Automatically use reaction symmetry when necessary #62
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Tests are now in place. Merging. |
schneiderfelipe
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* Set build action to run on central and dev repositories * Drop official support for PyPy3 (#53) * Invert minor imaginary frequencies (#50) * Use Rich library in the CLI (#47) * Improve reporting capabilities * Make get_y return a function and use a clever default for t_span (#48) * Create dependabot.yml (#54) * Solve a standard error due to randomness (#55) * Test only on the oldest supported and latest Python versions * Show initial and final concentrations in the output (#56) * Simple justification of text in the output * Automatically use reaction symmetry when necessary (#62) * Automatically introduce reaction symmetry when it exists * Add tests for get_reaction_entropies * Ensure standard state corrections are correct (#64) * Use bias in the CLI and make model objects immutable (#66) * Make model objects immutable and improve dotdict * Improve numerical stability when integrating the ODE system (#69) * Use the default integrator in general * Optionally use JAX for speed * Use an exact Jacobian using JAX * Use rtol and atol with solve_ivp * Improve reaction rate constants for equilibria * Allow the user to choose among ODE solvers * Allow the user to choose a simulation time * Improve CLI, plots, and some tests (#73) * Enlarge the default max simulation time * Base max. time and plot on active species * Select plot points according to simulation profile * Allow selection of tunneling correction in the CLI * Use an integrated keyword for --plot * Improve CLI help page * Refactor and allow fixing concentrations of selected compounds (#74) * Allow fixing concentrations of certain compounds * Improve testing convert_rate_constant * Improve tests and docs on equilibrium_constant * Improve get_k and its tests and docs * Change the default behavior of convert_rate_constant * Always use rate constants as a vector * Correct bug about equilibria adjustments * Correct and improve regressions * Reproduce some literature data as graphs * Match results from the literature and simplify API * Make flake8 more strict on function complexity * Make CLI receive only biases in kcal/mol * Optimize biases from experiments using get_bias * Update documentation * Update links (fix #82) * Make it future-proof and compatible with RTDs * Update docs with a new theme * Use MIT license * Make the program display a (better) startup notice * Inform we use semantic versioning
schneiderfelipe
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Oct 13, 2021
* Set build action to run on central and dev repositories * Drop official support for PyPy3 (#53) * Invert minor imaginary frequencies (#50) * Use Rich library in the CLI (#47) * Improve reporting capabilities * Make get_y return a function and use a clever default for t_span (#48) * Create dependabot.yml (#54) * Solve a standard error due to randomness (#55) * Test only on the oldest supported and latest Python versions * Show initial and final concentrations in the output (#56) * Simple justification of text in the output * Automatically use reaction symmetry when necessary (#62) * Automatically introduce reaction symmetry when it exists * Add tests for get_reaction_entropies * Ensure standard state corrections are correct (#64) * Use bias in the CLI and make model objects immutable (#66) * Make model objects immutable and improve dotdict * Improve numerical stability when integrating the ODE system (#69) * Use the default integrator in general * Optionally use JAX for speed * Use an exact Jacobian using JAX * Use rtol and atol with solve_ivp * Improve reaction rate constants for equilibria * Allow the user to choose among ODE solvers * Allow the user to choose a simulation time * Improve CLI, plots, and some tests (#73) * Enlarge the default max simulation time * Base max. time and plot on active species * Select plot points according to simulation profile * Allow selection of tunneling correction in the CLI * Use an integrated keyword for --plot * Improve CLI help page * Refactor and allow fixing concentrations of selected compounds (#74) * Allow fixing concentrations of certain compounds * Improve testing convert_rate_constant * Improve tests and docs on equilibrium_constant * Improve get_k and its tests and docs * Change the default behavior of convert_rate_constant * Always use rate constants as a vector * Correct bug about equilibria adjustments * Correct and improve regressions * Reproduce some literature data as graphs * Match results from the literature and simplify API * Make flake8 more strict on function complexity * Make CLI receive only biases in kcal/mol * Optimize biases from experiments using get_bias * Update documentation * Update links (fix #82) * Make it future-proof and compatible with RTDs * Update docs with a new theme * Use MIT license * Make the program display a (better) startup notice * Inform we use semantic versioning
schneiderfelipe
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Oct 13, 2021
