src/brains/SimInfo.hpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

/**
 * @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 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 globals 
         * @note
         */
        SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* globals);
        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 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) {
            sman_ = sman;
        }

        /** Returns the force field */
        ForceField* getForceField() {
            return forceField_;
        }

        Globals* getGlobals() {
            return globals_;
        }

        /** 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 seed (used for random number generator) */
        int getSeed() {
            return seed_;
        }

        /** Sets the seed*/
        void setSeed(int seed) {
            seed_ = seed;
        }

        /** 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];
        }
        
        /**
         * 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;
        }

        /** 
         * Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class
         * @see #SimCreator::setGlobalIndex
         */  
        int* getGlobalGroupMembershipPointer() {
            return &globalGroupMembership_[0];
        }

        /** 
         * Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class
         * @see #SimCreator::setGlobalIndex
         */        
        int* getGlobalMolMembershipPointer() {
            return &globalMolMembership_[0];
        }


        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);
                
        friend std::ostream& operator <<(ostream& o, SimInfo& info);
        
    private:

        
        /** Returns the unique atom types of local processor in an array */
        std::set<AtomType*> getUniqueAtomTypes();

        /** 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();

        void addExcludePairs(Molecule* mol);
        void removeExcludePairs(Molecule* mol);

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

        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 */

        /**
         * 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 is 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_;
        ForceField* forceField_;            
        PropertyMap properties_;                  /**< Generic Property */
        SnapshotManager* sman_;               /**< SnapshotManager */
        Globals* globals_;
        int seed_; /**< seed for random number generator */

        /** 
         * 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];
        }

        /** 
         * Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class
         * @see #SimCreator::divideMolecules
         */
        int* getMolToProcMapPointer() {
            return &molToProcMap_[0];
        }
        
    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:	1804
Committed:	Tue Nov 30 19:58:25 2004 UTC (19 years, 9 months ago) by tim
File size:	18309 byte(s)
Log Message:	fix Thermo
#	User	Rev	Content
1	tim	1804	/*
2			* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3			*
4			* Contact: oopse@oopse.org
5			*
6			* This program is free software; you can redistribute it and/or
7			* modify it under the terms of the GNU Lesser General Public License
8			* as published by the Free Software Foundation; either version 2.1
9			* of the License, or (at your option) any later version.
10			* All we ask is that proper credit is given for our work, which includes
11			* - but is not limited to - adding the above copyright notice to the beginning
12			* of your source code files, and to any copyright notice that you may distribute
13			* with programs based on this work.
14			*
15			* This program is distributed in the hope that it will be useful,
16			* but WITHOUT ANY WARRANTY; without even the implied warranty of
17			* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18			* GNU Lesser General Public License for more details.
19			*
20			* You should have received a copy of the GNU Lesser General Public License
21			* along with this program; if not, write to the Free Software
22			* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23			*
24			*/
25
26			/**
27			* @file SimInfo.hpp
28			* @author tlin
29			* @date 11/02/2004
30			* @version 1.0
31			*/
32
33			#ifndef BRAINS_SIMMODEL_HPP
34			#define BRAINS_SIMMODEL_HPP
35
36			#include <iostream>
37			#include <set>
38			#include <utility>
39			#include <vector>
40
41			#include "brains/Exclude.hpp"
42			#include "io/Globals.hpp"
43			#include "math/Vector3.hpp"
44			#include "types/MoleculeStamp.hpp"
45			#include "UseTheForce/ForceField.hpp"
46			#include "utils/PropertyMap.hpp"
47			#include "utils/LocalIndexManager.hpp"
48
49			//another nonsense macro declaration
50			#define __C
51			#include "brains/fSimulation.h"
52
53			namespace oopse{
54
55			//forward decalration
56			class SnapshotManager;
57			class Molecule;
58
59			/**
60			* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
61			* @brief As one of the heavy weight class of OOPSE, SimInfo
62			* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
63			* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
64			* cutoff groups, constrains).
65			* Another major change is the index. No matter single version or parallel version, atoms and
66			* rigid bodies have both global index and local index. Local index is not important to molecule as well as
67			* cutoff group.
68			*/
69			class SimInfo {
70			public:
71			typedef std::map<int, Molecule*>::iterator MoleculeIterator;
72
73			/**
74			* Constructor of SimInfo
75			* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
76			* second element is the total number of molecules with the same molecule stamp in the system
77			* @param ff pointer of a concrete ForceField instance
78			* @param globals
79			* @note
80			*/
81			SimInfo(std::vector<std::pair<MoleculeStamp, int> >& molStampPairs, ForceField ff, Globals* globals);
82			virtual ~SimInfo();
83
84			/**
85			* Adds a molecule
86			* @return return true if adding successfully, return false if the molecule is already in SimInfo
87			* @param mol molecule to be added
88			*/
89			bool addMolecule(Molecule* mol);
90
91			/**
92			* Removes a molecule from SimInfo
93			* @return true if removing successfully, return false if molecule is not in this SimInfo
94			*/
95			bool removeMolecule(Molecule* mol);
96
97			/** Returns the total number of molecules in the system. */
98			int getNGlobalMolecules() {
99			return nGlobalMols_;
100			}
101
102			/** Returns the total number of atoms in the system. */
103			int getNGlobalAtoms() {
104			return nGlobalAtoms_;
105			}
106
107			/** Returns the total number of cutoff groups in the system. */
108			int getNGlobalCutoffGroups() {
109			return nGlobalCutoffGroups_;
110			}
111
112			/**
113			* Returns the total number of integrable objects (total number of rigid bodies plus the total number
114			* of atoms which do not belong to the rigid bodies) in the system
115			*/
116			int getNGlobalIntegrableObjects() {
117			return nGlobalIntegrableObjects_;
118			}
119
120			/**
121			* Returns the number of local molecules.
122			* @return the number of local molecules
123			*/
124			int getNMolecules() {
125			return molecules_.size();
126			}
127
128			/** Returns the number of local atoms */
129			unsigned int getNAtoms() {
130			return nAtoms_;
131			}
132
133			/** Returns the number of local bonds */
134			unsigned int getNBonds(){
135			return nBonds_;
136			}
137
138			/** Returns the number of local bends */
139			unsigned int getNBends() {
140			return nBends_;
141			}
142
143			/** Returns the number of local torsions */
144			unsigned int getNTorsions() {
145			return nTorsions_;
146			}
147
148			/** Returns the number of local rigid bodies */
149			unsigned int getNRigidBodies() {
150			return nRigidBodies_;
151			}
152
153			/** Returns the number of local integrable objects */
154			unsigned int getNIntegrableObjects() {
155			return nIntegrableObjects_;
156			}
157
158			/** Returns the number of local cutoff groups */
159			unsigned int getNCutoffGroups() {
160			return nCutoffGroups_;
161			}
162
163			/** Returns the total number of constraints in this SimInfo */
164			unsigned int getNConstraints() {
165			return nConstraints_;
166			}
167
168			/**
169			* Returns the first molecule in this SimInfo and intialize the iterator.
170			* @return the first molecule, return NULL if there is not molecule in this SimInfo
171			* @param i the iterator of molecule array (user shouldn't change it)
172			*/
173			Molecule* beginMolecule(MoleculeIterator& i);
174
175			/**
176			* Returns the next avaliable Molecule based on the iterator.
177			* @return the next avaliable molecule, return NULL if reaching the end of the array
178			* @param i the iterator of molecule array
179			*/
180			Molecule* nextMolecule(MoleculeIterator& i);
181
182			/** Returns the number of degrees of freedom */
183			int getNdf() {
184			return ndf_;
185			}
186
187			/** Returns the number of raw degrees of freedom */
188			int getNdfRaw() {
189			return ndfRaw_;
190			}
191
192			/** Returns the number of translational degrees of freedom */
193			int getNdfTrans() {
194			return ndfTrans_;
195			}
196
197			//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
198
199			/** Returns the total number of z-constraint molecules in the system */
200			int getNZconstraint() {
201			return nZconstraint_;
202			}
203
204			/**
205			* Sets the number of z-constraint molecules in the system.
206			*/
207			void setNZconstraint(int nZconstraint) {
208			nZconstraint_ = nZconstraint;
209			}
210
211			/** Returns the snapshot manager. */
212			SnapshotManager* getSnapshotManager() {
213			return sman_;
214			}
215
216			/** Sets the snapshot manager. */
217			void setSnapshotManager(SnapshotManager* sman) {
218			sman_ = sman;
219			}
220
221			/** Returns the force field */
222			ForceField* getForceField() {
223			return forceField_;
224			}
225
226			Globals* getGlobals() {
227			return globals_;
228			}
229
230			/** Returns the velocity of center of mass of the whole system.*/
231			Vector3d getComVel();
232
233			/** Returns the center of the mass of the whole system.*/
234			Vector3d getCom();
235
236			/** Returns the seed (used for random number generator) */
237			int getSeed() {
238			return seed_;
239			}
240
241			/** Sets the seed*/
242			void setSeed(int seed) {
243			seed_ = seed;
244			}
245
246			/** main driver function to interact with fortran during the initialization and molecule migration */
247			void update();
248
249			/** Returns the local index manager */
250			LocalIndexManager* getLocalIndexManager() {
251			return &localIndexMan_;
252			}
253
254			int getMoleculeStampId(int globalIndex) {
255			//assert(globalIndex < molStampIds_.size())
256			return molStampIds_[globalIndex];
257			}
258
259			/** Returns the molecule stamp */
260			MoleculeStamp* getMoleculeStamp(int id) {
261			return moleculeStamps_[id];
262			}
263
264			/**
265			* Finds a molecule with a specified global index
266			* @return a pointer point to found molecule
267			* @param index
268			*/
269			Molecule* getMoleculeByGlobalIndex(int index) {
270			MoleculeIterator i;
271			i = molecules_.find(index);
272
273			return i != molecules_.end() ? i->second : NULL;
274			}
275
276			/** Calculate the maximum cutoff radius based on the atom types */
277			double calcMaxCutoffRadius();
278
279			double getRcut() {
280			return rcut_;
281			}
282
283			double getRsw() {
284			return rsw_;
285			}
286
287			std::string getFinalConfigFileName() {
288			return finalConfigFileName_;
289			}
290
291			void setFinalConfigFileName(const std::string& fileName) {
292			finalConfigFileName_ = fileName;
293			}
294
295			std::string getDumpFileName() {
296			return dumpFileName_;
297			}
298
299			void setDumpFileName(const std::string& fileName) {
300			dumpFileName_ = fileName;
301			}
302
303			std::string getStatFileName() {
304			return statFileName_;
305			}
306
307			void setStatFileName(const std::string& fileName) {
308			statFileName_ = fileName;
309			}
310
311			/**
312			* Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class
313			* @see #SimCreator::setGlobalIndex
314			*/
315			int* getGlobalGroupMembershipPointer() {
316			return &globalGroupMembership_[0];
317			}
318
319			/**
320			* Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class
321			* @see #SimCreator::setGlobalIndex
322			*/
323			int* getGlobalMolMembershipPointer() {
324			return &globalMolMembership_[0];
325			}
326
327
328			bool isFortranInitialized() {
329			return fortranInitialized_;
330			}
331
332			//below functions are just forward functions
333			//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
334			//the other hand, has-a relation need composing.
335			/**
336			* Adds property into property map
337			* @param genData GenericData to be added into PropertyMap
338			*/
339			void addProperty(GenericData* genData);
340
341			/**
342			* Removes property from PropertyMap by name
343			* @param propName the name of property to be removed
344			*/
345			void removeProperty(const std::string& propName);
346
347			/**
348			* clear all of the properties
349			*/
350			void clearProperties();
351
352			/**
353			* Returns all names of properties
354			* @return all names of properties
355			*/
356			std::vector<std::string> getPropertyNames();
357
358			/**
359			* Returns all of the properties in PropertyMap
360			* @return all of the properties in PropertyMap
361			*/
362			std::vector<GenericData*> getProperties();
363
364			/**
365			* Returns property
366			* @param propName name of property
367			* @return a pointer point to property with propName. If no property named propName
368			* exists, return NULL
369			*/
370			GenericData* getPropertyByName(const std::string& propName);
371
372			friend std::ostream& operator <<(ostream& o, SimInfo& info);
373
374			private:
375
376
377			/** Returns the unique atom types of local processor in an array */
378			std::set<AtomType*> getUniqueAtomTypes();
379
380			/** fill up the simtype struct*/
381			void setupSimType();
382
383			/**
384			* Setup Fortran Simulation
385			* @see #setupFortranParallel
386			*/
387			void setupFortranSim();
388
389			/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
390			void setupCutoff();
391
392			/** Calculates the number of degress of freedom in the whole system */
393			void calcNdf();
394			void calcNdfRaw();
395			void calcNdfTrans();
396
397			void addExcludePairs(Molecule* mol);
398			void removeExcludePairs(Molecule* mol);
399
400			/**
401			* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
402			* system.
403			*/
404			void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
405
406			std::map<int, Molecule> molecules_; /< Molecule array /
407
408			//degress of freedom
409			int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
410			int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
411			int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
412			int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
413
414			//number of global objects
415			int nGlobalMols_; /*< number of molecules in the system /
416			int nGlobalAtoms_; /*< number of atoms in the system /
417			int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
418			int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
419
420			/**
421			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
422			* corresponding content is the global index of cutoff group this atom belong to.
423			* It is filled by SimCreator once and only once, since it is never changed during the simulation.
424			*/
425			std::vector<int> globalGroupMembership_;
426
427			/**
428			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
429			* corresponding content is the global index of molecule this atom belong to.
430			* It is filled by SimCreator once and only once, since it is never changed during the simulation.
431			*/
432			std::vector<int> globalMolMembership_;
433
434
435			std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
436			std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
437
438			//number of local objects
439			int nAtoms_; /*< number of atoms in local processor /
440			int nBonds_; /*< number of bonds in local processor /
441			int nBends_; /*< number of bends in local processor /
442			int nTorsions_; /*< number of torsions in local processor /
443			int nRigidBodies_; /*< number of rigid bodies in local processor /
444			int nIntegrableObjects_; /*< number of integrable objects in local processor /
445			int nCutoffGroups_; /*< number of cutoff groups in local processor /
446			int nConstraints_; /*< number of constraints in local processors /
447
448			simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
449			Exclude exclude_;
450			ForceField* forceField_;
451			PropertyMap properties_; /*< Generic Property /
452			SnapshotManager* sman_; /*< SnapshotManager /
453			Globals* globals_;
454			int seed_; /*< seed for random number generator /
455
456			/**
457			* The reason to have a local index manager is that when molecule is migrating to other processors,
458			* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
459			* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
460			* to make a efficient data moving plan.
461			*/
462			LocalIndexManager localIndexMan_;
463
464			//file names
465			std::string finalConfigFileName_;
466			std::string dumpFileName_;
467			std::string statFileName_;
468
469			double rcut_; /*< cutoff radius/
470			double rsw_; /*< radius of switching function/
471
472			bool fortranInitialized_; /*< flag indicate whether fortran side is initialized /
473
474			#ifdef IS_MPI
475			//in Parallel version, we need MolToProc
476			public:
477
478			/**
479			* Finds the processor where a molecule resides
480			* @return the id of the processor which contains the molecule
481			* @param globalIndex global Index of the molecule
482			*/
483			int getMolToProc(int globalIndex) {
484			//assert(globalIndex < molToProcMap_.size());
485			return molToProcMap_[globalIndex];
486			}
487
488			/**
489			* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class
490			* @see #SimCreator::divideMolecules
491			*/
492			int* getMolToProcMapPointer() {
493			return &molToProcMap_[0];
494			}
495
496			private:
497
498			void setupFortranParallel();
499
500			/**
501			* The size of molToProcMap_ is equal to total number of molecules in the system.
502			* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
503			* once.
504			*/
505			std::vector<int> molToProcMap_;
506			#endif
507
508			};
509
510			} //namespace oopse
511			#endif //BRAINS_SIMMODEL_HPP