src/brains/SimInfo.hpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

/**
 * @file SimInfo.hpp
 * @author    tlin
 * @date  11/02/2004
 * @version 1.0
 */ 

#ifndef BRAINS_SIMMODEL_HPP
#define BRAINS_SIMMODEL_HPP

#include <iostream>
#include <vector>
#include <utility>

#include "brains/fSimulation.h"
#include "brains/SimInfo.hpp"
#include "primitives/Molecule.hpp"
#include "types/MoleculeStamp.hpp"
#include "utils/PropertyMap.hpp"
#include "io/Globals.hpp"

namespace oopse{

/**
 * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" 
 * @brief As one of the heavy weight class of OOPSE, SimInfo
 * One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
 * And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
 * cutoff groups, constrains).
 * Another major change is the index. No matter single version or parallel version,  atoms and
 * rigid bodies have both global index and local index. Local index is not important to molecule as well as
 * cutoff group. 
 */
class SimInfo {
    public:
        typedef std::map<int, Molecule*>::iterator  MoleculeIterator;

        /**
         * Constructor of SimInfo
         * @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
         * second element is the total number of molecules with the same molecule stamp in the system
         * @param ff pointer of a concrete ForceField instance
         * @param globals 
         * @note
         */
        SimInfo(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* globals);
        virtual ~SimInfo();

        /**
         * Adds a molecule
         * @return return true if adding successfully, return false if the molecule is already in SimInfo
         * @param mol molecule to be added
         */
        bool addMolecule(Molecule* mol);

        /**
         * Removes a molecule from SimInfo
         * @return true if removing successfully, return false if molecule is not in this SimInfo
         */
        bool removeMolecule(Molecule* mol);

        /** Returns the total number of molecules in the system. */
        int getNGlobalMolecules() {
            return nGlobalMols_;
        }

        /** Returns the total number of atoms in the system. */
        int getNGlobalAtoms() {
            return nGlobalAtoms_;
        }

        /** Returns the total number of cutoff groups in the system. */
        int getNGlobalCutoffGroups() {
            return nGlobalCutoffGroups_;
        }

        /**
         * Returns the total number of integrable objects (total number of rigid bodies plus the total number
         * of atoms which do not belong to the rigid bodies) in the system
         */
        int getNGlobalIntegrableObjects() {
            return nGlobalIntegrableObjects_;
        }
        
        /** 
         * Returns the number of local molecules.
         * @return the number of local molecules 
         */
        int getNMolecules() {
            return molecules_.size();
        }

        /** Returns the number of local atoms */
        unsigned int getNAtoms() {
            return nAtoms_;
        }

        /** Returns the number of local bonds */        
        unsigned int getNBonds(){
            return nBonds_;
        }

        /** Returns the number of local bends */        
        unsigned int getNBends() {
            return nBends_;
        }

        /** Returns the number of local torsions */        
        unsigned int getNTorsions() {
            return nTorsions_;
        }

        /** Returns the number of local rigid bodies */        
        unsigned int getNRigidBodies() {
            return nRigidBodies_;
        }

        /** Returns the number of local integrable objects */
        unsigned int getNIntegrableObjects() {
            return nIntegrableObjects_;
        }

        /** Returns the number of local cutoff groups */
        unsigned int getNCutoffGroups() {
            return nCutoffGroups_;
        }

        /** Returns the total number of constraints in this SimInfo */
        unsigned int getNConstraints() {
            return nConstraints_;
        }
        
        /**
         * Returns the first molecule in this SimInfo and intialize the iterator.
         * @return the first molecule, return NULL if there is not molecule in this SimInfo
         * @param i the iterator of molecule array (user shouldn't change it)
         */
        Molecule* beginMolecule(MoleculeIterator& i);

        /** 
          * Returns the next avaliable Molecule based on the iterator.
          * @return the next avaliable molecule, return NULL if reaching the end of the array 
          * @param i the iterator of molecule array
          */
        Molecule* nextMolecule(MoleculeIterator& i);

        /** Returns the number of degrees of freedom */
        int getNdf() {
            return ndf_;
        }

        /** Returns the number of raw degrees of freedom */
        int getNdfRaw() {
            return ndfRaw_;
        }

        /** Returns the number of translational degrees of freedom */
        int getNdfTrans() {
            return ndfTrans_;
        }

        //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
        
        /** Returns the total number of z-constraint molecules in the system */
        int getNZconstraint() {
            return nZconstraint_;
        }

        /** 
         * Sets the number of z-constraint molecules in the system.
         */
        int setNZconstraint(int nZconstraint) {
            nZconstraint_ = nZconstraint;
        }
        
        /** Returns the snapshot manager. */
        SnapshotManager* getSnapshotManager() {
            return sman_;
        }

        /** Sets the snapshot manager. */
        void setSnapshotManager(SnapshotManager* sman) {
            sman_ = sman;
        }

        /** Returns the force field */
        ForceField* getForceField() {
            return forceField_;
        }

        Globals* getGlobals() {
            return globals_;
        }

        /** Returns the velocity of center of mass of the whole system.*/
        Vector3d getComVel();

        /** Returns the center of the mass of the whole system.*/
        Vector3d getCom();

        /** Returns the seed (used for random number generator) */
        int getSeed() {
            return seed_;
        }

        /** Sets the seed*/
        void setSeed(int seed) {
            seed_ = seed;
        }

        /** main driver function to interact with fortran during the initialization and molecule migration */
        void update();

        /** Returns the local index manager */
        LocalIndexManager* getLocalIndexManager() {
            return &localIndexMan_;
        }

        int getMoleculeStampId(int globalIndex) {
            //assert(globalIndex < molStampIds_.size())
            return molStampIds_[globalIndex];
        }

        /** Returns the molecule stamp */
        MoleculeStamp* getMoleculeStamp(int id) {
            return moleculeStamps_[id];
        }
        
        /**
         * Finds a molecule with a specified global index
         * @return a pointer point to found molecule
         * @param index
         */
        Molecule* getMoleculeByGlobalIndex(int index) {
            std::map<int, Molecule*> i;
            i = molecules_.find(index);

            return i != molecules_.end() ? i->second : NULL;
        }

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

        double getRcut() {
            return rcut_;
        }

        double getRsw() {
            return rsw_;
        }
        
        std::string getFinalConfigFileName() {
            return finalConfigFileName_;
        }
        
        void setFinalConfigFileName(const std::string& fileName) {
            finalConfigFileName_ = fileName;
        }

        std::string getDumpFileName() {
            return dumpFileName_;
        }
        
        void setDumpFileName(const std::string& fileName) {
            dumpFileName_ = fileName;
        }

        std::string getStatFileName() {
            return statFileName_;
        }
        
        void setStatFileName(const std::string& fileName) {
            statFileName_ = fileName;
        }

        /** 
         * Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class
         * @see #SimCreator::setGlobalIndex
         */  
        int* getGlobalGroupMembershipPointer() {
            return globalGroupMembership_[0];
        }

        /** 
         * Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class
         * @see #SimCreator::setGlobalIndex
         */        
        int* getGlobalMolMembershipPointer() {
            return globalMolMembership_[0];
        }


        bool isFortranInitialized() {
            return fortranInitialized_;
        }
        
        //below functions are just forward functions
        //To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
        //the other hand, has-a relation need composing.
        /**
         * Adds property into property map
         * @param genData GenericData to be added into PropertyMap
         */
        void addProperty(GenericData* genData);

        /**
         * Removes property from PropertyMap by name
         * @param propName the name of property to be removed
         */
        void removeProperty(const std::string& propName);

        /**
         * clear all of the properties
         */
        void clearProperties();

        /**
         * Returns all names of properties
         * @return all names of properties
         */
        std::vector<std::string> getPropertyNames();

