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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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#include "brains/Exclude.hpp" |
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#include "io/Globals.hpp" |
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#include "math/Vector3.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "types/MoleculeStamp.hpp" |
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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 "selection/SelectionManager.hpp" |
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//another nonsense macro declaration |
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#define __C |
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#include "brains/fSimulation.h" |
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namespace oopse{ |
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//forward decalration |
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class SnapshotManager; |
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class Molecule; |
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//forward decalration |
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class SnapshotManager; |
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class Molecule; |
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class SelectionManager; |
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class StuntDouble; |
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/** |
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* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
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* @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules. |
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* The Molecule class maintains all of the concrete objects |
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* (atoms, bond, bend, torsions, rigid bodies, cutoff groups, constrains). |
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* In both the single and parallel versions, atoms and |
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* rigid bodies have both global and local indices. The local index is |
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* not relevant to molecules or cutoff groups. |
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*/ |
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class SimInfo { |
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public: |
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typedef std::map<int, Molecule*>::iterator MoleculeIterator; |
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/** |
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* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
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* @brief As one of the heavy weight class of OOPSE, SimInfo |
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* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules. |
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* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies, |
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* cutoff groups, constrains). |
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* Another major change is the index. No matter single version or parallel version, atoms and |
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* rigid bodies have both global index and local index. Local index is not important to molecule as well as |
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* cutoff group. |
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*/ |
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class SimInfo { |
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public: |
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typedef std::map<int, Molecule*>::iterator MoleculeIterator; |
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/** |
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* Constructor of SimInfo |
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* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the |
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* second element is the total number of molecules with the same molecule stamp in the system |
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* @param ff pointer of a concrete ForceField instance |
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* @param simParams |
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* @note |
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*/ |
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SimInfo(ForceField* ff, Globals* simParams); |
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virtual ~SimInfo(); |
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/** |
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* Constructor of SimInfo |
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* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the |
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* second element is the total number of molecules with the same molecule stamp in the system |
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* @param ff pointer of a concrete ForceField instance |
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* @param simParams |
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* @note |
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*/ |
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SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams); |
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virtual ~SimInfo(); |
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/** |
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* Adds a molecule |
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* @return return true if adding successfully, return false if the molecule is already in SimInfo |
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* @param mol molecule to be added |
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*/ |
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bool addMolecule(Molecule* mol); |
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/** |
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* Adds a molecule |
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* @return return true if adding successfully, return false if the molecule is already in SimInfo |
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* @param mol molecule to be added |
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*/ |
