SimCreator.hpp

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/*
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 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
/**
 * @file SimCreator.hpp
 * @author tlin
 * @date 11/02/2004
 * @version 1.0
 */
 
#ifndef BRAINS_SIMCREATOR_HPP
#define BRAINS_SIMCREATOR_HPP
 
#include <iostream>
 
#include "brains/ForceField.hpp"
#include "brains/SimInfo.hpp"
#include "io/Globals.hpp"
#include "primitives/Molecule.hpp"
 
namespace OpenMD {
 
  /**
   * @class SimCreator SimCreator.hpp "brains/SimCreator.hpp"
   *
   * The only responsibility of SimCreator is to parse the meta-data
   * file and create a SimInfo instance based on the information
   * returned by parser.
   */
  class SimCreator {
  public:
    virtual ~SimCreator() = default;
 
    /**
     * Setup Simulation
     * @return a pointer to SimInfo
     * @param mdFileName the meta-data file name
     * @param loadInitCoords should the initial coordinates be loaded from a
     * file?
     */
    SimInfo* createSim(const std::string& mdFileName,
                       bool loadInitCoords = true);
 
  private:
    /**
     * Parses the meta-data file
     * @param mdFileName the meta-data file name
     * @param rawMetaData the raw meta-data stream
     * @param mdFileVersion the version of code used to create the meta-data
     * file
     * @param metaDataStartingLine the starting line of the meta-data block
     * @return a pointer to the simulation parameters in a #Globals object
     */
    Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName,
                       int mdFileVersion, int metaDataStartingLine);
 
    /** create the molecules belong to current processor*/
    virtual void createMolecules(SimInfo* info);
 
    /**
     * Figure out the data storage layout based on what kinds of
     * objects are being simulated
     */
    void computeStorageLayouts(SimInfo* info);
 
    /**
     * Sets the global index for atoms, rigidbodies and cutoff groups
     * and fill up globalGroupMembership and globalMolMembership
     * arrays which map atoms' global index to the global index of the
     * groups (or molecules) they belong to.  These array are never
     * changed during the simulation.
     */
    void setGlobalIndex(SimInfo* info);
 
    void gatherParameters(SimInfo* info, const std::string& mdfile);
 
    /**
     * Divide the molecules among the processors
     */
 
    void divideMolecules(SimInfo* info);
 
    /** Load initial coordinates */
    void loadCoordinates(SimInfo* info, const std::string& mdFileName);
 
    std::string
        mdFileName_;  // save the meta-data file name which may be used later
  };
}  // namespace OpenMD
 
#endif  // BRAINS_SIMCREATOR_HPP