geometric 1.1.1

This is a geometry optimization code for molecular structures. The code works by calling external software for the energy and gradient through wrapper functions. Q-Chem, TeraChem, Psi4, Molpro, Gaussian 09/16, CFOUR, QUICK, BAGEL are supported quantum chemistry codes through the command line interface. The PySCF and QCArchive packages also provide interfaces to geomeTRIC for optimization. MM optimizations using OpenMM and Gromacs are also supported through the command line interface.

Documentation is hosted at https://geometric.readthedocs.io/ .

Authors: Lee-Ping Wang, Chenchen Song, Heejune Park

Contributors: Yudong Qiu (Psi4 engine, error handling); Daniel G. A. Smith (Testing framework, QCEngine JSON API); Tamas K. Stenczel (GitHub Actions, ASE engine); Sebastian Lee (Molpro engine); Chaya Stern (Travis, Conda); Qiming Sun (Custom engine); Alberto Gobbi (Batch energy/gradient, logging); Josh Horton (Convergence criteria, Gaussian engine); Akhil Shajan (QUICK engine); Xincheng Miao (BAGEL engine)

Contact Email: leeping@ucdavis.edu

If this code has benefited your research, please support us by citing:

Wang, L.-P.; Song, C. (2016) "Geometry optimization made simple with translation and rotation coordinates", J. Chem, Phys. 144, 214108. https://doi.org/10.1063/1.4952956

Park, H.; Pritchard, B. P.; Wang, L.-P. (2025) "High-Throughput Approach for Minimum Energy Pathway Search Using the Nudged Elastic Band Method with Efficient Data Handling and Parallel Computing", J. Chem. Theory Comput. 21, 12048. https://doi.org/10.1021/acs.jctc.5c01540

Quick Help

Package dependencies are: Python 2.7, 3.8+ NumPy, Scipy, NetworkX

To install the code from source, run "python setup.py install". To install the latest release from pip, run "pip install geometric". To install the latest release from conda-forge, run "conda install -c conda-forge geometric".

To execute the geometry optimizer, run "geometric-optimize". Use "-h" to see the list of command line options.

Generally, you will need a .xyz file for the coordinates and one of the supported quantum chemistry software packages installed on your system.

Supported QM packages are: TeraChem, Q-Chem, Molpro, Psi4, Gaussian 09/16, CFOUR, QUICK, BAGEL. Supported MM packages are: OpenMM, Gromacs.

Please refer to the example calculations for how to run the code.
The commands to execute the code are contained in "command.sh".

Funding Acknowledgments

We are grateful for funding support from NIH/NIAID Award R01 AI130684 and NSF Award 2408693.

Citation

If this code has benefited your research, please support us by citing our publications:

Wang, L.-P.; Song, C. (2016) "Geometry optimization made simple with translation and rotation coordinates", J. Chem, Phys. 144, 214108. DOI: 10.1063/1.4952956
(Cite this when the software is used.)

Park, H.; Pritchard, B. P.; Wang, L.-P. (2025) "High-Throughput Approach for Minimum Energy Pathway Search Using the Nudged Elastic Band Method with Efficient Data Handling and Parallel Computing", J. Chem. Theory Comput. 21, 12048. DOI: 10.1021/acs.jctc.5c01540
(Cite this when the NEB method is used.)