TARDIGRADE-EXAMPLES CLI
config_software.py
Configure software paths in a YAML file
usage: sphinx-build [-h] --config-file CONFIG_FILE
Named Arguments
- --config-file
The YAML file to write software paths
peta.py
Copy DNS results from the CU Peta library to the output directory
usage: sphinx-build [-h] --source-directory SOURCE_DIRECTORY
--output-directory OUTPUT_DIRECTORY
Named Arguments
- --source-directory
The source directory of DNS simulation results
- --output-directory
The output directory destination.
DNS_Abaqus.build_dynamic_elastic_cylinder.py
Create an Abaqus model of an elastic cylinder under dynamic compression
usage: abaqus cae -noGui build_dynamic_elastic_cylinder.py --
[-h] --model-name MODEL_NAME --diam DIAM --height HEIGHT --seed SEED
--material-E MATERIAL_E --material-nu MATERIAL_NU --material-rho
MATERIAL_RHO --total-force TOTAL_FORCE --duration DURATION --num-steps
NUM_STEPS [--fix-lateral-dofs] [--finite-rise FINITE_RISE]
Named Arguments
- --model-name
Specify the name of the model
- --diam
Specify the diameter (mm) of the cylinder
- --height
Specify the height (mm) of the cylinder
- --seed
Specify the approximate global seed size (mm) for meshing
- --material-E
Specify the elastic modulus (MPa) of the material
- --material-nu
Specify the Poisson ratio of the material
- --material-rho
Specify the density (g/cm^3) of the material. This value will be multiplied by 1.00e-9 to convert to units of tonne/mm^3
- --total-force
Specify the force applied to cylinder.
- --duration
Specify the duration of the simulation.
- --num-steps
Specify the number of fixed time increments.
- --fix-lateral-dofs
Option to force all x- and y-displacements to be fixed
Default:
False- --finite-rise
Optional extra number of time steps over which to to ramp force
DNS_Abaqus.build_elastic_cylinder.py
Create an Abaqus model of an elastic cylinder under static compression
usage: abaqus cae -noGui build_elastic_cylinder.py -- [-h] --model-name
MODEL_NAME --diam DIAM
--height HEIGHT --seed
SEED --material-E
MATERIAL_E
--material-nu
MATERIAL_NU
--material-rho
MATERIAL_RHO
--disp-fact DISP_FACT
--num-steps NUM_STEPS
--BCs BCS
Named Arguments
- --model-name
Specify the name of the model
- --diam
Specify the diameter (mm) of the cylinder
- --height
Specify the height (mm) of the cylinder
- --seed
Specify the approximate global seed size (mm) for meshing
- --material-E
Specify the elastic modulus (MPa) of the material
- --material-nu
Specify the Poisson ratio of the material
- --material-rho
Specify the density (g/cm^3) of the material. This value will be multiplied by 1.00e-9 to convert to units of tonne/mm^3
- --disp-fact
Specify the multiplicative factor of the sample height by which the model will be compressed
- --num-steps
Specify the fixed number of steps to simulate
- --BCs
The type of boundary conditions, either “slip” or “clamp”
DNS_Abaqus.dynamic_analytical_comparison.py
Plot dynamic Abaqus results against an analytical solution
usage: python dynamic_analytical_comparison.py [-h] -i INPUT_FILE
[INPUT_FILE ...]
[-o OUTPUT_FILE] --x-path
X_PATH --y-path Y_PATH
--x-label X_LABEL --y-label
Y_LABEL --x-units X_UNITS
--y-units Y_UNITS
[--diam DIAM]
[--height HEIGHT]
[--material-E MATERIAL_E]
[--material-rho MATERIAL_RHO]
[--total-force TOTAL_FORCE]
[--duration DURATION]
[--num-steps NUM_STEPS]
[--csv-file CSV_FILE]
[--series-plot SERIES_PLOT]
Named Arguments
- -o, --output-file
The output file for plotting
Default:
'dynamic_analytical_comparison.png'- --diam
Specify the diameter (mm) of the cylinder. This values will be multiplied by 1.e-3 to convert to units of m
- --height
Specify the height (mm) of the cylinder. This values will be multiplied by 1.e-3 to convert to units of m
- --material-E
Specify the elastic modulus (MPa) of the material. This value will be multiplied by 1.6 to convert to units of Pa.