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bool addMolecule(Molecule* mol); |
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/** |
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* Removes a molecule from SimInfo |
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* @return true if removing successfully, return false if molecule is not in this SimInfo |
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*/ |
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bool removeMolecule(Molecule* mol); |
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/** |
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* Removes a molecule from SimInfo |
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* @return true if removing successfully, return false if molecule is not in this SimInfo |
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*/ |
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bool removeMolecule(Molecule* mol); |
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/** Returns the total number of molecules in the system. */ |
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int getNGlobalMolecules() { |
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return nGlobalMols_; |
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} |
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/** Returns the total number of molecules in the system. */ |
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int getNGlobalMolecules() { |
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return nGlobalMols_; |
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} |
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/** Returns the total number of atoms in the system. */ |
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int getNGlobalAtoms() { |
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return nGlobalAtoms_; |
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} |
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/** Returns the total number of atoms in the system. */ |
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int getNGlobalAtoms() { |
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return nGlobalAtoms_; |
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} |
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/** Returns the total number of cutoff groups in the system. */ |
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int getNGlobalCutoffGroups() { |
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return nGlobalCutoffGroups_; |
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} |
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/** Returns the total number of cutoff groups in the system. */ |
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int getNGlobalCutoffGroups() { |
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return nGlobalCutoffGroups_; |
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} |
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/** |
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* Returns the total number of integrable objects (total number of rigid bodies plus the total number |
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* of atoms which do not belong to the rigid bodies) in the system |
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*/ |
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int getNGlobalIntegrableObjects() { |
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return nGlobalIntegrableObjects_; |
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} |
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/** |
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* Returns the total number of integrable objects (total number of rigid bodies plus the total number |
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* of atoms which do not belong to the rigid bodies) in the system |
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*/ |
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int getNGlobalIntegrableObjects() { |
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return nGlobalIntegrableObjects_; |
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} |
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/** |
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* Returns the total number of integrable objects (total number of rigid bodies plus the total number |
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* of atoms which do not belong to the rigid bodies) in the system |
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*/ |
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int getNGlobalRigidBodies() { |
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return nGlobalRigidBodies_; |
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} |
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/** |
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* Returns the total number of integrable objects (total number of rigid bodies plus the total number |
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* of atoms which do not belong to the rigid bodies) in the system |
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*/ |
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int getNGlobalRigidBodies() { |
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return nGlobalRigidBodies_; |
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} |
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int getNGlobalConstraints(); |
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/** |
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* Returns the number of local molecules. |
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* @return the number of local molecules |
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*/ |
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int getNMolecules() { |
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return molecules_.size(); |
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} |
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int getNGlobalConstraints(); |
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/** |
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* Returns the number of local molecules. |
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* @return the number of local molecules |
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*/ |
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int getNMolecules() { |
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return molecules_.size(); |
