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#include <utility> |
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|
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#include "brains/fSimulation.h" |
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#include "brains/SimInfo.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "types/MoleculeStamp.hpp" |
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#include "utils/PropertyMap.hpp" |
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|
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/** |
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* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
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* @brief |
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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, |
54 |
> |
* cutoff groups, constrains). |
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* Another major change is the index. No matter single version or parallel version, atoms and |
56 |
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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. |
58 |
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*/ |
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class SimInfo { |
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public: |
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SimInfo(); |
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typedef std::map<int, Molecule*>::iterator MoleculeIterator; |
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|
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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 globals |
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* @note |
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*/ |
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SimInfo(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* globals); |
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virtual ~SimInfo(); |
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|
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/** |
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*/ |
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bool removeMolecule(Molecule* mol); |
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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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|
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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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|
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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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/** |
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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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/** |
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* Returns the number of molecules. |
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* @return the number of molecules in this SimInfo |
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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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|
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/** Returns the total number of atoms in this SimInfo */ |
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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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|
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/** Returns the total number of bonds in this SimInfo */ |
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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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|
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/** Returns the total number of bends in this SimInfo */ |
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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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|
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/** Returns the total number of torsions in this SimInfo */ |
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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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|
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/** Returns the total number of rigid bodies in this SimInfo */ |
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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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|
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/** Returns the total number of integrable objects in this SimInfo */ |
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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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|
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/** Returns the total number of cutoff groups in this SimInfo */ |
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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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* @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(std::vector<Molecule*>::iterator& i); |
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Molecule* beginMolecule(MoleculeIterator& i); |
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|
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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(std::vector<Molecule*>::iterator& i); |
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Molecule* nextMolecule(MoleculeIterator& i); |
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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 ndfTrans_; |
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} |
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|
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//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying |
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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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/** |
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* Sets the number of z-constraint molecules in the system. |
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*/ |
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int setNZconstraint(int nZconstraint) { |
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nZconstraint_ = nZconstraint; |
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} |
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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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return forceField_; |
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} |
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|
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/** Sets the force field */ |
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void setForceField(ForceField* ff) { |
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forceField_ = ff; |
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} |
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|
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Globals* getGlobals() { |
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return globals_; |
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} |
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|
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void setGlobals(Globals* globals) { |
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globals_ = globals; |
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} |
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|
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int* getExcludeList() { |
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return exclude_.getExcludeList(); |
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} |
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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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|
