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38 #ifndef GMX_GMXPREPROCESS_TOPPUSH_H
39 #define GMX_GMXPREPROCESS_TOPPUSH_H
41 #include "gromacs/legacyheaders/typedefs.h"
43 #include "gpp_atomtype.h"
44 #include "gpp_bond_atomtype.h"
45 #include "gromacs/legacyheaders/warninp.h"
52 int nr; /* The number of entries in the list */
53 int nra2; /* The total number of entries in a */
54 atom_id *nra; /* The number of entries in each a array (dim nr) */
55 atom_id **a; /* The atom numbers (dim nr) the length of each element */
59 void generate_nbparams(int comb, int funct, t_params plist[],
63 void push_at (struct t_symtab *symtab, gpp_atomtype_t at,
64 t_bond_atomtype bat, char *line, int nb_funct,
65 t_nbparam ***nbparam, t_nbparam ***pair,
68 void push_bt(directive d, t_params bt[], int nral,
69 gpp_atomtype_t at, t_bond_atomtype bat, char *line,
72 void push_dihedraltype(directive d, t_params bt[],
73 t_bond_atomtype bat, char *line,
76 void push_cmaptype(directive d, t_params bt[], int nral, gpp_atomtype_t at,
77 t_bond_atomtype bat, char *line,
80 void push_nbt(directive d, t_nbparam **nbt, gpp_atomtype_t atype,
81 char *plines, int nb_funct,
85 push_gb_params(gpp_atomtype_t atype,
89 void push_atom(struct t_symtab *symtab,
97 void push_bond(directive d, t_params bondtype[], t_params bond[],
98 t_atoms *at, gpp_atomtype_t atype, char *line,
99 gmx_bool bBonded, gmx_bool bGenPairs, real fudgeQQ,
100 gmx_bool bZero, gmx_bool *bWarn_copy_A_B,
103 void push_cmap(directive d, t_params bondtype[], t_params bond[],
104 t_atoms *at, gpp_atomtype_t atype, char *line,
107 void push_vsitesn(directive d, t_params bond[],
108 t_atoms *at, char *line,
111 void push_mol(int nrmols, t_molinfo mols[], char *pline,
112 int *whichmol, int *nrcopies,
115 void push_molt(struct t_symtab *symtab, int *nmol, t_molinfo **mol, char *line,
118 void init_block2(t_block2 *b2, int natom);
120 void done_block2(t_block2 *b2);
122 void push_excl(char *line, t_block2 *b2);
124 void merge_excl(t_blocka *excl, t_block2 *b2);
126 void b_to_b2(t_blocka *b, t_block2 *b2);
128 void b2_to_b(t_block2 *b2, t_blocka *b);
130 int add_atomtype_decoupled(struct t_symtab *symtab, gpp_atomtype_t at,
131 t_nbparam ***nbparam, t_nbparam ***pair);
132 /* Add an atom type with all parameters set to zero (no interactions).
133 * Returns the atom type number.
136 void convert_moltype_couple(t_molinfo *mol, int atomtype_decouple,
138 int couple_lam0, int couple_lam1,
139 gmx_bool bCoupleIntra,
140 int nb_funct, t_params *nbp);
141 /* Setup mol such that the B-state has no interaction with the rest
142 * of the system, but full interaction with itself.