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, 8 months ago) by tim
File size:	18553 byte(s)
Log Message:	constraint is almost working
#	User	Rev	Content
1	tim	1842	/*
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	tim	1907
128			int getNGlobalConstraints();
129	tim	1842	/**
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	tim	1903
271			/** Return the total number of the molecule stamps */
272			int getNMoleculeStamp() {
273			return moleculeStamps_.size();
274			}
275	tim	1842	/**
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	tim	1843	globalGroupMembership_ = globalGroupMembership;
329	tim	1842	}
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	tim	1856
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	tim	1842
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	tim	1867	* It is filled by SimCreator once and only once, since it never changed during the simulation.
448	tim	1842	*/
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