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@leanfried
leanfried committed Dec 8, 2023
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Expand Up @@ -125,31 +125,31 @@ The files included in this publication use the following hierarchy:
set up log generation

- **jupyter_notebooks/**
- *convergence.ipynb* (no longer compatible)
Jupyter notebook for tracking convergence over the solve.
- *convergence.ipynb* (no longer compatible)
Jupyter notebook for tracking convergence over the solve.

- *interfacemetrics_adjacent_vicsweep.ipynb* (no longer compatible)
- *interfacemetrics_adjacent_vicsweep.ipynb* (no longer compatible)
Jupyter notebook for analyzing preliminary results for the adjacent filament dataset (Friedrich, L.M., & Gunther, R.T. (2023) Simulated inter-filament fusion in embedded 3D printing, submitted for publication.)

- *interfacemetrics_conicalNozzle.ipynb* (no longer compatible)
- *interfacemetrics_conicalNozzle.ipynb* (no longer compatible)
Jupyter notebook for analyzing OpenFOAM simulation data, for the stress mitigation dataset (Friedrich, L.M., Gunther, R.T. & Seppala, J.E. (2022) Simulated stress mitigation strategies in embedded 3D bioprinting, Physics of Fluids)

- *interfacemetrics_fusion.ipynb*
- *interfacemetrics_fusion.ipynb*
Jupyter notebook for analyzing results for the adjacent filament dataset (Friedrich, L.M., & Gunther, R.T. (2023) Simulated inter-filament fusion in embedded 3D printing, submitted for publication.)

- *interfacemetrics_LapRD.ipynb* (no longer compatible)
- *interfacemetrics_LapRD.ipynb* (no longer compatible)
Jupyter notebook for analyzing OpenFOAM simulation data, for the dataset that investigates models fitted to Laponite gels (unpublished)

- *interfacemetrics_viscsweep.ipynb* (no longer compatible)
- *interfacemetrics_viscsweep.ipynb* (no longer compatible)
Jupyter notebook for analyzing OpenFOAM simulation data, for the viscosity sweep dataset (Friedrich, L.M., & Seppala, J.E. (2021) Simulated filament shapes in embedded 3D printing, Soft Matter, doi: 10.1039/D1SM00731A)

- *interfacemetrics_yielding.ipynb* (no longer compatible)
- *interfacemetrics_yielding.ipynb* (no longer compatible)
Jupyter notebook for analyzing OpenFOAM simulation data, for the dataset that investigates yielded behaviors (unpublished)

- *noz3dscript.ipynb*
- *noz3dscript.ipynb*
Jupyter notebook for generating OpenFOAM input files.

- *videoCombine.ipynb*
- *videoCombine.ipynb*
Jupyter notebook for combining all of the time series for all simulations into one big video.

- **logs/**
Expand All @@ -161,10 +161,10 @@ The files included in this publication use the following hierarchy:
- *\__init\__.py*
Metadata about this project

- *colorBars.py*
- *colorBars.py*
Functions for creating color bars to be displayed on Paraview images.

- *comboscript.py*
- *comboscript.py*
Script for collecting interface points into csvs from vtk files and generating images from vtk files. Scripting for many folders and many images and tables.

- *paraview_csv.py*
Expand All @@ -179,7 +179,7 @@ The files included in this publication use the following hierarchy:
- *paraview_screenshots.py*
Functions for generating images of filaments from vtk files.

- *sim_metrics.py* (no longer compatible)
- *sim_metrics.py* (no longer compatible)
Functions for measuring cross-sections in paraview.

- **py/**
Expand All @@ -188,31 +188,31 @@ The files included in this publication use the following hierarchy:
- *\__init\__.py*
Metadata about this project

- *add_units.py*
- *add_units.py*
For adding units to tables generated in Paraview.

- *folder_parser.py*
- *folder_parser.py*
Tools for ending simulations early at a designated time.

- *folder_scraper.py*
- *folder_scraper.py*
Tools for reading legends quickly.

- *folder_stats.py*
- *folder_stats.py*
A class that scrapes metadata from a folder and keeps track of units

- *scrape_tools.py*
- *scrape_tools.py*
Functions for scraping values from legends.

- *scrape.py*
- *scrape.py*
A class for generating and reading legends for OpenFOAM simulations of embedded 3D printing of single filaments. Written for OpenFOAM v1912 and OpenFOAM 8. Scrapes input files for input variables.

- **cluster_tools/**
Files that handle simulations while they are running.

- *folder_loop.py*
- *folder_loop.py*
A tool for looping through all folders, running a function, and collecting errors into a table.

- *donescript.py*
- *donescript.py*
Functions for moving folders between computers, servers, for OpenFOAM simulations of embedded 3D printing of single filaments.

- *foldermover.py*
Expand All @@ -224,193 +224,193 @@ The files included in this publication use the following hierarchy:
- *backwards_read.py*
Function for reading text files from the bottom

- *file_export.py*
- *file_export.py*
Functions for exporting and importing tables and dictionaries

- *file_handling.py*
- *file_handling.py*
Functions that handle files that are in simulation folders

- *file_names.py*
- *file_names.py*
Functions for generating descriptive file names

- *plainIm.py*
- *plainIm.py*
Functions for exporting and importing tables as pandas dataframes

- **initialize/**
For creating OpenFOAM initialization files

- *block_points.py*
- *block_points.py*
For generating coordinates of blocks used for initializing the mesh

- *block.py*
- *block.py*
A class that describes blocks to initialize the mesh

- *boundary_input.py*
- *boundary_input.py*
A class that describes boundaries with defined properties

- *cd_vars.py*
- *cd_vars.py*
For handling variables that go into the controlDict

- *compile_XXX.py*
- *compile_XXX.py*
For generating specific files in the initialization folder

- *creator_adjacent.py*
- *creator_adjacent.py*
Functions for generating input files for disturbed filaments or fusion between filaments at a specific set of conditions.

