Publishing safe internal commits into public repo by BaoKhanhMa · Pull Request #87 · dssimmons-codes/AMDAT

BaoKhanhMa · 2026-07-07T15:04:32Z

AMDAT 1.1.0 — 2026-07-07

AMDAT now supports parallel execution with OpenMP multithreading, achieving enormous performance increase in numerous analyses supported in AMDAT, such as Mean Square Displacement, Incoherent Scattering Function, Radial Distribution Function,...

Highlights

Significant reduction of execution time due to the adoption of OpenMP multithreading.
Created a dedicated manual for running AMDAT with multithreading.

Analyses with multithreading enabled:

Analysis	Description	Maximum Speedup Tested (Compared to Serial)
`md`	Calculate Mean Displacement	7x
`msd`	Calculate Mean Square Displacement	10x
`msd_2d`	Calculate Mean Square Displacement for two-dimensional analysis	9x
`isfs`	Calculate Incoherent Scattering Function	20x
`vhs`	Calculate self part of Van Hove Function	12x
`vhd`	Calculate distinct part of Van Hove Function	20x
`raf`	Calculate Reorientation Autocorrelation Function	15x
`ngp`	Calculate Non Gaussian Parameter	30x
`composition`	Calculate Composition	7x
`rdf`	Calculate Radial Distribution Function	21x
`rnf`	Calculate Radial Count	23x
`orientational_correlation`	Calculate the orientational correlation of multibodies with an externally defined vector	6.5x
`neighbor_decorrelation_function`	Calculates an autocorrelation function for the mean number of initial neighbors that are still neighbors at a later displacement time.	8.5x

Migration Notes

No action required. OpenMP installation is already handled by conda.

(cherry picked from commit 229d62edc98b8faddc27f3476a6ab5e2a3ece63e)

…bb31f6faed80de

…d2927a5c33c9d0cc

Added link of exponential time spacing to time scheme documentation (cherry picked from commit 797d3ff4f6159d436e4594fbacb21057caa078fa)

…-safe adaptation of private commit 5345b431.

…on of private commit b9c795b.

…ptation of private commit fcfc2d9.

Public-safe adaptation of private commit f8b46f7.

Public-safe adaptation of private commit 6c74f81.

…ed to public-safe from 6809bb7.

…t. Public-safe adaptation from commit d096985.

…, and enables multithreading for Radial Distribution Function. Adapted from 986663f.

…ed from 5dea40f.

Change general manual wording to reflect partial implementation of multithreading. (cherry picked from commit 79c079a21e69488220d80191fc6cc8c180bd73a5)

Creating stub page for multithreading documentation. (cherry picked from commit 7c0cd87e030b9c6ddf19a6ef3ac856cdd8c7c44b)

Added flag for multithreaded. (cherry picked from commit a16651834d485384431a1f8519db3dc273cfe2f7)

Updated multithreading documentation. (cherry picked from commit 6f7a4b871a70aedbb15679304172b39540f8a18b)

More multithreading documentation. (cherry picked from commit 243e5ec3b11609e6da3f6a6f5d801690981aa417)

Updates the multithreading documentation initially (cherry picked from commit 044c2d98ef78ed5bfe831e715d2697915477ae70)

Added a badge for multithreading to the mean displacement documentation. (cherry picked from commit 6e10078bc2fbcd5d5b6cb7494fa2b915172c08b9)

(cherry picked from commit 31be0e63626e0d9ec4037a53a0f25601e8606fbe)

(cherry picked from commit 931459ffa24d4fe67dfc5c4813fafbd609b33507)

Added a badge for multithreading to radial_count documentation. (cherry picked from commit 7cb8360e675814c95a1beb33e929bed2dbd76cc4)

(cherry picked from commit 411ec9ce8d1ea0995c677158cd38b9b4a9d247cd)

Added a badge for multithreading to the VHD documentation. (cherry picked from commit e9672aa6b77ddcc82c1f49cb7d1a88c5342855e3)

Added a badge for multithreading support in the documentation. (cherry picked from commit e8adf1904fb8b062db4ee9c7561ce25b03e16b95)

Updated links in the analysis table and corrected formatting for CPU count in the threading formula. (cherry picked from commit be7134e8cf367d16a0411cb95e307cb1c8c4098d)

(cherry picked from commit 5f3a604facf9f2494228a2228a4a4fc1ba783031)

(cherry picked from commit cf6b2896b30856ded78473a0a52b41ad4df8218c)

(cherry picked from commit 2b04516b78012de14e650ebe3c50d7dd468842f8)

(cherry picked from commit 8cbf1ceab637de04e223b8a2e3bfc8f19fa34969)

This reverts commit 243e5ec3b11609e6da3f6a6f5d801690981aa417. (cherry picked from commit 8df31de0e0cdb36265b27d2cb8d58debeb39a950)

This reverts commit 8df31de0e0cdb36265b27d2cb8d58debeb39a950. (cherry picked from commit 1e57a77d39cce5a5125bb3c2dded8a7d9be14cd3)

This reverts commit 8cbf1ceab637de04e223b8a2e3bfc8f19fa34969. (cherry picked from commit 827ae1fc2fe5b0b1cdf258c4623390f14ce0a9cc)

…orrelation. Adapted from e3e8689

Public-safe adaptation of private commit 9821b95.

typo fix (cherry picked from commit f20e233b3597d45a70060faf5719167d0bf203e4)

BaoKhanhMa · 2026-07-07T15:19:57Z

Issues

How do I exclude the changes in check-version.yml?

