src/gromacs/gmxpreprocess/toppush.h

   1 /*
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   7  * Copyright (c) 2019,2020, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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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
  58 namespace gmx
  59 {
  60 template<typename>
  61 class ArrayRef;
  62 struct ExclusionBlock;
  63 } // namespace gmx
  64
  65 void generate_nbparams(int comb, int funct, InteractionsOfType* plist, PreprocessingAtomTypes* atype, warninp* wi);
  66
  67 void push_at(struct t_symtab*           symtab,
  68              PreprocessingAtomTypes*    at,
  69              PreprocessingBondAtomType* bat,
  70              char*                      line,
  71              int                        nb_funct,
  72              t_nbparam***               nbparam,
  73              t_nbparam***               pair,
  74              warninp*                   wi);
  75
  76 void push_bt(Directive                         d,
  77              gmx::ArrayRef<InteractionsOfType> bt,
  78              int                               nral,
  79              PreprocessingAtomTypes*           at,
  80              PreprocessingBondAtomType*        bat,
  81              char*                             line,
  82              warninp*                          wi);
  83
  84 void push_dihedraltype(Directive                         d,
  85                        gmx::ArrayRef<InteractionsOfType> bt,
  86                        PreprocessingBondAtomType*        bat,
  87                        char*                             line,
  88                        warninp*                          wi);
  89
  90 void push_cmaptype(Directive                         d,
  91                    gmx::ArrayRef<InteractionsOfType> bt,
  92                    int                               nral,
  93                    PreprocessingAtomTypes*           at,
  94                    PreprocessingBondAtomType*        bat,
  95                    char*                             line,
  96                    warninp*                          wi);
  97
  98 void push_nbt(Directive d, t_nbparam** nbt, PreprocessingAtomTypes* atype, char* plines, int nb_funct, warninp* wi);
  99
 100 void push_atom(struct t_symtab* symtab, t_atoms* at, PreprocessingAtomTypes* atype, char* line, warninp* wi);
 101
 102 void push_bond(Directive                         d,
 103                gmx::ArrayRef<InteractionsOfType> bondtype,
 104                gmx::ArrayRef<InteractionsOfType> bond,
 105                t_atoms*                          at,
 106                PreprocessingAtomTypes*           atype,
 107                char*                             line,
 108                bool                              bBonded,
 109                bool                              bGenPairs,
 110                real                              fudgeQQ,
 111                bool                              bZero,
 112                bool*                             bWarn_copy_A_B,
 113                warninp*                          wi);
 114
 115 void push_cmap(Directive                         d,
 116                gmx::ArrayRef<InteractionsOfType> bondtype,
 117                gmx::ArrayRef<InteractionsOfType> bond,
 118                t_atoms*                          at,
 119                PreprocessingAtomTypes*           atype,
 120                char*                             line,
 121                warninp*                          wi);
 122
 123 void push_vsitesn(Directive d, gmx::ArrayRef<InteractionsOfType> bond, t_atoms* at, char* line, warninp* wi);
 124
 125 void push_mol(gmx::ArrayRef<MoleculeInformation> mols, char* pline, int* whichmol, int* nrcopies, warninp* wi);
 126
 127 void push_molt(struct t_symtab* symtab, std::vector<MoleculeInformation>* mol, char* line, warninp* wi);
 128
 129 void push_excl(char* line, gmx::ArrayRef<gmx::ExclusionBlock> b2, warninp* wi);
 130
 131 int copy_nbparams(t_nbparam** param, int ftype, InteractionsOfType* plist, int nr);
 132
 133 void free_nbparam(t_nbparam** param, int nr);
 134
 135 int add_atomtype_decoupled(struct t_symtab*        symtab,
 136                            PreprocessingAtomTypes* at,
 137                            t_nbparam***            nbparam,
 138                            t_nbparam***            pair);
 139 /* Add an atom type with all parameters set to zero (no interactions).
 140  * Returns the atom type number.
 141  */
 142
 143 void convert_moltype_couple(MoleculeInformation* mol,
 144                             int                  atomtype_decouple,
 145                             real                 fudgeQQ,
 146                             int                  couple_lam0,
 147                             int                  couple_lam1,
 148                             bool                 bCoupleIntra,
 149                             int                  nb_funct,
 150                             InteractionsOfType*  nbp,
 151                             warninp*             wi);
 152 /* Setup mol such that the B-state has no interaction with the rest
 153  * of the system, but full interaction with itself.
 154  */
 155
 156 #endif