplus
+}
+#endif
-#endif /* _readir_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _resall_h
-#define _resall_h
+#ifndef GMX_GMXPREPROCESS_RESALL_H
+#define GMX_GMXPREPROCESS_RESALL_H
#include "typedefs.h"
#include "hackblock.h"
#include "gpp_atomtype.h"
-#include "grompp.h"
+#include "grompp-impl.h"
#ifdef __cplusplus
extern "C" {
}
#endif
-#endif /* _resall_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _specbond_h
-#define _specbond_h
+#ifndef GMX_GMXPREPROCESS_SPECBOND_H
+#define GMX_GMXPREPROCESS_SPECBOND_H
#include "pdb2top.h"
-extern int mk_specbonds(t_atoms *pdba, rvec x[], gmx_bool bInteractive,
- t_ssbond **specbonds, gmx_bool bVerbose);
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+int mk_specbonds(t_atoms *pdba, rvec x[], gmx_bool bInteractive,
+ t_ssbond **specbonds, gmx_bool bVerbose);
-extern gmx_bool yesno(void);
+gmx_bool yesno(void);
+
+#ifdef __cplusplus
+}
+#endif
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014, 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _ter_db_h
-#define _ter_db_h
+#ifndef GMX_GMXPREPROCESS_TER_DB_H
+#define GMX_GMXPREPROCESS_TER_DB_H
#include "sysstuff.h"
#include "hackblock.h"
-#include "grompp.h"
+#include "grompp-impl.h"
-extern int read_ter_db(const char *ffdir, char ter,
- t_hackblock **tbptr, gpp_atomtype_t atype);
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+int read_ter_db(const char *ffdir, char ter,
+ t_hackblock **tbptr, gpp_atomtype_t atype);
/* Read database for N&C terminal hacking */
-extern t_hackblock **filter_ter(int nrtp, t_restp rtp[],
- int nb, t_hackblock tb[],
- const char *resname,
- const char *rtpname,
- int *nret);
+t_hackblock **filter_ter(int nrtp, t_restp rtp[],
+ int nb, t_hackblock tb[],
+ const char *resname,
+ const char *rtpname,
+ int *nret);
/* Return a list of pointers to blocks that match residue name */
-extern t_hackblock *choose_ter(int nb, t_hackblock **tb, const char *title);
+t_hackblock *choose_ter(int nb, t_hackblock **tb, const char *title);
/* Interactively select one.. */
-#endif /* _ter_db_h */
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
#include <ctype.h>
#include "typedefs.h"
#include "string2.h"
-#include "grompp.h"
+#include "grompp-impl.h"
#include "gromacs/fileio/futil.h"
#include "smalloc.h"
#include "toputil.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _tomorse_h
-#define _tomorse_h
+#ifndef GMX_GMXPREPROCESS_TOMORSE_H
+#define GMX_GMXPREPROCESS_TOMORSE_H
#ifdef HAVE_CONFIG_H
#include <config.h>
#include <stdio.h>
#include "typedefs.h"
-extern void convert_harmonics(int nrmols, t_molinfo mols[], gpp_atomtype_t atype);
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+void convert_harmonics(int nrmols, t_molinfo mols[], gpp_atomtype_t atype);
-#endif /* _grompp_h */
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
#include "gmx_fatal.h"
#include "topdirs.h"
-/* Must correspond to the directive enum in grompp.h */
+/* Must correspond to the directive enum in grompp-impl.h */
static const char *directive_names[d_maxdir+1] = {
"defaults",
"atomtypes",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _topdirs_h
-#define _topdirs_h
+#ifndef GMX_GMXPREPROCESS_TOPDIRS_H
+#define GMX_GMXPREPROCESS_TOPDIRS_H
-#include "grompp.h"
+#include "grompp-impl.h"
