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 <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"

//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);
                
        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 */
        
#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:	1907
Committed:	Thu Jan 6 22:31:07 2005 UTC (19 years, 7 months ago) by tim
File size:	18553 byte(s)
Log Message:	constraint is almost working
#	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 <set>
38	#include <utility>
39	#include <vector>
40
41	#include "brains/Exclude.hpp"
42	#include "io/Globals.hpp"
43	#include "math/Vector3.hpp"
44	#include "types/MoleculeStamp.hpp"
45	#include "UseTheForce/ForceField.hpp"
46	#include "utils/PropertyMap.hpp"
47	#include "utils/LocalIndexManager.hpp"
48
49	//another nonsense macro declaration
50	#define __C
51	#include "brains/fSimulation.h"
52
53	namespace oopse{
54
55	//forward decalration
56	class SnapshotManager;
57	class Molecule;
58
59	/**
60	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
61	* @brief As one of the heavy weight class of OOPSE, SimInfo
62	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
63	* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
64	* cutoff groups, constrains).
65	* Another major change is the index. No matter single version or parallel version, atoms and
66	* rigid bodies have both global index and local index. Local index is not important to molecule as well as
67	* cutoff group.
68	*/
69	class SimInfo {
70	public:
71	typedef std::map<int, Molecule*>::iterator MoleculeIterator;
72
73	/**
74	* Constructor of SimInfo
75	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
76	* second element is the total number of molecules with the same molecule stamp in the system
77	* @param ff pointer of a concrete ForceField instance
78	* @param simParams
79	* @note
80	*/
81	SimInfo(std::vector<std::pair<MoleculeStamp, int> >& molStampPairs, ForceField ff, Globals* simParams);
82	virtual ~SimInfo();
83
84	/**
85	* Adds a molecule
86	* @return return true if adding successfully, return false if the molecule is already in SimInfo
87	* @param mol molecule to be added
88	*/
89	bool addMolecule(Molecule* mol);
90
91	/**
92	* Removes a molecule from SimInfo
93	* @return true if removing successfully, return false if molecule is not in this SimInfo
94	*/
95	bool removeMolecule(Molecule* mol);
96
97	/** Returns the total number of molecules in the system. */
98	int getNGlobalMolecules() {
99	return nGlobalMols_;
100	}
101
102	/** Returns the total number of atoms in the system. */
103	int getNGlobalAtoms() {
104	return nGlobalAtoms_;
105	}
106
107	/** Returns the total number of cutoff groups in the system. */
108	int getNGlobalCutoffGroups() {
109	return nGlobalCutoffGroups_;
110	}
111
112	/**
113	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
114	* of atoms which do not belong to the rigid bodies) in the system
115	*/
116	int getNGlobalIntegrableObjects() {
117	return nGlobalIntegrableObjects_;
118	}
119
120	/**
121	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
122	* of atoms which do not belong to the rigid bodies) in the system
123	*/
124	int getNGlobalRigidBodies() {
125	return nGlobalRigidBodies_;
126	}
127
128	int getNGlobalConstraints();
129	/**
130	* Returns the number of local molecules.
131	* @return the number of local molecules
132	*/
133	int getNMolecules() {
134	return molecules_.size();
135	}
136
137	/** Returns the number of local atoms */
138	unsigned int getNAtoms() {
139	return nAtoms_;
140	}
141
142	/** Returns the number of local bonds */
143	unsigned int getNBonds(){
144	return nBonds_;
145	}
146
147	/** Returns the number of local bends */
148	unsigned int getNBends() {
149	return nBends_;
150	}
151
152	/** Returns the number of local torsions */
153	unsigned int getNTorsions() {
154	return nTorsions_;
155	}
156
157	/** Returns the number of local rigid bodies */
158	unsigned int getNRigidBodies() {
159	return nRigidBodies_;
160	}
161
162	/** Returns the number of local integrable objects */
163	unsigned int getNIntegrableObjects() {
164	return nIntegrableObjects_;
165	}
166
167	/** Returns the number of local cutoff groups */
168	unsigned int getNCutoffGroups() {
169	return nCutoffGroups_;
170	}
171
172	/** Returns the total number of constraints in this SimInfo */
173	unsigned int getNConstraints() {
174	return nConstraints_;
175	}
176
177	/**
178	* Returns the first molecule in this SimInfo and intialize the iterator.
179	* @return the first molecule, return NULL if there is not molecule in this SimInfo
180	* @param i the iterator of molecule array (user shouldn't change it)
181	*/
182	Molecule* beginMolecule(MoleculeIterator& i);
183
184	/**
185	* Returns the next avaliable Molecule based on the iterator.
