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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 <set> |
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#include <utility> |
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#include <vector> |
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|
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#include "brains/Exclude.hpp" |
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#include "io/Globals.hpp" |
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#include "math/Vector3.hpp" |
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#include "types/MoleculeStamp.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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#include "utils/PropertyMap.hpp" |
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#include "utils/LocalIndexManager.hpp" |
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|
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//another nonsense macro declaration |
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#define __C |
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#include "brains/fSimulation.h" |
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|
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namespace oopse{ |
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|
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//forward decalration |
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class SnapshotManager; |
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class Molecule; |
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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 simParams |
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* @note |
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*/ |
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SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams); |
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virtual ~SimInfo(); |
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|
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/** |
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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 total number of integrable objects (total number of rigid bodies plus the total number |
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* of atoms which do not belong to the rigid bodies) in the system |
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*/ |
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int getNGlobalIntegrableObjects() { |
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return nGlobalIntegrableObjects_; |
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} |
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|
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/** |
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* Returns the total number of integrable objects (total number of rigid bodies plus the total number |
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* of atoms which do not belong to the rigid bodies) in the system |
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*/ |
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int getNGlobalRigidBodies() { |
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return nGlobalRigidBodies_; |
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} |
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|
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/** |
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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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void 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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|
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/** Returns the force field */ |
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ForceField* getForceField() { |
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return forceField_; |
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} |
