Add mass to MDAnalysis base units - #5439

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orbeckst merged 7 commits into
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Merged

Add mass to MDAnalysis base units#5439
orbeckst merged 7 commits into
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@sici17sici17 commented Jul 17, 2026•
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Fixes#3944

Changes made in this Pull Request:

  • Added mass to the MDAnalysis.units base-units documentation table.
  • Added "mass": "u" to MDANALYSIS_BASE_UNITS.
  • Updated the corresponding base-units test.

I did not update package/CHANGELOG because this is a small documentation/base-units table fix.

The SI value used for u is 1.66053892103219 × 10^-27 kg, which is consistent with the CODATA 2010 constants already used in MDAnalysis.units.

Note that the User Guide currently lists a newer value for u (1.66053906660(50) × 10^-27 kg). This PR intentionally keeps the MDAnalysis.units API documentation consistent with the existing CODATA 2010 values used by the module, following the maintainer guidance in the issue.

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes

PR Checklist

  • Issue raised/referenced?
  • Tests updated/added?
  • Documentation updated/added?
  • package/CHANGELOG file updated?
  • Is your name in package/AUTHORS? (If it is not, add it!)
  • LLM/AI disclosure was updated.

Developers Certificate of Origin

I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

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Documentation build overview

📚 MDAnalysis | 🛠️ Build #34363814 | 📁 Comparing c80bea3 against latest (3d3a53e)

🔍 Preview build

19 files changed · ± 19 modified

±Modified

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The failing checks appear unrelated to this PR. The GitHub Actions failures are in coordinates/test_xdr.py and concern lock file cleanup behavior, while this PR only changes MDAnalysis.units and its base-units test. The Azure Windows jobs also appear to have timed out after the 60 minute limit.

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Cycling PR to get CI to run again.

@orbeckstorbeckst reopened this Aug 31, 2026
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Can you merge the latest develope (or rebase)? There may have been updates addressing CI issues.

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.87%. Comparing base (ceb2e3e) to head (c80bea3).
⚠️ Report is 1 commits behind head on develop.

Additional details and impacted files
@@ Coverage Diff @@## develop #5439 +/- ##
========================================
Coverage 93.87% 93.87% ========================================
Files 182 182 Lines 22522 22522 Branches 3206 3206 ========================================
Hits 21143 21143 Misses 917 917 Partials 462 462

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

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Please add an entry to CHANGELOG (even though its docs, it does have an open issue associated with it and it clarifies some basic underlying assumptions). Also add yourself to AUTHORS.

Can you add a sentence after the base units table to mention CODATA2010 explicitly? See suggestion.

Comment threadpackage/MDAnalysis/units.py
@orbeckstorbeckst self-assigned this Aug 31, 2026
@orbeckstorbeckst added the AI-assisted Generated with AI/LLM assistance label Aug 31, 2026
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@sici17 please explain briefly how you used AI for this PR.

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Hi Orbecks, thanks a lot for the review. I rebased the branch onto the latest develop, added the CHANGELOG entry and my name to AUTHORS, and added the requested CODATA 2010 clarification.

About the AI usage, I can say more specificallly that I used ChatGPT/Codex to help understand the issue, locate the relevant definitions inside the code and the project, start and locate the tests and inspect the logs. I personally reviewed and applied all the changes. I made sure to understand everything I was doing before actually doing it.

I’ll verify the rendered documentation once the new Read the Docs build completes.

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Thanks, just a minor CHANGELOG rearrangement is needed.

Comment threadpackage/CHANGELOG Outdated
Comment on lines +79 to +81
* Mass (u) has been added to MDAnalysis base units and
clarified that physical constants use CODATA 2010 values
(Issue #3944, PR #5439)

@orbeckstorbeckstSep 1, 2026

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We add new entries at the top. Please move to directly under Fixes

@sici17
Update CHANGELOG
4a8c5c5
Move changelog entry to top of Fixes
@sici17

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Thanks, I moved the CHANGELOG entry to the top of the Fixes section.

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The run failures are not due to this PR but please reformat your CHANGELOG entry.

Comment threadpackage/CHANGELOG Outdated
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All looking good, thank you for your contribution.

I will merge despite the CI failures, given that they are clearly not a problem from your code.

