structure_desc.hpp

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//-----------------------------------------------------------------------------------
// d-SEAMS - Deferred Structural Elucidation Analysis for Molecular Simulations
// SPDX-License-Identifier: MIT
//-----------------------------------------------------------------------------------
 
#ifndef SEAMS_STRUCTURE_DESC_H_
#define SEAMS_STRUCTURE_DESC_H_
 
#include <mol_sys.hpp>
 
#include <string>
#include <vector>

 
namespace chill {
 
enum class CrystalKind { other = 0, sc, fcc, hcp, bcc };
 
struct TemplateHit {
  CrystalKind kind = CrystalKind::other;
  double rmsd = 1e300;
  const char *name = "other";
};

[[nodiscard]] std::vector<TemplateHit> classifyTemplates(
    const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    const std::vector<std::vector<int>> &nList, int kNeigh = 12);

[[nodiscard]] std::vector<double> soapSpectrum(
    const molSys::PointCloud<molSys::Point<double>, double> &yCloud, int iatom,
    const std::vector<std::vector<int>> &nList, int nMax, int lMax,
    double rcut);

[[nodiscard]] std::vector<std::vector<double>> soapSpectrumAll(
    const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    const std::vector<std::vector<int>> &nList, int nMax, int lMax,
    double rcut);

struct LinearClassifier {
  int nClasses = 0;
  int nFeat = 0;
  double ridge = 1e-6;
  std::vector<double> weights; // nClasses * nFeat, row-major
  std::vector<std::string> labels;
 
  void fit(const std::vector<std::vector<double>> &X,
           const std::vector<int> &y);
  [[nodiscard]] int predict(const std::vector<double> &x) const;
};

[[nodiscard]] std::vector<double> voronoiFeature(
    const molSys::PointCloud<molSys::Point<double>, double> &yCloud, int iatom,
    double candidateCutoff);

[[nodiscard]] std::vector<std::vector<double>> voronoiFeatures(
    const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    double candidateCutoff);
 
} // namespace chill
 
#endif // SEAMS_STRUCTURE_DESC_H_