The Kitchin Research Group

I have been thinking about ways to search my bibtex file with multiple criteria. Eventually, I want a decent natural language search like "au=kitchin and alloy" to find papers authored by me about alloys. For now, I am going to settle with a way to find these. This strategy will create a search function that prints the entries that are found. Here is the prototype idea:

(defun my-search (key start end)
  (when (and (re-search-forward "kitchin" end t)
           (re-search-forward "alloy" end t))
      (princ (format "%s\n" (buffer-substring start end)))))

(with-temp-buffer
  (insert-file-contents "../../bibliography/references.bib")
  (bibtex-map-entries  'my-search))

@ARTICLE{inoglu-2011-ident-sulfur,
  pdf =		 {[[file:bibtex-pdfs/inoglu-2011-ident-sulfur.pdf]]},
  org-notes =
                  {[[file:~/Dropbox/bibliography/notes.org::inoglu-2011-ident-sulfur]]},
  author =	 {Inoglu, Nilay and Kitchin, John R.},
  title =	 {Identification of Sulfur-Tolerant Bimetallic
                  Surfaces Using {DFT} Parametrized Models and
                  Atomistic Thermodynamics},
  journal =	 {ACS Catalysis},
  year =	 2011,
  pages =	 {399--407},
  abstract =	 {The identification of sulfur-tolerant alloys for
                  catalytic applications is difficult due to the
                  combinatorially large number of alloy compositions
                  and surface structures that may be
                  considered. Density functional theory calculations
                  (DFT) are not fast enough to enumerate all the
                  possible structures and their sulfur tolerance. In
                  this work, a DFT parametrized algebraic model that
                  accounts for structure and composition was used to
                  estimate the d-band properties and sulfur adsorption
                  energies of 370 transition metal-based bimetallic
                  alloy surfaces.  The estimated properties were
                  validated by DFT calculations for 110 of the surface
                  structures. We then utilized an atomistic
                  thermodynamic framework that includes surface
                  segregation, the presence of adsorbates, and effects
                  of environmental conditions to identify alloy
                  compositions and structures with enhanced sulfur
                  tolerance that are likely to be stable under the
                  environmental conditions. As a case study, we show
                  how this database can be used to identify
                  sulfur-tolerant Cu-based catalysts and compare the
                  results with what is known about these catalysts
                  experimentally.},
  doi =		 {10.1021/cs200039t},
  issn =	 {null},
  type =	 {Journal Article}
}
@ARTICLE{kitchin-2008-alloy,
  pdf =		 {[[file:bibtex-pdfs/kitchin-2008-alloy.pdf]]},
  org-notes =
                  {[[file:~/Dropbox/bibliography/notes.org::kitchin-2008-alloy]]},
  author =	 {Kitchin, J. R. and Reuter, K. and Scheffler, M.},
  title =	 {Alloy surface segregation in reactive environments:
                  First-principles atomistic thermodynamics study of
                  \ce{Ag_3Pd}(111) in oxygen atmospheres},
  journal =	 {Physical Review B},
  year =	 2008,
  volume =	 77,
  number =	 7,
  abstract =	 {We present a first-principles atomistic
                  thermodynamics framework to describe the structure,
                  composition, and segregation profile of an alloy
                  surface in contact with a (reactive)
                  environment. The method is illustrated with the
                  application to a Ag3Pd(111) surface in an oxygen
                  atmosphere, and we analyze trends in segregation,
                  adsorption, and surface free energies. We observe a
                  wide range of oxygen adsorption energies on the
                  various alloy surface configurations, including
                  binding that is stronger than on a Pd(111) surface
                  and weaker than that on a Ag(111) surface. This and
                  the consideration of even small amounts of
                  nonstoichiometries in the ordered bulk alloy are
                  found to be crucial to accurately model the Pd
                  surface segregation occurring in increasingly O-rich
                  gas phases.},
  doi =		 {https://doi.org/10.1103/PhysRevB.77.075437},
  pages =	 075437,
  issn =	 {1098-0121},
  type =	 {Journal Article}
}
@ARTICLE{tierney-2009-hydrog-dissoc,
  pdf =		 {[[file:bibtex-pdfs/tierney-2009-hydrog-dissoc.pdf]]},
  org-notes =
                  {[[file:~/Dropbox/bibliography/notes.org::tierney-2009-hydrog-dissoc]]},
  author =	 {Tierney, H. L. and Baber, A. E. and Kitchin,
                  J. R. and Sykes, E.  C. H.},
  title =	 {Hydrogen Dissociation and Spillover on Individual
                  Isolated Palladium Atoms},
  journal =	 {Physical Review Letters},
  year =	 2009,
  volume =	 103,
  number =	 24,
  abstract =	 {Using a combination of low-temperature scanning
                  tunneling microscopy and density functional theory
                  it is demonstrated how the nature of an inert host
                  metal of an alloy can affect the thermodynamics and
                  kinetics of a reaction pathway in a much more
                  profound way than simply a dilution, electronic, or
                  geometric effect. This study reveals that
                  individual, isolated Pd atoms can promote H-2
                  dissociation and spillover onto a Cu(111) surface,
                  but that the same mechanism is not observed for an
                  identical array of Pd atoms in Au(111).},
  pages =	 246102,
  doi =		 {10.1103/PhysRevLett.103.246102},
  issn =	 {0031-9007},
  url =		 {http://prl.aps.org/abstract/PRL/v103/i24/e246102},
  type =	 {Journal Article}
}

