include/mtop_util.h

   1 /*
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   4  *
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   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "typedefs.h"
  40
  41
  42 /* Returns the total number of charge groups in mtop */
  43 extern int
  44 ncg_mtop(const gmx_mtop_t *mtop);
  45
  46
  47 /* Returns a pointer to the t_atom struct belonging to atnr_global.
  48  * This can be an expensive operation, so if possible use
  49  * one of the atom loop constructs below.
  50  */
  51 extern void
  52 gmx_mtop_atomnr_to_atom(const gmx_mtop_t *mtop,int atnr_global,
  53                         t_atom **atom);
  54
  55
  56 /* Returns a pointer to the molecule interaction array ilist_mol[F_NRE]
  57  * and the local atom number in the molecule belonging to atnr_global.
  58  */
  59 extern void
  60 gmx_mtop_atomnr_to_ilist(const gmx_mtop_t *mtop,int atnr_global,
  61                          t_ilist **ilist_mol,int *atnr_offset);
  62
  63
  64 /* Returns the molecule block index
  65  * and the molecule number in the block
  66  * and the atom number offset for the atom indices in moltype
  67  * belonging to atnr_global.
  68  */
  69 extern void
  70 gmx_mtop_atomnr_to_molblock_ind(const gmx_mtop_t *mtop,int atnr_global,
  71                                 int *molb,int *molnr,int *atnr_mol);
  72
  73
  74 /* Returns atom name, global resnr and residue name  of atom atnr_global */
  75 extern void
  76 gmx_mtop_atominfo_global(const gmx_mtop_t *mtop,int atnr_global,
  77                          char **atomname,int *resnr,char **resname);
  78
  79
  80 /* Abstract type for atom loop over all atoms */
  81 typedef struct gmx_mtop_atomloop_all *gmx_mtop_atomloop_all_t;
  82
  83 /* Initialize an atom loop over all atoms in the system.
  84  * The order of the atoms will be as in the state struct.
  85  * Only use this when you really need to loop over all atoms,
  86  * i.e. when you use groups which might differ per molecule,
  87  * otherwise use gmx_mtop_atomloop_block.
  88  */
  89 extern gmx_mtop_atomloop_all_t
  90 gmx_mtop_atomloop_all_init(const gmx_mtop_t *mtop);
  91
  92 /* Loop to the next atom.
  93  * When not at the end:
  94  *   returns TRUE and at_global,
  95  *   writes the global atom number in *at_global
  96  *   and sets the pointer atom to the t_atom struct of that atom.
  97  * When at the end, destroys aloop and returns FALSE.
  98  * Use as:
  99  * gmx_mtop_atomloop_all_t aloop;
 100  * aloop = gmx_mtop_atomloop_all_init(mtop)
 101  * while (gmx_mtop_atomloop_all_next(aloop,&at_global,&atom)) {
 102  *     ...
 103  * }
 104  */
 105 extern bool
 106 gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
 107                            int *at_global,t_atom **atom);
 108
 109 /* Return the atomname, the residue number and residue name
 110  * of the current atom in the loop.
 111  */
 112 extern void
 113 gmx_mtop_atomloop_all_names(gmx_mtop_atomloop_all_t aloop,
 114                             char **atomname,int *resnr,char **resname);
 115
 116 /* Return the a pointer to the moltype struct of the current atom
 117  * in the loop and the atom number in the molecule.
 118  */
 119 extern void
 120 gmx_mtop_atomloop_all_moltype(gmx_mtop_atomloop_all_t aloop,
 121                               gmx_moltype_t **moltype,int *at_mol);
 122
 123
 124 /* Abstract type for atom loop over atoms in all molecule blocks */
 125 typedef struct gmx_mtop_atomloop_block *gmx_mtop_atomloop_block_t;
 126
 127 /* Initialize an atom loop over atoms in all molecule blocks the system.
