RASPA3: A Monte Carlo code for computing adsorption and diffusion in nanoporous materials and thermodynamics properties of fluids

Ran, Y. A.; Sharma, S.; Balestra, S. R. G.; Li, Z.; Calero, S.; Vlugt, T. J. H.; Snurr, R. Q.; Dubbeldam, D.

doi:10.1063/5.0226249

RASPA3: A Monte Carlo code for computing adsorption and diffusion in nanoporous materials and thermodynamics properties of fluids

Journal Article · Mon Sep 16 04:00:00 EDT 2024 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/5.0226249· OSTI ID:3010668

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University of Amsterdam (The Netherlands)
Delft University of Technology (The Netherlands)
Universidad Pablo de Olavide, Sevilla (Spain); Universidad de Sevilla (Spain)
Northwestern University, Evanston, IL (United States)
Eindhoven University of Technology (The Netherlands)

We present RASPA3, a molecular simulation code for computing adsorption and diffusion in nanoporous materials and thermodynamic and transport properties of fluids. It implements force field based classical Monte Carlo/molecular dynamics in various ensembles. In this article, we introduce the new additions and changes compared to RASPA2. RASPA3 is rewritten from the ground up in C++23 with speed and code readability in mind. Transition-matrix Monte Carlo is added to compute the density of states and free energies. The Monte Carlo code for rigid molecules is based on quaternions, and the atomic positions needed in the energy evaluation are recreated from the center of mass position and quaternion orientation. The expanded ensemble methodology for fractional molecules, with a scaling parameter λ between 0 and 1, now also keeps track of analytic expressions of dU/dλ, allowing independent verification of the chemical potential using thermodynamic integration. The source code is freely available under the MIT license on GitHub. Using this code, we compare four Monte Carlo (MC) insertion/deletion techniques: unbiased Metropolis MC, Configurational-Bias Monte Carlo (CBMC), Continuous Fractional Component MC (CFCMC), and CB/CFCMC. We compare particle distribution shapes, acceptance ratios, accuracy and speed of isotherm computation, enthalpies of adsorption, and chemical potentials, over a wide range of loadings and systems, for the grand canonical ensemble and for the Gibbs ensemble.

View Accepted Manuscript (DOE)

Research Organization:: University of Minnesota, Minneapolis, MN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB)

Grant/Contract Number:: SC0023454

OSTI ID:: 3010668

Alternate ID(s):: OSTI ID: 2510793

Journal Information:: Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Journal Issue: 11 Vol. 161; ISSN 1089-7690; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

References (73)

New‐Generation Anion‐Pillared Metal–Organic Frameworks with Customized Cages for Highly Efficient CO₂ Capture Hu, Yongqi; Jiang, Yunjia; Li, Jiahao Advanced Functional Materials, Vol. 33, Issue 14 https://doi.org/10.1002/adfm.202213915	journal	January 2023
Three‐Dimensional Triptycene‐Functionalized Covalent Organic Frameworks with hea Net for Hydrogen Adsorption Yu, Chengyang; Li, Hui; Wang, Yujie Angewandte Chemie International Edition, Vol. 61, Issue 13 https://doi.org/10.1002/anie.202117101	journal	February 2022
Improvement in molecule exchange efficiency in Gibbs ensemble Monte Carlo: Development and implementation of the continuous fractional component move Shi, Wei; Maginn, Edward J. Journal of Computational Chemistry, Vol. 29, Issue 15 https://doi.org/10.1002/jcc.20977	journal	November 2008
Cassandra: An open source Monte Carlo package for molecular simulation Shah, Jindal K.; Marin-Rimoldi, Eliseo; Mullen, Ryan Gotchy Journal of Computational Chemistry, Vol. 38, Issue 19 https://doi.org/10.1002/jcc.24807	journal	April 2017
Modeling of multi-scale transport phenomena in shale gas production — A critical review Wang, Hui; Chen, Li; Qu, Zhiguo Applied Energy, Vol. 262 https://doi.org/10.1016/j.apenergy.2020.114575	journal	March 2020
An ethane-trapping MOF PCN-250 for highly selective adsorption of ethane over ethylene Chen, Yongwei; Qiao, Zhiwei; Wu, Houxiao Chemical Engineering Science, Vol. 175 https://doi.org/10.1016/j.ces.2017.09.032	journal	January 2018
Measure-preserving integrators for molecular dynamics in the isothermal–isobaric ensemble derived from the Liouville operator Yu, Tang-Qing; Alejandre, José; López-Rendón, Roberto Chemical Physics, Vol. 370, Issue 1-3 https://doi.org/10.1016/j.chemphys.2010.02.014	journal	May 2010
Effects of thermostats/barostats on physical properties of liquids by molecular dynamics simulations Ke, Qia; Gong, Xiaoting; Liao, Shouwei Journal of Molecular Liquids, Vol. 365 https://doi.org/10.1016/j.molliq.2022.120116	journal	November 2022
GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids Nejahi, Younes; Soroush Barhaghi, Mohammad; Mick, Jason SoftwareX, Vol. 9 https://doi.org/10.1016/j.softx.2018.11.005	journal	January 2019
Adsorption — from theory to practice Dąbrowski, A. Advances in Colloid and Interface Science, Vol. 93, Issue 1-3 https://doi.org/10.1016/s0001-8686(00)00082-8	journal	October 2001
Topologically Guided, Automated Construction of Metal–Organic Frameworks and Their Evaluation for Energy-Related Applications Colón, Yamil J.; Gómez-Gualdrón, Diego A.; Snurr, Randall Q. Crystal Growth & Design, Vol. 17, Issue 11 https://doi.org/10.1021/acs.cgd.7b00848	journal	September 2017
Performance-Based Screening of Porous Materials for Carbon Capture Farmahini, Amir H.; Krishnamurthy, Shreenath; Friedrich, Daniel Chemical Reviews, Vol. 121, Issue 17 https://doi.org/10.1021/acs.chemrev.0c01266	journal	August 2021
Advances, Updates, and Analytics for the Computation-Ready, Experimental Metal–Organic Framework Database: CoRE MOF 2019 Chung, Yongchul G.; Haldoupis, Emmanuel; Bucior, Benjamin J. Journal of Chemical & Engineering Data, Vol. 64, Issue 12 https://doi.org/10.1021/acs.jced.9b00835	journal	November 2019
Brick-CFCMC: Open Source Software for Monte Carlo Simulations of Phase and Reaction Equilibria Using the Continuous Fractional Component Method Hens, Remco; Rahbari, Ahmadreza; Caro-Ortiz, Sebastián Journal of Chemical Information and Modeling, Vol. 60, Issue 6 https://doi.org/10.1021/acs.jcim.0c00334	journal	April 2020
