diff --git a/requirements-testing.txt b/requirements-testing.txt index 5cbd9a10..5370c1e0 100644 --- a/requirements-testing.txt +++ b/requirements-testing.txt @@ -4,7 +4,7 @@ pytest-cov==3.0.0 pycodestyle==2.8.0 pydocstyle==6.1.1 flake8==4.0.1 -mypy==0.910 +mypy==0.931 mypy-extensions==0.4.3 pylint==2.12.2 -black==21.12b0 +black==22.1.0 \ No newline at end of file diff --git a/scripts/generate_free_data.py b/scripts/generate_free_data.py new file mode 100644 index 00000000..326d9d29 --- /dev/null +++ b/scripts/generate_free_data.py @@ -0,0 +1,57 @@ +""" +This script generates the data/freed/compounds.json file by using the s4 package as an interface. +""" + +import numpy as np +from pymatgen.core.composition import Composition +from collections import OrderedDict +import json +import gzip + +from s4.thermo.exp.freed import ExpThermoDatabase + + +if __name__ == "__main__": + xp = ExpThermoDatabase() + temps = np.arange(300, 2100, 100) + data = {} + + # Acquire data + for c in xp.compositions: + if c.is_element: + continue + + formula, factor = c.get_integer_formula_and_factor() + + if not data.get(formula): + data[formula] = dict() + + phases = xp.compositions[c] + + for t in temps: + energies = [] + for p in phases: + if t > p.tmax: + continue + energies.append(p.dgf(t)) + + if not energies: + continue + + final_energy = min(energies) + g = final_energy / factor + + if data[formula].get(t): + data[formula][t].append(g) + else: + data[formula][t] = [g] + + # Clean the data + cleaned_data = {} + for f, energy_dict in data.items(): + cleaned_data[f] = {str(t): min(e) for t, e in energy_dict.items()} + + # Write to file + cleaned_data = OrderedDict(sorted(cleaned_data.items())) + with gzip.open("compounds.json.gz", "wt", encoding="ascii") as zipfile: + json.dump(cleaned_data, zipfile) diff --git a/scripts/generate_janaf_data.py b/scripts/generate_janaf_data.py index 17832be3..30246854 100644 --- a/scripts/generate_janaf_data.py +++ b/scripts/generate_janaf_data.py @@ -4,6 +4,7 @@ """ import os +import gzip import json from collections import OrderedDict import pandas @@ -74,6 +75,7 @@ formula, factor = Composition(f).get_integer_formula_and_factor() all_data[formula] = {temp: g / factor for temp, g in zip(temps, dGf)} -all_data = OrderedDict(sorted(all_data.items())) -with open("compounds.json", "w") as f: - json.dump(all_data, f) + all_data = OrderedDict(sorted(all_data.items())) + + with gzip.open("compounds.json.gz", "wt", encoding="ascii") as zipfile: + json.dump(all_data, zipfile) diff --git a/setup.cfg b/setup.cfg index 97fac142..2a76d2e8 100644 --- a/setup.cfg +++ b/setup.cfg @@ -24,6 +24,8 @@ ignore = D105,D2,D4 ignore_missing_imports = True [pylint.MASTER] +ignored-modules=scipy +extension-pkg-whitelist=scipy ignore-patterns=test_ disable=unsubscriptable-object, invalid-name, diff --git a/src/rxn_network/costs/competitiveness.py b/src/rxn_network/costs/competitiveness.py index 6edda756..07713b85 100644 --- a/src/rxn_network/costs/competitiveness.py +++ b/src/rxn_network/costs/competitiveness.py @@ -40,6 +40,7 @@ def __init__( use_minimize=False, basic_enumerator_kwargs: Optional[Dict] = None, minimize_enumerator_kwargs: Optional[Dict] = None, + quiet=True, name: str = "c_score", ): """ @@ -70,6 +71,10 @@ def __init__( if not self.minimize_enumerator_kwargs.get("calculators"): self.minimize_enumerator_kwargs["calculators"] = calcs + if quiet: + self.basic_enumerator_kwargs["quiet"] = True + self.minimize_enumerator_kwargs["quiet"] = True + def calculate(self, rxn: ComputedReaction) -> float: """ Calculates the competitiveness score for a given reaction by enumerating @@ -105,6 +110,8 @@ def get_competing_rxns(self, rxn: ComputedReaction) -> List[ComputedReaction]: A list of competing reactions """ + chemsys = rxn.chemical_system.split("-") + precursors = [r.reduced_formula for r in rxn.reactants] open_elem = self.open_elem @@ -116,6 +123,9 @@ def get_competing_rxns(self, rxn: ComputedReaction) -> List[ComputedReaction]: if open_phases: precursors = list(set(precursors) - set(open_phases)) + entries = self.entries.filter_by_stability(0.0).get_subset_in_chemsys(chemsys) + entries.update(rxn.entries) # add back entries which may have been filtered out + enumerators = [] if self.use_basic: kwargs = self.basic_enumerator_kwargs.copy() @@ -143,7 +153,7 @@ def get_competing_rxns(self, rxn: ComputedReaction) -> List[ComputedReaction]: rxns = set() for e in enumerators: - rxns.update(e.enumerate(self.entries)) + rxns.update(e.enumerate(entries)) if rxn in rxns: rxns.remove(rxn) diff --git a/src/rxn_network/data/__init__.py b/src/rxn_network/data/__init__.py index 20a921fc..febd8d41 100644 --- a/src/rxn_network/data/__init__.py +++ b/src/rxn_network/data/__init__.py @@ -10,6 +10,7 @@ cwd = Path(__file__).parent.resolve() PATH_TO_BARIN = cwd / "barin" +PATH_TO_FREED = cwd / "freed" PATH_TO_NIST = cwd / "nist" G_ELEMS = loadfn(cwd / "elements.json") diff --git a/src/rxn_network/data/barin/compounds.json b/src/rxn_network/data/barin/compounds.json deleted file mode 100644 index af830072..00000000 --- a/src/rxn_network/data/barin/compounds.json +++ /dev/null @@ -1,29803 +0,0 @@ -{ - "Ag2CO3": { - "298.15": -4.5271555983107525, - "300.0": -4.522719689765783, - "400.0": -4.284507255191983, - "500.0": -4.049891223106744 - }, - "Ag2O": { - "298.15": -0.334807452422209, - "300.0": -0.33409231763341707, - "400.0": -0.2917231724655744, - "500.0": -0.24767501518491603, - "600.0": -0.20325374410140973, - "700.0": -0.1587910159286981, - "800.0": -0.11455630174661577, - "900.0": -0.07073615845658668 - }, - "Ag2S": { - "298.15": -0.4200017707391529, - "300.0": -0.42050962008191817, - "400.0": -0.44777802050672105, - "450.0": -0.45913726294898016, - "500.0": -0.4744971144995533, - "600.0": -0.5040041977414438, - "700.0": -0.5326095892931184, - "800.0": -0.5604065676052892, - "860.0": -0.5765851966676674, - "900.0": -0.5756109550713423, - "1000.0": -0.5409942855848955, - "1100.0": -0.5068647368966113, - "1110.0": -0.5034756198540759, - "1200.0": -0.47994872173005365, - "1300.0": -0.4421398563747967, - "1400.0": -0.39849590571389026 - }, - "Ag2SO4": { - "298.15": -6.408229563913193, - "300.0": -6.4019591791708885, - "400.0": -6.062114690410231, - "500.0": -5.717523364935566, - "600.0": -5.37316005345153, - "700.0": -5.03126343877521, - "800.0": -4.720542555181296, - "900.0": -4.402007010272176, - "933.0": -4.281439430590789, - "1000.0": -4.052129905923832, - "1100.0": -3.7147521139708926, - "1200.0": -3.3825357296240166 - }, - "Ag2Te": { - "298.15": -8.593142536301464, - "300.0": -8.586944701465269, - "400.0": -8.254593581578476, - "500.0": -7.927611154743771 - }, - "Ag2WO4": { - "298.15": -0.4307184282987296, - "300.0": -0.4310811778292762, - "400.0": -0.45218283623478683, - "421.0": -0.45708513703331655, - "500.0": -0.48903818853832126, - "600.0": -0.5299148784947721, - "700.0": -0.5704495474652792, - "800.0": -0.5906495141805741 - }, - "Ag3AsO4": { - "298.15": -1.0063190190977704, - "300.0": -1.0061013693794425, - "400.0": -0.9629030824274935, - "500.0": -0.907848067962821, - "600.0": -0.8563894559867108, - "700.0": -0.8102995370626901, - "800.0": -0.7822330876706848, - "900.0": -0.7558560146637964, - "1000.0": -0.730826297056081, - "1100.0": -0.7068744637677042, - "1200.0": -0.6837621365357353, - "1300.0": -0.655011645171842, - "1400.0": -0.623452436014288, - "1500.0": -0.5922352478426779, - "1600.0": -0.5612875307509023, - "1633.91": -0.5508507085434616 - }, - "AgBr": { - "298.15": 0.5729991584514068, - "300.0": 0.570345904742266, - "400.0": 0.4611893888646438, - "500.0": 0.3691339222842185, - "600.0": 0.2785812751874862, - "700.0": 0.18937598348992699, - "800.0": 0.10141440446852758, - "900.0": 0.01462398821717858, - "1000.0": -0.0710367223533253, - "1100.0": -0.15559882005988804, - "1200.0": -0.23908303344711232, - "1300.0": -0.3152086135003913, - "1400.0": -0.38698119918711116, - "1500.0": -0.45769662909909514, - "1600.0": -0.5274274531424528, - "1700.0": -0.5962151284063891, - "1800.0": -0.6641425690693149, - "1900.0": -0.731230503675833, - "2000.0": -0.7975411178597511 - }, - "AgBrO3": { - "298.15": 0.740205963488786, - "300.0": 0.7454710138178624, - "400.0": 1.0597468428111338 - }, - "AgCN": { - "298.15": 1.6275742293841762, - "300.0": 1.6282789999006666, - "400.0": 1.6638388181665347, - "500.0": 1.695118191971953 - }, - "AgCl": { - "298.15": 0.6752530689763422, - "300.0": 0.6734911426851159, - "400.0": 0.5793524573721229, - "500.0": 0.48706897680106825, - "600.0": 0.39638159416441865, - "700.0": 0.30715557392225684, - "800.0": 0.2192872733515694, - "900.0": 0.13268341400164435, - "1000.0": 0.04731290305557776, - "1100.0": -0.03687608084813705, - "1200.0": -0.11989390198180142, - "1300.0": -0.1954805398754112, - "1400.0": -0.2666312692240511, - "1500.0": -0.3366626571641472, - "1600.0": -0.4056368893295076, - "1700.0": -0.4736161513539402, - "1800.0": -0.5406626288712528, - "1900.0": -0.6068281432429524, - "2000.0": -0.6721437872859428, - "2100.0": -0.736671746634032, - "2200.0": -0.8004327498318227 - }, - "AgF": { - "298.15": -0.20957595020522188, - "300.0": -0.2113275122241469, - "400.0": -0.3051863621850039, - "500.0": -0.39705527186400524, - "600.0": -0.48716225525178025, - "700.0": -0.5756524121605476, - "800.0": -0.6626190210410192, - "900.0": -0.7481553603439072, - "1000.0": -0.8323132514307179, - "1100.0": -0.915134151390657, - "1200.0": -0.9966595173129297, - "1300.0": -1.0706086001829291, - "1400.0": -1.140007767512644, - "1500.0": -1.208163222166199, - "1600.0": -1.275147514049704, - "1700.0": -1.3410331930692674, - "1800.0": -1.405882444858698, - "1900.0": -1.4697470907795018, - "2000.0": -1.5326893164654876 - }, - "AgI": { - "298.15": 0.8197828462184082, - "300.0": 0.8168083000679263, - "400.0": 0.6614685868155715, - "500.0": 0.5494308032381792, - "600.0": 0.4665269890998295, - "700.0": 0.3844626810178876, - "800.0": 0.30318605763084694, - "900.0": 0.2226971189387074, - "1000.0": 0.14299586494146907, - "1100.0": 0.0640719313668306, - "1200.0": -0.014053953240605354, - "1300.0": -0.08508031132162931, - "1400.0": -0.1519920532990247, - "1500.0": -0.21806428922001225, - "1600.0": -0.2833592047184, - "1700.0": -0.3479286211556945, - "1800.0": -0.41179326707649844, - "1900.0": -0.4750049638423186, - "2000.0": -0.5375948042700588 - }, - "AgNO3": { - "298.15": -0.3449540750052124, - "300.0": -0.33909826115496017, - "400.0": -0.024791339344784665, - "433.0": 0.07756621390316407, - "483.0": 0.22803471917389306, - "500.0": 0.27443556626695365, - "600.0": 0.5428494903268338 - }, - "AgP2": { - "298.15": -0.11591402141809017, - "300.0": -0.11462885165272509, - "400.0": -0.04593445483950069, - "500.0": 0.021402222302249304 - }, - "AgP3": { - "298.15": -0.5335216452556355, - "300.0": -0.5323608467578864, - "400.0": -0.4648583412593151, - "500.0": -0.3968583506902799, - "600.0": -0.3298636945344739, - "700.0": -0.2641542081440329, - "800.0": -0.19991644842038103, - "900.0": -0.1372851509034355 - }, - "Al(HO)3": { - "298.15": -11.971382275056579, - "300.0": -11.962494911558187, - "400.0": -11.479644193583761, - "500.0": -10.995694862745394 - }, - "Al2(SO4)3": { - "298.15": -7.39287688962888, - "300.0": -7.392192847656993, - "400.0": -7.351357614789746, - "500.0": -7.288912874174225, - "600.0": -7.2159691257174545, - "700.0": -7.136962277964405, - "800.0": -7.053405514671072, - "900.0": -6.929749381843887, - "1000.0": -6.6385858800825845, - "1100.0": -6.341473286020318, - "1200.0": -6.046526824869029, - "1300.0": -5.7538605036240345, - "1370.0": -5.550409838348899, - "1400.0": -5.476419298389694, - "1500.0": -5.231542636726138, - "1600.0": -4.989257043137914, - "1700.0": -4.7493863249959, - "1800.0": -4.51179574676018 - }, - "Al2CdO4": { - "298.15": 0.5967540705660583, - "300.0": 0.5952512510823652, - "400.0": 0.5146483053949111, - "500.0": 0.4357451003648753, - "600.0": 0.35901839251811907, - "700.0": 0.29387894110425133, - "800.0": 0.23001429518344738, - "900.0": 0.1672897192157898, - "1000.0": 0.10558084193366278, - "1100.0": 0.10572594174588143, - "1200.0": 0.1442292133453275, - "1300.0": 0.1827324849447736, - "1400.0": 0.22123575654421967, - "1500.0": 0.2597493924159671, - "1600.0": 0.2982630282877145, - "1700.0": 0.3367870284317632, - "1800.0": 0.37531102857581206, - "1900.0": 0.41384539299216205, - "2000.0": 0.45237975740851216 - }, - "Al2FeO4": { - "298.15": -19.481401352371257, - "300.0": -19.4739598048589, - "400.0": -19.071359647313685, - "500.0": -18.66923624629433, - "600.0": -18.268221822411213, - "700.0": -17.868160911579825, - "800.0": -17.468649307180403, - "900.0": -17.069106609964077, - "1000.0": -16.652981077065622, - "1100.0": -16.22751733482367, - "1200.0": -15.80141100769903, - "1300.0": -15.375325409118995, - "1400.0": -14.950255509224492, - "1500.0": -14.526242765104723, - "1600.0": -14.103318269576594, - "1700.0": -13.681305830010984, - "1800.0": -13.259935975328053, - "1900.0": -12.832243914541316, - "2000.0": -12.40467622502219, - "2073.0": -12.093115835371867 - }, - "Al2NiO4": { - "298.15": -18.62583067389635, - "300.0": -18.61819220521027, - "400.0": -18.205735624706488, - "500.0": -17.795434812841382, - "600.0": -17.38746596224407, - "700.0": -16.981279766482594, - "800.0": -16.577052418186067, - "900.0": -16.17446262491315, - "1000.0": -15.757290300512262, - "1100.0": -15.333515934655425, - "1200.0": -14.911088924197761, - "1300.0": -14.489978176322364, - "1400.0": -14.070204419573841, - "1500.0": -13.65176765395219, - "1600.0": -13.234709336546613, - "1700.0": -12.819091652990926, - "1800.0": -12.397058484880711, - "1900.0": -11.973418854563791, - "2000.0": -11.550919294200016 - }, - "Al2O": { - "298.15": -1.6554333933301548, - "300.0": -1.657309326616696, - "400.0": -1.756961804793997, - "500.0": -1.8536086440039123, - "600.0": -1.9476644151384945, - "700.0": -2.039326039371469, - "800.0": -2.1286246095197408, - "900.0": -2.215508304221802, - "1000.0": -2.2840368726782048, - "1100.0": -2.3424913684577136, - "1200.0": -2.399049202406079, - "1300.0": -2.453855474335519, - "1400.0": -2.507065648330555, - "1500.0": -2.558773002841897, - "1600.0": -2.6090915448648606, - "1700.0": -2.6580938243055554, - "1800.0": -2.705862755342392, - "1900.0": -2.7524708878814788, - "2000.0": -2.7979596790120222 - }, - "Al2O3": { - "298.15": -16.30273085891443, - "300.0": -16.29671958097966, - "400.0": -15.970659574379772, - "500.0": -15.644983045855035, - "600.0": -15.321016622260018, - "700.0": -14.998998681857653, - "800.0": -14.678784124835719, - "900.0": -14.360041294480572, - "1000.0": -14.026612290274443, - "1100.0": -13.686539787523156, - "1200.0": -13.347793911626441, - "1300.0": -13.010353934039694, - "1400.0": -12.674209490490613, - "1500.0": -12.339319123889995, - "1600.0": -12.005662105693231, - "1700.0": -11.673207343083424, - "1800.0": -11.341913378971368, - "1900.0": -11.011759484812456, - "2000.0": -10.682704203517487, - "2100.0": -10.354726806541855, - "2200.0": -10.027785836796356, - "2300.0": -9.70186056573639, - "2308.0": -9.675835877987746, - "2327.0": -9.621485634039564, - "2400.0": -9.415827378764247, - "2500.0": -9.136727889961692, - "2600.0": -8.860561490220418, - "2700.0": -8.587203808272802, - "2800.0": -8.304746295244618, - "2900.0": -7.819169773654941, - "3000.0": -7.336857997840184 - 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""" -from typing import Dict, Optional +from typing import Dict, Optional, List from pymatgen.core.composition import Composition +from pymatgen.entries.computed_entries import EnergyAdjustment from rxn_network.data import PATH_TO_BARIN, load_experimental_data from rxn_network.entries.experimental import ExperimentalReferenceEntry -G_COMPOUNDS = load_experimental_data(PATH_TO_BARIN / "compounds.json") +G_COMPOUNDS = load_experimental_data(PATH_TO_BARIN / "compounds.json.gz") class BarinReferenceEntry(ExperimentalReferenceEntry): @@ -25,7 +26,11 @@ class BarinReferenceEntry(ExperimentalReferenceEntry): REFERENCES = G_COMPOUNDS def __init__( - self, composition: Composition, temperature: float, data: Optional[Dict] = None + self, + composition: Composition, + temperature: float, + energy_adjustments: Optional[List[EnergyAdjustment]] = None, + data: Optional[Dict] = None, ): """ Args: @@ -34,4 +39,9 @@ def __init__( one of [300, 400, 500, ... 2000 K], then free energies will be interpolated. Defaults to 300 K. """ - super().__init__(composition, temperature, data) + super().