src/gromacs/mdlib/tests/constrtestdata.cpp

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  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,
  62                                          std::vector<real>        masses,
  63                                          std::vector<int>         constraints,
  64                                          std::vector<real>        constraintsR0,
  65                                          bool                     computeVirial,
  66                                          tensor                   virialScaledRef,
  67                                          bool                     compute_dHdLambda,
  68                                          float                    dHdLambdaRef,
  69                                          real                     initialTime,
  70                                          real                     timestep,
  71                                          const std::vector<RVec>& x,
  72                                          const std::vector<RVec>& xPrime,
  73                                          const std::vector<RVec>& v,
  74                                          real                     shakeTolerance,
  75                                          gmx_bool                 shakeUseSOR,
  76                                          int                      lincsNumIterations,
  77                                          int                      lincsExpansionOrder,
  78                                          real                     lincsWarnAngle)
  79 {
  80     title_    = title;    // Human-friendly name of the system
  81     numAtoms_ = numAtoms; // Number of atoms
  82
  83     // Masses of atoms
  84     masses_ = masses;
  85     invmass_.resize(numAtoms); // Vector of inverse masses
  86
  87     for (int i = 0; i < numAtoms; i++)
  88     {
  89         invmass_[i] = 1.0 / masses.at(i);
  90     }
  91
  92     // Saving constraints to check if they are satisfied after algorithm was applied
  93     constraints_   = constraints;   // Constraints indices (in type-i-j format)
  94     constraintsR0_ = constraintsR0; // Equilibrium distances for each type of constraint
  95
  96     invdt_ = 1.0 / timestep; // Inverse timestep
  97
  98     // Input record - data that usually comes from configuration file (.mdp)
  99     ir_.efep    = 0;
 100     ir_.init_t  = initialTime;
 101     ir_.delta_t = timestep;
 102     ir_.eI      = 0;
 103
 104     // MD atoms data
 105     md_.nMassPerturbed = 0;
 106     md_.lambda         = 0.0;
 107     md_.invmass        = invmass_.data();
 108     md_.nr             = numAtoms;
 109     md_.homenr         = numAtoms;
 110
 111     // Virial evaluation
 112     computeVirial_ = computeVirial;
 113     if (computeVirial)
 114     {
 115         for (int i = 0; i < DIM; i++)
 116         {
 117             for (int j = 0; j < DIM; j++)
 118             {
 119                 virialScaled_[i][j]    = 0;
 120                 virialScaledRef_[i][j] = virialScaledRef[i][j];
 121             }
 122         }
 123     }
 124
 125
 126     // Free energy evaluation
 127     compute_dHdLambda_ = compute_dHdLambda;
 128     dHdLambda_         = 0;
 129     if (compute_dHdLambda_)
 130     {
 131         ir_.efep      = efepYES;
 132         dHdLambdaRef_ = dHdLambdaRef;
 133     }
 134     else
 135     {
 136         ir_.efep      = efepNO;
 137         dHdLambdaRef_ = 0;
 138     }
 139
 140     int maxType = 0;
 141     for (index i = 0; i < ssize(constraints); i += 3)
 142     {
 143         if (maxType < constraints.at(i))
 144         {
 145             maxType = constraints.at(i);
 146         }
 147     }
 148     auto& iparams = mtop_.ffparams.iparams;
 149     iparams.resize(maxType + 1);
 150     for (index i = 0; i < ssize(constraints) / 3; i++)
 151     {
 152         iparams[constraints.at(3 * i)].constr.dA = constraintsR0.at(constraints.at(3 * i));
 153         iparams[constraints.at(3 * i)].constr.dB = constraintsR0.at(constraints.at(3 * i));
 154     }
 155     idef_ = std::make_unique<InteractionDefinitions>(mtop_.ffparams);
 156     for (index i = 0; i < ssize(constraints); i++)
 157     {
 158         idef_->il[F_CONSTR].iatoms.push_back(constraints.at(i));
 159     }
 160
 161     // Constraints and their parameters (global topology)
 162     InteractionList interactionList;
 163     interactionList.iatoms.resize(constraints.size());
 164     std::copy(constraints.begin(), constraints.end(), interactionList.iatoms.begin());
 165     InteractionList interactionListEmpty;
 166     interactionListEmpty.iatoms.resize(0);
 167
 168     gmx_moltype_t molType;
 169     molType.atoms.nr             = numAtoms;
 170     molType.ilist.at(F_CONSTR)   = interactionList;
 171     molType.ilist.at(F_CONSTRNC) = interactionListEmpty;
 172     mtop_.moltype.push_back(molType);
 173
 174     gmx_molblock_t molBlock;
 175     molBlock.type = 0;
 176     molBlock.nmol = 1;
 177     mtop_.molblock.push_back(molBlock);
 178
 179     mtop_.natoms                      = numAtoms;
 180     mtop_.bIntermolecularInteractions = false;
 181
 182     // Coordinates and velocities
 183     x_.resizeWithPadding(numAtoms);
 184     xPrime_.resizeWithPadding(numAtoms);
 185     xPrime0_.resizeWithPadding(numAtoms);
 186     xPrime2_.resizeWithPadding(numAtoms);
 187
 188     v_.resizeWithPadding(numAtoms);
 189     v0_.resizeWithPadding(numAtoms);
 190
 191     std::copy(x.begin(), x.end(), x_.begin());
 192     std::copy(xPrime.begin(), xPrime.end(), xPrime_.begin());
 193     std::copy(xPrime.begin(), xPrime.end(), xPrime0_.begin());
 194     std::copy(xPrime.begin(), xPrime.end(), xPrime2_.begin());
 195
 196     std::copy(v.begin(), v.end(), v_.begin());
 197     std::copy(v.begin(), v.end(), v0_.begin());
 198
 199     // SHAKE-specific parameters
 200     ir_.shake_tol = shakeTolerance;
 201     ir_.bShakeSOR = shakeUseSOR;
 202
 203     // LINCS-specific parameters
 204     ir_.nLincsIter     = lincsNumIterations;
 205     ir_.nProjOrder     = lincsExpansionOrder;
 206     ir_.LincsWarnAngle = lincsWarnAngle;
 207 }
 208
 209 /*! \brief
 210  * Reset the data structure so it can be reused.
 211  *
 212  * Set the coordinates and velocities back to their values before
 213  * constraining. The scaled virial tensor and dHdLambda are zeroed.
 214  *
 215  */
 216 void ConstraintsTestData::reset()
 217 {
 218     xPrime_  = xPrime0_;
 219     xPrime2_ = xPrime0_;
 220     v_       = v0_;
 221
 222     if (computeVirial_)
 223     {
 224         for (int i = 0; i < DIM; i++)
 225         {
 226             for (int j = 0; j < DIM; j++)
 227             {
 228                 virialScaled_[i][j] = 0;
 229             }
 230         }
 231     }
 232     dHdLambda_ = 0;
 233 }
 234
 235 } // namespace test
 236 } // namespace gmx