src/gromacs/mdlib/tests/constrtestdata.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018,2019, 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 SHAKE and LINCS tests.
  37  *
  38  * \todo Better tests for virial are needed.
  39  * \todo Tests for bigger systems to test threads synchronization,
  40  *       reduction, etc. on the GPU.
  41  * \todo Tests for algorithms for derivatives.
  42  * \todo Free-energy perturbation tests
  43  *
  44  * \author Artem Zhmurov <zhmurov@gmail.com>
  45  * \ingroup module_mdlib
  46  */
  47
  48 #include "gmxpre.h"
  49
  50 #include "constrtestdata.h"
  51
  52 #include "gromacs/utility/smalloc.h"
  53 #include "gromacs/utility/stringutil.h"
  54
  55 namespace gmx
  56 {
  57 namespace test
  58 {
  59
  60 ConstraintsTestData::ConstraintsTestData(const std::string &title,
  61                                          int numAtoms, std::vector<real> masses,
  62                                          std::vector<int> constraints, std::vector<real> constraintsR0,
  63                                          bool computeVirial, tensor virialScaledRef,
  64                                          bool compute_dHdLambda, float dHdLambdaRef,
  65                                          real initialTime, real timestep,
  66                                          const std::vector<RVec> &x, const std::vector<RVec> &xPrime, const std::vector<RVec> &v,
  67                                          real shakeTolerance, gmx_bool shakeUseSOR,
  68                                          int lincsNumIterations, int lincsExpansionOrder, real lincsWarnAngle)
  69 {
  70     title_    = title;    // Human-friendly name of the system
  71     numAtoms_ = numAtoms; // Number of atoms
  72
  73     // Masses of atoms
  74     masses_ = masses;
  75     invmass_.resize(numAtoms); // Vector of inverse masses
  76
  77     for (int i = 0; i < numAtoms; i++)
  78     {
  79         invmass_[i] = 1.0/masses.at(i);
  80     }
  81
  82     // Saving constraints to check if they are satisfied after algorithm was applied
  83     constraints_   = constraints;   // Constraints indices (in type-i-j format)
  84     constraintsR0_ = constraintsR0; // Equilibrium distances for each type of constraint
  85
  86     invdt_  = 1.0/timestep;         // Inverse timestep
  87
  88     // Communication record
  89     cr_.nnodes = 1;
  90     cr_.dd     = nullptr;
  91
  92     // Multisim data
  93     ms_.sim  = 0;
  94     ms_.nsim = 1;
  95
  96     // Input record - data that usually comes from configuration file (.mdp)
  97     ir_.efep           = 0;
  98     ir_.init_t         = initialTime;
  99     ir_.delta_t        = timestep;
 100     ir_.eI             = 0;
 101
 102     // MD atoms data
 103     md_.nMassPerturbed = 0;
 104     md_.lambda         = 0.0;
 105     md_.invmass        = invmass_.data();
 106     md_.nr             = numAtoms;
 107     md_.homenr         = numAtoms;
 108
 109     // Virial evaluation
 110     computeVirial_ = computeVirial;
 111     if (computeVirial)
 112     {
 113         for (int i = 0; i < DIM; i++)
 114         {
 115             for (int j = 0; j < DIM; j++)
 116             {
 117                 virialScaled_[i][j]    = 0;
 118                 virialScaledRef_[i][j] = virialScaledRef[i][j];
 119             }
 120         }
 121     }
 122
 123
 124     // Free energy evaluation
 125     compute_dHdLambda_ = compute_dHdLambda;
 126     dHdLambda_         = 0;
 127     if (compute_dHdLambda_)
 128     {
 129         ir_.efep                    = efepYES;
 130         dHdLambdaRef_               = dHdLambdaRef;
 131     }
 132     else
 133     {
 134         ir_.efep                    = efepNO;
 135         dHdLambdaRef_               = 0;
 136     }
 137
 138     // Constraints and their parameters (local topology)