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} |
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/** Returns the number of local atoms */ |
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unsigned int getNAtoms() { |
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return nAtoms_; |
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} |
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/** Returns the number of local atoms */ |
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unsigned int getNAtoms() { |
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return nAtoms_; |
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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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} |
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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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} |
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/** Returns the number of local bends */ |
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unsigned int getNBends() { |
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return nBends_; |
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} |
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/** Returns the number of local bends */ |
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unsigned int getNBends() { |
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return nBends_; |
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} |
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/** Returns the number of local torsions */ |
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unsigned int getNTorsions() { |
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return nTorsions_; |
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} |
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/** Returns the number of local torsions */ |
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unsigned int getNTorsions() { |
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return nTorsions_; |
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} |
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/** Returns the number of local rigid bodies */ |
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unsigned int getNRigidBodies() { |
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return nRigidBodies_; |
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} |
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/** Returns the number of local rigid bodies */ |
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unsigned int getNRigidBodies() { |
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return nRigidBodies_; |
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} |
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/** Returns the number of local integrable objects */ |
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unsigned int getNIntegrableObjects() { |
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return nIntegrableObjects_; |
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} |
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/** Returns the number of local integrable objects */ |
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unsigned int getNIntegrableObjects() { |
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return nIntegrableObjects_; |
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} |
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/** Returns the number of local cutoff groups */ |
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unsigned int getNCutoffGroups() { |
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return nCutoffGroups_; |
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} |
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/** Returns the number of local cutoff groups */ |
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unsigned int getNCutoffGroups() { |
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return nCutoffGroups_; |
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} |
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/** Returns the total number of constraints in this SimInfo */ |
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unsigned int getNConstraints() { |
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return nConstraints_; |
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} |
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/** Returns the total number of constraints in this SimInfo */ |
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unsigned int getNConstraints() { |
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return nConstraints_; |
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} |
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/** |
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* Returns the first molecule in this SimInfo and intialize the iterator. |
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* @return the first molecule, return NULL if there is not molecule in this SimInfo |
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* @param i the iterator of molecule array (user shouldn't change it) |
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*/ |
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Molecule* beginMolecule(MoleculeIterator& i); |
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/** |
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* Returns the first molecule in this SimInfo and intialize the iterator. |
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* @return the first molecule, return NULL if there is not molecule in this SimInfo |
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* @param i the iterator of molecule array (user shouldn't change it) |
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*/ |
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Molecule* beginMolecule(MoleculeIterator& i); |
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/** |
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* Returns the next avaliable Molecule based on the iterator. |
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* @return the next avaliable molecule, return NULL if reaching the end of the array |
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* @param i the iterator of molecule array |
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*/ |
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Molecule* nextMolecule(MoleculeIterator& i); |
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/** |
