From 52fe6f8f5be43d2654ffb04a1d4726691dfc9019 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Tue, 7 May 2024 15:36:14 -0700 Subject: [PATCH 1/2] [docs] fix normalization in g_ab() RDF equation - doc fix - see https://github.com/MDAnalysis/mdanalysis/discussions/4437#discussioncomment-9027091 (originally found by @rodpollet) --- package/MDAnalysis/analysis/rdf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package/MDAnalysis/analysis/rdf.py b/package/MDAnalysis/analysis/rdf.py index 0480c2adf13..9be624f2a06 100644 --- a/package/MDAnalysis/analysis/rdf.py +++ b/package/MDAnalysis/analysis/rdf.py @@ -32,7 +32,7 @@ .. math:: - g_{ab}(r) = (N_{a} N_{b})^{-1} \sum_{i=1}^{N_a} \sum_{j=1}^{N_b} + g_{ab}(r) = \frac{1}{N_{a}} \frac{1}{N_{b}/V} \sum_{i=1}^{N_a} \sum_{j=1}^{N_b} \langle \delta(|\mathbf{r}_i - \mathbf{r}_j| - r) \rangle which is normalized so that the RDF becomes 1 for large separations in a From 61d05a99cee7ea36e4dfcb27c1554ecfa7eb6c19 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Tue, 7 May 2024 15:40:15 -0700 Subject: [PATCH 2/2] [doc] fix missing HOLE link --- .../doc/sphinx/source/documentation_pages/analysis/hole2.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/package/doc/sphinx/source/documentation_pages/analysis/hole2.rst b/package/doc/sphinx/source/documentation_pages/analysis/hole2.rst index 60039568ac7..1d8b962a175 100644 --- a/package/doc/sphinx/source/documentation_pages/analysis/hole2.rst +++ b/package/doc/sphinx/source/documentation_pages/analysis/hole2.rst @@ -24,6 +24,8 @@ under the Apache v2.0 license.) `mdahole2 `_ and will be removed in MDAnalysis 3.0.0. +.. _HOLE: http://www.holeprogram.org/ + See Also --------