#ifdef __cplusplus
-extern "C"
-{
+extern "C" {
#endif
typedef struct tagDirStack {
struct tagDirStack *prev;
} DirStack;
-extern int ifunc_index(directive d, int type);
+int ifunc_index(directive d, int type);
-extern const char *dir2str (directive d);
+const char *dir2str (directive d);
-extern directive str2dir (char *dstr);
+directive str2dir (char *dstr);
-extern void DS_Init (DirStack **DS);
+void DS_Init (DirStack **DS);
-extern void DS_Done (DirStack **DS);
+void DS_Done (DirStack **DS);
-extern void DS_Push (DirStack **DS, directive d);
+void DS_Push (DirStack **DS, directive d);
-extern int DS_Search (DirStack *DS, directive d);
+int DS_Search (DirStack *DS, directive d);
-extern int DS_Check_Order (DirStack *DS, directive d);
+int DS_Check_Order (DirStack *DS, directive d);
#ifdef __cplusplus
}
#endif
-#endif /* _topdirs_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014, 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _topexcl_h
-#define _topexcl_h
+#ifndef GMX_GMXPREPROCESS_TOPEXCL_H
+#define GMX_GMXPREPROCESS_TOPEXCL_H
#include "topio.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
typedef struct {
int nr; /* nr atoms (0 <= i < nr) (atoms->nr) */
int nrex; /* with nrex lists of neighbours */
int ***a; /* like this: a[i][nre][nrx] */
} t_nextnb;
-extern void init_nnb(t_nextnb *nnb, int nr, int nrex);
+void init_nnb(t_nextnb *nnb, int nr, int nrex);
/* Initiate the arrays for nnb (see above) */
-extern void done_nnb(t_nextnb *nnb);
+void done_nnb(t_nextnb *nnb);
/* Cleanup the nnb struct */
#ifdef DEBUG_NNB
#define print_nnb(nnb, s) __print_nnb(nnb, s)
-extern void print_nnb(t_nextnb *nnb, char *s);
+void print_nnb(t_nextnb *nnb, char *s);
/* Print the nnb struct */
#else
#define print_nnb(nnb, s)
#endif
-extern void gen_nnb(t_nextnb *nnb, t_params plist[]);
+void gen_nnb(t_nextnb *nnb, t_params plist[]);
/* Generate a t_nextnb structure from bond information.
* With the structure you can either generate exclusions
* or generate angles and dihedrals. The structure must be
* initiated using init_nnb.
*/
-extern void nnb2excl (t_nextnb *nnb, t_blocka *excl);
+void nnb2excl (t_nextnb *nnb, t_blocka *excl);
/* generate exclusions from nnb */
-extern void generate_excl (int nrexcl, int nratoms,
- t_params plist[], t_blocka *excl);
+void generate_excl (int nrexcl, int nratoms,
+ t_params plist[], t_blocka *excl);
/* Generate an exclusion block from bonds and constraints in
* plist.
*/
-#endif /* _topexcl_h */
+#ifdef __cplusplus
+}
+#endif
+
+#endif
#include "warninp.h"
#include "vsite_parm.h"
-#include "grompp.h"
+#include "grompp-impl.h"
#include "toputil.h"
#include "toppush.h"
#include "topdirs.h"
bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
break;
case d_cmap:
- push_cmap(d, plist, mi0->plist, &(mi0->atoms), atype, pline,wi);
+ push_cmap(d, plist, mi0->plist, &(mi0->atoms), atype, pline, wi);
break;
case d_vsitesn:
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _topio_h
-#define _topio_h
+#ifndef GMX_GMXPREPROCESS_TOPIO_H
+#define GMX_GMXPREPROCESS_TOPIO_H
#include "typedefs.h"
#include "readir.h"
-#include "grompp.h"
+#include "grompp-impl.h"
#include "gpp_atomtype.h"
-extern double check_mol(gmx_mtop_t *mtop, warninp_t wi);