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|
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/** Returns the center of the mass of the whole system.*/ |
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Vector3d getCom(); |
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|
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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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|
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/** Sets the seed*/ |
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void setSeed(int seed) { |
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seed_ = seed; |
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} |
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|
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/** main driver function to interact with fortran during the initialization and molecule migration */ |
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void update(); |
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|
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/** Returns the local index manager */ |
240 |
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LocalIndexManager* getLocalIndexManager() { |
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return &localIndexMan_; |
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} |
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|
244 |
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int getMoleculeStampId(int globalIndex) { |
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//assert(globalIndex < molStampIds_.size()) |
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return molStampIds_[globalIndex]; |
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} |
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|
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/** Returns the molecule stamp */ |
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MoleculeStamp* getMoleculeStamp(int id) { |
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return moleculeStamps_[id]; |
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} |
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|
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/** |
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* Finds a molecule with a specified global index |
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* @return a pointer point to found molecule |
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* @param index |
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*/ |
259 |
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Molecule* getMoleculeByGlobalIndex(int index) { |
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std::map<int, Molecule*> i; |
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i = molecules_.find(index); |
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|
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return i != molecules_.end() ? i->second : NULL; |
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} |
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|
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/** Calculate the maximum cutoff radius based on the atom types */ |
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double calcMaxCutoffRadius(); |
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|
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double getRcut() { |
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return rcut_; |
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} |
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|
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double getRsw() { |
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return rsw_; |
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} |
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|
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std::string getFinalConfigFileName() { |
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return finalConfigFileName_; |
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} |
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|
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void setFinalConfigFileName(const std::string& fileName) { |
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finalConfigFileName_ = fileName; |
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} |
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|
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std::string getDumpFileName() { |
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return dumpFileName_; |
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} |
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|
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void setDumpFileName(const std::string& fileName) { |
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dumpFileName_ = fileName; |
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} |
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|
293 |
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std::string getStatFileName() { |
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return statFileName_; |
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} |
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|
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void setStatFileName(const std::string& fileName) { |
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statFileName_ = fileName; |
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} |
300 |
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|
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/** |
302 |
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* Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class |
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* @see #SimCreator::setGlobalIndex |
304 |
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*/ |
305 |
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int* getGlobalGroupMembershipPointer() { |
306 |
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return globalGroupMembership_[0]; |
307 |
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} |
308 |
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|
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/** |
310 |
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* Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class |
311 |
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* @see #SimCreator::setGlobalIndex |
312 |
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*/ |
313 |
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int* getGlobalMolMembershipPointer() { |
314 |
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return globalMolMembership_[0]; |
315 |
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} |
316 |
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|
317 |
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|
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bool isFortranInitialized() { |
319 |
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return fortranInitialized_; |
320 |
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} |
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|
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//below functions are just forward functions |
323 |
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//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
324 |
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//the other hand, has-a relation need composing. |
325 |
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/** |
326 |
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* Adds property into property map |
327 |
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* @param genData GenericData to be added into PropertyMap |
328 |
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*/ |
329 |
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void addProperty(GenericData* genData); |
330 |
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|
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/** |
