Merge pull request #2417 from ReactionMechanismGenerator/new-mopac

Upgrade to OpenMOPAC

Author: hwpang

.github/workflows/CI.yml

@@ -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

documentation/source/users/rmg/installation/anacondaDeveloper.rst

@@ -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.
 
 

documentation/source/users/rmg/installation/anacondaUser.rst

@@ -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 ::
 

documentation/source/users/rmg/installation/dependencies.rst

@@ -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.

environment.yml

@@ -23,7 +23,7 @@ dependencies:
   - rmg::lpsolve55
   - markupsafe
   - matplotlib >=1.5
-  - rmg::mopac
+  - conda-forge::mopac
   - mpmath
   - rmg::muq2
   - networkx
@@ -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