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+double check_mol(gmx_mtop_t *mtop, warninp_t wi);
/* Check mass and charge */
-extern char **do_top(gmx_bool bVerbose,
- const char *topfile,
- const char *topppfile,
- t_gromppopts *opts,
- gmx_bool bZero,
- t_symtab *symtab,
- t_params plist[],
- int *combination_rule,
- double *repulsion_power,
- real *fudgeQQ,
- gpp_atomtype_t atype,
- int *nrmols,
- t_molinfo **molinfo,
- t_inputrec *ir,
- int *nmolblock,
- gmx_molblock_t **molblock,
- gmx_bool bGB,
- warninp_t wi);
+char **do_top(gmx_bool bVerbose,
+ const char *topfile,
+ const char *topppfile,
+ t_gromppopts *opts,
+ gmx_bool bZero,
+ t_symtab *symtab,
+ t_params plist[],
+ int *combination_rule,
+ double *repulsion_power,
+ real *fudgeQQ,
+ gpp_atomtype_t atype,
+ int *nrmols,
+ t_molinfo **molinfo,
+ t_inputrec *ir,
+ int *nmolblock,
+ gmx_molblock_t **molblock,
+ gmx_bool bGB,
+ warninp_t wi);
/* This routine expects sys->molt[m].ilist to be of size F_NRE and ordered. */
void generate_qmexcl(gmx_mtop_t *sys, t_inputrec *ir, warninp_t wi);
-#endif /* _topio_h */
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _toppush_h
-#define _toppush_h
+#ifndef GMX_GMXPREPROCESS_TOPPUSH_H
+#define GMX_GMXPREPROCESS_TOPPUSH_H
#include "typedefs.h"
#include "toputil.h"
#include "gpp_bond_atomtype.h"
#include "warninp.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
typedef struct {
int nr; /* The number of entries in the list */
int nra2; /* The total number of entries in a */
/* i is nra[i] */
} t_block2;
-extern void generate_nbparams(int comb, int funct, t_params plist[],
- gpp_atomtype_t atype,
- warninp_t wi);
+void generate_nbparams(int comb, int funct, t_params plist[],
+ gpp_atomtype_t atype,
+ warninp_t wi);
-extern void push_at (t_symtab *symtab, gpp_atomtype_t at,
- t_bond_atomtype bat, char *line, int nb_funct,
- t_nbparam ***nbparam, t_nbparam ***pair,
- warninp_t wi);
+void push_at (t_symtab *symtab, gpp_atomtype_t at,
+ t_bond_atomtype bat, char *line, int nb_funct,
+ t_nbparam ***nbparam, t_nbparam ***pair,
+ warninp_t wi);
-extern void push_bt(directive d, t_params bt[], int nral,
- gpp_atomtype_t at, t_bond_atomtype bat, char *line,
- warninp_t wi);
+void push_bt(directive d, t_params bt[], int nral,
+ gpp_atomtype_t at, t_bond_atomtype bat, char *line,
+ warninp_t wi);
-extern void push_dihedraltype(directive d, t_params bt[],
- t_bond_atomtype bat, char *line,
- warninp_t wi);
+void push_dihedraltype(directive d, t_params bt[],
+ t_bond_atomtype bat, char *line,
+ warninp_t wi);
-extern void push_cmaptype(directive d, t_params bt[], int nral, gpp_atomtype_t at,
- t_bond_atomtype bat, char *line,
- warninp_t wi);
+void push_cmaptype(directive d, t_params bt[], int nral, gpp_atomtype_t at,
+ t_bond_atomtype bat, char *line,
+ warninp_t wi);
-extern void push_nbt(directive d, t_nbparam **nbt, gpp_atomtype_t atype,
- char *plines, int nb_funct,
- warninp_t wi);
+void push_nbt(directive d, t_nbparam **nbt, gpp_atomtype_t atype,
+ char *plines, int nb_funct,
+ warninp_t wi);
void
push_gb_params(gpp_atomtype_t atype,
char *line,
warninp_t wi);
-extern void push_atom(t_symtab *symtab,
- t_block *cgs,
- t_atoms *at,
- gpp_atomtype_t atype,
- char *line,
- int *lastcg,
- warninp_t wi);
+void push_atom(t_symtab *symtab,
