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37 * This implements nblib test systems
39 * \author Victor Holanda <victor.holanda@cscs.ch>
40 * \author Joe Jordan <ejjordan@kth.se>
41 * \author Prashanth Kanduri <kanduri@cscs.ch>
42 * \author Sebastian Keller <keller@cscs.ch>
43 * \author Artem Zhmurov <zhmurov@gmail.com>
45 #include "nblib/tests/testsystems.h"
46 #include "nblib/exception.h"
51 //! User class to hold ParticleTypes
52 //! Note: this is not part of NBLIB, users should write their own
58 ParticleType Ow(ParticleTypeName("Ow"), Mass(15.99940));
59 ParticleType H(ParticleTypeName("H"), Mass(1.008));
60 ParticleType OMet(ParticleTypeName("OMet"), Mass(15.999));
61 ParticleType CMet(ParticleTypeName("CMet"), Mass(15.035));
62 ParticleType Ar(ParticleTypeName("Ar"), Mass(39.94800));
64 particles_.insert(std::make_pair(Ow.name(), Ow));
65 particles_.insert(std::make_pair(H.name(), H));
66 particles_.insert(std::make_pair(OMet.name(), OMet));
67 particles_.insert(std::make_pair(CMet.name(), CMet));
68 particles_.insert(std::make_pair(Ar.name(), Ar));
70 c6_[Ow.name()] = 0.0026173456;
72 c6_[OMet.name()] = 0.0022619536;
73 c6_[CMet.name()] = 0.0088755241;
74 c6_[Ar.name()] = 0.0062647225;
76 c12_[Ow.name()] = 2.634129e-06;
78 c12_[OMet.name()] = 1.505529e-06;
79 c12_[CMet.name()] = 2.0852922e-05;
80 c12_[Ar.name()] = 9.847044e-06;
83 //! Get particle type using the string identifier
84 [[nodiscard]] ParticleType type(const std::string& particleTypeName) const
86 return particles_.at(ParticleTypeName(particleTypeName));
89 //! Get C6 parameter of a given particle
90 [[nodiscard]] C6 c6(const ParticleName& particleName) const
92 return c6_.at(ParticleTypeName(particleName.value()));
95 //! Get C12 parameter of a given particle
96 [[nodiscard]] C12 c12(const ParticleName& particleName) const
98 return c12_.at(ParticleTypeName(particleName.value()));
102 std::map<ParticleTypeName, ParticleType> particles_;
103 std::map<ParticleTypeName, C6> c6_;
104 std::map<ParticleTypeName, C12> c12_;
107 std::unordered_map<std::string, Charge> Charges{ { "Ow", Charge(-0.82) },
108 { "Hw", Charge(+0.41) },
109 { "OMet", Charge(-0.574) },
110 { "CMet", Charge(+0.176) },
111 { "HMet", Charge(+0.398) } };
113 WaterMoleculeBuilder::WaterMoleculeBuilder() : water_(MoleculeName("SOL"))
115 ParticleLibrary plib;
117 //! Add the particles
118 water_.addParticle(ParticleName("Oxygen"), Charges.at("Ow"), plib.type("Ow"));
119 water_.addParticle(ParticleName("H1"), Charges.at("Hw"), plib.type("H"));
120 water_.addParticle(ParticleName("H2"), Charges.at("Hw"), plib.type("H"));
122 HarmonicBondType ohBond(1., 1.);
123 water_.addInteraction(ParticleName("Oxygen"), ParticleName("H1"), ohBond);
124 water_.addInteraction(ParticleName("Oxygen"), ParticleName("H2"), ohBond);
127 Molecule WaterMoleculeBuilder::waterMolecule()
129 addExclusionsFromNames();
133 Molecule WaterMoleculeBuilder::waterMoleculeWithoutExclusions()
138 void WaterMoleculeBuilder::addExclusionsFromNames()
140 water_.addExclusion(ParticleName("H1"), ParticleName("Oxygen"));
141 water_.addExclusion(ParticleName("H2"), ParticleName("Oxygen"));
