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#ifndef __SIMINFO_H__ |
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#define __SIMINFO_H__ |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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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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#include <map> |
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#include <string> |
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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 "primitives/Atom.hpp" |
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#include "primitives/RigidBody.hpp" |
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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 "io/Globals.hpp" |
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#include "math/Vector3.hpp" |
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#include "math/SquareMatrix3.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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#include "utils/GenericData.hpp" |
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namespace oopse{ |
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//#include "Minimizer.hpp" |
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//#include "minimizers/OOPSEMinimizer.hpp" |
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//forward decalration |
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class SnapshotManager; |
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class Molecule; |
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class SelectionManager; |
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class StuntDouble; |
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/** |
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* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
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* @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules. |
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* The Molecule class maintains all of the concrete objects |
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* (atoms, bond, bend, torsions, rigid bodies, cutoff groups, constrains). |
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* In both the single and parallel versions, atoms and |
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* rigid bodies have both global and local indices. The local index is |
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* not relevant to molecules or cutoff groups. |
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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(ForceField* ff, Globals* simParams); |
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virtual ~SimInfo(); |
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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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* 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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public: |
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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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SimInfo(); |
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~SimInfo(); |
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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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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 atoms in the system. */ |
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int getNGlobalAtoms() { |
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return nGlobalAtoms_; |
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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 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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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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/** |
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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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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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/** |
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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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int n_dipoles; // number of dipoles |
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int getNGlobalConstraints(); |
