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 "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(MakeStamps* stamps, 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();

    /** 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;
    }
        
    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();

    /** 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);

    MakeStamps* stamps_;
    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 */

    /** 
     * 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*/

    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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	18021 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	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 "types/MoleculeStamp.hpp"
61	#include "UseTheForce/ForceField.hpp"
62	#include "utils/PropertyMap.hpp"
63	#include "utils/LocalIndexManager.hpp"
64
65	//another nonsense macro declaration
66	#define __C
67	#include "brains/fSimulation.h"
68
69	namespace oopse{
70
71	//forward decalration
72	class SnapshotManager;
73	class Molecule;
74	class SelectionManager;
75	/**
76	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
77	* @brief As one of the heavy weight class of OOPSE, SimInfo
78	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
79	* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
80	* cutoff groups, constrains).
81	* Another major change is the index. No matter single version or parallel version, atoms and
82	* rigid bodies have both global index and local index. Local index is not important to molecule as well as
83	* cutoff group.
84	*/
85	class SimInfo {
86	public:
87	typedef std::map<int, Molecule*>::iterator MoleculeIterator;
88
89	/**
90	* Constructor of SimInfo
91	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
92	* second element is the total number of molecules with the same molecule stamp in the system
93	* @param ff pointer of a concrete ForceField instance
94	* @param simParams
95	* @note
96	*/
97	SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp, int> >& molStampPairs, ForceField ff, Globals* simParams);
98	virtual ~SimInfo();
99
100	/**
101	* Adds a molecule
102	* @return return true if adding successfully, return false if the molecule is already in SimInfo
103	* @param mol molecule to be added
104	*/
105	bool addMolecule(Molecule* mol);
106
107	/**
108	* Removes a molecule from SimInfo
109	* @return true if removing successfully, return false if molecule is not in this SimInfo
110	*/
111	bool removeMolecule(Molecule* mol);
112
113	/** Returns the total number of molecules in the system. */
114	int getNGlobalMolecules() {
115	return nGlobalMols_;
116	}
117
118	/** Returns the total number of atoms in the system. */
119	int getNGlobalAtoms() {
120	return nGlobalAtoms_;
121	}
122
123	/** Returns the total number of cutoff groups in the system. */
124	int getNGlobalCutoffGroups() {
125	return nGlobalCutoffGroups_;
126	}
127
128	/**
129	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
130	* of atoms which do not belong to the rigid bodies) in the system
131	*/
132	int getNGlobalIntegrableObjects() {
133	return nGlobalIntegrableObjects_;
134	}
135
136	/**
137	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
138	* of atoms which do not belong to the rigid bodies) in the system
139	*/
140	int getNGlobalRigidBodies() {
141	return nGlobalRigidBodies_;
142	}
143
144	int getNGlobalConstraints();
145	/**
146	* Returns the number of local molecules.
147	* @return the number of local molecules
148	*/
149	int getNMolecules() {
150	return molecules_.size();
151	}
152
153	/** Returns the number of local atoms */
154	unsigned int getNAtoms() {
155	return nAtoms_;
156	}
157
158	/** Returns the number of local bonds */
159	unsigned int getNBonds(){
160	return nBonds_;
161	}
162
163	/** Returns the number of local bends */
164	unsigned int getNBends() {
165	return nBends_;
166	}
167
168	/** Returns the number of local torsions */
169	unsigned int getNTorsions() {
170	return nTorsions_;
171	}
172
173	/** Returns the number of local rigid bodies */
174	unsigned int getNRigidBodies() {
175	return nRigidBodies_;
176	}
177
178	/** Returns the number of local integrable objects */
179	unsigned int getNIntegrableObjects() {
180	return nIntegrableObjects_;
181	}
182
183	/** Returns the number of local cutoff groups */
184	unsigned int getNCutoffGroups() {
185	return nCutoffGroups_;
186	}
187
188	/** Returns the total number of constraints in this SimInfo */
189	unsigned int getNConstraints() {
190	return nConstraints_;
191	}
192
193	/**
194	* Returns the first molecule in this SimInfo and intialize the iterator.
195	* @return the first molecule, return NULL if there is not molecule in this SimInfo
196	* @param i the iterator of molecule array (user shouldn't change it)
197	*/
198	Molecule* beginMolecule(MoleculeIterator& i);
199
200	/**
201	* Returns the next avaliable Molecule based on the iterator.
