New publication in Catalysis Today

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In this paper we continue our exploration of using high-dimensional neural networks (NN) to model metal surface properties. Our first work started with modeling Au in a variety of structures using ReaxFF and a NN boes-2016-neural-networ. We then modeled atomic oxygen adsorbates on a Pd (111) surface boes-2017-neural-networ, and segregation of an Au-Pd alloy surface boes-2017-model-segreg. Our goal throughout this work has been to systematically build up complexity in the systems we are modeling, and to explore the limitations of these potentials for modeling surfaces. This current work happened in parallel with those works, and focused on modeling Pd adatom diffusion on Pd(111) surfaces. We show another example of how to train a neural network, and then to use it model the temperature dependent diffusion of adatoms on a metal surface using molecular dynamics and Arrhenius analysis.

@article{gao-2018-model-pallad,
  author =       {Tianyu Gao and John R. Kitchin},
  title =        {Modeling Palladium Surfaces With Density Functional Theory,
                  Neural Networks and Molecular Dynamics},
  journal =      {Catalysis Today},
  year =         2018,
  doi =          {10.1016/j.cattod.2018.03.045},
  url =          {https://doi.org/10.1016/j.cattod.2018.03.045},
  DATE_ADDED =   {Sun Apr 1 18:47:55 2018},
}

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New publication in Topics in Catalysis

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Single atom alloys are alloys in the extreme dilute limit, where single atoms of a reactive metal are surrounded by comparatively unreactive metals. This makes the single reactive atoms like single atom sites where reactions can occur. These sites are interesting because they are metallic, but their electronic structure is different than the atoms in more concentrated alloys. This means there is the opportunity for different, perhaps better catalytic performance for the single atom alloys. In this paper, we studied the electronic structure and some representative reaction pathways on a series of single atom alloy surfaces.

@article{Thirumalai2018,
  author =       "Thirumalai, Hari and Kitchin, John R.",
  title =        "Investigating the Reactivity of Single Atom Alloys Using
                  Density Functional Theory",
  journal =      "Topics in Catalysis",
  year =         "2018",
  month =        "Jan",
  day =          "25",
  abstract =     "Single atom alloys are gaining importance as atom-efficient
                  catalysts which can be extremely selective and active towards
                  the formation of desired products. They possess such desirable
                  characteristics because of the presence of a highly reactive
                  single atom in a less reactive host surface. In this work, we
                  calculated the electronic structure of several representative
                  single atom alloys. We examined single atom alloys of gold,
                  silver and copper doped with single atoms of platinum,
                  palladium, iridium, rhodium and nickel in the context of the
                  d-band model of Hammer and N{\o}rskov. The reactivity of these
                  alloys was probed through the dissociation of water and nitric
                  oxide and the hydrogenation of acetylene to ethylene. We
                  observed that these alloys exhibit a sharp peak in their atom
                  projected d-band density of states, which we hypothesize could
                  be the cause of high surface reactivity. We found that the
                  d-band centers and d-band widths of these systems correlated
                  linearly as with other alloys, but that the energy of
                  adsorption of a hydrogen atom on these surfaces could not be
                  correlated with the d-band center, or the average reactivity
                  of the surface. Finally, the single atom alloys, with the
                  exception of copper--palladium showed good catalytic behavior
                  by activating the reactant molecules more strongly than the
                  bulk atom behavior and showing favorable reaction pathways on
                  the free energy diagrams for the reactions investigated.",
  issn =         "1572-9028",
  doi =          "10.1007/s11244-018-0899-0",
  url =          "https://doi.org/10.1007/s11244-018-0899-0"
}

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New publication in Molecular Simulation

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This paper is our latest work using neural networks in molecular simulation. In this work, we build a Behler-Parinello neural network potential of bulk zirconia. The potential can describe several polymorphs of zirconia, as well as oxygen vacancy defect formation energies and diffusion barriers. We show that we can use the potential to model oxygen vacancy diffusion using molecular dynamics at different temperatures, and to use that data to estimate the effective diffusion activation energy. This is further evidence of the general utility of the neural network-based potential for molecular simulations with DFT accuracy.

