SequentialAnalyzer.hpp

/*
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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).
 */
 
#ifndef APPLICATIONS_SEQUENTIALPROPS_SEQUENTIALANALYZER_HPP
#define APPLICATIONS_SEQUENTIALPROPS_SEQUENTIALANALYZER_HPP
 
#include <string>
#include <vector>
 
#include "brains/BlockSnapshotManager.hpp"
#include "brains/SimInfo.hpp"
#include "primitives/StuntDouble.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
 
namespace OpenMD {
 
  /**
   * @class SequentialAnalyzer SequentialAnalyzer.hpp
   * "applications/sequentialProps/SequentialAnalyzer"
   * @brief Base class for Sequence Analyzer
   */
 
  class SequentialAnalyzer {
  public:
    SequentialAnalyzer(SimInfo* info, const std::string& filename,
                       const std::string& sele1, const std::string& sele2);
 
    virtual ~SequentialAnalyzer() = default;
    virtual void doSequence();
 
    void setOutputName(const std::string& filename) {
      outputFilename_ = filename;
    }
 
    const std::string& getOutputFileName() const { return outputFilename_; }
 
    void setStep(int step) {
      assert(step > 0);
      step_ = step;
    }
 
    int getStep() { return step_; }
 
    const std::string& getSequenceType() const { return sequenceType_; }
 
    void setSequenceType(const std::string& type) { sequenceType_ = type; }
 
    void setParameterString(const std::string& params) {
      paramString_ = params;
    }
 
  protected:
    virtual void preSequence() {}
    virtual void postSequence() {}
    virtual void writeSequence();
    virtual void doFrame(int frame) = 0;
 
    SimInfo* info_ {nullptr};
    Snapshot* currentSnapshot_;
    std::string dumpFilename_;
 
    SelectionManager seleMan1_;
    std::string selectionScript1_;
    SelectionEvaluator evaluator1_;
 
    SelectionManager seleMan2_;
    std::string selectionScript2_;
    SelectionEvaluator evaluator2_;
 
    int step_;
 
    std::string outputFilename_;
    int frame_;
    // int storageLayout_;
    std::vector<RealType> times_;
    std::vector<RealType> values_;
    std::string sequenceType_;
    std::string paramString_;
  };
}  // namespace OpenMD
 
#endif