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
 123 Molecule WaterMoleculeBuilder::waterMolecule()
 124 {
 125     addExclusionsFromNames();
 126     return water_;
 127 }
 128
 129 Molecule WaterMoleculeBuilder::waterMoleculeWithoutExclusions()
 130 {
 131     return water_;
 132 }
 133
 134 void WaterMoleculeBuilder::addExclusionsFromNames()
 135 {
 136     water_.addExclusion("H1", "Oxygen");
 137     water_.addExclusion("H2", "Oxygen");
 138     water_.addExclusion("H1", "H2");
 139 }
 140
 141 MethanolMoleculeBuilder::MethanolMoleculeBuilder() : methanol_(MoleculeName("MeOH"))
 142 {
 143     ParticleLibrary library;
 144
 145     //! Add the particles
 146     methanol_.addParticle(ParticleName("Me1"), Charges.at("CMet"), library.type("CMet"));
 147     methanol_.addParticle(ParticleName("O2"), Charges.at("OMet"), library.type("OMet"));
 148     methanol_.addParticle(ParticleName("H3"), Charges.at("HMet"), library.type("H"));
 149
 150     // Add the exclusions
 151     methanol_.addExclusion("Me1", "O2");
 152     methanol_.addExclusion("Me1", "H3");
 153     methanol_.addExclusion("H3", "O2");
 154 }
 155
 156 Molecule MethanolMoleculeBuilder::methanolMolecule()
 157 {
 158     return methanol_;
 159 }
 160
 161
 162 Topology WaterTopologyBuilder::buildTopology(int numMolecules)
 163 {
 164     ParticleLibrary library;
 165
 166     ParticleTypesInteractions interactions;
 167     std::vector<std::string>  typeNames = { "Ow", "H" };
 168     for (const auto& name : typeNames)
 169     {
 170         interactions.add(ParticleTypeName(name), library.c6(ParticleName(name)),
 171                          library.c12(ParticleName(name)));
 172     }
 173
 174     // Add some molecules to the topology
 175     TopologyBuilder topologyBuilder;
 176     topologyBuilder.addMolecule(water(), numMolecules);
 177
 178     // Add non-bonded interaction information
 179     topologyBuilder.addParticleTypesInteractions(interactions);
 180
 181     Topology topology = topologyBuilder.buildTopology();
 182     return topology;
 183 }
 184
 185 Molecule WaterTopologyBuilder::water()
 186 {
 187     return waterMolecule_.waterMolecule();
 188 }
 189
 190 Topology SpcMethanolTopologyBuilder::buildTopology(int numWater, int numMethanol)
 191 {
 192     ParticleLibrary library;
 193
 194     ParticleTypesInteractions interactions;
 195     std::vector<std::string>  typeNames = { "Ow", "H", "OMet", "CMet" };
 196     for (const auto& name : typeNames)
 197     {
 198         interactions.add(ParticleTypeName(name), library.c6(ParticleName(name)),
 199                          library.c12(ParticleName(name)));
 200     }
 201
 202     // Add some molecules to the topology
 203     TopologyBuilder topologyBuilder;
 204     topologyBuilder.addMolecule(methanol(), numMethanol);
 205     topologyBuilder.addMolecule(water(), numWater);
 206
 207     // Add non-bonded interaction information
 208     topologyBuilder.addParticleTypesInteractions(interactions);
 209
 210     Topology topology = topologyBuilder.buildTopology();
 211     return topology;
 212 }
 213
 214 Molecule SpcMethanolTopologyBuilder::methanol()
 215 {
 216     return methanolMolecule_.methanolMolecule();
 217 }
 218
 219 Molecule SpcMethanolTopologyBuilder::water()
 220 {
 221     return waterMolecule_.waterMolecule();
 222 }
 223
 224 ArgonTopologyBuilder::ArgonTopologyBuilder(const int& numParticles)
 225 {
 226     ParticleLibrary library;
 227
 228     ParticleTypesInteractions nbinteractions;
 229     nbinteractions.add(ParticleTypeName("Ar"), library.c6(ParticleName("Ar")),
 230                        library.c12(ParticleName("Ar")));
 231
 232     Molecule argonMolecule(MoleculeName("AR"));
 233     argonMolecule.addParticle(ParticleName("AR"), library.type("Ar"));
 234
 235     topologyBuilder_.addMolecule(argonMolecule, numParticles);
 236     topologyBuilder_.addParticleTypesInteractions((nbinteractions));
 237 }
 238
 239 Topology ArgonTopologyBuilder::argonTopology()
 240 {
