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 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 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 */

        /**
         * 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:	1738
Committed:	Sat Nov 13 05:08:12 2004 UTC (19 years, 9 months ago) by tim
File size:	17189 byte(s)
Log Message:	refactory, refactory, refactory
#	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	tim	1735	* @brief As one of the heavy weight class of OOPSE, SimInfo
51			* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
52			* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
53			* cutoff groups, constrains).
54			* Another major change is the index. No matter single version or parallel version, atoms and
55			* rigid bodies have both global index and local index. Local index is not important to molecule as well as
56			* cutoff group.
57	tim	1710	*/
58			class SimInfo {
59			public:
60	tim	1738	typedef std::map<int, Molecule*>::iterator MoleculeIterator;
61	tim	1733
62			/**
63			* Constructor of SimInfo
64			* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
65			* second element is the total number of molecules with the same molecule stamp in the system
66			* @param ff pointer of a concrete ForceField instance
67			* @param globals
68			* @note
69			*/
70			SimInfo(const std::vector<std::pair<MoleculeStamp, int> >& molStampPairs, ForceField ff, Globals* globals);
71	tim	1710	virtual ~SimInfo();
72	gezelter	1490
73	tim	1710	/**
74			* Adds a molecule
75			* @return return true if adding successfully, return false if the molecule is already in SimInfo
76			* @param mol molecule to be added
77			*/
78			bool addMolecule(Molecule* mol);
79	gezelter	1490
80	tim	1710	/**
81			* Removes a molecule from SimInfo
82			* @return true if removing successfully, return false if molecule is not in this SimInfo
83			*/
84			bool removeMolecule(Molecule* mol);
85	gezelter	1490
86	tim	1725	/** Returns the total number of molecules in the system. */
87			int getNGlobalMolecules() {
88	tim	1733	return nGlobalMols_;
89	tim	1725	}
90
91			/** Returns the total number of atoms in the system. */
92			int getNGlobalAtoms() {
93	tim	1733	return nGlobalAtoms_;
94	tim	1725	}
95
96			/** Returns the total number of cutoff groups in the system. */
97			int getNGlobalCutoffGroups() {
98	tim	1733	return nGlobalCutoffGroups_;
99	tim	1725	}
100
101	tim	1710	/**
102	tim	1725	* Returns the number of local molecules.
103			* @return the number of local molecules
104	tim	1710	*/
105			int getNMolecules() {
106			return molecules_.size();
107			}
108	gezelter	1490
109	tim	1725	/** Returns the number of local atoms */
110	tim	1710	unsigned int getNAtoms() {
111			return nAtoms_;
112			}
113	gezelter	1490
114	tim	1725	/** Returns the number of local bonds */
115	tim	1710	unsigned int getNBonds(){
116			return nBonds_;
117			}
118	gezelter	1490
119	tim	1725	/** Returns the number of local bends */
120	tim	1710	unsigned int getNBends() {
121			return nBends_;
122			}
123	gezelter	1490
124	tim	1725	/** Returns the number of local torsions */
125	tim	1710	unsigned int getNTorsions() {
126			return nTorsions_;
127			}
128	gezelter	1490
129	tim	1725	/** Returns the number of local rigid bodies */
130	tim	1710	unsigned int getNRigidBodies() {
131			return nRigidBodies_;
132			}
133	gezelter	1490
134	tim	1725	/** Returns the number of local integrable objects */
135	tim	1710	unsigned int getNIntegrableObjects() {
136			return nIntegrableObjects_;
137			}
138	gezelter	1490
139	tim	1725	/** Returns the number of local cutoff groups */
140	tim	1710	unsigned int getNCutoffGroups() {
141			return nCutoffGroups_;
142			}
143	gezelter	1490
144	tim	1710	/** Returns the total number of constraints in this SimInfo */
145			unsigned int getNConstraints() {
146			return nConstraints_;
147			}
148
149			/**
150			* Returns the first molecule in this SimInfo and intialize the iterator.
151			* @return the first molecule, return NULL if there is not molecule in this SimInfo
152			* @param i the iterator of molecule array (user shouldn't change it)
153			*/
154	tim	1726	Molecule* beginMolecule(MoleculeIterator& i);
155	gezelter	1490
156	tim	1710	/**
157			* Returns the next avaliable Molecule based on the iterator.
158			* @return the next avaliable molecule, return NULL if reaching the end of the array
159			* @param i the iterator of molecule array
160			*/
161	tim	1726	Molecule* nextMolecule(MoleculeIterator& i);
162	gezelter	1490
163	tim	1710	/** Returns the number of degrees of freedom */
164	tim	1722	int getNdf() {
165	tim	1710	return ndf_;
166			}
167	gezelter	1490
168	tim	1710	/** Returns the number of raw degrees of freedom */
169	tim	1722	int getNdfRaw() {
170	tim	1710	return ndfRaw_;
171			}
172	gezelter	1490
173	tim	1710	/** Returns the number of translational degrees of freedom */
174	tim	1722	int getNdfTrans() {
175	tim	1710	return ndfTrans_;
176			}
177	gezelter	1490
178	tim	1733	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
179
180			/** Returns the total number of z-constraint molecules in the system */
181			int getNZconstraint() {
182			return nZconstraint_;
183			}
184
185			/**
186			* Sets the number of z-constraint molecules in the system.
