ClusterSpecs.hh

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#ifndef CASM_ClusterSpecs
#define CASM_ClusterSpecs
 
#include <vector>
 
#include "casm/clusterography/ClusterOrbits.hh"
#include "casm/container/Permutation.hh"
#include "casm/crystallography/DoFDecl.hh"
#include "casm/global/enum.hh"
#include "casm/misc/cloneable_ptr.hh"
#include "casm/symmetry/PermuteIterator.hh"
#include "casm/symmetry/SymGroup.hh"
 
namespace CASM {
 
class SupercellSymInfo;
class SymGroup;
 
class ClusterSpecs : public notstd::Cloneable {
  ABSTRACT_CLONEABLE(ClusterSpecs)
 public:
  typedef std::vector<IntegralCluster> IntegralClusterVec;
  typedef std::vector<PrimPeriodicOrbit<IntegralCluster>> PeriodicOrbitVec;
  typedef std::vector<LocalOrbit<IntegralCluster>> LocalOrbitVec;
 
  std::string name() const;
  CLUSTER_PERIODICITY_TYPE periodicity_type() const;
 
  PeriodicOrbitVec make_periodic_orbits(
      IntegralClusterVec const &generating_elements) const;
  PeriodicOrbitVec make_periodic_orbits(std::ostream &status) const;
 
  LocalOrbitVec make_local_orbits(
      IntegralClusterVec const &generating_elements) const;
  LocalOrbitVec make_local_orbits(std::ostream &status) const;
 
 private:
  virtual std::string _name() const = 0;
  virtual CLUSTER_PERIODICITY_TYPE _periodicity_type() const = 0;
 
  virtual PeriodicOrbitVec _make_periodic_orbits(
      IntegralClusterVec const &generating_elements) const;
  virtual PeriodicOrbitVec _make_periodic_orbits(std::ostream &status) const;
 
  virtual LocalOrbitVec _make_local_orbits(
      IntegralClusterVec const &generating_elements) const;
  virtual LocalOrbitVec _make_local_orbits(std::ostream &status) const;
};
 
template <typename FunctorType>
void for_all_orbits(ClusterSpecs const &cluster_specs,
                    std::vector<IntegralCluster> const &generating_elements,
                    FunctorType const &f);
 
template <typename FunctorType>
void for_all_orbits(ClusterSpecs const &cluster_specs, std::ostream &status,
                    FunctorType const &f);
 
class PeriodicMaxLengthClusterSpecs : public ClusterSpecs {
  CLONEABLE(PeriodicMaxLengthClusterSpecs)
 public:
  static std::string const method_name; /*periodic_max_length*/
 
  PeriodicMaxLengthClusterSpecs(std::shared_ptr<Structure const> _shared_prim,
                                SymGroup const &_generating_group,
                                SiteFilterFunction const &_site_filter,
                                std::vector<double> const &_max_length,
                                std::vector<IntegralClusterOrbitGenerator> const
                                    &_custom_generators = {});
 
  std::shared_ptr<Structure const> shared_prim;
 
  SymGroup generating_group;
 
  PrimPeriodicSymCompare<IntegralCluster> sym_compare;
 
  SiteFilterFunction site_filter;
 
  std::vector<double> max_length;
 
  std::vector<IntegralClusterOrbitGenerator> custom_generators;
 
 private:
  std::string _name() const override;
  CLUSTER_PERIODICITY_TYPE _periodicity_type() const override;
 
  PeriodicOrbitVec _make_periodic_orbits(
      IntegralClusterVec const &generating_elements) const override;
  PeriodicOrbitVec _make_periodic_orbits(std::ostream &status) const override;
};
 
class LocalMaxLengthClusterSpecs : public ClusterSpecs {
  CLONEABLE(LocalMaxLengthClusterSpecs)
 public:
  static std::string const method_name; /*local_max_length*/
 
  LocalMaxLengthClusterSpecs(std::shared_ptr<Structure const> _shared_prim,
                             SymGroup const &_generating_group,
                             IntegralCluster const &_phenomenal,
                             SiteFilterFunction const &_site_filter,
                             std::vector<double> const &_max_length,
                             std::vector<double> const &_cutoff_radius,
                             bool _include_phenomenal_sites,
                             std::vector<IntegralClusterOrbitGenerator> const
                                 &_custom_generators = {});
 
  std::shared_ptr<Structure const> shared_prim;
 
  SymGroup generating_group;
 
  LocalSymCompare<IntegralCluster> sym_compare;
 
  IntegralCluster phenomenal;
 
  SiteFilterFunction site_filter;
 
  std::vector<double> max_length;
 
  std::vector<double> cutoff_radius;
 
  bool include_phenomenal_sites;
 
  std::vector<IntegralClusterOrbitGenerator> custom_generators;
 
 private:
  std::string _name() const override;
  CLUSTER_PERIODICITY_TYPE _periodicity_type() const override;
 
