Quickstart

Quickstart

Basic Workflow of FBTK

Structure building in FBTK follows these three essential steps. Understanding this flow will make your building process smooth.

graph LR
    A[Molecule<br/>Template Definition] --> B[Builder<br/>Packing & Placement]
    B --> C[System<br/>Physics, Analysis, Export]
    
    style A fill:#f9f,stroke:#333,stroke-width:2px
    style B fill:#bbf,stroke:#333,stroke-width:2px
    style C fill:#bfb,stroke:#333,stroke-width:2px

1. Molecule: This is your “template” or “blueprint.” You define a single molecular structure from SMILES or files. Even a single polymer chain is generated as one Molecule object here.
2. Builder: This is the “placer.” You specify “which molecules and how many” to pack into a box with a target density, and then execute the actual build().
3. System: This is the “realized system.” It contains the final coordinates and unit cell information (PBC). You can perform structural relaxation, RDF analysis, or save it to a file from here.

Quick Building from SMILES

import fbtk

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

# 2. Placement with Builder
builder = fbtk.Builder(density=0.789) # Specify target density (g/cm3)
builder.add_molecule(ethanol, count=200) # Add 200 instances of the template
system = builder.build() # Execute placement

# 3. Operations on System (Realized)
system.relax() # Structural relaxation
system.to_file("initial.mol2") # Save results

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