TARDIGRADE-EXAMPLES CLI
Common
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
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”
convert_tess.py
Convert a 3D tesselation file output by Neper to STL and create an Abaqus mesh
usage: python convert_tess.py [-h] --input-file INPUT_FILE
[--stl-file STL_FILE] [--mesh-file MESH_FILE]
[--seed-size SEED_SIZE]
Named Arguments
- --input-file
Input tesselation (.tess) file
- --stl-file
Optional filename to save STL of geometry without extension
- --mesh-file
Optional filename to create an Abaqus mesh without extension
- --seed-size
The approximate mesh size
Default:
1.0
convert_tess_cylinder.py
Convert a tesslation file output by Neper for a cylindrical geometry to STL and create Abaqus mesh
usage: python convert_tess_cylinder.py [-h] --input-file INPUT_FILE
[--stl-file STL_FILE]
[--mesh-file MESH_FILE]
[--seed-size SEED_SIZE]
Named Arguments
- --input-file
Input tesselation (.tess) file
- --stl-file
Optional filename to save STL of geometry without extension
- --mesh-file
Optional filename to create an Abaqus mesh without extension
- --seed-size
The approximate mesh size
Default:
1.0
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.
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
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.
modify_input.py
Modify Abaqus input file to output ‘COORD’ at integration points
usage: python 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
ODBextract_to_XDMF.py
Convert Abaqus DNS results to XDMF format
usage: python 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
ODBextract_to_XDMF_neper.py
Convert Abaqus DNS results of 3D bonded grains to XDMF format
usage: ODBextract_to_XDMF_neper.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]
[--element-type ELEMENT_TYPE]
[--init-ref INIT_REF]
[--sets-file SETS_FILE]
[--num-steps NUM_STEPS]
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
- --element-type
Abaqus element type
Default:
'C3D8'- --init-ref
A flag (any string) to specify if the reference configuration will be initialized manually
- --sets-file
A yaml file containing element set information
- --num-steps
Option to specify how many total timesteps should be written to the XDMF file excluding the reference state. For 1, the final state is used. For num_steps > 1, the final state is written and nearest evenly steps are written.
ODBextract_to_XDMF_neper_2d.py
Convert Abaqus DNS results of 2D bonded grains to XDMF format
usage: ODBextract_to_XDMF_neper_2d.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]
[--element-type ELEMENT_TYPE]
[--init-ref INIT_REF]
[--sets-file SETS_FILE]
[--num-steps NUM_STEPS]
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- --element-type
Abaqus element type
Default:
'C3D8'- --init-ref
A flag (any string) to specify if the reference configuration will be initialized manually
- --sets-file
A yaml file containing element set information
- --num-steps
Option to specify how many total timesteps should be written to the XDMF file excluding the reference state. For 1, the final state is used. For num_steps > 1, the final state is written and nearest evenly steps are written.
parse_sets_from_inp.py
Extract element IDs associated with element sets from Abaqus input file
usage: parse_sets_from_inp.py [-h] [-i INPUT_FILE] [-o OUTPUT_FILE]
Named Arguments
- -i, --input-file
Specify the Abaqus input file to containing element set information
- -o, --output-file
Specify the output yaml file name containing element set information
write_section_file.py
Write an Abaqus input file for the section definition of grains
usage: write_section_file.py [-h] -o OUTPUT_FILE --number-grains NUMBER_GRAINS
--material-name MATERIAL_NAME
Named Arguments
- -o, --output-file
The name of the Abaqus input file to write
- --number-grains
The number of sections to create corresponding to unqieu grains
- --material-name
The name of the material to assign to sections
DNS_GEOS
plot_force_displacement.py
Process force-displacement from GEOS DNS results
usage: python plot_force_displacement.py [-h] --csv-file CSV_FILE
--output-file OUTPUT_FILE
--output-csv OUTPUT_CSV
[--force-col FORCE_COL]
[--length-col LENGTH_COL]
[--force-factor FORCE_FACTOR]
[--disp-factor DISP_FACTOR]
[--filter-markers FILTER_MARKERS [FILTER_MARKERS ...]]
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
- --force-col
The column containing desired force information
Default:
'force_z'- --length-col
The column containing domain length data used for calculating displacement
Default:
'length_z'- --force-factor
The factor to scale force
Default:
1- --disp-factor
The factor to scale displacement
Default:
1- --filter-markers
Optional list of indices to plot markers on force displacement plot corresponding to frames for upscaling
vtk_to_xdmf.py
Convert GEOS DNS results to XDMF format using XML element tree
usage: python vtk_to_xdmf.py [-h] -i INPUT_FILE --file-root FILE_ROOT -o
OUTPUT_FILE [--dist-factor DIST_FACTOR]
[--stress-factor STRESS_FACTOR]
[--density-factor DENSITY_FACTOR]
Named Arguments
- -i, --input-file
Specify the main VTK PVD file containing GEOS DNS results
- --file-root
The root directory containing 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- --density-factor
Optional factor to scale current density (if provided in the DNS results to Mg/mm^3
Default:
1
vtk_to_xdmf_fast.py
Convert GEOS DNS results to XDMF format using VTK utilities
usage: python vtk_to_xdmf_fast.py [-h] -i INPUT_FILE --file-root FILE_ROOT -o
OUTPUT_FILE [--dist-factor DIST_FACTOR]
[--stress-factor STRESS_FACTOR]
[--density-factor DENSITY_FACTOR]
Named Arguments
- -i, --input-file
Specify the main VTK PVD file containing GEOS DNS results
- --file-root
The root directory containing 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- --density-factor
Optional factor to scale current density (if provided in the DNS results to Mg/mm^3
Default:
1
vtk_to_xdmf_fast_multi.py
Convert multiblock GEOS DNS results to XDMF format using VTK utilities
usage: python vtk_to_xdmf_fast_multi.py [-h] -i INPUT_FILE --file-root
FILE_ROOT -o OUTPUT_FILE
[--dist-factor DIST_FACTOR]
[--stress-factor STRESS_FACTOR]
[--density-factor DENSITY_FACTOR]
[--annulus-ratio ANNULUS_RATIO]
[--upscale-damage UPSCALE_DAMAGE]
[--num-ranks NUM_RANKS]
[--grain-particle-key GRAIN_PARTICLE_KEY]
[--binder-particle-key BINDER_PARTICLE_KEY]
Named Arguments
- -i, --input-file
Specify the main VTK PVD file containing GEOS DNS results
- --file-root
The root directory containing 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- --density-factor
Optional factor to scale current density (if provided in the DNS results to Mg/mm^3
Default:
1- --annulus-ratio
Optional fraction of the radius of points to keep in the final geometry
- --upscale-damage
Option to specify if damage will be upscaled
- --num-ranks
The number of ranks to collect data from
Default:
1000- --grain-particle-key
An integer specifying the particle key for grains
Default:
1- --binder-particle-key
An integer specifying the particle key for binder
Default:
2
DNS_Ratel
build_options_file.py
Write Ratel options file
usage: python 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’
cgns_to_xdmf.py
Convert Ratel DNS results to XDMF format
usage: python cgns_to_xdmf.py [-h] [-i INPUT_FILES [INPUT_FILES ...]]
