src/brains/SimInfo.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
/**
 * @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 "math/SquareMatrix3.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 SelectionManager;
  /**
   * @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(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 center of the mass and Center of Mass velocity of the whole system.*/ 
    void getComAll(Vector3d& com,Vector3d& comVel);

    /** Returns intertia tensor for the entire system and system Angular Momentum.*/
    void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
    
    /** Returns system angular momentum */
    Vector3d getAngularMomentum();

    /** 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;
    }

    double getRcut() {
      return rcut_;
    }

    double getRsw() {
      return rsw_;
    }

    double getList() {
      return rlist_;
    }
        
    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;
    }
        
    std::string getRestFileName() {
      return restFileName_;
    }
        
    void setRestFileName(const std::string& fileName) {
      restFileName_ = 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);


    /** Returns the unique atom types of local processor in an array */
    std::set<AtomType*> getUniqueAtomTypes();
        
    friend std::ostream& operator <<(std::ostream& o, SimInfo& info);

    void getCutoff(double& rcut, double& rsw);
        
  private:

    /** 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();

    /** Figure out which coulombic correction method to use and pass to fortran */
    void setupElectrostaticSummationMethod( int isError );

    /** Figure out which polynomial type to use for the switching function */
    void setupSwitchingFunction();

    /** Calculates the number of degress of freedom in the whole system */
    void calcNdf();
    void calcNdfRaw();
    void calcNdfTrans();

    ForceField* forceField_;      
    Globals* simParams_;

    std::map<int, Molecule*>  molecules_; /**< Molecule array */

    /**
     * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
     * system.
     */
    void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
        
    //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 */

    /** 
     * 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_;
    std::string restFileName_;
        
    double rcut_;       /**< cutoff radius*/
    double rsw_;        /**< radius of switching function*/
    double rlist_;      /**< neighbor list radius */

