From d89c611b6bc8e2fbee5cd365702042a652f6a720 Mon Sep 17 00:00:00 2001 From: sici17 Date: Fri, 17 Jul 2026 17:47:16 +0200 Subject: [PATCH 1/7] Update units.py --- package/MDAnalysis/units.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/package/MDAnalysis/units.py b/package/MDAnalysis/units.py index d52e46d86c..d698520e2c 100644 --- a/package/MDAnalysis/units.py +++ b/package/MDAnalysis/units.py @@ -47,6 +47,7 @@ charge :math:`e` :math:`1.602176565 \times 10^{-19}` As force kJ/(mol·Å) :math:`1.66053892103219 \times 10^{-11}` J/m speed Å/ps :math:`100` m/s + mass u :math:`1.66053892103219 \times 10^{-27}` kg =========== ============== =============================================== Implementation notes @@ -407,6 +408,7 @@ def __getitem__(self, key): "charge": "e", "force": "kJ/(mol*A)", "speed": "A/ps", + "mass": "u", } From 4576548ffc3199ba8b3a93ab705ca3ea182c7b65 Mon Sep 17 00:00:00 2001 From: sici17 Date: Fri, 17 Jul 2026 17:58:29 +0200 Subject: [PATCH 2/7] Update test_units.py --- testsuite/MDAnalysisTests/utils/test_units.py | 1 + 1 file changed, 1 insertion(+) diff --git a/testsuite/MDAnalysisTests/utils/test_units.py b/testsuite/MDAnalysisTests/utils/test_units.py index dad63d6b11..b37383f58a 100644 --- a/testsuite/MDAnalysisTests/utils/test_units.py +++ b/testsuite/MDAnalysisTests/utils/test_units.py @@ -181,6 +181,7 @@ def ref(): "charge": "e", "force": "kJ/(mol*A)", "speed": "A/ps", + "mass": "u", } return ref From 5113c40c88fa986244cc754cd0b29fee84c79437 Mon Sep 17 00:00:00 2001 From: sici17 Date: Tue, 1 Sep 2026 05:12:09 +0200 Subject: [PATCH 3/7] Address review feedback --- package/AUTHORS | 1 + package/CHANGELOG | 5 ++++- package/MDAnalysis/units.py | 7 +++++++ 3 files changed, 12 insertions(+), 1 deletion(-) diff --git a/package/AUTHORS b/package/AUTHORS index ed82321a9e..c8ba87c062 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -284,6 +284,7 @@ Chronological list of authors - Sai Udayagiri - Apoorva Verma - Aryaman Chaudhri + - Francesco Siciliani External code ------------- diff --git a/package/CHANGELOG b/package/CHANGELOG index c043f683f0..459bc45ac7 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -18,7 +18,7 @@ The rules for this file: spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521, harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9, ollyfutur, Amarendra22, charity-g, ParthUppal523, apoorva-01, RMeli, - raulloiscuns, Aryaman-Chaudhri + raulloiscuns, Aryaman-Chaudhri, sici17 * 2.11.0 @@ -76,6 +76,9 @@ Fixes to version 5.1.0 (Issue #5145, PR #5146) * Fixes incorrect assignment of secondary structure to proline residues in DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913) + * Mass (u) has been added to MDAnalysis base units and + clarified that physical constants use CODATA 2010 values + (Issue #3944, PR #5439) Enhancements * Added ASV benchmark for PDB trajectory reading (PR #5394) diff --git a/package/MDAnalysis/units.py b/package/MDAnalysis/units.py index d698520e2c..e5709b9994 100644 --- a/package/MDAnalysis/units.py +++ b/package/MDAnalysis/units.py @@ -50,6 +50,13 @@ mass u :math:`1.66053892103219 \times 10^{-27}` kg =========== ============== =============================================== + +MDAnalysis currently uses the NIST `CODATA 2010`_ values for physical constants. + +.. _`CODATA 2010`: + https://physics.nist.gov/cuu/Constants/ArchiveASCII/allascii_2010.txt + + Implementation notes -------------------- From 37ebeaf419c4e6cd6648e2db7377fdc16fb42df3 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Tue, 1 Sep 2026 16:27:01 -0700 Subject: [PATCH 4/7] Update package/MDAnalysis/units.py --- package/MDAnalysis/units.