src/gromacs/gmxpreprocess/toppush.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2018 by the GROMACS development team.
   7  * Copyright (c) 2019,2020, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   9  * and including many others, as listed in the AUTHORS file in the
  10  * top-level source directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
  18  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
  24  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
  28  * consider that scientific software is very special. Version
  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
  33  * official version at http://www.gromacs.org.
  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  38
  39 #ifndef GMX_GMXPREPROCESS_TOPPUSH_H
  40 #define GMX_GMXPREPROCESS_TOPPUSH_H
  41
  42 #include <vector>
  43
  44 #include "gromacs/utility/arrayref.h"
  45 #include "gromacs/utility/real.h"
  46
  47 enum class Directive : int;
  48 class PreprocessingAtomTypes;
  49 class PreprocessingBondAtomType;
  50 struct t_atoms;
  51 struct t_block;
  52 struct MoleculeInformation;
  53 struct t_nbparam;
  54 class InteractionOfType;
  55 struct InteractionsOfType;
  56 struct PreprocessResidue;
  57 struct warninp;
  58
  59 namespace gmx
  60 {
  61 struct ExclusionBlock;
  62 } // namespace gmx
  63
  64 void generate_nbparams(int comb, int funct, InteractionsOfType* plist, PreprocessingAtomTypes* atype, warninp* wi);
  65
  66 void push_at(struct t_symtab*           symtab,
  67              PreprocessingAtomTypes*    at,
  68              PreprocessingBondAtomType* bat,
  69              char*                      line,
  70              int                        nb_funct,
  71              t_nbparam***               nbparam,
  72              t_nbparam***               pair,
  73              warninp*                   wi);
  74
  75 void push_bt(Directive                         d,
  76              gmx::ArrayRef<InteractionsOfType> bt,
  77              int                               nral,
  78              PreprocessingAtomTypes*           at,
  79              PreprocessingBondAtomType*        bat,
  80              char*                             line,
  81              warninp*                          wi);
  82
  83 void push_dihedraltype(Directive                         d,
  84                        gmx::ArrayRef<InteractionsOfType> bt,
  85                        PreprocessingBondAtomType*        bat,
  86                        char*                             line,
  87                        warninp*                          wi);
  88
  89 void push_cmaptype(Directive                         d,
  90                    gmx::ArrayRef<InteractionsOfType> bt,
  91                    int                               nral,
  92                    PreprocessingAtomTypes*           at,
  93                    PreprocessingBondAtomType*        bat,
  94                    char*                             line,
  95                    warninp*                          wi);
  96
  97 void push_nbt(Directive d, t_nbparam** nbt, PreprocessingAtomTypes* atype, char* plines, int nb_funct, warninp* wi);
  98
  99 void push_atom(struct t_symtab* symtab, t_atoms* at, PreprocessingAtomTypes* atype, char* line, warninp* wi);
 100
 101 void push_bond(Directive                         d,
 102                gmx::ArrayRef<InteractionsOfType> bondtype,
 103                gmx::ArrayRef<InteractionsOfType> bond,
 104                t_atoms*                          at,
 105                PreprocessingAtomTypes*           atype,
 106                char*                             line,
 107                bool                              bBonded,
 108                bool                              bGenPairs,
 109                real                              fudgeQQ,
 110                bool                              bZero,
 111                bool*                             bWarn_copy_A_B,
 112                warninp*                          wi);
 113
 114 void push_cmap(Directive                         d,
 115                gmx::ArrayRef<InteractionsOfType> bondtype,
 116                gmx::ArrayRef<InteractionsOfType> bond,
 117                t_atoms*                          at,
 118                PreprocessingAtomTypes*           atype,
 119                char*                             line,
 120                warninp*                          wi);
 121
 122 void push_vsitesn(Directive d, gmx::ArrayRef<InteractionsOfType> bond, t_atoms* at, char* line, warninp* wi);
 123
 124 void push_mol(gmx::ArrayRef<MoleculeInformation> mols, char* pline, int* whichmol, int* nrcopies, warninp* wi);
 125
 126 void push_molt(struct t_symtab* symtab, std::vector<MoleculeInformation>* mol, char* line, warninp* wi);
 127
 128 void push_excl(char* line, gmx::ArrayRef<gmx::ExclusionBlock> b2, warninp* wi);
 129
 130 int copy_nbparams(t_nbparam** param, int ftype, InteractionsOfType* plist, int nr);
 131
 132 void free_nbparam(t_nbparam** param, int nr);
 133
 134 int add_atomtype_decoupled(struct t_symtab*        symtab,
 135                            PreprocessingAtomTypes* at,
 136                            t_nbparam***            nbparam,
 137                            t_nbparam***            pair);
 138 /* Add an atom type with all parameters set to zero (no interactions).
 139  * Returns the atom type number.
 140  */
 141
 142 void convert_moltype_couple(MoleculeInformation* mol,
 143                             int                  atomtype_decouple,
 144                             real                 fudgeQQ,
 145                             int                  couple_lam0,
 146                             int                  couple_lam1,
 147                             bool                 bCoupleIntra,
 148                             int                  nb_funct,
 149                             InteractionsOfType*  nbp,
 150                             warninp*             wi);
 151 /* Setup mol such that the B-state has no interaction with the rest
 152  * of the system, but full interaction with itself.
 153  */
 154
 155 #endif