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:
        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 number of molecules.
         * @return the number of molecules in this SimInfo
         */
        int getNMolecules() {
            return molecules_.size();
        }

        /** Returns the total number of atoms in this SimInfo */
        unsigned int getNAtoms() {
            return nAtoms_;
        }

        /** Returns the total number of bonds in this SimInfo */        
        unsigned int getNBonds(){
            return nBonds_;
        }

        /** Returns the total number of bends in this SimInfo */        
        unsigned int getNBends() {
            return nBends_;
        }

        /** Returns the total number of torsions in this SimInfo */        
        unsigned int getNTorsions() {
            return nTorsions_;
        }

        /** Returns the total number of rigid bodies in this SimInfo */        
        unsigned int getNRigidBodies() {
            return nRigidBodies_;
        }

        /** Returns the total number of integrable objects in this SimInfo */
        unsigned int getNIntegrableObjects() {
            return nIntegrableObjects_;
        }

        /** Returns the total number of cutoff groups in this SimInfo */
        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;
        }

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

        void calcNDF();
        void calcNDFRaw();
        void calcNDFTrans();

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

        int ndf_;
        int ndfRaw_;
        int ndfTrans_;
        
        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 */

        std::vector<std::pair<MoleculeStamp*, int> > moleculeStamps_;
        Globals* globals_;
};

} //namespace oopse
#endif //BRAINS_SIMMODEL_HPP
Revision:	1719
Committed:	Fri Nov 5 23:38:27 2004 UTC (19 years, 10 months ago) by tim
File size:	6317 byte(s)
Log Message:	Fix Exclude class etc.
#	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			SimInfo();
55			virtual ~SimInfo();
56	gezelter	1490
57	tim	1710	/**
58			* Adds a molecule
59			* @return return true if adding successfully, return false if the molecule is already in SimInfo
60			* @param mol molecule to be added
61			*/
62			bool addMolecule(Molecule* mol);
63	gezelter	1490
64	tim	1710	/**
65			* Removes a molecule from SimInfo
66			* @return true if removing successfully, return false if molecule is not in this SimInfo
67			*/
68			bool removeMolecule(Molecule* mol);
69	gezelter	1490
70	tim	1710	/**
71			* Returns the number of molecules.
72			* @return the number of molecules in this SimInfo
73			*/
74			int getNMolecules() {
75			return molecules_.size();
76			}
77	gezelter	1490
78	tim	1710	/** Returns the total number of atoms in this SimInfo */
79			unsigned int getNAtoms() {
80			return nAtoms_;
81			}
82	gezelter	1490
83	tim	1710	/** Returns the total number of bonds in this SimInfo */
84			unsigned int getNBonds(){
85			return nBonds_;
86			}
87	gezelter	1490
88	tim	1710	/** Returns the total number of bends in this SimInfo */
89			unsigned int getNBends() {
90			return nBends_;
91			}
92	gezelter	1490
93	tim	1710	/** Returns the total number of torsions in this SimInfo */
94			unsigned int getNTorsions() {
95			return nTorsions_;
96			}
97	gezelter	1490
98	tim	1710	/** Returns the total number of rigid bodies in this SimInfo */
99			unsigned int getNRigidBodies() {
100			return nRigidBodies_;
101			}
102	gezelter	1490
103	tim	1710	/** Returns the total number of integrable objects in this SimInfo */
104			unsigned int getNIntegrableObjects() {
105			return nIntegrableObjects_;
106			}
107	gezelter	1490
108	tim	1710	/** Returns the total number of cutoff groups in this SimInfo */
109			unsigned int getNCutoffGroups() {
110			return nCutoffGroups_;
111			}
112	gezelter	1490
113	tim	1710	/** Returns the total number of constraints in this SimInfo */
114			unsigned int getNConstraints() {
115			return nConstraints_;
116			}
117
118			/**
119			* Returns the first molecule in this SimInfo and intialize the iterator.
120			* @return the first molecule, return NULL if there is not molecule in this SimInfo
121			* @param i the iterator of molecule array (user shouldn't change it)
122			*/
123			Molecule* beginMolecule(std::vector<Molecule*>::iterator& i);
124	gezelter	1490
125	tim	1710	/**
126			* Returns the next avaliable Molecule based on the iterator.
127			* @return the next avaliable molecule, return NULL if reaching the end of the array
128			* @param i the iterator of molecule array
129			*/
130			Molecule* nextMolecule(std::vector<Molecule*>::iterator& i);
131	gezelter	1490
132	tim	1710	/** Returns the number of degrees of freedom */
133			int getNDF() {
134			return ndf_;
135			}
136	gezelter	1490
137	tim	1710	/** Returns the number of raw degrees of freedom */
138			int getNDFRaw() {
139			return ndfRaw_;
140			}
141	gezelter	1490
142	tim	1710	/** Returns the number of translational degrees of freedom */
143			int getNDFTrans() {
144			return ndfTrans_;
145			}
146	gezelter	1490
147	tim	1710	/** Returns the snapshot manager. */
148			SnapshotManager* getSnapshotManager() {
149			return sman_;
150			}
151	gezelter	1490
152	tim	1710	/** Sets the snapshot manager. */
153			void setSnapshotManager(SnapshotManager* sman) {
154			sman_ = sman;
155			}
156	tim	1712
157	tim	1719	/** Returns the force field */
158	tim	1712	ForceField* getForceField() {
159			return forceField_;
160			}
161	tim	1719
162			/** Sets the force field */
163	tim	1712	void setForceField(ForceField* ff) {
164			forceField_ = ff;
165			}
166	tim	1719
167			Globals* getGlobals() {
168			return globals_;
169			}
170
171			void setGlobals(Globals* globals) {
172			globals_ = globals;
173			}
174
175			int* getExcludeList() {
176			return exclude_.getExcludeList();
177			}
178
179	tim	1710	private:
180	gezelter	1490
181	tim	1710	void calcNDF();
182			void calcNDFRaw();
183			void calcNDFTrans();
184	gezelter	1490
185	tim	1719	void addExcludePairs(Molecule* mol);
186			void removeExcludePairs(Molecule* mol);
187
188	tim	1710	int ndf_;
189			int ndfRaw_;
190			int ndfTrans_;
191
192			int nAtoms_;
193			int nBonds_;
194			int nBends_;
195			int nTorsions_;
196			int nRigidBodies_;
197			int nIntegrableObjects_;
198			int nCutoffGroups_;
199			int nConstraints_;
200	gezelter	1490
201	tim	1719	simtype fInfo_;
202			Exclude exclude_;
203	tim	1712	ForceField* forceField_;
204	tim	1710
205			std::vector<Molecule> molecules_; /< Molecule array /
206			PropertyMap properties_; /** Generic Property */
207			SnapshotManager* sman_; /** SnapshotManager */
208	gezelter	1490
209	tim	1719	std::vector<std::pair<MoleculeStamp*, int> > moleculeStamps_;
210			Globals* globals_;
211	gezelter	1490	};
212
213	tim	1710	} //namespace oopse
214			#endif //BRAINS_SIMMODEL_HPP