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/package/MDAnalysis/units.py b/package/MDAnalysis/units.py index e5709b9994..9a3ae4235c 100644 --- a/package/MDAnalysis/units.py +++ b/package/MDAnalysis/units.py @@ -50,6 +50,11 @@ mass u :math:`1.66053892103219 \times 10^{-27}` kg =========== ============== =============================================== +MDAnalysis currently uses the NIST `CODATA 2010`_ values for physical constants. + +.. _`CODATA 2010`: + https://physics.nist.gov/cuu/Constants/ArchiveASCII/allascii_2010.txt + MDAnalysis currently uses the NIST `CODATA 2010`_ values for physical constants. From a1e370c406c7e98a206d3cdad89ed810ad5ebc26 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Tue, 1 Sep 2026 16:27:44 -0700 Subject: [PATCH 5/7] revert duplicated text addition --- package/MDAnalysis/units.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/package/MDAnalysis/units.py b/package/MDAnalysis/units.py index 9a3ae4235c..70b8a226bf 100644 --- a/package/MDAnalysis/units.py +++ b/package/MDAnalysis/units.py @@ -56,12 +56,6 @@ https://physics.nist.gov/cuu/Constants/ArchiveASCII/allascii_2010.txt -MDAnalysis currently uses the NIST `CODATA 2010`_ values for physical constants. - -.. _`CODATA 2010`: - https://physics.nist.gov/cuu/Constants/ArchiveASCII/allascii_2010.txt - - Implementation notes -------------------- From 4a8c5c553877d2038ae60faaa48d79008e1f2eb3 Mon Sep 17 00:00:00 2001 From: Francesco Siciliani Date: Thu, 3 Sep 2026 00:35:52 +0200 Subject: [PATCH 6/7] Update CHANGELOG Move changelog entry to top of Fixes --- package/CHANGELOG | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index 459bc45ac7..4ec3193cdb 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -23,6 +23,9 @@ The rules for this file: * 2.11.0 Fixes + * Mass (u) has been added to MDAnalysis base units and + clarified that physical constants use CODATA 2010 values + (Issue #3944, PR #5439) * Added `.gitattributes` to enforce LF (\n) as line endings and renormalized existing files to conform (Issue #5315, PR #5446) * `AtomGroup.rotate()` and the `rotateby` trajectory transformation now @@ -76,9 +79,6 @@ Fixes to version 5.1.0 (Issue #5145, PR #5146) * Fixes incorrect assignment of secondary structure to proline residues in DSSP by porting upstream PyDSSP 0.9.1 fix (Issue #4913) - * Mass (u) has been added to MDAnalysis base units and - clarified that physical constants use CODATA 2010 values - (Issue #3944, PR #5439) Enhancements * Added ASV benchmark for PDB trajectory reading (PR #5394) From c80bea377b88dde871270e90289036e374f56dfc Mon Sep 17 00:00:00 2001 From: Francesco Siciliani Date: Thu, 3 Sep 2026 01:40:35 +0200 Subject: [PATCH 7/7] Update CHANGELOG --- package/CHANGELOG | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/package/CHANGELOG b/package/CHANGELOG index 4ec3193cdb..b106b09dc3 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -23,9 +23,8 @@ The rules for this file: * 2.11.0 Fixes - * Mass (u) has been added to MDAnalysis base units and - clarified that physical constants use CODATA 2010 values - (Issue #3944, PR #5439) + * Mass (u) has been added to MDAnalysis base units and clarified that physical + constants use CODATA 2010 values (Issue #3944, PR #5439) * Added `.gitattributes` to enforce LF (\n) as line endings and renormalized existing files to conform (Issue #5315, PR #5446) * `AtomGroup.rotate()` and the `rotateby` trajectory transformation now