src/brains/SimInfo.hpp

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

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

#ifndef BRAINS_SIMMODEL_HPP
#define BRAINS_SIMMODEL_HPP

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

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

namespace oopse{

/**
 * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" 
 * @brief
 */
class SimInfo {
    public:
        typedef std::vector<Molecule*>::iterator MoleculeIterator;
        SimInfo();
        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() {

#ifdef IS_MPI
        int nmols;
        int totNMols;

        nmols = getNMolecules();
        MPI_Allreduce(&nmols, &totNMols, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);

        return totNMols;
#else
            return getNMolecules();
#endif
        }

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

#ifdef IS_MPI
        int totNAtoms;
        MPI_Allreduce(&nAtoms_, &totNAtoms, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
        return totNAtoms;
#else
            return nAtoms_;
#endif
        }

        /** Returns the total number of cutoff groups in the system. */
        int getNGlobalCutoffGroups() {
#ifdef IS_MPI
        int totNGroups;
        MPI_Allreduce(&nCutoffGroups_, &totNGroups, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
        return totNGroups;
#else
            return nCutoffGroups_;
#endif
        }
        
        /** 
         * 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(std::vector<Molecule*>::iterator& 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(std::vector<Molecule*>::iterator& 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_;
        }

        /** Returns the snapshot manager. */
        SnapshotManager* getSnapshotManager() {
            return sman_;
        }

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

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

        /** Sets the force field */
        void setForceField(ForceField* ff) {
            forceField_ = ff;
        }

        Globals* getGlobals() {
            return globals_;
        }
        
        void setGlobals(Globals* globals) {
            globals_ = globals;
        }

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

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

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

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

        
        void update();


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


        /**
         *
         */
        void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);

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

        /** Returns the molecule stamp */
        MoleculeStamp* getMoleculeStamp(int id) {
            return moleculeStamps_[id];
        }
        
        /**
         * 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];
        }

        /**
         * Finds a molecule with a specified global index
         * @return a pointer point to found molecule
         * @param index
         */
        Molecule* getMoleculeByGlobalIndex(int index) {
            std::map<int, Molecule*> i;
            i = globalIndexToMol_.find(index);

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


        friend std::ostream& operator <<(ostream& o, SimInfo& info);
        
    private:

        void calcNdf();
        void calcNdfRaw();
        void calcNdfTrans();

        int* getExcludeList() {
            return exclude_.getExcludeList();
        }

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

        //degress of freedom
        int ndf_;           /** number of degress of freedom */
        int ndfRaw_;
        int ndfTrans_; /**< number of translation degress of freedom */

        //number of local objects
        int nAtoms_;
        int nBonds_;
        int nBends_;
        int nTorsions_;
        int nRigidBodies_;
        int nIntegrableObjects_;
        int nCutoffGroups_;
        int nConstraints_;

        simtype fInfo_;
        Exclude exclude_;
        ForceField* forceField_;
        
        std::vector<Molecule*> molecules_; /**< Molecule array */
        PropertyMap properties_;                  /**< Generic Property */
        SnapshotManager* sman_;               /**< SnapshotManager */

        Globals* globals_;

        int seed_; /**< seed for random number generator */

        LocalIndexManager localIndexMan_;

        //
        std::vector<int> molToProcMap_;
        std::map<int, Molecule*> globalIndexToMol_;
        std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
        std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */      

};