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|
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Globals* getSimParams() { |
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return simParams_; |
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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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MoleculeIterator 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 <<(std::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*> 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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ForceField* forceField_; |
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Globals* simParams_; |
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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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int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */ |
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int nGlobalRigidBodies_; /**< number of rigid bodies in this system */ |
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/** |
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* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 431 |
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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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/** |
| 437 |
< |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 438 |
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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. |
| 440 |
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*/ |
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std::vector<int> globalMolMembership_; |
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|
| 443 |
< |
|
| 444 |
< |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
| 445 |
< |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
| 446 |
< |
|
| 447 |
< |
//number of local objects |
| 448 |
< |
int nAtoms_; /**< number of atoms in local processor */ |
| 449 |
< |
int nBonds_; /**< number of bonds in local processor */ |
| 450 |
< |
int nBends_; /**< number of bends in local processor */ |
| 451 |
< |
int nTorsions_; /**< number of torsions in local processor */ |
| 452 |
< |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
| 453 |
< |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
| 454 |
< |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
| 455 |
< |
int nConstraints_; /**< number of constraints in local processors */ |
| 456 |
< |
|
| 457 |
< |
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
| 458 |
< |
Exclude exclude_; |
| 459 |
< |
PropertyMap properties_; /**< Generic Property */ |
| 460 |
< |
SnapshotManager* sman_; /**< SnapshotManager */ |
| 461 |
< |
|
| 462 |
< |
int seed_; /**< seed for random number generator */ |
| 463 |
< |
|
| 464 |
< |
/** |
| 465 |
< |
* The reason to have a local index manager is that when molecule is migrating to other processors, |
| 466 |
< |
* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
| 467 |
< |
* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager |
| 468 |
< |
* to make a efficient data moving plan. |
| 469 |
< |
*/ |
| 470 |
< |
LocalIndexManager localIndexMan_; |
| 471 |
< |
|
| 472 |
< |
//file names |
| 473 |
< |
std::string finalConfigFileName_; |
| 474 |
< |
std::string dumpFileName_; |
| 475 |
< |
std::string statFileName_; |
| 476 |
< |
|
| 477 |
< |
double rcut_; /**< cutoff radius*/ |
| 478 |
< |
double rsw_; /**< radius of switching function*/ |
| 479 |
< |
|
| 480 |
< |
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
| 481 |
< |
|
| 482 |
< |
#ifdef IS_MPI |
| 483 |
< |
//in Parallel version, we need MolToProc |
| 484 |
< |
public: |
| 485 |
< |
|
| 486 |
< |
/** |
| 487 |
< |
* Finds the processor where a molecule resides |
| 488 |
< |
* @return the id of the processor which contains the molecule |
| 489 |
< |
* @param globalIndex global Index of the molecule |
| 490 |
< |
*/ |
| 491 |
< |
int getMolToProc(int globalIndex) { |
| 492 |
< |
