This file defines low-level functions necessary for computing energies and forces for listed interactions.
- Author
- Mark Abraham mark..nosp@m.j.ab.nosp@m.raham.nosp@m.@gma.nosp@m.il.co.nosp@m.m
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int | anonymous_namespace{bonded.cpp}::pbc_rvec_sub (const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx) |
| Compute dx = xi - xj, modulo PBC if non-NULL. More...
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void | make_dp_periodic (real *dp) |
| Make a dihedral fall in the range (-pi,pi)
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template<BondedKernelFlavor flavor> |
void | anonymous_namespace{bonded.cpp}::spreadBondForces (const real bondForce, const rvec dx, const int ai, const int aj, rvec4 *f, int shiftIndex, const t_graph *g, rvec *fshift) |
| Spreads and accumulates the bonded forces to the two atoms and adds the virial contribution when needed. More...
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template<BondedKernelFlavor flavor> |
real | anonymous_namespace{bonded.cpp}::morse_bonds (int nbonds, const t_iatom forceatoms[], const t_iparams forceparams[], const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const t_graph *g, real lambda, real *dvdlambda, const t_mdatoms *md, t_fcdata *fcd, int *global_atom_index) |
| Morse potential bond. More...
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int | anonymous_namespace{bonded.cpp}::cmap_setup_grid_index (int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2) |
| Mysterious undocumented function.
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real | cmap_dihs (int nbonds, const t_iatom forceatoms[], const t_iparams forceparams[], const gmx_cmap_t *cmap_grid, const rvec x[], rvec4 f[], rvec fshift[], const struct t_pbc *pbc, const struct t_graph *g, real lambda, real *dvdlambda, const t_mdatoms *md, t_fcdata *fcd, int *global_atom_index) |
| Compute CMAP dihedral energies and forces.
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real | calculateSimpleBond (const int ftype, const int numForceatoms, const t_iatom forceatoms[], const t_iparams forceparams[], const rvec x[], rvec4 f[], rvec fshift[], const struct t_pbc *pbc, const struct t_graph *g, const real lambda, real *dvdlambda, const t_mdatoms *md, t_fcdata *fcd, int *global_atom_index, const BondedKernelFlavor bondedKernelFlavor) |
| Calculates bonded interactions for simple bonded types. More...
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int | nrnbIndex (int ftype) |
| Getter for finding the flop count for an ftype interaction.
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