Merge pull request #2826 from JacksonBurns/release/rmg_33

RMG-Py Version 3.3.0

Author: JacksonBurns

CONTRIBUTING.md

@@ -29,7 +29,7 @@ Thank you for contributing to RMG-Py! Please take a moment to review our guideli
 
 ### **Do you want to contribute to the documentation?**
 
-* Documentation is [hosted here](http://reactionmechanismgenerator.github.io/RMG-Py/) using [Sphinx](https://www.sphinx-doc.org/en/master/). 
+* Documentation is [hosted here](https://reactionmechanismgenerator.github.io/RMG-Py/) using [Sphinx](https://www.sphinx-doc.org/en/master/). 
 
 * The live version of the documentation is hosted on the `gh-pages` branch which is updated upon pushes to the `main` branch of RMG-Py.
 

README.md

@@ -22,12 +22,12 @@ Gaussian, Q-Chem, Molpro, Orca, Psi4, and TeraChem.
 
 ## How to Install
 You can either download the source from GitHub and compile yourself, or download the binaries from Anaconda.
-Please see the [Download and Install](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html) page for detailed instructions.
+Please see the [Download and Install](https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html) page for detailed instructions.
 
 ## Documentation
-- [RMG Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/users/rmg/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
-- [Arkane Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/users/arkane/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
-- [RMG API Reference](http://reactionmechanismgenerator.github.io/RMG-Py/reference/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_API_Reference.pdf))
+- [RMG Documentation](https://ReactionMechanismGenerator.github.io/RMG-Py/users/rmg/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
+- [Arkane Documentation](https://ReactionMechanismGenerator.github.io/RMG-Py/users/arkane/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
+- [RMG API Reference](https://reactionmechanismgenerator.github.io/RMG-Py/reference/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_API_Reference.pdf))
 
 ## How to Contribute
 Please see the [Contributor Guidelines](https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/CONTRIBUTING.md)
@@ -44,10 +44,10 @@ perform thermodynamics and kinetics searches
 - [Issues Page](https://github.com/ReactionMechanismGenerator/RMG-Py/issues/): view current issues and feature requests
 
 ## Credits
-- [Professor William H. Green's research group](http://cheme.scripts.mit.edu/green-group/) at the 
-[Massachusetts Institute of Technology](http://web.mit.edu/) 
-- [Professor Richard H. West's research group](http://www.northeastern.edu/comocheng/) at 
-[Northeastern University](http://www.northeastern.edu/). 
+- [Professor William H. Green's research group](https://greengroup.mit.edu/) at the 
+[Massachusetts Institute of Technology](https://web.mit.edu/) 
+- [Professor Richard H. West's research group](https://www.northeastern.edu/comocheng/) at 
+[Northeastern University](https://www.northeastern.edu/). 
 
 ## Resources and References
 The resources and relevant publications are listed [here](https://rmg.mit.edu/resources) on the RMG-website. 

arkane/README.md

@@ -13,13 +13,13 @@ Arkane is distributed via the [RMG-Py repository](https://github.com/ReactionMec
 as a [root module](https://github.com/ReactionMechanismGenerator/RMG-Py/tree/main/arkane).
 
 ## How to Install
-Please follow the [installation instructions](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html)
+Please follow the [installation instructions](https://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html)
 for RMG-Py.
 
 ## Documentation
-- [RMG Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/users/rmg/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
-- [Arkane Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/users/arkane/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
-- [RMG API Reference](http://reactionmechanismgenerator.github.io/RMG-Py/reference/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_API_Reference.pdf))
+- [RMG Documentation](https://ReactionMechanismGenerator.github.io/RMG-Py/users/rmg/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
+- [Arkane Documentation](https://ReactionMechanismGenerator.github.io/RMG-Py/users/arkane/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_and_Arkane_Documentation.pdf))
+- [RMG API Reference](https://reactionmechanismgenerator.github.io/RMG-Py/reference/index.html) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/main/documentation/RMG-Py_API_Reference.pdf))
 
 ## How to cite
 A. Grinberg Dana, M.S. Johnson, J.W. Allen, S. Sharma, S. Raman, M. Liu, C.W. Gao, C.A. Grambow, M.J. Goldman,
@@ -32,7 +32,7 @@ A statistical mechanics, thermodynamics, transition state theory, and master equ
 DOI: [10.1002/kin.21637](https://doi.org/10.1002/kin.21637)
 
 ## How to Contribute
-Please see the [Contributor Guidelines](https://github.com/ReactionMechanismGenerator/RMG-Py/wiki/RMG-Contributor-Guidelines)
+Please see the [Contributor Guidelines](https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/CONTRIBUTING.md)
 for details on how to contribute to RMG-Py or RMG-database.
 
