src/brains/SimInfo.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @file SimInfo.hpp
 * @author    tlin
 * @date  11/02/2004
 * @version 1.0
 */ 

#ifndef BRAINS_SIMMODEL_HPP
#define BRAINS_SIMMODEL_HPP

#include <iostream>
#include <set>
#include <utility>
#include <vector>

#include "brains/Exclude.hpp"
#include "io/Globals.hpp"
#include "math/Vector3.hpp"
#include "math/SquareMatrix3.hpp"
#include "types/MoleculeStamp.hpp"
#include "UseTheForce/ForceField.hpp"
#include "utils/PropertyMap.hpp"
#include "utils/LocalIndexManager.hpp"

//another nonsense macro declaration
#define __C
#include "brains/fSimulation.h"

namespace oopse{

  //forward decalration 
  class SnapshotManager;
  class Molecule;
  class SelectionManager;
  /**
   * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" 
   * @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules.
   * The Molecule class maintains all of the concrete objects 
   * (atoms, bond, bend, torsions, rigid bodies, cutoff groups, constrains).
   * In both the  single and parallel versions,  atoms and
   * rigid bodies have both global and local indices.  The local index is 
   * not relevant to molecules or cutoff groups.
   */
  class SimInfo {
  public:
    typedef std::map<int, Molecule*>::iterator  MoleculeIterator;

    /**
     * Constructor of SimInfo
     * @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
     * second element is the total number of molecules with the same molecule stamp in the system
     * @param ff pointer of a concrete ForceField instance
     * @param simParams 
     * @note
     */
    SimInfo(ForceField* ff, Globals* simParams);
    virtual ~SimInfo();

    /**
     * Adds a molecule
     * @return return true if adding successfully, return false if the molecule is already in SimInfo
     * @param mol molecule to be added
     */
    bool addMolecule(Molecule* mol);

    /**
     * Removes a molecule from SimInfo
     * @return true if removing successfully, return false if molecule is not in this SimInfo
     */
    bool removeMolecule(Molecule* mol);

    /** Returns the total number of molecules in the system. */
    int getNGlobalMolecules() {
      return nGlobalMols_;
    }

    /** Returns the total number of atoms in the system. */
    int getNGlobalAtoms() {
      return nGlobalAtoms_;
    }

    /** Returns the total number of cutoff groups in the system. */
    int getNGlobalCutoffGroups() {
      return nGlobalCutoffGroups_;
    }

    /**
     * Returns the total number of integrable objects (total number of rigid bodies plus the total number
     * of atoms which do not belong to the rigid bodies) in the system
     */
    int getNGlobalIntegrableObjects() {
      return nGlobalIntegrableObjects_;
    }

    /**
     * Returns the total number of integrable objects (total number of rigid bodies plus the total number
     * of atoms which do not belong to the rigid bodies) in the system
     */
    int getNGlobalRigidBodies() {
      return nGlobalRigidBodies_;
    }

    int getNGlobalConstraints();
    /** 
     * Returns the number of local molecules.
     * @return the number of local molecules 
     */
    int getNMolecules() {
      return molecules_.size();
    }

    /** Returns the number of local atoms */
    unsigned int getNAtoms() {
      return nAtoms_;
    }

    /** Returns the number of local bonds */        
    unsigned int getNBonds(){
      return nBonds_;
    }

    /** Returns the number of local bends */        
    unsigned int getNBends() {
      return nBends_;
    }

    /** Returns the number of local torsions */        
    unsigned int getNTorsions() {
      return nTorsions_;
    }

    /** Returns the number of local rigid bodies */        
    unsigned int getNRigidBodies() {
      return nRigidBodies_;
    }

    /** Returns the number of local integrable objects */
    unsigned int getNIntegrableObjects() {
      return nIntegrableObjects_;
    }

    /** Returns the number of local cutoff groups */
    unsigned int getNCutoffGroups() {
      return nCutoffGroups_;
    }

    /** Returns the total number of constraints in this SimInfo */
    unsigned int getNConstraints() {
      return nConstraints_;
    }
        
