app.py

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():
                file_choice = gr.Radio(
                    ["Use example CIF (NdSiRu.cif)", "Upload custom CIF"],
                    label="Choose CIF source",
                    value="Use example CIF (NdSiRu.cif)"
                )
                example_file = gr.File(value="NdSiRu.cif", visible=False, interactive=False)
                custom_file = gr.File(label="Upload CIF file", file_types=[".cif"], visible=False)
                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
    def update_file_visibility(choice):
        return gr.update(visible=choice == "Use example CIF (NdSiRu.cif)"), gr.update(visible=choice == "Upload custom CIF")

    file_choice.change(
        update_file_visibility,
        inputs=[file_choice],
        outputs=[example_file, custom_file]
    )

    def get_active_file(choice, example, custom):
        return example if choice == "Use example CIF (NdSiRu.cif)" else custom

    convert_cif_button.click(
        lambda choice, example, custom: cif_to_slices(get_active_file(choice, example, custom)),
        inputs=[file_choice, example_file, custom_file],
        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]
    )

iface.launch(share=True)