I wasn't familiar with github-workflow back then, so I edited the check-version file to make it skipped the check in the internal remote. However, I already reverted that change in the internal version, but my cherry-picking process still picked the changes somehow. Ultimately, I don't want to keep that change, but I am also hesitated to redo the entire screening process of the commits just to exclude one particular file.

That specific line in the workflow is also the reason why this PR failed the VERSION check

pkawak · 2026-07-07T23:24:32Z

Issues

How do I exclude the changes in check-version.yml?

I wasn't familiar with github-workflow back then, so I edited the check-version file to make it skipped the check in the internal remote. However, I already reverted that change in the internal version, but my cherry-picking process still picked the changes somehow. Ultimately, I don't want to keep that change, but I am also hesitated to redo the entire screening process of the commits just to exclude one particular file.

That specific line in the workflow is also the reason why this PR failed the VERSION check

Is there a specific commit that leads to this behavior?

pkawak

Excellent work, @BaoKhanhMa

I left you one small comment on .github/workflows/check-version.yml that may fix the failing unit test (version check).

pkawak · 2026-07-07T23:25:50Z

Is this where that skip happens? If so, we need to just edit it out. Why are we not checking when its a pull request. That doesn't make much sense to me.

Removed VERSION check skip for pull requests (included in error).

pkawak · 2026-07-08T17:23:36Z

From a brief analysis, I can see several issues with this pull request. I have to investigate a little more carefully. I will analyze this weekend and get back to you.

BaoKhanhMa · 2026-07-09T02:33:11Z

From a brief analysis, I can see several issues with this pull request. I have to investigate a little more carefully. I will analyze this weekend and get back to you.

Yes, please take your time. Thank you, Dr. Kawak.

BaoKhanhMa and others added 30 commits June 25, 2026 19:13

Enable multithreading for system.cpp (Line~ 4100)

8c71903

(cherry picked from commit 229d62edc98b8faddc27f3476a6ab5e2a3ece63e)

Adding high-resolution clock. Adapted from 1176fd45ecde950126c1d8c392…

1b8cffd

…bb31f6faed80de

Enabling Multithreading: ISFS - Adapted from bf5a91e1ae1e345e48630a57…

0060c42

…d2927a5c33c9d0cc

Padding MSD - Adapted from f6130411ca27fd890fe953e4a0d590200f92bcfc

646375f

Update README.md

e01bbc2

Added link of exponential time spacing to time scheme documentation (cherry picked from commit 797d3ff4f6159d436e4594fbacb21057caa078fa)

Enable multithreading for MD, MSD, Van Hove, and BAF analyses: Public…

1f87c2c

…-safe adaptation of private commit 5345b431.

Update README for public multithreading changes: Public-safe adaptati…

0644b02

…on of private commit b9c795b.

Add padding support to bond autocorrelation function: Public-safe ada…

e4fff85

…ptation of private commit fcfc2d9.

Add padding support to mean displacement

8098af3

Public-safe adaptation of private commit f8b46f7.

Update control handling for multithreading

ecf7463

Public-safe adaptation of private commit 6c74f81.

Change environment.yml to make conda use latest C/C++ compiler. Adapt…

cd2bc2a

…ed to public-safe from 6809bb7.

Enable multithreading for Non Gaussian Parameter and Van Hove Distinc…

f9416b6

…t. Public-safe adaptation from commit d096985.

Create isf.md. Public-safe adaptation from 88a17cf.

25d947b

Update trajectory_lists.md. Adapted from c599974

cfaebff

Creates OpenMP loop parallelism for time loop in analysis_onetime.cpp…

b858e50

…, and enables multithreading for Radial Distribution Function. Adapted from 986663f.

Enables multithreading for Composition and Composition vs time. Adapt…

1759439

…ed from 5dea40f.