 128  */
 129 extern gmx_mtop_atomloop_block_t
 130 gmx_mtop_atomloop_block_init(const gmx_mtop_t *mtop);
 131
 132 /* Loop to the next atom.
 133  * When not at the end:
 134  *   returns TRUE
 135  *   sets the pointer atom to the t_atom struct of that atom
 136  *   and return the number of molecules corresponding to this atom.
 137  * When at the end, destroys aloop and returns FALSE.
 138  * Use as:
 139  * gmx_mtop_atomloop_block_t aloop;
 140  * aloop = gmx_mtop_atomloop_block_init(mtop)
 141  * while (gmx_mtop_atomloop_block_next(aloop,&atom,&nmol)) {
 142  *     ...
 143  * }
 144  */
 145 extern bool
 146 gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
 147                              t_atom **atom,int *nmol);
 148
 149
 150 /* Abstract type for ilist loop over all ilists */
 151 typedef struct gmx_mtop_ilistloop *gmx_mtop_ilistloop_t;
 152
 153 /* Initialize an ilist loop over all molecule types in the system. */
 154 extern gmx_mtop_ilistloop_t
 155 gmx_mtop_ilistloop_init(const gmx_mtop_t *mtop);
 156
 157
 158 /* Loop to the next molecule,
 159  * When not at the end:
 160  *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 161  *   writes the number of molecules for this ilist in *nmol.
 162  * When at the end, destroys iloop and returns FALSE.
 163  */
 164 extern bool
 165 gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
 166                         t_ilist **ilist_mol,int *nmol);
 167
 168
 169 /* Abstract type for ilist loop over all ilists of all molecules */
 170 typedef struct gmx_mtop_ilistloop_all *gmx_mtop_ilistloop_all_t;
 171
 172 /* Initialize an ilist loop over all molecule types in the system.
 173  * Only use this when you really need to loop over all molecules,
 174  * i.e. when you use groups which might differ per molecule,
 175  * otherwise use gmx_mtop_ilistloop.
 176  */
 177 extern gmx_mtop_ilistloop_all_t
 178 gmx_mtop_ilistloop_all_init(const gmx_mtop_t *mtop);
 179
 180 /* Loop to the next molecule,
 181  * When not at the end:
 182  *   returns TRUE and a pointer to the next array ilist_mol[F_NRE],
 183  *   writes the atom offset which should be added to iatoms in atnr_offset.
 184  * When at the end, destroys iloop and returns FALSE.
 185  */
 186 extern bool
 187 gmx_mtop_ilistloop_all_next(gmx_mtop_ilistloop_all_t iloop,
 188                             t_ilist **ilist_mol,int *atnr_offset);
 189
 190
 191 /* Returns the total number of interactions in the system of type ftype */
 192 extern int
 193 gmx_mtop_ftype_count(const gmx_mtop_t *mtop,int ftype);
 194
 195
 196 /* Returns a charge group index for the whole system */
 197 extern t_block
 198 gmx_mtop_global_cgs(const gmx_mtop_t *mtop);
 199
 200
 201 /* Returns a single t_atoms struct for the whole system */
 202 extern t_atoms
 203 gmx_mtop_global_atoms(const gmx_mtop_t *mtop);
 204
 205
 206 /* Make all charge groups the size of one atom.
 207  * When bKeepSingleMolCG==TRUE keep charge groups for molecules
 208  * that consist of a single charge group.
 209  */
 210 extern void
 211 gmx_mtop_make_atomic_charge_groups(gmx_mtop_t *mtop,bool bKeepSingleMolCG);
 212
 213
 214 /* Generate a 'local' topology for the whole system.
 215  * When ir!=NULL the free energy interactions will be sorted to the end.
 216  */
 217 extern gmx_localtop_t *
 218 gmx_mtop_generate_local_top(const gmx_mtop_t *mtop,const t_inputrec *ir);
 219
 220
 221 /* Converts a gmx_mtop_t struct to t_topology.
 222  * All memory relating only to mtop will be freed.
 223  */
 224 extern t_topology
 225 gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop);