IntegralCluster_json_io.cc

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#include "casm/clusterography/io/json/IntegralCluster_json_io.hh"
 
#include "casm/casm_io/Log.hh"
#include "casm/casm_io/container/json_io.hh"
#include "casm/casm_io/json/InputParser.hh"
#include "casm/casm_io/json/InputParser_impl.hh"
#include "casm/casm_io/json/jsonParser.hh"
#include "casm/clusterography/ClusterInvariants.hh"
#include "casm/clusterography/ClusterOrbits.hh"
#include "casm/clusterography/ClusterOrbits_impl.hh"
#include "casm/clusterography/IntegralCluster.hh"
#include "casm/crystallography/Structure.hh"
#include "casm/crystallography/io/UnitCellCoordIO.hh"
#include "casm/global/enum/json_io.hh"
 
namespace CASM {
 
jsonParser &to_json(const IntegralCluster &clust, jsonParser &json) {
  json.put_obj();
  ClusterInvariants invariants{clust};
  if (invariants.displacement().size()) {
    json["min_length"] = invariants.displacement().front();
    json["max_length"] = invariants.displacement().back();
  } else {
    json["min_length"] = 0.0;
    json["max_length"] = 0.0;
  }
  json["sites"].put_array(clust.begin(), clust.end());
  return json;
}
 
void from_json(IntegralCluster &clust, const jsonParser &json) {
  clust = jsonConstructor<IntegralCluster>::from_json(json, clust.prim());
}
 
IntegralCluster jsonConstructor<IntegralCluster>::from_json(
    const jsonParser &json, Structure const &prim) {
  jsonParser tmp{json};  // TODO: this shouldn't be necessary
  InputParser<IntegralCluster> parser{tmp, prim};
  std::stringstream ss;
  ss << "Error: Invalid cluster JSON object";
  report_and_throw_if_invalid(parser, err_log(), std::runtime_error{ss.str()});
  return *parser.value;
}
 
void parse(InputParser<IntegralCluster> &parser, Structure const &prim) {
  std::string name;
  const jsonParser &json = parser.self;
  if (json.contains("sites")) {
    name = "sites";
  } else if (json.contains("prototype")) {
    name = "prototype";
  } else {
    parser.error.insert(
        "Error reading IntegralCluster from JSON: Expected 'sites' or "
        "'prototype' containing a list of cluster site coordinates.");
    return;
  }
 
  double xtal_tol = prim.lattice().tol();
  CASM::COORD_TYPE coord_type;
  parser.optional_else(coord_type, "coordinate_mode", INTEGRAL);
 
  parser.value = notstd::make_unique<IntegralCluster>(prim);
  auto &clust = *parser.value;
 
  if (coord_type == INTEGRAL) {
    parser.require(clust.elements(), name);
  } else {
    std::vector<Eigen::Vector3d> coord_vec;
    parser.require(coord_vec, name);
 
    try {
      for (const auto &coord : coord_vec) {
        xtal::Coordinate tcoord{coord, prim.lattice(), coord_type};
        clust.elements().emplace_back(
            xtal::UnitCellCoord::from_coordinate(prim, tcoord, xtal_tol));
      }
    } catch (std::exception &e) {
      parser.error.insert("Error: could not read coordinates from '" + name +
                          "'");
      return;
    }
  }
  return;
}
}  // namespace CASM