bonded.cpp File Reference

#include "gmxpre.h"
#include "bonded.h"
#include "config.h"
#include <cassert>
#include <cmath>
#include <cstdint>
#include <algorithm>
#include <array>
#include <filesystem>
#include <type_traits>
#include <vector>
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/listed_forces/disre.h"
#include "gromacs/listed_forces/orires.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/pbc_simd.h"
#include "gromacs/simd/simd.h"
#include "gromacs/simd/simd_math.h"
#include "gromacs/simd/vector_operations.h"
#include "gromacs/topology/idef.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
#include "listed_internal.h"
#include "restcbt.h"

Include dependency graph for bonded.cpp:

Description

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

Typedefs
using	anonymous_namespace{bonded.cpp}::BondedFunction = real(*)(int nbonds, const t_iatom iatoms[], const t_iparams iparams[], const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, real lambda, real *dvdlambda, gmx::ArrayRef< const real > charge, t_fcdata *fcd, t_disresdata *disresdata, t_oriresdata *oriresdata, int *ddgatindex)
	Type of CPU function to compute a bonded interaction.
using	anonymous_namespace{bonded.cpp}::CmapForceStructure = std::array< real, 4 >

Functions
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...
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, rvec *fshift)
	Spreads and accumulates the bonded forces to the two atoms and adds the virial contribution when needed. More...
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, real lambda, real *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)
	Morse potential bond. More...
int	anonymous_namespace{bonded.cpp}::cmap_setup_grid_index (int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2)
	Mysterious undocumented function.
gmx::RVec	anonymous_namespace{bonded.cpp}::processCmapForceComponent (const gmx::RVec a, const gmx::RVec b, const real df, const real gaa, const real fga, const real gbb, const real hgb, const int dim)
CmapForceStructure	anonymous_namespace{bonded.cpp}::applyCmapForceComponent (const gmx::RVec forceComponent)
void	anonymous_namespace{bonded.cpp}::accumulateCmapForces (const rvec x[], rvec4 f[], rvec fshift[], const t_pbc *pbc, const gmx::RVec r_ij, const gmx::RVec r_kj, const gmx::RVec r_kl, const gmx::RVec a, const gmx::RVec b, gmx::RVec h, const real ra2r, const real rb2r, const real rgr, const real rg, const int ai, const int aj, const int ak, const int al, const real df, const int t1, const int t2)
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.
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 real lambda, real *dvdlambda, gmx::ArrayRef< const real > charge, t_fcdata *fcd, t_disresdata *disresdata, t_oriresdata *oriresdata, int gmx_unused *global_atom_index, const 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
const EnumerationArray < BondedKernelFlavor, std::string >	c_bondedKernelFlavorStrings
	Helper strings for human-readable messages. More...
const int	anonymous_namespace{bonded.cpp}::cmap_coeff_matrix []
	Mysterious CMAP coefficient matrix. More...

Function Documentation

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.

Returns

the energy or 0 when bondedKernelFlavor did not request the energy.

Variable Documentation

const EnumerationArray<BondedKernelFlavor, std::string> c_bondedKernelFlavorStrings

Initial value:

= {
    "forces, using SIMD when available",
    "forces, not using SIMD",
    "forces, virial, and energy (ie. not using SIMD)",
    "forces and energy (ie. not using SIMD)"
}

Helper strings for human-readable messages.