pairs.cpp File Reference

#include "gmxpre.h"
#include "pairs.h"
#include <cmath>
#include "gromacs/listed_forces/bonded.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/nblist.h"
#include "gromacs/mdtypes/simulation_workload.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.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/tables/forcetable.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "listed_internal.h"

Include dependency graph for pairs.cpp:

Description

This file defines functions for "pair" interactions (i.e. listed non-bonded interactions, e.g. 1-4 interactions)

Author

Mark Abraham mark..nosp@m.j.ab.nosp@m.raham.nosp@m.@gma.nosp@m.il.co.nosp@m.m

Functions
static void	warning_rlimit (const rvec *x, int ai, int aj, int *global_atom_index, real r, real rlimit)
	Issue a warning if a listed interaction is beyond a table limit.
static real	evaluate_single (real r2, real tabscale, const real *vftab, real tableStride, real qq, real c6, real c12, real *velec, real *vvdw)
	Compute the energy and force for a single pair interaction.
static real	free_energy_evaluate_single (real r2, real sc_r_power, real alpha_coul, real alpha_vdw, real tabscale, const real *vftab, real tableStride, real qqA, real c6A, real c12A, real qqB, real c6B, real c12B, const real LFC[2], const real LFV[2], const real DLF[2], const real lfac_coul[2], const real lfac_vdw[2], const real dlfac_coul[2], const real dlfac_vdw[2], real sigma6_def, real sigma6_min, real sigma2_def, real sigma2_min, real *velectot, real *vvdwtot, real *dvdl)
	Compute the energy and force for a single pair interaction under FEP.
template<BondedKernelFlavor flavor>
static real	do_pairs_general (int ftype, int nbonds, const t_iatom iatoms[], const t_iparams iparams[], const rvec x[], rvec4 f[], rvec fshift[], const struct t_pbc *pbc, const struct t_graph *g, const real *lambda, real *dvdl, const t_mdatoms *md, const t_forcerec *fr, gmx_grppairener_t *grppener, int *global_atom_index)
	Calculate pair interactions, supports all types and conditions.
template<typename T , int pack_size, typename pbc_type >
static void	do_pairs_simple (int nbonds, const t_iatom iatoms[], const t_iparams iparams[], const rvec x[], rvec4 f[], const pbc_type pbc, const t_mdatoms *md, const real scale_factor)
	Calculate pairs, only for plain-LJ + plain Coulomb normal type. More...
void	do_pairs (int ftype, int nbonds, const t_iatom iatoms[], const t_iparams iparams[], const rvec x[], rvec4 f[], rvec fshift[], const struct t_pbc *pbc, const struct t_graph *g, const real *lambda, real *dvdl, const t_mdatoms *md, const t_forcerec *fr, const bool havePerturbedInteractions, const gmx::StepWorkload &stepWork, gmx_grppairener_t *grppener, int *global_atom_index)
	Calculate all listed pair interactions. More...

Function Documentation

void do_pairs	(	int	ftype,
		int	nbonds,
		const t_iatom	iatoms[],
		const t_iparams	iparams[],
		const rvec	x[],
		rvec4	f[],
		rvec	fshift[],
		const struct t_pbc *	pbc,
		const struct t_graph *	g,
		const real *	lambda,
		real *	dvdl,
		const t_mdatoms *	md,
		const t_forcerec *	fr,
		const bool	havePerturbedInteractions,
		const gmx::StepWorkload &	stepWork,
		gmx_grppairener_t *	grppener,
		int *	global_atom_index
	)

Calculate all listed pair interactions.

Calculate VdW/charge listed pair interactions (usually 1-4 interactions).

template<typename T , int pack_size, typename pbc_type >

static void do_pairs_simple ( int  nbonds, const t_iatom  iatoms[], const t_iparams  iparams[], const rvec  x[], rvec4  f[], const pbc_type  pbc, const t_mdatoms *  md, const real  scale_factor  )

static

Calculate pairs, only for plain-LJ + plain Coulomb normal type.

This function is templated for real/SimdReal and for optimization.