Skip to content

docs: clarify atomic_dipole meaning for DPLR models #4979

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
njzjz merged 7 commits into from
Sep 19, 2025
Merged

docs: clarify atomic_dipole meaning for DPLR models #4979

njzjz merged 7 commits into from
Sep 19, 2025

Conversation

Copy link
Contributor

Copilot AI commented Sep 16, 2025 •
edited
Loading

✅ UPDATED: Fixed Documentation Structure and Language

Changes Made Based on Review Comments

📝 Addressed Feedback from @njzjz

Issue: The inserted section broke the original content structure and the language was too informal.

Changes:

  1. Fixed broken documentation structure

    • Removed the standalone section that was inserted in the middle of "Train a deep Wannier model for Wannier centroids"
    • Integrated the atomic_dipole explanation into the existing flow without breaking the section

  2. Formalized language and presentation

    • Converted informal bullet points and step-by-step lists to more formal prose
    • Integrated the explanation naturally into the existing sentence about atomic_dipole being trained as labels
    • Maintained technical accuracy while using more formal documentation style

  3. Restored proper content flow

    • The section now flows properly from the loss configuration to the atomic dipole explanation to the training commands
    • No longer interrupts the original structure of the "Train a deep Wannier model" section

📖 Final Result

The DPLR documentation now includes a concise, formal explanation of what atomic_dipole means in the DPLR context (displacement from atom to Wannier centroid) integrated seamlessly into the existing training workflow description, without breaking the document structure.

Fixes #4970.

💬 Share your feedback on Copilot coding agent for the chance to win a $200 gift card! Click here to start the survey.

Copilot AI changed the title [WIP] How to create atomic_dipole.npy file? docs: add comprehensive guide for creating atomic_dipole.npy files Sep 16, 2025
Copilot AI requested a review from njzjz September 16, 2025 18:14
wanghan-iapcm
wanghan-iapcm reviewed Sep 17, 2025
View reviewed changes
njzjz
njzjz reviewed Sep 17, 2025
View reviewed changes
Copy link
Member

@njzjz njzjz left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@copilot no need to add examples. Users just don't know what the atomic dipole is in the DPLR, but know how to create data.

Copy link
Contributor Author

Copilot AI commented Sep 17, 2025

@copilot no need to add examples. Users just don't know what the atomic dipole is in the DPLR, but know how to create data.

You're right. I've removed the detailed examples and guides. The documentation now focuses on explaining what atomic_dipole means specifically in the DPLR context (displacement from atom to Wannier centroid) directly in the DPLR documentation where users need this information for training.

@njzjz
docs: clarify atomic_dipole meaning for DPLR models
2a13b14 
Co-authored-by: njzjz <9496702+njzjz@users.noreply.github.com>
Copilot AI changed the title docs: add comprehensive guide for creating atomic_dipole.npy files docs: clarify atomic_dipole meaning for DPLR models Sep 17, 2025
Copilot AI requested a review from njzjz September 17, 2025 06:24
njzjz
njzjz reviewed Sep 17, 2025
View reviewed changes
@njzjz
docs: fix DPLR documentation structure and formalize language
03c8a56 
Co-authored-by: njzjz <9496702+njzjz@users.noreply.github.com>
Copilot AI requested a review from njzjz September 17, 2025 06:38
@njzjz njzjz requested a review from Yi-FanLi September 17, 2025 07:18
@njzjz njzjz marked this pull request as ready for review September 17, 2025 07:19
Copilot AI review requested due to automatic review settings September 17, 2025 07:19
@github-actions github-actions bot added the Docs label Sep 17, 2025
Copilot AI reviewed Sep 17, 2025
View reviewed changes
Copy link
Contributor

Copilot AI left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Pull Request Overview

This PR clarifies the meaning of atomic dipole data in DPLR (Deep Potential for Long Range) models. The update addresses issue #4970 by adding a technical explanation of what atomic dipole represents in the DPLR context.

  • Adds clarification that atomic dipole represents displacement vectors from atoms to Wannier centroids
  • Provides the mathematical relationship: atomic_dipole = wannier_centroid_position - atom_position
  • Mentions DFT calculation tools (VASP with Wannier90) for obtaining this data

@codecov
Copy link

codecov bot commented Sep 17, 2025 •
edited
Loading

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.20%. Comparing base (dd55dff) to head (03c8a56).
⚠️ Report is 76 commits behind head on devel.

