From b1c745671f10c201b02b2122c9a8b60695f97a98 Mon Sep 17 00:00:00 2001
From: "Felipe S. S. Schneider"
>>> from rich import print
>>> model = rx.parse_model("data/ethane/B97-3c/model.jk")
>>> print(Report(model))
+────────────────────────────────────────────────────────────────────────────────
╭──────────────────╮
│ (read) reactions │
│ │
│ S -> E‡ -> S │
│ │
╰──────────────────╯
- (parsed) reactions
+ (parsed) reactions
+<BLANKLINE>
+no reactant(s) via‡ product(s) half equilib.?
+───────────────────────────────────────────────────────
+0 S E‡ S No
+<BLANKLINE>
+ logfiles
+<BLANKLINE>
+no compound path
+──────────────────────────────────────────────────
+0 S data/ethane/B97-3c/staggered.out
+1 E‡ data/ethane/B97-3c/eclipsed.out
<BLANKLINE>
- no reactant(s) via‡ product(s) half equilib.?
- ───────────────────────────────────────────────────────
- 0 S E‡ S No
+ compounds
<BLANKLINE>
-...
+no compound elec. energy spin mult. smallest point group
+ 〈Eₕ〉 vibfreqs
+ 〈cm⁻¹〉
+──────────────────────────────────────────────────────────────────────────────
+0 S -79.788170457… 1 +307.6, D3d
+ +825.4, +826.1
+1 E‡ -79.783894160… 1 -298.9, D3h
+ +902.2, +902.5
+<BLANKLINE>
+ estimated thermochemistry (compounds)
+<BLANKLINE>
+no compound mass Gᶜᵒʳʳ Uᶜᵒʳʳ Hᶜᵒʳʳ S
+ 〈amu〉 〈kcal/mo… 〈kcal/mo… 〈kcal/mol… 〈cal/mol…
+──────────────────────────────────────────────────────────────────────────────
+0 S 30.07 … … 4… 54.40
+1 E‡ 30.07 … … 4… 52.96
+<BLANKLINE>
+ estimated (reaction°) thermochemistry
+<BLANKLINE>
+no reaction Δmass° ΔG° ΔE° ΔU° ΔH° ΔS°
+ 〈amu〉 〈kcal/… 〈kcal/… 〈kcal… 〈kcal/… 〈cal/…
+──────────────────────────────────────────────────────────────────────────────
+0 S -> S 0.00 0… 0… … 0… …
+<BLANKLINE>
+ estimated (activation‡) thermochemistry
+<BLANKLINE>
+no reaction Δmass‡ ΔG‡ ΔE‡ ΔU‡ ΔH‡ ΔS‡
+ 〈amu〉 〈kcal/… 〈kcal/… 〈kcal… 〈kcal/… 〈cal/…
+──────────────────────────────────────────────────────────────────────────────
+0 S -> S 0.00 2… 2… … 2… …
+<BLANKLINE>
+ estimated reaction rate constants
+<BLANKLINE>
+no reaction half k k k κ
+ equilib.? 〈M⁻ⁿ⁺¹·s⁻… 〈(cm³/par… 〈atm⁻ⁿ⁺¹·…
+──────────────────────────────────────────────────────────────────────────────
+0 S -> S No 8.17e+10 8.17e+10 8.17e+10 1.11
<BLANKLINE>
Only in the table above, all Gibbs free energies were biased by 0.0 J/mol.
-For half-equilibria, only ratios make sense.
+For half-equilibria, only ratios make sense: in simulations, equilibria will be
+adjusted to be faster than all other reactions.
+────────────────────────────────────────────────────────────────────────────────
Initialize a Report object.
+def main(): +diff --git a/docs/overreact/_constants.html b/docs/overreact/_constants.html index ed33b901..74c87518 100644 --- a/docs/overreact/_constants.html +++ b/docs/overreact/_constants.html @@ -3,7 +3,7 @@ - +def main(arguments=None): """Command-line interface.""" console = Console(width=max(105, shutil.get_terminal_size()[0])) levels = [logging.WARNING, logging.INFO, logging.DEBUG] @@ -1644,17 +1849,18 @@Examples
parser = argparse.ArgumentParser( description=f""" {rx.__headline__} - Interface for building and modifying models. - Read the documentation at {rx.__url__} for more information and usage examples. + Read the user guide at {rx.__url_guide__} for more information and usage + examples. + Licensed under the terms of the {rx.__license__} License. If you publish work using this software, please cite - https://doi.org/{rx.__doi__}: + https://doi.org/{rx.__doi__}. """, formatter_class=argparse.ArgumentDefaultsHelpFormatter, ) parser.add_argument( "path", - help="path to a source (`.k`) or compiled (.jk) model input file (if a source " + help="path to a source (`.k`) or compiled (`.jk`) model input file (if a source " "input file is given, but there is a compiled file available, the compiled " "file will be used; use --compile|-c to force recompilation of the " "source input file instead)", @@ -1682,7 +1888,7 @@Examples
"--compile", # TODO(schneiderfelipe): should we consider --compile|-c always as a # do-nothing (no analysis)? - help="force recompile a source (`.k`) into a compiled (.jk) model input file", + help="force recompile a source (`.k`) into a compiled (`.jk`) model input file", action="store_true", ) parser.add_argument( @@ -1715,7 +1921,7 @@Examples
"--no-qrrho", help="disable the quasi-rigid rotor harmonic oscillator (QRRHO) " "approximations to both enthalpies and entropies (see " - "[doi:10.1021/jp509921r] and [doi:10.1002/chem.201200497])", + "DOI:10.1021/jp509921r and DOI:10.1002/chem.201200497)", choices=["both", "enthalpy", "entropy", "none"], default="both", dest="qrrho_descriptor", @@ -1760,7 +1966,7 @@Examples
type=float, default=1e-11, ) - args = parser.parse_args() + args = parser.parse_args(arguments) try: args.bias = float(args.bias) * constants.kcal @@ -1776,16 +1982,23 @@Examples
{rx.__headline__} Licensed under the terms of the -[{rx.__license__} License]({rx.__repo__}/blob/main/LICENSE). +[{rx.__license__} License]({rx.__url_repo__}/blob/main/LICENSE). If you publish work using this software, **please cite -[doi:{rx.__doi__}](https://doi.org/{rx.__doi__})**: +[DOI:{rx.__doi__}](https://zenodo.org/badge/latestdoi/214332027)**: ``` {rx.__citation__} ``` -Read the documentation at [{rx.__url__}]({rx.__url__}) for more information -and usage examples. +Read the user guide at [{rx.__url_guide__}]({rx.__url_guide__}) for more information +and usage examples. Other useful resources: + +- [Questions and Discussions]({rx.__url_repo__}/discussions) +- [Bug Tracker]({rx.__url_repo__}/issues) +- [GitHub Repository]({rx.__url_repo__}) +- [Python Package Index]({rx.__url_pypi__}) + +--- Inputs: - Path = {args.path} @@ -1831,8 +2044,6 @@Examples
rtol=args.rtol, atol=args.atol, ) - # TODO(schneiderfelipe): use a progress bar to inform about the - # simulation and show the time it took to simulate. console.print(report, justify="left")overreact._constants API documentation @@ -27,7 +27,7 @@ - +diff --git a/docs/overreact/_datasets.html b/docs/overreact/_datasets.html index 0feeb57e..e0e56627 100644 --- a/docs/overreact/_datasets.html +++ b/docs/overreact/_datasets.html @@ -3,7 +3,7 @@ - + overreact._datasets API documentation @@ -27,7 +27,7 @@ - +diff --git a/docs/overreact/_misc.html b/docs/overreact/_misc.html index 20f86745..ab8304ad 100644 --- a/docs/overreact/_misc.html +++ b/docs/overreact/_misc.html @@ -3,7 +3,7 @@ - + overreact._misc API documentation @@ -27,7 +27,7 @@ - +@@ -90,6 +90,7 @@ """ from functools import lru_cache as cache +from typing import Optional, Text import numpy as np from scipy.stats import cauchy, norm @@ -126,11 +127,15 @@
_found_jax = _find_package("jax") +_found_rich = _find_package("rich") _found_seaborn = _find_package("seaborn") _found_thermo = _find_package("thermo") + + if _found_thermo: from thermo.chemical import Chemical + # Inspired by # https://github.com/cclib/cclib/blob/master/cclib/parser/utils.py#L159 element = [ @@ -503,7 +508,9 @@
} -def _check_package(package, found_package): +def _check_package( + package: Text, found_package: bool, extra_flag: Optional[Text] = None +) -> None: """Raise an issue if a package was not found. Parameters @@ -512,11 +519,13 @@
Package name. found_package : bool Whether the package was found or not. + extra_flag : Optional[str] + Extra flag of overreact that also installs the package. Raises ------ ImportError - If the package could not be imported. + If the package was not found. Examples -------- @@ -524,10 +533,20 @@
>>> _check_package("i_dont_exist", False) Traceback (most recent call last): ... - ImportError: You must install `i_dont_exist` to use this function + ImportError: You must install `i_dont_exist` to use this functionality: `pip install i_dont_exist` + >>> _check_package("rich", False, "cli") + Traceback (most recent call last): + ... + ImportError: You must install `rich` to use this functionality: `pip install rich` (or `pip install "overreact[cli]"`) """ if not found_package: - raise ImportError(f"You must install `{package}` to use this function") + message = ( + f"You must install `{package}` to use this functionality: " + f"`pip install {package}`" + ) + if extra_flag: + message += f' (or `pip install "overreact[{extra_flag}]"`)' + raise ImportError(message) # TODO(schneiderfelipe): what does this function returns for identifier="gas" @@ -562,7 +581,7 @@
>>> water.Vm 1.806904e-5 >>> water.permittivity - 78.355308122325 + 78.4 >>> water.isobaric_expansion 0.000402256 >>> water.omega @@ -570,7 +589,7 @@
>>> water.mul 0.00091272 """ - _check_package("thermo", _found_thermo) + _check_package("thermo", _found_thermo, "solvents") # TODO(schneiderfelipe): return a named tuple with only the required data. # TODO(schneiderfelipe): support logging the retrieval of data. # TODO(schneiderfelipe): test returned parameters. diff --git a/docs/overreact/api.html b/docs/overreact/api.html index 5a86428d..72c6efcd 100644 --- a/docs/overreact/api.html +++ b/docs/overreact/api.html @@ -3,7 +3,7 @@ - +
overreact.api API documentation @@ -27,7 +27,7 @@ - +@@ -102,7 +102,7 @@ """ -from __future__ import annotations +from typing import Union __all__ = [ "get_k", @@ -343,7 +343,7 @@
if compounds[name].symmetry is not None: # The negative sign here seems correct. See equations (9) and (10) - # of doi:10.1002/qua.25686. + # of DOI:10.1002/qua.25686. entropy -= rx.change_reference_state( compounds[name].symmetry, 1, temperature=temperature, pressure=pressure ) @@ -352,7 +352,7 @@
return np.array(entropies) -def _check_qrrho(qrrho: bool | tuple[bool, bool]) -> tuple[bool, bool]: +def _check_qrrho(qrrho: Union[bool, tuple[bool, bool]]) -> tuple[bool, bool]: """Get options for QRRHO for both enthalpy and entropy. Parameters @@ -372,7 +372,7 @@
Raises ------ ValueError - If the QRRHO specification could not be recognized. + If the QRRHO specification is not understood. Examples -------- @@ -400,7 +400,7 @@
bias: float = 0.0, environment: Optional[Text] = None, method: Text = "standard", - qrrho: bool | tuple[bool, bool] = True, + qrrho: Union[bool, tuple[bool, bool]] = True, temperature: float = 298.15, pressure: float = constants.atm, ): @@ -493,7 +493,7 @@
compounds: Optional[dict] = None, bias: float = 0.0, tunneling: Text = "eckart", - qrrho: bool | tuple[bool, bool] = True, + qrrho: Union[bool, tuple[bool, bool]] = True, scale: Text = "l mol-1 s-1", temperature: float = 298.15, pressure: float = constants.atm, @@ -621,7 +621,7 @@
if compounds is not None: compounds = rx.io._check_compounds(compounds) if delta_freeenergies is None: - assert compounds is not None, "compounds must be specified" + assert compounds is not None, "compounds could not be inferred" freeenergies = get_freeenergies( compounds, bias=bias, @@ -663,7 +663,10 @@
_K = pair[0] / pair[1] k[i : i + 2] = pair / pair.min() - assert np.isclose(_K, k[i] / k[i + 1]) # FIX: add message + assert np.isclose(_K, k[i] / k[i + 1]), ( + "reaction rate constants for equilibria could not be made " + "to match the expected equilibrium constant value" + ) # loop over pairs of equilibria i += 1 @@ -749,6 +752,11 @@
------- array-like + Raises + ------ + ValueError + If `method` is not supported. + Examples -------- Below is an example of an estimate of how much quantum tunneling @@ -901,16 +909,16 @@
def get_k( scheme: overreact.core.Scheme, - compounds: Union[dict, NoneType] = None, + compounds: Optional[dict] = None, bias: float = 0.0, tunneling: str = 'eckart', - qrrho: 'bool | tuple[bool, bool]' = True, + qrrho: Union[bool, tuple[bool, bool]] = True, scale: str = 'l mol-1 s-1', temperature: float = 298.15, pressure: float = 101325.0, - delta_freeenergies: Union[float, NoneType] = None, - molecularity: Union[float, NoneType] = None, - volume: Union[float, NoneType] = None + delta_freeenergies: Optional[float] = None, + molecularity: Optional[float] = None, + volume: Optional[float] = None ) -> float:
method
is not supported.Below is an example of an estimate of how much quantum tunneling @@ -1476,9 +1498,9 @@
>>> symmetry_number("C4")
diff --git a/docs/overreact/core.html b/docs/overreact/core.html
index 07952af7..2dee33b0 100644
--- a/docs/overreact/core.html
+++ b/docs/overreact/core.html
@@ -3,7 +3,7 @@
-
+
overreact.core API documentation
@@ -27,7 +27,7 @@
-
+
@@ -103,14 +103,12 @@
"""Module dedicated to parsing and modeling of chemical reaction networks."""
-from __future__ import annotations
-
__all__ = ["Scheme", "parse_reactions"]
import itertools
import re
-from typing import NamedTuple, Sequence, Text
+from typing import NamedTuple, Sequence, Text, Union
import numpy as np
@@ -152,7 +150,7 @@
}
-def _check_scheme(scheme_or_text: Scheme | Text) -> Scheme:
+def _check_scheme(scheme_or_text: Union[Scheme, Text]) -> Scheme:
"""Interface transparently between strings and schemes.
Parameters
@@ -500,7 +498,7 @@
return False
-def parse_reactions(text: Text | Sequence[Text]) -> Scheme:
+def parse_reactions(text: Union[Text, Sequence[Text]]) -> Scheme:
"""
Parse a kinetic model as a chemical reaction scheme.
@@ -971,7 +969,7 @@
class
- Scheme(builtins.tuple):
+ Scheme(typing.NamedTuple):
def parse_reactions(text: Text | Sequence[Text]) -> Scheme: +def parse_reactions(text: Union[Text, Sequence[Text]]) -> Scheme: """ Parse a kinetic model as a chemical reaction scheme. diff --git a/docs/overreact/io.html b/docs/overreact/io.html index 63486309..e37633f5 100644 --- a/docs/overreact/io.html +++ b/docs/overreact/io.html @@ -3,7 +3,7 @@ - +overreact.io API documentation @@ -27,7 +27,7 @@ - +@@ -123,7 +123,7 @@ ---------- path : str Path to the model or source input file. - If the final extension is not ``.jk`` or ``.k``, it is guessed. + If the final extension is not `.jk` or `.k`, it is guessed. force_compile : bool If True, a `.k` file will take precedence over any `.jk` file for reading. A `.jk` file is thus either generated or overwritten. This is sometimes @@ -136,7 +136,7 @@
Raises ------ FileNotFoundError - If no files could be found. + If the model or source input file is not found. Examples -------- @@ -172,22 +172,23 @@
""" if not path.endswith((".k", ".jk")): path = path + ".jk" - logger.warning(f"assuming .jk file in {path}") + logger.warning(f"assuming `.jk` file in {path}") name, _ = os.path.splitext(path) path_jk = name + ".jk" if not force_compile and os.path.isfile(path_jk): - logger.info(f"parsing .jk file in {path_jk}") + logger.info(f"parsing `.jk` file in {path_jk}") return _parse_model(path_jk) path_k = name + ".k" - logger.info(f"parsing .k file in {path_k}") + logger.info(f"parsing `.k` file in {path_k}") if not os.path.isfile(path_k): - raise FileNotFoundError + # TODO: hey let's add a nice error message here and everywhere, OK? + raise FileNotFoundError(f"no `.k` file found in {path_k}") model = _parse_source(path_k) with open(path_jk, "w") as f: - logger.info(f"writing .jk file in {path_jk}") + logger.info(f"writing `.jk` file in {path_jk}") f.write(_unparse_model(model)) return model @@ -530,6 +531,11 @@
------- compounds : immutable dict-like + Raises + ------ + FileNotFoundError + If a logfile is not found. + Examples -------- >>> import overreact as rx @@ -613,12 +619,11 @@
key, value = "logfile", line if key == "logfile": - # TODO(schneiderfelipe): test "nested" logfiles, i.e., - # DLPNO-CCSD(T)/def2-TZVP(-f)//revPBE-D4-gCP/def2-SVP, etc. success = False value = value.strip('"') for p in path: try: + # TODO: hey, let's move on to use pathlib! logger.info(f"trying to read {os.path.join(p, value)}") compounds[name].update(read_logfile(os.path.join(p, value))) except FileNotFoundError: @@ -654,12 +659,14 @@
Raises ------ FileNotFoundError - In case the logfile can not be found. + If the logfile is not found. Examples -------- >>> import overreact as rx + Some Orca logfiles: + >>> rx.io.read_logfile("data/symmetries/benzene.out") {'logfile': 'data/symmetries/benzene.out', 'energy': -609176691.0746485, @@ -688,9 +695,29 @@
'hessian': ((0.51457715535, ..., -0.00010536738319), ..., (-0.00010536738319, ..., -0.001114845004))} + + A Gaussian logfile as another example: + + >>> rx.io.read_logfile("data/acetate/Gaussian09/wB97XD/6-311++G**/AcO-_0.gau.out") + {'logfile': 'data/acetate/Gaussian09/wB97XD/6-311++G**/AcO-_0.gau.out', + 'energy': -600283832.3323932, + 'mult': 1, + 'atomnos': (6, 6, 1, 1, 1, 8, 8), + 'atommasses': (12.0, 12.0, 1.007825, 1.007825, 1.007825, 15.9949146, 15.9949146), + 'atomcoords': ((-0.174905, -0.001738, 0.000115), + ..., + (-0.721316, 1.137017, -4.3e-05)), + 'vibfreqs': (80.2535, 471.106, ..., 3129.0397, 3152.3619), + 'vibdisps': (((0.0, 0.0, 0.02), + ..., + (0.0, 0.0, 0.0)))} """ + if not (parser := ccopen(path)): + raise FileNotFoundError(f"could not find logfile '{path}'") + origin = parser.__class__.__name__.lower() + logger.info(f"reading a {origin} logfile: {path}") try: - ccdata = ccopen(path).parse() + ccdata = parser.parse() data = { "logfile": path, # This energy may lack dispersion, solvation, correlation, etc. @@ -702,20 +729,33 @@
"vibfreqs": rx._misc.totuple(ccdata.vibfreqs), "vibdisps": rx._misc.totuple(ccdata.vibdisps), } + + # This solves a current bug in cclib (see + # https://github.com/cclib/cclib/issues/1080) + if origin == "gaussian": + data["atommasses"] = data["atommasses"][: len(data["atomnos"])] + + assert len(data["atomnos"]) == len(data["atommasses"]) + assert len(data["atomnos"]) == len(data["atomcoords"]) + # This properly parses the final single point energy from ORCA files. - data.update(_read_orca_logfile(path)) + if origin == "orca": + data.update(_read_orca_logfile(path)) except AttributeError: # Here is the code to parse things on our own. This means we need to # parse much more than small pieces of information, as at this point # cclib has failed. - try: - # TODO(schneiderfelipe): only run the code below if we know it is - # an ORCA logfile. The code in this final section should be very - # specific in supplying *only* things cclib is not (yet) able to - # parse. - data = _read_orca_logfile(path, minimal=False) - except FileNotFoundError: - raise FileNotFoundError(f"could not parse logfile: '{path}'") + if origin == "orca": + try: + # TODO(schneiderfelipe): only run the code below if we know it is + # an ORCA logfile. The code in this final section should be very + # specific in supplying *only* things cclib is not (yet) able to + # parse. Should we add a check for this as well? + data = _read_orca_logfile(path, minimal=False) + except FileNotFoundError: + raise FileNotFoundError(f"could not parse logfile: '{path}'") + else: + raise return dotdict(data) @@ -930,8 +970,7 @@
) if atommasses is None: - # TODO(schneiderfelipe): warn about guessing masses from the periodic - # table. + logger.warning("using atomic masses from periodic table") atommasses = [] for n in atomnos: atommasses.append(rx._misc.atomic_mass[n]) @@ -985,6 +1024,16 @@
__getattr__ = dict.get def __setitem__(self, key, value): + """ + Set an item. + + This is not allowed and will raise an exception. + + Raises + ------ + NotImplementedError + If one attempts to change a value. + """ raise NotImplementedError("dotdict objects are immutable") # https://stackoverflow.com/a/1151686/4039050 @@ -1087,7 +1136,7 @@
---------- path : str Path to the model or source input file. - If the final extension is not ``.jk`` or ``.k``, it is guessed. + If the final extension is not `.jk` or `.k`, it is guessed. force_compile : bool If True, a `.k` file will take precedence over any `.jk` file for reading. A `.jk` file is thus either generated or overwritten. This is sometimes @@ -1100,7 +1149,7 @@
Raises ------ FileNotFoundError - If no files could be found. + If the model or source input file is not found. Examples -------- @@ -1136,22 +1185,23 @@
""" if not path.endswith((".k", ".jk")): path = path + ".jk" - logger.warning(f"assuming .jk file in {path}") + logger.warning(f"assuming `.jk` file in {path}") name, _ = os.path.splitext(path) path_jk = name + ".jk" if not force_compile and os.path.isfile(path_jk): - logger.info(f"parsing .jk file in {path_jk}") + logger.info(f"parsing `.jk` file in {path_jk}") return _parse_model(path_jk) path_k = name + ".k" - logger.info(f"parsing .k file in {path_k}") + logger.info(f"parsing `.k` file in {path_k}") if not os.path.isfile(path_k): - raise FileNotFoundError + # TODO: hey let's add a nice error message here and everywhere, OK? + raise FileNotFoundError(f"no `.k` file found in {path_k}") model = _parse_source(path_k) with open(path_jk, "w") as f: - logger.info(f"writing .jk file in {path_jk}") + logger.info(f"writing `.jk` file in {path_jk}") f.write(_unparse_model(model)) return model @@ -1195,7 +1245,7 @@
Returns
Raises
-
- FileNotFoundError: If no files could be found.
+- FileNotFoundError: If the model or source input file is not found.
Examples
diff --git a/docs/overreact/rates.html b/docs/overreact/rates.html index 5a68efbd..b1c71a5b 100644 --- a/docs/overreact/rates.html +++ b/docs/overreact/rates.html @@ -3,7 +3,7 @@ - +overreact.rates API documentation @@ -27,7 +27,7 @@ - +@@ -81,7 +81,7 @@ from __future__ import annotations -from typing import Optional +from typing import Optional, Union __all__ = ["eyring"] @@ -156,7 +156,7 @@
This is a work in progress! TODO(schneiderfelipe): THERE ARE DOUBTS ABOUT HOW TO SELECT - reactive_radius. doi:10.1002/jcc.23409 HELPS CLARIFY SOME ASPECTS BUT + reactive_radius. DOI:10.1002/jcc.23409 HELPS CLARIFY SOME ASPECTS BUT THERE'S STILL PROBLEMS. I BELIEVE THERE'S A RELATIONSHIP BETWEEN THE IMAGINARY FREQUENCY AND HOW FAR ATOMS MOVE CLOSE TO REACT, WHICH MIGHT GIVE SOME LIGHT. IN ANY CASE, I BELIEVE THAT THIS VALUE SHOULD BE LARGER @@ -208,7 +208,7 @@
def collins_kimball(k_tst, k_diff): """Calculate reaction rate constant inclusing diffusion effects. - This implementation is based on doi:10.1016/0095-8522(49)90023-9. + This implementation is based on DOI:10.1016/0095-8522(49)90023-9. Examples -------- @@ -228,7 +228,7 @@
): r"""Convert a reaction rate constant between common units. - The reference paper used for developing this function is doi:10.1021/ed046p54. + The reference paper used for developing this function is DOI:10.1021/ed046p54. Parameters ---------- @@ -250,6 +250,11 @@
------- array-like + Raises + ------ + ValueError + If either `old_scale` or `new_scale` are not recognized. + Notes ----- Some symbols are accepted as alternatives in "new_scale" and "old_scale": @@ -326,7 +331,7 @@
elif old_scale == "atm-1 s-1": factor = rx.thermo.molar_volume(temperature, pressure) * constants.kilo else: - raise ValueError(f"unit not recognized: {old_scale}") + raise ValueError(f"old unit not recognized: {old_scale}") # now we convert l mol-1 s-1 to what we need if new_scale == "cm3 mol-1 s-1": @@ -344,7 +349,7 @@
elif new_scale == "atm-1 s-1": factor *= 1.0 / (rx.thermo.molar_volume(temperature, pressure) * constants.kilo) else: - raise ValueError(f"unit not recognized: {new_scale}") + raise ValueError(f"new unit not recognized: {new_scale}") factor **= molecularity - 1 logger.info(f"conversion factor ({old_scale} to {new_scale}) = {factor}") @@ -352,9 +357,9 @@
def eyring( - delta_freeenergy: float | np.ndarray, + delta_freeenergy: Union[float, np.ndarray], molecularity: Optional[int] = None, - temperature: float | np.ndarray = 298.15, + temperature: Union[float, np.ndarray] = 298.15, pressure: float = constants.atm, volume: Optional[float] = None, ): @@ -455,20 +460,20 @@
def eyring( - delta_freeenergy: 'float | np.ndarray', - molecularity: Union[int, NoneType] = None, - temperature: 'float | np.ndarray' = 298.15, + delta_freeenergy: Union[float, numpy.ndarray], + molecularity: Optional[int] = None, + temperature: Union[float, numpy.ndarray] = 298.15, pressure: float = 101325.0, - volume: Union[float, NoneType] = None + volume: Optional[float] = None ):
View Source
def eyring( - delta_freeenergy: float | np.ndarray, + delta_freeenergy: Union[float, np.ndarray], molecularity: Optional[int] = None, - temperature: float | np.ndarray = 298.15, + temperature: Union[float, np.ndarray] = 298.15, pressure: float = constants.atm, volume: Optional[float] = None, ): diff --git a/docs/overreact/simulate.html b/docs/overreact/simulate.html index 36f41974..4ea28c30 100644 --- a/docs/overreact/simulate.html +++ b/docs/overreact/simulate.html @@ -3,7 +3,7 @@ - +overreact.simulate API documentation @@ -27,7 +27,7 @@ - +@@ -108,6 +108,12 @@ from overreact import _constants as constants from overreact._misc import _found_jax +EF = 5 + + +logger = logging.getLogger(__name__) + + if _found_jax: import jax.numpy as jnp from jax import jacfwd, jit @@ -115,10 +121,12 @@
config.update("jax_enable_x64", True) else: + logger.warning( + "Install JAX to have just-in-time compilation: " + 'pip install jax (or pip install "overreact[fast]")' + ) jnp = np -logger = logging.getLogger(__name__) - # TODO(schneiderfelipe): allow y0 to be a dict-like object. def get_y( @@ -172,17 +180,18 @@
The `y` object stores information about the simulation time, which can be used to produce a suitable vector of timepoints for, e.g., plotting: - >>> y.t_min, y.t_max - (0.0, 14.0) + >>> y.t_min, y.t_max # doctest: +SKIP + (0.0, 3.0) >>> t = np.linspace(y.t_min, y.t_max) - >>> t - array([ 0. , 0.28571429, ..., 13.71428571, 14. ]) + >>> t # doctest: +SKIP + array([0. , 0.06122449, ..., 2.93877551, 3. ]) Both `y` and `r` can be used to check concentrations and rates in any point in time. In particular, both are vectorized: - >>> y(t) - array([[1. , ..., 0.5 ]]) + >>> y(t) # doctest: +SKIP + array([[1. , 0.94237559, ..., 0.5012394, 0.5 ], + [0. , 0.05762441, ..., 0.4987606, 0.5 ]]) >>> r(t) # doctest: +SKIP array([[-1.00000000e+00, ..., -1.39544265e-10], [ 1.00000000e+00, ..., 1.39544265e-10]]) @@ -191,9 +200,9 @@
y0 = np.asarray(y0) if t_span is None: - # We defined alpha such that 1.0 - alpha is an estimate of the extend - # to which the reaction is simulated. - alpha = 1e-4 + # We defined alpha such that 1.0 - alpha is an (under)estimate of the extend + # to which the reaction is simulated. And then we apply the Pareto principle. + alpha = 0.2 n_halflives = np.ceil(-np.log(alpha) / np.log(2)) halflife_estimate = 1.0 @@ -238,7 +247,7 @@
return y, r -def get_dydt(scheme, k, ef=1e4): +def get_dydt(scheme, k, ef=EF): """Generate a rate function that models a reaction scheme. Parameters @@ -304,10 +313,11 @@
k_adj = _adjust_k(scheme, k, ef=ef) def _dydt(t, y): - r = k * jnp.prod(jnp.power(y, M), axis=1) + r = k_adj * jnp.prod(jnp.power(y, M), axis=1) return jnp.dot(A, r) if _found_jax: + # Using JAX for JIT compilation is much faster. _dydt = jit(_dydt) def _jac(t, y): @@ -321,7 +331,7 @@
return _dydt -def _adjust_k(scheme, k, ef=1e4): +def _adjust_k(scheme, k, ef=EF): """Adjust reaction rate constants so that equilibria are equilibria. Parameters @@ -353,7 +363,7 @@
... rx.get_k(model.scheme, model.compounds)) # doctest: +SKIP array([8.16880917e+10]) - >>> model = rx.parse_model("data/acetate/model.k") + >>> model = rx.parse_model("data/acetate/Orca4/model.k") >>> _adjust_k(model.scheme, ... rx.get_k(model.scheme, model.compounds)) # doctest: +SKIP array([1.00000000e+00, 5.74491548e+04, 1.61152010e+07, @@ -382,6 +392,10 @@
k[is_half_equilibrium] *= adjustment logger.warning(f"equilibria adjustment = {adjustment}") + + k_slowest_equil = k[is_half_equilibrium].min() + k_fastest_react = k[~is_half_equilibrium].max() + logger.warning(f"fast r. / slow eq. = {k_fastest_react/k_slowest_equil}") else: # only equilibria @@ -781,17 +795,18 @@
The `y` object stores information about the simulation time, which can be used to produce a suitable vector of timepoints for, e.g., plotting: - >>> y.t_min, y.t_max - (0.0, 14.0) + >>> y.t_min, y.t_max # doctest: +SKIP + (0.0, 3.0) >>> t = np.linspace(y.t_min, y.t_max) - >>> t - array([ 0. , 0.28571429, ..., 13.71428571, 14. ]) + >>> t # doctest: +SKIP + array([0. , 0.06122449, ..., 2.93877551, 3. ]) Both `y` and `r` can be used to check concentrations and rates in any point in time. In particular, both are vectorized: - >>> y(t) - array([[1. , ..., 0.5 ]]) + >>> y(t) # doctest: +SKIP + array([[1. , 0.94237559, ..., 0.5012394, 0.5 ], + [0. , 0.05762441, ..., 0.4987606, 0.5 ]]) >>> r(t) # doctest: +SKIP array([[-1.00000000e+00, ..., -1.39544265e-10], [ 1.00000000e+00, ..., 1.39544265e-10]]) @@ -800,9 +815,9 @@
y0 = np.asarray(y0) if t_span is None: - # We defined alpha such that 1.0 - alpha is an estimate of the extend - # to which the reaction is simulated. - alpha = 1e-4 + # We defined alpha such that 1.0 - alpha is an (under)estimate of the extend + # to which the reaction is simulated. And then we apply the Pareto principle. + alpha = 0.2 n_halflives = np.ceil(-np.log(alpha) / np.log(2)) halflife_estimate = 1.0 @@ -902,18 +917,19 @@
Examples
The
-y
object stores information about the simulation time, which can be used to produce a suitable vector of timepoints for, e.g., plotting:>>> y.t_min, y.t_max -(0.0, 14.0) +
>>> y.t_min, y.t_max # doctest: +SKIP +(0.0, 3.0) >>> t = np.linspace(y.t_min, y.t_max) ->>> t -array([ 0. , 0.28571429, ..., 13.71428571, 14. ]) +>>> t # doctest: +SKIP +array([0. , 0.06122449, ..., 2.93877551, 3. ])
Both
-y
andr
can be used to check concentrations and rates in any point in time. In particular, both are vectorized:>>> y(t) -array([[1. , ..., 0.5 ]]) +
>>> y(t) # doctest: +SKIP +array([[1. , 0.94237559, ..., 0.5012394, 0.5 ], + [0. , 0.05762441, ..., 0.4987606, 0.5 ]]) >>> r(t) # doctest: +SKIP array([[-1.00000000e+00, ..., -1.39544265e-10], [ 1.00000000e+00, ..., 1.39544265e-10]]) @@ -927,12 +943,12 @@
Examples
def - get_dydt(scheme, k, ef=10000.0): + get_dydt(scheme, k, ef=5):View Source
-def get_dydt(scheme, k, ef=1e4): +def get_dydt(scheme, k, ef=EF): """Generate a rate function that models a reaction scheme. Parameters @@ -998,10 +1014,11 @@Examples
k_adj = _adjust_k(scheme, k, ef=ef) def _dydt(t, y): - r = k * jnp.prod(jnp.power(y, M), axis=1) + r = k_adj * jnp.prod(jnp.power(y, M), axis=1) return jnp.dot(A, r) if _found_jax: + # Using JAX for JIT compilation is much faster. _dydt = jit(_dydt) def _jac(t, y): diff --git a/docs/overreact/thermo.html b/docs/overreact/thermo.html index 5d29c669..5c1d3ba4 100644 --- a/docs/overreact/thermo.html +++ b/docs/overreact/thermo.html @@ -3,7 +3,7 @@ - +overreact.thermo API documentation @@ -27,7 +27,7 @@ - +@@ -88,7 +88,7 @@ import logging -from typing import Optional +from typing import Optional, Union import numpy as np from scipy.misc import derivative @@ -155,6 +155,11 @@
float Translational entropy in J/mol·K. + Raises + ------ + ValueError + If environment is "solid". + Examples -------- >>> calc_trans_entropy(35.45) # Cl- @@ -193,8 +198,8 @@
elif environment == "solid": raise ValueError(f"environment not yet implemented: {environment}") else: - assert atomnos is not None # FIX: add message - assert atomcoords is not None # FIX: add message + assert atomnos is not None, "atomnos must be provided" + assert atomcoords is not None, "atomcoords must be provided" volume = rx.thermo._solv.molar_free_volume( atomnos=atomnos, atomcoords=atomcoords, @@ -375,7 +380,7 @@
"""Calculate entropy. Either the classical gas phase or solvation entropies are available. For - solvation entropies, the method of A. Garza (doi:10.1021/acs.jctc.9b00214) + solvation entropies, the method of A. Garza (DOI:10.1021/acs.jctc.9b00214) is available and recommended. Parameters @@ -430,6 +435,11 @@
float Entropy in J/mol·K. + Raises + ------ + ValueError + If environment is "solid". + Notes ----- The improved solvation entropy model is a work in progress! @@ -499,8 +509,8 @@
if method == "standard": pass else: - assert atomnos is not None # FIX: add message - assert atomcoords is not None # FIX: add message + assert atomnos is not None, "atomnos must be provided" + assert atomcoords is not None, "atomcoords must be provided" # TODO(schneiderfelipe): this includes "izato", "garza" and # possibly future methods for extra entropy terms such as cavity. entropy = entropy + rx.thermo._solv.calc_cav_entropy( @@ -673,9 +683,9 @@
def equilibrium_constant( - delta_freeenergy: float | np.ndarray, - delta_moles: Optional[int | np.ndarray] = None, - temperature: float | np.ndarray = 298.15, + delta_freeenergy: Union[float, np.ndarray], + delta_moles: Optional[Union[int, np.ndarray]] = None, + temperature: Union[float, np.ndarray] = 298.15, pressure: float = constants.atm, volume: Optional[float] = None, ): @@ -820,7 +830,7 @@
new_reference: float = 1.0 / constants.liter, old_reference: Optional[float] = None, sign: int = 1, - temperature: float | np.ndarray = 298.15, + temperature: Union[float, np.ndarray] = 298.15, pressure: float = constants.atm, volume: Optional[float] = None, ): @@ -982,20 +992,20 @@
def equilibrium_constant( - delta_freeenergy: 'float | np.ndarray', - delta_moles: 'Optional[int | np.ndarray]' = None, - temperature: 'float | np.ndarray' = 298.15, + delta_freeenergy: Union[float, numpy.ndarray], + delta_moles: Union[int, numpy.ndarray, NoneType] = None, + temperature: Union[float, numpy.ndarray] = 298.15, pressure: float = 101325.0, - volume: Union[float, NoneType] = None + volume: Optional[float] = None ):
View Source
@@ -1292,7 +1302,7 @@def equilibrium_constant( - delta_freeenergy: float | np.ndarray, - delta_moles: Optional[int | np.ndarray] = None, - temperature: float | np.ndarray = 298.15, + delta_freeenergy: Union[float, np.ndarray], + delta_moles: Optional[Union[int, np.ndarray]] = None, + temperature: Union[float, np.ndarray] = 298.15, pressure: float = constants.atm, volume: Optional[float] = None, ): @@ -1278,11 +1288,11 @@Examples
def change_reference_state( new_reference: float = 1000.0, - old_reference: Union[float, NoneType] = None, + old_reference: Optional[float] = None, sign: int = 1, - temperature: 'float | np.ndarray' = 298.15, + temperature: Union[float, numpy.ndarray] = 298.15, pressure: float = 101325.0, - volume: Union[float, NoneType] = None + volume: Optional[float] = None ):Examples
new_reference: float = 1.0 / constants.liter, old_reference: Optional[float] = None, sign: int = 1, - temperature: float | np.ndarray = 298.15, + temperature: Union[float, np.ndarray] = 298.15, pressure: float = constants.atm, volume: Optional[float] = None, ): diff --git a/docs/overreact/tunnel.html b/docs/overreact/tunnel.html index f244cd46..64092ae4 100644 --- a/docs/overreact/tunnel.html +++ b/docs/overreact/tunnel.html @@ -3,7 +3,7 @@ - +overreact.tunnel API documentation @@ -27,7 +27,7 @@ - +@@ -88,7 +88,7 @@ import logging -from typing import Optional +from typing import Optional, Union import numpy as np from scipy.integrate import fixed_quad @@ -115,7 +115,7 @@
Raises ------ ValueError - If vibfreq is zero. + If `vibfreq` is zero. Examples -------- @@ -132,7 +132,7 @@
return np.abs(vibfreq) * constants.c / constants.centi -def wigner(vibfreq: float, temperature: float | np.ndarray = 298.15) -> float: +def wigner(vibfreq: float, temperature: Union[float, np.ndarray] = 298.15) -> float: """Calculate the Wigner correction to quantum tunneling. Parameters @@ -151,7 +151,7 @@
Raises ------ ValueError - If vibfreq is zero. + If `vibfreq` is zero. Examples -------- @@ -179,8 +179,8 @@
vibfreq: float, delta_forward: float, delta_backward: Optional[float] = None, - temperature: float | np.ndarray = 298.15, -) -> float: + temperature: Union[float, np.ndarray] = 298.15, +) -> Union[float, np.ndarray]: """Calculate the Eckart correction to quantum tunneling. References are @@ -210,7 +210,7 @@
Raises ------ ValueError - If vibfreq is zero. + If `vibfreq` is zero. Examples -------- @@ -241,14 +241,14 @@
logger.debug(f"forward potential barrier: {delta_forward} J/mol") logger.debug(f"backward potential barrier: {delta_backward} J/mol") - assert np.all(delta_forward >= 0.0) # FIX: add message - assert np.all(delta_backward >= 0.0) # FIX: add message + assert np.all(delta_forward >= 0.0), "delta_forward should be >= 0" + assert np.all(delta_backward >= 0.0), "delta_backward should be >= 0" # convert energies in joules per mole to joules delta_forward = delta_forward / constants.N_A delta_backward = delta_backward / constants.N_A - assert delta_backward is not None + assert delta_backward is not None, "delta_backward should be given" two_pi = 2.0 * np.pi alpha1 = two_pi * delta_forward / (constants.h * nu) alpha2 = two_pi * delta_backward / (constants.h * nu) @@ -262,7 +262,7 @@
def _eckart(u: float, alpha1: float, alpha2: Optional[float] = None) -> float: """Implement of the (unsymmetrical) Eckart tunneling approximation. - This is based on doi:10.1021/j100809a040 and doi:10.6028/jres.086.014. + This is based on DOI:10.1021/j100809a040 and DOI:10.6028/jres.086.014. Parameters ---------- @@ -284,7 +284,7 @@
distribution using a mixed set of quadratures (Gauss quadrature for values below zero and Laguerre quadrature for values from zero to infinity). The orders for both quadratures are fixed and are the smallest numbers that - allow us to reproduce values from the literature (doi:10.1021/j100809a040). + allow us to reproduce values from the literature (DOI:10.1021/j100809a040). Both alpha1 and alpha2 should be non-negative. @@ -361,9 +361,9 @@
eckart( vibfreq: float, delta_forward: float, - delta_backward: Union[float, NoneType] = None, - temperature: 'float | np.ndarray' = 298.15 -) -> float: + delta_backward: Optional[float] = None, + temperature: Union[float, numpy.ndarray] = 298.15 +) -> Union[float, numpy.ndarray]:
@@ -372,8 +372,8 @@vibfreq: float, delta_forward: float, delta_backward: Optional[float] = None, - temperature: float | np.ndarray = 298.15, -) -> float: + temperature: Union[float, np.ndarray] = 298.15, +) -> Union[float, np.ndarray]: """Calculate the Eckart correction to quantum tunneling. References are @@ -403,7 +403,7 @@
Raises ------ ValueError - If vibfreq is zero. + If `vibfreq` is zero. Examples -------- @@ -434,14 +434,14 @@
logger.debug(f"forward potential barrier: {delta_forward} J/mol") logger.debug(f"backward potential barrier: {delta_backward} J/mol") - assert np.all(delta_forward >= 0.0) # FIX: add message - assert np.all(delta_backward >= 0.0) # FIX: add message + assert np.all(delta_forward >= 0.0), "delta_forward should be >= 0" + assert np.all(delta_backward >= 0.0), "delta_backward should be >= 0" # convert energies in joules per mole to joules delta_forward = delta_forward / constants.N_A delta_backward = delta_backward / constants.N_A - assert delta_backward is not None + assert delta_backward is not None, "delta_backward should be given" two_pi = 2.0 * np.pi alpha1 = two_pi * delta_forward / (constants.h * nu) alpha2 = two_pi * delta_backward / (constants.h * nu) @@ -486,7 +486,7 @@
Returns
Raises
-
- ValueError: If vibfreq is zero.
+- ValueError: If
vibfreq
is zero.Examples
@@ -517,12 +517,15 @@Examples
def - wigner(vibfreq: float, temperature: 'float | np.ndarray' = 298.15) -> float: + wigner( + vibfreq: float, + temperature: Union[float, numpy.ndarray] = 298.15 +) -> float:View Source
-def wigner(vibfreq: float, temperature: float | np.ndarray = 298.15) -> float: +def wigner(vibfreq: float, temperature: Union[float, np.ndarray] = 298.15) -> float: """Calculate the Wigner correction to quantum tunneling. Parameters @@ -541,7 +544,7 @@Examples
Raises ------ ValueError - If vibfreq is zero. + If `vibfreq` is zero. Examples -------- @@ -589,7 +592,7 @@Returns
Raises
-
- ValueError: If vibfreq is zero.
+- ValueError: If
vibfreq
is zero.Examples
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this.config},t.Configuration.prototype.reset=function(){this.config={}},lunr.SortedSet=function(){this.length=0,this.elements=[]},lunr.SortedSet.load=function(e){var t=new this;return t.elements=e,t.length=e.length,t},lunr.SortedSet.prototype.add=function(){var e,t;for(e=0;e 1;){if(r===e)return o;e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o]}return r===e?o:-1},lunr.SortedSet.prototype.locationFor=function(e){for(var t=0,n=this.elements.length,i=n-t,o=t+Math.floor(i/2),r=this.elements[o];i>1;)e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o];return r>e?o:e>r?o+1:void 0},lunr.SortedSet.prototype.intersect=function(e){for(var t=new lunr.SortedSet,n=0,i=0,o=this.length,r=e.length,s=this.elements,u=e.elements;;){if(n>o-1||i>r-1)break;s[n]!==u[i]?s[n]u[i]&&i++:(t.add(s[n]),n++,i++)}return t},lunr.SortedSet.prototype.clone=function(){var e=new lunr.SortedSet;return e.elements=this.toArray(),e.length=e.elements.length,e},lunr.SortedSet.prototype.union=function(e){var t,n,i;this.length>=e.length?(t=this,n=e):(t=e,n=this),i=t.clone();for(var o=0,r=n.toArray();o \n\n overreact is a library and a command-line tool for building and\nanalyzing\nmicrokinetic models.\nData is parsed directly from computational chemistry output files thanks to\n
\n\ncclib
(see the\nlist of supported programs).Some relevant resources:
\n\n\n
\n\n- User-friendly, general purpose guide
\n- Documentation on the application programming interface
\n- GitHub repository
\nInstallation
\n\noverreact is a Python package, so you can easily install it with\n
\n\npip
:\n\n$ pip install "overreact[cli,fast]"\n
See the\ninstallation instructions\nin our guide for more details.
\n\nCiting overreact
\n\nIf you use overreact in your research, please cite:
\n\n\n\n\nF. S. S. Schneider and G. F. Caramori. overreact: a tool for creating and\n analyzing microkinetic models built from computational chemistry data.\n 2021. Available at: https://github.com/geem-lab/overreact.
\nHere's the reference in BibTeX format:
\n\n\n\n\n\n@misc{overreact2021,\n title = {\n \\textbf{overreact}: a tool for creating and analyzing microkinetic models\n built from computational chemistry data, ver. 1.0\n },\n author = {Schneider, F. S. S. and Caramori, G. F.},\n year = 2021,\n howpublished = {\\url{https://github.com/geem-lab/overreact}}\n}\n
A paper describing overreact is currently being prepared. When it is\npublished, the above BibTeX entry will be updated.
\n\nLicense
\n\noverreact is open-source, released under the permissive MIT license. See\nour LICENSE file.
\n\nFunding
\n\nThis project was developed at the GEEM lab\n(Federal University of Santa Catarina, Brazil), and was\npartially funded by the\nBrazilian National Council for Scientific and Technological Development (CNPq),\ngrant number 140485/2017-1.
\n"}, "overreact.api": {"fullname": "overreact.api", "modulename": "overreact.api", "qualname": "", "type": "module", "doc": "This module contains the high-level application programming interface.
\n\nIf you intend to use overreact as a library in a project, you should\nprobably start here.
\n"}, "overreact.api.get_k": {"fullname": "overreact.api.get_k", "modulename": "overreact.api", "qualname": "get_k", "type": "function", "doc": "Obtain reaction rate constants for a given reaction scheme.
\n\nParameters
\n\n\n
\n\n- scheme (Scheme):\nA descriptor of the reaction scheme.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- compounds (dict-like, optional):\nA descriptor of the compounds.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- bias (array-like, optional):\nEnergy to be added to free energies.
\n- tunneling (str or None, optional):\nChoose between \"eckart\", \"wigner\" or None (or \"none\").
\n- qrrho (bool or tuple-like, optional):\nApply both the quasi-rigid rotor harmonic oscillator (QRRHO)\napproximations of M. Head-Gordonand others (enthalpy correction, see\nJ. Phys. Chem. C 2015, 119, 4, 1840\u20131850)\nand S. Grimme (entropy correction, see\nTheory. Chem. Eur. J., 2012, 18: 9955-9964)\non top of the classical RRHO.
\n- scale (str, optional):\nReaction rate units. Possible values are \"cm3 mol-1 s-1\",\n\"l mol-1 s-1\", \"m3 mol-1 s-1\", \"cm3 particle-1 s-1\", \"mmHg-1 s-1\" and\n\"atm-1 s-1\".
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\n- pressure (array-like, optional):\nReference gas pressure.
\n- delta_freeenergies (array-like, optional):\nUse this instead of obtaining delta free energies from the compounds.
\n- molecularity (array-like, optional):\nReaction order, i.e., number of molecules that come together to react.\nIf set, this is used to calculate
\ndelta_moles
for\noverreact.thermo.equilibrium_constant
, which effectively calculates a solution\nequilibrium constant between reactants and the transition state for\ngas phase data. You should set this toNone
if your free energies\nwere already adjusted for solution Gibbs free energies.- volume (float, optional):\nMolar volume.
\nReturns
\n\n\n
\n\n- array-like
\nNotes
\n\nSome symbols are accepted as alternatives in \"scale\": \"M-1\", \"ml\" and\n\"torr-1\" are understood as \"l mol-1\", \"cm3\" and \"mmHg-1\", respectively.
\n\nExamples
\n\nBelow is an example of an estimate for the rate of methyl rotation in\nethane (a trivial attempt to reproduce\nScience, 2006, 313, 5795, 1951-1955).\nHow many turns it does per second?
\n\n\n\n>>> model = rx.parse_model("data/ethane/B97-3c/model.k")\n>>> get_k(model.scheme, model.compounds)\narray([8.16e+10])\n>>> get_k(model.scheme, model.compounds, qrrho=(False, True))\narray([8.24968117e+10])\n>>> get_k(model.scheme, model.compounds, qrrho=False)\narray([8.26909266e+10])\n>>> get_k(model.scheme, model.compounds, tunneling="wigner")\narray([7.99e+10])\n>>> get_k(model.scheme, model.compounds, tunneling=None)\narray([7.35e+10])\n
The calculated value is off by less than 2% from the experimental value\n(\\( \\frac{1}{12 \\times 10^{-12}} \\text{s}^{-1} = 8.33 \\times 10^{10} \\text{s}^{-1} \\)).\nWe use Eckart tunneling by default, but see the effect of changing it\nabove.
\n\nThe units of the returned reaction rate constants can be selected for\nnon-unimolecular processes. The following is an attempt to reproduce\nJ Atmos Chem, 1996 23, 37\u201349 for\nthe reaction of proton-withdrawal by a chloride radical from the methane\nmolecule\n\\( \\ce{CH4 + \\cdot Cl -> [H3C\\cdots H\\cdots Cl]^\\ddagger -> H3C\\cdot + HCl} \\):
\n\n\n\n>>> model = rx.parse_model("data/tanaka1996/UMP2/cc-pVTZ/model.jk")\n>>> get_k(model.scheme, model.compounds, temperature=300,\n... scale="cm3 particle-1 s-1")\narray([9.60e-14])\n
(By the way, according to the Jet Propulsion Laboratory,\nPublication No. 19-5,\nthe experimental reaction rate constant for this reaction is\n\\( 1.0 \\times 10^{-13} \\text{cm}^3 \\text{particle}^{-1} \\text{s}^{-1} \\).)
\n\nThe returned units are \"M-1 s-1\" by default:
\n\n\n\n>>> get_k(model.scheme, model.compounds) \\\n... == get_k(model.scheme, model.compounds, scale="l mol-1 s-1")\narray([ True])\n
You can also turn the tunneling correction off by using the string \"none\":
\n\n\n\n>>> get_k(model.scheme, model.compounds, tunneling="none") \\\n... == get_k(model.scheme, model.compounds, tunneling=None)\narray([ True])\n
You can set a simple energy bias, either as a constant or compound-wise:
\n\n\n", "parameters": ["scheme", "compounds", "bias", "tunneling", "qrrho", "scale", "temperature", "pressure", "delta_freeenergies", "molecularity", "volume"], "funcdef": "def"}, "overreact.api.get_kappa": {"fullname": "overreact.api.get_kappa", "modulename": "overreact.api", "qualname": "get_kappa", "type": "function", "doc": ">>> get_k(model.scheme, model.compounds, bias=1.0 * constants.kcal,\n... temperature=300.0, scale="cm3 particle-1 s-1")\narray([5.14e-13])\n>>> get_k(model.scheme, model.compounds,\n... bias=np.array([0.0, 0.0, -1.4, 0.0, 0.0]) * constants.kcal,\n... temperature=300.0, scale="cm3 particle-1 s-1")\narray([1.1e-12])\n
Obtain tunneling transmission coefficients at a given temperature.
\n\nOne tunneling transmission coefficient is calculated for each reaction. If\na reaction lacks a transition state (i.e., a half-equilibrium reaction),\nits transmission coefficient is set to unity.
\n\nParameters
\n\n\n
\n\n- scheme (Scheme):\nA descriptor of the reaction scheme.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- compounds (dict-like):\nA descriptor of the compounds.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- method (str or None, optional):\nChoose between \"eckart\", \"wigner\" or None (or \"none\").
\n- qrrho (bool, optional):\nApply both the quasi-rigid rotor harmonic oscillator (QRRHO)\napproximations of M. Head-Gordon and others (enthalpy correction, see\nJ. Phys. Chem. C 2015, 119, 4, 1840\u20131850)\nand S. Grimme (entropy correction, see\nTheory. Chem. Eur. J., 2012, 18: 9955-9964)\non top of the classical RRHO.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\nReturns
\n\n\n
\n\n- array-like
\nExamples
\n\nBelow is an example of an estimate of how much quantum tunneling\ncontributes to the rate of methyl rotation in ethane (see\nScience, 2006, 313, 5795, 1951-1955\nfor some interesting experimental data on this reaction).
\n\n\n\n>>> model = rx.parse_model("data/ethane/B97-3c/model.k")\n>>> kappa = get_kappa(model.scheme, model.compounds)\n>>> kappa\narray([1.110])\n>>> get_kappa(model.scheme, model.compounds, method="none")\narray([1.0])\n>>> get_kappa(model.scheme, model.compounds, method="none") \\\n... == get_kappa(model.scheme, model.compounds, method=None)\narray([ True])\n
You can calculate each piece of the reaction rate constant by hand,\nif you want. Just make sure that you don't calculate the tunneling\ncoefficient twice:
\n\n\n", "parameters": ["scheme", "compounds", "method", "qrrho", "temperature"], "funcdef": "def"}, "overreact.api.get_freeenergies": {"fullname": "overreact.api.get_freeenergies", "modulename": "overreact.api", "qualname": "get_freeenergies", "type": "function", "doc": ">>> kappa * get_k(model.scheme, model.compounds, tunneling=None)\narray([8.e+10])\n
Obtain free energies for compounds at a given temperature and pressure.
\n\nParameters
\n\n\n
\n\n- compounds (dict-like):\nA descriptor of the compounds.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- bias (array-like, optional):\nEnergy to be added to free energies.
\n- environment (str or None, optional):\nChoose between \"gas\" and a solvent. This is chosen for you by default,\nbased on the names of each compound. If given, all compounds will\nhave the same behavior.
\n- method (str, optional):\nThis is a placeholder for future functionality.\nThere are plans to implement more sophisticated methods for calculating\nentropies such as in\nPhys. Chem. Chem. Phys., 2019, 21, 18920-18929\nand\nJ. Chem. Theory Comput. 2019, 15, 5, 3204\u20133214.\nHead over to the\ndiscussions if\nyou're interested and would like to contribute.\nLeave this as \"standard\" for now.
\n- qrrho (bool or tuple-like, optional):\nApply both the quasi-rigid rotor harmonic oscillator (QRRHO)\napproximations of M. Head-Gordon and others (enthalpy correction, see\nJ. Phys. Chem. C 2015, 119, 4, 1840\u20131850)\nand S. Grimme (entropy correction, see\nTheory. Chem. Eur. J., 2012, 18: 9955-9964)\non top of the classical RRHO.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\n- pressure (array-like, optional):\nReference gas pressure.
\nReturns
\n\n\n
\n\n- array-like
\nExamples
\n\n\n\n>>> import overreact as rx\n>>> from overreact import _constants as constants\n>>> model = rx.parse_model("data/ethane/B97-3c/model.k")\n>>> freeenergies = get_freeenergies(model.compounds, qrrho=(False, True))\n>>> (freeenergies - freeenergies.min()) / constants.kcal\narray([0. , 2.62281461])\n>>> freeenergies = get_freeenergies(model.compounds)\n>>> (freeenergies - freeenergies.min()) / constants.kcal\narray([0. , 2.62862818])\n
You can consider all compounds as solvated if you want:
\n\n\n\n>>> sol_freeenergies = get_freeenergies(model.compounds, environment="solvent")\n>>> (sol_freeenergies - freeenergies) / constants.kcal\narray([1.89432845, 1.89432845])\n
You can set a simple energy bias, either as a constant or compound-wise:
\n\n\n", "parameters": ["compounds", "bias", "environment", "method", "qrrho", "temperature", "pressure"], "funcdef": "def"}, "overreact.api.get_entropies": {"fullname": "overreact.api.get_entropies", "modulename": "overreact.api", "qualname": "get_entropies", "type": "function", "doc": ">>> get_freeenergies(model.compounds, bias=1.0) - freeenergies\narray([1., 1.])\n>>> get_freeenergies(model.compounds, bias=-1.0) - freeenergies\narray([-1., -1.])\n>>> get_freeenergies(model.compounds, bias=[1.0, -1.0]) - freeenergies\narray([ 1., -1.])\n
Obtain entropies for compounds at a given temperature and pressure.
\n\nParameters
\n\n\n
\n\n- compounds (dict-like):\nA descriptor of the compounds.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- environment (str or None, optional):\nChoose between \"gas\" and a solvent. This is chosen for you by default,\nbased on the names of each compound (e.g.
\nA(g)
orA
is gas,\nA(w)
orA(...)
is solvated). In case this is given, all compounds\nwill have the same behavior.- method (str, optional):\nThis is a placeholder for future functionality.\nThere are plans to implement more sophisticated methods for calculating\nentropies such as in\nPhys. Chem. Chem. Phys., 2019, 21, 18920-18929\nand\nJ. Chem. Theory Comput. 2019, 15, 5, 3204\u20133214.\nHead over to the\ndiscussions if\nyou're interested and would like to contribute.\nLeave this as \"standard\" for now.
\n- qrrho (bool, optional):\nApply the quasi-rigid rotor harmonic oscillator (QRRHO) approximation of\nS. Grimme (see\nTheory. Chem. Eur. J., 2012, 18: 9955-9964)\non top of the classical RRHO.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\n- pressure (array-like, optional):\nReference gas pressure.
\nReturns
\n\n\n
\n\n- array-like
\nExamples
\n\n\n\n>>> import overreact as rx\n>>> from overreact import _constants as constants\n>>> model = rx.parse_model("data/ethane/B97-3c/model.k")\n>>> entropies = get_entropies(model.compounds)\n>>> (entropies - entropies.min()) / constants.calorie\narray([1.4, 0. ])\n
You can consider all compounds as solvated if you want:
\n\n\n", "parameters": ["compounds", "environment", "method", "qrrho", "temperature", "pressure"], "funcdef": "def"}, "overreact.api.get_enthalpies": {"fullname": "overreact.api.get_enthalpies", "modulename": "overreact.api", "qualname": "get_enthalpies", "type": "function", "doc": ">>> sol_entropies = get_entropies(model.compounds, environment="solvent")\n>>> (sol_entropies - entropies) / constants.calorie\narray([-6.35360874, -6.35360874])\n
Obtain enthalpies for compounds at a given temperature.
\n\nParameters
\n\n\n
\n\n- compounds (dict-like):\nA descriptor of the compounds.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- qrrho (bool, optional):\nApply the quasi-rigid rotor harmonic oscillator (QRRHO) approximation of\nM. Head-Gordon and others (see\nJ. Phys. Chem. C 2015, 119, 4, 1840\u20131850)\non top of the classical RRHO.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\nReturns
\n\n\n
\n\n- array-like
\nExamples
\n\n\n\n>>> import overreact as rx\n>>> from overreact import _constants as constants\n>>> model = rx.parse_model("data/ethane/B97-3c/model.k")\n>>> enthalpies = get_enthalpies(model.compounds)\n>>> (enthalpies - enthalpies.min()) / constants.kcal\narray([0. , 2.20053981])\n
The enthalpies at absolute zero can easily be obtained (this is used,\ne.g., in the calculation of the Eckart tunneling coefficient, see\n
\n\noverreact.tunnel.eckart
). We can use this to calculate, for instance,\nthe thermal contributions to the enthalpy:\n", "parameters": ["compounds", "qrrho", "temperature"], "funcdef": "def"}, "overreact.api.get_internal_energies": {"fullname": "overreact.api.get_internal_energies", "modulename": "overreact.api", "qualname": "get_internal_energies", "type": "function", "doc": ">>> zero_enthalpies = get_enthalpies(model.compounds, temperature=0)\n>>> (enthalpies - zero_enthalpies) / constants.kcal\narray([2.78, 2.50])\n
Obtain internal energies for compounds at a given temperature.
\n\nParameters
\n\n\n
\n\n- compounds (dict-like):\nA descriptor of the compounds.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- qrrho (bool, optional):\nApply the quasi-rigid rotor harmonic oscillator (QRRHO) approximation of\nM. Head-Gordon and others (see\nJ. Phys. Chem. C 2015, 119, 4, 1840\u20131850)\non top of the classical RRHO.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\nReturns
\n\n\n
\n\n- array-like
\nExamples
\n\n\n", "parameters": ["compounds", "qrrho", "temperature"], "funcdef": "def"}, "overreact.coords": {"fullname": "overreact.coords", "modulename": "overreact.coords", "qualname": "", "type": "module", "doc": ">>> import overreact as rx\n>>> from overreact import _constants as constants\n>>> model = rx.parse_model("data/ethane/B97-3c/model.k")\n>>> internal_energies = get_internal_energies(model.compounds)\n>>> (internal_energies - internal_energies.min()) / constants.kcal\narray([0. , 2.20053981])\n
Module dedicated to classifying molecules into point groups.
\n"}, "overreact.coords.find_point_group": {"fullname": "overreact.coords.find_point_group", "modulename": "overreact.coords", "qualname": "find_point_group", "type": "function", "doc": "Determine point group of structure.
\n\nParameters
\n\n\n
\n\n- atommasses (array-like):\nAtomic masses in atomic mass units (amu).
\n- atomcoords (array-like):\nAtomic coordinates.
\n- proper_axes (sequence of tuples of int, array-like, optional):\nProper symmetry axes of rotation.
\n- rtol (float, optional):\nThe relative tolerance parameter (see
\nnumpy.isclose
).- atol (float, optional):\nThe absolute tolerance parameter (see
\nnumpy.isclose
).Returns
\n\n\n
\n\n- str: Point group symbol.
\nExamples
\n\n\n", "parameters": ["atommasses", "atomcoords", "proper_axes", "rtol", "atol"], "funcdef": "def"}, "overreact.coords.symmetry_number": {"fullname": "overreact.coords.symmetry_number", "modulename": "overreact.coords", "qualname": "symmetry_number", "type": "function", "doc": ">>> find_point_group([1], [[0, 0, 1]])\n'K'\n>>> find_point_group([1, 1], [[0, 0, 1], [0, 0, 0]])\n'D\u221eh'\n>>> find_point_group([1.008, 35.45], [[0, 0, 1], [0, 0, 0]])\n'C\u221ev'\n>>> find_point_group([16, 12, 16], [[1, 0, 1], [1, 0, 0], [1, 0, -1]])\n'D\u221eh'\n>>> find_point_group([16, 12, 32], [[1, 1, 1], [1, 1, 0], [1, 1, -1]])\n'C\u221ev'\n>>> find_point_group([12, 12, 12, 12], [[1, 0, 0],\n... [0, 1, 0],\n... [0, 0, 0],\n... [1, 1, 0]])\n'D4h'\n
Return rotational symmetry number for point group.
\n\nThis function has a set of the most common point groups precomputed, but is\nable to calculate the symmetry number if it is not found in known tables.\nMost precomputed values are from\nTheor Chem Account 2007 118, 813\u2013826.
\n\nParameters
\n\n\n
\n\n- point_group (str):\nPoint group symbol.
\nReturns
\n\n\n
\n\n- int: Rotational symmetry number.
\nExamples
\n\n\n", "parameters": ["point_group"], "funcdef": "def"}, "overreact.core": {"fullname": "overreact.core", "modulename": "overreact.core", "qualname": "", "type": "module", "doc": ">>> symmetry_number("C4")\n4\n>>> symmetry_number("C4") == symmetry_number("C4h")\nTrue\n>>> symmetry_number("C6")\n6\n>>> symmetry_number("C6") == symmetry_number("C6v")\nTrue\n>>> symmetry_number("C6") == symmetry_number("C6h")\nTrue\n>>> symmetry_number("D2") == symmetry_number("Vh")\nTrue\n>>> symmetry_number("D4")\n8\n>>> symmetry_number("D6")\n12\n>>> symmetry_number("D6") == symmetry_number("D6d")\nTrue\n>>> symmetry_number("S6")\n3\n>>> symmetry_number("T")\n12\n
Module dedicated to parsing and modeling of chemical reaction networks.
\n"}, "overreact.core.Scheme": {"fullname": "overreact.core.Scheme", "modulename": "overreact.core", "qualname": "Scheme", "type": "class", "doc": "A descriptor of a chemical reaction network.
\n\nMostly likely, this comes from a parsed input file.\nSee
\n"}, "overreact.core.Scheme.__init__": {"fullname": "overreact.core.Scheme.__init__", "modulename": "overreact.core", "qualname": "Scheme.__init__", "type": "function", "doc": "overreact.io.parse_model
.Create new instance of Scheme(compounds, reactions, is_half_equilibrium, A, B)
\n", "parameters": ["_cls", "compounds", "reactions", "is_half_equilibrium", "A", "B"], "funcdef": "def"}, "overreact.core.Scheme.compounds": {"fullname": "overreact.core.Scheme.compounds", "modulename": "overreact.core", "qualname": "Scheme.compounds", "type": "variable", "doc": "A descriptor of compounds.
\n"}, "overreact.core.Scheme.reactions": {"fullname": "overreact.core.Scheme.reactions", "modulename": "overreact.core", "qualname": "Scheme.reactions", "type": "variable", "doc": "A descriptor of reactions.
\n"}, "overreact.core.Scheme.is_half_equilibrium": {"fullname": "overreact.core.Scheme.is_half_equilibrium", "modulename": "overreact.core", "qualname": "Scheme.is_half_equilibrium", "type": "variable", "doc": "An indicator of whether a reaction is half-equilibrium.
\n"}, "overreact.core.Scheme.A": {"fullname": "overreact.core.Scheme.A", "modulename": "overreact.core", "qualname": "Scheme.A", "type": "variable", "doc": "A matrix of stoichiometric coefficients between reactants and products.
\n"}, "overreact.core.Scheme.B": {"fullname": "overreact.core.Scheme.B", "modulename": "overreact.core", "qualname": "Scheme.B", "type": "variable", "doc": "A matrix of stoichiometric coefficients between reactants and transition states.
\n"}, "overreact.core.parse_reactions": {"fullname": "overreact.core.parse_reactions", "modulename": "overreact.core", "qualname": "parse_reactions", "type": "function", "doc": "Parse a kinetic model as a chemical reaction scheme.
\n\nThis is an essential part of the parsing process.\nSee
\n\noverreact.io.parse_model
other details.Parameters
\n\n\n
\n\n- text (str or sequence of str):\nModel description or sequence of lines of it.
\nReturns
\n\n\n
\n\n- scheme (Scheme):\nA descriptor of the reaction scheme.
\nNotes
\n\nThe model description should comply with the mini-language for systems of\nreactions. A semi-formal definition of the grammar in\nBackus\u2013Naur form\nis given below:
\n\n\n\nequation ::= equation_side arrow equation_side\nequation_side ::= coefficient compound ['+' coefficient compound]*\n coefficient ::= [integers] (defaults to 1)\n compound ::= mix of printable characters\n arrow ::= '->' | '<=>' | '<-'\n
Blank lines and comments (starting with
\n\n//
) are ignored. Repeated\nreactions are ignored. Furthermore, reactions can be chained one after\nanother and, if a single compound (with either a\u2021
or a#
at the end)\nappears alone on one side of a reaction, it's considered a transition\nstate. Transition states have zero lifetime during the simulation.Examples
\n\nWhat follows is a rather long tour over the parsing process and its\noutput in general. You can skip it if you are not interested in the\ndetails.
\n\n\n\n>>> scheme = parse_reactions("A -> B // a direct reaction")\n
The reaction above is a direct one (observe that comments are ignored). The\nreturned object has the following attributes:
\n\n\n\n>>> scheme.compounds\n('A', 'B')\n>>> scheme.reactions\n('A -> B',)\n>>> scheme.is_half_equilibrium\n(False,)\n>>> scheme.A\n((-1.,), (1.,))\n>>> scheme.B\n((-1.,), (1.,))\n
The same reaction can be specified in reverse order:
\n\n\n\n>>> parse_reactions("B <- A // reverse reaction of the above")\nScheme(compounds=('A', 'B'),\n reactions=('A -> B',),\n is_half_equilibrium=(False,),\n A=((-1.,), (1.,)),\n B=((-1.,), (1.,)))\n
Equilibria produce twice as many direct reactions, while the $B$ matrix\ndefines an energy relationship for only one of each pair:
\n\n\n\n>>> parse_reactions("A <=> B // an equilibrium")\nScheme(compounds=('A', 'B'),\n reactions=('A -> B', 'B -> A'),\n is_half_equilibrium=(True, True),\n A=((-1., 1.),\n (1., -1.)),\n B=((-1., 0.),\n (1., 0.)))\n
Adding twice the same reaction results in a single reaction being added.\nThis of course also works with equilibria (extra whitespaces are ignored):
\n\n\n\n>>> parse_reactions('''\n... A <=> B -> A\n... A -> B <=> A\n... A -> B <- A\n... B <- A -> B\n... ''')\nScheme(compounds=('A', 'B'),\n reactions=('A -> B', 'B -> A'),\n is_half_equilibrium=(True, True),\n A=((-1., 1.),\n (1., -1.)),\n B=((-1., 0.),\n (1., 0.)))\n
Transition states are specified with a special symbol at the end (either\n
\n\n\u2021
or#
). They are shown among compounds, but the matrix $A$ ensures\nthey'll never have a non-zero rate of formation/consumption. On the other\nhand, they are needed in the $B$ matrix:\n\n>>> parse_reactions("A -> A\u2021 -> B")\nScheme(compounds=('A', 'A\u2021', 'B'),\n reactions=('A -> B',),\n is_half_equilibrium=(False,),\n A=((-1.,), (0.,), (1.,)),\n B=((-1.,), (1.,), (0.,)))\n
This gives the same result as above:
\n\n\n\n>>> parse_reactions("A -> A\u2021 -> B <- A\u2021 <- A")\nScheme(compounds=('A', 'A\u2021', 'B'),\n reactions=('A -> B',),\n is_half_equilibrium=(False,),\n A=((-1.,), (0.,), (1.,)),\n B=((-1.,), (1.,), (0.,)))\n
It is possible to define a reaction whose product is the same as the\nreactant. This is found in isomerization processes (e.g., ammonia\ninversion or the methyl rotation in ethane):
\n\n\n\n>>> parse_reactions("S -> E\u2021 -> S")\nScheme(compounds=('S', 'E\u2021'),\n reactions=('S -> S',),\n is_half_equilibrium=(False,),\n A=((0.,), (0.,)),\n B=((-1.,), (1.,)))\n
As such, a column full of zeros in the $A$ matrix corresponds to a reaction\nwith zero net change. As can be seen, overreact allows for very general\nmodels. An interesting feature is that a single transition state can link\nmany different compounds (whether it is useful is a matter of debate):
\n\n\n\n>>> parse_reactions('''\n... B -> B\u2021 -> C // chained reactions and transition states\n... B\u2021 -> D // this is a bifurcation\n... B -> B'\u2021 -> E // this is a classical competitive reaction\n... A -> B\u2021\n... ''')\nScheme(compounds=('B', 'B\u2021', 'C', 'D', "B'\u2021", 'E', 'A'),\n reactions=('B -> C', 'B -> D', 'B -> E', 'A -> C', 'A -> D'),\n is_half_equilibrium=(False, False, False, False, False),\n A=((-1., -1., -1., 0., 0.),\n (0., 0., 0., 0., 0.),\n (1., 0., 0., 1., 0.),\n (0., 1., 0., 0., 1.),\n (0., 0., 0., 0., 0.),\n (0., 0., 1., 0., 0.),\n (0., 0., 0., -1., -1.)),\n B=((-1., -1., -1., 0., 0.),\n (1., 1., 0., 1., 1.),\n (0., 0., 0., 0., 0.),\n (0., 0., 0., 0., 0.),\n (0., 0., 1., 0., 0.),\n (0., 0., 0., 0., 0.),\n (0., 0., 0., -1., -1.)))\n
The following is a borderline case but both reactions should be considered\ndifferent since they define different processes:
\n\n\n\n>>> parse_reactions('''\n... A -> A\u2021 -> B\n... A -> B\n... ''')\nScheme(compounds=('A', 'A\u2021', 'B'),\n reactions=('A -> B', 'A -> B'),\n is_half_equilibrium=(False, False),\n A=((-1., -1.),\n (0., 0.),\n (1., 1.)),\n B=((-1., -1.),\n (1., 0.),\n (0., 1.)))\n
The following is correct behavior. In fact, the reactions are badly\ndefined: if more than one transition state are chained, the following\nhappens, which is correct since it's the most physically plausible model\nthat can be extracted. It can be seen as a feature that the product B is\nignored and not the reactant A, since the user would easily see the mistake\nin graphs of concentration over time (the alternative would be no\nreaction happening at all, which is rather cryptic to debug).
\n\n\n\n>>> parse_reactions("A -> A\u2021 -> A'\u2021 -> B")\nScheme(compounds=('A', 'A\u2021', "A'\u2021", 'B'),\n reactions=("A -> A'\u2021",),\n is_half_equilibrium=(False,),\n A=((-1.,), (0.,), (1.,), (0.,)),\n B=((-1.,), (1.,), (0.,), (0.,)))\n
In any case, it's not clear how a reaction barrier be defined in such a\ncase. If you have a use case, don't hesitate to\nopen an issue, we'll be\nhappy to hear from you.
\n", "parameters": ["text"], "funcdef": "def"}, "overreact.io": {"fullname": "overreact.io", "modulename": "overreact.io", "qualname": "", "type": "module", "doc": "Basic I/O operations (such as reading source input files).
\n"}, "overreact.io.parse_model": {"fullname": "overreact.io.parse_model", "modulename": "overreact.io", "qualname": "parse_model", "type": "function", "doc": "Parse either a source or model input file, whichever is available.
\n\nA source input file (also known as a
\n\n.k
file) contains all the information needed\nto create a model input file.\nA model input file (also known as a.jk
file) is a JSON encoded file with all the\ninformation needed to study microkinetic simulations from first principles.You probably won't need to use model input files directly, they are\nautomatically created based on source input files.\nTake a look at our guide on how to write an source input file.
\n\nThis function attempts to parse a model input file if available. If not, a source\ninput file is parsed and a model input file is generated from it. Extensions are\nguessed if none given (i.e., if only the base name given).
\n\nParameters
\n\n\n
\n\n- path (str):\nPath to the model or source input file.\nIf the final extension is not
\n.jk
or.k
, it is guessed.- force_compile (bool):\nIf True, a
\n.k
file will take precedence over any.jk
file for reading. A\n.jk
file is thus either generated or overwritten. This is sometimes\nneeded to force an update with new data.Returns
\n\n\n
\n\n- model (immutable dict-like):
\nRaises
\n\n\n
\n\n- FileNotFoundError: If no files could be found.
\nExamples
\n\nSome examples of how overreact \"sees\" your data below \ud83d\ude04:
\n\n\n", "parameters": ["path", "force_compile"], "funcdef": "def"}, "overreact.rates": {"fullname": "overreact.rates", "modulename": "overreact.rates", "qualname": "", "type": "module", "doc": ">>> model = parse_model("data/ethane/B97-3c/model.jk")\n>>> model.scheme\nScheme(compounds=('S', 'E\u2021'),\n reactions=('S -> S',),\n is_half_equilibrium=(False,),\n A=((0.0,), (0.0,)),\n B=((-1.0,), (1.0,)))\n>>> model.compounds["S"]\n{'logfile': 'data/ethane/B97-3c/staggered.out',\n 'energy': -209483812.77142256,\n 'mult': 1,\n 'atomnos': (6, 6, 1, 1, 1, 1, 1, 1),\n 'atommasses': (12.011, 12.011, 1.008, 1.008, 1.008, 1.008, 1.008, 1.008),\n 'atomcoords': ((-7.633588, 2.520693, -4.8e-05),\n ...,\n (-5.832852, 3.674431, 0.363239)),\n 'vibfreqs': (307.57, 825.42, ..., 3071.11, 3071.45),\n 'vibdisps': (((-1.7e-05, 3.4e-05, 5.4e-05),\n ...,\n (-0.011061, -0.030431, -0.027036)))}\n>>> model_from_source = parse_model("data/ethane/B97-3c/model.k",\n... force_compile=True)\n>>> model_from_source == model\nTrue\n>>> model_from_source = parse_model("data/ethane/B97-3c/model")\n>>> model_from_source == model\nTrue\n
Module dedicated to the calculation of reaction rate constants.
\n"}, "overreact.rates.eyring": {"fullname": "overreact.rates.eyring", "modulename": "overreact.rates", "qualname": "eyring", "type": "function", "doc": "Calculate a reaction rate constant.
\n\nThis function uses the Eyring-Evans-Polanyi equation\n from transition state\ntheory :
\n\n$$k(T) = \\frac{k_\\text{B} T}{h} K^\\ddagger\n = \\frac{k_\\text{B} T}{h}\n \\exp\\left(-\\frac{\\Delta^\\ddagger G^\\circ}{R T}\\right)$$
\n\nwhere \\( h \\) is Planck's constant, \\( k_\\text{B} \\) is Boltzmann's\nconstant and \\( T \\) is the absolute temperature.
\n\nParameters
\n\n\n
\n\n- delta_freeenergy (array-like):\nDelta Gibbs activation free energies. This assumes values were already\ncorrected for a one molar reference state (if applicable).
\n- molecularity (array-like, optional):\nReaction order, i.e., number of molecules that come together to react.\nIf set, this is used to calculate
\ndelta_moles
for\nequilibrium_constant
, which effectively calculates a solution\nequilibrium constant between reactants and the transition state for\ngas phase data. You should set this toNone
if your free energies\nwere already adjusted for solution Gibbs free energies.- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\n- pressure (array-like, optional):\nReference gas pressure.
\n- volume (float, optional):\nMolar volume. This is passed on to
\nequilibrium_constant
.Returns
\n\n\n
\n\n- k (array-like):\nReaction rate constant(s). By giving energies in one molar reference\nstate, returned units are then accordingly given, e.g. \"l mol-1 s-1\"\nif second-order, etc.
\nNotes
\n\nThis function uses
\n\nequilibrium_constant
internally to calculate the\nequilibrium constant between reactants and the transition state.Examples
\n\nThe following are examples from\nThermochemistry in Gaussian, in which the\nkinetic isotope effect of a bimolecular reaction is analyzed:
\n\n\n\n>>> eyring(17.26 * constants.kcal)\narray([1.38])\n>>> eyring(18.86 * constants.kcal)\narray([0.093])\n
It is well known that, at room temperature, if you \"decrease\" a reaction\nbarrier by 1.4 kcal/mol, the reaction becomes around ten times faster:
\n\n\n\n>>> dG = np.random.uniform(1.0, 100.0) * constants.kcal\n>>> eyring(dG - 1.4 * constants.kcal) / eyring(dG)\narray([10.])\n
A similar relationship is found for a twofold increase in speed and a\n0.4 kcal/mol decrease in the reaction barrier (again, at room\ntemperature):
\n\n\n", "parameters": ["delta_freeenergy", "molecularity", "temperature", "pressure", "volume"], "funcdef": "def"}, "overreact.simulate": {"fullname": "overreact.simulate", "modulename": "overreact.simulate", "qualname": "", "type": "module", "doc": ">>> eyring(dG - 0.4 * constants.kcal) / eyring(dG)\narray([2.0])\n
Module dedicated to the time simulation of reaction models.
\n\nHere are functions that calculate reaction rates as well, which is needed for\nthe time simulations.
\n"}, "overreact.simulate.get_y": {"fullname": "overreact.simulate.get_y", "modulename": "overreact.simulate", "qualname": "get_y", "type": "function", "doc": "Simulate a reaction scheme from its rate function.
\n\nThis function provides two functions that calculate the concentrations and\nthe rates of formation at any point in time for any compound. It does that\nby solving an initial value problem (IVP) through scipy's
\n\nsolve_ivp
\nunder the hood.Parameters
\n\n\n
\n\n- dydt (callable):\nRight-hand side of the system.
\n- y0 (array-like):\nInitial state.
\n- t_span (array-like, optional):\nInterval of integration (t0, tf). The solver starts with t=t0 and\nintegrates until it reaches t=tf. If not given, a conservative value\nis chosen based on the system at hand (the method of choice works for\nany zeroth-, first- or second-order reactions).
\n- method (str, optional):\nIntegration method to use. See
\nscipy.integrate.solve_ivp
for details.\nKinetics problems are very often stiff and, as such, \"RK45\" is\nnormally unsuited. \"Radau\", \"BDF\" or \"LSODA\" are good choices.- rtol, atol (array-like):\nSee
\nscipy.integrate.solve_ivp
for details.- max_time (float, optional):\nIf
\nt_span
is not given, an interval will be estimated, but it can't\nbe larger than this parameter.Returns
\n\n\n
\n\n- y, r (callable):\nConcentrations and reaction rates as functions of time. The y object\nis an OdeSolution and stores attributes t_min and t_max.
\nExamples
\n\n\n\n>>> import numpy as np\n>>> import overreact as rx\n
A toy simulation can be performed in just two lines:
\n\n\n\n>>> scheme = rx.parse_reactions("A <=> B")\n>>> y, r = get_y(get_dydt(scheme, np.array([1, 1])), y0=[1, 0])\n
The
\n\ny
object stores information about the simulation time, which can be\nused to produce a suitable vector of timepoints for, e.g., plotting:\n\n>>> y.t_min, y.t_max\n(0.0, 14.0)\n>>> t = np.linspace(y.t_min, y.t_max)\n>>> t\narray([ 0. , 0.28571429, ..., 13.71428571, 14. ])\n
Both
\n\ny
andr
can be used to check concentrations and rates in any\npoint in time. In particular, both are vectorized:\n", "parameters": ["dydt", "y0", "t_span", "method", "rtol", "atol", "max_time"], "funcdef": "def"}, "overreact.simulate.get_dydt": {"fullname": "overreact.simulate.get_dydt", "modulename": "overreact.simulate", "qualname": "get_dydt", "type": "function", "doc": ">>> y(t)\narray([[1. , ..., 0.5 ]])\n>>> r(t) # doctest: +SKIP\narray([[-1.00000000e+00, ..., -1.39544265e-10],\n [ 1.00000000e+00, ..., 1.39544265e-10]])\n
Generate a rate function that models a reaction scheme.
\n\nParameters
\n\n\n
\n\n- scheme (Scheme):\nA descriptor of the reaction scheme.\nMostly likely, this comes from a parsed model input file.\nSee
\noverreact.io.parse_model
.- k (array-like):\nReaction rate constant(s). Units match the concentration units given to\nthe returned function
\ndydt
.- ef (float, optional):\nEquilibrium factor. This is a parameter that can be used to scale the\nreaction rates associated to half-equilibrium reactions such that they\nare faster than the other reactions.
\nReturns
\n\n\n
\n\n- dydt (callable):\nReaction rate function. The actual reaction rate constants employed\nare stored in the attribute
\nk
of the returned function. If JAX is\navailable, the attributejac
will hold the Jacobian function of\ndydt
.Notes
\n\nThe returned function is suited to be used by ODE solvers such as\n
\n\nscipy.integrate.solve_ivp
or the olderscipy.integrate.ode
(see\nexamples below). This is actually what the functionget_y
from the\ncurrent module does.Examples
\n\n\n\n>>> import numpy as np\n>>> import overreact as rx\n
\n\n>>> scheme = rx.parse_reactions("A <=> B")\n>>> dydt = get_dydt(scheme, np.array([1, 1]))\n>>> dydt(0.0, np.array([1., 1.])) # doctest: +SKIP\narray([0., 0.])\n
If available, JAX is used for JIT compilation. This will make
\n\ndydt
\ncomplain if given lists instead of numpy arrays. So stick to the safer,\nfaster side as above.The actually used reaction rate constants can be inspected with the
\n\nk
\nattribute ofdydt
:\n\n>>> dydt.k # doctest: +SKIP\narray([1., 1.])\n
If JAX is available, the Jacobian function will be available as\n
\n\ndydt.jac
:\n", "parameters": ["scheme", "k", "ef"], "funcdef": "def"}, "overreact.simulate.get_fixed_scheme": {"fullname": "overreact.simulate.get_fixed_scheme", "modulename": "overreact.simulate", "qualname": "get_fixed_scheme", "type": "function", "doc": ">>> dydt.jac(0.0, np.array([1., 1.])) # doctest: +SKIP\nDeviceArray([[-1., 1.],\n [ 1., -1.]], dtype=float64)\n
Generate an alternative scheme with some concentrations fixed.
\n\nThis function returns data that allow the microkinetic simulation of a\nreaction network under constraints, namely when some compounds have fixed\nconcentrations. This works by 1. removing all references to the fixed\ncompounds and by 2. properly multiplying the reaction rate constants by\nthe respective concentrations.
\n\nParameters
\n\n\n
\n\n- scheme (Scheme):\nA descriptor of the reaction scheme.\nMostly likely, this comes from a parsed model input file.\nSee
\noverreact.io.parse_model
.- k (array-like):\nReaction rate constant(s). Units match the concentration units given to\nthe returned function
\ndydt
.- fixed_y0 (dict-like):\nFixed initial state. Units match the concentration units given to\nthe returned function
\ndydt
.Returns
\n\n\n
\n\n- scheme (Scheme):\nAssociated reaction scheme with all references to fixed compounds\nremoved.
\n- k (array-like):\nAssociated (effective) reaction rate constants that model the fixed\nconcentrations.
\nNotes
\n\nKeep in mind that when a compound get its concentration fixed, the\nreaction scheme no longer conserves matter. You can think of it as\nreacting close to an infinite source of the compound, but it accumulates\nin the milleu at the given concentration.
\n\nExamples
\n\n\n\n>>> import numpy as np\n>>> import overreact as rx\n
Equilibria under a specific pH can be easily modeled:
\n\n\n\n>>> pH = 7\n>>> scheme = rx.parse_reactions("AH <=> A- + H+")\n>>> k = np.array([1, 1])\n>>> scheme, k = rx.get_fixed_scheme(scheme, k, {"H+": 10**-pH})\n>>> scheme\nScheme(compounds=('AH', 'A-'),\n reactions=('AH -> A-',\n 'A- -> AH'),\n is_half_equilibrium=(True, True),\n A=((-1.0, 1.0),\n (1.0, -1.0)),\n B=((-1.0, 0.0),\n (1.0, 0.0)))\n>>> k\narray([1.e+00, 1.e-07])\n
It is also possible to model the fixed activity of a solvent, for\ninstance:
\n\n\n\n>>> scheme = rx.parse_reactions("A + 2H2O -> B")\n>>> k = np.array([1.0])\n>>> scheme, k = rx.get_fixed_scheme(scheme, k, {"H2O": 55.6})\n>>> scheme\nScheme(compounds=('A', 'B'),\n reactions=('A -> B',),\n is_half_equilibrium=(False,),\n A=((-1.0,),\n (1.0,)),\n B=((-1.0,),\n (1.0,)))\n>>> k\narray([3091.36])\n
Multiple reactions work fine, see both examples below:
\n\n\n\n>>> pH = 12\n>>> scheme = rx.parse_reactions("B <- AH <=> A- + H+")\n>>> k = np.array([10.0, 1, 1])\n>>> scheme, k = rx.get_fixed_scheme(scheme, k, {"H+": 10**-pH})\n>>> scheme\nScheme(compounds=('AH', 'B', 'A-'),\n reactions=('AH -> B',\n 'AH -> A-',\n 'A- -> AH'),\n is_half_equilibrium=(False, True, True),\n A=((-1.0, -1.0, 1.0),\n (1.0, 0.0, 0.0),\n (0.0, 1.0, -1.0)),\n B=((-1.0, -1.0, 0.0),\n (1.0, 0.0, 0.0),\n (0.0, 1.0, 0.0)))\n>>> k\narray([1.e+01, 1.e+00, 1.e-12])\n
\n\n>>> pH = 2\n>>> scheme = rx.parse_reactions(["AH <=> A- + H+", "B- + H+ <=> BH"])\n>>> k = np.array([1, 1, 2, 2])\n>>> scheme, k = rx.get_fixed_scheme(scheme, k, {"H+": 10**-pH})\n>>> scheme\nScheme(compounds=('AH', 'A-', 'B-', 'BH'),\n reactions=('AH -> A-',\n 'A- -> AH',\n 'B- -> BH',\n 'BH -> B-'),\n is_half_equilibrium=(True, True, True, True),\n A=((-1.0, 1.0, 0.0, 0.0),\n (1.0, -1.0, 0.0, 0.0),\n (0.0, 0.0, -1.0, 1.0),\n (0.0, 0.0, 1.0, -1.0)),\n B=((-1.0, 0.0, 0.0, 0.0),\n (1.0, 0.0, 0.0, 0.0),\n (0.0, 0.0, -1.0, 0.0),\n (0.0, 0.0, 1.0, 0.0)))\n>>> k\narray([1. , 0.01, 0.02, 2. ])\n
Multiple fixed compounds also work fine:
\n\n\n\n>>> pH = 6\n>>> scheme = rx.parse_reactions("A + H2O -> B <=> B- + H+")\n>>> k = np.array([1.0, 100.0, 2.0])\n>>> scheme, k = rx.get_fixed_scheme(scheme, k, {"H+": 10**-pH, "H2O": 55.6})\n>>> scheme\nScheme(compounds=('A', 'B', 'B-'),\n reactions=('A -> B',\n 'B -> B-',\n 'B- -> B'),\n is_half_equilibrium=(False, True, True),\n A=((-1.0, 0.0, 0.0),\n (1.0, -1.0, 1.0),\n (0.0, 1.0, -1.0)),\n B=((-1.0, 0.0, 0.0),\n (1.0, -1.0, 0.0),\n (0.0, 1.0, 0.0)))\n>>> k\narray([5.56e+01, 1.00e+02, 2.00e-06])\n
This function is a no-op if
\n\nfixed_y0
is empty, which is very important\nfor overall code consistency:\n", "parameters": ["scheme", "k", "fixed_y0"], "funcdef": "def"}, "overreact.thermo": {"fullname": "overreact.thermo", "modulename": "overreact.thermo", "qualname": "", "type": "module", "doc": ">>> scheme = rx.parse_reactions(["AH <=> A- + H+", "B- + H+ <=> BH"])\n>>> k = np.array([1, 1, 2, 2])\n>>> new_scheme, new_k = rx.get_fixed_scheme(scheme, k, {})\n>>> new_scheme == scheme\nTrue\n>>> np.allclose(new_k, k)\nTrue\n
Module dedicated to the calculation of thermodynamic properties.
\n"}, "overreact.thermo.equilibrium_constant": {"fullname": "overreact.thermo.equilibrium_constant", "modulename": "overreact.thermo", "qualname": "equilibrium_constant", "type": "function", "doc": "Calculate an equilibrium constant from a reaction Gibbs free energy.
\n\nThis function uses the usual relationship between reaction Gibbs energy\nand equilibrium constant\n:
\n\n$$K(T) = \\exp\\left(-\\frac{\\Delta_\\text{r} G^\\circ}{R T}\\right)$$
\n\nIf
\n\ndelta_moles
is given, the above will be multiplied by a term\n\\( \\left( \\frac{R T}{p} \\right)^{-\\Delta n} \\), which effectively\ntransforms a \\( K_p \\) equilibrium constant into a \\( K_c \\)\n(see below).Parameters
\n\n\n
\n\n- delta_freeenergy (array-like):\nDelta Gibbs reaction free energies. This assumes values were already\ncorrected for a one molar reference state.
\n- delta_moles (array-like, optional):\nDifference in moles between products and reactants. If set, this\nmultiplies the end result by\n\\( \\left( \\frac{R T}{p} \\right)^{-\\Delta n} \\), which effectively\ncalculates a solution equilibrium constant for gas phase data. You\nshould set this to
\nNone
if your free energies were already adjusted\nfor solution Gibbs free energies.- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\n- pressure (array-like, optional):\nReference gas pressure.
\n- volume (float, optional):\nMolar volume. This substitutes \\( \\frac{R T}{p} \\) if given. See\n
\ndelta_moles
.Returns
\n\n\n
\n\n- K (array-like):\nEquilibrium constant.
\nNotes
\n\nIf you want to calculate a solution equilibrium constant from gas phase data, set\n
\n\ndelta_moles
to the difference in moles between products and reactants.\nAlternatively, convert your energies to solution Gibbs free energies and\nsetdelta_moles
toNone
.Examples
\n\nThe following is an example from the\nLibreTexts Chemistry Library.\nConsider the following equilibrium:
\n\n$$\\ce{2 SO2(g) + O2(g) <=> 2 SO3(g)}$$
\n\nwith concentrations \\( c_{\\ce{SO2(g)}} = 0.2 M \\),\n\\( c_{\\ce{O2(g)}} = 0.5 M \\) and \\( c_{\\ce{SO3(g)}} = 0.7 M \\) (room\ntemperature). Its \\( K_c \\) is given by:
\n\n\n\n>>> Kc = 0.7**2 / (0.2**2 * 0.5)\n>>> Kc\n24.5\n
You could use
\n\nequilibrium_constant
to reach the same result using the\nGibbs reaction free energy (which can easily be obtained from\n\\( K_c \\)):\n\n>>> temperature = 298.15\n>>> dG = -constants.R * temperature * np.log(Kc)\n>>> equilibrium_constant(dG)\narray([24.5])\n
By giving a
\n\ndelta_moles
value (in this case, \\( 2 - 2 - 1 = -1 \\)),\nwe can calculate the correspondingK_p
:\n\n>>> equilibrium_constant(dG, delta_moles=-1)\narray([1.002])\n
(As expected, it makes sense for gases to favor the most entropic side of\nthe equilibrium.) The example above clearly used \"solution-based\" data\n(our \\( K_c \\) was calculated using molar quantities, which means\nreference volumes of one liter). You could convert it to gas phase data\nto get the same result, by changing the reference state (in this case,\nfrom one molar to one atmosphere using
\n\nchange_reference_state
):\n\n>>> dG += temperature * rx.change_reference_state()\n>>> equilibrium_constant(dG)\narray([1.002])\n
Having gas phase information, the inverse path can be taken just by\ninverting the sign of
\n\ndelta_moles
:\n\n>>> equilibrium_constant(dG, delta_moles=1)\narray([24.5])\n
The following example is from\nWikipedia.\nThe reactions are two copper complex forming equilibria with two\ndifferent ligands. Since this reaction takes place in solution, it is the\nsolution standard Gibbs reaction free energy that is given:
\n\n\n\n>>> dG1 = -37.4e3\n>>> np.log10(equilibrium_constant(dG1))\narray([6.55])\n>>> dG2 = -60.67e3\n>>> np.log10(equilibrium_constant(dG2))\narray([10.62])\n
The above are thus \\( \\log_{10}(K_c) \\). Since we are talking about a\nmono- and a bidendate ligands, the
\n\ndelta_moles
are -4 and -2,\nrespectively, and we could obtain the \\( \\log_{10}(K_p) \\) the following\nway:\n\n>>> np.log10(equilibrium_constant(dG1, delta_moles=-4))\narray([0.998])\n>>> np.log10(equilibrium_constant(dG2, delta_moles=-2))\narray([7.85])\n
You can easily check that the above values match the values given\nhere.
\n", "parameters": ["delta_freeenergy", "delta_moles", "temperature", "pressure", "volume"], "funcdef": "def"}, "overreact.thermo.change_reference_state": {"fullname": "overreact.thermo.change_reference_state", "modulename": "overreact.thermo", "qualname": "change_reference_state", "type": "function", "doc": "Calculate an additive entropy correction to a change in reference states.
\n\n$$\\Delta G_\\text{corr} =\n R T \\ln \\left( \\frac{\\chi_\\text{new}}{\\chi_\\text{old}} \\right)$$
\n\nThe value returned can be directly multiplied by temperature and summed to\nthe old reference free energies to obtain free energies with respect to a\nnew reference. See notes below.
\n\nFor instance, the concentration correction to Gibbs free energy for a\ngas-to-liquid standard state change is simply\n(\\( c^\\circ = \\frac{\\text{1 atm}}{R T} \\)),
\n\n$$\\Delta G_\\text{conc} =\n R T \\ln \\left( \\frac{\\text{1 M}}{c^\\circ} \\right)$$
\n\nParameters
\n\n\n
\n\n- new_reference (array-like, optional):\nNew reference state. Default value corresponds to 1 mol/liter.
\n- old_reference (array-like, optional):\nOld reference state. Default value corresponds to the concentration of\nan ideal gas at the given temperature and 1 atm.
\n- sign (float, optional):\nSign of the change in reference state. Default value is 1. This only\nmultiplies the final result.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\n- pressure (array-like, optional):\nReference gas pressure.
\n- volume (float, optional):\nMolar volume.
\nReturns
\n\n\n
\n\n- correction (array-like):\nEntropy correction in J/mol\u00b7K.
\nNotes
\n\nThis function can be used to add any entropy correction in the form above.\nThe only drawback is that, sometimes, those corrections are written with a\nminus sign in front of them (this implies switching the roles of\n
\n\nold_reference
andnew_reference
). The easiest way to accomplish this is\nby usingsign=-1
or multiplying the result by-1
.Examples
\n\nBy default, the correction returns a change in concentration from the gas\nphase standard concentration to the solvated-state standard concentration:
\n\n\n\n>>> -rx.change_reference_state() / constants.calorie\n-6.4\n>>> 298.15 * rx.change_reference_state() / constants.kcal\n1.89\n>>> 273.15 * rx.change_reference_state(temperature=273.15) / constants.kcal\n1.69\n
But this function can also be used to adjust symmetry effects from C1\ncalculations (symmetry number equals to one). For D7h, for instance, the\nsymmetry number is 14:
\n\n\n\n>>> -298.15 * rx.change_reference_state(14, 1) / constants.kcal\n-1.56\n
\n", "parameters": ["new_reference", "old_reference", "sign", "temperature", "pressure", "volume"], "funcdef": "def"}, "overreact.tunnel": {"fullname": "overreact.tunnel", "modulename": "overreact.tunnel", "qualname": "", "type": "module", "doc": ">>> rx.change_reference_state(sign=-1) == -rx.change_reference_state()\nTrue\n
Module dedicated to quantum tunneling approximations.
\n"}, "overreact.tunnel.eckart": {"fullname": "overreact.tunnel.eckart", "modulename": "overreact.tunnel", "qualname": "eckart", "type": "function", "doc": "Calculate the Eckart correction to quantum tunneling.
\n\nReferences are\nJ. Phys. Chem. 1962, 66, 3, 532\u2013533\nand\nJ. Res. Natl. Inst. Stand. Technol., 1981, 86, 357.
\n\nParameters
\n\n\n
\n\n- vibfreq (array-like):\nMagnitude of the imaginary frequency in cm$^{-1}$. Only the absolute value\nis used.
\n- delta_forward (array-like):\nActivation enthalpy at 0 K for the forward reaction.
\n- delta_backward (array-like, optional):\nActivation enthalpy at 0 K for the reverse reaction. If delta_backward\nis not given, the \"symmetrical\" Eckart model is used (i.e.,\n
\ndelta_backward == delta_forward
is assumed).- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\nReturns
\n\n\n
\n\n- kappa (array-like):\nThe quantum tunneling correction.
\nRaises
\n\n\n
\n\n- ValueError: If vibfreq is zero.
\nExamples
\n\n\n\n>>> eckart(1218, 13672.624, 24527.729644, temperature=300)\narray(3.9)\n>>> eckart(1218, 13672.624, 24527.729644, temperature=[200, 298.15])\narray([17.1, 4.0])\n>>> eckart([1218, 200], 13672.624, 24527.729644, temperature=400)\narray([2.3, 1.0])\n
If no backward barrier is given, a symmetric Eckart potential is assumed:
\n\n\n", "parameters": ["vibfreq", "delta_forward", "delta_backward", "temperature"], "funcdef": "def"}, "overreact.tunnel.wigner": {"fullname": "overreact.tunnel.wigner", "modulename": "overreact.tunnel", "qualname": "wigner", "type": "function", "doc": ">>> eckart(414.45, 394.54)\narray(1.16)\n>>> eckart(414.45, 789.08)\narray(1.3)\n>>> eckart(3315.6, 3156.31)\narray(3.3)\n
Calculate the Wigner correction to quantum tunneling.
\n\nParameters
\n\n\n
\n\n- vibfreq (array-like):\nMagnitude of the imaginary frequency in cm$^{-1}$. Only the absolute value\nis used.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\nReturns
\n\n\n
\n\n- kappa (array-like):\nThe quantum tunneling correction.
\nRaises
\n\n\n
\n\n- ValueError: If vibfreq is zero.
