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from backend.latmathcher.plots import plot_atom_list
from backend.latmathcher import atoms_to_greed
from backend.latmathcher import PipelineLatMatch
from backend.db_utils.utils import structure_ato_list
from backend.db_utils.parse_c2db import from_c2db_structure, read_c2db_json
from backend.db_utils.structure_database import DBInstance
from ase.io import read
from CifFile import ReadCif
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import os
import shutil
import numpy as np
import periodictable
import ast
def create_directory(directory_path):
if not os.path.exists(directory_path):
os.makedirs(directory_path)
print(f"Directory '{directory_path}' created successfully.")
else:
print(f"Directory '{directory_path}' already exists.")
def get_atomic_number(element_symbol):
# Find the element in the periodic table and return its atomic number
element = getattr(periodictable, element_symbol)
return element.number
def compute_supercell_a(file_material_a, file_material_b,inter_distance , max_angle, max_strain):
#
ip = "test_ip" # get_client_ip(response)
db_latmatcher_path = "DB/LatMatcher"
create_directory("DB")
create_directory("DB/LatMatcher")
new_directory = db_latmatcher_path + "/{}__ma{}__ms{}_on{}".format(ip, max_angle, max_strain,
len(os.listdir(db_latmatcher_path)))
if not os.path.exists(new_directory):
os.makedirs(new_directory)
path_to_move = new_directory
file1 = process_file(file_material_a, path_to_move+"/")
file2 = process_file(file_material_b, path_to_move+"/")
file_source_a="."+file1.split(".")[-1]
file_source_b = "."+file2.split(".")[-1]
print("fa, fb:",file_source_a, file_source_b)
if file_source_a == "c2db.json":
A_structure = from_c2db_structure(read_c2db_json(file1))
A_cell=A_structure["cell"]
if file_source_b == "c2db.json":
B_structure = from_c2db_structure(read_c2db_json(file2))
B_cell=B_structure["cell"]
if file_source_a == ".xyz":
A_structure = extract_from_xyz(file1)
A_cell = A_structure["cell"]
if file_source_b == ".xyz":
B_structure = extract_from_xyz(file2)
B_cell=B_structure["cell"]
if file_source_a == "bespoke.json":
A_structure = extract_from_bespoke(file1)
A_cell = A_structure["cell"]
if file_source_b == "bespoke.json":
B_structure = extract_from_bespoke(file2)
B_cell=B_structure["cell"]
inter_distance=[0,0,inter_distance]
super_xyz, min_supercel= compute_supercell(A_cell, B_cell, A_structure, B_structure, inter_distance )
rez=min_supercel.rez
# Write the new file:
name = "solution"
file12 = path_to_move + "/" + name + ".xyz"
xyz_content = f"{len(super_xyz)}\n"
xyz_content +="Lattice=\"{}\"".format(np.array2string(min_supercel.get_new_structure()['lattice_vectors'],
separator=', ',
max_line_width=np.inf).replace("\n"," ").replace("[","").replace("]","").replace(",",""))+" pbc=\"T T F\""+"\n"
xyz_content += "\n".join([f"{atom[0]} {' '.join(map(str, atom[1]))}" for atom in super_xyz])
# Write the content to a file
with open(file12, 'w') as file:
file.write(xyz_content)
plot=plot_supercel(super_xyz, min_supercel)
return file12, str(rez[0]), str((rez[1], rez[2])),plot, xyz_content
def compute_supercell_b():
pass
def compute_supercell(A_cell, B_cell,A_structure,B_structure,inter_distance ):
min_supercel = PipelineLatMatch(A_cell, B_cell, Aatoms3D=structure_ato_list(A_structure),
Batoms3D=structure_ato_list(B_structure), dim=(10, 10), optimize_angle=True,
optimize_strain=True)
new_structure = min_supercel.get_new_structure(inter_distance)
super_xyz = structure_ato_list(new_structure)
return super_xyz, min_supercel
def plot_supercel(super_xyz, min_supercel):
fig = plt.figure()
atoms = atoms_to_greed(super_xyz, lat_v=min_supercel.sc_vec3, dim=(10, 10, 0))
plot_atom_list(atoms, marker=".")
x = [0.0, min_supercel.sc_vec3[0][0], min_supercel.sc_vec3[0][0] + min_supercel.sc_vec3[0][1],
min_supercel.sc_vec3[0][1], 0.0]
y = [0.0, min_supercel.sc_vec3[1][0], min_supercel.sc_vec3[1][0] + min_supercel.sc_vec3[1][1],
min_supercel.sc_vec3[1][1], 0.0]
plt.gca().add_patch(patches.Polygon(xy=list(zip(x, y)), fill=True, alpha=0.4, color="green"))
plt.ylim(-15, 15)
plt.xlim(-10, 20)
# super_a = [super_xyz[i] for i in range(len(new_structure["host_guest"])) if
# new_structure["host_guest"][i] == "host"]
# super_b = [super_xyz[i] for i in range(len(new_structure["host_guest"])) if
# new_structure["host_guest"][i] == "guest"]
#
# atoms = atoms_to_greed(super_a, lat_v=min_supercel.sc_vec3, dim=(10, 10, 0))
# plot_atom_list(atoms, marker=".")
# atoms = atoms_to_greed(super_b, lat_v=min_supercel.sc_vec3, dim=(10, 10, 0))
# plot_atom_list(atoms, marker="*")
#
# x = [0.0, min_supercel.sc_vec3[0][0], min_supercel.sc_vec3[0][0] + min_supercel.sc_vec3[0][1],
# min_supercel.sc_vec3[0][1], 0.0]
# y = [0.0, min_supercel.sc_vec3[1][0], min_supercel.sc_vec3[1][0] + min_supercel.sc_vec3[1][1],
# min_supercel.sc_vec3[1][1], 0.0]
# plt.gca().add_patch(patches.Polygon(xy=list(zip(x, y)), fill=True, alpha=0.4, color="green"))
# plt.ylim(-15, 15)
# plt.xlim(-15, 15)
return fig
# Utility tools for working with files
def file_json(file_path):
file = file_path.split("/")[-1]
ext = file.split(".")[-1]
if ext == "json":
return True
else:
return False
def get_file_name(file_path):
file = file_path.split("/")[-1]
file_name = file.split(".")[-2]
return file_name
def process_file(fileobj, path_to_move):
file_path = path_to_move + os.path.basename(fileobj.name)
shutil.copyfile(fileobj.name, file_path)
return file_path
def extract_from_xyz(file):
structure={'cell':[], 'atoms':[],
'positions':[],
"pbc":[ True, True, False] }
atoms = read(file)
lattice_vectors = atoms.cell
atom_symbols = atoms.get_chemical_symbols()
positions = atoms.get_positions()
structure["cell"] = np.array([[lattice_vectors[0][0], lattice_vectors[0][1], 0],
[lattice_vectors[1][0], lattice_vectors[1][1], 0],
[0,0,1]])
structure['atoms'] = [get_atomic_number(element_symbol) for element_symbol in atom_symbols]
structure['positions'] = positions
print(structure)
return structure
def extract_from_bespoke(file):
read_element = DBInstance().from_json_file(file)
structure = read_element.structure
structure["cell"]=np.array(structure["cell"])
return structure |