- --material-rho
Specify the density (g/cm^3) of the material. This value will be multiplied by 1.00e3 to convert to units of kg/m^3
- --total-force
Specify the force (N) applied to cylinder.
- --duration
Specify the duration of the simulation.
- --num-steps
Specify the number of fixed time increments.
required named arguments
- -i, --input-file
The HDF5 dataset file containing Abaqus results
- --x-path
The HDF5 path to the x data
- --y-path
The HDF5 path to the y data
- --x-label
The label (without units) for the x data
- --y-label
The label (without units) for the y data.
- --x-units
The dependent (x-axis) units string.
- --y-units
The independent (y-axis) units string.
- --csv-file
Name of output CSV file.
- --series-plot
Name of the output series convergence plot for summation terms.
DNS_Abaqus.extract_history.py
Plot Abaqus history output for force versus displacement
usage: python extract_history.py [-h] -i INPUT_FILE [INPUT_FILE ...] --x-path
X_PATH --y-path Y_PATH --x-label X_LABEL
--y-label Y_LABEL --x-units X_UNITS
--y-units Y_UNITS [--csv_file CSV_FILE] -o
OUTPUT_FILE
Named Arguments
- -o, --output-file
The output file for plotting
required named arguments
- -i, --input-file
The Xarray Dataset file(s)
- --x-path
The HDF5 path to the x data
- --y-path
The HDF5 path to the y data
- --x-label
The label (without units) for the x data
- --y-label
The label (without units) for the y data.
- --x-units
The dependent (x-axis) units string.
- --y-units
The independent (y-axis) units string.
- --csv_file
Name of output CSV file.
DNS_Abaqus.extract_frames.py
Extracts 3D field output from a completed Abaqus simulation to save as 2D image
usage: abaqus cae -noGui extract_frames.py -- [-h] -i INPUT_FILE -o
OUTPUT_FILE [--frame FRAME]
--field FIELD
Named Arguments
- -i, --input-file
The Abaqus input file created by
build_model.py.- -o, --output-file
The modified Abaqus input file
- --frame
Simulation frame number to extract field output. Final frame will be plotted if nothing is specified.
- --field
Field to extract
DNS_Abaqus.modify_input.py
Modify Abaqus input file to output ‘COORD’ at integration points
usage: modify_input.py [-h] [-i INPUT_FILE] [-o OUTPUT_FILE]
Named Arguments
- -i, --input-file
The Abaqus input file created by
build_model.py.- -o, --output-file
The modified Abaqus input file
DNS_Abaqus.ODBextract_to_XDMF.py
Convert Abaqus DNS results to XDMF format
usage: ODBextract_to_XDMF.py [-h] [-i INPUT_FILE] [-o OUTPUT_FILE]
[--elem-path ELEM_PATH] [--node-path NODE_PATH]
[--mesh-path MESH_PATH] [-c COLLOCATION_OPTION]
[--velocities VELOCITIES]
[--accelerations ACCELERATIONS]
[--specific-frames SPECIFIC_FRAMES [SPECIFIC_FRAMES ...]]
[--ref-density REF_DENSITY]
[--dump-all-33-stresses DUMP_ALL_33_STRESSES]
Named Arguments
- -i, --input-file
Specify the input hdf5 file generated from odb_extract
- -o, --output-file
Specify the output filename for the h5 + XDMF file pair
- --elem-path
Specify the hdf5 group path to element fields
- --node-path
Specify the hdf5 group path to nodal fields
- --mesh-path
Specify the hdf5 group path to mesh data
- -c, --collocation-option
Specify the method for collocation, either “qp” for quadrature points or “center” for element center.
Default:
'ip'- --velocities
String specifying “True” or “False” if velocities are to be extracted
Default:
'False'- --accelerations
String specifying “True” or “False” if accelerations are to be extracted
Default:
'False'- --specific-frames
A list of floats corresponding to the frames to extract
- --ref-density
The reference density of the material in g/cm^3
Default:
2.0- --dump-all-33-stresses
Optional filename to dump all 33 stresses from DNS
DNS_Ratel.build_options_file.py
Write Ratel options file
usage: build_options_file.py [-h] -o OUTPUT_FILE --material-E MATERIAL_E
--material-nu MATERIAL_NU --material-rho
MATERIAL_RHO --top-id TOP_ID --bottom-id
BOTTOM_ID --num-steps NUM_STEPS --displacement
DISPLACEMENT --BCs BCS
Named Arguments
- -o, --output-file
The name of the Ratel options file to output
- --material-E
The material’s elastic modulus
- --material-nu
The material’s Poisson ratio
- --material-rho
The material’s density
- --top-id
The id of the top surface
- --bottom-id
The id of the bottom surface
- --num-steps
The number of steps for the simulation
- --displacement
The displacement to apply to the top surface
- --BCs
The type of boundary conditions, either ‘slip’ or ‘clamp’
DNS_Ratel.plot_force_displacement.py
Process force-displacement from Ratel DNS results
usage: python plot_force_displacement.py [-h] --csv-file CSV_FILE
--output-file OUTPUT_FILE
--output-csv OUTPUT_CSV --face-id
FACE_ID --final-disp FINAL_DISP
[--force-col FORCE_COL]
[--header-row HEADER_ROW]
[--force-factor FORCE_FACTOR]
Named Arguments
- --csv-file
The csv file containing force results
- --output-file
The name of the output file of collected results
- --output-csv
The name of the output csv file
- --face-id
The face id (or ids) of forces to process
- --final-disp
The final displacement (mm) to linearly ramp over simulation duration
- --force-col
The column containing desired force information
Default:
'force_z'- --header-row
The row containing the headers
Default:
0- --force-factor
The factor to scale force
Default:
1
DNS_Ratel.vtk_to_xdmf.py
Convert Ratel DNS results to XDMF format
usage: vtk_to_xdmf.py [-h] [-i INPUT_FILES [INPUT_FILES ...]] [-o OUTPUT_FILE]
[--dist-factor DIST_FACTOR]
[--stress-factor STRESS_FACTOR]
[--ref-density REF_DENSITY]
[--density-factor DENSITY_FACTOR]
[--dump-all-33-stresses DUMP_ALL_33_STRESSES]
Named Arguments
- -i, --input-files
Specify the input VTK files containing Ratel DNS results
- -o, --output-file
Specify the output filename for the h5 + XDMF file pair
- --dist-factor
Optional argument to scale DNS displacements and coordinates
Default:
1- --stress-factor
Optional argument to scale DNS stresses
Default:
1- --ref-density
Optional argument to specify the reference density to be converted to current density by the Jacobian of deformation if current density is not reported in the DNS results
Default:
2e-09- --density-factor
Optional factor to scale current density (if provided in the DNS results to Mg/tonne^3
Default:
1- --dump-all-33-stresses
Optional filename to dump all 33 stresses from DNS
Filter.bounds_from_DNS.py
Create a csv containing the extents of a DNS file
usage: bounds_from_DNS.py [-h] -d DNS_FILE -o OUTPUT_FILE [--coord COORD]
Named Arguments
- -d, --dns-file
The name of the input XDMF file containing DNS results
- -o, --output-file
The name of the output csv file of bounding information
- --coord
The name of the coordinate field
Default:
'coord'
Filter.build_filter_config.py
Write the configuration file for the Micromorphic Filter
usage: build_filter_config.py [-h] -o OUTPUT_FILE --job-name JOB_NAME
--dns-file DNS_FILE --macro-file MACRO_FILE
--volume VOLUME --density DENSITY
--cauchy-stress CAUCHY_STRESS --displacement
DISPLACEMENT [--velocity VELOCITY]
[--acceleration ACCELERATION]
[--max-parallel MAX_PARALLEL]
Named Arguments
- -o, --output-file
Specify the output filename for filter configuration
- --job-name
Specify the name of the job for the Micromorphic Filter
- --dns-file
Specify the name of the XDMF file containing DNS data
- --macro-file
Specify the name of the macroscale filter domain file
- --volume
Specify the string identifying volume quantities located in “dns-file”
- --density
Specify the string identifying density quantities located in “dns-file”
- --cauchy-stress
Specify the string identifying stress quantities located in “dns-file”
- --displacement
Specify the string identifying displacement quantities located in “dns-file”
- --velocity
Optional string identifying velocity quantities located in “dns-file”
- --acceleration
Optional string identifying acceleration quantities located in “dns-file”
- --max-parallel
Optional parameter defining the number of parallel processes for the Micromorphic Filter
Filter.collect_multi_domain_errors.py
Collect balance equation errors across filter domain studies
usage: python collect_multi_domain_errors.py [-h] --csv-files CSV_FILES
[CSV_FILES ...] --num-domains
NUM_DOMAINS [NUM_DOMAINS ...]
