interatomic distance

backend/latmathcher/pipeline.py

@@ -97,7 +97,7 @@ class PipelineLatMatch:
 
         return self.superA_xyz, self.superB_xyz
 
-    def get_new_structure(self):
+    def get_new_structure(self, inter_distance=[0,0,0]):
 
         structure = {"atoms": [],
                      "lattice_vectors": self.sc_vec3,
@@ -124,6 +124,8 @@ class PipelineLatMatch:
         for element in superB_xyz:
             structure["host_guest"].append("guest")
             symbol = element[0]
+            pos=element[1].tolist()+inter_distance
+
             positions.append(element[1].tolist())
             atomic_number = getattr(periodictable, symbol)
             if atomic_number is not None:

interface_connection/latmatcher_interface.py

@@ -80,8 +80,8 @@ def compute_supercell_a(file_material_a, file_material_b,inter_distance , max_an
         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 )
+    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:
@@ -110,13 +110,13 @@ def compute_supercell_a(file_material_a, file_material_b,inter_distance , max_an
 def compute_supercell_b():
     pass
 
-def compute_supercell(A_cell, B_cell,A_structure,B_structure ):
+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()
+    new_structure = min_supercel.get_new_structure(inter_distance)
     super_xyz = structure_ato_list(new_structure)
     return super_xyz,    min_supercel