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* Returns the next avaliable Molecule based on the iterator. |
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* @return the next avaliable molecule, return NULL if reaching the end of the array |
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* @param i the iterator of molecule array |
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*/ |
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Molecule* nextMolecule(MoleculeIterator& i); |
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/** Returns the number of degrees of freedom */ |
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int getNdf() { |
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return ndf_; |
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} |
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/** Returns the number of degrees of freedom */ |
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int getNdf() { |
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return ndf_ - getFdf(); |
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} |
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/** Returns the number of raw degrees of freedom */ |
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int getNdfRaw() { |
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return ndfRaw_; |
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} |
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/** Returns the number of raw degrees of freedom */ |
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int getNdfRaw() { |
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return ndfRaw_; |
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} |
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/** Returns the number of translational degrees of freedom */ |
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int getNdfTrans() { |
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return ndfTrans_; |
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} |
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/** Returns the number of translational degrees of freedom */ |
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int getNdfTrans() { |
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return ndfTrans_; |
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} |
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//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying |
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/** sets the current number of frozen degrees of freedom */ |
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void setFdf(int fdf) { |
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fdf_local = fdf; |
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} |
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|
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int getFdf(); |
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|
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//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying |
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/** Returns the total number of z-constraint molecules in the system */ |
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int getNZconstraint() { |
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return nZconstraint_; |
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} |
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/** Returns the total number of z-constraint molecules in the system */ |
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int getNZconstraint() { |
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return nZconstraint_; |
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} |
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/** |
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* Sets the number of z-constraint molecules in the system. |
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*/ |
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void setNZconstraint(int nZconstraint) { |
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nZconstraint_ = nZconstraint; |
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} |
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/** |
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* Sets the number of z-constraint molecules in the system. |
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*/ |
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void setNZconstraint(int nZconstraint) { |
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nZconstraint_ = nZconstraint; |
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} |
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/** Returns the snapshot manager. */ |
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SnapshotManager* getSnapshotManager() { |
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return sman_; |
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} |
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/** Returns the snapshot manager. */ |
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SnapshotManager* getSnapshotManager() { |
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return sman_; |
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} |
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/** Sets the snapshot manager. */ |
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void setSnapshotManager(SnapshotManager* sman); |
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/** Sets the snapshot manager. */ |
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void setSnapshotManager(SnapshotManager* sman); |
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/** Returns the force field */ |
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ForceField* getForceField() { |
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return forceField_; |
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} |
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/** Returns the force field */ |
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> |
ForceField* getForceField() { |
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> |
return forceField_; |
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> |
} |
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|
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< |
Globals* getSimParams() { |
| 258 |
< |
return simParams_; |
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< |
} |
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> |
