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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* |
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* Contact: oopse@oopse.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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|
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/** |
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* @file SimInfo.hpp |
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* @author tlin |
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* @date 11/02/2004 |
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* @version 1.0 |
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*/ |
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|
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#ifndef BRAINS_SIMMODEL_HPP |
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#define BRAINS_SIMMODEL_HPP |
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|
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#include <iostream> |
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#include <vector> |
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#include <utility> |
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|
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#include "brains/fSimulation.h" |
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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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#include "io/Globals.hpp" |
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|
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namespace oopse{ |
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|
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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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/** |
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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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* 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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/** |
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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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/** 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 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 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 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 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 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 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 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 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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|
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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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/** |
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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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/** |
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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 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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|
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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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|
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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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|
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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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} |
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|
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/** Sets the snapshot manager. */ |
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void setSnapshotManager(SnapshotManager* sman) { |
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sman_ = sman; |
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} |
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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* getGlobals() { |
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return globals_; |
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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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/** 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 */ |
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LocalIndexManager* getLocalIndexManager() { |
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return &localIndexMan_; |
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} |
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|
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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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*/ |
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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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|
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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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} |
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|
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/** |
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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 |
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*/ |
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int* getGlobalGroupMembershipPointer() { |
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return globalGroupMembership_[0]; |
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} |
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|
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/** |
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* Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class |
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* @see #SimCreator::setGlobalIndex |
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*/ |
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int* getGlobalMolMembershipPointer() { |
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return globalMolMembership_[0]; |
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} |
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|
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|
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bool isFortranInitialized() { |
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return fortranInitialized_; |
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} |
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|
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//below functions are just forward functions |
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//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
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//the other hand, has-a relation need composing. |
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/** |
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* Adds property into property map |
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* @param genData GenericData to be added into PropertyMap |
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*/ |
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void addProperty(GenericData* genData); |
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|
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/** |
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* Removes property from PropertyMap by name |
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* @param propName the name of property to be removed |
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*/ |
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void removeProperty(const std::string& propName); |
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|
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/** |
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* clear all of the properties |
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*/ |
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void clearProperties(); |
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|
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/** |
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* Returns all names of properties |
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* @return all names of properties |
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*/ |
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std::vector<std::string> getPropertyNames(); |
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|
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/** |
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* Returns all of the properties in PropertyMap |
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* @return all of the properties in PropertyMap |
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*/ |
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std::vector<GenericData*> getProperties(); |
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|
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/** |
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* Returns property |
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* @param propName name of property |
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* @return a pointer point to property with propName. If no property named propName |
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* exists, return NULL |
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*/ |
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GenericData* getPropertyByName(const std::string& propName); |
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|
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friend std::ostream& operator <<(ostream& o, SimInfo& info); |
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|
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private: |
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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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std::set<AtomType*> SimInfo::getUniqueAtomTypes(); |
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|
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/** fill up the simtype struct*/ |
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void setupSimType(); |
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|
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/** |
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* Setup Fortran Simulation |
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* @see #setupFortranParallel |
