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 "brains/SimInfo.hpp"
#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 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(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 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.
         */
        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;
        }

        /** 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*> SimInfo::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:	1739
Committed:	Mon Nov 15 18:02:15 2004 UTC (19 years, 8 months ago) by tim
File size:	17620 byte(s)
Log Message:	finish DumpReader, DumpWriter.Next Step is LJFF and integrators
#	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 "brains/SimInfo.hpp"
42	#include "primitives/Molecule.hpp"
43	#include "types/MoleculeStamp.hpp"
44	#include "utils/PropertyMap.hpp"
45	#include "io/Globals.hpp"
46
47	namespace oopse{
48
49	/**
50	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
51	* @brief As one of the heavy weight class of OOPSE, SimInfo
52	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
53	* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
54	* cutoff groups, constrains).
55	* Another major change is the index. No matter single version or parallel version, atoms and
56	* rigid bodies have both global index and local index. Local index is not important to molecule as well as
57	* cutoff group.
58	*/
59	class SimInfo {
60	public:
61	typedef std::map<int, Molecule*>::iterator MoleculeIterator;
62
63	/**
64	* Constructor of SimInfo
65	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
66	* second element is the total number of molecules with the same molecule stamp in the system
67	* @param ff pointer of a concrete ForceField instance
68	* @param globals
69	* @note
70	*/
71	SimInfo(const std::vector<std::pair<MoleculeStamp, int> >& molStampPairs, ForceField ff, Globals* globals);
72	virtual ~SimInfo();
73
74	/**
75	* Adds a molecule
76	* @return return true if adding successfully, return false if the molecule is already in SimInfo
77	* @param mol molecule to be added
78	*/
79	bool addMolecule(Molecule* mol);
80
81	/**
82	* Removes a molecule from SimInfo
83	* @return true if removing successfully, return false if molecule is not in this SimInfo
84	*/
85	bool removeMolecule(Molecule* mol);
86
87	/** Returns the total number of molecules in the system. */
88	int getNGlobalMolecules() {
89	return nGlobalMols_;
90	}
91
92	/** Returns the total number of atoms in the system. */
93	int getNGlobalAtoms() {
94	return nGlobalAtoms_;
95	}
96
97	/** Returns the total number of cutoff groups in the system. */
98	int getNGlobalCutoffGroups() {
99	return nGlobalCutoffGroups_;
100	}
101
102	/**
103	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
104	* of atoms which do not belong to the rigid bodies) in the system
105	*/
106	int getNGlobalIntegrableObjects() {
107	return nGlobalIntegrableObjects_;
108	}
109
110	/**
111	* Returns the number of local molecules.
112	* @return the number of local molecules
113	*/
114	int getNMolecules() {
115	return molecules_.size();
116	}
117
118	/** Returns the number of local atoms */
119	unsigned int getNAtoms() {
120	return nAtoms_;
121	}
122
123	/** Returns the number of local bonds */
124	unsigned int getNBonds(){
125	return nBonds_;
126	}
127
128	/** Returns the number of local bends */
129	unsigned int getNBends() {
130	return nBends_;
131	}
132
133	/** Returns the number of local torsions */
134	unsigned int getNTorsions() {
135	return nTorsions_;
136	}
137
138	/** Returns the number of local rigid bodies */
139	unsigned int getNRigidBodies() {
140	return nRigidBodies_;
141	}
142
143	/** Returns the number of local integrable objects */
144	unsigned int getNIntegrableObjects() {
145	return nIntegrableObjects_;
146	}
147
148	/** Returns the number of local cutoff groups */
149	unsigned int getNCutoffGroups() {
150	return nCutoffGroups_;
151	}
152
153	/** Returns the total number of constraints in this SimInfo */
154	unsigned int getNConstraints() {
155	return nConstraints_;
156	}
157
158	/**
159	* Returns the first molecule in this SimInfo and intialize the iterator.
160	* @return the first molecule, return NULL if there is not molecule in this SimInfo
161	* @param i the iterator of molecule array (user shouldn't change it)
162	*/
163	Molecule* beginMolecule(MoleculeIterator& i);
164
165	/**
166	* Returns the next avaliable Molecule based on the iterator.
