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35 /*! \libinternal \file
36 * \brief Declares interface to box deformation code.
38 * \author Mark Abraham <mark.j.abraham@gmail.com>
39 * \ingroup module_mdlib
43 #ifndef GMX_MDRUN_BOXDEFORMATION_H
44 #define GMX_MDRUN_BOXDEFORMATION_H
48 #include "gromacs/math/vectypes.h"
49 #include "gromacs/utility/basedefinitions.h"
50 #include "gromacs/utility/classhelpers.h"
51 #include "gromacs/utility/gmxmpi.h"
65 //! Trivial constructor.
66 BoxDeformation(double timeStep, int64_t initialStep, const tensor& deformationTensor, const matrix& referenceBox);
68 //! Deform \c x and \c box at this \c step;
69 void apply(ArrayRef<RVec> x, matrix box, int64_t step);
72 //! The integrator time step.
74 //! The initial step number (from the .tpr, which permits checkpointing to work correctly).
76 //! Non-zero elements provide a scaling factor for deformation in that box dimension.
77 tensor deformationTensor_;
78 //! The initial box, ie from the .tpr file.
81 GMX_DISALLOW_COPY_AND_ASSIGN(BoxDeformation);
84 /*! \brief Factory function for box deformation module.
86 * If the \c inputrec specifies the use of box deformation during the
87 * update phase, communicates the \c initialBox from SIMMASTER to
88 * other ranks, and constructs and returns an object to manage that
91 * \throws NotImplementedError if the \c inputrec specifies an
92 * unsupported combination.
94 std::unique_ptr<BoxDeformation> prepareBoxDeformation(const matrix& initialBox,
97 MPI_Comm communicator,
98 const t_inputrec& inputrec);