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 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;
        }

        /** Calculate the maximum cutoff radius based on the atom types */
        double calcMaxCutoffRadius();

        double getRcut() {
            return rcut_;
        }
        
        void setRcut(double rcut) {
            rcut_ = rcut;
        }

        double getRsw() {
            return rsw_;
        }
        void setRsw(double rsw) {
            rsw_ = 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];
        }
        
        //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();

        /** 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*/
        
#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:	1735
Committed:	Fri Nov 12 17:40:03 2004 UTC (19 years, 9 months ago) by tim
File size:	17076 byte(s)
Log Message:	SimCreator and SimInfo are ready for unit test
#	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	1726	typedef MoleculeIterator 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			* <p>
70			* The major change of SimInfo
71			* </p>
72			*/
73			SimInfo(const std::vector<std::pair<MoleculeStamp, int> >& molStampPairs, ForceField ff, Globals* globals);
74	tim	1710	virtual ~SimInfo();
75	gezelter	1490
76	tim	1710	/**
77			* Adds a molecule
78			* @return return true if adding successfully, return false if the molecule is already in SimInfo
79			* @param mol molecule to be added
80			*/
81			bool addMolecule(Molecule* mol);
82	gezelter	1490
83	tim	1710	/**
84			* Removes a molecule from SimInfo
85			* @return true if removing successfully, return false if molecule is not in this SimInfo
86			*/
87			bool removeMolecule(Molecule* mol);
88	gezelter	1490
89	tim	1725	/** Returns the total number of molecules in the system. */
90			int getNGlobalMolecules() {
91	tim	1733	return nGlobalMols_;
92	tim	1725	}
93
94			/** Returns the total number of atoms in the system. */
95			int getNGlobalAtoms() {
96	tim	1733	return nGlobalAtoms_;
97	tim	1725	}
98
99			/** Returns the total number of cutoff groups in the system. */
100			int getNGlobalCutoffGroups() {
101	tim	1733	return nGlobalCutoffGroups_;
102	tim	1725	}
103
104	tim	1710	/**
105	tim	1725	* Returns the number of local molecules.
106			* @return the number of local molecules
107	tim	1710	*/
108			int getNMolecules() {
109			return molecules_.size();
110			}
111	gezelter	1490
112	tim	1725	/** Returns the number of local atoms */
113	tim	1710	unsigned int getNAtoms() {
114			return nAtoms_;
115			}
116	gezelter	1490
117	tim	1725	/** Returns the number of local bonds */
118	tim	1710	unsigned int getNBonds(){
119			return nBonds_;
120			}
121	gezelter	1490
122	tim	1725	/** Returns the number of local bends */
123	tim	1710	unsigned int getNBends() {
124			return nBends_;
125			}
126	gezelter	1490
127	tim	1725	/** Returns the number of local torsions */
128	tim	1710	unsigned int getNTorsions() {
129			return nTorsions_;
130			}
131	gezelter	1490
132	tim	1725	/** Returns the number of local rigid bodies */
133	tim	1710	unsigned int getNRigidBodies() {
134			return nRigidBodies_;
135			}
136	gezelter	1490
137	tim	1725	/** Returns the number of local integrable objects */
138	tim	1710	unsigned int getNIntegrableObjects() {
139			return nIntegrableObjects_;
140			}
141	gezelter	1490
142	tim	1725	/** Returns the number of local cutoff groups */
143	tim	1710	unsigned int getNCutoffGroups() {
144			return nCutoffGroups_;
145			}
146	gezelter	1490
147	tim	1710	/** Returns the total number of constraints in this SimInfo */
148			unsigned int getNConstraints() {
149			return nConstraints_;
150			}
151
152			/**
153			* Returns the first molecule in this SimInfo and intialize the iterator.
154			* @return the first molecule, return NULL if there is not molecule in this SimInfo
155			* @param i the iterator of molecule array (user shouldn't change it)
156			*/
157	tim	1726	Molecule* beginMolecule(MoleculeIterator& i);
158	gezelter	1490
159	tim	1710	/**
160			* Returns the next avaliable Molecule based on the iterator.
161			* @return the next avaliable molecule, return NULL if reaching the end of the array
162			* @param i the iterator of molecule array
163			*/
164	tim	1726	Molecule* nextMolecule(MoleculeIterator& i);
165	gezelter	1490
166	tim	1710	/** Returns the number of degrees of freedom */
167	tim	1722	int getNdf() {
168	tim	1710	return ndf_;
169			}
170	gezelter	1490
171	tim	1710	/** Returns the number of raw degrees of freedom */
172	tim	1722	int getNdfRaw() {
173	tim	1710	return ndfRaw_;
174			}
175	gezelter	1490
176	tim	1710	/** Returns the number of translational degrees of freedom */
177	tim	1722	int getNdfTrans() {
178	tim	1710	return ndfTrans_;
179			}
180	gezelter	1490
181	tim	1733	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