+ t_block *cgs,
+ t_atoms *at,
+ gpp_atomtype_t atype,
+ char *line,
+ int *lastcg,
+ warninp_t wi);
-extern void push_bond(directive d, t_params bondtype[], t_params bond[],
- t_atoms *at, gpp_atomtype_t atype, char *line,
- gmx_bool bBonded, gmx_bool bGenPairs, real fudgeQQ,
- gmx_bool bZero, gmx_bool *bWarn_copy_A_B,
- warninp_t wi);
+void push_bond(directive d, t_params bondtype[], t_params bond[],
+ t_atoms *at, gpp_atomtype_t atype, char *line,
+ gmx_bool bBonded, gmx_bool bGenPairs, real fudgeQQ,
+ gmx_bool bZero, gmx_bool *bWarn_copy_A_B,
+ warninp_t wi);
-extern void push_cmap(directive d, t_params bondtype[], t_params bond[],
- t_atoms *at, gpp_atomtype_t atype, char *line,
- warninp_t wi);
+void push_cmap(directive d, t_params bondtype[], t_params bond[],
+ t_atoms *at, gpp_atomtype_t atype, char *line,
+ warninp_t wi);
-extern void push_vsitesn(directive d, t_params bond[],
- t_atoms *at, char *line,
- warninp_t wi);
+void push_vsitesn(directive d, t_params bond[],
+ t_atoms *at, char *line,
+ warninp_t wi);
-extern void push_mol(int nrmols, t_molinfo mols[], char *pline,
- int *whichmol, int *nrcopies,
- warninp_t wi);
+void push_mol(int nrmols, t_molinfo mols[], char *pline,
+ int *whichmol, int *nrcopies,
+ warninp_t wi);
-extern void push_molt(t_symtab *symtab, int *nmol, t_molinfo **mol, char *line,
- warninp_t wi);
+void push_molt(t_symtab *symtab, int *nmol, t_molinfo **mol, char *line,
+ warninp_t wi);
-extern void init_block2(t_block2 *b2, int natom);
+void init_block2(t_block2 *b2, int natom);
-extern void done_block2(t_block2 *b2);
+void done_block2(t_block2 *b2);
-extern void push_excl(char *line, t_block2 *b2);
+void push_excl(char *line, t_block2 *b2);
-extern void merge_excl(t_blocka *excl, t_block2 *b2);
+void merge_excl(t_blocka *excl, t_block2 *b2);
-extern void b_to_b2(t_blocka *b, t_block2 *b2);
+void b_to_b2(t_blocka *b, t_block2 *b2);
-extern void b2_to_b(t_block2 *b2, t_blocka *b);
+void b2_to_b(t_block2 *b2, t_blocka *b);
-extern int add_atomtype_decoupled(t_symtab *symtab, gpp_atomtype_t at,
- t_nbparam ***nbparam, t_nbparam ***pair);
+int add_atomtype_decoupled(t_symtab *symtab, gpp_atomtype_t at,
+ t_nbparam ***nbparam, t_nbparam ***pair);
/* Add an atom type with all parameters set to zero (no interactions).
* Returns the atom type number.
*/
-extern void convert_moltype_couple(t_molinfo *mol, int atomtype_decouple,
- real fudgeQQ,
- int couple_lam0, int couple_lam1,
- gmx_bool bCoupleIntra,
- int nb_funct, t_params *nbp);
+void convert_moltype_couple(t_molinfo *mol, int atomtype_decouple,
+ real fudgeQQ,
+ int couple_lam0, int couple_lam1,
+ gmx_bool bCoupleIntra,
+ int nb_funct, t_params *nbp);
/* Setup mol such that the B-state has no interaction with the rest
* of the system, but full interaction with itself.
*/
-#endif /* _toppush_h */
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _topshake_h
-#define _topshake_h
+#ifndef GMX_GMXPREPROCESS_TOPSHAKE_H
+#define GMX_GMXPREPROCESS_TOPSHAKE_H
#include "topio.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
void make_shake (t_params plist[], t_atoms *atoms, int nshake);
-#endif /* _topshake_h */
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * 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.
