app.py

import os
import polars as pl

import gradio as gr
import numpy as np
import pandas as pd
import plotly.graph_objs as go
from datasets import concatenate_datasets, load_dataset
from pymatgen.analysis.phase_diagram import PDPlotter, PhaseDiagram
from pymatgen.core import Composition, Structure, Element
from pymatgen.core.composition import Composition
from pymatgen.entries.computed_entries import (
    ComputedStructureEntry,
    GibbsComputedStructureEntry,
)

HF_TOKEN = os.environ.get("HF_TOKEN")

subsets = [
    "compatible_pbe",
    "compatible_pbesol",
    "compatible_scan",
]

# polars_dfs = {
#     subset: pl.read_parquet(
#         "hf://datasets/LeMaterial/LeMat1/{}/train-*.parquet".format(subset),
#         storage_options={
#             "token": HF_TOKEN,
#         },
#     )
#     for subset in subsets
# }

# # Load only the train split of the dataset

subsets_ds = {}
for subset in subsets:
    dataset = load_dataset(
        "LeMaterial/leMat1",
        subset,
        token=HF_TOKEN,
        columns=[
            "lattice_vectors",
            "species_at_sites",
            "cartesian_site_positions",
            "energy",
            "energy_corrected",
            "immutable_id",
            "elements",
            "functional",
        ],
    )
    subsets_ds[subset] = dataset["train"]

# Convert the train split to a pandas DataFrame
# df = pd.concat([x.to_pandas() for x in datasets])
# train_df = dataset.to_pandas()
# del dataset

# dataset_element_combination_dict = {}

# isubset = lambda x: set(x).issubset(element_list)
# isintersection = lambda x: len(set(x).intersection(element_list)) > 0
# for element_1 in Element:
#     for element_2 in Element:
#         for element_3 in Element:
#             if element_1 != element_2 and element_2 != element_3 and element_3 != element_1:
#                 print("processing {},{},{}".format(*element_list))
#                 element_list = [element_1.name, element_2.name, element_3.name]
#                 dataset_element_combination_dict(sorted(tuple(element_list))) = dataset.filter(
#                     lambda example: isintersection(example["elements"])
#                     and isubset(example["elements"])
#                 )


def create_phase_diagram(
    elements,
    max_e_above_hull,
    color_scheme,
    plot_style,
    functional,
    finite_temp,
    **kwargs,
):
    # Split elements and remove any whitespace
    element_list = [el.strip() for el in elements.split("-")]

    # Filter entries based on functional
    if functional == "PBE":
        entries_df = subsets_ds["compatible_pbe"].to_pandas()
        # entries_df = train_df[train_df["functional"] == "pbe"]
    elif functional == "PBESol":
        entries_df = subsets_ds["compatible_pbesol"].to_pandas()
        # entries_df = train_df[train_df["functional"] == "pbesol"]
    elif functional == "SCAN":
        entries_df = subsets_ds["compatible_scan"].to_pandas()
        # entries_df = train_df[train_df["functional"] == "scan"]

    # entries_df = df.to_pandas()

    entries_df = entries_df[~entries_df['immutable_id'].isna()]

    isubset = lambda x: set(x).issubset(element_list)
    isintersection = lambda x: len(set(x).intersection(element_list)) > 0
    entries_df = entries_df[
        [isintersection(l) and isubset(l) for l in entries_df.elements.values.tolist()]
    ]

    # df = df.filter((df.col("elements").list.contains(x) for x in element_list))
    # df = df.filter(
    #     pl.col("elements")
    #     .list.eval(pl.element().is_in(element_list))
    #     .list.any()
    #     .alias("check")
    # )

    # entries_df = df.to_pandas()

    # Fetch all entries from the Materials Project database
    entries = [
        ComputedStructureEntry(
            Structure(
                [x.tolist() for x in row["lattice_vectors"].tolist()],
                row["species_at_sites"],
                row["cartesian_site_positions"],
                coords_are_cartesian=True,
            ),
            energy=row["energy"],
            correction=(
                row["energy_corrected"] - row["energy"]
                if not np.isnan(row["energy_corrected"])
                else 0
            ),
            entry_id=row["immutable_id"],
            parameters={"run_type": row["functional"]},
        )
        for n, row in entries_df.iterrows()
    ]
    # TODO: Fetch elemental entries (they are usually GGA calculations)
    # entries.extend([e for e in entries if e.composition.is_element])

    if finite_temp:
        entries = GibbsComputedStructureEntry.from_entries(entries)

    # Build the phase diagram
    try:
        phase_diagram = PhaseDiagram(entries)
    except ValueError as e:
        return go.Figure().add_annotation(text=str(e))

    # Generate plotly figure
    if plot_style == "2D":
        plotter = PDPlotter(phase_diagram, show_unstable=True, backend="plotly")
        fig = plotter.get_plot()
    else:
        # For 3D plots, limit to ternary systems
        if len(element_list) == 3:
            plotter = PDPlotter(
                phase_diagram, show_unstable=True, backend="plotly", ternary_style="3d"
            )
            fig = plotter.get_plot()
        else:
            return go.Figure().add_annotation(
                text="3D plots are only available for ternary systems."
            )

    # Adjust the maximum energy above hull
    # (This is a placeholder as PDPlotter does not support direct filtering)

    # Return the figure
    return fig


# Define Gradio interface components
elements_input = gr.Textbox(
    label="Elements (e.g., 'Li-Fe-O')",
    placeholder="Enter elements separated by '-'",
    value="Li-Fe-O",
)
max_e_above_hull_slider = gr.Slider(
    minimum=0, maximum=1, value=0.1, label="Maximum Energy Above Hull (eV)"
)
color_scheme_dropdown = gr.Dropdown(
    choices=["Energy Above Hull", "Formation Energy"], label="Color Scheme"
)
plot_style_dropdown = gr.Dropdown(choices=["2D", "3D"], label="Plot Style")
functional_dropdown = gr.Dropdown(choices=["PBE", "PBESol", "SCAN"], label="Functional")
finite_temp_toggle = gr.Checkbox(label="Enable Finite Temperature Estimation")

warning_message = "This application uses energy correction schemes directly"
warning_message += " from the data providers (Alexandria, MP) and has the 2020 MP"
warning_message += " Compatibility scheme applied to OQMD. However, because we did"
warning_message += " not directly apply the compatibility schemes to Alexandria, MP"
warning_message += " we have noticed discrepencies in the data. While the correction"
warning_message += " scheme will be standardized in a soon to be released update, for"
warning_message += " now please take caution when analyzing the results of this"
warning_message += " application."


message = '<div class="alert"><span class="closebtn" onclick="this.parentElement.style.display="none";">&times;</span>{}</div>Generate a phase diagram for a set of elements using LeMat-Bulk data.'.format(
    warning_message
)

# Create Gradio interface
iface = gr.Interface(
    fn=create_phase_diagram,
    inputs=[
        elements_input,
        max_e_above_hull_slider,
        color_scheme_dropdown,
        plot_style_dropdown,
        functional_dropdown,
        finite_temp_toggle,
    ],
    outputs=gr.Plot(label="Phase Diagram"),
    title="LeMaterial - Phase Diagram Viewer",
    description=message,
)

# Launch the app
iface.launch()