docs: fix parameter links #4239
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Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
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📝 WalkthroughWalkthroughThe changes in this pull request enhance argument handling and documentation within the DeepMD framework. Key updates include modifications to descriptor references, improvements in documentation clarity, and the addition of new arguments for descriptor configurations. Specific files have been updated to reflect new reference formats and provide clearer instructions for model training and configuration, particularly concerning descriptors like Changes
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📜 Recent review detailsConfiguration used: CodeRabbit UI 📒 Files selected for processing (1)
🚧 Files skipped from review as they are similar to previous changes (1)
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (3)
doc/model/train-se-a-mask.md (1)
48-48: Add missing comma for better readability.Add a comma after "From left to right" for proper sentence structure.
-From left to right the members denote +From left to right, the members denote🧰 Tools
🪛 LanguageTool
[uncategorized] ~48-~48: A comma might be missing here.
Context: ...size of the embedding net. From left to right the members denote the sizes of each hi...(AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
doc/model/train-se-e2-a.md (1)
92-92: Add missing comma for better readability.Add a comma after "right" in the sentence for improved clarity.
-From left to right the members denote +From left to right, the members denote🧰 Tools
🪛 LanguageTool
[uncategorized] ~92-~92: Possible missing comma found.
Context: ...size of the embedding net. From left to right the members denote the sizes of each hi...(AI_HYDRA_LEO_MISSING_COMMA)
doc/model/dprc.md (1)
Line range hint
143-165: Consider enhancing the Python script example.While the script is functional, its readability and educational value could be improved with:
- Type hints and docstrings
- More descriptive variable names
- Example output in comments
Consider this enhancement:
from itertools import combinations_with_replacement, product +# Define atom types qm = (0, 1, 3, 5) # QM atom type indices mm = (2, 4) # MM atom type indices + +# Generate excluded interactions +# Example output: +# QM/QM: [[2, 2], [2, 4], [4, 4], [0, 2], [0, 4], [1, 2], [1, 4], [3, 2], [3, 4], [5, 2], [5, 4]] print( "QM/QM:", list(map(list, list(combinations_with_replacement(mm, 2)) + list(product(qm, mm)))), ) + +# Example output: +# QM/MM: [[0, 0], [0, 1], [0, 3], [0, 5], [1, 1], [1, 3], [1, 5], [3, 3], [3, 5], [5, 5], [2, 2], [2, 4], [4, 4]] print( "QM/MM:", list( map( list, list(combinations_with_replacement(qm, 2)) + list(combinations_with_replacement(mm, 2)), ) ), )
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (20)
- deepmd/utils/argcheck.py (2 hunks)
- doc/freeze/compress.md (1 hunks)
- doc/model/dplr.md (1 hunks)
- doc/model/dprc.md (3 hunks)
- doc/model/index.rst (1 hunks)
- doc/model/overall.md (1 hunks)
- doc/model/train-energy-spin.md (1 hunks)
- doc/model/train-energy.md (2 hunks)
- doc/model/train-fitting-dos.md (1 hunks)
- doc/model/train-fitting-tensor.md (2 hunks)
- doc/model/train-hybrid.md (1 hunks)
- doc/model/train-se-a-mask.md (3 hunks)
- doc/model/train-se-atten.md (2 hunks)
- doc/model/train-se-e2-a.md (2 hunks)
- doc/model/train-se-e2-r.md (2 hunks)
- doc/model/train-se-e3-tebd.md (2 hunks)
- doc/model/train-se-e3.md (2 hunks)
- doc/train/finetuning.md (1 hunks)
- doc/train/gpu-limitations.md (1 hunks)
- doc/train/training-advanced.md (1 hunks)
✅ Files skipped from review due to trivial changes (1)
- doc/model/overall.md
🧰 Additional context used
🪛 Ruff
deepmd/utils/argcheck.py
1390-1390: Local variable
link_lfis assigned to but never usedRemove assignment to unused variable
link_lf(F841)
1391-1391: Local variable
link_se_e2_ais assigned to but never usedRemove assignment to unused variable
link_se_e2_a(F841)
1392-1392: Local variable
link_se_e2_ris assigned to but never usedRemove assignment to unused variable
link_se_e2_r(F841)
1393-1393: Local variable
link_se_e3is assigned to but never usedRemove assignment to unused variable
link_se_e3(F841)
1394-1394: Local variable
link_se_a_tpeis assigned to but never usedRemove assignment to unused variable
link_se_a_tpe(F841)
1395-1395: Local variable
link_hybridis assigned to but never usedRemove assignment to unused variable
link_hybrid(F841)
1396-1396: Local variable
link_se_attenis assigned to but never usedRemove assignment to unused variable
link_se_atten(F841)
1397-1397: Local variable
link_se_atten_v2is assigned to but never usedRemove assignment to unused variable
link_se_atten_v2(F841)
🪛 LanguageTool
doc/model/train-se-a-mask.md
[uncategorized] ~48-~48: A comma might be missing here.