    /**
     * Returns the first molecule in this SimInfo and intialize the iterator.
     * @return the first molecule, return NULL if there is not molecule in this SimInfo
     * @param i the iterator of molecule array (user shouldn't change it)
     */
    Molecule* beginMolecule(MoleculeIterator& i);

    /** 
     * Returns the next avaliable Molecule based on the iterator.
     * @return the next avaliable molecule, return NULL if reaching the end of the array 
     * @param i the iterator of molecule array
     */
    Molecule* nextMolecule(MoleculeIterator& i);

    /** Returns the number of degrees of freedom */
    int getNdf() {
      return ndf_ - getFdf();
    }

    /** Returns the number of raw degrees of freedom */
    int getNdfRaw() {
      return ndfRaw_;
    }

    /** Returns the number of translational degrees of freedom */
    int getNdfTrans() {
      return ndfTrans_;
    }

    /** sets the current number of frozen degrees of freedom */
    void setFdf(int fdf) {
      fdf_local = fdf;
    }

    int getFdf(); 
    
    //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
        
    /** Returns the total number of z-constraint molecules in the system */
    int getNZconstraint() {
      return nZconstraint_;
    }

    /** 
     * Sets the number of z-constraint molecules in the system.
     */
    void setNZconstraint(int nZconstraint) {
      nZconstraint_ = nZconstraint;
    }
        
    /** Returns the snapshot manager. */
    SnapshotManager* getSnapshotManager() {
      return sman_;
    }

    /** Sets the snapshot manager. */
    void setSnapshotManager(SnapshotManager* sman);
        
    /** Returns the force field */
    ForceField* getForceField() {
      return forceField_;
    }

    Globals* getSimParams() {
      return simParams_;
    }

    /** Returns the velocity of center of mass of the whole system.*/
    Vector3d getComVel();

    /** Returns the center of the mass of the whole system.*/
    Vector3d getCom();
   /** Returns the center of the mass and Center of Mass velocity of the whole system.*/ 
    void getComAll(Vector3d& com,Vector3d& comVel);

    /** Returns intertia tensor for the entire system and system Angular Momentum.*/
    void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
    
    /** Returns system angular momentum */
    Vector3d getAngularMomentum();

    /** main driver function to interact with fortran during the initialization and molecule migration */
    void update();

    /** Returns the local index manager */
    LocalIndexManager* getLocalIndexManager() {
      return &localIndexMan_;
    }

    int getMoleculeStampId(int globalIndex) {
      //assert(globalIndex < molStampIds_.size())
      return molStampIds_[globalIndex];
    }

    /** Returns the molecule stamp */
    MoleculeStamp* getMoleculeStamp(int id) {
      return moleculeStamps_[id];
    }

    /** Return the total number of the molecule stamps */
    int getNMoleculeStamp() {
      return moleculeStamps_.size();
    }
    /**
     * Finds a molecule with a specified global index
     * @return a pointer point to found molecule
     * @param index
     */
    Molecule* getMoleculeByGlobalIndex(int index) {
      MoleculeIterator i;
      i = molecules_.find(index);

      return i != molecules_.end() ? i->second : NULL;
    }

    double getRcut() {
      return rcut_;
    }

    double getRsw() {
      return rsw_;
    }

    double getList() {
      return rlist_;
    }
        
    std::string getFinalConfigFileName() {
      return finalConfigFileName_;
    }
        
    void setFinalConfigFileName(const std::string& fileName) {
      finalConfigFileName_ = fileName;
    }

    std::string getDumpFileName() {
      return dumpFileName_;
    }
        
    void setDumpFileName(const std::string& fileName) {
      dumpFileName_ = fileName;
    }

    std::string getStatFileName() {
      return statFileName_;
    }
        
    void setStatFileName(const std::string& fileName) {
      statFileName_ = fileName;
    }
        
    std::string getRestFileName() {
      return restFileName_;
    }
        
    void setRestFileName(const std::string& fileName) {
      restFileName_ = fileName;
    }

    /** 
     * Sets GlobalGroupMembership
     * @see #SimCreator::setGlobalIndex
     */  
    void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
      assert(globalGroupMembership.size() == nGlobalAtoms_);
      globalGroupMembership_ = globalGroupMembership;
    }