@orbeckst
orbeckst merged commit 8b8875c into MDAnalysis:developSep 3, 2026
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
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})();
(function(){
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var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Add mass to MDAnalysis base units - #5439
Merged
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
Sep 3, 2026
Merged
Add mass to MDAnalysis base units#5439
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
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@sici17
@sici17sici17
commented
Jul 17, 2026•

edited by orbeckst

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Fixes#3944
Changes made in this Pull Request:
  • Added mass to the MDAnalysis.units base-units documentation table.
  • Added "mass": "u" to MDANALYSIS_BASE_UNITS.
  • Updated the corresponding base-units test.
I did not update package/CHANGELOG because this is a small documentation/base-units table fix.
The SI value used for u is 1.66053892103219 × 10^-27 kg, which is consistent with the CODATA 2010 constants already used in MDAnalysis.units.
Note that the User Guide currently lists a newer value for u (1.66053906660(50) × 10^-27 kg). This PR intentionally keeps the MDAnalysis.units API documentation consistent with the existing CODATA 2010 values used by the module, following the maintainer guidance in the issue.
LLM / AI generated code disclosure
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes
PR Checklist
  •  Issue raised/referenced?
  •  Tests updated/added?
  •  Documentation updated/added?
  • package/CHANGELOG file updated?
  •  Is your name in package/AUTHORS? (If it is not, add it!)
  •  LLM/AI disclosure was updated.
Developers Certificate of Origin
I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.
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Documentation build overview
📚 MDAnalysis | 🛠️ Build #34363814 | 📁 Comparing c80bea3 against latest (3d3a53e)
 🔍 Preview build 
19 files changed · ± 19 modified
±Modified
@sici17
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Jul 20, 2026

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The failing checks appear unrelated to this PR. The GitHub Actions failures are in coordinates/test_xdr.py and concern lock file cleanup behavior, while this PR only changes MDAnalysis.units and its base-units test. The Azure Windows jobs also appear to have timed out after the 60 minute limit.
@orbeckst
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Cycling PR to get CI to run again.
@orbeckstorbeckst
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Aug 31, 2026
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Can you merge the latest develope (or rebase)? There may have been updates addressing CI issues.
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Aug 31, 2026•

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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 93.87%. Comparing base (ceb2e3e) to head (c80bea3).
⚠️ Report is 1 commits behind head on develop.
Additional details and impacted files
@@ Coverage Diff @@## develop #5439 +/- ##
========================================
Coverage 93.87% 93.87% ========================================
Files 182 182 Lines 22522 22522 Branches 3206 3206 ========================================
Hits 21143 21143 Misses 917 917 Partials 462 462 
☔ View full report in Codecov by Harness.

📢 Have feedback on the report? Share it here.
 🚀 New features to boost your workflow: 
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Please add an entry to CHANGELOG (even though its docs, it does have an open issue associated with it and it clarifies some basic underlying assumptions). Also add yourself to AUTHORS.
Can you add a sentence after the base units table to mention CODATA2010 explicitly? See suggestion.
Comment threadpackage/MDAnalysis/units.py
@orbeckstorbeckst
self-assigned this
Aug 31, 2026
@orbeckstorbeckst
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@sici17 please explain briefly how you used AI for this PR.
@sici17
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Sep 1, 2026

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Hi Orbecks, thanks a lot for the review. I rebased the branch onto the latest develop, added the CHANGELOG entry and my name to AUTHORS, and added the requested CODATA 2010 clarification.
About the AI usage, I can say more specificallly that I used ChatGPT/Codex to help understand the issue, locate the relevant definitions inside the code and the project, start and locate the tests and inspect the logs. I personally reviewed and applied all the changes. I made sure to understand everything I was doing before actually doing it.
I’ll verify the rendered documentation once the new Read the Docs build completes.
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Thanks, just a minor CHANGELOG rearrangement is needed.
Comment threadpackage/CHANGELOG
Outdated


Comment on lines

+79
 to 
+81

 * Mass (u) has been added to MDAnalysis base units and
 clarified that physical constants use CODATA 2010 values
 (Issue #3944, PR #5439)
@orbeckstorbeckstSep 1, 2026

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We add new entries at the top. Please move to directly under Fixes
@sici17
Update CHANGELOG
4a8c5c5
Move changelog entry to top of Fixes
@sici17
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Thanks, I moved the CHANGELOG entry to the top of the Fixes section.
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The run failures are not due to this PR but please reformat your CHANGELOG entry.
Comment threadpackage/CHANGELOG
Outdated

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All looking good, thank you for your contribution.
I will merge despite the CI failures, given that they are clearly not a problem from your code.
@orbeckst
orbeckst
merged commit 8b8875c
into
MDAnalysis:developSep 3, 2026

