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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_gromos(ParticleTypeName("Ar_gromos"), Mass(39.94800));
63 ParticleType Ar_opls(ParticleTypeName("Ar_opls"), Mass(39.94800));
65 particles_.insert(std::make_pair(Ow.name(), Ow));
66 particles_.insert(std::make_pair(H.name(), H));
67 particles_.insert(std::make_pair(OMet.name(), OMet));
68 particles_.insert(std::make_pair(CMet.name(), CMet));
69 particles_.insert(std::make_pair(Ar_gromos.name(), Ar_gromos));
70 particles_.insert(std::make_pair(Ar_opls.name(), Ar_opls));
72 c6_[Ow.name()] = 0.0026173456;
74 c6_[OMet.name()] = 0.0022619536;
75 c6_[CMet.name()] = 0.0088755241;
76 c6_[Ar_gromos.name()] = 0.0062647225;
77 c6_[Ar_opls.name()] = 0.0058560692;
79 c12_[Ow.name()] = 2.634129e-06;
81 c12_[OMet.name()] = 1.505529e-06;
82 c12_[CMet.name()] = 2.0852922e-05;
83 c12_[Ar_gromos.name()] = 9.847044e-06;
84 c12_[Ar_opls.name()] = 8.203193e-06;
87 //! Get particle type using the string identifier
88 [[nodiscard]] ParticleType type(const std::string& particleTypeName) const
90 return particles_.at(ParticleTypeName(particleTypeName));
93 //! Get C6 parameter of a given particle
94 [[nodiscard]] C6 c6(const ParticleName& particleName) const
96 return c6_.at(ParticleTypeName(particleName.value()));
99 //! Get C12 parameter of a given particle
100 [[nodiscard]] C12 c12(const ParticleName& particleName) const
102 return c12_.at(ParticleTypeName(particleName.value()));
106 std::map<ParticleTypeName, ParticleType> particles_;
107 std::map<ParticleTypeName, C6> c6_;
108 std::map<ParticleTypeName, C12> c12_;
111 std::unordered_map<std::string, Charge> Charges{ { "Ow", Charge(-0.82) },
112 { "Hw", Charge(+0.41) },
113 { "OMet", Charge(-0.574) },
114 { "CMet", Charge(+0.176) },
115 { "HMet", Charge(+0.398) } };
117 WaterMoleculeBuilder::WaterMoleculeBuilder() : water_(MoleculeName("SOL"))
119 ParticleLibrary plib;
121 //! Add the particles
122 water_.addParticle(ParticleName("Oxygen"), Charges.at("Ow"), plib.type("Ow"));
123 water_.addParticle(ParticleName("H1"), Charges.at("Hw"), plib.type("H"));
124 water_.addParticle(ParticleName("H2"), Charges.at("Hw"), plib.type("H"));
126 HarmonicBondType ohBond(1., 1.);
127 water_.addInteraction(ParticleName("Oxygen"), ParticleName("H1"), ohBond);
128 water_.addInteraction(ParticleName("Oxygen"), ParticleName("H2"), ohBond);
131 Molecule WaterMoleculeBuilder::waterMolecule()
133 addExclusionsFromNames();
137 Molecule WaterMoleculeBuilder::waterMoleculeWithoutExclusions()
142 void WaterMoleculeBuilder::addExclusionsFromNames()
144 water_.addExclusion(ParticleName("H1"), ParticleName("Oxygen"));
145 water_.addExclusion(ParticleName("H2"), ParticleName("Oxygen"));
146 water_.addExclusion(ParticleName("H1"), ParticleName("H2"));
149 MethanolMoleculeBuilder::MethanolMoleculeBuilder() : methanol_(MoleculeName("MeOH"))
151 ParticleLibrary library;
153 //! Add the particles
154 methanol_.addParticle(ParticleName("Me1"), Charges.at("CMet"), library.type("CMet"));
155 methanol_.addParticle(ParticleName("O2"), Charges.at("OMet"), library.type("OMet"));
156 methanol_.addParticle(ParticleName("H3"), Charges.at("HMet"), library.type("H"));
158 // Add the exclusions
159 methanol_.addExclusion(ParticleName("Me1"), ParticleName("O2"));
160 methanol_.addExclusion(ParticleName("Me1"), ParticleName("H3"));
161 methanol_.addExclusion(ParticleName("H3"), ParticleName("O2"));
163 HarmonicBondType ohBond(1.01, 1.02);
164 methanol_.addInteraction(ParticleName("O2"), ParticleName("H3"), ohBond);
166 HarmonicBondType ometBond(1.1, 1.2);
167 methanol_.addInteraction(ParticleName("O2"), ParticleName("Me1"), ometBond);
169 HarmonicAngle ochAngle(Degrees(108.52), 397.5);
170 methanol_.addInteraction(ParticleName("O2"), ParticleName("Me1"), ParticleName("H3"), ochAngle);
173 Molecule MethanolMoleculeBuilder::methanolMolecule()
179 Topology WaterTopologyBuilder::buildTopology(int numMolecules)
181 ParticleLibrary library;
183 ParticleTypesInteractions interactions;
184 std::vector<std::string> typeNames = { "Ow", "H" };
185 for (const auto& name : typeNames)
188 ParticleTypeName(name), library.c6(ParticleName(name)), library.c12(ParticleName(name)));
191 // Add some molecules to the topology
192 TopologyBuilder topologyBuilder;
193 topologyBuilder.addMolecule(water(), numMolecules);
195 // Add non-bonded interaction information
196 topologyBuilder.addParticleTypesInteractions(interactions);
198 Topology topology = topologyBuilder.buildTopology();
202 Molecule WaterTopologyBuilder::water()
204 return waterMolecule_.waterMolecule();
207 Topology SpcMethanolTopologyBuilder::buildTopology(int numWater, int numMethanol)
