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37 * Implements nblib Topology and TopologyBuilder
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>
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"
61 TopologyBuilder::TopologyBuilder() : numParticles_(0) {}
63 ExclusionLists<int> TopologyBuilder::createExclusionsLists() const
65 const auto& moleculesList = molecules_;
67 std::vector<gmx::ExclusionBlock> exclusionBlockGlobal;
68 exclusionBlockGlobal.reserve(numParticles_);
70 size_t particleNumberOffset = 0;
71 for (const auto& molNumberTuple : moleculesList)
73 const Molecule& molecule = std::get<0>(molNumberTuple);
74 size_t numMols = std::get<1>(molNumberTuple);
75 const auto& exclusions = molecule.getExclusions();
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()));
82 std::vector<gmx::ExclusionBlock> exclusionBlockPerMolecule = toGmxExclusionBlock(exclusions);
84 // duplicate the exclusionBlockPerMolecule for the number of Molecules of (numMols)
85 for (size_t i = 0; i < numMols; ++i)
87 auto offsetExclusions = offsetGmxBlock(exclusionBlockPerMolecule, particleNumberOffset);
89 std::copy(std::begin(offsetExclusions),
90 std::end(offsetExclusions),
91 std::back_inserter(exclusionBlockGlobal));
93 particleNumberOffset += molecule.numParticlesInMolecule();
97 gmx::ListOfLists<int> exclusionsListOfListsGlobal;
98 for (const auto& block : exclusionBlockGlobal)
100 exclusionsListOfListsGlobal.pushBack(block.atomNumber);
103 std::vector<int> listRanges(exclusionsListOfListsGlobal.listRangesView().begin(),
104 exclusionsListOfListsGlobal.listRangesView().end());
105 std::vector<int> listElements(exclusionsListOfListsGlobal.elementsView().begin(),
106 exclusionsListOfListsGlobal.elementsView().end());
107 ExclusionLists<int> exclusionListsGlobal;
108 exclusionListsGlobal.ListRanges = std::move(listRanges);
109 exclusionListsGlobal.ListElements = std::move(listElements);
111 return exclusionListsGlobal;
114 ListedInteractionData TopologyBuilder::createInteractionData(const ParticleSequencer& particleSequencer)
116 ListedInteractionData interactionData;
118 // this code is doing the compile time equivalent of
119 // for (int i = 0; i < interactionData.size(); ++i)
120 // create(get<i>(interactionData));
122 auto create = [this, &particleSequencer](auto& interactionDataElement) {
123 using InteractionType = typename std::decay_t<decltype(interactionDataElement)>::type;
125 // first compression stage: each bond per molecule listed once,
126 // eliminates duplicates from multiple identical molecules
127 auto compressedDataStage1 = detail::collectInteractions<InteractionType>(this->molecules_);
128 auto& expansionArrayStage1 = std::get<0>(compressedDataStage1);
129 auto& moleculeInteractions = std::get<1>(compressedDataStage1);
131 // second compression stage: recognize bond duplicates among bonds from all molecules put together
132 auto compressedDataStage2 = detail::eliminateDuplicateInteractions(moleculeInteractions);
133 auto& expansionArrayStage2 = std::get<0>(compressedDataStage2);
134 auto& uniqueInteractionInstances = std::get<1>(compressedDataStage2);
136 // combine stage 1 + 2 expansion arrays
137 std::vector<size_t> expansionArray(expansionArrayStage1.size());
138 std::transform(begin(expansionArrayStage1),
139 end(expansionArrayStage1),
140 begin(expansionArray),
141 [& S2 = expansionArrayStage2](size_t S1Element) { return S2[S1Element]; });
143 // add data about InteractionType instances
144 interactionDataElement.parameters = std::move(uniqueInteractionInstances);
146 interactionDataElement.indices.resize(expansionArray.size());
147 // coordinateIndices contains the particle sequence IDs of all interaction coordinates of type <BondType>
148 auto coordinateIndices = detail::sequenceIDs<InteractionType>(this->molecules_, particleSequencer);
149 // zip coordinateIndices(i,j,...) + expansionArray(k) -> interactionDataElement.indices(i,j,...,k)
150 std::transform(begin(coordinateIndices),
151 end(coordinateIndices),
152 begin(expansionArray),
153 begin(interactionDataElement.indices),
154 [](auto coordinateIndex, auto interactionIndex) {
155 std::array<int, coordinateIndex.size() + 1> ret{ 0 };
156 for (int i = 0; i < int(coordinateIndex.size()); ++i)
158 ret[i] = coordinateIndex[i];
160 ret[coordinateIndex.size()] = interactionIndex;
165 for_each_tuple(create, interactionData);
167 return interactionData;
170 template<typename T, class Extractor>
171 std::vector<T> TopologyBuilder::extractParticleTypeQuantity(Extractor&& extractor)