//assert(globalIndex < molToProcMap_.size()); |
| 493 |
< |
return molToProcMap_[globalIndex]; |
| 494 |
< |
} |
| 495 |
< |
|
| 496 |
< |
/** |
| 497 |
< |
* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class |
| 498 |
< |
* @see #SimCreator::divideMolecules |
| 499 |
< |
*/ |
| 500 |
< |
int* getMolToProcMapPointer() { |
| 501 |
< |
return &molToProcMap_[0]; |
| 502 |
< |
} |
| 503 |
< |
|
| 504 |
< |
private: |
| 505 |
< |
|
| 506 |
< |
void setupFortranParallel(); |
| 507 |
< |
|
| 508 |
< |
/** |
| 509 |
< |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
| 510 |
< |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
| 511 |
< |
* once. |
| 512 |
< |
*/ |
| 513 |
< |
std::vector<int> molToProcMap_; |
| 514 |
< |
#endif |
| 515 |
< |
|
| 516 |
< |
}; |
| 517 |
< |
|
| 518 |
< |
} //namespace oopse |
| 519 |
< |
#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 |
> |
* |
| 15 |
> |
* 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 simParams |
| 79 |
> |
* @note |
| 80 |
> |
*/ |
| 81 |
> |
SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams); |
| 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 total number of integrable objects (total number of rigid bodies plus the total number |
| 122 |
> |
* of atoms which do not belong to the rigid bodies) in the system |
| 123 |
> |
*/ |
| 124 |
> |
int getNGlobalRigidBodies() { |
| 125 |
> |
return nGlobalRigidBodies_; |
| 126 |
> |
} |
| 127 |
> |
|
| 128 |
> |
/** |
| 129 |
> |
* Returns the number of local molecules. |
| 130 |
> |
* @return the number of local molecules |
| 131 |
> |
*/ |
| 132 |
> |
int getNMolecules() { |
| 133 |
> |
return molecules_.size(); |
| 134 |
> |
} |
| 135 |
> |
|
| 136 |
> |
/** Returns the number of local atoms */ |
| 137 |
> |
unsigned int getNAtoms() { |
| 138 |
> |
return nAtoms_; |
| 139 |
> |
} |
| 140 |
> |
|
| 141 |
> |
/** Returns the number of local bonds */ |
| 142 |
> |
unsigned int getNBonds(){ |
| 143 |
> |
return nBonds_; |
| 144 |
> |
} |
| 145 |
> |
|
| 146 |
> |
/** Returns the number of local bends */ |
| 147 |
> |
unsigned int getNBends() { |
| 148 |
> |
return nBends_; |
| 149 |
> |
} |
| 150 |
> |
|
| 151 |
> |
/** Returns the number of local torsions */ |
| 152 |
> |
unsigned int getNTorsions() { |
| 153 |
> |
return nTorsions_; |
| 154 |
> |
} |
| 155 |
> |
|
| 156 |
> |
/** Returns the number of local rigid bodies */ |
| 157 |
> |
unsigned int getNRigidBodies() { |
| 158 |
> |
return nRigidBodies_; |
| 159 |
> |
} |
| 160 |
> |
|
| 161 |
> |
/** Returns the number of local integrable objects */ |
| 162 |
> |
unsigned int getNIntegrableObjects() { |
| 163 |
> |
return nIntegrableObjects_; |
| 164 |
> |
} |
| 165 |
> |
|
| 166 |
> |
/** Returns the number of local cutoff groups */ |
| 167 |
> |
unsigned int getNCutoffGroups() { |
| 168 |
> |
return nCutoffGroups_; |
| 169 |
> |
} |
| 170 |
> |
|
| 171 |
> |
/** Returns the total number of constraints in this SimInfo */ |
| 172 |
> |
unsigned int getNConstraints() { |
| 173 |
> |
return nConstraints_; |
| 174 |
> |
} |
| 175 |
> |
|
| 176 |
> |
/** |
| 177 |
> |
* Returns the first molecule in this SimInfo and intialize the iterator. |
| 178 |
> |
* @return the first molecule, return NULL if there is not molecule in this SimInfo |
| 179 |
> |
* @param i the iterator of molecule array (user shouldn't change it) |
| 180 |
> |
*/ |
| 181 |
> |
Molecule* beginMolecule(MoleculeIterator& i); |
| 182 |
> |
|
| 183 |
> |
/** |
| 184 |
> |
* Returns the next avaliable Molecule based on the iterator. |
| 185 |
> |
* @return the next avaliable molecule, return NULL if reaching the end of the array |
| 186 |
> |
* @param i the iterator of molecule array |
| 187 |
> |
*/ |
| 188 |
> |
Molecule* nextMolecule(MoleculeIterator& i); |
| 189 |
> |
|
| 190 |
> |
/** Returns the number of degrees of freedom */ |
| 191 |
> |
int getNdf() { |
| 192 |
> |
return ndf_; |
| 193 |
> |
} |
| 194 |
> |
|
| 195 |
> |
/** Returns the number of raw degrees of freedom */ |
| 196 |
> |
int getNdfRaw() { |
| 197 |
> |
return ndfRaw_; |
| 198 |
> |
} |
| 199 |
> |
|
| 200 |
> |
/** Returns the number of translational degrees of freedom */ |
| 201 |
> |
int getNdfTrans() { |
| 202 |
> |
return ndfTrans_; |
| 203 |
> |
} |
| 204 |
> |
|
| 205 |
> |
//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying |
| 206 |
> |
|
| 207 |
> |
/** Returns the total number of z-constraint molecules in the system */ |
| 208 |
> |
int getNZconstraint() { |
| 209 |
> |
return nZconstraint_; |
| 210 |
> |
} |
| 211 |
> |
|
| 212 |
> |
/** |
| 213 |
> |
* Sets the number of z-constraint molecules in the system. |
| 214 |
> |
*/ |
| 215 |
> |
void setNZconstraint(int nZconstraint) { |
| 216 |
> |
nZconstraint_ = nZconstraint; |
| 217 |
> |
} |
| 218 |
> |
|
| 219 |
> |
/** Returns the snapshot manager. */ |
| 220 |
> |
SnapshotManager* getSnapshotManager() { |
| 221 |
> |
return sman_; |
| 222 |
> |
} |
| 223 |
> |
|
| 224 |
> |
/** Sets the snapshot manager. */ |
| 225 |
> |
void setSnapshotManager(SnapshotManager* sman); |
| 226 |
> |
|
| 227 |
> |
/** Returns the force field */ |
| 228 |
> |
ForceField* getForceField() { |
| 229 |
> |
return forceField_; |
| 230 |
> |
} |
| 231 |
> |
|
| 232 |
> |
Globals* getSimParams() { |
| 233 |
> |
return simParams_; |
| 234 |
> |
} |
| 235 |
> |
|
| 236 |
> |
/** Returns the velocity of center of mass of the whole system.*/ |
| 237 |
> |
Vector3d getComVel(); |
| 238 |
> |
|
| 239 |
> |
/** Returns the center of the mass of the whole system.*/ |
| 240 |
> |
Vector3d getCom(); |
| 241 |
> |
|
| 242 |
> |
/** Returns the seed (used for random number generator) */ |
| 243 |
> |
int getSeed() { |
| 244 |
> |
return seed_; |
| 245 |
> |
} |
| 246 |
> |
|
| 247 |
> |
/** Sets the seed*/ |
| 248 |
> |
void setSeed(int seed) { |
| 249 |
> |
seed_ = seed; |
| 250 |
> |
} |
| 251 |
> |
|
| 252 |
> |
/** main driver function to interact with fortran during the initialization and molecule migration */ |
| 253 |
> |
void update(); |
| 254 |
> |
|
| 255 |
> |
/** Returns the local index manager */ |
| 256 |
> |
LocalIndexManager* getLocalIndexManager() { |
| 257 |
> |
return &localIndexMan_; |
| 258 |
> |
} |
| 259 |
> |
|
| 260 |
> |
int getMoleculeStampId(int globalIndex) { |
| 261 |
> |
//assert(globalIndex < molStampIds_.size()) |
| 262 |
> |
return molStampIds_[globalIndex]; |
| 263 |
> |
} |
| 264 |
> |
|
| 265 |
> |
/** Returns the molecule stamp */ |
| 266 |
> |
MoleculeStamp* getMoleculeStamp(int id) { |
| 267 |
> |
return moleculeStamps_[id]; |
| 268 |
> |
} |
| 269 |
> |
|
| 270 |
> |
/** |
| 271 |
> |
* Finds a molecule with a specified global index |
| 272 |
> |
* @return a pointer point to found molecule |
| 273 |
> |
* @param index |
| 274 |
> |
*/ |
| 275 |
> |
Molecule* getMoleculeByGlobalIndex(int index) { |
| 276 |
> |
MoleculeIterator i; |
| 277 |
> |
i = molecules_.find(index); |
| 278 |
> |
|
| 279 |
> |
return i != molecules_.end() ? i->second : NULL; |
| 280 |
> |
} |
| 281 |
> |
|
| 282 |
> |
/** Calculate the maximum cutoff radius based on the atom types */ |
| 283 |
> |
double calcMaxCutoffRadius(); |
| 284 |
> |
|
| 285 |
> |
double getRcut() { |
| 286 |
> |
return rcut_; |
| 287 |
> |
} |
| 288 |
> |
|
| 289 |
> |
double getRsw() { |
| 290 |
> |
return rsw_; |
| 291 |
> |
} |
| 292 |
> |
|
| 293 |
> |
std::string getFinalConfigFileName() { |
| 294 |
> |
return finalConfigFileName_; |
| 295 |
> |
} |
| 296 |
> |
|
| 297 |
> |
void setFinalConfigFileName(const std::string& fileName) { |
| 298 |
> |
finalConfigFileName_ = fileName; |
| 299 |
> |
} |
| 300 |
> |
|
| 301 |
> |
std::string getDumpFileName() { |
| 302 |
> |
return dumpFileName_; |
| 303 |
> |
} |
| 304 |
> |
|
| 305 |
> |
void setDumpFileName(const std::string& fileName) { |
| 306 |
> |
dumpFileName_ = fileName; |
| 307 |
> |
} |
| 308 |
> |
|
| 309 |
> |
std::string getStatFileName() { |
| 310 |
> |
return statFileName_; |
| 311 |
> |
} |
| 312 |
> |
|
| 313 |
> |
void setStatFileName(const std::string& fileName) { |
| 314 |
> |
statFileName_ = fileName; |
| 315 |
> |
} |
| 316 |
> |
|
| 317 |
> |
/** |
| 318 |
> |
* Sets GlobalGroupMembership |
| 319 |
> |
* @see #SimCreator::setGlobalIndex |
| 320 |
> |
*/ |
