Replication data of C6 group for: "A thermalized electrokinetics model including stochastic reactions suitable for multiscale simulations of reaction-advection-diffusion systems" (doi:10.18419/darus-2258)

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Replication data of C6 group for: "A thermalized electrokinetics model including stochastic reactions suitable for multiscale simulations of reaction-advection-diffusion systems"

doi:10.18419/darus-2258

DaRUS

2022-07-20

1

Tischler, Ingo; Holm, Christian; Weeber, Rudolf; Kuron, Michael; Weik, Florian; Kaufmann, Robert, 2022, "Replication data of C6 group for: "A thermalized electrokinetics model including stochastic reactions suitable for multiscale simulations of reaction-advection-diffusion systems"", https://doi.org/10.18419/darus-2258, DaRUS, V1

Replication data of C6 group for: "A thermalized electrokinetics model including stochastic reactions suitable for multiscale simulations of reaction-advection-diffusion systems"

doi:10.18419/darus-2258

Tischler, Ingo (University of Stuttgart)

Holm, Christian (University of Stuttgart)

Weeber, Rudolf (University of Stuttgart)

Kuron, Michael (University of Stuttgart)

Weik, Florian (University of Stuttgart)

Kaufmann, Robert (University of Stuttgart)

358283783 - SFB 1333

390740016 - SimTech

DaRUS

Tischler, Ingo

Holm, Christian

Tischler, Ingo

2021-12-02

https://doi.org/10.18419/darus-2258

Chemistry, Physics, Advection-Reaction-Diffusion, Reaction-Diffusion systems

Simulation Physics, Computational physics

All primary data files of measurements and processed data of the journal article mentioned under related publications from C6 group can be found here. <br/> The data is structured according to figures and schemes in the research article and contains the following data types: text files, .ipynb (jupyter notebooks), .py (python files)

pystencils and ESPResSo script files

<p>The important script of this dataverse is the `fluctuating_reactive_ek.ipynb` jupyter notebook. To run this notebook properly one would need the 3 additional files `poisson.py`, `ideal_gas_md_hist.dat` and `coulomb_gas_md_hist.dat`, which hold the MD data to compare to and help to solve the poisson equation. The `fluctuating_reactive_ek_validation.ipynb` uses more time steps, which were used to create the data in the corresponding publication.</p> <p>In the performance folder, there are the scripts that were used to measure calculation time of the method in the bwunicluster. The measured times are also included here., In the espresso folder there is the note of the espresso commit used and the patch apllied to it. Also there are the scripts to run the ESPResSo simulations.</p>

Tischler I, Weik F, Kaufmann R, Kuron M, Weeber R, Holm C. A thermalized electrokinetics model including stochastic reactions suitable for multiscale simulations of reaction-advection-diffusion systems. J. Comput. Sci., 2022, 101770

10.1016/j.jocs.2022.101770

Tischler I, Weik F, Kaufmann R, Kuron M, Weeber R, Holm C. A thermalized electrokinetics model including stochastic reactions suitable for multiscale simulations of reaction-advection-diffusion systems. J. Comput. Sci., 2022, 101770

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coulomb_gas_md_hist.dat

text/x-fixed-field

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fluctuating_reactive_ek.ipynb

application/x-ipynb+json

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fluctuating_reactive_ek_validation.ipynb

application/x-ipynb+json

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ideal_gas_md_hist.dat

text/x-fixed-field

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poisson.py

text/x-python

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base_version

text/plain; charset=US-ASCII

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reactions.patch

application/octet-stream

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fluct_diff_react_system.py

text/x-python

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loaded.pvsm

application/octet-stream

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reaction_diffusion_fluctuation.py

text/x-python

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react_fig.dat

text/x-fixed-field

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measure_time_system_size.sh

application/x-sh

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measure_time_system_size_gpu.sh

application/x-sh

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plot_system_size_scaling.py

text/x-python

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speed_test.py

text/x-python

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start_sims_size.sh

application/x-sh

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timings_scaling.tar

application/x-tar