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#ifndef __SIMINFO_H__ |
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#define __SIMINFO_H__ |
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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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#include <map> |
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#include <string> |
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/** |
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* @file SimInfo.hpp |
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* @author tlin |
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* @date 11/02/2004 |
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* @version 1.0 |
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*/ |
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|
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#ifndef BRAINS_SIMMODEL_HPP |
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#define BRAINS_SIMMODEL_HPP |
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|
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#include <iostream> |
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#include <vector> |
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#include <utility> |
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#include "primitives/Atom.hpp" |
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#include "primitives/RigidBody.hpp" |
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#include "brains/fSimulation.h" |
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#include "primitives/Molecule.hpp" |
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#include "brains/Exclude.hpp" |
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#include "brains/SkipList.hpp" |
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#include "primitives/AbstractClasses.hpp" |
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#include "types/MakeStamps.hpp" |
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#include "brains/SimState.hpp" |
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#include "restraints/Restraints.hpp" |
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#include "types/MoleculeStamp.hpp" |
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#include "utils/PropertyMap.hpp" |
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#include "io/Globals.hpp" |
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#define __C |
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#include "brains/fSimulation.h" |
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#include "utils/GenericData.hpp" |
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namespace oopse{ |
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|
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/** |
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* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
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* @brief |
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*/ |
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class SimInfo { |
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public: |
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typedef MoleculeIterator MoleculeIterator; |
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|
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//#include "Minimizer.hpp" |
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//#include "minimizers/OOPSEMinimizer.hpp" |
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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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* <p> |
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* The major change of SimInfo |
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* </p> |
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*/ |
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SimInfo(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* globals); |
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virtual ~SimInfo(); |
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|
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/** |
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* Adds a molecule |
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* @return return true if adding successfully, return false if the molecule is already in SimInfo |
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* @param mol molecule to be added |
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*/ |
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bool addMolecule(Molecule* mol); |
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|
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double roundMe( double x ); |
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class OOPSEMinimizer; |
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class SimInfo{ |
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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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public: |
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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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SimInfo(); |
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~SimInfo(); |
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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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int n_atoms; // the number of atoms |
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Atom **atoms; // the array of atom objects |
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/** Returns the total number of cutoff groups in the system. */ |
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int getNGlobalCutoffGroups() { |
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return nGlobalCutoffGroups_; |
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} |
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|
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/** |
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* Returns the number of local molecules. |
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* @return the number of local molecules |
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*/ |
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int getNMolecules() { |
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return molecules_.size(); |
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} |
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|
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vector<RigidBody*> rigidBodies; // A vector of rigid bodies |
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vector<StuntDouble*> integrableObjects; |
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|
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double tau[9]; // the stress tensor |
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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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int n_bonds; // number of bends |
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int n_bends; // number of bends |
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int n_torsions; // number of torsions |
