mopac-step

=================== SEAMM MOPAC plug-in

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A SEAMM plug-in to setup, run and analyze semiempirical calculations with MOPAC.

This plug-in provides a graphical user interface (GUI) for setting up and running simulations using the semiempirical quantum chemistry code MOPAC_.

• Free software: BSD license
• Documentation: https://molssi-seamm.github.io/mopac_step/index.html
• Code: https://github.com/molssi-seamm/mopac_step

.. _MOPAC: http://openmopac.net

Features

• Single-point energies
• Structural optimization
• IR and Raman vibrational frequencies
• Temperature dependent thermodynamic functions
• Results can be stored in flowchart variables or tables_.

.. _tables: https://molssi-seamm.github.io/table_step/index.html

seamm-mopac Docker image

There is a Docker image available for the SEAMM MOPAC plug-in for running mopac. It is available at the Github Container Registry (ghcr.io) as

.. code-block:: bash

ghcr.io/molssi-seamm/seamm-mopac:<version>

Where is the explicit version tag for the desired image. The tag latest is quite confusing, and does not mean the latest version of the image, so we recomend using explcit versions rather than latest.

The container can also be run standalone with the following command:

.. code-block:: bash

docker run --rm -v $PWD:/home ghcr.io/molssi-seamm/seamm-mopac:<version> ?mopac <input file>?

where <input file> is the input file for the MOPAC calculation. By default, mopac is run using the input file mopac.dat. The output files will be written to the current directory. The --rm option removes the container after it exits, and the -v option mounts the current directory to the /home directory in the container.

Acknowledgements

This package was created with Cookiecutter_ and the molssi-seamm/cookiecutter-seamm-plugin_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter .. _molssi-seamm/cookiecutter-seamm-plugin: https://github.com/molssi-seamm/cookiecutter-seamm-plugin

Developed by the Molecular Sciences Software Institute (MolSSI_), which receives funding from the National Science Foundation_ under awards OAC-1547580 and CHE-2136142.

.. _MolSSI: https://www.molssi.org .. _National Science Foundation: https://www.nsf.gov

======= History

2024.12.9 -- Add the force constants as a property.

• Add the force constants as a property of the configuration when running thermodynamics, IR, or force constants calculations.

2024.10.15 -- Bugfix: error if used in a loop and previous directories deleted.

• The code crashed if called with a loop in the flowchart, and the last directory of a previous loop iteration was deleted before running the next iteration.

2024.8.21 -- Bugfix for PM7-TS and optimization, GUI clean up for CI calculations.

• Calculations using PM7-TS do not write information to the AUX file, so added code to get the energy from the output file.
• For optimizations, the option for the frequency of calculating the force constants and the maximum radius of convergence were missing from the GUI for the EF method. The frequency also was not being correctly handled in the input to MOPAC.
• The GUI for using CI calculations was cleaned up.

2024.8.17 -- Added CI calculations and better handling of transition states

• Added ability to do the various types of CI calculations that MOPAC supports.
• Improved the handling of TS calculations and added NLLSQ and SIGMA methods in the optimization step.
• Added option to correctly handle transition states in the thermodynamics step and improved the output to include the imaginary and low-lying frequencies.

2024.7.29 -- Bugfix in bond analysis for atoms and mopac.ini

• Fixed a bug in the bond analysis that caused the code to crash for calculations on atoms.
• Fixed a bug in the mopac.ini file created if it did not exists that caused the code to crash when the calculation was run.

2024.5.14 -- Added output of energy & gradients to JSON

• To support the Energy Scan step.

2024.3.17 -- Updated installation

• Updated the installation to reflect the new way to install SEAMM plug-ins to support both Conda and Docker

2024.1.16 -- Added support for containers.

• Added access to the new PM6-ORG parameterization and made it the default, though PM7 is still preferred for materials simulation. PM6-ORG handle organic and biomolecules well.
• Made the Lewis structure analysis more robust and added information to the output.
• Provided an option for the Lewis structure calculation to set the charge of the system to that calculaed by the Lewis structure.
• Added support for containers
• Made default to run serially, since parallel doesn't provide much benefit.
• Fixed bug in analysis if optimization doesn't converge.