__init__( + composition=composition, + temperature=temperature, + energy_adjustments=energy_adjustments, + data=data, + ) diff --git a/src/rxn_network/entries/entry_set.py b/src/rxn_network/entries/entry_set.py index 7acb88e7..6a190e9e 100644 --- a/src/rxn_network/entries/entry_set.py +++ b/src/rxn_network/entries/entry_set.py @@ -7,6 +7,7 @@ import warnings from copy import deepcopy from typing import Dict, Iterable, List, Optional, Set, Union +from functools import cached_property from monty.dev import deprecated from monty.json import MontyDecoder, MSONable @@ -24,6 +25,7 @@ from rxn_network.entries.barin import BarinReferenceEntry from rxn_network.entries.experimental import ExperimentalReferenceEntry from rxn_network.entries.gibbs import GibbsComputedEntry +from rxn_network.entries.freed import FREEDReferenceEntry from rxn_network.entries.nist import NISTReferenceEntry from rxn_network.thermo.utils import expand_pd @@ -61,10 +63,22 @@ def add(self, entry: Union[GibbsComputedEntry, ExperimentalReferenceEntry]): """ Add an entry to the set. - :param element: Entry + Args: + entry: An entry object. """ self.entries.add(entry) + def update( + self, entries: Iterable[Union[GibbsComputedEntry, ExperimentalReferenceEntry]] + ): + """ + Add an iterable of entries to the set. + + Args: + entry: An iterable of entry objects. + """ + self.entries.update(entries) + def discard(self, entry: Union[GibbsComputedEntry, ExperimentalReferenceEntry]): """ Discard an entry. @@ -162,11 +176,7 @@ def get_min_entry_by_formula(self, formula: str) -> ComputedEntry: Returns: Ground state computed entry object. """ - comp = Composition(formula).reduced_composition - possible_entries = filter( - lambda x: x.composition.reduced_composition == comp, self.entries - ) - return sorted(possible_entries, key=lambda x: x.energy_per_atom)[0] + return self.min_entries_by_formula[Composition(formula).reduced_formula] def get_stabilized_entry( self, entry: ComputedEntry, tol: float = 1e-6 @@ -275,6 +285,7 @@ def from_pd( temperature: float, include_nist_data=True, include_barin_data=False, + include_freed_data=False, ) -> "GibbsEntrySet": """ Constructor method for building a GibbsEntrySet from an existing phase diagram. @@ -339,6 +350,17 @@ def from_pd( logging.warning( f"Compound {formula} is in Barin tables but not at this temperature! {error}" ) + if include_freed_data and formula in FREEDReferenceEntry.REFERENCES: + try: + e = FREEDReferenceEntry( + composition=Composition(formula), temperature=temperature + ) + experimental = True + new_entries.append(e) + except ValueError as error: + logging.warning( + f"Compound {formula} is in FREED tables but not at this temperature! {error}" + ) if experimental: experimental_formulas.append(formula) @@ -369,6 +391,7 @@ def from_entries( temperature: float, include_nist_data=True, include_barin_data=False, + include_freed_data=False, ) -> "GibbsEntrySet": """ Constructor method for initializing GibbsEntrySet from T = 0 K @@ -396,6 +419,7 @@ def from_entries( temperature, include_nist_data=include_nist_data, include_barin_data=include_barin_data, + include_freed_data=include_freed_data, ) pd_dict = expand_pd(list(e_set)) @@ -407,11 +431,30 @@ def from_entries( return cls(list(new_entries)) - @property + @cached_property def entries_list(self) -> List[ComputedEntry]: """Returns a list of all entries in the entry set.""" return list(sorted(self.entries, key=lambda e: e.composition.reduced_formula)) + @cached_property + def min_entries_by_formula(self) -> Dict[str, ComputedEntry]: + """ + Returns a dict of minimum energy entries in the entry set, indexed by + formula. + """ + min_entries = {} + for e in self.entries: + formula = e.composition.reduced_formula + if formula not in min_entries: + entries = filter( + lambda x: x.composition.reduced_formula == formula, self.entries + ) + min_entries[formula] = sorted(entries, key=lambda x: x.energy_per_atom)[ + 0 + ] + + return min_entries + @property def chemsys(self) -> set: """ diff --git a/src/rxn_network/entries/experimental.py b/src/rxn_network/entries/experimental.py index 15342013..24f5dda1 100644 --- a/src/rxn_network/entries/experimental.py +++ b/src/rxn_network/entries/experimental.py @@ -2,14 +2,15 @@ Implements an Entry that looks up NIST pre-tabulated Gibbs free energies """ import hashlib -from typing import Any, Dict, List, Optional -from monty.json import MSONable +from typing import Dict, List, Optional from pymatgen.core.composition import Composition +from pymatgen.entries.computed_entries import ComputedEntry, EnergyAdjustment +from monty.json import MontyDecoder from scipy.interpolate import interp1d -class ExperimentalReferenceEntry(MSONable): +class ExperimentalReferenceEntry(ComputedEntry): """ An Entry class for experimental reference data, to be sub-classed for specific data sources. Given a composition, automatically finds the Gibbs free energy of formation, dGf(T) from tabulated @@ -22,6 +23,7 @@ def __init__( self, composition: Composition, temperature: float, + energy_adjustments: Optional[List[EnergyAdjustment]] = None, data: Optional[dict] = None, ): """ @@ -32,18 +34,23 @@ def __init__( interpolated. Defaults to 300 K. data: Optional dictionary containing entry data """ - self._composition = Composition(composition) - self.temperature = temperature - self.data = data if data else {} # type: Dict[Any, Any] + formula = Composition(composition).reduced_formula + entry_id = self.__class__.__name__ - formula = self._composition.reduced_formula + self._temperature = temperature self._validate_temperature(formula, temperature) - self._energy = self._get_energy(formula, temperature) + energy = self._get_energy(formula, temperature) + + super().__init__( + composition, + energy, + energy_adjustments=energy_adjustments, + data=data, + entry_id=entry_id, + ) - self._formula = formula self.name = formula - self.entry_id = self.__class__.__name__ def get_new_temperature( self, new_temperature: float @@ -96,38 +103,9 @@ def _get_energy(cls, formula: str, temperature: float) -> float: return data[temperature] @property - def composition(self) -> Composition: - """ - :return: the composition of the entry. - """ - return self._composition - - @property - def energy(self) -> float: - """The energy of the entry, as supplied by the reference tables.""" - return self._energy - - @property - def energy_per_atom(self) -> float: - """The energy of the entry, as supplied by the reference tables.""" - return self.energy / self.composition.num_atoms - - @property - def correction_uncertainty(self) -> float: - """Uncertainty of experimental data is not supplied.""" - return 0 - - @property - def correction_uncertainty_per_atom(self) -> float: - """Uncertainty of experimental data is not supplied.""" - return 0 - - @property - def energy_adjustments(self) -> List: - """ - Returns a list of energy adjustments. Not implemented for experimental data. - """ - return [] + def temperature(self) -> float: + """Returns temperature used to calculate entry's energy""" + return self._temperature @property def is_experimental(self) -> bool: @@ -139,17 +117,46 @@ def is_element(self) -> bool: """Returns True if the entry is an element.""" return self.composition.is_element + def as_dict(self): + """ + Returns: + A dict representation of the Entry. + """ + d = super().as_dict() + + d["temperature"] = self.temperature + + del d["energy"] + del d["entry_id"] + del d["parameters"] + del d["correction"] + + return d + + @classmethod + def from_dict(cls, d): + dec = MontyDecoder() + entry = cls( + composition=d["composition"], + temperature=d["temperature"], + energy_adjustments=dec.process_decoded(d["energy_adjustments"]), + data=d["data"], + ) + return entry + def __repr__(self): output = [ - f"{self.__class__.__name__} | {self._formula}", + f"{self.__class__.__name__} | {self.composition.reduced_formula}", f"Gibbs Energy ({self.temperature} K) = {self.energy:.4f}", ] return "\n".join(output) def __eq__(self, other): if isinstance(other, self.__class__): - return (self._formula == other._formula) and ( - self.temperature == other.temperature + return ( + (self.composition.reduced_formula == other.composition.reduced_formula) + and (self.temperature == other.temperature) + and (set(self.energy_adjustments) == set(other.energy_adjustments)) ) return False diff --git a/src/rxn_network/entries/freed.py b/src/rxn_network/entries/freed.py new file mode 100644 index 00000000..ea69aae9 --- /dev/null +++ b/src/rxn_network/entries/freed.py @@ -0,0 +1,48 @@ +""" +Implements an Entry that looks up pre-tabulated Gibbs free energies from the NIST-JANAF +tables. +""" +from typing import Dict, Optional, List + +from pymatgen.core.composition import Composition +from pymatgen.entries.computed_entries import EnergyAdjustment + +from rxn_network.data import PATH_TO_FREED, load_experimental_data +from rxn_network.entries.experimental import ExperimentalReferenceEntry + +G_COMPOUNDS = load_experimental_data(PATH_TO_FREED / "compounds.json.gz") + + +class FREEDReferenceEntry(ExperimentalReferenceEntry): + """ + An Entry class for FREED experimental reference data. Given a composition, + automatically finds the Gibbs free energy of formation, dGf(T) from tabulated + reference values. + + Reference: + https://www.thermart.net/freed-thermodynamic-database/ + """ + + REFERENCES = G_COMPOUNDS + + def __init__( + self, + composition: Composition, + temperature: float, + energy_adjustments: Optional[List[EnergyAdjustment]] = None, + data: Optional[Dict] = None, + ): + """ + Args: + composition: Composition object (within pymatgen). + temperature: Temperature in Kelvin. If temperature is not selected from + one of [300, 400, 500, ... 2000 K], then free energies will be + interpolated. Defaults to 300 K. + data: Optional dictionary containing entry data + """ + super().__init__( + composition=composition, + temperature=temperature, + energy_adjustments=energy_adjustments, + data=data, + ) diff --git a/src/rxn_network/entries/nist.py b/src/rxn_network/entries/nist.py index 25abf6f7..db093f1d 100644 --- a/src/rxn_network/entries/nist.py +++ b/src/rxn_network/entries/nist.py @@ -2,14 +2,15 @@ Implements an Entry that looks up pre-tabulated Gibbs free energies from the NIST-JANAF tables. """ -from typing import Dict, Optional +from typing import Dict, Optional, List from pymatgen.core.composition import Composition +from pymatgen.entries.computed_entries import EnergyAdjustment from rxn_network.data import PATH_TO_NIST, load_experimental_data from rxn_network.entries.experimental import ExperimentalReferenceEntry -G_COMPOUNDS = load_experimental_data(PATH_TO_NIST / "compounds.json") +G_COMPOUNDS = load_experimental_data(PATH_TO_NIST / "compounds.json.gz") class NISTReferenceEntry(ExperimentalReferenceEntry): @@ -27,7 +28,11 @@ class NISTReferenceEntry(ExperimentalReferenceEntry): REFERENCES = G_COMPOUNDS def __init__( - self, composition: Composition, temperature: float, data: Optional[Dict] = None + self, + composition: Composition, + temperature: float, + energy_adjustments: Optional[List[EnergyAdjustment]] = None, + data: Optional[Dict] = None, ): """ Args: @@ -37,4 +42,9 @@ def __init__( interpolated. Defaults to 300 K. data: Optional dictionary containing entry data """ - super().__init__(composition, temperature, data) + super().