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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:
ParticleLibrary()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
type(const std::string & particleTypeName) const84 [[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
c6(const ParticleName & particleName) const90 [[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
c12(const ParticleName & particleName) const96 [[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
WaterMoleculeBuilder()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
waterMolecule()127 Molecule WaterMoleculeBuilder::waterMolecule()
128 {
129 addExclusionsFromNames();
130 return water_;
131 }
132
waterMoleculeWithoutExclusions()133 Molecule WaterMoleculeBuilder::waterMoleculeWithoutExclusions()
134 {
135 return water_;
136 }
137
addExclusionsFromNames()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
MethanolMoleculeBuilder()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
methanolMolecule()169 Molecule MethanolMoleculeBuilder::methanolMolecule()
170 {
171 return methanol_;
172 }
173
174
buildTopology(int numMolecules)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(ParticleTypeName(name), library.c6(ParticleName(name)),
184 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
water()198 Molecule WaterTopologyBuilder::water()
199 {
200 return waterMolecule_.waterMolecule();
201 }
202
buildTopology(int numWater,int numMethanol)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(ParticleTypeName(name), library.c6(ParticleName(name)),
212 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
methanol()227 Molecule SpcMethanolTopologyBuilder::methanol()
228 {
229 return methanolMolecule_.methanolMolecule();
230 }
231
water()232 Molecule SpcMethanolTopologyBuilder::water()
233 {
234 return waterMolecule_.waterMolecule();
235 }
236
ArgonTopologyBuilder(const int & numParticles)237 ArgonTopologyBuilder::ArgonTopologyBuilder(const int& numParticles)
238 {
239 ParticleLibrary library;
240
241 ParticleTypesInteractions nbinteractions;
242 nbinteractions.add(ParticleTypeName("Ar"), library.c6(ParticleName("Ar")),
243 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
argonTopology()252 Topology ArgonTopologyBuilder::argonTopology()
253 {
254 return topologyBuilder_.buildTopology();
255 }
256
ArgonSimulationStateBuilder()257 ArgonSimulationStateBuilder::ArgonSimulationStateBuilder() :
258 box_(6.05449),
259 topology_(ArgonTopologyBuilder(12).argonTopology())
260 {
261
262 coordinates_ = {
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 },
267 };
268
269 velocities_ = {
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 },
274 };
275 forces_ = {
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 },
280 };
281 }
282
setCoordinate(int particleNum,int dimension,real value)283 void ArgonSimulationStateBuilder::setCoordinate(int particleNum, int dimension, real value)
284 {
285 if (dimension < 0 or dimension > 2)
286 {
287 throw InputException("Must provide a valid dimension\n");
288 }
289 coordinates_.at(particleNum)[dimension] = value;
290 }
291
setVelocity(int particleNum,int dimension,real value)292 void ArgonSimulationStateBuilder::setVelocity(int particleNum, int dimension, real value)
293 {
294 if (dimension < 0 or dimension > 2)
295 {
296 throw InputException("Must provide a valid dimension\n");
297 }
298 velocities_.at(particleNum)[dimension] = value;
299 }
300
setupSimulationState()301 SimulationState ArgonSimulationStateBuilder::setupSimulationState()
302 {
303 return SimulationState(coordinates_, velocities_, forces_, box_, topology_);
304 }
305
topology() const306 const Topology& ArgonSimulationStateBuilder::topology() const
307 {
308 return topology_;
309 }
310
box()311 Box& ArgonSimulationStateBuilder::box()
312 {
313 return box_;
314 }
315
coordinates()316 std::vector<Vec3>& ArgonSimulationStateBuilder::coordinates()
317 {
318 return coordinates_;
319 }
320
velocities()321 std::vector<Vec3>& ArgonSimulationStateBuilder::velocities()
322 {
323 return velocities_;
324 }
325
SpcMethanolSimulationStateBuilder()326 SpcMethanolSimulationStateBuilder::SpcMethanolSimulationStateBuilder() :
327 box_(3.01000),
328 topology_(SpcMethanolTopologyBuilder().buildTopology(1, 1))
329 {
330 coordinates_ = {
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
337 };
338
339 velocities_ = {
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 },
342 };
343
344 forces_ = {
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 },
347 };
348 }
349
setupSimulationState()350 SimulationState SpcMethanolSimulationStateBuilder::setupSimulationState()
351 {
352 return SimulationState(coordinates_, velocities_, forces_, box_, topology_);
353 }
354
coordinates()355 std::vector<Vec3>& SpcMethanolSimulationStateBuilder::coordinates()
356 {
357 return coordinates_;
358 }
359
velocities()360 std::vector<Vec3>& SpcMethanolSimulationStateBuilder::velocities()
361 {
362 return velocities_;
363 }
364
365 } // namespace nblib
366