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 <vector>
#include <utility>

#include "brains/fSimulation.h"
#include "primitives/Molecule.hpp"
#include "types/MoleculeStamp.hpp"
#include "utils/PropertyMap.hpp"
#include "io/Globals.hpp"

namespace oopse{

/**
 * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" 
 * @brief
 */
class SimInfo {
    public:
        typedef MoleculeIterator 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
         * <p>
         * The major change of SimInfo
         * </p>
         */
        SimInfo(const 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 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.
         */
        int 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) {
            std::map<int, Molecule*> i;
            i = molecules_.find(index);

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

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

        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;
        }

        int* getGlobalGroupMembershipPointer() {
            return globalGroupMembership_[0];
        }

        //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:

        void setupSimType();

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

        /** 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 stamps into 
         */
        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 */

        /**
         * 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_; 
        
        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 */

        LocalIndexManager localIndexMan_;

        std::string finalConfigFileName_;
        std::string dumpFileName_;
        std::string statFileName_;
        
#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];
        }

        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:	1733
Committed:	Fri Nov 12 06:19:04 2004 UTC (19 years, 9 months ago) by tim
File size:	14411 byte(s)
Log Message:	OOPSE = Object-Obfuscated Parallel Simulation Engine
#	User	Rev	Content
1	tim	1710	/*
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	gezelter	1490
26	tim	1710	/**
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	tim	1719
36			#include <iostream>
37	gezelter	1490	#include <vector>
38	tim	1719	#include <utility>
39	gezelter	1490
40	tim	1710	#include "brains/fSimulation.h"
41	tim	1492	#include "primitives/Molecule.hpp"
42	tim	1719	#include "types/MoleculeStamp.hpp"
43	tim	1710	#include "utils/PropertyMap.hpp"
44	tim	1719	#include "io/Globals.hpp"
45	gezelter	1490
46	tim	1710	namespace oopse{
47	gezelter	1490
48	tim	1710	/**
49			* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
50			* @brief
51			*/
52			class SimInfo {
53			public:
54	tim	1726	typedef MoleculeIterator MoleculeIterator;
55	tim	1733
56			/**
57			* Constructor of SimInfo
58			* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
59			* second element is the total number of molecules with the same molecule stamp in the system
60			* @param ff pointer of a concrete ForceField instance
61			* @param globals
62			* @note
63			* <p>
64			* The major change of SimInfo
65			* </p>
66			*/
67			SimInfo(const std::vector<std::pair<MoleculeStamp, int> >& molStampPairs, ForceField ff, Globals* globals);
68	tim	1710	virtual ~SimInfo();
69	gezelter	1490
70	tim	1710	/**
71			* Adds a molecule
72			* @return return true if adding successfully, return false if the molecule is already in SimInfo
73			* @param mol molecule to be added
74			*/
75			bool addMolecule(Molecule* mol);
76	gezelter	1490
77	tim	1710	/**
78			* Removes a molecule from SimInfo
79			* @return true if removing successfully, return false if molecule is not in this SimInfo
80			*/
81			bool removeMolecule(Molecule* mol);
82	gezelter	1490
83	tim	1725	/** Returns the total number of molecules in the system. */
84			int getNGlobalMolecules() {
85	tim	1733	return nGlobalMols_;
86	tim	1725	}
87
88			/** Returns the total number of atoms in the system. */
89			int getNGlobalAtoms() {
90	tim	1733	return nGlobalAtoms_;
91	tim	1725	}
92
93			/** Returns the total number of cutoff groups in the system. */
94			int getNGlobalCutoffGroups() {
95	tim	1733	return nGlobalCutoffGroups_;
96	tim	1725	}
97
98	tim	1710	/**
99	tim	1725	* Returns the number of local molecules.
100			* @return the number of local molecules
101	tim	1710	*/
102			int getNMolecules() {
103			return molecules_.size();
104			}
105	gezelter	1490
106	tim	1725	/** Returns the number of local atoms */
107	tim	1710	unsigned int getNAtoms() {
108			return nAtoms_;
109			}
110	gezelter	1490
111	tim	1725	/** Returns the number of local bonds */
112	tim	1710	unsigned int getNBonds(){
113			return nBonds_;
114			}
115	gezelter	1490
116	tim	1725	/** Returns the number of local bends */
117	tim	1710	unsigned int getNBends() {
118			return nBends_;
119			}
120	gezelter	1490
121	tim	1725	/** Returns the number of local torsions */
122	tim	1710	unsigned int getNTorsions() {
123			return nTorsions_;
124			}
125	gezelter	1490
126	tim	1725	/** Returns the number of local rigid bodies */
127	tim	1710	unsigned int getNRigidBodies() {
128			return nRigidBodies_;
129			}
130	gezelter	1490
131	tim	1725	/** Returns the number of local integrable objects */
132	tim	1710	unsigned int getNIntegrableObjects() {
133			return nIntegrableObjects_;
134			}
135	gezelter	1490
136	tim	1725	/** Returns the number of local cutoff groups */
137	tim	1710	unsigned int getNCutoffGroups() {
138			return nCutoffGroups_;
139			}
140	gezelter	1490
141	tim	1710	/** Returns the total number of constraints in this SimInfo */
142			unsigned int getNConstraints() {
143			return nConstraints_;
144			}
145
146			/**
147			* Returns the first molecule in this SimInfo and intialize the iterator.
148			* @return the first molecule, return NULL if there is not molecule in this SimInfo
149			* @param i the iterator of molecule array (user shouldn't change it)
150			*/
151	tim	1726	Molecule* beginMolecule(MoleculeIterator& i);
152	gezelter	1490
153	tim	1710	/**
154			* Returns the next avaliable Molecule based on the iterator.
155			* @return the next avaliable molecule, return NULL if reaching the end of the array
156			* @param i the iterator of molecule array
157			*/
158	tim	1726	Molecule* nextMolecule(MoleculeIterator& i);
159	gezelter	1490
160	tim	1710	/** Returns the number of degrees of freedom */
161	tim	1722	int getNdf() {
162	tim	1710	return ndf_;
163			}
164	gezelter	1490
165	tim	1710	/** Returns the number of raw degrees of freedom */
166	tim	1722	int getNdfRaw() {
167	tim	1710	return ndfRaw_;
168			}
169	gezelter	1490
170	tim	1710	/** Returns the number of translational degrees of freedom */
171	tim	1722	int getNdfTrans() {
172	tim	1710	return ndfTrans_;
173			}
174	gezelter	1490
175	tim	1733	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
176
177			/** Returns the total number of z-constraint molecules in the system */
178			int getNZconstraint() {
179			return nZconstraint_;
180			}
181
182			/**
183			* Sets the number of z-constraint molecules in the system.
184			*/
185			int setNZconstraint(int nZconstraint) {
186			nZconstraint_ = nZconstraint;
187			}
188
189	tim	1710	/** Returns the snapshot manager. */
190			SnapshotManager* getSnapshotManager() {
191			return sman_;
192			}
193	gezelter	1490
194	tim	1710	/** Sets the snapshot manager. */
195			void setSnapshotManager(SnapshotManager* sman) {
196			sman_ = sman;
197			}
198	tim	1712
199	tim	1719	/** Returns the force field */
200	tim	1712	ForceField* getForceField() {
201			return forceField_;
202			}
203	tim	1719
204			Globals* getGlobals() {
205			return globals_;
206			}
207
208	tim	1725	/** Returns the velocity of center of mass of the whole system.*/
209			Vector3d getComVel();
210	tim	1722
211	tim	1725	/** Returns the center of the mass of the whole system.*/
212	tim	1722	Vector3d getCom();
213
214	tim	1725	/** Returns the seed (used for random number generator) */
215	tim	1722	int getSeed() {
216			return seed_;
217			}
218
219	tim	1725	/** Sets the seed*/
220	tim	1722	void setSeed(int seed) {
221			seed_ = seed;
222			}
223	tim	1725
224	tim	1733	/** main driver function to interact with fortran during the initialization and molecule migration */
225	tim	1725	void update();
226
227			/** Returns the local index manager */
228			LocalIndexManager* getLocalIndexManager() {
229			return localIndexMan_;
230			}
231
232			int getMoleculeStampId(int globalIndex) {
233			//assert(globalIndex < molStampIds_.size())
234			return molStampIds_[globalIndex];
235			}
236
237			/** Returns the molecule stamp */
238			MoleculeStamp* getMoleculeStamp(int id) {
239			return moleculeStamps_[id];
240			}
241
242			/**
243			* Finds a molecule with a specified global index
244			* @return a pointer point to found molecule
245			* @param index
246			*/
247			Molecule* getMoleculeByGlobalIndex(int index) {
248			std::map<int, Molecule*> i;
249	tim	1726	i = molecules_.find(index);
250	tim	1725
251	tim	1726	return i != molecules_.end() ? i->second : NULL;
252	tim	1725	}
253
254	tim	1733	/** Returns the unique atom types of local processor in an array */
255			std::set<AtomType*> SimInfo::getUniqueAtomTypes();
256
257			std::string getFinalConfigFileName() {
258			return finalConfigFileName_;
259			}
260
261			void setFinalConfigFileName(const std::string& fileName) {
262			finalConfigFileName_ = fileName;
263			}
264
265
266			std::string getDumpFileName() {
267			return dumpFileName_;
268			}
269
270			void setDumpFileName(const std::string& fileName) {
271			dumpFileName_ = fileName;
272			}
273
274			std::string getStatFileName() {
275			return statFileName_;
276			}
277
278			void setStatFileName(const std::string& fileName) {
279			statFileName_ = fileName;
280			}
281
282			int* getGlobalGroupMembershipPointer() {
283			return globalGroupMembership_[0];
284			}
285
286			//below functions are just forward functions
