include/typedefs.h

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