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36 * \brief SHAKE and LINCS tests.
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
44 * \author Artem Zhmurov <zhmurov@gmail.com>
45 * \ingroup module_mdlib
50 #include "constrtestdata.h"
52 #include "gromacs/utility/smalloc.h"
53 #include "gromacs/utility/stringutil.h"
60 ConstraintsTestData::ConstraintsTestData(const std::string& title,
62 std::vector<real> masses,
63 std::vector<int> constraints,
64 std::vector<real> constraintsR0,
66 tensor virialScaledRef,
67 bool compute_dHdLambda,
71 const std::vector<RVec>& x,
72 const std::vector<RVec>& xPrime,
73 const std::vector<RVec>& v,
76 int lincsNumIterations,
77 int lincsExpansionOrder,
80 title_ = title; // Human-friendly name of the system
81 numAtoms_ = numAtoms; // Number of atoms
85 invmass_.resize(numAtoms); // Vector of inverse masses
87 for (int i = 0; i < numAtoms; i++)
89 invmass_[i] = 1.0 / masses.at(i);
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
96 invdt_ = 1.0 / timestep; // Inverse timestep
98 // Input record - data that usually comes from configuration file (.mdp)
99 ir_.efep = FreeEnergyPerturbationType::No;
100 ir_.init_t = initialTime;
101 ir_.delta_t = timestep;
102 ir_.eI = IntegrationAlgorithm::MD;
105 computeVirial_ = computeVirial;
108 for (int i = 0; i < DIM; i++)
110 for (int j = 0; j < DIM; j++)
112 virialScaled_[i][j] = 0;
113 virialScaledRef_[i][j] = virialScaledRef[i][j];
118 // Free energy evaluation
119 hasMassPerturbed_ = false;
121 compute_dHdLambda_ = compute_dHdLambda;
123 if (compute_dHdLambda_)
125 ir_.efep = FreeEnergyPerturbationType::Yes;
126 dHdLambdaRef_ = dHdLambdaRef;
130 ir_.efep = FreeEnergyPerturbationType::No;
135 for (index i = 0; i < ssize(constraints); i += 3)
137 if (maxType < constraints.at(i))
139 maxType = constraints.at(i);
142 auto& iparams = mtop_.ffparams.iparams;
143 iparams.resize(maxType + 1);
144 for (index i = 0; i < ssize(constraints) / 3; i++)
146 iparams[constraints.at(3 * i)].constr.dA = constraintsR0.at(constraints.at(3 * i));
147 iparams[constraints.at(3 * i)].constr.dB = constraintsR0.at(constraints.at(3 * i));
149 idef_ = std::make_unique<InteractionDefinitions>(mtop_.ffparams);
150 for (index i = 0; i < ssize(constraints); i++)
152 idef_->il[F_CONSTR].iatoms.push_back(constraints.at(i));
155 // Constraints and their parameters (global topology)
156 InteractionList interactionList;
157 interactionList.iatoms.resize(constraints.size());
158 std::copy(constraints.begin(), constraints.end(), interactionList.iatoms.begin());
159 InteractionList interactionListEmpty;
160 interactionListEmpty.iatoms.resize(0);
162 gmx_moltype_t molType;
163 molType.atoms.nr = numAtoms;
164 molType.ilist.at(F_CONSTR) = interactionList;
165 molType.ilist.at(F_CONSTRNC) = interactionListEmpty;
166 mtop_.moltype.push_back(molType);
168 gmx_molblock_t molBlock;
171 mtop_.molblock.push_back(molBlock);
173 mtop_.natoms = numAtoms;
174 mtop_.bIntermolecularInteractions = false;
176 // Coordinates and velocities
177 x_.resizeWithPadding(numAtoms);
178 xPrime_.resizeWithPadding(numAtoms);
179 xPrime0_.resizeWithPadding(numAtoms);
180 xPrime2_.resizeWithPadding(numAtoms);
182 v_.resizeWithPadding(numAtoms);
183 v0_.resizeWithPadding(numAtoms);
185 std::copy(x.begin(), x.end(), x_.begin());
186 std::copy(xPrime.begin(), xPrime.end(), xPrime_.begin());
187 std::copy(xPrime.begin(), xPrime.end(), xPrime0_.begin());
188 std::copy(xPrime.begin(), xPrime.end(), xPrime2_.begin());
190 std::copy(v.begin(), v.end(), v_.begin());
191 std::copy(v.begin(), v.end(), v0_.begin());
193 // SHAKE-specific parameters
194 ir_.shake_tol = shakeTolerance;
195 ir_.bShakeSOR = shakeUseSOR;
197 // LINCS-specific parameters
198 ir_.nLincsIter = lincsNumIterations;
199 ir_.nProjOrder = lincsExpansionOrder;
200 ir_.LincsWarnAngle = lincsWarnAngle;
204 * Reset the data structure so it can be reused.
206 * Set the coordinates and velocities back to their values before
207 * constraining. The scaled virial tensor and dHdLambda are zeroed.
210 void ConstraintsTestData::reset()
218 for (int i = 0; i < DIM; i++)
220 for (int j = 0; j < DIM; j++)
222 virialScaled_[i][j] = 0;