182
183			/** Returns the total number of z-constraint molecules in the system */
184			int getNZconstraint() {
185			return nZconstraint_;
186			}
187
188			/**
189			* Sets the number of z-constraint molecules in the system.
190			*/
191			int setNZconstraint(int nZconstraint) {
192			nZconstraint_ = nZconstraint;
193			}
194
195	tim	1710	/** Returns the snapshot manager. */
196			SnapshotManager* getSnapshotManager() {
197			return sman_;
198			}
199	gezelter	1490
200	tim	1710	/** Sets the snapshot manager. */
201			void setSnapshotManager(SnapshotManager* sman) {
202			sman_ = sman;
203			}
204	tim	1712
205	tim	1719	/** Returns the force field */
206	tim	1712	ForceField* getForceField() {
207			return forceField_;
208			}
209	tim	1719
210			Globals* getGlobals() {
211			return globals_;
212			}
213
214	tim	1725	/** Returns the velocity of center of mass of the whole system.*/
215			Vector3d getComVel();
216	tim	1722
217	tim	1725	/** Returns the center of the mass of the whole system.*/
218	tim	1722	Vector3d getCom();
219
220	tim	1725	/** Returns the seed (used for random number generator) */
221	tim	1722	int getSeed() {
222			return seed_;
223			}
224
225	tim	1725	/** Sets the seed*/
226	tim	1722	void setSeed(int seed) {
227			seed_ = seed;
228			}
229	tim	1725
230	tim	1733	/** main driver function to interact with fortran during the initialization and molecule migration */
231	tim	1725	void update();
232
233			/** Returns the local index manager */
234			LocalIndexManager* getLocalIndexManager() {
235	tim	1735	return &localIndexMan_;
236	tim	1725	}
237
238			int getMoleculeStampId(int globalIndex) {
239			//assert(globalIndex < molStampIds_.size())
240			return molStampIds_[globalIndex];
241			}
242
243			/** Returns the molecule stamp */
244			MoleculeStamp* getMoleculeStamp(int id) {
245			return moleculeStamps_[id];
246			}
247
248			/**
249			* Finds a molecule with a specified global index
250			* @return a pointer point to found molecule
251			* @param index
252			*/
253			Molecule* getMoleculeByGlobalIndex(int index) {
254			std::map<int, Molecule*> i;
255	tim	1726	i = molecules_.find(index);
256	tim	1725
257	tim	1726	return i != molecules_.end() ? i->second : NULL;
258	tim	1725	}
259
260	tim	1735	/** Calculate the maximum cutoff radius based on the atom types */
261			double calcMaxCutoffRadius();
262	tim	1733
263	tim	1735	double getRcut() {
264			return rcut_;
265			}
266
267			void setRcut(double rcut) {
268			rcut_ = rcut;
269			}
270
271			double getRsw() {
272			return rsw_;
273			}
274			void setRsw(double rsw) {
275			rsw_ = rsw;
276			}
277
278	tim	1733	std::string getFinalConfigFileName() {
279			return finalConfigFileName_;
280			}
281
282			void setFinalConfigFileName(const std::string& fileName) {
283			finalConfigFileName_ = fileName;
284			}
285
286
287			std::string getDumpFileName() {
288			return dumpFileName_;
289			}
290
291			void setDumpFileName(const std::string& fileName) {
292			dumpFileName_ = fileName;
293			}
294
295			std::string getStatFileName() {
296			return statFileName_;
297			}
298
299			void setStatFileName(const std::string& fileName) {
300			statFileName_ = fileName;
301			}
302
303	tim	1735	/**
304			* Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class
305			* @see #SimCreator::setGlobalIndex
306			*/
307	tim	1733	int* getGlobalGroupMembershipPointer() {
308			return globalGroupMembership_[0];
309			}
310
311	tim	1735	/**
312			* Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class
313			* @see #SimCreator::setGlobalIndex
314			*/
315			int* getGlobalMolMembershipPointer() {
316			return globalMolMembership_[0];
317			}
318
319	tim	1733	//below functions are just forward functions
320			//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
321			//the other hand, has-a relation need composing.
322			/**
323			* Adds property into property map
324			* @param genData GenericData to be added into PropertyMap
325			*/
326			void addProperty(GenericData* genData);
327
328			/**
329			* Removes property from PropertyMap by name
330			* @param propName the name of property to be removed
331			*/
332			void removeProperty(const std::string& propName);
333
334			/**
335			* clear all of the properties
336			*/
337			void clearProperties();
338
339			/**
340			* Returns all names of properties
341			* @return all names of properties
342			*/
343			std::vector<std::string> getPropertyNames();
344
345			/**
346			* Returns all of the properties in PropertyMap
347			* @return all of the properties in PropertyMap
348			*/
349			std::vector<GenericData*> getProperties();
350
351			/**
352			* Returns property
353			* @param propName name of property
354			* @return a pointer point to property with propName. If no property named propName
355			* exists, return NULL
356			*/