--output-file OUTPUT_FILE
Named Arguments
- --csv-files
A list of csv files containing balance equation errors
- --num-domains
A list of integers corresponding to the number of filtering domains associated with results contained in each csv file.
- --output-file
The name of the output file of collected results
Filter.collect_multi_domain_stats.py
Collect statistics of a homogenized micromorphic quantity across filter domain studies
usage: python collect_multi_domain_stats.py [-h] --csv-files CSV_FILES
[CSV_FILES ...] --num-domains
NUM_DOMAINS [NUM_DOMAINS ...]
[--output-file OUTPUT_FILE]
[--box-plot BOX_PLOT]
[--narrow NARROW]
Named Arguments
- --csv-files
A list of csv files containing information to collect
- --num-domains
A list of integers corresponding to the number of filtering domains associated with results contained in each csv file.
- --output-file
The name of the output file of collected results
- --box-plot
The name of an optional box and whisker plot
- --narrow
Optional flag to make a narrow box plot
Filter.force_bounds.py
Create a csv file containing information for a bounding box encompassing all DNS points
usage: force_bounds.py [-h] -o OUTPUT_FILE --xmin XMIN --xmax XMAX --ymin YMIN
--ymax YMAX --zmin ZMIN --zmax ZMAX
Named Arguments
- -o, --output-file
The name of the output csv file of bounding informaiton
- --xmin
The minimum x-value
- --xmax
The maximum x-value
- --ymin
The minimum y-value
- --ymax
The maximum y-value
- --zmin
The minimum z-value
- --zmax
The maximum z-value
Filter.parse_balance_errors.py
Parse balance equation errors from Micromorphic Filter standard output
usage: parse_balance_errors.py [-h] [-i INPUT_FILE] --output-csv OUTPUT_CSV
[--output-plot OUTPUT_PLOT]
Named Arguments
- -i, --input-file
The standard out file produced when running the Micromorphic Filter
- --output-csv
Name of output csv file summarizing output for each timestep
- --output-plot
Optional filename to plot balance equation errors
Filter.run_micromorphic_filter.py
Run the Micromorphic Filter
usage: run_micromorphic_filter.py [-h] --config-file CONFIG_FILE
Named Arguments
- --config-file
Specify the filter configuration file
Filter.single_macroscale.py
Write a single macroscale domain file for the Micromorphic Filter
usage: single_macroscale.py [-h] -o OUTPUT_FILE
[--single-points SINGLE_POINTS SINGLE_POINTS SINGLE_POINTS SINGLE_POINTS SINGLE_POINTS SINGLE_POINTS]
[--csv-file CSV_FILE]
Named Arguments
- -o, --output-file
Specify the output filename for the h5 + XDMF file pair
- --single-points
Specify the X, Y, and Z extents for the a single element macro domain
- --csv-file
Specify a csv file containing the bounds of a DNS file
Filter.visualize_results.py
Post-process Micromorphic Filter Output
usage: visualize_results.py [-h] -i INPUT_FILE [--average AVERAGE]
[--num-domains NUM_DOMAINS]
[--plot-cauchy-couple PLOT_CAUCHY_COUPLE]
[--plot-cauchy-stress PLOT_CAUCHY_STRESS]
[--plot-PK2-stress PLOT_PK2_STRESS]
[--plot-symm-stress PLOT_SYMM_STRESS]
[--plot-SIGMA-stress PLOT_SIGMA_STRESS]
[--plot-stress-diff PLOT_STRESS_DIFF]
[--plot-body-couples PLOT_BODY_COUPLES]
[--plot-spin-inertias PLOT_SPIN_INERTIAS]
[--plot-spin-diff PLOT_SPIN_DIFF]
[--plot-rotation-diff PLOT_ROTATION_DIFF]
[--plot-stretch-diff PLOT_STRETCH_DIFF]
[--plot-stress-norms PLOT_STRESS_NORMS]
[--csv-cauchy CSV_CAUCHY] [--csv-PK2 CSV_PK2]
[--csv-GLstrain CSV_GLSTRAIN]
[--csv-ref-mod CSV_REF_MOD]
[--csv-cur-mod CSV_CUR_MOD]
[--csv-estrain CSV_ESTRAIN] [--csv-symm CSV_SYMM]
[--csv-stress-diff CSV_STRESS_DIFF]
[--csv-m CSV_M] [--csv-M CSV_M]
[--csv-stress33-all CSV_STRESS33_ALL]
[--csv-all-quantities-single-domain CSV_ALL_QUANTITIES_SINGLE_DOMAIN]
[--rho-binder RHO_BINDER] [--rho-grain RHO_GRAIN]
Named Arguments
- -i, --input-file
The XDMF Micromorphic Filter results file
- --average