        /**
         * Returns all of the properties in PropertyMap
         * @return all of the properties in PropertyMap
         */      
        std::vector<GenericData*> getProperties();

        /**
         * Returns property 
         * @param propName name of property
         * @return a pointer point to property with propName. If no property named propName
         * exists, return NULL
         */      
        GenericData* getPropertyByName(const std::string& propName);
                
        friend std::ostream& operator <<(ostream& o, SimInfo& info);
        
    private:

        
        /** Returns the unique atom types of local processor in an array */
        std::set<AtomType*> SimInfo::getUniqueAtomTypes();

        /** fill up the simtype struct*/
        void setupSimType();

        /**
         * Setup Fortran Simulation
         * @see #setupFortranParallel
         */
        void setupFortranSim();

        /** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
        void setupCutoff();

        /** Calculates the number of degress of freedom in the whole system */
        void calcNdf();
        void calcNdfRaw();
        void calcNdfTrans();

        void addExcludePairs(Molecule* mol);
        void removeExcludePairs(Molecule* mol);

        /**
         * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
         * system.
         */
        void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);

        std::map<int, Molecule*>  molecules_; /**< Molecule array */
        
        //degress of freedom
        int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
        int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
        int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
        int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
        
        //number of global objects
        int nGlobalMols_;       /**< number of molecules in the system */
        int nGlobalAtoms_;   /**< number of atoms in the system */
        int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
        int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */

        /**
         * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
         * corresponding content is the global index of cutoff group this atom belong to. 
         * It is filled by SimCreator once and only once, since it is never changed during the simulation.
         */
        std::vector<int> globalGroupMembership_; 

        /**
         * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
         * corresponding content is the global index of molecule this atom belong to. 
         * It is filled by SimCreator once and only once, since it is never changed during the simulation.
         */
        std::vector<int> globalMolMembership_;        

        
        std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
        std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */        
        
        //number of local objects
        int nAtoms_;                        /**< number of atoms in local processor */
        int nBonds_;                        /**< number of bonds in local processor */
        int nBends_;                        /**< number of bends in local processor */
        int nTorsions_;                    /**< number of torsions in local processor */
        int nRigidBodies_;              /**< number of rigid bodies in local processor */
        int nIntegrableObjects_;    /**< number of integrable objects in local processor */
        int nCutoffGroups_;             /**< number of cutoff groups in local processor */
        int nConstraints_;              /**< number of constraints in local processors */

        simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
        Exclude exclude_;
        ForceField* forceField_;            
        PropertyMap properties_;                  /**< Generic Property */
        SnapshotManager* sman_;               /**< SnapshotManager */
        Globals* globals_;
        int seed_; /**< seed for random number generator */

        /** 
         * The reason to have a local index manager is that when molecule is migrating to other processors, 
         * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
         * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
         * to make a efficient data moving plan.
         */        
        LocalIndexManager localIndexMan_;

        //file names
        std::string finalConfigFileName_;
        std::string dumpFileName_;
        std::string statFileName_;

        double rcut_;       /**< cutoff radius*/
        double rsw_;        /**< radius of switching function*/

        bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
        
#ifdef IS_MPI
    //in Parallel version, we need MolToProc
    public:
                
        /**
         * Finds the processor where a molecule resides
         * @return the id of the processor which contains the molecule
         * @param globalIndex global Index of the molecule
         */
        int getMolToProc(int globalIndex) {
            //assert(globalIndex < molToProcMap_.size());
            return molToProcMap_[globalIndex];
        }

        /** 
         * Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class
         * @see #SimCreator::divideMolecules
         */
        int* getMolToProcMapPointer() {
            return &molToProcMap_[0];
        }
        
    private:

        void setupFortranParallel();
        
        /** 
         * The size of molToProcMap_ is equal to total number of molecules in the system.
         *  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
         * once.
         */        
        std::vector<int> molToProcMap_; 
#endif