| 321 |
> |
void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) { |
| 322 |
> |
assert(globalGroupMembership.size() == nGlobalAtoms_); |
| 323 |
> |
globalGroupMembership_ = globalGroupMembership_; |
| 324 |
> |
} |
| 325 |
> |
|
| 326 |
> |
/** |
| 327 |
> |
* Sets GlobalMolMembership |
| 328 |
> |
* @see #SimCreator::setGlobalIndex |
| 329 |
> |
*/ |
| 330 |
> |
void setGlobalMolMembership(const std::vector<int>& globalMolMembership) { |
| 331 |
> |
assert(globalMolMembership.size() == nGlobalAtoms_); |
| 332 |
> |
globalMolMembership_ = globalMolMembership; |
| 333 |
> |
} |
| 334 |
> |
|
| 335 |
> |
|
| 336 |
> |
bool isFortranInitialized() { |
| 337 |
> |
return fortranInitialized_; |
| 338 |
> |
} |
| 339 |
> |
|
| 340 |
> |
//below functions are just forward functions |
| 341 |
> |
//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
| 342 |
> |
//the other hand, has-a relation need composing. |
| 343 |
> |
/** |
| 344 |
> |
* Adds property into property map |
| 345 |
> |
* @param genData GenericData to be added into PropertyMap |
| 346 |
> |
*/ |
| 347 |
> |
void addProperty(GenericData* genData); |
| 348 |
> |
|
| 349 |
> |
/** |
| 350 |
> |
* Removes property from PropertyMap by name |
| 351 |
> |
* @param propName the name of property to be removed |
| 352 |
> |
*/ |
| 353 |
> |
void removeProperty(const std::string& propName); |
| 354 |
> |
|
| 355 |
> |
/** |
| 356 |
> |
* clear all of the properties |
| 357 |
> |
*/ |
| 358 |
> |
void clearProperties(); |
| 359 |
> |
|
| 360 |
> |
/** |
| 361 |
> |
* Returns all names of properties |
| 362 |
> |
* @return all names of properties |
| 363 |
> |
*/ |
| 364 |
> |
std::vector<std::string> getPropertyNames(); |
| 365 |
> |
|
| 366 |
> |
/** |
| 367 |
> |
* Returns all of the properties in PropertyMap |
| 368 |
> |
* @return all of the properties in PropertyMap |
| 369 |
> |
*/ |
| 370 |
> |
std::vector<GenericData*> getProperties(); |
| 371 |
> |
|
| 372 |
> |
/** |
| 373 |
> |
* Returns property |
| 374 |
> |
* @param propName name of property |
| 375 |
> |
* @return a pointer point to property with propName. If no property named propName |
| 376 |
> |
* exists, return NULL |
| 377 |
> |
*/ |
| 378 |
> |
GenericData* getPropertyByName(const std::string& propName); |
| 379 |
> |
|
| 380 |
> |
friend std::ostream& operator <<(std::ostream& o, SimInfo& info); |
| 381 |
> |
|
| 382 |
> |
private: |
| 383 |
> |
|
| 384 |
> |
|
| 385 |
> |
/** Returns the unique atom types of local processor in an array */ |
| 386 |
> |
std::set<AtomType*> getUniqueAtomTypes(); |
| 387 |
> |
|
| 388 |
> |
/** fill up the simtype struct*/ |
| 389 |
> |
void setupSimType(); |
| 390 |
> |
|
| 391 |
> |
/** |
| 392 |
> |
* Setup Fortran Simulation |
| 393 |
> |
* @see #setupFortranParallel |
| 394 |
> |
*/ |
| 395 |
> |
void setupFortranSim(); |
| 396 |
> |
|
| 397 |
> |
/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */ |
| 398 |
> |
void setupCutoff(); |
| 399 |
> |
|
| 400 |
> |
/** Calculates the number of degress of freedom in the whole system */ |
| 401 |
> |
void calcNdf(); |
| 402 |
> |
void calcNdfRaw(); |
| 403 |
> |
void calcNdfTrans(); |
| 404 |
> |
|
| 405 |
> |
void addExcludePairs(Molecule* mol); |
| 406 |
> |
void removeExcludePairs(Molecule* mol); |
| 407 |
> |
|
| 408 |
> |
/** |
| 409 |
> |
* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole |
| 410 |
> |
* system. |
| 411 |
> |
*/ |
| 412 |
> |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
| 413 |
> |
|
| 414 |
> |
ForceField* forceField_; |
| 415 |
> |
Globals* simParams_; |
| 416 |
> |
|
| 417 |
> |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
| 418 |
> |
|
| 419 |
> |
//degress of freedom |
| 420 |
> |
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
| 421 |
> |
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
| 422 |
> |
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
| 423 |
> |
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
| 424 |
> |
|
| 425 |
> |
//number of global objects |
| 426 |
> |
int nGlobalMols_; /**< number of molecules in the system */ |
| 427 |
> |
