SOFTWARE

new codes

PySIDT (https://github.com/zadorlab/PySIDT) a package containing a set of low-data machine-learning algorithms for prediction of chemical properties based on the subgraph isomorphic tree generation (SIDT) approach originally developed in Johnson and Green 2024. While the algorithm in that work was specific to rate coefficients, this implementation can be applied to prediction of arbitrary properties. This implementation also incorporates uncertainty prepruning, as detailed in Pang et al. 2024.
KinCat (https://github.com/sandialabs/KinCat) is an open-source software for parallel kinetic Monte Carlo (KMC) simulations, with a focus on heterogeneous catalysis applications. It implements lattice KMC on CPU/GPU architectures using Kokkos for performance portability.
Sella (https://github.com/zadorlab/sella) is a utility for finding first order saddle points and minima on PESs. See: https://pubs.acs.org/doi/full/10.1021/acs.jctc.9b00869 , https://aip.scitation.org/doi/10.1063/5.0060146, and https://pubs.acs.org/doi/10.1021/acs.jctc.2c00395
TChem (https://github.com/sandialabs/TChem) is an open source software library for solving complex computational chemistry problems and analyzing detailed chemical kinetic models. See: https://doi.org/10.1016/j.cpc.2022.108628
CSPlib (https://github.com/sandialabs/CSPlib) is an open source software for analysis of chemical kinetic models. See: https://doi.org/10.1016/j.cpc.2023.109069
Tines (https://github.com/sandialabs/Tines) is a performance portable math library providing a stiff time integrator solving ODEs and DAEs and a batched eigensolver on heterogeneous computing platforms.
Pynta (https://github.com/zadorlab/pynta) is an automated workflow for reaction path exploration of adsorbates on crystal facets. See: https://doi.org/10.1021/acs.jcim.3c00948
AdTherm (https://github.com/franklingoldsmith/adtherm) is a code to compute anharmonic partition functions for adsorbates using classical phase space sampling. The code is currently under development, but we plan to release it soon as part of our forthcoming first manuscript.
MPNN (https://github.com/sandialabs/MPNN) is a small library for Minima-preserving neural network construction.

codes expanded by us

RMG (https://github.com/ReactionMechanismGenerator/RMG-Py) automatically generates detailed microkinetic mechanisms. As part of the ECC-2017 project, RMG-Cat was merged into RMG, and the surface chemistry capability was expanded to include (i) better thermodynamic and kinetic databases, and (ii) new functionality for linear scaling relations.
AutoTST (https://github.com/ReactionMechanismGenerator/AutoTST) is a toolkit for performing end-to-end automated Transition State Theory calculations, from chemical description to validated reaction rate. As part of ECC-2017 it was rewritten and expanded with more robust geometry prediction algorithms, conformer searches, symmetry detection, and hindered rotor treatments.
NWChem (https://github.com/nwchemgit/nwchem) is an electronic structure theory package. The ECC- 2017 project supported the implementation of new DFT functionals, improvements for optimizers with fractional occupation, space-group symmetry, RPA and other beyond DFT developments, and various other enhancements.
NWChemEx (https://github.com/NWChemEx-Project) is a developing exascale version of NWChem. The ECC-2017 project supported SYCL GPU developments in the PW DFT code for the exascale machine being installed at the Argonne Leadership Class Facility in 2021-2022 time frame.
EMSL Arrows (https://arrows.emsl.pnnl.gov/api/) is a web application that uses NWChem and chemical computational databases to perform materials and chemical modeling. The ECC-2017 project supported a periodic builder, surface generation, and simulation workflow to carry out pathway/free energy methods including NEB, metadynamics, WHAM, and TAMD.
ASE (https://gitlab.com/ase/ase/) is a toolkit for manipulating atomic systems which interfaces with a variety of electronic structure theory packages. In addition to various other enhancements, the ECC supported the creation of a new NWChem interface in ASE.

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