src/gromacs/gmxpreprocess/grompp-impl.h

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  37
  38 #ifndef GMX_GMXPREPROCESS_GROMPP_IMPL_H
  39 #define GMX_GMXPREPROCESS_GROMPP_IMPL_H
  40
  41 #include "gromacs/topology/atom_id.h"
  42 #include "gromacs/topology/atoms.h"
  43 #include "gromacs/topology/block.h"
  44 #include "gromacs/topology/idef.h"
  45 #include "gromacs/utility/basedefinitions.h"
  46 #include "gromacs/utility/real.h"
  47
  48 struct t_block;
  49 struct t_blocka;
  50
  51 #define MAXSLEN 32
  52
  53 typedef struct {
  54     gmx_bool bSet;              /* Has this combination been set        */
  55     real     c[4];              /* The non-bonded parameters            */
  56 } t_nbparam;
  57 /* The t_nbparam struct is used to temporary store the explicit
  58  * non-bonded parameter combinations, which will be copied to t_params.
  59  */
  60
  61 typedef struct {
  62     atom_id    a[MAXATOMLIST];   /* The atom list (eg. bonds: particle  */
  63     /* i = a[0] (ai), j = a[1] (aj))    */
  64     real       c[MAXFORCEPARAM]; /* Force parameters (eg. b0 = c[0])    */
  65     char       s[MAXSLEN];       /* A string (instead of parameters),    *
  66                                   * read from the .rtp file in pdb2gmx   */
  67     atom_id   &ai() { return a[0]; }
  68     atom_id   &aj() { return a[1]; }
  69     atom_id   &ak() { return a[2]; }
  70     atom_id   &al() { return a[3]; }
  71     atom_id   &am() { return a[4]; }
  72
  73     real      &c0() { return c[0]; }
  74     real      &c1() { return c[1]; }
  75     real      &c2() { return c[2]; }
  76 } t_param;
  77
  78 typedef struct {
  79     int          nr;    /* The number of bonds in this record   */
  80     int          maxnr; /* The amount of elements in the array  */
  81     t_param     *param; /* Array of parameters (dim: nr)        */
  82
  83     /* CMAP tmp data, there are probably better places for this */
  84     int         grid_spacing; /* Cmap grid spacing */
  85     int         nc;           /* Number of cmap angles */
  86
  87     real       *cmap;         /* Temporary storage of the raw cmap grid data */
  88     int         ncmap;        /* Number of allocated elements in cmap grid*/
  89
  90     int        *cmap_types;   /* Store the five atomtypes followed by a number that identifies the type */
  91     int         nct;          /* Number of allocated elements in cmap_types */
  92
  93 } t_params;
  94
  95 typedef struct {
  96     int            nr;          /* The number of exclusions             */
  97     atom_id       *e;           /* The excluded atoms                   */
  98 } t_excls;
  99
 100 typedef struct {
 101     char            **name;
 102     int               nrexcl;       /* Number of exclusions per atom    */
 103     gmx_bool          excl_set;     /* Have exclusions been generated?  */
 104     gmx_bool          bProcessed;   /* Has the mol been processed           */
 105     t_atoms           atoms;        /* Atoms                                */
 106     t_block           cgs;          /* Charge groups                        */
 107     t_block           mols;         /* Molecules                            */
 108     t_blocka          excls;        /* Exclusions                           */
 109     t_params          plist[F_NRE]; /* Parameters in old style              */
 110 } t_molinfo;
 111
 112 typedef struct {
 113     char *name;
 114     int   nr;
 115 } t_mols;
 116
 117 gmx_bool is_int(double x);
 118 /* Returns TRUE when x is integer */
 119
 120 /* Must correspond to strings in topdirs.c */
 121 typedef enum {
 122     d_defaults,
 123     d_atomtypes,
 124     d_bondtypes,
 125     d_constrainttypes,
 126     d_pairtypes,
 127     d_angletypes,
 128     d_dihedraltypes,
 129     d_nonbond_params,
 130     d_implicit_genborn_params,
 131     d_implicit_surface_params,
 132     d_cmaptypes,
 133     d_moleculetype,
 134     d_atoms,
 135     d_vsites2,
 136     d_vsites3,
 137     d_vsites4,
 138     d_vsitesn,
 139     d_bonds,
 140     d_exclusions,
 141     d_pairs,
 142     d_pairs_nb,
 143     d_angles,
 144     d_dihedrals,
 145     d_constraints,
 146     d_settles,
 147     d_polarization,
 148     d_water_polarization,
 149     d_thole_polarization,
 150     d_system,
 151     d_molecules,
 152     d_position_restraints,
 153     d_angle_restraints,
 154     d_angle_restraints_z,
 155     d_distance_restraints,
 156     d_orientation_restraints,
 157     d_dihedral_restraints,
 158     d_cmap,
 159     d_intermolecular_interactions,
 160     d_maxdir,
 161     d_invalid,
 162     d_none
 163 } directive;
 164
 165 #endif