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Upgrade to OpenMOPAC #2417

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merged 14 commits into from
May 10, 2023
Merged

Upgrade to OpenMOPAC #2417

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a88238b
switch to conda-force mopac in environment.yml, skip install step in CI
JacksonBurns Apr 20, 2023
0915745
add libfortran for mopac, float cantera to potentially unsupported ver.
JacksonBurns Apr 20, 2023
77be5e5
Use newer pydas and pydqed.
JacksonBurns May 2, 2023
f38d45a
change mopac unit tests
JacksonBurns May 8, 2023
2068326
update documentation regarding use of MOPAC
JacksonBurns May 8, 2023
0fe291c
delete NO_LICENSE and NO_MOPAC checks since it will now be included a…
JacksonBurns May 8, 2023
ebea50e
format mopac.py with black, remove checks for old unsupported versions
JacksonBurns May 9, 2023
853a9cb
fix typo (delta not selta), decrease required close enough, format wi…
JacksonBurns May 9, 2023
dd98e07
set reproduce threshold to half a percent
JacksonBurns May 9, 2023
795de00
Update rmgpy/qm/mopac.py
JacksonBurns May 9, 2023
101f8b5
black formatting, rename variables for PEP8
JacksonBurns May 9, 2023
3b444a9
module-level point group dictionary should be all caps (PEP8)
JacksonBurns May 9, 2023
b20c813
remove dead, untested, and undocumented MOPAC_DIR lines
JacksonBurns May 9, 2023
ddf97ee
Remove conda-forge::libgfortran-ng>=10.0 from environment.yml for MacOS
rwest May 10, 2023
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10 changes: 0 additions & 10 deletions .github/workflows/CI.yml
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Expand Up @@ -86,16 +86,6 @@ jobs:
julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' || true
ln -sfn $(which python-jl) $(which python)

# Attempt to install MOPAC
- name: Install MOPAC
env:
MOPACKEY: ${{ secrets.MOPACKEY }}
timeout-minutes: 1
continue-on-error: true # allowed to fail on pull request from a forked repository
run: |
set +o pipefail
yes 'Yes' | ${CONDA_PREFIX}/bin/mopac "$MOPACKEY"

# non-regression testing
- name: Unit tests
run: make test-unittests
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4 changes: 0 additions & 4 deletions documentation/source/users/rmg/installation/anacondaDeveloper.rst
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Expand Up @@ -137,10 +137,6 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux

python-jl replace/with/path/to/rmg.py input.py

#. Optional: If you wish to use the :ref:`QMTP interface <qm>` with `MOPAC <http://openmopac.net/>`_ to run quantum mechanical calculations for improved thermochemistry estimates of cyclic species, please obtain a legal license through the `MOPAC License Request Form <http://openmopac.net/form.php>`_. Once you have it, type the following into your terminal ::

mopac password_string_here

You may now use RMG-Py, Arkane, as well as any of the :ref:`Standalone Modules <modules>` included in the RMG-Py package.


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4 changes: 0 additions & 4 deletions documentation/source/users/rmg/installation/anacondaUser.rst
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Expand Up @@ -22,10 +22,6 @@ Binary Installation Using Anaconda for Unix-Based Systems: Linux and Mac OSX

source activate rmg_env

#. Optional: If you wish to use the :ref:`QMTP interface <qm>` with `MOPAC <http://openmopac.net/>`_ to run quantum mechanical calculations for improved thermochemistry estimates of cyclic species, please obtain a legal license through the `MOPAC License Request Form <http://openmopac.net/form.php>`_. Once you have it, type the following into your terminal ::

mopac password_string_here

#. You may now run an RMG test job. Save the `Minimal Example Input File <https://raw.githubusercontent.com/ReactionMechanismGenerator/RMG-Py/master/examples/rmg/minimal/input.py>`_
to a local directory. Use the terminal to run your RMG job inside that folder using the following command ::

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3 changes: 1 addition & 2 deletions documentation/source/users/rmg/installation/dependencies.rst
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Expand Up @@ -63,5 +63,4 @@ All of RMG's dependencies except the ones listed below are freely available and
If you wish to do on-the-fly quantum chemistry calculations of thermochemistry (advisable for fused cyclic species in particular, where the ring corrections to group additive estimates are lacking),
the then you will need the third-party software for the QM calculations:

* **gaussian**: Gaussian03 and Gaussian09 are currently supported and commercially available. See `https://gaussian.com <https://gaussian.com>`_ for more details.
* **mopac** MOPAC can be found at `http://openmopac.net/ <http://openmopac.net/>`_. Though it is not free for industrial use, it is free for non-profit and academic research use.
* **gaussian**: Gaussian03 and Gaussian09 are currently supported and commercially available. See `https://gaussian.com <https://gaussian.com>`_ for more details.
6 changes: 3 additions & 3 deletions environment.yml
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Expand Up @@ -23,7 +23,7 @@ dependencies:
- rmg::lpsolve55
- markupsafe
- matplotlib >=1.5
- rmg::mopac
- conda-forge::mopac
- mpmath
- rmg::muq2
- networkx
Expand All @@ -34,9 +34,9 @@ dependencies:
- conda-forge::openbabel >= 3
- pandas
- psutil
- rmg::pydas >=1.0.2
- rmg::pydas >=1.0.3
- pydot
- rmg::pydqed >=1.0.1
- rmg::pydqed >=1.0.3
- rmg::pyjulia
- pymongo
- pyparsing
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