332 |
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* Removes property from PropertyMap by name |
333 |
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* @param propName the name of property to be removed |
334 |
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*/ |
335 |
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void removeProperty(const std::string& propName); |
336 |
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|
337 |
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/** |
338 |
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* clear all of the properties |
339 |
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*/ |
340 |
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void clearProperties(); |
341 |
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|
342 |
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/** |
343 |
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* Returns all names of properties |
344 |
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* @return all names of properties |
345 |
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*/ |
346 |
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std::vector<std::string> getPropertyNames(); |
347 |
+ |
|
348 |
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/** |
349 |
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* Returns all of the properties in PropertyMap |
350 |
+ |
* @return all of the properties in PropertyMap |
351 |
+ |
*/ |
352 |
+ |
std::vector<GenericData*> getProperties(); |
353 |
+ |
|
354 |
+ |
/** |
355 |
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* Returns property |
356 |
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* @param propName name of property |
357 |
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* @return a pointer point to property with propName. If no property named propName |
358 |
+ |
* exists, return NULL |
359 |
+ |
*/ |
360 |
+ |
GenericData* getPropertyByName(const std::string& propName); |
361 |
+ |
|
362 |
+ |
friend std::ostream& operator <<(ostream& o, SimInfo& info); |
363 |
+ |
|
364 |
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private: |
365 |
|
|
366 |
+ |
|
367 |
+ |
/** Returns the unique atom types of local processor in an array */ |
368 |
+ |
std::set<AtomType*> SimInfo::getUniqueAtomTypes(); |
369 |
+ |
|
370 |
+ |
/** fill up the simtype struct*/ |
371 |
+ |
void setupSimType(); |
372 |
+ |
|
373 |
+ |
/** |
374 |
+ |
* Setup Fortran Simulation |
375 |
+ |
* @see #setupFortranParallel |
376 |
+ |
*/ |
377 |
+ |
void setupFortranSim(); |
378 |
+ |
|
379 |
+ |
/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */ |
380 |
+ |
void setupCutoff(); |
381 |
+ |
|
382 |
+ |
/** Calculates the number of degress of freedom in the whole system */ |
383 |
|
void calcNdf(); |
384 |
|
void calcNdfRaw(); |
385 |
|
void calcNdfTrans(); |
387 |
|
void addExcludePairs(Molecule* mol); |
388 |
|
void removeExcludePairs(Molecule* mol); |
389 |
|
|
390 |
< |
int ndf_; |
391 |
< |
int ndfRaw_; |
392 |
< |
int ndfTrans_; |
390 |
> |
/** |
391 |
> |
* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole |
392 |
> |
* system. |
393 |
> |
*/ |
394 |
> |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
395 |
> |
|
396 |
> |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
397 |
|
|
398 |
< |
int nAtoms_; |
399 |
< |
int nBonds_; |
400 |
< |
int nBends_; |
401 |
< |
int nTorsions_; |
402 |
< |
int nRigidBodies_; |
403 |
< |
int nIntegrableObjects_; |
404 |
< |
int nCutoffGroups_; |
405 |
< |
int nConstraints_; |
398 |
> |
//degress of freedom |
399 |
> |
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
400 |
> |
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
401 |
> |
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
402 |
> |
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
403 |
> |
|
404 |
> |
//number of global objects |
405 |
> |
int nGlobalMols_; /**< number of molecules in the system */ |
406 |
> |
int nGlobalAtoms_; /**< number of atoms in the system */ |
407 |
> |
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
408 |
> |
int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */ |
409 |
|
|
410 |
< |
simtype fInfo_; |
411 |
< |
Exclude exclude_; |
412 |
< |
ForceField* forceField_; |
410 |
> |
/** |
411 |
> |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
412 |
> |
* corresponding content is the global index of cutoff group this atom belong to. |
413 |
> |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
414 |
> |
*/ |
415 |
> |
std::vector<int> globalGroupMembership_; |
416 |
> |
|
417 |
> |
/** |
418 |
> |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
419 |
> |
* corresponding content is the global index of molecule this atom belong to. |
420 |
> |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
421 |
> |
*/ |
422 |
> |
std::vector<int> globalMolMembership_; |
423 |
> |
|
424 |
|
|
425 |
< |
std::vector<Molecule*> molecules_; /**< Molecule array */ |
426 |
< |
PropertyMap properties_; /** Generic Property */ |
427 |
< |
SnapshotManager* sman_; /** SnapshotManager */ |
425 |
> |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
426 |
> |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
427 |
> |
|
428 |
> |
//number of local objects |
429 |
> |
int nAtoms_; /**< number of atoms in local processor */ |
430 |
> |
int nBonds_; /**< number of bonds in local processor */ |
431 |
> |
int nBends_; /**< number of bends in local processor */ |
432 |
> |
int nTorsions_; /**< number of torsions in local processor */ |
433 |
> |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
434 |
> |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
435 |
> |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
436 |
> |
int nConstraints_; /**< number of constraints in local processors */ |
437 |
|
|
438 |
< |
std::vector<std::pair<MoleculeStamp*, int> > moleculeStamps_; |
438 |
> |
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
439 |
> |
Exclude exclude_; |
440 |
> |
ForceField* forceField_; |
441 |
> |
PropertyMap properties_; /**< Generic Property */ |
442 |
> |
SnapshotManager* sman_; /**< SnapshotManager */ |
443 |
|
Globals* globals_; |
444 |
+ |
int seed_; /**< seed for random number generator */ |
445 |
|
|
446 |
< |
int seed_; |
446 |
> |
/** |
447 |
> |
* The reason to have a local index manager is that when molecule is migrating to other processors, |
448 |
> |
* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
449 |
> |
* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager |
450 |
> |
* to make a efficient data moving plan. |
451 |
> |
*/ |
452 |
> |
LocalIndexManager localIndexMan_; |
453 |
> |
|
454 |
> |
//file names |
455 |
> |
std::string finalConfigFileName_; |
456 |
> |
std::string dumpFileName_; |
457 |
> |
std::string statFileName_; |
458 |
> |
|
459 |
> |
double rcut_; /**< cutoff radius*/ |
460 |
> |
double rsw_; /**< radius of switching function*/ |
461 |
> |
|
462 |
> |
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
463 |
> |
|
464 |
> |
#ifdef IS_MPI |
465 |
> |
//in Parallel version, we need MolToProc |
466 |
> |
public: |
467 |
> |
|
468 |
> |
/** |
469 |
> |
* Finds the processor where a molecule resides |
470 |
> |
* @return the id of the processor which contains the molecule |
471 |
> |
* @param globalIndex global Index of the molecule |
472 |
> |
*/ |
473 |
> |
int getMolToProc(int globalIndex) { |
474 |
> |
//assert(globalIndex < molToProcMap_.size()); |
475 |
> |
return molToProcMap_[globalIndex]; |
476 |
> |
} |
477 |
> |
|
478 |
> |
/** |
479 |
> |
* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class |
480 |
> |
* @see #SimCreator::divideMolecules |
481 |
> |
*/ |
482 |
> |
int* getMolToProcMapPointer() { |
483 |
> |
return &molToProcMap_[0]; |
484 |
> |
} |
485 |
> |
|
486 |
> |
private: |
487 |
> |
|
488 |
> |
void setupFortranParallel(); |
489 |
> |
|
490 |
> |
/** |
491 |
> |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
492 |
> |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
493 |
> |
* once. |
494 |
> |
*/ |
495 |
> |
std::vector<int> molToProcMap_; |
496 |
> |
#endif |
497 |
> |
|
498 |
|
}; |
499 |
|
|
500 |
|
} //namespace oopse |