Nalu-Wind Helper Scripts

Scripts to help with Nalu-Wind

Contents

Plot mesh refinement

[plotmesh.py](plotmesh.py): Plots the mesh refinement levels, turbine locations, and cut-slices

Usage

$ module load canopy
$ plotmesh.py YAMLFILE

Here YAMLFILE is a yaml file containing the mesh definition, refinement windows, and (optionally) the slice mesh parameters.

Output:

Each different colored rectangle represents a halving of the mesh resolution (8x refinement). The arrow in the middle of the domain points in the wind direction.

If you include the slice_mesh section in the YAML file, then it will also include the areas where the sections are being taken, like this:

The plotmesh.py script will also plot the probes in the data_probes section. If you include the following in your input file

  data_probes:
    exodus_name: exoprobe/probes3.exo
    output_frequency: 1
    search_method: stk_kdtree
    search_tolerance: 1.0e-5 #1.0e-3
    search_expansion_factor: 2.0
 
    specifications:
    - name: probe_surface
      from_target_part: Unspecified-2-HEX
      line_of_site_specifications:        
        - name: Probe1 # boostProbes2/probes/Probe1
          number_of_points: 3
          tip_coordinates:  [10, 0, 0]
          tail_coordinates:  [20, 0, 0]
        - name: Probe2 # boostProbes2/probes/Probe2
          number_of_points: 11
          tip_coordinates:  [100, 0, 0]
          tail_coordinates:  [120, 0, 0]
      plane_specifications:        
        - name: boostProbes2/planes/p1/Plane1
          corner_coordinates:  [25, -100, 0]
          edge1_vector:    [450, 0, 0]
          edge2_vector:    [0, 200, 0]
          edge1_numPoints: 51
          edge2_numPoints: 21
          #offset_vector:   [0, 0, 1]
          #offset_spacings: [0, 100]
        - name: ./Plane2 #boostProbes2/planes/p2/Plane2
          edge1_numPoints: 31
          edge2_numPoints: 31
          corner_coordinates:  [100, 0, 0]
          edge1_vector:    [10, 0, 0]
          edge2_vector:    [0, 10, 0]
          offset_vector:   [1, 0, 0]
          offset_spacings: [0, 100]
        - name: boostProbes2/planes/p3/Plane3
          edge1_numPoints: 21
          edge2_numPoints: 21
          corner_coordinates:  [126, -70, -70]
          edge1_vector:    [0, 140, 0]
          edge2_vector:    [0, 0, 140]
          offset_vector:   [1, 0, 0]
          offset_spacings: [-20, 20]
      output_variables:
        - field_name: velocity
          field_size: 3

Then the output of plotmesh.py will look like:

Mesh refinement script

[buildrefinemesh.sh](buildrefinemesh.sh): Creates a mesh, does local refinement

Usage

buildrefinemesh.sh YAMLFILE [OPTIONS]

Arguments
  YAMFILE   : a yaml file containing the mesh definitions

Options: 
  -o|--output-mesh OUTFILE  : Output filename (default: refinedmesh.exo)
  -n|--ncores      NPU      : Number of cores to use (default: 8)
  --no-createmesh           : Do not create basic mesh
  --no-preproc              : Do not use the preprocessor to define mesh refinem ent zones
  --no-refine               : Do not use mesh_adapt to refine mesh
  -h|--help                 : This help file

The argument YAMLFILE should point to a yaml input file like this:

nalu_abl_mesh:
  output_db: mesh_abl.exo
  spec_type: bounding_box
  fluid_part_name: fluid_part

  vertices:
  - [0.0, 0.0, 0.0]
  - [1000.0, 1000.0, 300.0]
  mesh_dimensions: [100, 100, 30]

  xmin_boundary_name: west
  xmax_boundary_name: east
  ymin_boundary_name: south
  ymax_boundary_name: north
  zmin_boundary_name: lower
  zmax_boundary_name: upper

# Mandatory section for Nalu preprocessing
nalu_preprocess:
  # Name of the input exodus database
  input_db: mesh_abl.exo
  # Name of the output exodus database
  output_db: mesh_abl.exo

  # Nalu preprocessor expects a list of tasks to be performed on the mesh and
  # field data structures
  tasks:
    - mesh_local_refinement

  mesh_local_refinement:
    fluid_parts: [fluid_part]
    write_percept_files: true
    percept_file_prefix: adapt
    search_tolerance: 11.0
    turbine_locations:
      - [ 200.0, 200.0, 0.0 ]
      - [ 230.0, 300.0, 0.0 ]
    turbine_diameters: 15.0        # Provide a list for variable diameters
    turbine_heights: 50.0          # Provide a list for variable tower heights
    orientation:
      type: wind_direction
      wind_direction: 225.0
    refinement_levels:             # Numbers are for upstream, downstream, lateral and vertical length in turbine diameters
      - [ 7.0, 12.0, 7.0, 7.0 ]
      - [ 5.0, 10.0, 5.0, 5.0 ]
      - [ 3.0, 6.0, 3.0, 3.0 ]

When you execute the script, for instance

$ ./buildrefinemesh.sh testmesh.yaml -o testmesh.exo

the first stage should be the mesh creation part

Nalu ABL Mesh Generation Utility
Input file: testmesh.yaml
HexBlockBase: Registering parts to meta data
	Mesh block: fluid_part
Num. nodes = 41616; Num elements = 37500
	Generating nodes...done
	Generating elements...done
	Creating element connectivity... done
	Generating X Sideset: west
	Generating X Sideset: east
	Generating Y Sideset: south
	Generating Y Sideset: north
	Generating Z Sideset: lower
	Generating Z Sideset: upper
	Finalizing bulk data modifications ... done
	Generating coordinates...
	 Generating x spacing: constant_spacing
	 Generating y spacing: constant_spacing
	 Generating z spacing: constant_spacing
Writing mesh to file: mesh_abl.exo

Followed by the preprocessing stage which marks out areas for local refinement:

Nalu Preprocessing Utility
Input file: testmesh.yaml
Found 1 tasks
    - mesh_local_refinement

Performing metadata updates... 
Metadata update completed
Reading mesh bulk data... done.

--------------------------------------------------
Begin task: mesh_local_refinement

Then it will run mesh_adapt through the multiple stages of refinement:

Running mesh refinement step
------------------
STAGE 1 REFINEMENT: tempmesh0.e --> tempmesh1.e
------------------
mpirun -n 8 mesh_adapt --refine=DEFAULT --input_mesh=tempmesh0.e --output_mesh=tempmesh1.e --RAR_info=adapt1.yaml --ioss_read_options="auto-decomp:yes" 
INFO: ioss_read_options=auto-decomp:yes ioss_write_options=
PerceptMesh:: opening tempmesh0.e

Using decomposition method 'RIB' on 8 processors.

At the very end, it will copy over the final mesh and report the new mesh blocks which are included:

‘tempmesh2.e’ -> ‘testmesh.exo’

New mesh blocks: 
 eb_names =
  "fluid_part",
  "fluid_part.pyramid_5._urpconv",
  "fluid_part.tetrahedron_4._urpconv",
  "fluid_part.pyramid_5._urpconv.Tetrahedron_4._urpconv" ;
}

Slice mesh utility

[slicemesh.sh](slicemesh.sh): Creates the slice geometry for a mesh

Usage

./slicemesh.sh MESHYAMLFILE [OPTIONS]

where MESHYAMLFILE is the yaml file containing the slice mesh parameters.

Optional Arguments:

  -y|--yaml-output YAMLFILE    Print out the corresponding yaml inputs needed to include the slice mesh 
                               output during the simulation.  YAMLFILE is the main simulation yamlfile
  -v|--extra-vars  VARLIST     An extra list of variables to include when writing out the sliced meshes.
                               VARLIST is of the form "var1:N var2:N ..." where var1, var2, are the
                               variable names, and N is the number of components for that variable

The MESHYAMLFILE input file defining the slices to take:

slice_mesh:
  output_db: temp.exo # sliceplanes.exo

  slices:
    # X-Y plane
    - axis1: [1.0, 0.0, 0.0]
      axis2: [0.0, 1.0, 0.0]
      axis3: [0.0, 0.0, 1.0]
      origin: [0.0, 0.0, 0.0]
      grid_lengths: [2500.0, 2500.0]
      grid_dx: [4.0, 4.0]
      num_planes: 1
      plane_offsets: [0.0]
      part_name_prefix: turbineHH

    # Y-Z plane 
    - axis1: [1.0, 1.0, 0.0]
      axis2: [0.0, 0.0, 1.0]
      axis3: [-1,  1.0, 0.0]
      origin: [0.0, 00, -100.0]
      grid_lengths: [3000.0, 200.0]
      grid_dx: [4.0, 4.0]
      num_planes: 1
      plane_offsets: [0.0]
      part_name_prefix: turbineSlice2

If you execute it with the input files:

$ slicemesh.sh mesh1.yaml 
yamlfile    = mesh1.yaml
simyamlfile = 
extravars   = 
Loading modules
Output mesh name = temp.exo
Slice Mesh Generation Utility
Input file: mesh1.yaml
Loading slice inputs... 
Initializing slices... 
Slice: Registering parts to meta data: 
  -  turbineHH_1
Slice: Registering parts to meta data: 
  -  turbineSlice2_1
Generating slices for: turbineHH
Creating nodes... 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
Creating elements... 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
Generating coordinate field
 - turbineHH_1
Generating slices for: turbineSlice2
Creating nodes... 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
Creating elements... 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
Generating coordinate field
 - turbineSlice2_1
Writing mesh to file: temp.exo

Memory usage: Avg:  156.043 MB; Min:  156.043 MB; Max:  156.043 MB

If you execute it with the -y option, like slicemesh.sh mesh1test.yaml -y alm_simulation.yaml, then some additional output will be generated:

# === Auto-generated YAML below ======

# Goes under [realms:]
- name: ioRealm
  mesh: temp.exo
  type: input_output
  automatic_decomposition_type: rcb

  field_registration:
    specifications:
    - field_name: velocity_slice
      target_name: &fieldreg [ turbineHH_1, turbineSlice2_1 ]
      field_size: 3
      field_type: node_rank
  output:
    output_data_base_name: ./sliceDataInstantaneous/temp.exo
    output_frequency: 1
    output_node_set: no
    output_variables:
    - velocity_slice
transfers:
- name: turbineHH_1
  type: geometric
  realm_pair: [realm_1, ioRealm]
  to_target_name: turbineHH_1
  from_target_name: ['fluid_part', 'fluid_part.Pyramid_5._urpconv', 'fluid_part.Tetrahedron_4._urpconv']
  objective: input_output
  transfer_variables:
  - [velocity, velocity_slice]
- name: turbineSlice2_1
  type: geometric
  realm_pair: [realm_1, ioRealm]
  to_target_name: turbineSlice2_1
  from_target_name: ['fluid_part', 'fluid_part.Pyramid_5._urpconv', 'fluid_part.Tetrahedron_4._urpconv']
  objective: input_output
  transfer_variables:
  - [velocity, velocity_slice]

# === End auto-generated YAML ======

These yaml parameters can be added to alm_simulation.yaml to extract the slice during simulations.

Plot FAST output

[plotFAST.py](plotFAST.py): Plots FAST output

Usage

$ module load canopy
$ plotFAST.py FAST.T1.out [FAST.T2.out  ... ]

Output:

It's pretty self-explanatory. Check the variables on the left you would like to plot, and hit Plot. If the output files get updated, hit Reload data to reread the files from disk.

Backup and write a restart YAML file

[restartbackupnalu.py](restartbackupnalu.py): Retarts and backups up a simulation from a YAML file

This script takes in the current YAML input file, then automatically sets up the right restart parameters and spits out a new YAML file. Works on both ABL and FAST turbine runs. Optionally backups all the restart/output files so they don't get overwritten.

Usage

usage: restartbackupnalu.py [-h] [--dobackup] [--Nsteps NSTEPS]
                            [--suffix SUFFIX]
                            yamlfile [yamlfile ...]

Create a restart YAML file for Nalu.

positional arguments:
  yamlfile

optional arguments:
  -h, --help            show this help message and exit
  --dobackup            Backup files [default=False]
  --addNsteps ADDNSTEPS
                        Add another ADDNSTEPS to the run [default 100]
  --runToNsteps RUNTONSTEPS
                        Run until RUNTONSTEPS are reached [default is
                        ADDNSTEPS, not RUNTONSTEPS]
  --suffix SUFFIX       Suffix to attach to backup files [default is date/time
                        based suffix]

Plot sample planes

[plotSamplePlaneGUI.py](plotSamplePlaneGUI.py): GUI to plot the sample planes

Usage

usage: plotSamplePlaneGUI.py [-h] [--nogui] [--planenum PLANENUM]
                             [--varnum VARNUM]
                             [PLANEFILE [PLANEFILE ...]]

Plot sample mesh

positional arguments:
  PLANEFILE            Plot this sample plane

optional arguments:
  -h, --help           show this help message and exit
  --nogui              Use command line only [default=False]
  --planenum PLANENUM  Plot this plane number
  --varnum VARNUM      Plot this variable number

For example, let's say you created a set of planes with the following specifications:

   specifications:
    - name: probe_surface
      from_target_part: Unspecified-2-HEX
      plane_specifications:
        - name: Probes/Plane3
          edge1_numPoints: 21
          edge2_numPoints: 21
          corner_coordinates:  [126, -70, -70]
          edge1_vector:    [0, 140, 0]
          edge2_vector:    [0, 0, 140]
          offset_vector:   [1, 0, 0]
          offset_spacings: [-20, 20]
      output_variables:
        - field_name: velocity
          field_size: 3

These planes can be plotted by loading them in plotSamplePlaneGUI.py:

$ plotSamplePlaneGUI.py Plane3*_1.dat

On the left hand side there are the different plane files, plot variables, and plane numbers in each file. Select the parameters to display, and hit the Plot button to see something like:

Convert sample planes to VTK

[convertSamplePlane2VTK.py](convertSamplePlane2VTK.py): This script converts the text output sample planes to ASCII VTK format.

Usage

usage: convertSamplePlane2VTK.py [-h] [--planenum PLANENUM]
                                 PLANEFILE [PLANEFILE ...]

Convert sample planes to ASCII VTK format

positional arguments:
  PLANEFILE            Sample plane file(s) to convert

optional arguments:
  -h, --help           show this help message and exit
  --planenum PLANENUM  Convert only this offset plane number [default: convert
                       all planes]

Example

$ convertSamplePlane2VTK.py --planenum 0 HHplane_0009[0-3]*.dat
Converting HHplane_0009000_0.dat
 -> writing HHplane_0009000_0_plane0.vtk
Converting HHplane_0009100_0.dat
 -> writing HHplane_0009100_0_plane0.vtk
Converting HHplane_0009200_0.dat
 -> writing HHplane_0009200_0_plane0.vtk
Converting HHplane_0009300_0.dat
 -> writing HHplane_0009300_0_plane0.vtk

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