src/gromacs/gmxpreprocess/toppush.h

   1 /*
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  38
  39 #ifndef GMX_GMXPREPROCESS_TOPPUSH_H
  40 #define GMX_GMXPREPROCESS_TOPPUSH_H
  41
  42 #include <vector>
  43
  44 #include "gromacs/utility/real.h"
  45
  46 enum class Directive : int;
  47 class PreprocessingAtomTypes;
  48 class PreprocessingBondAtomType;
  49 struct t_atoms;
  50 struct t_block;
  51 struct MoleculeInformation;
  52 struct t_nbparam;
  53 class InteractionOfType;
  54 struct InteractionsOfType;
  55 struct PreprocessResidue;
  56 struct warninp;
  57 enum class CombinationRule : int;
  58 namespace gmx
  59 {
  60 template<typename>
  61 class ArrayRef;
  62 struct ExclusionBlock;
  63 } // namespace gmx
  64
  65 void generate_nbparams(CombinationRule         comb,
  66                        int                     funct,
  67                        InteractionsOfType*     plist,
  68                        PreprocessingAtomTypes* atype,
  69                        warninp*                wi);
  70
  71 void push_at(struct t_symtab*           symtab,
  72              PreprocessingAtomTypes*    at,
  73              PreprocessingBondAtomType* bat,
  74              char*                      line,
  75              int                        nb_funct,
  76              t_nbparam***               nbparam,
  77              t_nbparam***               pair,
  78              warninp*                   wi);
  79
  80 void push_bt(Directive                         d,
  81              gmx::ArrayRef<InteractionsOfType> bt,
  82              int                               nral,
  83              PreprocessingAtomTypes*           at,
  84              PreprocessingBondAtomType*        bat,
  85              char*                             line,
  86              warninp*                          wi);
  87
  88 void push_dihedraltype(Directive                         d,
  89                        gmx::ArrayRef<InteractionsOfType> bt,
  90                        PreprocessingBondAtomType*        bat,
  91                        char*                             line,
  92                        warninp*                          wi);
  93
  94 void push_cmaptype(Directive                         d,
  95                    gmx::ArrayRef<InteractionsOfType> bt,
  96                    int                               nral,
  97                    PreprocessingAtomTypes*           at,
  98                    PreprocessingBondAtomType*        bat,
  99                    char*                             line,
 100                    warninp*                          wi);
 101
 102 void push_nbt(Directive d, t_nbparam** nbt, PreprocessingAtomTypes* atype, char* plines, int nb_funct, warninp* wi);
 103
 104 void push_atom(struct t_symtab* symtab, t_atoms* at, PreprocessingAtomTypes* atype, char* line, warninp* wi);
 105
 106 void push_bond(Directive                         d,
 107                gmx::ArrayRef<InteractionsOfType> bondtype,
 108                gmx::ArrayRef<InteractionsOfType> bond,
 109                t_atoms*                          at,
 110                PreprocessingAtomTypes*           atype,
 111                char*                             line,
 112                bool                              bBonded,
 113                bool                              bGenPairs,
 114                real                              fudgeQQ,
 115                bool                              bZero,
 116                bool*                             bWarn_copy_A_B,
 117                warninp*                          wi);
 118
 119 void push_cmap(Directive                         d,
 120                gmx::ArrayRef<InteractionsOfType> bondtype,
 121                gmx::ArrayRef<InteractionsOfType> bond,
 122                t_atoms*                          at,
 123                PreprocessingAtomTypes*           atype,
 124                char*                             line,
 125                warninp*                          wi);
 126
 127 void push_vsitesn(Directive d, gmx::ArrayRef<InteractionsOfType> bond, t_atoms* at, char* line, warninp* wi);
 128
 129 void push_mol(gmx::ArrayRef<MoleculeInformation> mols, char* pline, int* whichmol, int* nrcopies, warninp* wi);
 130
 131 void push_molt(struct t_symtab* symtab, std::vector<MoleculeInformation>* mol, char* line, warninp* wi);
 132
 133 void push_excl(char* line, gmx::ArrayRef<gmx::ExclusionBlock> b2, warninp* wi);
 134
 135 int copy_nbparams(t_nbparam** param, int ftype, InteractionsOfType* plist, int nr);
 136
 137 void free_nbparam(t_nbparam** param, int nr);
 138
 139 int add_atomtype_decoupled(struct t_symtab*        symtab,
 140                            PreprocessingAtomTypes* at,
 141                            t_nbparam***            nbparam,
 142                            t_nbparam***            pair);
 143 /* Add an atom type with all parameters set to zero (no interactions).
 144  * Returns the atom type number.
 145  */
 146
 147 void convert_moltype_couple(MoleculeInformation* mol,
 148                             int                  atomtype_decouple,
 149                             real                 fudgeQQ,
 150                             int                  couple_lam0,
 151                             int                  couple_lam1,
 152                             bool                 bCoupleIntra,
 153                             int                  nb_funct,
 154                             InteractionsOfType*  nbp,
 155                             warninp*             wi);
 156 /* Setup mol such that the B-state has no interaction with the rest
 157  * of the system, but full interaction with itself.
 158  */
 159
 160 #endif