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*/ |
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void setupFortranSim(); |
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|
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/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */ |
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void setupCutoff(); |
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|
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/** Calculates the number of degress of freedom in the whole system */ |
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void calcNdf(); |
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void calcNdfRaw(); |
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void calcNdfTrans(); |
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|
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void addExcludePairs(Molecule* mol); |
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void removeExcludePairs(Molecule* mol); |
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|
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/** |
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* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole |
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* system. |
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*/ |
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void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
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|
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std::map<int, Molecule*> molecules_; /**< Molecule array */ |
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|
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//degress of freedom |
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int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
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int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
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int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
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int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
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|
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//number of global objects |
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int nGlobalMols_; /**< number of molecules in the system */ |
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int nGlobalAtoms_; /**< number of atoms in the system */ |
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int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
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|
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/** |
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* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
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* corresponding content is the global index of cutoff group this atom belong to. |
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* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
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*/ |
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std::vector<int> globalGroupMembership_; |
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|
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/** |
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* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
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* corresponding content is the global index of molecule this atom belong to. |
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* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
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*/ |
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std::vector<int> globalMolMembership_; |
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|
414 |
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|
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std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
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std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
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|
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//number of local objects |
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int nAtoms_; /**< number of atoms in local processor */ |
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int nBonds_; /**< number of bonds in local processor */ |
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int nBends_; /**< number of bends in local processor */ |
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int nTorsions_; /**< number of torsions in local processor */ |
423 |
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int nRigidBodies_; /**< number of rigid bodies in local processor */ |
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int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
425 |
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int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
426 |
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int nConstraints_; /**< number of constraints in local processors */ |
427 |
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|
428 |
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simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
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Exclude exclude_; |