};

} //namespace oopse
#endif //BRAINS_SIMMODEL_HPP
Revision:	1739
Committed:	Mon Nov 15 18:02:15 2004 UTC (19 years, 9 months ago) by tim
File size:	17620 byte(s)
Log Message:	finish DumpReader, DumpWriter.Next Step is LJFF and integrators
#	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	1739	#include "brains/SimInfo.hpp"
42	tim	1492	#include "primitives/Molecule.hpp"
43	tim	1719	#include "types/MoleculeStamp.hpp"
44	tim	1710	#include "utils/PropertyMap.hpp"
45	tim	1719	#include "io/Globals.hpp"
46	gezelter	1490
47	tim	1710	namespace oopse{
48	gezelter	1490
49	tim	1710	/**
50			* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
51	tim	1735	* @brief As one of the heavy weight class of OOPSE, SimInfo
52			* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
53			* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
54			* cutoff groups, constrains).
55			* Another major change is the index. No matter single version or parallel version, atoms and
56			* rigid bodies have both global index and local index. Local index is not important to molecule as well as
57			* cutoff group.
58	tim	1710	*/
59			class SimInfo {
60			public:
61	tim	1738	typedef std::map<int, Molecule*>::iterator MoleculeIterator;
62	tim	1733
63			/**
64			* Constructor of SimInfo
65			* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
66			* second element is the total number of molecules with the same molecule stamp in the system
67			* @param ff pointer of a concrete ForceField instance
68			* @param globals
69			* @note
70			*/
71			SimInfo(const std::vector<std::pair<MoleculeStamp, int> >& molStampPairs, ForceField ff, Globals* globals);
72	tim	1710	virtual ~SimInfo();
73	gezelter	1490
74	tim	1710	/**
75			* Adds a molecule
76			* @return return true if adding successfully, return false if the molecule is already in SimInfo
77			* @param mol molecule to be added
78			*/
79			bool addMolecule(Molecule* mol);
80	gezelter	1490
81	tim	1710	/**
82			* Removes a molecule from SimInfo
83			* @return true if removing successfully, return false if molecule is not in this SimInfo
84			*/
85			bool removeMolecule(Molecule* mol);
86	gezelter	1490
87	tim	1725	/** Returns the total number of molecules in the system. */
88			int getNGlobalMolecules() {
89	tim	1733	return nGlobalMols_;
90	tim	1725	}
91
92			/** Returns the total number of atoms in the system. */
93			int getNGlobalAtoms() {
94	tim	1733	return nGlobalAtoms_;
95	tim	1725	}
96
97			/** Returns the total number of cutoff groups in the system. */
98			int getNGlobalCutoffGroups() {
99	tim	1733	return nGlobalCutoffGroups_;
100	tim	1725	}
101	tim	1739
102			/**
103			* Returns the total number of integrable objects (total number of rigid bodies plus the total number
104			* of atoms which do not belong to the rigid bodies) in the system
105			*/
106			int getNGlobalIntegrableObjects() {
107			return nGlobalIntegrableObjects_;
108			}
109	tim	1725
110	tim	1710	/**
111	tim	1725	* Returns the number of local molecules.
112			* @return the number of local molecules
113	tim	1710	*/
114			int getNMolecules() {
115			return molecules_.size();
116			}
117	gezelter	1490
118	tim	1725	/** Returns the number of local atoms */
119	tim	1710	unsigned int getNAtoms() {
120			return nAtoms_;
121			}
122	gezelter	1490
123	tim	1725	/** Returns the number of local bonds */
124	tim	1710	unsigned int getNBonds(){
125			return nBonds_;
126			}
127	gezelter	1490
128	tim	1725	/** Returns the number of local bends */
129	tim	1710	unsigned int getNBends() {
130			return nBends_;
131			}
132	gezelter	1490
133	tim	1725	/** Returns the number of local torsions */
134	tim	1710	unsigned int getNTorsions() {
135			return nTorsions_;
136			}
137	gezelter	1490
138	tim	1725	/** Returns the number of local rigid bodies */
139	tim	1710	unsigned int getNRigidBodies() {
140			return nRigidBodies_;
141			}
142	gezelter	1490
