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_gromos(ParticleTypeName("Ar_gromos"), Mass(39.94800));
  63         ParticleType Ar_opls(ParticleTypeName("Ar_opls"), Mass(39.94800));
  64
  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));
  71
  72         c6_[Ow.name()]        = 0.0026173456;
  73         c6_[H.name()]         = 0;
  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;
  78
  79         c12_[Ow.name()]        = 2.634129e-06;
  80         c12_[H.name()]         = 0;
  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;
  85     }
  86
  87     //! Get particle type using the string identifier
  88     [[nodiscard]] ParticleType type(const std::string& particleTypeName) const
  89     {
  90         return particles_.at(ParticleTypeName(particleTypeName));
  91     }
  92
  93     //! Get C6 parameter of a given particle
  94     [[nodiscard]] C6 c6(const ParticleName& particleName) const
  95     {
  96         return c6_.at(ParticleTypeName(particleName.value()));
  97     }
  98
  99     //! Get C12 parameter of a given particle
 100     [[nodiscard]] C12 c12(const ParticleName& particleName) const
 101     {
 102         return c12_.at(ParticleTypeName(particleName.value()));
 103     }
 104
 105 private:
 106     std::map<ParticleTypeName, ParticleType> particles_;
 107     std::map<ParticleTypeName, C6>           c6_;
 108     std::map<ParticleTypeName, C12>          c12_;
 109 };
 110
 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) } };
 116
 117 WaterMoleculeBuilder::WaterMoleculeBuilder() : water_(MoleculeName("SOL"))
 118 {
 119     ParticleLibrary plib;
 120
 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"));
 125
 126     HarmonicBondType ohBond(1., 1.);
 127     water_.addInteraction(ParticleName("Oxygen"), ParticleName("H1"), ohBond);
 128     water_.addInteraction(ParticleName("Oxygen"), ParticleName("H2"), ohBond);
 129 }
 130
 131 Molecule WaterMoleculeBuilder::waterMolecule()
 132 {
 133     addExclusionsFromNames();
 134     return water_;
 135 }
 136
 137 Molecule WaterMoleculeBuilder::waterMoleculeWithoutExclusions()
 138 {
 139     return water_;
 140 }
 141
 142 void WaterMoleculeBuilder::addExclusionsFromNames()
 143 {
 144     water_.addExclusion(ParticleName("H1"), ParticleName("Oxygen"));
 145     water_.addExclusion(ParticleName("H2"), ParticleName("Oxygen"));
 146     water_.addExclusion(ParticleName("H1"), ParticleName("H2"));
 147 }
 148
 149 MethanolMoleculeBuilder::MethanolMoleculeBuilder() : methanol_(MoleculeName("MeOH"))
 150 {
 151     ParticleLibrary library;
 152
 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"));
 157
 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"));
 162
 163     HarmonicBondType ohBond(1.01, 1.02);
 164     methanol_.addInteraction(ParticleName("O2"), ParticleName("H3"), ohBond);
 165
 166     HarmonicBondType ometBond(1.1, 1.2);
 167     methanol_.addInteraction(ParticleName("O2"), ParticleName("Me1"), ometBond);
 168
 169     HarmonicAngle ochAngle(397.5, Degrees(108.52));
 170     methanol_.addInteraction(ParticleName("O2"), ParticleName("Me1"), ParticleName("H3"), ochAngle);
 171 }
 172
 173 Molecule MethanolMoleculeBuilder::methanolMolecule()
 174 {
 175     return methanol_;
 176 }
 177
 178
 179 Topology WaterTopologyBuilder::buildTopology(int numMolecules)
 180 {
 181     ParticleLibrary library;
 182
 183     ParticleTypesInteractions interactions;
 184     std::vector<std::string>  typeNames = { "Ow", "H" };
 185     for (const auto& name : typeNames)
 186     {
 187         interactions.add(
 188                 ParticleTypeName(name), library.c6(ParticleName(name)), library.c12(ParticleName(name)));
 189     }
 190
 191     // Add some molecules to the topology
 192     TopologyBuilder topologyBuilder;
 193     topologyBuilder.addMolecule(water(), numMolecules);
 194
 195     // Add non-bonded interaction information
 196     topologyBuilder.addParticleTypesInteractions(interactions);
 197
 198     Topology topology = topologyBuilder.buildTopology();
 199     return topology;
 200 }
 201
 202 Molecule WaterTopologyBuilder::water()
 203 {
 204     return waterMolecule_.waterMolecule();
 205 }
 206
 207 Topology SpcMethanolTopologyBuilder::buildTopology(int numWater, int numMethanol)
 208 {
 209     ParticleLibrary library;
 210
 211     ParticleTypesInteractions interactions;
 212     std::vector<std::string>  typeNames = { "Ow", "H", "OMet", "CMet" };
 213     for (const auto& name : typeNames)
 214     {
 215         interactions.add(
 216                 ParticleTypeName(name), library.c6(ParticleName(name)), library.c12(ParticleName(name)));
 217     }
 218
 219     // Add some molecules to the topology
 220     TopologyBuilder topologyBuilder;
 221     topologyBuilder.addMolecule(methanol(), numMethanol);
 222     topologyBuilder.addMolecule(water(), numWater);
 223
 224     // Add non-bonded interaction information
 225     topologyBuilder.addParticleTypesInteractions(interactions);
 226
 227     Topology topology = topologyBuilder.buildTopology();
 228     return topology;
 229 }
 230
 231 Molecule SpcMethanolTopologyBuilder::methanol()
 232 {
 233     return methanolMolecule_.methanolMolecule();
 234 }
 235
 236 Molecule SpcMethanolTopologyBuilder::water()
 237 {
 238     return waterMolecule_.waterMolecule();
 239 }
 240
 241 ArgonTopologyBuilder::ArgonTopologyBuilder(const int& numParticles, const fftypes forceField)
 242 {
 243     ParticleLibrary library;
 244
 245     ParticleTypesInteractions nbinteractions;
 246
 247     Molecule argonMolecule(MoleculeName("AR"));
 248
 249     std::string particleName;
 250
 251     if (forceField == fftypes::GROMOS43A1)
 252     {
 253         particleName = "Ar_gromos";
 254     }
 255     else if (forceField == fftypes::OPLSA)
 256     {
 257         particleName = "Ar_opls";
 258     }
 259
 260     nbinteractions.add(ParticleTypeName(particleName),
 261                        library.c6(ParticleName(particleName)),
 262                        library.c12(ParticleName(particleName)));
 263     argonMolecule.addParticle(ParticleName("AR"), library.type(particleName));
 264
 265     topologyBuilder_.addMolecule(argonMolecule, numParticles);
 266     topologyBuilder_.addParticleTypesInteractions((nbinteractions));
 267 }
 268
 269 Topology ArgonTopologyBuilder::argonTopology()
 270 {
 271     return topologyBuilder_.buildTopology();
 272 }
 273
 274 ArgonSimulationStateBuilder::ArgonSimulationStateBuilder(const fftypes forceField) :
 275     box_(6.05449), topology_(ArgonTopologyBuilder(12, forceField).argonTopology())
 276 {
 277
 278     coordinates_ = {
 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 },
 283     };
 284
 285     velocities_ = {
 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 },
 290     };
 291     forces_ = {
 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 },
 296     };
 297 }
 298
 299 void ArgonSimulationStateBuilder::setCoordinate(int particleNum, int dimension, real value)
 300 {
 301     if (dimension < 0 or dimension > 2)
 302     {
 303         throw InputException("Must provide a valid dimension\n");
 304     }
 305     coordinates_.at(particleNum)[dimension] = value;
 306 }
 307
 308 void ArgonSimulationStateBuilder::setVelocity(int particleNum, int dimension, real value)
 309 {
 310     if (dimension < 0 or dimension > 2)
 311     {
 312         throw InputException("Must provide a valid dimension\n");
 313     }
 314     velocities_.at(particleNum)[dimension] = value;
 315 }
 316
 317 SimulationState ArgonSimulationStateBuilder::setupSimulationState()
 318 {
 319     return SimulationState(coordinates_, velocities_, forces_, box_, topology_);
 320 }
 321
 322 const Topology& ArgonSimulationStateBuilder::topology() const
 323 {
 324     return topology_;
 325 }
 326
 327 Box& ArgonSimulationStateBuilder::box()
 328 {
 329     return box_;
 330 }
 331
 332 std::vector<Vec3>& ArgonSimulationStateBuilder::coordinates()
 333 {
 334     return coordinates_;
 335 }
 336
 337 std::vector<Vec3>& ArgonSimulationStateBuilder::velocities()
 338 {
 339     return velocities_;
 340 }
 341
 342 SpcMethanolSimulationStateBuilder::SpcMethanolSimulationStateBuilder() :
 343     box_(3.01000), topology_(SpcMethanolTopologyBuilder().buildTopology(1, 1))
 344 {
 345     coordinates_ = {
 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
 352     };
 353
 354     velocities_ = {
 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 },
 357     };
 358
 359     forces_ = {
 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 },
 362     };
 363 }
 364
 365 SimulationState SpcMethanolSimulationStateBuilder::setupSimulationState()
 366 {
 367     return SimulationState(coordinates_, velocities_, forces_, box_, topology_);
 368 }
 369
 370 std::vector<Vec3>& SpcMethanolSimulationStateBuilder::coordinates()
 371 {
 372     return coordinates_;
 373 }
 374
 375 std::vector<Vec3>& SpcMethanolSimulationStateBuilder::velocities()
 376 {
 377     return velocities_;
 378 }
 379
 380 } // namespace nblib