Globals* getSimParams() { |
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> |
return simParams_; |
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> |
} |
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/** Returns the velocity of center of mass of the whole system.*/ |
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Vector3d getComVel(); |
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/** Returns the velocity of center of mass of the whole system.*/ |
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> |
Vector3d getComVel(); |
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/** Returns the center of the mass of the whole system.*/ |
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Vector3d getCom(); |
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> |
/** Returns the center of the mass of the whole system.*/ |
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> |
Vector3d getCom(); |
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> |
/** Returns the center of the mass and Center of Mass velocity of the whole system.*/ |
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> |
void getComAll(Vector3d& com,Vector3d& comVel); |
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| 269 |
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/** Returns the seed (used for random number generator) */ |
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< |
int getSeed() { |
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< |
return seed_; |
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} |
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> |
/** Returns intertia tensor for the entire system and system Angular Momentum.*/ |
| 270 |
> |
void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum); |
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|
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/** Returns system angular momentum */ |
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> |
Vector3d getAngularMomentum(); |
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|
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/** Sets the seed*/ |
| 276 |
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void setSeed(int seed) { |
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< |
seed_ = seed; |
| 278 |
< |
} |
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> |
/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/ |
| 276 |
> |
void getGyrationalVolume(RealType &vol); |
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> |
/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/ |
| 278 |
> |
void getGyrationalVolume(RealType &vol, RealType &detI); |
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> |
/** main driver function to interact with fortran during the initialization and molecule migration */ |
| 280 |
> |
void update(); |
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|
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/** main driver function to interact with fortran during the initialization and molecule migration */ |
| 283 |
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void update(); |
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> |
/** Returns the local index manager */ |
| 283 |
> |
LocalIndexManager* getLocalIndexManager() { |
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> |
return &localIndexMan_; |
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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 getMoleculeStampId(int globalIndex) { |
| 288 |
> |
//assert(globalIndex < molStampIds_.size()) |
| 289 |
> |
return molStampIds_[globalIndex]; |
| 290 |
> |
} |
| 291 |
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|
| 292 |
< |
int getMoleculeStampId(int globalIndex) { |
| 293 |
< |
//assert(globalIndex < molStampIds_.size()) |
| 294 |
< |
return molStampIds_[globalIndex]; |
| 295 |
< |
} |
| 292 |
> |
/** Returns the molecule stamp */ |
| 293 |
> |
MoleculeStamp* getMoleculeStamp(int id) { |
| 294 |
> |
return moleculeStamps_[id]; |
| 295 |
> |
} |
| 296 |
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|
| 297 |
< |
/** Returns the molecule stamp */ |
| 298 |
< |
MoleculeStamp* getMoleculeStamp(int id) { |
| 299 |
< |
return moleculeStamps_[id]; |
| 300 |
< |
} |
| 297 |
> |
/** Return the total number of the molecule stamps */ |
| 298 |
> |
int getNMoleculeStamp() { |
| 299 |
> |
return moleculeStamps_.size(); |
| 300 |
> |
} |
| 301 |
> |
/** |
| 302 |
> |
* Finds a molecule with a specified global index |
| 303 |
> |
* @return a pointer point to found molecule |
| 304 |
> |
* @param index |
| 305 |
> |
*/ |
| 306 |
> |
Molecule* getMoleculeByGlobalIndex(int index) { |
| 307 |
> |
MoleculeIterator i; |
| 308 |
> |
i = molecules_.find(index); |
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|
| 310 |
< |
/** Return the total number of the molecule stamps */ |
| 311 |
< |
int getNMoleculeStamp() { |
| 289 |
< |
return moleculeStamps_.size(); |
| 290 |
< |
} |
| 291 |
< |
/** |
| 292 |
< |
* Finds a molecule with a specified global index |
| 293 |
< |
* @return a pointer point to found molecule |
| 294 |
< |
* @param index |
| 295 |
< |
*/ |
| 296 |
< |
Molecule* getMoleculeByGlobalIndex(int index) { |
| 297 |
< |
MoleculeIterator i; |
| 298 |
< |
i = molecules_.find(index); |
| 310 |
> |
return i != molecules_.end() ? i->second : NULL; |
| 311 |
> |
} |
| 312 |
|
|
| 313 |
< |
return i != molecules_.end() ? i->second : NULL; |
| 314 |
< |
} |
| 313 |
> |
RealType getRcut() { |
| 314 |
> |
return rcut_; |
| 315 |
> |
} |
| 316 |
|
|
| 317 |
< |
/** Calculate the maximum cutoff radius based on the atom types */ |
| 318 |
< |
double calcMaxCutoffRadius(); |
| 317 |
> |
RealType getRsw() { |
| 318 |
> |
return rsw_; |
| 319 |
> |
} |
| 320 |
|
|
| 321 |
< |
double getRcut() { |
| 322 |
< |
return rcut_; |
| 323 |
< |
} |
| 321 |
> |
RealType getList() { |
| 322 |
> |
return rlist_; |
| 323 |
> |
} |
| 324 |
> |
|
| 325 |
> |
std::string getFinalConfigFileName() { |
| 326 |
> |
return finalConfigFileName_; |
| 327 |
> |
} |
| 328 |
|
|
| 329 |
< |
double getRsw() { |
| 330 |
< |
return rsw_; |
| 331 |
< |
} |
| 329 |
> |
void setFinalConfigFileName(const std::string& fileName) { |
| 330 |
> |
finalConfigFileName_ = fileName; |
| 331 |
> |
} |
| 332 |
> |
|
| 333 |
> |
std::string getRawMetaData() { |
| 334 |
> |
return rawMetaData_; |
| 335 |
> |
} |
| 336 |
> |
void setRawMetaData(const std::string& rawMetaData) { |
| 337 |
> |
rawMetaData_ = rawMetaData; |
| 338 |
> |
} |
| 339 |
|
|
| 340 |
< |
std::string getFinalConfigFileName() { |
| 341 |
< |