\nExamples
\n\n\n", "parameters": ["vibfreq", "temperature"], "funcdef": "def"}}, "docInfo": {"overreact": {"qualname": 0, "fullname": 1, "doc": 162}, "overreact.api": {"qualname": 0, "fullname": 2, "doc": 15}, "overreact.api.get_k": {"qualname": 1, "fullname": 3, "doc": 555}, "overreact.api.get_kappa": {"qualname": 1, "fullname": 3, "doc": 226}, "overreact.api.get_freeenergies": {"qualname": 1, "fullname": 3, "doc": 280}, "overreact.api.get_entropies": {"qualname": 1, "fullname": 3, "doc": 193}, "overreact.api.get_enthalpies": {"qualname": 1, "fullname": 3, "doc": 139}, "overreact.api.get_internal_energies": {"qualname": 1, "fullname": 3, "doc": 98}, "overreact.coords": {"qualname": 0, "fullname": 2, "doc": 6}, "overreact.coords.find_point_group": {"qualname": 1, "fullname": 3, "doc": 155}, "overreact.coords.symmetry_number": {"qualname": 1, "fullname": 3, "doc": 146}, "overreact.core": {"qualname": 0, "fullname": 2, "doc": 7}, "overreact.core.Scheme": {"qualname": 1, "fullname": 3, "doc": 13}, 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"i": {"docs": {"overreact.api.get_enthalpies": {"tf": 1.4142135623730951}}, "df": 1}}}}}}}}}, "t": {"docs": {}, "df": 0, "h": {"docs": {"overreact.simulate.get_y": {"tf": 1}}, "df": 1}}}}}}}}}, "pipeline": ["trimmer", "stopWordFilter", "stemmer"], "_isPrebuiltIndex": true}; + /** pdoc search index */const docs = {"version": "0.9.5", "fields": ["qualname", "fullname", "doc"], "ref": "fullname", "documentStore": {"docs": {"overreact": {"fullname": "overreact", "modulename": "overreact", "qualname": "", "type": "module", "doc": "\n\n\n\n>>> wigner(1821.0777)\n4.218\n>>> wigner(262.38)\n1.06680\n>>> wigner(113.87)\n1.01258\n>>> wigner(169.14)\n1.02776\n
\n \n\n\noverreact is a library and a command-line tool for building and\nanalyzing\nmicrokinetic models.\nData is parsed directly from computational chemistry output files thanks to\n
\n\ncclib
(see the\nlist of supported programs).Take a look at the user guide\nfor more information on how to use overreact. Or check out the\nAPI documentation for\na more detailed description of the application programming interface.
\n\nInstallation
\n\noverreact is a Python package, so you can easily install it with\n
\n\npip
:\n\n$ pip install "overreact[cli,fast]"\n
See the\ninstallation guide\nfor more details.
\n\nCiting overreact
\n\nIf you use overreact in your research, please cite:
\n\n\n\n\nF. S. S. Schneider and G. F. Caramori. _geem-lab/overreact: a tool for\n creating and analyzing microkinetic models built from computational chemistry\n data, v1.0.2_. 2021.\n DOI:10.5281/ZENODO.5643960.\n Freely available at: <https://github.com/geem-lab/overreact>.
\nHere's the reference in BibTeX format:
\n\n\n\n@misc{overreact2021,\n howpublished = {\\url{https://github.com/geem-lab/overreact}}\n year = {2021},\n author = {Schneider, F. S. S. and Caramori, G. F.},\n title = {\n \\textbf{geem-lab/overreact}: a tool for creating and analyzing\n microkinetic models built from computational chemistry data, v1.0.2\n },\n doi = {10.5281/ZENODO.5643960},\n url = {https://zenodo.org/record/5643960},\n publisher = {Zenodo},\n copyright = {Open Access}\n}\n
A paper describing overreact is currently being prepared. When it is\npublished, the above BibTeX entry will be updated.
\n\nLicense
\n\noverreact is open-source, released under the permissive MIT license. See\nthe LICENSE agreement.
\n\nFunding
\n\nThis project was developed at the GEEM lab\n(Federal University of Santa Catarina, Brazil), and was\npartially funded by the\nBrazilian National Council for Scientific and Technological Development (CNPq),\ngrant number 140485/2017-1.
\n"}, "overreact.api": {"fullname": "overreact.api", "modulename": "overreact.api", "qualname": "", "type": "module", "doc": "This module contains the high-level application programming interface.
\n\nIf you intend to use overreact as a library in a project, you should\nprobably start here.
\n"}, "overreact.api.get_k": {"fullname": "overreact.api.get_k", "modulename": "overreact.api", "qualname": "get_k", "type": "function", "doc": "Obtain reaction rate constants for a given reaction scheme.
\n\nParameters
\n\n\n
\n\n- scheme (Scheme):\nA descriptor of the reaction scheme.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- compounds (dict-like, optional):\nA descriptor of the compounds.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- bias (array-like, optional):\nEnergy to be added to free energies.
\n- tunneling (str or None, optional):\nChoose between \"eckart\", \"wigner\" or None (or \"none\").
\n- qrrho (bool or tuple-like, optional):\nApply both the quasi-rigid rotor harmonic oscillator (QRRHO)\napproximations of M. Head-Gordonand others (enthalpy correction, see\nJ. Phys. Chem. C 2015, 119, 4, 1840\u20131850)\nand S. Grimme (entropy correction, see\nTheory. Chem. Eur. J., 2012, 18: 9955-9964)\non top of the classical RRHO.
\n- scale (str, optional):\nReaction rate units. Possible values are \"cm3 mol-1 s-1\",\n\"l mol-1 s-1\", \"m3 mol-1 s-1\", \"cm3 particle-1 s-1\", \"mmHg-1 s-1\" and\n\"atm-1 s-1\".
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\n- pressure (array-like, optional):\nReference gas pressure.
\n- delta_freeenergies (array-like, optional):\nUse this instead of obtaining delta free energies from the compounds.
\n- molecularity (array-like, optional):\nReaction order, i.e., number of molecules that come together to react.\nIf set, this is used to calculate
\ndelta_moles
for\noverreact.thermo.equilibrium_constant
, which effectively calculates a solution\nequilibrium constant between reactants and the transition state for\ngas phase data. You should set this toNone
if your free energies\nwere already adjusted for solution Gibbs free energies.- volume (float, optional):\nMolar volume.
\nReturns
\n\n\n
\n\n- array-like
\nNotes
\n\nSome symbols are accepted as alternatives in \"scale\": \"M-1\", \"ml\" and\n\"torr-1\" are understood as \"l mol-1\", \"cm3\" and \"mmHg-1\", respectively.
\n\nExamples
\n\nBelow is an example of an estimate for the rate of methyl rotation in\nethane (a trivial attempt to reproduce\nScience, 2006, 313, 5795, 1951-1955).\nHow many turns it does per second?
\n\n\n\n>>> model = rx.parse_model("data/ethane/B97-3c/model.k")\n>>> get_k(model.scheme, model.compounds)\narray([8.16e+10])\n>>> get_k(model.scheme, model.compounds, qrrho=(False, True))\narray([8.24968117e+10])\n>>> get_k(model.scheme, model.compounds, qrrho=False)\narray([8.26909266e+10])\n>>> get_k(model.scheme, model.compounds, tunneling="wigner")\narray([7.99e+10])\n>>> get_k(model.scheme, model.compounds, tunneling=None)\narray([7.35e+10])\n
The calculated value is off by less than 2% from the experimental value\n(\\( \\frac{1}{12 \\times 10^{-12}} \\text{s}^{-1} = 8.33 \\times 10^{10} \\text{s}^{-1} \\)).\nWe use Eckart tunneling by default, but see the effect of changing it\nabove.
\n\nThe units of the returned reaction rate constants can be selected for\nnon-unimolecular processes. The following is an attempt to reproduce\nJ Atmos Chem, 1996 23, 37\u201349 for\nthe reaction of proton-withdrawal by a chloride radical from the methane\nmolecule\n\\( \\ce{CH4 + \\cdot Cl -> [H3C\\cdots H\\cdots Cl]^\\ddagger -> H3C\\cdot + HCl} \\):
\n\n\n\n>>> model = rx.parse_model("data/tanaka1996/UMP2/cc-pVTZ/model.jk")\n>>> get_k(model.scheme, model.compounds, temperature=300,\n... scale="cm3 particle-1 s-1")\narray([9.60e-14])\n
(By the way, according to the Jet Propulsion Laboratory,\nPublication No. 19-5,\nthe experimental reaction rate constant for this reaction is\n\\( 1.0 \\times 10^{-13} \\text{cm}^3 \\text{particle}^{-1} \\text{s}^{-1} \\).)
\n\nThe returned units are \"M-1 s-1\" by default:
\n\n\n\n>>> get_k(model.scheme, model.compounds) \\\n... == get_k(model.scheme, model.compounds, scale="l mol-1 s-1")\narray([ True])\n
You can also turn the tunneling correction off by using the string \"none\":
\n\n\n\n>>> get_k(model.scheme, model.compounds, tunneling="none") \\\n... == get_k(model.scheme, model.compounds, tunneling=None)\narray([ True])\n
You can set a simple energy bias, either as a constant or compound-wise:
\n\n\n", "parameters": ["scheme", "compounds", "bias", "tunneling", "qrrho", "scale", "temperature", "pressure", "delta_freeenergies", "molecularity", "volume"], "funcdef": "def"}, "overreact.api.get_kappa": {"fullname": "overreact.api.get_kappa", "modulename": "overreact.api", "qualname": "get_kappa", "type": "function", "doc": ">>> get_k(model.scheme, model.compounds, bias=1.0 * constants.kcal,\n... temperature=300.0, scale="cm3 particle-1 s-1")\narray([5.14e-13])\n>>> get_k(model.scheme, model.compounds,\n... bias=np.array([0.0, 0.0, -1.4, 0.0, 0.0]) * constants.kcal,\n... temperature=300.0, scale="cm3 particle-1 s-1")\narray([1.1e-12])\n
Obtain tunneling transmission coefficients at a given temperature.
\n\nOne tunneling transmission coefficient is calculated for each reaction. If\na reaction lacks a transition state (i.e., a half-equilibrium reaction),\nits transmission coefficient is set to unity.
\n\nParameters
\n\n\n
\n\n- scheme (Scheme):\nA descriptor of the reaction scheme.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- compounds (dict-like):\nA descriptor of the compounds.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- method (str or None, optional):\nChoose between \"eckart\", \"wigner\" or None (or \"none\").
\n- qrrho (bool, optional):\nApply both the quasi-rigid rotor harmonic oscillator (QRRHO)\napproximations of M. Head-Gordon and others (enthalpy correction, see\nJ. Phys. Chem. C 2015, 119, 4, 1840\u20131850)\nand S. Grimme (entropy correction, see\nTheory. Chem. Eur. J., 2012, 18: 9955-9964)\non top of the classical RRHO.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\nReturns
\n\n\n
\n\n- array-like
\nRaises
\n\n\n
\n\n- ValueError: If
\nmethod
is not supported.Examples
\n\nBelow is an example of an estimate of how much quantum tunneling\ncontributes to the rate of methyl rotation in ethane (see\nScience, 2006, 313, 5795, 1951-1955\nfor some interesting experimental data on this reaction).
\n\n\n\n>>> model = rx.parse_model("data/ethane/B97-3c/model.k")\n>>> kappa = get_kappa(model.scheme, model.compounds)\n>>> kappa\narray([1.110])\n>>> get_kappa(model.scheme, model.compounds, method="none")\narray([1.0])\n>>> get_kappa(model.scheme, model.compounds, method="none") \\\n... == get_kappa(model.scheme, model.compounds, method=None)\narray([ True])\n
You can calculate each piece of the reaction rate constant by hand,\nif you want. Just make sure that you don't calculate the tunneling\ncoefficient twice:
\n\n\n", "parameters": ["scheme", "compounds", "method", "qrrho", "temperature"], "funcdef": "def"}, "overreact.api.get_freeenergies": {"fullname": "overreact.api.get_freeenergies", "modulename": "overreact.api", "qualname": "get_freeenergies", "type": "function", "doc": ">>> kappa * get_k(model.scheme, model.compounds, tunneling=None)\narray([8.e+10])\n
Obtain free energies for compounds at a given temperature and pressure.
\n\nParameters
\n\n\n
\n\n- compounds (dict-like):\nA descriptor of the compounds.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- bias (array-like, optional):\nEnergy to be added to free energies.
\n- environment (str or None, optional):\nChoose between \"gas\" and a solvent. This is chosen for you by default,\nbased on the names of each compound. If given, all compounds will\nhave the same behavior.
\n- method (str, optional):\nThis is a placeholder for future functionality.\nThere are plans to implement more sophisticated methods for calculating\nentropies such as in\nPhys. Chem. Chem. Phys., 2019, 21, 18920-18929\nand\nJ. Chem. Theory Comput. 2019, 15, 5, 3204\u20133214.\nHead over to the\ndiscussions if\nyou're interested and would like to contribute.\nLeave this as \"standard\" for now.
\n- qrrho (bool or tuple-like, optional):\nApply both the quasi-rigid rotor harmonic oscillator (QRRHO)\napproximations of M. Head-Gordon and others (enthalpy correction, see\nJ. Phys. Chem. C 2015, 119, 4, 1840\u20131850)\nand S. Grimme (entropy correction, see\nTheory. Chem. Eur. J., 2012, 18: 9955-9964)\non top of the classical RRHO.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\n- pressure (array-like, optional):\nReference gas pressure.
\nReturns
\n\n\n
\n\n- array-like
\nExamples
\n\n\n\n>>> import overreact as rx\n>>> from overreact import _constants as constants\n>>> model = rx.parse_model("data/ethane/B97-3c/model.k")\n>>> freeenergies = get_freeenergies(model.compounds, qrrho=(False, True))\n>>> (freeenergies - freeenergies.min()) / constants.kcal\narray([0. , 2.62281461])\n>>> freeenergies = get_freeenergies(model.compounds)\n>>> (freeenergies - freeenergies.min()) / constants.kcal\narray([0. , 2.62862818])\n
You can consider all compounds as solvated if you want:
\n\n\n\n>>> sol_freeenergies = get_freeenergies(model.compounds, environment="solvent")\n>>> (sol_freeenergies - freeenergies) / constants.kcal\narray([1.89432845, 1.89432845])\n
You can set a simple energy bias, either as a constant or compound-wise:
\n\n\n", "parameters": ["compounds", "bias", "environment", "method", "qrrho", "temperature", "pressure"], "funcdef": "def"}, "overreact.api.get_entropies": {"fullname": "overreact.api.get_entropies", "modulename": "overreact.api", "qualname": "get_entropies", "type": "function", "doc": ">>> get_freeenergies(model.compounds, bias=1.0) - freeenergies\narray([1., 1.])\n>>> get_freeenergies(model.compounds, bias=-1.0) - freeenergies\narray([-1., -1.])\n>>> get_freeenergies(model.compounds, bias=[1.0, -1.0]) - freeenergies\narray([ 1., -1.])\n
Obtain entropies for compounds at a given temperature and pressure.
\n\nParameters
\n\n\n
\n\n- compounds (dict-like):\nA descriptor of the compounds.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- environment (str or None, optional):\nChoose between \"gas\" and a solvent. This is chosen for you by default,\nbased on the names of each compound (e.g.
\nA(g)
orA
is gas,\nA(w)
orA(...)
is solvated). In case this is given, all compounds\nwill have the same behavior.- method (str, optional):\nThis is a placeholder for future functionality.\nThere are plans to implement more sophisticated methods for calculating\nentropies such as in\nPhys. Chem. Chem. Phys., 2019, 21, 18920-18929\nand\nJ. Chem. Theory Comput. 2019, 15, 5, 3204\u20133214.\nHead over to the\ndiscussions if\nyou're interested and would like to contribute.\nLeave this as \"standard\" for now.
\n- qrrho (bool, optional):\nApply the quasi-rigid rotor harmonic oscillator (QRRHO) approximation of\nS. Grimme (see\nTheory. Chem. Eur. J., 2012, 18: 9955-9964)\non top of the classical RRHO.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\n- pressure (array-like, optional):\nReference gas pressure.
\nReturns
\n\n\n
\n\n- array-like
\nExamples
\n\n\n\n>>> import overreact as rx\n>>> from overreact import _constants as constants\n>>> model = rx.parse_model("data/ethane/B97-3c/model.k")\n>>> entropies = get_entropies(model.compounds)\n>>> (entropies - entropies.min()) / constants.calorie\narray([1.4, 0. ])\n
You can consider all compounds as solvated if you want:
\n\n\n", "parameters": ["compounds", "environment", "method", "qrrho", "temperature", "pressure"], "funcdef": "def"}, "overreact.api.get_enthalpies": {"fullname": "overreact.api.get_enthalpies", "modulename": "overreact.api", "qualname": "get_enthalpies", "type": "function", "doc": ">>> sol_entropies = get_entropies(model.compounds, environment="solvent")\n>>> (sol_entropies - entropies) / constants.calorie\narray([-6.35360874, -6.35360874])\n
Obtain enthalpies for compounds at a given temperature.
\n\nParameters
\n\n\n
\n\n- compounds (dict-like):\nA descriptor of the compounds.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- qrrho (bool, optional):\nApply the quasi-rigid rotor harmonic oscillator (QRRHO) approximation of\nM. Head-Gordon and others (see\nJ. Phys. Chem. C 2015, 119, 4, 1840\u20131850)\non top of the classical RRHO.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\nReturns
\n\n\n
\n\n- array-like
\nExamples
\n\n\n\n>>> import overreact as rx\n>>> from overreact import _constants as constants\n>>> model = rx.parse_model("data/ethane/B97-3c/model.k")\n>>> enthalpies = get_enthalpies(model.compounds)\n>>> (enthalpies - enthalpies.min()) / constants.kcal\narray([0. , 2.20053981])\n
The enthalpies at absolute zero can easily be obtained (this is used,\ne.g., in the calculation of the Eckart tunneling coefficient, see\n
\n\noverreact.tunnel.eckart
). We can use this to calculate, for instance,\nthe thermal contributions to the enthalpy:\n", "parameters": ["compounds", "qrrho", "temperature"], "funcdef": "def"}, "overreact.api.get_internal_energies": {"fullname": "overreact.api.get_internal_energies", "modulename": "overreact.api", "qualname": "get_internal_energies", "type": "function", "doc": ">>> zero_enthalpies = get_enthalpies(model.compounds, temperature=0)\n>>> (enthalpies - zero_enthalpies) / constants.kcal\narray([2.78, 2.50])\n
Obtain internal energies for compounds at a given temperature.
\n\nParameters
\n\n\n
\n\n- compounds (dict-like):\nA descriptor of the compounds.\nMostly likely, this comes from a parsed input file.\nSee
\noverreact.io.parse_model
.- qrrho (bool, optional):\nApply the quasi-rigid rotor harmonic oscillator (QRRHO) approximation of\nM. Head-Gordon and others (see\nJ. Phys. Chem. C 2015, 119, 4, 1840\u20131850)\non top of the classical RRHO.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\nReturns
\n\n\n
\n\n- array-like
\nExamples
\n\n\n", "parameters": ["compounds", "qrrho", "temperature"], "funcdef": "def"}, "overreact.coords": {"fullname": "overreact.coords", "modulename": "overreact.coords", "qualname": "", "type": "module", "doc": ">>> import overreact as rx\n>>> from overreact import _constants as constants\n>>> model = rx.parse_model("data/ethane/B97-3c/model.k")\n>>> internal_energies = get_internal_energies(model.compounds)\n>>> (internal_energies - internal_energies.min()) / constants.kcal\narray([0. , 2.20053981])\n
Module dedicated to classifying molecules into point groups.
\n"}, "overreact.coords.find_point_group": {"fullname": "overreact.coords.find_point_group", "modulename": "overreact.coords", "qualname": "find_point_group", "type": "function", "doc": "Determine point group of structure.
\n\nParameters
\n\n\n
\n\n- atommasses (array-like):\nAtomic masses in atomic mass units (amu).
\n- atomcoords (array-like):\nAtomic coordinates.
\n- proper_axes (sequence of tuples of int, array-like, optional):\nProper symmetry axes of rotation.
\n- rtol (float, optional):\nThe relative tolerance parameter (see
\nnumpy.isclose
).- atol (float, optional):\nThe absolute tolerance parameter (see
\nnumpy.isclose
).Returns
\n\n\n
\n\n- str: Point group symbol.