143	tim	1725	/** Returns the number of local integrable objects */
144	tim	1710	unsigned int getNIntegrableObjects() {
145			return nIntegrableObjects_;
146			}
147	gezelter	1490
148	tim	1725	/** Returns the number of local cutoff groups */
149	tim	1710	unsigned int getNCutoffGroups() {
150			return nCutoffGroups_;
151			}
152	gezelter	1490
153	tim	1710	/** Returns the total number of constraints in this SimInfo */
154			unsigned int getNConstraints() {
155			return nConstraints_;
156			}
157
158			/**
159			* Returns the first molecule in this SimInfo and intialize the iterator.
160			* @return the first molecule, return NULL if there is not molecule in this SimInfo
161			* @param i the iterator of molecule array (user shouldn't change it)
162			*/
163	tim	1726	Molecule* beginMolecule(MoleculeIterator& i);
164	gezelter	1490
165	tim	1710	/**
166			* Returns the next avaliable Molecule based on the iterator.
167			* @return the next avaliable molecule, return NULL if reaching the end of the array
168			* @param i the iterator of molecule array
169			*/
170	tim	1726	Molecule* nextMolecule(MoleculeIterator& i);
171	gezelter	1490
172	tim	1710	/** Returns the number of degrees of freedom */
173	tim	1722	int getNdf() {
174	tim	1710	return ndf_;
175			}
176	gezelter	1490
177	tim	1710	/** Returns the number of raw degrees of freedom */
178	tim	1722	int getNdfRaw() {
179	tim	1710	return ndfRaw_;
180			}
181	gezelter	1490
182	tim	1710	/** Returns the number of translational degrees of freedom */
183	tim	1722	int getNdfTrans() {
184	tim	1710	return ndfTrans_;
185			}
186	gezelter	1490
187	tim	1733	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
188
189			/** Returns the total number of z-constraint molecules in the system */
190			int getNZconstraint() {
191			return nZconstraint_;
192			}
193
194			/**
195			* Sets the number of z-constraint molecules in the system.
196			*/
197			int setNZconstraint(int nZconstraint) {
198			nZconstraint_ = nZconstraint;
199			}
200
201	tim	1710	/** Returns the snapshot manager. */
202			SnapshotManager* getSnapshotManager() {
203			return sman_;
204			}
205	gezelter	1490
206	tim	1710	/** Sets the snapshot manager. */
207			void setSnapshotManager(SnapshotManager* sman) {
208			sman_ = sman;
209			}
210	tim	1712
211	tim	1719	/** Returns the force field */
212	tim	1712	ForceField* getForceField() {
213			return forceField_;
214			}
215	tim	1719
216			Globals* getGlobals() {
217			return globals_;
218			}
219
220	tim	1725	/** Returns the velocity of center of mass of the whole system.*/
221			Vector3d getComVel();
222	tim	1722
223	tim	1725	/** Returns the center of the mass of the whole system.*/
224	tim	1722	Vector3d getCom();
225
226	tim	1725	/** Returns the seed (used for random number generator) */
227	tim	1722	int getSeed() {
228			return seed_;
229			}
230
231	tim	1725	/** Sets the seed*/
232	tim	1722	void setSeed(int seed) {
233			seed_ = seed;
234			}
235	tim	1725
236	tim	1733	/** main driver function to interact with fortran during the initialization and molecule migration */
237	tim	1725	void update();
238
239			/** Returns the local index manager */
240			LocalIndexManager* getLocalIndexManager() {
241	tim	1735	return &localIndexMan_;
242	tim	1725	}
243
244			int getMoleculeStampId(int globalIndex) {
245			//assert(globalIndex < molStampIds_.size())
246			return molStampIds_[globalIndex];
247			}
248
249			/** Returns the molecule stamp */
250			MoleculeStamp* getMoleculeStamp(int id) {
251			return moleculeStamps_[id];
252			}
253
254			/**
255			* Finds a molecule with a specified global index
256			* @return a pointer point to found molecule
257			* @param index
258			*/
259			Molecule* getMoleculeByGlobalIndex(int index) {
260			std::map<int, Molecule*> i;
261	tim	1726	i = molecules_.find(index);
262	tim	1725
263	tim	1726	return i != molecules_.end() ? i->second : NULL;
264	tim	1725	}
265