24 of 25 checks passed

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Add mass to MDAnalysis base units - #5439
Merged
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
Sep 3, 2026
Merged
Add mass to MDAnalysis base units#5439
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
Conversation
@sici17
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Jul 17, 2026•

edited by orbeckst

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Fixes#3944
Changes made in this Pull Request:
  • Added mass to the MDAnalysis.units base-units documentation table.
  • Added "mass": "u" to MDANALYSIS_BASE_UNITS.
  • Updated the corresponding base-units test.
I did not update package/CHANGELOG because this is a small documentation/base-units table fix.
The SI value used for u is 1.66053892103219 × 10^-27 kg, which is consistent with the CODATA 2010 constants already used in MDAnalysis.units.
Note that the User Guide currently lists a newer value for u (1.66053906660(50) × 10^-27 kg). This PR intentionally keeps the MDAnalysis.units API documentation consistent with the existing CODATA 2010 values used by the module, following the maintainer guidance in the issue.
LLM / AI generated code disclosure
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes
PR Checklist
  •  Issue raised/referenced?
  •  Tests updated/added?
  •  Documentation updated/added?
  • package/CHANGELOG file updated?
  •  Is your name in package/AUTHORS? (If it is not, add it!)
  •  LLM/AI disclosure was updated.
Developers Certificate of Origin
I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.
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Documentation build overview
📚 MDAnalysis | 🛠️ Build #34363814 | 📁 Comparing c80bea3 against latest (3d3a53e)
 🔍 Preview build 
19 files changed · ± 19 modified
±Modified
@sici17
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The failing checks appear unrelated to this PR. The GitHub Actions failures are in coordinates/test_xdr.py and concern lock file cleanup behavior, while this PR only changes MDAnalysis.units and its base-units test. The Azure Windows jobs also appear to have timed out after the 60 minute limit.
@orbeckst
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Cycling PR to get CI to run again.
@orbeckstorbeckst
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Aug 31, 2026
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Can you merge the latest develope (or rebase)? There may have been updates addressing CI issues.
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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 93.87%. Comparing base (ceb2e3e) to head (c80bea3).
⚠️ Report is 1 commits behind head on develop.
Additional details and impacted files
@@ Coverage Diff @@## develop #5439 +/- ##
========================================
Coverage 93.87% 93.87% ========================================
Files 182 182 Lines 22522 22522 Branches 3206 3206 ========================================
Hits 21143 21143 Misses 917 917 Partials 462 462 
☔ View full report in Codecov by Harness.

📢 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.
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Please add an entry to CHANGELOG (even though its docs, it does have an open issue associated with it and it clarifies some basic underlying assumptions). Also add yourself to AUTHORS.
Can you add a sentence after the base units table to mention CODATA2010 explicitly? See suggestion.
Comment threadpackage/MDAnalysis/units.py
@orbeckstorbeckst
self-assigned this
Aug 31, 2026
@orbeckstorbeckst
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AI-assisted
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@sici17 please explain briefly how you used AI for this PR.
@sici17
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Sep 1, 2026

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Hi Orbecks, thanks a lot for the review. I rebased the branch onto the latest develop, added the CHANGELOG entry and my name to AUTHORS, and added the requested CODATA 2010 clarification.
About the AI usage, I can say more specificallly that I used ChatGPT/Codex to help understand the issue, locate the relevant definitions inside the code and the project, start and locate the tests and inspect the logs. I personally reviewed and applied all the changes. I made sure to understand everything I was doing before actually doing it.
I’ll verify the rendered documentation once the new Read the Docs build completes.
orbeckst
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Thanks, just a minor CHANGELOG rearrangement is needed.
Comment threadpackage/CHANGELOG
Outdated


Comment on lines

+79
 to 
+81

 * Mass (u) has been added to MDAnalysis base units and
 clarified that physical constants use CODATA 2010 values
 (Issue #3944, PR #5439)
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We add new entries at the top. Please move to directly under Fixes
@sici17
Update CHANGELOG
4a8c5c5
Move changelog entry to top of Fixes
@sici17
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Thanks, I moved the CHANGELOG entry to the top of the Fixes section.
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The run failures are not due to this PR but please reformat your CHANGELOG entry.
Comment threadpackage/CHANGELOG
Outdated

orbeckst
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All looking good, thank you for your contribution.
I will merge despite the CI failures, given that they are clearly not a problem from your code.
@orbeckst
orbeckst
merged commit 8b8875c
into
MDAnalysis:developSep 3, 2026

24 of 25 checks passed

@orbeckstorbeckst
mentioned this pull request
Sep 3, 2026

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mass unit not listed in 'Base units' table


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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Add mass to MDAnalysis base units - #5439
Merged
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
Sep 3, 2026
Merged
Add mass to MDAnalysis base units#5439
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
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Jul 17, 2026•

