FAQ

Matlantis

• Types of Release Models
• Controlling Token Usage
• How to configure EntraID in Matlantis
• Using Background Jobs Effectively
• How to Set Up an SSH Connection

Installation

• How to install Open Babel
• How to install LAMMPS package (matlantis-lammps)
• How to install PLUMED

Tutorial

• #Appendix: Matlantis Operation Status
• #Appendix: Service Role and User Type
• 0_[For Administrator] Authentication and User Registration
• 1_User authentication
• 2_Matlantis Dashboard screen
• 3_JupyterLab interface (Notebook environment)

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Reaction Pathway

• NEB Calculation: Notes on Preparing Initial and Final States

trouble shooting

• ImportError in ASE 3.27: Migration of Filter Classes
• Kernel error on Python 3.13
• Troubleshooting nglview JavaScript Errors
• Bug in ASE NPT.set_strain_rate (ASE 3.25 or later)
• Jupyter Notebook won't open (blank screen)
• Troubleshooting Blank Notebook Cells

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Tips

• Atomic Level Explanation via PFP Descriptors and Shapley Values
• LAMMPS Inputs creation for matlantis-lammps
• Handling Isotopes in ASE
• How to Get Token Usage History and Issues with Garbled Text
• Parallel Computation Within a Notebook Using joblib
• Introduction of pfcc-ase-extras

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Modeling

• Generating ASE Atoms object from SMILES
• How to Create a Polycrystal Containing Grain Boundaries

Molecular Dynamics

• NotImplementedError in ASE NPT-MD (convert_atoms_to_upper)
• How to Run Metadynamics Simulations Using PLUMED in Matlantis

Visualization

• Visualizing Bader Charge
• HTML File Generation with view_ngl

LightPFP

• Switching LightPFP Users