  LocalOrbitVec _make_local_orbits(
      IntegralClusterVec const &generating_elements) const override;
  LocalOrbitVec _make_local_orbits(std::ostream &status) const override;
};
 
class GenericPeriodicClusterSpecs : public ClusterSpecs {
  CLONEABLE(GenericPeriodicClusterSpecs)
 
  typedef PrimPeriodicSymCompare<IntegralCluster> SymCompareType;
 
  GenericPeriodicClusterSpecs(
      std::string _method_name, std::shared_ptr<Structure const> _shared_prim,
      SymGroup const &_generating_group, SymCompareType const &_sym_compare,
      SiteFilterFunction _site_filter,
      std::vector<ClusterFilterFunction> _cluster_filter,
      std::vector<CandidateSitesFunction> _candidate_sites,
      std::vector<IntegralClusterOrbitGenerator> _custom_generators);
 
  std::shared_ptr<Structure const> shared_prim;
 
  SymGroup generating_group;
 
  SymCompareType sym_compare;
 
  SiteFilterFunction site_filter;
 
  std::vector<ClusterFilterFunction> cluster_filter;
 
  std::vector<CandidateSitesFunction> candidate_sites;
 
  std::vector<IntegralClusterOrbitGenerator> custom_generators;
 
 private:
  std::string m_method_name;
 
  std::string _name() const override;
  CLUSTER_PERIODICITY_TYPE _periodicity_type() const override;
 
  PeriodicOrbitVec _make_periodic_orbits(
      IntegralClusterVec const &generating_elements) const override;
  PeriodicOrbitVec _make_periodic_orbits(std::ostream &status) const override;
};
 
class GenericLocalClusterSpecs : public ClusterSpecs {
  CLONEABLE(GenericLocalClusterSpecs)
 
  typedef LocalSymCompare<IntegralCluster> SymCompareType;
 
  GenericLocalClusterSpecs(
      std::string _method_name, std::shared_ptr<Structure const> _shared_prim,
      SymGroup const &_generating_group, SymCompareType const &_sym_compare,
      SiteFilterFunction _site_filter,
      std::vector<ClusterFilterFunction> _cluster_filter,
      std::vector<CandidateSitesFunction> _candidate_sites,
      std::vector<IntegralClusterOrbitGenerator> _custom_generators);
 
  std::shared_ptr<Structure const> shared_prim;
 
  SymGroup generating_group;
 
  SymCompareType sym_compare;
 
  SiteFilterFunction site_filter;
 
  std::vector<ClusterFilterFunction> cluster_filter;
 
  std::vector<CandidateSitesFunction> candidate_sites;
 
  std::vector<IntegralClusterOrbitGenerator> custom_generators;
 
 private:
  std::string m_method_name;
 
  std::string _name() const override;
  CLUSTER_PERIODICITY_TYPE _periodicity_type() const override;
 
  LocalOrbitVec _make_local_orbits(
      IntegralClusterVec const &generating_elements) const override;
  LocalOrbitVec _make_local_orbits(std::ostream &status) const override;
};
 
// ** Filter functions **
 
bool all_sites_filter(const xtal::Site &site);
 
bool alloy_sites_filter(const xtal::Site &site);
 
SiteFilterFunction dof_sites_filter(const std::vector<DoFKey> &dofs = {});
 
ClusterFilterFunction all_clusters_filter();
 
ClusterFilterFunction max_length_cluster_filter(double max_length);
 
// /// Accept clusters with max pair distance (using closest images) less than
// max_length ClusterFilterFunction within_scel_max_length_cluster_filter(
//   double max_length,
//   Eigen::Matrix3l const &superlattice_matrix);
 
CandidateSitesFunction empty_neighborhood();
 
CandidateSitesFunction origin_neighborhood();
 
// /// Sites in the supercell defined by the superlattice_matrix
// CandidateSitesFunction scel_neighborhood(Eigen::Matrix3l const
// &superlattice_matrix);
 
CandidateSitesFunction max_length_neighborhood(double max_length);
 
CandidateSitesFunction cutoff_radius_neighborhood(
    IntegralCluster const &phenomenal, double cutoff_radius,
    bool include_phenomenal_sites = false);
 
// /// Sites within cutoff_radius distance (using closest images) to any site in
// the phenomenal cluster CandidateSitesFunction
// within_scel_cutoff_radius_neighborhood(
//   IntegralCluster const &phenomenal,
//   double cutoff_radius,
//   Eigen::Matrix3l const &superlattice_matrix);
 
}  // namespace CASM
#endif