Boolean whether or not homogenized DNS results will be averaged
Default:
False- --num-domains
Specify the number of filter domains
Default:
1- --plot-cauchy-couple
Optional filename to plot Cauchy couple vs. simulation time
- --plot-cauchy-stress
Optional filename to plot Cauchy stress vs. Eulerian strain
- --plot-PK2-stress
Optional filename to plot PK2 stress vs. Green-Lagrange strain
- --plot-symm-stress
Optional filename to plot symmetric micro stress vs. Eulerian strain
- --plot-SIGMA-stress
Optional filename to plot Symmetric micro stress vs. Green-Lagrange strain
- --plot-stress-diff
Optional filename to plot difference between Cauchy and symmetric micro stresses vs. simulation time
- --plot-body-couples
Optional filename to plot body couples vs. simulation time
- --plot-spin-inertias
Optional filename to plot micro spin inertias vs. simulation time
- --plot-spin-diff
Optional filename to plot difference between body couples and micro spin inertias vs. simulation time
- --plot-rotation-diff
Optional filename to plot difference between macro and micro rotations vs. simulation time
- --plot-stretch-diff
Optional filename to plot differences between macro and micro stretches vs. simulation time
- --plot-stress-norms
Optional filename to plot norms of cauchy stress, symmetric micro stress, difference between Cauchy and symmetric micro stresses, and higher order stress.
- --csv-cauchy
Optional filename for csv output of Cauchy stress summary statistics
- --csv-PK2
Optional filename for csv output of PK2 stress summary statistics
- --csv-GLstrain
Optional filename for csv output of Green-Lagrange strain summary statistics
- --csv-ref-mod
Optional filename for csv output of ‘moduli’ calculation (S_{ij} / E_{ij}) in reference configuration summary statistics
- --csv-cur-mod
Optional filename for csv output of ‘moduli’ calculation (sigma_{ij} / e_{ij}) in the current configuration summary statistics
- --csv-estrain
Optional filename for csv output of Eulerian strain summary statistics
- --csv-symm
Optional filename for csv output of symmetric micro stress summary statistics
- --csv-stress-diff
Optional filename for csv output of difference between Cauchy and symmetric micro stresses summary statistics
- --csv-m
Optional filename for csv output of couple stress (current configuration) summary statistics
- --csv-M
Optional filename for csv output of couple stress (reference configuration) summary statistics
- --csv-stress33-all
Optional filename for csv output of all Cauchy 33 values
- --csv-all-quantities-single-domain
Optional filename for csv output of all quantities for a single domain
- --rho-binder
The density of the binder material, required if ‘–csv-all-quantities-single-domain’ is specified
- --rho-grain
The density of the grain material, required if ‘–csv-all-quantities-single-domain’ is specified
Filter.xdmf_local_paths.py
Create a copy of an XDMF file with absolute H5 paths replaced with relative paths
usage: xdmf_local_paths.py [-h] -i INPUT_FILE -o OUTPUT_FILE --oldpath OLDPATH
--newpath NEWPATH
Named Arguments
- -i, --input-file
The XDMF file output by the Micromorphic Filter with absolute H5 paths
- -o, --output-file
The new XDMF file with relative H5 paths
- --oldpath
The absolute path to be replaced by
--newpath- --newpath
The relative path to replace
--oldpath
Filter.xdmf_tomfoolery.py
Modify an XDMF file by combining elements from separate ‘blocks’
usage: xdmf_tomfoolery.py [-h] -o OUTPUT_FILE --input-file INPUT_FILE
Named Arguments
- -o, --output-file
Specify the output filename for the h5 + XDMF file pair
- --input-file
Specify the XDMF mesh file to operate on
Calibrate.build_calibration_map.py
Create a yaml file to map calibration results
usage: python build_calibration_map.py [-h] --calibrated-elements
CALIBRATED_ELEMENTS
[CALIBRATED_ELEMENTS ...]
