bonded.cpp File Reference

#include "gmxpre.h"
#include "bonded.h"
#include "config.h"
#include <assert.h>
#include <cmath>
#include <algorithm>
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc-simd.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/simd/simd.h"
#include "gromacs/simd/simd_math.h"
#include "gromacs/simd/vector_operations.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "listed-internal.h"
#include "pairs.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

Functions
static void gmx_simdcall	gmx_hack_simd_gather_rvec_dist_two_index (const rvec *v, const int *index0, const int *index1, real *buf, gmx_simd_float_t *dx, gmx_simd_float_t *dy, gmx_simd_float_t *dz)
	Store differences between indexed rvecs in SIMD registers. More...
static int	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...
real	morse_bonds (int nbonds, const t_iatom forceatoms[], const t_iparams forceparams[], const rvec x[], rvec 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...
static int	cmap_setup_grid_index (int ip, int grid_spacing, int *ipm1, int *ipp1, int *ipp2)
	Mysterious undocumented function.
real	cmap_dihs (int nbonds, const t_iatom forceatoms[], const t_iparams forceparams[], const gmx_cmap_t *cmap_grid, const rvec x[], rvec 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.

Variables
const int	cmap_coeff_matrix []
	Mysterious CMAP coefficient matrix. More...

Function Documentation

static void gmx_simdcall gmx_hack_simd_gather_rvec_dist_two_index ( const rvec *  v, const int *  index0, const int *  index1, real *  buf, gmx_simd_float_t *  dx, gmx_simd_float_t *  dy, gmx_simd_float_t *  dz  )

inlinestatic

Store differences between indexed rvecs in SIMD registers.

Returns SIMD register with the difference vectors: v[index0[i]] - v[index1[i]]

Parameters

[in]	v	Array of rvecs
[in]	index0	Index into the vector array
[in]	index1	Index into the vector array
[in,out]	buf	Aligned tmp buffer of size 3*GMX_SIMD_REAL_WIDTH
[out]	dx	SIMD register with x difference
[out]	dy	SIMD register with y difference
[out]	dz	SIMD register with z difference

real morse_bonds	(	int	nbonds,
		const t_iatom	forceatoms[],
		const t_iparams	forceparams[],
		const rvec	x[],
		rvec	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.

By Frank Everdij. Three parameters needed:

b0 = equilibrium distance in nm be = beta in nm^-1 (actually, it's nu_e*Sqrt(2*pi*pi*mu/D_e)) cb = well depth in kJ/mol

Note: the potential is referenced to be +cb at infinite separation and zero at the equilibrium distance!

static int pbc_rvec_sub ( const t_pbc *  pbc, const rvec  xi, const rvec  xj, rvec  dx  )

static

Compute dx = xi - xj, modulo PBC if non-NULL.

Todo:

This kind of code appears in many places. Consolidate it

Variable Documentation

const int cmap_coeff_matrix[]

Initial value:

= {
    1, 0, -3,  2, 0, 0,  0,  0, -3,  0,  9, -6,  2,  0, -6,  4,
    0, 0,  0,  0, 0, 0,  0,  0,  3,  0, -9,  6, -2,  0,  6, -4,
    0, 0,  0,  0, 0, 0,  0,  0,  0,  0,  9, -6,  0,  0, -6,  4,
    0, 0,  3, -2, 0, 0,  0,  0,  0,  0, -9,  6,  0,  0,  6, -4,
    0, 0,  0,  0, 1, 0, -3,  2, -2,  0,  6, -4,  1,  0, -3,  2,
    0, 0,  0,  0, 0, 0,  0,  0, -1,  0,  3, -2,  1,  0, -3,  2,
    0, 0,  0,  0, 0, 0,  0,  0,  0,  0, -3,  2,  0,  0,  3, -2,
    0, 0,  0,  0, 0, 0,  3, -2,  0,  0, -6,  4,  0,  0,  3, -2,
    0, 1, -2,  1, 0, 0,  0,  0,  0, -3,  6, -3,  0,  2, -4,  2,
    0, 0,  0,  0, 0, 0,  0,  0,  0,  3, -6,  3,  0, -2,  4, -2,
    0, 0,  0,  0, 0, 0,  0,  0,  0,  0, -3,  3,  0,  0,  2, -2,
    0, 0, -1,  1, 0, 0,  0,  0,  0,  0,  3, -3,  0,  0, -2,  2,
    0, 0,  0,  0, 0, 1, -2,  1,  0, -2,  4, -2,  0,  1, -2,  1,
    0, 0,  0,  0, 0, 0,  0,  0,  0, -1,  2, -1,  0,  1, -2,  1,
    0, 0,  0,  0, 0, 0,  0,  0,  0,  0,  1, -1,  0,  0, -1,  1,
    0, 0,  0,  0, 0, 0, -1,  1,  0,  0,  2, -2,  0,  0, -1,  1
}

Mysterious CMAP coefficient matrix.