NMGC Software Matrix

NMGC (Co-)developed Software for Electronic Structure Calculations

CP2K

CP2K is a free, open-source quantum chemistry software package designed to perform molecular dynamics and Monte Carlo simulations of clusters and periodic systems. CP2K can be run in both MPI and OpenMP modes, and built-in farming procedures allow for capacity jobs at DOE Leadership Computing Facilities. The NMGC team contributes to CP2K through the development first principles Monte Carlo (FPMC) modules for simulations of phase, adsorption, and chemical equilibria and through algorithms for the incorporation of nuclear quantum effects. CP2K can be downloaded from: (www.cp2k.org), and NMGC will make workflows for FPMC simulations of adsorption equilibria available to the community.

J. Hutter, M. Iannuzzi, F. Schiffmann, and J. Vandevondele, J. (2014). Cp2k: Atomistic simulations of condensed matter systems. WIREs Comput. Mol. Sci. 4, 15-25 (2014). DOI: 10.1002/wcms.1159

E.O. Fetisov, M.S. Shah, J.R. Long, M. Tsapatsis, and J.I. Siepmann, “First principles Monte Carlo simulations of unary and binary adsorption: CO2, N2, and H2O in Mg-MOF-74,” Chem. Comm. 54, 10816-10819 (2018). DOI: 10.1039/C8CC06178E

PySCF

PySCF is a free, open-source quantum chemistry and solid-state physics software package designed to perform electronic structure calculations in molecular and periodic systems. The NMGC team contributes to PySCF through the development of approaches for quantum embedding calculations. This code is hosted on Github and is free for download at https://github.com/Goodpaster/pbpe. Future goals are the development of robust quantum methods for highly accurate calculations in large systems.

Q. Sun, T.C. Berkelbach, N.S. Blunt, G.H. Booth, S. Guo, Z. Li, J. Liu, J. McClain, E.R. Sayfutyarova, S. Sharma, S. Wouters, and G.K.-L. Chan, “PySCF: the Python‐based simulations of chemistry framework,” WIREs Comput. Mol. Sci. 8, e1340 (2018). DOI: 10.1002/wcms.1340

D.V. Chulhai and J.D. Goodpaster, “Projection-Based Correlated Wave Function in Density Functional Theory Embedding for Periodic Systems,” J. Chem. Theory Comput. 14, 1928 (2018). DOI: 10.1021/acs.jctc.7b01154

QMMM

QMMM is a computer program for performing single-point calculations (energies, gradients, and Hessians), geometry optimizations, and molecular dynamics using combined quantum mechanics (QM) and molecular mechanics (MM) methods. The boundary between the QM and MM regions can be treated by a number of schemes, including the redistributed charge (RC) scheme, the redistributed charge and dipole (RCD) scheme, the polarized-boundary RC (PBRC) scheme, the polarized-boundary RCD (PBRCD) scheme, the flexible-boundary RC (FBRC), and the flexible-boundary RCD (FBRCD) scheme. QMMM calls a QM package and an MM package to perform required single-level calculations. QMMM was tested with GAMESS, Gaussian (both Gaussian 09 and Gaussian 16), and ORCA for the QM package and with TINKER for the MM package; it contains 156 sample runs that can be used to learn and test the program. After completing a free license form, the QMMM can be freely downloaded from: https://comp.chem.umn.edu/qmmm/.

QMMM 2017 by H. Lin, Y. Zhang, S. Pezeshki, B. Wang, X.-P. Wu, L. Gagliardi, and D.G. Truhlar, University of Minnesota, Minneapolis, 2017.

NMGC (Co-)developed Software for Molecular Modeling and Simulations

MCCCS-MN

MCCCS-MN is a free, open-source Monte Carlo software tailored for simulations of phase and adsorption equilibria in the Gibbs ensemble using the TraPPE force field. MCCCS-MN is particularly efficient for equilibria involving multiple condensed phases and articulated molecules. MCCCS–MN uses hybrid MPI/OpenMP for parallel execution, has been adapted to processors with high-bandwidth MCDRAM, and workflows with specific I/O handling allow for capacity jobs at DOE Leadership Computing Facilities. The NMGC team is the sole developer of MCCCS-MN. MCCCS-Towhee, a more user-friendly version with support for a variety of force fields but slower version, is freely available for download (http://towhee.sourceforge.net/).