[-o OUTPUT_FILE] [--dist-factor DIST_FACTOR]
[--stress-factor STRESS_FACTOR]
[--density-factor DENSITY_FACTOR]
[--dump-all-33-stresses DUMP_ALL_33_STRESSES]
[--damage DAMAGE]
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- --density-factor
Optional factor to scale current density (if provided in the DNS results to Mg/mm^3
Default:
1- --dump-all-33-stresses
Optional filename to dump all 33 stresses from DNS
- --damage
Optional filename to dump all 33 stresses from DNS
Default:
False
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]
[--filter-markers FILTER_MARKERS [FILTER_MARKERS ...]]
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- --filter-markers
Optional list of indices to plot markers on force displacement plot corresponding to frames for upscaling
vtk_to_xdmf.py
Convert Ratel DNS results to XDMF format
usage: python 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/mm^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: python 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'
build_filter_config.py
Write the configuration file for the Micromorphic Filter
usage: python 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]
[--damage DAMAGE]
[--max-parallel MAX_PARALLEL]
[--sets-file SETS_FILE]
[--micro-averaging-domains MICRO_AVERAGING_DOMAINS]
[--update-filter-domains UPDATE_FILTER_DOMAINS]
[--plot-micro-domains PLOT_MICRO_DOMAINS]
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”
- --damage
Optional string identifying damage quantities located in “dns-file”
- --max-parallel
Optional parameter defining the number of parallel processes for the Micromorphic Filter
- --sets-file
Optional yaml file containing prescribed micro-averaging domains
- --micro-averaging-domains
Micro-averaging domain detection method. Options include “auto,” “prescribed,” “spectral,” or “HDBSCAN_recursive”
- --update-filter-domains
Option to update filter and microaveraging domains for each time step
- --plot-micro-domains
Option to request filter to plot micro averaging domains
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
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
force_bounds.py
Create a csv file containing information for a bounding box encompassing all DNS points
usage: python 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
parse_balance_errors.py
Parse balance equation errors from Micromorphic Filter standard output
usage: python 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
run_micromorphic_filter.py
Run the Micromorphic Filter
usage: python run_micromorphic_filter.py [-h] --config-file CONFIG_FILE
[--damage-class DAMAGE_CLASS]
Named Arguments
- --config-file
Specify the filter configuration file
- --damage-class
Flag to request the FilterMicroDomainDamage filter class
single_macroscale.py
Write a single macroscale domain file for the Micromorphic Filter
usage: python 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]
[--dimension DIMENSION]
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
- --dimension
The spatial dimension of the macroscale
Default:
3
visualize_results.py
Post-process Micromorphic Filter Output
usage: python 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]
[--plot-better-stress-norms PLOT_BETTER_STRESS_NORMS]
[--plot-best-stress-norms PLOT_BEST_STRESS_NORMS]
[--plot-norm-histories PLOT_NORM_HISTORIES]
[--p-q-plots P_Q_PLOTS]
[--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] [--dim DIM]
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.
- --plot-better-stress-norms
Optional filename to plot norms of PK2 stress, Symmetric micro stress, difference between PK2 and Symmetric micro stresses, and higher order stress, all against norms of Green-Lagrange strain, Micro strain, and Micro-deformation.
- --plot-best-stress-norms
Optional filename to plot norm of PK2 stress vs Green-Lagrange strain, Symmetric micro stress vs Micro strain, and higher order stress vs micro-deformation
- --plot-norm-histories
Optional filename to plot norm of p and q invariants of Pk2 stress, Symmetric micro stress, and higher order stress, and the norms of Green-Lagrange strain, Micro strain, and Micro-deformation. All plots have an x-axis of pseudo-time
- --p-q-plots
Optional filename to plot p-q invariants of PK2 stress, Symmetric micro stress, difference btween PK2 and Symmtric 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
- --dim
The dimension of the arrays, ‘2’ for 2d or ‘3’ for 3d
Default:
3
xdmf_3d_calculations.py
Create an XDMF file containing a variety of derived quantities
usage: xdmf_3d_calculations.py [-h] [-i INPUT_FILE] [-o OUTPUT_FILE]
[--num-elements NUM_ELEMENTS] --write-type
WRITE_TYPE
[--calibration-map-file CALIBRATION_MAP_FILE]
Named Arguments
- -i, --input-file
Specify the input filename for the h5 + XDMF file pair (no suffix)
- -o, --output-file
Specify the output filenmae for the h5 + XDMF file pair (no suffix)
- --num-elements
The number of macroscale elements
- --write-type
The type of quantities to write to XDMF. Choose “filter_stress_measures” to calculate stress invariants directly on filter results. Choose “calibration” results to display calibrations on static mesh.
- --calibration-map-file
A csv file containing previously calibrated parameters. Required if “–write-type calibration”
xdmf_local_paths.py
Create a copy of an XDMF file with absolute H5 paths replaced with relative paths
usage: python 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
xdmf_tomfoolery.py
Modify an XDMF file by combining elements from separate ‘blocks’
usage: python 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 file mapping calibration results for each macroscale element
usage: python build_calibration_map.py [-h] --output-file OUTPUT_FILE
[--calibrated-elements CALIBRATED_ELEMENTS [CALIBRATED_ELEMENTS ...]]
[--calibrated-files CALIBRATED_FILES [CALIBRATED_FILES ...]]
[--map-type MAP_TYPE]
[--material-type MATERIAL_TYPE]
[--best-parameters-yml-no-BCs BEST_PARAMETERS_YML_NO_BCS]
[--boundary-csv BOUNDARY_CSV]
[--previous-calibration-map PREVIOUS_CALIBRATION_MAP]
[--input-csv INPUT_CSV]
Named Arguments
- --output-file
The name of the output csv file
- --calibrated-elements
A list of elements with associated calibration files
- --calibrated-files
A list of files containing calibration results
- --map-type
The type of calibration map to generate. ‘full_csv’ (default) to create a csv file containing material parameters mapped for every element. ‘ignore_boundary_yaml’ to create a new calibration map with boundary element parameters swapped with best_parameters_yml_no_BCs. ‘trim_for_tardigrade’ to modify a previously generated csv file for Tardigrade
Default:
'full_csv'- --material-type
The material type: ‘elastic’, ‘plastic’, or ‘full_plastic’
- --best-parameters-yml-no-BCs
A yaml file containing the ‘best’ calibration using the kernel density estimate for elements not on the boundary
- --boundary-csv
A csv file containing list of boundary elements
- --previous-calibration-map
A csv file containing a previous calibration map for all elements to be modified
- --input-csv
An input, previously generated csv file using ‘map_type=full_csv’ to be trimmed for Tardigrade
calibrate_element.py
Calibrate micromorphic linear elasticity on a single filter domain (i.e. macroscale element)
usage: python calibrate_element.py [-h] [-i INPUT_FILE] [-o OUTPUT_FILE]
[--Emod EMOD] [--nu NU] [--L L]
[--element ELEMENT]
[--increment INCREMENT [INCREMENT ...]]
