src/brains/SimInfo.hpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @file SimInfo.hpp
 * @author    tlin
 * @date  11/02/2004
 * @version 1.0
 */ 

#ifndef BRAINS_SIMMODEL_HPP
#define BRAINS_SIMMODEL_HPP

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

#include "brains/Exclude.hpp"
#include "io/Globals.hpp"
#include "math/Vector3.hpp"
#include "types/MoleculeStamp.hpp"
#include "UseTheForce/ForceField.hpp"
#include "utils/PropertyMap.hpp"
#include "utils/LocalIndexManager.hpp"
#include "selection/SelectionManager.hpp"
//another nonsense macro declaration
#define __C
#include "brains/fSimulation.h"

namespace oopse{

//forward decalration 
class SnapshotManager;
class Molecule;

/**
 * @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 simParams 
         * @note
         */
        SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
        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 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 getNGlobalRigidBodies() {
            return nGlobalRigidBodies_;
        }

        int getNGlobalConstraints();
        /** 
         * 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.
         */
        void setNZconstraint(int nZconstraint) {
            nZconstraint_ = nZconstraint;
        }
        
        /** Returns the snapshot manager. */
        SnapshotManager* getSnapshotManager() {
            return sman_;
        }

        /** Sets the snapshot manager. */
        void setSnapshotManager(SnapshotManager* sman);
        
        /** Returns the force field */
        ForceField* getForceField() {
            return forceField_;
        }

        Globals* getSimParams() {
            return simParams_;
        }

        /** 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];
        }

        /** Return the total number of the molecule stamps */
        int getNMoleculeStamp() {
            return moleculeStamps_.size();
        }
        /**
         * Finds a molecule with a specified global index
         * @return a pointer point to found molecule
         * @param index
         */
        Molecule* getMoleculeByGlobalIndex(int index) {
            MoleculeIterator 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;
        }

        /** 
         * Sets GlobalGroupMembership
         * @see #SimCreator::setGlobalIndex
         */  
        void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
            assert(globalGroupMembership.size() == nGlobalAtoms_);
            globalGroupMembership_ = globalGroupMembership;
        }

        /** 
         * Sets GlobalMolMembership
         * @see #SimCreator::setGlobalIndex
         */        
        void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
            assert(globalMolMembership.size() == nGlobalAtoms_);
            globalMolMembership_ = globalMolMembership;
        }


        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);

        /**
         * add all exclude pairs of a molecule into exclude list.
         */
        void addExcludePairs(Molecule* mol);

        /**
         * remove all exclude pairs which belong to a molecule from exclude list
         */

        void removeExcludePairs(Molecule* mol);


        SelectionManager* getSelectionManager() {
            return selectMan_;
        }
        
        friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
        
    private:

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

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

        ForceField* forceField_;      
        Globals* simParams_;

        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 */
        int nGlobalRigidBodies_; /**< number of rigid bodies 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 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_;      
        PropertyMap properties_;                  /**< Generic Property */
        SnapshotManager* sman_;               /**< SnapshotManager */

        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 */

        SelectionManager* selectMan_;
#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];
        }

        /** 
         * Set MolToProcMap array
         * @see #SimCreator::divideMolecules
         */
        void setMolToProcMap(const std::vector<int>& molToProcMap) {
            molToProcMap_ = molToProcMap;
        }
        
