Qsurf.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_QSURF_HPP
#define APPLICATIONS_SEQUENTIALPROPS_QSURF_HPP
 
#include "applications/sequentialProps/SequentialAnalyzer.hpp"
#include "math/Vector3.hpp"
 
namespace OpenMD {
 
  /**
   * @class Qsurf
   * @brief Tetrahedral order parameter Q field, output frame-by-frame as
   *        OpenDX volumetric data files.
   *
   * For each frame, computes the Errington-Debenedetti rescaled
   * tetrahedrality parameter Q for every molecule in sele1 (using
   * neighbors from sele2), Gaussian-coarse-grains Q onto a 3D voxel
   * grid, and writes the resulting scalar field to a numbered OpenDX
   * (.dx) file.
   *
   * Output is a series of per-frame .dx files plus a Tcl script
   * for loading the entire series into VMD as an animated
   * isosurface.  The user can interactively adjust the isovalue
   * threshold in VMD's Isosurface representation.
   */
  class Qsurf : public SequentialAnalyzer {
  public:
    Qsurf(SimInfo* info, const std::string& filename,
          const std::string& sele1, const std::string& sele2,
          RealType rCut, RealType voxelSize, RealType gaussWidth);
 
    virtual void doSequence() override;
 
  protected:
    virtual void doFrame(int) override {}  // unused; work is in doSequence
 
  private:
    void writeDXFrame(const std::string& fname,
                      const std::vector<std::vector<std::vector<RealType>>>& field,
                      const Vector3d& origin,
                      RealType time);
 
    void writeVMDScript(const std::string& scriptName,
                        const std::string& baseName,
                        int nFramesWritten);
 
    RealType rCut_;
    RealType voxelSize_;
    RealType gaussWidth_;
 
    int nBinsX_;
    int nBinsY_;
    int nBinsZ_;
  };
}  // namespace OpenMD
 
#endif