box.cpp File Reference

#include "gmxpre.h"
#include "box.h"
#include "config.h"
#include <cmath>
#include <cstdio>
#include <filesystem>
#include <memory>
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/nsgrid.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/functions.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/block.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/mpicomm.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/vec.h"
#include "domdec_internal.h"

Include dependency graph for box.cpp:

Description

This file defines functions used by the domdec module for (bounding) box and pbc information generation.

Author

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

Functions
static void	calc_pos_av_stddev (gmx::ArrayRef< const gmx::RVec > x, rvec av, rvec stddev, const gmx::MpiComm *mpiComm)
	Calculates the average and standard deviation in 3D of atoms.
static void	set_tric_dir (const gmx::IVec *numDomains, gmx_ddbox_t *ddbox, const matrix box)
	Determines if dimensions require triclinic treatment and stores this info in ddbox.
static void	low_set_ddbox (int numPbcDimensions, int numBoundedDimensions, const gmx::IVec *numDomains, const matrix box, bool calculateUnboundedSize, gmx::ArrayRef< const gmx::RVec > x, const gmx::MpiComm *mpiComm, gmx_ddbox_t *ddbox)
	This function calculates bounding box and pbc info and populates ddbox.
void	set_ddbox (const gmx_domdec_t &dd, bool mainRankHasTheSystemState, const matrix box, bool calculateUnboundedSize, gmx::ArrayRef< const gmx::RVec > x, gmx_ddbox_t *ddbox)
	Set the box and PBC data in ddbox.
void	set_ddbox_MpiComm (DDRole ddRole, const gmx::MpiComm &mpiComm, const gmx::IVec *numDomains, const t_inputrec &ir, const matrix box, gmx::ArrayRef< const gmx::RVec > x, gmx_ddbox_t *ddbox)
	Set the box and PBC data in ddbox.
gmx_ddbox_t	get_ddbox (const gmx::IVec &numDomains, const t_inputrec &ir, const matrix box, gmx::ArrayRef< const gmx::RVec > x)
	Computes and returns a domain decomposition box.