ReactionMechanismGenerator · jonwzheng · Nov 13, 2024 · Aug 6, 2024 · Aug 6, 2024 · Aug 6, 2024
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1 @@
+Initial commit
diff --git a/documentation/source/theory/rmg/dynamics.rst b/documentation/source/theory/rmg/dynamics.rst
@@ -67,31 +67,31 @@ for movement from surface to bulk core based on flux or dynamics criterion.
 Key Parameters for Dynamics Criterion and Surface Algorithm
 ===========================================================
 
-* **toleranceMoveEdgeReactionToCore**
+* ``toleranceMoveEdgeReactionToCore``
 
   An edge reaction will be pulled directly into the bulk core if its dynamics number
   ever exceeds this value.
 
-* **toleranceMoveEdgeReactionToSurface**
+* ``toleranceMoveEdgeReactionToSurface``
 
   An edge reaction will be pulled into the surface if its dynamics number
   ever exceeds this value.
 
-* **toleranceMoveEdgeReactionToCoreInterrupt**
+* ``toleranceMoveEdgeReactionToCoreInterrupt``
 
   When any reaction's dynamics number exceeds this value the simulation will be interrupted.
 
-* **toleranceMoveEdgeReactionToSurfaceInterrupt**
+* ``toleranceMoveEdgeReactionToSurfaceInterrupt``
 
   When the dynamics number of any reaction that would be valid for movement to the surface
   exceeds this value the simulation will be interrupted
 
-* **toleranceMoveSurfaceReactionToCore**
+* ``toleranceMoveSurfaceReactionToCore``
 
   A surface reaction will be pulled into the bulk core if its dynamics number
   ever exceeds this value.  Note this is done on the fly during simulation.
 
-* **toleranceMoveSurfaceSpeciesToCore**
+* ``toleranceMoveSurfaceSpeciesToCore``
 
   A surface species will be pulled into the bulk core if it's rate ratio
   ever exceeds this value.  Note this is done on the fly during simulation.
diff --git a/documentation/source/theory/rmg/prune.rst b/documentation/source/theory/rmg/prune.rst
@@ -12,30 +12,30 @@ in order to achieve both low memory consumption and mechanism accuracy. Pruning
 Key Parameters in Pruning
 =========================
 
-* toleranceKeepInEdge
+* ``toleranceKeepInEdge``
 
-  Any edge species to prune should have peak flux along the whole conversion course lower than toleranceKeepInEdge :math:`*` characteristic flux. Thus, larger values will lead to smaller edge mechanisms.
+  Any edge species to prune should have peak flux along the whole conversion course lower than ``toleranceKeepInEdge`` :math:`*` characteristic flux. Thus, larger values will lead to smaller edge mechanisms.
 
-* toleranceMoveToCore
+* ``toleranceMoveToCore``
 
-  Any edge species to enter core model should have flux at some point larger than toleranceMoveToCore :math:`*` characteristic flux Thus, in general, smaller values will lead to larger core mechanisms.
+  Any edge species to enter core model should have flux at some point larger than ``toleranceMoveToCore`` :math:`*` characteristic flux Thus, in general, smaller values will lead to larger core mechanisms.
 
-* toleranceInterrupSimulation
+* ``toleranceInterruptSimulation``
 
-  Once flux of any edge species exceeds toleranceInterruptSimulation :math:`*` characteristic flux, dynamic simulation will be stopped.
+  Once flux of any edge species exceeds ``toleranceInterruptSimulation`` :math:`*` characteristic flux, dynamic simulation will be stopped.
   Usually this tolerance will be set a very high value so that any flux's exceeding that means mechanism is too incomplete to continue 
   dynamic simulation.
 
-* maximumEdgeSpecies
+* ``maximumEdgeSpecies``
 
   If dynamic simulation isn't interrupted in half way and total number of the edge species whose peak fluxes are higher than 
-  toleranceKeepInEdge :math:`*` characteristic flux exceeds maximumEdgeSpecies, such excessive amount of edge species with lowest peak fluxes will be pruned.
+  ``toleranceKeepInEdge`` :math:`*` characteristic flux exceeds ``maximumEdgeSpecies``, such excessive amount of edge species with lowest peak fluxes will be pruned.
 