* Set build action to run on main and dev repositories * Drop official support for PyPy3 (#53) Co-authored-by: Felipe S. S. Schneider <schneiderfelipe@posgrad.ufsc.br> * Invert small imaginary frequencies (#50) * Use Rich library in the CLI (#47) * Use Rich library in the CLI * Improve reporting capabilities Co-authored-by: Felipe S. S. Schneider <schneiderfelipe@posgrad.ufsc.br> * Make get_y return a function and use a clever default for t_span (#48) * Create dependabot.yml (#54) * Solve a common error due to randomness (#55) Co-authored-by: Felipe S. S. Schneider <schneiderfelipe@posgrad.ufsc.br> * Run tests on macOS as well (#45) * Run all essential tests on macOS as well * Test only on the oldest supported and latest Python versions Co-authored-by: Felipe S. S. Schneider <schneiderfelipe@posgrad.ufsc.br> * Do not test on macOS anymore, only on Ubuntu/Linux (#57) Co-authored-by: Felipe S. S. Schneider <schneiderfelipe@posgrad.ufsc.br> * Show initial and final concentrations in the output (#56) * Simple justification of text in the output * Show initial and final concentrations in the output Co-authored-by: Felipe S. S. Schneider <schneiderfelipe@posgrad.ufsc.br> * Automatically use reaction symmetry when necessary (#62) * Create a function for calculating reaction symmetries * Automatically introduce reaction symmetry when it exists * Add tests for get_reaction_entropies * Ensure standard state corrections are correct (#64) * Use bias in the CLI and make model objects immutable (#66) * Use bias in the CLI * Make model objects immutable and improve dotdict * Improve numerical stability when integrating the ODE system (#69) * Use the default integrator in general * Optionally use JAX for speed * Use an exact Jacobian using JAX * Use rtol and atol with solve_ivp * Improve reaction rate constants for equilibria * Allow the user to choose among ODE solvers * Allow the user to choose a simulation time Co-authored-by: Felipe S. S. Schneider <schneiderfelipe@posgrad.ufsc.br> * Improve CLI, plots, and some tests (#73) * Test more liquid viscosities * Check and manage some TODOs and docs * Enlarge the default max simulation time * Base max. time and plot on active species * Select plot points according to simulation profile * Allow selection of tunneling correction in the CLI * Use an integrated keyword for --plot * Improve CLI help page Co-authored-by: Felipe S. S. Schneider <schneiderfelipe@posgrad.ufsc.br> * Refactor and allow fixing concentrations of selected compounds (#74) * Allow fixing concentrations of certain compounds * Improve testing convert_rate_constant * Improve tests and docs on equilibrium_constant * Improve testing eyring * Improve get_k and its tests and docs * Change default behavior of convert_rate_constant * Always use rate constants as a vector * Correct bug about equilibria adjustments * Correct and improve regressions * Reproduce some literature data as graphs * Match results from the literature and simplify API * Add a get_bias function for fitting experimental/reference kinetic data (#79) * Make flake8 be more strict on function complexity * Make CLI receive only biases in kcal/mol * Optimize biases from experiments using get_bias * Bump actions/setup-python from 1 to 2.2.2 (#85) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 1 to 2.2.2. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v1...v2.2.2) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Make documentation awesome 🎉 (#83) * Set build action to run on central and dev repositories * Drop official support for PyPy3 (#53) * Invert minor imaginary frequencies (#50) * Use Rich library in the CLI (#47) * Improve reporting capabilities * Make get_y return a function and use a clever default for t_span (#48) * Create dependabot.yml (#54) * Solve a standard error due to randomness (#55) * Test only on the oldest supported and latest Python versions * Show initial and final concentrations in the output (#56) * Simple justification of text in the output * Automatically use reaction symmetry when necessary (#62) * Automatically introduce reaction symmetry when it exists * Add tests for get_reaction_entropies * Ensure standard state corrections are correct (#64) * Use bias in the CLI and make model objects immutable (#66) * Make model objects immutable and improve dotdict * Improve numerical stability when integrating the ODE system (#69) * Use the default integrator in general * Optionally use JAX for speed * Use an exact Jacobian using JAX * Use rtol and atol with solve_ivp * Improve reaction rate constants for equilibria * Allow the user to choose among ODE solvers * Allow the user to choose a simulation time * Improve CLI, plots, and some tests (#73) * Enlarge the default max simulation time * Base max. time and plot on active species * Select plot points according to simulation profile * Allow selection of tunneling correction in the CLI * Use an integrated keyword for --plot * Improve CLI help page * Refactor and allow fixing concentrations of selected compounds (#74) * Allow fixing concentrations of certain compounds * Improve testing convert_rate_constant * Improve tests and docs on equilibrium_constant * Improve get_k and its tests and docs * Change the default behavior of convert_rate_constant * Always use rate constants as a vector * Correct bug about equilibria adjustments * Correct and improve regressions * Reproduce some literature data as graphs * Match results from the literature and simplify API * Make flake8 more strict on function complexity * Make CLI receive only biases in kcal/mol * Optimize biases from experiments using get_bias * Update documentation * Update links (fix #82) * Make it future-proof and compatible with RTDs * Update docs with a new theme * Use MIT license * Make the program display a (better) startup notice * Inform we use semantic versioning * Update docs & README.md (#87) * Move docs to https://geem-lab.github.io/overreact-docs/ * Update README.md Co-authored-by: Felipe S. S. Schneider <schneiderfelipe@posgrad.ufsc.br> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
schneiderfelipe
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Oct 13, 2021
* Create a function for calculating reaction symmetries * Automatically introduce reaction symmetry when it exists * Add tests for get_reaction_entropies
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This PR introduces automatic detection and usage of reaction symmetry (#8). The only thing it still lacks is some proper testing.
An important use case is an explicit-implicit aquation:
n H2O + A <=> A·nH2O(I believe that if the product structure is strongly bound, results will be comfortably comparable to the experiment). I'll try to add a simple test like this soon.Closes #8.