186	* @return the next avaliable molecule, return NULL if reaching the end of the array
187	* @param i the iterator of molecule array
188	*/
189	Molecule* nextMolecule(MoleculeIterator& i);
190
191	/** Returns the number of degrees of freedom */
192	int getNdf() {
193	return ndf_;
194	}
195
196	/** Returns the number of raw degrees of freedom */
197	int getNdfRaw() {
198	return ndfRaw_;
199	}
200
201	/** Returns the number of translational degrees of freedom */
202	int getNdfTrans() {
203	return ndfTrans_;
204	}
205
206	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
207
208	/** Returns the total number of z-constraint molecules in the system */
209	int getNZconstraint() {
210	return nZconstraint_;
211	}
212
213	/**
214	* Sets the number of z-constraint molecules in the system.
215	*/
216	void setNZconstraint(int nZconstraint) {
217	nZconstraint_ = nZconstraint;
218	}
219
220	/** Returns the snapshot manager. */
221	SnapshotManager* getSnapshotManager() {
222	return sman_;
223	}
224
225	/** Sets the snapshot manager. */
226	void setSnapshotManager(SnapshotManager* sman);
227
228	/** Returns the force field */
229	ForceField* getForceField() {
230	return forceField_;
231	}
232
233	Globals* getSimParams() {
234	return simParams_;
235	}
236
237	/** Returns the velocity of center of mass of the whole system.*/
238	Vector3d getComVel();
239
240	/** Returns the center of the mass of the whole system.*/
241	Vector3d getCom();
242
243	/** Returns the seed (used for random number generator) */
244	int getSeed() {
245	return seed_;
246	}
247
248	/** Sets the seed*/
249	void setSeed(int seed) {
250	seed_ = seed;
251	}
252
253	/** main driver function to interact with fortran during the initialization and molecule migration */
254	void update();
255
256	/** Returns the local index manager */
257	LocalIndexManager* getLocalIndexManager() {
258	return &localIndexMan_;
259	}
260
261	int getMoleculeStampId(int globalIndex) {
262	//assert(globalIndex < molStampIds_.size())
263	return molStampIds_[globalIndex];
264	}
265
266	/** Returns the molecule stamp */
267	MoleculeStamp* getMoleculeStamp(int id) {
268	return moleculeStamps_[id];
269	}
270
271	/** Return the total number of the molecule stamps */
272	int getNMoleculeStamp() {
273	return moleculeStamps_.size();
274	}
275	/**
276	* Finds a molecule with a specified global index
277	* @return a pointer point to found molecule
278	* @param index
279	*/
280	Molecule* getMoleculeByGlobalIndex(int index) {
281	MoleculeIterator i;
282	i = molecules_.find(index);
283
284	return i != molecules_.end() ? i->second : NULL;
285	}
286
287	/** Calculate the maximum cutoff radius based on the atom types */
288	double calcMaxCutoffRadius();
289
290	double getRcut() {
291	return rcut_;
292	}
293
294	double getRsw() {
295	return rsw_;
296	}
297
298	std::string getFinalConfigFileName() {
299	return finalConfigFileName_;
300	}
301
302	void setFinalConfigFileName(const std::string& fileName) {
303	finalConfigFileName_ = fileName;
304	}
305
306	std::string getDumpFileName() {
307	return dumpFileName_;
308	}
309
310	void setDumpFileName(const std::string& fileName) {
311	dumpFileName_ = fileName;
312	}
313
314	std::string getStatFileName() {
315	return statFileName_;
316	}
317
318	void setStatFileName(const std::string& fileName) {
319	statFileName_ = fileName;
320	}
321
322	/**
323	* Sets GlobalGroupMembership
324	* @see #SimCreator::setGlobalIndex
325	*/
326	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
327	assert(globalGroupMembership.size() == nGlobalAtoms_);
328	globalGroupMembership_ = globalGroupMembership;
329	}
330
331	/**
332	* Sets GlobalMolMembership
333	* @see #SimCreator::setGlobalIndex
334	*/
335	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
336	assert(globalMolMembership.size() == nGlobalAtoms_);
337	globalMolMembership_ = globalMolMembership;
338	}
339
340
341	bool isFortranInitialized() {
342	return fortranInitialized_;
343	}
344
345	//below functions are just forward functions
346	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
347	//the other hand, has-a relation need composing.