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int n_oriented; // number of of atoms with orientation |
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int ndf; // number of actual degrees of freedom |
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int ndfRaw; // number of settable degrees of freedom |
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int ndfTrans; // number of translational degrees of freedom |
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int nZconstraints; // the number of zConstraints |
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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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int setTemp; // boolean to set the temperature at each sampleTime |
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int resetIntegrator; // boolean to reset the integrator |
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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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int n_dipoles; // number of dipoles |
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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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int n_exclude; |
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Exclude* excludes; // the exclude list for ignoring pairs in fortran |
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int nGlobalExcludes; |
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int* globalExcludes; // same as above, but these guys participate in |
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// no long range forces. |
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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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int* identArray; // array of unique identifiers for the atoms |
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int* molMembershipArray; // map of atom numbers onto molecule numbers |
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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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int n_constraints; // the number of constraints on the system |
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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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int n_SRI; // the number of short range interactions |
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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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double lrPot; // the potential energy from the long range calculations. |
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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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double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the |
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// column vectors of the x, y, and z box vectors. |
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// h1 h2 h3 |
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// [ Xx Yx Zx ] |
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// [ Xy Yy Zy ] |
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// [ Xz Yz Zz ] |
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// |
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double HmatInv[3][3]; |
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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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double boxL[3]; // The Lengths of the 3 column vectors of Hmat |
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double boxVol; |
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int orthoRhombic; |
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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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double dielectric; // the dielectric of the medium for reaction field |
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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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int usePBC; // whether we use periodic boundry conditions. |
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int useLJ; |
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int useSticky; |
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int useCharges; |
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int useDipoles; |
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int useReactionField; |
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int useGB; |
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int useEAM; |
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bool haveCutoffGroups; |
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bool useInitXSstate; |
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double orthoTolerance; |
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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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double dt, run_time; // the time step and total time |
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double sampleTime, statusTime; // the position and energy dump frequencies |
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double target_temp; // the target temperature of the system |
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double thermalTime; // the temp kick interval |
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double currentTime; // Used primarily for correlation Functions |
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double resetTime; // Use to reset the integrator periodically |
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short int have_target_temp; |
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/** |
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* Sets the number of z-constraint molecules in the system. |
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*/ |
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int setNZconstraint(int nZconstraint) { |
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nZconstraint_ = nZconstraint; |
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} |
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|
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/** Returns the snapshot manager. */ |
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SnapshotManager* getSnapshotManager() { |
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return sman_; |
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} |
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|
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int n_mol; // n_molecules; |
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Molecule* molecules; // the array of molecules |
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|
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int nComponents; // the number of components in the system |
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int* componentsNmol; // the number of molecules of each component |
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MoleculeStamp** compStamps;// the stamps matching the components |
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LinkedMolStamp* headStamp; // list of stamps used in the simulation |
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|