-* minCoreSizeForPrune
+* ``minCoreSizeForPrune``
 
   Ensures that a minimum number of species are in the core before pruning occurs, in order to avoid pruning the model when it is far away from completeness.  The default value is set to 50 species. 
 
-* minSpeciesExistIterationsForPrune
+* ``minSpeciesExistIterationsForPrune``
 
   Set the number of iterations an edge species must stay in the job before it can be pruned.  The default value is 2 iterations.  
 
@@ -46,20 +46,20 @@ How Pruning Works
 
   The goal of pruning is to delete those "useless" edge species. So "usefulness" should be defined and it's natural to have flux as a 
   criterion for "usefulness". Since flux changes with reactant conversion, peak flux is chosen here to make decision of pruning or not.
-  Every time pruning is triggered, edge species with peak flux lower than toleranceKeepInEdge :math:`*` characteristic flux will be deleted.
+  Every time pruning is triggered, edge species with peak flux lower than ``toleranceKeepInEdge`` :math:`*` characteristic flux will be deleted.
 
 .. figure:: fluxDiagramWithTolerance.png
 
-  However, pruning is not always triggered because of toleranceInterruptSimulation. As mentioned above, in order to prune, RMG needs to figure out
+  However, pruning is not always triggered because of ``toleranceInterruptSimulation``. As mentioned above, in order to prune, RMG needs to figure out
   the peak flux of each edge species, which requires dynamic simulation to complete. If some run of dynamic simulation is terminated in half way
-  by toleranceInterruptSimulation, pruning is rejected although there might be some edge species with peak fluxes lower than 
-  toleranceKeepInEdge :math:`*` characteristic flux. Since pruning requires to complete dynamic simulation, setting toleranceInterruptSimulation to be positive infinity, 
-  as an extreme case, means always enabling pruning. Another extreme case would be that it has same value as toleranceMoveToCore where 
+  by ``toleranceInterruptSimulation``, pruning is rejected although there might be some edge species with peak fluxes lower than 
+  ``toleranceKeepInEdge`` :math:`*` characteristic flux. Since pruning requires to complete dynamic simulation, setting ``toleranceInterruptSimulation`` to be positive infinity, 
+  as an extreme case, means always enabling pruning. Another extreme case would be that it has same value as ``toleranceMoveToCore`` where 
   no pruning occurs.
 
-  In summary, each run of dynamic simulation will proceed towards terminationConversion unless some flux exceeds 
-  toleranceInterruptSimulation :math:`*` characteristic flux.Following complete simulation is the pruning of edge species whose flux is not high enough be kept
-  in the edge, which is followed by pruning of excessive amount of edge species to make sure total edge species number is no greater than maximumEdgeSpecies.
+  In summary, each run of dynamic simulation will proceed towards ``terminationConversion`` unless some flux exceeds 
+  ``toleranceInterruptSimulation`` :math:`*` characteristic flux. Following complete simulation is the pruning of edge species whose flux is not high enough be kept
+  in the edge, which is followed by pruning of excessive amount of edge species to make sure total edge species number is no greater than ``maximumEdgeSpecies``.
 
 
 

diff --git a/documentation/source/users/arkane/credits.rst b/documentation/source/users/arkane/credits.rst
@@ -9,7 +9,7 @@ Project Supervisors:
 - Prof. William H. Green (whgreen@mit.edu)
 - Prof. Richard H. West (r.west@northeastern.edu)
 - Prof. C. Franklin Goldsmith (franklin_Goldsmith@brown.edu)
-- Asst. Prof. Alon Grinberg Dana (alon@technion.ac.il)
+- Prof. Alon Grinberg Dana (alon@technion.ac.il)
 
 Developers: (rmg_dev@mit.edu)
 
