Gecko Hamaker

An Open-Science Software Tool

for the Calculation of

van der Waals-London Dispersion (vdW-Ld) Interactions

Based on algorithms developed by V. Adrian Parsegian1 and others, Gecko Hamaker calculates Hamaker coefficients, interaction free energies, forces, and torques for a wide range of geometries and materials, using the full Lifshitz theory for vdW-Ld interactions. Gecko Hamaker also provides a web service for the distribution of over 100 materials’ full spectral optical properties.

How to Install and Run Gecko Hamaker

Installers and documentation for Gecko Hamaker are available on Sourceforge:

Gecko Hamaker

http://sourceforge.net/projects/geckoproj

The latest version is Gecko Hamaker 2.1; installers are available for Windows x86 and x64, MacOS, and Linux.

Basic Overview

Recent advances in vdW-Ld theory2 have facilitated the implementation of an open-source, open-data design tool that renders tractable an understanding and predictive design capability for vdW-Ld interactions in a wide variety of contexts. The Gecko Hamaker open-source software project is a full implementation of the fully retarded Lifshitz formulations3 for isotropic and anisotropic plane-plane4 and cylinder-cylinder2 interactions with intervening interlayer materials, planar systems of up to 99 layers, 5 and graded interfaces6 for the modeling of grain boundaries or other continuously changing systems, accompanied by a database of material optical properties spectra. The software and source code are distributed freely on Sourceforge under the GNU General Public License.7  The machine-readable optical property database is available for download and as a web service and makes available the full spectral optical properties of over 100 materials from both ab initio calculations8,9 and experimental measurements.10-17

Gecko Hamaker is a database application which runs with the help of MariaDB, an open source database available for free download.  Gecko Hamaker allows the user to either connect to an external web service which provides a database of over 100 material optical properties, or to connect to a local MariaDB server.  Gecko Hamaker calculates a London Dispersion spectrum1 for the materials in the database.  The user may then set up the layer configuration for the calculation by creating a project and assigning database materials to layers in the project. Gecko Hamaker then automatically calculates Hamaker coefficients, interaction free energies, forces and torques for your project.

Hamaker coefficients represent the London Dispersion Force of the van der Waals attraction between two materials. London Dispersion Forces arise from the interaction between fluctuating dipoles whose frequencies lie in the optical and UV regions of the spectrum.  Therefore, Hamaker constants may be calculated from the complex dielectric constants measured in the optical/UV portions of the spectrum.

 

Development of Gecko Hamaker, an open-source software tool, began in 2004 as a student project at Cornell University.  Since 2012, development has been supported by DOE-BES-DMSE-BMM under awards DE-SC0008068 (Case Western Reserve University) and DE-SC0008176 (University of Massachusetts – Amherst).

1.  V.A. Parsegian, Van der Waals forces: a handbook for biologists, chemists, engineers, and physicists. Cambridge University Press, 2006.

2. A. Siber, R. Rajter, R. French, W. Ching, V. Parsegian, and R. Podgornik, “Dispersion interactions between optically anisotropic cylinders at all separations: Retardation effects for insulating and semiconducting single-wall carbon nanotubes,” Physical Review B, 80 [16] (2009).

3. E.M. Lifshitz, “The Theory of Molecular Attractive Forces between Solids,” Journal of Experimental and Theoretical Physics USSR, 29 94–110 (1956).

4. R.F. Rajter and R.H. French, “New perspectives on van der Waals-London interactions of materials. From planar interfaces to carbon nanotubes,” J. Phys.: Conf. Ser., 94 [1] 012001 (2008).

5. R. Podgornik, R. French, and V. Parsegian, “Nonadditivity in van der Waals interactions within multilayers,” Journal of Chemical Physics, 124 [4] (2006).

6. K. van Benthem, G. Tan, R.H. French, L.K. DeNoyer, R. Podgornik, and V.A. Parsegian, “Graded interface models for more accurate determination of van der Waals–London dispersion interactions across grain boundaries,” Phys. Rev. B, 74 [20] 205110 (2006).

7. GNU General Public License, Version 2 - http://www.gnu.org/licenses/gpl-2.0.html.

8. R.F. Rajter, R.H. French, W.Y. Ching, R. Podgornik, and V.A. Parsegian, “Chirality-dependent properties of carbon nanotubes: electronic structure, optical dispersion properties, Hamaker coefficients and van der Waals-London dispersion interactions,” RSC Adv., [3] 823–842 (2012).

9. L. Poudel, P. Rulis, L. Liang, and W.-Y. Ching, “Electronic structure, stacking energy, partial charge, and hydrogen bonding in four periodic B-DNA models,” Phys. Rev. E, (Accepted 2014).

10. R.H. French, S.J. Glass, F.S. Ohuchi, Y.-N. Xu, and W.Y. Ching, “Experimental and theoretical determination of the electronic structure and optical properties of three phases of ZrO2,” Phys. Rev. B, 49 [8] 5133–5142 (1994).

11. R. French, R. Cannon, L. DeNoyer, and Y. Chiang, “Full Spectral Calculation of Nonretarded Hamaker Constants for Ceramic Systems from Interband Transitions Strengths,” Solid State Ionics, 75 13–33 (1995).

12. R. French, H. Mullejans, D. Jones, G. Duscher, R. Cannon, and M. Ruhle, “Dispersion forces and Hamaker constants for intergranular films in silicon nitride from spatially resolved-valence electron energy loss spectrum imaging,” Acta Materialia, 46 [7] 2271–2287 (1998).

13. R. French, H. Mullejans, and D. Jones, “Optical properties of aluminum oxide: Determined from vacuum ultraviolet and electron energy-loss spectroscopies,” Journal of the American Ceramic Society, 81 [10] 2549–2557 (1998).

14. R. French, “Origins and applications of London dispersion forces and Hamaker constants in ceramics,” Journal of the American Ceramic Society, 83 [9] 2117–2146 (2000).

15. G. Tan, M. Lemon, D. Jones, and R. French, “Optical properties and London dispersion interaction of amorphous and crystalline SiO$_2$ determined by vacuum ultraviolet spectroscopy and spectroscopic ellipsometry,” Physical Review B, 72 [20] (2005).

16. R. French, V. Parsegian, R. Podgornik, R. Rajter, A. Jagota, J. Luo, D. Asthagiri, M. Chaudhury, et al., “Long range interactions in nanoscale science,” Reviews of Modern Physics, 82 [2] 1887–1944 (2010).

17. D.M. Dryden, G.L. Tan, and R.H. French, “Optical Properties and van der Waals-London Dispersion Interactions in Berlinite Aluminum Phosphate from Vacuum Ultraviolet Spectroscopy,” Journal of the American Ceramic Society, 97 [4] 1143–1150 (2014).