pdom.export

Helper functions to export simulation results.

pdom.export.fit_dark(cfg, result, result_raw)

Export function for fit: Adsorption - Desorption experiment in the dark.

Parameters:

• cfg (dict) – simulation config
• result (tuple) – fit_t, fit_y, k_ads, k_des
• result_raw – raw fit function result

Result:

• plot with fit and initial data points fit_dark.pdf
• space separated data file containing the fit fit_dark-values_calculated.txt
• space separated data file containing initial data points fit_dark-values_experiment.txt
• .json with the fitted parameters fit_dark.json
• .txt files with corresponding units (LaTeX formatted)

pdom.export.fit_single(cfg, result, result_raw)

Export function for fit: single species degradation model.

Parameters:

• cfg (dict) – simulation config
• result (tuple) – fit_t, fit_y, k_ads, k_des, k_reac
• result_raw – raw fit function result

Result:

• plot with fit and initial data points fit_single.pdf
• space separated data file containing the fit fit_single-values_calculated.txt
• space separated data file containing initial data points fit_single-values_experiment.txt
• .json with the fitted parameters fit_single.json
• .txt files with corresponding units (LaTeX formatted)

pdom.export.fit_toc(cfg, sd_error, t, fit)

Export function for fit: TOC.

Parameters:

• cfg (dict) – simulation config
• sd_error (float) – standard derivation error
• t (ndarray) – fit time series
• fit (ndarray) – fit toc series

Result:

• plot with fit and initial data points | fit_toc.pdf
• space separated data file containing the fit | fit_toc-values_calculated.txt
• space separated data file containing initial data points | fit_toc-values_experiment.txt
• .json with the fitted parameters | fit_toc.json
• .txt files with corresponding units (LaTeX formatted)

pdom.export.multi_species(cfg, t, N_surf, N_vol)

Export function for incremental and fragmentation multi species model simulations.

Parameters:

• cfg (dict) – simulation config
• t (ndarray) – fit time series
• N_surf (ndarray) – number of molecules on the surface
• N_vol (ndarray) – number of molecules in solution

Result:

• plot with concentration development in solution and TOC c_volume-toc.pdf
• plot of the segments in solution and on the surface volume_segments.pdf, solution_segments.pdf
• space separated data file containing the concentrations in solution multi_species-values_volume.txt
• space separated data file containing the concentrations on the surface multi_species-values_surface.txt
• .txt files with corresponding units (LaTeX formatted)

pdom.export.multi_species_bonds(cfg, t, N_surf_detail, N_vol_detail)

Export function for incremental and fragmentation multi species model simulations.

Parameters:

• cfg (dict) – simulation config
• t (ndarray) – fit time series
• N_surf_detail (ndarray) – number of molecules on the surface
• N_vol_detail (ndarray) – number of molecules in solution

Result:

• same files as multi_species()
• plot of the average excess bond count excess_bonds.pdf
• space separated data file containing the average number of excess bonds multi_species-excess_bonds

pdom.export.single_species(cfg, t, N_surf, N_vol)

Export function single species model simulations.

Parameters:

• cfg (dict) – simulation config
• t (ndarray) – fit time series
• N_surf (ndarray) – number of molecules on the surface
• N_vol (ndarray) – number of molecules in solution

Result:

• plot with concentration development in solution and on the surface single_species.pdf
• space separated data file containing the concentrations in solution single_species-values_volume.txt
• space separated data file containing the concentrations on the surface single_species-values_surface.txt
• .txt files with corresponding units (LaTeX formatted)