For light-harvesting complexes (i.e. the Fenna-Matthews-Olson complex) or model systems with less than 8 sites, you can calculate absorption spectra, two-dimensional echo-spectra, and track the exciton populations and coherences.
== method ==
This tool employs a variant of the reduced hierarchy equations of motion (HEOM) method  for generalized spectral densities and implemented on massively parallel graphics processing units (GPU-HEOM) [2,3].
GPU-HEOM handles non-Markovian effects and works well in the biologically relevant temperature range.
== assumptions ==
* independent phonon baths attached to each site, the same shape of the spectral density J(omega) is taken for each independent bath
* decomposition of the vibronic spectral density into a superposition of shifted Lorentzian peaks
* high-temperature approximation
* for two-dimensional spectra, the program computes up to six Feynman pathways , and constructs the manifolds for the two exciton states as described in 
== caveats ==
* convergence must be verified by increasing the hierarchy depth (be careful, this quickly exhausts the available GPU memory) and by decreasing the time-step. We recommend to start from the examples provided.
* at lower temperatures (for the FMO complex typically below 100 K), the high-temperature approximation becomes invalid
* activation of excited-state absorption mode in two-dimensional spectroscopy requires longer computation times and consumes more memory. Use this option with caution.
== examples ==
The examples are a good starting point for own explorations. A short tutorial will be published soon, see also [http://quantumdynamics.wordpress.com quantumdynamics.wordpress.com] for additional background information and tutorials.
== references ==
# Y. Tanimura and R. Kubo (1989): Time Evolution of a Quantum System in Contact with a Nearly Gaussian-Markoffian Noise Bath, [http://jpsj.ipap.jp/link?JPSJ/58/101/ J. Phys. Soc. Jpn. vol. 58, p. 101]
# C. Kreisbeck and T. Kramer (2012): Long-Lived Electronic Coherence in Dissipative Exciton-Dynamics of Light Harvesting Complexes, [http://dx.doi.org/10.1021/jz3012029 Journal of Physical Chemistry Letters, vol. 3, p. 2828]
# C. Kreisbeck, T. Kramer, M. Rodríguez, B.Hein (2011): High-performance solution of hierarchical equations of motions for studying energy-transfer in light-harvesting complexes, [http://dx.doi.org/10.1088/1367-2630/14/2/023018 Journal of Chemical Theory and Computation, vol. 7, p. 2166]
# S. Mukamel, [http://worldcatlibraries.org/wcpa/isbn/9780195132915 Principles of nonlinear optical spectroscopy]
# B. Hein, C. Kreisbeck, T. Kramer, M. Rodríguez (2012): Modelling of Oscillations in Two-Dimensional Echo-Spectra of the Fenna-Matthews-Olson Complex, [http://dx.doi.org/10.1088/1367-2630/14/2/023018 New Journal of Physics vol. 14, p. 023018]
nanohub.org GPU deployment
We appreciate contributions by B. Hein for calculating absorption and two-dimensional echo-spectra and by M. Rodríguez.
Emmy-Noether Programme of the Deutsche Forschungsgemeinschaft, grant KR 2889/2
German Academic Exchange Service (DAAD)
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