Case 1: Small Molecule Pure Substance (Benzene)

In this case, we use benzene as a representative example of a small molecule pure substance. We will explain the basic flow of creating a molecule object from SMILES, packing it into a unit cell at a specified density, and performing structural relaxation.

Target System

Compound: Benzene
Composition: 150 molecules (Total atoms: 1,800)
Initial Target Density: 0.80 g/cm³

Calculation Code (run.py)

import fbtk

# 1. Create a molecule object from SMILES
benzene = fbtk.Molecule.from_smiles("c1ccccc1", name="benzene")

# 2. Initialize the Builder
builder = fbtk.Builder(density=0.80)

# 3. Add molecules to the system
builder.add_molecule(benzene, count=150)

# 4. Build the system
system = builder.build()

# 5. Execute structural relaxation (Pre-relaxation)
print("Starting relaxation for Benzene...")
system.relax()

# 6. Output results
benzene.to_file("benzene.mol")        # Individual molecule
system.to_file("benzene_cell.mol2")   # Relaxed unit cell
print("Done.")

Reviewing the Execution Log

During execution, the standard output displays the progress of the optimization process.

Atoms:     1800       | Bonds:     1800
--------------------------------------------------------------------------------
       | Fmax           | FRMS           | Total E          |
Iter   | (kcal/mol/Å)   | (kcal/mol/Å)   | (kcal/mol)       | Status
--------------------------------------------------------------------------------
     0 |     36968.7497 |      6300.0166 | 686143734596.2736 |
    10 |      4785.6728 |       229.2529 |      156059.5598 |
    20 |      2074.8591 |       129.3691 |       87049.2019 |
   ...
   980 |         2.0817 |         0.1992 |       18859.4087 |
   990 |        36.2483 |         1.3258 |       18848.6857 |
--------------------------------------------------------------------------------
=== Optimization Finished ===
Reason: Max-Iter
Total Time: 14.335s    (Avg: 14.335ms / step)
Final Energy: 18852.1265      kcal/mol
Final Fmax:   2.3571          kcal/mol/Å
Final FRMS:   0.2088          kcal/mol/Å
Min Distance: 1.0809          Å (Atoms 553 and 559)
--------------------------------------------------------------------------------

Result Explanation

Effect of Structural Relaxation

If the Min Distance (closest interatomic distance) after relaxation is secured at 1.0 Å or more, it can be said that local “atomic collisions” have been resolved and a physically reasonable initial structure has been obtained.

Integration with ASE

By using the to_ase() method, you can convert the system to an ASE Atoms object, allowing for easy integration with external MD software and various Calculators.

atoms = system.to_ase()
# atoms.calc = SomeCalculator(...)