include/typedefs.h

   1 /*
   2  *
   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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  20  * If you want to redistribute modifications, please consider that
  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 extern char *gmx_step_str(gmx_large_int_t i,char *buf);
 120 /* Prints a gmx_large_int_t value in buf and returns the pointer to buf.
 121  * buf should be large enough to contain i: 22 chars.
 122  * When multiple gmx_large_int_t values are printed in the same printf call,
 123  * be sure to call gmx_step_str with different buffers.
 124  */
 125
 126 /* Functions to initiate and delete structures *
 127  * These functions are defined in gmxlib/typedefs.c
 128  */
 129 void init_block(t_block *block);
 130 void init_blocka(t_blocka *block);
 131 void init_atom (t_atoms *at);
 132 void init_mtop(gmx_mtop_t *mtop);
 133 void init_top (t_topology *top);
 134 void init_inputrec(t_inputrec *ir);
 135 void init_gtc_state(t_state *state,int ngtc);
 136 void init_state(t_state *state,int natoms,int ngtc);
 137
 138 void copy_blocka(const t_blocka *src,t_blocka *dest);
 139
 140 void done_block(t_block *block);
 141 void done_blocka(t_blocka *block);
 142 void done_atom (t_atoms *at);
 143 void done_moltype(gmx_moltype_t *molt);
 144 void done_molblock(gmx_molblock_t *molb);
 145 void done_mtop(gmx_mtop_t *mtop,bool bDoneSymtab);
 146 void done_top(t_topology *top);
 147 void done_inputrec(t_inputrec *ir);
 148 void done_state(t_state *state);
 149
 150 void set_box_rel(t_inputrec *ir,t_state *state);
 151 /* Set state->box_rel used in mdrun to preserve the box shape */
 152
 153 void preserve_box_shape(t_inputrec *ir,matrix box_rel,matrix b);
 154 /* Preserve the box shape, b can be box or boxv */
 155
 156 void stupid_fill_block(t_block *grp, int natom,bool bOneIndexGroup);
 157 /* Fill a block structure with numbers identical to the index
 158  * (0, 1, 2, .. natom-1)
 159  * If bOneIndexGroup, then all atoms are  lumped in one index group,
 160  * otherwise there is one atom per index entry
 161  */
 162
 163 void stupid_fill_blocka(t_blocka *grp, int natom);
 164 /* Fill a block structure with numbers identical to the index
 165  * (0, 1, 2, .. natom-1)
 166  * There is one atom per index entry
 167  */
 168
 169 void init_t_atoms(t_atoms *atoms, int natoms, bool bPdbinfo);
 170 /* allocate memory for the arrays, set nr to natoms and nres to 0
 171  * set pdbinfo to NULL or allocate memory for it */
 172
 173 extern void t_atoms_set_resinfo(t_atoms *atoms,int atom_ind,t_symtab *symtab,
 174                                 const char *resname,int resnr,unsigned char ic,
 175                                 unsigned char chain);
 176 /* Set the residue name, number, insertion code and chain identifier
 177  * of atom index atom_ind.
 178  */
 179
 180 void free_t_atoms(t_atoms *atoms,bool bFreeNames);
 181 /* free all the arrays and set the nr and nres to 0 */
 182
 183 t_atoms *mtop2atoms(gmx_mtop_t *mtop);
 184 /* generate a t_atoms struct for the system from gmx_mtop_t */
 185
 186 real max_cutoff(real cutoff1,real cutoff2);
 187 /* Returns the maximum of the cut-off's, taking into account that 0=inf. */
 188
 189 #ifdef __cplusplus
 190 }
 191 #endif
 192
 193
 194 #endif  /* _typedefs_h */