===================
SEAMM MOPAC plug-in
===================
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:target: https://pypi.python.org/pypi/mopac_step
:alt: PyPi VERSION
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 <version> 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
=======
2024.10.15 -- 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.
Raw data
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"description": "===================\nSEAMM MOPAC plug-in\n===================\n\n.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/mopac_step\n :target: https://github.com/molssi-seamm/mopac_step/pulls\n :alt: GitHub pull requests\n\n.. image:: https://github.com/molssi-seamm/mopac_step/workflows/CI/badge.svg\n :target: https://github.com/molssi-seamm/mopac_step/actions\n :alt: Build Status\n\n.. image:: https://codecov.io/gh/molssi-seamm/mopac_step/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/molssi-seamm/mopac_step\n :alt: Code Coverage\n\n.. image:: https://github.com/molssi-seamm/mopac_step/workflows/CodeQL/badge.svg\n :target: https://github.com/molssi-seamm/mopac_step/security/code-scanning\n :alt: Code Quality\n\n.. image:: https://github.com/molssi-seamm/mopac_step/workflows/Release/badge.svg\n :target: https://molssi-seamm.github.io/mopac_step/index.html\n :alt: Documentation Status\n\n.. image:: https://img.shields.io/pypi/v/mopac_step.svg\n :target: https://pypi.python.org/pypi/mopac_step\n :alt: PyPi VERSION\n\nA SEAMM plug-in to setup, run and analyze semiempirical calculations\nwith MOPAC.\n\nThis plug-in provides a graphical user interface (GUI) for setting up\nand running simulations using the semiempirical quantum chemistry code\nMOPAC_.\n\n* Free software: BSD license\n* Documentation: https://molssi-seamm.github.io/mopac_step/index.html\n* Code: https://github.com/molssi-seamm/mopac_step\n\n.. _MOPAC: http://openmopac.net\n\nFeatures\n--------\n\n* Single-point energies\n* Structural optimization\n* IR and Raman vibrational frequencies\n* Temperature dependent thermodynamic functions\n* Results can be stored in flowchart variables or tables_.\n\n.. _tables: https://molssi-seamm.github.io/table_step/index.html\n\nseamm-mopac Docker image\n------------------------\nThere is a Docker image available for the SEAMM MOPAC plug-in for running mopac. It is\navailable at the Github Container Registry (ghcr.io) as\n\n.. code-block:: bash\n\n ghcr.io/molssi-seamm/seamm-mopac:<version>\n\nWhere <version> is the explicit version tag for the desired image. The tag `latest` is\nquite confusing, and does not mean the latest version of the image, so we recomend using\nexplcit versions rather than `latest`.\n\nThe container can also be run standalone with the following command:\n\n.. code-block:: bash\n\n docker run --rm -v $PWD:/home ghcr.io/molssi-seamm/seamm-mopac:<version> ?mopac <input file>?\n\nwhere `<input file>` is the input file for the MOPAC calculation. By default, mopac is\nrun using the input file `mopac.dat`. The output files will be written to the current\ndirectory. The `--rm` option removes the container after it exits, and the `-v` option\nmounts the current directory to the `/home` directory in the container.\n\nAcknowledgements\n----------------\n\nThis package was created with Cookiecutter_ and the `molssi-seamm/cookiecutter-seamm-plugin`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin\n\nDeveloped by the Molecular Sciences Software Institute (MolSSI_),\nwhich receives funding from the `National Science Foundation`_ under\nawards OAC-1547580 and CHE-2136142.\n\n.. _MolSSI: https://www.molssi.org\n.. _`National Science Foundation`: https://www.nsf.gov\n\n\n=======\nHistory\n=======\n2024.10.15 -- Bugfix: error if used in a loop and previous directories deleted.\n * The code crashed if called with a loop in the flowchart, and the last directory of\n a previous loop iteration was deleted before running the next iteration.\n \n2024.8.21 -- Bugfix for PM7-TS and optimization, GUI clean up for CI calculations.\n * Calculations using PM7-TS do not write information to the AUX file, so added code to\n get the energy from the output file.\n * For optimizations, the option for the frequency of calculating the force constants\n and the maximum radius of convergence were missing from the GUI for the EF\n method. The frequency also was not being correctly handled in the input to MOPAC.