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Fixes#3944
Changes made in this Pull Request:
  • Added mass to the MDAnalysis.units base-units documentation table.
  • Added "mass": "u" to MDANALYSIS_BASE_UNITS.
  • Updated the corresponding base-units test.
I did not update package/CHANGELOG because this is a small documentation/base-units table fix.
The SI value used for u is 1.66053892103219 × 10^-27 kg, which is consistent with the CODATA 2010 constants already used in MDAnalysis.units.
Note that the User Guide currently lists a newer value for u (1.66053906660(50) × 10^-27 kg). This PR intentionally keeps the MDAnalysis.units API documentation consistent with the existing CODATA 2010 values used by the module, following the maintainer guidance in the issue.
LLM / AI generated code disclosure
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes
PR Checklist
  •  Issue raised/referenced?
  •  Tests updated/added?
  •  Documentation updated/added?
  • package/CHANGELOG file updated?
  •  Is your name in package/AUTHORS? (If it is not, add it!)
  •  LLM/AI disclosure was updated.
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I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.
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Documentation build overview
📚 MDAnalysis | 🛠️ Build #34363814 | 📁 Comparing c80bea3 against latest (3d3a53e)
 🔍 Preview build 
19 files changed · ± 19 modified
±Modified
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The failing checks appear unrelated to this PR. The GitHub Actions failures are in coordinates/test_xdr.py and concern lock file cleanup behavior, while this PR only changes MDAnalysis.units and its base-units test. The Azure Windows jobs also appear to have timed out after the 60 minute limit.
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Cycling PR to get CI to run again.
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Can you merge the latest develope (or rebase)? There may have been updates addressing CI issues.
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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 93.87%. Comparing base (ceb2e3e) to head (c80bea3).
⚠️ Report is 1 commits behind head on develop.
Additional details and impacted files
@@ Coverage Diff @@## develop #5439 +/- ##
========================================
Coverage 93.87% 93.87% ========================================
Files 182 182 Lines 22522 22522 Branches 3206 3206 ========================================
Hits 21143 21143 Misses 917 917 Partials 462 462 
☔ View full report in Codecov by Harness.

📢 Have feedback on the report? Share it here.
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Please add an entry to CHANGELOG (even though its docs, it does have an open issue associated with it and it clarifies some basic underlying assumptions). Also add yourself to AUTHORS.
Can you add a sentence after the base units table to mention CODATA2010 explicitly? See suggestion.
Comment threadpackage/MDAnalysis/units.py
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@sici17 please explain briefly how you used AI for this PR.
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Hi Orbecks, thanks a lot for the review. I rebased the branch onto the latest develop, added the CHANGELOG entry and my name to AUTHORS, and added the requested CODATA 2010 clarification.
About the AI usage, I can say more specificallly that I used ChatGPT/Codex to help understand the issue, locate the relevant definitions inside the code and the project, start and locate the tests and inspect the logs. I personally reviewed and applied all the changes. I made sure to understand everything I was doing before actually doing it.
I’ll verify the rendered documentation once the new Read the Docs build completes.
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Thanks, just a minor CHANGELOG rearrangement is needed.
Comment threadpackage/CHANGELOG
Outdated


Comment on lines

+79
 to 
+81

 * Mass (u) has been added to MDAnalysis base units and
 clarified that physical constants use CODATA 2010 values
 (Issue #3944, PR #5439)
@orbeckstorbeckstSep 1, 2026

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We add new entries at the top. Please move to directly under Fixes
@sici17
Update CHANGELOG
4a8c5c5
Move changelog entry to top of Fixes
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Thanks, I moved the CHANGELOG entry to the top of the Fixes section.
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The run failures are not due to this PR but please reformat your CHANGELOG entry.
Comment threadpackage/CHANGELOG
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All looking good, thank you for your contribution.
I will merge despite the CI failures, given that they are clearly not a problem from your code.
@orbeckst
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merged commit 8b8875c
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MDAnalysis:developSep 3, 2026

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Add mass to MDAnalysis base units - #5439
Merged
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
Sep 3, 2026
Merged
Add mass to MDAnalysis base units#5439
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
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commented
Jul 17, 2026•

