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, 8 months ago) by tim
File size:	14411 byte(s)
Log Message:	OOPSE = Object-Obfuscated Parallel Simulation Engine
#	Content
1	/*
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 <vector>
38	#include <utility>
39
40	#include "brains/fSimulation.h"
41	#include "primitives/Molecule.hpp"
42	#include "types/MoleculeStamp.hpp"
43	#include "utils/PropertyMap.hpp"
44	#include "io/Globals.hpp"
45
46	namespace oopse{
47
48	/**
49	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
50	* @brief
51	*/
52	class SimInfo {
53	public:
54	typedef MoleculeIterator MoleculeIterator;
55
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	virtual ~SimInfo();
69
70	/**
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
77	/**
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
83	/** Returns the total number of molecules in the system. */
84	int getNGlobalMolecules() {
85	return nGlobalMols_;
86	}
87
88	/** Returns the total number of atoms in the system. */
89	int getNGlobalAtoms() {
90	return nGlobalAtoms_;
91	}
92
93	/** Returns the total number of cutoff groups in the system. */
94	int getNGlobalCutoffGroups() {
95	return nGlobalCutoffGroups_;
96	}
97
98	/**
99	* Returns the number of local molecules.
100	* @return the number of local molecules
101	*/
102	int getNMolecules() {
103	return molecules_.size();
104	}
105
106	/** Returns the number of local atoms */
107	unsigned int getNAtoms() {
108	return nAtoms_;
109	}
110
111	/** Returns the number of local bonds */
112	unsigned int getNBonds(){
113	return nBonds_;
114	}
115
116	/** Returns the number of local bends */
117	unsigned int getNBends() {
118	return nBends_;
119	}
120
121	/** Returns the number of local torsions */
122	unsigned int getNTorsions() {
123	return nTorsions_;
124	}
125
126	/** Returns the number of local rigid bodies */
127	unsigned int getNRigidBodies() {
128	return nRigidBodies_;
129	}
130
131	/** Returns the number of local integrable objects */
132	unsigned int getNIntegrableObjects() {
133	return nIntegrableObjects_;
134	}
135
136	/** Returns the number of local cutoff groups */
137	unsigned int getNCutoffGroups() {
138	return nCutoffGroups_;
139	}
140
141	/** 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	Molecule* beginMolecule(MoleculeIterator& i);
152
153	/**
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	Molecule* nextMolecule(MoleculeIterator& i);
159
160	/** Returns the number of degrees of freedom */
161	int getNdf() {
162	return ndf_;
163	}
164
165	/** Returns the number of raw degrees of freedom */
166	int getNdfRaw() {
167	return ndfRaw_;
168	}
169
170	/** Returns the number of translational degrees of freedom */
171	int getNdfTrans() {
172	return ndfTrans_;
173	}
174
175	//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	/** Returns the snapshot manager. */
190	SnapshotManager* getSnapshotManager() {
191	return sman_;
192	}
193
194	/** Sets the snapshot manager. */
195	void setSnapshotManager(SnapshotManager* sman) {
196	sman_ = sman;
197	}
198
199	/** Returns the force field */
200	ForceField* getForceField() {
201	return forceField_;
202	}
203
204	Globals* getGlobals() {
205	return globals_;
206	}
207
208	/** Returns the velocity of center of mass of the whole system.*/
209	Vector3d getComVel();
210
211	/** Returns the center of the mass of the whole system.*/
212	Vector3d getCom();
213
214	/** Returns the seed (used for random number generator) */
215	int getSeed() {
216	return seed_;
217	}
218
219	/** Sets the seed*/
220	void setSeed(int seed) {
221	seed_ = seed;
222	}
223
224	/** main driver function to interact with fortran during the initialization and molecule migration */
225	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	i = molecules_.find(index);
250
251	return i != molecules_.end() ? i->second : NULL;
252	}
253
254	/** 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	friend std::ostream& operator <<(ostream& o, SimInfo& info);
327
328	private:
329
330	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	void calcNdf();
340	void calcNdfRaw();
341	void calcNdfTrans();
342
343	void addExcludePairs(Molecule* mol);
344	void removeExcludePairs(Molecule* mol);
345
346	/**
347	* Adds molecule stamps into
348	*/
349	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
350
351	std::map<int, Molecule> molecules_; /< Molecule array /
352
353	//degress of freedom
354	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
364	/**
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	//number of local objects
375	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
384	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
385	Exclude exclude_;
386	ForceField* forceField_;
387	PropertyMap properties_; /*< Generic Property /
388	SnapshotManager* sman_; /*< SnapshotManager /
389	Globals* globals_;
390	int seed_; /*< seed for random number generator /
391
392	LocalIndexManager localIndexMan_;
393
394	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
412	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	};
429
430	} //namespace oopse
431	#endif //BRAINS_SIMMODEL_HPP