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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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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 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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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 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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int n_constraints; // the number of constraints on the system |
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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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int n_SRI; // the number of short range interactions |
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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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double lrPot; // the potential energy from the long range calculations. |
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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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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 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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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 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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double dielectric; // the dielectric of the medium for reaction field |
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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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int usePBC; // whether we use periodic boundry conditions. |
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int useDirectionalAtoms; |
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int useLennardJones; |
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int useElectrostatics; |
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int useCharges; |
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int useDipoles; |
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int useSticky; |
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int useGayBerne; |
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int useEAM; |
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int useShapes; |
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int useFLARB; |
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int useReactionField; |
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bool haveCutoffGroups; |
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bool useInitXSstate; |
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double orthoTolerance; |
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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 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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/** Returns the number of degrees of freedom */ |
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int getNdf() { |
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return ndf_ - getFdf(); |
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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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> |
/** 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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< |
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 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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< |
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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> |
/** sets the current number of frozen degrees of freedom */ |
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> |
void setFdf(int fdf) { |
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> |
fdf_local = fdf; |
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> |
} |
| 227 |
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|
| 228 |
< |
int seed; //seed for random number generator |
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> |
int getFdf(); |
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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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> |
} |
| 236 |
|
|
| 237 |
< |
int useSolidThermInt; // is solid-state thermodynamic integration being used |
| 238 |
< |
int useLiquidThermInt; // is liquid thermodynamic integration being used |
| 239 |
< |
double thermIntLambda; // lambda for TI |
| 240 |
< |
double thermIntK; // power of lambda for TI |
| 241 |
< |
double vRaw; // unperturbed potential for TI |
| 242 |
< |
double vHarm; // harmonic potential for TI |
| 243 |
< |
int i; // just an int |
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> |
/** |
| 238 |
> |
* 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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> |
} |
| 243 |
> |
|
| 244 |
> |
/** Returns the snapshot manager. */ |
| 245 |
> |
SnapshotManager* getSnapshotManager() { |
| 246 |
> |
return sman_; |
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> |
} |
| 248 |
|
|
| 249 |
< |
vector<double> mfact; |
| 250 |
< |
vector<int> FglobalGroupMembership; |
| 251 |
< |
int ngroup; |
| 252 |
< |
int* globalGroupMembership; |
| 249 |
> |
/** Sets the snapshot manager. */ |
| 250 |
> |
void setSnapshotManager(SnapshotManager* sman); |
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> |
|
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> |
/** Returns the force field */ |
| 253 |
> |
ForceField* getForceField() { |
| 254 |
> |
return forceField_; |
| 255 |
> |
} |
| 256 |
|
|
| 257 |
< |
// refreshes the sim if things get changed (load balanceing, volume |
| 258 |
< |
// adjustment, etc.) |
| 257 |
> |
Globals* getSimParams() { |
| 258 |
> |
return simParams_; |
| 259 |
> |
} |
| 260 |
|
|
| 261 |
< |
void refreshSim( void ); |
| 262 |
< |
|
| 261 |
> |
/** Returns the velocity of center of mass of the whole system.*/ |
| 262 |
> |
Vector3d getComVel(); |
| 263 |
|
|
| 264 |
< |
// sets the internal function pointer to fortran. |
| 264 |
> |
/** Returns the center of the mass of the whole system.*/ |
| 265 |
> |
Vector3d getCom(); |
| 266 |
> |
/** Returns the center of the mass and Center of Mass velocity of the whole system.*/ |
| 267 |
> |
void getComAll(Vector3d& com,Vector3d& comVel); |
| 268 |
|
|
| 269 |
+ |
/** Returns intertia tensor for the entire system and system Angular Momentum.*/ |
| 270 |
+ |
void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum); |
| 271 |
+ |
|
| 272 |
+ |
/** Returns system angular momentum */ |
| 273 |
+ |
Vector3d getAngularMomentum(); |
| 274 |
|
|
| 275 |
< |
int getNDF(); |
| 276 |
< |
int getNDFraw(); |
| 277 |
< |
int getNDFtranslational(); |
| 278 |
< |
int getTotIntegrableObjects(); |
| 279 |
< |
void setBox( double newBox[3] ); |
| 280 |
< |
void setBoxM( double newBox[3][3] ); |
| 165 |
< |
void getBoxM( double theBox[3][3] ); |
| 166 |
< |
void scaleBox( double scale ); |
| 167 |
< |
|
| 168 |
< |
void setDefaultRcut( double theRcut ); |
| 169 |
< |
void setDefaultRcut( double theRcut, double theRsw ); |
| 170 |
< |
void checkCutOffs( void ); |
| 171 |
< |
|
| 172 |
< |
double getRcut( void ) { return rCut; } |
| 173 |
< |
double getRlist( void ) { return rList; } |
| 174 |
< |
double getRsw( void ) { return rSw; } |
| 175 |
< |
double getMaxCutoff( void ) { return maxCutoff; } |
| 176 |
< |
|
| 177 |
< |
void setTime( double theTime ) { currentTime = theTime; } |
| 178 |
< |
void incrTime( double the_dt ) { currentTime += the_dt; } |
| 179 |
< |
void decrTime( double the_dt ) { currentTime -= the_dt; } |
| 180 |
< |
double getTime( void ) { return currentTime; } |
| 181 |
< |
|
| 182 |
< |
void wrapVector( double thePos[3] ); |
| 275 |
> |
/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/ |
| 276 |
> |
void getGyrationalVolume(RealType &vol); |
| 277 |
> |
/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/ |
| 278 |
> |
void getGyrationalVolume(RealType &vol, RealType &detI); |
| 279 |
> |
/** main driver function to interact with fortran during the initialization and molecule migration */ |
| 280 |
> |
void update(); |
| 281 |
|
|
| 282 |
< |
SimState* getConfiguration( void ) { return myConfiguration; } |
| 283 |
< |
|
| 284 |
< |
void addProperty(GenericData* prop); |
| 285 |
< |
GenericData* getProperty(const string& propName); |
| 188 |
< |
//vector<GenericData*>& getProperties() {return properties;} |
| 282 |
> |
/** Returns the local index manager */ |
| 283 |
> |
LocalIndexManager* getLocalIndexManager() { |
| 284 |
> |
return &localIndexMan_; |
| 285 |
> |
} |
| 286 |
|
|
| 287 |
< |
int getSeed(void) { return seed; } |
| 288 |
< |
void setSeed(int theSeed) { seed = theSeed;} |
| 287 |
> |
int getMoleculeStampId(int globalIndex) { |
| 288 |
> |
//assert(globalIndex < molStampIds_.size()) |
| 289 |
> |
return molStampIds_[globalIndex]; |
| 290 |
> |
} |
| 291 |
|
|
| 292 |
< |