return finalConfigFileName_; |
| 342 |
< |
} |
| 340 |
> |
std::string getDumpFileName() { |
| 341 |
> |
return dumpFileName_; |
| 342 |
> |
} |
| 343 |
|
|
| 344 |
< |
void setFinalConfigFileName(const std::string& fileName) { |
| 345 |
< |
finalConfigFileName_ = fileName; |
| 346 |
< |
} |
| 344 |
> |
void setDumpFileName(const std::string& fileName) { |
| 345 |
> |
dumpFileName_ = fileName; |
| 346 |
> |
} |
| 347 |
|
|
| 348 |
< |
std::string getDumpFileName() { |
| 349 |
< |
return dumpFileName_; |
| 350 |
< |
} |
| 348 |
> |
std::string getStatFileName() { |
| 349 |
> |
return statFileName_; |
| 350 |
> |
} |
| 351 |
|
|
| 352 |
< |
void setDumpFileName(const std::string& fileName) { |
| 353 |
< |
dumpFileName_ = fileName; |
| 354 |
< |
} |
| 329 |
< |
|
| 330 |
< |
std::string getStatFileName() { |
| 331 |
< |
return statFileName_; |
| 332 |
< |
} |
| 352 |
> |
void setStatFileName(const std::string& fileName) { |
| 353 |
> |
statFileName_ = fileName; |
| 354 |
> |
} |
| 355 |
|
|
| 356 |
< |
void setStatFileName(const std::string& fileName) { |
| 357 |
< |
statFileName_ = fileName; |
| 358 |
< |
} |
| 356 |
> |
std::string getRestFileName() { |
| 357 |
> |
return restFileName_; |
| 358 |
> |
} |
| 359 |
> |
|
| 360 |
> |
void setRestFileName(const std::string& fileName) { |
| 361 |
> |
restFileName_ = fileName; |
| 362 |
> |
} |
| 363 |
|
|
| 364 |
< |
/** |
| 365 |
< |
* Sets GlobalGroupMembership |
| 366 |
< |
* @see #SimCreator::setGlobalIndex |
| 367 |
< |
*/ |
| 368 |
< |
void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) { |
| 369 |
< |
assert(globalGroupMembership.size() == nGlobalAtoms_); |
| 370 |
< |
globalGroupMembership_ = globalGroupMembership; |
| 371 |
< |
} |
| 364 |
> |
/** |
| 365 |
> |
* Sets GlobalGroupMembership |
| 366 |
> |
* @see #SimCreator::setGlobalIndex |
| 367 |
> |
*/ |
| 368 |
> |
void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) { |
| 369 |
> |
assert(globalGroupMembership.size() == nGlobalAtoms_); |
| 370 |
> |
globalGroupMembership_ = globalGroupMembership; |
| 371 |
> |
} |
| 372 |
|
|
| 373 |
< |
/** |
| 374 |
< |
* Sets GlobalMolMembership |
| 375 |
< |
* @see #SimCreator::setGlobalIndex |
| 376 |
< |
*/ |
| 377 |
< |
void setGlobalMolMembership(const std::vector<int>& globalMolMembership) { |
| 378 |
< |
assert(globalMolMembership.size() == nGlobalAtoms_); |
| 379 |
< |
globalMolMembership_ = globalMolMembership; |
| 380 |
< |
} |
| 373 |
> |
/** |
| 374 |
> |
* Sets GlobalMolMembership |
| 375 |
> |
* @see #SimCreator::setGlobalIndex |
| 376 |
> |
*/ |
| 377 |
> |
void setGlobalMolMembership(const std::vector<int>& globalMolMembership) { |
| 378 |
> |
assert(globalMolMembership.size() == nGlobalAtoms_); |
| 379 |
> |
globalMolMembership_ = globalMolMembership; |
| 380 |
> |
} |
| 381 |
|
|
| 382 |
|
|
| 383 |
< |
bool isFortranInitialized() { |
| 384 |
< |
return fortranInitialized_; |
| 385 |
< |
} |
| 383 |
> |
bool isFortranInitialized() { |
| 384 |
> |
return fortranInitialized_; |
| 385 |
> |
} |
| 386 |
|
|
| 387 |
< |
//below functions are just forward functions |
| 388 |
< |
//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
| 389 |
< |
//the other hand, has-a relation need composing. |
| 364 |
< |
/** |
| 365 |
< |
* Adds property into property map |
| 366 |
< |
* @param genData GenericData to be added into PropertyMap |
| 367 |
< |
*/ |
| 368 |
< |
void addProperty(GenericData* genData); |
| 387 |
> |
bool getCalcBoxDipole() { |
| 388 |
> |
return calcBoxDipole_; |
| 389 |
> |
} |
| 390 |
|
|
| 391 |
< |
/** |
| 392 |
< |
* Removes property from PropertyMap by name |
| 393 |
< |
* @param propName the name of property to be removed |
| 394 |
< |
*/ |
| 395 |
< |
void removeProperty(const std::string& propName); |
| 391 |
> |
//below functions are just forward functions |
| 392 |
> |
//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
| 393 |
> |
//the other hand, has-a relation need composing. |
| 394 |
> |
/** |
| 395 |
> |
* Adds property into property map |
| 396 |
> |
* @param genData GenericData to be added into PropertyMap |
| 397 |
> |
*/ |
| 398 |
> |
void addProperty(GenericData* genData); |
| 399 |
|
|
| 400 |
< |
/** |
| 401 |
< |
* clear all of the properties |
| 402 |
< |
*/ |
| 403 |
< |
void clearProperties(); |
| 400 |
> |
/** |
| 401 |
> |
* Removes property from PropertyMap by name |
| 402 |
> |
* @param propName the name of property to be removed |
| 403 |
> |
*/ |
| 404 |
> |
void removeProperty(const std::string& propName); |
| 405 |
|
|
| 406 |
< |
/** |
| 407 |
< |
* Returns all names of properties |
| 408 |
< |
* @return all names of properties |
| 409 |
< |
*/ |
| 385 |
< |
std::vector<std::string> getPropertyNames(); |
| 406 |
> |
/** |
| 407 |
> |
* clear all of the properties |
| 408 |
> |
*/ |
| 409 |
> |
void clearProperties(); |
| 410 |
|
|
| 411 |
< |
/** |
| 412 |
< |
* Returns all of the properties in PropertyMap |
| 413 |
< |
* @return all of the properties in PropertyMap |
| 414 |
< |
*/ |
| 415 |
< |
std::vector<GenericData*> getProperties(); |
| 411 |
> |
/** |
| 412 |
> |
* Returns all names of properties |
| 413 |
> |
* @return all names of properties |
| 414 |
> |
*/ |
| 415 |
> |
std::vector<std::string> getPropertyNames(); |
| 416 |
|
|
| 417 |
< |
/** |
| 418 |
< |
* Returns property |
| 419 |
< |
* @param propName name of property |
| 420 |
< |
* @return a pointer point to property with propName. If no property named propName |
| 421 |
< |
* exists, return NULL |
| 398 |
< |
*/ |
| 399 |
< |
GenericData* getPropertyByName(const std::string& propName); |
| 417 |
> |
/** |
| 418 |
> |
* Returns all of the properties in PropertyMap |
| 419 |
> |
* @return all of the properties in PropertyMap |
| 420 |
> |
*/ |
| 421 |
> |
std::vector<GenericData*> getProperties(); |
| 422 |
|
|
| 423 |
< |
/** |
| 424 |
< |
* add all exclude pairs of a molecule into exclude list. |
| 425 |
< |
*/ |
| 426 |
< |
void addExcludePairs(Molecule* mol); |
| 423 |
> |
/** |
| 424 |
> |
* Returns property |
| 425 |
> |
* @param propName name of property |
| 426 |
> |
* @return a pointer point to property with propName. If no property named propName |
| 427 |
> |
* exists, return NULL |
| 428 |
> |
*/ |
| 429 |
> |
GenericData* getPropertyByName(const std::string& propName); |
| 430 |
|
|
| 431 |
< |
/** |
| 432 |
< |
* remove all exclude pairs which belong to a molecule from exclude list |
| 433 |
< |
*/ |
| 431 |
> |
/** |
| 432 |
> |
* add all exclude pairs of a molecule into exclude list. |
| 433 |
> |
*/ |
| 434 |
> |
void addExcludePairs(Molecule* mol); |
| 435 |
|
|
| 436 |
< |
void removeExcludePairs(Molecule* mol); |
| 436 |
> |