@@ -24,10 +24,10 @@ Developers: (rmg_dev@mit.edu)
 - Dr. D.S. Ranasinghe
 - Dr. R.J. Gillis
 - Dr. A.M. Payne
-- Asst. Prof. Y.-P. Li
-- X. Dong
-- K.A. Spiekermann
-- H. Wu
+- Prof. Y.-P. Li
+- Dr. X. Dong
+- Dr. K.A. Spiekermann
+- Mr. H. Wu
 - Dr. E.E. Dames
 - Dr. Z.J. Buras,
 - Dr. N.M. Vandewiele
@@ -41,11 +41,4 @@ Developers: (rmg_dev@mit.edu)
 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,
-D.S. Ranasinghe, R.J. Gillis, A.M. Payne, Y.-P. Li, X. Dong, K.A. Spiekermann, H. Wu, E.E. Dames, Z.J. Buras,
-N.M. Vandewiele, N.W. Yee, S.S. Merchant, B. Buesser, C.A. Class, C.F. Goldsmith, R.H. West, W.H. Green,
-"Automated reaction kinetics and network exploration (Arkane):
-A statistical mechanics, thermodynamics, transition state theory, and master equation software",
-*International Journal of Chemical Kinetics* 2023, 55(6), 300-323.
-
-DOI: `10.1002/kin.21637 <https://doi.org/10.1002/kin.21637>`_
+Please refer to the ``Arkane`` reference in the `CITATIONS.bib file <https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/CITATIONS.bib>`_.
diff --git a/documentation/source/users/rmg/credits.rst b/documentation/source/users/rmg/credits.rst
@@ -16,26 +16,29 @@ Project Supervisors:
 
 Current Developers: (rmg_dev@mit.edu)
 
-- Dr. Alon Grinberg Dana
+- Prof. Alon Grinberg Dana
 - Dr. Matt Johnson
-- Yen-Ting Wang
-- Xiaorui Dong
-- Hao-Wei Pang
+- Dr. Anna Doner
 - Oscar Wu
-- Kevin Spiekermann
 - Jonathan Zheng
 - Jackson Burns
 - Nathan Morgan
+- Prof. Richard H. West
 - Prof. C. Franklin Goldsmith
-- Dr. Katrin Blondal
 - Dr. Bjarne Kreitz
+- Chao Xu
 - Chris Blais
 - Sevy Harris
 - Nora Khalil
 
 Previous Developers: 
 
+- Dr. Xiaorui Dong
+- Dr. Hao-Wei Pang
+- Dr. Kevin Spiekermann
+- Yen-Ting Wang
 - Dr. Joshua W. Allen
+- Dr. Katrin Blondal
 - Dr. Yunsie Chung
 - Dr. David Farina
 - Dr. Mark Goldman
@@ -66,25 +69,4 @@ Previous Developers:
 How to Cite
 ***********
 
-C.W. Gao, J.W. Allen, W.H. Green, R.H. West,
-"Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms",
-*Computer Physics Communications* 2016, 203, 212-225.
-
-DOI: `10.1016/j.cpc.2016.02.013 <https://doi.org/10.1016/j.cpc.2016.02.013>`_
-
-
-M. Liu, A. Grinberg Dana, M.S. Johnson, M.J. Goldman, A. Jocher, A.M. Payne, C.A. Grambow, K. Han, N.W. Yee,
-E.J. Mazeau, K. Blondal, R.H. West, C.F. Goldsmith, W.H. Green,
-"Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation",
-*Journal of Chemical Information and Modeling* 2021, 61(6), 2686–2696.
-
-DOI: `10.1021/acs.jcim.0c01480 <https://doi.org/10.1021/acs.jcim.0c01480>`_
-
-
-
-M.S. Johnson, X. Dong, A. Grinberg Dana, Y. Chung, D. Farina, R.J. Gillis, M. Liu, N.W. Yee, K. Blondal,
-E. Mazeau, C.A. Grambow, A.M. Payne, K.A. Spiekermann, H.-W. Pang, C.F. Goldsmith, R.H. West, W.H. Green,
-"The RMG Database for Chemical Property Prediction",
-*Chemical Information* 2022, 62(20), 4906–4915.
-
-DOI: `10.1021/acs.jcim.2c00965 <https://doi.org/10.1021/acs.jcim.2c00965>`_
+Please refer to the ``RMG``, ``RMG3``, and ``RMG_Database`` citations in the `CITATIONS.bib file <https://github.com/ReactionMechanismGenerator/RMG-Py/blob/main/CITATIONS.bib>`_.