VibronicToolkit

Tools for vibronic Hamiltonians. This package aims for correctness and readability rather than performance, so these tools are mainly useful for verifying other implementations.

Tested with Julia 1.0.

Installation

pkg> add https://github.com/0/VibronicToolkit.jl.git

In order to run the driver scripts in bin/, you will also need to

pkg> add ArgParse
pkg> add PyPlot

Application project

If you're working with a clone of this repository, you can use the basic application project in bin/, which already has VibronicToolkit, ArgParse, and PyPlot as dependencies. From the repository root, run

julia --project=bin

and then

pkg> dev .

to create bin/Manifest.toml with a development version of VibronicToolkit.

Units

• The input energy parameters define the unit of energy E.
• The input frequency parameters are in units of E (i.e. hbar = 1).
• Positions are dimensionless, so the other input parameters are also in units of E.
• Reciprocal temperatures are in units of reciprocal energy (i.e. k_B = 1).
• Heat capacities are dimensionless (in units of k_B).

Examples

To run the following examples, you should set the project (e.g. using --project or JULIA_PROJECT) to a Julia project that has the prerequisites installed.

• julia bin/analytical.jl --conf examples/s2m2_uncoupled.json --beta 43.21
• julia bin/sos.jl --conf examples/s2m2_uncoupled.json --beta 43.21 --basis-size 30
• julia bin/trotter.jl --conf examples/s2m2_uncoupled.json --beta 43.21 --basis-size 30 --num-links 20
• julia bin/sampling.jl --conf examples/s2m2_uncoupled.json --beta 43.21 --num-links 20 --num-samples 1000000
• julia bin/sampling.jl --conf examples/s2m2_uncoupled.json --beta 43.21 --dbeta 1e-4 --num-links 20 --num-samples 1000000
• julia bin/pes.jl --conf examples/s2m2_coupled.json --num-links 20 --sampling-conf examples/s2m2_simple.json --sampling-beta 43.21 --extent -2,2,-1,1 --out-path pes.pdf --contour
• julia bin/iterative_decomposition.jl --conf examples/s2m2_coupled.json --out-conf decomp.json --out-vs decomp.dat

Testing

To run all the tests, activate the package before calling test:

pkg> activate .
(VibronicToolkit) pkg> test

Publications

The following publications contain data created using this package:

• Neil Raymond, Dmitri Iouchtchenko, Pierre-Nicholas Roy, and Marcel Nooijen. A path integral methodology for obtaining thermodynamic properties of nonadiabatic systems using Gaussian mixture distributions. The Journal of Chemical Physics 148, 194110 (2018). doi:10.1063/1.5025058, arXiv:1805.05971.

Acknowledgements

Thanks to Neil Raymond for designing the parameter file format and helping to verify this implementation!

License

Provided under the terms of the MIT license. See LICENSE for more information.