include/typedefs.h

   1 /*
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   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
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  21  * scientific software is very special. Version control is crucial -
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  35
  36 #ifndef _typedefs_h
  37 #define _typedefs_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #define STRLEN 4096
  44 #define NOTSET -12345
  45 #define BIG_STRLEN 1048576
  46
  47 #include <sys/types.h>
  48 #include <sysstuff.h>
  49 #include "types/simple.h"
  50 #include "types/enums.h"
  51 #include "types/block.h"
  52 #include "types/symtab.h"
  53 #include "types/idef.h"
  54 #include "types/atoms.h"
  55 #include "types/trx.h"
  56 #include "types/topology.h"
  57 #include "types/energy.h"
  58 #include "types/inputrec.h"
  59 #include "types/ishift.h"
  60 #include "types/graph.h"
  61 #include "types/nrnb.h"
  62 #include "types/nblist.h"
  63 #include "types/nsgrid.h"
  64 #include "types/commrec.h"
  65 #include "types/forcerec.h"
  66 #include "types/fcdata.h"
  67 #include "types/mdatom.h"
  68 #include "types/pbc.h"
  69 #include "types/ifunc.h"
  70 #include "types/filenm.h"
  71 #include "types/group.h"
  72 #include "types/state.h"
  73 #include "types/shellfc.h"
  74 #include "types/constr.h"
  75 #include "types/matrix.h"
  76 #include "types/oenv.h"
  77
  78 #ifdef __cplusplus
  79 extern "C" {
  80 #endif
  81
  82 /*
  83  * Memory (re)allocation can be VERY slow, especially with some
  84  * MPI libraries that replace the standard malloc and realloc calls.
  85  * To avoid slow memory allocation we use over_alloc to set the memory
  86  * allocation size for large data blocks. Since this scales the size
  87  * with a factor, we use log(n) realloc calls instead of n.
  88  * This can reduce allocation times from minutes to seconds.
  89  */
  90 /* This factor leads to 4 realloc calls to double the array size */
  91 #define OVER_ALLOC_FAC 1.19
  92
  93 extern void set_over_alloc_dd(bool set);
  94   /* Turns over allocation for variable size atoms/cg/top arrays on or off,
  95    * default is off.
  96    */
  97
  98 extern int over_alloc_dd(int n);
  99   /* Returns n when domain decomposition over allocation is off.
 100    * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
 101    * This is to avoid frequent reallocation
 102    * during domain decomposition in mdrun.
 103    */
 104
 105 /* Over allocation for small data types: int, real etc. */
 106 #define over_alloc_small(n) (OVER_ALLOC_FAC*(n) + 8000)
 107
 108 /* Over allocation for large data types: complex structs */
 109 #define over_alloc_large(n) (OVER_ALLOC_FAC*(n) + 1000)
 110
 111 extern int gmx_large_int_to_int(gmx_large_int_t step,const char *warn);
 112 /* Convert a gmx_large_int_t value to int.
 113  * If warn!=NULL a warning message will be written
 114  * to stderr when step does not fit in an int,
 115  * the first line is:
 116  * "WARNING during %s:", where warn is printed in %s.
 117  */
 118
 119 #define STEPSTRSIZE 22
 120
 121 extern char *gmx_step_str(gmx_large_int_t i,char *buf);
 122 /* Prints a gmx_large_int_t value in buf and returns the pointer to buf.
 123  * buf should be large enough to contain i: STEPSTRSIZE (22) chars.
 124  * When multiple gmx_large_int_t values are printed in the same printf call,
 125  * be sure to call gmx_step_str with different buffers.
 126  */
 127
 128 /* Functions to initiate and delete structures *
 129  * These functions are defined in gmxlib/typedefs.c
 130  */
 131 void init_block(t_block *block);
 132 void init_blocka(t_blocka *block);
 133 void init_atom (t_atoms *at);
 134 void init_mtop(gmx_mtop_t *mtop);
 135 void init_top (t_topology *top);
 136 void init_inputrec(t_inputrec *ir);
 137 void init_gtc_state(t_state *state,int ngtc, int nnhpres, int nhchainlength);
 138 void init_state(t_state *state,int natoms,int ngtc, int nnhpres, int nhchainlength);
 139
 140 void copy_blocka(const t_blocka *src,t_blocka *dest);
 141
 142 void done_block(t_block *block);
 143 void done_blocka(t_blocka *block);
 144 void done_atom (t_atoms *at);
 145 void done_moltype(gmx_moltype_t *molt);
 146 void done_molblock(gmx_molblock_t *molb);
 147 void done_mtop(gmx_mtop_t *mtop,bool bDoneSymtab);
 148 void done_top(t_topology *top);
 149 void done_inputrec(t_inputrec *ir);
 150 void done_state(t_state *state);
 151
 152 void set_box_rel(t_inputrec *ir,t_state *state);
 153 /* Set state->box_rel used in mdrun to preserve the box shape */
 154
 155 void preserve_box_shape(t_inputrec *ir,matrix box_rel,matrix b);
 156 /* Preserve the box shape, b can be box or boxv */
 157
 158 void stupid_fill_block(t_block *grp, int natom,bool bOneIndexGroup);
 159 /* Fill a block structure with numbers identical to the index
 160  * (0, 1, 2, .. natom-1)
 161  * If bOneIndexGroup, then all atoms are  lumped in one index group,
 162  * otherwise there is one atom per index entry
 163  */
 164
 165 void stupid_fill_blocka(t_blocka *grp, int natom);
 166 /* Fill a block structure with numbers identical to the index
 167  * (0, 1, 2, .. natom-1)
 168  * There is one atom per index entry
 169  */
 170
 171 extern void init_t_atoms(t_atoms *atoms, int natoms, bool bPdbinfo);
 172 /* allocate memory for the arrays, set nr to natoms and nres to 0
 173  * set pdbinfo to NULL or allocate memory for it */
 174
 175 extern t_atoms *copy_t_atoms(t_atoms *src);
 176 /* copy an atoms struct from src to a new one */
 177
 178 extern void add_t_atoms(t_atoms *atoms,int natom_extra,int nres_extra);
 179 /* allocate extra space for more atoms and or residues */
 180
 181 extern void t_atoms_set_resinfo(t_atoms *atoms,int atom_ind,t_symtab *symtab,
 182                                 const char *resname,int resnr,unsigned char ic,
 183                                 unsigned char chain);
 184 /* Set the residue name, number, insertion code and chain identifier
 185  * of atom index atom_ind.
 186  */
 187
 188 void free_t_atoms(t_atoms *atoms,bool bFreeNames);
 189 /* Free all the arrays and set the nr and nres to 0.
 190  * bFreeNames tells if to free the atom and residue name strings,
 191  * don't free them if they still need to be used in e.g. the topology struct.
 192  */
 193
 194 t_atoms *mtop2atoms(gmx_mtop_t *mtop);
 195 /* generate a t_atoms struct for the system from gmx_mtop_t */
 196
 197 real max_cutoff(real cutoff1,real cutoff2);
 198 /* Returns the maximum of the cut-off's, taking into account that 0=inf. */
 199
 200 #ifdef __cplusplus
 201 }
 202 #endif
 203
 204
 205 #endif  /* _typedefs_h */