include/typedefs.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team,
   6  * check out http://www.gromacs.org for more information.
   7  * Copyright (c) 2012, by the GROMACS development team, led by
   8  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
   9  * others, as listed in the AUTHORS file in the top-level source
  10  * directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
  18  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
  24  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
  28  * consider that scientific software is very special. Version
  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
  33  * official version at http://www.gromacs.org.
  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  38
  39 #ifndef _typedefs_h
  40 #define _typedefs_h
  41
  42
  43 /* DEPRECATED! value for signaling unitialized variables */
  44 #define NOTSET -12345
  45
  46 #include <sys/types.h>
  47 #include "visibility.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/nbnxn_pairlist.h"
  64 #include "types/nsgrid.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 GMX_LIBGMX_EXPORT
  94 void set_over_alloc_dd(gmx_bool set);
  95   /* Turns over allocation for variable size atoms/cg/top arrays on or off,
  96    * default is off.
  97    */
  98
  99 GMX_LIBGMX_EXPORT
 100 int over_alloc_dd(int n);
 101   /* Returns n when domain decomposition over allocation is off.
 102    * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
 103    * This is to avoid frequent reallocation
 104    * during domain decomposition in mdrun.
 105    */
 106
 107 /* Over allocation for small data types: int, real etc. */
 108 #define over_alloc_small(n) (OVER_ALLOC_FAC*(n) + 8000)
 109
 110 /* Over allocation for large data types: complex structs */
 111 #define over_alloc_large(n) (OVER_ALLOC_FAC*(n) + 1000)
 112
 113 GMX_LIBGMX_EXPORT
 114 int gmx_large_int_to_int(gmx_large_int_t step,const char *warn);
 115 /* Convert a gmx_large_int_t value to int.
 116  * If warn!=NULL a warning message will be written
 117  * to stderr when step does not fit in an int,
 118  * the first line is:
 119  * "WARNING during %s:", where warn is printed in %s.
 120  */
 121
 122 #define STEPSTRSIZE 22
 123
 124 GMX_LIBGMX_EXPORT
 125 char *gmx_step_str(gmx_large_int_t i,char *buf);
 126 /* Prints a gmx_large_int_t value in buf and returns the pointer to buf.
 127  * buf should be large enough to contain i: STEPSTRSIZE (22) chars.
 128  * When multiple gmx_large_int_t values are printed in the same printf call,
 129  * be sure to call gmx_step_str with different buffers.
 130  */
 131
 132 /* Functions to initiate and delete structures *
 133  * These functions are defined in gmxlib/typedefs.c
 134  */
 135 GMX_LIBGMX_EXPORT
 136 void init_block(t_block *block);
 137 GMX_LIBGMX_EXPORT
 138 void init_blocka(t_blocka *block);
 139 GMX_LIBGMX_EXPORT
 140 void init_atom (t_atoms *at);
 141 GMX_LIBGMX_EXPORT
 142 void init_mtop(gmx_mtop_t *mtop);
 143 GMX_LIBGMX_EXPORT
 144 void init_top (t_topology *top);
 145 void init_inputrec(t_inputrec *ir);
 146 GMX_LIBGMX_EXPORT
 147 void init_energyhistory(energyhistory_t * enerhist);
 148 GMX_LIBGMX_EXPORT
 149 void done_energyhistory(energyhistory_t * enerhist);
 150 GMX_LIBGMX_EXPORT
 151 void init_gtc_state(t_state *state,int ngtc, int nnhpres, int nhchainlength);
 152 GMX_LIBGMX_EXPORT
 153 void init_state(t_state *state,int natoms,int ngtc, int nnhpres, int nhchainlength, int nlambda);
 154 GMX_LIBGMX_EXPORT
 155 void init_df_history(df_history_t *dfhist, int nlambda, real wl_delta);
 156 GMX_LIBGMX_EXPORT
 157 void copy_df_history(df_history_t * df_dest, df_history_t *df_source);
 158
 159 GMX_LIBGMX_EXPORT
 160 void copy_blocka(const t_blocka *src,t_blocka *dest);
 161
 162 GMX_LIBGMX_EXPORT
 163 void done_block(t_block *block);
 164 GMX_LIBGMX_EXPORT
 165 void done_blocka(t_blocka *block);
 166 GMX_LIBGMX_EXPORT
 167 void done_atom (t_atoms *at);
 168 void done_moltype(gmx_moltype_t *molt);
 169 void done_molblock(gmx_molblock_t *molb);
 170 void done_mtop(gmx_mtop_t *mtop,gmx_bool bDoneSymtab);
 171 void done_top(t_topology *top);
 172 void done_inputrec(t_inputrec *ir);
 173 GMX_LIBGMX_EXPORT
 174 void done_state(t_state *state);
 175
 176 GMX_LIBGMX_EXPORT
 177 void set_box_rel(t_inputrec *ir,t_state *state);
 178 /* Set state->box_rel used in mdrun to preserve the box shape */
 179
 180 GMX_LIBGMX_EXPORT
 181 void preserve_box_shape(t_inputrec *ir,matrix box_rel,matrix b);
 182 /* Preserve the box shape, b can be box or boxv */
 183
 184 GMX_LIBGMX_EXPORT
 185 void stupid_fill_block(t_block *grp, int natom,gmx_bool bOneIndexGroup);
 186 /* Fill a block structure with numbers identical to the index
 187  * (0, 1, 2, .. natom-1)
 188  * If bOneIndexGroup, then all atoms are  lumped in one index group,
 189  * otherwise there is one atom per index entry
 190  */
 191
 192 GMX_LIBGMX_EXPORT
 193 void stupid_fill_blocka(t_blocka *grp, int natom);
 194 /* Fill a block structure with numbers identical to the index
 195  * (0, 1, 2, .. natom-1)
 196  * There is one atom per index entry
 197  */
 198
 199 GMX_LIBGMX_EXPORT
 200 void init_t_atoms(t_atoms *atoms, int natoms, gmx_bool bPdbinfo);
 201 /* allocate memory for the arrays, set nr to natoms and nres to 0
 202  * set pdbinfo to NULL or allocate memory for it */
 203
 204 t_atoms *copy_t_atoms(t_atoms *src);
 205 /* copy an atoms struct from src to a new one */
 206
 207 void add_t_atoms(t_atoms *atoms,int natom_extra,int nres_extra);
 208 /* allocate extra space for more atoms and or residues */
 209
 210 GMX_LIBGMX_EXPORT
 211 void t_atoms_set_resinfo(t_atoms *atoms,int atom_ind,t_symtab *symtab,
 212                                 const char *resname,int resnr,unsigned char ic,
 213                                 int chainnum, char chainid);
 214 /* Set the residue name, number, insertion code and chain identifier
 215  * of atom index atom_ind.
 216  */
 217
 218 GMX_LIBGMX_EXPORT
 219 void free_t_atoms(t_atoms *atoms,gmx_bool bFreeNames);
 220 /* Free all the arrays and set the nr and nres to 0.
 221  * bFreeNames tells if to free the atom and residue name strings,
 222  * don't free them if they still need to be used in e.g. the topology struct.
 223  */
 224
 225 t_atoms *mtop2atoms(gmx_mtop_t *mtop);
 226 /* generate a t_atoms struct for the system from gmx_mtop_t */
 227
 228 GMX_LIBGMX_EXPORT
 229 real max_cutoff(real cutoff1,real cutoff2);
 230 /* Returns the maximum of the cut-off's, taking into account that 0=inf. */
 231
 232 #ifdef __cplusplus
 233 }
 234 #endif
 235
 236
 237 #endif  /* _typedefs_h */