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Andrei tomut commited on May 1

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1fcd924

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1 Parent(s): c8c4db0

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Files changed (25) hide show

.idea/latmatcher.iml +1 -1
.idea/misc.xml +1 -1
Example_LatmatherExample.py +10 -4
app.py +1 -1
backend/__pycache__/__init__.cpython-310.pyc +0 -0
backend/__pycache__/__init__.cpython-38.pyc +0 -0
backend/db_utils/__pycache__/__init__.cpython-310.pyc +0 -0
backend/db_utils/__pycache__/parse_c2db.cpython-310.pyc +0 -0
backend/db_utils/__pycache__/parse_jarvis.cpython-310.pyc +0 -0
backend/db_utils/__pycache__/structure_database.cpython-310.pyc +0 -0
backend/db_utils/__pycache__/structure_propriety.cpython-310.pyc +0 -0
backend/db_utils/__pycache__/utils.cpython-310.pyc +0 -0
backend/db_utils/vasp_utils/__pycache__/__init__.cpython-310.pyc +0 -0
backend/db_utils/vasp_utils/__pycache__/band_structure.cpython-310.pyc +0 -0
backend/latmathcher/__pycache__/__init__.cpython-310.pyc +0 -0
backend/latmathcher/__pycache__/__init__.cpython-38.pyc +0 -0
backend/latmathcher/__pycache__/geometry.cpython-310.pyc +0 -0
backend/latmathcher/__pycache__/geometry.cpython-38.pyc +0 -0
backend/latmathcher/__pycache__/latmatcher.cpython-310.pyc +0 -0
backend/latmathcher/__pycache__/latmatcher.cpython-38.pyc +0 -0
backend/latmathcher/__pycache__/pipeline.cpython-310.pyc +0 -0
backend/latmathcher/__pycache__/pipeline.cpython-38.pyc +0 -0
backend/latmathcher/__pycache__/plots.cpython-310.pyc +0 -0
backend/latmathcher/__pycache__/utils.cpython-310.pyc +0 -0
interface_connection/latmatcher_interface.py +5 -3

.idea/latmatcher.iml CHANGED Viewed

@@ -2,7 +2,7 @@
 <module type="PYTHON_MODULE" version="4">
   <component name="NewModuleRootManager">
     <content url="file://$MODULE_DIR$" />
-    <orderEntry type="inheritedJdk" />
     <orderEntry type="sourceFolder" forTests="false" />
   </component>
   <component name="PyDocumentationSettings">

 <module type="PYTHON_MODULE" version="4">
   <component name="NewModuleRootManager">
     <content url="file://$MODULE_DIR$" />
+    <orderEntry type="jdk" jdkName="BespokeMaterialsConda" jdkType="Python SDK" />
     <orderEntry type="sourceFolder" forTests="false" />
   </component>
   <component name="PyDocumentationSettings">

.idea/misc.xml CHANGED Viewed

@@ -1,4 +1,4 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.11 (latmatcher)" project-jdk-type="Python SDK" />
 </project>

 <?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="BespokeMaterialsConda" project-jdk-type="Python SDK" />
 </project>

Example_LatmatherExample.py CHANGED Viewed

@@ -10,10 +10,16 @@ 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))
@@ -21,12 +27,12 @@ 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()

 import matplotlib.patches as patches
+#
+# filepathA = "EXAMPLES/1WSe2-1.xyz"
+# filepathB = "EXAMPLES/2C2-1.xyz"
+filepathA = "/Users/voicutomut/Documents/GitLab/bespoke-interface/DB_experiments/C2DB_json_colection/WSe2-1cfbe6183886.json"
+filepathB = "/Users/voicutomut/Documents/GitLab/bespoke-interface/DB_experiments/C2DB_json_colection/C2-a6735a4a3797.json"
+A_structure = from_c2db_structure(read_c2db_json(filepathA))
+B_structure = from_c2db_structure(read_c2db_json(filepathB))
+print("Astr:",A_structure)
 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( dist=[0,0,0.1])

app.py CHANGED Viewed

@@ -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=" min Angle:", step=1, value=90)
             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)

                     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=" min Angle:", step=1, value=5)
             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)

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interface_connection/latmatcher_interface.py CHANGED Viewed

@@ -82,6 +82,7 @@ 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,
                                                               max_angle, max_strain )
     rez=min_supercel.rez
@@ -107,8 +108,9 @@ def compute_supercell_a(file_material_a, file_material_b,inter_distance , max_an
     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)
-    return file12, str(rez[0]), str((rez[1], rez[2])),plot, xyz_content_dd
 def compute_supercell_b():
     pass
@@ -137,8 +139,8 @@ def  plot_supercel(super_xyz, min_supercel):
     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)*3, max(y)*3)
-    plt.xlim(min(x)*3, max(x)*3)
     # 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

         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,
                                                               max_angle, max_strain )
     rez=min_supercel.rez
     atoms= atoms_to_greed(super_xyz, lat_v=min_supercel.sc_vec3, dim=(3,3,0))
     xyz_content_dd=generate_xyz_text(atoms)
+    # plot_atom_list(atoms, marker=".")
     plot=plot_supercel(super_xyz, min_supercel)
+    return file12, str(rez[2]), str((rez[0], rez[1])),plot, xyz_content_dd
 def compute_supercell_b():
     pass
     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)*3+1, max(y)*3+1)
+    plt.xlim(min(x)*3+1, max(x)*3+1)
     # 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