P. Bai, M.Y. Jeon, L. Ren, C. Knight, M.W. Deem, M. Tsapatsis, and J.I. Siepmann, “Discovery of optimal zeolites for challenging separations and chemical transformations using predictive materials modeling,” Nat. Commun. 6, art. no. 5912 (2014). DOI: 10.1038/ncomms6912

RASPA

RASPA is a software package for simulating adsorption and diffusion of molecules in flexible nanoporous materials. The code implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo in various ensembles. Applications of RASPA include computing coexistence properties, adsorption isotherms for single and multiple components, self- and collective diffusivities, and visualization. RASPA is particularly efficient for gas adsorption in a wide variety of porous materials. The NMGC team contributes to the development of RASPA. Information on RASPA is provided at https://www.iraspa.org/, and is available for download from a git server (obtain login information from the developers).

D. Dubbeldam, S. Calero, D.E. Ellis, and R.Q. Snurr, “RASPA: Molecular simulation software for adsorption and diffusion in flexible nanoporous materials,” Molec. Sim. 42, 81-101 (2016). DOI: 10.1080/08927022.2015.1010082

NMGC (Co-)developed Software for Machine Learning

chemical_VAE

Chemical Variational Autoencoder (chemical_VAE) is a free, open-source software for machine learning of molecular properties. chemical_VAE utilizes molecular SMILES that are encoded into a code vector representation and can be decoded from the code representation back to molecular SMILES. The autoencoder may also be jointly trained with property prediction to help shape the latent space. The new latent space can then be optimized upon to find the molecules with the most optimized properties of interest. chemical_VAE is currently being extended in conjunction with MOFid to capture adsorption of molecules in porous materials. chemical_VAE can be downloaded from: https://github.com/aspuru-guzik-group/chemical_vae.

R. Gómez-Bombarelli, J. Wei, D. Duvenaud, J. Hernández-Lobato, B. Sánchez-Lengeling, D. Sheberla, J. Aguilera-Iparraguirre, T. Hirzel, R. Adams, and A. Aspuru-Guzik, "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules," ACS Central Science 4, 268-276 (2018). DOI: 10.1021/acscentsci.7b00572

NMGC (Co-)developed Databases

CoRE MOF

Computation-Ready Experimental (CoRE) MOF is a database that enables high-throughput computational screening by using Github's versioning system to manage and curate the data. CoRE MOF provides cleaned atomic coordinates and pore characteristics of structures while solving issues such as solvent molecules and partially occupied/disordered atoms in experimental crystal structures. The database is available for download from http://gregchung.github.io/CoRE-MOFs/. CoRE MOF V2 will include additional structures, open-metal-site detection, free and structural solvent, optimized structures, and DDEC partial charges.

Nanoporous Materials Explorer

The Nanoporous Materials Explorer App is a database containing information on thousands of materials' computational properties. The application aims to present the accumulation of data in a new, interactive way. The Nanoporous Materials Explorer App data are predicted, measured, and maintained by the NMGC in partnership with the Materials Project. A detailed manual is available at The Materials Project site, and the App is also available (after registration) at The Materials Project.

Currently, more than 500,000 nanoporous materials have data, such as structures and point charges, recorded in a searchable format through the Nanoporous Materials Explorer.

Polymatic

Polymatic is a set of codes for the structure generation of amorphous polymers via a stimulated polymerization algorithm. In conjunction with a simulation package Polymatic performs energy minimization and molecular dynamics simulations during the polymerization. Currently, Polymatic has 1300 independent users and is available for download at https://nanohub.org/resources/17278. Future plans for Polymatic include extensions to include NPM/polymer composites.

NMGC (Co-)developed Software for Pore Analytics, Generation of Porous Structures, and Hierarchical Workflows

pyIAST

pyIAST is a user-friendly, open-source Python that can fit data into analytical isotherm models or use interpolation to characterize the pure-component adsorption isotherms. pyIAST is hosted on Github and is free for download at https://github.com/CorySimon/pyIAST, with additional documents available at http://pyiast.readthedocs.org/en/latest/. Users may also contribute to the source code via the Github system. Communication with pyIAST authors is done via email and Github's messaging system.

Zeo++

Zeo++ is an open-source software for performing high-throughput geometry-based analysis of porous materials and their voids. Zeo++ serves approximately 800 registered users, who can communicate with the developer via email. Registration is required by LBNL for downloading the code from zeoplusplus.org. Future plans for Zeo++ include the addition of functionality for hard and soft nanoporous materials.

Educational Games


Master of Filtering

Master of Filtering (MOF) is a game being developed by the NMGC to engage youth and citizen scientists with concepts of porous materials and separations. A video tutorial of the game is available at https://www.youtube.com/watch?v=Hys6_XcYOyE. The long range goal for this game is the crowdsourcing of nanoporous material design through gamification.