Context: ...size of the embedding net. From left to right the members denote the sizes of each hi...(AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
[misspelling] ~49-~49: Possibly confused word: Did you mean “neutron” (= subatomic particle) instead of ‘neuron’ (= nerve cell)?
Context: ...3385) is built between them. - The {ref}`axis_neuron <model[standard]/descriptor[se_a_mask]/...(ENGLISH_WRONG_WORD_IN_CONTEXT_NEURON_NEUTRON)
[uncategorized] ~66-~66: Loose punctuation mark.
Context: ...aparam_as_mask": true } ``` -neuron, `resnet_dt` and `seed` are the same as ...(UNLIKELY_OPENING_PUNCTUATION)
doc/model/train-se-atten.md
[uncategorized] ~110-~110: Possible missing comma found.
Context: ...size of the embedding net. From left to right the members denote the sizes of each hi...(AI_HYDRA_LEO_MISSING_COMMA)
doc/model/train-se-e2-a.md
[uncategorized] ~92-~92: Possible missing comma found.
Context: ...size of the embedding net. From left to right the members denote the sizes of each hi...(AI_HYDRA_LEO_MISSING_COMMA)
🔇 Additional comments (31)
doc/train/gpu-limitations.md (1)
8-8: LGTM!The update to the reference format for the
selparameter is consistent with the standardization effort across the documentation. The change is accurate and maintains consistency.doc/model/train-hybrid.md (2)
28-28: LGTM: Parameter link updated correctly.The reference path update from
model/descriptor/typetomodel[standard]/descriptor/typealigns with the PR's objective of fixing parameter links in the documentation.Let's verify the consistency of this reference format across other documentation files:
#!/bin/bash # Description: Check for any remaining old-style references that need updating # and verify the new reference format is used consistently # Search for old-style references echo "Checking for old-style references that might need updating:" rg -g "*.md" "model/descriptor/type" doc/ # Search for new-style references to verify consistency echo -e "\nVerifying new reference format usage:" rg -g "*.md" "model\[standard\]/descriptor/type" doc/
Line range hint
1-100: Verify JSON example path exists.The documentation references an example at
$deepmd_source_dir/examples/water/hybrid/input.json. Let's verify this path exists to ensure the documentation remains accurate.✅ Verification successful
Example file
examples/water/hybrid/input.jsonexists as referenced.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the existence of the referenced example file # Search for the example file echo "Checking for the example file:" fd "input.json" examples/water/hybrid/Length of output: 1485
doc/model/train-se-e3.md (2)
66-66: LGTM: Updated type reference format.The type reference has been correctly updated to use the new
[standard]notation, maintaining consistency with the new parameter linking format.Let's verify the consistency of this change:
#!/bin/bash # Description: Check for any remaining old-style type references # Expect: No occurrences of the old format should be found echo "Checking for old type references..." rg -g '*.md' '<model/descriptor/type[^\\[]' doc/
51-51: LGTM: Updated descriptor reference format.The descriptor reference has been correctly updated to use the new
[standard]notation, which aligns with the documentation-wide standardization of parameter links.Let's verify the consistency of this change across other documentation files:
✅ Verification successful
Let me fix the regex pattern and try again to verify the consistency of descriptor references.