266	tim	1735	/** Calculate the maximum cutoff radius based on the atom types */
267			double calcMaxCutoffRadius();
268	tim	1733
269	tim	1735	double getRcut() {
270			return rcut_;
271			}
272
273			double getRsw() {
274			return rsw_;
275			}
276
277	tim	1733	std::string getFinalConfigFileName() {
278			return finalConfigFileName_;
279			}
280
281			void setFinalConfigFileName(const std::string& fileName) {
282			finalConfigFileName_ = fileName;
283			}
284
285			std::string getDumpFileName() {
286			return dumpFileName_;
287			}
288
289			void setDumpFileName(const std::string& fileName) {
290			dumpFileName_ = fileName;
291			}
292
293			std::string getStatFileName() {
294			return statFileName_;
295			}
296
297			void setStatFileName(const std::string& fileName) {
298			statFileName_ = fileName;
299			}
300
301	tim	1735	/**
302			* Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class
303			* @see #SimCreator::setGlobalIndex
304			*/
305	tim	1733	int* getGlobalGroupMembershipPointer() {
306			return globalGroupMembership_[0];
307			}
308
309	tim	1735	/**
310			* Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class
311			* @see #SimCreator::setGlobalIndex
312			*/
313			int* getGlobalMolMembershipPointer() {
314			return globalMolMembership_[0];
315			}
316	tim	1738
317
318			bool isFortranInitialized() {
319			return fortranInitialized_;
320			}
321	tim	1735
322	tim	1733	//below functions are just forward functions
323			//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
324			//the other hand, has-a relation need composing.
325			/**
326			* Adds property into property map
327			* @param genData GenericData to be added into PropertyMap
328			*/
329			void addProperty(GenericData* genData);
330
331			/**
332			* Removes property from PropertyMap by name
333			* @param propName the name of property to be removed
334			*/
335			void removeProperty(const std::string& propName);
336
337			/**
338			* clear all of the properties
339			*/
340			void clearProperties();
341
342			/**
343			* Returns all names of properties
344			* @return all names of properties
345			*/
346			std::vector<std::string> getPropertyNames();
347
348			/**
349			* Returns all of the properties in PropertyMap
350			* @return all of the properties in PropertyMap
351			*/
352			std::vector<GenericData*> getProperties();
353
354			/**
355			* Returns property
356			* @param propName name of property
357			* @return a pointer point to property with propName. If no property named propName
358			* exists, return NULL
359			*/
360			GenericData* getPropertyByName(const std::string& propName);
361
362	tim	1725	friend std::ostream& operator <<(ostream& o, SimInfo& info);
363
364	tim	1710	private:
365	gezelter	1490
366	tim	1735
367			/** Returns the unique atom types of local processor in an array */
368			std::set<AtomType*> SimInfo::getUniqueAtomTypes();
369
370			/** fill up the simtype struct*/
371	tim	1733	void setupSimType();
372
373			/**
374			* Setup Fortran Simulation
375			* @see #setupFortranParallel
376			*/
377			void setupFortranSim();
378
379	tim	1738	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
380			void setupCutoff();
381
382	tim	1733	/** Calculates the number of degress of freedom in the whole system */
383	tim	1722	void calcNdf();
384			void calcNdfRaw();
385			void calcNdfTrans();
386	gezelter	1490
387	tim	1719	void addExcludePairs(Molecule* mol);
388			void removeExcludePairs(Molecule* mol);
389
390	tim	1733	/**
391	tim	1735	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
392			* system.
393	tim	1733	*/
394			void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
395
396			std::map<int, Molecule> molecules_; /< Molecule array /
397
398	tim	1725	//degress of freedom
399	tim	1733	int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
400			int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
401			int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
