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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/arrayref.h"
50 #include "gromacs/utility/basedefinitions.h"
51 #include "gromacs/utility/classhelpers.h"
62 //! Trivial constructor.
63 BoxDeformation(double timeStep,
64 gmx_int64_t initialStep,
65 const tensor &deformationTensor,
66 const matrix &referenceBox);
68 //! Deform \c x and \c box at this \c step;
69 void apply(ArrayRef<RVec> x,
74 //! The integrator time step.
76 //! The initial step number (from the .tpr, which permits checkpointing to work correctly).
77 gmx_int64_t initialStep_;
78 //! Non-zero elements provide a scaling factor for deformation in that box dimension.
79 tensor deformationTensor_;
80 //! The initial box, ie from the .tpr file.
83 GMX_DISALLOW_COPY_AND_ASSIGN(BoxDeformation);
86 /*! \brief Factory function for box deformation module.
88 * If the \c inputrec specifies the use of box deformation during the
89 * update phase, communicates the \c initialBox from SIMMASTER to
90 * other ranks, and constructs and returns an object to manage that
93 * \throws NotImplementedError if the \c inputrec specifies an
94 * unsupported combination.
96 std::unique_ptr<BoxDeformation>
97 prepareBoxDeformation(const matrix &initialBox,
99 const t_inputrec &inputrec);