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