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Marcus Kinetics #247

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mjohnson541 wants to merge 57 commits intomainReactionMechanismGenerator/ReactionMechanismSimulator.jl:mainfrom marcusReactionMechanismGenerator/ReactionMechanismSimulator.jl:marcusCopy head branch name to clipboard

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Commits on Jun 23, 2024

• ignore automatically generated files

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• Add channels

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• Remove yml file as it's not used anymore, using CondaPkg to manage env

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• Switch to CondaPkg, PythonCall, PythonPlot

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• Remove unused dependency

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• Update version

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• bump to 1.10

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• No need to install env beforehand

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• Install with CondaPkg

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• Switch to 1.10 and no need to create env

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• export env path for CondaPkg

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• Update build to use CondaPkg

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• Update installation instruction

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• Use PythonPlot instead of PyPlot

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• Switch to PythonPlot

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• Switch parsing to PythonCall and PythonPlot

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• Switch plotting to pythonplot

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• Use PythonCall syntax in module

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• Don't set jacobian prototype if jacobian is not sparse

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• Switch to pythoncall syntax in test

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• Import necessary packages

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• Use SciMLSensitivity

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• Change rtol

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• Add propane mech test file

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Commits on Jun 29, 2024

• ensure SciMLSensitivity.extract_local_sensitivities is called

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• clean up automatic mechanism string output

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• adapt automatic mechanism analysis tests

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• make compat for PythonCall and CondaPkg more specific for release

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Commits on Jul 1, 2024

• move conda install to import and on test

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• clean up conda installs

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Commits on Aug 3, 2024

• run rops and flux diagram generation in tests

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• decode to utf-8

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• 0-index python objects

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• adapt getcolor

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• avoid pydot 2.0.0

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• remove CondaPkg.toml

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• increment version

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Commits on Sep 21, 2024

• include electronchange in reaction reconstruction in phase

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• add Marcus kinetics type and allow dGrxn dependence of kinetics

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• handle dGrxn and d dependence of reactions in interfaces and phase calculations

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• adapt Domains to dGrxn and d dependence of forward rate coefficient calculations

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• add a Marcus reaction to the ORR.rms mechanism for testing

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• fix variable naminng

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Commits on Sep 23, 2024

• update documentation build action

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• loosen solve tolerances

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• fix getKc call in ReactiveInternalInterface

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• add phi and d to newer domains

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• doc build tweak

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Commits on Sep 25, 2024

• phase electron change fixes

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• missing domain tweaks for phi/d

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• fix typo

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• tweak docs build

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• tweak docs

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• fix FragmentBasedReactiveFilmGrowthInterfaceConstantT interface

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• fix

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• revert documentation

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• add documentation workflow

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