402			int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
403
404			//number of global objects
405			int nGlobalMols_; /*< number of molecules in the system /
406			int nGlobalAtoms_; /*< number of atoms in the system /
407			int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
408	tim	1739	int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
409	tim	1725
410	tim	1733	/**
411			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
412			* corresponding content is the global index of cutoff group this atom belong to.
413			* It is filled by SimCreator once and only once, since it is never changed during the simulation.
414			*/
415			std::vector<int> globalGroupMembership_;
416	tim	1735
417			/**
418			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
419			* corresponding content is the global index of molecule this atom belong to.
420			* It is filled by SimCreator once and only once, since it is never changed during the simulation.
421			*/
422			std::vector<int> globalMolMembership_;
423
424	tim	1733
425			std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
426			std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
427
428	tim	1725	//number of local objects
429	tim	1733	int nAtoms_; /*< number of atoms in local processor /
430			int nBonds_; /*< number of bonds in local processor /
431			int nBends_; /*< number of bends in local processor /
432			int nTorsions_; /*< number of torsions in local processor /
433			int nRigidBodies_; /*< number of rigid bodies in local processor /
434			int nIntegrableObjects_; /*< number of integrable objects in local processor /
435			int nCutoffGroups_; /*< number of cutoff groups in local processor /
436			int nConstraints_; /*< number of constraints in local processors /
437	gezelter	1490
438	tim	1733	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
439	tim	1719	Exclude exclude_;
440	tim	1733	ForceField* forceField_;
441	tim	1725	PropertyMap properties_; /*< Generic Property /
442			SnapshotManager* sman_; /*< SnapshotManager /
443	tim	1719	Globals* globals_;
444	tim	1725	int seed_; /*< seed for random number generator /
445
446	tim	1735	/**
447			* The reason to have a local index manager is that when molecule is migrating to other processors,
448			* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
449			* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
450			* to make a efficient data moving plan.
451			*/
452	tim	1725	LocalIndexManager localIndexMan_;
453
454	tim	1735	//file names
455	tim	1733	std::string finalConfigFileName_;
456			std::string dumpFileName_;
457			std::string statFileName_;
458	tim	1735
459			double rcut_; /*< cutoff radius/
460			double rsw_; /*< radius of switching function/
461	tim	1738
462			bool fortranInitialized_; /*< flag indicate whether fortran side is initialized /
463	tim	1733
464			#ifdef IS_MPI
465			//in Parallel version, we need MolToProc
466			public:
467
468			/**
469			* Finds the processor where a molecule resides
470			* @return the id of the processor which contains the molecule
471			* @param globalIndex global Index of the molecule
472			*/
473			int getMolToProc(int globalIndex) {
474			//assert(globalIndex < molToProcMap_.size());
475			return molToProcMap_[globalIndex];
476			}
477	tim	1725
478	tim	1735	/**
479			* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class
480			* @see #SimCreator::divideMolecules
481			*/
482	tim	1733	int* getMolToProcMapPointer() {
483			return &molToProcMap_[0];
484			}
485
486			private:
487
488			void setupFortranParallel();
489
490			/**
491			* The size of molToProcMap_ is equal to total number of molecules in the system.
492			* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
493			* once.
494			*/
495			std::vector<int> molToProcMap_;
496			#endif
497
498	gezelter	1490	};
499
500	tim	1710	} //namespace oopse
501			#endif //BRAINS_SIMMODEL_HPP