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 "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 As one of the heavy weight class of OOPSE, SimInfo
 * One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
 * And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
 * cutoff groups, constrains).
 * Another major change is the index. No matter single version or parallel version,  atoms and
 * rigid bodies have both global index and local index. Local index is not important to molecule as well as
 * cutoff group. 
 */
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(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, 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_;
        }

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

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

        //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();

        /** 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;
        }

        /** Calculate the maximum cutoff radius based on the atom types */
        double calcMaxCutoffRadius();

        double getRcut() {
            return rcut_;
        }

        double getRsw() {
            return rsw_;
        }
        
        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;
        }

        /** 
         * 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();

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

        /**
         * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
         * system.
         */
        void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);

        ForceField* forceField_;      
        Globals* simParams_;

        std::map<int, Molecule*>  molecules_; /**< Molecule array */
        
        //degress of freedom
        int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
        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_;

        double rcut_;       /**< cutoff radius*/
        double rsw_;        /**< radius of switching function*/

        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:	2097
Committed:	Wed Mar 9 17:30:29 2005 UTC (19 years, 4 months ago) by tim
File size:	19248 byte(s)
Log Message:	adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
#	User	Rev	Content
1	gezelter	1930	/*
2			* 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	1490
49	gezelter	1930	#ifndef BRAINS_SIMMODEL_HPP
50			#define BRAINS_SIMMODEL_HPP
51
52			#include <iostream>
53			#include <set>
54			#include <utility>
55	gezelter	1490	#include <vector>
56
57	tim	1492	#include "brains/Exclude.hpp"
58	gezelter	1930	#include "io/Globals.hpp"
59			#include "math/Vector3.hpp"
60			#include "types/MoleculeStamp.hpp"
61			#include "UseTheForce/ForceField.hpp"
62			#include "utils/PropertyMap.hpp"
63			#include "utils/LocalIndexManager.hpp"
64	tim	2000
65	gezelter	1930	//another nonsense macro declaration
66	gezelter	1490	#define __C
67	tim	1492	#include "brains/fSimulation.h"
68	gezelter	1490
69	gezelter	1930	namespace oopse{
70	gezelter	1490
71	gezelter	1930	//forward decalration
72			class SnapshotManager;
73			class Molecule;
74	tim	2000	class SelectionManager;
75	gezelter	1930	/**
76			* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
77			* @brief As one of the heavy weight class of OOPSE, SimInfo
78			* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
79			* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
80			* cutoff groups, constrains).
81			* Another major change is the index. No matter single version or parallel version, atoms and
82			* rigid bodies have both global index and local index. Local index is not important to molecule as well as
83			* cutoff group.
84			*/
85			class SimInfo {
86			public:
87			typedef std::map<int, Molecule*>::iterator MoleculeIterator;
88	gezelter	1490
89	gezelter	1930	/**
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			SimInfo(std::vector<std::pair<MoleculeStamp, int> >& molStampPairs, ForceField ff, Globals* simParams);
98			virtual ~SimInfo();
99	gezelter	1490
100	gezelter	1930	/**
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	1490
107	gezelter	1930	/**
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	1490
113	gezelter	1930	/** Returns the total number of molecules in the system. */
114			int getNGlobalMolecules() {
115			return nGlobalMols_;
116			}
117	gezelter	1490
118	gezelter	1930	/** Returns the total number of atoms in the system. */
119			int getNGlobalAtoms() {
120			return nGlobalAtoms_;
121			}
122	gezelter	1490
123	gezelter	1930	/** Returns the total number of cutoff groups in the system. */
124			int getNGlobalCutoffGroups() {
125			return nGlobalCutoffGroups_;
126			}
127	gezelter	1490
128	gezelter	1930	/**
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	1490
136	gezelter	1930	/**
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	1490
144	gezelter	1930	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	1490
153	gezelter	1930	/** Returns the number of local atoms */
154			unsigned int getNAtoms() {
155			return nAtoms_;
156			}
157	gezelter	1490
158	gezelter	1930	/** Returns the number of local bonds */
159			unsigned int getNBonds(){
160			return nBonds_;
161			}
162	gezelter	1490
163	gezelter	1930	/** Returns the number of local bends */
164			unsigned int getNBends() {
165			return nBends_;
166			}
167	gezelter	1490
168	gezelter	1930	/** Returns the number of local torsions */
169			unsigned int getNTorsions() {
170			return nTorsions_;
171			}
172	gezelter	1490
173	gezelter	1930	/** Returns the number of local rigid bodies */
174			unsigned int getNRigidBodies() {
175			return nRigidBodies_;
176			}
177	gezelter	1490
178	gezelter	1930	/** Returns the number of local integrable objects */