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ForceField* forceField_; |
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PropertyMap properties_; /**< Generic Property */ |
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SnapshotManager* sman_; /**< SnapshotManager */ |
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Globals* globals_; |
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int seed_; /**< seed for random number generator */ |
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|
436 |
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/** |
437 |
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* The reason to have a local index manager is that when molecule is migrating to other processors, |
438 |
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* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
439 |
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* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager |
440 |
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* to make a efficient data moving plan. |
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*/ |
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LocalIndexManager localIndexMan_; |
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|
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//file names |
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std::string finalConfigFileName_; |
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std::string dumpFileName_; |
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std::string statFileName_; |
448 |
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|
449 |
< |
double rcut_; /**< cutoff radius*/ |
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double rsw_; /**< radius of switching function*/ |
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< |
|
452 |
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bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
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< |
|
454 |
< |
#ifdef IS_MPI |
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//in Parallel version, we need MolToProc |
456 |
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public: |
457 |
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|
458 |
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/** |
459 |
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* Finds the processor where a molecule resides |
460 |
< |
* @return the id of the processor which contains the molecule |
461 |
< |
* @param globalIndex global Index of the molecule |
462 |
< |
*/ |
463 |
< |
int getMolToProc(int globalIndex) { |
464 |
< |
//assert(globalIndex < molToProcMap_.size()); |
465 |
< |
return molToProcMap_[globalIndex]; |
466 |
< |
} |
467 |
< |
|
468 |
< |
/** |
469 |
< |
* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class |
470 |
< |
* @see #SimCreator::divideMolecules |
471 |
< |
*/ |
472 |
< |
int* getMolToProcMapPointer() { |
473 |
< |
return &molToProcMap_[0]; |
474 |
< |
} |
475 |
< |
|
476 |
< |
private: |
477 |
< |
|
478 |
< |
void setupFortranParallel(); |
479 |
< |
|
480 |
< |
/** |
481 |
< |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
482 |
< |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
483 |
< |
* once. |
484 |
< |
*/ |
485 |
< |
std::vector<int> molToProcMap_; |
486 |
< |
#endif |
487 |
< |
|
488 |
< |
}; |
489 |
< |
|
490 |
< |
} //namespace oopse |
491 |
< |
#endif //BRAINS_SIMMODEL_HPP |
1 |
> |
/* |
2 |
> |
* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
3 |
> |
* |
4 |
> |
* Contact: oopse@oopse.org |
5 |
> |
* |
6 |
> |
* This program is free software; you can redistribute it and/or |
7 |
> |
* modify it under the terms of the GNU Lesser General Public License |
8 |
> |
* as published by the Free Software Foundation; either version 2.1 |
9 |
> |
* of the License, or (at your option) any later version. |
10 |
> |
* All we ask is that proper credit is given for our work, which includes |
11 |
> |
* - but is not limited to - adding the above copyright notice to the beginning |
12 |
> |
* of your source code files, and to any copyright notice that you may distribute |
13 |
> |
* with programs based on this work. |
14 |
> |
* |
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> |
* This program is distributed in the hope that it will be useful, |
16 |
> |
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
17 |
> |
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
18 |
> |
* GNU Lesser General Public License for more details. |
19 |
> |
* |
20 |
> |
* You should have received a copy of the GNU Lesser General Public License |
21 |
> |
* along with this program; if not, write to the Free Software |
22 |
> |
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
23 |
> |
* |
24 |
> |
*/ |
25 |
> |
|
26 |
> |
/** |
27 |
> |
* @file SimInfo.hpp |
28 |
> |
* @author tlin |
29 |
> |
* @date 11/02/2004 |
30 |
> |
* @version 1.0 |
31 |
> |
*/ |
32 |
> |
|
33 |
> |
#ifndef BRAINS_SIMMODEL_HPP |
34 |
> |
#define BRAINS_SIMMODEL_HPP |
35 |
> |
|
36 |
> |
#include <iostream> |
37 |
> |
#include <set> |
38 |
> |
#include <utility> |
39 |
> |
#include <vector> |
40 |
> |
|
41 |
> |
#include "brains/Exclude.hpp" |
42 |
> |
#include "io/Globals.hpp" |
43 |
> |
#include "math/Vector3.hpp" |
44 |
> |
#include "types/MoleculeStamp.hpp" |
45 |
> |
#include "UseTheForce/ForceField.hpp" |
46 |
> |
#include "utils/PropertyMap.hpp" |
47 |
> |
#include "utils/LocalIndexManager.hpp" |
48 |
> |
|
49 |
> |
//another nonsense macro declaration |
