/
structure_creator.py
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/
structure_creator.py
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import numpy as np
import warnings
import os
from pyscal.atoms import Atoms
from pyscal.attributes import read_yaml
structures = read_yaml(os.path.join(os.path.dirname(__file__), "data/structure_data.yaml"))
def make_crystal(structure, lattice_constant = 1.00, repetitions = None, ca_ratio = 1.633, noise = 0, element=None,
return_structure_dict=False):
"""
Create a basic crystal structure and return it as a list of `Atom` objects
and box dimensions.
Parameters
----------
structure : {'sc', 'bcc', 'fcc', 'hcp', 'diamond', 'a15' or 'l12'}
type of the crystal structure
lattice_constant : float, optional
lattice constant of the crystal structure, default 1
repetitions : list of ints of len 3, optional
of type `[nx, ny, nz]`, repetions of the unit cell in x, y and z directions.
default `[1, 1, 1]`.
ca_ratio : float, optional
ratio of c/a for hcp structures, default 1.633
noise : float, optional
If provided add normally distributed noise with standard deviation `noise` to the atomic positions.
Returns
-------
atoms : list of `Atom` objects
list of all atoms as created by user input
box : list of list of floats
list of the type `[[xlow, xhigh], [ylow, yhigh], [zlow, zhigh]]` where each of them are the lower
and upper limits of the simulation box in x, y and z directions respectively.
Examples
--------
>>> atoms, box = make_crystal('bcc', lattice_constant=3.48, repetitions=[2,2,2])
>>> sys = System()
>>> sys.assign_atoms(atoms, box)
"""
if repetitions == None:
nx = 1
ny = 1
nz = 1
elif isinstance(repetitions, int):
nx = repetitions
ny = repetitions
nz = repetitions
else:
nx = repetitions[0]
ny = repetitions[1]
nz = repetitions[2]
if structure in structures.keys():
sdict = structures[structure]
else:
raise ValueError("Unknown crystal structure")
unique_types = np.unique(sdict["species"])
print(element)
if element is not None:
if isinstance(element, str):
element = [element]
if not (len(element) == len(unique_types)):
raise ValueError("Elements should equal number of species in the system")
element_dict = dict([x for x in zip(unique_types, element)])
else:
element = [None for x in range(len(unique_types))]
element_dict = dict([x for x in zip(unique_types, element)])
m = 0
co = 1
natoms = sdict["natoms"]*nx*ny*nz
positions = []
types = []
ids = []
species = []
xh = nx*lattice_constant*sdict["scaling_factors"][0]
yh = ny*lattice_constant*sdict["scaling_factors"][1]
zh = nz*lattice_constant*sdict["scaling_factors"][2]
box = [[xh, 0, 0], [0, yh, 0], [0, 0, zh]]
#create structure
for i in range(1, nx+1):
for j in range(1, ny+1):
for k in range(1, nz+1):
for l in range(1, sdict["natoms"]+1):
m += 1
posx = ((lattice_constant*sdict["positions"][l-1][0])+(lattice_constant*sdict["scaling_factors"][0]*(float(i)-1)))
posy = ((lattice_constant*sdict["positions"][l-1][1])+(lattice_constant*sdict["scaling_factors"][1]*(float(j)-1)))
posz = ((lattice_constant*sdict["positions"][l-1][2])+(lattice_constant*sdict["scaling_factors"][2]*(float(k)-1)))
if noise > 0:
posx = np.random.normal(loc=posx, scale=noise)
posy = np.random.normal(loc=posy, scale=noise)
posz = np.random.normal(loc=posz, scale=noise)
positions.append([posx, posy, posz])
ids.append(co)
types.append(sdict["species"][l-1])
species.append(element_dict[sdict["species"][l-1]])
co += 1
atoms = {}
atoms['positions'] = positions
atoms['ids'] = ids
atoms['types'] = types
atoms['species'] = species
atoms['ghost'] = [False for x in range(len(types))]
patoms = Atoms()
patoms.from_dict(atoms)
if return_structure_dict:
return patoms, box, sdict
return patoms, box
def _update_list_of_elements():
"""
Only run when needed to update database
"""
import mendeleev
from mendeleev import element
el_list = dir(mendeleev)
el_dict = {}
for el in el_list:
if len(el) == 2:
if el=="db":
break
chem = element(el)
struct = chem.lattice_structure
lc = chem.lattice_constant
if (struct is not None) and (lc is not None):
if struct.lower() in ['sc', 'bcc', 'fcc', 'hex', 'dia']:
el_dict[el] = {}
if struct.lower() == "dia":
struct = "diamond"
elif struct.lower() == "hex":
struct = "hcp"
el_dict[el]["structure"] = str(struct.lower())
el_dict[el]["lattice_constant"] = float(lc)
return el_dict