357			GenericData* getPropertyByName(const std::string& propName);
358
359	tim	1725	friend std::ostream& operator <<(ostream& o, SimInfo& info);
360
361	tim	1710	private:
362	gezelter	1490
363	tim	1735
364			/** Returns the unique atom types of local processor in an array */
365			std::set<AtomType*> SimInfo::getUniqueAtomTypes();
366
367			/** fill up the simtype struct*/
368	tim	1733	void setupSimType();
369
370			/**
371			* Setup Fortran Simulation
372			* @see #setupFortranParallel
373			*/
374			void setupFortranSim();
375
376			/** Calculates the number of degress of freedom in the whole system */
377	tim	1722	void calcNdf();
378			void calcNdfRaw();
379			void calcNdfTrans();
380	gezelter	1490
381	tim	1719	void addExcludePairs(Molecule* mol);
382			void removeExcludePairs(Molecule* mol);
383
384	tim	1733	/**
385	tim	1735	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
386			* system.
387	tim	1733	*/
388			void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
389
390			std::map<int, Molecule> molecules_; /< Molecule array /
391
392	tim	1725	//degress of freedom
393	tim	1733	int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
394			int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
395			int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
396			int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
397
398			//number of global objects
399			int nGlobalMols_; /*< number of molecules in the system /
400			int nGlobalAtoms_; /*< number of atoms in the system /
401			int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
402	tim	1725
403	tim	1733	/**
404			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
405			* corresponding content is the global index of cutoff group this atom belong to.
406			* It is filled by SimCreator once and only once, since it is never changed during the simulation.
407			*/
408			std::vector<int> globalGroupMembership_;
409	tim	1735
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 molecule 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> globalMolMembership_;
416
417	tim	1733
418			std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
419			std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
420
421	tim	1725	//number of local objects
422	tim	1733	int nAtoms_; /*< number of atoms in local processor /
423			int nBonds_; /*< number of bonds in local processor /
424			int nBends_; /*< number of bends in local processor /
425			int nTorsions_; /*< number of torsions in local processor /
426			int nRigidBodies_; /*< number of rigid bodies in local processor /
427			int nIntegrableObjects_; /*< number of integrable objects in local processor /
428			int nCutoffGroups_; /*< number of cutoff groups in local processor /
429			int nConstraints_; /*< number of constraints in local processors /
430	gezelter	1490
431	tim	1733	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
432	tim	1719	Exclude exclude_;
433	tim	1733	ForceField* forceField_;
434	tim	1725	PropertyMap properties_; /*< Generic Property /
435			SnapshotManager* sman_; /*< SnapshotManager /
436	tim	1719	Globals* globals_;
437	tim	1725	int seed_; /*< seed for random number generator /
438
439	tim	1735	/**
440			* The reason to have a local index manager is that when molecule is migrating to other processors,
441			* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
442			* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
443			* to make a efficient data moving plan.
444			*/
445	tim	1725	LocalIndexManager localIndexMan_;
446
447	tim	1735	//file names
448	tim	1733	std::string finalConfigFileName_;
449			std::string dumpFileName_;
450			std::string statFileName_;
451	tim	1735
452			double rcut_; /*< cutoff radius/
453			double rsw_; /*< radius of switching function/
454	tim	1733
455			#ifdef IS_MPI
456			//in Parallel version, we need MolToProc
457			public:
458
459			/**
460			* Finds the processor where a molecule resides
461			* @return the id of the processor which contains the molecule
462			* @param globalIndex global Index of the molecule
463			*/
464			int getMolToProc(int globalIndex) {
465			//assert(globalIndex < molToProcMap_.size());
466			return molToProcMap_[globalIndex];
467			}
468	tim	1725
469	tim	1735	/**
470			* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class
471			* @see #SimCreator::divideMolecules
472			*/
473	tim	1733	int* getMolToProcMapPointer() {
474			return &molToProcMap_[0];
475			}
476
477			private:
478
479			void setupFortranParallel();
480
481			/**
482			* The size of molToProcMap_ is equal to total number of molecules in the system.
483			* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
484			* once.
485			*/
486			std::vector<int> molToProcMap_;
487			#endif
488
489	gezelter	1490	};
490
491	tim	1710	} //namespace oopse
492			#endif //BRAINS_SIMMODEL_HPP