A Python Multiscale Thermochemistry Toolbox (pMuTT) for thermochemical and kinetic parameter estimation

Lym, Jonathan; Wittreich, Gerhard R.; Vlachos, Dionisios G.

doi:10.1016/j.cpc.2019.106864

A Python Multiscale Thermochemistry Toolbox (pMuTT) for thermochemical and kinetic parameter estimation

Journal Article · 17 August 2019 · Computer Physics Communications

DOI:https://doi.org/10.1016/j.cpc.2019.106864· OSTI ID:1799392

^[1]; ^[2]; Vlachos, Dionisios G. ^[2]

Univ. of Delaware, Newark, DE (United States); OSTI
Univ. of Delaware, Newark, DE (United States)

Estimating the thermochemical properties of systems is important in many fields such as material science and catalysis. The Python multiscale thermochemistry toolbox (pMuTT) is a Python software library developed to streamline the conversion of ab-initio data to thermochemical properties using statistical mechanics, to perform thermodynamic analysis, and to create input files for kinetic modeling software. Its open-source implementation in Python leverages existing scientific codes, encourages users to write scripts for their needs, and allows the code to be expanded easily. The core classes developed include a statistical mechanical model in which energy modes can be included or excluded to suit the application, empirical models for rapid thermodynamic property estimation, and a reaction model to calculate kinetic parameters or changes in thermodynamic properties. In addition, pMuTT supports other features, such as Brønsted–Evans–Polanyi (BEP) relationships, coverage effects, and ab-initio phase diagrams.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Delaware, Newark, DE (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE), Energy Efficiency Office. Advanced Manufacturing Office

Grant/Contract Number:: EE0007888

OSTI ID:: 1799392

Alternate ID(s):: OSTI ID: 1575937

Journal Information:: Computer Physics Communications, Journal Name: Computer Physics Communications Vol. 247; ISSN 0010-4655

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (34)

Scaling Relationships for Adsorption Energies on Transition Metal Oxide, Sulfide, and Nitride Surfaces Fernández, Eva M.; Moses, Poul G.; Toftelund, Anja Angewandte Chemie International Edition, Vol. 47, Issue 25 https://doi.org/10.1002/anie.200705739	journal	June 2008
DFT-Based Coverage-Dependent Model of Pt-Catalyzed NO Oxidation Getman, Rachel B.; Schneider, William F. ChemCatChem, Vol. 2, Issue 11 https://doi.org/10.1002/cctc.201000146	journal	August 2010
Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory Grimme, Stefan Chemistry - A European Journal, Vol. 18, Issue 32 https://doi.org/10.1002/chem.201200497	journal	July 2012
Understanding Trends in Catalytic Activity: The Effect of Adsorbate–Adsorbate Interactions for CO Oxidation Over Transition Metals Grabow, Lars C.; Hvolbæk, Britt; Nørskov, Jens K. Topics in Catalysis, Vol. 53, Issue 5-6 https://doi.org/10.1007/s11244-010-9455-2	journal	February 2010
The PANDAT software package and its applications Chen, S. -L.; Daniel, S.; Zhang, F. Calphad, Vol. 26, Issue 2 https://doi.org/10.1016/S0364-5916(02)00034-2	journal	June 2002
Thermo-Calc & DICTRA, computational tools for materials science Andersson, J-O; Helander, Thomas; Höglund, Lars Calphad, Vol. 26, Issue 2 https://doi.org/10.1016/S0364-5916(02)00037-8	journal	June 2002
Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis Ong, Shyue Ping; Richards, William Davidson; Jain, Anubhav Computational Materials Science, Vol. 68 https://doi.org/10.1016/j.commatsci.2012.10.028	journal	February 2013
Language-oriented rule-based reaction network generation and analysis: Description of RING Rangarajan, Srinivas; Bhan, Aditya; Daoutidis, Prodromos Computers & Chemical Engineering, Vol. 45 https://doi.org/10.1016/j.compchemeng.2012.06.008	journal	October 2012
Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms Gao, Connie W.; Allen, Joshua W.; Green, William H. Computer Physics Communications, Vol. 203 https://doi.org/10.1016/j.cpc.2016.02.013	journal	June 2016
Exploring the limits: A low-pressure, low-temperature Haber–Bosch process Vojvodic, Aleksandra; Medford, Andrew James; Studt, Felix Chemical Physics Letters, Vol. 598 https://doi.org/10.1016/j.cplett.2014.03.003	journal	April 2014
Effect of multiscale model uncertainty on identification of optimal catalyst properties Ulissi, Z.; Prasad, V.; Vlachos, D. G. Journal of Catalysis, Vol. 281, Issue 2 https://doi.org/10.1016/j.jcat.2011.05.019	journal	July 2011
Scaling Relations for Adsorption Energies on Doped Molybdenum Phosphide Surfaces Fields, Meredith; Tsai, Charlie; Chen, Leanne D. ACS Catalysis, Vol. 7, Issue 4 https://doi.org/10.1021/acscatal.6b03403	journal	March 2017
How to Conceptualize Catalytic Cycles? The Energetic Span Model Kozuch, Sebastian; Shaik, Sason Accounts of Chemical Research, Vol. 44, Issue 2 https://doi.org/10.1021/ar1000956	journal	February 2011
A Theoretical and Computational Analysis of Linear Free Energy Relations for the Estimation of Activation Energies Sutton, Jonathan E.; Vlachos, Dionisios G. ACS Catalysis, Vol. 2, Issue 8 https://doi.org/10.1021/cs3003269	journal	July 2012
Trends in the Hydrogen Evolution Activity of Metal Carbide Catalysts Michalsky, Ronald; Zhang, Yin-Jia; Peterson, Andrew A. ACS Catalysis, Vol. 4, Issue 5 https://doi.org/10.1021/cs500056u	journal	March 2014
Coverage-Induced Conformational Effects on Activity and Selectivity: Hydrogenation and Decarbonylation of Furfural on Pd(111) Wang, Shengguang; Vorotnikov, Vassili; Vlachos, Dionisios G. ACS Catalysis, Vol. 5, Issue 1 https://doi.org/10.1021/cs5015145	journal	November 2014
Microkinetic Modeling and Reduced Rate Expressions of Ethylene Hydrogenation and Ethane Hydrogenolysis on Platinum Salciccioli, M.; Chen, Y.; Vlachos, D. G. Industrial & Engineering Chemistry Research, Vol. 50, Issue 1 https://doi.org/10.1021/ie100364a	journal	January 2011
Development of transition-state theory Laidler, Keith J.; King, M. Christine The Journal of Physical Chemistry, Vol. 87, Issue 15 https://doi.org/10.1021/j100238a002	journal	July 1983
A Method for Evaluating and Correlating Thermodynamic Da ta Shomate, C. Howard The Journal of Physical Chemistry, Vol. 58, Issue 4 https://doi.org/10.1021/j150514a018	journal	April 1954
A Linear Scaling Relation for CO Oxidation on CeO ₂ -Supported Pd Liu, Jin-Xun; Su, Yaqiong; Filot, Ivo A. W. Journal of the American Chemical Society, Vol. 140, Issue 13 https://doi.org/10.1021/jacs.7b13624	journal	March 2018
Thermodynamic Properties and Kinetic Parameters for Cyclic Ether Formation from Hydroperoxyalkyl Radicals Wijaya, Catherina D.; Sumathi, Raman; Green, William H. The Journal of Physical Chemistry A, Vol. 107, Issue 24 https://doi.org/10.1021/jp027471n	journal	June 2003
Thermodynamic Consistency in Microkinetic Development of Surface Reaction Mechanisms Mhadeshwar, A. B.; Wang, H.; Vlachos, D. G. The Journal of Physical Chemistry B, Vol. 107, Issue 46 https://doi.org/10.1021/jp034954y	journal	November 2003
Microkinetic Modeling for Water-Promoted CO Oxidation, Water−Gas Shift, and Preferential Oxidation of CO on Pt Mhadeshwar, A. B.; Vlachos, D. G. The Journal of Physical Chemistry B, Vol. 108, Issue 39 https://doi.org/10.1021/jp048698g	journal	September 2004
Density Functional Theory (DFT) Study of Enthalpy of Formation. 1. Consistency of DFT Energies and Atom Equivalents for Converting DFT Energies into Enthalpies of Formation Mole, Susan J.; Zhou, Xuefeng; Liu, Ruifeng The Journal of Physical Chemistry, Vol. 100, Issue 35 https://doi.org/10.1021/jp960801h	journal	January 1996
Heats of Formation from G2, G2(MP2), and G2(MP2,SVP) Total Energies Nicolaides, Athanassios; Rauk, Arvi; Glukhovtsev, Mikhail N. The Journal of Physical Chemistry, Vol. 100, Issue 44 https://doi.org/10.1021/jp9613753	journal	January 1996
Introducing structural sensitivity into adsorption–energy scaling relations by means of coordination numbers Calle-Vallejo, Federico; Loffreda, David; Koper, Marc T. M. Nature Chemistry, Vol. 7, Issue 5 https://doi.org/10.1038/nchem.2226	journal	April 2015
Patched bimetallic surfaces are active catalysts for ammonia decomposition Guo, Wei; Vlachos, Dionisios G. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9619	journal	October 2015
Using scaling relations to understand trends in the catalytic activity of transition metals Jones, G.; Bligaard, T.; Abild-Pedersen, F. Journal of Physics: Condensed Matter, Vol. 20, Issue 6 https://doi.org/10.1088/0953-8984/20/6/064239	journal	January 2008
Correlations in coverage-dependent atomic adsorption energies on Pd(111) Kitchin, John R. Physical Review B, Vol. 79, Issue 20 https://doi.org/10.1103/PhysRevB.79.205412	journal	May 2009
Scaling Properties of Adsorption Energies for Hydrogen-Containing Molecules on Transition-Metal Surfaces Abild-Pedersen, F.; Greeley, J.; Studt, F. Physical Review Letters, Vol. 99, Issue 1 https://doi.org/10.1103/PhysRevLett.99.016105	journal	July 2007
Matplotlib: A 2D Graphics Environment Hunter, John D. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.55	journal	January 2007
Python for Scientific Computing Oliphant, Travis E. Computing in Science & Engineering, Vol. 9, Issue 3 https://doi.org/10.1109/MCSE.2007.58	journal	January 2007
Python for Scientists and Engineers Millman, K. Jarrod; Aivazis, Michael Computing in Science & Engineering, Vol. 13, Issue 2 https://doi.org/10.1109/MCSE.2011.36	journal	March 2011
The NumPy Array: A Structure for Efficient Numerical Computation van der Walt, Stéfan; Colbert, S. Chris; Varoquaux, Gaël Computing in Science & Engineering, Vol. 13, Issue 2 https://doi.org/10.1109/MCSE.2011.37	journal	March 2011

