Scine::Swoose  2.1.0
This is the SCINE module Swoose.
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Pages
ConnectivityGenerator.h
Go to the documentation of this file.
1 
8 #ifndef MMPARAMETRIZATION_CONNECTIVITYGENERATOR_H
9 #define MMPARAMETRIZATION_CONNECTIVITYGENERATOR_H
10 
11 #include <list>
12 #include <memory>
13 #include <vector>
14 
15 namespace Scine {
16 
17 namespace Core {
18 struct Log;
19 } // namespace Core
20 
21 namespace Utils {
22 class Settings;
23 class BondOrderCollection;
24 } // namespace Utils
25 
26 namespace MMParametrization {
27 struct ParametrizationData;
28 
37  public:
41  ConnectivityGenerator(ParametrizationData& data, std::shared_ptr<Utils::Settings> settings, Core::Log& log);
55 
56  private:
57  // The data used within all MM parametrization classes
58  ParametrizationData& data_;
59  // The settings
60  std::shared_ptr<Utils::Settings> settings_;
61  // Logger
62  Core::Log& log_;
63  // The threshold for a bond's bond order to be considered a bond
64  double bondOrderThreshold_ = 0.4;
65 };
66 
67 } // namespace MMParametrization
68 } // namespace Scine
69 
70 #endif // MMPARAMETRIZATION_CONNECTIVITYGENERATOR_H
This class handles the generation of the connectivity of the molecular system.
Definition: ConnectivityGenerator.h:36
void refineListsOfNeighbors()
Refines the connectivity based on information obtained from quantum-chemically calculated bond orders...
Definition: ConnectivityGenerator.cpp:51
void generateInitialListsOfNeighbors()
This function generates the connectivity as a vector of lists of neighbor atom indices and updates th...
Definition: ConnectivityGenerator.cpp:29
ConnectivityGenerator(ParametrizationData &data, std::shared_ptr< Utils::Settings > settings, Core::Log &log)
Constructor.
Definition: ConnectivityGenerator.cpp:23
This struct holds all objects used inside the MM parametrization algorithm.
Definition: ParametrizationData.h:29