private: |
| 292 |
> |
/** Returns the molecule stamp */ |
| 293 |
> |
MoleculeStamp* getMoleculeStamp(int id) { |
| 294 |
> |
return moleculeStamps_[id]; |
| 295 |
> |
} |
| 296 |
|
|
| 297 |
< |
SimState* myConfiguration; |
| 297 |
> |
/** Return the total number of the molecule stamps */ |
| 298 |
> |
int getNMoleculeStamp() { |
| 299 |
> |
return moleculeStamps_.size(); |
| 300 |
> |
} |
| 301 |
> |
/** |
| 302 |
> |
* Finds a molecule with a specified global index |
| 303 |
> |
* @return a pointer point to found molecule |
| 304 |
> |
* @param index |
| 305 |
> |
*/ |
| 306 |
> |
Molecule* getMoleculeByGlobalIndex(int index) { |
| 307 |
> |
MoleculeIterator i; |
| 308 |
> |
i = molecules_.find(index); |
| 309 |
|
|
| 310 |
< |
int boxIsInit, haveRcut, haveRsw; |
| 310 |
> |
return i != molecules_.end() ? i->second : NULL; |
| 311 |
> |
} |
| 312 |
|
|
| 313 |
< |
double rList, rCut; // variables for the neighborlist |
| 314 |
< |
double rSw; // the switching radius |
| 313 |
> |
RealType getRcut() { |
| 314 |
> |
return rcut_; |
| 315 |
> |
} |
| 316 |
|
|
| 317 |
< |
double maxCutoff; |
| 317 |
> |
RealType getRsw() { |
| 318 |
> |
return rsw_; |
| 319 |
> |
} |
| 320 |
|
|
| 321 |
< |
double distXY; |
| 322 |
< |
double distYZ; |
| 323 |
< |
double distZX; |
| 324 |
< |
|
| 325 |
< |
void calcHmatInv( void ); |
| 326 |
< |
void calcBoxL(); |
| 327 |
< |
double calcMaxCutOff(); |
| 321 |
> |
RealType getList() { |
| 322 |
> |
return rlist_; |
| 323 |
> |
} |
| 324 |
> |
|
| 325 |
> |
std::string getFinalConfigFileName() { |
| 326 |
> |
return finalConfigFileName_; |
| 327 |
> |
} |
| 328 |
|
|
| 329 |
< |
|
| 330 |
< |
//Addtional Properties of SimInfo |
| 331 |
< |
map<string, GenericData*> properties; |
| 215 |
< |
void getFortranGroupArrays(SimInfo* info, |
| 216 |
< |
vector<int>& FglobalGroupMembership, |
| 217 |
< |
vector<double>& mfact); |
| 329 |
> |
void setFinalConfigFileName(const std::string& fileName) { |
| 330 |
> |
finalConfigFileName_ = fileName; |
| 331 |
> |
} |
| 332 |
|
|
| 333 |
+ |
std::string getRawMetaData() { |
| 334 |
+ |
return rawMetaData_; |
| 335 |
+ |
} |
| 336 |
+ |
void setRawMetaData(const std::string& rawMetaData) { |
| 337 |
+ |
rawMetaData_ = rawMetaData; |
| 338 |
+ |
} |
| 339 |
+ |
|
| 340 |
+ |
std::string getDumpFileName() { |
| 341 |
+ |
return dumpFileName_; |
| 342 |
+ |
} |
| 343 |
+ |
|
| 344 |
+ |
void setDumpFileName(const std::string& fileName) { |
| 345 |
+ |
dumpFileName_ = fileName; |
| 346 |
+ |
} |
| 347 |
|
|
| 348 |
< |
}; |
| 348 |
> |
std::string getStatFileName() { |
| 349 |
> |
return statFileName_; |
| 350 |
> |
} |
| 351 |
> |
|
| 352 |
> |
void setStatFileName(const std::string& fileName) { |
| 353 |
> |
statFileName_ = fileName; |
| 354 |
> |
} |
| 355 |
> |
|
| 356 |
> |
std::string getRestFileName() { |
| 357 |
> |
return restFileName_; |
| 358 |
> |
} |
| 359 |
> |
|
| 360 |
> |
void setRestFileName(const std::string& fileName) { |
| 361 |
> |
restFileName_ = fileName; |
| 362 |
> |
} |
| 363 |
|
|
| 364 |
+ |
/** |
| 365 |
+ |
* Sets GlobalGroupMembership |
| 366 |
+ |
* @see #SimCreator::setGlobalIndex |
| 367 |
+ |
*/ |
| 368 |
+ |
void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) { |
| 369 |
+ |
assert(globalGroupMembership.size() == nGlobalAtoms_); |
| 370 |
+ |
globalGroupMembership_ = globalGroupMembership; |
| 371 |
+ |
} |
| 372 |
|
|
| 373 |
+ |
/** |
| 374 |
+ |
* Sets GlobalMolMembership |
| 375 |
+ |
* @see #SimCreator::setGlobalIndex |
| 376 |
+ |
*/ |
| 377 |
+ |
void setGlobalMolMembership(const std::vector<int>& globalMolMembership) { |
| 378 |
+ |
assert(globalMolMembership.size() == nGlobalAtoms_); |
| 379 |
+ |
globalMolMembership_ = globalMolMembership; |
| 380 |
+ |
} |
| 381 |
+ |
|
| 382 |
+ |
|
| 383 |
+ |
bool isFortranInitialized() { |
| 384 |
+ |
return fortranInitialized_; |
| 385 |
+ |
} |
| 386 |
+ |
|
| 387 |
+ |
bool getCalcBoxDipole() { |
| 388 |
+ |
return calcBoxDipole_; |
| 389 |
+ |
} |
| 390 |
+ |
|
| 391 |
+ |
//below functions are just forward functions |
| 392 |
+ |
//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
| 393 |
+ |
//the other hand, has-a relation need composing. |
| 394 |
+ |
/** |
| 395 |
+ |
* Adds property into property map |
| 396 |
+ |
* @param genData GenericData to be added into PropertyMap |
| 397 |
+ |
*/ |
| 398 |
+ |
void addProperty(GenericData* genData); |
| 399 |
+ |
|
| 400 |
+ |
/** |
| 401 |
+ |
* Removes property from PropertyMap by name |
| 402 |
+ |
* @param propName the name of property to be removed |
| 403 |
+ |
*/ |
| 404 |
+ |