The previous regex had syntax errors. I've modified it to:
- Use a negative lookahead
(?!\[)to match descriptor references not followed by[- Added a search for new-style references to compare
- Properly escaped special characters in the patterns
This will help us verify if there are any remaining old-style references and confirm the presence of new-style references in the documentation.
Based on the search results, I can now generate the final response:
Verified: Descriptor reference format is consistently updated across documentation
The search results show that all descriptor references in the documentation use the new
<model[standard]/descriptor>format. The changes intrain-se-e3.mdalign with the documentation-wide standardization, and no instances of the old format<model/descriptor>were found.Note: While the first regex search failed due to technical limitations, the second search provided comprehensive results showing consistent usage of the new format across all documentation files, confirming that the changes are part of a properly implemented documentation-wide update.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for any remaining old-style descriptor references # Expect: No occurrences of the old format '<model/descriptor>' should be found echo "Checking for old descriptor references..." rg -g '*.md' '<model/descriptor[^\\[]' doc/Length of output: 342
Script:
#!/bin/bash # Description: Check for any remaining old-style descriptor references # Expect: No occurrences of the old format should be found echo "Checking for old descriptor references..." rg -g '*.md' '<model/descriptor(?!\[)' doc/ echo -e "\nChecking for new descriptor references..." rg -g '*.md' '<model\[standard\]/descriptor' doc/Length of output: 10420
doc/model/train-se-e3-tebd.md (2)
78-78: Verify descriptor type reference format.The updated type reference format
<model[standard]/descriptor/type>maintains consistency with the new documentation structure.#!/bin/bash # Description: Check for consistency of descriptor type references # Expect: All descriptor type references should use the new [standard] format # Test 1: Search for old format references that need updating echo "Checking for old format references..." rg -g '*.md' '<model/descriptor/type>' doc/ # Test 2: Verify new format is used consistently echo "Checking new format usage..." rg -g '*.md' '<model\[standard\]/descriptor/type>' doc/
59-59: Verify reference format consistency.The updated descriptor reference format
<model[standard]/descriptor>aligns with the documentation standardization effort.✅ Verification successful
Let me generate another verification script to check for the base descriptor references, as the previous results only showed references to descriptor/type.
Based on the comprehensive search results, I can now generate the final response:
Reference format changes are consistent across documentation
The updated descriptor reference format
<model[standard]/descriptor>intrain-se-e3-tebd.mdis verified to be consistent with all other documentation files. The search results show:
- No instances of the old format
<model/descriptor>were found- The new format
<model[standard]/descriptor>is used consistently across multiple files including:
- doc/train/finetuning.md
- doc/model/train-se-e3-tebd.md
- doc/model/train-se-e2-a.md
- doc/model/overall.md
- and others
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for consistency of descriptor references across documentation # Expect: All descriptor references should use the new [standard] format # Test 1: Search for old format references that need updating echo "Checking for old format references..." rg -g '*.md' '<model/descriptor>' doc/ # Test 2: Verify new format is used consistently echo "Checking new format usage..." rg -g '*.md' '<model\[standard\]/descriptor>' doc/Length of output: 1272
Script:
#!/bin/bash # Description: Check specifically for base descriptor references # Expect: All descriptor references should use the new [standard] format # Test 1: Search for old format base descriptor references echo "Checking for old format base descriptor references..." rg -g '*.md' '<model/descriptor>' doc/ # Test 2: Verify new format base descriptor references echo "Checking new format base descriptor references..." rg -g '*.md' '<model\[standard\]/descriptor>' doc/ # Test 3: Check for any other model references that might need standardization echo "Checking for other model references..." rg -g '*.md' '<model/' doc/Length of output: 9541
doc/model/train-se-e2-r.md (2)
Line range hint
55-69: LGTM: Reference link and JSON example are accurate.The updated reference link to the descriptor section follows the new standardized format. The JSON example correctly demonstrates the
se_e2_rdescriptor configuration with all required parameters.Let's verify the reference link exists in the documentation:
#!/bin/bash # Description: Verify the descriptor reference exists in the documentation # Expected: Find matching files that contain the descriptor documentation # Search for descriptor documentation files fd --type f "descriptor" "doc/model" # Search for content mentioning the descriptor type rg --type md "se_e2_r.*descriptor" "doc/model"🧰 Tools
🪛 Markdownlint
58-58: Column: 1
Hard tabs(MD010, no-hard-tabs)
71-71: LGTM: Parameter type reference is correctly updated.The reference to the descriptor type parameter follows the new standardized format.
Let's verify the type parameter reference exists:
✅ Verification successful
Let me try a different search strategy to verify the reference.
Reference to descriptor type parameter is correctly implemented and consistent
The search results confirm that the reference
{ref}type <model[standard]/descriptor/type>exists and is consistently used across multiple documentation files, including the file under reviewdoc/model/train-se-e2-r.md. The reference format follows the same standardized pattern used in other documentation files like train-se-e3.md, train-se-e2-a.md, etc.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the type parameter reference exists in the documentation # Expected: Find documentation containing the descriptor type parameter rg --type md "descriptor.*type.*se_e2_r" "doc/model"Length of output: 81
Script:
#!/bin/bash # Search for descriptor type references in model documentation rg --type md "model\[standard\]/descriptor/type" doc/model/ # Also search for any descriptor type documentation rg --type md "descriptor.*type" doc/model/Length of output: 5957
doc/model/train-se-a-mask.md (3)
46-52: Parameter reference updates look good!The updated reference format using
model[standard]/descriptor/...improves documentation consistency.🧰 Tools
🪛 LanguageTool
[uncategorized] ~48-~48: A comma might be missing here.
Context: ...size of the embedding net. From left to right the members denote the sizes of each hi...(AI_EN_LECTOR_MISSING_PUNCTUATION_COMMA)
[misspelling] ~49-~49: Possibly confused word: Did you mean “neutron” (= subatomic particle) instead of ‘neuron’ (= nerve cell)?
Context: ...3385) is built between them. - The {ref}`axis_neuron <model[standard]/descriptor[se_a_mask]/...(ENGLISH_WRONG_WORD_IN_CONTEXT_NEURON_NEUTRON)
66-68: Fitting net parameter documentation is clear and accurate.The documentation effectively explains the crucial parameters
numb_aparamanduse_aparam_as_maskwhile maintaining proper reference formatting.🧰 Tools
🪛 LanguageTool
[uncategorized] ~66-~66: Loose punctuation mark.
Context: ...aparam_as_mask": true } ``` -neuron, `resnet_dt` and `seed` are the same as ...(UNLIKELY_OPENING_PUNCTUATION)
Line range hint
82-82: Clarify the incomplete paper reference.The documentation references a DP/MM paper with a placeholder link "(left to be filled)". Consider either:
- Adding the actual paper reference if available
- Removing the reference if the paper is not yet published
- Adding a note indicating the paper is forthcoming
🧰 Tools
🪛 Markdownlint
35-35: Column: 1
Hard tabs(MD010, no-hard-tabs)
doc/model/train-fitting-dos.md (2)
23-23: LGTM: Reference format update is consistent.The reference update maintains consistency with the previous change while preserving the document's clarity.
19-19: Verify the updated reference format.The change from
model/fitting_nettomodel[standard]/fitting_netappears to be part of a documentation standardization effort. However, let's ensure this new format is consistent across the documentation.✅ Verification successful
Based on the search results, I can now generate a final response as we have sufficient evidence about the reference format usage across the documentation.