50 |
> |
#define __C |
51 |
> |
#include "brains/fSimulation.h" |
52 |
> |
|
53 |
> |
namespace oopse{ |
54 |
> |
|
55 |
> |
//forward decalration |
56 |
> |
class SnapshotManager; |
57 |
> |
class Molecule; |
58 |
> |
|
59 |
> |
/** |
60 |
> |
* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
61 |
> |
* @brief As one of the heavy weight class of OOPSE, SimInfo |
62 |
> |
* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules. |
63 |
> |
* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies, |
64 |
> |
* cutoff groups, constrains). |
65 |
> |
* Another major change is the index. No matter single version or parallel version, atoms and |
66 |
> |
* rigid bodies have both global index and local index. Local index is not important to molecule as well as |
67 |
> |
* cutoff group. |
68 |
> |
*/ |
69 |
> |
class SimInfo { |
70 |
> |
public: |
71 |
> |
typedef std::map<int, Molecule*>::iterator MoleculeIterator; |
72 |
> |
|
73 |
> |
/** |
74 |
> |
* Constructor of SimInfo |
75 |
> |
* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the |
76 |
> |
* second element is the total number of molecules with the same molecule stamp in the system |
77 |
> |
* @param ff pointer of a concrete ForceField instance |
78 |
> |
* @param globals |
79 |
> |
* @note |
80 |
> |
*/ |
81 |
> |
SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* globals); |
82 |
> |
virtual ~SimInfo(); |
83 |
> |
|
84 |
> |
/** |
85 |
> |
* Adds a molecule |
86 |
> |
* @return return true if adding successfully, return false if the molecule is already in SimInfo |
87 |
> |
* @param mol molecule to be added |
88 |
> |
*/ |
89 |
> |
bool addMolecule(Molecule* mol); |
90 |
> |
|
91 |
> |
/** |
92 |
> |
* Removes a molecule from SimInfo |
93 |
> |
* @return true if removing successfully, return false if molecule is not in this SimInfo |
94 |
> |
*/ |
95 |
> |
bool removeMolecule(Molecule* mol); |
96 |
> |
|
97 |
> |
/** Returns the total number of molecules in the system. */ |
98 |
> |
int getNGlobalMolecules() { |
99 |
> |
return nGlobalMols_; |
100 |
> |
} |
101 |
> |
|
102 |
> |
/** Returns the total number of atoms in the system. */ |
103 |
> |
int getNGlobalAtoms() { |
104 |
> |
return nGlobalAtoms_; |
105 |
> |
} |
106 |
> |
|
107 |
> |
/** Returns the total number of cutoff groups in the system. */ |
108 |
> |
int getNGlobalCutoffGroups() { |
109 |
> |
return nGlobalCutoffGroups_; |
110 |
> |
} |
111 |
> |
|
112 |
> |
/** |
113 |
> |
* Returns the total number of integrable objects (total number of rigid bodies plus the total number |
114 |
> |
* of atoms which do not belong to the rigid bodies) in the system |
115 |
> |
*/ |
116 |
> |
int getNGlobalIntegrableObjects() { |
117 |
> |
return nGlobalIntegrableObjects_; |
118 |
> |
} |
119 |
> |
|
120 |
> |
/** |
121 |
> |
* Returns the number of local molecules. |
122 |
> |
* @return the number of local molecules |
123 |
> |
*/ |
124 |
> |
int getNMolecules() { |
125 |
> |
return molecules_.size(); |
126 |
> |
} |
127 |
> |
|
128 |
> |
/** Returns the number of local atoms */ |
129 |
> |
unsigned int getNAtoms() { |
130 |
> |
return nAtoms_; |
131 |
> |
} |
132 |
> |
|
133 |
> |
/** Returns the number of local bonds */ |
134 |
> |
unsigned int getNBonds(){ |
135 |
> |
return nBonds_; |
136 |
> |
} |
137 |
> |
|
138 |
> |
/** Returns the number of local bends */ |
139 |
> |
unsigned int getNBends() { |
140 |
> |
return nBends_; |
141 |
> |
} |
142 |
> |
|
143 |
> |
/** Returns the number of local torsions */ |
144 |
> |
unsigned int getNTorsions() { |
145 |
> |
return nTorsions_; |
146 |
> |
} |
147 |
> |
|
148 |
> |
/** Returns the number of local rigid bodies */ |
149 |
> |
unsigned int getNRigidBodies() { |
150 |
> |
return nRigidBodies_; |
151 |
> |
} |
152 |
> |
|
153 |
> |
/** Returns the number of local integrable objects */ |
154 |
> |
unsigned int getNIntegrableObjects() { |
155 |
> |
return nIntegrableObjects_; |
156 |
> |
} |
157 |
> |
|
158 |
> |
/** Returns the number of local cutoff groups */ |
159 |
> |
unsigned int getNCutoffGroups() { |
160 |
> |
return nCutoffGroups_; |
161 |
> |
} |
162 |
> |
|
163 |
> |
/** Returns the total number of constraints in this SimInfo */ |
164 |
> |
unsigned int getNConstraints() { |
165 |
> |
return nConstraints_; |
166 |
> |
} |
167 |
> |
|
168 |
> |
/** |
169 |
> |
* Returns the first molecule in this SimInfo and intialize the iterator. |
170 |
> |
* @return the first molecule, return NULL if there is not molecule in this SimInfo |
171 |
> |
* @param i the iterator of molecule array (user shouldn't change it) |
172 |
> |
*/ |
173 |
> |
Molecule* beginMolecule(MoleculeIterator& i); |
174 |
> |
|
175 |
> |
/** |
176 |
> |
* Returns the next avaliable Molecule based on the iterator. |
177 |
> |
* @return the next avaliable molecule, return NULL if reaching the end of the array |
178 |
> |
* @param i the iterator of molecule array |
179 |
> |
*/ |
180 |
> |
Molecule* nextMolecule(MoleculeIterator& i); |
181 |
> |
|
182 |
> |
/** Returns the number of degrees of freedom */ |
183 |
> |
int getNdf() { |
184 |
> |
return ndf_; |
185 |
> |
} |
186 |
> |
|
187 |
> |
/** Returns the number of raw degrees of freedom */ |
188 |
> |
int getNdfRaw() { |
189 |
> |
return ndfRaw_; |
190 |
> |
} |
191 |
> |
|
192 |
> |
/** Returns the number of translational degrees of freedom */ |
193 |
> |
int getNdfTrans() { |
194 |
> |
return ndfTrans_; |
195 |
> |
} |
196 |
> |
|
197 |
> |
//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying |
198 |
> |
|
199 |
> |