--case CASE [--plot-file PLOT_FILE]
[--average AVERAGE] [--UQ-file UQ_FILE]
[--cal-norm CAL_NORM]
[--bound-half-width BOUND_HALF_WIDTH]
[--dev-norm-errors DEV_NORM_ERRORS]
[--input-elastic-parameters INPUT_ELASTIC_PARAMETERS]
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 list of one or more increments to perform calibration
- --case
The calibration ‘case’. 1: two parameter, 2: 7 parameter, 3: 7 parameter plus tau7 without error for M, 4: all 18 parameters, 5: 7 parameter plus tau7 with error for M, 6: 11 higher order parameters, 7: 7 parameters using fixed higher order parameters determined from case 6, 8: 7 parameters using initial guess and tighter bounds for higher order parameters determined from case 6
- --plot-file
Optional root filename to for plotting results
- --average
Boolean whether or not homogenized DNS results will be averaged
Default:
False- --UQ-file
Optional csv filename to store function evaluations and parameter sets for UQ
- --cal-norm
The type of norm to use for calibration (“L1”, “L2”, or “L1-L2”)
Default:
'L1'- --bound-half-width
The uniform parameter bound “half-width” to apply for all parameters to be calibrated. Bounds for lambda will be [0., bound_half_width]. All other parameter bounds will be [-1*bound_half_width, bound_half_width]
Default:
100000.0- --dev-norm-errors
Boolean whether to inclue deviatoric stress norms during calibration
Default:
False- --input-elastic-parameters
Yaml file containing previously calibrated elastic parameters
calibrate_element_plastic.py
Calibrate micromorphic elastoplasticity on a single filter domain (i.e. macroscale element)
usage: python calibrate_element_plastic.py [-h] [-i INPUT_FILE]
[-o OUTPUT_FILE]
[--element ELEMENT]
[--increment INCREMENT [INCREMENT ...]]
--case CASE --input-parameters
INPUT_PARAMETERS
[--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
- --element
The macro (filter) element to calibrate
Default:
0- --increment
An optional list of one or more increments to perform calibration
- --case
Specify the calibration ‘case’. 1: two parameter, 2: 7 parameter, 3: 7 parameter plus tau7, 4: all 18 parameters
- --input-parameters
A yaml file containing previously calibrated parameters
- --plot-file
Optional root filename to for plotting results
- --average
Boolean whether or not homogenized DNS results will be averaged
Default:
False- --UQ-file
Optional csv filename to store function evaluations and parameter sets for UQ
calibrate_qp.py
Calibrate micromorphic linear elasticity on a single filter domain (i.e. macroscale element) and quadrature point
usage: python calibrate_qp.py [-h] [-i INPUT_FILE] [-o OUTPUT_FILE]
[--Emod EMOD] [--nu NU] [--L L]
[--element ELEMENT] [--qp QP]
[--increment INCREMENT [INCREMENT ...]] --case
CASE [--plot-file PLOT_FILE]
[--UQ-file UQ_FILE] [--cal-norm CAL_NORM]
[--bound-half-width BOUND_HALF_WIDTH]
[--dev-norm-errors DEV_NORM_ERRORS]
[--input-elastic-parameters INPUT_ELASTIC_PARAMETERS]
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- --qp
The quadrature point of the macro (filter) element to calibrate
Default:
0- --increment
An optional list of one or more increments to perform calibration
- --case
The calibration ‘case’. 1: two parameter, 2: 7 parameter, 3: 7 parameter plus tau7 without error for M, 4: all 18 parameters, 5: 7 parameter plus tau7 with error for M, 6: 11 higher order parameters, 7: 7 parameters using fixed higher order parameters determined from case 6, 8: 7 parameters using initial guess and tighter bounds for higher order parameters determined from case 6
- --plot-file
Optional root filename to for plotting results
- --UQ-file
Optional csv filename to store function evaluations and parameter sets for UQ
- --cal-norm
The type of norm to use for calibration (“L1”, “L2”, or “L1-L2”)
Default:
'L1'- --bound-half-width
The uniform parameter bound “half-width” to apply for all parameters to be calibrated. Bounds for lambda will be [0., bound_half_width]. All other parameter bounds will be [-1*bound_half_width, bound_half_width]
Default:
100000.0- --dev-norm-errors
Boolean whether to inclue deviatoric stress norms during calibration
Default:
False- --input-elastic-parameters
Yaml file containing previously calibrated elastic parameters
identify_z_boundary_elements.py
Read in macroscale XDMF file of a cylindrical geometry and identify element found on the z-boundary
usage: python identify_z_boundary_elements.py [-h] --macro-file MACRO_FILE
--output-file OUTPUT_FILE
Named Arguments
- --macro-file
The macroscale filter domain XDMF file, less extension
- --output-file
Output csv filename containing list of boundary elements
identify_z_boundary_elements.py
Read in macroscale XDMF file of a cylindrical geometry and identify element found on the z-boundary
usage: python identify_z_boundary_elements.py [-h] --macro-file MACRO_FILE
--output-file OUTPUT_FILE
Named Arguments
- --macro-file
The macroscale filter domain XDMF file, less extension
- --output-file
Output csv filename containing list of boundary elements
elastic_map_to_material_card.py
Unpack a csv file of elastic parameters and call function to write elastic yaml file
usage: python elastic_map_to_material_card.py [-h] --map-file MAP_FILE
--element-number ELEMENT_NUMBER
--output-file OUTPUT_FILE
Named Arguments
- --map-file
CSV file containing previously calibrated elastic parameters
- --element-number
The id of the element to extract calibration data
- --output-file
The name of the yml material card to write
summarize_calibration_results.py
Summarize results of parameter calibration
usage: python 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
The calibration ‘case’. 1: two parameter, 2: 7 parameter, 3: 7 parameter plus tau7 without error for M, 4: all 18 parameters, 5: 7 parameter plus tau7 with error for M, 6: 11 higher order parameters, 7: 7 parameters using fixed higher order parameters determined from case 6, 8: 7 parameters using initial guess and tighter bounds for higher order parameters determined from case 6
