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Update app.py
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app.py
CHANGED
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@@ -159,18 +159,15 @@ def relax_wrapper(structure_file, task_name, steps, fmax, charge, spin, relax_ce
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# ==== UI ====
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with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
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with gr.Tabs():
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# -------- HOME TAB --------
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with gr.Tab("Home"):
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with gr.Row():
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# Columna izquierda con acordeones
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with gr.Column(scale=1):
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gr.Markdown("## Learn more about OrbMol")
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with gr.Accordion("What is OrbMol?", open=False):
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gr.Markdown("""
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OrbMol is a suite of quantum-accurate machine learning models for molecular predictions. Built on the **Orb-v3 architecture**, OrbMol provides fast and accurate calculations of energies, forces, and molecular properties at the level of advanced quantum chemistry methods.
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The models combine the transferability of universal potentials with quantum-level accuracy, making them suitable for a wide range of applications in chemistry, materials science, and drug discovery.
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""")
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with gr.Accordion("Available Models", open=False):
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@@ -186,57 +183,21 @@ The models combine the transferability of universal potentials with quantum-leve
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**OMat**
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- **Training dataset**: OMat24 (>100M inorganic calculations, from Materials Project, Alexandria, and far-from-equilibrium samples)
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- **Level of theory**: PBE/PBE+U with Materials Project settings; VASP 54 pseudopotentials; no dispersion
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- **Inputs**: No support for spin and charge
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- **Applications**: inorganic discovery, photovoltaics, alloys, superconductors, electronic/optical materials
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- **Caveats**: magnetic effects may be incompletely captured
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""")
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with gr.Accordion("Supported File Formats", open=False):
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gr.Markdown("""
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OrbMol supports
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- `.xyz` - XYZ coordinate files
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- `.pdb` - Protein Data Bank format
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- `.cif` - Crystallographic Information File
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- `.traj` - ASE trajectory format
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- `.mol` - MDL Molfile
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- `.sdf` - Structure Data File
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All formats are automatically converted internally for processing.
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""")
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with gr.Accordion("How to Use", open=False):
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gr.Markdown("""
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**Single Point Energy**: Upload a molecular structure and select a model to calculate energies and forces.
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**Molecular Dynamics**: Run time-dependent simulations to observe molecular behavior at different temperatures and conditions.
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**Relaxation/Optimization**: Find the minimum-energy configuration of your molecular structure.
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Each tab provides specific parameters you can adjust to customize your calculations.
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""")
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with gr.Accordion("Technical Foundation", open=False):
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gr.Markdown("""
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All models are based on the **Orb-v3 architecture**, the latest generation of Orb universal interatomic potentials.
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Key features:
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- Graph neural network architecture
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- Equivariant message passing
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- Multi-task learning across different quantum chemistry methods
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- Billions of training examples across diverse chemical spaces
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- Sub-kcal/mol accuracy on test sets
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""")
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with gr.Accordion("Resources & Support", open=False):
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gr.Markdown("""
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- [Orb-v3 paper](https://arxiv.org/abs/2504.06231)
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- [Orb-Models GitHub repository](https://github.com/orbital-materials/orb-models)
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- For issues/questions, please open a GitHub issue or contact the developers
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**Citation**: If you use OrbMol in your research, please cite the Orb-v3 paper and the relevant dataset papers (OMol25/OMat24).
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""")
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# Columna derecha con contenido principal
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with gr.Column(scale=2):
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gr.Image("logo_color_text.png",
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show_share_button=False,
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show_fullscreen_button=False)
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gr.Markdown("# OrbMol — Quantum-Accurate Molecular Predictions")
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gr.Markdown("""
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Welcome to the OrbMol demo!
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## Quick Start
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Use the tabs above to access different functionalities:
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1. **Single Point Energy**: Calculate energies and forces for a given molecular structure
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2. **Molecular Dynamics**: Run MD simulations using OrbMol-trained potentials
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3. **Relaxation / Optimization**: Optimize molecular structures to their minimum-energy configurations
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Simply upload a molecular structure file in any supported format (`.xyz`, `.pdb`, `.cif`, `.traj`, `.mol`, `.sdf`) and select the appropriate model for your system.
