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35 /*! \inpublicapi \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 #ifndef NBLIB_TOPOLOGY_H
46 #define NBLIB_TOPOLOGY_H
47
48 #include <vector>
49
50 #include "nblib/interactions.h"
51 #include "nblib/listed_forces/definitions.h"
52 #include "nblib/molecules.h"
53 #include "nblib/particlesequencer.h"
54
55 namespace nblib
56 {
57
58 /*! \brief A list of exclusion lists, optimized for performance
59 *
60 * This struct is to hold data that comes from, and will be copied into,
61 * gmx::ListOfLists. Since the ListElements and ListRanges are sufficient
62 * to create a gmx::ListOfLists, they are stored in the topoology instead
63 * of a gmx::ListOfLists to avoid dependencies.
64 */
65 template<typename T>
66 struct ExclusionLists
67 {
68 //! Ranges of the concatenated lists
69 std::vector<int> ListRanges;
70 //! Elements of the concatenated lists
71 std::vector<T> ListElements;
72 };
73
74 /*! \inpublicapi
75 * \ingroup nblib
76 * \brief System Topology
77 *
78 * Contains all topology information meant to be used by the simulation
79 * engine internally. Private constructor ensures that a Topology object
80 * exists in a scope in a valid state after it has been built using a
81 * Topology Builder.
82 */
83 class Topology final
84 {
85
86 public:
87 //! Returns the total number of particles in the system
88 int numParticles() const;
89
90 //! Returns a vector of particle types
91 std::vector<ParticleType> getParticleTypes() const;
92
93 //! Return the ParticleType ID of all particles
94 std::vector<int> getParticleTypeIdOfAllParticles() const;
95
96 //! Returns a vector of particles partial charges
97 std::vector<real> getCharges() const;
98
99 //! Returns exclusions in a format that can be used to create gmx::ListOfLists
100 ExclusionLists<int> exclusionLists() const;
101
102 //! Returns the unique ID of a specific particle belonging to a molecule in the global space
103 int sequenceID(MoleculeName moleculeName, int moleculeNr, ResidueName residueName, ParticleName particleName) const;
104
105 //! Returns a map of non-bonded force parameters indexed by ParticleType names
106 NonBondedInteractionMap getNonBondedInteractionMap() const;
107
108 //! Returns the interaction data
109 ListedInteractionData getInteractionData() const;
110
111 //! Returns the combination rule used to generate the NonBondedInteractionMap
112 CombinationRule getCombinationRule() const;
113
114 private:
115 Topology() = default;
116
117 friend class TopologyBuilder;
118
119 //! Total number of particles in the system
120 int numParticles_;
121 //! unique collection of ParticleTypes
122 std::vector<ParticleType> particleTypes_;
123 //! store an ID of each particles's type
124 std::vector<int> particleTypeIdOfAllParticles_;
125 //! Storage for particles partial charges
126 std::vector<real> charges_;
127 //! Information about exclusions.
128 ExclusionLists<int> exclusionLists_;
129 //! Associate molecule, residue and particle names with sequence numbers
130 ParticleSequencer particleSequencer_;
131 //! Map that should hold all nonbonded interactions for all particle types
132 NonBondedInteractionMap nonBondedInteractionMap_;
133 //! data about bonds for all supported types
134 ListedInteractionData interactionData_;
135 //! Combination Rule used to generate the nonbonded interactions
136 CombinationRule combinationRule_;
137 };
138
139 /*! \brief Topology Builder
140 *
141 * \libinternal
142 * \ingroup nblib
143 *
144 * A helper class to assist building of topologies. They also ensure that
145 * topologies only exist in a valid state within the scope of the
146 * simulation program.
147 *
148 */
149 class TopologyBuilder final
150 {
151 public:
152 //! Constructor
153 TopologyBuilder();
154
155 /*! \brief
156 * Builds and Returns a valid Topology
157 *
158 * This function accounts for all the molecules added along with their
159 * exclusions and returns a topology with a valid state that is usable
160 * by the GROMACS back-end.
161 */
162 Topology buildTopology();
163
164 //! Adds a molecules of a certain type into the topology
165 TopologyBuilder& addMolecule(const Molecule& moleculeType, int nMolecules);
166
167 //! Add non-bonded interaction map to the topology
168 void addParticleTypesInteractions(const ParticleTypesInteractions& particleTypesInteractions);
169
170 private:
171 //! Internally stored topology
172 Topology topology_;
173
174 //! Total number of particles in the system
175 int numParticles_;
176
177 //! List of molecule types and number of molecules
178 std::vector<std::tuple<Molecule, int>> molecules_;
179
180 //! Builds an exclusions list aggregating exclusions from all molecules
181 ExclusionLists<int> createExclusionsLists() const;
182
183 //! Gather interaction data from molecules
184 ListedInteractionData createInteractionData(const ParticleSequencer&);
185
186 //! Helper function to extract quantities like mass, charge, etc from the system
187 template<typename T, class Extractor>
188 std::vector<T> extractParticleTypeQuantity(Extractor&& extractor);
189
190 //! Distinct collection of ParticleTypes
191 std::unordered_map<std::string, ParticleType> particleTypes_;
192
193 //! ParticleType nonbonded parameters
194 ParticleTypesInteractions particleTypesInteractions_;
195 };
196
197 //! utility function to extract Particle quantities and expand them to the full
198 //! array of length numParticles()
199 template<class F>
expandQuantity(const Topology & topology,F && particleTypeExtractor)200 inline auto expandQuantity(const Topology& topology, F&& particleTypeExtractor)
201 {
202 using ValueType = decltype((std::declval<ParticleType>().*std::declval<F>())());
203
204 std::vector<ValueType> ret;
205 ret.reserve(topology.numParticles());
206
207 const std::vector<ParticleType>& particleTypes = topology.getParticleTypes();
208
209 for (size_t id : topology.getParticleTypeIdOfAllParticles())
210 {
211 ret.push_back((particleTypes[id].*particleTypeExtractor)());
212 }
213
214 return ret;
215 }
216
217 } // namespace nblib
218
219 #endif // NBLIB_TOPOLOGY_H
220