ReactionMechanismGenerator · JacksonBurns · Jul 11, 2025 · Jul 10, 2025 · Jul 10, 2025 · Jul 10, 2025
diff --git a/CONTRIBUTING.md b/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.
 

diff --git a/README.md b/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. 

diff --git a/arkane/README.md b/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

diff --git a/arkane/encorr/corr.py b/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

diff --git a/arkane/ess/gaussian.py b/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

diff --git a/arkane/main.py b/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, '')

diff --git a/arkane/statmech.py b/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

diff --git a/documentation/RMG-Py_API_Reference.pdf b/documentation/RMG-Py_API_Reference.pdf
diff --git a/documentation/RMG-Py_and_Arkane_Documentation.pdf b/documentation/RMG-Py_and_Arkane_Documentation.pdf
diff --git a/documentation/source/latex-rmg.rst b/documentation/source/latex-rmg.rst
@@ -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

diff --git a/documentation/source/reference/molecule/graph.rst b/documentation/source/reference/molecule/graph.rst
@@ -1,3 +1,5 @@
+.. _rmgpy.molecule.graph.Graph:
+
 **************************
 rmgpy.molecule.graph.Graph
 **************************

diff --git a/documentation/source/reference/molecule/group.rst b/documentation/source/reference/molecule/group.rst
@@ -1,3 +1,5 @@
+.. _rmgpy.molecule.Group:
+
 ********************
 rmgpy.molecule.Group
 ********************

diff --git a/documentation/source/reference/molecule/molecule.rst b/documentation/source/reference/molecule/molecule.rst
@@ -1,3 +1,5 @@
+.. _rmgpy.molecule.Molecule:
+
 ***********************
 rmgpy.molecule.Molecule
 ***********************

diff --git a/documentation/source/users/arkane/faq.rst b/documentation/source/users/arkane/faq.rst
@@ -30,8 +30,8 @@ data and physical quantities.
 
 .. [#f2] No longer distributed
 
-.. _MultiWell: https://clasp-research.engin.umich.edu/multiwell/
-.. _UNIMOL: http://www.ccl.net/cca/software/SOURCES/FORTRAN/unimol/index.shtml
-.. _ChemRate: https://kinetics.nist.gov/ChemRate/
-.. _Variflex: http://web.archive.org/web/20181126234555/http://ftp.tcg.anl.gov/pub/variflex/Summary.vrfx
+.. _MultiWell: https://web.archive.org/web/20220927051103/https://multiwell.engin.umich.edu/about/
+.. _UNIMOL: https://server.ccl.net//cca/software/SOURCES/FORTRAN/unimol/index.shtml
+.. _ChemRate: https://web.archive.org/web/20220621125921/https://kinetics.nist.gov/ChemRate/
+.. _Variflex: https://web.archive.org/web/20181126234555/http://ftp.tcg.anl.gov/pub/variflex/Summary.vrfx
 .. _MESMER: https://sourceforge.net/projects/mesmer/
diff --git a/documentation/source/users/arkane/input.rst b/documentation/source/users/arkane/input.rst
@@ -170,7 +170,7 @@ Frequency Scale Factor
 ======================
 
 Frequency scale factors are empirically fit to experiment for different ``modelChemistry``.
-Refer to NIST website for values (http://cccbdb.nist.gov/vibscalejust.asp).
+Refer to NIST website for values (https://cccbdb.nist.gov/vibscalejustx.asp).
 For CBS-QB3, which is not included in the link above, ``frequencyScaleFactor = 0.99`` according to Montgomery et al.
 (*J. Chem. Phys. 1999, 110, 2822–2827*).
 The frequency scale factor is automatically assigned according to the supplied ``modelChemistry``, if available
@@ -617,7 +617,7 @@ systems in literature. For example, if the user is interested in a pressure-depe
 formula C7H8, the single exponential down parameters for toluene in helium availabe from literature could be used for
 all unimolecular isomers in the network (assuming helium is the bath gas). One helpful literature source for calculated
 exponential down parameters is the following paper:
-http://www.sciencedirect.com/science/article/pii/S1540748914001084#s0060
+http://www.sciencedirect.com/science/article/pii/S1540748914001084
 