187			*/
188			int setNZconstraint(int nZconstraint) {
189			nZconstraint_ = nZconstraint;
190			}
191
192	tim	1710	/** Returns the snapshot manager. */
193			SnapshotManager* getSnapshotManager() {
194			return sman_;
195			}
196	gezelter	1490
197	tim	1710	/** Sets the snapshot manager. */
198			void setSnapshotManager(SnapshotManager* sman) {
199			sman_ = sman;
200			}
201	tim	1712
202	tim	1719	/** Returns the force field */
203	tim	1712	ForceField* getForceField() {
204			return forceField_;
205			}
206	tim	1719
207			Globals* getGlobals() {
208			return globals_;
209			}
210
211	tim	1725	/** Returns the velocity of center of mass of the whole system.*/
212			Vector3d getComVel();
213	tim	1722
214	tim	1725	/** Returns the center of the mass of the whole system.*/
215	tim	1722	Vector3d getCom();
216
217	tim	1725	/** Returns the seed (used for random number generator) */
218	tim	1722	int getSeed() {
219			return seed_;
220			}
221
222	tim	1725	/** Sets the seed*/
223	tim	1722	void setSeed(int seed) {
224			seed_ = seed;
225			}
226	tim	1725
227	tim	1733	/** main driver function to interact with fortran during the initialization and molecule migration */
228	tim	1725	void update();
229
230			/** Returns the local index manager */
231			LocalIndexManager* getLocalIndexManager() {
232	tim	1735	return &localIndexMan_;
233	tim	1725	}
234
235			int getMoleculeStampId(int globalIndex) {
236			//assert(globalIndex < molStampIds_.size())
237			return molStampIds_[globalIndex];
238			}
239
240			/** Returns the molecule stamp */
241			MoleculeStamp* getMoleculeStamp(int id) {
242			return moleculeStamps_[id];
243			}
244
245			/**
246			* Finds a molecule with a specified global index
247			* @return a pointer point to found molecule
248			* @param index
249			*/
250			Molecule* getMoleculeByGlobalIndex(int index) {
251			std::map<int, Molecule*> i;
252	tim	1726	i = molecules_.find(index);
253	tim	1725
254	tim	1726	return i != molecules_.end() ? i->second : NULL;
255	tim	1725	}
256
257	tim	1735	/** Calculate the maximum cutoff radius based on the atom types */
258			double calcMaxCutoffRadius();
259	tim	1733
260	tim	1735	double getRcut() {
261			return rcut_;
262			}
263
264			double getRsw() {
265			return rsw_;
266			}
267
268	tim	1733	std::string getFinalConfigFileName() {
269			return finalConfigFileName_;
270			}
271
272			void setFinalConfigFileName(const std::string& fileName) {
273			finalConfigFileName_ = fileName;
274			}
275
276			std::string getDumpFileName() {
277			return dumpFileName_;
278			}
279
280			void setDumpFileName(const std::string& fileName) {
281			dumpFileName_ = fileName;
282			}
283
284			std::string getStatFileName() {
285			return statFileName_;
286			}
287
288			void setStatFileName(const std::string& fileName) {
289			statFileName_ = fileName;
290			}
291
292	tim	1735	/**
293			* Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class
294			* @see #SimCreator::setGlobalIndex
295			*/
296	tim	1733	int* getGlobalGroupMembershipPointer() {
297			return globalGroupMembership_[0];
298			}
299
300	tim	1735	/**
301			* Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class
302			* @see #SimCreator::setGlobalIndex
303			*/
304			int* getGlobalMolMembershipPointer() {
305			return globalMolMembership_[0];
306			}
307	tim	1738
308
309			bool isFortranInitialized() {
310			return fortranInitialized_;
311			}
312	tim	1735
313	tim	1733	//below functions are just forward functions
314			//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
315			//the other hand, has-a relation need composing.