348	/**
349	* Adds property into property map
350	* @param genData GenericData to be added into PropertyMap
351	*/
352	void addProperty(GenericData* genData);
353
354	/**
355	* Removes property from PropertyMap by name
356	* @param propName the name of property to be removed
357	*/
358	void removeProperty(const std::string& propName);
359
360	/**
361	* clear all of the properties
362	*/
363	void clearProperties();
364
365	/**
366	* Returns all names of properties
367	* @return all names of properties
368	*/
369	std::vector<std::string> getPropertyNames();
370
371	/**
372	* Returns all of the properties in PropertyMap
373	* @return all of the properties in PropertyMap
374	*/
375	std::vector<GenericData*> getProperties();
376
377	/**
378	* Returns property
379	* @param propName name of property
380	* @return a pointer point to property with propName. If no property named propName
381	* exists, return NULL
382	*/
383	GenericData* getPropertyByName(const std::string& propName);
384
385	/**
386	* add all exclude pairs of a molecule into exclude list.
387	*/
388	void addExcludePairs(Molecule* mol);
389
390	/**
391	* remove all exclude pairs which belong to a molecule from exclude list
392	*/
393
394	void removeExcludePairs(Molecule* mol);
395
396	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
397
398	private:
399
400
401	/** Returns the unique atom types of local processor in an array */
402	std::set<AtomType*> getUniqueAtomTypes();
403
404	/** fill up the simtype struct*/
405	void setupSimType();
406
407	/**
408	* Setup Fortran Simulation
409	* @see #setupFortranParallel
410	*/
411	void setupFortranSim();
412
413	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
414	void setupCutoff();
415
416	/** Calculates the number of degress of freedom in the whole system */
417	void calcNdf();
418	void calcNdfRaw();
419	void calcNdfTrans();
420
421	/**
422	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
423	* system.
424	*/
425	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
426
427	ForceField* forceField_;
428	Globals* simParams_;
429
430	std::map<int, Molecule> molecules_; /< Molecule array /
431
432	//degress of freedom
433	int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
434	int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
435	int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
436	int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
437
438	//number of global objects
439	int nGlobalMols_; /*< number of molecules in the system /
440	int nGlobalAtoms_; /*< number of atoms in the system /
441	int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
442	int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
443	int nGlobalRigidBodies_; /*< number of rigid bodies in this system /
444	/**
445	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
446	* corresponding content is the global index of cutoff group this atom belong to.
447	* It is filled by SimCreator once and only once, since it never changed during the simulation.
448	*/
449	std::vector<int> globalGroupMembership_;
450
451	/**
452	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
453	* corresponding content is the global index of molecule this atom belong to.
454	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
455	*/
456	std::vector<int> globalMolMembership_;
457
458
459	std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
460	std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
461
462	//number of local objects
463	int nAtoms_; /*< number of atoms in local processor /
464	int nBonds_; /*< number of bonds in local processor /
465	int nBends_; /*< number of bends in local processor /
466	int nTorsions_; /*< number of torsions in local processor /
467	int nRigidBodies_; /*< number of rigid bodies in local processor /
468	int nIntegrableObjects_; /*< number of integrable objects in local processor /
469	int nCutoffGroups_; /*< number of cutoff groups in local processor /
470	int nConstraints_; /*< number of constraints in local processors /
471
472	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
473	Exclude exclude_;
474	PropertyMap properties_; /*< Generic Property /
475	SnapshotManager* sman_; /*< SnapshotManager /
476
477	int seed_; /*< seed for random number generator /
478
479	/**
480	* The reason to have a local index manager is that when molecule is migrating to other processors,
481	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
482	* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
483	* to make a efficient data moving plan.
484	*/
485	LocalIndexManager localIndexMan_;
486
487	//file names
488	std::string finalConfigFileName_;
489	std::string dumpFileName_;
490	std::string statFileName_;
491
492	double rcut_; /*< cutoff radius/
493	double rsw_; /*< radius of switching function/
494
495	bool fortranInitialized_; /*< flag indicate whether fortran side is initialized /
496
497	#ifdef IS_MPI
498	//in Parallel version, we need MolToProc
499	public:
500
501	/**
502	* Finds the processor where a molecule resides
503	* @return the id of the processor which contains the molecule
504	* @param globalIndex global Index of the molecule
505	*/
506	int getMolToProc(int globalIndex) {
507	//assert(globalIndex < molToProcMap_.size());
508	return molToProcMap_[globalIndex];
509	}
510
511	/**
512	* Set MolToProcMap array
513	* @see #SimCreator::divideMolecules
514	*/
515	void setMolToProcMap(const std::vector<int>& molToProcMap) {
516	molToProcMap_ = molToProcMap;
517	}
518
519	private:
520
521	void setupFortranParallel();
522
523	/**
524	* The size of molToProcMap_ is equal to total number of molecules in the system.
525	* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
526	* once.
527	*/
528	std::vector<int> molToProcMap_;
529	#endif
530
531	};
532
533	} //namespace oopse
534	#endif //BRAINS_SIMMODEL_HPP
535