/** |
| 437 |
> |
* remove all exclude pairs which belong to a molecule from exclude list |
| 438 |
> |
*/ |
| 439 |
|
|
| 440 |
+ |
void removeExcludePairs(Molecule* mol); |
| 441 |
|
|
| 442 |
< |
SelectionManager* getSelectionManager() { |
| 443 |
< |
return selectMan_; |
| 444 |
< |
} |
| 442 |
> |
|
| 443 |
> |
/** Returns the unique atom types of local processor in an array */ |
| 444 |
> |
std::set<AtomType*> getUniqueAtomTypes(); |
| 445 |
|
|
| 446 |
< |
friend std::ostream& operator <<(std::ostream& o, SimInfo& info); |
| 418 |
< |
|
| 419 |
< |
private: |
| 446 |
> |
friend std::ostream& operator <<(std::ostream& o, SimInfo& info); |
| 447 |
|
|
| 448 |
+ |
void getCutoff(RealType& rcut, RealType& rsw); |
| 449 |
|
|
| 450 |
< |
/** Returns the unique atom types of local processor in an array */ |
| 423 |
< |
std::set<AtomType*> getUniqueAtomTypes(); |
| 450 |
> |
private: |
| 451 |
|
|
| 452 |
< |
/** fill up the simtype struct*/ |
| 453 |
< |
void setupSimType(); |
| 452 |
> |
/** fill up the simtype struct*/ |
| 453 |
> |
void setupSimType(); |
| 454 |
|
|
| 455 |
< |
/** |
| 456 |
< |
* Setup Fortran Simulation |
| 457 |
< |
* @see #setupFortranParallel |
| 458 |
< |
*/ |
| 459 |
< |
void setupFortranSim(); |
| 455 |
> |
/** |
| 456 |
> |
* Setup Fortran Simulation |
| 457 |
> |
* @see #setupFortranParallel |
| 458 |
> |
*/ |
| 459 |
> |
void setupFortranSim(); |
| 460 |
|
|
| 461 |
< |
/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */ |
| 462 |
< |
void setupCutoff(); |
| 461 |
> |
/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */ |
| 462 |
> |
void setupCutoff(); |
| 463 |
|
|
| 464 |
< |
/** Calculates the number of degress of freedom in the whole system */ |
| 465 |
< |
void calcNdf(); |
| 439 |
< |
void calcNdfRaw(); |
| 440 |
< |
void calcNdfTrans(); |
| 464 |
> |
/** Figure out which coulombic correction method to use and pass to fortran */ |
| 465 |
> |
void setupElectrostaticSummationMethod( int isError ); |
| 466 |
|
|
| 467 |
< |
/** |
| 468 |
< |
* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole |
| 444 |
< |
* system. |
| 445 |
< |
*/ |
| 446 |
< |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
| 467 |
> |
/** Figure out which polynomial type to use for the switching function */ |
| 468 |
> |
void setupSwitchingFunction(); |
| 469 |
|
|
| 470 |
< |
ForceField* forceField_; |
| 471 |
< |
Globals* simParams_; |
| 470 |
> |
/** Determine if we need to accumulate the simulation box dipole */ |
| 471 |
> |
void setupAccumulateBoxDipole(); |
| 472 |
|
|
| 473 |
< |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
| 473 |
> |
/** Calculates the number of degress of freedom in the whole system */ |
| 474 |
> |
void calcNdf(); |
| 475 |
> |
void calcNdfRaw(); |
| 476 |
> |
void calcNdfTrans(); |
| 477 |
> |
|
| 478 |
> |
ForceField* forceField_; |
| 479 |
> |
Globals* simParams_; |
| 480 |
> |
|
| 481 |
> |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
| 482 |
> |
|
| 483 |
> |
/** |
| 484 |
> |
* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole |
| 485 |
> |
* system. |
| 486 |
> |
*/ |
| 487 |
> |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
| 488 |
|
|
| 489 |
< |
//degress of freedom |
| 490 |
< |
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
| 491 |
< |
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
| 492 |
< |
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
| 493 |
< |
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
| 489 |
> |
//degress of freedom |
| 490 |
> |
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
| 491 |
> |
int fdf_local; /**< number of frozen degrees of freedom */ |
| 492 |
> |
int fdf_; /**< number of frozen degrees of freedom */ |
| 493 |
> |
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
| 494 |
> |
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
| 495 |
> |
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
| 496 |
|
|
| 497 |
< |
//number of global objects |
| 498 |
< |
int nGlobalMols_; /**< number of molecules in the system */ |
| 499 |
< |
int nGlobalAtoms_; /**< number of atoms in the system */ |
| 500 |
< |
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
| 501 |
< |
int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */ |
| 502 |
< |
int nGlobalRigidBodies_; /**< number of rigid bodies in this system */ |
| 503 |
< |
/** |
| 504 |
< |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 505 |
< |
* corresponding content is the global index of cutoff group this atom belong to. |
| 506 |
< |
* It is filled by SimCreator once and only once, since it never changed during the simulation. |
| 507 |
< |
*/ |
| 508 |
< |
std::vector<int> globalGroupMembership_; |
| 497 |
> |
//number of global objects |
| 498 |
> |
int nGlobalMols_; /**< number of molecules in the system */ |
| 499 |
> |
int nGlobalAtoms_; /**< number of atoms in the system */ |
| 500 |
> |
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
| 501 |
> |
int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */ |
| 502 |
> |
int nGlobalRigidBodies_; /**< number of rigid bodies in this system */ |
| 503 |
> |
/** |
| 504 |
> |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 505 |
> |
* corresponding content is the global index of cutoff group this atom belong to. |
| 506 |
> |
* It is filled by SimCreator once and only once, since it never changed during the simulation. |
| 507 |
> |
*/ |
| 508 |
> |
std::vector<int> globalGroupMembership_; |
| 509 |
|
|
| 510 |
< |
/** |
| 511 |
< |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 512 |
< |
* corresponding content is the global index of molecule this atom belong to. |
| 513 |
< |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
| 514 |
< |
*/ |
| 515 |
< |
std::vector<int> globalMolMembership_; |
| 510 |
> |
/** |
| 511 |
> |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 512 |
> |
* corresponding content is the global index of molecule this atom belong to. |
| 513 |
> |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
| 514 |
> |
*/ |
| 515 |
> |
std::vector<int> globalMolMembership_; |
| 516 |
|
|
| 517 |
|
|
| 518 |
< |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
| 519 |
< |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
| 518 |
> |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
| 519 |
> |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
| 520 |
|
|
| 521 |
< |
//number of local objects |
| 522 |
< |
int nAtoms_; /**< number of atoms in local processor */ |
| 523 |
< |
int nBonds_; /**< number of bonds in local processor */ |
| 524 |
< |
int nBends_; /**< number of bends in local processor */ |
| 525 |
< |
