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#include "UseTheForce/ForceField.hpp" |
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#include "utils/PropertyMap.hpp" |
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#include "utils/LocalIndexManager.hpp" |
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#include "nonbonded/SwitchingFunction.hpp" |
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|
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//another nonsense macro declaration |
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#define __OPENMD_C |
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#include "brains/fSimulation.h" |
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using namespace std; |
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namespace OpenMD{ |
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enum CutoffMethod { |
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HARD, |
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SWITCHING_FUNCTION, |
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SHIFTED_POTENTIAL, |
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SHIFTED_FORCE |
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}; |
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|
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//forward decalration |
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//forward declaration |
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class SnapshotManager; |
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class Molecule; |
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class SelectionManager; |
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return nAtoms_; |
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} |
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|
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/** Returns the number of effective cutoff groups on local processor */ |
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unsigned int getNLocalCutoffGroups(); |
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|
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/** Returns the number of local bonds */ |
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unsigned int getNBonds(){ |
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return nBonds_; |
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/** Overloaded version of gyrational volume that also returns |
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det(I) so dV/dr can be calculated*/ |
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void getGyrationalVolume(RealType &vol, RealType &detI); |
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/** main driver function to interact with fortran during the |
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initialization and molecule migration */ |
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|
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void update(); |
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/** |
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* Do final bookkeeping before Force managers need their data. |
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*/ |
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void prepareTopology(); |
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|
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|
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/** Returns the local index manager */ |
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LocalIndexManager* getLocalIndexManager() { |
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return &localIndexMan_; |
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return globalMolMembership_[id]; |
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} |
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|
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RealType getCutoffRadius() { |
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return cutoffRadius_; |
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} |
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/** |
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* returns a vector which maps the local atom index on this |
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* processor to the global atom index. With only one processor, |
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* these should be identical. |
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*/ |
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vector<int> getGlobalAtomIndices(); |
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|
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RealType getSwitchingRadius() { |
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return switchingRadius_; |
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} |
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/** |
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* returns a vector which maps the local cutoff group index on |
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* this processor to the global cutoff group index. With only one |
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* processor, these should be identical. |
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*/ |
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vector<int> getGlobalGroupIndices(); |
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|
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RealType getListRadius() { |
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return listRadius_; |
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} |
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|
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string getFinalConfigFileName() { |
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return finalConfigFileName_; |
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} |
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|
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bool isFortranInitialized() { |
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return fortranInitialized_; |
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bool isTopologyDone() { |
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return topologyDone_; |
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} |
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bool getCalcBoxDipole() { |
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*/ |
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void removeInteractionPairs(Molecule* mol); |
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|
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/** Returns the unique atom types of local processor in an array */ |
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set<AtomType*> getUniqueAtomTypes(); |
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/** Returns the set of atom types present in this simulation */ |
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set<AtomType*> getSimulatedAtomTypes(); |
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private: |
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/** fill up the simtype struct*/ |
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void setupSimType(); |
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/** fill up the simtype struct and other simulation-related variables */ |
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void setupSimVariables(); |
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|
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/** |
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* Setup Fortran Simulation |
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* @see #setupFortranParallel |
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*/ |
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void setupFortranSim(); |
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|
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/** Figure out the cutoff radius */ |
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void setupCutoffRadius(); |
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/** Figure out the cutoff method */ |
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void setupCutoffMethod(); |
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/** Figure out the switching radius */ |
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void setupSwitchingRadius(); |
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/** Figure out the neighbor list skin thickness */ |
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void setupSkinThickness(); |
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/** Figure out which polynomial type to use for the switching function */ |
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void setupSwitchingFunction(); |
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/** Determine if we need to accumulate the simulation box dipole */ |
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void setupAccumulateBoxDipole(); |
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bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */ |
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bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */ |
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|
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public: |
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bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; } |
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bool usesDirectionalAtoms() { return usesDirectionalAtoms_; } |
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bool usesMetallicAtoms() { return usesMetallicAtoms_; } |
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bool usesAtomicVirial() { return usesAtomicVirial_; } |
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bool requiresPrepair() { return requiresPrepair_; } |
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bool requiresSkipCorrection() { return requiresSkipCorrection_;} |
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bool requiresSelfCorrection() { return requiresSelfCorrection_;} |
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|
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private: |
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/// Data structures holding primary simulation objects |
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map<int, Molecule*> molecules_; /**< map holding pointers to LOCAL molecules */ |
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simtype fInfo_; /**< A dual struct shared by C++ |
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and Fortran to pass |
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information about what types |
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of calculation are |
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required */ |
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|
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|
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/// Stamps are templates for objects that are then used to create |
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/// groups of objects. For example, a molecule stamp contains |
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/// information on how to build that molecule (i.e. the topology, |
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* the simulation. It should be nGlobalAtoms_ in size. |
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*/ |
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vector<int> globalGroupMembership_; |
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public: |
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vector<int> getGlobalGroupMembership() { return globalGroupMembership_; } |
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private: |
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|
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/** |
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* A vector that maps between the global index of an atom and the |
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* by SimCreator once and only once, since it is never changed |
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* during the simulation. It shoudl be nGlobalAtoms_ in size. |
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*/ |
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vector<int> globalMolMembership_; |
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vector<int> globalMolMembership_; |
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|
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/** |
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* A vector that maps between the local index of an atom and the |
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* index of the AtomType. |
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*/ |
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vector<int> identArray_; |
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public: |
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vector<int> getIdentArray() { return identArray_; } |
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private: |
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|
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/** |
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* A vector which contains the fractional contribution of an |
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* atom's mass to the total mass of the cutoffGroup that atom |
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* belongs to. In the case of single atom cutoff groups, the mass |
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* factor for that atom is 1. For massless atoms, the factor is |
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* also 1. |
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*/ |
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vector<RealType> massFactors_; |
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public: |
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vector<RealType> getMassFactors() { return massFactors_; } |
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> |
|
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PairList getExcludedInteractions() { return excludedInteractions_; } |
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PairList getOneTwoInteractions() { return oneTwoInteractions_; } |
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PairList getOneThreeInteractions() { return oneThreeInteractions_; } |
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PairList getOneFourInteractions() { return oneFourInteractions_; } |
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> |
|
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private: |
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> |
|
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|
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/// lists to handle atoms needing special treatment in the non-bonded interactions |
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PairList excludedInteractions_; /**< atoms excluded from interacting with each other */ |
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string statFileName_; |
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string restFileName_; |
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|
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RealType cutoffRadius_; /**< cutoff radius for non-bonded interactions */ |
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RealType switchingRadius_; /**< inner radius of switching function */ |
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RealType listRadius_; /**< Verlet neighbor list radius */ |
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RealType skinThickness_; /**< Verlet neighbor list skin thickness */ |
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CutoffMethod cutoffMethod_; /**< Cutoff Method for most non-bonded interactions */ |
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|
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bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */ |
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> |
bool topologyDone_; /** flag to indicate whether the topology has |
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been scanned and all the relevant |
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bookkeeping has been done*/ |
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|
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bool calcBoxDipole_; /**< flag to indicate whether or not we calculate |
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the simulation box dipole moment */ |
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} |
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|
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private: |
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|
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void setupFortranParallel(); |
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|
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/** |
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* The size of molToProcMap_ is equal to total number of molecules |
