Merge pull request #2707 from ReactionMechanismGenerator/fix/docs-wik…

…i2website

[Docs] Update docs website with GitHub wiki info

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.

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``.
 
 
 

documentation/source/users/arkane/credits.rst

@@ -27,7 +27,7 @@ Developers: (rmg_dev@mit.edu)
 - Prof. Y.-P. Li
 - Dr. X. Dong
 - Dr. K.A. Spiekermann
-- Mr. H. Wu
+- H. Wu
 - Dr. E.E. Dames
 - Dr. Z.J. Buras,
 - Dr. N.M. Vandewiele

documentation/source/users/rmg/features.rst

@@ -4,30 +4,30 @@
 Overview of Features
 ********************
 
-Thermodynamics estimation using group additivity.
+**Thermodynamics estimation using group additivity.**
 	Group additivity based on Benson's groups provide fast and reliable thermochemistry estimates. A standalone utility for estimating heat of formation, entropy, and heat capacity is also included.
 
-Rate-based model enlargement 
+**Rate-based model enlargement.**
  	Reactions are added to the model based on their rate, fastest first.
 
-Rate-based termination. 
+**Rate-based termination.** 
 	The model enlargement stops when all excluded reactions are slower than a given threshold.
 	This provides a controllable error bound on the kinetic model that is generated.
 
-Extensible libraries
+**Extensible libraries.**
 	Ability to include reaction models on top of the provided reaction families.
 
-Pressure-dependent reaction networks. 
+**Pressure-dependent reaction networks.**
 	Dissociation, combination, and isomerization reactions have the potential to have rate coefficients that are dependent on both temperature and pressure, and RMG is able to estimate both for networks of arbitrary complexity with a bounded error.
 
-Simultaneous mechanism generation for several conditions.
+**Simultaneous mechanism generation for several conditions.**
 	Concurrent generation of a reaction mechanism over multiple temperature and pressure conditions. 
 	Mechanisms generated this way are valid over a range of reaction conditions.
 
-Dynamic simulation to a target conversion or time.
+**Dynamic simulation to a target conversion or time.**
 	Often the desired simulation time is not known *a priori*, so a target conversion is preferred.
 
-Transport properties estimation using group additivity 
+**Transport properties estimation using group additivity.**
 	The Lennard-Jones sigma and epsilon parameters are estimated using empirical correlations (based on a species' critical properties and acentric factor).
 	The critical properties are estimated using a group-additivity approach; the acentric factor is also estimated using empirical correlations.
 	A standalone application for estimating these parameters is provided, and the output is stored in CHEMKIN-readable format.

documentation/source/users/rmg/input.rst

@@ -647,9 +647,9 @@ this is more likely to kick out species RMG might otherwise have added to core.
 
 Advanced Setting: Taking Multiple Species At A Time
 ----------------------------------------------------
-Taking multiple objects (species, reactions or pdepNetworks) during a given simulation can often decrease your overall model generation time
+Taking multiple objects (``Species``, ``Reaction`` or ``PDepNetwork``) during a given simulation can often decrease your overall model generation time
 over only taking one.  For this purpose there is a ``maxNumObjsPerIter`` parameter that allows RMG to take
-that many species, reactions or pdepNetworks from a given simulation. This is done in the order they trigger their respective criteria.
+that many ``Species``, ``Reaction`` or ``PDepNetwork`` from a given simulation. This is done in the order they trigger their respective criteria.
 
 You can also set ``terminateAtMaxObjects=True`` to cause it to terminate when it has the maximum
 number of objects allowed rather than waiting around until it hits an interrupt tolerance.  This
@@ -669,6 +669,14 @@ For example ::
 Note that this can also result in larger models, however, sometimes these larger models (from taking more than one
 object at a time) pick up chemistry that would otherwise have been missed.
 
+
+Advanced Settings: Other 
+----------------------------------------------------
+- ``dynamicsTimeScale``: The time before which the dynamics criterion cannot be used to bring reactions into the model. This is useful because the math behind the dynamics criterion breaks down as ``t`` approaches 0, thus restricting the use of the dynamics criterion until later times may reduce the number of junk species/reactions added to the model.
+
+- ``ignoreOverallFluxCriterion``: Causes RMG to use the given flux criterion only for determining if a ``PDepNetwork`` should be explored and not whether species should enter the model. Lets you run pressure dependence alongside the dynamics criterion without the flux criterion.
+
+
 .. _ontheflyquantumcalculations:
 
 On the fly Quantum Calculations
@@ -1033,7 +1041,7 @@ It is now possible to concatenate different model and simulator blocks into the
 
 There must be the same number of each of these blocks (although only having one simulator block and many model blocks is enabled as well) and RMG will enter each stage these define in the order they were put in the input file.
 