--calibrated-files CALIBRATED_FILES
[CALIBRATED_FILES ...]
--ignore-boundary-yml
IGNORE_BOUNDARY_YML
--ignore-boundary-summary-file
IGNORE_BOUNDARY_SUMMARY_FILE
--output-file OUTPUT_FILE
Named Arguments
- --calibrated-elements
A list of elements with associated calibration files
- --calibrated-files
A list of files containing calibration results
- --ignore-boundary-yml
A yaml file containing the ‘best’ calibration using the kernel density estimate
- --ignore-boundary-summary-file
A csv file containing a summary of calibrated parameters for each element
- --output-file
The name of the output yaml file
Calibrate.calibrate_element.py
Calibrate micromorphic linear elasticity for averaged output on a single filter domain (i.e. macroscale element)
usage: calibrate_element.py [-h] [-i INPUT_FILE] [-o OUTPUT_FILE]
[--Emod EMOD] [--nu NU] [--L L]
[--element ELEMENT] [--increment INCREMENT] --case
CASE [--plot-file PLOT_FILE] [--average AVERAGE]
[--UQ-file UQ_FILE]
Named Arguments
- -i, --input-file
The homogenized XDMF file output by the Micromorphic Filter
- -o, --output-file
The resulting list of parameters stored in a yaml file
- --Emod
DNS elastic modulus, used for initial parameter estimation.
- --nu
DNS Poisson’s ratio, used for initial parameter estimation.
- --L
DNS max dimension (width, height, depth, etc.), used for initial parameter estimation.
- --element
The macro (filter) element to calibrate
Default:
0- --increment
An optional argument to callibrate only for specific increment
- --case
Specify the calibration ‘case’. 1: two parameter, 2: 7 parameter, 3: 7 parameter plus tau7, 4: all 18 parameters
- --plot-file
Optional root filename to plot Cauchy and symmetric micro stress comparison between DNS and calibration results
- --average
Boolean whether or not homogenized DNS results will be averaged
Default:
True- --UQ-file
Optional csv filename to store function evaluations and parameter sets for UQ
Calibrate.joint_probability_distributions.py
Create a joint probability distribution plot to summarize calibration results
usage: joint_probability_distributions.py [-h] -o OUTPUT_FILE
[--num-params NUM_PARAMS]
--csv-files CSV_FILES
[CSV_FILES ...] --num-domains
NUM_DOMAINS [NUM_DOMAINS ...]
[--distribution-plots DISTRIBUTION_PLOTS]
[--full-kde FULL_KDE]
Named Arguments
- -o, --output-file
Specify the output filename for the joint probability distribution plot
- --num-params
Optionally specify the number of parameters to make a joint probability plot with if not all are desired
- --csv-files
The csv files containing calibration results
- --num-domains
A list of integers corresponding to the number of filtering domains associated with results contained in each csv file
- --distribution-plots
Optional root file name for distribution plots of each parameter
- --full-kde
Optional root file name for KDE of each parameter
Calibrate.summarize_calibration_results.py
Summarize results of parameter calibration
usage: summarize_calibration_results.py [-h] --parameter-sets PARAMETER_SETS
[PARAMETER_SETS ...] --case CASE
[--results-csv RESULTS_CSV]
[--summary-csv SUMMARY_CSV]
[--kde-hist-plot KDE_HIST_PLOT]
[--kde-plot KDE_PLOT]
[--kde-best KDE_BEST]
[--kde-best-parameters KDE_BEST_PARAMETERS]
Named Arguments
- --parameter-sets
Specify the list of yaml files containing calibration results
- --case
Specify the calibration “case”. 1: two parameter, 2: 7 parameter, 3: 7 parameter plus tau7, 4: all 18 parameters
- --results-csv
Optional filename to store all calibrated parameter values
- --summary-csv
Optional filename to store summary statistics of calibrated parameters
- --kde-hist-plot
Optional root filename to plot kernel density estimate of each calibrated parameter with histogram
- --kde-plot
Optional root filename to plot kernel density estimate of each calibrated parameter
- --kde-best
Optional root filename to plot kernel density estimate of each calibrated parameter with maximum value in title
- --kde-best-parameters
Optional root filename to output a yaml file containing the “best” parameters sampled from the kernel density estimate associated with “–kde-best”
Calibrate.summarize_calibration_results_ignore_boundary.py
Summarize results of parameter calibration while ignoring elements on the z-boundary
usage: summarize_calibration_results_ignore_boundary.py [-h] --parameter-sets
PARAMETER_SETS
[PARAMETER_SETS ...]