    /** 
     * Sets GlobalMolMembership
     * @see #SimCreator::setGlobalIndex
     */        
    void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
      assert(globalMolMembership.size() == nGlobalAtoms_);
      globalMolMembership_ = globalMolMembership;
    }


    bool isFortranInitialized() {
      return fortranInitialized_;
    }
        
    //below functions are just forward functions
    //To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
    //the other hand, has-a relation need composing.
    /**
     * Adds property into property map
     * @param genData GenericData to be added into PropertyMap
     */
    void addProperty(GenericData* genData);

    /**
     * Removes property from PropertyMap by name
     * @param propName the name of property to be removed
     */
    void removeProperty(const std::string& propName);

    /**
     * clear all of the properties
     */
    void clearProperties();

    /**
     * Returns all names of properties
     * @return all names of properties
     */
    std::vector<std::string> getPropertyNames();

    /**
     * Returns all of the properties in PropertyMap
     * @return all of the properties in PropertyMap
     */      
    std::vector<GenericData*> getProperties();

    /**
     * Returns property 
     * @param propName name of property
     * @return a pointer point to property with propName. If no property named propName
     * exists, return NULL
     */      
    GenericData* getPropertyByName(const std::string& propName);

    /**
     * add all exclude pairs of a molecule into exclude list.
     */
    void addExcludePairs(Molecule* mol);

    /**
     * remove all exclude pairs which belong to a molecule from exclude list
     */

    void removeExcludePairs(Molecule* mol);


    /** Returns the unique atom types of local processor in an array */
    std::set<AtomType*> getUniqueAtomTypes();
        
    friend std::ostream& operator <<(std::ostream& o, SimInfo& info);

    void getCutoff(double& rcut, double& rsw);
        
  private:

    /** fill up the simtype struct*/
    void setupSimType();

    /**
     * Setup Fortran Simulation
     * @see #setupFortranParallel
     */
    void setupFortranSim();

    /** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
    void setupCutoff();

    /** Figure out which coulombic correction method to use and pass to fortran */
    void setupElectrostaticSummationMethod( int isError );

    /** Figure out which polynomial type to use for the switching function */
    void setupSwitchingFunction();

    /** Calculates the number of degress of freedom in the whole system */
    void calcNdf();
    void calcNdfRaw();
    void calcNdfTrans();

    ForceField* forceField_;      
    Globals* simParams_;

    std::map<int, Molecule*>  molecules_; /**< Molecule array */

    /**
     * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
     * system.
     */
    void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
        
    //degress of freedom
    int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
    int fdf_local;       /**< number of frozen degrees of freedom */
    int fdf_;            /**< number of frozen degrees of freedom */
    int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
    int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
    int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
        
    //number of global objects
    int nGlobalMols_;       /**< number of molecules in the system */
    int nGlobalAtoms_;   /**< number of atoms in the system */
    int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
    int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
    int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
    /**
     * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
     * corresponding content is the global index of cutoff group this atom belong to. 
     * It is filled by SimCreator once and only once, since it never changed during the simulation.
     */
    std::vector<int> globalGroupMembership_; 

    /**
     * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
     * corresponding content is the global index of molecule this atom belong to. 
     * It is filled by SimCreator once and only once, since it is never changed during the simulation.
     */
    std::vector<int> globalMolMembership_;        

        
    std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
    std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */        
        
    //number of local objects
    int nAtoms_;                        /**< number of atoms in local processor */
    int nBonds_;                        /**< number of bonds in local processor */
    int nBends_;                        /**< number of bends in local processor */
    int nTorsions_;                    /**< number of torsions in local processor */
    int nRigidBodies_;              /**< number of rigid bodies in local processor */
    int nIntegrableObjects_;    /**< number of integrable objects in local processor */
    int nCutoffGroups_;             /**< number of cutoff groups in local processor */
    int nConstraints_;              /**< number of constraints in local processors */

    simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
    Exclude exclude_;      
    PropertyMap properties_;                  /**< Generic Property */
    SnapshotManager* sman_;               /**< SnapshotManager */