 ## How to Give Feedback

arkane/encorr/corr.py

@@ -221,7 +221,7 @@ def assign_frequency_scale_factor(level_of_theory: Union[LevelOfTheory, Composit
 
     Sources:
         [1] I.M. Alecu, J. Zheng, Y. Zhao, D.G. Truhlar, J. Chem. Theory Comput. 2010, 6, 2872, DOI: 10.1021/ct100326h
-        [2] http://cccbdb.nist.gov/vibscalejust.asp
+        [2] https://cccbdb.nist.gov/vibscalejustx.asp
         [3] http://comp.chem.umn.edu/freqscale/190107_Database_of_Freq_Scale_Factors_v4.pdf
         [4] Calculated as described in 10.1021/ct100326h
         [5] J.A. Montgomery, M.J. Frisch, J. Chem. Phys. 1999, 110, 2822–2827, DOI: 10.1063/1.477924

arkane/ess/gaussian.py

@@ -524,7 +524,7 @@ def _load_scan_specs(self, letter_spec, get_after_letter_spec=False):
         parameters after letter_spec is found. If not specified or False, it will
         return the preceeding letters, which are typically the atom numbers.
 
-        More information about the syntax can be found http://gaussian.com/opt/
+        More information about the syntax can be found https://gaussian.com/opt/
         """
         output = []
         reached_input_spec_section = False

arkane/main.py

@@ -465,7 +465,7 @@ def log_header(level=logging.INFO):
     logging.log(level, '#   Authors: RMG Developers (rmg_dev@mit.edu)                  #')
     logging.log(level, '#   P.I.s:   William H. Green (whgreen@mit.edu)                #')
     logging.log(level, '#            Richard H. West (r.west@neu.edu)                  #')
-    logging.log(level, '#   Website: http://reactionmechanismgenerator.github.io/      #')
+    logging.log(level, '#   Website: https://reactionmechanismgenerator.github.io/      #')
     logging.log(level, '#                                                              #')
     logging.log(level, '################################################################')
     logging.log(level, '')

arkane/statmech.py

@@ -1002,7 +1002,7 @@ def project_rotors(conformer, hessian, rotors, linear, is_ts, get_projected_out_
     constant matrix and use this to determine the vibrational frequencies. The
     list of vibrational frequencies is returned in cm^-1.
 
-    Refer to Gaussian whitepaper (http://gaussian.com/vib/) for procedure to calculate
+    Refer to Gaussian whitepaper (https://gaussian.com/vib/) for procedure to calculate
     harmonic oscillator vibrational frequencies using the force constant matrix.
     """
     n_rotors = 0

documentation/RMG-Py_API_Reference.pdf

@@ -8,19 +8,19 @@ RMG is an automatic chemical reaction mechanism generator
 that constructs kinetic models composed of elementary chemical reaction 
 steps using a general understanding of how molecules react. This documentation is for the newer Python version of RMG that we call RMG-Py.
 
-+---------------------------------------------+----------------------------------------------------------------------------------------+
-| I want to...                                | Resource                                                                               |
-+=============================================+========================================================================================+
-| analyze models & search databases           | `RMG website resources <https://rmg.mit.edu/>`__  (no download needed)                 |
-+---------------------------------------------+----------------------------------------------------------------------------------------+
-| create mechanisms automatically             | Download RMG with the RMG User's Guide                                                 |
-+---------------------------------------------+----------------------------------------------------------------------------------------+
-| make transition state theory calculations   | Run Arkane after downloading RMG. See the Arkane User's Guide                          |
-+---------------------------------------------+----------------------------------------------------------------------------------------+
-| post an issue with RMG                      | `GitHub issues page <https://github.com/ReactionMechanismGenerator/RMG-Py/issues>`__   |
-+---------------------------------------------+----------------------------------------------------------------------------------------+
-| contribute to the RMG project               | `RMG developer's wiki <https://github.com/ReactionMechanismGenerator/RMG-Py/wiki>`__   |
-+---------------------------------------------+----------------------------------------------------------------------------------------+
++---------------------------------------------+---------------------------------------------------------------------------------------------------------------+
+| I want to...                                | Resource                                                                                                      |
++=============================================+===============================================================================================================+
+| analyze models & search databases           | `RMG website resources <https://rmg.mit.edu/>`__  (no download needed)                                        |
++---------------------------------------------+---------------------------------------------------------------------------------------------------------------+
+| create mechanisms automatically             | Download RMG with the RMG User's Guide                                                                        |
++---------------------------------------------+---------------------------------------------------------------------------------------------------------------+
+| make transition state theory calculations   | Run Arkane after downloading RMG. See the Arkane User's Guide                                                 |
++---------------------------------------------+---------------------------------------------------------------------------------------------------------------+
+| post an issue with RMG                      | `GitHub issues page <https://github.com/ReactionMechanismGenerator/RMG-Py/issues>`__                          |
++---------------------------------------------+---------------------------------------------------------------------------------------------------------------+
+| contribute to the RMG project               | `Contributor guidelines <https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/CONTRIBUTING.md>`__   |
++---------------------------------------------+---------------------------------------------------------------------------------------------------------------+
 
 Arkane is developed and distributed as part of RMG-Py, but can be used as a stand-alone
 application for Thermochemistry, Transition State Theory, and Master Equation chemical kinetics