pbc_aiuc.h File Reference

#include "gromacs/pbcutil/ishift.h"

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Description

Structure and basic routines to handle periodic boundary conditions.

This file contains CPU

Todo:

CPU, GPU and SIMD routines essentially do the same operations on different data-types. Currently this leads to code duplication, which has to be resolved. For details, see Issue #2863 https://gitlab.com/gromacs/gromacs/-/issues/2863

Author

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

Berk Hess hess@.nosp@m.kth..nosp@m.se

Artem Zhmurov zhmur.nosp@m.ov@g.nosp@m.mail..nosp@m.com

Classes
struct	PbcAiuc
	Compact and ordered version of the PBC matrix. More...

Functions
static void	setPbcAiuc (int numPbcDim, const matrix box, PbcAiuc *pbcAiuc)
	Set the PBC data-structure. More...
static void	pbcDxAiuc (const PbcAiuc &pbcAiuc, const rvec &r1, const rvec &r2, rvec dr)
	Computes the vector between two points taking PBC into account. More...

Function Documentation

static void pbcDxAiuc ( const PbcAiuc &  pbcAiuc, const rvec &  r1, const rvec &  r2, rvec  dr  )

inlinestatic

Computes the vector between two points taking PBC into account.

Computes the vector dr between points r2 and r1, taking into account the periodic boundary conditions, described in pbcAiuc object. Note that this routine always does the PBC arithmetic for all directions, multiplying the displacements by zeroes if the corresponding direction is not periodic. For triclinic boxes only distances up to half the smallest box diagonal element are guaranteed to be the shortest. This means that distances from 0.5/sqrt(2) times a box vector length (e.g. for a rhombic dodecahedron) can use a more distant periodic image.

Todo:

This routine operates on rvec types and uses PbcAiuc to define periodic box, but essentially does the same thing as SIMD and GPU version. These will have to be unified in future to avoid code duplication. See Issue #2863: https://gitlab.com/gromacs/gromacs/-/issues/2863

Parameters

[in]	pbcAiuc	PBC object.
[in]	r1	Coordinates of the first point.
[in]	r2	Coordinates of the second point.
[out]	dr	Resulting distance.

static void setPbcAiuc ( int  numPbcDim, const matrix  box, PbcAiuc *  pbcAiuc  )

inlinestatic

Set the PBC data-structure.

Parameters

[in]	numPbcDim	Number of periodic dimensions: 0 - no periodicity. 1 - periodicity along X-axis. 2 - periodicity in XY plane. 3 - periodicity along all dimensions.
[in]	box	Matrix, describing the periodic cell.
[out]	pbcAiuc	Pointer to PbcAiuc structure to be initialized.