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