    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:	2469
Committed:	Fri Dec 2 15:38:03 2005 UTC (18 years, 7 months ago) by tim
File size:	18593 byte(s)
Log Message:	End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	/**
43	* @file SimInfo.hpp
44	* @author tlin
45	* @date 11/02/2004
46	* @version 1.0
47	*/
48
49	#ifndef BRAINS_SIMMODEL_HPP
50	#define BRAINS_SIMMODEL_HPP
51
52	#include <iostream>
53	#include <set>
54	#include <utility>
55	#include <vector>
56
57	#include "brains/Exclude.hpp"
58	#include "io/Globals.hpp"
59	#include "math/Vector3.hpp"
60	#include "math/SquareMatrix3.hpp"
61	#include "types/MoleculeStamp.hpp"
62	#include "UseTheForce/ForceField.hpp"
63	#include "utils/PropertyMap.hpp"
64	#include "utils/LocalIndexManager.hpp"
65
66	//another nonsense macro declaration
67	#define __C
68	#include "brains/fSimulation.h"
69
70	namespace oopse{
71
72	//forward decalration
73	class SnapshotManager;
74	class Molecule;
75	class SelectionManager;
76	/**
77	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
78	* @brief As one of the heavy weight class of OOPSE, SimInfo
79	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
80	* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
81	* cutoff groups, constrains).
82	* Another major change is the index. No matter single version or parallel version, atoms and
83	* rigid bodies have both global index and local index. Local index is not important to molecule as well as
84	* cutoff group.
85	*/
86	class SimInfo {
87	public:
88	typedef std::map<int, Molecule*>::iterator MoleculeIterator;
89
90	/**
91	* Constructor of SimInfo
92	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
93	* second element is the total number of molecules with the same molecule stamp in the system
94	* @param ff pointer of a concrete ForceField instance
95	* @param simParams
96	* @note
97	*/
98	SimInfo(ForceField* ff, Globals* simParams);
99	virtual ~SimInfo();
100
101	/**
102	* Adds a molecule
103	* @return return true if adding successfully, return false if the molecule is already in SimInfo
104	* @param mol molecule to be added
105	*/
106	bool addMolecule(Molecule* mol);
107
108	/**
109	* Removes a molecule from SimInfo
110	* @return true if removing successfully, return false if molecule is not in this SimInfo
111	*/
112	bool removeMolecule(Molecule* mol);
113
114	/** Returns the total number of molecules in the system. */
115	int getNGlobalMolecules() {
116	return nGlobalMols_;
117	}
118
119	/** Returns the total number of atoms in the system. */
120	int getNGlobalAtoms() {
121	return nGlobalAtoms_;
122	}
123
124	/** Returns the total number of cutoff groups in the system. */
125	int getNGlobalCutoffGroups() {
126	return nGlobalCutoffGroups_;
127	}
128
129	/**
130	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
131	* of atoms which do not belong to the rigid bodies) in the system
132	*/
133	int getNGlobalIntegrableObjects() {
134	return nGlobalIntegrableObjects_;
135	}
136
137	/**
138	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
139	* of atoms which do not belong to the rigid bodies) in the system
140	*/
141	int getNGlobalRigidBodies() {
142	return nGlobalRigidBodies_;
143	}
144
145	int getNGlobalConstraints();
146	/**
147	* Returns the number of local molecules.
148	* @return the number of local molecules
149	*/
150	int getNMolecules() {
151	return molecules_.size();
152	}
153
154	/** Returns the number of local atoms */
155	unsigned int getNAtoms() {
156	return nAtoms_;
157	}
158
159	/** Returns the number of local bonds */
160	unsigned int getNBonds(){
161	return nBonds_;
162	}
163
164	/** Returns the number of local bends */
165	unsigned int getNBends() {
166	return nBends_;
167	}
168
169	/** Returns the number of local torsions */
170	unsigned int getNTorsions() {
171	return nTorsions_;
172	}
173
174	/** Returns the number of local rigid bodies */
175	unsigned int getNRigidBodies() {
176	return nRigidBodies_;
177	}
178
179	/** Returns the number of local integrable objects */
180	unsigned int getNIntegrableObjects() {
181	return nIntegrableObjects_;
182	}
183
184	/** Returns the number of local cutoff groups */
185	unsigned int getNCutoffGroups() {
186	return nCutoffGroups_;
187	}
188
189	/** Returns the total number of constraints in this SimInfo */
190	unsigned int getNConstraints() {
191	return nConstraints_;
192	}
193
194	/**
195	* Returns the first molecule in this SimInfo and intialize the iterator.
196	* @return the first molecule, return NULL if there is not molecule in this SimInfo
197	* @param i the iterator of molecule array (user shouldn't change it)
198	*/
199	Molecule* beginMolecule(MoleculeIterator& i);
200
201	/**
202	* Returns the next avaliable Molecule based on the iterator.
203	* @return the next avaliable molecule, return NULL if reaching the end of the array
204	* @param i the iterator of molecule array
205	*/
206	Molecule* nextMolecule(MoleculeIterator& i);
207
208	/** Returns the number of degrees of freedom */
209	int getNdf() {
210	return ndf_;
211	}
212
213	/** Returns the number of raw degrees of freedom */