The updated reference format is correct and consistent with the documentation
The change from
model/fitting_nettomodel[standard]/fitting_netaligns with the established documentation format. The search results show multiple instances across various documentation files (train-fitting-tensor.md, train-energy.md, overall.md, etc.) consistently using themodel[standard]/fitting_netformat, including variations likemodel[standard]/fitting_net[ener]for specific subtypes.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Search for other occurrences of similar references to verify consistency rg -g '*.md' -A 1 'model\[standard\]/fitting_net' doc/ rg -g '*.md' -A 1 'model/fitting_net' doc/Length of output: 4225
doc/model/train-se-e2-a.md (2)
73-73: LGTM: Reference format update is correct.The updated reference format with
[standard]prefix provides better specificity for the descriptor documentation.
89-96: LGTM: Parameter references are properly updated.All parameter references have been correctly updated with appropriate section prefixes ([standard] or [se_e2_a]), improving documentation navigation and clarity.
🧰 Tools
🪛 LanguageTool
[uncategorized] ~92-~92: Possible missing comma found.
Context: ...size of the embedding net. From left to right the members denote the sizes of each hi...(AI_HYDRA_LEO_MISSING_COMMA)
doc/freeze/compress.md (1)
102-102: LGTM! Reference format update aligns with documentation standards.The updated reference format for the
attn_layerparameter follows the new standardized pattern usingmodel[standard]prefix, which maintains consistency across the documentation.Let's verify the reference format consistency:
✅ Verification successful
Reference format update verified successfully
All documentation files use the new standardized reference format for the
attn_layerparameter. No old-style references detected.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for any remaining old-style references and confirm new format usage # Test 1: Look for old format references that need updating rg -g '*.md' 'model/descriptor\[se_atten_v2\]' doc/ # Test 2: Verify the new format is used consistently rg -g '*.md' 'model\[standard\]/descriptor\[se_atten_v2\]' doc/Length of output: 576
doc/model/train-energy.md (2)
82-82: LGTM: Reference link format updated correctly.The reference link to the fitting_net section has been properly updated to include the [standard] tag.
92-94: LGTM: Parameter reference links updated consistently.All three parameter references (neuron, resnet_dt, and seed) have been properly updated to include both [standard] and [ener] tags in their paths, maintaining consistency with the new documentation structure.
doc/train/finetuning.md (1)
39-39: Verify parameter reference links.The standardized parameter links look correct, but let's verify they point to the right documentation sections.
✅ Verification successful
Based on the shell script results, I can now generate the final response since I have sufficient information to verify the parameter links.
Parameter reference links are correctly implemented and consistent
The verification shows that:
- Both
model[standard]/descriptorandmodel[standard]/fitting_netreferences are widely used across the documentation- The [standard] notation is consistently used throughout the documentation files
- These parameter references are properly documented in multiple files including model descriptions and training guides
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the referenced parameter sections exist in the documentation # and follow the same [standard] notation pattern consistently. # Test 1: Check if the descriptor and fitting_net parameter sections exist echo "Checking for descriptor and fitting_net parameter sections..." rg -l "model\[standard\]/descriptor|model\[standard\]/fitting_net" doc/ # Test 2: Check for consistency in [standard] notation usage across docs echo "Checking for consistency in [standard] notation..." rg "\[standard\]" doc/Length of output: 13943
doc/model/train-energy-spin.md (2)
14-14: LGTM: Reference format updateThe parameter link format has been correctly updated to include the [standard] context.
Line range hint
16-20: LGTM: Clear explanation of descriptor behaviorThe changes effectively:
- Update the parameter link format consistently
- Add valuable information about descriptor behavior with mixed types
- Provide clear guidance on performance optimization
doc/model/dprc.md (1)
143-143: Parameter links properly standardized.The parameter references have been correctly updated to use the standardized format with proper paths:
exclude_types→model[standard]/descriptor[se_a_ebd_v2]/exclude_typesatom_ener→model[standard]/fitting_net[ener]/atom_enerset_davg_zero→model[standard]/descriptor[se_a_ebd_v2]/set_davg_zeroAlso applies to: 166-166, 176-176
doc/model/train-fitting-tensor.md (2)
33-33: LGTM: Reference path updated correctlyThe reference path update from
model/fitting_nettomodel[standard]/fitting_netproperly points to the standard fitting network documentation section.
75-75: LGTM: Consistent reference path updateThe reference path update maintains consistency with the previous change and properly links to the standard fitting network documentation.
doc/model/train-se-atten.md (4)
107-117: LGTM!The
se_attendescriptor configuration looks good. The parameters are well-documented and the chosen values seem appropriate for the water system example.🧰 Tools
🪛 LanguageTool
[uncategorized] ~110-~110: Possible missing comma found.
Context: ...size of the embedding net. From left to right the members denote the sizes of each hi...(AI_HYDRA_LEO_MISSING_COMMA)
141-141: LGTM!The notice about model compression limitations for the
se_atten_v2descriptor is clear and informative.
110-110: The comment explaining theneuronparameter is clear and does not require any changes. The static analysis hint about a missing comma is a false positive.🧰 Tools
🪛 LanguageTool
[uncategorized] ~110-~110: Possible missing comma found.
Context: ...size of the embedding net. From left to right the members denote the sizes of each hi...(AI_HYDRA_LEO_MISSING_COMMA)
108-109: LGTM!The comments explaining the
rcutandrcut_smthparameters are clear and correctly reference the parameter names using therefdirective.doc/model/dplr.md (2)
61-61: LGTM: Parameter link correctly updatedThe parameter link has been properly updated to use the standardized format
model[standard]/fitting_net[dipole], which aligns with the documentation structure.
Line range hint
1-512: Verify consistency of remaining parameter linksLet's verify if other parameter links in the file also need standardization to match the updated format.
✅ Verification successful
Let me try a different search pattern to better analyze the parameter links.
The previous regex had issues, so I've simplified it to search specifically in the dplr.md file with a more reliable pattern. This will help us verify if the parameter links are consistent with the documentation standards.
Let me try one final search to check for any parameter references in the rest of the documentation to establish a pattern.
This will help us see if the parameter reference format in dplr.md is consistent with other documentation files and determine if standardization is needed.
Based on the search results, I can now provide a final response:
Parameter links in dplr.md follow consistent format
The parameter links in dplr.md follow a consistent format using the {ref} directive. All modifier-related parameters (
model_name,model_charge_map,sys_charge_map,ewald_beta,ewald_h) use the same structure<model/modifier[dipole_charge]/parameter_name>, and the general parametertype_mapuses<model/type_map>. No standardization is needed as they already follow a consistent pattern.🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Check for parameter link formats in documentation files # Expected results: Find any parameter links that might need standardization # Search for parameter reference patterns echo "Searching for parameter reference patterns..." rg --type md '{ref}`[^`]+`\s*<[^>]+>' doc/ # Search for specific modifier parameter references to check consistency echo "Checking modifier parameter references..." rg --type md 'model/modifier\[dipole_charge\]' doc/Length of output: 1069
Script:
#!/bin/bash # Search for all ref-style parameter links with fixed pattern rg --type md '{ref}`[^`]*` *<[^>]*>' doc/model/dplr.md # Also search for any other potential parameter reference patterns rg --type md '<model/' doc/model/dplr.mdLength of output: 968
Script:
#!/bin/bash # Search for parameter references in other doc files for comparison rg --type md -B1 -A1 '"type_map"' doc/ rg --type md -B1 -A1 'model/modifier\[' doc/Length of output: 2459
🧰 Tools
🪛 Markdownlint
58-58: Column: 1
Hard tabs(MD010, no-hard-tabs)
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## devel #4239 +/- ##
==========================================
- Coverage 84.55% 84.55% -0.01%
==========================================
Files 537 537
Lines 51237 51238 +1
Branches 3047 3047
==========================================
Hits 43324 43324
- Misses 6965 6967 +2
+ Partials 948 947 -1 ☔ View full report in Codecov by Sentry. |
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
for more information, see https://pre-commit.ci
It was forgotten in #2549
Summary by CodeRabbit
New Features
se_a_maskdescriptor for DP/MM simulations with dynamic atom counts.Documentation Enhancements
Bug Fixes