# -*- coding: utf-8 -*- from __future__ import annotations from typing import Any from .backends import dispatch_structure_backend, safe_float, to_builtin AMU_TO_G = 1.66053906660e-24 ANG3_TO_CM3 = 1.0e-24 def get_lattice_inf(structure: Any, *, backend: str='auto') -> dict[str, Any]: b = dispatch_structure_backend(structure, backend) if b == 'pymatgen': l = structure.lattice; a,bv,c = l.abc; al,be,ga = l.angles return {'backend':'pymatgen','a':float(a),'b':float(bv),'c':float(c), 'alpha':float(al),'beta':float(be),'gamma':float(ga), 'abc':[float(a),float(bv),float(c)], 'angles':[float(al),float(be),float(ga)], 'volume':float(l.volume),'matrix':to_builtin(l.matrix), 'reciprocal_matrix':to_builtin(l.reciprocal_lattice.matrix)} raise RuntimeError(f'unsupported backend {b!r}') def _species_occ_list(site: Any) -> list[dict[str, Any]]: ret=[] for sp,occ in site.species.items(): d={'symbol':getattr(sp,'symbol',str(sp)),'species':str(sp),'occupancy':float(occ)} try: d['Z']=int(sp.Z) except Exception: pass try: d['oxidation_state']=float(sp.oxi_state) except Exception: pass ret.append(d) return ret def _species_string(site: Any) -> str: parts=[] for s in _species_occ_list(site): occ=s['occupancy']; parts.append(s['species'] if abs(occ-1)<1e-12 else f"{s['species']}:{occ:.6g}") return ','.join(parts) def _site_to_dict(site: Any, index: int, *, include_cartesian=True) -> dict[str, Any]: sp=_species_occ_list(site) d={'index':int(index),'species_string':_species_string(site),'species':sp, 'frac_coords':[float(x) for x in site.frac_coords], 'occupancy_sum':float(sum(x['occupancy'] for x in sp))} if include_cartesian: d['cart_coords']=[float(x) for x in site.coords] try: d['label']=str(site.label) except Exception: pass try: d['properties']=to_builtin(site.properties) except Exception: pass return d def get_site_inf(structure: Any, *, backend: str='auto', max_sites: int|None=None, include_cartesian=True) -> dict[str, Any]: b=dispatch_structure_backend(structure, backend) if b == 'pymatgen': sites=structure.sites if max_sites is None else structure.sites[:int(max_sites)] return {'backend':'pymatgen','n_sites':len(structure.sites),'n_returned_sites':len(sites), 'sites':[_site_to_dict(site,i,include_cartesian=include_cartesian) for i,site in enumerate(sites)]} raise RuntimeError(f'unsupported backend {b!r}') def get_composition_inf(structure: Any, *, backend: str='auto') -> dict[str, Any]: b=dispatch_structure_backend(structure, backend) if b == 'pymatgen': c=structure.composition; elems=[] for el,amt in c.items(): d={'symbol':getattr(el,'symbol',str(el)),'amount':float(amt)} try: d['Z']=int(el.Z) except Exception: pass elems.append(d) ret={'backend':'pymatgen','formula':c.formula,'alphabetical_formula':c.alphabetical_formula, 'reduced_formula':c.reduced_formula,'num_atoms':float(c.num_atoms), 'elements':elems,'as_dict':{str(k):float(v) for k,v in c.as_dict().items()}} for name in ['chemical_system','anonymized_formula']: try: ret[name]=getattr(c,name) except Exception: pass return ret raise RuntimeError(f'unsupported backend {b!r}') def _site_mass(site: Any) -> tuple[float,float]: occ_total=0.0; mass=0.0 for sp,amt in site.species.items(): occ=float(amt); occ_total += occ try: mass += occ*float(sp.atomic_mass) except Exception: pass return occ_total, mass def get_density_inf(structure: Any, *, backend: str='auto') -> dict[str, Any]: b=dispatch_structure_backend(structure, backend) if b == 'pymatgen': eff=0.0; mass_amu=0.0 for site in structure.sites: o,m=_site_mass(site); eff+=o; mass_amu+=m vol=float(structure.volume); mass_g=mass_amu*AMU_TO_G; vol_cm3=vol*ANG3_TO_CM3 ret={'backend':'pymatgen','n_sites':len(structure.sites),'effective_atoms':eff, 'total_mass_amu':mass_amu,'volume_ang3':vol, 'atomic_density_atom_per_ang3': eff/vol if vol>0 else None, 'mass_density_g_cm3': mass_g/vol_cm3 if vol_cm3>0 else None} try: ret['pymatgen_density_g_cm3']=float(structure.density) except Exception: pass return ret raise RuntimeError(f'unsupported backend {b!r}') def get_crystal_inf(structure: Any, *, backend: str='auto', include_sites=True, max_sites: int|None=None, include_symmetry=True, symprec: float=1e-3) -> dict[str, Any]: b=dispatch_structure_backend(structure, backend) if b != 'pymatgen': raise RuntimeError(f'unsupported backend {b!r}') ret={'backend':'pymatgen','source_type':type(structure).__name__, 'composition':get_composition_inf(structure,backend='pymatgen'), 'lattice':get_lattice_inf(structure,backend='pymatgen'), 'density':get_density_inf(structure,backend='pymatgen'), 'charge':safe_float(getattr(structure,'charge',None)), 'is_ordered':bool(getattr(structure,'is_ordered',False))} if include_sites: ret['site_info']=get_site_inf(structure,backend='pymatgen',max_sites=max_sites) if include_symmetry: try: from .symmetry import get_spg_inf ret['spacegroup']=get_spg_inf(structure,backend='pymatgen',symprec=symprec) except Exception as exc: ret['spacegroup']={'ok':False,'error':f'{type(exc).__name__}: {exc}'} return ret def get_neighbor_inf(structure: Any, *, site_index: int=0, radius: float=5.0, backend: str='auto') -> dict[str, Any]: b=dispatch_structure_backend(structure, backend) if b == 'pymatgen': idx=int(site_index); center=structure.sites[idx]; nbs=structure.get_neighbors(center, float(radius)) return {'backend':'pymatgen','site_index':idx,'center':_site_to_dict(center,idx), 'radius':float(radius),'n_neighbors':len(nbs), 'neighbors':[{'index':i,'species_string':str(nn.species_string),'distance':float(nn.nn_distance), 'frac_coords':[float(x) for x in nn.frac_coords],'cart_coords':[float(x) for x in nn.coords]} for i,nn in enumerate(nbs)]} raise RuntimeError(f'unsupported backend {b!r}')