boxdeformation.cpp File Reference

#include "gmxpre.h"
#include "boxdeformation.h"
#include <array>
#include <memory>
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/boxmatrix.h"
#include "gromacs/math/invertmatrix.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/real.h"

Include dependency graph for boxdeformation.cpp:

Description

Defines the box deformation code.

Todo:

The .mdp specification should have a boolean for this module.

Todo:

grompp should set up fields in the tpr file that carry the information about the original box, then the deform module would can be build alongside the update module, rather than need to be set up before the checkpoint is read.

Author

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

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

Functions
std::unique_ptr< BoxDeformation >	gmx::buildBoxDeformation (const Matrix3x3 &initialBox, DDRole ddRole, NumRanks numRanks, MPI_Comm communicator, const t_inputrec &inputrec)
	Factory function for box deformation module. More...
void	gmx::setBoxDeformationFlowMatrix (const matrix boxDeformationVelocity, const matrix box, matrix flowMatrix)
	Set a matrix for computing the flow velocity at coordinates. More...