 
 Option #2: Directly Enter Molecular Properties
@@ -1056,7 +1056,7 @@ An example of the ``network`` function is given below along with a scheme of the
 
 .. image:: acetyl+O2.jpg
 
-Image source: `J.W. Allen, PhD dissertation, MIT 2013 <http://hdl.handle.net/1721.1/81677>`_,
+Image source: `J.W. Allen, PhD dissertation, MIT 2013 <https://dspace.mit.edu/handle/1721.1/81677>`_,
 calculated at the RQCISD(T)/CBS//B3LYP/6-311++G(d,p) level of theory
 
 Pressure Dependent Rate Calculation

diff --git a/documentation/source/users/arkane/introduction.rst b/documentation/source/users/arkane/introduction.rst
@@ -31,7 +31,7 @@ License
 =======
 
 Arkane is provided as free, open source code under the terms of the
-`MIT/X11 License <http://www.opensource.org/licenses/mit-license.php>`_. The
+`MIT/X11 License <https://opensource.org/license/mit>`_. The
 full, official license is reproduced below
 
 

diff --git a/documentation/source/users/rmg/installation/anacondaDeveloper.rst b/documentation/source/users/rmg/installation/anacondaDeveloper.rst
@@ -121,7 +121,7 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
     python replace/with/path/to/rmg.py input.py
 
 You may now use RMG-Py, Arkane, as well as any of the :ref:`Standalone Modules <modules>` included in the RMG-Py package.
-For more information about using conda, please check out the `conda user guide <https://conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_.
+For more information about using conda, please check out the `conda user guide <https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_.
 
 
 Debugging

diff --git a/documentation/source/users/rmg/installation/anacondaDeveloperWindows.rst b/documentation/source/users/rmg/installation/anacondaDeveloperWindows.rst
@@ -10,7 +10,7 @@ Installation by Source Using Anaconda Environment for Windows
     .. image:: images/AnacondaInstallWindows.png
         :align: center
 
-#. Install `Git <http://git-scm.com/download/win>`_, the open source version control package. When asked, append Git tools to your Command Prompt. It is also recommended to commit Unix-style line endings:
+#. Install `Git <https://git-scm.com/download/win>`_, the open source version control package. When asked, append Git tools to your Command Prompt. It is also recommended to commit Unix-style line endings:
 
     .. image:: images/InstallGit.png
         :align: center
@@ -44,7 +44,7 @@ Installation by Source Using Anaconda Environment for Windows
 
 #. If you set any new environment variables, you must now close and reopen the command prompt so that those environment variables can be refreshed and used.
 
-#. 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 command prompt ::
+#. Optional: If you wish to use the :ref:`QMTP interface <qm>` with `MOPAC <https://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 <https://openmopac.net/form.php>`_.  Once you have it, type the following into your command prompt ::
 
     mopac password_string_here
 

diff --git a/documentation/source/users/rmg/installation/anacondaUser.rst b/documentation/source/users/rmg/installation/anacondaUser.rst
@@ -15,7 +15,7 @@ Binary Installation Using Anaconda for Unix-Based Systems: Linux and Mac OSX
 
     conda activate rmg_env
 
-   For more information about using conda, please check out the `conda user guide <https://conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_.
+   For more information about using conda, please check out the `conda user guide <https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_.
 
    To install a specific version of RMG, add the version to the install command::
 

diff --git a/documentation/source/users/rmg/installation/anacondaUserWindows.rst b/documentation/source/users/rmg/installation/anacondaUserWindows.rst
@@ -17,7 +17,7 @@ Binary Installation Using Anaconda for Windows
 
     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 command prompt (while the environment is activated) ::
+#. Optional: If you wish to use the :ref:`QMTP interface <qm>` with `MOPAC <https://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 <https://openmopac.net/form.php>`_.Once you have it, type the following into your command prompt (while the environment is activated) ::
 
     mopac password_string_here