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36 * \brief Defines the class to accumulate the data needed for the Leap-Frog integrator tests
38 * \author Artem Zhmurov <zhmurov@gmail.com>
39 * \ingroup module_mdlib
43 #include "leapfrogtestdata.h"
50 #include <unordered_map>
53 #include <gtest/gtest.h>
55 #include "gromacs/gpu_utils/gpu_utils.h"
56 #include "gromacs/math/vec.h"
57 #include "gromacs/math/vectypes.h"
58 #include "gromacs/mdtypes/mdatom.h"
59 #include "gromacs/utility/smalloc.h"
60 #include "gromacs/utility/stringutil.h"
62 #include "testutils/refdata.h"
63 #include "testutils/testasserts.h"
70 LeapFrogTestData::LeapFrogTestData(int numAtoms, real timestep, const rvec v0, const rvec f0, int numTCoupleGroups, int nstpcouple) :
79 inverseMasses_(numAtoms),
80 inverseMassesPerDim_(numAtoms),
81 numTCoupleGroups_(numTCoupleGroups)
83 mdAtoms_.nr = numAtoms_;
85 for (int i = 0; i < numAtoms_; i++)
87 // Typical PBC box size is tens of nanometers
88 x_[i][XX] = (i%21)*1.0;
89 x_[i][YY] = 6.5 + (i%13)*(-1.0);
90 x_[i][ZZ] = (i%32)*(0.0);
92 for (int d = 0; d < DIM; d++)
95 // Thermal velocity is ~1 nm/ps (|v0| = 1-2 nm/ps)
97 // TODO Check what value typical MD forces have (now ~ 1 kJ/mol/nm)
100 x0_[i][d] = x_[i][d];
101 v0_[i][d] = v_[i][d];
103 // Atom masses are ~1-100 g/mol
104 inverseMasses_[i] = 1.0/(1.0 + i%100);
105 for (int d = 0; d < DIM; d++)
107 inverseMassesPerDim_[i][d] = inverseMasses_[i];
110 mdAtoms_.invmass = inverseMasses_.data();
111 mdAtoms_.invMassPerDim = as_rvec_array(inverseMassesPerDim_.data());
113 // Temperature coupling
114 snew(mdAtoms_.cTC, numAtoms_);
116 // To do temperature coupling at each step
117 inputRecord_.nsttcouple = 1;
119 if (numTCoupleGroups_ == 0)
121 inputRecord_.etc = etcNO;
122 for (int i = 0; i < numAtoms_; i++)
126 kineticEnergyData_.ngtc = 1;
127 t_grp_tcstat temperatureCouplingGroupData;
128 temperatureCouplingGroupData.lambda = 1.0;
129 kineticEnergyData_.tcstat.emplace_back(temperatureCouplingGroupData);
133 inputRecord_.etc = etcYES;
134 for (int i = 0; i < numAtoms_; i++)
136 mdAtoms_.cTC[i] = i % numTCoupleGroups_;
138 kineticEnergyData_.ngtc = numTCoupleGroups_;
139 for (int i = 0; i < numTCoupleGroups; i++)
141 real tCoupleLambda = 1.0 - (i + 1.0)/10.0;
142 t_grp_tcstat temperatureCouplingGroupData;
143 temperatureCouplingGroupData.lambda = tCoupleLambda;
144 kineticEnergyData_.tcstat.emplace_back(temperatureCouplingGroupData);
148 inputRecord_.eI = eiMD;
149 inputRecord_.delta_t = timestep_;
153 state_.box[XX][XX] = 10.0;
154 state_.box[XX][YY] = 0.0;
155 state_.box[XX][ZZ] = 0.0;
157 state_.box[YY][XX] = 0.0;
158 state_.box[YY][YY] = 10.0;
159 state_.box[YY][ZZ] = 0.0;
161 state_.box[ZZ][XX] = 0.0;
162 state_.box[ZZ][YY] = 0.0;
163 state_.box[ZZ][ZZ] = 10.0;
165 kineticEnergyData_.bNEMD = false;
166 kineticEnergyData_.cosacc.cos_accel = 0.0;
168 kineticEnergyData_.nthreads = 1;
169 snew(kineticEnergyData_.ekin_work_alloc, kineticEnergyData_.nthreads);
170 snew(kineticEnergyData_.ekin_work, kineticEnergyData_.nthreads);
171 snew(kineticEnergyData_.dekindl_work, kineticEnergyData_.nthreads);
173 mdAtoms_.homenr = numAtoms_;
174 mdAtoms_.haveVsites = false;
175 mdAtoms_.havePartiallyFrozenAtoms = false;
176 mdAtoms_.cFREEZE = nullptr;
178 update_ = std::make_unique<Update>(&inputRecord_, nullptr);
179 update_->setNumAtoms(numAtoms);
181 doPressureCouple_ = (nstpcouple != 0);
183 if (doPressureCouple_)
185 inputRecord_.epc = epcPARRINELLORAHMAN;
186 inputRecord_.nstpcouple = nstpcouple;
187 dtPressureCouple_ = inputRecord_.nstpcouple*inputRecord_.delta_t;
189 velocityScalingMatrix_[XX][XX] = 1.2;
190 velocityScalingMatrix_[XX][YY] = 0.0;
191 velocityScalingMatrix_[XX][ZZ] = 0.0;
193 velocityScalingMatrix_[YY][XX] = 0.0;
194 velocityScalingMatrix_[YY][YY] = 0.8;
195 velocityScalingMatrix_[YY][ZZ] = 0.0;
197 velocityScalingMatrix_[ZZ][XX] = 0.0;
198 velocityScalingMatrix_[ZZ][YY] = 0.0;
199 velocityScalingMatrix_[ZZ][ZZ] = 0.9;
203 inputRecord_.epc = epcNO;
204 velocityScalingMatrix_[XX][XX] = 1.0;
205 velocityScalingMatrix_[XX][YY] = 0.0;
206 velocityScalingMatrix_[XX][ZZ] = 0.0;
208 velocityScalingMatrix_[YY][XX] = 0.0;
209 velocityScalingMatrix_[YY][YY] = 1.0;
210 velocityScalingMatrix_[YY][ZZ] = 0.0;
212 velocityScalingMatrix_[ZZ][XX] = 0.0;
213 velocityScalingMatrix_[ZZ][YY] = 0.0;
214 velocityScalingMatrix_[ZZ][ZZ] = 1.0;
219 LeapFrogTestData::~LeapFrogTestData()