include/typedefs.h

   1 /*
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   8  *          GROningen MAchine for Chemical Simulations
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  10  *                        VERSION 3.2.0
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  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
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  36
  37 #ifndef _typedefs_h
  38 #define _typedefs_h
  39
  40 #ifdef HAVE_CONFIG_H
  41 #include <config.h>
  42 #endif
  43
  44 #ifdef CPLUSPLUS
  45 extern "C" {
  46 #endif
  47
  48 #define STRLEN 4096
  49 #define NOTSET -12345
  50
  51 #include <sys/types.h>
  52 #include <sysstuff.h>
  53 #include <types/simple.h>
  54 #include <types/enums.h>
  55 #include <types/block.h>
  56 #include <types/symtab.h>
  57 #include <types/idef.h>
  58 #include <types/atoms.h>
  59 #include <types/trx.h>
  60 #include <types/topology.h>
  61 #include <types/energy.h>
  62 #include <types/inputrec.h>
  63 #include <types/ishift.h>
  64 #include <types/graph.h>
  65 #include <types/nrnb.h>
  66 #include <types/nblist.h>
  67 #include <types/nsgrid.h>
  68 #include <types/commrec.h>
  69 #include <types/forcerec.h>
  70 #include <types/fcdata.h>
  71 #include <types/mdatom.h>
  72 #include <types/pbc.h>
  73 #include <types/ifunc.h>
  74 #include <types/filenm.h>
  75 #include <types/group.h>
  76 #include <types/state.h>
  77 #include <types/shellfc.h>
  78 #include <types/constr.h>
  79 #include <types/matrix.h>
  80
  81 /*
  82  * Memory (re)allocation can be VERY slow, especially with some
  83  * MPI libraries that replace the standard malloc and realloc calls.
  84  * To avoid slow memory allocation we use over_alloc to set the memory
  85  * allocation size for large data blocks. Since this scales the size
  86  * with a factor, we use log(n) realloc calls instead of n.
  87  * This can reduce allocation times from minutes to seconds.
  88  */
  89 /* This factor leads to 4 realloc calls to double the array size */
  90 #define OVER_ALLOC_FAC 1.19
  91
  92 extern void set_over_alloc_dd(bool set);
  93   /* Turns over allocation for variable size atoms/cg/top arrays on or off,
  94    * default is off.
  95    */
  96
  97 extern int over_alloc_dd(int n);
  98   /* Returns n when domain decomposition over allocation is off.
  99    * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
 100    * This is to avoid frequent reallocation
 101    * during domain decomposition in mdrun.
 102    */
 103
 104 /* Over allocation for small data types: int, real etc. */
 105 #define over_alloc_small(n) (OVER_ALLOC_FAC*(n) + 8000)
 106
 107 /* Over allocation for large data types: complex structs */
 108 #define over_alloc_large(n) (OVER_ALLOC_FAC*(n) + 1000)
 109
 110 /* Functions to initiate and delete structures *
 111  * These functions are defined in gmxlib/typedefs.c
 112  */
 113 void init_block(t_block *block);
 114 void init_blocka(t_blocka *block);
 115 void init_atom (t_atoms *at);
 116 void init_mtop(gmx_mtop_t *mtop);
 117 void init_top (t_topology *top);
 118 void init_inputrec(t_inputrec *ir);
 119 void init_gtc_state(t_state *state,int ngtc);
 120 void init_state(t_state *state,int natoms,int ngtc);
 121
 122 void copy_blocka(const t_blocka *src,t_blocka *dest);
 123
 124 void done_block(t_block *block);
 125 void done_blocka(t_blocka *block);
 126 void done_atom (t_atoms *at);
 127 void done_moltype(gmx_moltype_t *molt);
 128 void done_molblock(gmx_molblock_t *molb);
 129 void done_mtop(gmx_mtop_t *mtop,bool bDoneSymtab);
 130 void done_top(t_topology *top);
 131 void done_inputrec(t_inputrec *ir);
 132 void done_state(t_state *state);
 133
 134 void set_box_rel(t_inputrec *ir,t_state *state);
 135 /* Set state->box_rel used in mdrun to preserve the box shape */
 136
 137 void preserve_box_shape(t_inputrec *ir,matrix box_rel,matrix b);
 138 /* Preserve the box shape, b can be box or boxv */
 139
 140 void stupid_fill_block(t_block *grp, int natom,bool bOneIndexGroup);
 141 /* Fill a block structure with numbers identical to the index
 142  * (0, 1, 2, .. natom-1)
 143  * If bOneIndexGroup, then all atoms are  lumped in one index group,
 144  * otherwise there is one atom per index entry
 145  */
 146
 147 void stupid_fill_blocka(t_blocka *grp, int natom);
 148 /* Fill a block structure with numbers identical to the index
 149  * (0, 1, 2, .. natom-1)
 150  * There is one atom per index entry
 151  */
 152
 153 void init_t_atoms(t_atoms *atoms, int natoms, bool bPdbinfo);
 154 /* allocate memory for the arrays, set nr to natoms and nres to 0
 155  * set pdbinfo to NULL or allocate memory for it */
 156
 157 void free_t_atoms(t_atoms *atoms,bool bFreeNames);
 158 /* free all the arrays and set the nr and nres to 0 */
 159
 160 t_atoms *mtop2atoms(gmx_mtop_t *mtop);
 161 /* generate a t_atoms struct for the system from gmx_mtop_t */
 162
 163 #ifdef CPLUSPLUS
 164 }
 165 #endif
 166
 167
 168 #endif  /* _typedefs_h */