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Merged
aplowman merged 43 commits into from
Jan 13, 2026
Merged

Support CIPHER, a phase-field simulation code. #403

aplowman merged 43 commits into from
Jan 13, 2026

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@aplowman
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@aplowman aplowman commented Jul 10, 2025 •
edited by gcapes
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Will fix #392. Some points below are from my chat with Aiden a few weeks ago.

Port existing functionality from old-matflow:

  • Initial basic support
  • Generate a Docker image for test running CIPHER locally (in serial) to assist development
  • Check if we still need the parameter: delete_VTIs
  • Support the other generate_phase_field_input methods:
  • Respect the num_VTU_files parameter
  • Document the environment requirements (cipher_processing_env and cipher_env)
  • Quick tests on:
    • CSF3 (UoM)
    • CSF4 (UoM)
    • CSD3 (UoC)
  • Merge my CIPHER PR to reduce memory usage
  • Release a new version of cipher-parse, containing:
    • Fixed GitHub actions workflows (updates required)
    • small fixes identified so far
    • support for generating mappings in separate files (already implemented)
    • simplified/more modern dependencies (e.g. we won't need integration with old-matflow now)
  • Re-implement (and publish to docs site as demos, with suggested resource requirements) pertinent workflows/post-processing from the abnormal grain growth work:
    • "grain growth reversal" simulations in 2D and 3D:
      • sampling two textures from MTEX, and generating with Dream3D a volume element with a nucleus and these textures
      • interface binning
      • ability to change grain size
      • with/without nucleus
    • Processing results to allow plots of nucleus vs matrix growth curves (maybe as a new task)
  • Ability to separate VE-generation workflow from simulation workflow
    • The parameter import functionality that is in old-matflow is not yet re-implemented in new-matflow, but we can define a task to load the VE from an existing workflow (I think I did this somewhere else).

Possible new features requested (possibly in cipher-parse):

  • Recreate VE with centre shifted if anomalous grain happens to be the edge of the VE
    • Need to discuss with Aiden more
  • Integrate Sam's reshuffle algorithm which clusters orientations together
    • Need to discuss with Aiden more

@aplowman aplowman added the enhancement New feature or request label Jul 10, 2025
@gcapes gcapes mentioned this pull request Aug 7, 2025
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2 tasks
@gcapes gcapes mentioned this pull request Sep 9, 2025
Open
aplowman and others added 12 commits September 18, 2025 15:12
@aplowman @gcapes
feat: initial support for CIPHER simulations
61394ce
@gcapes
Remove resource request from cipher demo
df8b593 
This is specific to running on Windows with Docker,
which should be set by the user.
@gcapes
Add combine_phases to inputs in task schema
3b2206d 
- Set default value here instead of in the python script.
@gcapes
Add schema for from_random_voronoi_with_orientations method
54f1068
@gcapes
Implement from volume element method
0d75620
@gcapes
Fix function name to match file name
6d9a27d
@gcapes
Implement from_random_voronoi_orientations_gradient method
71576e3
@gcapes
Add environment definitions for cipher
a599deb
@gcapes
Add Aiden's old workflow file
71cb666 
This is clearly incompatible with the current Matflow.
@gcapes
Start to implement tasks using new task schemas
a9aaf3b 
Started with the easier ones:

Remove dropbox archiving
Adapt task syntax for
- sample texture from model ODF mtex for phase 1
- Visualise orientations and move straight after sampling tasks
- visualise VE VTK
@gcapes
Move CIPHER definitions from workflow to template components
4a5ce2e
@gcapes
Implement remaining CIPHER tasks
0d82b11
gcapes and others added 13 commits October 1, 2025 09:55
@gcapes
Fix indentation to match other env definitions
91361c3
@gcapes
Add simulate_grain_growth task to workflow
d2b9bed
@aplowman
build: merge
e0c7d0e
@aplowman
fix: demo of how to implement from_statistics_dual_phase_orientations
9d70a28
@gcapes
Implement dual phase orientations with Dream3D
3bfbfda 
Remove explanation from previous commit.

Note that this workflow gives an error:

```
ValueError: Action 0 input 'orientations' of schema 'generate_volume_element_from_statistics_dual_phase_orientations_Dream3D' is not a schema input, but nor is it an action output from a preceding action.
```
@gcapes
Add original single-phase workflows
2dc7806 
These are in thd old matflow format.
@gcapes
Fix various syntax errors
7ccfac1 
Debugging the workflow turned up some incorrect syntax,
incorrect filenames (scripts not matching the first function names),
missing default values for input parameters.

It also turns out that Dream3D needs the full path to the precipitates file.
@gcapes
Save dream3d hdf5 file by using absolute path in json pipline file
f05ea10
@gcapes
Use compact notation for output file parser
94b128d
@gcapes
Convert orientations to old matflow format
52c2412 
I still get this error that I got before converting to old matflow
orientations format:

```
  File "/home/mbexegc2/projects/lightform/cipher-workflows/cipher-aiden_2025-10-29_133031/artifacts/submissions/0/scripts/generate_volume_element_from_statistics_dual_phase_orientations_Dream3D_act_3.py", line 40, in parse_dream_3D_volume_element_from_stats
    ori_1 = validate_orientations(orientations_phase_1)
  File "/home/mbexegc2/projects/lightform/cipher-workflows/.venv/lib/python3.10/site-packages/damask_parse/utils.py", line 983, in validate_orientations
    ori_type = orientations.get('type')
AttributeError: 'Orientations' object has no attribute 'get'
```
@gcapes
Convert orientations to old matflow format
3d6fac9
@gcapes
Revert "Convert orientations to old matflow format"
0b0f993 
This reverts commit 52c2412.
@gcapes
Convert orientations to numpy so we can edit them
099d3d5
gcapes added 14 commits November 6, 2025 16:13
@gcapes
Rename CIPHER workflows more descriptively
3645cc5
@gcapes
Use new matflow syntax
f1dbc20
@gcapes
Add placeholder tasks to single phase microstructure workflow
ce0be31 
These are commented out because there's an error from the
generate_phase_field_input_from_volume_element task.
@gcapes
Add skeleton task schema to return a volume element
96670cc 
This just returns the unaltered volume element.
@gcapes
Add completed task schema but with hard-coded values
2e44947 
The demo workflow uses paths on my machine,
and the clustering regions/values are hard-coded.

I expect these both need updating.
@gcapes
Fix typo
6b05a6a
@gcapes
Define quaternion replacement ranges through input parameters
c2b72ae
@gcapes
Add quaternions as demo data file
30691d6
@gcapes
Save misorientations plot
07b8050
@gcapes
Remove old comment
daab0a8
@gcapes
Add workflow doc attribute
58578f8
@gcapes
Add docstring for clustering.py
df4c373
@gcapes
Rename single phase microstructure workflow
3a2874b
@gcapes
Add doc attributes to cipher workflows
2b74ea2
@gcapes gcapes marked this pull request as ready for review January 7, 2026 15:41
@gcapes gcapes requested a review from a team as a code owner January 7, 2026 15:41
@dkfellows dkfellows marked this pull request as draft January 8, 2026 13:36
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dkfellows commented Jan 8, 2026

I've marked this as a Draft PR because it's still being baked.

@gcapes
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gcapes commented Jan 8, 2026

Not sure what you mean "baked", but I think it's ready for review, so I'm going to re-mark it as such.

@gcapes gcapes marked this pull request as ready for review January 8, 2026 13:49
@dkfellows
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dkfellows commented Jan 8, 2026

Well, you have merge conflicts...

@gcapes
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gcapes commented Jan 8, 2026

Two of the merge conflicts (to template components) are easy to resolve - keep both sets of changes. What I'm unclear about is where the demo data has moved to. Looks all to have been deleted, so this will need some advice as part of the review.

@aplowman aplowman merged commit f3f4117 into develop Jan 13, 2026
23 checks passed
@aplowman aplowman deleted the software/cipher branch January 13, 2026 13:55
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Support CIPHER

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@aplowman @dkfellows @gcapes