int nGlobalAtoms_; /**< number of atoms in the system */ |
| 428 |
> |
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
| 429 |
> |
int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */ |
| 430 |
> |
int nGlobalRigidBodies_; /**< number of rigid bodies in this system */ |
| 431 |
> |
/** |
| 432 |
> |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 433 |
> |
* corresponding content is the global index of cutoff group this atom belong to. |
| 434 |
> |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
| 435 |
> |
*/ |
| 436 |
> |
std::vector<int> globalGroupMembership_; |
| 437 |
> |
|
| 438 |
> |
/** |
| 439 |
> |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 440 |
> |
* corresponding content is the global index of molecule this atom belong to. |
| 441 |
> |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
| 442 |
> |
*/ |
| 443 |
> |
std::vector<int> globalMolMembership_; |
| 444 |
> |
|
| 445 |
> |
|
| 446 |
> |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
| 447 |
> |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
| 448 |
> |
|
| 449 |
> |
//number of local objects |
| 450 |
> |
int nAtoms_; /**< number of atoms in local processor */ |
| 451 |
> |
int nBonds_; /**< number of bonds in local processor */ |
| 452 |
> |
int nBends_; /**< number of bends in local processor */ |
| 453 |
> |
int nTorsions_; /**< number of torsions in local processor */ |
| 454 |
> |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
| 455 |
> |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
| 456 |
> |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
| 457 |
> |
int nConstraints_; /**< number of constraints in local processors */ |
| 458 |
> |
|
| 459 |
> |
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
| 460 |
> |
Exclude exclude_; |
| 461 |
> |
PropertyMap properties_; /**< Generic Property */ |
| 462 |
> |
SnapshotManager* sman_; /**< SnapshotManager */ |
| 463 |
> |
|
| 464 |
> |
int seed_; /**< seed for random number generator */ |
| 465 |
> |
|
| 466 |
> |
/** |
| 467 |
> |
* The reason to have a local index manager is that when molecule is migrating to other processors, |
| 468 |
> |
* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
| 469 |
> |
* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager |
| 470 |
> |
* to make a efficient data moving plan. |
| 471 |
> |
*/ |
| 472 |
> |
LocalIndexManager localIndexMan_; |
| 473 |
> |
|
| 474 |
> |
//file names |
| 475 |
> |
std::string finalConfigFileName_; |
| 476 |
> |
std::string dumpFileName_; |
| 477 |
> |
std::string statFileName_; |
| 478 |
> |
|
| 479 |
> |
double rcut_; /**< cutoff radius*/ |
| 480 |
> |
double rsw_; /**< radius of switching function*/ |
| 481 |
> |
|
| 482 |
> |
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
| 483 |
> |
|
| 484 |
> |
#ifdef IS_MPI |
| 485 |
> |
//in Parallel version, we need MolToProc |
| 486 |
> |
public: |
| 487 |
> |
|
| 488 |
> |
/** |
| 489 |
> |
* Finds the processor where a molecule resides |
| 490 |
> |
* @return the id of the processor which contains the molecule |
| 491 |
> |
* @param globalIndex global Index of the molecule |
| 492 |
> |
*/ |
| 493 |
> |
int getMolToProc(int globalIndex) { |
| 494 |
> |
//assert(globalIndex < molToProcMap_.size()); |
| 495 |
> |
return molToProcMap_[globalIndex]; |
| 496 |
> |
} |
| 497 |
> |
|
| 498 |
> |
/** |
| 499 |
> |
* Set MolToProcMap array |
| 500 |
> |
* @see #SimCreator::divideMolecules |
| 501 |
> |
*/ |
| 502 |
> |
void setMolToProcMap(const std::vector<int>& molToProcMap) { |
| 503 |
> |
molToProcMap_ = molToProcMap; |
| 504 |
> |
} |
| 505 |
> |
|
| 506 |
> |
private: |
| 507 |
> |
|
| 508 |
> |
void setupFortranParallel(); |
| 509 |
> |
|
| 510 |
> |
/** |
| 511 |
> |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
| 512 |
> |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
| 513 |
> |
* once. |
| 514 |
> |
*/ |
| 515 |
> |
std::vector<int> molToProcMap_; |
| 516 |
> |
#endif |
| 517 |
> |
|
| 518 |
> |
}; |
| 519 |
> |
|
| 520 |
> |
} //namespace oopse |
| 521 |
> |
#endif //BRAINS_SIMMODEL_HPP |
| 522 |
> |
|