287			//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
288			//the other hand, has-a relation need composing.
289			/**
290			* Adds property into property map
291			* @param genData GenericData to be added into PropertyMap
292			*/
293			void addProperty(GenericData* genData);
294
295			/**
296			* Removes property from PropertyMap by name
297			* @param propName the name of property to be removed
298			*/
299			void removeProperty(const std::string& propName);
300
301			/**
302			* clear all of the properties
303			*/
304			void clearProperties();
305
306			/**
307			* Returns all names of properties
308			* @return all names of properties
309			*/
310			std::vector<std::string> getPropertyNames();
311
312			/**
313			* Returns all of the properties in PropertyMap
314			* @return all of the properties in PropertyMap
315			*/
316			std::vector<GenericData*> getProperties();
317
318			/**
319			* Returns property
320			* @param propName name of property
321			* @return a pointer point to property with propName. If no property named propName
322			* exists, return NULL
323			*/
324			GenericData* getPropertyByName(const std::string& propName);
325
326	tim	1725	friend std::ostream& operator <<(ostream& o, SimInfo& info);
327
328	tim	1710	private:
329	gezelter	1490
330	tim	1733	void setupSimType();
331
332			/**
333			* Setup Fortran Simulation
334			* @see #setupFortranParallel
335			*/
336			void setupFortranSim();
337
338			/** Calculates the number of degress of freedom in the whole system */
339	tim	1722	void calcNdf();
340			void calcNdfRaw();
341			void calcNdfTrans();
342	gezelter	1490
343	tim	1719	void addExcludePairs(Molecule* mol);
344			void removeExcludePairs(Molecule* mol);
345
346	tim	1733	/**
347			* Adds molecule stamps into
348			*/
349			void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
350
351			std::map<int, Molecule> molecules_; /< Molecule array /
352
353	tim	1725	//degress of freedom
354	tim	1733	int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
355			int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
356			int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
357			int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
358
359			//number of global objects
360			int nGlobalMols_; /*< number of molecules in the system /
361			int nGlobalAtoms_; /*< number of atoms in the system /
362			int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
363	tim	1725
364	tim	1733	/**
365			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
366			* corresponding content is the global index of cutoff group this atom belong to.
367			* It is filled by SimCreator once and only once, since it is never changed during the simulation.
368			*/
369			std::vector<int> globalGroupMembership_;
370
371			std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
372			std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
373
374	tim	1725	//number of local objects
375	tim	1733	int nAtoms_; /*< number of atoms in local processor /
376			int nBonds_; /*< number of bonds in local processor /
377			int nBends_; /*< number of bends in local processor /
378			int nTorsions_; /*< number of torsions in local processor /
379			int nRigidBodies_; /*< number of rigid bodies in local processor /
380			int nIntegrableObjects_; /*< number of integrable objects in local processor /
381			int nCutoffGroups_; /*< number of cutoff groups in local processor /
382			int nConstraints_; /*< number of constraints in local processors /
383	gezelter	1490
384	tim	1733	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
385	tim	1719	Exclude exclude_;
386	tim	1733	ForceField* forceField_;
387	tim	1725	PropertyMap properties_; /*< Generic Property /
388			SnapshotManager* sman_; /*< SnapshotManager /
389	tim	1719	Globals* globals_;
390	tim	1725	int seed_; /*< seed for random number generator /
391
392			LocalIndexManager localIndexMan_;
393
394	tim	1733	std::string finalConfigFileName_;
395			std::string dumpFileName_;
396			std::string statFileName_;
397
398			#ifdef IS_MPI
399			//in Parallel version, we need MolToProc
400			public:
401
402			/**
403			* Finds the processor where a molecule resides
404			* @return the id of the processor which contains the molecule
405			* @param globalIndex global Index of the molecule
406			*/
407			int getMolToProc(int globalIndex) {
408			//assert(globalIndex < molToProcMap_.size());
409			return molToProcMap_[globalIndex];
410			}
411	tim	1725
412	tim	1733	int* getMolToProcMapPointer() {
413			return &molToProcMap_[0];
414			}
415
416			private:
417
418			void setupFortranParallel();
419
420			/**
421			* The size of molToProcMap_ is equal to total number of molecules in the system.
422			* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
423			* once.
424			*/
425			std::vector<int> molToProcMap_;
426			#endif
427
428	gezelter	1490	};
429
430	tim	1710	} //namespace oopse
431			#endif //BRAINS_SIMMODEL_HPP