In Silico Evolution of High-Performing Metal Organic Frameworks for Methane Adsorption Beauregard, Nicole; Pardakhti, Maryam; Srivastava, Ranjan Journal of Chemical Information and Modeling, Vol. 61, Issue 7 https://doi.org/10.1021/acs.jcim.0c01479	journal	July 2021
New Features of the Open Source Monte Carlo Software Brick-CFCMC: Thermodynamic Integration and Hybrid Trial Moves Polat, H. Mert; Salehi, Hirad S.; Hens, Remco Journal of Chemical Information and Modeling, Vol. 61, Issue 8 https://doi.org/10.1021/acs.jcim.1c00652	journal	August 2021
Interpretable Graph Transformer Network for Predicting Adsorption Isotherms of Metal–Organic Frameworks Chen, Pin; Jiao, Rui; Liu, Jinyu Journal of Chemical Information and Modeling, Vol. 62, Issue 22 https://doi.org/10.1021/acs.jcim.2c00876	journal	November 2022
Direct Free Energy Calculation in the Continuous Fractional Component Gibbs Ensemble Poursaeidesfahani, Ali; Torres-Knoop, Ariana; Dubbeldam, David Journal of Chemical Theory and Computation, Vol. 12, Issue 4 https://doi.org/10.1021/acs.jctc.5b01230	journal	March 2016
A Universal Standard Archive File for Adsorption Data Evans, Jack D.; Bon, Volodymyr; Senkovska, Irena Langmuir, Vol. 37, Issue 14 https://doi.org/10.1021/acs.langmuir.1c00122	journal	April 2021
Reaction Ensemble Monte Carlo Simulation of Complex Molecular Systems Rosch, Thomas W.; Maginn, Edward J. Journal of Chemical Theory and Computation, Vol. 7, Issue 2 https://doi.org/10.1021/ct100615j	journal	December 2010
Monte Carlo Simulation Methods for Computing Liquid–Vapor Saturation Properties of Model Systems Rane, Kaustubh S.; Murali, Sabharish; Errington, Jeffrey R. Journal of Chemical Theory and Computation, Vol. 9, Issue 6 https://doi.org/10.1021/ct400074p	journal	May 2013
A Comparison of Advanced Monte Carlo Methods for Open Systems: CFCMC vs CBMC Torres-Knoop, Ariana; Balaji, Sayee Prasaad; Vlugt, Thijs J. H. Journal of Chemical Theory and Computation, Vol. 10, Issue 3 https://doi.org/10.1021/ct4009766	journal	February 2014
Continuous Fractional Component Monte Carlo: An Adaptive Biasing Method for Open System Atomistic Simulations Shi, Wei; Maginn, Edward J. Journal of Chemical Theory and Computation, Vol. 3, Issue 4 https://doi.org/10.1021/ct7000039	journal	May 2007
Effect of the Integration Method on the Accuracy and Computational Efficiency of Free Energy Calculations Using Thermodynamic Integration Jorge, Miguel; Garrido, Nuno M.; Queimada, António J. Journal of Chemical Theory and Computation, Vol. 6, Issue 4 https://doi.org/10.1021/ct900661c	journal	February 2010
Understanding Inflections and Steps in Carbon Dioxide Adsorption Isotherms in Metal-Organic Frameworks Walton, Krista S.; Millward, Andrew R.; Dubbeldam, David Journal of the American Chemical Society, Vol. 130, Issue 2, p. 406-407 https://doi.org/10.1021/ja076595g	journal	January 2008
Separation and Molecular-Level Segregation of Complex Alkane Mixtures in Metal−Organic Frameworks Dubbeldam, David; Galvin, Casey J.; Walton, Krista S. Journal of the American Chemical Society, Vol. 130, Issue 33 https://doi.org/10.1021/ja804039c	journal	July 2008
Adsorption of Linear and Branched Alkanes in the Zeolite Silicalite-1 Vlugt, T. J. H.; Zhu, W.; Kapteijn, F. Journal of the American Chemical Society, Vol. 120, Issue 22 https://doi.org/10.1021/ja974336t	journal	June 1998
Application of Consistency Criteria To Calculate BET Areas of Micro- And Mesoporous Metal–Organic Frameworks Gómez-Gualdrón, Diego A.; Moghadam, Peyman Z.; Hupp, Joseph T. Journal of the American Chemical Society, Vol. 138, Issue 1 https://doi.org/10.1021/jacs.5b10266	journal	December 2015
