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38 #ifndef GMX_LEGACYHEADERS_TYPES_GENBORN_H
39 #define GMX_LEGACYHEADERS_TYPES_GENBORN_H
45 #include "gromacs/legacyheaders/types/simple.h"
54 typedef struct gbtmpnbls *gbtmpnbls_t;
56 /* Struct to hold all the information for GB */
59 int nr; /* number of atoms, length of arrays below */
60 int n12; /* number of 1-2 (bond) interactions */
61 int n13; /* number of 1-3 (angle) terms */
62 int n14; /* number of 1-4 (torsion) terms */
63 int nalloc; /* Allocation of local arrays (with DD) */
66 /* Arrays below that end with _globalindex are used for setting up initial values of
67 * all gb parameters and values. They all have length natoms, which for DD is the
69 * Values are then taken from these arrays to local copies, that have names without
70 * _globalindex, in the routine make_local_gb(), which is called once for single
71 * node runs, and for DD at every call to dd_partition_system
74 real *gpol; /* Atomic polarisation energies */
75 real *gpol_globalindex; /* */
76 real *gpol_still_work; /* Work array for Still model */
77 real *gpol_hct_work; /* Work array for HCT/OBC models */
78 real *bRad; /* Atomic Born radii */
79 real *vsolv; /* Atomic solvation volumes */
80 real *vsolv_globalindex; /* */
81 real *gb_radius; /* Radius info, copied from atomtypes */
82 real *gb_radius_globalindex;
84 int *use; /* Array that till if this atom does GB */
85 int *use_globalindex; /* Global array for parallelization */
87 real es; /* Solvation energy and derivatives */
88 real *asurf; /* Atomic surface area */
89 rvec *dasurf; /* Surface area derivatives */
90 real as; /* Total surface area */
92 real *drobc; /* Parameters for OBC chain rule calculation */
93 real *param; /* Precomputed factor rai*atype->S_hct for HCT/OBC */
94 real *param_globalindex; /* */
96 real *log_table; /* Table for logarithm lookup */
98 real obc_alpha; /* OBC parameters */
99 real obc_beta; /* OBC parameters */
100 real obc_gamma; /* OBC parameters */
101 real gb_doffset; /* Dielectric offset for Still/HCT/OBC */
102 real gb_epsilon_solvent; /* */
103 real epsilon_r; /* Used for inner dielectric */
105 real sa_surface_tension; /* Surface tension for non-polar solvation */
107 real *work; /* Used for parallel summation and in the chain rule, length natoms */
108 real *buf; /* Used for parallel summation and in the chain rule, length natoms */
109 int *count; /* Used for setting up the special gb nblist, length natoms */
110 gbtmpnbls_t nblist_work; /* Used for setting up the special gb nblist, dim natoms*nblist_work_nalloc */
111 int nblist_work_nalloc; /* Length of second dimension of nblist_work */