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- Organic molecules and biomolecules
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- Drug-like compounds
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- Metal-organic complexes
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- Molecules in solution
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- Systems where you need to specify charge and spin
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**Choose OMat for:**
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- Inorganic crystals and materials
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- Periodic systems
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- Bulk materials and alloys
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- Solid-state compounds
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Explore the accordions on the left to learn more about each model's capabilities, training data, and limitations.
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""")
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gr.Markdown("## Try an Example")
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gr.Markdown("""
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To get started quickly, navigate to any of the calculation tabs above and try one of these examples:
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- **Single Point Energy**: Upload a small molecule to see energy and force predictions
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- **Molecular Dynamics**: Run a short simulation at 300K to observe thermal motion
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- **Relaxation**: Optimize a distorted structure to find its equilibrium geometry
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""")
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# -------- SPE
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with gr.Tab("Single Point Energy"):
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with gr.Row():
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with gr.Column(scale=2):
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[spe_out, spe_status, spe_viewer]
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# -------- MD
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with gr.Tab("Molecular Dynamics"):
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with gr.Row():
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with gr.Column(scale=2):
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[md_status, md_traj, md_log, md_script, md_explain, md_viewer]
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# -------- Relax
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with gr.Tab("Relaxation / Optimization"):
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with gr.Row():
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with gr.Column(scale=2):
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# ==== UI ====
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with gr.Blocks(theme=gr.themes.Ocean(), title="OrbMol Demo") as demo:
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with gr.Tabs():
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# -------- HOME TAB (NUEVA) --------
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with gr.Tab("Home"):
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with gr.Row():
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with gr.Column(scale=1):
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gr.Markdown("## Learn more about OrbMol")
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with gr.Accordion("What is OrbMol?", open=False):
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gr.Markdown("""
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OrbMol is a suite of quantum-accurate machine learning models for molecular predictions. Built on the **Orb-v3 architecture**, OrbMol provides fast and accurate calculations of energies, forces, and molecular properties at the level of advanced quantum chemistry methods.
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""")
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with gr.Accordion("Available Models", open=False):
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**OMat**
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- **Training dataset**: OMat24 (>100M inorganic calculations, from Materials Project, Alexandria, and far-from-equilibrium samples)
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- **Level of theory**: PBE/PBE+U with Materials Project settings; VASP 54 pseudopotentials; no dispersion
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- **Inputs**: No support for spin and charge
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- **Applications**: inorganic discovery, photovoltaics, alloys, superconductors, electronic/optical materials
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""")
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with gr.Accordion("Supported File Formats", open=False):
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gr.Markdown("""
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OrbMol supports: `.xyz`, `.pdb`, `.cif`, `.traj`, `.mol`, `.sdf`
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""")
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with gr.Accordion("Resources & Support", open=False):
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gr.Markdown("""
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- [Orb-v3 paper](https://arxiv.org/abs/2504.06231)
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- [Orb-Models GitHub repository](https://github.com/orbital-materials/orb-models)
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""")
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with gr.Column(scale=2):
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gr.Image("logo_color_text.png",
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show_share_button=False,
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show_fullscreen_button=False)
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gr.Markdown("# OrbMol — Quantum-Accurate Molecular Predictions")
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gr.Markdown("""
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Welcome to the OrbMol demo! Use the tabs above to access different functionalities:
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1. **Single Point Energy**: Calculate energies and forces
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2. **Molecular Dynamics**: Run MD simulations
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3. **Relaxation / Optimization**: Optimize structures
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Supported formats: `.xyz`, `.pdb`, `.cif`, `.traj`, `.mol`, `.sdf`
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""")
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# -------- SPE (IDÉNTICA A LA QUE FUNCIONABA) --------
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with gr.Tab("Single Point Energy"):
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with gr.Row():
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with gr.Column(scale=2):
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[spe_out, spe_status, spe_viewer]
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)
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# -------- MD (IDÉNTICA A LA QUE FUNCIONABA) --------
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with gr.Tab("Molecular Dynamics"):
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with gr.Row():
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with gr.Column(scale=2):
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[md_status, md_traj, md_log, md_script, md_explain, md_viewer]
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)
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# -------- Relax (IDÉNTICA A LA QUE FUNCIONABA) --------
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with gr.Tab("Relaxation / Optimization"):
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with gr.Row():
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with gr.Column(scale=2):
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