src/gromacs/mdlib/boxdeformation.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35 /*! \internal \file
  36  * \brief Defines the box deformation code.
  37  *
  38  * \todo The .mdp specification should have a boolean for this module.
  39  *
  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.
  44  *
  45  * \author Berk Hess <hess@kth.se>
  46  * \author Mark Abraham <mark.j.abraham@gmail.com>
  47  * \ingroup module_mdlib
  48  */
  49 #include "gmxpre.h"
  50
  51 #include "boxdeformation.h"
  52
  53 #include "gromacs/compat/make_unique.h"
  54 #include "gromacs/gmxlib/network.h"
  55 #include "gromacs/math/invertmatrix.h"
  56 #include "gromacs/math/vec.h"
  57 #include "gromacs/mdtypes/commrec.h"
  58 #include "gromacs/mdtypes/inputrec.h"
  59 #include "gromacs/mdtypes/md_enums.h"
  60 #include "gromacs/utility/exceptions.h"
  61
  62 namespace gmx
  63 {
  64
  65 std::unique_ptr<BoxDeformation>
  66 prepareBoxDeformation(const matrix     &initialBox,
  67                       t_commrec        *cr,
  68                       const t_inputrec &inputrec)
  69 {
  70     if (!inputrecDeform(&inputrec))
  71     {
  72         return nullptr;
  73     }
  74     if (!EI_DYNAMICS(inputrec.eI))
  75     {
  76         GMX_THROW(NotImplementedError("Box deformation is only supported with dynamical integrators"));
  77     }
  78
  79     matrix box;
  80     // Only the rank that read the tpr has the global state, and thus
  81     // the initial box, so we pass that around.
  82     if (SIMMASTER(cr))
  83     {
  84         copy_mat(initialBox, box);
  85     }
  86     if (PAR(cr))
  87     {
  88         gmx_bcast(sizeof(box), box, cr);
  89     }
  90
  91     return compat::make_unique<BoxDeformation>(inputrec.delta_t,
  92                                                inputrec.init_step,
  93                                                inputrec.deform,
  94                                                box);
  95 }
  96
  97 BoxDeformation::BoxDeformation(double        timeStep,
  98                                int64_t       initialStep,
  99                                const tensor &deformationTensor,
 100                                const matrix &referenceBox)
 101     : timeStep_(timeStep),
 102       initialStep_(initialStep)
 103 {
 104     copy_mat(deformationTensor, deformationTensor_);
 105     copy_mat(referenceBox, referenceBox_);
 106 }
 107
 108 void
 109 BoxDeformation::apply(ArrayRef<RVec> x,
 110                       matrix         box,
 111                       int64_t        step)
 112 {
 113     matrix updatedBox, invbox, mu;
 114
 115     double elapsedTime = (step + 1 - initialStep_) * timeStep_;
 116     copy_mat(box, updatedBox);
 117     for (int i = 0; i < DIM; i++)
 118     {
 119         for (int j = 0; j < DIM; j++)
 120         {
 121             if (deformationTensor_[i][j] != 0)
 122             {
 123                 updatedBox[i][j] =
 124                     referenceBox_[i][j] + elapsedTime * deformationTensor_[i][j];
 125             }
 126         }
 127     }
 128     /* We correct the off-diagonal elements,
 129      * which can grow indefinitely during shearing,
 130      * so the shifts do not get messed up.
 131      */
 132     for (int i = 1; i < DIM; i++)
 133     {
 134         for (int j = i-1; j >= 0; j--)
 135         {
 136             while (updatedBox[i][j] - box[i][j] > 0.5 * updatedBox[j][j])
 137             {
 138                 rvec_dec(updatedBox[i], updatedBox[j]);
 139             }
 140             while (updatedBox[i][j] - box[i][j] < -0.5 * updatedBox[j][j])
 141             {
 142                 rvec_inc(updatedBox[i], updatedBox[j]);
 143             }
 144         }
 145     }
 146     invertBoxMatrix(box, invbox);
 147     // Return the updated box
 148     copy_mat(updatedBox, box);
 149     mmul_ur0(box, invbox, mu);
 150
 151     for (auto &thisX : x)
 152     {
 153         thisX[XX] = mu[XX][XX]*thisX[XX] + mu[YY][XX]*thisX[YY] + mu[ZZ][XX]*thisX[ZZ];
 154         thisX[YY] = mu[YY][YY]*thisX[YY] + mu[ZZ][YY]*thisX[ZZ];
 155         thisX[ZZ] = mu[ZZ][ZZ]*thisX[ZZ];
 156     }
 157 }
 158
 159 }  // namespace gmx