Transferable Potentials for Phase Equilibria. 4. United-Atom Description of Linear and Branched Alkenes and Alkylbenzenes Wick, Collin D.; Martin, Marcus G.; Siepmann, J. Ilja The Journal of Physical Chemistry B, Vol. 104, Issue 33 https://doi.org/10.1021/jp001044x	journal	August 2000
Transferable Potentials for Phase Equilibria. 6. United-Atom Description for Ethers, Glycols, Ketones, and Aldehydes Stubbs, John M.; Potoff, Jeffrey J.; Siepmann, J. Ilja The Journal of Physical Chemistry B, Vol. 108, Issue 45 https://doi.org/10.1021/jp049459w	journal	November 2004
Transferable Potentials for Phase Equilibria. 7. Primary, Secondary, and Tertiary Amines, Nitroalkanes and Nitrobenzene, Nitriles, Amides, Pyridine, and Pyrimidine Wick, Collin D.; Stubbs, John M.; Rai, Neeraj The Journal of Physical Chemistry B, Vol. 109, Issue 40 https://doi.org/10.1021/jp0504827	journal	October 2005
Self-Diffusion and Transport Diffusion of Light Gases in Metal-Organic Framework Materials Assessed Using Molecular Dynamics Simulations Skoulidas, Anastasios I.; Sholl, David S. The Journal of Physical Chemistry B, Vol. 109, Issue 33 https://doi.org/10.1021/jp051771y	journal	August 2005
Transferable Potentials for Phase Equilibria. 9. Explicit Hydrogen Description of Benzene and Five-Membered and Six-Membered Heterocyclic Aromatic Compounds Rai, Neeraj; Siepmann, J. Ilja The Journal of Physical Chemistry B, Vol. 111, Issue 36 https://doi.org/10.1021/jp073586l	journal	September 2007
Use of the Grand Canonical Transition-Matrix Monte Carlo Method to Model Gas Adsorption in Porous Materials Siderius, Daniel W.; Shen, Vincent K. The Journal of Physical Chemistry C, Vol. 117, Issue 11 https://doi.org/10.1021/jp400480q	journal	March 2013
Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes Martin, Marcus G.; Siepmann, J. Ilja https://doi.org/10.1021/jp972543+		March 1998
Molecular Simulations of Adsorption Isotherms for Linear and Branched Alkanes and Their Mixtures in Silicalite Vlugt, T. J. H.; Krishna, R.; Smit, B. The Journal of Physical Chemistry B, Vol. 103, Issue 7 https://doi.org/10.1021/jp982736c	journal	February 1999
Novel Configurational-Bias Monte Carlo Method for Branched Molecules. Transferable Potentials for Phase Equilibria. 2. United-Atom Description of Branched Alkanes Martin, Marcus G.; Siepmann, J. Ilja The Journal of Physical Chemistry B, Vol. 103, Issue 21 https://doi.org/10.1021/jp984742e	journal	May 1999
Functional materials discovery using energy–structure–function maps Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz Nature, Vol. 543, Issue 7647 https://doi.org/10.1038/nature21419	journal	March 2017
Carbon dioxide capture and conversion by an acid-base resistant metal-organic framework Liang, Linfeng; Liu, Caiping; Jiang, Feilong Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01166-3	journal	November 2017
Exceptional hydrogen storage achieved by screening nearly half a million metal-organic frameworks Ahmed, Alauddin; Seth, Saona; Purewal, Justin Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09365-w	journal	April 2019
Understanding the diversity of the metal-organic framework ecosystem Moosavi, Seyed Mohamad; Nandy, Aditya; Jablonka, Kevin Maik Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-17755-8	journal	August 2020
Robust ultrathin nanoporous MOF membrane with intra-crystalline defects for fast water transport Wang, Xueling; Lyu, Qiang; Tong, Tiezheng Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-021-27873-6	journal	January 2022
Inverse design of nanoporous crystalline reticular materials with deep generative models Yao, Zhenpeng; Sánchez-Lengeling, Benjamín; Bobbitt, N. Scott Nature Machine Intelligence, Vol. 3, Issue 1 https://doi.org/10.1038/s42256-020-00271-1	journal	January 2021
A multi-modal pre-training transformer for universal transfer learning in metal–organic frameworks Kang, Yeonghun; Park, Hyunsoo; Smit, Berend Nature Machine Intelligence, Vol. 5, Issue 3 https://doi.org/10.1038/s42256-023-00628-2	journal	March 2023
Energy-based descriptors to rapidly predict hydrogen storage in metal–organic frameworks Bucior, Benjamin J.; Bobbitt, N. Scott; Islamoglu, Timur Molecular Systems Design & Engineering, Vol. 4, Issue 1 https://doi.org/10.1039/c8me00050f	journal	January 2019
Symplectic quaternion scheme for biophysical molecular dynamics Miller, T. F.; Eleftheriou, M.; Pattnaik, P. The Journal of Chemical Physics, Vol. 116, Issue 20 https://doi.org/10.1063/1.1473654	journal	May 2002
Equation of State Calculations by Fast Computing Machines Metropolis, Nicholas; Rosenbluth, Arianna W.; Rosenbluth, Marshall N. The Journal of Chemical Physics, Vol. 21, Issue 6 https://doi.org/10.1063/1.1699114	journal	June 1953
Asymptotic Behavior of the Radial Distribution Function Lebowitz, J. L.; Percus, J. K. Journal of Mathematical Physics, Vol. 4, Issue 2 https://doi.org/10.1063/1.1703948	journal	February 1963
Monte Carlo Calculation of the Average Extension of Molecular Chains Rosenbluth, Marshall N.; Rosenbluth, Arianna W. The Journal of Chemical Physics, Vol. 23, Issue 2 https://doi.org/10.1063/1.1741967	journal	February 1955
New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles Lyubartsev, A. P.; Martsinovski, A. A.; Shevkunov, S. V. The Journal of Chemical Physics, Vol. 96, Issue 3 https://doi.org/10.1063/1.462133	journal	February 1992
Monte Carlo simulation of the chemical potential of polymers in an expanded ensemble Escobedo, Fernando A.; de Pablo, Juan J. The Journal of Chemical Physics, Vol. 103, Issue 7 https://doi.org/10.1063/1.470504	journal	August 1995
Use the force! Reduced variance estimators for densities, radial distribution functions, and local mobilities in molecular simulations Rotenberg, Benjamin The Journal of Chemical Physics, Vol. 153, Issue 15 https://doi.org/10.1063/5.0029113	journal	October 2020
Computation of pair distribution functions and three-dimensional densities with a reduced variance principle Borgis, Daniel; Assaraf, Roland; Rotenberg, Benjamin Molecular Physics, Vol. 111, Issue 22-23 https://doi.org/10.1080/00268976.2013.838316	journal	December 2013
Improving the accuracy of computing chemical potentials in CFCMC simulations Rahbari, A.; Hens, R.; Dubbeldam, D. Molecular Physics, Vol. 117, Issue 23-24 https://doi.org/10.1080/00268976.2019.1631497	journal	June 2019
Explicit reversible integrators for extended systems dynamics Martyna, Glenn J.; Tuckerman, Mark E.; Tobias, Douglas J. Molecular Physics, Vol. 87, Issue 5 https://doi.org/10.1080/00268979600100761	journal	April 1996
A new perspective on the order- n algorithm for computing correlation functions Dubbeldam, David; Ford, Denise C.; Ellis, Donald E. Molecular Simulation, Vol. 35, Issue 12-13 https://doi.org/10.1080/08927020902818039	journal	October 2009
On the inner workings of Monte Carlo codes Dubbeldam, David; Torres-Knoop, Ariana; Walton, Krista S. Molecular Simulation, Vol. 39, Issue 14-15 https://doi.org/10.1080/08927022.2013.819102	journal	December 2013
Experiences with the publicly available multipurpose simulation code, Music Chempath, Shaji; Düren, Tina; Sarkisov, Lev Molecular Simulation, Vol. 39, Issue 14-15 https://doi.org/10.1080/08927022.2013.819103	journal	December 2013
MCCCS Towhee: a tool for Monte Carlo molecular simulation Martin, Marcus G. Molecular Simulation, Vol. 39, Issue 14-15 https://doi.org/10.1080/08927022.2013.828208	journal	December 2013
RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials Dubbeldam, David; Calero, Sofía; Ellis, Donald E. Molecular Simulation, Vol. 42, Issue 2 https://doi.org/10.1080/08927022.2015.1010082	journal	February 2015
Continuous fractional component Monte Carlo simulations of high-density adsorption in metal–organic frameworks Sikora, Benjamin J.; Colón, Yamil J.; Snurr, Randall Q. Molecular Simulation, Vol. 41, Issue 16-17 https://doi.org/10.1080/08927022.2015.1043629	journal	July 2015
Automated analysis and benchmarking of GCMC simulation programs in application to gas adsorption Gowers, Richard J.; Farmahini, Amir H.; Friedrich, Daniel Molecular Simulation, Vol. 44, Issue 4 https://doi.org/10.1080/08927022.2017.1375492	journal	September 2017
iRASPA: GPU-accelerated visualization software for materials scientists Dubbeldam, David; Calero, Sofía; Vlugt, Thijs J. H. Molecular Simulation, Vol. 44, Issue 8 https://doi.org/10.1080/08927022.2018.1426855	journal	January 2018
DL_MONTE: a multipurpose code for Monte Carlo simulation Brukhno, A. V.; Grant, J.; Underwood, T. L. Molecular Simulation https://doi.org/10.1080/08927022.2019.1569760	journal	February 2019
Recent advances in the continuous fractional component Monte Carlo methodology Rahbari, A.; Hens, R.; Ramdin, M. Molecular Simulation, Vol. 47, Issue 10-11 https://doi.org/10.1080/08927022.2020.1828585	journal	October 2020
Molecular Simulations of Methane Adsorption in Silicalite Snurr, Randall Q.; June, R. Larry; Bell, Alexis T. Molecular Simulation, Vol. 8, Issue 1-2 https://doi.org/10.1080/08927029108022468	journal	December 1991
A Liouville-operator derived measure-preserving integrator for molecular dynamics simulations in the isothermal–isobaric ensemble Tuckerman, Mark E.; Alejandre, José; López-Rendón, Roberto Journal of Physics A: Mathematical and General, Vol. 39, Issue 19 https://doi.org/10.1088/0305-4470/39/19/s18	journal	April 2006
Better Than Counting: Density Profiles from Force Sampling de las Heras, Daniel; Schmidt, Matthias Physical Review Letters, Vol. 120, Issue 21 https://doi.org/10.1103/physrevlett.120.218001	journal	May 2018
On the location and disorder of the tetrapropylammonium (TPA) ion in zeolite ZSM-5 with improved framework accuracy van Koningsveld, H.; van Bekkum, H.; Jansen, J. C. Acta Crystallographica Section B Structural Science, Vol. 43, Issue 2 https://doi.org/10.1107/s0108768187098173	journal	April 1987
A Chemically Functionalizable Nanoporous Material [Cu₃(TMA)₂(H₂O)₃]_n Chui, Stephen S.-Y.; Lo, Samuel M.-F.; Charmant, Jonathan P. H. Science, Vol. 283, Issue 5405, p. 1148-1150 https://doi.org/10.1126/science.283.5405.1148	journal	February 1999
Barely porous organic cages for hydrogen isotope separation Liu, Ming; Zhang, Linda; Little, Marc A. Science, Vol. 366, Issue 6465 https://doi.org/10.1126/science.aax7427	journal	October 2019
Balancing volumetric and gravimetric uptake in highly porous materials for clean energy Chen, Zhijie; Li, Penghao; Anderson, Ryther Science, Vol. 368, Issue 6488 https://doi.org/10.1126/science.aaz8881	journal	April 2020
Rational design of mixed-matrix metal-organic framework membranes for molecular separations Datta, Shuvo Jit; Mayoral, Alvaro; Murthy Srivatsa Bettahalli, Narasimha Science, Vol. 376, Issue 6597 https://doi.org/10.1126/science.abe0192	journal	June 2022

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