edited by orbeckst

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Fixes#3944
Changes made in this Pull Request:
  • Added mass to the MDAnalysis.units base-units documentation table.
  • Added "mass": "u" to MDANALYSIS_BASE_UNITS.
  • Updated the corresponding base-units test.
I did not update package/CHANGELOG because this is a small documentation/base-units table fix.
The SI value used for u is 1.66053892103219 × 10^-27 kg, which is consistent with the CODATA 2010 constants already used in MDAnalysis.units.
Note that the User Guide currently lists a newer value for u (1.66053906660(50) × 10^-27 kg). This PR intentionally keeps the MDAnalysis.units API documentation consistent with the existing CODATA 2010 values used by the module, following the maintainer guidance in the issue.
LLM / AI generated code disclosure
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes
PR Checklist
  •  Issue raised/referenced?
  •  Tests updated/added?
  •  Documentation updated/added?
  • package/CHANGELOG file updated?
  •  Is your name in package/AUTHORS? (If it is not, add it!)
  •  LLM/AI disclosure was updated.
Developers Certificate of Origin
I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.
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Documentation build overview
📚 MDAnalysis | 🛠️ Build #34363814 | 📁 Comparing c80bea3 against latest (3d3a53e)
 🔍 Preview build 
19 files changed · ± 19 modified
±Modified
@sici17
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Jul 20, 2026

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The failing checks appear unrelated to this PR. The GitHub Actions failures are in coordinates/test_xdr.py and concern lock file cleanup behavior, while this PR only changes MDAnalysis.units and its base-units test. The Azure Windows jobs also appear to have timed out after the 60 minute limit.
@orbeckst
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Cycling PR to get CI to run again.
@orbeckstorbeckst
reopened this
Aug 31, 2026
@orbeckst
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Can you merge the latest develope (or rebase)? There may have been updates addressing CI issues.
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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 93.87%. Comparing base (ceb2e3e) to head (c80bea3).
⚠️ Report is 1 commits behind head on develop.
Additional details and impacted files
@@ Coverage Diff @@## develop #5439 +/- ##
========================================
Coverage 93.87% 93.87% ========================================
Files 182 182 Lines 22522 22522 Branches 3206 3206 ========================================
Hits 21143 21143 Misses 917 917 Partials 462 462 
☔ View full report in Codecov by Harness.

📢 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.
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Please add an entry to CHANGELOG (even though its docs, it does have an open issue associated with it and it clarifies some basic underlying assumptions). Also add yourself to AUTHORS.
Can you add a sentence after the base units table to mention CODATA2010 explicitly? See suggestion.
Comment threadpackage/MDAnalysis/units.py
@orbeckstorbeckst
self-assigned this
Aug 31, 2026
@orbeckstorbeckst
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the 
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Generated with AI/LLM assistance
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@sici17 please explain briefly how you used AI for this PR.
@sici17
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Sep 1, 2026

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Hi Orbecks, thanks a lot for the review. I rebased the branch onto the latest develop, added the CHANGELOG entry and my name to AUTHORS, and added the requested CODATA 2010 clarification.
About the AI usage, I can say more specificallly that I used ChatGPT/Codex to help understand the issue, locate the relevant definitions inside the code and the project, start and locate the tests and inspect the logs. I personally reviewed and applied all the changes. I made sure to understand everything I was doing before actually doing it.
I’ll verify the rendered documentation once the new Read the Docs build completes.
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Thanks, just a minor CHANGELOG rearrangement is needed.
Comment threadpackage/CHANGELOG
Outdated


Comment on lines

+79
 to 
+81

 * Mass (u) has been added to MDAnalysis base units and
 clarified that physical constants use CODATA 2010 values
 (Issue #3944, PR #5439)
@orbeckstorbeckstSep 1, 2026

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We add new entries at the top. Please move to directly under Fixes
@sici17
Update CHANGELOG
4a8c5c5
Move changelog entry to top of Fixes
@sici17
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Thanks, I moved the CHANGELOG entry to the top of the Fixes section.
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The run failures are not due to this PR but please reformat your CHANGELOG entry.
Comment threadpackage/CHANGELOG
Outdated

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All looking good, thank you for your contribution.
I will merge despite the CI failures, given that they are clearly not a problem from your code.
@orbeckst
orbeckst
merged commit 8b8875c
into
MDAnalysis:developSep 3, 2026

24 of 25 checks passed

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Sep 3, 2026

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mass unit not listed in 'Base units' table


