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NdSiRu.cif

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+# generated using pymatgen
+data_NdSiRu
+_symmetry_space_group_name_H-M   P4/nmm
+_cell_length_a   4.22194715
+_cell_length_b   4.22194715
+_cell_length_c   6.93978618
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   129
+_chemical_formula_structural   NdSiRu
+_chemical_formula_sum   'Nd2 Si2 Ru2'
+_cell_volume   123.70056259
+_cell_formula_units_Z   2
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+  2  '-y+1/2, x+1/2, z'
+  3  '-x, -y, z'
+  4  'y+1/2, -x+1/2, z'
+  5  'x+1/2, -y+1/2, -z'
+  6  '-y, -x, -z'
+  7  '-x+1/2, y+1/2, -z'
+  8  'y, x, -z'
+  9  '-x+1/2, -y+1/2, -z'
+  10  'y, -x, -z'
+  11  'x+1/2, y+1/2, -z'
+  12  '-y, x, -z'
+  13  '-x, y, z'
+  14  'y+1/2, x+1/2, z'
+  15  'x, -y, z'
+  16  '-y+1/2, -x+1/2, z'
+loop_
+ _atom_type_symbol
+ _atom_type_oxidation_number
+  Nd2+  2.0
+  Si4-  -4.0
+  Ru2+  2.0
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Nd2+  Nd0  2  0.00000000  0.50000000  0.31849090  1
+  Si4-  Si1  2  0.00000000  0.50000000  0.82833210  1
+  Ru2+  Ru2  2  0.00000000  0.00000000  0.00000000  1

app.py

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+import gradio as gr
+from slices.core import SLICES
+from pymatgen.core.structure import Structure
+from pymatgen.io.cif import CifWriter
+from pymatgen.io.ase import AseAtomsAdaptor
+from ase.io import write as ase_write
+import tempfile
+from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+import os
+# Initialize SLICES backend
+backend = SLICES(relax_model="chgnet", fmax=0.4, steps=25)
+
+def wrap_structure(structure):
+    """Wrap all atoms back into the unit cell."""
+    for i, site in enumerate(structure):
+        frac_coords = site.frac_coords % 1.0
+        structure.replace(i, species=site.species, coords=frac_coords, coords_are_cartesian=False)
+    return structure
+
+def get_primitive_structure(structure):
+    """Convert the structure to its primitive cell."""
+    analyzer = SpacegroupAnalyzer(structure)
+    return analyzer.get_primitive_standard_structure()
+
+def visualize_structure(structure):
+    """Generate an image of the structure."""
+    atoms = AseAtomsAdaptor.get_atoms(structure)
+    with tempfile.NamedTemporaryFile(suffix='.png', delete=False) as temp_file:
+        ase_write(temp_file.name, atoms, format='png', rotation='10x,10y,10z')
+    return temp_file.name
+
+def process_structure(structure):
+    """Wrap and convert to primitive cell."""
+    structure = wrap_structure(structure)
+    return get_primitive_structure(structure)
+
+def cif_to_slices(cif_file):
+    try:
+        structure = Structure.from_file(cif_file.name)
+        structure = process_structure(structure)
+        slices_string = backend.structure2SLICES(structure)
+        image_file = visualize_structure(structure)
+        return slices_string, image_file, None, slices_string, slices_string  # Added another slices_string for aug_slices_input
+    except Exception as e:
+        return str(e), None, None, "", ""
+
+
+def slices_to_cif(slices_string):
+    try:
+        structure, energy = backend.SLICES2structure(slices_string)
+        structure = process_structure(structure)
+        with tempfile.NamedTemporaryFile(mode='w', suffix='.cif', delete=False) as temp_file:
+            CifWriter(structure).write_file(temp_file.name)
+        image_file = visualize_structure(structure)
+        return temp_file.name, image_file, f"Conversion successful. Energy: {energy:.4f} eV/atom"
+    except Exception as e:
+        return None, None, f"Conversion failed. Error: {str(e)}"
+
+def augment_and_canonicalize_slices(slices_string, num_augmentations):
+    try:
+        augmented_slices = backend.SLICES2SLICESAug_atom_order(slices_string,num=num_augmentations)
+        unique_augmented_slices = list(set(augmented_slices))
+        canonical_slices = list(set([backend.get_canonical_SLICES(s) for s in unique_augmented_slices]))
+        return augmented_slices, canonical_slices
+    except Exception as e:
+        return [], [], str(e)
+
+
+
+
+# Gradio interface
+with gr.Blocks() as iface:
+    gr.Markdown("# Crystal Structure and SLICES Converter", elem_classes=["center"])
+    with gr.Row(elem_classes=["center"]):
+        gr.Image("1.png", label="SLICES Representation", show_label=False, width=600, height=250)
+    gr.Markdown("SLICES provides a text-based encoding of crystal structures, allowing for efficient manipulation and generation of new materials.", elem_classes=["center"])
+    
+    with gr.Tab("CIF-SLICES Conversion"):
+        with gr.Row():
+            with gr.Column():
+                cif_input = gr.File(label="Upload CIF file", file_types=[".cif"], value="NdSiRu.cif")
+                convert_cif_button = gr.Button("Convert CIF to SLICES")
+                slices_input = gr.Textbox(label="Enter SLICES String")
+                convert_slices_button = gr.Button("Convert SLICES to CIF")
+            with gr.Column():
+                slices_output = gr.Textbox(label="SLICES String")
+                cif_output = gr.File(label="Download CIF", file_types=[".cif"])
+                conversion_status = gr.Textbox(label="Conversion Status")
+        with gr.Row():
+            cif_image = gr.Image(label="Original Structure")
+            slices_image = gr.Image(label="Converted Structure")
+    
+    with gr.Tab("SLICES Augmentation and Canonicalization"):
+        aug_slices_input = gr.Textbox(label="Enter SLICES String")
+        num_augmentations = gr.Slider(minimum=1, maximum=50, step=1, value=10, label="Number of Augmentations")
+        augment_button = gr.Button("Augment and Canonicalize")
+        aug_slices_output = gr.Textbox(label="Augmented SLICES Strings")
+        canon_slices_output = gr.Textbox(label="Canonical SLICES Strings")
+    
+    # Event handlers
+    convert_cif_button.click(
+        cif_to_slices,
+        inputs=[cif_input],
+        outputs=[slices_output, cif_image, conversion_status, slices_input, aug_slices_input]
+    )
+    convert_slices_button.click(
+        slices_to_cif,
+        inputs=[slices_input],
+        outputs=[cif_output, slices_image, conversion_status]
+    )
+    augment_button.click(
+        augment_and_canonicalize_slices,
+        inputs=[aug_slices_input, num_augmentations],
+        outputs=[aug_slices_output, canon_slices_output]
+    )
+
+# Launch the interface
+iface.launch(share=True)

requirements.txt

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+slices==2.0.4