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40 #include "visibility.h"
51 gmx_bool bSet
; /* Has this combination been set */
52 real c
[4]; /* The non-bonded parameters */
54 /* The t_nbparam struct is used to temporary store the explicit
55 * non-bonded parameter combinations, which will be copied to t_params.
59 atom_id a
[MAXATOMLIST
]; /* The atom list (eg. bonds: particle */
60 /* i = a[0] (AI), j = a[1] (AJ)) */
61 real c
[MAXFORCEPARAM
]; /* Force parameters (eg. b0 = c[0]) */
62 char s
[MAXSLEN
]; /* A string (instead of parameters), *
63 * read from the .rtp file in pdb2gmx */
67 int nr
; /* The number of bonds in this record */
68 int maxnr
; /* The amount of elements in the array */
69 t_param
*param
; /* Array of parameters (dim: nr) */
71 /* CMAP tmp data, there are probably better places for this */
72 int grid_spacing
; /* Cmap grid spacing */
73 int nc
; /* Number of cmap angles */
75 real
*cmap
; /* Temporary storage of the raw cmap grid data */
76 int ncmap
; /* Number of allocated elements in cmap grid*/
78 int *cmap_types
; /* Store the five atomtypes followed by a number that identifies the type */
79 int nct
; /* Number of allocated elements in cmap_types */
84 int nr
; /* The number of exclusions */
85 atom_id
*e
; /* The excluded atoms */
90 int nrexcl
; /* Number of exclusions per atom */
91 gmx_bool excl_set
; /* Have exclusions been generated? */
92 gmx_bool bProcessed
; /* Has the mol been processed */
93 t_atoms atoms
; /* Atoms */
94 t_block cgs
; /* Charge groups */
95 t_block mols
; /* Molecules */
96 t_blocka excls
; /* Exclusions */
97 t_params plist
[F_NRE
]; /* Parameters in old style */
105 GMX_LIBGMXPREPROCESS_EXPORT
106 gmx_bool
is_int(double x
);
107 /* Returns TRUE when x is integer */
118 d_implicit_genborn_params
,
119 d_implicit_surface_params
,
136 d_water_polarization
,
137 d_thole_polarization
,
140 d_position_restraints
,
142 d_angle_restraints_z
,
143 d_distance_restraints
,
144 d_orientation_restraints
,
145 d_dihedral_restraints
,
152 static const char *ds
[d_maxdir
+1] = {
161 "implicit_genborn_params",
162 "implicit_surface_params",
164 /* All the directives above can not appear after moleculetype */
180 "water_polarization",
181 "thole_polarization",
184 "position_restraints",
186 "angle_restraints_z",
187 "distance_restraints",
188 "orientation_restraints",
189 "dihedral_restraints",
198 #endif /* _grompp_h */