    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:	292
Committed:	Fri Feb 4 22:44:15 2005 UTC (20 years, 8 months ago) by tim
File size:	19640 byte(s)
Log Message:	adding SelectionManager into SimInfo
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	/**
43	* @file SimInfo.hpp
44	* @author tlin
45	* @date 11/02/2004
46	* @version 1.0
47	*/
48
49	#ifndef BRAINS_SIMMODEL_HPP
50	#define BRAINS_SIMMODEL_HPP
51
52	#include <iostream>
53	#include <set>
54	#include <utility>
55	#include <vector>
56
57	#include "brains/Exclude.hpp"
58	#include "io/Globals.hpp"
59	#include "math/Vector3.hpp"
60	#include "types/MoleculeStamp.hpp"
61	#include "UseTheForce/ForceField.hpp"
62	#include "utils/PropertyMap.hpp"
63	#include "utils/LocalIndexManager.hpp"
64	#include "selection/SelectionManager.hpp"
65	//another nonsense macro declaration
66	#define __C
67	#include "brains/fSimulation.h"
68
69	namespace oopse{
70
71	//forward decalration
72	class SnapshotManager;
73	class Molecule;
74
75	/**
76	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
77	* @brief As one of the heavy weight class of OOPSE, SimInfo
78	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
79	* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
80	* cutoff groups, constrains).
81	* Another major change is the index. No matter single version or parallel version, atoms and
82	* rigid bodies have both global index and local index. Local index is not important to molecule as well as
83	* cutoff group.
84	*/
85	class SimInfo {
86	public:
87	typedef std::map<int, Molecule*>::iterator MoleculeIterator;
88
89	/**
90	* Constructor of SimInfo
91	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
92	* second element is the total number of molecules with the same molecule stamp in the system
93	* @param ff pointer of a concrete ForceField instance
94	* @param simParams
95	* @note
96	*/
97	SimInfo(std::vector<std::pair<MoleculeStamp, int> >& molStampPairs, ForceField ff, Globals* simParams);
98	virtual ~SimInfo();
99
100	/**
101	* Adds a molecule
102	* @return return true if adding successfully, return false if the molecule is already in SimInfo
103	* @param mol molecule to be added
104	*/
105	bool addMolecule(Molecule* mol);
106
107	/**
108	* Removes a molecule from SimInfo
109	* @return true if removing successfully, return false if molecule is not in this SimInfo
110	*/
111	bool removeMolecule(Molecule* mol);
112
113	/** Returns the total number of molecules in the system. */
114	int getNGlobalMolecules() {
115	return nGlobalMols_;
116	}
117
118	/** Returns the total number of atoms in the system. */
119	int getNGlobalAtoms() {
120	return nGlobalAtoms_;
121	}
122
123	/** Returns the total number of cutoff groups in the system. */
124	int getNGlobalCutoffGroups() {
125	return nGlobalCutoffGroups_;
126	}
127
128	/**
129	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
130	* of atoms which do not belong to the rigid bodies) in the system
131	*/
132	int getNGlobalIntegrableObjects() {
133	return nGlobalIntegrableObjects_;
134	}
135
136	/**
137	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
138	* of atoms which do not belong to the rigid bodies) in the system
139	*/
140	int getNGlobalRigidBodies() {
141	return nGlobalRigidBodies_;
142	}
143
144	int getNGlobalConstraints();
145	/**
146	* Returns the number of local molecules.
147	* @return the number of local molecules
148	*/
149	int getNMolecules() {
150	return molecules_.size();
151	}
152
153	/** Returns the number of local atoms */
154	unsigned int getNAtoms() {
155	return nAtoms_;
156	}
157
158	/** Returns the number of local bonds */
159	unsigned int getNBonds(){
160	return nBonds_;
161	}
162
163	/** Returns the number of local bends */
164	unsigned int getNBends() {
165	return nBends_;
166	}
167
168	/** Returns the number of local torsions */
169	unsigned int getNTorsions() {
170	return nTorsions_;
171	}
172
173	/** Returns the number of local rigid bodies */
174	unsigned int getNRigidBodies() {
175	return nRigidBodies_;
176	}
177
178	/** Returns the number of local integrable objects */
179	unsigned int getNIntegrableObjects() {
180	return nIntegrableObjects_;
181	}
182
183	/** Returns the number of local cutoff groups */
184	unsigned int getNCutoffGroups() {
185	return nCutoffGroups_;
186	}
187
188	/** Returns the total number of constraints in this SimInfo */
189	unsigned int getNConstraints() {
190	return nConstraints_;
191	}
192
193	/**
194	* Returns the first molecule in this SimInfo and intialize the iterator.
195	* @return the first molecule, return NULL if there is not molecule in this SimInfo
196	* @param i the iterator of molecule array (user shouldn't change it)
197	*/
198	Molecule* beginMolecule(MoleculeIterator& i);
199
200	/**
201	* Returns the next avaliable Molecule based on the iterator.
202	* @return the next avaliable molecule, return NULL if reaching the end of the array
203	* @param i the iterator of molecule array
204	*/