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@sici17@orbeckst

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Add mass to MDAnalysis base units - #5439
Merged
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
Sep 3, 2026
Merged
Add mass to MDAnalysis base units#5439
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
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Jul 17, 2026•

edited by orbeckst

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Fixes#3944
Changes made in this Pull Request:
  • Added mass to the MDAnalysis.units base-units documentation table.
  • Added "mass": "u" to MDANALYSIS_BASE_UNITS.
  • Updated the corresponding base-units test.
I did not update package/CHANGELOG because this is a small documentation/base-units table fix.
The SI value used for u is 1.66053892103219 × 10^-27 kg, which is consistent with the CODATA 2010 constants already used in MDAnalysis.units.
Note that the User Guide currently lists a newer value for u (1.66053906660(50) × 10^-27 kg). This PR intentionally keeps the MDAnalysis.units API documentation consistent with the existing CODATA 2010 values used by the module, following the maintainer guidance in the issue.
LLM / AI generated code disclosure
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes
PR Checklist
  •  Issue raised/referenced?
  •  Tests updated/added?
  •  Documentation updated/added?
  • package/CHANGELOG file updated?
  •  Is your name in package/AUTHORS? (If it is not, add it!)
  •  LLM/AI disclosure was updated.
Developers Certificate of Origin
I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.
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Documentation build overview
📚 MDAnalysis | 🛠️ Build #34363814 | 📁 Comparing c80bea3 against latest (3d3a53e)
 🔍 Preview build 
19 files changed · ± 19 modified
±Modified
@sici17
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Jul 20, 2026

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The failing checks appear unrelated to this PR. The GitHub Actions failures are in coordinates/test_xdr.py and concern lock file cleanup behavior, while this PR only changes MDAnalysis.units and its base-units test. The Azure Windows jobs also appear to have timed out after the 60 minute limit.
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Cycling PR to get CI to run again.
@orbeckstorbeckst
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Aug 31, 2026
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Can you merge the latest develope (or rebase)? There may have been updates addressing CI issues.
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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 93.87%. Comparing base (ceb2e3e) to head (c80bea3).
⚠️ Report is 1 commits behind head on develop.
Additional details and impacted files
@@ Coverage Diff @@## develop #5439 +/- ##
========================================
Coverage 93.87% 93.87% ========================================
Files 182 182 Lines 22522 22522 Branches 3206 3206 ========================================
Hits 21143 21143 Misses 917 917 Partials 462 462 
☔ View full report in Codecov by Harness.

📢 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.
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Please add an entry to CHANGELOG (even though its docs, it does have an open issue associated with it and it clarifies some basic underlying assumptions). Also add yourself to AUTHORS.
Can you add a sentence after the base units table to mention CODATA2010 explicitly? See suggestion.
Comment threadpackage/MDAnalysis/units.py
@orbeckstorbeckst
self-assigned this
Aug 31, 2026
@orbeckstorbeckst
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@sici17 please explain briefly how you used AI for this PR.
@sici17
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Sep 1, 2026

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Hi Orbecks, thanks a lot for the review. I rebased the branch onto the latest develop, added the CHANGELOG entry and my name to AUTHORS, and added the requested CODATA 2010 clarification.
About the AI usage, I can say more specificallly that I used ChatGPT/Codex to help understand the issue, locate the relevant definitions inside the code and the project, start and locate the tests and inspect the logs. I personally reviewed and applied all the changes. I made sure to understand everything I was doing before actually doing it.
I’ll verify the rendered documentation once the new Read the Docs build completes.
orbeckst
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Sep 1, 2026
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Thanks, just a minor CHANGELOG rearrangement is needed.
Comment threadpackage/CHANGELOG
Outdated


Comment on lines

+79
 to 
+81

 * Mass (u) has been added to MDAnalysis base units and
 clarified that physical constants use CODATA 2010 values
 (Issue #3944, PR #5439)
@orbeckstorbeckstSep 1, 2026

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We add new entries at the top. Please move to directly under Fixes
@sici17
Update CHANGELOG
4a8c5c5
Move changelog entry to top of Fixes
@sici17
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Sep 2, 2026

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Thanks, I moved the CHANGELOG entry to the top of the Fixes section.
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Sep 2, 2026

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The run failures are not due to this PR but please reformat your CHANGELOG entry.
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All looking good, thank you for your contribution.
I will merge despite the CI failures, given that they are clearly not a problem from your code.
@orbeckst
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MDAnalysis:developSep 3, 2026

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mass unit not listed in 'Base units' table


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, 'i');
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injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Add mass to MDAnalysis base units - #5439
Merged
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
Sep 3, 2026
Merged
Add mass to MDAnalysis base units#5439
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
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@sici17
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Jul 17, 2026•