/** Returns the total number of z-constraint molecules in the system */ |
200 |
> |
int getNZconstraint() { |
201 |
> |
return nZconstraint_; |
202 |
> |
} |
203 |
> |
|
204 |
> |
/** |
205 |
> |
* Sets the number of z-constraint molecules in the system. |
206 |
> |
*/ |
207 |
> |
void setNZconstraint(int nZconstraint) { |
208 |
> |
nZconstraint_ = nZconstraint; |
209 |
> |
} |
210 |
> |
|
211 |
> |
/** Returns the snapshot manager. */ |
212 |
> |
SnapshotManager* getSnapshotManager() { |
213 |
> |
return sman_; |
214 |
> |
} |
215 |
> |
|
216 |
> |
/** Sets the snapshot manager. */ |
217 |
> |
void setSnapshotManager(SnapshotManager* sman); |
218 |
> |
|
219 |
> |
/** Returns the force field */ |
220 |
> |
ForceField* getForceField() { |
221 |
> |
return forceField_; |
222 |
> |
} |
223 |
> |
|
224 |
> |
Globals* getGlobals() { |
225 |
> |
return globals_; |
226 |
> |
} |
227 |
> |
|
228 |
> |
/** Returns the velocity of center of mass of the whole system.*/ |
229 |
> |
Vector3d getComVel(); |
230 |
> |
|
231 |
> |
/** Returns the center of the mass of the whole system.*/ |
232 |
> |
Vector3d getCom(); |
233 |
> |
|
234 |
> |
/** Returns the seed (used for random number generator) */ |
235 |
> |
int getSeed() { |
236 |
> |
return seed_; |
237 |
> |
} |
238 |
> |
|
239 |
> |
/** Sets the seed*/ |
240 |
> |
void setSeed(int seed) { |
241 |
> |
seed_ = seed; |
242 |
> |
} |
243 |
> |
|
244 |
> |
/** main driver function to interact with fortran during the initialization and molecule migration */ |
245 |
> |
void update(); |
246 |
> |
|
247 |
> |
/** Returns the local index manager */ |
248 |
> |
LocalIndexManager* getLocalIndexManager() { |
249 |
> |
return &localIndexMan_; |
250 |
> |
} |
251 |
> |
|
252 |
> |
int getMoleculeStampId(int globalIndex) { |
253 |
> |
//assert(globalIndex < molStampIds_.size()) |
254 |
> |
return molStampIds_[globalIndex]; |
255 |
> |
} |
256 |
> |
|
257 |
> |
/** Returns the molecule stamp */ |
258 |
> |
MoleculeStamp* getMoleculeStamp(int id) { |
259 |
> |
return moleculeStamps_[id]; |
260 |
> |
} |
261 |
> |
|
262 |
> |
/** |
263 |
> |
* Finds a molecule with a specified global index |
264 |
> |
* @return a pointer point to found molecule |
265 |
> |
* @param index |
266 |
> |
*/ |
267 |
> |
Molecule* getMoleculeByGlobalIndex(int index) { |
268 |
> |
MoleculeIterator i; |
269 |
> |
i = molecules_.find(index); |
270 |
> |
|
271 |
> |
return i != molecules_.end() ? i->second : NULL; |
272 |
> |
} |
273 |
> |
|
274 |
> |
/** Calculate the maximum cutoff radius based on the atom types */ |
275 |
> |
double calcMaxCutoffRadius(); |
276 |
> |
|
277 |
> |
double getRcut() { |
278 |
> |
return rcut_; |
279 |
> |
} |
280 |
> |
|
281 |
> |
double getRsw() { |
282 |
> |
return rsw_; |
283 |
> |
} |
284 |
> |
|
285 |
> |
std::string getFinalConfigFileName() { |
286 |
> |
return finalConfigFileName_; |
287 |
> |
} |
288 |
> |
|
289 |
> |
void setFinalConfigFileName(const std::string& fileName) { |
290 |
> |
finalConfigFileName_ = fileName; |
291 |
> |
} |
292 |
> |
|
293 |
> |
std::string getDumpFileName() { |
294 |
> |
return dumpFileName_; |
295 |
> |
} |
296 |
> |
|
297 |
> |
void setDumpFileName(const std::string& fileName) { |
298 |
> |
dumpFileName_ = fileName; |
299 |
> |
} |
300 |
> |
|
301 |
> |
std::string getStatFileName() { |
302 |
> |
return statFileName_; |
303 |
> |
} |
304 |
> |
|
305 |
> |
void setStatFileName(const std::string& fileName) { |
306 |
> |
statFileName_ = fileName; |
307 |
> |
} |
308 |
> |
|
309 |
> |
/** |
310 |
> |
* Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class |
311 |
> |
* @see #SimCreator::setGlobalIndex |
312 |
> |
*/ |
313 |
> |
int* getGlobalGroupMembershipPointer() { |
314 |
> |
return &globalGroupMembership_[0]; |
315 |
> |
} |
316 |
> |
|
317 |
> |
/** |
318 |
> |
* Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class |
319 |
> |
* @see #SimCreator::setGlobalIndex |
320 |
> |
*/ |
321 |
> |
int* getGlobalMolMembershipPointer() { |
322 |
> |
return &globalMolMembership_[0]; |
323 |
> |
} |
324 |
> |
|
325 |
> |
|
326 |
> |
bool isFortranInitialized() { |
327 |
> |
return fortranInitialized_; |
328 |
> |
} |
329 |
> |
|
330 |
> |
//below functions are just forward functions |
331 |
> |
//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
332 |
> |
//the other hand, has-a relation need composing. |
333 |
> |
/** |
334 |
> |
* Adds property into property map |
335 |
> |
* @param genData GenericData to be added into PropertyMap |
336 |
> |
*/ |
337 |
> |
void addProperty(GenericData* genData); |
338 |
> |
|
339 |
> |
/** |
340 |
> |
* Removes property from PropertyMap by name |
341 |
> |
* @param propName the name of property to be removed |
342 |
> |
*/ |
343 |
> |
void removeProperty(const std::string& propName); |
344 |
> |
|
345 |
> |
/** |
346 |
> |
* clear all of the properties |
347 |
> |
*/ |
348 |
> |
void clearProperties(); |
349 |
> |
|
350 |
> |
/** |
351 |
> |
* Returns all names of properties |
352 |
> |
* @return all names of properties |
353 |
> |
*/ |
354 |
> |
std::vector<std::string> getPropertyNames(); |
355 |
> |
|
356 |
> |
/** |
357 |
> |
* Returns all of the properties in PropertyMap |
358 |
> |
* @return all of the properties in PropertyMap |
359 |
> |
*/ |
360 |
> |
std::vector<GenericData*> getProperties(); |
361 |
> |
|
362 |
> |
/** |
363 |
> |
* Returns property |
364 |
> |
* @param propName name of property |
365 |
> |
* @return a pointer point to property with propName. If no property named propName |
366 |
> |
* exists, return NULL |
367 |
> |
*/ |
368 |
> |
GenericData* getPropertyByName(const std::string& propName); |