    /** 
     * The reason to have a local index manager is that when molecule is migrating to other processors, 
     * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
     * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
     * to make a efficient data moving plan.
     */        
    LocalIndexManager localIndexMan_;

    //file names
    std::string finalConfigFileName_;
    std::string dumpFileName_;
    std::string statFileName_;
    std::string restFileName_;
        
    double rcut_;       /**< cutoff radius*/
    double rsw_;        /**< radius of switching function*/
    double rlist_;      /**< neighbor list radius */

    bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */

#ifdef IS_MPI
    //in Parallel version, we need MolToProc
  public:
                
    /**
     * Finds the processor where a molecule resides
     * @return the id of the processor which contains the molecule
     * @param globalIndex global Index of the molecule
     */
    int getMolToProc(int globalIndex) {
      //assert(globalIndex < molToProcMap_.size());
      return molToProcMap_[globalIndex];
    }

    /** 
     * Set MolToProcMap array
     * @see #SimCreator::divideMolecules
     */
    void setMolToProcMap(const std::vector<int>& molToProcMap) {
      molToProcMap_ = molToProcMap;
    }
        
  private:

    void setupFortranParallel();
        
    /** 
     * The size of molToProcMap_ is equal to total number of molecules in the system.
     *  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
     * once.
     */        
    std::vector<int> molToProcMap_; 

#endif

  };