-To enable easier manipulation of staging a new parameter in the model block was developed maxNumSpecies that is the number of core species at which that stage (or if it is the last stage the entire model generation process) will terminate.
+To enable easier manipulation of staging a new parameter in the model block was developed ``maxNumSpecies`` that is the number of core species at which that stage (or if it is the last stage the entire model generation process) will terminate.
 
 For example ::
 

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

@@ -127,6 +127,7 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
     python-jl 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>`_.
 
 
 Debugging

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

@@ -15,6 +15,8 @@ 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>`_.
+
 #. 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/kinetics.rst

@@ -6,6 +6,8 @@ Kinetics Estimation
 This section gives in-depth descriptions of algorithms used for determining 
 kinetic parameters. For general usage of the kinetic database see :ref:`kineticsDatabase`. 
 
+
+
 Priority of Kinetic Databases
 -----------------------------
 When multiple sources are available for kinetic parameters, the following priority
@@ -49,27 +51,27 @@ parameters
 
 The rank of 0 is assigned to kinetics that are generally default values for top level nodes 
 that we have little faith in.  It is never used in generation and its value will in fact be overriden
-by averages of its child nodes, which generates an averaged rate rule with rank 11.  
+by averages of its child nodes, which generates an averaged rate rule with rank 10. 
 
 Only non-zero rules are used in generation.  A rank of 1 is assigned to the most trustworthy kinetics, while a rank of 10 is considered very poor.
 Thus, a rate rule of rank 3 will be given priority over a rate rule of rank 5.  
 
-Short Glossary:  
+**Short Glossary:**
 
-FCI (Full Configuration Interaction):  Exact solution to Schrodinger equation within the chosen basis
+**FCI (Full Configuration Interaction):**  Exact solution to Schrodinger equation within the chosen basis
 set and Born-Oppenheimer approximation; possible for about 12 electrons with reasonably sized basis set
 (cost grows factorially with number of electrons).  
 
-Wn (Weizmann-n):  Composite methods often with sub-kJ/mol accuracies; W1 is possible for about 9 heavy 
+**Wn (Weizmann-n):**  Composite methods often with sub-kJ/mol accuracies; W1 is possible for about 9 heavy 
 atoms; W1 aims to reproduce CCSD(T)/CBS; W4 aims to reproduce CCSDTQ5/CBS.  
 
-HEAT (High Accuracy Extrapolated ab inito thermochemistry):  Sub-kJ/mol accuracies; essentially
+**HEAT (High Accuracy Extrapolated ab inito thermochemistry):**  Sub-kJ/mol accuracies; essentially
 CCSDTQ with various corrections; similar in cost to Wn.  
 
-CBS (Complete Basis Set):  Typically obtained by extrapolating to the complete basis set limit,
+**CBS (Complete Basis Set):**  Typically obtained by extrapolating to the complete basis set limit,
 i.e., successive cc-pVDZ, cc-pVTZ, cc-pVQZ, etc. calculations with some extrapolation formula.  
 
-CCSD(T)-F12:  Coupled cluster with explicit electron correlation; chemical accuracy (1 kcal/mol)
+**CCSD(T)-F12:**  Coupled cluster with explicit electron correlation; chemical accuracy (1 kcal/mol)
 possible with double-zeta basis sets.  
 
 Kinetic Families
@@ -113,3 +115,19 @@ up to more and more general nodes. In the worst case, the root nodes may be used
 
 A :ref:`Full List of the Kinetics Families <kinetics_families_db>` in RMG is available.
 
+Reverse Rates
+-------------
+Rates in the reverse direction are calculated from the forward rate (as defined by the family) 
+and the equilibrium constant (as calculated from thermodynamic parameters).
+
+Reaction Comments
+-----------------
+Reaction comments are saved by RMG to the ``chem_annotated.inp`` Chemkin input file. 
+These comments contain information about the source of the reaction rate and are read by RMG when 
+loading the Chemkin file. These comments are compiled from many different locations in the code.
+
+Comments attached to the kinetics attribute of the entry used are included first. 
+These can occur if there is a comment hard-coded in the kinetics database, or if the rate rule was 
+derived from a training reaction, in which case ``From Training reaction # for rate rule ##`` 
+is automatically added. Then, comments describing the match are added based on the details of 
+how the kinetics were estiamted. Finally, additional metadata about the reaction type are included.