app.py

import gradio as gr
import torch
import numpy as np
import tempfile
import os

from ase.io import read
from ase import units
from ase.optimize import LBFGS
from ase.md.verlet import VelocityVerlet
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.md import MDLogger
from ase.io.trajectory import Trajectory

import py3Dmol

from orb_models.forcefield import pretrained
from orb_models.forcefield.calculator import ORBCalculator

# -----------------------------
# Global model
# -----------------------------
model_calc = None

def load_orbmol_model():
    """Load OrbMol model once"""
    global model_calc
    if model_calc is None:
        try:
            print("Loading OrbMol model...")
            orbff = pretrained.orb_v3_conservative_inf_omat(
                device="cpu",
                precision="float32-high"
            )
            model_calc = ORBCalculator(orbff, device="cpu")
            print("✅ OrbMol model loaded successfully")
        except Exception as e:
            print(f"❌ Error loading model: {e}")
            model_calc = None
    return model_calc

# -----------------------------
# Single-point calculation
# -----------------------------
def predict_molecule(xyz_content, charge=0, spin_multiplicity=1):
    try:
        calc = load_orbmol_model()
        if calc is None:
            return "❌ Error: Could not load OrbMol model", ""

        if not xyz_content.strip():
            return "❌ Error: Please enter XYZ coordinates", ""

        with tempfile.NamedTemporaryFile(mode='w', suffix='.xyz', delete=False) as f:
            f.write(xyz_content)
            xyz_file = f.name

        atoms = read(xyz_file)
        atoms.info = {"charge": int(charge), "spin": int(spin_multiplicity)}
        atoms.calc = calc

        energy = atoms.get_potential_energy()
        forces = atoms.get_forces()

        result = f"🔋 **Total Energy**: {energy:.6f} eV\n\n⚡ **Atomic Forces**:\n"
        for i, f in enumerate(forces):
            result += f"Atom {i+1}: [{f[0]:.4f}, {f[1]:.4f}, {f[2]:.4f}] eV/Å\n"

        max_force = np.max(np.linalg.norm(forces, axis=1))
        result += f"\n📊 **Max Force**: {max_force:.4f} eV/Å"

        os.unlink(xyz_file)
        return result, "✅ Calculation completed with OrbMol"
    except Exception as e:
        return f"❌ Error during calculation: {str(e)}", "Error"

# -----------------------------
# Helper: convert trajectory → HTML animation
# -----------------------------
def traj_to_html(traj_file):
    traj = Trajectory(traj_file)
    view = py3Dmol.view(width=400, height=400)
    for atoms in traj:
        symbols = atoms.get_chemical_symbols()
        xyz = atoms.get_positions()
        mol = ""
        for s, (x, y, z) in zip(symbols, xyz):
            mol += f"{s} {x} {y} {z}\n"
        view.addModel(mol, "xyz")
    view.setStyle({"stick": {}})
    view.zoomTo()
    view.animate({"loop": "forward"})
    return view._make_html()

# -----------------------------
# Molecular dynamics simulation
# -----------------------------
def run_md(xyz_content, charge=0, spin_multiplicity=1, steps=100, temperature=300, timestep=1.0):
    try:
        calc = load_orbmol_model()
        if calc is None:
            return "❌ Error: Could not load OrbMol model", ""

        if not xyz_content.strip():
            return "❌ Error: Please enter XYZ coordinates", ""

        with tempfile.NamedTemporaryFile(mode='w', suffix='.xyz', delete=False) as f:
            f.write(xyz_content)
            xyz_file = f.name

        atoms = read(xyz_file)
        atoms.info = {"charge": int(charge), "spin": int(spin_multiplicity)}
        atoms.calc = calc

        # Pre-relaxation
        opt = LBFGS(atoms)
        opt.run(fmax=0.05, steps=20)

        # Velocities
        MaxwellBoltzmannDistribution(atoms, temperature_K=2 * temperature)

        # MD setup
        dyn = VelocityVerlet(atoms, timestep=timestep * units.fs)

        traj_file = tempfile.NamedTemporaryFile(suffix=".traj", delete=False)
        traj = Trajectory(traj_file.name, "w", atoms)
        dyn.attach(traj.write, interval=1)

        dyn.run(steps)

        html = traj_to_html(traj_file.name)

        os.unlink(xyz_file)
        return f"✅ MD completed: {steps} steps at {temperature} K", html
    except Exception as e:
        return f"❌ Error during MD simulation: {str(e)}", ""

# -----------------------------
# Gradio UI
# -----------------------------
with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol + MD Demo") as demo:
    gr.Markdown("# OrbMol Demo with Molecular Dynamics")

    with gr.Tab("Single Point Energy"):
        xyz_input = gr.Textbox(label="XYZ Coordinates", lines=12)
        charge_input = gr.Slider(value=0, minimum=-10, maximum=10, step=1, label="Charge")
        spin_input = gr.Slider(value=1, minimum=1, maximum=11, step=1, label="Spin Multiplicity")
        run_btn = gr.Button("Run OrbMol Calculation")
        results_output = gr.Textbox(label="Results", lines=15)
        status_output = gr.Textbox(label="Status")
        run_btn.click(
            predict_molecule,
            inputs=[xyz_input, charge_input, spin_input],
            outputs=[results_output, status_output],
        )

    with gr.Tab("Molecular Dynamics"):
        xyz_input_md = gr.Textbox(label="XYZ Coordinates", lines=12)
        charge_input_md = gr.Slider(value=0, minimum=-10, maximum=10, step=1, label="Charge")
        spin_input_md = gr.Slider(value=1, minimum=1, maximum=11, step=1, label="Spin Multiplicity")
        steps_input = gr.Slider(value=100, minimum=10, maximum=1000, step=10, label="Steps")
        temp_input = gr.Slider(value=300, minimum=10, maximum=1000, step=10, label="Temperature (K)")
        timestep_input = gr.Slider(value=1.0, minimum=0.1, maximum=5.0, step=0.1, label="Timestep (fs)")
        run_md_btn = gr.Button("Run MD Simulation")
        md_status = gr.Textbox(label="MD Status", lines=2)
        md_view = gr.HTML()
        run_md_btn.click(
            run_md,
            inputs=[xyz_input_md, charge_input_md, spin_input_md, steps_input, temp_input, timestep_input],
            outputs=[md_status, md_view],
        )

print("🚀 Starting OrbMol model loading...")
load_orbmol_model()

if __name__ == "__main__":
    demo.launch(server_name="0.0.0.0", server_port=7860, show_error=True)