179			unsigned int getNIntegrableObjects() {
180			return nIntegrableObjects_;
181			}
182	gezelter	1490
183	gezelter	1930	/** Returns the number of local cutoff groups */
184			unsigned int getNCutoffGroups() {
185			return nCutoffGroups_;
186			}
187	gezelter	1490
188	gezelter	1930	/** Returns the total number of constraints in this SimInfo */
189			unsigned int getNConstraints() {
190			return nConstraints_;
191			}
192
193			/**
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	1490
200	gezelter	1930	/**
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	1490
207	gezelter	1930	/** Returns the number of degrees of freedom */
208			int getNdf() {
209			return ndf_;
210			}
211	gezelter	1490
212	gezelter	1930	/** Returns the number of raw degrees of freedom */
213			int getNdfRaw() {
214			return ndfRaw_;
215			}
216	gezelter	1490
217	gezelter	1930	/** Returns the number of translational degrees of freedom */
218			int getNdfTrans() {
219			return ndfTrans_;
220			}
221	gezelter	1490
222	gezelter	1930	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
223
224			/** Returns the total number of z-constraint molecules in the system */
225			int getNZconstraint() {
226			return nZconstraint_;
227			}
228	gezelter	1490
229	gezelter	1930	/**
230			* Sets the number of z-constraint molecules in the system.
231			*/
232			void setNZconstraint(int nZconstraint) {
233			nZconstraint_ = nZconstraint;
234			}
235
236			/** Returns the snapshot manager. */
237			SnapshotManager* getSnapshotManager() {
238			return sman_;
239			}
240	gezelter	1490
241	gezelter	1930	/** Sets the snapshot manager. */
242			void setSnapshotManager(SnapshotManager* sman);
243
244			/** Returns the force field */
245			ForceField* getForceField() {
246			return forceField_;
247			}
248	gezelter	1490
249	gezelter	1930	Globals* getSimParams() {
250			return simParams_;
251			}
252	gezelter	1490
253	gezelter	1930	/** Returns the velocity of center of mass of the whole system.*/
254			Vector3d getComVel();
255	gezelter	1490
256	gezelter	1930	/** Returns the center of the mass of the whole system.*/
257			Vector3d getCom();
258	gezelter	1490
259	gezelter	1930	/** main driver function to interact with fortran during the initialization and molecule migration */
260			void update();
261	gezelter	1490
262	gezelter	1930	/** Returns the local index manager */
263			LocalIndexManager* getLocalIndexManager() {
264			return &localIndexMan_;
265			}
266	gezelter	1490
267	gezelter	1930	int getMoleculeStampId(int globalIndex) {
268			//assert(globalIndex < molStampIds_.size())
269			return molStampIds_[globalIndex];
270			}
271	gezelter	1490
272	gezelter	1930	/** Returns the molecule stamp */
273			MoleculeStamp* getMoleculeStamp(int id) {
274			return moleculeStamps_[id];
275			}
276	gezelter	1490
277	gezelter	1930	/** Return the total number of the molecule stamps */
278			int getNMoleculeStamp() {
279			return moleculeStamps_.size();
280			}
281			/**
282			* Finds a molecule with a specified global index
283			* @return a pointer point to found molecule
284			* @param index
285			*/
286			Molecule* getMoleculeByGlobalIndex(int index) {
287			MoleculeIterator i;
288			i = molecules_.find(index);
289	gezelter	1490
290	gezelter	1930	return i != molecules_.end() ? i->second : NULL;
291			}
292	gezelter	1490
293	gezelter	1930	/** Calculate the maximum cutoff radius based on the atom types */
294			double calcMaxCutoffRadius();
295	gezelter	1490
296	gezelter	1930	double getRcut() {
297			return rcut_;
298			}
299	gezelter	1490
300	gezelter	1930	double getRsw() {
301			return rsw_;
302			}
303
304			std::string getFinalConfigFileName() {
305			return finalConfigFileName_;
306			}
307
308			void setFinalConfigFileName(const std::string& fileName) {
309			finalConfigFileName_ = fileName;
310			}
311	gezelter	1490
312	gezelter	1930	std::string getDumpFileName() {
313			return dumpFileName_;
314			}
315
316			void setDumpFileName(const std::string& fileName) {
317			dumpFileName_ = fileName;
318			}
319	gezelter	1490
320	gezelter	1930	std::string getStatFileName() {
321			return statFileName_;
322			}
323
324			void setStatFileName(const std::string& fileName) {
325			statFileName_ = fileName;
326			}
327	gezelter	1490
328	gezelter	1930	/**
329			* Sets GlobalGroupMembership
330			* @see #SimCreator::setGlobalIndex
331			*/
332			void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
333			assert(globalGroupMembership.size() == nGlobalAtoms_);
334			globalGroupMembership_ = globalGroupMembership;
335			}
336	gezelter	1490
337	gezelter	1930	/**
338			* Sets GlobalMolMembership
339			* @see #SimCreator::setGlobalIndex
340			*/
341			void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
342			assert(globalMolMembership.size() == nGlobalAtoms_);
343			globalMolMembership_ = globalMolMembership;
344			}
345
346
347			bool isFortranInitialized() {
348			return fortranInitialized_;
349			}
350
351			//below functions are just forward functions
352			//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
353			//the other hand, has-a relation need composing.
354			/**
355			* Adds property into property map
356			* @param genData GenericData to be added into PropertyMap
357			*/
358			void addProperty(GenericData* genData);
359
360			/**
361			* Removes property from PropertyMap by name
362			* @param propName the name of property to be removed
363			*/
364			void removeProperty(const std::string& propName);
365
366			/**
367			* clear all of the properties
368			*/
369			void clearProperties();
370
371			/**
372			* Returns all names of properties
373			* @return all names of properties
374			*/
375			std::vector<std::string> getPropertyNames();
376
377			/**
378			* Returns all of the properties in PropertyMap
379			* @return all of the properties in PropertyMap
380			*/
381			std::vector<GenericData*> getProperties();
382
383			/**
384			* Returns property
385			* @param propName name of property
386			* @return a pointer point to property with propName. If no property named propName
387			* exists, return NULL
388			*/
389			GenericData* getPropertyByName(const std::string& propName);
390
391			/**
392			* add all exclude pairs of a molecule into exclude list.
393			*/
394			void addExcludePairs(Molecule* mol);
395
396			/**
397			* remove all exclude pairs which belong to a molecule from exclude list
398			*/
399
400			void removeExcludePairs(Molecule* mol);
401	tim	1976
402
403	tim	2006	/** Returns the unique atom types of local processor in an array */
404			std::set<AtomType*> getUniqueAtomTypes();
405	tim	1976
406	gezelter	1930	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
407	tim	2010
408			void getCutoff(double& rcut, double& rsw);
409	gezelter	1930
410			private:
411
412			/** fill up the simtype struct*/
413			void setupSimType();
414
415			/**
416			* Setup Fortran Simulation
417			* @see #setupFortranParallel
418			*/
419			void setupFortranSim();
420
421			/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
422			void setupCutoff();
423
424			/** Calculates the number of degress of freedom in the whole system */
425			void calcNdf();
426			void calcNdfRaw();
427			void calcNdfTrans();
428
429			/**
430			* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
431			* system.
432			*/
433			void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
434
435			ForceField* forceField_;
436			Globals* simParams_;
437
438			std::map<int, Molecule> molecules_; /< Molecule array /
439
440			//degress of freedom
441			int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
442			int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
443			int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
444			int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
445
446			//number of global objects
447			int nGlobalMols_; /*< number of molecules in the system /
448			int nGlobalAtoms_; /*< number of atoms in the system /
449			int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
450			int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
451			int nGlobalRigidBodies_; /*< number of rigid bodies in this system /
452			/**
453			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
454			* corresponding content is the global index of cutoff group this atom belong to.
455			* It is filled by SimCreator once and only once, since it never changed during the simulation.
456			*/
457			std::vector<int> globalGroupMembership_;
458
459			/**
460			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
461			* corresponding content is the global index of molecule this atom belong to.
462			* It is filled by SimCreator once and only once, since it is never changed during the simulation.
463			*/
464			std::vector<int> globalMolMembership_;
465
466
467			std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
468			std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
469
470			//number of local objects
471			int nAtoms_; /*< number of atoms in local processor /
472			int nBonds_; /*< number of bonds in local processor /
473			int nBends_; /*< number of bends in local processor /
474			int nTorsions_; /*< number of torsions in local processor /
475			int nRigidBodies_; /*< number of rigid bodies in local processor /
476			int nIntegrableObjects_; /*< number of integrable objects in local processor /
477			int nCutoffGroups_; /*< number of cutoff groups in local processor /
478			int nConstraints_; /*< number of constraints in local processors /
479
480			simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
481			Exclude exclude_;
482			PropertyMap properties_; /*< Generic Property /
483			SnapshotManager* sman_; /*< SnapshotManager /
484
485			/**
486			* The reason to have a local index manager is that when molecule is migrating to other processors,
487			* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
488			* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
489			* to make a efficient data moving plan.
490			*/
491			LocalIndexManager localIndexMan_;
492
493			//file names
494			std::string finalConfigFileName_;
495			std::string dumpFileName_;
496			std::string statFileName_;
497
498			double rcut_; /*< cutoff radius/
499			double rsw_; /*< radius of switching function/
500
501			bool fortranInitialized_; /*< flag indicate whether fortran side is initialized /
502	tim	1976
503	gezelter	1930	#ifdef IS_MPI
504			//in Parallel version, we need MolToProc
505			public:
506
507			/**
508			* Finds the processor where a molecule resides
509			* @return the id of the processor which contains the molecule
510			* @param globalIndex global Index of the molecule
511			*/
512			int getMolToProc(int globalIndex) {
513			//assert(globalIndex < molToProcMap_.size());
514			return molToProcMap_[globalIndex];
515			}
516
517			/**
518			* Set MolToProcMap array
519			* @see #SimCreator::divideMolecules
520			*/
521			void setMolToProcMap(const std::vector<int>& molToProcMap) {
522			molToProcMap_ = molToProcMap;
523			}
524
525			private:
526
527			void setupFortranParallel();
528
529			/**
530			* The size of molToProcMap_ is equal to total number of molecules in the system.
531			* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
532			* once.
533			*/
534			std::vector<int> molToProcMap_;
535	tim	1976
536	gezelter	1930	#endif
537
538	gezelter	1490	};
539
540	gezelter	1930	} //namespace oopse
541			#endif //BRAINS_SIMMODEL_HPP
542	gezelter	1490