} //namespace oopse
#endif //BRAINS_SIMMODEL_HPP
Revision:	1725
Committed:	Wed Nov 10 22:01:06 2004 UTC (20 years, 11 months ago) by tim
File size:	9600 byte(s)
Log Message:	another painful day (1) SimCreator, SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom File will be removed) (3) ForceField (at least LJ) and BondType, BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint
#	User	Rev	Content
1	tim	1710	/*
2			* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3			*
4			* Contact: oopse@oopse.org
5			*
6			* This program is free software; you can redistribute it and/or
7			* modify it under the terms of the GNU Lesser General Public License
8			* as published by the Free Software Foundation; either version 2.1
9			* of the License, or (at your option) any later version.
10			* All we ask is that proper credit is given for our work, which includes
11			* - but is not limited to - adding the above copyright notice to the beginning
12			* of your source code files, and to any copyright notice that you may distribute
13			* with programs based on this work.
14			*
15			* This program is distributed in the hope that it will be useful,
16			* but WITHOUT ANY WARRANTY; without even the implied warranty of
17			* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18			* GNU Lesser General Public License for more details.
19			*
20			* You should have received a copy of the GNU Lesser General Public License
21			* along with this program; if not, write to the Free Software
22			* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23			*
24			*/
25	gezelter	1490
26	tim	1710	/**
27			* @file SimInfo.hpp
28			* @author tlin
29			* @date 11/02/2004
30			* @version 1.0
31			*/
32
33			#ifndef BRAINS_SIMMODEL_HPP
34			#define BRAINS_SIMMODEL_HPP
35	tim	1719
36			#include <iostream>
37	gezelter	1490	#include <vector>
38	tim	1719	#include <utility>
39	gezelter	1490
40	tim	1710	#include "brains/fSimulation.h"
41	tim	1492	#include "primitives/Molecule.hpp"
42	tim	1719	#include "types/MoleculeStamp.hpp"
43	tim	1710	#include "utils/PropertyMap.hpp"
44	tim	1719	#include "io/Globals.hpp"
45	gezelter	1490
46	tim	1710	namespace oopse{
47	gezelter	1490
48	tim	1710	/**
49			* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
50			* @brief
51			*/
52			class SimInfo {
53			public:
54	tim	1725	typedef std::vector<Molecule*>::iterator MoleculeIterator;
55	tim	1710	SimInfo();
56			virtual ~SimInfo();
57	gezelter	1490
58	tim	1710	/**
59			* Adds a molecule
60			* @return return true if adding successfully, return false if the molecule is already in SimInfo
61			* @param mol molecule to be added
62			*/
63			bool addMolecule(Molecule* mol);
64	gezelter	1490
65	tim	1710	/**
66			* Removes a molecule from SimInfo
67			* @return true if removing successfully, return false if molecule is not in this SimInfo
68			*/
69			bool removeMolecule(Molecule* mol);
70	gezelter	1490
71	tim	1725	/** Returns the total number of molecules in the system. */
72			int getNGlobalMolecules() {
73
74			#ifdef IS_MPI
75			int nmols;
76			int totNMols;
77
78			nmols = getNMolecules();
79			MPI_Allreduce(&nmols, &totNMols, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
80
81			return totNMols;
82			#else
83			return getNMolecules();
84			#endif
85			}
86
87			/** Returns the total number of atoms in the system. */
88			int getNGlobalAtoms() {
89
90			#ifdef IS_MPI
91			int totNAtoms;
92			MPI_Allreduce(&nAtoms_, &totNAtoms, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
93			return totNAtoms;
94			#else
95			return nAtoms_;
96			#endif
97			}
98
99			/** Returns the total number of cutoff groups in the system. */
100			int getNGlobalCutoffGroups() {
101			#ifdef IS_MPI
102			int totNGroups;
103			MPI_Allreduce(&nCutoffGroups_, &totNGroups, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD);
104			return totNGroups;
105			#else
106			return nCutoffGroups_;
107			#endif
108			}
109
110	tim	1710	/**
111	tim	1725	* Returns the number of local molecules.
112			* @return the number of local molecules
113	tim	1710	*/
114			int getNMolecules() {
115			return molecules_.size();
116			}
117	gezelter	1490
118	tim	1725	/** Returns the number of local atoms */
119	tim	1710	unsigned int getNAtoms() {
120			return nAtoms_;
121			}
122	gezelter	1490
123	tim	1725	/** Returns the number of local bonds */
124	tim	1710	unsigned int getNBonds(){
125			return nBonds_;
126			}
127	gezelter	1490
128	tim	1725	/** Returns the number of local bends */
129	tim	1710	unsigned int getNBends() {
130			return nBends_;
131			}
132	gezelter	1490
133	tim	1725	/** Returns the number of local torsions */
134	tim	1710	unsigned int getNTorsions() {
135			return nTorsions_;
136			}
137	gezelter	1490
138	tim	1725	/** Returns the number of local rigid bodies */
139	tim	1710	unsigned int getNRigidBodies() {
140			return nRigidBodies_;
141			}
142	gezelter	1490
143	tim	1725	/** Returns the number of local integrable objects */
144	tim	1710	unsigned int getNIntegrableObjects() {
145			return nIntegrableObjects_;
146			}
147	gezelter	1490
148	tim	1725	/** Returns the number of local cutoff groups */
149	tim	1710	unsigned int getNCutoffGroups() {
150			return nCutoffGroups_;
151			}
152	gezelter	1490
153	tim	1710	/** Returns the total number of constraints in this SimInfo */