205	Molecule* nextMolecule(MoleculeIterator& i);
206
207	/** Returns the number of degrees of freedom */
208	int getNdf() {
209	return ndf_;
210	}
211
212	/** Returns the number of raw degrees of freedom */
213	int getNdfRaw() {
214	return ndfRaw_;
215	}
216
217	/** Returns the number of translational degrees of freedom */
218	int getNdfTrans() {
219	return ndfTrans_;
220	}
221
222	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
223
224	/** Returns the total number of z-constraint molecules in the system */
225	int getNZconstraint() {
226	return nZconstraint_;
227	}
228
229	/**
230	* Sets the number of z-constraint molecules in the system.
231	*/
232	void setNZconstraint(int nZconstraint) {
233	nZconstraint_ = nZconstraint;
234	}
235
236	/** Returns the snapshot manager. */
237	SnapshotManager* getSnapshotManager() {
238	return sman_;
239	}
240
241	/** Sets the snapshot manager. */
242	void setSnapshotManager(SnapshotManager* sman);
243
244	/** Returns the force field */
245	ForceField* getForceField() {
246	return forceField_;
247	}
248
249	Globals* getSimParams() {
250	return simParams_;
251	}
252
253	/** Returns the velocity of center of mass of the whole system.*/
254	Vector3d getComVel();
255
256	/** Returns the center of the mass of the whole system.*/
257	Vector3d getCom();
258
259	/** Returns the seed (used for random number generator) */
260	int getSeed() {
261	return seed_;
262	}
263
264	/** Sets the seed*/
265	void setSeed(int seed) {
266	seed_ = seed;
267	}
268
269	/** main driver function to interact with fortran during the initialization and molecule migration */
270	void update();
271
272	/** Returns the local index manager */
273	LocalIndexManager* getLocalIndexManager() {
274	return &localIndexMan_;
275	}
276
277	int getMoleculeStampId(int globalIndex) {
278	//assert(globalIndex < molStampIds_.size())
279	return molStampIds_[globalIndex];
280	}
281
282	/** Returns the molecule stamp */
283	MoleculeStamp* getMoleculeStamp(int id) {
284	return moleculeStamps_[id];
285	}
286
287	/** Return the total number of the molecule stamps */
288	int getNMoleculeStamp() {
289	return moleculeStamps_.size();
290	}
291	/**
292	* Finds a molecule with a specified global index
293	* @return a pointer point to found molecule
294	* @param index
295	*/
296	Molecule* getMoleculeByGlobalIndex(int index) {
297	MoleculeIterator i;
298	i = molecules_.find(index);
299
300	return i != molecules_.end() ? i->second : NULL;
301	}
302
303	/** Calculate the maximum cutoff radius based on the atom types */
304	double calcMaxCutoffRadius();
305
306	double getRcut() {
307	return rcut_;
308	}
309
310	double getRsw() {
311	return rsw_;
312	}
313
314	std::string getFinalConfigFileName() {
315	return finalConfigFileName_;
316	}
317
318	void setFinalConfigFileName(const std::string& fileName) {
319	finalConfigFileName_ = fileName;
320	}
321
322	std::string getDumpFileName() {
323	return dumpFileName_;
324	}
325
326	void setDumpFileName(const std::string& fileName) {
327	dumpFileName_ = fileName;
328	}
329
330	std::string getStatFileName() {
331	return statFileName_;
332	}
333
334	void setStatFileName(const std::string& fileName) {
335	statFileName_ = fileName;
336	}
337
338	/**
339	* Sets GlobalGroupMembership
340	* @see #SimCreator::setGlobalIndex
341	*/
342	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
343	assert(globalGroupMembership.size() == nGlobalAtoms_);
344	globalGroupMembership_ = globalGroupMembership;
345	}
346
347	/**
348	* Sets GlobalMolMembership
349	* @see #SimCreator::setGlobalIndex
350	*/
351	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
352	assert(globalMolMembership.size() == nGlobalAtoms_);
353	globalMolMembership_ = globalMolMembership;
354	}
355
356
357	bool isFortranInitialized() {
358	return fortranInitialized_;
359	}
360
361	//below functions are just forward functions
362	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
363	//the other hand, has-a relation need composing.
364	/**
365	* Adds property into property map
366	* @param genData GenericData to be added into PropertyMap
367	*/
368	void addProperty(GenericData* genData);
369
370	/**
371	* Removes property from PropertyMap by name
372	* @param propName the name of property to be removed
373	*/
374	void removeProperty(const std::string& propName);
375
376	/**
377	* clear all of the properties
378	*/
379	void clearProperties();
380
381	/**
382	* Returns all names of properties
383	* @return all names of properties
384	*/
385	std::vector<std::string> getPropertyNames();
386
387	/**
388	* Returns all of the properties in PropertyMap
389	* @return all of the properties in PropertyMap
390	*/
391	std::vector<GenericData*> getProperties();
392
393	/**
394	* Returns property
395	* @param propName name of property
396	* @return a pointer point to property with propName. If no property named propName
397	* exists, return NULL
398	*/
399	GenericData* getPropertyByName(const std::string& propName);
400
