src/gromacs/listed-forces/bonded.h

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  37 /*! \libinternal \file
  38  *
  39  * \brief This file contains declarations necessary for low-level
  40  * functions for computing energies and forces for bonded interactions.
  41  *
  42  * \author Mark Abraham <mark.j.abraham@gmail.com>
  43  * \inlibraryapi
  44  * \ingroup module_listed-forces
  45  */
  46
  47 #ifndef GMX_LISTED_FORCES_BONDED_H
  48 #define GMX_LISTED_FORCES_BONDED_H
  49
  50 #include <cstdio>
  51
  52 #include "gromacs/gmxlib/nrnb.h"
  53 #include "gromacs/math/vec.h"
  54 #include "gromacs/mdtypes/fcdata.h"
  55 #include "gromacs/mdtypes/forcerec.h"
  56 #include "gromacs/mdtypes/interaction_const.h"
  57 #include "gromacs/mdtypes/mdatom.h"
  58 #include "gromacs/topology/idef.h"
  59 #include "gromacs/topology/ifunc.h"
  60 #include "gromacs/utility/basedefinitions.h"
  61
  62
  63 struct t_graph;
  64 struct t_pbc;
  65
  66 /*! \brief Calculate bond-angle. No PBC is taken into account (use mol-shift) */
  67 real bond_angle(const rvec xi, const rvec xj, const rvec xk,
  68                 const struct t_pbc *pbc,
  69                 rvec r_ij, rvec r_kj, real *costh,
  70                 int *t1, int *t2);  /* out */
  71
  72 /*! \brief Calculate dihedral-angle. No PBC is taken into account (use mol-shift) */
  73 real dih_angle(const rvec xi, const rvec xj, const rvec xk, const rvec xl,
  74                const struct t_pbc *pbc,
  75                rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n, /* out */
  76                real *sign,
  77                int *t1, int *t2, int *t3);
  78
  79 /*! \brief Do an update of the forces for dihedral potentials */
  80 void do_dih_fup(int i, int j, int k, int l, real ddphi,
  81                 rvec r_ij, rvec r_kj, rvec r_kl,
  82                 rvec m, rvec n, rvec4 f[], rvec fshift[],
  83                 const struct t_pbc *pbc, const struct t_graph *g,
  84                 const rvec *x, int t1, int t2, int t3);
  85
  86 /*! \brief Make a dihedral fall in the range (-pi,pi) */
  87 void make_dp_periodic(real *dp);
  88
  89 /*! \brief Compute CMAP dihedral energies and forces */
  90 real
  91     cmap_dihs(int nbonds,
  92               const t_iatom forceatoms[], const t_iparams forceparams[],
  93               const gmx_cmap_t *cmap_grid,
  94               const rvec x[], rvec4 f[], rvec fshift[],
  95               const struct t_pbc *pbc, const struct t_graph *g,
  96               real gmx_unused lambda, real gmx_unused *dvdlambda,
  97               const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
  98               int  gmx_unused *global_atom_index);
  99
 100 //! \cond
 101 /*************************************************************************
 102  *
 103  *  Bonded force functions
 104  *
 105  *************************************************************************/
 106 t_ifunc bonds, g96bonds, morse_bonds, cubic_bonds, FENE_bonds, restraint_bonds;
 107 t_ifunc angles, g96angles, cross_bond_bond, cross_bond_angle, urey_bradley, quartic_angles, linear_angles;
 108 t_ifunc restrangles;
 109 t_ifunc pdihs, idihs, rbdihs;
 110 t_ifunc restrdihs, cbtdihs;
 111 t_ifunc tab_bonds, tab_angles, tab_dihs;
 112 t_ifunc polarize, anharm_polarize, water_pol, thole_pol, angres, angresz, dihres, unimplemented;
 113
 114 /* As pdihs(), but without calculating energies and shift forces */
 115 void
 116     pdihs_noener(int nbonds,
 117                  const t_iatom forceatoms[], const t_iparams forceparams[],
 118                  const rvec x[], rvec4 f[],
 119                  const struct t_pbc gmx_unused *pbc,
 120                  const struct t_graph gmx_unused *g,
 121                  real lambda,
 122                  const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
 123                  int gmx_unused *global_atom_index);
 124
 125 /* TODO these declarations should be internal to the module */
 126
 127 /* As angles(), but using SIMD to calculate many angles at once.
 128  * This routines does not calculate energies and shift forces.
 129  */
 130 void
 131     angles_noener_simd(int nbonds,
 132                        const t_iatom forceatoms[], const t_iparams forceparams[],
 133                        const rvec x[], rvec4 f[],
 134                        const struct t_pbc *pbc,
 135                        const struct t_graph gmx_unused *g,
 136                        real gmx_unused lambda,
 137                        const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
 138                        int gmx_unused *global_atom_index);
 139
 140 /* As pdihs_noener(), but using SIMD to calculate many dihedrals at once. */
 141 void
 142     pdihs_noener_simd(int nbonds,
 143                       const t_iatom forceatoms[], const t_iparams forceparams[],
 144                       const rvec x[], rvec4 f[],
 145                       const struct t_pbc *pbc,
 146                       const struct t_graph gmx_unused *g,
 147                       real gmx_unused lambda,
 148                       const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
 149                       int gmx_unused *global_atom_index);
 150
 151 /* As rbdihs(), when not needing energy or shift force, using SIMD to calculate many dihedrals at once. */
 152 void
 153     rbdihs_noener_simd(int nbonds,
 154                        const t_iatom forceatoms[], const t_iparams forceparams[],
 155                        const rvec x[], rvec4 f[],
 156                        const struct t_pbc *pbc,
 157                        const struct t_graph gmx_unused *g,
 158                        real gmx_unused lambda,
 159                        const t_mdatoms gmx_unused *md, t_fcdata gmx_unused *fcd,
 160                        int gmx_unused *global_atom_index);
 161
 162 //! \endcond
 163
 164 #endif