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.io.trajectory import Trajectory import py3Dmol from orb_models.forcefield import pretrained from orb_models.forcefield.calculator import ORBCalculator # ----------------------------- # Global OrbMol 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("āœ… OrbMol model loaded successfully") except Exception as e: print(f"āŒ 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 "āŒ Error: Could not load OrbMol model", "" if not xyz_content.strip(): return "āŒ 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"šŸ”‹ **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/ƅ\n" max_force = np.max(np.linalg.norm(forces, axis=1)) result += f"\nšŸ“Š **Max Force**: {max_force:.4f} eV/ƅ" os.unlink(xyz_file) return result, "āœ… Calculation completed with OrbMol" except Exception as e: return f"āŒ Error during calculation: {str(e)}", "Error" # ----------------------------- # Trajectory → HTML for Gradio # ----------------------------- 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.render() # āœ… en Gradio funciona mejor que _make_html() # ----------------------------- # MD 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 "āŒ Error: Could not load OrbMol model", "" if not xyz_content.strip(): return "āŒ 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-relax opt = LBFGS(atoms) opt.run(fmax=0.05, steps=20) # Initialize 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"āœ… MD completed: {steps} steps at {temperature} K", html except Exception as e: return f"āŒ Error during MD simulation: {str(e)}", "" # ----------------------------- # Examples # ----------------------------- examples = [ ["""2 Hydrogen molecule H 0.0 0.0 0.0 H 0.0 0.0 0.74""", 0, 1], ["""3 Water molecule O 0.0000 0.0000 0.0000 H 0.7571 0.0000 0.5864 H -0.7571 0.0000 0.5864""", 0, 1], ["""5 Methane C 0.0000 0.0000 0.0000 H 1.0890 0.0000 0.0000 H -0.3630 1.0267 0.0000 H -0.3630 -0.5133 0.8887 H -0.3630 -0.5133 -0.8887""", 0, 1] ] # ----------------------------- # Gradio UI # ----------------------------- with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol + MD Demo") as demo: with gr.Tab("Single Point Energy"): with gr.Row(): with gr.Column(scale=2): with gr.Column(variant="panel"): gr.Markdown("# OrbMol Demo - Quantum-Accurate Molecular Predictions") xyz_input = gr.Textbox( label="XYZ Coordinates", lines=12, placeholder="Paste XYZ here" ) with gr.Row(): charge_input = gr.Slider(value=0, label="Charge", minimum=-10, maximum=10, step=1) spin_input = gr.Slider(value=1, maximum=11, minimum=1, step=1, label="Spin Multiplicity") run_btn = gr.Button("Run OrbMol Prediction", variant="primary", size="lg") with gr.Column(variant="panel", min_width=500): gr.Markdown("## Results") results_output = gr.Textbox(label="Energy & Forces", lines=15, interactive=False) status_output = gr.Textbox(label="Status", interactive=False, max_lines=1) gr.Examples(examples=examples, inputs=[xyz_input, charge_input, spin_input]) 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", variant="primary") 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("šŸš€ Starting OrbMol model loading...") load_orbmol_model() if __name__ == "__main__": demo.launch(server_name="0.0.0.0", server_port=7860, show_error=True)