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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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|
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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 */ |
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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 */ |
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int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
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int nConstraints_; /**< number of constraints in local processors */ |
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|
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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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|
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/** |
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* The reason to have a local index manager is that when molecule is migrating to other processors, |
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* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
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* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager |
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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_; |
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|
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double rcut_; /**< cutoff radius*/ |
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double rsw_; /**< radius of switching function*/ |
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|
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bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
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|
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#ifdef IS_MPI |
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//in Parallel version, we need MolToProc |
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public: |
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|
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/** |
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* Finds the processor where a molecule resides |
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* @return the id of the processor which contains the molecule |
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* @param globalIndex global Index of the molecule |
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*/ |
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int getMolToProc(int globalIndex) { |
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//assert(globalIndex < molToProcMap_.size()); |
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return molToProcMap_[globalIndex]; |
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} |
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|
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/** |
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* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class |
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* @see #SimCreator::divideMolecules |
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*/ |
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int* getMolToProcMapPointer() { |
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return &molToProcMap_[0]; |
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} |
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|
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private: |
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|
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void setupFortranParallel(); |
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|
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/** |
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* The size of molToProcMap_ is equal to total number of molecules in the system. |
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* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
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* once. |
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*/ |
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std::vector<int> molToProcMap_; |
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#endif |
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|
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}; |
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|
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} //namespace oopse |
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#endif //BRAINS_SIMMODEL_HPP |