void removeProperty(const std::string& propName); |
| 405 |
+ |
|
| 406 |
+ |
/** |
| 407 |
+ |
* clear all of the properties |
| 408 |
+ |
*/ |
| 409 |
+ |
void clearProperties(); |
| 410 |
+ |
|
| 411 |
+ |
/** |
| 412 |
+ |
* Returns all names of properties |
| 413 |
+ |
* @return all names of properties |
| 414 |
+ |
*/ |
| 415 |
+ |
std::vector<std::string> getPropertyNames(); |
| 416 |
+ |
|
| 417 |
+ |
/** |
| 418 |
+ |
* Returns all of the properties in PropertyMap |
| 419 |
+ |
* @return all of the properties in PropertyMap |
| 420 |
+ |
*/ |
| 421 |
+ |
std::vector<GenericData*> getProperties(); |
| 422 |
+ |
|
| 423 |
+ |
/** |
| 424 |
+ |
* Returns property |
| 425 |
+ |
* @param propName name of property |
| 426 |
+ |
* @return a pointer point to property with propName. If no property named propName |
| 427 |
+ |
* exists, return NULL |
| 428 |
+ |
*/ |
| 429 |
+ |
GenericData* getPropertyByName(const std::string& propName); |
| 430 |
+ |
|
| 431 |
+ |
/** |
| 432 |
+ |
* add all exclude pairs of a molecule into exclude list. |
| 433 |
+ |
*/ |
| 434 |
+ |
void addExcludePairs(Molecule* mol); |
| 435 |
+ |
|
| 436 |
+ |
/** |
| 437 |
+ |
* remove all exclude pairs which belong to a molecule from exclude list |
| 438 |
+ |
*/ |
| 439 |
+ |
|
| 440 |
+ |
void removeExcludePairs(Molecule* mol); |
| 441 |
+ |
|
| 442 |
+ |
|
| 443 |
+ |
/** Returns the unique atom types of local processor in an array */ |
| 444 |
+ |
std::set<AtomType*> getUniqueAtomTypes(); |
| 445 |
+ |
|
| 446 |
+ |
friend std::ostream& operator <<(std::ostream& o, SimInfo& info); |
| 447 |
+ |
|
| 448 |
+ |
void getCutoff(RealType& rcut, RealType& rsw); |
| 449 |
+ |
|
| 450 |
+ |
private: |
| 451 |
+ |
|
| 452 |
+ |
/** fill up the simtype struct*/ |
| 453 |
+ |
void setupSimType(); |
| 454 |
+ |
|
| 455 |
+ |
/** |
| 456 |
+ |
* Setup Fortran Simulation |
| 457 |
+ |
* @see #setupFortranParallel |
| 458 |
+ |
*/ |
| 459 |
+ |
void setupFortranSim(); |
| 460 |
+ |
|
| 461 |
+ |
/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */ |
| 462 |
+ |
void setupCutoff(); |
| 463 |
+ |
|
| 464 |
+ |
/** Figure out which coulombic correction method to use and pass to fortran */ |
| 465 |
+ |
void setupElectrostaticSummationMethod( int isError ); |
| 466 |
+ |
|
| 467 |
+ |
/** Figure out which polynomial type to use for the switching function */ |
| 468 |
+ |
void setupSwitchingFunction(); |
| 469 |
+ |
|
| 470 |
+ |
/** Determine if we need to accumulate the simulation box dipole */ |
| 471 |
+ |
void setupAccumulateBoxDipole(); |
| 472 |
+ |
|
| 473 |
+ |
/** Calculates the number of degress of freedom in the whole system */ |
| 474 |
+ |
void calcNdf(); |
| 475 |
+ |
void calcNdfRaw(); |
| 476 |
+ |
void calcNdfTrans(); |
| 477 |
+ |
|
| 478 |
+ |
ForceField* forceField_; |
| 479 |
+ |
Globals* simParams_; |
| 480 |
+ |
|
| 481 |
+ |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
| 482 |
+ |
|
| 483 |
+ |
/** |
| 484 |
+ |
* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole |
| 485 |
+ |
* system. |
| 486 |
+ |
*/ |
| 487 |
+ |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
| 488 |
+ |
|
| 489 |
+ |
//degress of freedom |
| 490 |
+ |
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
| 491 |
+ |
int fdf_local; /**< number of frozen degrees of freedom */ |
| 492 |
+ |
int fdf_; /**< number of frozen degrees of freedom */ |
| 493 |
+ |
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
| 494 |
+ |
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
| 495 |
+ |
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
| 496 |
+ |
|
| 497 |
+ |
//number of global objects |
| 498 |
+ |
int nGlobalMols_; /**< number of molecules in the system */ |
| 499 |
+ |
int nGlobalAtoms_; /**< number of atoms in the system */ |
| 500 |
+ |
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
| 501 |
+ |
int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */ |
| 502 |
+ |
int nGlobalRigidBodies_; /**< number of rigid bodies in this system */ |
| 503 |
+ |
/** |
| 504 |
+ |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 505 |
+ |
* corresponding content is the global index of cutoff group this atom belong to. |
| 506 |
+ |
* It is filled by SimCreator once and only once, since it never changed during the simulation. |
| 507 |
+ |
*/ |
| 508 |
+ |
std::vector<int> globalGroupMembership_; |
| 509 |
+ |
|
| 510 |
+ |
/** |
| 511 |
+ |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
| 512 |
+ |
* corresponding content is the global index of molecule this atom belong to. |
| 513 |