2023.12.18 -- Added readonly flag

• Added a flag to prepare the input but not run the calculation.

2023.11.15 -- More updates for v2022.1.0

• Added PM6-ORG Hamiltonian to options
• Added other new data types for the AUX file.

2023.11.14 -- Updated for MOPAC v2022.1.0

• MOPAC v2022.1.0 added GRADIENT_NORM_UPDATED to the AUX file. This updates adds it to the results recognized by the plug-in

2023.10.30 -- Updated to standard structure handling

• Adds IUPAC names, InChI and InChIKey as possible names for configurations
• Cleaned up output to be properly indented and laid out.

2023.8.30 -- Support for spacegroup symmetry

2023.7.27 -- Bugfix: printing bond order info

• If the bond orders were printed but not used on the system, the code crashed.

2023.7.26 -- Added output of bond orders

• Also added capability to use the bond orders to put bond multiplicities on the structure.

2023.7.24 -- Bugfix in Lewis structure with bond orders

• Major issue in getting the bonds from the Lewis structure where the atoms and bond orders were mixed up.

2023.6.5 -- Bugfix working around MOPAC problem

• MOPAC is not consistent about putting end of file and end of program markers in the AUX file. This caused carashed in SEAMM, which this fixes until MOPAC can be corrected.

2023.4.24 -- Bugfixes for Lewis structure

• Correctly handle periodic systems in Lewis structure.
• Fixed and issue with the Lewis structure GUI not displaying all the widgets.

2023.3.31 -- Bugfix Lewis structure could reference a variable before it was set, and crash.

2023.3.15 -- Bugfix A copy of the input and output files for MOPAC was inadvertently written to the main job directory. This has been fixed.

2023.2.13 -- Added Lewis Structure step Provide access to the 'LEWIS' keyword in MOPAC for generating the Lewis dot structure. This step also allows assigning the bonds of the system using either the connectivity or the Lewis structure.

2022.11.18 -- Printing spins on atoms Fixed an oversight that preventing printing spins on the atoms, and storing them on the structure. Also increased the precision of the AUX file so have coordinates to seven decimals, which should maintain symmetry better.

2022.11.4 -- Added ForceConstant substep Calculates and writes the Hessian (force constant) matrix to disk. Works for both molecular and periodic systems, and provides an option to control which parts of the Hessian matrix are written. Defaults to the full matrix. Also provides options to control the units of the output, with default of N/m for the atom block of the Hessian as well as the atom-cell off-diagonal block, and GPa for the cell block.

2021.2.11 (11 February 2021)

• Updated the README file to give a better description.
• Updated the short description in setup.py to work with the new installer.
• Added keywords for better searchability.

2021.2.4 (4 February 2021)

• Updated for compatibility with the new system classes in MolSystem 2021.2.2 release.

2020.12.5 (5 December 2020)

• Internal: switching CI from TravisCI to GitHub Actions, and in the process moving documentation from ReadTheDocs to GitHub Pages where it is consolidated with the main SEAMM documentation.

2020.11.2 (2 November 2020)

• Updated to be compatible with the new command-line argument handling.

2020.10.7 (7 October 2020)

• Updated to handle citations using the new framework.

2020.9.29 (29 September 2020)

• Updated to be compatible with the new system classes in MolSystem.

2020.8.1 (1 August 2020)

• Fixed bug caused by coordinates being strings, not numbers, in some cases.

2020.7.0 (23 July 2020)

• Improved the text output when running.

0.9 (15 April 2020)

• General bug fixes and cleanup of the code.

0.7.0 (17 December 2019)

• Consolidating minor changes and making a uniform release at year's end.

0.5.1 (29 August 2019)

• First version that runs correctly and generates output.

0.2.0 (13 August 2019)

• First release on PyPI.