__init__( + composition=composition, + temperature=temperature, + energy_adjustments=energy_adjustments, + data=data, + ) diff --git a/src/rxn_network/enumerators/basic.py b/src/rxn_network/enumerators/basic.py index 5cfb0535..c838f980 100644 --- a/src/rxn_network/enumerators/basic.py +++ b/src/rxn_network/enumerators/basic.py @@ -84,8 +84,6 @@ def __init__( self.quiet = quiet self._stabilize = False - if "ChempotDistanceCalculator" in self.calculators: - self._stabilize = True # ChempotDistanceCalculator requires stable entries self.open_phases: Optional[List] = None self._build_pd = False @@ -248,12 +246,14 @@ def _get_rxns( ): continue - if not (precursor_func(r) or precursor_func(p)): + if not (precursor_func(r) or (p and precursor_func(p))): continue if p and not (target_func(r) or target_func(p)): continue - suggested_rxns = self._react(r, p, calculators, pd, grand_pd) + suggested_rxns = self._react( + r, p, calculators, filtered_entries, pd, grand_pd + ) for rxn in suggested_rxns: if ( @@ -271,12 +271,25 @@ def _get_rxns( return rxns - def _react(self, reactants, products, calculators, pd=None, grand_pd=None): + def _react( + self, + reactants, + products, + calculators, + filtered_entries=None, + pd=None, + grand_pd=None, + ): """ Generates reactions from a list of reactants, products, and optional calculator(s) """ - _ = (pd, grand_pd, self) # unused arguments in BasicEnumerator class + _ = ( + filtered_entries, + pd, + grand_pd, + self, + ) # unused arguments in BasicEnumerator class forward_rxn = ComputedReaction.balance(reactants, products) backward_rxn = forward_rxn.reverse() @@ -474,7 +487,7 @@ def estimate_max_num_reactions(self, entries: List[ComputedEntry]) -> int: num_combos = comb(len(entries), i) num_total_combos += num_combos_with_open * num_combos - return num_total_combos ** 2 + return num_total_combos**2 def _get_open_combos(self, open_entries): """Get all possible combinations of open entries. For a single entry, diff --git a/src/rxn_network/enumerators/minimize.py b/src/rxn_network/enumerators/minimize.py index 361f5703..df3466d6 100644 --- a/src/rxn_network/enumerators/minimize.py +++ b/src/rxn_network/enumerators/minimize.py @@ -18,7 +18,6 @@ from rxn_network.enumerators.utils import ( apply_calculators, get_computed_rxn, - get_open_computed_rxn, ) @@ -75,7 +74,15 @@ def estimate_max_num_reactions(self, entries: List[ComputedEntry]) -> int: """ return comb(len(entries), 2) * 2 - def _react(self, reactants, products, calculators, pd=None, grand_pd=None): + def _react( + self, + reactants, + products, + calculators, + filtered_entries=None, + pd=None, + grand_pd=None, + ): """React method for MinimizeGibbsEnumerator, which uses the interfacial reaction approach (see _react_interface())""" r = list(reactants) @@ -87,7 +94,12 @@ def _react(self, reactants, products, calculators, pd=None, grand_pd=None): r1 = r[1] return self._react_interface( - r0.composition, r1.composition, pd, grand_pd, calculators=calculators + r0.composition, + r1.composition, + filtered_entries, + pd, + grand_pd, + calculators=calculators, ) @staticmethod @@ -98,7 +110,7 @@ def _get_rxn_iterable(combos, open_combos): return product(combos, [None]) @staticmethod - def _react_interface(r1, r2, pd, grand_pd=None, calculators=None): + def _react_interface(r1, r2, filtered_entries, pd, grand_pd=None, calculators=None): """Simple API for InterfacialReactivity module from pymatgen.""" chempots = None @@ -124,11 +136,7 @@ def _react_interface(r1, r2, pd, grand_pd=None, calculators=None): rxns = [] for _, _, _, rxn, _ in interface.get_kinks(): - if grand_pd: - rxn = get_open_computed_rxn(rxn, pd.all_entries, chempots) - else: - rxn = get_computed_rxn(rxn, pd.all_entries) - + rxn = get_computed_rxn(rxn, filtered_entries, chempots) rxn = apply_calculators(rxn, calculators) rxns.append(rxn) @@ -185,7 +193,15 @@ def __init__( self.chempots = {self.open_elem: self.mu} self._build_grand_pd = True - def _react(self, reactants, products, calculators, pd=None, grand_pd=None): + def _react( + self, + reactants, + products, + calculators, + filtered_entries=None, + pd=None, + grand_pd=None, + ): """Same as the MinimizeGibbsEnumerator react function, but with ability to specify open element and grand potential phase diagram""" r = list(reactants) @@ -206,6 +222,7 @@ def _react(self, reactants, products, calculators, pd=None, grand_pd=None): return self._react_interface( r0.composition, r1.composition, + filtered_entries, pd, grand_pd=grand_pd, calculators=calculators, diff --git a/src/rxn_network/enumerators/utils.py b/src/rxn_network/enumerators/utils.py index e2e19cbf..28710d10 100644 --- a/src/rxn_network/enumerators/utils.py +++ b/src/rxn_network/enumerators/utils.py @@ -5,7 +5,7 @@ from typing import Dict, Iterable, List, Optional, Set, Tuple, Union from pymatgen.analysis.phase_diagram import PhaseDiagram -from pymatgen.core.composition import Composition, Element +from pymatgen.core.composition import Element from pymatgen.entries.computed_entries import ComputedEntry, Entry import rxn_network.costs.calculators as calcs @@ -15,7 +15,7 @@ from rxn_network.reactions.open import OpenComputedReaction -def initialize_entry(formula: str, entry_set: GibbsEntrySet, stabilize: bool = True): +def initialize_entry(formula: str, entry_set: GibbsEntrySet, stabilize: bool = False): """ Acquire a (stabilized) entry by user-specified formula. @@ -28,14 +28,14 @@ def initialize_entry(formula: str, entry_set: GibbsEntrySet, stabilize: bool = T """ try: entry = entry_set.get_min_entry_by_formula(formula) - except IndexError: + except KeyError: entry = entry_set.get_interpolated_entry(formula) warnings.warn( f"Using interpolated entry for {entry.composition.reduced_formula}" ) if stabilize: - entry = entry_set.get_stabilized_entry(entry, tol=1e-1) + entry = entry_set.get_stabilized_entry(entry, tol=1e-3) return entry @@ -157,24 +157,9 @@ def stabilize_entries( return new_entries -def get_min_entry_by_comp(comp: Composition, entries: Iterable[Entry]) -> Entry: - """ - Gets the entry with the lowest energy for a given composition from a set of provided entries. - - Args: - comp: Composition object - entries: Iterable of entries - - Returns: - Entry with the lowest enegy per