209 ParticleLibrary library;
211 ParticleTypesInteractions interactions;
212 std::vector<std::string> typeNames = { "Ow", "H", "OMet", "CMet" };
213 for (const auto& name : typeNames)
216 ParticleTypeName(name), library.c6(ParticleName(name)), library.c12(ParticleName(name)));
219 // Add some molecules to the topology
220 TopologyBuilder topologyBuilder;
221 topologyBuilder.addMolecule(methanol(), numMethanol);
222 topologyBuilder.addMolecule(water(), numWater);
224 // Add non-bonded interaction information
225 topologyBuilder.addParticleTypesInteractions(interactions);
227 Topology topology = topologyBuilder.buildTopology();
231 Molecule SpcMethanolTopologyBuilder::methanol()
233 return methanolMolecule_.methanolMolecule();
236 Molecule SpcMethanolTopologyBuilder::water()
238 return waterMolecule_.waterMolecule();
241 ArgonTopologyBuilder::ArgonTopologyBuilder(const int& numParticles, const fftypes forceField)
243 ParticleLibrary library;
245 ParticleTypesInteractions nbinteractions;
247 Molecule argonMolecule(MoleculeName("AR"));
249 std::string particleName;
251 if (forceField == fftypes::GROMOS43A1)
253 particleName = "Ar_gromos";
255 else if (forceField == fftypes::OPLSA)
257 particleName = "Ar_opls";
260 nbinteractions.add(ParticleTypeName(particleName),
261 library.c6(ParticleName(particleName)),
262 library.c12(ParticleName(particleName)));
263 argonMolecule.addParticle(ParticleName("AR"), library.type(particleName));
265 topologyBuilder_.addMolecule(argonMolecule, numParticles);
266 topologyBuilder_.addParticleTypesInteractions((nbinteractions));
269 Topology ArgonTopologyBuilder::argonTopology()
271 return topologyBuilder_.buildTopology();
274 ArgonSimulationStateBuilder::ArgonSimulationStateBuilder(const fftypes forceField) :
275 box_(6.05449), topology_(ArgonTopologyBuilder(12, forceField).argonTopology())
279 { 0.794, 1.439, 0.610 }, { 1.397, 0.673, 1.916 }, { 0.659, 1.080, 0.573 },
280 { 1.105, 0.090, 3.431 }, { 1.741, 1.291, 3.432 }, { 1.936, 1.441, 5.873 },
281 { 0.960, 2.246, 1.659 }, { 0.382, 3.023, 2.793 }, { 0.053, 4.857, 4.242 },
282 { 2.655, 5.057, 2.211 }, { 4.114, 0.737, 0.614 }, { 5.977, 5.104, 5.217 },
286 { 0.0055, -0.1400, 0.2127 }, { 0.0930, -0.0160, -0.0086 }, { 0.1678, 0.2476, -0.0660 },
287 { 0.1591, -0.0934, -0.0835 }, { -0.0317, 0.0573, 0.1453 }, { 0.0597, 0.0013, -0.0462 },
288 { 0.0484, -0.0357, 0.0168 }, { 0.0530, 0.0295, -0.2694 }, { -0.0550, -0.0896, 0.0494 },
289 { -0.0799, -0.2534, -0.0079 }, { 0.0436, -0.1557, 0.1849 }, { -0.0214, 0.0446, 0.0758 },
292 { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
293 { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
294 { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
295 { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
299 void ArgonSimulationStateBuilder::setCoordinate(int particleNum, int dimension, real value)
301 if (dimension < 0 or dimension > 2)
303 throw InputException("Must provide a valid dimension\n");
305 coordinates_.at(particleNum)[dimension] = value;
308 void ArgonSimulationStateBuilder::setVelocity(int particleNum, int dimension, real value)
310 if (dimension < 0 or dimension > 2)
312 throw InputException("Must provide a valid dimension\n");
314 velocities_.at(particleNum)[dimension] = value;
317 SimulationState ArgonSimulationStateBuilder::setupSimulationState()
319 return SimulationState(coordinates_, velocities_, forces_, box_, topology_);
322 const Topology& ArgonSimulationStateBuilder::topology() const
327 Box& ArgonSimulationStateBuilder::box()
332 std::vector<Vec3>& ArgonSimulationStateBuilder::coordinates()
337 std::vector<Vec3>& ArgonSimulationStateBuilder::velocities()
342 SpcMethanolSimulationStateBuilder::SpcMethanolSimulationStateBuilder() :
343 box_(3.01000), topology_(SpcMethanolTopologyBuilder().buildTopology(1, 1))
346 { 1.970, 1.460, 1.209 }, // Me1
347 { 1.978, 1.415, 1.082 }, // O2
348 { 1.905, 1.460, 1.030 }, // H3
349 { 1.555, 1.511, 0.703 }, // Ow
350 { 1.498, 1.495, 0.784 }, // Hw1
351 { 1.496, 1.521, 0.623 }, // Hw2
355 { -0.8587, -0.1344, -0.0643 }, { 0.0623, -0.1787, 0.0036 }, { -0.5020, -0.9564, 0.0997 },
356 { 0.869, 1.245, 1.665 }, { 0.169, 0.275, 1.565 }, { 0.269, 2.275, 1.465 },
360 { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 },
361 { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 },
365 SimulationState SpcMethanolSimulationStateBuilder::setupSimulationState()
367 return SimulationState(coordinates_, velocities_, forces_, box_, topology_);
370 std::vector<Vec3>& SpcMethanolSimulationStateBuilder::coordinates()
375 std::vector<Vec3>& SpcMethanolSimulationStateBuilder::velocities()