369 |
> |
|
370 |
> |
friend std::ostream& operator <<(ostream& o, SimInfo& info); |
371 |
> |
|
372 |
> |
private: |
373 |
> |
|
374 |
> |
|
375 |
> |
/** Returns the unique atom types of local processor in an array */ |
376 |
> |
std::set<AtomType*> getUniqueAtomTypes(); |
377 |
> |
|
378 |
> |
/** fill up the simtype struct*/ |
379 |
> |
void setupSimType(); |
380 |
> |
|
381 |
> |
/** |
382 |
> |
* Setup Fortran Simulation |
383 |
> |
* @see #setupFortranParallel |
384 |
> |
*/ |
385 |
> |
void setupFortranSim(); |
386 |
> |
|
387 |
> |
/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */ |
388 |
> |
void setupCutoff(); |
389 |
> |
|
390 |
> |
/** Calculates the number of degress of freedom in the whole system */ |
391 |
> |
void calcNdf(); |
392 |
> |
void calcNdfRaw(); |
393 |
> |
void calcNdfTrans(); |
394 |
> |
|
395 |
> |
void addExcludePairs(Molecule* mol); |
396 |
> |
void removeExcludePairs(Molecule* mol); |
397 |
> |
|
398 |
> |
/** |
399 |
> |
* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole |
400 |
> |
* system. |
401 |
> |
*/ |
402 |
> |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
403 |
> |
|
404 |
> |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
405 |
> |
|
406 |
> |
//degress of freedom |
407 |
> |
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
408 |
> |
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
409 |
> |
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
410 |
> |
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
411 |
> |
|
412 |
> |
//number of global objects |
413 |
> |
int nGlobalMols_; /**< number of molecules in the system */ |
414 |
> |
int nGlobalAtoms_; /**< number of atoms in the system */ |
415 |
> |
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
416 |
> |
int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */ |
417 |
> |
|
418 |
> |
/** |
419 |
> |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
420 |
> |
* corresponding content is the global index of cutoff group this atom belong to. |
421 |
> |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
422 |
> |
*/ |
423 |
> |
std::vector<int> globalGroupMembership_; |
424 |
> |
|
425 |
> |
/** |
426 |
> |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
427 |
> |
* corresponding content is the global index of molecule this atom belong to. |
428 |
> |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
429 |
> |
*/ |
430 |
> |
std::vector<int> globalMolMembership_; |
431 |
> |
|
432 |
> |
|
433 |
> |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
434 |
> |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
435 |
> |
|
436 |
> |
//number of local objects |
437 |
> |
int nAtoms_; /**< number of atoms in local processor */ |
438 |
> |
int nBonds_; /**< number of bonds in local processor */ |
439 |
> |
int nBends_; /**< number of bends in local processor */ |
440 |
> |
int nTorsions_; /**< number of torsions in local processor */ |
441 |
> |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
442 |
> |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
443 |
> |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
444 |
> |
int nConstraints_; /**< number of constraints in local processors */ |
445 |
> |
|
446 |
> |
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
447 |
> |
Exclude exclude_; |
448 |
> |
ForceField* forceField_; |
449 |
> |
PropertyMap properties_; /**< Generic Property */ |
450 |
> |
SnapshotManager* sman_; /**< SnapshotManager */ |
451 |
> |
Globals* globals_; |
452 |
> |
int seed_; /**< seed for random number generator */ |
453 |
> |
|
454 |
> |
/** |
455 |
> |
* The reason to have a local index manager is that when molecule is migrating to other processors, |
456 |
> |
* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
457 |
> |
* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager |
458 |
> |
* to make a efficient data moving plan. |
459 |
> |
*/ |
460 |
> |
LocalIndexManager localIndexMan_; |
461 |
> |
|
462 |
> |
//file names |
463 |
> |
std::string finalConfigFileName_; |
464 |
> |
std::string dumpFileName_; |
465 |
> |
std::string statFileName_; |
466 |
> |
|
467 |
> |
double rcut_; /**< cutoff radius*/ |
468 |
> |
double rsw_; /**< radius of switching function*/ |
469 |
> |
|
470 |
> |
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
471 |
> |
|
472 |
> |
#ifdef IS_MPI |
473 |
> |
//in Parallel version, we need MolToProc |
474 |
> |
public: |
475 |
> |
|
476 |
> |
/** |
477 |
> |
* Finds the processor where a molecule resides |
478 |
> |
* @return the id of the processor which contains the molecule |
479 |
> |
* @param globalIndex global Index of the molecule |
480 |
> |
*/ |
481 |
> |
int getMolToProc(int globalIndex) { |
482 |
> |
//assert(globalIndex < molToProcMap_.size()); |
483 |
> |
return molToProcMap_[globalIndex]; |
484 |
> |
} |
485 |
> |
|
486 |
> |
/** |
487 |
> |
* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class |
488 |
> |
* @see #SimCreator::divideMolecules |
489 |
> |
*/ |
490 |
> |
int* getMolToProcMapPointer() { |
491 |
> |
return &molToProcMap_[0]; |
492 |
> |
} |
493 |
> |
|
494 |
> |
private: |
495 |
> |
|
496 |
> |
void setupFortranParallel(); |
497 |
> |
|
498 |
> |
/** |
499 |
> |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
500 |
> |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
501 |
> |
* once. |
502 |
> |
*/ |
503 |
> |
std::vector<int> molToProcMap_; |
504 |
> |
#endif |
505 |
> |
|
506 |
> |
}; |
507 |
> |
|
508 |
> |
} //namespace oopse |
509 |
> |
#endif //BRAINS_SIMMODEL_HPP |