site.hpp

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

 
namespace site {
 
enum class Kind {
  unspecified,
  cationHead,
  anion,
  tail,
  donorH,
  acceptor,
  polar,
  apolar,
  waterO,
  waterH,
  solvent
};
 
enum class Family {
  waterIce,      // default; CHILL/TUM allowed
  ionicLiquid,   // CHILL/TUM refused
  moltenSalt,    // CHILL/TUM refused
  des,           // CHILL/TUM refused
  electrolyte,   // CHILL/TUM only if the caller also names a waterIce subset
  confinedIL,    // CHILL/TUM refused
  confinedWater, // 2D RDF / monolayer rings; bulk CHILL refused
  networkFormer  // silica / BeF2; Franzblau yes, CHILL no
};
 
struct Table {
  Family family = Family::waterIce;
  std::unordered_map<int, Kind> typeToKind;   // LAMMPS type ID
  std::unordered_map<int, Kind> atomOverride; // atom ID wins over type
  Kind of(const molSys::Point<double> &p) const;
  Kind ofType(int typeId) const;
};
 
std::vector<int>
indicesOf(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
          const Table &table, Kind kind);
 
int lammpsTypeOfKind(const Table &table, Kind kind); // error if not unique
 
// One vertex per molID that carries ionKind (cationHead or anion).
// Coordinates: unweighted geometric COM of atoms of that molID whose
// kind is ionKind, unwrapped with gen::relDist to the first atom of
// the group (createMolIDAtomIDMultiMap, mol_sys.hpp:187-190). Copies
// box / boxLow from src. Point::type is 1 for cationHead molecules
// and 2 for anion molecules so neighList(merged, 1, 2) is legal.
// A molecule that is already one tagged site (UA, or one designated
// type per ion) is a no-op: the COM is that site.
molSys::PointCloud<molSys::Point<double>, double>
ionCloud(const molSys::PointCloud<molSys::Point<double>, double> &src,
         const Table &table);
 
Table parseSiteSpec(std::string_view spec);
 
} // namespace site
 
#endif // SEAMS_SITE_H_