316			/**
317			* Adds property into property map
318			* @param genData GenericData to be added into PropertyMap
319			*/
320			void addProperty(GenericData* genData);
321
322			/**
323			* Removes property from PropertyMap by name
324			* @param propName the name of property to be removed
325			*/
326			void removeProperty(const std::string& propName);
327
328			/**
329			* clear all of the properties
330			*/
331			void clearProperties();
332
333			/**
334			* Returns all names of properties
335			* @return all names of properties
336			*/
337			std::vector<std::string> getPropertyNames();
338
339			/**
340			* Returns all of the properties in PropertyMap
341			* @return all of the properties in PropertyMap
342			*/
343			std::vector<GenericData*> getProperties();
344
345			/**
346			* Returns property
347			* @param propName name of property
348			* @return a pointer point to property with propName. If no property named propName
349			* exists, return NULL
350			*/
351			GenericData* getPropertyByName(const std::string& propName);
352
353	tim	1725	friend std::ostream& operator <<(ostream& o, SimInfo& info);
354
355	tim	1710	private:
356	gezelter	1490
357	tim	1735
358			/** Returns the unique atom types of local processor in an array */
359			std::set<AtomType*> SimInfo::getUniqueAtomTypes();
360
361			/** fill up the simtype struct*/
362	tim	1733	void setupSimType();
363
364			/**
365			* Setup Fortran Simulation
366			* @see #setupFortranParallel
367			*/
368			void setupFortranSim();
369
370	tim	1738	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
371			void setupCutoff();
372
373	tim	1733	/** Calculates the number of degress of freedom in the whole system */
374	tim	1722	void calcNdf();
375			void calcNdfRaw();
376			void calcNdfTrans();
377	gezelter	1490
378	tim	1719	void addExcludePairs(Molecule* mol);
379			void removeExcludePairs(Molecule* mol);
380
381	tim	1733	/**
382	tim	1735	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
383			* system.
384	tim	1733	*/
385			void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
386
387			std::map<int, Molecule> molecules_; /< Molecule array /
388
389	tim	1725	//degress of freedom
390	tim	1733	int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
391			int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
392			int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
393			int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
394
395			//number of global objects
396			int nGlobalMols_; /*< number of molecules in the system /
397			int nGlobalAtoms_; /*< number of atoms in the system /
398			int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
399	tim	1725
400	tim	1733	/**
401			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
402			* corresponding content is the global index of cutoff group this atom belong to.
403			* It is filled by SimCreator once and only once, since it is never changed during the simulation.
404			*/
405			std::vector<int> globalGroupMembership_;
406	tim	1735
407			/**
408			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
409			* corresponding content is the global index of molecule this atom belong to.
410			* It is filled by SimCreator once and only once, since it is never changed during the simulation.
411			*/
412			std::vector<int> globalMolMembership_;
413
414	tim	1733
415			std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
416			std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
417
418	tim	1725	//number of local objects
419	tim	1733	int nAtoms_; /*< number of atoms in local processor /
420			int nBonds_; /*< number of bonds in local processor /
421			int nBends_; /*< number of bends in local processor /
422			int nTorsions_; /*< number of torsions in local processor /
423			int nRigidBodies_; /*< number of rigid bodies in local processor /
424			int nIntegrableObjects_; /*< number of integrable objects in local processor /
425			int nCutoffGroups_; /*< number of cutoff groups in local processor /
426			int nConstraints_; /*< number of constraints in local processors /
427	gezelter	1490
428	tim	1733	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
429	tim	1719	Exclude exclude_;
430	tim	1733	ForceField* forceField_;
431	tim	1725	PropertyMap properties_; /*< Generic Property /
432			SnapshotManager* sman_; /*< SnapshotManager /
433	tim	1719	Globals* globals_;
434	tim	1725	int seed_; /*< seed for random number generator /
435
436	tim	1735	/**
437			* The reason to have a local index manager is that when molecule is migrating to other processors,
438			* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
439			* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
440			* to make a efficient data moving plan.
441			*/
442	tim	1725	LocalIndexManager localIndexMan_;
443
444	tim	1735	//file names
445	tim	1733	std::string finalConfigFileName_;
446			std::string dumpFileName_;
447			std::string statFileName_;
448	tim	1735
449			double rcut_; /*< cutoff radius/
450			double rsw_; /*< radius of switching function/
451	tim	1738
452			bool fortranInitialized_; /*< flag indicate whether fortran side is initialized /
453	tim	1733
454			#ifdef IS_MPI
455			//in Parallel version, we need MolToProc
456			public:
457
458			/**
459			* Finds the processor where a molecule resides
460			* @return the id of the processor which contains the molecule
461			* @param globalIndex global Index of the molecule
462			*/
463			int getMolToProc(int globalIndex) {
464			//assert(globalIndex < molToProcMap_.size());
465			return molToProcMap_[globalIndex];
466			}
467	tim	1725
468	tim	1735	/**
469			* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class
470			* @see #SimCreator::divideMolecules
471			*/
472	tim	1733	int* getMolToProcMapPointer() {
473			return &molToProcMap_[0];
474			}
475
476			private:
477
478			void setupFortranParallel();
479
480			/**
481			* The size of molToProcMap_ is equal to total number of molecules in the system.
482			* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
483			* once.
484			*/
485			std::vector<int> molToProcMap_;
486			#endif
487
488	gezelter	1490	};
489
490	tim	1710	} //namespace oopse
491			#endif //BRAINS_SIMMODEL_HPP