- --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”
summarize_calibration_results_from_csv.py
Summarize results of parameter calibration from a calibration map csv
usage: python summarize_calibration_results_from_csv.py [-h] --parameter-csv
PARAMETER_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]
[--boundary-csv BOUNDARY_CSV]
Named Arguments
- --parameter-csv
Specify the list of yaml files containing calibration results
- --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”
- --boundary-csv
A csv file containing list of boundary elements
summarize_calibration_results_ignore_boundary.py
Summarize results of parameter calibration while ignoring elements on the z-boundary
usage: python 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
The calibration ‘case’. 1: two parameter, 2: 7 parameter, 3: 7 parameter plus tau7 without error for M, 4: all 18 parameters, 5: 7 parameter plus tau7 with error for M, 6: 11 higher order parameters, 7: 7 parameters using fixed higher order parameters determined from case 6, 8: 7 parameters using initial guess and tighter bounds for higher order parameters determined from case 6
- --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]
[--brazil-lines BRAZIL_LINES]
[--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
- --brazil-lines
The option to define load lines for a brazilina disk simulation
- --xdmf
The option to convert default exodus mesh to XDMF (binary)
- --ascii
The option to convert binary XDMF mesh to ascii
Default:
False
annulus_from_bounds.py
Create an annular mesh from the bounds of a DNS file
usage: python annulus_from_bounds.py [-h] --output-file OUTPUT_FILE
--bounds-file BOUNDS_FILE --seed-size
SEED_SIZE --annulus-ratio ANNULUS_RATIO
Named Arguments
- --output-file
The output filename
- --bounds-file
The file containing the bounds of the DNS
- --seed-size
The approximate mesh size
- --annulus-ratio
The fraction of the radius to keep in the final geometry
brazilian_disk_apparatus.py
Create a Brazilian Disk specimen and loading apparatus
usage: python brazilian_disk_apparatus.py [-h] --output-file OUTPUT_FILE
--specimen-seed-size
SPECIMEN_SEED_SIZE
--platen-seed-size PLATEN_SEED_SIZE
--height HEIGHT --width WIDTH
--chord CHORD --app-rad APP_RAD
--app-dep APP_DEP --spec-rad
SPEC_RAD --spec-dep SPEC_DEP
[--tol TOL] [--x0 X0] [--y0 Y0]
[--z0 Z0]
[--export-platens EXPORT_PLATENS]
Named Arguments
- --output-file
The output filename
- --specimen-seed-size
The approximate mesh size for the specimen
- --platen-seed-size
The approximate mesh size for the platens
- --height
The height of a single Brazilian disk compression platen
- --width
The base width of a Brazilian disk compression platen
- --chord
The chord distance of the Brazilian disk compression platen
- --app-rad
The radius of curvature of the Brazilian disk compression platen
- --app-dep
The extrusion depth of the Brazilian disk compression platen
- --spec-rad
The radius of the Brazilian disk compression specimen
- --spec-dep
The extrusion depth of the Brazilian disk compression specimen
- --tol
A tolerance / gap distance to insert between Brazilian disk compression specimen and platens
Default:
0.001- --x0
The x-location to move geometry for the center of the Brazil Disk
Default:
0.0- --y0
The y-location to move geometry for the center of the Brazil Disk
Default:
0.0- --z0
The z-location to move geometry for the center of the Brazil Disk
Default:
0.0- --export-platens
Flag to export platen meshes of the brazilian disk apparatus
Default:
'True'
brazilian_disk_apparatus_symmetry.py
Create a Brazilian Disk specimen and loading apparatus using 1/8th symmetry
usage: python brazilian_disk_apparatus_symmetry.py [-h] --output-file
OUTPUT_FILE
--specimen-seed-size
SPECIMEN_SEED_SIZE
--platen-seed-size
PLATEN_SEED_SIZE --height
HEIGHT --width WIDTH
--chord CHORD --app-rad
APP_RAD --app-dep APP_DEP
--spec-rad SPEC_RAD
--spec-dep SPEC_DEP
[--tol TOL]
[--symmetry SYMMETRY]
[--x0 X0] [--y0 Y0]
[--z0 Z0]
[--export-platens EXPORT_PLATENS]
Named Arguments
- --output-file
The output filename
- --specimen-seed-size
The approximate mesh size for the specimen
- --platen-seed-size
The approximate mesh size for the platen
- --height
The height of a single Brazilian disk compression platen
- --width
The base width of a Brazilian disk compression platen
- --chord
The chord distance of the Brazilian disk compression platen
- --app-rad
The radius of curvature of the Brazilian disk compression platen
- --app-dep
The extrusion depth of the Brazilian disk compression platen
- --spec-rad
The radius of the Brazilian disk compression specimen
- --spec-dep
The extrusion depth of the Brazilian disk compression specimen
- --tol
A tolerance / gap distance to insert between Brazilian disk compression specimen and platens
Default:
0.001- --symmetry
Type of symmetry to create, either “eighth” or “quarter” or “half”
Default:
'eighth'- --x0
The x-location to move geometry for the center of the Brazil Disk
Default:
0.0- --y0
The y-location to move geometry for the center of the Brazil Disk
Default:
0.0- --z0
The z-location to move geometry for the center of the Brazil Disk
Default:
0.0- --export-platens
Flag to export platen meshes of the brazilian disk apparatus
Default:
'True'
Brazil_disk_normalized_force_vs_displacements.py
Process force-displacement from Tardigrade-MOOSE results
usage: python Brazil_disk_normalized_force_vs_displacements.py
[-h] --input-file INPUT_FILE [--radius RADIUS] [--thickness THICKNESS]
[--force-factor FORCE_FACTOR] [--disp-factor DISP_FACTOR] --plot-file
PLOT_FILE --csv-file CSV_FILE
Named Arguments
- --input-file
The csv file containing force vs displacement results
- --radius
The specimen initial radius
Default:
1- --thickness
The specimen initial thickness
Default:
1- --force-factor
The factor to scale force
Default:
1- --disp-factor
The factor to scale displacement
Default:
1- --plot-file
The name of the output file of collected results
- --csv-file
