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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,
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)
70 title_ = title; // Human-friendly name of the system
71 numAtoms_ = numAtoms; // Number of atoms
75 invmass_.resize(numAtoms); // Vector of inverse masses
77 for (int i = 0; i < numAtoms; i++)
79 invmass_[i] = 1.0/masses.at(i);
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
86 invdt_ = 1.0/timestep; // Inverse timestep
88 // Communication record
96 // Input record - data that usually comes from configuration file (.mdp)
98 ir_.init_t = initialTime;
99 ir_.delta_t = timestep;
103 md_.nMassPerturbed = 0;
105 md_.invmass = invmass_.data();
107 md_.homenr = numAtoms;
110 computeVirial_ = computeVirial;
113 for (int i = 0; i < DIM; i++)
115 for (int j = 0; j < DIM; j++)
117 virialScaled_[i][j] = 0;
118 virialScaledRef_[i][j] = virialScaledRef[i][j];
124 // Free energy evaluation
125 compute_dHdLambda_ = compute_dHdLambda;
127 if (compute_dHdLambda_)
130 dHdLambdaRef_ = dHdLambdaRef;
138 // Constraints and their parameters (local topology)
139 for (int i = 0; i < F_NRE; i++)
143 idef_.il[F_CONSTR].nr = constraints.size();
145 snew(idef_.il[F_CONSTR].iatoms, constraints.size());
147 for (unsigned i = 0; i < constraints.size(); i++)
151 if (maxType < constraints.at(i))
153 maxType = constraints.at(i);
156 idef_.il[F_CONSTR].iatoms[i] = constraints.at(i);
158 snew(idef_.iparams, maxType + 1);
159 for (unsigned i = 0; i < constraints.size()/3; i++)
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));
165 // Constraints and their parameters (global topology)
166 InteractionList interactionList;
167 interactionList.iatoms.resize(constraints.size());
168 for (unsigned i = 0; i < constraints.size(); i++)
170 interactionList.iatoms.at(i) = constraints.at(i);
172 InteractionList interactionListEmpty;
173 interactionListEmpty.iatoms.resize(0);
175 gmx_moltype_t molType;
176 molType.atoms.nr = numAtoms;
177 molType.ilist.at(F_CONSTR) = interactionList;
178 molType.ilist.at(F_CONSTRNC) = interactionListEmpty;
179 mtop_.moltype.push_back(molType);
181 gmx_molblock_t molBlock;
184 mtop_.molblock.push_back(molBlock);
186 mtop_.natoms = numAtoms;
187 mtop_.ffparams.iparams.resize(maxType + 1);
188 for (int i = 0; i <= maxType; i++)
190 mtop_.ffparams.iparams.at(i) = idef_.iparams[i];
192 mtop_.bIntermolecularInteractions = false;
194 // Coordinates and velocities
195 x_.resizeWithPadding(numAtoms);
196 xPrime_.resizeWithPadding(numAtoms);
197 xPrime0_.resizeWithPadding(numAtoms);
198 xPrime2_.resizeWithPadding(numAtoms);
200 v_.resizeWithPadding(numAtoms);
201 v0_.resizeWithPadding(numAtoms);
203 std::copy(x.begin(), x.end(), x_.begin());
204 std::copy(xPrime.begin(), xPrime.end(), xPrime_.begin());
205 std::copy(xPrime.begin(), xPrime.end(), xPrime0_.begin());
206 std::copy(xPrime.begin(), xPrime.end(), xPrime2_.begin());
208 std::copy(v.begin(), v.end(), v_.begin());
209 std::copy(v.begin(), v.end(), v0_.begin());
211 // SHAKE-specific parameters
212 ir_.shake_tol = shakeTolerance;
213 ir_.bShakeSOR = shakeUseSOR;
215 // LINCS-specific parameters
216 ir_.nLincsIter = lincsNumIterations;
217 ir_.nProjOrder = lincsExpansionOrder;
218 ir_.LincsWarnAngle = lincsWarnAngle;
222 * Reset the data structure so it can be reused.
224 * Set the coordinates and velocities back to their values before
225 * constraining. The scaled virial tensor and dHdLambda are zeroed.
228 void ConstraintsTestData::reset()
236 for (int i = 0; i < DIM; i++)
238 for (int j = 0; j < DIM; j++)
240 virialScaled_[i][j] = 0;
248 * Cleaning up the memory.
250 ConstraintsTestData::~ConstraintsTestData()
252 sfree(idef_.il[F_CONSTR].iatoms);
253 sfree(idef_.iparams);