angle+

Example_LatmatherExample.py

@@ -0,0 +1,52 @@
+import os
+os.environ['KMP_DUPLICATE_LIB_OK']='True'
+
+from backend.latmathcher import PipelineLatMatch
+from backend.db_utils.parse_c2db import from_c2db_structure, read_c2db_json
+from backend.db_utils.utils import structure_ato_list
+from backend.latmathcher.plots import plot_atom_list
+from backend.latmathcher import atoms_to_greed
+import matplotlib.pyplot as plt
+import matplotlib.patches as patches
+
+
+
+filepathA = "EXAMPLES/WSe2-1cfbe6183886.json"
+filepathB = "EXAMPLES/C2-a6735a4a3797.json"
+
+
+A_structure = from_c2db_structure(read_c2db_json(filepathA))
+B_structure = from_c2db_structure(read_c2db_json(filepathB))
+
+min_supercel = PipelineLatMatch(A_structure["cell"],B_structure["cell"],
+                                Aatoms3D=structure_ato_list(A_structure),
+                                Batoms3D=structure_ato_list(B_structure),
+                                dim=(10, 10), optimize_angle=True, optimize_strain=True)
+
+
+print(min_supercel.Alat)
+print(min_supercel.Blat)
+new_structure = min_supercel.get_new_structure()
+
+
+
+super_xyz = structure_ato_list(new_structure)
+
+atoms = atoms_to_greed(super_xyz, lat_v=min_supercel.sc_vec3, dim=(10,10,0))
+print(atoms)
+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(min(y) - 10, max(y) + 10)
+plt.xlim(min(x) - 10, max(x) + 10)
+
+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"]
+
+plt.show()
+print(min_supercel.sc_vec)
+print(min_supercel.Alat)
+print(min_supercel.Blat)
+print(new_structure)
+plt.show()

app.py

@@ -18,7 +18,7 @@ with gr.Blocks() as latmatcher:
                     example_file_b = gr.File(label="example file:",value="EXAMPLES/2C-1.xyz" )
                     file_material_b = gr.File(label="material B file", )
 
-            max_angle = gr.Slider(0, 180, label=" max Angle:", step=1)
+            max_angle = gr.Slider(0, 180, label=" min Angle:", step=1)
             max_strain = gr.Slider(0, 1, label=" max Strain:", step=0.05)
             inter_distance = gr.Slider(-0.05, 10, label=" Inter-layer distance:",info="If set to -0.05 is computed automatically.", step=0.05)
 

backend/latmathcher/pipeline.py

@@ -8,7 +8,7 @@ from .latmatcher import LatMatch, SR
 class PipelineLatMatch:
 
     def __init__(self, Alat3D, Blat3D, Aatoms3D=None, Batoms3D=None, dim=10, sc_vec=None, optimize_angle=True,
-                 optimize_strain=True, dz=4):
+                 optimize_strain=True, dz=4, min_angle=5 * np.pi / 180, max_strain=0.1):
 
         self.Alat3D = Alat3D
         self.Blat3D = Blat3D
@@ -24,6 +24,8 @@ class PipelineLatMatch:
         else:
             self.matcher4 = LatMatch(scdim=dim, reference=self.Alat, target=self.Blat,
                                      optimize_angle=optimize_angle, optimize_strain=optimize_strain)
+            self.matcher4.setMaxStrain([max_strain, max_strain])
+            self.matcher4.setMaxStrain(min_angle)
             self.sc_vec = self.matcher4.supercell()
             self.rez = self.matcher4.result
 

interface_connection/latmatcher_interface.py

@@ -82,7 +82,8 @@ def compute_supercell_a(file_material_a, file_material_b,inter_distance , max_an
         B_cell=B_structure["cell"]
 
     inter_distance=[0,0,inter_distance]
-    super_xyz, min_supercel, new_structure= compute_supercell(A_cell, B_cell, A_structure, B_structure, inter_distance )
+    super_xyz, min_supercel, new_structure= compute_supercell(A_cell, B_cell, A_structure, B_structure, inter_distance,
+                                                              max_angle, max_strain )
     rez=min_supercel.rez
 
     # Write the new file:
@@ -103,7 +104,7 @@ def compute_supercell_a(file_material_a, file_material_b,inter_distance , max_an
     # Write the content to a file
     with open(file12, 'w') as file:
         file.write(xyz_content)
-    atoms= atoms_to_greed(super_xyz, lat_v=min_supercel.sc_vec3, dim=(5,5,0))
+    atoms= atoms_to_greed(super_xyz, lat_v=min_supercel.sc_vec3, dim=(3,3,0))
     xyz_content_dd=generate_xyz_text(atoms)
 
     plot=plot_supercel(super_xyz, min_supercel)
@@ -112,11 +113,11 @@ 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,inter_distance ):
-
+def compute_supercell(A_cell, B_cell,A_structure,B_structure,inter_distance,min_angle, max_strain):
+    min_angle=min_angle/180*np.pi
     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)
+                                    optimize_strain=True,min_angle=min_angle, max_strain=max_strain)
 
     new_structure = min_supercel.get_new_structure(inter_distance)
     super_xyz = structure_ato_list(new_structure)