} //namespace oopse
#endif //BRAINS_SIMMODEL_HPP

Revision:	945
Committed:	Tue Apr 25 02:09:01 2006 UTC (19 years ago) by gezelter
Original Path:	*trunk/src/brains/SimInfo.hpp*
File size:	18760 byte(s)
Log Message:	Adding spherical boundary conditions to LD integrator
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file SimInfo.hpp
44			* @author tlin
45			* @date 11/02/2004
46			* @version 1.0
47			*/
48	gezelter	2
49	gezelter	246	#ifndef BRAINS_SIMMODEL_HPP
50			#define BRAINS_SIMMODEL_HPP
51
52			#include <iostream>
53			#include <set>
54			#include <utility>
55	gezelter	2	#include <vector>
56
57	tim	3	#include "brains/Exclude.hpp"
58	gezelter	246	#include "io/Globals.hpp"
59			#include "math/Vector3.hpp"
60	chuckv	555	#include "math/SquareMatrix3.hpp"
61	gezelter	246	#include "types/MoleculeStamp.hpp"
62			#include "UseTheForce/ForceField.hpp"
63			#include "utils/PropertyMap.hpp"
64			#include "utils/LocalIndexManager.hpp"
65	tim	316
66	gezelter	246	//another nonsense macro declaration
67	gezelter	2	#define __C
68	tim	3	#include "brains/fSimulation.h"
69	gezelter	2
70	gezelter	246	namespace oopse{
71	gezelter	2
72	gezelter	507	//forward decalration
73			class SnapshotManager;
74			class Molecule;
75			class SelectionManager;
76			/**
77			* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
78	gezelter	945	* @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules.
79			* The Molecule class maintains all of the concrete objects
80			* (atoms, bond, bend, torsions, rigid bodies, cutoff groups, constrains).
81			* In both the single and parallel versions, atoms and
82			* rigid bodies have both global and local indices. The local index is
83			* not relevant to molecules or cutoff groups.
84	gezelter	507	*/
85			class SimInfo {
86			public:
87			typedef std::map<int, Molecule*>::iterator MoleculeIterator;
88	gezelter	2
89	gezelter	507	/**
90			* Constructor of SimInfo
91			* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
92			* second element is the total number of molecules with the same molecule stamp in the system
93			* @param ff pointer of a concrete ForceField instance
94			* @param simParams
95			* @note
96			*/
97	tim	770	SimInfo(ForceField* ff, Globals* simParams);
98	gezelter	507	virtual ~SimInfo();
99	gezelter	2
100	gezelter	507	/**
101			* Adds a molecule
102			* @return return true if adding successfully, return false if the molecule is already in SimInfo
103			* @param mol molecule to be added
104			*/
105			bool addMolecule(Molecule* mol);
106	gezelter	2
107	gezelter	507	/**
108			* Removes a molecule from SimInfo
109			* @return true if removing successfully, return false if molecule is not in this SimInfo
110			*/
111			bool removeMolecule(Molecule* mol);
112	gezelter	2
113	gezelter	507	/** Returns the total number of molecules in the system. */
114			int getNGlobalMolecules() {
115			return nGlobalMols_;
116			}
117	gezelter	2
118	gezelter	507	/** Returns the total number of atoms in the system. */
119			int getNGlobalAtoms() {
120			return nGlobalAtoms_;
121			}
122	gezelter	2
123	gezelter	507	/** Returns the total number of cutoff groups in the system. */
124			int getNGlobalCutoffGroups() {
125			return nGlobalCutoffGroups_;
126			}
127	gezelter	2
128	gezelter	507	/**
129			* Returns the total number of integrable objects (total number of rigid bodies plus the total number
130			* of atoms which do not belong to the rigid bodies) in the system
131			*/
132			int getNGlobalIntegrableObjects() {
133			return nGlobalIntegrableObjects_;
134			}
135	gezelter	2
136	gezelter	507	/**
137			* Returns the total number of integrable objects (total number of rigid bodies plus the total number
138			* of atoms which do not belong to the rigid bodies) in the system
139			*/
140			int getNGlobalRigidBodies() {
141			return nGlobalRigidBodies_;
142			}
143	gezelter	2
144	gezelter	507	int getNGlobalConstraints();
145			/**
146			* Returns the number of local molecules.
147			* @return the number of local molecules
148			*/
149			int getNMolecules() {
150			return molecules_.size();
151			}
152	gezelter	2
153	gezelter	507	/** Returns the number of local atoms */
154			unsigned int getNAtoms() {
155			return nAtoms_;
156			}
157	gezelter	2
158	gezelter	507	/** Returns the number of local bonds */
159			unsigned int getNBonds(){
160			return nBonds_;
161			}
162	gezelter	2
163	gezelter	507	/** Returns the number of local bends */
164			unsigned int getNBends() {
165			return nBends_;
166			}
167	gezelter	2
168	gezelter	507	/** Returns the number of local torsions */
169			unsigned int getNTorsions() {
170			return nTorsions_;
171			}
172	gezelter	2
173	gezelter	507	/** Returns the number of local rigid bodies */
