Robert Q. Topper

Professor of Chemistry

Software and Data Archive

This page consists of a public archive of software that we have used in our published work, as well as structural and other data for molecular, cluster, and nanoparticle systems. All files will be available for a minimum of ten years following their publication. In some cases the data is available in a publically available Supplementary Information file. If so, a link to that file is provided.

If you need data from previously published work which is not yet available here, please send an email to TopperNanoGroup_AT_gmail.com. 

Software

1. S.L. Topper and R.Q. Topper, TransRot. The GitHub archive contains full documentation on how to set up, install and run our machine-portable Java software for simulated annealing Monte Carlo optimization calculations of nanoparticles, guest-host systems and surface -adsorbate interactions. The code is currently still under development. A test run is provided as well as a few case studies. https://github.com/steventopper/Transrot

2. R.Q. Topper, PHOENIX. This Fortran program uses path integral Monte Carlo methods enhanced with adaptively optimized stratified sampling to calculate the partition functions (and hence free energies) of a toy 2D harmonic oscillator as well as diatomic and triatomic molecules. The code compiles and runs efficiently under gfortran, and calculations using partial averaging are now possible for some systems. It is easily adaptable to other 2D systems and diatomic / triatomic molecules. Although this code is useful, please note that the FPIMC code at University of Minnesota by Truhlar et al. is the most up-to-date code available. PHOENIX is still under development. Note: this project will be ported to GitHub in the near future. For now... Click here to download PHOENIX 8.1

3. R.Q. Topper and I. M. Markus, Annie. A zip file is provided of the last version of Annie, our Fortran software for simulated annealing Monte Carlo optimization calculations of ammonium halide nanoparticles. Includes full documentation and a test run. Note: Ths project is no longer active. All of Annie's functionality is now fully implemented in TransRot; this archive is here for historical purposes only since all of its capabilties (and many new ones) are now available in TransRot. Click here 

Molecular, cluster, and nanoparticle data

1. R.Q. Topper, W.V. Feldmann, I.M. Markus, D. Bergin, P.R. Sweeney. Simulated Annealing and Density Functional Theory Calculations of Structural and Energetic Properties of the Ammonium Chloride Clusters (NH4Cl)n, (NH4+)(NH4Cl)n, and (Cl–)(NH4Cl)n, n = 1–13.  Journal of Physical Chemistry A2011, 115, 38, 10423 - 10432. https://doi.org/10.1021/jp2069732

  • Supporting information is available which includes Cartesian coordinates in xyz format for M06-2X/6-31G(d,p) optimized geometries of all of the molecules and clusters presented in this work. Click here

2. J.J. Biswakarma, V. Ciocoi, R.Q. Topper. Energetics, Thermodynamics, and Hydrogen Bonding Diversity in Ammonium Halide Clusters.  Journal of Physical Chemistry A2016, 120, 40, 7924–7934. https://doi.org/10.1021/acs.jpca.6b06788

  • Supporting information is available which includes 
    • Cartesian coordinates in xyz format of the (NH4Br)n clusters (n = 1–13) optimized at the M06-2X/6-31G(d,p) level and (NH4F)n clusters (n = 1–5) optimized at the RI-MP2/aug-cc-pVTZ level of theory.
    • A table of all parameters used to form the interaction potential used in the MW-SSA calculations of (NH4Br)n and (NH4Cl)n 
    • Click here

3. J.R. Cendagorta, J. Tolpin,* E. Schneider, R.Q. Topper, M.E. Tuckerman. Comparison of the performance of machine learning models in representing high-dimensional free energy surfaces and generating observables. Journal of Physical Chemistry B,124(18), pp.3647-3660(2020). https://pubs.acs.org/doi/10.1021/acs.jpcb.0c01218 

  • Supporting information is available which includes the details of hyperparameter tuning for the various machine learning methods as well as the tabulated hyperparameters for this work. Click here

4. A.J.V. Lomboy, R.Q. Topper. Nonuniform Proton Transfer and Strong Hydrogen Bonding within Cation, Anion, and Neutral Clusters of Ammonia and Hydrogen Fluoride.  Journal of Physical Chemistry A 2021, 125, 12, 2546–2557. https://doi.org/10.1021/acs.jpca.1c00732 .

  • Supporting information is available which includes Cartesian coordinates in xyz format and unscaled harmonic frequencies of all component molecules and molecular clusters, optimized at the MP2/aug-cc-pVQZ level of theory. Click here

5. R.Q. Topper,  S.L. Topper, S. Lee. TransRot: A portable software package for simulated annealing Monte Carlo geometry optimization of atomic and molecular clusters, in "Physical Chemistry Research at Undergraduate Institutions," T. Hopkins and C.A. Parish, Eds., ACS Symposium Series (accepted for publication, 2022)

  • A zip file is provided which includes the Cartesian coordinates (which are provided in xyz format) and energies for (H2O)n clusters (n=2 to 8) which have been "nearly optimized" using TransRot, within the TIP-4P potential. Click here