Delete interface_connection

interface_connection/__init__.py

@@ -1,3 +0,0 @@
-
-from .latmatcher_interface import compute_supercell, compute_supercell_a, compute_supercell_b
-from .gpaw_interface import gpaw_calc_energy

interface_connection/gpaw_interface.py

@@ -1,66 +0,0 @@
-from gpaw import GPAW
-import periodictable
-from .latmatcher_interface import extract_from_xyz, process_file, extract_from_bespoke
-from backend.soft_gpaw.experiment import bespoke_structure_to_ase
-
-
-def get_atomic_number(element_name):
-    # Find the element
-    element = getattr(periodictable, element_name, None)
-
-    # Check if the element exists
-    if element is not None and hasattr(element, 'number'):
-        return element.number
-    else:
-        return "Element not found"
-
-
-def gpaw_calc_energy(file_gpaw_format,
-                     file_gpaw,
-                     convergence_forces,
-                     hund,
-                     xc, basis,
-                     beta, method,
-                     weight, backend,
-                     ecut, mode_name,
-                     maxiter, kpts,
-                     log_file_name, mail):
-    path_to_move = "/Users/voicutomut/Documents/GitHub/BespokeMaterials/DB/OnlineGPAW"
-    # https://wiki.fysik.dtu.dk/gpaw/documentation/basic.html
-
-    # TODO: ad proper kpts:
-    kpts = None
-    mode = {"name": mode_name,
-            "ecut": ecut}
-    mixer = {"beta": beta, "method": method,
-             "weight": weight, "backend": backend}
-    poissonsolver = {}#{'dipolelayer': 'xy',}
-
-    log_file_name = path_to_move + "/{}".format(log_file_name)
-    calc = GPAW(mode=mode,
-                xc=xc,
-                basis=basis,
-                convergence={'forces': convergence_forces},
-                poissonsolver=poissonsolver,
-                hund=hund,
-                mixer=mixer,
-                maxiter=maxiter,
-                txt=log_file_name,
-
-                )
-
-    file1 = process_file(file_gpaw, path_to_move + "/")
-    if file_gpaw_format == ".xyz":
-        structure = extract_from_xyz(file1)
-    elif file_gpaw_format == "bespoke.json":
-        structure = extract_from_bespoke(file1)
-
-    print("structure:", structure)
-    lattice = bespoke_structure_to_ase(b_structure=structure)
-    print("lattice", lattice)
-
-    lattice.calc = calc
-
-    energy = lattice.get_potential_energy()
-
-    return energy

interface_connection/latmatcher_interface.py

@@ -1,191 +0,0 @@
-
-
-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
-
-
-import matplotlib.pyplot as plt
-import matplotlib.patches as patches
-import os
-import shutil
-import numpy as np
-import periodictable
-import ast
-
-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, file_source_a, file_source_b, max_angle, max_strain):
-
-
-    #
-    ip = "test_ip"  # get_client_ip(response)
-
-    db_latmatcher_path = "/Users/voicutomut/Documents/GitHub/BespokeMaterials/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+"/")
-
-
-    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"]
-
-
-    super_xyz, min_supercel= compute_supercell(A_cell, B_cell, A_structure, B_structure )
-    rez=min_supercel.rez
-
-    # Write the new file:
-    name = "solution"
-    file12 = path_to_move + "/" + name + ".xyz"
-
-    xyz_content = "{"+"'lattice_vectors':{}".format(np.array2string(min_supercel.get_new_structure()['lattice_vectors'],
-                                                                  separator=', ',
-                                                                   max_line_width=np.inf).replace("\n"," "))+"}\n\n"
-
-    xyz_content += f"{len(super_xyz)}\n\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
-
-def compute_supercell_b():
-    pass
-
-def compute_supercell(A_cell, B_cell,A_structure,B_structure ):
-
-    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()
-    super_xyz = structure_ato_list(new_structure)
-    return super_xyz,    min_supercel
-
-
-
-
-def  plot_supercel(super_xyz, min_supercel):
-    fig = plt.figure()
-    new_structure=min_supercel.get_new_structure()
-    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] }
-
-    with open(file, 'r') as xyz_file:
-        lines = xyz_file.readlines()[4:]  # Skipping the first two line
-
-    with open(file, 'r') as xyz_file:
-        dict_string = xyz_file.readlines()[:1][0]
-        print(dict_string)
-
-
-    lattice = ast.literal_eval(dict_string)['lattice_vectors']
-
-
-    structure["cell"]=np.array([[lattice[0][0], lattice[0][1], 0],
-                                [lattice[1][0], lattice[1][1], 0],
-                                [0,0,1]])
-
-
-    atom_xyz=np.array([line.split()[1:4] for line in lines], dtype=float)
-
-    atomic_symbols = []
-    for line in lines:
-        atomic_symbols.append(line.split()[0])
-    structure['atoms']=[get_atomic_number(element_symbol) for element_symbol  in atomic_symbols]
-
-    structure['positions']=atom_xyz
-
-
-
-    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