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 (19 years, 8 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
#	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 <vector>
38	#include <utility>
39
40	#include "brains/fSimulation.h"
41	#include "primitives/Molecule.hpp"
42	#include "types/MoleculeStamp.hpp"
43	#include "utils/PropertyMap.hpp"
44	#include "io/Globals.hpp"
45
46	namespace oopse{
47
48	/**
49	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
50	* @brief
51	*/
52	class SimInfo {
53	public:
54	typedef std::vector<Molecule*>::iterator MoleculeIterator;
55	SimInfo();
56	virtual ~SimInfo();
57
58	/**
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
65	/**
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
71	/** 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	/**
111	* Returns the number of local molecules.
112	* @return the number of local molecules
113	*/
114	int getNMolecules() {
115	return molecules_.size();
116	}
117
118	/** Returns the number of local atoms */
119	unsigned int getNAtoms() {
120	return nAtoms_;
121	}
122
123	/** Returns the number of local bonds */
124	unsigned int getNBonds(){
125	return nBonds_;
126	}
127
128	/** Returns the number of local bends */
129	unsigned int getNBends() {
130	return nBends_;
131	}
132
133	/** Returns the number of local torsions */
134	unsigned int getNTorsions() {
135	return nTorsions_;
136	}
137
138	/** Returns the number of local rigid bodies */
139	unsigned int getNRigidBodies() {
140	return nRigidBodies_;
141	}
142
143	/** Returns the number of local integrable objects */
144	unsigned int getNIntegrableObjects() {
145	return nIntegrableObjects_;
146	}
147
148	/** Returns the number of local cutoff groups */
149	unsigned int getNCutoffGroups() {
150	return nCutoffGroups_;
151	}
152
153	/** 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
165	/**
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
172	/** Returns the number of degrees of freedom */
173	int getNdf() {
174	return ndf_;
175	}
176
177	/** Returns the number of raw degrees of freedom */
178	int getNdfRaw() {
179	return ndfRaw_;
180	}
181
182	/** Returns the number of translational degrees of freedom */
183	int getNdfTrans() {
184	return ndfTrans_;
185	}
186
187	/** Returns the snapshot manager. */
188	SnapshotManager* getSnapshotManager() {
189	return sman_;
190	}
191
192	/** Sets the snapshot manager. */
193	void setSnapshotManager(SnapshotManager* sman) {
194	sman_ = sman;
195	}
196
197	/** Returns the force field */
198	ForceField* getForceField() {
199	return forceField_;
200	}
201
202	/** Sets the force field */
203	void setForceField(ForceField* ff) {
204	forceField_ = ff;
205	}
206
207	Globals* getGlobals() {
208	return globals_;
209	}
210
211	void setGlobals(Globals* globals) {
212	globals_ = globals;
213	}
214
215	/** Returns the velocity of center of mass of the whole system.*/
216	Vector3d getComVel();
217
218	/** Returns the center of the mass of the whole system.*/
219	Vector3d getCom();
220
221	/** Returns the seed (used for random number generator) */
222	int getSeed() {
223	return seed_;
224	}
225
226	/** Sets the seed*/
227	void setSeed(int seed) {
228	seed_ = seed;
229	}
230
231
232	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	private:
282
283	void calcNdf();
284	void calcNdfRaw();
285	void calcNdfTrans();
286
287	int* getExcludeList() {
288	return exclude_.getExcludeList();
289	}
290
291	void addExcludePairs(Molecule* mol);
292	void removeExcludePairs(Molecule* mol);
293
294	//degress of freedom
295	int ndf_; /** number of degress of freedom */
296	int ndfRaw_;
297	int ndfTrans_; /*< number of translation degress of freedom /
298
299	//number of local objects
300	int nAtoms_;
301	int nBonds_;
302	int nBends_;
303	int nTorsions_;
304	int nRigidBodies_;
305	int nIntegrableObjects_;
306	int nCutoffGroups_;
307	int nConstraints_;
308
309	simtype fInfo_;
310	Exclude exclude_;
311	ForceField* forceField_;
312
313	std::vector<Molecule> molecules_; /< Molecule array /
314	PropertyMap properties_; /*< Generic Property /
315	SnapshotManager* sman_; /*< SnapshotManager /
316
317	Globals* globals_;
318
319	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	};
330
331	} //namespace oopse
332	#endif //BRAINS_SIMMODEL_HPP