 241     return topologyBuilder_.buildTopology();
 242 }
 243
 244 ArgonSimulationStateBuilder::ArgonSimulationStateBuilder() :
 245     box_(6.05449),
 246     topology_(ArgonTopologyBuilder(12).argonTopology())
 247 {
 248
 249     coordinates_ = {
 250         { 0.794, 1.439, 0.610 }, { 1.397, 0.673, 1.916 }, { 0.659, 1.080, 0.573 },
 251         { 1.105, 0.090, 3.431 }, { 1.741, 1.291, 3.432 }, { 1.936, 1.441, 5.873 },
 252         { 0.960, 2.246, 1.659 }, { 0.382, 3.023, 2.793 }, { 0.053, 4.857, 4.242 },
 253         { 2.655, 5.057, 2.211 }, { 4.114, 0.737, 0.614 }, { 5.977, 5.104, 5.217 },
 254     };
 255
 256     velocities_ = {
 257         { 0.0055, -0.1400, 0.2127 },   { 0.0930, -0.0160, -0.0086 }, { 0.1678, 0.2476, -0.0660 },
 258         { 0.1591, -0.0934, -0.0835 },  { -0.0317, 0.0573, 0.1453 },  { 0.0597, 0.0013, -0.0462 },
 259         { 0.0484, -0.0357, 0.0168 },   { 0.0530, 0.0295, -0.2694 },  { -0.0550, -0.0896, 0.0494 },
 260         { -0.0799, -0.2534, -0.0079 }, { 0.0436, -0.1557, 0.1849 },  { -0.0214, 0.0446, 0.0758 },
 261     };
 262     forces_ = {
 263         { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
 264         { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
 265         { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
 266         { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 }, { 0.0000, 0.0000, 0.0000 },
 267     };
 268 }
 269
 270 void ArgonSimulationStateBuilder::setCoordinate(int particleNum, int dimension, real value)
 271 {
 272     if (dimension < 0 or dimension > 2)
 273     {
 274         throw InputException("Must provide a valid dimension\n");
 275     }
 276     coordinates_.at(particleNum)[dimension] = value;
 277 }
 278
 279 void ArgonSimulationStateBuilder::setVelocity(int particleNum, int dimension, real value)
 280 {
 281     if (dimension < 0 or dimension > 2)
 282     {
 283         throw InputException("Must provide a valid dimension\n");
 284     }
 285     velocities_.at(particleNum)[dimension] = value;
 286 }
 287
 288 SimulationState ArgonSimulationStateBuilder::setupSimulationState()
 289 {
 290     return SimulationState(coordinates_, velocities_, forces_, box_, topology_);
 291 }
 292
 293 const Topology& ArgonSimulationStateBuilder::topology() const
 294 {
 295     return topology_;
 296 }
 297
 298 Box& ArgonSimulationStateBuilder::box()
 299 {
 300     return box_;
 301 }
 302
 303 std::vector<Vec3>& ArgonSimulationStateBuilder::coordinates()
 304 {
 305     return coordinates_;
 306 }
 307
 308 std::vector<Vec3>& ArgonSimulationStateBuilder::velocities()
 309 {
 310     return velocities_;
 311 }
 312
 313 SpcMethanolSimulationStateBuilder::SpcMethanolSimulationStateBuilder() :
 314     box_(3.01000),
 315     topology_(SpcMethanolTopologyBuilder().buildTopology(1, 1))
 316 {
 317     coordinates_ = {
 318         { 1.970, 1.460, 1.209 }, // Me1
 319         { 1.978, 1.415, 1.082 }, // O2
 320         { 1.905, 1.460, 1.030 }, // H3
 321         { 1.555, 1.511, 0.703 }, // Ow
 322         { 1.498, 1.495, 0.784 }, // Hw1
 323         { 1.496, 1.521, 0.623 }, // Hw2
 324     };
 325
 326     velocities_ = {
 327         { -0.8587, -0.1344, -0.0643 }, { 0.0623, -0.1787, 0.0036 }, { -0.5020, -0.9564, 0.0997 },
 328         { 0.869, 1.245, 1.665 },       { 0.169, 0.275, 1.565 },     { 0.269, 2.275, 1.465 },
 329     };
 330
 331     forces_ = {
 332         { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 },
 333         { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 }, { 0.000, 0.000, 0.000 },
 334     };
 335 }
 336
 337 SimulationState SpcMethanolSimulationStateBuilder::setupSimulationState()
 338 {
 339     return SimulationState(coordinates_, velocities_, forces_, box_, topology_);
 340 }
 341
 342 std::vector<Vec3>& SpcMethanolSimulationStateBuilder::coordinates()
 343 {
 344     return coordinates_;
 345 }
 346
 347 std::vector<Vec3>& SpcMethanolSimulationStateBuilder::velocities()
 348 {
 349     return velocities_;
 350 }
 351
 352 } // namespace nblib