- *creator.py*
- *creator.py*
Functions for generating all files.

- *dict_list.py*
- *dict_list.py*
A class useful for creating OpenFOAM files in the correct format

- *export.py*
- *export.py*
Tools for exporting files

- *file_creator.py*
- *file_creator.py*
A class that holds all input parameters

- *file_group.py*
- *file_group.py*
A class that holds all strings to be exported as files

- *file_plotter.py*
- *file_plotter.py*
A class that creates plots representing the input boundaries

- *fluid.py*
- *fluid.py*
A class that holds rheological data about a fluid

- *fv_sol_grp.py*
- *fv_sol_grp.py*
A class that holds fvsolution variables for a given solve variable (e.g. interFoam)

- *fv_vars.py*
- *fv_vars.py*
A class that holds all fvsolution and fvschemes variables

- *geometry_file.py*
- *geometry_file.py*
A class that holds a table summarizing the geometry for export

- *initialize_tools.py*
- *initialize_tools.py*
A class that creates common headers and footers for files

- *mesh_vars.py*
- *mesh_vars.py*
A class that describes the meshing variables

- *ncreate3d.py*
- *ncreate3d.py*
Imports dependencies

- *noz_vars.py*
- *noz_vars.py*
Describes the geometry of the nozzle

- *real_boundaries.py*
- *real_boundaries.py*
Creates coordinates and boundary conditions for all boundaries

- *transport_group.py*
- *transport_group.py*
Classes that describe rheology, density, etc. of fluids

- **plot/**
Tools for plotting results

- *cells_plot.py*
- *cells_plot.py*
Plot the number of cells over time

- *colors.py*
- *colors.py*
Handle colors for all plots

- *combo_plot.py*
- *combo_plot.py*
A class for plotting the same variables across multiple axes, for different sets of data. Reshapes input data so x and y data that is unevenly spaced is plotted categorically instead.

- *convergence_plot.py*
- *convergence_plot.py*
Plot residuals over time

- *folder_plots.py*
- *folder_plots.py*
A class for plotting many folders on many plots

- *legend.py*
- *legend.py*
For creating several types of legends

- *markers.py*
- *markers.py*
For determining what markers should be plotted

- *measurement_plot.py*
- *measurement_plot.py*
For plotting measurements of cross-sections across different simulations

- *meta_plot.py*
- *meta_plot.py*
A class for plotting metadata

- *multi_plot.py*
- *multi_plot.py*
A class for plotting measurements directly against an input variable.

- *pic_plot.py*
- *pic_plot.py*
For plotting pictures collected using ParaView

- *plot_adjacent.py*
- *plot_adjacent.py*
Tools for plotting common variables used in simulations of fused filaments and disturbed filaments

- *rate_plot.py*
- *rate_plot.py*
For plotting the simulation rate as circles as a function of input variables

- *sizes.py*
- *sizes.py*
For determining the size of the plot, font sizes, based on default settings

- *super_summary_plot.py*
- *super_summary_plot.py*
For plotting measurements of cross-sections at a specific slice and time, directly against input variables

- *time_plot.py*
- *time_plot.py*
For plotting simulation time as text as a function of input variables

- *trace_plots.py*
- *trace_plots.py*
For plotting measurements of cross-sections against position in the filament

- *txt_plot.py*
- *txt_plot.py*
For plotting simulation names as a function of input variables

- *value_plot.py*
- *value_plot.py*
A class for plotting data as squares or circles

- *varPlots.py*
- *varPlots.py*
Generic class for creating plots and handling the variables to plot against

- *xs_plot.py*
- *xs_plot.py*
Plot cross-sections

- **points/**
For handling tables of interface points

- *folder_points.py*
- *folder_points.py*
For importing and exporting points files

- *points_tools.py*
- *points_tools.py*
For selecting and sorting points

- *slice_points.py*
- *slice_points.py*
For sorting and labeling points belonging to different segments

- **summarize/**
For measuring cross-sections and summarizing data across folders

- *ideals.py*
- *ideals.py*
Ideal values of cross-section measurements

- *legend_summary.py*
- *legend_summary.py*
For scraping all legends together into one table.

- *log_reader.py*
- *log_reader.py*
For scraping values from logs

- *steady.py*
- *steady.py*
For determining when simulations reach steady state based on measurements of cross-sections

- *sum_and_steady.py*
- *sum_and_steady.py*
For summarizing data and finding steady state

- *summarizer_adjacent.py*
- *summarizer_adjacent.py*
For measuring cross-sections of disturbed and fused filaments

- *summarizer_single.py*
- *summarizer_single.py*
For measuring cross-sections of single filaments

- *summarizer.py*
- *summarizer.py*
For measuring cross sections, generically

- *super_summary.py*
- *super_summary.py*
For collecting summary data at a slice and time for all folders and combining into a single table

- **tools/**
Expand All @@ -419,17 +419,17 @@ The files included in this publication use the following hierarchy:
- *config.py*
script for importing packages and setting environmental variables, e.g. folders

- *logs.py*
- *logs.py*
For generating log files

- *strings.py*
- *strings.py*
For converting variable names between their English, code, shortened, and symbolic forms

- *val_tools.py*
- *val_tools.py*
For converting variables to floats

- **video/**
For generating videos

- *video_funcs.py*
- *video_funcs.py*
Tools generating videos

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