edited by orbeckst

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Fixes#3944
Changes made in this Pull Request:
  • Added mass to the MDAnalysis.units base-units documentation table.
  • Added "mass": "u" to MDANALYSIS_BASE_UNITS.
  • Updated the corresponding base-units test.
I did not update package/CHANGELOG because this is a small documentation/base-units table fix.
The SI value used for u is 1.66053892103219 × 10^-27 kg, which is consistent with the CODATA 2010 constants already used in MDAnalysis.units.
Note that the User Guide currently lists a newer value for u (1.66053906660(50) × 10^-27 kg). This PR intentionally keeps the MDAnalysis.units API documentation consistent with the existing CODATA 2010 values used by the module, following the maintainer guidance in the issue.
LLM / AI generated code disclosure
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes
PR Checklist
  •  Issue raised/referenced?
  •  Tests updated/added?
  •  Documentation updated/added?
  • package/CHANGELOG file updated?
  •  Is your name in package/AUTHORS? (If it is not, add it!)
  •  LLM/AI disclosure was updated.
Developers Certificate of Origin
I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.
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Documentation build overview
📚 MDAnalysis | 🛠️ Build #34363814 | 📁 Comparing c80bea3 against latest (3d3a53e)
 🔍 Preview build 
19 files changed · ± 19 modified
±Modified
@sici17
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The failing checks appear unrelated to this PR. The GitHub Actions failures are in coordinates/test_xdr.py and concern lock file cleanup behavior, while this PR only changes MDAnalysis.units and its base-units test. The Azure Windows jobs also appear to have timed out after the 60 minute limit.
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Cycling PR to get CI to run again.
@orbeckstorbeckst
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Can you merge the latest develope (or rebase)? There may have been updates addressing CI issues.
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Aug 31, 2026•

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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 93.87%. Comparing base (ceb2e3e) to head (c80bea3).
⚠️ Report is 1 commits behind head on develop.
Additional details and impacted files
@@ Coverage Diff @@## develop #5439 +/- ##
========================================
Coverage 93.87% 93.87% ========================================
Files 182 182 Lines 22522 22522 Branches 3206 3206 ========================================
Hits 21143 21143 Misses 917 917 Partials 462 462 
☔ View full report in Codecov by Harness.

📢 Have feedback on the report? Share it here.
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Please add an entry to CHANGELOG (even though its docs, it does have an open issue associated with it and it clarifies some basic underlying assumptions). Also add yourself to AUTHORS.
Can you add a sentence after the base units table to mention CODATA2010 explicitly? See suggestion.
Comment threadpackage/MDAnalysis/units.py
@orbeckstorbeckst
self-assigned this
Aug 31, 2026
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@sici17 please explain briefly how you used AI for this PR.
@sici17
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Sep 1, 2026

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Hi Orbecks, thanks a lot for the review. I rebased the branch onto the latest develop, added the CHANGELOG entry and my name to AUTHORS, and added the requested CODATA 2010 clarification.
About the AI usage, I can say more specificallly that I used ChatGPT/Codex to help understand the issue, locate the relevant definitions inside the code and the project, start and locate the tests and inspect the logs. I personally reviewed and applied all the changes. I made sure to understand everything I was doing before actually doing it.
I’ll verify the rendered documentation once the new Read the Docs build completes.
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Thanks, just a minor CHANGELOG rearrangement is needed.
Comment threadpackage/CHANGELOG
Outdated


Comment on lines

+79
 to 
+81

 * Mass (u) has been added to MDAnalysis base units and
 clarified that physical constants use CODATA 2010 values
 (Issue #3944, PR #5439)
@orbeckstorbeckstSep 1, 2026

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We add new entries at the top. Please move to directly under Fixes
@sici17
Update CHANGELOG
4a8c5c5
Move changelog entry to top of Fixes
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Thanks, I moved the CHANGELOG entry to the top of the Fixes section.
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The run failures are not due to this PR but please reformat your CHANGELOG entry.
Comment threadpackage/CHANGELOG
Outdated

orbeckst
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Sep 3, 2026
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All looking good, thank you for your contribution.
I will merge despite the CI failures, given that they are clearly not a problem from your code.
@orbeckst
orbeckst
merged commit 8b8875c
into
MDAnalysis:developSep 3, 2026

24 of 25 checks passed

@orbeckstorbeckst
mentioned this pull request
Sep 3, 2026

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mass unit not listed in 'Base units' table


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@sici17@orbeckst

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Add mass to MDAnalysis base units - #5439
Merged
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
Sep 3, 2026
Merged
Add mass to MDAnalysis base units#5439
orbeckst merged 7 commits into
MDAnalysis:developfrom 
sici17:patch-1
Conversation
@sici17
@sici17sici17
commented
Jul 17, 2026•