142 water_.addExclusion(ParticleName("H1"), ParticleName("H2"));
145 MethanolMoleculeBuilder::MethanolMoleculeBuilder() : methanol_(MoleculeName("MeOH"))
147 ParticleLibrary library;
149 //! Add the particles
150 methanol_.addParticle(ParticleName("Me1"), Charges.at("CMet"), library.type("CMet"));
151 methanol_.addParticle(ParticleName("O2"), Charges.at("OMet"), library.type("OMet"));
152 methanol_.addParticle(ParticleName("H3"), Charges.at("HMet"), library.type("H"));
154 // Add the exclusions
155 methanol_.addExclusion(ParticleName("Me1"), ParticleName("O2"));
156 methanol_.addExclusion(ParticleName("Me1"), ParticleName("H3"));
157 methanol_.addExclusion(ParticleName("H3"), ParticleName("O2"));
159 HarmonicBondType ohBond(1.01, 1.02);
160 methanol_.addInteraction(ParticleName("O2"), ParticleName("H3"), ohBond);
162 HarmonicBondType ometBond(1.1, 1.2);
163 methanol_.addInteraction(ParticleName("O2"), ParticleName("Me1"), ometBond);
165 DefaultAngle ochAngle(Degrees(108.52), 397.5);
166 methanol_.addInteraction(ParticleName("O2"), ParticleName("Me1"), ParticleName("H3"), ochAngle);
169 Molecule MethanolMoleculeBuilder::methanolMolecule()
175 Topology WaterTopologyBuilder::buildTopology(int numMolecules)
177 ParticleLibrary library;
179 ParticleTypesInteractions interactions;
180 std::vector<std::string> typeNames = { "Ow", "H" };
181 for (const auto& name : typeNames)
183 interactions.add(ParticleTypeName(name), library.c6(ParticleName(name)),
184 library.c12(ParticleName(name)));
187 // Add some molecules to the topology
188 TopologyBuilder topologyBuilder;
189 topologyBuilder.addMolecule(water(), numMolecules);
191 // Add non-bonded interaction information
192 topologyBuilder.addParticleTypesInteractions(interactions);
194 Topology topology = topologyBuilder.buildTopology();
198 Molecule WaterTopologyBuilder::water()
200 return waterMolecule_.waterMolecule();
203 Topology SpcMethanolTopologyBuilder::buildTopology(int numWater, int numMethanol)
205 ParticleLibrary library;
207 ParticleTypesInteractions interactions;
208 std::vector<std::string> typeNames = { "Ow", "H", "OMet", "CMet" };
209 for (const auto& name : typeNames)
211 interactions.add(ParticleTypeName(name), library.c6(ParticleName(name)),
212 library.c12(ParticleName(name)));
215 // Add some molecules to the topology
216 TopologyBuilder topologyBuilder;
217 topologyBuilder.addMolecule(methanol(), numMethanol);
218 topologyBuilder.addMolecule(water(), numWater);
220 // Add non-bonded interaction information
221 topologyBuilder.addParticleTypesInteractions(interactions);
223 Topology topology = topologyBuilder.buildTopology();
227 Molecule SpcMethanolTopologyBuilder::methanol()
229 return methanolMolecule_.methanolMolecule();
232 Molecule SpcMethanolTopologyBuilder::water()
234 return waterMolecule_.waterMolecule();
237 ArgonTopologyBuilder::ArgonTopologyBuilder(const int& numParticles)
239 ParticleLibrary library;
241 ParticleTypesInteractions nbinteractions;
242 nbinteractions.add(ParticleTypeName("Ar"), library.c6(ParticleName("Ar")),
243 library.c12(ParticleName("Ar")));
245 Molecule argonMolecule(MoleculeName("AR"));