 139     for (int i = 0; i < F_NRE; i++)
 140     {
 141         idef_.il[i].nr = 0;
 142     }
 143     idef_.il[F_CONSTR].nr   = constraints.size();
 144
 145     snew(idef_.il[F_CONSTR].iatoms, constraints.size());
 146     int maxType = 0;
 147     for (index i = 0; i < ssize(constraints); i++)
 148     {
 149         if (i % 3 == 0)
 150         {
 151             if (maxType < constraints.at(i))
 152             {
 153                 maxType = constraints.at(i);
 154             }
 155         }
 156         idef_.il[F_CONSTR].iatoms[i] = constraints.at(i);
 157     }
 158     snew(idef_.iparams, maxType + 1);
 159     for (index i = 0; i < ssize(constraints)/3; i++)
 160     {
 161         idef_.iparams[constraints.at(3*i)].constr.dA = constraintsR0.at(constraints.at(3*i));
 162         idef_.iparams[constraints.at(3*i)].constr.dB = constraintsR0.at(constraints.at(3*i));
 163     }
 164
 165     // Constraints and their parameters (global topology)
 166     InteractionList interactionList;
 167     interactionList.iatoms.resize(constraints.size());
 168     std::copy(constraints.begin(), constraints.end(), interactionList.iatoms.begin());
 169     InteractionList interactionListEmpty;
 170     interactionListEmpty.iatoms.resize(0);
 171
 172     gmx_moltype_t molType;
 173     molType.atoms.nr             = numAtoms;
 174     molType.ilist.at(F_CONSTR)   = interactionList;
 175     molType.ilist.at(F_CONSTRNC) = interactionListEmpty;
 176     mtop_.moltype.push_back(molType);
 177
 178     gmx_molblock_t molBlock;
 179     molBlock.type = 0;
 180     molBlock.nmol = 1;
 181     mtop_.molblock.push_back(molBlock);
 182
 183     mtop_.natoms = numAtoms;
 184     mtop_.ffparams.iparams.resize(maxType + 1);
 185     for (int i = 0; i <= maxType; i++)
 186     {
 187         mtop_.ffparams.iparams.at(i) = idef_.iparams[i];
 188     }
 189     mtop_.bIntermolecularInteractions = false;
 190
 191     // Coordinates and velocities
 192     x_.resizeWithPadding(numAtoms);
 193     xPrime_.resizeWithPadding(numAtoms);
 194     xPrime0_.resizeWithPadding(numAtoms);
 195     xPrime2_.resizeWithPadding(numAtoms);
 196
 197     v_.resizeWithPadding(numAtoms);
 198     v0_.resizeWithPadding(numAtoms);
 199
 200     std::copy(x.begin(), x.end(), x_.begin());
 201     std::copy(xPrime.begin(), xPrime.end(), xPrime_.begin());
 202     std::copy(xPrime.begin(), xPrime.end(), xPrime0_.begin());
 203     std::copy(xPrime.begin(), xPrime.end(), xPrime2_.begin());
 204
 205     std::copy(v.begin(), v.end(), v_.begin());
 206     std::copy(v.begin(), v.end(), v0_.begin());
 207
 208     // SHAKE-specific parameters
 209     ir_.shake_tol            = shakeTolerance;
 210     ir_.bShakeSOR            = shakeUseSOR;
 211
 212     // LINCS-specific parameters
 213     ir_.nLincsIter     = lincsNumIterations;
 214     ir_.nProjOrder     = lincsExpansionOrder;
 215     ir_.LincsWarnAngle = lincsWarnAngle;
 216 }
 217
 218 /*! \brief
 219  * Reset the data structure so it can be reused.
 220  *
 221  * Set the coordinates and velocities back to their values before
 222  * constraining. The scaled virial tensor and dHdLambda are zeroed.
 223  *
 224  */
 225 void ConstraintsTestData::reset()
 226 {
 227     xPrime_  = xPrime0_;
 228     xPrime2_ = xPrime0_;
 229     v_       = v0_;
 230
 231     if (computeVirial_)
 232     {
 233         for (int i = 0; i < DIM; i++)
 234         {
 235             for (int j = 0; j < DIM; j++)
 236             {
 237                 virialScaled_[i][j] = 0;
 238             }
 239         }
 240     }
 241     dHdLambda_         = 0;
 242 }
 243
 244 /*! \brief
 245  * Cleaning up the memory.
 246  */
 247 ConstraintsTestData::~ConstraintsTestData()
 248 {
 249     sfree(idef_.il[F_CONSTR].iatoms);
 250     sfree(idef_.iparams);
 251 }
 252
 253 } // namespace test
 254 } // namespace gmx