@article{wang-2018-densit-funct,
  author =       {Chen Wang and Akshay Tharval and John R. Kitchin},
  title =        {A Density Functional Theory Parameterised Neural Network Model
                  of Zirconia},
  journal =      {Molecular Simulation},
  volume =       0,
  number =       0,
  pages =        {1-8},
  year =         2018,
  doi =          {10.1080/08927022.2017.1420185},
  url =          {https://doi.org/10.1080/08927022.2017.1420185},
  eprint =       { https://doi.org/10.1080/08927022.2017.1420185 },
  publisher =    {Taylor \& Francis},
}

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New publication in J. Phys. Chem. Lett.

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DFT calculations are extensively used to predict the chemical properties of metal alloy surfaces, but they are expensive which limits the number of calculations that can be practically be calculated. In this paper, we explore a perturbation approach known as alchemy to take previously calculated results and extend them to new compositions. We use oxygen reduction as a prototype reaction, and show that alchemy is often much faster than DFT, with an accuracy within 0.1 eV of the DFT. There are cases where the accuracy is not as good suggesting that further improvements to the perturbation model could be beneficial. Overall, alchemy appears to be a useful tool in high-throughput screening research.

@article{saravanan-2017-alchem-predic,
  title =        {Alchemical Predictions for Computational Catalysis: Potential
                  and Limitations},
  year =         2017,
  Author =       {Saravanan, Karthikeyan and Kitchin, John R. and von
                  Lilienfeld, O. Anatole and Keith, John A.},
  Bdsk-Url-1 =   {https://doi.org/10.1021/acs.jpclett.7b01974},
  Doi =          {10.1021/acs.jpclett.7b01974},
  Eprint =       {https://doi.org/10.1021/acs.jpclett.7b01974},
  Journal =      {The Journal of Physical Chemistry Letters},
  Note =         {PMID: 28938798},
  Number =       {ja},
  Pages =        {null},
  Url =          {https://doi.org/10.1021/acs.jpclett.7b01974},
  Volume =       0,
}

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New publication in Journal of Physics Condensed Matter

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The Atomic Simulation Environment is a powerful python library for setting up, running and analyzing molecular simulations. I have been using it and contributing to it since around 2002 when I used the ASE-2 version in Python 1.5! The new ase-3 version is much simpler to use, and much more powerful. This paper describes some of its design principles and capabilities. If you use ASE, please cite this paper!

@article{larsen-2017-atomic-simul,
  author =       {Ask Hjorth Larsen and Jens J{\o}rgen Mortensen and Jakob
                  Blomqvist and Ivano E Castelli and Rune Christensen and
                  Marcin Dułak and Jesper Friis and Michael N Groves and
                  Bj{\o}rk Hammer and Cory Hargus and Eric D Hermes and Paul C
                  Jennings and Peter Bjerre Jensen and James Kermode and John
                  R Kitchin and Esben Leonhard Kolsbjerg and Joseph Kubal and
                  Kristen Kaasbjerg and Steen Lysgaard and J{\'o}n Bergmann
                  Maronsson and Tristan Maxson and Thomas Olsen and Lars
                  Pastewka and Andrew Peterson and Carsten Rostgaard and Jakob
                  Schi{\o}tz and Ole Sch{\"u}tt and Mikkel Strange and Kristian
                  S Thygesen and Tejs Vegge and Lasse Vilhelmsen and Michael
                  Walter and Zhenhua Zeng and Karsten W Jacobsen},
  title =        {The Atomic Simulation Environment-A Python Library for Working
                  With Atoms},
  journal =      {Journal of Physics: Condensed Matter},
  volume =       29,
  number =       27,
  pages =        273002,
  year =         2017,
  url =          {http://stacks.iop.org/0953-8984/29/i=27/a=273002},
  abstract =     {The atomic simulation environment (ASE) is a software package
                  written in the Python programming language with the aim of
                  setting up, steering, and analyzing atomistic simulations. In
                  ASE, tasks are fully scripted in Python. The powerful syntax
                  of Python combined with the NumPy array library make it
                  possible to perform very complex simulation tasks. For
                  example, a sequence of calculations may be performed with the
                  use of a simple 'for-loop' construction. Calculations of
                  energy, forces, stresses and other quantities are performed
                  through interfaces to many external electronic structure codes
                  or force fields using a uniform interface. On top of this
                  calculator interface, ASE provides modules for performing many
                  standard simulation tasks such as structure optimization,
                  molecular dynamics, handling of constraints and performing
                  nudged elastic band calculations.},
}

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