246 argonMolecule.addParticle(ParticleName("AR"), library.type("Ar"));
248 topologyBuilder_.addMolecule(argonMolecule, numParticles);
249 topologyBuilder_.addParticleTypesInteractions((nbinteractions));
252 Topology ArgonTopologyBuilder::argonTopology()
254 return topologyBuilder_.buildTopology();
257 ArgonSimulationStateBuilder::ArgonSimulationStateBuilder() :
259 topology_(ArgonTopologyBuilder(12).argonTopology())
263 { 0.794, 1.439, 0.610 }, { 1.397, 0.673, 1.916 }, { 0.659, 1.080, 0.573 },
264 { 1.105, 0.090, 3.431 }, { 1.741, 1.291, 3.432 }, { 1.936, 1.441, 5.873 },
265 { 0.960, 2.246, 1.659 }, { 0.382, 3.023, 2.793 }, { 0.053, 4.857, 4.242 },
266 { 2.655, 5.057, 2.211 }, { 4.114, 0.737, 0.614 }, { 5.977, 5.104, 5.217 },
270 { 0.0055, -0.1400, 0.2127 }, { 0.0930, -0.0160, -0.0086 }, { 0.1678, 0.2476, -0.0660 },
271 { 0.1591, -0.0934, -0.0835 }, { -0.0317, 0.0573, 0.1453 }, { 0.0597, 0.0013, -0.0462 },
272 { 0.0484, -0.0357, 0.0168 }, { 0.0530, 0.0295, -0.2694 }, { -0.0550, -0.0896, 0.0494 },
273 { -0.0799, -0.2534, -0.0079 }, { 0.0436, -0.1557, 0.1849 }, { -0.0214, 0.0446, 0.0758 },
276 { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
277 { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
278 { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
279 { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
283 void ArgonSimulationStateBuilder::setCoordinate(int particleNum, int dimension, real value)
285 if (dimension < 0 or dimension > 2)
287 throw InputException("Must provide a valid dimension\n");
289 coordinates_.at(particleNum)[dimension] = value;
292 void ArgonSimulationStateBuilder::setVelocity(int particleNum, int dimension, real value)
294 if (dimension < 0 or dimension > 2)
296 throw InputException("Must provide a valid dimension\n");
298 velocities_.at(particleNum)[dimension] = value;
301 SimulationState ArgonSimulationStateBuilder::setupSimulationState()
303 return SimulationState(coordinates_, velocities_, forces_, box_, topology_);
306 const Topology& ArgonSimulationStateBuilder::topology() const
311 Box& ArgonSimulationStateBuilder::box()
316 std::vector<Vec3>& ArgonSimulationStateBuilder::coordinates()
321 std::vector<Vec3>& ArgonSimulationStateBuilder::velocities()
326 SpcMethanolSimulationStateBuilder::SpcMethanolSimulationStateBuilder() :
328 topology_(SpcMethanolTopologyBuilder().buildTopology(1, 1))
331 { 1.970, 1.460, 1.209 }, // Me1
332 { 1.978, 1.415, 1.082 }, // O2
333 { 1.905, 1.460, 1.030 }, // H3
334 { 1.555, 1.511, 0.703 }, // Ow
335 { 1.498, 1.495, 0.784 }, // Hw1
336 { 1.496, 1.521, 0.623 }, // Hw2
340 { -0.8587, -0.1344, -0.0643 }, { 0.0623, -0.1787, 0.0036 }, { -0.5020, -0.9564, 0.0997 },
341 { 0.869, 1.245, 1.665 }, { 0.169, 0.275, 1.565 }, { 0.269, 2.275, 1.465 },
345 { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 },
346 { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 },
350 SimulationState SpcMethanolSimulationStateBuilder::setupSimulationState()
352 return SimulationState(coordinates_, velocities_, forces_, box_, topology_);
355 std::vector<Vec3>& SpcMethanolSimulationStateBuilder::coordinates()
360 std::vector<Vec3>& SpcMethanolSimulationStateBuilder::velocities()