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38 #ifndef GMX_GMXPREPROCESS_TOPPUSH_H
39 #define GMX_GMXPREPROCESS_TOPPUSH_H
41 #include "gromacs/fileio/warninp.h"
42 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
43 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
44 #include "gromacs/gmxpreprocess/toputil.h"
47 int nr; /* The number of entries in the list */
48 int nra2; /* The total number of entries in a */
49 int *nra; /* The number of entries in each a array (dim nr) */
50 int **a; /* The atom numbers (dim nr) the length of each element */
54 void generate_nbparams(int comb, int funct, t_params plist[],
58 void push_at (struct t_symtab *symtab, gpp_atomtype_t at,
59 t_bond_atomtype bat, char *line, int nb_funct,
60 t_nbparam ***nbparam, t_nbparam ***pair,
63 void push_bt(directive d, t_params bt[], int nral,
64 gpp_atomtype_t at, t_bond_atomtype bat, char *line,
67 void push_dihedraltype(directive d, t_params bt[],
68 t_bond_atomtype bat, char *line,
71 void push_cmaptype(directive d, t_params bt[], int nral, gpp_atomtype_t at,
72 t_bond_atomtype bat, char *line,
75 void push_nbt(directive d, t_nbparam **nbt, gpp_atomtype_t atype,
76 char *plines, int nb_funct,
79 void push_atom(struct t_symtab *symtab,
87 void push_bond(directive d, t_params bondtype[], t_params bond[],
88 t_atoms *at, gpp_atomtype_t atype, char *line,
89 gmx_bool bBonded, gmx_bool bGenPairs, real fudgeQQ,
90 gmx_bool bZero, gmx_bool *bWarn_copy_A_B,
93 void push_cmap(directive d, t_params bondtype[], t_params bond[],
94 t_atoms *at, gpp_atomtype_t atype, char *line,
97 void push_vsitesn(directive d, t_params bond[],
98 t_atoms *at, char *line,
101 void push_mol(int nrmols, t_molinfo mols[], char *pline,
102 int *whichmol, int *nrcopies,
105 void push_molt(struct t_symtab *symtab, int *nmol, t_molinfo **mol, char *line,
108 void init_block2(t_block2 *b2, int natom);
110 void done_block2(t_block2 *b2);
112 void push_excl(char *line, t_block2 *b2, warninp_t wi);
114 void merge_excl(t_blocka *excl, t_block2 *b2, warninp_t wi);
116 void b_to_b2(t_blocka *b, t_block2 *b2);
118 void b2_to_b(t_block2 *b2, t_blocka *b);
120 int add_atomtype_decoupled(struct t_symtab *symtab, gpp_atomtype_t at,
121 t_nbparam ***nbparam, t_nbparam ***pair);
122 /* Add an atom type with all parameters set to zero (no interactions).
123 * Returns the atom type number.
126 void convert_moltype_couple(t_molinfo *mol, int atomtype_decouple,
128 int couple_lam0, int couple_lam1,
129 gmx_bool bCoupleIntra,
130 int nb_funct, t_params *nbp,
132 /* Setup mol such that the B-state has no interaction with the rest
133 * of the system, but full interaction with itself.