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|
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char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. ) |
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char mixingRule[100]; // the mixing rules for Lennard jones/van der walls |
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BaseIntegrator *the_integrator; // the integrator of the simulation |
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/** Sets the snapshot manager. */ |
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void setSnapshotManager(SnapshotManager* sman) { |
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sman_ = sman; |
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} |
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|
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OOPSEMinimizer* the_minimizer; // the energy minimizer |
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Restraints* restraint; |
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bool has_minimizer; |
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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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< |
string finalName; // the name of the eor file to be written |
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string sampleName; // the name of the dump file to be written |
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string statusName; // the name of the stat file to be written |
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Globals* getGlobals() { |
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return globals_; |
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} |
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|
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int seed; //seed for random number generator |
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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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int useSolidThermInt; // is solid-state thermodynamic integration being used |
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int useLiquidThermInt; // is liquid thermodynamic integration being used |
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double thermIntLambda; // lambda for TI |
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double thermIntK; // power of lambda for TI |
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double vRaw; // unperturbed potential for TI |
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double vHarm; // harmonic potential for TI |
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int i; // just an int |
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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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vector<double> mfact; |
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vector<int> FglobalGroupMembership; |
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int ngroup; |
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int* globalGroupMembership; |
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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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// refreshes the sim if things get changed (load balanceing, volume |
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// adjustment, etc.) |
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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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void refreshSim( void ); |
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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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// sets the internal function pointer to fortran. |
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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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int getNDF(); |
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int getNDFraw(); |
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int getNDFtranslational(); |
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int getTotIntegrableObjects(); |
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void setBox( double newBox[3] ); |
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< |
void setBoxM( double newBox[3][3] ); |
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< |
void getBoxM( double theBox[3][3] ); |
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void scaleBox( double scale ); |
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|
| 246 |
< |
void setDefaultRcut( double theRcut ); |
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void setDefaultRcut( double theRcut, double theRsw ); |
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void checkCutOffs( void ); |
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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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> |
/** |
| 243 |
> |
* Finds a molecule with a specified global index |
| 244 |
> |
* @return a pointer point to found molecule |
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> |
* @param index |
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> |
*/ |
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> |
Molecule* getMoleculeByGlobalIndex(int index) { |
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> |
std::map<int, Molecule*> i; |
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> |
i = molecules_.find(index); |
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|
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< |
double getRcut( void ) { return rCut; } |
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double getRlist( void ) { return rList; } |
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< |
double getRsw( void ) { return rSw; } |
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< |
double getMaxCutoff( void ) { return maxCutoff; } |
| 172 |
< |
|
| 173 |
< |
void setTime( double theTime ) { currentTime = theTime; } |
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< |
void incrTime( double the_dt ) { currentTime += the_dt; } |
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void decrTime( double the_dt ) { currentTime -= the_dt; } |
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double getTime( void ) { return currentTime; } |
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> |
return i != molecules_.end() ? i->second : NULL; |
| 252 |
> |
} |
| 253 |
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|
| 254 |
< |
void wrapVector( double thePos[3] ); |
| 254 |
> |
/** Returns the unique atom types of local processor in an array */ |
| 255 |
> |
std::set<AtomType*> SimInfo::getUniqueAtomTypes(); |
| 256 |
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|
| 257 |
< |
SimState* getConfiguration( void ) { return myConfiguration; } |
| 258 |
< |
|
| 259 |
< |
void addProperty(GenericData* prop); |
| 260 |
< |
GenericData* getProperty(const string& propName); |
| 261 |
< |
//vector<GenericData*>& getProperties() {return properties;} |
| 257 |
> |
std::string getFinalConfigFileName() { |
| 258 |
> |
return finalConfigFileName_; |
| 259 |
> |
} |
| 260 |
> |
|
| 261 |
> |
void setFinalConfigFileName(const std::string& fileName) { |
| 262 |
> |
finalConfigFileName_ = fileName; |
| 263 |