edited by orbeckst

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Fixes#3944
Changes made in this Pull Request:
  • Added mass to the MDAnalysis.units base-units documentation table.
  • Added "mass": "u" to MDANALYSIS_BASE_UNITS.
  • Updated the corresponding base-units test.
I did not update package/CHANGELOG because this is a small documentation/base-units table fix.
The SI value used for u is 1.66053892103219 × 10^-27 kg, which is consistent with the CODATA 2010 constants already used in MDAnalysis.units.
Note that the User Guide currently lists a newer value for u (1.66053906660(50) × 10^-27 kg). This PR intentionally keeps the MDAnalysis.units API documentation consistent with the existing CODATA 2010 values used by the module, following the maintainer guidance in the issue.
LLM / AI generated code disclosure
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes
PR Checklist
  •  Issue raised/referenced?
  •  Tests updated/added?
  •  Documentation updated/added?
  • package/CHANGELOG file updated?
  •  Is your name in package/AUTHORS? (If it is not, add it!)
  •  LLM/AI disclosure was updated.
Developers Certificate of Origin
I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.
@read-the-docs-community
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commented
Jul 17, 2026•

edited

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Documentation build overview
📚 MDAnalysis | 🛠️ Build #34363814 | 📁 Comparing c80bea3 against latest (3d3a53e)
 🔍 Preview build 
19 files changed · ± 19 modified
±Modified
@sici17
sici17
commented
Jul 20, 2026

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ContributorAuthor
The failing checks appear unrelated to this PR. The GitHub Actions failures are in coordinates/test_xdr.py and concern lock file cleanup behavior, while this PR only changes MDAnalysis.units and its base-units test. The Azure Windows jobs also appear to have timed out after the 60 minute limit.
@orbeckst
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Aug 31, 2026

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Cycling PR to get CI to run again.
@orbeckstorbeckst
reopened this
Aug 31, 2026
@orbeckst
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Aug 31, 2026

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Can you merge the latest develope (or rebase)? There may have been updates addressing CI issues.
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Aug 31, 2026•

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Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 93.87%. Comparing base (ceb2e3e) to head (c80bea3).
⚠️ Report is 1 commits behind head on develop.
Additional details and impacted files
@@ Coverage Diff @@## develop #5439 +/- ##
========================================
Coverage 93.87% 93.87% ========================================
Files 182 182 Lines 22522 22522 Branches 3206 3206 ========================================
Hits 21143 21143 Misses 917 917 Partials 462 462 
☔ View full report in Codecov by Harness.

📢 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.
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Please add an entry to CHANGELOG (even though its docs, it does have an open issue associated with it and it clarifies some basic underlying assumptions). Also add yourself to AUTHORS.
Can you add a sentence after the base units table to mention CODATA2010 explicitly? See suggestion.
Comment threadpackage/MDAnalysis/units.py
@orbeckstorbeckst
self-assigned this
Aug 31, 2026
@orbeckstorbeckst
added
the 
AI-assisted
Generated with AI/LLM assistance
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Aug 31, 2026
@orbeckst
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@sici17 please explain briefly how you used AI for this PR.
@sici17
sici17
commented
Sep 1, 2026

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ContributorAuthor
Hi Orbecks, thanks a lot for the review. I rebased the branch onto the latest develop, added the CHANGELOG entry and my name to AUTHORS, and added the requested CODATA 2010 clarification.
About the AI usage, I can say more specificallly that I used ChatGPT/Codex to help understand the issue, locate the relevant definitions inside the code and the project, start and locate the tests and inspect the logs. I personally reviewed and applied all the changes. I made sure to understand everything I was doing before actually doing it.
I’ll verify the rendered documentation once the new Read the Docs build completes.
orbeckst
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requested changes
Sep 1, 2026
View reviewed changes
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Thanks, just a minor CHANGELOG rearrangement is needed.
Comment threadpackage/CHANGELOG
Outdated


Comment on lines

+79
 to 
+81

 * Mass (u) has been added to MDAnalysis base units and
 clarified that physical constants use CODATA 2010 values
 (Issue #3944, PR #5439)
@orbeckstorbeckstSep 1, 2026

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We add new entries at the top. Please move to directly under Fixes
@sici17
Update CHANGELOG
4a8c5c5
Move changelog entry to top of Fixes
@sici17
sici17
commented
Sep 2, 2026

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Thanks, I moved the CHANGELOG entry to the top of the Fixes section.
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Sep 2, 2026

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The run failures are not due to this PR but please reformat your CHANGELOG entry.
Comment threadpackage/CHANGELOG
Outdated

orbeckst
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Sep 3, 2026
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All looking good, thank you for your contribution.
I will merge despite the CI failures, given that they are clearly not a problem from your code.
@orbeckst
orbeckst
merged commit 8b8875c
into
MDAnalysis:developSep 3, 2026

24 of 25 checks passed

@orbeckstorbeckst
mentioned this pull request
Sep 3, 2026

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mass unit not listed in 'Base units' table


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