}
else
{
- gmx_fatal(FARGS, "Increase MAXSLEN in include/grompp.h to at least %d,"
+ gmx_fatal(FARGS, "Increase MAXSLEN in include/grompp-impl.h to at least %d,"
" or shorten your definition of bonds like %s to at most %d",
strlen(s)+1, s, MAXSLEN-1);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _toputil_h
-#define _toputil_h
+#ifndef GMX_GMXPREPROCESS_TOPUTIL_H
+#define GMX_GMXPREPROCESS_TOPUTIL_H
-#include "grompp.h"
+#include "grompp-impl.h"
#include "gpp_atomtype.h"
#ifdef __cplusplus
}
#endif
-#endif /* _toputil_h */
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _vsite_parm_h
-#define _vsite_parm_h
+#ifndef GMX_GMXPREPROCESS_VSITE_PARM_H
+#define GMX_GMXPREPROCESS_VSITE_PARM_H
#include "typedefs.h"
-#include "grompp.h"
+#include "grompp-impl.h"
#include "gpp_atomtype.h"
-extern int set_vsites(gmx_bool bVerbose, t_atoms *atoms, gpp_atomtype_t atype,
- t_params plist[]);
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+int set_vsites(gmx_bool bVerbose, t_atoms *atoms, gpp_atomtype_t atype,
+ t_params plist[]);
/* set parameters for virtual sites, return number of virtual sites */
-extern void set_vsites_ptype(gmx_bool bVerbose, gmx_moltype_t *molt);
+void set_vsites_ptype(gmx_bool bVerbose, gmx_moltype_t *molt);
/* set ptype to VSite for virtual sites */
-extern void clean_vsite_bondeds(t_params *ps, int natoms, gmx_bool bRmVSiteBds);
+void clean_vsite_bondeds(t_params *ps, int natoms, gmx_bool bRmVSiteBds);
/* remove all bonded interaction (bonds, angles and diherals) that
have become obsolete due to virtual site constructions */
-#endif /* _vsite_parm_h */
+#ifdef __cplusplus
+}
+#endif
+
+#endif
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "x2top.h"
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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.
+ *
+ * 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.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 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 research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_GMXPREPROCESS_X2TOP_H
+#define GMX_GMXPREPROCESS_X2TOP_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+#if 0
+}
+#endif
+
+int gmx_x2top(int argc, char *argv[]);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _xlate_h
-#define _xlate_h
+#ifndef GMX_GMXPREPROCESS_XLATE_H
+#define GMX_GMXPREPROCESS_XLATE_H
#include "index.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
/* If bResname is true renames atoms based on residue names,
* otherwise renames atoms based on rtp entry names.
*/
-extern void rename_atoms(const char *xlfile, const char *ffdir,
- t_atoms *atoms, t_symtab *symtab, const t_restp *restp,
- gmx_bool bResname, gmx_residuetype_t rt, gmx_bool bReorderNum,
- gmx_bool bVerbose);
+void rename_atoms(const char *xlfile, const char *ffdir,
+ t_atoms *atoms, t_symtab *symtab, const t_restp *restp,
+ gmx_bool bResname, gmx_residuetype_t rt, gmx_bool bReorderNum,
+ gmx_bool bVerbose);
+
+#ifdef __cplusplus
+}
+#endif
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
#include "typedefs.h"
#include "types/commrec.h"
-#include "grompp.h"
#ifdef __cplusplus
extern "C" {
void gb_pd_send(t_commrec *cr, real *send_data, int nr);
-/* Functions for setting up the F_GB12,13,14 lists in grompp */
-int
-init_gb_plist(t_params *p_list);
-
-int
-convert_gb_params(gmx_ffparams_t *ffparams, t_functype ftype, t_params *gb_plist, t_ilist *il);
-