The name of the output csv file
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
[--phi-BC PHI_BC]
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
- --phi-BC
Optional string specifying nodeset to force micro deformation components to be zero
build_elastic_MOOSE_input_deck_brazil_disk_platens.py
Write MOOSE input file for symmetric Brazilian disk simulation with platens
usage: python build_elastic_MOOSE_input_deck_brazil_disk_platens.py
[-h] -o OUTPUT_FILE --mesh MESH --material-E MATERIAL_E --material-nu
MATERIAL_NU --platen-E PLATEN_E --platen-nu PLATEN_NU --disp DISP
--duration DURATION --specimen-top-surface SPECIMEN_TOP_SURFACE
--specimen-bottom-surface SPECIMEN_BOTTOM_SURFACE --top-platen-contact
TOP_PLATEN_CONTACT --bottom-platen-contact BOTTOM_PLATEN_CONTACT
--top-platen-fixture TOP_PLATEN_FIXTURE --top-platen-side
TOP_PLATEN_SIDE --top-platen-back TOP_PLATEN_BACK
--bottom-platen-fixture BOTTOM_PLATEN_FIXTURE --bottom-platen-side
BOTTOM_PLATEN_SIDE --bottom-platen-back BOTTOM_PLATEN_BACK
[--contact-type CONTACT_TYPE]
[--friction-coefficient FRICTION_COEFFICIENT]
Named Arguments
- -o, --output-file
Specify the name of Tardigrade-MOOSE file to write
- --mesh
Specify the mesh file
- --material-E
The elastic modulus of the specimen material
- --material-nu
The Poisson ratio of the specimen material
- --platen-E
The elastic modulus of the platen material
- --platen-nu
The Poisson ratio of the platen material
- --disp
Specify the compressive displacement to be applied
- --duration
Specify the duration of the simulation
- --specimen-top-surface
Specify the name of the specimen top contact surface
- --specimen-bottom-surface
Specify the name of the specimen bottom contact surface
- --top-platen-contact
Specify the name of the top platen contact surface
- --bottom-platen-contact
Specify the name of the bottom platen contact surface
- --top-platen-fixture
Specify the name of the top platen fixture surface
- --top-platen-side
Specify the name of the top platen side surface
- --top-platen-back
Specify the name of the top platen back surface
- --bottom-platen-fixture
Specify the name of the bottom platen fixture surface
- --bottom-platen-side
Specify the name of the bottom platen side surface
- --bottom-platen-back
Specify the name of the bottom platen back surface
- --contact-type
The option for specifying contact, either “frictionless” or “friction”
Default:
'friction'- --friction-coefficient
The fricition coefficient if contact_type=”friction”
build_elastic_MOOSE_input_deck_brazil_disk_platens_symmetry.py
Write MOOSE input file for eighth symmetry Brazilian disk simulation with platens
usage: python build_elastic_MOOSE_input_deck_brazil_disk_platens_symmetry.py
[-h] -o OUTPUT_FILE --mesh MESH --material-E MATERIAL_E --material-nu
MATERIAL_NU --platen-E PLATEN_E --platen-nu PLATEN_NU --disp DISP
--duration DURATION --specimen-bottom-surface SPECIMEN_BOTTOM_SURFACE
--bottom-platen-contact BOTTOM_PLATEN_CONTACT --top-symmetry
TOP_SYMMETRY --back-symmetry BACK_SYMMETRY --side-set SIDE_SET
--bottom-platen-fixture BOTTOM_PLATEN_FIXTURE
[--contact-type CONTACT_TYPE]
[--friction-coefficient FRICTION_COEFFICIENT] [--symmetry SYMMETRY]
Named Arguments
- -o, --output-file
Specify the name of Tardigrade-MOOSE file to write
- --mesh
Specify the mesh file
- --material-E
The elastic modulus of the specimen material
- --material-nu
The Poisson ratio of the specimen material
- --platen-E
The elastic modulus of the platen material
- --platen-nu
The Poisson ratio of the platen material
- --disp
Specify the compressive displacement to be applied
- --duration
Specify the duration of the simulation
- --specimen-bottom-surface
Specify the name of the specimen bottom contact surface
- --bottom-platen-contact
Specify the name of the bottom platen contact surface
- --top-symmetry
Specify the name of the top symmetry surface(s)
- --back-symmetry
Specify the name of the back symmetry surface(s)
- --side-set
Specify the name of the side surface(s) to restrict motion in x-direction
- --bottom-platen-fixture
Specify the name of the bottom platen fixture surface
- --contact-type
The option for specifying contact, either “frictionless” or “friction”
Default:
'friction'- --friction-coefficient
The friction coefficient if contact_type=”friction”
- --symmetry
Type of symmetry to enforce, either “eighth” or “quarter”
Default:
'eighth'
build_elastic_MOOSE_input_deck_brazil_disk_rigid_platens.py
Write MOOSE input file for Brazilian disk simulation with rigid platens
usage: python build_elastic_MOOSE_input_deck_brazil_disk_rigid_platens.py
[-h] -o OUTPUT_FILE --mesh MESH --material-E MATERIAL_E --material-nu
MATERIAL_NU --platen-radius PLATEN_RADIUS --disp DISP --duration
DURATION --specimen-bottom-surface SPECIMEN_BOTTOM_SURFACE
[--specimen-top-surface SPECIMEN_TOP_SURFACE]
[--top-symmetry TOP_SYMMETRY] [--back-symmetry BACK_SYMMETRY]
[--side-symmetry SIDE_SYMMETRY] [--xc-bot XC_BOT] [--yc-bot YC_BOT]
[--xc-top XC_TOP] [--yc-top YC_TOP] [--geometry GEOMETRY]
Named Arguments
- -o, --output-file
Specify the name of Tardigrade-MOOSE file to write
- --mesh
Specify the mesh file
- --material-E
The elastic modulus of the specimen material
- --material-nu
The Poisson ratio of the specimen material
- --platen-radius
The radius of curvature of the Brazilian disk compression platen
- --disp
Specify the compressive displacement to be applied
- --duration
Specify the duration of the simulation
- --specimen-bottom-surface
Specify the name of the specimen bottom contact surface
- --specimen-top-surface
Specify the name of the specimen top contact surface. Required if “geometry” = “full.”
- --top-symmetry
Specify the name of the top symmetry surface. Required if “geometry” = “quarter” or “eighth.”
- --back-symmetry
Specify the name of the back symmetry surface. Required if “geometry” = “quarter” or “eighth” or “half”
- --side-symmetry
Specify the name of the side symmetry surface. Required if “geometry” = “quarter” or “eighth.”