+ |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
| 514 |
+ |
*/ |
| 515 |
+ |
std::vector<int> globalMolMembership_; |
| 516 |
+ |
|
| 517 |
+ |
|
| 518 |
+ |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
| 519 |
+ |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
| 520 |
+ |
|
| 521 |
+ |
//number of local objects |
| 522 |
+ |
int nAtoms_; /**< number of atoms in local processor */ |
| 523 |
+ |
int nBonds_; /**< number of bonds in local processor */ |
| 524 |
+ |
int nBends_; /**< number of bends in local processor */ |
| 525 |
+ |
int nTorsions_; /**< number of torsions in local processor */ |
| 526 |
+ |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
| 527 |
+ |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
| 528 |
+ |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
| 529 |
+ |
int nConstraints_; /**< number of constraints in local processors */ |
| 530 |
+ |
|
| 531 |
+ |
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
| 532 |
+ |
Exclude exclude_; |
| 533 |
+ |
PropertyMap properties_; /**< Generic Property */ |
| 534 |
+ |
SnapshotManager* sman_; /**< SnapshotManager */ |
| 535 |
+ |
|
| 536 |
+ |
/** |
| 537 |
+ |
* The reason to have a local index manager is that when molecule is migrating to other processors, |
| 538 |
+ |
* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
| 539 |
+ |
* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager |
| 540 |
+ |
* to make a efficient data moving plan. |
| 541 |
+ |
*/ |
| 542 |
+ |
LocalIndexManager localIndexMan_; |
| 543 |
+ |
|
| 544 |
+ |
// unparsed MetaData block for storing in Dump and EOR files: |
| 545 |
+ |
std::string rawMetaData_; |
| 546 |
+ |
|
| 547 |
+ |
//file names |
| 548 |
+ |
std::string finalConfigFileName_; |
| 549 |
+ |
std::string dumpFileName_; |
| 550 |
+ |
std::string statFileName_; |
| 551 |
+ |
std::string restFileName_; |
| 552 |
+ |
|
| 553 |
+ |
RealType rcut_; /**< cutoff radius*/ |
| 554 |
+ |
RealType rsw_; /**< radius of switching function*/ |
| 555 |
+ |
RealType rlist_; /**< neighbor list radius */ |
| 556 |
+ |
|
| 557 |
+ |
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
| 558 |
+ |
|
| 559 |
+ |
bool calcBoxDipole_; /**< flag to indicate whether or not we calculate the simulation box dipole moment */ |
| 560 |
+ |
|
| 561 |
+ |
public: |
| 562 |
+ |
/** |
| 563 |
+ |
* return an integral objects by its global index. In MPI version, if the StuntDouble with specified |
| 564 |
+ |
* global index does not belong to local processor, a NULL will be return. |
| 565 |
+ |
*/ |
| 566 |
+ |
StuntDouble* getIOIndexToIntegrableObject(int index); |
| 567 |
+ |
void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v); |
| 568 |
+ |
private: |
| 569 |
+ |
std::vector<StuntDouble*> IOIndexToIntegrableObject; |
| 570 |
+ |
//public: |
| 571 |
+ |
//void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v); |
| 572 |
+ |
/** |
| 573 |
+ |
* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified |
| 574 |
+ |
* global index does not belong to local processor, a NULL will be return. |
| 575 |
+ |
*/ |
| 576 |
+ |
//StuntDouble* getStuntDoubleFromGlobalIndex(int index); |
| 577 |
+ |
//private: |
| 578 |
+ |
//std::vector<StuntDouble*> sdByGlobalIndex_; |
| 579 |
+ |
|
| 580 |
+ |
#ifdef IS_MPI |
| 581 |
+ |
//in Parallel version, we need MolToProc |
| 582 |
+ |
public: |
| 583 |
+ |
|
| 584 |
+ |
/** |
| 585 |
+ |
* Finds the processor where a molecule resides |
| 586 |
+ |
* @return the id of the processor which contains the molecule |
| 587 |
+ |
* @param globalIndex global Index of the molecule |
| 588 |
+ |
*/ |
| 589 |
+ |
int getMolToProc(int globalIndex) { |
| 590 |
+ |
//assert(globalIndex < molToProcMap_.size()); |
| 591 |
+ |
return molToProcMap_[globalIndex]; |
| 592 |
+ |
} |
| 593 |
+ |
|
| 594 |
+ |
/** |
| 595 |
+ |
* Set MolToProcMap array |
| 596 |
+ |
* @see #SimCreator::divideMolecules |
| 597 |
+ |
*/ |
| 598 |
+ |
void setMolToProcMap(const std::vector<int>& molToProcMap) { |
| 599 |
+ |
molToProcMap_ = molToProcMap; |
| 600 |
+ |
} |
| 601 |
+ |
|
| 602 |
+ |
|
| 603 |
+ |
|
| 604 |
+ |
private: |
| 605 |
+ |
|
| 606 |
+ |
void setupFortranParallel(); |
| 607 |
+ |
|
| 608 |
+ |
/** |
| 609 |
+ |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
| 610 |
+ |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
| 611 |
+ |
* once. |
| 612 |
+ |
*/ |
| 613 |
+ |
std::vector<int> molToProcMap_; |
| 614 |
+ |
|
| 615 |
|
#endif |
| 616 |
+ |
|
| 617 |
+ |
}; |
| 618 |
+ |
|
| 619 |
+ |
} //namespace oopse |
| 620 |
+ |
#endif //BRAINS_SIMMODEL_HPP |
| 621 |
+ |
|
