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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @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/PairList.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"
#include "nonbonded/Electrostatic.hpp"

//another nonsense macro declaration
#define __OPENMD_C
#include "brains/fSimulation.h"

namespace OpenMD{

  //forward decalration 
  class SnapshotManager;
  class Molecule;
  class SelectionManager;
  class StuntDouble;
  class Electrostatic;
  /**
   * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" 
   * @brief One of the heavy weight classes of OpenMD, SimInfo maintains a list of molecules.
    * The Molecule class maintains all of the concrete objects 
    * (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups, 
    * constraints). In both the single and parallel versions, atoms and
    * rigid bodies have both global and local indices.  The local index is 
    * not relevant to molecules or cutoff groups.
    */
  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 torsions */        
    unsigned int getNInversions() {
      return nInversions_;
    }
    /** 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_ - getFdf();
    }

    /** Returns the number of raw degrees of freedom */
    int getNdfRaw() {
      return ndfRaw_;
    }

    /** Returns the number of translational degrees of freedom */
    int getNdfTrans() {
      return ndfTrans_;
    }

    /** sets the current number of frozen degrees of freedom */
    void setFdf(int fdf) {
      fdf_local = fdf;
    }

    int getFdf(); 
    
    //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();

    /** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
    void getGyrationalVolume(RealType &vol);
    /** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
    void getGyrationalVolume(RealType &vol, RealType &detI);
    /** 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;
    }

    int getGlobalMolMembership(int id){
      return globalMolMembership_[id];
    }

    RealType getRcut() {
      return rcut_;
    }

    RealType getRsw() {
      return rsw_;
    }

    RealType getList() {
      return rlist_;
    }
        
    std::string getFinalConfigFileName() {
      return finalConfigFileName_;
    }

    void setFinalConfigFileName(const std::string& fileName) {
      finalConfigFileName_ = fileName;
    }

    std::string getRawMetaData() {
      return rawMetaData_;
    }
    void setRawMetaData(const std::string& rawMetaData) {
      rawMetaData_ = rawMetaData;
    }
        
    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() == static_cast<size_t>(nGlobalAtoms_));
      globalGroupMembership_ = globalGroupMembership;
    }

    /** 
     * Sets GlobalMolMembership
     * @see #SimCreator::setGlobalIndex
     */        
    void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
      assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
      globalMolMembership_ = globalMolMembership;
    }


    bool isFortranInitialized() {
      return fortranInitialized_;
    }
        
    bool getCalcBoxDipole() {
      return calcBoxDipole_;
    }

    bool getUseAtomicVirial() {
      return useAtomicVirial_;
    }

    //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 special interaction pairs (including excluded
     * interactions) in a molecule into the appropriate lists.
     */
    void addInteractionPairs(Molecule* mol);

    /**
     * remove all special interaction pairs which belong to a molecule
     * from the appropriate lists.
     */
    void removeInteractionPairs(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(RealType& rcut, RealType& 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();

    /** Determine if we need to accumulate the simulation box dipole */
    void setupAccumulateBoxDipole();

    /** 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 fdf_local;       /**< number of frozen degrees of freedom */
    int fdf_;            /**< number of frozen degrees of freedom */
    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 globalMolMembership_  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 nInversions_;         /**< number of inversions 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*/
    PairList excludedInteractions_;      
    PairList oneTwoInteractions_;      
    PairList oneThreeInteractions_;      
    PairList oneFourInteractions_;      
    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_;

    // unparsed MetaData block for storing in Dump and EOR files:
    std::string rawMetaData_;

    //file names
    std::string finalConfigFileName_;
    std::string dumpFileName_;
    std::string statFileName_;
    std::string restFileName_;
        
    RealType rcut_;       /**< cutoff radius*/
    RealType rsw_;        /**< radius of switching function*/
    RealType rlist_;      /**< neighbor list radius */

    int ljsp_; /**< use shifted potential for LJ*/
    int ljsf_; /**< use shifted force for LJ*/

    bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
    
    bool calcBoxDipole_; /**< flag to indicate whether or not we calculate 
                            the simulation box dipole moment */
    
    bool useAtomicVirial_; /**< flag to indicate whether or not we use 
                              Atomic Virials to calculate the pressure */

    public:
     /**
      * return an integral objects by its global index. In MPI version, if the StuntDouble with specified
      * global index does not belong to local processor, a NULL will be return.
      */
      StuntDouble* getIOIndexToIntegrableObject(int index);
      void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
    private:
      std::vector<StuntDouble*> IOIndexToIntegrableObject;
  //public:
    //void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
    /**
     * return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
     * global index does not belong to local processor, a NULL will be return.
     */
    //StuntDouble* getStuntDoubleFromGlobalIndex(int index);
  //private:
    //std::vector<StuntDouble*> sdByGlobalIndex_;
    
    //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_; 


  };

} //namespace OpenMD
#endif //BRAINS_SIMMODEL_HPP

Revision:	1503
Committed:	Sat Oct 2 19:54:41 2010 UTC (15 years, 1 month ago) by gezelter
File size:	21460 byte(s)
Log Message:	Changes to remove more of the low level stuff from the fortran side.