--element-sets
ELEMENT_SETS
[ELEMENT_SETS ...]
--macro-file
MACRO_FILE --case CASE
[--results-csv RESULTS_CSV]
[--summary-csv SUMMARY_CSV]
[--kde-hist-plot KDE_HIST_PLOT]
[--kde-plot KDE_PLOT]
[--kde-best KDE_BEST]
[--kde-best-parameters KDE_BEST_PARAMETERS]
Named Arguments
- --parameter-sets
Specify the list of yaml files containing calibration results
- --element-sets
List of elements of the macro domain which have been calibrated
- --macro-file
The macroscale filter domain XDMF file, less extension
- --case
Specify the calibration “case”. 1: two parameter, 2: 7 parameter, 3: 7 parameter plus tau7, 4: all 18 parameters
- --results-csv
Optional filename to store all calibrated parameter values
- --summary-csv
Optional filename to store summary statistics of calibrated parameters
- --kde-hist-plot
Optional root filename to plot kernel density estimate of each calibrated parameter with histogram
- --kde-plot
Optional root filename to plot kernel density estimate of each calibrated parameter
- --kde-best
Optional root filename to plot kernel density estimate of each calibrated parameter with maximum value in title
- --kde-best-parameters
Optional root filename to output a yaml file containing the “best” parameters sampled from the kernel density estimate associated with “–kde-best”
Tardigrade_MOOSE.add_element_blocks_to_mesh.py
Create a cylinder mesh from the bounds of a DNS file.
usage: python cylinder_from_bounds.py [-h] --output-file OUTPUT_FILE
--bounds-file BOUNDS_FILE --seed-size
SEED_SIZE [--cut CUT] [--xdmf XDMF]
[--ascii ASCII]
Named Arguments
- --output-file
The output filename
- --bounds-file
The file containing the bounds of the DNS
- --seed-size
The approximate mesh size
- --cut
The option to cut geometry into octants, pass string “True” if desired
- --xdmf
The option to convert default exodus mesh to XDMF (binary)
- --ascii
The option to convert binary XDMF mesh to ascii
Tardigrade_MOOSE.build_dynamic_Tardigrade_input_deck.py
Write Tardigrade-MOOSE input file for dynamic simulation
usage: build_dynamic_Tardigrade_input_deck.py [-h] -o OUTPUT_FILE --mesh MESH
[--parameter-sets PARAMETER_SETS [PARAMETER_SETS ...]]
[--calibration-map CALIBRATION_MAP]
--BCs BCS --pressure PRESSURE
--start START --duration
DURATION --dt DT --ref-density
REF_DENSITY --height HEIGHT
Named Arguments
- -o, --output-file
The name of Tardigrade-MOOSE file to write
- --mesh
The mesh file
- --parameter-sets
List of yaml files containing calibration results, required if calibration-map is not provided
- --calibration-map
Optional yaml file containing names of calibration files
- --BCs
The type of boundary conditions, either “slip” or “clamp”
- --pressure
The pressure to be applied
- --start
The time when heaviside pressure is applied
- --duration
The duration of the simulation
- --dt
The fixed time increment
- --ref-density
Density in reference configuration (Mg/mm^3)
- --height
Height of the geometry
Tardigrade_MOOSE.build_Tardigrade_input_deck.py
Write Tardigrade-MOOSE input file
usage: build_Tardigrade_input_deck.py [-h] -o OUTPUT_FILE --mesh MESH
[--parameter-sets PARAMETER_SETS [PARAMETER_SETS ...]]
