Automated documentation rebuild

Author: github-actions

_sources/latex-rmg.rst.txt

@@ -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

_sources/reference/molecule/graph.rst.txt

@@ -1,3 +1,5 @@
+.. _rmgpy.molecule.graph.Graph:
+
 **************************
 rmgpy.molecule.graph.Graph
 **************************

_sources/reference/molecule/group.rst.txt

@@ -1,3 +1,5 @@
+.. _rmgpy.molecule.Group:
+
 ********************
 rmgpy.molecule.Group
 ********************

_sources/reference/molecule/molecule.rst.txt

@@ -1,3 +1,5 @@
+.. _rmgpy.molecule.Molecule:
+
 ***********************
 rmgpy.molecule.Molecule
 ***********************

_sources/users/arkane/faq.rst.txt

@@ -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/

_sources/users/arkane/input.rst.txt

@@ -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

_sources/users/arkane/introduction.rst.txt

@@ -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
 
 

_sources/users/rmg/installation/anacondaDeveloper.rst.txt

@@ -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

_sources/users/rmg/installation/anacondaDeveloperWindows.rst.txt

@@ -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
 

_sources/users/rmg/installation/anacondaUser.rst.txt

@@ -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::