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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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class SnapshotManager; |
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class Molecule; |
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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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* Setup Fortran Simulation |
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*/ |
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void setupFortran(); |
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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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|
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int getGlobalMolMembership(int id){ |
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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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RealType getSwitchingRadius() { |
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return switchingRadius_; |
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} |
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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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void removeInteractionPairs(Molecule* mol); |
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|
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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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|
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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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/** fill up the simtype struct and other simulation-related variables */ |
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void setupSimVariables(); |
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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 and cutoff method */ |
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void setupCutoffs(); |
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/** Figure out the switching radius and polynomial type for the switching function */ |
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void setupSwitching(); |
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/** Figure out the simulation variables associated with electrostatics */ |
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void setupElectrostatics(); |
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/** Figure out the neighbor list skin thickness */ |
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void setupNeighborlists(); |
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|
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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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|
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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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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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* 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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vector<int> getIdentArray() { return identArray_; } |
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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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SwitchingFunctionType sft_; /**< Type of switching function in use */ |
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|
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bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */ |
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|
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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 |