[--calibration-map CALIBRATION_MAP]
--BCs BCS --disp DISP --duration
DURATION [--disp-point DISP_POINT]
Named Arguments
- -o, --output-file
The name of Tardigrade-MOOSE file to write
- --mesh
The mesh file
- --parameter-sets
List of yaml files containing calibration results, required if calibration-map is not provided
- --calibration-map
Optional yaml file containing names of calibration files
- --BCs
The type of boundary conditions, either “slip” or “clamp”
- --disp
The compressive displacement to be applied
- --duration
The duration of the simulation
- --disp-point
Optional string of coordinates to query x-displacement
Tardigrade_MOOSE.cylinder_from_bounds.py
Create a cylinder mesh from the bounds of a DNS file.
usage: python cylinder_from_bounds.py [-h] --output-file OUTPUT_FILE
--bounds-file BOUNDS_FILE --seed-size
SEED_SIZE [--cut CUT] [--xdmf XDMF]
[--ascii ASCII]
Named Arguments
- --output-file
The output filename
- --bounds-file
The file containing the bounds of the DNS
- --seed-size
The approximate mesh size
- --cut
The option to cut geometry into octants, pass string “True” if desired
- --xdmf
The option to convert default exodus mesh to XDMF (binary)
- --ascii
The option to convert binary XDMF mesh to ascii
Tardigrade_MOOSE.plot_dynamic_displacement.py
Process displacement vs time from Tardigrade-MOOSE results
usage: python plot_dynamic_displacement.py [-h] --csv-file CSV_FILE
--output-file OUTPUT_FILE
--output-csv OUTPUT_CSV
[--disp-factor DISP_FACTOR]
Named Arguments
- --csv-file
The csv file containing force results
- --output-file
The name of the output file of collected results
- --output-csv
The name of the output csv file
- --disp-factor
The factor to scale displacement
Default:
1
Tardigrade_MOOSE.plot_force_displacement.py
Process force-displacement from Tardigrade-MOOSE results
usage: python plot_force_displacement.py [-h] --csv-file CSV_FILE
--output-file OUTPUT_FILE
--output-csv OUTPUT_CSV --final-disp
FINAL_DISP
[--force-factor FORCE_FACTOR]
Named Arguments
- --csv-file
The csv file containing force results
- --output-file
The name of the output file of collected results
- --output-csv
The name of the output csv file
- --final-disp
The final displacement (mm) to linearly ramp over simulation duration
- --force-factor
The factor to scale force
Default:
1
Tardigrade_MOOSE.summarize_micro_macro_force_displacements.py
Plot mutliple force displacement plots against each other
usage: python summarize_micro_macro_force_displacements.py
[-h] --csv-files CSV_FILES [CSV_FILES ...] --plot-labels PLOT_LABELS
[PLOT_LABELS ...] --output-file OUTPUT_FILE --output-csv OUTPUT_CSV
[--convergence-plot CONVERGENCE_PLOT]
Named Arguments
- --csv-files
The csv files containing force results
- --plot-labels
The plot labels, same size as ‘–csv-files’
- --output-file
The name of the output plot
- --output-csv
The name of the output csv file
- --convergence-plot
Optional file name for convergence plot
Tardigrade_MOOSE.write_elastic_material_card.py
Write elastic Tardigrade-MOOSE input card (.yml)
usage: write_elastic_material_card.py [-h] -o OUTPUT_FILE [--lamb LAMB]
[--mu MU] [--eta ETA] [--tau TAU]
[--kappa KAPPA] [--nu NU]
[--sigma SIGMA] [--tau1 TAU1]
[--tau2 TAU2] [--tau3 TAU3]
[--tau4 TAU4] [--tau5 TAU5]
[--tau6 TAU6] [--tau7 TAU7]
[--tau8 TAU8] [--tau9 TAU9]
[--tau10 TAU10] [--tau11 TAU11]
Named Arguments
- -o, --output-file
Specify the name of Tardigrade-MOOSE file to write
- --lamb
Specify lambda
Default:
0.0- --mu
Specify mu
Default:
0.0- --eta
Specify eta
Default:
0.0- --tau
Specify tau
Default:
0.0- --kappa
Specify kappa
Default:
0.0- --nu
Specify nu
Default:
0.0- --sigma
Specify sigma
Default:
0.0- --tau1
Specify tau1
Default:
0.0- --tau2
Specify tau2
Default:
0.0- --tau3
Specify tau3
Default:
0.0- --tau4
Specify tau4
Default:
0.0- --tau5
Specify tau5
Default:
0.0- --tau6
Specify tau6
Default:
0.0- --tau7
Specify tau7
Default:
0.001- --tau8
Specify tau8
Default:
0.0- --tau9
Specify tau9
Default:
0.0- --tau10
Specify tau10
Default:
0.0- --tau11
Specify tau11
Default:
0.0