6. pyclupan modules on ZDD construction¶

Initialization

from pyclupan.dd.dd_node import DDNodeHandler
from pyclupan.dd.dd_constructor import DDConstructor

# Number of sites in supercell and element occupation
n_expand = 4
n_sites = np.array([1,1,3]) * n_expand
elements_lattice = [[0,1],[0,1],[2,3]]

dd_handler = DDNodeHandler(n_sites=n_sites,
                           elements_lattice=elements_lattice)
dd_const = DDConstructor(dd_handler)

#. identifying lattice (primitive cell)

from mlptools.common.readvasp import Poscar
from mlptools.common.structure import Structure

lattice_prim = Poscar('POSCAR').get_structure_class()

Entire set of structures
```
gs = dd_const.one_of_k()
```

Restricting ZDD to structures a composition

comp = [1/2, 1/2, 2/3, 1/3] # or comp = [1/2, None, 2/3, None]
gs &= dd_const.composition(comp)

Nonequivalent derivative structures

from pyclupan.common.supercell import Supercell
from pyclupan.common.symmetry import get_permutation

H = np.array([[1,0,0],[0,2,0],[0,0,2]])

sup = Supercell(st_prim=lattice_prim, hnf=H)
lattice_sup = sup.get_supercell()

site_perm, site_perm_lt = get_permutation(lattice_sup,
                                          superperiodic=True,
                                          hnf=H)

gs = dd_const.one_of_k()
gs = dd_const.nonequivalent_permutations(site_perm, gs=gs)

Eliminating end members (imcomplete structures)
```
gs &= dd_const.no_endmembers()
```

Electroneutrality (Charge balance) in ionic structures

charge = [4,3,-4,-3]
gs = dd_const.charge_balance(charge, gs=gs, eps=1e-5)

Excluding stuctures including a cluster

# orb is the orbit of a cluster
orbit_dd = dd_handler.convert_to_orbit_dd(orb)
gs = dd_const.excluding_clusters(orbit_dd, gs=gs)

# Example
# orb can be obtained by find_orbits_supercell in Cluster class

from pyclupan.derivative.preamble import preamble_ds_enum_from_cluster_yaml

pre_data = preamble_ds_enum_from_cluster_yaml('clusters.yaml', n_expand)
dd_handler, lattice_prim, hnf_all, clusters_ele = pre_data

cluster_ids = [136]
for H in hnf_all:
    orbits = clusters_ele.find_orbits_supercell(lattice_sup,
                                                H, ids=cluster_ids)
    for orb in orbits:
        orbit_dd = dd_handler.convert_to_orbit_dd(orb)
        gs = dd_const.excluding_clusters(orbit_dd, gs=gs)

Generating structure lists

from pyclupan.common.io.yaml import Yaml
from pyclupan.derivative.derivative import DSSet

res = dd_handler.convert_graphs_to_labelings(gs)
active_labelings, inactive_labeling, active_sites, inactive_sites = res
ds_set = DSSet(active_labelings=active_labelings,
               inactive_labeling=inactive_labeling,
               active_sites=active_sites,
               inactive_sites=inactive_sites,
               primitive_cell=lattice_prim,
               n_expand=n_expand,
               elements=dd_handler.elements,
               comp=comp,
               hnf=H,
               supercell=lattice_sup,
               supercell_id=idx)

# or

res = dd_handler.convert_graphs_to_labelings(gs)
ds_set = DSSet(labelings_info=res,
               primitive_cell=st_prim,
               n_expand=n_expand,
               elements=dd_handler.elements,
               comp=comp,
               hnf=hnf,
               supercell=st_sup,
               supercell_id=idx)

ds_set_all = [ds_set]

# ds_set_all including multiple ds_set is possible to use
yaml = Yaml()
yaml.write_derivative_yaml(st_prim, ds_set_all, filename='derivative.yaml')
joblib.dump(ds_set_all, 'derivative.pkl', compress=3)

6. pyclupan modules on ZDD construction¶

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