- --xc-bot
Specify the x-position of the center of the circular bottom surface arc
Default:
0.0- --yc-bot
Specify the y-position of the center of the circular bottom surface arc
Default:
0.0- --xc-top
Specify the x-position of the center of the circular top surface arc
Default:
0.0- --yc-top
Specify the y-position of the center of the circular top surface arc
Default:
0.0- --geometry
Specify the geometry/symmetry type: “full,” “half,” “quarter,” or “eighth”
Default:
'full'
build_GED_Tardigrade_input_deck_from_csv.py
Write Tardigrade-MOOSE input file for a gradient-enhanced damage plasticity simulation
usage: python build_GED_Tardigrade_input_deck_from_csv.py [-h] -o OUTPUT_FILE
--mesh MESH
--parameter-csv
PARAMETER_CSV --BCs
BCS --disp DISP
--duration DURATION
[--damage-parameter DAMAGE_PARAMETER]
Named Arguments
- -o, --output-file
Specify the name of Tardigrade-MOOSE file to write
- --mesh
Specify the mesh file
- --parameter-csv
CSV file containing calibration data
- --BCs
Specify the type of boundary conditions, either “slip” or “clamp”
- --disp
Specify the compressive displacement to be applied
- --duration
Specify the duration of the simulation
- --damage-parameter
The value of the damage parameter
Default:
0.095
build_plastic_Tardigrade_input_deck.py
Write Tardigrade-MOOSE input file for a plastic simulation
usage: python build_plastic_Tardigrade_input_deck.py [-h] -o OUTPUT_FILE
--mesh MESH
--calibration-map
CALIBRATION_MAP --BCs
BCS --disp DISP
--duration DURATION
Named Arguments
- -o, --output-file
Specify the name of Tardigrade-MOOSE file to write
- --mesh
Specify the mesh file
- --calibration-map
CSV file containing calibration data
- --BCs
Specify the type of boundary conditions, either “slip”, “slip_plane”, “clamp”, or “brazil”
- --disp
Specify the compressive displacement to be applied
- --duration
Specify the duration of the simulation
build_plastic_Tardigrade_input_deck_brazil_disk_platens.py
Write Tardigrade-MOOSE input file for Brazilian disk simulation with platens
usage: python build_plastic_Tardigrade_input_deck_brazil_disk_platens.py
[-h] -o OUTPUT_FILE --mesh MESH --parameter-sets PARAMETER_SETS
[PARAMETER_SETS ...] --disp DISP --duration DURATION
--specimen-top-surface SPECIMEN_TOP_SURFACE --specimen-bottom-surface
SPECIMEN_BOTTOM_SURFACE --top-platen-contact TOP_PLATEN_CONTACT
--bottom-platen-contact BOTTOM_PLATEN_CONTACT --top-platen-fixture
TOP_PLATEN_FIXTURE --bottom-platen-fixture BOTTOM_PLATEN_FIXTURE
[--contact-type CONTACT_TYPE]
Named Arguments
- -o, --output-file
Specify the name of Tardigrade-MOOSE file to write
- --mesh
Specify the mesh file
- --parameter-sets
Specify the list of yaml files containing calibration results
- --disp
Specify the compressive displacement to be applied
- --duration
Specify the duration of the simulation
- --specimen-top-surface
Specify the name of the specimen top contact surface
- --specimen-bottom-surface
Specify the name of the specimen bottom contact surface
- --top-platen-contact
Specify the name of the top platen contact surface
- --bottom-platen-contact
Specify the name of the bottom platen contact surface
- --top-platen-fixture
Specify the name of the top platen fixture surface
- --bottom-platen-fixture
Specify the name of the bottom platen fixture surface
- --contact-type
The option for specifying contact, either “frictionless” or “friction”
Default:
'frictionless'
build_plastic_Tardigrade_input_deck_brazil_disk_platens_symmetry.py
Write Tardigrade-MOOSE input file for eighth symmetry Brazilian disk simulation with platens
usage: python build_plastic_Tardigrade_input_deck_brazil_disk_platens_symmetry.py
[-h] -o OUTPUT_FILE --mesh MESH --parameter-sets PARAMETER_SETS
[PARAMETER_SETS ...] --disp DISP --duration DURATION
--specimen-bottom-surface SPECIMEN_BOTTOM_SURFACE
--bottom-platen-contact BOTTOM_PLATEN_CONTACT --top-symmetry
TOP_SYMMETRY --back-symmetry BACK_SYMMETRY --side-set SIDE_SET
--bottom-platen-fixture BOTTOM_PLATEN_FIXTURE
[--contact-type CONTACT_TYPE] [--symmetry SYMMETRY] [--phi-BC PHI_BC]
Named Arguments
- -o, --output-file
Specify the name of Tardigrade-MOOSE file to write
- --mesh
Specify the mesh file
- --parameter-sets
Specify the list of yaml files containing calibration results
- --disp
Specify the compressive displacement to be applied
- --duration
Specify the duration of the simulation
- --specimen-bottom-surface
Specify the name of the specimen bottom contact surface
- --bottom-platen-contact
Specify the name of the bottom platen contact surface
- --top-symmetry
Specify the name of the top symmetry surface(s)
- --back-symmetry
Specify the name of the back symmetry surface(s)
- --side-set
Specify the name of the side surface(s) to restrict motion in x-direction
- --bottom-platen-fixture
Specify the name of the bottom platen fixture surface
- --contact-type
The option for specifying contact, either “frictionless” or “friction”
Default:
'frictionless'- --symmetry
Type of symmetry to enforce, either “eighth” or “quarter”
Default:
'eighth'- --phi-BC
Optional string specifying nodeset to force micro deformation components to be zero
build_plastic_Tardigrade_input_deck_platens.py
Write Tardigrade-MOOSE input file for a plastic simulation with platens
usage: python build_plastic_Tardigrade_input_deck_platens.py
[-h] -o OUTPUT_FILE --mesh MESH --calibration-map CALIBRATION_MAP
--disp DISP --duration DURATION --specimen-top-surface
SPECIMEN_TOP_SURFACE --specimen-bottom-surface SPECIMEN_BOTTOM_SURFACE
--top-platen-contact TOP_PLATEN_CONTACT --bottom-platen-contact
BOTTOM_PLATEN_CONTACT --top-platen-fixture TOP_PLATEN_FIXTURE
--bottom-platen-fixture BOTTOM_PLATEN_FIXTURE
[--contact-type CONTACT_TYPE]
Named Arguments
- -o, --output-file
Specify the name of Tardigrade-MOOSE file to write
- --mesh
Specify the mesh file
- --calibration-map
CSV file containing calibration data
- --disp
Specify the compressive displacement to be applied
- --duration
Specify the duration of the simulation
- --specimen-top-surface
Specify the name of the specimen top contact surface
- --specimen-bottom-surface
Specify the name of the specimen bottom contact surface
- --top-platen-contact
Specify the name of the top platen contact surface
- --bottom-platen-contact
Specify the name of the bottom platen contact surface
- --top-platen-fixture
Specify the name of the top platen fixture surface
- --bottom-platen-fixture
Specify the name of the bottom platen fixture surface
- --contact-type
The option for specifying contact, either “frictionless” or “friction”
Default:
'frictionless'
build_Tardigrade_input_deck.py
Write Tardigrade-MOOSE input file
usage: python build_Tardigrade_input_deck.py [-h] -o OUTPUT_FILE --mesh MESH
--BCs BCS --disp DISP --duration
DURATION
[--calibration-map CALIBRATION_MAP]
[--elastic-material-card ELASTIC_MATERIAL_CARD]
[--disp-point DISP_POINT]
[--phi-BC PHI_BC]
Named Arguments
- -o, --output-file
The name of Tardigrade-MOOSE file to write
- --mesh
The mesh file
- --BCs
The type of boundary conditions, either “slip” or “clamp”
- --disp
The compressive displacement to be applied
- --duration
The duration of the simulation
- --calibration-map
CSV file containing calibration data, first method for specifying material parameters
- --elastic-material-card
YML file containing elastic material parameters, second method for specifying material parameters
- --disp-point
Optional string of coordinates to query x-displacement
- --phi-BC
Optional string specifying nodeset to force micro deformation components to be zero
build_Tardigrade_input_deck_brazil_disk_kernel_platens.py
Write MOOSE input file for Brazilian disk simulation with nodal kernel contact
usage: python build_Tardigrade_input_deck_brazil_disk_kernel_platens.py
[-h] -o OUTPUT_FILE --mesh MESH --parameter-sets PARAMETER_SETS
[PARAMETER_SETS ...] --platen-radius PLATEN_RADIUS --disp DISP
--duration DURATION --specimen-bottom-surface SPECIMEN_BOTTOM_SURFACE
[--specimen-top-surface SPECIMEN_TOP_SURFACE]
[--top-symmetry TOP_SYMMETRY] [--back-symmetry BACK_SYMMETRY]
[--side-symmetry SIDE_SYMMETRY] [--xc-bot XC_BOT] [--yc-bot YC_BOT]
[--xc-top XC_TOP] [--yc-top YC_TOP] [--geometry GEOMETRY]
[--material-type MATERIAL_TYPE] [--phi-BC PHI_BC] [--phis PHIS]
[--extra-stress-output EXTRA_STRESS_OUTPUT]
[--higher-order-stress-output HIGHER_ORDER_STRESS_OUTPUT]
Named Arguments
- -o, --output-file
Specify the name of Tardigrade-MOOSE file to write
- --mesh
Specify the mesh file
- --parameter-sets
Specify the list of yaml files containing calibration results
- --platen-radius
The radius of curvature of the Brazilian disk compression platen
- --disp
Specify the compressive displacement to be applied
- --duration
Specify the duration of the simulation
- --specimen-bottom-surface
Specify the name of the specimen bottom contact surface
- --specimen-top-surface
Specify the name of the specimen top contact surface. Required if “geometry” = “full.”
- --top-symmetry
Specify the name of the top symmetry surface. Required if “geometry” = “quarter” or “eighth.”
- --back-symmetry
Specify the name of the back symmetry surface. Required if “geometry” = “quarter” or “eighth” or “half”
- --side-symmetry
Specify the name of the side symmetry surface. Required if “geometry” = “quarter” or “eighth.”
- --xc-bot
Specify the x-position of the center of the circular bottom surface arc
Default:
0.0- --yc-bot
Specify the y-position of the center of the circular bottom surface arc
Default:
0.0- --xc-top
Specify the x-position of the center of the circular top surface arc
Default:
0.0- --yc-top
Specify the y-position of the center of the circular top surface arc
Default:
0.0- --geometry
Specify the geometry/symmetry type: “full,” “half,” “quarter,” or “eighth”
Default:
'full'- --material-type
Specify the material type: “elastic” or “plastic”
Default:
'elastic'- --phi-BC
Optional string specifying nodeset to force micro deformation components to be zero
- --phis
Either “on” to activate phi coupling kernels, or “off” to deactivate
Default:
'on'- --extra-stress-output
Either “on” to output second order stress variables, or “off” to deactivate
Default:
'off'- --higher-order-stress-output
Either “on” to output higher order stress variables, or “off” to deactivate
Default:
'off'
build_Tardigrade_input_deck_brazil_disk_rigid_platens.py
Write MOOSE input file for Brazilian disk simulation with rigid contact platens
usage: python build_Tardigrade_input_deck_brazil_disk_rigid_platens.py
[-h] -o OUTPUT_FILE --mesh MESH --parameter-sets PARAMETER_SETS
[PARAMETER_SETS ...] --platen-radius PLATEN_RADIUS --disp DISP
--duration DURATION --specimen-bottom-surface SPECIMEN_BOTTOM_SURFACE
[--specimen-top-surface SPECIMEN_TOP_SURFACE]
[--top-symmetry TOP_SYMMETRY] [--back-symmetry BACK_SYMMETRY]
[--side-symmetry SIDE_SYMMETRY] [--xc-bot XC_BOT] [--yc-bot YC_BOT]
[--xc-top XC_TOP] [--yc-top YC_TOP] [--geometry GEOMETRY]
[--material-type MATERIAL_TYPE] [--phi-BC PHI_BC] [--platens PLATENS]
Named Arguments
- -o, --output-file
Specify the name of Tardigrade-MOOSE file to write
- --mesh
Specify the mesh file
- --parameter-sets
Specify the list of yaml files containing calibration results
- --platen-radius
The radius of curvature of the Brazilian disk compression platen
- --disp
Specify the compressive displacement to be applied
- --duration
Specify the duration of the simulation
- --specimen-bottom-surface
Specify the name of the specimen bottom contact surface
- --specimen-top-surface
Specify the name of the specimen top contact surface. Required if “geometry” = “full.”
- --top-symmetry
Specify the name of the top symmetry surface. Required if “geometry” = “quarter” or “eighth.”
- --back-symmetry
Specify the name of the back symmetry surface. Required if “geometry” = “quarter” or “eighth” or “half”
- --side-symmetry
Specify the name of the side symmetry surface. Required if “geometry” = “quarter” or “eighth.”
- --xc-bot
Specify the x-position of the center of the circular bottom surface arc
Default:
0.0- --yc-bot
Specify the y-position of the center of the circular bottom surface arc
Default:
0.0- --xc-top
Specify the x-position of the center of the circular top surface arc
Default:
0.0- --yc-top
Specify the y-position of the center of the circular top surface arc
Default:
0.0- --geometry
Specify the geometry/symmetry type: “full,” “half,” “quarter,” or “eighth”
Default:
'full'- --material-type
Specify the material type: “elastic” or “plastic”
Default:
'elastic'- --phi-BC
Optional string specifying nodeset to force micro deformation components to be zero
- --platens
Either “cylinder” for cylindrical BCs or “flat” for flat plane BCs
Default:
'cylinder'
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]
[--brazil-lines BRAZIL_LINES]
[--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
- --brazil-lines
The option to define load lines for a brazilina disk simulation
- --xdmf
The option to convert default exodus mesh to XDMF (binary)
- --ascii
The option to convert binary XDMF mesh to ascii
Default:
False
cylinder_from_bounds_with_platens.py
Create a cylinder mesh from the bounds of a DNS file with platens.
