Programmatic usage
==================

Four-state pipeline (from a CIF)
--------------------------------

.. code-block:: python

   from mag4 import (
       run_cif_analysis, expand_supercell,
       find_dimers, build_reference_bath,
       generate_four_states, find_unique_configs,
       find_symmetry_ops,
   )
   from mag4.lattice import get_cartesian_coords

   crystal, couplings = run_cif_analysis("Gd2S3.cif", "Gd",
                                         cutoff=7.0, tol=0.01)
   crystal = expand_supercell(crystal, 2, 1, 1)

   atoms    = crystal.target_species
   ref_bath = build_reference_bath(len(atoms))
   dimers   = find_dimers(atoms, crystal.lattice_matrix, couplings, tol=0.05)

   cart    = get_cartesian_coords(atoms, crystal.lattice_matrix)
   sym_ops = find_symmetry_ops(cart, crystal.lattice_vectors)

   all_cfgs = []
   for name, _ in couplings:
       if dimers[name]:
           all_cfgs.extend(generate_four_states(ref_bath, dimers[name][0], name))

   unique = find_unique_configs(all_cfgs, sym_ops)
   print(f"{len(unique)} unique configurations to compute "
         f"(out of {len(all_cfgs)} raw)")

Multi-sublattice LSWT and T_c
-----------------------------

.. code-block:: python

   from pymatgen.core import Structure
   from mag4.io_cif import get_distance_shells
   from mag4.magnon import (
       get_sublattice_bonds, build_qmesh, build_jq_matrices,
       compute_eigenvalues_all_q, analyse_ordering,
       compute_tc, compute_tc_lswt,
   )

   shells   = get_distance_shells("Gd2O2S.cif", "Gd", cutoff=7.0)
   j_values = {"J1": 0.26, "J2": 0.26, "J3": 0.12}
   bonds    = get_sublattice_bonds("Gd2O2S.cif", "Gd", 7.0, shells, j_values)

   structure       = Structure.from_file("Gd2O2S.cif")
   q_cart, q_frac  = build_qmesh(structure, 30, 30, 20)
   Jq              = build_jq_matrices(bonds, q_cart)
   evals           = compute_eigenvalues_all_q(Jq)

   ordering = analyse_ordering(Jq, evals, q_frac, q_cart, structure)
   tc_lt    = compute_tc(evals, S=3.5, lam0=ordering["lam0"])
   tc_sw    = compute_tc_lswt(bonds, S=3.5, ordering_lt=ordering,
                              q_cart=q_cart, evals_lt=evals)

M – L – M angles
----------------

.. code-block:: python

   from pymatgen.core import Structure
   from mag4.analysis import (
       group_into_shells, find_bridging_angles,
   )
   from mag4.analysis.bond_angles import get_mm_pairs

   structure = Structure.from_file("Gd2S3.cif")
   pairs     = get_mm_pairs(structure, "Gd", cutoff=7.0)
   shells    = group_into_shells(pairs)
   for shell in shells:
       for p in shell["pairs"]:
           angles = find_bridging_angles(
               structure, p["site_i"], p["site_j"], p["image"],
               ligand_elements=["S"], bond_cutoff=3.5)

WIEN2k moment extraction
------------------------

.. code-block:: python

   from mag4.analysis import find_cases, build_table

   cases = find_cases(".")
   table = build_table(cases, atom_indices=list(range(9, 17)))
   print("\\n".join(table))