174			unsigned int getNRigidBodies() {
175			return nRigidBodies_;
176			}
177	gezelter	2
178	gezelter	507	/** Returns the number of local integrable objects */
179			unsigned int getNIntegrableObjects() {
180			return nIntegrableObjects_;
181			}
182	gezelter	2
183	gezelter	507	/** Returns the number of local cutoff groups */
184			unsigned int getNCutoffGroups() {
185			return nCutoffGroups_;
186			}
187	gezelter	2
188	gezelter	507	/** Returns the total number of constraints in this SimInfo */
189			unsigned int getNConstraints() {
190			return nConstraints_;
191			}
192	gezelter	246
193	gezelter	507	/**
194			* Returns the first molecule in this SimInfo and intialize the iterator.
195			* @return the first molecule, return NULL if there is not molecule in this SimInfo
196			* @param i the iterator of molecule array (user shouldn't change it)
197			*/
198			Molecule* beginMolecule(MoleculeIterator& i);
199	gezelter	2
200	gezelter	507	/**
201			* Returns the next avaliable Molecule based on the iterator.
202			* @return the next avaliable molecule, return NULL if reaching the end of the array
203			* @param i the iterator of molecule array
204			*/
205			Molecule* nextMolecule(MoleculeIterator& i);
206	gezelter	2
207	gezelter	507	/** Returns the number of degrees of freedom */
208			int getNdf() {
209	gezelter	945	return ndf_ - getFdf();
210	gezelter	507	}
211	gezelter	2
212	gezelter	507	/** Returns the number of raw degrees of freedom */
213			int getNdfRaw() {
214			return ndfRaw_;
215			}
216	gezelter	2
217	gezelter	507	/** Returns the number of translational degrees of freedom */
218			int getNdfTrans() {
219			return ndfTrans_;
220			}
221	gezelter	2
222	gezelter	945	/** sets the current number of frozen degrees of freedom */
223			void setFdf(int fdf) {
224			fdf_local = fdf;
225			}
226
227			int getFdf();
228
229	gezelter	507	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
230	gezelter	246
231	gezelter	507	/** Returns the total number of z-constraint molecules in the system */
232			int getNZconstraint() {
233			return nZconstraint_;
234			}
235	gezelter	2
236	gezelter	507	/**
237			* Sets the number of z-constraint molecules in the system.
238			*/
239			void setNZconstraint(int nZconstraint) {
240			nZconstraint_ = nZconstraint;
241			}
242	gezelter	246
243	gezelter	507	/** Returns the snapshot manager. */
244			SnapshotManager* getSnapshotManager() {
245			return sman_;
246			}
247	gezelter	2
248	gezelter	507	/** Sets the snapshot manager. */
249			void setSnapshotManager(SnapshotManager* sman);
250	gezelter	246
251	gezelter	507	/** Returns the force field */
252			ForceField* getForceField() {
253			return forceField_;
254			}
255	gezelter	2
256	gezelter	507	Globals* getSimParams() {
257			return simParams_;
258			}
259	gezelter	2
260	gezelter	507	/** Returns the velocity of center of mass of the whole system.*/
261			Vector3d getComVel();
262	gezelter	2
263	gezelter	507	/** Returns the center of the mass of the whole system.*/
264			Vector3d getCom();
265	chuckv	555	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
266			void getComAll(Vector3d& com,Vector3d& comVel);
267	gezelter	2
268	chuckv	555	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
269			void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
270
271			/** Returns system angular momentum */
272			Vector3d getAngularMomentum();
273
274	gezelter	507	/** main driver function to interact with fortran during the initialization and molecule migration */
275			void update();
276	gezelter	2
277	gezelter	507	/** Returns the local index manager */
278			LocalIndexManager* getLocalIndexManager() {
279			return &localIndexMan_;
280			}
281	gezelter	2
282	gezelter	507	int getMoleculeStampId(int globalIndex) {
283			//assert(globalIndex < molStampIds_.size())
284			return molStampIds_[globalIndex];
285			}
286	gezelter	2
287	gezelter	507	/** Returns the molecule stamp */
288			MoleculeStamp* getMoleculeStamp(int id) {
289			return moleculeStamps_[id];
290			}
291	gezelter	2
292	gezelter	507	/** Return the total number of the molecule stamps */
293			int getNMoleculeStamp() {
294			return moleculeStamps_.size();
295			}
296			/**
297			* Finds a molecule with a specified global index
298			* @return a pointer point to found molecule
299			* @param index
300			*/
301			Molecule* getMoleculeByGlobalIndex(int index) {
302			MoleculeIterator i;
303			i = molecules_.find(index);
304	gezelter	2
305	gezelter	507	return i != molecules_.end() ? i->second : NULL;
306			}
307	gezelter	2
308	gezelter	507	double getRcut() {
309			return rcut_;
310			}
311	gezelter	2
312	gezelter	507	double getRsw() {
313			return rsw_;
314			}
315	gezelter	764
316			double getList() {
317			return rlist_;
