src/gromacs/gmxpreprocess/toppush.h

   1 /*
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  37
  38 #ifndef GMX_GMXPREPROCESS_TOPPUSH_H
  39 #define GMX_GMXPREPROCESS_TOPPUSH_H
  40
  41 #include <vector>
  42
  43 #include "gromacs/utility/arrayref.h"
  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
  58 namespace gmx
  59 {
  60 struct ExclusionBlock;
  61 } // namespace gmx
  62
  63 void generate_nbparams(int comb, int funct, InteractionsOfType* plist, PreprocessingAtomTypes* atype, warninp* wi);
  64
  65 void push_at(struct t_symtab*           symtab,
  66              PreprocessingAtomTypes*    at,
  67              PreprocessingBondAtomType* bat,
  68              char*                      line,
  69              int                        nb_funct,
  70              t_nbparam***               nbparam,
  71              t_nbparam***               pair,
  72              warninp*                   wi);
  73
  74 void push_bt(Directive                         d,
  75              gmx::ArrayRef<InteractionsOfType> bt,
  76              int                               nral,
  77              PreprocessingAtomTypes*           at,
  78              PreprocessingBondAtomType*        bat,
  79              char*                             line,
  80              warninp*                          wi);
  81
  82 void push_dihedraltype(Directive                         d,
  83                        gmx::ArrayRef<InteractionsOfType> bt,
  84                        PreprocessingBondAtomType*        bat,
  85                        char*                             line,
  86                        warninp*                          wi);
  87
  88 void push_cmaptype(Directive                         d,
  89                    gmx::ArrayRef<InteractionsOfType> bt,
  90                    int                               nral,
  91                    PreprocessingAtomTypes*           at,
  92                    PreprocessingBondAtomType*        bat,
  93                    char*                             line,
  94                    warninp*                          wi);
  95
  96 void push_nbt(Directive d, t_nbparam** nbt, PreprocessingAtomTypes* atype, char* plines, int nb_funct, warninp* wi);
  97
  98 void push_atom(struct t_symtab* symtab, t_atoms* at, PreprocessingAtomTypes* atype, char* line, warninp* wi);
  99
 100 void push_bond(Directive                         d,
 101                gmx::ArrayRef<InteractionsOfType> bondtype,
 102                gmx::ArrayRef<InteractionsOfType> bond,
 103                t_atoms*                          at,
 104                PreprocessingAtomTypes*           atype,
 105                char*                             line,
 106                bool                              bBonded,
 107                bool                              bGenPairs,
 108                real                              fudgeQQ,
 109                bool                              bZero,
 110                bool*                             bWarn_copy_A_B,
 111                warninp*                          wi);
 112
 113 void push_cmap(Directive                         d,
 114                gmx::ArrayRef<InteractionsOfType> bondtype,
 115                gmx::ArrayRef<InteractionsOfType> bond,
 116                t_atoms*                          at,
 117                PreprocessingAtomTypes*           atype,
 118                char*                             line,
 119                warninp*                          wi);
 120
 121 void push_vsitesn(Directive d, gmx::ArrayRef<InteractionsOfType> bond, t_atoms* at, char* line, warninp* wi);
 122
 123 void push_mol(gmx::ArrayRef<MoleculeInformation> mols, char* pline, int* whichmol, int* nrcopies, warninp* wi);
 124
 125 void push_molt(struct t_symtab* symtab, std::vector<MoleculeInformation>* mol, char* line, warninp* wi);
 126
 127 void push_excl(char* line, gmx::ArrayRef<gmx::ExclusionBlock> b2, warninp* wi);
 128
 129 int copy_nbparams(t_nbparam** param, int ftype, InteractionsOfType* plist, int nr);
 130
 131 void free_nbparam(t_nbparam** param, int nr);
 132
 133 int add_atomtype_decoupled(struct t_symtab*        symtab,
 134                            PreprocessingAtomTypes* at,
 135                            t_nbparam***            nbparam,
 136                            t_nbparam***            pair);
 137 /* Add an atom type with all parameters set to zero (no interactions).
 138  * Returns the atom type number.
 139  */
 140
 141 void convert_moltype_couple(MoleculeInformation* mol,
 142                             int                  atomtype_decouple,
 143                             real                 fudgeQQ,
 144                             int                  couple_lam0,
 145                             int                  couple_lam1,
 146                             bool                 bCoupleIntra,
 147                             int                  nb_funct,
 148                             InteractionsOfType*  nbp,
 149                             warninp*             wi);
 150 /* Setup mol such that the B-state has no interaction with the rest
 151  * of the system, but full interaction with itself.
 152  */
 153
 154 #endif