\n * The GUI for using CI calculations was cleaned up.\n \n2024.8.17 -- Added CI calculations and better handling of transition states\n * Added ability to do the various types of CI calculations that MOPAC supports.\n * Improved the handling of TS calculations and added NLLSQ and SIGMA methods in\n the optimization step.\n * Added option to correctly handle transition states in the thermodynamics step and\n improved the output to include the imaginary and low-lying frequencies.\n \n2024.7.29 -- Bugfix in bond analysis for atoms and mopac.ini\n * Fixed a bug in the bond analysis that caused the code to crash for calculations on\n atoms. \n * Fixed a bug in the mopac.ini file created if it did not exists that caused the code\n to crash when the calculation was run.\n\n2024.5.14 -- Added output of energy & gradients to JSON\n * To support the Energy Scan step.\n \n2024.3.17 -- Updated installation\n * Updated the installation to reflect the new way to install SEAMM plug-ins to support\n both Conda and Docker\n \n2024.1.16 -- Added support for containers.\n * Added access to the new PM6-ORG parameterization and made it the default, though PM7\n is still preferred for materials simulation. PM6-ORG handle organic and biomolecules\n well.\n * Made the Lewis structure analysis more robust and added information to the output.\n * Provided an option for the Lewis structure calculation to set the charge of the\n system to that calculaed by the Lewis structure.\n * Added support for containers\n * Made default to run serially, since parallel doesn't provide much benefit.\n * Fixed bug in analysis if optimization doesn't converge.\n\n2023.12.18 -- Added readonly flag\n * Added a flag to prepare the input but not run the calculation.\n \n2023.11.15 -- More updates for v2022.1.0\n * Added PM6-ORG Hamiltonian to options\n * Added other new data types for the AUX file.\n \n2023.11.14 -- Updated for MOPAC v2022.1.0\n * MOPAC v2022.1.0 added GRADIENT_NORM_UPDATED to the AUX file. This updates adds it to\n the results recognized by the plug-in\n \n2023.10.30 -- Updated to standard structure handling\n * Adds IUPAC names, InChI and InChIKey as possible names for configurations\n * Cleaned up output to be properly indented and laid out.\n \n2023.8.30 -- Support for spacegroup symmetry\n\n2023.7.27 -- Bugfix: printing bond order info\n * If the bond orders were printed but not used on the system, the code crashed.\n \n2023.7.26 -- Added output of bond orders\n * Also added capability to use the bond orders to put bond multiplicities on the\n structure.\n \n2023.7.24 -- Bugfix in Lewis structure with bond orders\n * Major issue in getting the bonds from the Lewis structure where the atoms and bond\n orders were mixed up.\n \n2023.6.5 -- Bugfix working around MOPAC problem\n * MOPAC is not consistent about putting end of file and end of program markers in the\n AUX file. This caused carashed in SEAMM, which this fixes until MOPAC can be\n corrected.\n \n2023.4.24 -- Bugfixes for Lewis structure\n * Correctly handle periodic systems in Lewis structure.\n * Fixed and issue with the Lewis structure GUI not displaying all the widgets.\n \n2023.3.31 -- Bugfix\n Lewis structure could reference a variable before it was set, and crash.\n \n2023.3.15 -- Bugfix\n A copy of the input and output files for MOPAC was inadvertently written to the main\n job directory. This has been fixed.\n \n2023.2.13 -- Added Lewis Structure step\n Provide access to the 'LEWIS' keyword in MOPAC for generating the Lewis dot\n structure. This step also allows assigning the bonds of the system using either the\n connectivity or the Lewis structure.\n \n2022.11.18 -- Printing spins on atoms\n Fixed an oversight that preventing printing spins on the atoms, and storing them on\n the structure. Also increased the precision of the AUX file so have coordinates to\n seven decimals, which should maintain symmetry better.\n \n2022.11.4 -- Added ForceConstant substep\n Calculates and writes the Hessian (force constant) matrix to disk. Works for both\n molecular and periodic systems, and provides an option to control which parts of the\n Hessian matrix are written. Defaults to the full matrix. 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