318			}
319	gezelter	246
320	gezelter	507	std::string getFinalConfigFileName() {
321			return finalConfigFileName_;
322			}
323	gezelter	246
324	gezelter	507	void setFinalConfigFileName(const std::string& fileName) {
325			finalConfigFileName_ = fileName;
326			}
327	gezelter	2
328	gezelter	507	std::string getDumpFileName() {
329			return dumpFileName_;
330			}
331	gezelter	246
332	gezelter	507	void setDumpFileName(const std::string& fileName) {
333			dumpFileName_ = fileName;
334			}
335	gezelter	2
336	gezelter	507	std::string getStatFileName() {
337			return statFileName_;
338			}
339	gezelter	246
340	gezelter	507	void setStatFileName(const std::string& fileName) {
341			statFileName_ = fileName;
342			}
343	chrisfen	417
344	gezelter	507	std::string getRestFileName() {
345			return restFileName_;
346			}
347	chrisfen	417
348	gezelter	507	void setRestFileName(const std::string& fileName) {
349			restFileName_ = fileName;
350			}
351	gezelter	2
352	gezelter	507	/**
353			* Sets GlobalGroupMembership
354			* @see #SimCreator::setGlobalIndex
355			*/
356			void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
357			assert(globalGroupMembership.size() == nGlobalAtoms_);
358			globalGroupMembership_ = globalGroupMembership;
359			}
360	gezelter	2
361	gezelter	507	/**
362			* Sets GlobalMolMembership
363			* @see #SimCreator::setGlobalIndex
364			*/
365			void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
366			assert(globalMolMembership.size() == nGlobalAtoms_);
367			globalMolMembership_ = globalMolMembership;
368			}
369	gezelter	246
370
371	gezelter	507	bool isFortranInitialized() {
372			return fortranInitialized_;
373			}
374	gezelter	246
375	gezelter	507	//below functions are just forward functions
376			//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
377			//the other hand, has-a relation need composing.
378			/**
379			* Adds property into property map
380			* @param genData GenericData to be added into PropertyMap
381			*/
382			void addProperty(GenericData* genData);
383	gezelter	246
384	gezelter	507	/**
385			* Removes property from PropertyMap by name
386			* @param propName the name of property to be removed
387			*/
388			void removeProperty(const std::string& propName);
389	gezelter	246
390	gezelter	507	/**
391			* clear all of the properties
392			*/
393			void clearProperties();
394	gezelter	246
395	gezelter	507	/**
396			* Returns all names of properties
397			* @return all names of properties
398			*/
399			std::vector<std::string> getPropertyNames();
400	gezelter	246
401	gezelter	507	/**
402			* Returns all of the properties in PropertyMap
403			* @return all of the properties in PropertyMap
404			*/
405			std::vector<GenericData*> getProperties();
406	gezelter	246
407	gezelter	507	/**
408			* Returns property
409			* @param propName name of property
410			* @return a pointer point to property with propName. If no property named propName
411			* exists, return NULL
412			*/
413			GenericData* getPropertyByName(const std::string& propName);
414	gezelter	246
415	gezelter	507	/**
416			* add all exclude pairs of a molecule into exclude list.
417			*/
418			void addExcludePairs(Molecule* mol);
419	gezelter	246
420	gezelter	507	/**
421			* remove all exclude pairs which belong to a molecule from exclude list
422			*/
423	gezelter	246
424	gezelter	507	void removeExcludePairs(Molecule* mol);
425	tim	292
426
427	gezelter	507	/** Returns the unique atom types of local processor in an array */
428			std::set<AtomType*> getUniqueAtomTypes();
429	tim	292
430	gezelter	507	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
431	tim	326
432	gezelter	507	void getCutoff(double& rcut, double& rsw);
433	gezelter	246
434	gezelter	507	private:
435	gezelter	246
436	gezelter	507	/** fill up the simtype struct*/
437			void setupSimType();
438	gezelter	246
439	gezelter	507	/**
440			* Setup Fortran Simulation
441			* @see #setupFortranParallel
442			*/
443			void setupFortranSim();
444	gezelter	246
445	gezelter	507	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
446			void setupCutoff();
447	gezelter	246
448	chrisfen	598	/** Figure out which coulombic correction method to use and pass to fortran */
449	chrisfen	604	void setupElectrostaticSummationMethod( int isError );
450	chrisfen	598
451	chrisfen	726	/** Figure out which polynomial type to use for the switching function */
452			void setupSwitchingFunction();
453
454	gezelter	507	/** Calculates the number of degress of freedom in the whole system */
455			void calcNdf();
456			void calcNdfRaw();
457			void calcNdfTrans();
458	gezelter	246
459	tim	770	ForceField* forceField_;
460			Globals* simParams_;
461
462			std::map<int, Molecule> molecules_; /< Molecule array /
463
464	gezelter	507	/**
465			* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
466			* system.
467			*/
468			void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
469	gezelter	246
470	gezelter	507	//degress of freedom
471			int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
472	gezelter	945	int fdf_local; /*< number of frozen degrees of freedom /
473			int fdf_; /*< number of frozen degrees of freedom /
474	gezelter	507	int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
475			int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
476			int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
477	gezelter	246
478	gezelter	507	//number of global objects
479			int nGlobalMols_; /*< number of molecules in the system /
480			int nGlobalAtoms_; /*< number of atoms in the system /
481			int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
482			int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
483			int nGlobalRigidBodies_; /*< number of rigid bodies in this system /
484			/**
485			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
486			* corresponding content is the global index of cutoff group this atom belong to.
487			* It is filled by SimCreator once and only once, since it never changed during the simulation.
488			*/
489			std::vector<int> globalGroupMembership_;
490	gezelter	246
491	gezelter	507	/**
492			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
493			* corresponding content is the global index of molecule this atom belong to.
494			* It is filled by SimCreator once and only once, since it is never changed during the simulation.
495			*/
496			std::vector<int> globalMolMembership_;
497	gezelter	246
498
499	gezelter	507	std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
500			std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
501	gezelter	246
502	gezelter	507	//number of local objects
503			int nAtoms_; /*< number of atoms in local processor /
504			int nBonds_; /*< number of bonds in local processor /
505			int nBends_; /*< number of bends in local processor /
506			int nTorsions_; /*< number of torsions in local processor /
507			int nRigidBodies_; /*< number of rigid bodies in local processor /
508			int nIntegrableObjects_; /*< number of integrable objects in local processor /
509			int nCutoffGroups_; /*< number of cutoff groups in local processor /
510			int nConstraints_; /*< number of constraints in local processors /
511	gezelter	246
512	gezelter	507	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
513			Exclude exclude_;
514			PropertyMap properties_; /*< Generic Property /
515			SnapshotManager* sman_; /*< SnapshotManager /
516	gezelter	246
517	gezelter	507	/**
518			* The reason to have a local index manager is that when molecule is migrating to other processors,
519			* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
520			* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
521			* to make a efficient data moving plan.
522			*/
523			LocalIndexManager localIndexMan_;
524	gezelter	246
525	gezelter	507	//file names
526			std::string finalConfigFileName_;
527			std::string dumpFileName_;
528			std::string statFileName_;
529			std::string restFileName_;
530	chrisfen	417
531	gezelter	507	double rcut_; /*< cutoff radius/
532			double rsw_; /*< radius of switching function/
533	gezelter	764	double rlist_; /*< neighbor list radius /
534	gezelter	246
535	gezelter	507	bool fortranInitialized_; /*< flag indicate whether fortran side is initialized /
536	tim	292
537	gezelter	246	#ifdef IS_MPI
538			//in Parallel version, we need MolToProc
539	gezelter	507	public:
540	gezelter	246
541	gezelter	507	/**
542			* Finds the processor where a molecule resides
543			* @return the id of the processor which contains the molecule
544			* @param globalIndex global Index of the molecule
545			*/
546			int getMolToProc(int globalIndex) {
547			//assert(globalIndex < molToProcMap_.size());
548			return molToProcMap_[globalIndex];
549			}
550	gezelter	246
551	gezelter	507	/**
552			* Set MolToProcMap array
553			* @see #SimCreator::divideMolecules
554			*/
555			void setMolToProcMap(const std::vector<int>& molToProcMap) {
556			molToProcMap_ = molToProcMap;
557			}
558	gezelter	246
559	gezelter	507	private:
560	gezelter	246
561	gezelter	507	void setupFortranParallel();
562	gezelter	246
563	gezelter	507	/**
564			* The size of molToProcMap_ is equal to total number of molecules in the system.
565			* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
566			* once.
567			*/
568			std::vector<int> molToProcMap_;
569	tim	292
570	gezelter	246	#endif
571
572	gezelter	507	};
573	gezelter	2
574	gezelter	246	} //namespace oopse
575			#endif //BRAINS_SIMMODEL_HPP
576	gezelter	2