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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 |
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*/ |
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class SimInfo { |
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public: |
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SimInfo(); |
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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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/** |
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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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*/ |
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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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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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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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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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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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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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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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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(std::vector<Molecule*>::iterator& 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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|
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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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/** 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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/** 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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Vector3d getComVel(); |
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|
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Vector3d getCom(); |
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|
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int getSeed() { |
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return seed_; |
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} |
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|
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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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private: |
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|
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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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int ndf_; |
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int ndfRaw_; |
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int ndfTrans_; |
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|
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int nAtoms_; |
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int nBonds_; |
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int nBends_; |
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int nTorsions_; |
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int nRigidBodies_; |
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int nIntegrableObjects_; |
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int nCutoffGroups_; |
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int nConstraints_; |
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|
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simtype fInfo_; |
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Exclude exclude_; |
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ForceField* forceField_; |
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|
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std::vector<Molecule*> molecules_; /**< Molecule array */ |
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PropertyMap properties_; /** Generic Property */ |
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SnapshotManager* sman_; /** SnapshotManager */ |
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|
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std::vector<std::pair<MoleculeStamp*, int> > moleculeStamps_; |
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Globals* globals_; |
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|
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int seed_; |
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}; |
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|
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} //namespace oopse |
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#endif //BRAINS_SIMMODEL_HPP |