202	* @return the next avaliable molecule, return NULL if reaching the end of the array
203	* @param i the iterator of molecule array
204	*/
205	Molecule* nextMolecule(MoleculeIterator& i);
206
207	/** Returns the number of degrees of freedom */
208	int getNdf() {
209	return ndf_;
210	}
211
212	/** Returns the number of raw degrees of freedom */
213	int getNdfRaw() {
214	return ndfRaw_;
215	}
216
217	/** Returns the number of translational degrees of freedom */
218	int getNdfTrans() {
219	return ndfTrans_;
220	}
221
222	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
223
224	/** Returns the total number of z-constraint molecules in the system */
225	int getNZconstraint() {
226	return nZconstraint_;
227	}
228
229	/**
230	* Sets the number of z-constraint molecules in the system.
231	*/
232	void setNZconstraint(int nZconstraint) {
233	nZconstraint_ = nZconstraint;
234	}
235
236	/** Returns the snapshot manager. */
237	SnapshotManager* getSnapshotManager() {
238	return sman_;
239	}
240
241	/** Sets the snapshot manager. */
242	void setSnapshotManager(SnapshotManager* sman);
243
244	/** Returns the force field */
245	ForceField* getForceField() {
246	return forceField_;
247	}
248
249	Globals* getSimParams() {
250	return simParams_;
251	}
252
253	/** Returns the velocity of center of mass of the whole system.*/
254	Vector3d getComVel();
255
256	/** Returns the center of the mass of the whole system.*/
257	Vector3d getCom();
258
259	/** main driver function to interact with fortran during the initialization and molecule migration */
260	void update();
261
262	/** Returns the local index manager */
263	LocalIndexManager* getLocalIndexManager() {
264	return &localIndexMan_;
265	}
266
267	int getMoleculeStampId(int globalIndex) {
268	//assert(globalIndex < molStampIds_.size())
269	return molStampIds_[globalIndex];
270	}
271
272	/** Returns the molecule stamp */
273	MoleculeStamp* getMoleculeStamp(int id) {
274	return moleculeStamps_[id];
275	}
276
277	/** Return the total number of the molecule stamps */
278	int getNMoleculeStamp() {
279	return moleculeStamps_.size();
280	}
281	/**
282	* Finds a molecule with a specified global index
283	* @return a pointer point to found molecule
284	* @param index
285	*/
286	Molecule* getMoleculeByGlobalIndex(int index) {
287	MoleculeIterator i;
288	i = molecules_.find(index);
289
290	return i != molecules_.end() ? i->second : NULL;
291	}
292
293	/** Calculate the maximum cutoff radius based on the atom types */
294	double calcMaxCutoffRadius();
295
296	double getRcut() {
297	return rcut_;
298	}
299
300	double getRsw() {
301	return rsw_;
302	}
303
304	std::string getFinalConfigFileName() {
305	return finalConfigFileName_;
306	}
307
308	void setFinalConfigFileName(const std::string& fileName) {
309	finalConfigFileName_ = fileName;
310	}
311
312	std::string getDumpFileName() {
313	return dumpFileName_;
314	}
315
316	void setDumpFileName(const std::string& fileName) {
317	dumpFileName_ = fileName;
318	}
319
320	std::string getStatFileName() {
321	return statFileName_;
322	}
323
324	void setStatFileName(const std::string& fileName) {
325	statFileName_ = fileName;
326	}
327
328	std::string getRestFileName() {
329	return restFileName_;
330	}
331
332	void setRestFileName(const std::string& fileName) {
333	restFileName_ = fileName;
334	}
335
336	/**
337	* Sets GlobalGroupMembership
338	* @see #SimCreator::setGlobalIndex
339	*/
340	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
341	assert(globalGroupMembership.size() == nGlobalAtoms_);
342	globalGroupMembership_ = globalGroupMembership;
343	}
344
345	/**
346	* Sets GlobalMolMembership
347	* @see #SimCreator::setGlobalIndex
348	*/
349	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
350	assert(globalMolMembership.size() == nGlobalAtoms_);
351	globalMolMembership_ = globalMolMembership;
352	}
353
354
355	bool isFortranInitialized() {
356	return fortranInitialized_;
357	}
358
359	//below functions are just forward functions
360	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
361	//the other hand, has-a relation need composing.
362	/**
363	* Adds property into property map
364	* @param genData GenericData to be added into PropertyMap
365	*/
366	void addProperty(GenericData* genData);
367
368	/**
369	* Removes property from PropertyMap by name
370	* @param propName the name of property to be removed
371	*/
372	void removeProperty(const std::string& propName);
373
374	/**
375	* clear all of the properties
376	*/
377	void clearProperties();
378
379	/**
380	* Returns all names of properties
381	* @return all names of properties
382	*/
383	std::vector<std::string> getPropertyNames();
384
385	/**
386	* Returns all of the properties in PropertyMap
387	* @return all of the properties in PropertyMap
388	*/
389	std::vector<GenericData*> getProperties();
390
391	/**
392	* Returns property
393	* @param propName name of property
394	* @return a pointer point to property with propName. If no property named propName
395	* exists, return NULL