167	* @return the next avaliable molecule, return NULL if reaching the end of the array
168	* @param i the iterator of molecule array
169	*/
170	Molecule* nextMolecule(MoleculeIterator& i);
171
172	/** Returns the number of degrees of freedom */
173	int getNdf() {
174	return ndf_;
175	}
176
177	/** Returns the number of raw degrees of freedom */
178	int getNdfRaw() {
179	return ndfRaw_;
180	}
181
182	/** Returns the number of translational degrees of freedom */
183	int getNdfTrans() {
184	return ndfTrans_;
185	}
186
187	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
188
189	/** Returns the total number of z-constraint molecules in the system */
190	int getNZconstraint() {
191	return nZconstraint_;
192	}
193
194	/**
195	* Sets the number of z-constraint molecules in the system.
196	*/
197	int setNZconstraint(int nZconstraint) {
198	nZconstraint_ = nZconstraint;
199	}
200
201	/** Returns the snapshot manager. */
202	SnapshotManager* getSnapshotManager() {
203	return sman_;
204	}
205
206	/** Sets the snapshot manager. */
207	void setSnapshotManager(SnapshotManager* sman) {
208	sman_ = sman;
209	}
210
211	/** Returns the force field */
212	ForceField* getForceField() {
213	return forceField_;
214	}
215
216	Globals* getGlobals() {
217	return globals_;
218	}
219
220	/** Returns the velocity of center of mass of the whole system.*/
221	Vector3d getComVel();
222
223	/** Returns the center of the mass of the whole system.*/
224	Vector3d getCom();
225
226	/** Returns the seed (used for random number generator) */
227	int getSeed() {
228	return seed_;
229	}
230
231	/** Sets the seed*/
232	void setSeed(int seed) {
233	seed_ = seed;
234	}
235
236	/** main driver function to interact with fortran during the initialization and molecule migration */
237	void update();
238
239	/** Returns the local index manager */
240	LocalIndexManager* getLocalIndexManager() {
241	return &localIndexMan_;
242	}
243
244	int getMoleculeStampId(int globalIndex) {
245	//assert(globalIndex < molStampIds_.size())
246	return molStampIds_[globalIndex];
247	}
248
249	/** Returns the molecule stamp */
250	MoleculeStamp* getMoleculeStamp(int id) {
251	return moleculeStamps_[id];
252	}
253
254	/**
255	* Finds a molecule with a specified global index
256	* @return a pointer point to found molecule
257	* @param index
258	*/
259	Molecule* getMoleculeByGlobalIndex(int index) {
260	std::map<int, Molecule*> i;
261	i = molecules_.find(index);
262
263	return i != molecules_.end() ? i->second : NULL;
264	}
265
266	/** Calculate the maximum cutoff radius based on the atom types */
267	double calcMaxCutoffRadius();
268
269	double getRcut() {
270	return rcut_;
271	}
272
273	double getRsw() {
274	return rsw_;
275	}
276
277	std::string getFinalConfigFileName() {
278	return finalConfigFileName_;
279	}
280
281	void setFinalConfigFileName(const std::string& fileName) {
282	finalConfigFileName_ = fileName;
283	}
284
285	std::string getDumpFileName() {
286	return dumpFileName_;
287	}
288
289	void setDumpFileName(const std::string& fileName) {
290	dumpFileName_ = fileName;
291	}
292
293	std::string getStatFileName() {
294	return statFileName_;
295	}
296
297	void setStatFileName(const std::string& fileName) {
298	statFileName_ = fileName;
299	}
300
301	/**
302	* Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class
303	* @see #SimCreator::setGlobalIndex
304	*/
305	int* getGlobalGroupMembershipPointer() {
306	return globalGroupMembership_[0];
307	}
308
309	/**
310	* Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class
311	* @see #SimCreator::setGlobalIndex
312	*/
313	int* getGlobalMolMembershipPointer() {
314	return globalMolMembership_[0];
315	}
316
317
318	bool isFortranInitialized() {
319	return fortranInitialized_;
320	}
321
322	//below functions are just forward functions
323	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
324	//the other hand, has-a relation need composing.