214	int getNdfRaw() {
215	return ndfRaw_;
216	}
217
218	/** Returns the number of translational degrees of freedom */
219	int getNdfTrans() {
220	return ndfTrans_;
221	}
222
223	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
224
225	/** Returns the total number of z-constraint molecules in the system */
226	int getNZconstraint() {
227	return nZconstraint_;
228	}
229
230	/**
231	* Sets the number of z-constraint molecules in the system.
232	*/
233	void setNZconstraint(int nZconstraint) {
234	nZconstraint_ = nZconstraint;
235	}
236
237	/** Returns the snapshot manager. */
238	SnapshotManager* getSnapshotManager() {
239	return sman_;
240	}
241
242	/** Sets the snapshot manager. */
243	void setSnapshotManager(SnapshotManager* sman);
244
245	/** Returns the force field */
246	ForceField* getForceField() {
247	return forceField_;
248	}
249
250	Globals* getSimParams() {
251	return simParams_;
252	}
253
254	/** Returns the velocity of center of mass of the whole system.*/
255	Vector3d getComVel();
256
257	/** Returns the center of the mass of the whole system.*/
258	Vector3d getCom();
259	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
260	void getComAll(Vector3d& com,Vector3d& comVel);
261
262	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
263	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
264
265	/** Returns system angular momentum */
266	Vector3d getAngularMomentum();
267
268	/** main driver function to interact with fortran during the initialization and molecule migration */
269	void update();
270
271	/** Returns the local index manager */
272	LocalIndexManager* getLocalIndexManager() {
273	return &localIndexMan_;
274	}
275
276	int getMoleculeStampId(int globalIndex) {
277	//assert(globalIndex < molStampIds_.size())
278	return molStampIds_[globalIndex];
279	}
280
281	/** Returns the molecule stamp */
282	MoleculeStamp* getMoleculeStamp(int id) {
283	return moleculeStamps_[id];
284	}
285
286	/** Return the total number of the molecule stamps */
287	int getNMoleculeStamp() {
288	return moleculeStamps_.size();
289	}
290	/**
291	* Finds a molecule with a specified global index
292	* @return a pointer point to found molecule
293	* @param index
294	*/
295	Molecule* getMoleculeByGlobalIndex(int index) {
296	MoleculeIterator i;
297	i = molecules_.find(index);
298
299	return i != molecules_.end() ? i->second : NULL;
300	}
301
302	double getRcut() {
303	return rcut_;
304	}
305
306	double getRsw() {
307	return rsw_;
308	}
309
310	double getList() {
311	return rlist_;
312	}
313
314	std::string getFinalConfigFileName() {
315	return finalConfigFileName_;
316	}
317
318	void setFinalConfigFileName(const std::string& fileName) {
319	finalConfigFileName_ = fileName;
320	}
321
322	std::string getDumpFileName() {
323	return dumpFileName_;
324	}
325
326	void setDumpFileName(const std::string& fileName) {
327	dumpFileName_ = fileName;
328	}
329
330	std::string getStatFileName() {
331	return statFileName_;
332	}
333
334	void setStatFileName(const std::string& fileName) {
335	statFileName_ = fileName;
336	}
337
338	std::string getRestFileName() {
339	return restFileName_;
340	}
341
342	void setRestFileName(const std::string& fileName) {
343	restFileName_ = fileName;
344	}
345
346	/**
347	* Sets GlobalGroupMembership
348	* @see #SimCreator::setGlobalIndex
349	*/
350	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
351	assert(globalGroupMembership.size() == nGlobalAtoms_);
352	globalGroupMembership_ = globalGroupMembership;
353	}
354
355	/**
356	* Sets GlobalMolMembership
357	* @see #SimCreator::setGlobalIndex
358	*/
359	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
360	assert(globalMolMembership.size() == nGlobalAtoms_);
361	globalMolMembership_ = globalMolMembership;
362	}
363
364
365	bool isFortranInitialized() {
366	return fortranInitialized_;
367	}
368
369	//below functions are just forward functions
370	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
371	//the other hand, has-a relation need composing.
372	/**
373	* Adds property into property map
374	* @param genData GenericData to be added into PropertyMap
375	*/
376	void addProperty(GenericData* genData);
377
378	/**
379	* Removes property from PropertyMap by name
380	* @param propName the name of property to be removed
381	*/
382	void removeProperty(const std::string& propName);
383
384	/**
385	* clear all of the properties
386	*/
387	void clearProperties();
388
389	/**
390	* Returns all names of properties
391	* @return all names of properties
392	*/
393	std::vector<std::string> getPropertyNames();
394
395	/**
396	* Returns all of the properties in PropertyMap
397	* @return all of the properties in PropertyMap
398	*/
399	std::vector<GenericData*> getProperties();
400
401	/**
402	* Returns property
403	* @param propName name of property
404	* @return a pointer point to property with propName. If no property named propName
405	* exists, return NULL
406	*/
407	GenericData* getPropertyByName(const std::string& propName);
408
409	/**
410	* add all exclude pairs of a molecule into exclude list.
411	*/
