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.

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

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.

• 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).

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

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

pkg> activate .
(VibronicToolkit) pkg> test

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.

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

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