173 auto& moleculesList = molecules_;
177 ret.reserve(numParticles_);
179 for (auto& molNumberTuple : moleculesList)
181 Molecule& molecule = std::get<0>(molNumberTuple);
182 size_t numMols = std::get<1>(molNumberTuple);
184 for (size_t i = 0; i < numMols; ++i)
186 for (auto& particleData : molecule.particleData())
188 auto particleTypesMap = molecule.particleTypesMap();
189 ret.push_back(extractor(particleData, particleTypesMap));
197 Topology TopologyBuilder::buildTopology()
199 assert((!(numParticles_ < 0) && "It should not be possible to have negative particles"));
200 if (numParticles_ == 0)
202 throw InputException("You cannot build a topology with no particles");
204 topology_.numParticles_ = numParticles_;
206 topology_.exclusionLists_ = createExclusionsLists();
207 topology_.charges_ = extractParticleTypeQuantity<real>(
208 [](const auto& data, [[maybe_unused]] auto& map) { return data.charge_; });
210 // map unique ParticleTypes to IDs
211 std::unordered_map<std::string, int> nameToId;
212 for (auto& name_particleType_tuple : particleTypes_)
214 topology_.particleTypes_.push_back(name_particleType_tuple.second);
215 nameToId[name_particleType_tuple.first] = nameToId.size();
218 topology_.particleTypeIdOfAllParticles_ =
219 extractParticleTypeQuantity<int>([&nameToId](const auto& data, [[maybe_unused]] auto& map) {
220 return nameToId[data.particleTypeName_];
223 ParticleSequencer particleSequencer;
224 particleSequencer.build(molecules_);
225 topology_.particleSequencer_ = std::move(particleSequencer);
227 topology_.combinationRule_ = particleTypesInteractions_.getCombinationRule();
228 topology_.nonBondedInteractionMap_ = particleTypesInteractions_.generateTable();
230 topology_.interactionData_ = createInteractionData(topology_.particleSequencer_);
232 // Check whether there is any missing term in the particleTypesInteractions compared to the
233 // list of particletypes
234 for (const auto& particleType1 : particleTypes_)
236 for (const auto& particleType2 : particleTypes_)
238 auto interactionKey = std::make_tuple(ParticleTypeName(particleType1.first),
239 ParticleTypeName(particleType2.first));
240 if (topology_.nonBondedInteractionMap_.count(interactionKey) == 0)
242 std::string message =
243 formatString("Missing nonbonded interaction parameters for pair {} {}",
245 particleType2.first);
246 throw InputException(message);
254 TopologyBuilder& TopologyBuilder::addMolecule(const Molecule& molecule, const int nMolecules)
257 * 1. Push-back a tuple of molecule type and nMolecules
258 * 2. Append exclusion list into the data structure
261 molecules_.emplace_back(molecule, nMolecules);
262 numParticles_ += nMolecules * molecule.numParticlesInMolecule();
264 auto particleTypesInMolecule = molecule.particleTypesMap();
266 for (const auto& name_type_tuple : particleTypesInMolecule)
268 // If we already have the particleType, we need to make
269 // sure that the type's parameters are actually the same
270 // otherwise we would overwrite them
271 if (particleTypes_.count(name_type_tuple.first) > 0)
273 if (!(particleTypes_.at(name_type_tuple.first) == name_type_tuple.second))
275 throw InputException("Differing ParticleTypes with identical names encountered");
280 // Note: insert does nothing if the key already exists
281 particleTypes_.insert(particleTypesInMolecule.begin(), particleTypesInMolecule.end());
286 void TopologyBuilder::addParticleTypesInteractions(const ParticleTypesInteractions& particleTypesInteractions)
288 particleTypesInteractions_.merge(particleTypesInteractions);
291 int Topology::numParticles() const
293 return numParticles_;
296 std::vector<real> Topology::getCharges() const
301 std::vector<ParticleType> Topology::getParticleTypes() const
303 return particleTypes_;
306 std::vector<int> Topology::getParticleTypeIdOfAllParticles() const
308 return particleTypeIdOfAllParticles_;
311 int Topology::sequenceID(MoleculeName moleculeName, int moleculeNr, ResidueName residueName, ParticleName particleName) const
313 return particleSequencer_(moleculeName, moleculeNr, residueName, particleName);
316 NonBondedInteractionMap Topology::getNonBondedInteractionMap() const
318 return nonBondedInteractionMap_;
321 ListedInteractionData Topology::getInteractionData() const
323 return interactionData_;
326 CombinationRule Topology::getCombinationRule() const
328 return combinationRule_;
331 ExclusionLists<int> Topology::exclusionLists() const
333 return exclusionLists_;