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36 * \brief Defines the box deformation code.
38 * \todo The .mdp specification should have a boolean for this module.
40 * \todo grompp should set up fields in the tpr file that carry the
41 * information about the original box, then the deform module would
42 * can be build alongside the update module, rather than need to be
43 * set up before the checkpoint is read.
45 * \author Berk Hess <hess@kth.se>
46 * \author Mark Abraham <mark.j.abraham@gmail.com>
47 * \ingroup module_mdlib
51 #include "boxdeformation.h"
55 #include "gromacs/gmxlib/network.h"
56 #include "gromacs/math/invertmatrix.h"
57 #include "gromacs/math/vec.h"
58 #include "gromacs/mdtypes/commrec.h"
59 #include "gromacs/mdtypes/inputrec.h"
60 #include "gromacs/mdtypes/md_enums.h"
61 #include "gromacs/utility/arrayref.h"
62 #include "gromacs/utility/exceptions.h"
67 std::unique_ptr<BoxDeformation> prepareBoxDeformation(const matrix& initialBox,
70 MPI_Comm communicator,
71 const t_inputrec& inputrec)
73 if (!inputrecDeform(&inputrec))
77 if (!EI_DYNAMICS(inputrec.eI))
79 GMX_THROW(NotImplementedError(
80 "Box deformation is only supported with dynamical integrators"));
84 // Only the rank that read the tpr has the global state, and thus
85 // the initial box, so we pass that around.
86 // (numRanks != NumRanks::Multiple helps clang static analyzer to
87 // understand that box is defined in all cases)
88 if (ddRole == DDRole::Master || numRanks != NumRanks::Multiple)
90 copy_mat(initialBox, box);
92 if (numRanks == NumRanks::Multiple)
94 gmx_bcast(sizeof(box), box, communicator);
97 return std::make_unique<BoxDeformation>(inputrec.delta_t, inputrec.init_step, inputrec.deform, box);
100 BoxDeformation::BoxDeformation(double timeStep,
102 const tensor& deformationTensor,
103 const matrix& referenceBox) :
105 initialStep_(initialStep)
107 copy_mat(deformationTensor, deformationTensor_);
108 copy_mat(referenceBox, referenceBox_);
111 void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
113 matrix updatedBox, invbox, mu;
115 double elapsedTime = (step + 1 - initialStep_) * timeStep_;
116 copy_mat(box, updatedBox);
117 for (int i = 0; i < DIM; i++)
119 for (int j = 0; j < DIM; j++)
121 if (deformationTensor_[i][j] != 0)
123 updatedBox[i][j] = referenceBox_[i][j] + elapsedTime * deformationTensor_[i][j];
127 /* We correct the off-diagonal elements,
128 * which can grow indefinitely during shearing,
129 * so the shifts do not get messed up.
131 for (int i = 1; i < DIM; i++)
133 for (int j = i - 1; j >= 0; j--)
135 while (updatedBox[i][j] - box[i][j] > 0.5 * updatedBox[j][j])
137 rvec_dec(updatedBox[i], updatedBox[j]);
139 while (updatedBox[i][j] - box[i][j] < -0.5 * updatedBox[j][j])
141 rvec_inc(updatedBox[i], updatedBox[j]);
145 invertBoxMatrix(box, invbox);
146 // Return the updated box
147 copy_mat(updatedBox, box);
148 mmul_ur0(box, invbox, mu);
150 for (auto& thisX : x)
152 thisX[XX] = mu[XX][XX] * thisX[XX] + mu[YY][XX] * thisX[YY] + mu[ZZ][XX] * thisX[ZZ];
153 thisX[YY] = mu[YY][YY] * thisX[YY] + mu[ZZ][YY] * thisX[ZZ];
154 thisX[ZZ] = mu[ZZ][ZZ] * thisX[ZZ];