atom for the given composition - """ - possible_entries = filter( - lambda e: e.composition.reduced_composition == comp.reduced_composition, entries - ) - return sorted(possible_entries, key=lambda e: e.energy_per_atom)[0] - - -def get_computed_rxn(rxn: Reaction, entries: Iterable[Entry]) -> ComputedReaction: +def get_computed_rxn( + rxn: Reaction, entries: GibbsEntrySet, chempots=None +) -> ComputedReaction: """ Provided with a Reaction object and a list of possible entries, this function returns a new ComputedReaction object containing a selection of those entries. @@ -186,32 +171,16 @@ def get_computed_rxn(rxn: Reaction, entries: Iterable[Entry]) -> ComputedReactio Returns: A ComputedReaction object transformed from a normal Reaction object """ - reactant_entries = [get_min_entry_by_comp(r, entries) for r in rxn.reactants] - product_entries = [get_min_entry_by_comp(p, entries) for p in rxn.products] - - rxn = ComputedReaction.balance(reactant_entries, product_entries) - return rxn - - -def get_open_computed_rxn( - rxn: Reaction, entries: Iterable[Entry], chempots: Dict[Element, float] -) -> OpenComputedReaction: - """ - Provided with a Reaction object and a list of possible entries, as well as a - dictionary of chemical potentials of open elements, this function returns a new - OpenComputedReaction object containing a selection of those entries. - - Args: - rxn: Reaction object - entries: Iterable of entries - chempots: Dictionary of chemical potentials of open elements - ` - Returns: - An OpenComputedReaction object transformed from a normal Reaction object - """ - reactant_entries = [get_min_entry_by_comp(r, entries) for r in rxn.reactants] - product_entries = [get_min_entry_by_comp(p, entries) for p in rxn.products] - - rxn = OpenComputedReaction.balance(reactant_entries, product_entries, chempots) + reactant_entries = [ + entries.get_min_entry_by_formula(r.reduced_formula) for r in rxn.reactants + ] + product_entries = [ + entries.get_min_entry_by_formula(p.reduced_formula) for p in rxn.products + ] + + if chempots: + rxn = OpenComputedReaction.balance(reactant_entries, product_entries, chempots) + else: + rxn = ComputedReaction.balance(reactant_entries, product_entries) return rxn diff --git a/src/rxn_network/pathways/pathway_set.py b/src/rxn_network/pathways/pathway_set.py index 7acc8e0a..99426931 100644 --- a/src/rxn_network/pathways/pathway_set.py +++ b/src/rxn_network/pathways/pathway_set.py @@ -98,7 +98,7 @@ def from_paths( return cls( reaction_set=reaction_set, indices=indices, - coefficients=coefficients, + coefficients=coefficients, # type: ignore costs=costs, ) diff --git a/src/rxn_network/reactions/plotting.py b/src/rxn_network/reactions/plotting.py index 7e910de9..0fead4d0 100644 --- a/src/rxn_network/reactions/plotting.py +++ b/src/rxn_network/reactions/plotting.py @@ -21,8 +21,8 @@ def plot_energy_distance_scatter(df: DataFrame) -> px.scatter: fig = px.scatter( df, - x="energy", - y="chempot_distance", + x="chempot_distance", + y="c_score", hover_name="rxn", labels={ "energy": r"$\Delta G_{\mathrm{rxn}} ~ \mathrm{\left(" diff --git a/src/rxn_network/thermo/__init__.py b/src/rxn_network/thermo/__init__.py index f39e099b..fa366d50 100644 --- a/src/rxn_network/thermo/__init__.py +++ b/src/rxn_network/thermo/__init__.py @@ -2,5 +2,3 @@ Thermodynamic functions for the reaction network package, including chemical potential diagrams. """ - -from rxn_network.thermo.chempot_diagram import ChemicalPotentialDiagram diff --git a/src/rxn_network/thermo/chempot_diagram.py b/src/rxn_network/thermo/chempot_diagram.py index 17efe9e0..f0df0ea2 100644 --- a/src/rxn_network/thermo/chempot_diagram.py +++ b/src/rxn_network/thermo/chempot_diagram.py @@ -2,20 +2,23 @@ This module implements added features to the ChemicalPotentialDiagram class from pymatgen. """ -import warnings + from functools import cached_property -from typing import Dict, List, Optional +from typing import Dict, List, Optional, Tuple import numpy as np from pymatgen.analysis.chempot_diagram import ChemicalPotentialDiagram as ChempotDiagram -from pymatgen.analysis.phase_diagram import PDEntry +from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram from pymatgen.core.composition import Element -from scipy.spatial import KDTree +from scipy.spatial import HalfspaceIntersection, KDTree + +from rxn_network.entries.entry_set import GibbsEntrySet class ChemicalPotentialDiagram(ChempotDiagram): - """This class is an extension of the ChemicalPotentialDiagram class from pymatgen. - Several features have been added to the original class for the purpose of + """ + This class is an extension of the ChemicalPotentialDiagram class from pymatgen. + Several features have been added to the original class for the purpose of efficiently calculating the shortest distance between two chemical potential domains. """ @@ -35,7 +38,7 @@ def __init__( of with 2+ elements limits: Bounds of elemental chemical potentials (min, max), which are used to construct the border hyperplanes used in the - HalfSpaceIntersection algorithm; these constrain the space over which the + HalfspaceIntersection algorithm; these constrain the space over which the domains are calculated and also determine the size of the plotted diagram. Any elemental limits not specified are covered in the default_min_limit argument @@ -46,13 +49,13 @@ def __init__( super().