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, 8 months ago) by tim
File size:	17076 byte(s)
Log Message:	SimCreator and SimInfo are ready for unit test
#	Content
1	/*
2	* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3	*
4	* Contact: oopse@oopse.org
5	*
6	* This program is free software; you can redistribute it and/or
7	* modify it under the terms of the GNU Lesser General Public License
8	* as published by the Free Software Foundation; either version 2.1
9	* of the License, or (at your option) any later version.
10	* All we ask is that proper credit is given for our work, which includes
11	* - but is not limited to - adding the above copyright notice to the beginning
12	* of your source code files, and to any copyright notice that you may distribute
13	* with programs based on this work.
14	*
15	* This program is distributed in the hope that it will be useful,
16	* but WITHOUT ANY WARRANTY; without even the implied warranty of
17	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18	* GNU Lesser General Public License for more details.
19	*
20	* You should have received a copy of the GNU Lesser General Public License
21	* along with this program; if not, write to the Free Software
22	* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23	*
24	*/
25
26	/**
27	* @file SimInfo.hpp
28	* @author tlin
29	* @date 11/02/2004
30	* @version 1.0
31	*/
32
33	#ifndef BRAINS_SIMMODEL_HPP
34	#define BRAINS_SIMMODEL_HPP
35
36	#include <iostream>
37	#include <vector>
38	#include <utility>
39
40	#include "brains/fSimulation.h"
41	#include "primitives/Molecule.hpp"
42	#include "types/MoleculeStamp.hpp"
43	#include "utils/PropertyMap.hpp"
44	#include "io/Globals.hpp"
45
46	namespace oopse{
47
48	/**
49	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
50	* @brief 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	*/
58	class SimInfo {
59	public:
60	typedef MoleculeIterator MoleculeIterator;
61
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	virtual ~SimInfo();
75
76	/**
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
83	/**
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
89	/** Returns the total number of molecules in the system. */
90	int getNGlobalMolecules() {
91	return nGlobalMols_;
92	}
93
94	/** Returns the total number of atoms in the system. */
95	int getNGlobalAtoms() {
96	return nGlobalAtoms_;
97	}
98
99	/** Returns the total number of cutoff groups in the system. */
100	int getNGlobalCutoffGroups() {
101	return nGlobalCutoffGroups_;
102	}
103
104	/**
105	* Returns the number of local molecules.
106	* @return the number of local molecules
107	*/
108	int getNMolecules() {
109	return molecules_.size();
110	}
111
112	/** Returns the number of local atoms */
113	unsigned int getNAtoms() {
114	return nAtoms_;
115	}
116
117	/** Returns the number of local bonds */
118	unsigned int getNBonds(){
119	return nBonds_;
120	}
121
122	/** Returns the number of local bends */
123	unsigned int getNBends() {
124	return nBends_;
125	}
126
127	/** Returns the number of local torsions */
128	unsigned int getNTorsions() {
129	return nTorsions_;
130	}
131
132	/** Returns the number of local rigid bodies */
133	unsigned int getNRigidBodies() {
134	return nRigidBodies_;
135	}
136
137	/** Returns the number of local integrable objects */
138	unsigned int getNIntegrableObjects() {
139	return nIntegrableObjects_;
140	}
141
142	/** Returns the number of local cutoff groups */
143	unsigned int getNCutoffGroups() {
144	return nCutoffGroups_;
145	}
146
147	/** 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	Molecule* beginMolecule(MoleculeIterator& i);
158
159	/**
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	Molecule* nextMolecule(MoleculeIterator& i);
165
166	/** Returns the number of degrees of freedom */
167	int getNdf() {
168	return ndf_;
169	}
170
171	/** Returns the number of raw degrees of freedom */
172	int getNdfRaw() {
173	return ndfRaw_;
174	}
175
176	/** Returns the number of translational degrees of freedom */
177	int getNdfTrans() {
178	return ndfTrans_;
179	}
180
181	//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	/** Returns the snapshot manager. */
196	SnapshotManager* getSnapshotManager() {
197	return sman_;
198	}
199
200	/** Sets the snapshot manager. */
201	void setSnapshotManager(SnapshotManager* sman) {
202	sman_ = sman;
203	}
204
205	/** Returns the force field */
206	ForceField* getForceField() {
207	return forceField_;
208	}
209
210	Globals* getGlobals() {
211	return globals_;
212	}
213
214	/** Returns the velocity of center of mass of the whole system.*/
215	Vector3d getComVel();
216
217	/** Returns the center of the mass of the whole system.*/
218	Vector3d getCom();
219
220	/** Returns the seed (used for random number generator) */
221	int getSeed() {
222	return seed_;
223	}
224
225	/** Sets the seed*/
226	void setSeed(int seed) {
227	seed_ = seed;
228	}
229
230	/** main driver function to interact with fortran during the initialization and molecule migration */
231	void update();
232
233	/** Returns the local index manager */
234	LocalIndexManager* getLocalIndexManager() {
235	return &localIndexMan_;
236	}
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	i = molecules_.find(index);
256
257	return i != molecules_.end() ? i->second : NULL;
258	}
259
260	/** Calculate the maximum cutoff radius based on the atom types */
261	double calcMaxCutoffRadius();
262
263	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	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	/**
304	* Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class
305	* @see #SimCreator::setGlobalIndex
306	*/
307	int* getGlobalGroupMembershipPointer() {
308	return globalGroupMembership_[0];
309	}
310
311	/**
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	//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	friend std::ostream& operator <<(ostream& o, SimInfo& info);
360
361	private:
362
363
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	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	void calcNdf();
378	void calcNdfRaw();
379	void calcNdfTrans();
380
381	void addExcludePairs(Molecule* mol);
382	void removeExcludePairs(Molecule* mol);
383
384	/**
385	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
386	* system.
387	*/
388	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
389
390	std::map<int, Molecule> molecules_; /< Molecule array /
391
392	//degress of freedom
393	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
403	/**
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
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
418	std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
419	std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
420
421	//number of local objects
422	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
431	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
432	Exclude exclude_;
433	ForceField* forceField_;
434	PropertyMap properties_; /*< Generic Property /
435	SnapshotManager* sman_; /*< SnapshotManager /
436	Globals* globals_;
437	int seed_; /*< seed for random number generator /
438
439	/**
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	LocalIndexManager localIndexMan_;
446
447	//file names
448	std::string finalConfigFileName_;
449	std::string dumpFileName_;
450	std::string statFileName_;
451
452	double rcut_; /*< cutoff radius/
453	double rsw_; /*< radius of switching function/
454
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
469	/**
470	* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class
471	* @see #SimCreator::divideMolecules
472	*/
473	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	};
490
491	} //namespace oopse
492	#endif //BRAINS_SIMMODEL_HPP