412	void addExcludePairs(Molecule* mol);
413
414	/**
415	* remove all exclude pairs which belong to a molecule from exclude list
416	*/
417
418	void removeExcludePairs(Molecule* mol);
419
420
421	/** Returns the unique atom types of local processor in an array */
422	std::set<AtomType*> getUniqueAtomTypes();
423
424	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
425
426	void getCutoff(double& rcut, double& rsw);
427
428	private:
429
430	/** fill up the simtype struct*/
431	void setupSimType();
432
433	/**
434	* Setup Fortran Simulation
435	* @see #setupFortranParallel
436	*/
437	void setupFortranSim();
438
439	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
440	void setupCutoff();
441
442	/** Figure out which coulombic correction method to use and pass to fortran */
443	void setupElectrostaticSummationMethod( int isError );
444
445	/** Figure out which polynomial type to use for the switching function */
446	void setupSwitchingFunction();
447
448	/** Calculates the number of degress of freedom in the whole system */
449	void calcNdf();
450	void calcNdfRaw();
451	void calcNdfTrans();
452
453	ForceField* forceField_;
454	Globals* simParams_;
455
456	std::map<int, Molecule> molecules_; /< Molecule array /
457
458	/**
459	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
460	* system.
461	*/
462	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
463
464	//degress of freedom
465	int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
466	int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
467	int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
468	int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
469
470	//number of global objects
471	int nGlobalMols_; /*< number of molecules in the system /
472	int nGlobalAtoms_; /*< number of atoms in the system /
473	int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
474	int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
475	int nGlobalRigidBodies_; /*< number of rigid bodies in this system /
476	/**
477	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
478	* corresponding content is the global index of cutoff group this atom belong to.
479	* It is filled by SimCreator once and only once, since it never changed during the simulation.
480	*/
481	std::vector<int> globalGroupMembership_;
482
483	/**
484	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
485	* corresponding content is the global index of molecule this atom belong to.
486	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
487	*/
488	std::vector<int> globalMolMembership_;
489
490
491	std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
492	std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
493
494	//number of local objects
495	int nAtoms_; /*< number of atoms in local processor /
496	int nBonds_; /*< number of bonds in local processor /
497	int nBends_; /*< number of bends in local processor /
498	int nTorsions_; /*< number of torsions in local processor /
499	int nRigidBodies_; /*< number of rigid bodies in local processor /
500	int nIntegrableObjects_; /*< number of integrable objects in local processor /
501	int nCutoffGroups_; /*< number of cutoff groups in local processor /
502	int nConstraints_; /*< number of constraints in local processors /
503
504	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
505	Exclude exclude_;
506	PropertyMap properties_; /*< Generic Property /
507	SnapshotManager* sman_; /*< SnapshotManager /
508
509	/**
510	* The reason to have a local index manager is that when molecule is migrating to other processors,
511	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
512	* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
513	* to make a efficient data moving plan.
514	*/
515	LocalIndexManager localIndexMan_;
516
517	//file names
518	std::string finalConfigFileName_;
519	std::string dumpFileName_;
520	std::string statFileName_;
521	std::string restFileName_;
522
523	double rcut_; /*< cutoff radius/
524	double rsw_; /*< radius of switching function/
525	double rlist_; /*< neighbor list radius /
526
527	bool fortranInitialized_; /*< flag indicate whether fortran side is initialized /
528
529	#ifdef IS_MPI
530	//in Parallel version, we need MolToProc
531	public:
532
533	/**
534	* Finds the processor where a molecule resides
535	* @return the id of the processor which contains the molecule
536	* @param globalIndex global Index of the molecule
537	*/
538	int getMolToProc(int globalIndex) {
539	//assert(globalIndex < molToProcMap_.size());
540	return molToProcMap_[globalIndex];
541	}
542
543	/**
544	* Set MolToProcMap array
545	* @see #SimCreator::divideMolecules
546	*/
547	void setMolToProcMap(const std::vector<int>& molToProcMap) {
548	molToProcMap_ = molToProcMap;
549	}
550
551	private:
552
553	void setupFortranParallel();
554
555	/**
556	* The size of molToProcMap_ is equal to total number of molecules in the system.
557	* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
558	* once.
559	*/
560	std::vector<int> molToProcMap_;
561
562	#endif
563
564	};
565
566	} //namespace oopse
567	#endif //BRAINS_SIMMODEL_HPP
568