325	/**
326	* Adds property into property map
327	* @param genData GenericData to be added into PropertyMap
328	*/
329	void addProperty(GenericData* genData);
330
331	/**
332	* Removes property from PropertyMap by name
333	* @param propName the name of property to be removed
334	*/
335	void removeProperty(const std::string& propName);
336
337	/**
338	* clear all of the properties
339	*/
340	void clearProperties();
341
342	/**
343	* Returns all names of properties
344	* @return all names of properties
345	*/
346	std::vector<std::string> getPropertyNames();
347
348	/**
349	* Returns all of the properties in PropertyMap
350	* @return all of the properties in PropertyMap
351	*/
352	std::vector<GenericData*> getProperties();
353
354	/**
355	* Returns property
356	* @param propName name of property
357	* @return a pointer point to property with propName. If no property named propName
358	* exists, return NULL
359	*/
360	GenericData* getPropertyByName(const std::string& propName);
361
362	friend std::ostream& operator <<(ostream& o, SimInfo& info);
363
364	private:
365
366
367	/** Returns the unique atom types of local processor in an array */
368	std::set<AtomType*> SimInfo::getUniqueAtomTypes();
369
370	/** fill up the simtype struct*/
371	void setupSimType();
372
373	/**
374	* Setup Fortran Simulation
375	* @see #setupFortranParallel
376	*/
377	void setupFortranSim();
378
379	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
380	void setupCutoff();
381
382	/** Calculates the number of degress of freedom in the whole system */
383	void calcNdf();
384	void calcNdfRaw();
385	void calcNdfTrans();
386
387	void addExcludePairs(Molecule* mol);
388	void removeExcludePairs(Molecule* mol);
389
390	/**
391	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
392	* system.
393	*/
394	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
395
396	std::map<int, Molecule> molecules_; /< Molecule array /
397
398	//degress of freedom
399	int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
400	int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
401	int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
402	int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
403
404	//number of global objects
405	int nGlobalMols_; /*< number of molecules in the system /
406	int nGlobalAtoms_; /*< number of atoms in the system /
407	int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
408	int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
409
410	/**
411	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
412	* corresponding content is the global index of cutoff group this atom belong to.
413	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
414	*/
415	std::vector<int> globalGroupMembership_;
416
417	/**
418	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
419	* corresponding content is the global index of molecule this atom belong to.
420	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
421	*/
422	std::vector<int> globalMolMembership_;
423
424
425	std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
426	std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
427
428	//number of local objects
429	int nAtoms_; /*< number of atoms in local processor /
430	int nBonds_; /*< number of bonds in local processor /
431	int nBends_; /*< number of bends in local processor /
432	int nTorsions_; /*< number of torsions in local processor /
433	int nRigidBodies_; /*< number of rigid bodies in local processor /
434	int nIntegrableObjects_; /*< number of integrable objects in local processor /
435	int nCutoffGroups_; /*< number of cutoff groups in local processor /
436	int nConstraints_; /*< number of constraints in local processors /
437
438	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
439	Exclude exclude_;
440	ForceField* forceField_;
441	PropertyMap properties_; /*< Generic Property /
442	SnapshotManager* sman_; /*< SnapshotManager /
443	Globals* globals_;
444	int seed_; /*< seed for random number generator /
445
446	/**
447	* The reason to have a local index manager is that when molecule is migrating to other processors,
448	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
449	* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
450	* to make a efficient data moving plan.
451	*/
452	LocalIndexManager localIndexMan_;
453
454	//file names
455	std::string finalConfigFileName_;
456	std::string dumpFileName_;
457	std::string statFileName_;
458
459	double rcut_; /*< cutoff radius/
460	double rsw_; /*< radius of switching function/
461
462	bool fortranInitialized_; /*< flag indicate whether fortran side is initialized /
463
464	#ifdef IS_MPI
465	//in Parallel version, we need MolToProc
466	public:
467
468	/**
469	* Finds the processor where a molecule resides
470	* @return the id of the processor which contains the molecule
471	* @param globalIndex global Index of the molecule
472	*/
473	int getMolToProc(int globalIndex) {
474	//assert(globalIndex < molToProcMap_.size());
475	return molToProcMap_[globalIndex];
476	}
477
478	/**
479	* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class
480	* @see #SimCreator::divideMolecules
481	*/
482	int* getMolToProcMapPointer() {
483	return &molToProcMap_[0];
484	}
485
486	private:
487
488	void setupFortranParallel();
489
490	/**
491	* The size of molToProcMap_ is equal to total number of molecules in the system.
492	* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
493	* once.
494	*/
495	std::vector<int> molToProcMap_;
496	#endif
497
498	};
499
500	} //namespace oopse
501	#endif //BRAINS_SIMMODEL_HPP