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35 /*! \internal \file
36 * \brief
37 * Implements nblib Topology and TopologyBuilder
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 <algorithm>
46 #include <numeric>
47
48 #include "gromacs/topology/exclusionblocks.h"
49 #include "gromacs/utility/listoflists.h"
50 #include "gromacs/utility/smalloc.h"
51 #include "nblib/exception.h"
52 #include "nblib/particletype.h"
53 #include "nblib/sequencing.hpp"
54 #include "nblib/topology.h"
55 #include "nblib/util/util.hpp"
56 #include "nblib/topologyhelpers.h"
57
58 namespace nblib
59 {
60
TopologyBuilder()61 TopologyBuilder::TopologyBuilder() : numParticles_(0) {}
62
createExclusionsLists() const63 ExclusionLists<int> TopologyBuilder::createExclusionsLists() const
64 {
65 const auto& moleculesList = molecules_;
66
67 std::vector<gmx::ExclusionBlock> exclusionBlockGlobal;
68 exclusionBlockGlobal.reserve(numParticles_);
69
70 size_t particleNumberOffset = 0;
71 for (const auto& molNumberTuple : moleculesList)
72 {
73 const Molecule& molecule = std::get<0>(molNumberTuple);
74 size_t numMols = std::get<1>(molNumberTuple);
75 const auto& exclusions = molecule.getExclusions();
76
77 // Note this is a programming error as all particles should exclude at least themselves and empty topologies are not allowed.
78 const std::string message =
79 "No exclusions found in the " + molecule.name().value() + " molecule.";
80 assert((!exclusions.empty() && message.c_str()));
81
82 std::vector<gmx::ExclusionBlock> exclusionBlockPerMolecule = toGmxExclusionBlock(exclusions);
83
84 // duplicate the exclusionBlockPerMolecule for the number of Molecules of (numMols)
85 for (size_t i = 0; i < numMols; ++i)
86 {
87 auto offsetExclusions = offsetGmxBlock(exclusionBlockPerMolecule, particleNumberOffset);
88
89 std::copy(std::begin(offsetExclusions), std::end(offsetExclusions),
90 std::back_inserter(exclusionBlockGlobal));
91
92 particleNumberOffset += molecule.numParticlesInMolecule();
93 }
94 }
95
96 gmx::ListOfLists<int> exclusionsListOfListsGlobal;
97 for (const auto& block : exclusionBlockGlobal)
98 {
99 exclusionsListOfListsGlobal.pushBack(block.atomNumber);
100 }
101
102 std::vector<int> listRanges(exclusionsListOfListsGlobal.listRangesView().begin(),
103 exclusionsListOfListsGlobal.listRangesView().end());
104 std::vector<int> listElements(exclusionsListOfListsGlobal.elementsView().begin(),
105 exclusionsListOfListsGlobal.elementsView().end());
106 ExclusionLists<int> exclusionListsGlobal;
107 exclusionListsGlobal.ListRanges = std::move(listRanges);
108 exclusionListsGlobal.ListElements = std::move(listElements);
109
110 return exclusionListsGlobal;
111 }
112
createInteractionData(const ParticleSequencer & particleSequencer)113 ListedInteractionData TopologyBuilder::createInteractionData(const ParticleSequencer& particleSequencer)
114 {
115 ListedInteractionData interactionData;
116
117 // this code is doing the compile time equivalent of
118 // for (int i = 0; i < interactionData.size(); ++i)
119 // create(get<i>(interactionData));
120
121 auto create = [this, &particleSequencer](auto& interactionDataElement) {
122 using InteractionType = typename std::decay_t<decltype(interactionDataElement)>::type;
123
124 // first compression stage: each bond per molecule listed once,
125 // eliminates duplicates from multiple identical molecules
126 auto compressedDataStage1 = detail::collectInteractions<InteractionType>(this->molecules_);
127 auto& expansionArrayStage1 = std::get<0>(compressedDataStage1);
128 auto& moleculeInteractions = std::get<1>(compressedDataStage1);
129
130 // second compression stage: recognize bond duplicates among bonds from all molecules put together
131 auto compressedDataStage2 = detail::eliminateDuplicateInteractions(moleculeInteractions);
132 auto& expansionArrayStage2 = std::get<0>(compressedDataStage2);
133 auto& uniqueInteractionInstances = std::get<1>(compressedDataStage2);
134
135 // combine stage 1 + 2 expansion arrays
136 std::vector<size_t> expansionArray(expansionArrayStage1.size());
137 std::transform(begin(expansionArrayStage1), end(expansionArrayStage1), begin(expansionArray),
138 [& S2 = expansionArrayStage2](size_t S1Element) { return S2[S1Element]; });
139
140 // add data about InteractionType instances
141 interactionDataElement.parameters = std::move(uniqueInteractionInstances);
142
143 interactionDataElement.indices.resize(expansionArray.size());
144 // coordinateIndices contains the particle sequence IDs of all interaction coordinates of type <BondType>
145 auto coordinateIndices = detail::sequenceIDs<InteractionType>(this->molecules_, particleSequencer);
146 // zip coordinateIndices(i,j,...) + expansionArray(k) -> interactionDataElement.indices(i,j,...,k)
147 std::transform(begin(coordinateIndices), end(coordinateIndices), begin(expansionArray),
148 begin(interactionDataElement.indices),
149 [](auto coordinateIndex, auto interactionIndex) {
150 std::array<int, coordinateIndex.size() + 1> ret{ 0 };
151 for (int i = 0; i < int(coordinateIndex.size()); ++i)
152 {
153 ret[i] = coordinateIndex[i];
154 }
155 ret[coordinateIndex.size()] = interactionIndex;
156 return ret;
157 });
158 };
159
160 for_each_tuple(create, interactionData);
161
162 return interactionData;
163 }
164
165 template<typename T, class Extractor>
extractParticleTypeQuantity(Extractor && extractor)166 std::vector<T> TopologyBuilder::extractParticleTypeQuantity(Extractor&& extractor)
167 {
168 auto& moleculesList = molecules_;
169
170 // returned object
171 std::vector<T> ret;
172 ret.reserve(numParticles_);
173
174 for (auto& molNumberTuple : moleculesList)
175 {
176 Molecule& molecule = std::get<0>(molNumberTuple);
177 size_t numMols = std::get<1>(molNumberTuple);
178
179 for (size_t i = 0; i < numMols; ++i)
180 {
181 for (auto& particleData : molecule.particleData())
182 {
183 auto particleTypesMap = molecule.particleTypesMap();
184 ret.push_back(extractor(particleData, particleTypesMap));
185 }
186 }
187 }
188
189 return ret;
190 }
191
buildTopology()192 Topology TopologyBuilder::buildTopology()
193 {
194 assert((!(numParticles_ < 0) && "It should not be possible to have negative particles"));
195 if (numParticles_ == 0)
196 {
197 throw InputException("You cannot build a topology with no particles");
198 }
199 topology_.numParticles_ = numParticles_;
200
201 topology_.exclusionLists_ = createExclusionsLists();
202 topology_.charges_ = extractParticleTypeQuantity<real>(
203 [](const auto& data, [[maybe_unused]] auto& map) { return data.charge_; });
204
205 // map unique ParticleTypes to IDs
206 std::unordered_map<std::string, int> nameToId;
207 for (auto& name_particleType_tuple : particleTypes_)
208 {
209 topology_.particleTypes_.push_back(name_particleType_tuple.second);
210 nameToId[name_particleType_tuple.first] = nameToId.size();
211 }
212
213 topology_.particleTypeIdOfAllParticles_ =
214 extractParticleTypeQuantity<int>([&nameToId](const auto& data, [[maybe_unused]] auto& map) {
215 return nameToId[data.particleTypeName_];
216 });
217
218 ParticleSequencer particleSequencer;
219 particleSequencer.build(molecules_);
220 topology_.particleSequencer_ = std::move(particleSequencer);
221
222 topology_.combinationRule_ = particleTypesInteractions_.getCombinationRule();
223 topology_.nonBondedInteractionMap_ = particleTypesInteractions_.generateTable();
224
225 topology_.interactionData_ = createInteractionData(topology_.particleSequencer_);
226
227 // Check whether there is any missing term in the particleTypesInteractions compared to the
228 // list of particletypes
229 for (const auto& particleType1 : particleTypes_)
230 {
231 for (const auto& particleType2 : particleTypes_)
232 {
233 auto interactionKey = std::make_tuple(ParticleTypeName(particleType1.first),
234 ParticleTypeName(particleType2.first));
235 if (topology_.nonBondedInteractionMap_.count(interactionKey) == 0)
236 {
237 std::string message =
238 formatString("Missing nonbonded interaction parameters for pair {} {}",
239 particleType1.first, particleType2.first);
240 throw InputException(message);
241 }
242 }
243 }
244
245 return topology_;
246 }
247
addMolecule(const Molecule & molecule,const int nMolecules)248 TopologyBuilder& TopologyBuilder::addMolecule(const Molecule& molecule, const int nMolecules)
249 {
250 /*
251 * 1. Push-back a tuple of molecule type and nMolecules
252 * 2. Append exclusion list into the data structure
253 */
254
255 molecules_.emplace_back(molecule, nMolecules);
256 numParticles_ += nMolecules * molecule.numParticlesInMolecule();
257
258 auto particleTypesInMolecule = molecule.particleTypesMap();
259
260 for (const auto& name_type_tuple : particleTypesInMolecule)
261 {
262 // If we already have the particleType, we need to make
263 // sure that the type's parameters are actually the same
264 // otherwise we would overwrite them
265 if (particleTypes_.count(name_type_tuple.first) > 0)
266 {
267 if (!(particleTypes_.at(name_type_tuple.first) == name_type_tuple.second))
268 {
269 throw InputException("Differing ParticleTypes with identical names encountered");
270 }
271 }
272 }
273
274 // Note: insert does nothing if the key already exists
275 particleTypes_.insert(particleTypesInMolecule.begin(), particleTypesInMolecule.end());
276
277 return *this;
278 }
279
addParticleTypesInteractions(const ParticleTypesInteractions & particleTypesInteractions)280 void TopologyBuilder::addParticleTypesInteractions(const ParticleTypesInteractions& particleTypesInteractions)
281 {
282 particleTypesInteractions_.merge(particleTypesInteractions);
283 }
284
numParticles() const285 int Topology::numParticles() const
286 {
287 return numParticles_;
288 }
289
getCharges() const290 std::vector<real> Topology::getCharges() const
291 {
292 return charges_;
293 }
294
getParticleTypes() const295 std::vector<ParticleType> Topology::getParticleTypes() const
296 {
297 return particleTypes_;
298 }
299
getParticleTypeIdOfAllParticles() const300 std::vector<int> Topology::getParticleTypeIdOfAllParticles() const
301 {
302 return particleTypeIdOfAllParticles_;
303 }
304
sequenceID(MoleculeName moleculeName,int moleculeNr,ResidueName residueName,ParticleName particleName) const305 int Topology::sequenceID(MoleculeName moleculeName, int moleculeNr, ResidueName residueName, ParticleName particleName) const
306 {
307 return particleSequencer_(moleculeName, moleculeNr, residueName, particleName);
308 }
309
getNonBondedInteractionMap() const310 NonBondedInteractionMap Topology::getNonBondedInteractionMap() const
311 {
312 return nonBondedInteractionMap_;
313 }
314
getInteractionData() const315 ListedInteractionData Topology::getInteractionData() const
316 {
317 return interactionData_;
318 }
319
getCombinationRule() const320 CombinationRule Topology::getCombinationRule() const
321 {
322 return combinationRule_;
323 }
324
exclusionLists() const325 ExclusionLists<int> Topology::exclusionLists() const
326 {
327 return exclusionLists_;
328 }
329
330 } // namespace nblib
331