firecode 2.0.0

FIRECODE: Filtering Refiner and Embedder for Conformationally Dense Ensembles

FIRECODE - Filtering Refiner and Embedder for Conformationally Dense Ensembles

FIRECODE is a computational chemistry workflow driver and hub for the generation, optimization and refinement of conformational ensembles, including transition state and thermochemical utilities.

Calculators

• xTB (native)
• tblite (via ASE)
• AIMNET2 (via ASE)
• UMA (via ASE)

Interfaces / utilities

• CREST (conformational search)
• GOAT (conformational search)
• racerts (conformational search)
• ETKDG (via rdkit, conformational search)
• TSCoDe (conformational embedding)
• prism_pruner (conformational pruning)
• ML-FSM (two-ended TS search)
• Sella (saddle point optimization)

...plus frequency calculation, NEB optimization, and more are all implemented in the code in a calculator-agnostic way.

Installation

The package is distributed via pip, and the use of uv is highly recommended. The default installation is minimalistic, and torch/GPU support requires dedicated installs:

uv pip install firecode           # XTB, TBLITE, ORCA
uv pip install firecode[aimnet2]  # + AIMNET2
uv pip install firecode[uma]      # + UMA/OMOL
uv pip install firecode[full]     # + AIMNET2, UMA/OMOL

More installation details in the documentation.

Usage

Installation exposes the main program working on a plain text file as well as a standalone optimizer.

🔥 firecode [-h] [-s] [-t] input.txt [-n NAME] [-p]

    positional arguments:
      inpufile.txt            Input filename, can be any text file.

    optional arguments:
      -h, --help              Show this help message and exit.
      -s, --setup             Guided setup of the calculation settings.
      -n, --name NAME         Specify a custom name for the run.
      -cl,--command_line      Read instructions from the command line instead of from an input file.
      -p, --profile           Profile the run through cProfiler.

🔥 firecode_opt [-h] [-i] [-t TEMPERATURE] [-c CALCULATOR] [-m METHOD] [-s SOLVENT] [-o] [-f] [--ts] [--irc] [--cfile CFILE] [-n] [--debug]
                    filenames [filenames ...]

positional arguments:
  filenames             Input filename(s), in .xyz format

options:
  -h, --help            show this help message and exit
  -i, --interactive     Set options interactively.
  -t TEMPERATURE, --temperature TEMPERATURE
                        Temperature, in degrees Celsius.
  -c CALCULATOR, --calculator CALCULATOR
                        Calculator (default UMA).
  -m METHOD, --method METHOD
                        Method (default OMOL for UMA).
  -s SOLVENT, --solvent SOLVENT
                        Solvent (default ch2cl2).
  -o, --opt             Optimize the geometry.
  -f, --freq            Perform vibrational analysis.
  --ts, --saddle        Optimize to a TS.
  --irc                 Run an IRC calculation.
  --cfile CFILE         Uses a constraint file.
  -n, --newfile         Write optimized structure to a new file (*_opt.xyz).
  --debug               Does not delete optimization data.

Documentation

Documentation on how to install and use the program can be found on readthedocs.