int nTorsions_; /**< number of torsions in local processor */ |
| 526 |
< |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
| 527 |
< |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
| 528 |
< |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
| 529 |
< |
int nConstraints_; /**< number of constraints in local processors */ |
| 521 |
> |
//number of local objects |
| 522 |
> |
int nAtoms_; /**< number of atoms in local processor */ |
| 523 |
> |
int nBonds_; /**< number of bonds in local processor */ |
| 524 |
> |
int nBends_; /**< number of bends in local processor */ |
| 525 |
> |
int nTorsions_; /**< number of torsions in local processor */ |
| 526 |
> |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
| 527 |
> |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
| 528 |
> |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
| 529 |
> |
int nConstraints_; /**< number of constraints in local processors */ |
| 530 |
|
|
| 531 |
< |
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
| 532 |
< |
Exclude exclude_; |
| 533 |
< |
PropertyMap properties_; /**< Generic Property */ |
| 534 |
< |
SnapshotManager* sman_; /**< SnapshotManager */ |
| 531 |
> |
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
| 532 |
> |
Exclude exclude_; |
| 533 |
> |
PropertyMap properties_; /**< Generic Property */ |
| 534 |
> |
SnapshotManager* sman_; /**< SnapshotManager */ |
| 535 |
|
|
| 536 |
< |
int seed_; /**< seed for random number generator */ |
| 536 |
> |
/** |
| 537 |
> |
* The reason to have a local index manager is that when molecule is migrating to other processors, |
| 538 |
> |
* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
| 539 |
> |
* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager |
| 540 |
> |
* to make a efficient data moving plan. |
| 541 |
> |
*/ |
| 542 |
> |
LocalIndexManager localIndexMan_; |
| 543 |
|
|
| 544 |
< |
/** |
| 545 |
< |
* The reason to have a local index manager is that when molecule is migrating to other processors, |
| 502 |
< |
* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
| 503 |
< |
* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager |
| 504 |
< |
* to make a efficient data moving plan. |
| 505 |
< |
*/ |
| 506 |
< |
LocalIndexManager localIndexMan_; |
| 544 |
> |
// unparsed MetaData block for storing in Dump and EOR files: |
| 545 |
> |
std::string rawMetaData_; |
| 546 |
|
|
| 547 |
< |
//file names |
| 548 |
< |
std::string finalConfigFileName_; |
| 549 |
< |
std::string dumpFileName_; |
| 550 |
< |
std::string statFileName_; |
| 547 |
> |
//file names |
| 548 |
> |
std::string finalConfigFileName_; |
| 549 |
> |
std::string dumpFileName_; |
| 550 |
> |
std::string statFileName_; |
| 551 |
> |
std::string restFileName_; |
| 552 |
> |
|
| 553 |
> |
RealType rcut_; /**< cutoff radius*/ |
| 554 |
> |
RealType rsw_; /**< radius of switching function*/ |
| 555 |
> |
RealType rlist_; /**< neighbor list radius */ |
| 556 |
|
|
| 557 |
< |
double rcut_; /**< cutoff radius*/ |
| 514 |
< |
double rsw_; /**< radius of switching function*/ |
| 557 |
> |
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
| 558 |
|
|
| 559 |
< |
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
| 559 |
> |
bool calcBoxDipole_; /**< flag to indicate whether or not we calculate the simulation box dipole moment */ |
| 560 |
|
|
| 561 |
< |
SelectionManager* selectMan_; |
| 561 |
> |
public: |
| 562 |
> |
/** |
| 563 |
> |
* return an integral objects by its global index. In MPI version, if the StuntDouble with specified |
| 564 |
> |
* global index does not belong to local processor, a NULL will be return. |
| 565 |
> |
*/ |
| 566 |
> |
StuntDouble* getIOIndexToIntegrableObject(int index); |
| 567 |
> |
void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v); |
| 568 |
> |
private: |
| 569 |
> |
std::vector<StuntDouble*> IOIndexToIntegrableObject; |
| 570 |
> |
//public: |
| 571 |
> |
//void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v); |
| 572 |
> |
/** |
| 573 |
> |
* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified |
| 574 |
> |
* global index does not belong to local processor, a NULL will be return. |
| 575 |
> |
*/ |
| 576 |
> |
//StuntDouble* getStuntDoubleFromGlobalIndex(int index); |
| 577 |
> |
//private: |
| 578 |
> |
//std::vector<StuntDouble*> sdByGlobalIndex_; |
| 579 |
> |
|
| 580 |
|
#ifdef IS_MPI |
| 581 |
|
//in Parallel version, we need MolToProc |
| 582 |
< |
public: |
| 582 |
> |
public: |
| 583 |
|
|
| 584 |
< |
/** |
| 585 |
< |
* Finds the processor where a molecule resides |
| 586 |
< |
* @return the id of the processor which contains the molecule |
| 587 |
< |
* @param globalIndex global Index of the molecule |
| 588 |
< |
*/ |
| 589 |
< |
int getMolToProc(int globalIndex) { |
| 590 |
< |
//assert(globalIndex < molToProcMap_.size()); |
| 591 |
< |
return molToProcMap_[globalIndex]; |
| 592 |
< |
} |
| 584 |
> |
/** |
| 585 |
> |
* Finds the processor where a molecule resides |
| 586 |
> |
* @return the id of the processor which contains the molecule |
| 587 |
> |
* @param globalIndex global Index of the molecule |
| 588 |
> |
*/ |
| 589 |
> |
int getMolToProc(int globalIndex) { |
| 590 |
> |
//assert(globalIndex < molToProcMap_.size()); |
| 591 |
> |
return molToProcMap_[globalIndex]; |
| 592 |
> |
} |
| 593 |
|
|
| 594 |
< |
/** |
| 595 |
< |
* Set MolToProcMap array |
| 596 |
< |
* @see #SimCreator::divideMolecules |
| 597 |
< |
*/ |
| 598 |
< |
void setMolToProcMap(const std::vector<int>& molToProcMap) { |
| 599 |
< |
molToProcMap_ = molToProcMap; |
| 600 |
< |
} |
| 594 |
> |
/** |
| 595 |
> |
* Set MolToProcMap array |
| 596 |
> |
* @see #SimCreator::divideMolecules |
| 597 |
> |
*/ |
| 598 |
> |
void setMolToProcMap(const std::vector<int>& molToProcMap) { |
| 599 |
> |
molToProcMap_ = molToProcMap; |
| 600 |
> |
} |
| 601 |
> |
|
| 602 |
> |
|
| 603 |
|
|
| 604 |
< |
private: |
| 604 |
> |
private: |
| 605 |
|
|
| 606 |
< |
void setupFortranParallel(); |
| 606 |
> |
void setupFortranParallel(); |
| 607 |
|
|
| 608 |
< |
/** |
| 609 |
< |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
| 610 |
< |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
| 611 |
< |
* once. |
| 612 |
< |
*/ |
| 613 |
< |
std::vector<int> molToProcMap_; |
| 608 |
> |
/** |
| 609 |
> |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
| 610 |
> |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
| 611 |
> |
* once. |
| 612 |
> |
*/ |
| 613 |
> |
std::vector<int> molToProcMap_; |
| 614 |
|
|
| 615 |
|
#endif |
| 616 |
|
|
| 617 |
< |
}; |
| 617 |
> |
}; |
| 618 |
|
|
| 619 |
|
} //namespace oopse |
| 620 |
|
#endif //BRAINS_SIMMODEL_HPP |