/* Functions for calculating adjustments due to ie chain rule terms */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
#include "smalloc.h"
#include "genborn.h"
#include "vec.h"
-#include "grompp.h"
#include "gromacs/fileio/pdbio.h"
#include "names.h"
#include "physics.h"
}
-int init_gb_plist(t_params *p_list)
-{
- p_list->nr = 0;
- p_list->param = NULL;
-
- return 0;
-}
-
-
-
int init_gb_still(const t_commrec *cr,
const t_atomtypes *atype, t_idef *idef, t_atoms *atoms,
gmx_genborn_t *born, int natoms)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
#include "smalloc.h"
#include "genborn.h"
#include "vec.h"
-#include "grompp.h"
#include "gromacs/fileio/pdbio.h"
#include "names.h"
#include "physics.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
#endif
#include "typedefs.h"
-#include "grompp.h"
-
int
calc_gb_rad_still_sse2_double(t_commrec *cr, t_forcerec *fr, int natoms, gmx_localtop_t *top,
calc_gb_rad_hct_obc_sse2_double(t_commrec *cr, t_forcerec *fr, int natoms, gmx_localtop_t *top,
double *x, t_nblist *nl, gmx_genborn_t *born, t_mdatoms *md, int gb_algorithm);
-
-
#endif /* _genborn_sse2_double_h */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
#include "smalloc.h"
#include "genborn.h"
#include "vec.h"
-#include "grompp.h"
#include "gromacs/fileio/pdbio.h"
#include "names.h"
#include "physics.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * 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.
#endif
#include "typedefs.h"
-#include "grompp.h"
-
float
calc_gb_chainrule_sse2_single(int natoms, t_nblist *nl, float *dadx, float *dvda,
calc_gb_rad_hct_obc_sse2_single(t_commrec *cr, t_forcerec * fr, int natoms, gmx_localtop_t *top,
float *x, t_nblist *nl, gmx_genborn_t *born, t_mdatoms *md, int gb_algorithm);
-
#endif /* _genborn_sse_h */
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+# Copyright (c) 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.
COMPILE_FLAGS "${OpenMP_C_FLAGS}")
install(TARGETS mdrun DESTINATION ${BIN_INSTALL_DIR} COMPONENT mdrun)
else()
- file(GLOB GMX_GENERAL_SOURCES gmx/*.c gmx/*.cpp)
file(GLOB GMX_MAIN_SOURCES gmx/gmx.cpp gmx/legacymodules.cpp)
- list(REMOVE_ITEM GMX_GENERAL_SOURCES ${GMX_MAIN_SOURCES})
if(GMX_X11)
file(GLOB VIEW_SOURCES view/*.cpp)
else()
file(GLOB VIEW_SOURCES view/view.cpp)
endif()
- add_library(gmx_objlib OBJECT ${GMX_GENERAL_SOURCES})
add_library(view_objlib OBJECT ${VIEW_SOURCES})
add_executable(gmx
${GMX_MAIN_SOURCES}
- $<TARGET_OBJECTS:gmx_objlib>
$<TARGET_OBJECTS:mdrun_objlib>
$<TARGET_OBJECTS:view_objlib>)
target_link_libraries(gmx
#include "gromacs/tools/check.h"
#include "gromacs/tools/dump.h"
#include "gromacs/tools/convert_tpr.h"
-
-#include "legacycmainfunctions.h"
+#include "gromacs/gmxpreprocess/grompp.h"
+#include "gromacs/gmxpreprocess/pdb2gmx.h"
+#include "gromacs/gmxpreprocess/protonate.h"
+#include "gromacs/gmxpreprocess/x2top.h"
namespace
{
compressed_x_output.cpp
# files with code for test fixtures
moduletest.cpp
- # pseudo libraries for code for grompp and mdrun
+ # pseudo-library for code for mdrun
$<TARGET_OBJECTS:mdrun_objlib>
- $<TARGET_OBJECTS:gmx_objlib>
)
gmx_register_integration_test(
${testname}
#include "gromacs/utility/file.h"
#include "gromacs/legacyheaders/network.h"
#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/gmxpreprocess/grompp.h"
#include "programs/mdrun/mdrun_main.h"
-#include "programs/gmx/legacycmainfunctions.h"
namespace gmx
{
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff