api/nblib/tests/testsystems.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * This implements nblib test systems
  38  *
  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>
  44  */
  45 #include "nblib/tests/testsystems.h"
  46 #include "nblib/exception.h"
  47
  48 namespace nblib
  49 {
  50
  51 //! User class to hold ParticleTypes
  52 //! Note: this is not part of NBLIB, users should write their own
  53 class ParticleLibrary
  54 {
  55 public:
  56     ParticleLibrary()
  57     {
  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));
  63
  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));
  69
  70         c6_[Ow.name()]   = 0.0026173456;
  71         c6_[H.name()]    = 0;
  72         c6_[OMet.name()] = 0.0022619536;
  73         c6_[CMet.name()] = 0.0088755241;
  74         c6_[Ar.name()]   = 0.0062647225;
  75
  76         c12_[Ow.name()]   = 2.634129e-06;
  77         c12_[H.name()]    = 0;
  78         c12_[OMet.name()] = 1.505529e-06;
  79         c12_[CMet.name()] = 2.0852922e-05;
  80         c12_[Ar.name()]   = 9.847044e-06;
  81     }
  82
  83     //! Get particle type using the string identifier
  84     [[nodiscard]] ParticleType type(const std::string& particleTypeName) const
  85     {
  86         return particles_.at(ParticleTypeName(particleTypeName));
  87     }
  88
  89     //! Get C6 parameter of a given particle
  90     [[nodiscard]] C6 c6(const ParticleName& particleName) const
  91     {
  92         return c6_.at(ParticleTypeName(particleName.value()));
  93     }
  94
  95     //! Get C12 parameter of a given particle
  96     [[nodiscard]] C12 c12(const ParticleName& particleName) const
  97     {
  98         return c12_.at(ParticleTypeName(particleName.value()));
  99     }
 100
 101 private:
 102     std::map<ParticleTypeName, ParticleType> particles_;
 103     std::map<ParticleTypeName, C6>           c6_;
 104     std::map<ParticleTypeName, C12>          c12_;
 105 };
 106
 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) } };
 112
 113 WaterMoleculeBuilder::WaterMoleculeBuilder() : water_(MoleculeName("SOL"))
 114 {
 115     ParticleLibrary plib;
 116
 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"));
 121
 122     HarmonicBondType ohBond(1., 1.);
 123     water_.addInteraction(ParticleName("Oxygen"), ParticleName("H1"), ohBond);
 124     water_.addInteraction(ParticleName("Oxygen"), ParticleName("H2"), ohBond);
 125 }
 126
 127 Molecule WaterMoleculeBuilder::waterMolecule()
 128 {
 129     addExclusionsFromNames();
 130     return water_;
 131 }
 132
 133 Molecule WaterMoleculeBuilder::waterMoleculeWithoutExclusions()
 134 {
 135     return water_;
 136 }
 137
 138 void WaterMoleculeBuilder::addExclusionsFromNames()
 139 {
 140     water_.addExclusion(ParticleName("H1"), ParticleName("Oxygen"));
 141     water_.addExclusion(ParticleName("H2"), ParticleName("Oxygen"));
 142     water_.addExclusion(ParticleName("H1"), ParticleName("H2"));
 143 }
 144
 145 MethanolMoleculeBuilder::MethanolMoleculeBuilder() : methanol_(MoleculeName("MeOH"))
 146 {
 147     ParticleLibrary library;
 148
 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"));
 153
 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"));
 158
 159     HarmonicBondType ohBond(1.01, 1.02);
 160     methanol_.addInteraction(ParticleName("O2"), ParticleName("H3"), ohBond);
 161
 162     HarmonicBondType ometBond(1.1, 1.2);
 163     methanol_.addInteraction(ParticleName("O2"), ParticleName("Me1"), ometBond);
 164
 165     HarmonicAngleType ochAngle(Degrees(108.52), 397.5);
 166     methanol_.addInteraction(ParticleName("O2"), ParticleName("Me1"), ParticleName("H3"), ochAngle);
 167 }
 168
 169 Molecule MethanolMoleculeBuilder::methanolMolecule()
 170 {
 171     return methanol_;
 172 }
 173
 174
 175 Topology WaterTopologyBuilder::buildTopology(int numMolecules)
 176 {
 177     ParticleLibrary library;
 178
 179     ParticleTypesInteractions interactions;
 180     std::vector<std::string>  typeNames = { "Ow", "H" };
 181     for (const auto& name : typeNames)
 182     {
 183         interactions.add(
 184                 ParticleTypeName(name), library.c6(ParticleName(name)), library.c12(ParticleName(name)));
 185     }
 186
 187     // Add some molecules to the topology
 188     TopologyBuilder topologyBuilder;
 189     topologyBuilder.addMolecule(water(), numMolecules);
 190
 191     // Add non-bonded interaction information
 192     topologyBuilder.addParticleTypesInteractions(interactions);
 193
 194     Topology topology = topologyBuilder.buildTopology();
 195     return topology;
 196 }
 197
 198 Molecule WaterTopologyBuilder::water()
 199 {
 200     return waterMolecule_.waterMolecule();
 201 }
 202
 203 Topology SpcMethanolTopologyBuilder::buildTopology(int numWater, int numMethanol)
 204 {
 205     ParticleLibrary library;
 206
 207     ParticleTypesInteractions interactions;
 208     std::vector<std::string>  typeNames = { "Ow", "H", "OMet", "CMet" };
 209     for (const auto& name : typeNames)
 210     {
 211         interactions.add(
 212                 ParticleTypeName(name), library.c6(ParticleName(name)), library.c12(ParticleName(name)));
 213     }
 214
 215     // Add some molecules to the topology
 216     TopologyBuilder topologyBuilder;
 217     topologyBuilder.addMolecule(methanol(), numMethanol);
 218     topologyBuilder.addMolecule(water(), numWater);
 219
 220     // Add non-bonded interaction information
 221     topologyBuilder.addParticleTypesInteractions(interactions);
 222
 223     Topology topology = topologyBuilder.buildTopology();
 224     return topology;
 225 }
 226
 227 Molecule SpcMethanolTopologyBuilder::methanol()
 228 {
 229     return methanolMolecule_.methanolMolecule();
 230 }
 231
 232 Molecule SpcMethanolTopologyBuilder::water()
 233 {
 234     return waterMolecule_.waterMolecule();
 235 }
 236
 237 ArgonTopologyBuilder::ArgonTopologyBuilder(const int& numParticles)
 238 {
 239     ParticleLibrary library;
 240
 241     ParticleTypesInteractions nbinteractions;
 242     nbinteractions.add(
 243             ParticleTypeName("Ar"), library.c6(ParticleName("Ar")), library.c12(ParticleName("Ar")));
 244
 245     Molecule argonMolecule(MoleculeName("AR"));
 246     argonMolecule.addParticle(ParticleName("AR"), library.type("Ar"));
 247
 248     topologyBuilder_.addMolecule(argonMolecule, numParticles);
 249     topologyBuilder_.addParticleTypesInteractions((nbinteractions));
 250 }
 251
 252 Topology ArgonTopologyBuilder::argonTopology()
 253 {
 254     return topologyBuilder_.buildTopology();
 255 }
 256
 257 ArgonSimulationStateBuilder::ArgonSimulationStateBuilder() :
 258     box_(6.05449), topology_(ArgonTopologyBuilder(12).argonTopology())
 259 {
 260
 261     coordinates_ = {
 262         { 0.794, 1.439, 0.610 }, { 1.397, 0.673, 1.916 }, { 0.659, 1.080, 0.573 },
 263         { 1.105, 0.090, 3.431 }, { 1.741, 1.291, 3.432 }, { 1.936, 1.441, 5.873 },
 264         { 0.960, 2.246, 1.659 }, { 0.382, 3.023, 2.793 }, { 0.053, 4.857, 4.242 },
 265         { 2.655, 5.057, 2.211 }, { 4.114, 0.737, 0.614 }, { 5.977, 5.104, 5.217 },
 266     };
 267
 268     velocities_ = {
 269         { 0.0055, -0.1400, 0.2127 },   { 0.0930, -0.0160, -0.0086 }, { 0.1678, 0.2476, -0.0660 },
 270         { 0.1591, -0.0934, -0.0835 },  { -0.0317, 0.0573, 0.1453 },  { 0.0597, 0.0013, -0.0462 },
 271         { 0.0484, -0.0357, 0.0168 },   { 0.0530, 0.0295, -0.2694 },  { -0.0550, -0.0896, 0.0494 },
 272         { -0.0799, -0.2534, -0.0079 }, { 0.0436, -0.1557, 0.1849 },  { -0.0214, 0.0446, 0.0758 },
 273     };
 274     forces_ = {
 275         { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
 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     };
 280 }
 281
 282 void ArgonSimulationStateBuilder::setCoordinate(int particleNum, int dimension, real value)
 283 {
 284     if (dimension < 0 or dimension > 2)
 285     {
 286         throw InputException("Must provide a valid dimension\n");
 287     }
 288     coordinates_.at(particleNum)[dimension] = value;
 289 }
 290
 291 void ArgonSimulationStateBuilder::setVelocity(int particleNum, int dimension, real value)
 292 {
 293     if (dimension < 0 or dimension > 2)
 294     {
 295         throw InputException("Must provide a valid dimension\n");
 296     }
 297     velocities_.at(particleNum)[dimension] = value;
 298 }
 299
 300 SimulationState ArgonSimulationStateBuilder::setupSimulationState()
 301 {
 302     return SimulationState(coordinates_, velocities_, forces_, box_, topology_);
 303 }
 304
 305 const Topology& ArgonSimulationStateBuilder::topology() const
 306 {
 307     return topology_;
 308 }
 309
 310 Box& ArgonSimulationStateBuilder::box()
 311 {
 312     return box_;
 313 }
 314
 315 std::vector<Vec3>& ArgonSimulationStateBuilder::coordinates()
 316 {
 317     return coordinates_;
 318 }
 319
 320 std::vector<Vec3>& ArgonSimulationStateBuilder::velocities()
 321 {
 322     return velocities_;
 323 }
 324
 325 SpcMethanolSimulationStateBuilder::SpcMethanolSimulationStateBuilder() :
 326     box_(3.01000), topology_(SpcMethanolTopologyBuilder().buildTopology(1, 1))
 327 {
 328     coordinates_ = {
 329         { 1.970, 1.460, 1.209 }, // Me1
 330         { 1.978, 1.415, 1.082 }, // O2
 331         { 1.905, 1.460, 1.030 }, // H3
 332         { 1.555, 1.511, 0.703 }, // Ow
 333         { 1.498, 1.495, 0.784 }, // Hw1
 334         { 1.496, 1.521, 0.623 }, // Hw2
 335     };
 336
 337     velocities_ = {
 338         { -0.8587, -0.1344, -0.0643 }, { 0.0623, -0.1787, 0.0036 }, { -0.5020, -0.9564, 0.0997 },
 339         { 0.869, 1.245, 1.665 },       { 0.169, 0.275, 1.565 },     { 0.269, 2.275, 1.465 },
 340     };
 341
 342     forces_ = {
 343         { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 },
 344         { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 },
 345     };
 346 }
 347
 348 SimulationState SpcMethanolSimulationStateBuilder::setupSimulationState()
 349 {
 350     return SimulationState(coordinates_, velocities_, forces_, box_, topology_);
 351 }
 352
 353 std::vector<Vec3>& SpcMethanolSimulationStateBuilder::coordinates()
 354 {
 355     return coordinates_;
 356 }
 357
 358 std::vector<Vec3>& SpcMethanolSimulationStateBuilder::velocities()
 359 {
 360     return velocities_;
 361 }
 362
 363 } // namespace nblib