Multithreading enabled for Radial Count. Adapted from 80a0f72

ac194c5

Update overview.md

3e86b82

Change general manual wording to reflect partial implementation of multithreading. (cherry picked from commit 79c079a21e69488220d80191fc6cc8c180bd73a5)

Create multithreading.md

f452cd1

Creating stub page for multithreading documentation. (cherry picked from commit 7c0cd87e030b9c6ddf19a6ef3ac856cdd8c7c44b)

Update msd.md

f40b124

Added flag for multithreaded. (cherry picked from commit a16651834d485384431a1f8519db3dc273cfe2f7)

Update overview.md

00dff24

Updated multithreading documentation. (cherry picked from commit 6f7a4b871a70aedbb15679304172b39540f8a18b)

Update overview.md

018760f

More multithreading documentation. (cherry picked from commit 243e5ec3b11609e6da3f6a6f5d801690981aa417)

Enhance separate multithreading documentation in Manual

2ea4f41

Updates the multithreading documentation initially (cherry picked from commit 044c2d98ef78ed5bfe831e715d2697915477ae70)

Add multithreading badge to mean displacement doc

eab3fdb

Added a badge for multithreading to the mean displacement documentation. (cherry picked from commit 6e10078bc2fbcd5d5b6cb7494fa2b915172c08b9)

Add multithreading badge to msd_2d documentation

207ded3

(cherry picked from commit 31be0e63626e0d9ec4037a53a0f25601e8606fbe)

Add multithreading badge to ngp documentation

c7fbb32

(cherry picked from commit 931459ffa24d4fe67dfc5c4813fafbd609b33507)

Add multithreading badge to radial_count.md

521cd11

Added a badge for multithreading to radial_count documentation. (cherry picked from commit 7cb8360e675814c95a1beb33e929bed2dbd76cc4)

Update rdf.md

55a6d4e

(cherry picked from commit 411ec9ce8d1ea0995c677158cd38b9b4a9d247cd)

Add multithreading badge to vhd.md

02870f7

Added a badge for multithreading to the VHD documentation. (cherry picked from commit e9672aa6b77ddcc82c1f49cb7d1a88c5342855e3)

Add multithreading badge to vhs documentation

cc7d865

Added a badge for multithreading support in the documentation. (cherry picked from commit e8adf1904fb8b062db4ee9c7561ce25b03e16b95)

BaoKhanhMa and others added 13 commits July 3, 2026 10:33

Fix links and formatting in multithreading documentation

9e8a218

Updated links in the analysis table and corrected formatting for CPU count in the threading formula. (cherry picked from commit be7134e8cf367d16a0411cb95e307cb1c8c4098d)

Update multithreading.md

14ee3ed

(cherry picked from commit 5f3a604facf9f2494228a2228a4a4fc1ba783031)

Fix typo in multithreading documentation

2f9992c

(cherry picked from commit cf6b2896b30856ded78473a0a52b41ad4df8218c)

Update multithreading.md

53556ad

(cherry picked from commit 2b04516b78012de14e650ebe3c50d7dd468842f8)

Update trajectory_bin_list.md

a75cbf5

(cherry picked from commit 8cbf1ceab637de04e223b8a2e3bfc8f19fa34969)

Revert "Update overview.md"

521b47d

This reverts commit 243e5ec3b11609e6da3f6a6f5d801690981aa417. (cherry picked from commit 8df31de0e0cdb36265b27d2cb8d58debeb39a950)

Revert "Revert "Update overview.md""

ce2e850

This reverts commit 8df31de0e0cdb36265b27d2cb8d58debeb39a950. (cherry picked from commit 1e57a77d39cce5a5125bb3c2dded8a7d9be14cd3)

Revert "Update trajectory_bin_list.md"

3e7d63f

This reverts commit 8cbf1ceab637de04e223b8a2e3bfc8f19fa34969. (cherry picked from commit 827ae1fc2fe5b0b1cdf258c4623390f14ce0a9cc)

Multithreading enabled for Orientational_Correlation and Neighbor_Dec…

0f398be

…orrelation. Adapted from e3e8689

Clean control timing after multithreading changes

39d63d0

Public-safe adaptation of private commit 9821b95.

Update multithreading.md

dcb7f25

typo fix (cherry picked from commit f20e233b3597d45a70060faf5719167d0bf203e4)

Cherry-pick the remaining Documentation changes.

3b97b6f

Remove sync audit CSV from public branch

6a0618f

pkawak requested changes Jul 7, 2026

View reviewed changes

Update VERSION check logic in workflow

e7ccd71

Removed VERSION check skip for pull requests (included in error).

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Publishing safe internal commits into public repo#87

Publishing safe internal commits into public repo#87
BaoKhanhMa wants to merge 44 commits into
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BaoKhanhMa commented Jul 7, 2026

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BaoKhanhMa commented Jul 7, 2026 •

edited

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pkawak commented Jul 7, 2026

Issues

How do I exclude the changes in check-version.yml?

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BaoKhanhMa commented Jul 9, 2026

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BaoKhanhMa commented Jul 7, 2026

AMDAT 1.1.0 — 2026-07-07

Highlights

Analyses with multithreading enabled:

Migration Notes

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BaoKhanhMa commented Jul 7, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Issues

How do I exclude the changes in check-version.yml?

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pkawak commented Jul 7, 2026

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How do I exclude the changes in check-version.yml?

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BaoKhanhMa commented Jul 9, 2026

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BaoKhanhMa commented Jul 7, 2026 •

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