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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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* @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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#ifndef BRAINS_SIMMODEL_HPP
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#define BRAINS_SIMMODEL_HPP
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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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#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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//another nonsense macro declaration
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#define __C
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#include "brains/fSimulation.h"
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namespace oopse{
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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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* @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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* 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(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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* 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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* 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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/** 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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/** 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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/** 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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* 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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* 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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/** 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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/** 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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/** 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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/** 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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/** 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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/** 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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/** 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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/** 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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* 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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* 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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/** 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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/** 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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/** 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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//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
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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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* 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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/** Returns the snapshot manager. */
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SnapshotManager* getSnapshotManager() {
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return sman_;
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}
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/** Sets the snapshot manager. */
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void setSnapshotManager(SnapshotManager* sman);
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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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Globals* getGlobals() {
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return globals_;
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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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/** Returns the center of the mass of the whole system.*/
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Vector3d getCom();
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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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/** 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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/** main driver function to interact with fortran during the initialization and molecule migration */
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void update();
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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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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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/** 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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* 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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return i != molecules_.end() ? i->second : NULL;
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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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double getRcut() {
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return rcut_;
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}
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double getRsw() {
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return rsw_;
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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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void setFinalConfigFileName(const std::string& fileName) {
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finalConfigFileName_ = fileName;
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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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void setDumpFileName(const std::string& fileName) {
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dumpFileName_ = fileName;
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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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void setStatFileName(const std::string& fileName) {
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statFileName_ = fileName;
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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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* 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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bool isFortranInitialized() {
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return fortranInitialized_;
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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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* 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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* clear all of the properties
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*/
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void clearProperties();
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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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* 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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* 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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friend std::ostream& operator <<(ostream& o, SimInfo& info);
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private:
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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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/** fill up the simtype struct*/
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void setupSimType();
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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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/** 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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/** 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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void addExcludePairs(Molecule* mol);
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void removeExcludePairs(Molecule* mol);
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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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std::map<int, Molecule*> molecules_; /**< Molecule array */
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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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//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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/**
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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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| 421 |
* 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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* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
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| 427 |
* corresponding content is the global index of molecule this atom belong to.
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| 428 |
* 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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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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//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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| 443 |
int nCutoffGroups_; /**< number of cutoff groups in local processor */
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| 444 |
int nConstraints_; /**< number of constraints in local processors */
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| 445 |
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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 */
|
| 453 |
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/**
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| 455 |
* The reason to have a local index manager is that when molecule is migrating to other processors,
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| 456 |
* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
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| 457 |
* 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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//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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double rcut_; /**< cutoff radius*/
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double rsw_; /**< radius of switching function*/
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bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
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| 471 |
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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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| 475 |
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| 476 |
/**
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| 477 |
* Finds the processor where a molecule resides
|
| 478 |
* @return the id of the processor which contains the molecule
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| 479 |
* @param globalIndex global Index of the molecule
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*/
|
| 481 |
int getMolToProc(int globalIndex) {
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| 482 |
//assert(globalIndex < molToProcMap_.size());
|
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return molToProcMap_[globalIndex];
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}
|
| 485 |
|
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/**
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| 487 |
* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class
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| 488 |
* @see #SimCreator::divideMolecules
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| 489 |
*/
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int* getMolToProcMapPointer() {
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return &molToProcMap_[0];
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}
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| 493 |
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| 494 |
private:
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| 495 |
|
| 496 |
void setupFortranParallel();
|
| 497 |
|
| 498 |
/**
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| 499 |
* The size of molToProcMap_ is equal to total number of molecules in the system.
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| 500 |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
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| 501 |
* once.
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| 502 |
*/
|
| 503 |
std::vector<int> molToProcMap_;
|
| 504 |
#endif
|
| 505 |
|
| 506 |
};
|
| 507 |
|
| 508 |
} //namespace oopse
|
| 509 |
#endif //BRAINS_SIMMODEL_HPP
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