> |
} |
| 264 |
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|
| 186 |
– |
int getSeed(void) { return seed; } |
| 187 |
– |
void setSeed(int theSeed) { seed = theSeed;} |
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|
| 266 |
< |
private: |
| 266 |
> |
std::string getDumpFileName() { |
| 267 |
> |
return dumpFileName_; |
| 268 |
> |
} |
| 269 |
> |
|
| 270 |
> |
void setDumpFileName(const std::string& fileName) { |
| 271 |
> |
dumpFileName_ = fileName; |
| 272 |
> |
} |
| 273 |
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|
| 274 |
< |
SimState* myConfiguration; |
| 274 |
> |
std::string getStatFileName() { |
| 275 |
> |
return statFileName_; |
| 276 |
> |
} |
| 277 |
> |
|
| 278 |
> |
void setStatFileName(const std::string& fileName) { |
| 279 |
> |
statFileName_ = fileName; |
| 280 |
> |
} |
| 281 |
|
|
| 282 |
< |
int boxIsInit, haveRcut, haveRsw; |
| 282 |
> |
int* getGlobalGroupMembershipPointer() { |
| 283 |
> |
return globalGroupMembership_[0]; |
| 284 |
> |
} |
| 285 |
|
|
| 286 |
< |
double rList, rCut; // variables for the neighborlist |
| 287 |
< |
double rSw; // the switching radius |
| 286 |
> |
//below functions are just forward functions |
| 287 |
> |
//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
| 288 |
> |
//the other hand, has-a relation need composing. |
| 289 |
> |
/** |
| 290 |
> |
* Adds property into property map |
| 291 |
> |
* @param genData GenericData to be added into PropertyMap |
| 292 |
> |
*/ |
| 293 |
> |
void addProperty(GenericData* genData); |
| 294 |
|
|
| 295 |
< |
double maxCutoff; |
| 295 |
> |
/** |
| 296 |
> |
* Removes property from PropertyMap by name |
| 297 |
> |
* @param propName the name of property to be removed |
| 298 |
> |
*/ |
| 299 |
> |
void removeProperty(const std::string& propName); |
| 300 |
|
|
| 301 |
< |
double distXY; |
| 302 |
< |
double distYZ; |
| 303 |
< |
double distZX; |
| 304 |
< |
|
| 204 |
< |
void calcHmatInv( void ); |
| 205 |
< |
void calcBoxL(); |
| 206 |
< |
double calcMaxCutOff(); |
| 301 |
> |
/** |
| 302 |
> |
* clear all of the properties |
| 303 |
> |
*/ |
| 304 |
> |
void clearProperties(); |
| 305 |
|
|
| 306 |
< |
|
| 307 |
< |
//Addtional Properties of SimInfo |
| 308 |
< |
map<string, GenericData*> properties; |
| 309 |
< |
void getFortranGroupArrays(SimInfo* info, |
| 310 |
< |
vector<int>& FglobalGroupMembership, |
| 213 |
< |
vector<double>& mfact); |
| 306 |
> |
/** |
| 307 |
> |
* Returns all names of properties |
| 308 |
> |
* @return all names of properties |
| 309 |
> |
*/ |
| 310 |
> |
std::vector<std::string> getPropertyNames(); |
| 311 |
|
|
| 312 |
+ |
/** |
| 313 |
+ |
* Returns all of the properties in PropertyMap |
| 314 |
+ |
* @return all of the properties in PropertyMap |
| 315 |
+ |
*/ |
| 316 |
+ |
std::vector<GenericData*> getProperties(); |
| 317 |
|
|
| 318 |
< |
}; |
| 318 |
> |
/** |
| 319 |
> |
* Returns property |
| 320 |
> |
* @param propName name of property |
| 321 |
> |
* @return a pointer point to property with propName. If no property named propName |
| 322 |
> |
* exists, return NULL |
| 323 |
> |
*/ |
| 324 |
> |
GenericData* getPropertyByName(const std::string& propName); |
| 325 |
> |
|
| 326 |
> |
friend std::ostream& operator <<(ostream& o, SimInfo& info); |
| 327 |
> |
|
| 328 |
> |
private: |
| 329 |
|
|
| 330 |
+ |
void setupSimType(); |
| 331 |
|
|
| 332 |
+ |
/** |
| 333 |
+ |
* Setup Fortran Simulation |
| 334 |
+ |
* @see #setupFortranParallel |
| 335 |
+ |
*/ |
| 336 |
+ |
void setupFortranSim(); |
| 337 |
+ |
|
| 338 |
+ |
/** Calculates the number of degress of freedom in the whole system */ |
| 339 |
+ |
void calcNdf(); |
| 340 |
+ |
void calcNdfRaw(); |
| 341 |
+ |
void calcNdfTrans(); |
| 342 |
+ |
|
| 343 |
+ |
void addExcludePairs(Molecule* mol); |
| 344 |
+ |
void removeExcludePairs(Molecule* mol); |
| 345 |
+ |
|
| 346 |
+ |
/** |
| 347 |
+ |
* Adds molecule stamps into |
| 348 |
+ |
*/ |
| 349 |
+ |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
| 350 |
+ |
|
| 351 |
+ |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
| 352 |
+ |
|
| 353 |
+ |
//degress of freedom |
| 354 |
+ |
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
| 355 |
+ |
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
| 356 |
+ |
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
| 357 |
+ |
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
| 358 |
+ |
|
| 359 |
+ |
//number of global objects |
| 360 |
+ |
int nGlobalMols_; /**< number of molecules in the system */ |
| 361 |
+ |
int nGlobalAtoms_; /**< number of atoms in the system */ |
| 362 |
+ |
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
| 363 |
+ |
|
| 364 |
+ |
/** |
| 365 |
+ |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 366 |
+ |
* corresponding content is the global index of cutoff group this atom belong to. |
| 367 |
+ |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
| 368 |
+ |
*/ |
| 369 |
+ |
std::vector<int> globalGroupMembership_; |
| 370 |
+ |
|
| 371 |
+ |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
| 372 |
+ |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
| 373 |
+ |
|
| 374 |
+ |
//number of local objects |
| 375 |
+ |
int nAtoms_; /**< number of atoms in local processor */ |
| 376 |
+ |
int nBonds_; /**< number of bonds in local processor */ |
| 377 |
+ |
int nBends_; /**< number of bends in local processor */ |
| 378 |
+ |
int nTorsions_; /**< number of torsions in local processor */ |
| 379 |
+ |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
| 380 |
+ |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
| 381 |
+ |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
| 382 |
+ |
int nConstraints_; /**< number of constraints in local processors */ |
| 383 |
+ |
|
| 384 |
+ |
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
| 385 |
+ |
Exclude exclude_; |
| 386 |
+ |
ForceField* forceField_; |
| 387 |
+ |
PropertyMap properties_; /**< Generic Property */ |
| 388 |
+ |
SnapshotManager* sman_; /**< SnapshotManager */ |
| 389 |
+ |
Globals* globals_; |
| 390 |
+ |
int seed_; /**< seed for random number generator */ |
| 391 |
+ |
|
| 392 |
+ |
LocalIndexManager localIndexMan_; |
| 393 |
+ |
|
| 394 |
+ |
std::string finalConfigFileName_; |
| 395 |
+ |
std::string dumpFileName_; |
| 396 |
+ |
std::string statFileName_; |
| 397 |
+ |
|
| 398 |
+ |
#ifdef IS_MPI |
| 399 |
+ |
//in Parallel version, we need MolToProc |
| 400 |
+ |
public: |
| 401 |
+ |
|
| 402 |
+ |
/** |
| 403 |
+ |
* Finds the processor where a molecule resides |
| 404 |
+ |
* @return the id of the processor which contains the molecule |
| 405 |
+ |
* @param globalIndex global Index of the molecule |
| 406 |
+ |
*/ |
| 407 |
+ |
int getMolToProc(int globalIndex) { |
| 408 |
+ |
//assert(globalIndex < molToProcMap_.size()); |
| 409 |
+ |
return molToProcMap_[globalIndex]; |
| 410 |
+ |
} |
| 411 |
+ |
|
| 412 |
+ |
int* getMolToProcMapPointer() { |
| 413 |
+ |
return &molToProcMap_[0]; |
| 414 |
+ |
} |
| 415 |
+ |
|
| 416 |
+ |
private: |
| 417 |
+ |
|
| 418 |
+ |
void setupFortranParallel(); |
| 419 |
+ |
|
| 420 |
+ |
/** |
| 421 |
+ |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
| 422 |
+ |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
| 423 |
+ |
* once. |
| 424 |
+ |
*/ |
| 425 |
+ |
std::vector<int> molToProcMap_; |
| 426 |
|
#endif |
| 427 |
+ |
|
| 428 |
+ |
}; |
| 429 |
+ |
|
| 430 |
+ |
} //namespace oopse |
| 431 |
+ |
#endif //BRAINS_SIMMODEL_HPP |