usage: python cylinder_from_bounds_with_platens.py [-h] --output-file
OUTPUT_FILE --bounds-file
BOUNDS_FILE --seed-size
SEED_SIZE
[--platen-rad-factor PLATEN_RAD_FACTOR]
[--platen-depth PLATEN_DEPTH]
[--xdmf XDMF]
[--ascii ASCII]
[--gap GAP]
Named Arguments
- --output-file
The output filename
- --bounds-file
The file containing the bounds of the DNS
- --seed-size
The approximate mesh size
- --platen-rad-factor
The factor to multiply the specimen radius by to determine the specimen radius
Default:
1.5- --platen-depth
The thickness of the platens
Default:
1.0- --xdmf
The option to convert default exodus mesh to XDMF (binary)
- --ascii
The option to convert binary XDMF mesh to ascii
Default:
False- --gap
An initial gap to place between specimen and platens
extract_exodus_data.py
Process results from a MOOSE exodus simulation results file
usage: python extract_exodus_data.py [-h] --exodus-file EXODUS_FILE
[--output-cell-data OUTPUT_CELL_DATA]
[--output-node-data OUTPUT_NODE_DATA]
[--output-plot-base-name OUTPUT_PLOT_BASE_NAME]
[--output-dt-plot-base-name OUTPUT_DT_PLOT_BASE_NAME]
[--stress-norms-plot-base STRESS_NORMS_PLOT_BASE]
[--xdmf-file XDMF_FILE]
[--higher-order-stresses HIGHER_ORDER_STRESSES]
Named Arguments
- --exodus-file
The MOOSE exodus simulation results file
- --output-cell-data
Optional output netcdf file containing xarray of collected cell data
- --output-node-data
Optional output netcdf file containing xarray of collected node data
- --output-plot-base-name
Optional basename for field output plots
- --output-dt-plot-base-name
Optional basename for dt history plots
- --stress-norms-plot-base
Optional basename for stress norm history plots
- --xdmf-file
Optional basename for writing cell data to an XDMF file
- --higher-order-stresses
Either ‘on’ to include higher order stresses in norm calculation, or ‘off’
Default:
'off'
finite_stVK_calculation.py
Solution for uniaxial stress of a cylinder for finite deformation using the St. Venant-Kirchhoff elasticity model
usage: python finite_stVK_calculation.py [-h] [--diameter DIAMETER]
[--material-E MATERIAL_E]
[--material-nu MATERIAL_NU]
[--eps-z EPS_Z]
Named Arguments
- --diameter
The diameter of the cylinder in millimeters
Default:
5.0- --material-E
The elastic modulus in MPa
Default:
250.0- --material-nu
The Poisson ratio
Default:
0.2- --eps-z
The applied nominal strain in the z-direction
Default:
-0.01
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
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]
[--force-field FORCE_FIELD]
[--time-field TIME_FIELD]
[--disp-field DISP_FIELD]
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
Default:
1- --force-factor
The factor to scale force
Default:
1- --force-field
The column label for force values
Default:
'bot_react_z'- --time-field
The column label for time values
Default:
'time'- --disp-field
Optional column label for displacement values
plot_lateral_displacement.py
Process lateral displacement from Tardigrade-MOOSE results
usage: python plot_lateral_displacement.py [-h] --csv-file CSV_FILE
--output-file OUTPUT_FILE
--output-csv OUTPUT_CSV
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
process_calibration_map_to_parameter_csv.py
Process a calibration map file to a parameter csv for Tardigrade-MOOSE
usage: python process_calibration_map_to_parameter_csv.py [-h] -o OUTPUT_FILE
--calibration-map
CALIBRATION_MAP
Named Arguments
- -o, --output-file
Specify the name of the output csv to write
- --calibration-map
CSV file containing calibration data
summarize_dynamic_displacements.py
Plot mutliple dynamic displacement plots against each other
usage: python summarize_dynamic_displacements.py [-h] --csv-files CSV_FILES
[CSV_FILES ...]
--plot-labels PLOT_LABELS
[PLOT_LABELS ...]
--output-file OUTPUT_FILE
--output-csv OUTPUT_CSV
[--disp-factor DISP_FACTOR]
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
- --disp-factor
The factor to scale displacement
Default:
1
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] [--force-field FORCE_FIELD]
[--disp-field DISP_FIELD] [--x-label X_LABEL] [--y-label Y_LABEL]
[--brazil-exp-file BRAZIL_EXP_FILE]
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
- --force-field
The column label for force values
Default:
'force'- --disp-field
Optional column label for displacement values
Default:
'disp'- --x-label
The label for the x data
Default:
'Displacement (mm)'- --y-label
The label for the y data
Default:
'Force (N)'- --brazil-exp-file
Optional csv file containing Brazil disk data
summarize_micro_macro_lateral_displacements.py
Plot mutliple lateral displacement plots against each other
usage: python summarize_micro_macro_lateral_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
uniformly_refine_mesh.py
Uniformly refine an exodus mesh and update a calibration map with new element IDs
usage: python uniformly_refine_mesh.py [-h] --input-mesh INPUT_MESH
--output-mesh OUTPUT_MESH
--refinement-level REFINEMENT_LEVEL
--calibration-map-in
CALIBRATION_MAP_IN
[--calibration-map-out CALIBRATION_MAP_OUT]
Named Arguments
- --input-mesh
The input exodus mesh file to refine
- --output-mesh
The output exodus mesh file
- --refinement-level
The uniform refinement level, 1: refine by 1 level (each hex element is split into 8), 2: refinement by 2 levels (each hex element is split into 24)
- --calibration-map-in
The original calibration map file
- --calibration-map-out
The output calibration map file with updated element ids
write_elastic_material_card.py
Write elastic Tardigrade-MOOSE input card (.yml)
usage: python 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
write_plastic_material_card.py
Write elastoplastic Tardigrade-MOOSE input card
usage: python write_plastic_material_card.py [-h] -o OUTPUT_FILE
[--output-type OUTPUT_TYPE]
--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] [--cu0 CU0]
[--Hu HU] [--cchi0 CCHI0]
[--Hchi HCHI]
[--cnablachi0 CNABLACHI0]
[--Hnablachi HNABLACHI]
Named Arguments
- -o, --output-file
The name of Tardigrade-MOOSE file to write
- --output-type
The type of material card to write, either ‘yaml’ or ‘csv’
Default:
'yaml'- --lamb
The elastic lambda parameter
- --mu
The elastic mu parameter
- --eta
The elastic mu parameter
Default:
0.0- --tau
The elastic tau parameter
Default:
0.0- --kappa
The elastic kappa parameter
Default:
0.0- --nu
The elastic nu parameter
Default:
0.0- --sigma
The elastic sigma parameter
Default:
0.0- --tau1
The elastic tau1 parameter
Default:
0.0- --tau2
The elastic tau2 parameter
Default:
0.0- --tau3
The elastic tau3 parameter
Default:
0.0- --tau4
The elastic tau4 parameter
Default:
0.0- --tau5
The elastic tau5 parameter
Default:
0.0- --tau6
The elastic tau6 parameter
Default:
0.0- --tau7
The elastic tau7 parameter
Default:
0.001- --tau8
The elastic tau8 parameter
Default:
0.0- --tau9
The elastic tau9 parameter
Default:
0.0- --tau10
The elastic tau10 parameter
Default:
0.0- --tau11
The elastic tau11 parameter
Default:
0.0- --cu0
The plastic initial macro cohesion parameter, $c^{u,0}$
Default:
10000000000.0- --Hu
The plastic macro hardening parameter, $H^u$
Default:
10000.0- --cchi0
The plastic initial micro cohesion parameter, $c^{chi,0}$
Default:
10000000000.0- --Hchi
The plastic micro hardening parameter, $H^{chi}$
Default:
10000.0- --cnablachi0
The plastic initial micro gradient cohesion parameter, $c^{ ablachi,0}$
Default:
10000000000.0- --Hnablachi
The plastic micro gradient hardening parameter, $H^{ ablachi}$
Default:
10000.0