/*
+ * 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,
- * 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
+ * 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
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * GROMACS is distributed in the hope that it will be useful,
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+ * Lesser General Public License for more details.
*
- * 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.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
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*
- * For more info, check our website at http://www.gromacs.org
+ * 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.
*
- * And Hey:
- * Gromacs Runs On Most of All Computer Systems
+ * 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 _typedefs_h
#define NOTSET -12345
#include <sys/types.h>
-#include "sysstuff.h"
-#include "types/simple.h"
-#include "types/enums.h"
-#include "types/block.h"
-#include "types/symtab.h"
-#include "types/idef.h"
-#include "types/atoms.h"
-#include "types/trx.h"
-#include "types/topology.h"
-#include "types/energy.h"
-#include "types/inputrec.h"
-#include "types/ishift.h"
-#include "types/graph.h"
-#include "types/nrnb.h"
-#include "types/nblist.h"
-#include "types/nbnxn_pairlist.h"
-#include "types/nsgrid.h"
-#include "types/forcerec.h"
-#include "types/fcdata.h"
-#include "types/mdatom.h"
-#include "types/pbc.h"
-#include "types/ifunc.h"
-#include "types/filenm.h"
-#include "types/group.h"
-#include "types/state.h"
-#include "types/shellfc.h"
-#include "types/constr.h"
-#include "types/matrix.h"
-#include "types/oenv.h"
+
+#include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/constr.h"
+#include "gromacs/legacyheaders/types/energy.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/fcdata.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/group.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/legacyheaders/types/nblist.h"
+#include "gromacs/legacyheaders/types/nrnb.h"
+#include "gromacs/legacyheaders/types/nsgrid.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/legacyheaders/types/shellfc.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/state.h"
+#include "gromacs/topology/topology.h"
#ifdef __cplusplus
extern "C" {
#endif
-/*
- * Memory (re)allocation can be VERY slow, especially with some
- * MPI libraries that replace the standard malloc and realloc calls.
- * To avoid slow memory allocation we use over_alloc to set the memory
- * allocation size for large data blocks. Since this scales the size
- * with a factor, we use log(n) realloc calls instead of n.
- * This can reduce allocation times from minutes to seconds.
- */
-/* This factor leads to 4 realloc calls to double the array size */
-#define OVER_ALLOC_FAC 1.19
-
-void set_over_alloc_dd(gmx_bool set);
-/* Turns over allocation for variable size atoms/cg/top arrays on or off,
- * default is off.
- */
-
-int over_alloc_dd(int n);
-/* Returns n when domain decomposition over allocation is off.
- * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
- * This is to avoid frequent reallocation
- * during domain decomposition in mdrun.
- */
-
-/* Over allocation for small data types: int, real etc. */
-#define over_alloc_small(n) (int)(OVER_ALLOC_FAC*(n) + 8000)
-
-/* Over allocation for large data types: complex structs */
-#define over_alloc_large(n) (int)(OVER_ALLOC_FAC*(n) + 1000)
-
-int gmx_large_int_to_int(gmx_large_int_t step, const char *warn);
-/* Convert a gmx_large_int_t value to int.
+int gmx_int64_to_int(gmx_int64_t step, const char *warn);
+/* Convert a gmx_int64_t value to int.
* If warn!=NULL a warning message will be written
* to stderr when step does not fit in an int,
* the first line is:
* "WARNING during %s:", where warn is printed in %s.
*/
-#define STEPSTRSIZE 22
-
-char *gmx_step_str(gmx_large_int_t i, char *buf);
-/* Prints a gmx_large_int_t value in buf and returns the pointer to buf.
- * buf should be large enough to contain i: STEPSTRSIZE (22) chars.
- * When multiple gmx_large_int_t values are printed in the same printf call,
- * be sure to call gmx_step_str with different buffers.
- */
-
/* Functions to initiate and delete structures *
* These functions are defined in gmxlib/typedefs.c
*/
-void init_block(t_block *block);
-void init_blocka(t_blocka *block);
-void init_atom (t_atoms *at);
-void init_mtop(gmx_mtop_t *mtop);
-void init_top (t_topology *top);
void init_inputrec(t_inputrec *ir);
void init_energyhistory(energyhistory_t * enerhist);
void done_energyhistory(energyhistory_t * enerhist);
void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength);
void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda);
-void init_df_history(df_history_t *dfhist, int nlambda, real wl_delta);
+t_state *serial_init_local_state(t_state *state_global);
+void init_df_history(df_history_t *dfhist, int nlambda);
+void done_df_history(df_history_t *dfhist);
void copy_df_history(df_history_t * df_dest, df_history_t *df_source);
-
-void copy_blocka(const t_blocka *src, t_blocka *dest);
-
-void done_block(t_block *block);
-void done_blocka(t_blocka *block);
-void done_atom (t_atoms *at);
-void done_moltype(gmx_moltype_t *molt);
-void done_molblock(gmx_molblock_t *molb);
-void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab);
-void done_top(t_topology *top);
void done_inputrec(t_inputrec *ir);
void done_state(t_state *state);
void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b);
/* Preserve the box shape, b can be box or boxv */
-void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup);
-/* Fill a block structure with numbers identical to the index
- * (0, 1, 2, .. natom-1)
- * If bOneIndexGroup, then all atoms are lumped in one index group,
- * otherwise there is one atom per index entry
- */
-
-void stupid_fill_blocka(t_blocka *grp, int natom);
-/* Fill a block structure with numbers identical to the index
- * (0, 1, 2, .. natom-1)
- * There is one atom per index entry
- */
-
-void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
-/* allocate memory for the arrays, set nr to natoms and nres to 0
- * set pdbinfo to NULL or allocate memory for it */
-
-t_atoms *copy_t_atoms(t_atoms *src);
-/* copy an atoms struct from src to a new one */
-
-void add_t_atoms(t_atoms *atoms, int natom_extra, int nres_extra);
-/* allocate extra space for more atoms and or residues */
-
-void t_atoms_set_resinfo(t_atoms *atoms, int atom_ind, t_symtab *symtab,
- const char *resname, int resnr, unsigned char ic,
- int chainnum, char chainid);
-/* Set the residue name, number, insertion code and chain identifier
- * of atom index atom_ind.
- */
-
-void free_t_atoms(t_atoms *atoms, gmx_bool bFreeNames);
-/* Free all the arrays and set the nr and nres to 0.
- * bFreeNames tells if to free the atom and residue name strings,
- * don't free them if they still need to be used in e.g. the topology struct.
- */
-
-t_atoms *mtop2atoms(gmx_mtop_t *mtop);
-/* generate a t_atoms struct for the system from gmx_mtop_t */
-
real max_cutoff(real cutoff1, real cutoff2);
/* Returns the maximum of the cut-off's, taking into account that 0=inf. */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff