Skip to content

keithgroup/bebop-qc

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

27 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

BEBOP

The bond energy/bond order population (BEBOP) program is a computational chemistry algorithm that computes accurate molecular energies at equilibrium and bond energies using well-conditioned Hartree-Fock orbital populations and bond orders from approximate quantum chemistry methods.

Installation

git clone https://github.com/keithgroup/bebop-qc
cd bebop-qc
pip install .

Preparing BEBOP Input Files

Currently, we have developed BEBOP-1 and BEBOP-2 models, and each of these models require output from the MinPop algorithm when running Hartree-Fock. Below is an example of how to do this in Gaussian 16 for each model.

  1. Optimize your molecular structure using your preferred level of theory (e.g., B3LYP/CBSB7 and B3LYP/cc-pVTZ+1d).
BEBOP-1:
# Opt B3LYP/CBSB7
BEBOP-2:
# Opt B3LYP/cc-pVTZ+1d
  1. Run Hartree-Fock on the optimized structure in Gaussian.
BEBOP-1 and BEBOP-2:
# SP ROHF/CBSB3 Pop=(Full) IOp(6/27=122,6/12=3)

Usage

Execute bebop1 and bebop2 for BEBOP-1 and BEBOP-2, respectively. Run this in the command line:

BEBOP-1:
bebop1 -f {name_file} --be --sort --json > {name_file}.bop
BEBOP-2
bebop2 -f {name_file} -parameter_folder {parameter_folder} --be --sort --json --ionicity > {name_file}.bop

where {name_file} is the Hartree-Fock Gaussian output file and {parameter_folder} is the name or path of the BEBOP-2 parameter folder. Note that BEBOP-2 parameters are stored in json files under the opt_parameters folders.

Some examples of BEBOP-1 and BEBOP-2 output files are found in the examples directory.

Some details of the parsers used in bebop1 and bebop2 source codes.

BEBOP-1:
$ bebop1 -h
usage: bebop1 [-h] -f F [--be] [--sort] [--json]

compute BEBOP atomization energies and bond energies (i.e., gross and net)

optional arguments:
  -h, --help  show this help message and exit
  -f F        name of the Gaussian Hartree-Fock output file
  --be        compute BEBOP bond energies (net and gross bond energies)
  --sort      sort the net BEBOP bond energies (from lowest to highest in energy)
  --json      save the job output into JSON
BEBOP-2:
$ bebop2 -h
usage: bebop2 [-h] -f F [-param_folder PARAM_FOLDER] [--be] [--sort] [--json] [--ionicity]

compute BEBOP atomization energies and bond energies (i.e., gross and net)

optional arguments:
  -h, --help            show this help message and exit
  -f F                  name of the Gaussian Hartree-Fock output file
  -param_folder PARAM_FOLDER
                        name of BEBOP-2's parameter path/folder (default: opt_parameters)
  --be                  compute BEBOP bond energies (net and gross bond energies)
  --sort                sort the net BEBOP bond energies (from lowest to highest in energy)
  --json                save the job output into JSON
  --ionicity            percent of ionicity per each bond and entire molecule

Citations

Please cite:

BEBOP-1: Barbaro Zulueta, Sonia V. Tulyani, Phillip R. Westmoreland, Michael J. Frisch, E. James Petersson, George A. Petersson, and John A. Keith Journal of Chemical Theory and Computation 2022 18 (8), 4774-4794 DOI: 10.1021/acs.jctc.2c00334

BEBOP-2: Barbaro Zulueta, George A. Petersson, and John A. Keith; Many-Body Bond and Charge Model Contributions to BEBOP Model 2024 (in preparation).

License

Distributed under the MIT License. See LICENSE for more information.

About

No description, website, or topics provided.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages