Gromacs
2022.2
|
#include <string>
#include "gromacs/math/vectypes.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/libgromacs_export.h"
This file contains declarations necessary for low-level functions for computing energies and forces for bonded interactions.
Classes | |
struct | gmx::EnumerationArray< EnumType, DataType, ArraySize > |
Wrapper for a C-style array with size and indexing defined by an enum. Useful for declaring arrays of enum names for debug or other printing. An ArrayRef<DataType> may be constructed from an object of this type. More... | |
class | gmx::ArrayRef< typename > |
STL-like interface to a C array of T (or part of a std container of T). More... | |
Enumerations | |
enum | BondedKernelFlavor { BondedKernelFlavor::ForcesSimdWhenAvailable, BondedKernelFlavor::ForcesNoSimd, BondedKernelFlavor::ForcesAndVirialAndEnergy, BondedKernelFlavor::ForcesAndEnergy, BondedKernelFlavor::Count } |
For selecting which flavor of bonded kernel is used for simple bonded types. More... | |
Functions | |
real | bond_angle (const rvec xi, const rvec xj, const rvec xk, const struct t_pbc *pbc, rvec r_ij, rvec r_kj, real *costh, int *t1, int *t2) |
Calculate bond-angle. No PBC is taken into account (use mol-shift) | |
real | dih_angle (const rvec xi, const rvec xj, const rvec xk, const rvec xl, const struct t_pbc *pbc, rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n, int *t1, int *t2, int *t3) |
Calculate dihedral-angle. No PBC is taken into account (use mol-shift) | |
void | do_dih_fup (int i, int j, int k, int l, real ddphi, rvec r_ij, rvec r_kj, rvec r_kl, rvec m, rvec n, rvec4 f[], rvec fshift[], const struct t_pbc *pbc, const rvec *x, int t1, int t2, int t3) |
Do an update of the forces for dihedral potentials. | |
void | make_dp_periodic (real *dp) |
Make a dihedral fall in the range (-pi,pi) | |
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, real gmx_unused lambda, real gmx_unused *dvdlambda, gmx::ArrayRef< const real >, t_fcdata gmx_unused *fcd, t_disresdata gmx_unused *disresdata, t_oriresdata gmx_unused *oriresdata, int gmx_unused *global_atom_index) |
Compute CMAP dihedral energies and forces. | |
static constexpr bool | computeEnergy (const BondedKernelFlavor flavor) |
Returns whether the energy should be computed. | |
static constexpr bool | computeVirial (const BondedKernelFlavor flavor) |
Returns whether the virial should be computed. | |
static constexpr bool | computeEnergyOrVirial (const BondedKernelFlavor flavor) |
Returns whether the energy and/or virial should be computed. | |
real | calculateSimpleBond (int ftype, int numForceatoms, const t_iatom forceatoms[], const t_iparams forceparams[], const rvec x[], rvec4 f[], rvec fshift[], const struct t_pbc *pbc, real lambda, real *dvdlambda, gmx::ArrayRef< const real > charge, t_fcdata *fcd, t_disresdata *disresdata, t_oriresdata *oriresdata, int gmx_unused *global_atom_index, BondedKernelFlavor bondedKernelFlavor) |
Calculates bonded interactions for simple bonded types. More... | |
int | nrnbIndex (int ftype) |
Getter for finding the flop count for an ftype interaction. | |
Variables | |
LIBGROMACS_EXPORT const gmx::EnumerationArray < BondedKernelFlavor, std::string, BondedKernelFlavor::Count > | c_bondedKernelFlavorStrings |
Helper strings for human-readable messages. | |
|
strong |
For selecting which flavor of bonded kernel is used for simple bonded types.
real calculateSimpleBond | ( | int | ftype, |
int | numForceatoms, | ||
const t_iatom | forceatoms[], | ||
const t_iparams | forceparams[], | ||
const rvec | x[], | ||
rvec4 | f[], | ||
rvec | fshift[], | ||
const struct t_pbc * | pbc, | ||
real | lambda, | ||
real * | dvdlambda, | ||
gmx::ArrayRef< const real > | charge, | ||
t_fcdata * | fcd, | ||
t_disresdata * | disresdata, | ||
t_oriresdata * | oriresdata, | ||
int gmx_unused * | global_atom_index, | ||
BondedKernelFlavor | bondedKernelFlavor | ||
) |
Calculates bonded interactions for simple bonded types.
Exits with an error when the bonded type is not simple All pointers should be non-null, except for pbc and g which can be nullptr.
bondedKernelFlavor
did not request the energy.