Similar Records

Microkinetic modeling of aqueous phase biomass conversion: Application to ethylene glycol reforming

Journal Article · 2019 · Chemical Engineering Science · OSTI ID:1566433

Python Group Additivity (pGrAdd) software for estimating species thermochemical properties

Journal Article · 2022 · Computer Physics Communications · OSTI ID:1977048

Uncertainty Quantification and Error Propagation in the Enthalpy and Entropy of Surface Reactions Arising from a Single DFT Functional

Journal Article · 2021 · Journal of Physical Chemistry. C · OSTI ID:2212398

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
catalysis
microkinetics
rate constant
statistical mechanics
thermochemistry

A Python Multiscale Thermochemistry Toolbox (pMuTT) for thermochemical and kinetic parameter estimation Lym, Jonathan https://doi.org/10.17632/b7f7d28ynd The current record is supplemented by this dataset	dataset	January 2019
A Python Multiscale Thermochemistry Toolbox (pMuTT) for thermochemical and kinetic parameter estimation Lym, Jonathan https://doi.org/10.17632/b7f7d28ynd.1 The current record is supplemented by this dataset	dataset	January 2019

A Python Multiscale Thermochemistry Toolbox (pMuTT) for thermochemical and kinetic parameter estimation

Citation Formats

References (34)

Linked Research (2)

Similar Records

Related Subjects