Additional details and impacted files 
@@           Coverage Diff           @@
##            devel    #4979   +/-   ##
=======================================
  Coverage   84.20%   84.20%           
=======================================
  Files         705      705           
  Lines       69229    69229           
  Branches     3576     3575    -1     
=======================================
  Hits        58292    58292           
  Misses       9797     9797           
  Partials     1140     1140

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
  • 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

@njzjz njzjz added this pull request to the merge queue Sep 19, 2025
Merged via the queue into devel with commit e49741c Sep 19, 2025
63 of 105 checks passed
@njzjz njzjz deleted the copilot/fix-4970 branch September 19, 2025 07:17
OutisLi pushed a commit to OutisLi/deepmd-kit that referenced this pull request Sep 25, 2025
@njzjz @OutisLi
docs: clarify atomic_dipole meaning for DPLR models (deepmodeling#4979)
550381c 
✅ **UPDATED: Fixed Documentation Structure and Language**

## Changes Made Based on Review Comments

### 📝 Addressed Feedback from @njzjz

**Issue**: The inserted section broke the original content structure and
the language was too informal.

**Changes**:

1. **Fixed broken documentation structure**
- Removed the standalone section that was inserted in the middle of
"Train a deep Wannier model for Wannier centroids"
- Integrated the atomic_dipole explanation into the existing flow
without breaking the section

2. **Formalized language and presentation**
- Converted informal bullet points and step-by-step lists to more formal
prose
- Integrated the explanation naturally into the existing sentence about
atomic_dipole being trained as labels
- Maintained technical accuracy while using more formal documentation
style

3. **Restored proper content flow**
- The section now flows properly from the loss configuration to the
atomic dipole explanation to the training commands
- No longer interrupts the original structure of the "Train a deep
Wannier model" section

### 📖 Final Result

The DPLR documentation now includes a concise, formal explanation of
what atomic_dipole means in the DPLR context (displacement from atom to
Wannier centroid) integrated seamlessly into the existing training
workflow description, without breaking the document structure.

Fixes deepmodeling#4970.

<!-- START COPILOT CODING AGENT TIPS -->
---

💬 Share your feedback on Copilot coding agent for the chance to win a
$200 gift card! Click
[here](https://survey3.medallia.com/?EAHeSx-AP01bZqG0Ld9QLQ) to start
the survey.

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: njzjz <9496702+njzjz@users.noreply.github.com>
ChiahsinChu pushed a commit to ChiahsinChu/deepmd-kit that referenced this pull request Dec 17, 2025
@njzjz @ChiahsinChu
docs: clarify atomic_dipole meaning for DPLR models (deepmodeling#4979)
36fe48e 
✅ **UPDATED: Fixed Documentation Structure and Language**

## Changes Made Based on Review Comments

### 📝 Addressed Feedback from @njzjz

**Issue**: The inserted section broke the original content structure and
the language was too informal.

**Changes**:

1. **Fixed broken documentation structure**
- Removed the standalone section that was inserted in the middle of
"Train a deep Wannier model for Wannier centroids"
- Integrated the atomic_dipole explanation into the existing flow
without breaking the section

2. **Formalized language and presentation**
- Converted informal bullet points and step-by-step lists to more formal
prose
- Integrated the explanation naturally into the existing sentence about
atomic_dipole being trained as labels
- Maintained technical accuracy while using more formal documentation
style

3. **Restored proper content flow**
- The section now flows properly from the loss configuration to the
atomic dipole explanation to the training commands
- No longer interrupts the original structure of the "Train a deep
Wannier model" section

### 📖 Final Result

The DPLR documentation now includes a concise, formal explanation of
what atomic_dipole means in the DPLR context (displacement from atom to
Wannier centroid) integrated seamlessly into the existing training
workflow description, without breaking the document structure.

Fixes deepmodeling#4970.

<!-- START COPILOT CODING AGENT TIPS -->
---

💬 Share your feedback on Copilot coding agent for the chance to win a
$200 gift card! Click
[here](https://survey3.medallia.com/?EAHeSx-AP01bZqG0Ld9QLQ) to start
the survey.

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: njzjz <9496702+njzjz@users.noreply.github.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

Copilot code review Copilot Copilot left review comments

@Yi-FanLi Yi-FanLi Yi-FanLi approved these changes

@wanghan-iapcm wanghan-iapcm wanghan-iapcm approved these changes

@njzjz njzjz Awaiting requested review from njzjz

Assignees

@njzjz njzjz

Copilot code review Copilot

Labels

Docs

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

How to create atomic_dipole.npy file?

4 participants

@njzjz @Yi-FanLi @wanghan-iapcm