Update interface_connection/latmatcher_interface.py

interface_connection/latmatcher_interface.py

@@ -6,6 +6,8 @@ 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
@@ -49,6 +51,11 @@ def compute_supercell_a(file_material_a, file_material_b, file_source_a, file_so
     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"]
@@ -164,32 +171,19 @@ def extract_from_xyz(file):
                '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']
 
+    atoms = read(file)
+    lattice_vectors = atoms.cell
+    atom_symbols = atoms.get_chemical_symbols()
+    positions = atoms.get_positions()
 
-    structure["cell"]=np.array([[lattice[0][0], lattice[0][1], 0],
-                                [lattice[1][0], lattice[1][1], 0],
+    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]])
-
-
-    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
-
-
+    structure['atoms'] = [get_atomic_number(element_symbol) for element_symbol  in atom_symbols]
+    structure['positions'] = positions
+    print(structure)
 
     return structure