154			unsigned int getNConstraints() {
155			return nConstraints_;
156			}
157
158			/**
159			* Returns the first molecule in this SimInfo and intialize the iterator.
160			* @return the first molecule, return NULL if there is not molecule in this SimInfo
161			* @param i the iterator of molecule array (user shouldn't change it)
162			*/
163			Molecule* beginMolecule(std::vector<Molecule*>::iterator& i);
164	gezelter	1490
165	tim	1710	/**
166			* Returns the next avaliable Molecule based on the iterator.
167			* @return the next avaliable molecule, return NULL if reaching the end of the array
168			* @param i the iterator of molecule array
169			*/
170			Molecule* nextMolecule(std::vector<Molecule*>::iterator& i);
171	gezelter	1490
172	tim	1710	/** Returns the number of degrees of freedom */
173	tim	1722	int getNdf() {
174	tim	1710	return ndf_;
175			}
176	gezelter	1490
177	tim	1710	/** Returns the number of raw degrees of freedom */
178	tim	1722	int getNdfRaw() {
179	tim	1710	return ndfRaw_;
180			}
181	gezelter	1490
182	tim	1710	/** Returns the number of translational degrees of freedom */
183	tim	1722	int getNdfTrans() {
184	tim	1710	return ndfTrans_;
185			}
186	gezelter	1490
187	tim	1710	/** Returns the snapshot manager. */
188			SnapshotManager* getSnapshotManager() {
189			return sman_;
190			}
191	gezelter	1490
192	tim	1710	/** Sets the snapshot manager. */
193			void setSnapshotManager(SnapshotManager* sman) {
194			sman_ = sman;
195			}
196	tim	1712
197	tim	1719	/** Returns the force field */
198	tim	1712	ForceField* getForceField() {
199			return forceField_;
200			}
201	tim	1719
202			/** Sets the force field */
203	tim	1712	void setForceField(ForceField* ff) {
204			forceField_ = ff;
205			}
206	tim	1719
207			Globals* getGlobals() {
208			return globals_;
209			}
210
211			void setGlobals(Globals* globals) {
212			globals_ = globals;
213			}
214
215	tim	1725	/** Returns the velocity of center of mass of the whole system.*/
216			Vector3d getComVel();
217	tim	1722
218	tim	1725	/** Returns the center of the mass of the whole system.*/
219	tim	1722	Vector3d getCom();
220
221	tim	1725	/** Returns the seed (used for random number generator) */
222	tim	1722	int getSeed() {
223			return seed_;
224			}
225
226	tim	1725	/** Sets the seed*/
227	tim	1722	void setSeed(int seed) {
228			seed_ = seed;
229			}
230	tim	1725
231	tim	1722
232	tim	1725	void update();
233
234
235			/** Returns the local index manager */
236			LocalIndexManager* getLocalIndexManager() {
237			return localIndexMan_;
238			}
239
240
241			/**
242			*
243			*/
244			void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
245
246			int getMoleculeStampId(int globalIndex) {
247			//assert(globalIndex < molStampIds_.size())
248			return molStampIds_[globalIndex];
249			}
250
251			/** Returns the molecule stamp */
252			MoleculeStamp* getMoleculeStamp(int id) {
253			return moleculeStamps_[id];
254			}
255
256			/**
257			* Finds the processor where a molecule resides
258			* @return the id of the processor which contains the molecule
259			* @param globalIndex global Index of the molecule
260			*/
261			int getMolToProc(int globalIndex) {
262			//assert(globalIndex < molToProcMap_.size());
263			return molToProcMap_[globalIndex];
264			}
265
266			/**
267			* Finds a molecule with a specified global index
268			* @return a pointer point to found molecule
269			* @param index
270			*/
271			Molecule* getMoleculeByGlobalIndex(int index) {
272			std::map<int, Molecule*> i;
273			i = globalIndexToMol_.find(index);
274
275			return i != globalIndexToMol_.end() ? i->second : NULL;
276			}
277
278
279			friend std::ostream& operator <<(ostream& o, SimInfo& info);
280
281	tim	1710	private:
282	gezelter	1490
283	tim	1722	void calcNdf();
284			void calcNdfRaw();
285			void calcNdfTrans();
286	gezelter	1490
287	tim	1725	int* getExcludeList() {
288			return exclude_.getExcludeList();
289			}
290
291	tim	1719	void addExcludePairs(Molecule* mol);
292			void removeExcludePairs(Molecule* mol);
293
294	tim	1725	//degress of freedom
295			int ndf_; /** number of degress of freedom */
296	tim	1710	int ndfRaw_;
297	tim	1725	int ndfTrans_; /*< number of translation degress of freedom /
298
299			//number of local objects
300	tim	1710	int nAtoms_;
301			int nBonds_;
302			int nBends_;
303			int nTorsions_;
304			int nRigidBodies_;
305			int nIntegrableObjects_;
306			int nCutoffGroups_;
307			int nConstraints_;
308	gezelter	1490
309	tim	1719	simtype fInfo_;
310			Exclude exclude_;
311	tim	1712	ForceField* forceField_;
312	tim	1710
313			std::vector<Molecule> molecules_; /< Molecule array /
314	tim	1725	PropertyMap properties_; /*< Generic Property /
315			SnapshotManager* sman_; /*< SnapshotManager /
316	gezelter	1490
317	tim	1719	Globals* globals_;
318	tim	1722
319	tim	1725	int seed_; /*< seed for random number generator /
320
321			LocalIndexManager localIndexMan_;
322
323			//
324			std::vector<int> molToProcMap_;
325			std::map<int, Molecule*> globalIndexToMol_;
326			std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
327			std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
328
329	gezelter	1490	};
330
331	tim	1710	} //namespace oopse
332			#endif //BRAINS_SIMMODEL_HPP