Quickstart

FBTK allows you to go from a simple SMILES string to a fully relaxed bulk system in just a few lines of code.

Quick construction from SMILES

Ethanol Bulk

This example creates a bulk system containing Ethanol and Water, relaxes the structure to remove overlaps, and exports it for MD simulation.

import fbtk

# 1. Define Molecule
ethanol = fbtk.Molecule.from_smiles("CCO", name="Ethanol")

# 2. Build System
builder = fbtk.Builder(density=0.789) # Specify target density (g/cm3)
builder.add_molecule(ethanol, count=200)
system = builder.build()

# 3. Structural Relaxation (Overlap Removal)
system.relax() # 1000 steps (default)

# 4. Save the result (.mol2 preserves unit cell information)
system.to_file("initial.mol2")

# (Optional) Export to ASE
# atoms = system.to_ase()
# atoms.write("initial.data", format="lammps-data")

What’s Happening?

Smart Packing: Molecules are randomly placed and rotated while avoiding severe overlaps.
Internal 3D Generation: 3D structures for “Ethanol” and “Water” are generated on-the-fly from SMILES using the internal VSEPR/UFF engine.
Fast Relaxation: The relax() method uses a high-performance Rust implementation of the Universal Force Field (UFF) and the FIRE optimizer to stabilize the system in milliseconds.
Format Interoperability: The resulting System object can be converted to an ASE Atoms object or exported to a .mol2 file (complete with unit cell parameters and connectivity) for use in AmberTools or LAMMPS.

Next Steps

System Building: Learn how to create polymers and more complex mixtures.
Analysis: Learn how to compute RDF and MSD at high speed.
CLI: Run builds and analysis directly from the command line without Python code.