__init__( entries=entries, limits=limits, default_min_limit=default_min_limit ) + self._hs_int = self._get_halfspace_intersection() - @cached_property - def domains(self) -> Dict[str, np.ndarray]: - """ - Mapping of formulas to array of domain boundary points. Cached for speed. - """ - return self._get_domains() + num_hyperplanes = len(self._hyperplanes) + num_border_hyperplanes = len(self._border_hyperplanes) + self._border_hyperplane_indices = list( + range(num_hyperplanes, num_hyperplanes + num_border_hyperplanes) + ) def shortest_domain_distance(self, f1: str, f2: str) -> float: """ @@ -64,34 +67,131 @@ def shortest_domain_distance(self, f1: str, f2: str) -> float: Shortest distance between domain boundaries in the full (hyper)dimensional space, calculated using KDTree. """ - pts1 = self.domains[f1] - pts2 = self.domains[f2] + + if f1 in self.domains: + pts1 = self.domains[f1] + elif f1 in self.metastable_domains: + pts1 = self.metastable_domains[f1] + else: + raise ValueError(f"Formula {f1} not in domains!") + + if f2 in self.domains: + pts2 = self.domains[f2] + elif f2 in self.metastable_domains: + pts2 = self.metastable_domains[f2] + else: + raise ValueError(f"Formula {f2} not in domains!") tree = KDTree(pts1) return min(tree.query(pts2)[0]) - def shortest_elemental_domain_distances(self, f1: str, f2: str) -> float: + def add_entry(self, entry): """ + Adds an entry to existing chemical potential diagram. Uses scipy's + add_halfspaces() method to save some time/memory. + Args: - f1: chemical formula (1) - f2: chemical formula (2) + entry: Returns: - Shortest distance between domain boundaries along one elemental axis. + None + """ - warnings.warn( - "Use with caution; this function may not result in anything meaningful!" + if entry in self.entries: + return + if not set(entry.composition.elements).issubset(self.elements): + raise ValueError("New entry is not within the same chemical system!") + + hyperplane = self._get_hyperplane(entry) + self._hyperplanes = np.vstack([self._hyperplanes, hyperplane]) + self._hyperplane_entries.append(entry) + self._hs_int.add_halfspaces([hyperplane], restart=True) + self._entry_dict[entry.composition.reduced_formula] = entry + self.entries.append(entry) + + try: + del self.domains # clear cache + except AttributeError: + pass + + def _get_halfspace_intersection(self): + hs_hyperplanes = np.vstack([self._hyperplanes, self._border_hyperplanes]) + interior_point = np.min(self.lims, axis=1) + 1e-1 + return HalfspaceIntersection(hs_hyperplanes, interior_point, incremental=True) + + def _get_domains(self) -> Dict[str, np.ndarray]: + """Returns a dictionary of domains as {formula: np.ndarray}""" + domains = {entry.composition.reduced_formula: [] for entry in self._hyperplane_entries} # type: ignore + entries = self._hyperplane_entries + + for intersection, facet in zip( + self.hs_int.intersections, self.hs_int.dual_facets + ): + for v in facet: + if v not in self._border_hyperplane_indices: + if v > max(self._border_hyperplane_indices): + v = v - len(self._border_hyperplane_indices) + this_entry = entries[v] + formula = this_entry.composition.reduced_formula + domains[formula].append(intersection) + + return {k: np.array(v) for k, v in domains.items() if v} + + def _get_hyperplanes_and_entries(self) -> Tuple[np.ndarray, List[PDEntry]]: + """Returns both the array of hyperplanes, as well as a list of the minimum + entries""" + data = np.array([self._get_hyperplane(e) for e in self._min_entries]) + vec = [self.el_refs[el].energy_per_atom for el in self.elements] + [1] + form_e = -np.dot(data, vec) + + inds = np.where(form_e < -PhaseDiagram.formation_energy_tol)[0].tolist() + + inds.extend([self._min_entries.index(el) for el in self.el_refs.values()]) + + hyperplanes = data[inds] + hyperplane_entries = [self._min_entries[i] for i in inds] + + return hyperplanes, hyperplane_entries + + def _get_hyperplane(self, entry): + data = np.array( + [entry.composition.get_atomic_fraction(el) for el in self.elements] + + [-entry.energy_per_atom] ) + return data + + @property + def hs_int(self): + """Returns the scipy HalfSpaceIntersection object""" + return self._hs_int + + @cached_property + def domains(self) -> Dict[str, np.ndarray]: + """ + Mapping of formulas to array of domain boundary points. Cached for speed. + """ + return self._get_domains() + + @cached_property + def metastable_domains(self) -> Dict[str, np.ndarray]: + """Gets a dictionary of the chemical potential domains for metastable chemical + formulas. This corresponds to the domains of the relevant phases if they were + just barely stable""" + return self._get_metastable_domains() + + def _get_metastable_domains(self): + e_set = GibbsEntrySet(self.entries) + e_dict = e_set.min_entries_by_formula + stable_formulas = list(self.domains.keys()) - pts1 = self.domains[f1] - pts2 = self.domains[f2] - pts1 = pts1[~np.isclose(pts1, self.default_min_limit).any(axis=1)] - pts2 = pts2[~np.isclose(pts2, self.default_min_limit).any(axis=1)] - num_elems = pts1.shape[1] + metastable_entries = [e for f, e in e_dict.items() if f not in stable_formulas] + metastable_domains = {} - mesh = np.meshgrid(pts1, pts2) - diff = abs(mesh[0] - mesh[1]) - diff = diff.reshape(-1, num_elems) + for e in metastable_entries: + formula = e.composition.reduced_formula + new_entry = e_set.get_stabilized_entry(e) + cpd = ChemicalPotentialDiagram(list(e_dict.values()) + [new_entry]) + metastable_domains[formula] = cpd.domains[formula] - return diff.min(axis=0) + return metastable_domains diff --git a/tests/costs/test_calculators.py b/tests/costs/test_calculators.py index 1efbc082..5493c5c3 100644 --- a/tests/costs/test_calculators.py +++ b/tests/costs/test_calculators.py @@ -27,12 +27,6 @@ } -@pytest.fixture(params=["Cl_Mn_Na_O_Y_entries.json.gz"]) -def entries(request): - entries = loadfn(TEST_FILES_PATH / request.param) - return GibbsEntrySet(entries) - - @pytest.fixture( params=[ [["Y2O3", "Mn2O3"], ["YMnO3"]],