new output

.idea/.gitignore

@@ -0,0 +1,8 @@
+# Default ignored files
+/shelf/
+/workspace.xml
+# Editor-based HTTP Client requests
+/httpRequests/
+# Datasource local storage ignored files
+/dataSources/
+/dataSources.local.xml

.idea/inspectionProfiles/Project_Default.xml

@@ -0,0 +1,62 @@
+<component name="InspectionProjectProfileManager">
+  <profile version="1.0">
+    <option name="myName" value="Project Default" />
+    <inspection_tool class="PyCompatibilityInspection" enabled="true" level="WARNING" enabled_by_default="true">
+      <option name="ourVersions">
+        <value>
+          <list size="2">
+            <item index="0" class="java.lang.String" itemvalue="3.9" />
+            <item index="1" class="java.lang.String" itemvalue="3.11" />
+          </list>
+        </value>
+      </option>
+    </inspection_tool>
+    <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
+      <option name="ignoredPackages">
+        <value>
+          <list size="25">
+            <item index="0" class="java.lang.String" itemvalue="numpy" />
+            <item index="1" class="java.lang.String" itemvalue="pandas" />
+            <item index="2" class="java.lang.String" itemvalue="symengine" />
+            <item index="3" class="java.lang.String" itemvalue="gpyopt" />
+            <item index="4" class="java.lang.String" itemvalue="matplotlib" />
+            <item index="5" class="java.lang.String" itemvalue="pennylane" />
+            <item index="6" class="java.lang.String" itemvalue="torch" />
+            <item index="7" class="java.lang.String" itemvalue="ase" />
+            <item index="8" class="java.lang.String" itemvalue="wget" />
+            <item index="9" class="java.lang.String" itemvalue="kahypar" />
+            <item index="10" class="java.lang.String" itemvalue="certifi" />
+            <item index="11" class="java.lang.String" itemvalue="tensorly-torch" />
+            <item index="12" class="java.lang.String" itemvalue="scipy" />
+            <item index="13" class="java.lang.String" itemvalue="setuptools" />
+            <item index="14" class="java.lang.String" itemvalue="tensorly" />
+            <item index="15" class="java.lang.String" itemvalue="evaluate" />
+            <item index="16" class="java.lang.String" itemvalue="transformers" />
+            <item index="17" class="java.lang.String" itemvalue="fastapi" />
+            <item index="18" class="java.lang.String" itemvalue="gradio" />
+            <item index="19" class="java.lang.String" itemvalue="uvicorn" />
+            <item index="20" class="java.lang.String" itemvalue="Requests" />
+            <item index="21" class="java.lang.String" itemvalue="datasets" />
+            <item index="22" class="java.lang.String" itemvalue="torchvision" />
+            <item index="23" class="java.lang.String" itemvalue="memory_profiler" />
+            <item index="24" class="java.lang.String" itemvalue="mendeleev" />
+          </list>
+        </value>
+      </option>
+    </inspection_tool>
+    <inspection_tool class="PyPep8Inspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
+      <option name="ignoredErrors">
+        <list>
+          <option value="E701" />
+        </list>
+      </option>
+    </inspection_tool>
+    <inspection_tool class="PyUnresolvedReferencesInspection" enabled="true" level="WARNING" enabled_by_default="true">
+      <option name="ignoredIdentifiers">
+        <list>
+          <option value="six.xrange" />
+        </list>
+      </option>
+    </inspection_tool>
+  </profile>
+</component>

.idea/inspectionProfiles/profiles_settings.xml

@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

.idea/latmatcher.iml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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">
+    <option name="format" value="PLAIN" />
+    <option name="myDocStringFormat" value="Plain" />
+  </component>
+</module>

.idea/misc.xml

@@ -0,0 +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>

.idea/modules.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/latmatcher.iml" filepath="$PROJECT_DIR$/.idea/latmatcher.iml" />
+    </modules>
+  </component>
+</project>

.idea/vcs.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="Git" />
+  </component>
+</project>

app.py

@@ -22,6 +22,7 @@ with gr.Blocks() as latmatcher:
 
             max_angle = gr.Slider(0, 180, label=" max 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)
 
             msc_button = gr.Button("Compute minimum super cel")
 
@@ -31,10 +32,12 @@ with gr.Blocks() as latmatcher:
 
             plot_overlap = gr.Plot()
 
+            file_txt = gr.Text(label="Result:", info=" You can use the text below to create a 3D plot in Speck \n(high-quality atomistic system rendering).")
+
             msc_button.click(compute_supercell_a,
-                             inputs=[file_material_a, file_material_b, file_source_a, file_source_b, max_angle,
+                             inputs=[file_material_a, file_material_b, inter_distance, max_angle,
                                      max_strain],
-                             outputs=[file_material_ab, file_angle, file_strain, plot_overlap])
+                             outputs=[file_material_ab, file_angle, file_strain, plot_overlap, file_txt])
 
         with gr.TabItem(label="data"):
             with gr.Row():

interface_connection/latmatcher_interface.py

@@ -32,7 +32,7 @@ def get_atomic_number(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):
+def compute_supercell_a(file_material_a, file_material_b,inter_distance , max_angle, max_strain):
 
 
     #
@@ -105,7 +105,7 @@ def compute_supercell_a(file_material_a, file_material_b, file_source_a, file_so
 
 
     plot=plot_supercel(super_xyz, min_supercel)
-    return file12, str(rez[0]), str((rez[1], rez[2])),plot
+    return file12, str(rez[0]), str((rez[1], rez[2])),plot, xyz_content
 
 def compute_supercell_b():
     pass