401	/**
402	* add all exclude pairs of a molecule into exclude list.
403	*/
404	void addExcludePairs(Molecule* mol);
405
406	/**
407	* remove all exclude pairs which belong to a molecule from exclude list
408	*/
409
410	void removeExcludePairs(Molecule* mol);
411
412
413	SelectionManager* getSelectionManager() {
414	return selectMan_;
415	}
416
417	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
418
419	private:
420
421
422	/** Returns the unique atom types of local processor in an array */
423	std::set<AtomType*> getUniqueAtomTypes();
424
425	/** fill up the simtype struct*/
426	void setupSimType();
427
428	/**
429	* Setup Fortran Simulation
430	* @see #setupFortranParallel
431	*/
432	void setupFortranSim();
433
434	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
435	void setupCutoff();
436
437	/** Calculates the number of degress of freedom in the whole system */
438	void calcNdf();
439	void calcNdfRaw();
440	void calcNdfTrans();
441
442	/**
443	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
444	* system.
445	*/
446	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
447
448	ForceField* forceField_;
449	Globals* simParams_;
450
451	std::map<int, Molecule> molecules_; /< Molecule array /
452
453	//degress of freedom
454	int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
455	int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
456	int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
457	int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
458
459	//number of global objects
460	int nGlobalMols_; /*< number of molecules in the system /
461	int nGlobalAtoms_; /*< number of atoms in the system /
462	int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
463	int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
464	int nGlobalRigidBodies_; /*< number of rigid bodies in this system /
465	/**
466	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
467	* corresponding content is the global index of cutoff group this atom belong to.
468	* It is filled by SimCreator once and only once, since it never changed during the simulation.
469	*/
470	std::vector<int> globalGroupMembership_;
471
472	/**
473	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
474	* corresponding content is the global index of molecule this atom belong to.
475	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
476	*/
477	std::vector<int> globalMolMembership_;
478
479
480	std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
481	std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
482
483	//number of local objects
484	int nAtoms_; /*< number of atoms in local processor /
485	int nBonds_; /*< number of bonds in local processor /
486	int nBends_; /*< number of bends in local processor /
487	int nTorsions_; /*< number of torsions in local processor /
488	int nRigidBodies_; /*< number of rigid bodies in local processor /
489	int nIntegrableObjects_; /*< number of integrable objects in local processor /
490	int nCutoffGroups_; /*< number of cutoff groups in local processor /
491	int nConstraints_; /*< number of constraints in local processors /
492
493	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
494	Exclude exclude_;
495	PropertyMap properties_; /*< Generic Property /
496	SnapshotManager* sman_; /*< SnapshotManager /
497
498	int seed_; /*< seed for random number generator /
499
500	/**
501	* The reason to have a local index manager is that when molecule is migrating to other processors,
502	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
503	* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
504	* to make a efficient data moving plan.
505	*/
506	LocalIndexManager localIndexMan_;
507
508	//file names
509	std::string finalConfigFileName_;
510	std::string dumpFileName_;
511	std::string statFileName_;
512
513	double rcut_; /*< cutoff radius/
514	double rsw_; /*< radius of switching function/
515
516	bool fortranInitialized_; /*< flag indicate whether fortran side is initialized /
517
518	SelectionManager* selectMan_;
519	#ifdef IS_MPI
520	//in Parallel version, we need MolToProc
521	public:
522
523	/**
524	* Finds the processor where a molecule resides
525	* @return the id of the processor which contains the molecule
526	* @param globalIndex global Index of the molecule
527	*/
528	int getMolToProc(int globalIndex) {
529	//assert(globalIndex < molToProcMap_.size());
530	return molToProcMap_[globalIndex];
531	}
532
533	/**
534	* Set MolToProcMap array
535	* @see #SimCreator::divideMolecules
536	*/
537	void setMolToProcMap(const std::vector<int>& molToProcMap) {
538	molToProcMap_ = molToProcMap;
539	}
540
541	private:
542
543	void setupFortranParallel();
544
545	/**
546	* The size of molToProcMap_ is equal to total number of molecules in the system.
547	* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
548	* once.
549	*/
550	std::vector<int> molToProcMap_;
551
552	#endif
553
554	};
555
556	} //namespace oopse
557	#endif //BRAINS_SIMMODEL_HPP
558