That is not too bad. If I had a parser like this one , I could do some reasonable searches. I could try integrating it with reftex or something similar for selecting citations. I would like that a lot.

What if I wanted to find articles with Kitchin as an author, and alloy in the title? This is my best effort at doing that, where I explicitly match the fields in the bibtex entries.

(find-file "~/Dropbox/bibliography/references.bib")
(bibtex-map-entries (lambda (bibtex-key start end)
                      (let* ((entry (bibtex-parse-entry))
                             (title (cdr (assoc "title" entry)))
                             (authors (cdr (assoc "author" entry))))
                        (when (and title (string-match "alloy" title)
                                   authors (string-match "kitchin" authors))
                          (princ (buffer-substring start end)))))))

@ARTICLE{kitchin-2008-alloy,
  pdf =		 {[[file:bibtex-pdfs/kitchin-2008-alloy.pdf]]},
  org-notes =
                  {[[file:~/Dropbox/bibliography/notes.org::kitchin-2008-alloy]]},
  author =	 {Kitchin, J. R. and Reuter, K. and Scheffler, M.},
  title =	 {Alloy surface segregation in reactive environments:
                  First-principles atomistic thermodynamics study of
                  \ce{Ag_3Pd}(111) in oxygen atmospheres},
  journal =	 {Physical Review B},
  year =	 2008,
  volume =	 77,
  number =	 7,
  abstract =	 {We present a first-principles atomistic
                  thermodynamics framework to describe the structure,
                  composition, and segregation profile of an alloy
                  surface in contact with a (reactive)
                  environment. The method is illustrated with the
                  application to a Ag3Pd(111) surface in an oxygen
                  atmosphere, and we analyze trends in segregation,
                  adsorption, and surface free energies. We observe a
                  wide range of oxygen adsorption energies on the
                  various alloy surface configurations, including
                  binding that is stronger than on a Pd(111) surface
                  and weaker than that on a Ag(111) surface. This and
                  the consideration of even small amounts of
                  nonstoichiometries in the ordered bulk alloy are
                  found to be crucial to accurately model the Pd
                  surface segregation occurring in increasingly O-rich
                  gas phases.},
  doi =		 {https://doi.org/10.1103/PhysRevB.77.075437},
  pages =	 075437,
  issn =	 {1098-0121},
  type =	 {Journal Article}
}

This is a more precise search, which yields only one entry. That is not exactly nimble searching, but it does provide precision. I need to think about this some more.

Copyright (C) 2014 by John Kitchin. See the License for information about copying.

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