\nExamples
\n\n\n", "parameters": ["atommasses", "atomcoords", "proper_axes", "rtol", "atol"], "funcdef": "def"}, "overreact.coords.symmetry_number": {"fullname": "overreact.coords.symmetry_number", "modulename": "overreact.coords", "qualname": "symmetry_number", "type": "function", "doc": ">>> find_point_group([1], [[0, 0, 1]])\n'K'\n>>> find_point_group([1, 1], [[0, 0, 1], [0, 0, 0]])\n'D\u221eh'\n>>> find_point_group([1.008, 35.45], [[0, 0, 1], [0, 0, 0]])\n'C\u221ev'\n>>> find_point_group([16, 12, 16], [[1, 0, 1], [1, 0, 0], [1, 0, -1]])\n'D\u221eh'\n>>> find_point_group([16, 12, 32], [[1, 1, 1], [1, 1, 0], [1, 1, -1]])\n'C\u221ev'\n>>> find_point_group([12, 12, 12, 12], [[1, 0, 0],\n... [0, 1, 0],\n... [0, 0, 0],\n... [1, 1, 0]])\n'D4h'\n
Return rotational symmetry number for point group.
\n\nThis function has a set of the most common point groups precomputed, but is\nable to calculate the symmetry number if it is not found in known tables.\nMost precomputed values are from\nTheor Chem Account 2007 118, 813\u2013826.
\n\nParameters
\n\n\n
\n\n- point_group (str):\nPoint group symbol.
\nReturns
\n\n\n
\n\n- int: Rotational symmetry number.
\nRaises
\n\n\n
\n\n- ValueError: If point group is not found in precomputed values.
\nExamples
\n\n\n", "parameters": ["point_group"], "funcdef": "def"}, "overreact.core": {"fullname": "overreact.core", "modulename": "overreact.core", "qualname": "", "type": "module", "doc": ">>> symmetry_number("C4")\n4\n>>> symmetry_number("C4") == symmetry_number("C4h")\nTrue\n>>> symmetry_number("C6")\n6\n>>> symmetry_number("C6") == symmetry_number("C6v")\nTrue\n>>> symmetry_number("C6") == symmetry_number("C6h")\nTrue\n>>> symmetry_number("D2") == symmetry_number("Vh")\nTrue\n>>> symmetry_number("D4")\n8\n>>> symmetry_number("D6")\n12\n>>> symmetry_number("D6") == symmetry_number("D6d")\nTrue\n>>> symmetry_number("S6")\n3\n>>> symmetry_number("T")\n12\n
Module dedicated to parsing and modeling of chemical reaction networks.
\n"}, "overreact.core.Scheme": {"fullname": "overreact.core.Scheme", "modulename": "overreact.core", "qualname": "Scheme", "type": "class", "doc": "A descriptor of a chemical reaction network.
\n\nMostly likely, this comes from a parsed input file.\nSee
\n"}, "overreact.core.Scheme.__init__": {"fullname": "overreact.core.Scheme.__init__", "modulename": "overreact.core", "qualname": "Scheme.__init__", "type": "function", "doc": "overreact.io.parse_model
.Create new instance of Scheme(compounds, reactions, is_half_equilibrium, A, B)
\n", "parameters": ["_cls", "compounds", "reactions", "is_half_equilibrium", "A", "B"], "funcdef": "def"}, "overreact.core.Scheme.compounds": {"fullname": "overreact.core.Scheme.compounds", "modulename": "overreact.core", "qualname": "Scheme.compounds", "type": "variable", "doc": "A descriptor of compounds.
\n"}, "overreact.core.Scheme.reactions": {"fullname": "overreact.core.Scheme.reactions", "modulename": "overreact.core", "qualname": "Scheme.reactions", "type": "variable", "doc": "A descriptor of reactions.
\n"}, "overreact.core.Scheme.is_half_equilibrium": {"fullname": "overreact.core.Scheme.is_half_equilibrium", "modulename": "overreact.core", "qualname": "Scheme.is_half_equilibrium", "type": "variable", "doc": "An indicator of whether a reaction is half-equilibrium.
\n"}, "overreact.core.Scheme.A": {"fullname": "overreact.core.Scheme.A", "modulename": "overreact.core", "qualname": "Scheme.A", "type": "variable", "doc": "A matrix of stoichiometric coefficients between reactants and products.
\n"}, "overreact.core.Scheme.B": {"fullname": "overreact.core.Scheme.B", "modulename": "overreact.core", "qualname": "Scheme.B", "type": "variable", "doc": "A matrix of stoichiometric coefficients between reactants and transition states.
\n"}, "overreact.core.parse_reactions": {"fullname": "overreact.core.parse_reactions", "modulename": "overreact.core", "qualname": "parse_reactions", "type": "function", "doc": "Parse a kinetic model as a chemical reaction scheme.
\n\nThis is an essential part of the parsing process.\nSee
\n\noverreact.io.parse_model
other details.Parameters
\n\n\n
\n\n- text (str or sequence of str):\nModel description or sequence of lines of it.
\nReturns
\n\n\n
\n\n- scheme (Scheme):\nA descriptor of the reaction scheme.
\nNotes
\n\nThe model description should comply with the mini-language for systems of\nreactions. A semi-formal definition of the grammar in\nBackus\u2013Naur form\nis given below:
\n\n\n\nequation ::= equation_side arrow equation_side\nequation_side ::= coefficient compound ['+' coefficient compound]*\n coefficient ::= [integers] (defaults to 1)\n compound ::= mix of printable characters\n arrow ::= '->' | '<=>' | '<-'\n
Blank lines and comments (starting with
\n\n//
) are ignored. Repeated\nreactions are ignored. Furthermore, reactions can be chained one after\nanother and, if a single compound (with either a\u2021
or a#
at the end)\nappears alone on one side of a reaction, it's considered a transition\nstate. Transition states have zero lifetime during the simulation.Examples
\n\nWhat follows is a rather long tour over the parsing process and its\noutput in general. You can skip it if you are not interested in the\ndetails.
\n\n\n\n>>> scheme = parse_reactions("A -> B // a direct reaction")\n
The reaction above is a direct one (observe that comments are ignored). The\nreturned object has the following attributes:
\n\n\n\n>>> scheme.compounds\n('A', 'B')\n>>> scheme.reactions\n('A -> B',)\n>>> scheme.is_half_equilibrium\n(False,)\n>>> scheme.A\n((-1.,), (1.,))\n>>> scheme.B\n((-1.,), (1.,))\n
The same reaction can be specified in reverse order:
\n\n\n\n>>> parse_reactions("B <- A // reverse reaction of the above")\nScheme(compounds=('A', 'B'),\n reactions=('A -> B',),\n is_half_equilibrium=(False,),\n A=((-1.,), (1.,)),\n B=((-1.,), (1.,)))\n
Equilibria produce twice as many direct reactions, while the $B$ matrix\ndefines an energy relationship for only one of each pair:
\n\n\n\n>>> parse_reactions("A <=> B // an equilibrium")\nScheme(compounds=('A', 'B'),\n reactions=('A -> B', 'B -> A'),\n is_half_equilibrium=(True, True),\n A=((-1., 1.),\n (1., -1.)),\n B=((-1., 0.),\n (1., 0.)))\n
Adding twice the same reaction results in a single reaction being added.\nThis of course also works with equilibria (extra whitespaces are ignored):
\n\n\n\n>>> parse_reactions('''\n... A <=> B -> A\n... A -> B <=> A\n... A -> B <- A\n... B <- A -> B\n... ''')\nScheme(compounds=('A', 'B'),\n reactions=('A -> B', 'B -> A'),\n is_half_equilibrium=(True, True),\n A=((-1., 1.),\n (1., -1.)),\n B=((-1., 0.),\n (1., 0.)))\n
Transition states are specified with a special symbol at the end (either\n
\n\n\u2021
or#
). They are shown among compounds, but the matrix $A$ ensures\nthey'll never have a non-zero rate of formation/consumption. On the other\nhand, they are needed in the $B$ matrix:\n\n>>> parse_reactions("A -> A\u2021 -> B")\nScheme(compounds=('A', 'A\u2021', 'B'),\n reactions=('A -> B',),\n is_half_equilibrium=(False,),\n A=((-1.,), (0.,), (1.,)),\n B=((-1.,), (1.,), (0.,)))\n
This gives the same result as above:
\n\n\n\n>>> parse_reactions("A -> A\u2021 -> B <- A\u2021 <- A")\nScheme(compounds=('A', 'A\u2021', 'B'),\n reactions=('A -> B',),\n is_half_equilibrium=(False,),\n A=((-1.,), (0.,), (1.,)),\n B=((-1.,), (1.,), (0.,)))\n
It is possible to define a reaction whose product is the same as the\nreactant. This is found in isomerization processes (e.g., ammonia\ninversion or the methyl rotation in ethane):
\n\n\n\n>>> parse_reactions("S -> E\u2021 -> S")\nScheme(compounds=('S', 'E\u2021'),\n reactions=('S -> S',),\n is_half_equilibrium=(False,),\n A=((0.,), (0.,)),\n B=((-1.,), (1.,)))\n
As such, a column full of zeros in the $A$ matrix corresponds to a reaction\nwith zero net change. As can be seen, overreact allows for very general\nmodels. An interesting feature is that a single transition state can link\nmany different compounds (whether it is useful is a matter of debate):
\n\n\n\n>>> parse_reactions('''\n... B -> B\u2021 -> C // chained reactions and transition states\n... B\u2021 -> D // this is a bifurcation\n... B -> B'\u2021 -> E // this is a classical competitive reaction\n... A -> B\u2021\n... ''')\nScheme(compounds=('B', 'B\u2021', 'C', 'D', "B'\u2021", 'E', 'A'),\n reactions=('B -> C', 'B -> D', 'B -> E', 'A -> C', 'A -> D'),\n is_half_equilibrium=(False, False, False, False, False),\n A=((-1., -1., -1., 0., 0.),\n (0., 0., 0., 0., 0.),\n (1., 0., 0., 1., 0.),\n (0., 1., 0., 0., 1.),\n (0., 0., 0., 0., 0.),\n (0., 0., 1., 0., 0.),\n (0., 0., 0., -1., -1.)),\n B=((-1., -1., -1., 0., 0.),\n (1., 1., 0., 1., 1.),\n (0., 0., 0., 0., 0.),\n (0., 0., 0., 0., 0.),\n (0., 0., 1., 0., 0.),\n (0., 0., 0., 0., 0.),\n (0., 0., 0., -1., -1.)))\n
The following is a borderline case but both reactions should be considered\ndifferent since they define different processes:
\n\n\n\n>>> parse_reactions('''\n... A -> A\u2021 -> B\n... A -> B\n... ''')\nScheme(compounds=('A', 'A\u2021', 'B'),\n reactions=('A -> B', 'A -> B'),\n is_half_equilibrium=(False, False),\n A=((-1., -1.),\n (0., 0.),\n (1., 1.)),\n B=((-1., -1.),\n (1., 0.),\n (0., 1.)))\n
The following is correct behavior. In fact, the reactions are badly\ndefined: if more than one transition state are chained, the following\nhappens, which is correct since it's the most physically plausible model\nthat can be extracted. It can be seen as a feature that the product B is\nignored and not the reactant A, since the user would easily see the mistake\nin graphs of concentration over time (the alternative would be no\nreaction happening at all, which is rather cryptic to debug).
\n\n\n\n>>> parse_reactions("A -> A\u2021 -> A'\u2021 -> B")\nScheme(compounds=('A', 'A\u2021', "A'\u2021", 'B'),\n reactions=("A -> A'\u2021",),\n is_half_equilibrium=(False,),\n A=((-1.,), (0.,), (1.,), (0.,)),\n B=((-1.,), (1.,), (0.,), (0.,)))\n
In any case, it's not clear how a reaction barrier be defined in such a\ncase. If you have a use case, don't hesitate to\nopen an issue, we'll be\nhappy to hear from you.
\n", "parameters": ["text"], "funcdef": "def"}, "overreact.io": {"fullname": "overreact.io", "modulename": "overreact.io", "qualname": "", "type": "module", "doc": "Basic I/O operations (such as reading source input files).
\n"}, "overreact.io.parse_model": {"fullname": "overreact.io.parse_model", "modulename": "overreact.io", "qualname": "parse_model", "type": "function", "doc": "Parse either a source or model input file, whichever is available.
\n\nA source input file (also known as a
\n\n.k
file) contains all the information needed\nto create a model input file.\nA model input file (also known as a.jk
file) is a JSON encoded file with all the\ninformation needed to study microkinetic simulations from first principles.You probably won't need to use model input files directly, they are\nautomatically created based on source input files.\nTake a look at our guide on how to write an source input file.
\n\nThis function attempts to parse a model input file if available. If not, a source\ninput file is parsed and a model input file is generated from it. Extensions are\nguessed if none given (i.e., if only the base name given).
\n\nParameters
\n\n\n
\n\n- path (str):\nPath to the model or source input file.\nIf the final extension is not
\n.jk
or.k
, it is guessed.- force_compile (bool):\nIf True, a
\n.k
file will take precedence over any.jk
file for reading. A\n.jk
file is thus either generated or overwritten. This is sometimes\nneeded to force an update with new data.Returns
\n\n\n
\n\n- model (immutable dict-like):
\nRaises
\n\n\n
\n\n- FileNotFoundError: If the model or source input file is not found.
\nExamples
\n\nSome examples of how overreact \"sees\" your data below \ud83d\ude04:
\n\n\n", "parameters": ["path", "force_compile"], "funcdef": "def"}, "overreact.rates": {"fullname": "overreact.rates", "modulename": "overreact.rates", "qualname": "", "type": "module", "doc": ">>> model = parse_model("data/ethane/B97-3c/model.jk")\n>>> model.scheme\nScheme(compounds=('S', 'E\u2021'),\n reactions=('S -> S',),\n is_half_equilibrium=(False,),\n A=((0.0,), (0.0,)),\n B=((-1.0,), (1.0,)))\n>>> model.compounds["S"]\n{'logfile': 'data/ethane/B97-3c/staggered.out',\n 'energy': -209483812.77142256,\n 'mult': 1,\n 'atomnos': (6, 6, 1, 1, 1, 1, 1, 1),\n 'atommasses': (12.011, 12.011, 1.008, 1.008, 1.008, 1.008, 1.008, 1.008),\n 'atomcoords': ((-7.633588, 2.520693, -4.8e-05),\n ...,\n (-5.832852, 3.674431, 0.363239)),\n 'vibfreqs': (307.57, 825.42, ..., 3071.11, 3071.45),\n 'vibdisps': (((-1.7e-05, 3.4e-05, 5.4e-05),\n ...,\n (-0.011061, -0.030431, -0.027036)))}\n>>> model_from_source = parse_model("data/ethane/B97-3c/model.k",\n... force_compile=True)\n>>> model_from_source == model\nTrue\n>>> model_from_source = parse_model("data/ethane/B97-3c/model")\n>>> model_from_source == model\nTrue\n
Module dedicated to the calculation of reaction rate constants.
\n"}, "overreact.rates.eyring": {"fullname": "overreact.rates.eyring", "modulename": "overreact.rates", "qualname": "eyring", "type": "function", "doc": "Calculate a reaction rate constant.
\n\nThis function uses the Eyring-Evans-Polanyi equation\n from transition state\ntheory :
\n\n$$k(T) = \\frac{k_\\text{B} T}{h} K^\\ddagger\n = \\frac{k_\\text{B} T}{h}\n \\exp\\left(-\\frac{\\Delta^\\ddagger G^\\circ}{R T}\\right)$$
\n\nwhere \\( h \\) is Planck's constant, \\( k_\\text{B} \\) is Boltzmann's\nconstant and \\( T \\) is the absolute temperature.
\n\nParameters
\n\n\n
\n\n- delta_freeenergy (array-like):\nDelta Gibbs activation free energies. This assumes values were already\ncorrected for a one molar reference state (if applicable).
\n- molecularity (array-like, optional):\nReaction order, i.e., number of molecules that come together to react.\nIf set, this is used to calculate
\ndelta_moles
for\nequilibrium_constant
, which effectively calculates a solution\nequilibrium constant between reactants and the transition state for\ngas phase data. You should set this toNone
if your free energies\nwere already adjusted for solution Gibbs free energies.- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\n- pressure (array-like, optional):\nReference gas pressure.
\n- volume (float, optional):\nMolar volume. This is passed on to
\nequilibrium_constant
.Returns
\n\n\n
\n\n- k (array-like):\nReaction rate constant(s). By giving energies in one molar reference\nstate, returned units are then accordingly given, e.g. \"l mol-1 s-1\"\nif second-order, etc.
\nNotes
\n\nThis function uses
\n\nequilibrium_constant
internally to calculate the\nequilibrium constant between reactants and the transition state.Examples
\n\nThe following are examples from\nThermochemistry in Gaussian, in which the\nkinetic isotope effect of a bimolecular reaction is analyzed:
\n\n\n\n>>> eyring(17.26 * constants.kcal)\narray([1.38])\n>>> eyring(18.86 * constants.kcal)\narray([0.093])\n
It is well known that, at room temperature, if you \"decrease\" a reaction\nbarrier by 1.4 kcal/mol, the reaction becomes around ten times faster:
\n\n\n\n>>> dG = np.random.uniform(1.0, 100.0) * constants.kcal\n>>> eyring(dG - 1.4 * constants.kcal) / eyring(dG)\narray([10.])\n
A similar relationship is found for a twofold increase in speed and a\n0.4 kcal/mol decrease in the reaction barrier (again, at room\ntemperature):
\n\n\n", "parameters": ["delta_freeenergy", "molecularity", "temperature", "pressure", "volume"], "funcdef": "def"}, "overreact.simulate": {"fullname": "overreact.simulate", "modulename": "overreact.simulate", "qualname": "", "type": "module", "doc": ">>> eyring(dG - 0.4 * constants.kcal) / eyring(dG)\narray([2.0])\n
Module dedicated to the time simulation of reaction models.
\n\nHere are functions that calculate reaction rates as well, which is needed for\nthe time simulations.
\n"}, "overreact.simulate.get_y": {"fullname": "overreact.simulate.get_y", "modulename": "overreact.simulate", "qualname": "get_y", "type": "function", "doc": "Simulate a reaction scheme from its rate function.
\n\nThis function provides two functions that calculate the concentrations and\nthe rates of formation at any point in time for any compound. It does that\nby solving an initial value problem (IVP) through scipy's
\n\nsolve_ivp
\nunder the hood.Parameters
\n\n\n
\n\n- dydt (callable):\nRight-hand side of the system.
\n- y0 (array-like):\nInitial state.
\n- t_span (array-like, optional):\nInterval of integration (t0, tf). The solver starts with t=t0 and\nintegrates until it reaches t=tf. If not given, a conservative value\nis chosen based on the system at hand (the method of choice works for\nany zeroth-, first- or second-order reactions).
\n- method (str, optional):\nIntegration method to use. See
\nscipy.integrate.solve_ivp
for details.\nKinetics problems are very often stiff and, as such, \"RK45\" is\nnormally unsuited. \"Radau\", \"BDF\" or \"LSODA\" are good choices.- rtol, atol (array-like):\nSee
\nscipy.integrate.solve_ivp
for details.- max_time (float, optional):\nIf
\nt_span
is not given, an interval will be estimated, but it can't\nbe larger than this parameter.Returns
\n\n\n
\n\n- y, r (callable):\nConcentrations and reaction rates as functions of time. The y object\nis an OdeSolution and stores attributes t_min and t_max.
\nExamples
\n\n\n\n>>> import numpy as np\n>>> import overreact as rx\n
A toy simulation can be performed in just two lines:
\n\n\n\n>>> scheme = rx.parse_reactions("A <=> B")\n>>> y, r = get_y(get_dydt(scheme, np.array([1, 1])), y0=[1, 0])\n
The
\n\ny
object stores information about the simulation time, which can be\nused to produce a suitable vector of timepoints for, e.g., plotting:\n\n>>> y.t_min, y.t_max # doctest: +SKIP\n(0.0, 3.0)\n>>> t = np.linspace(y.t_min, y.t_max)\n>>> t # doctest: +SKIP\narray([0. , 0.06122449, ..., 2.93877551, 3. ])\n
Both
\n\ny
andr
can be used to check concentrations and rates in any\npoint in time. In particular, both are vectorized:\n", "parameters": ["dydt", "y0", "t_span", "method", "rtol", "atol", "max_time"], "funcdef": "def"}, "overreact.simulate.get_dydt": {"fullname": "overreact.simulate.get_dydt", "modulename": "overreact.simulate", "qualname": "get_dydt", "type": "function", "doc": ">>> y(t) # doctest: +SKIP\narray([[1. , 0.94237559, ..., 0.5012394, 0.5 ],\n [0. , 0.05762441, ..., 0.4987606, 0.5 ]])\n>>> r(t) # doctest: +SKIP\narray([[-1.00000000e+00, ..., -1.39544265e-10],\n [ 1.00000000e+00, ..., 1.39544265e-10]])\n
Generate a rate function that models a reaction scheme.