396	*/
397	GenericData* getPropertyByName(const std::string& propName);
398
399	/**
400	* add all exclude pairs of a molecule into exclude list.
401	*/
402	void addExcludePairs(Molecule* mol);
403
404	/**
405	* remove all exclude pairs which belong to a molecule from exclude list
406	*/
407
408	void removeExcludePairs(Molecule* mol);
409
410
411	/** Returns the unique atom types of local processor in an array */
412	std::set<AtomType*> getUniqueAtomTypes();
413
414	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
415
416	void getCutoff(double& rcut, double& rsw);
417
418	private:
419
420	/** fill up the simtype struct*/
421	void setupSimType();
422
423	/**
424	* Setup Fortran Simulation
425	* @see #setupFortranParallel
426	*/
427	void setupFortranSim();
428
429	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
430	void setupCutoff();
431
432	/** Calculates the number of degress of freedom in the whole system */
433	void calcNdf();
434	void calcNdfRaw();
435	void calcNdfTrans();
436
437	/**
438	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
439	* system.
440	*/
441	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
442
443	MakeStamps* stamps_;
444	ForceField* forceField_;
445	Globals* simParams_;
446
447	std::map<int, Molecule> molecules_; /< Molecule array /
448
449	//degress of freedom
450	int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
451	int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
452	int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
453	int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
454
455	//number of global objects
456	int nGlobalMols_; /*< number of molecules in the system /
457	int nGlobalAtoms_; /*< number of atoms in the system /
458	int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
459	int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
460	int nGlobalRigidBodies_; /*< number of rigid bodies in this system /
461	/**
462	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
463	* corresponding content is the global index of cutoff group this atom belong to.
464	* It is filled by SimCreator once and only once, since it never changed during the simulation.
465	*/
466	std::vector<int> globalGroupMembership_;
467
468	/**
469	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
470	* corresponding content is the global index of molecule this atom belong to.
471	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
472	*/
473	std::vector<int> globalMolMembership_;
474
475
476	std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
477	std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
478
479	//number of local objects
480	int nAtoms_; /*< number of atoms in local processor /
481	int nBonds_; /*< number of bonds in local processor /
482	int nBends_; /*< number of bends in local processor /
483	int nTorsions_; /*< number of torsions in local processor /
484	int nRigidBodies_; /*< number of rigid bodies in local processor /
485	int nIntegrableObjects_; /*< number of integrable objects in local processor /
486	int nCutoffGroups_; /*< number of cutoff groups in local processor /
487	int nConstraints_; /*< number of constraints in local processors /
488
489	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
490	Exclude exclude_;
491	PropertyMap properties_; /*< Generic Property /
492	SnapshotManager* sman_; /*< SnapshotManager /
493
494	/**
495	* The reason to have a local index manager is that when molecule is migrating to other processors,
496	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
497	* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
498	* to make a efficient data moving plan.
499	*/
500	LocalIndexManager localIndexMan_;
501
502	//file names
503	std::string finalConfigFileName_;
504	std::string dumpFileName_;
505	std::string statFileName_;
506	std::string restFileName_;
507
508	double rcut_; /*< cutoff radius/
509	double rsw_; /*< radius of switching function/
510
511	bool fortranInitialized_; /*< flag indicate whether fortran side is initialized /
512
513	#ifdef IS_MPI
514	//in Parallel version, we need MolToProc
515	public:
516
517	/**
518	* Finds the processor where a molecule resides
519	* @return the id of the processor which contains the molecule
520	* @param globalIndex global Index of the molecule
521	*/
522	int getMolToProc(int globalIndex) {
523	//assert(globalIndex < molToProcMap_.size());
524	return molToProcMap_[globalIndex];
525	}
526
527	/**
528	* Set MolToProcMap array
529	* @see #SimCreator::divideMolecules
530	*/
531	void setMolToProcMap(const std::vector<int>& molToProcMap) {
532	molToProcMap_ = molToProcMap;
533	}
534
535	private:
536
537	void setupFortranParallel();
538
539	/**
540	* The size of molToProcMap_ is equal to total number of molecules in the system.
541	* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
542	* once.
543	*/
544	std::vector<int> molToProcMap_;
545
546	#endif
547
548	};
549
550	} //namespace oopse
551	#endif //BRAINS_SIMMODEL_HPP
552