\n\nParameters
\n\n\n
\n\n- scheme (Scheme):\nA descriptor of the reaction scheme.\nMostly likely, this comes from a parsed model input file.\nSee
\noverreact.io.parse_model
.- k (array-like):\nReaction rate constant(s). Units match the concentration units given to\nthe returned function
\ndydt
.- ef (float, optional):\nEquilibrium factor. This is a parameter that can be used to scale the\nreaction rates associated to half-equilibrium reactions such that they\nare faster than the other reactions.
\nReturns
\n\n\n
\n\n- dydt (callable):\nReaction rate function. The actual reaction rate constants employed\nare stored in the attribute
\nk
of the returned function. If JAX is\navailable, the attributejac
will hold the Jacobian function of\ndydt
.Notes
\n\nThe returned function is suited to be used by ODE solvers such as\n
\n\nscipy.integrate.solve_ivp
or the olderscipy.integrate.ode
(see\nexamples below). This is actually what the functionget_y
from the\ncurrent module does.Examples
\n\n\n\n>>> import numpy as np\n>>> import overreact as rx\n
\n\n>>> scheme = rx.parse_reactions("A <=> B")\n>>> dydt = get_dydt(scheme, np.array([1, 1]))\n>>> dydt(0.0, np.array([1., 1.])) # doctest: +SKIP\narray([0., 0.])\n
If available, JAX is used for JIT compilation. This will make
\n\ndydt
\ncomplain if given lists instead of numpy arrays. So stick to the safer,\nfaster side as above.The actually used reaction rate constants can be inspected with the
\n\nk
\nattribute ofdydt
:\n\n>>> dydt.k # doctest: +SKIP\narray([1., 1.])\n
If JAX is available, the Jacobian function will be available as\n
\n\ndydt.jac
:\n", "parameters": ["scheme", "k", "ef"], "funcdef": "def"}, "overreact.simulate.get_fixed_scheme": {"fullname": "overreact.simulate.get_fixed_scheme", "modulename": "overreact.simulate", "qualname": "get_fixed_scheme", "type": "function", "doc": ">>> dydt.jac(0.0, np.array([1., 1.])) # doctest: +SKIP\nDeviceArray([[-1., 1.],\n [ 1., -1.]], dtype=float64)\n
Generate an alternative scheme with some concentrations fixed.
\n\nThis function returns data that allow the microkinetic simulation of a\nreaction network under constraints, namely when some compounds have fixed\nconcentrations. This works by 1. removing all references to the fixed\ncompounds and by 2. properly multiplying the reaction rate constants by\nthe respective concentrations.
\n\nParameters
\n\n\n
\n\n- scheme (Scheme):\nA descriptor of the reaction scheme.\nMostly likely, this comes from a parsed model input file.\nSee
\noverreact.io.parse_model
.- k (array-like):\nReaction rate constant(s). Units match the concentration units given to\nthe returned function
\ndydt
.- fixed_y0 (dict-like):\nFixed initial state. Units match the concentration units given to\nthe returned function
\ndydt
.Returns
\n\n\n
\n\n- scheme (Scheme):\nAssociated reaction scheme with all references to fixed compounds\nremoved.
\n- k (array-like):\nAssociated (effective) reaction rate constants that model the fixed\nconcentrations.
\nNotes
\n\nKeep in mind that when a compound get its concentration fixed, the\nreaction scheme no longer conserves matter. You can think of it as\nreacting close to an infinite source of the compound, but it accumulates\nin the milleu at the given concentration.
\n\nExamples
\n\n\n\n>>> import numpy as np\n>>> import overreact as rx\n
Equilibria under a specific pH can be easily modeled:
\n\n\n\n>>> pH = 7\n>>> scheme = rx.parse_reactions("AH <=> A- + H+")\n>>> k = np.array([1, 1])\n>>> scheme, k = rx.get_fixed_scheme(scheme, k, {"H+": 10**-pH})\n>>> scheme\nScheme(compounds=('AH', 'A-'),\n reactions=('AH -> A-',\n 'A- -> AH'),\n is_half_equilibrium=(True, True),\n A=((-1.0, 1.0),\n (1.0, -1.0)),\n B=((-1.0, 0.0),\n (1.0, 0.0)))\n>>> k\narray([1.e+00, 1.e-07])\n
It is also possible to model the fixed activity of a solvent, for\ninstance:
\n\n\n\n>>> scheme = rx.parse_reactions("A + 2H2O -> B")\n>>> k = np.array([1.0])\n>>> scheme, k = rx.get_fixed_scheme(scheme, k, {"H2O": 55.6})\n>>> scheme\nScheme(compounds=('A', 'B'),\n reactions=('A -> B',),\n is_half_equilibrium=(False,),\n A=((-1.0,),\n (1.0,)),\n B=((-1.0,),\n (1.0,)))\n>>> k\narray([3091.36])\n
Multiple reactions work fine, see both examples below:
\n\n\n\n>>> pH = 12\n>>> scheme = rx.parse_reactions("B <- AH <=> A- + H+")\n>>> k = np.array([10.0, 1, 1])\n>>> scheme, k = rx.get_fixed_scheme(scheme, k, {"H+": 10**-pH})\n>>> scheme\nScheme(compounds=('AH', 'B', 'A-'),\n reactions=('AH -> B',\n 'AH -> A-',\n 'A- -> AH'),\n is_half_equilibrium=(False, True, True),\n A=((-1.0, -1.0, 1.0),\n (1.0, 0.0, 0.0),\n (0.0, 1.0, -1.0)),\n B=((-1.0, -1.0, 0.0),\n (1.0, 0.0, 0.0),\n (0.0, 1.0, 0.0)))\n>>> k\narray([1.e+01, 1.e+00, 1.e-12])\n
\n\n>>> pH = 2\n>>> scheme = rx.parse_reactions(["AH <=> A- + H+", "B- + H+ <=> BH"])\n>>> k = np.array([1, 1, 2, 2])\n>>> scheme, k = rx.get_fixed_scheme(scheme, k, {"H+": 10**-pH})\n>>> scheme\nScheme(compounds=('AH', 'A-', 'B-', 'BH'),\n reactions=('AH -> A-',\n 'A- -> AH',\n 'B- -> BH',\n 'BH -> B-'),\n is_half_equilibrium=(True, True, True, True),\n A=((-1.0, 1.0, 0.0, 0.0),\n (1.0, -1.0, 0.0, 0.0),\n (0.0, 0.0, -1.0, 1.0),\n (0.0, 0.0, 1.0, -1.0)),\n B=((-1.0, 0.0, 0.0, 0.0),\n (1.0, 0.0, 0.0, 0.0),\n (0.0, 0.0, -1.0, 0.0),\n (0.0, 0.0, 1.0, 0.0)))\n>>> k\narray([1. , 0.01, 0.02, 2. ])\n
Multiple fixed compounds also work fine:
\n\n\n\n>>> pH = 6\n>>> scheme = rx.parse_reactions("A + H2O -> B <=> B- + H+")\n>>> k = np.array([1.0, 100.0, 2.0])\n>>> scheme, k = rx.get_fixed_scheme(scheme, k, {"H+": 10**-pH, "H2O": 55.6})\n>>> scheme\nScheme(compounds=('A', 'B', 'B-'),\n reactions=('A -> B',\n 'B -> B-',\n 'B- -> B'),\n is_half_equilibrium=(False, True, True),\n A=((-1.0, 0.0, 0.0),\n (1.0, -1.0, 1.0),\n (0.0, 1.0, -1.0)),\n B=((-1.0, 0.0, 0.0),\n (1.0, -1.0, 0.0),\n (0.0, 1.0, 0.0)))\n>>> k\narray([5.56e+01, 1.00e+02, 2.00e-06])\n
This function is a no-op if
\n\nfixed_y0
is empty, which is very important\nfor overall code consistency:\n", "parameters": ["scheme", "k", "fixed_y0"], "funcdef": "def"}, "overreact.thermo": {"fullname": "overreact.thermo", "modulename": "overreact.thermo", "qualname": "", "type": "module", "doc": ">>> scheme = rx.parse_reactions(["AH <=> A- + H+", "B- + H+ <=> BH"])\n>>> k = np.array([1, 1, 2, 2])\n>>> new_scheme, new_k = rx.get_fixed_scheme(scheme, k, {})\n>>> new_scheme == scheme\nTrue\n>>> np.allclose(new_k, k)\nTrue\n
Module dedicated to the calculation of thermodynamic properties.
\n"}, "overreact.thermo.equilibrium_constant": {"fullname": "overreact.thermo.equilibrium_constant", "modulename": "overreact.thermo", "qualname": "equilibrium_constant", "type": "function", "doc": "Calculate an equilibrium constant from a reaction Gibbs free energy.
\n\nThis function uses the usual relationship between reaction Gibbs energy\nand equilibrium constant\n:
\n\n$$K(T) = \\exp\\left(-\\frac{\\Delta_\\text{r} G^\\circ}{R T}\\right)$$
\n\nIf
\n\ndelta_moles
is given, the above will be multiplied by a term\n\\( \\left( \\frac{R T}{p} \\right)^{-\\Delta n} \\), which effectively\ntransforms a \\( K_p \\) equilibrium constant into a \\( K_c \\)\n(see below).Parameters
\n\n\n
\n\n- delta_freeenergy (array-like):\nDelta Gibbs reaction free energies. This assumes values were already\ncorrected for a one molar reference state.
\n- delta_moles (array-like, optional):\nDifference in moles between products and reactants. If set, this\nmultiplies the end result by\n\\( \\left( \\frac{R T}{p} \\right)^{-\\Delta n} \\), which effectively\ncalculates a solution equilibrium constant for gas phase data. You\nshould set this to
\nNone
if your free energies were already adjusted\nfor solution Gibbs free energies.- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\n- pressure (array-like, optional):\nReference gas pressure.
\n- volume (float, optional):\nMolar volume. This substitutes \\( \\frac{R T}{p} \\) if given. See\n
\ndelta_moles
.Returns
\n\n\n
\n\n- K (array-like):\nEquilibrium constant.
\nNotes
\n\nIf you want to calculate a solution equilibrium constant from gas phase data, set\n
\n\ndelta_moles
to the difference in moles between products and reactants.\nAlternatively, convert your energies to solution Gibbs free energies and\nsetdelta_moles
toNone
.Examples
\n\nThe following is an example from the\nLibreTexts Chemistry Library.\nConsider the following equilibrium:
\n\n$$\\ce{2 SO2(g) + O2(g) <=> 2 SO3(g)}$$
\n\nwith concentrations \\( c_{\\ce{SO2(g)}} = 0.2 M \\),\n\\( c_{\\ce{O2(g)}} = 0.5 M \\) and \\( c_{\\ce{SO3(g)}} = 0.7 M \\) (room\ntemperature). Its \\( K_c \\) is given by:
\n\n\n\n>>> Kc = 0.7**2 / (0.2**2 * 0.5)\n>>> Kc\n24.5\n
You could use
\n\nequilibrium_constant
to reach the same result using the\nGibbs reaction free energy (which can easily be obtained from\n\\( K_c \\)):\n\n>>> temperature = 298.15\n>>> dG = -constants.R * temperature * np.log(Kc)\n>>> equilibrium_constant(dG)\narray([24.5])\n
By giving a
\n\ndelta_moles
value (in this case, \\( 2 - 2 - 1 = -1 \\)),\nwe can calculate the correspondingK_p
:\n\n>>> equilibrium_constant(dG, delta_moles=-1)\narray([1.002])\n
(As expected, it makes sense for gases to favor the most entropic side of\nthe equilibrium.) The example above clearly used \"solution-based\" data\n(our \\( K_c \\) was calculated using molar quantities, which means\nreference volumes of one liter). You could convert it to gas phase data\nto get the same result, by changing the reference state (in this case,\nfrom one molar to one atmosphere using
\n\nchange_reference_state
):\n\n>>> dG += temperature * rx.change_reference_state()\n>>> equilibrium_constant(dG)\narray([1.002])\n
Having gas phase information, the inverse path can be taken just by\ninverting the sign of
\n\ndelta_moles
:\n\n>>> equilibrium_constant(dG, delta_moles=1)\narray([24.5])\n
The following example is from\nWikipedia.\nThe reactions are two copper complex forming equilibria with two\ndifferent ligands. Since this reaction takes place in solution, it is the\nsolution standard Gibbs reaction free energy that is given:
\n\n\n\n>>> dG1 = -37.4e3\n>>> np.log10(equilibrium_constant(dG1))\narray([6.55])\n>>> dG2 = -60.67e3\n>>> np.log10(equilibrium_constant(dG2))\narray([10.62])\n
The above are thus \\( \\log_{10}(K_c) \\). Since we are talking about a\nmono- and a bidendate ligands, the
\n\ndelta_moles
are -4 and -2,\nrespectively, and we could obtain the \\( \\log_{10}(K_p) \\) the following\nway:\n\n>>> np.log10(equilibrium_constant(dG1, delta_moles=-4))\narray([0.998])\n>>> np.log10(equilibrium_constant(dG2, delta_moles=-2))\narray([7.85])\n
You can easily check that the above values match the values given\nhere.
\n", "parameters": ["delta_freeenergy", "delta_moles", "temperature", "pressure", "volume"], "funcdef": "def"}, "overreact.thermo.change_reference_state": {"fullname": "overreact.thermo.change_reference_state", "modulename": "overreact.thermo", "qualname": "change_reference_state", "type": "function", "doc": "Calculate an additive entropy correction to a change in reference states.
\n\n$$\\Delta G_\\text{corr} =\n R T \\ln \\left( \\frac{\\chi_\\text{new}}{\\chi_\\text{old}} \\right)$$
\n\nThe value returned can be directly multiplied by temperature and summed to\nthe old reference free energies to obtain free energies with respect to a\nnew reference. See notes below.
\n\nFor instance, the concentration correction to Gibbs free energy for a\ngas-to-liquid standard state change is simply\n(\\( c^\\circ = \\frac{\\text{1 atm}}{R T} \\)),
\n\n$$\\Delta G_\\text{conc} =\n R T \\ln \\left( \\frac{\\text{1 M}}{c^\\circ} \\right)$$
\n\nParameters
\n\n\n
\n\n- new_reference (array-like, optional):\nNew reference state. Default value corresponds to 1 mol/liter.
\n- old_reference (array-like, optional):\nOld reference state. Default value corresponds to the concentration of\nan ideal gas at the given temperature and 1 atm.
\n- sign (float, optional):\nSign of the change in reference state. Default value is 1. This only\nmultiplies the final result.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\n- pressure (array-like, optional):\nReference gas pressure.
\n- volume (float, optional):\nMolar volume.
\nReturns
\n\n\n
\n\n- correction (array-like):\nEntropy correction in J/mol\u00b7K.
\nNotes
\n\nThis function can be used to add any entropy correction in the form above.\nThe only drawback is that, sometimes, those corrections are written with a\nminus sign in front of them (this implies switching the roles of\n
\n\nold_reference
andnew_reference
). The easiest way to accomplish this is\nby usingsign=-1
or multiplying the result by-1
.Examples
\n\nBy default, the correction returns a change in concentration from the gas\nphase standard concentration to the solvated-state standard concentration:
\n\n\n\n>>> -rx.change_reference_state() / constants.calorie\n-6.4\n>>> 298.15 * rx.change_reference_state() / constants.kcal\n1.89\n>>> 273.15 * rx.change_reference_state(temperature=273.15) / constants.kcal\n1.69\n
But this function can also be used to adjust symmetry effects from C1\ncalculations (symmetry number equals to one). For D7h, for instance, the\nsymmetry number is 14:
\n\n\n\n>>> -298.15 * rx.change_reference_state(14, 1) / constants.kcal\n-1.56\n
\n", "parameters": ["new_reference", "old_reference", "sign", "temperature", "pressure", "volume"], "funcdef": "def"}, "overreact.tunnel": {"fullname": "overreact.tunnel", "modulename": "overreact.tunnel", "qualname": "", "type": "module", "doc": ">>> rx.change_reference_state(sign=-1) == -rx.change_reference_state()\nTrue\n
Module dedicated to quantum tunneling approximations.
\n"}, "overreact.tunnel.eckart": {"fullname": "overreact.tunnel.eckart", "modulename": "overreact.tunnel", "qualname": "eckart", "type": "function", "doc": "Calculate the Eckart correction to quantum tunneling.
\n\nReferences are\nJ. Phys. Chem. 1962, 66, 3, 532\u2013533\nand\nJ. Res. Natl. Inst. Stand. Technol., 1981, 86, 357.
\n\nParameters
\n\n\n
\n\n- vibfreq (array-like):\nMagnitude of the imaginary frequency in cm$^{-1}$. Only the absolute value\nis used.
\n- delta_forward (array-like):\nActivation enthalpy at 0 K for the forward reaction.
\n- delta_backward (array-like, optional):\nActivation enthalpy at 0 K for the reverse reaction. If delta_backward\nis not given, the \"symmetrical\" Eckart model is used (i.e.,\n
\ndelta_backward == delta_forward
is assumed).- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\nReturns
\n\n\n
\n\n- kappa (array-like):\nThe quantum tunneling correction.
\nRaises
\n\n\n
\n\n- ValueError: If
\nvibfreq
is zero.Examples
\n\n\n\n>>> eckart(1218, 13672.624, 24527.729644, temperature=300)\narray(3.9)\n>>> eckart(1218, 13672.624, 24527.729644, temperature=[200, 298.15])\narray([17.1, 4.0])\n>>> eckart([1218, 200], 13672.624, 24527.729644, temperature=400)\narray([2.3, 1.0])\n
If no backward barrier is given, a symmetric Eckart potential is assumed:
\n\n\n", "parameters": ["vibfreq", "delta_forward", "delta_backward", "temperature"], "funcdef": "def"}, "overreact.tunnel.wigner": {"fullname": "overreact.tunnel.wigner", "modulename": "overreact.tunnel", "qualname": "wigner", "type": "function", "doc": ">>> eckart(414.45, 394.54)\narray(1.16)\n>>> eckart(414.45, 789.08)\narray(1.3)\n>>> eckart(3315.6, 3156.31)\narray(3.3)\n
Calculate the Wigner correction to quantum tunneling.
\n\nParameters
\n\n\n
\n\n- vibfreq (array-like):\nMagnitude of the imaginary frequency in cm$^{-1}$. Only the absolute value\nis used.
\n- temperature (array-like, optional):\nAbsolute temperature in Kelvin.
\nReturns
\n\n\n
\n\n- kappa (array-like):\nThe quantum tunneling correction.
\nRaises
\n\n\n
\n\n- ValueError: If
\nvibfreq
is zero.Examples
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"df": 0, "i": {"docs": {}, "df": 0, "c": {"docs": {"overreact.core.parse_reactions": {"tf": 1}, "overreact.rates.eyring": {"tf": 1}}, "df": 2, "s": {"docs": {"overreact.simulate.get_y": {"tf": 1}}, "df": 1}}}}}}}, "(": {"docs": {}, "df": 0, "t": {"docs": {"overreact.rates.eyring": {"tf": 1}, "overreact.thermo.equilibrium_constant": {"tf": 1}}, "df": 2}}, "^": {"docs": {}, "df": 0, "\\": {"docs": {}, "df": 0, "d": {"docs": {}, "df": 0, "d": {"docs": {}, "df": 0, "a": {"docs": {}, "df": 0, "g": {"docs": {}, "df": 0, "g": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "r": {"docs": {"overreact.rates.eyring": {"tf": 1}}, "df": 1}}}}}}}}}}}}}, "pipeline": ["trimmer", "stopWordFilter"], "_isPrebuiltIndex": true}; // mirrored in build-search-index.js (part 1) // Also split on html tags. this is a cheap heuristic, but good enough. - elasticlunr.tokenizer.setSeperator(/[\s\-.;&]+|<[^>]*>/); + elasticlunr.tokenizer.setSeperator(/[\s\-.;&_]+|<[^>]*>/); let searchIndex; if (docs._isPrebuiltIndex) { @@ -14,6 +14,7 @@ window.pdocSearch = (function(){ console.time("building search index"); // mirrored in build-search-index.js (part 2) searchIndex = elasticlunr(function () { + this.pipeline.remove(elasticlunr.stemmer); this.addField("qualname"); this.addField("fullname"); this.addField("doc");>>> wigner(1821.0777)\n4.218\n>>> wigner(262.38)\n1.06680\n>>> wigner(113.87)\n1.01258\n>>> wigner(169.14)\n1.02776\n