From ec992572160515ed3e5ac04c76423835e57bf64b Mon Sep 17 00:00:00 2001 From: Jenna Bradley <55467578+janbridley@users.noreply.github.com> Date: Fri, 3 Oct 2025 11:36:26 -0400 Subject: [PATCH 1/7] Update __init__.py --- hoomd/md/pair/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hoomd/md/pair/__init__.py b/hoomd/md/pair/__init__.py index 6344f6cf90..bcec25731b 100644 --- a/hoomd/md/pair/__init__.py +++ b/hoomd/md/pair/__init__.py @@ -6,7 +6,7 @@ .. math:: - U_\mathrm{pair,total} = \frac{1}{2} \sum_{i=0}^\mathrm{N_particles-1} + U_\mathrm{pair,total} = \frac{1}{2} \sum_{i=0}^\mathrm{N_{particles}-1} \sum_{j \ne i, (i,j) \notin \mathrm{exclusions}} U_\mathrm{pair}(r_{ij}) From d3a96284ff2ea37a6c514e32197e857e64ddda34 Mon Sep 17 00:00:00 2001 From: janbridley Date: Fri, 3 Oct 2025 12:31:04 -0400 Subject: [PATCH 2/7] Update other typos --- hoomd/hpmc/external/external.py | 2 +- hoomd/hpmc/pair/pair.py | 4 ++-- hoomd/md/external/wall.py | 2 +- hoomd/md/pair/aniso.py | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/hoomd/hpmc/external/external.py b/hoomd/hpmc/external/external.py index 02af8f8e9a..378fb40f56 100644 --- a/hoomd/hpmc/external/external.py +++ b/hoomd/hpmc/external/external.py @@ -76,7 +76,7 @@ def energy(self): .. math:: - U = \\sum_{i=0}^\\mathrm{N_particles-1} + U = \\sum_{i=0}^\\mathrm{N_{particles}-1} U_{\\mathrm{external},i} See `hoomd.hpmc.integrate` for the full expression which includes diff --git a/hoomd/hpmc/pair/pair.py b/hoomd/hpmc/pair/pair.py index 96a6ff75a3..bb634a4e1c 100644 --- a/hoomd/hpmc/pair/pair.py +++ b/hoomd/hpmc/pair/pair.py @@ -83,8 +83,8 @@ def energy(self): .. math:: - U = \\sum_{i=0}^\\mathrm{N_particles-1} - \\sum_{j=i+1}^\\mathrm{N_particles-1} + U = \\sum_{i=0}^\\mathrm{N_{particles}-1} + \\sum_{j=i+1}^\\mathrm{N_{particles}-1} U_{\\mathrm{pair},ij} See `hoomd.hpmc.integrate` for the full expression which includes diff --git a/hoomd/md/external/wall.py b/hoomd/md/external/wall.py index 572ab6991f..3714bdd523 100644 --- a/hoomd/md/external/wall.py +++ b/hoomd/md/external/wall.py @@ -6,7 +6,7 @@ .. math:: - U_\mathrm{wall} = \sum_{i=0}^{\mathrm{N_particles-1}} + U_\mathrm{wall} = \sum_{i=0}^{\mathrm{N_{particles}-1}} \sum_{w \in walls} U_w(d_i), where :math:`d_i` is the signed distance between particle :math:`i` and the wall diff --git a/hoomd/md/pair/aniso.py b/hoomd/md/pair/aniso.py index bd08565d7f..b0f6c08253 100644 --- a/hoomd/md/pair/aniso.py +++ b/hoomd/md/pair/aniso.py @@ -6,7 +6,7 @@ .. math:: - U_\mathrm{pair,total} = \frac{1}{2} \sum_{i=0}^\mathrm{N_particles-1} + U_\mathrm{pair,total} = \frac{1}{2} \sum_{i=0}^\mathrm{N_{particles}-1} \sum_{j \ne i, (i,j) \notin \mathrm{exclusions}} U_\mathrm{pair}(r_{ij}, \mathbf{q}_i, \mathbf{q}_j) From 6a26d7c94b1b2f2a6c602a30baad54e18ef73703 Mon Sep 17 00:00:00 2001 From: janbridley Date: Fri, 3 Oct 2025 12:33:57 -0400 Subject: [PATCH 3/7] Fix one more --- hoomd/hpmc/integrate.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hoomd/hpmc/integrate.py b/hoomd/hpmc/integrate.py index 1735b5facb..e842e8847c 100644 --- a/hoomd/hpmc/integrate.py +++ b/hoomd/hpmc/integrate.py @@ -157,7 +157,7 @@ .. math:: U_\mathrm{external} = - \sum_{i=0}^\mathrm{N_particles-1} U_{\mathrm{external},i}(\vec{r}_i, + \sum_{i=0}^\mathrm{N_{particles}-1} U_{\mathrm{external},i}(\vec{r}_i, \mathbf{q}_i) Potential classes in `hoomd.hpmc.pair` evaluate From 4eaac1f171c64bc7dd44ad075e84575366e70395 Mon Sep 17 00:00:00 2001 From: janbridley Date: Fri, 3 Oct 2025 13:24:04 -0400 Subject: [PATCH 4/7] Address style comment --- hoomd/hpmc/external/external.py | 2 +- hoomd/hpmc/pair/pair.py | 4 ++-- hoomd/md/external/wall.py | 2 +- hoomd/md/pair/__init__.py | 2 +- hoomd/md/pair/aniso.py | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/hoomd/hpmc/external/external.py b/hoomd/hpmc/external/external.py index 378fb40f56..5dc43bbb9a 100644 --- a/hoomd/hpmc/external/external.py +++ b/hoomd/hpmc/external/external.py @@ -76,7 +76,7 @@ def energy(self): .. math:: - U = \\sum_{i=0}^\\mathrm{N_{particles}-1} + U = \\sum_{i=0}^{N_\mathrm{particles}-1} U_{\\mathrm{external},i} See `hoomd.hpmc.integrate` for the full expression which includes diff --git a/hoomd/hpmc/pair/pair.py b/hoomd/hpmc/pair/pair.py index bb634a4e1c..0aad7e64b5 100644 --- a/hoomd/hpmc/pair/pair.py +++ b/hoomd/hpmc/pair/pair.py @@ -83,8 +83,8 @@ def energy(self): .. math:: - U = \\sum_{i=0}^\\mathrm{N_{particles}-1} - \\sum_{j=i+1}^\\mathrm{N_{particles}-1} + U = \\sum_{i=0}^{N_\mathrm{particles}-1} + \\sum_{j=i+1}^{N_\mathrm{particles}-1} U_{\\mathrm{pair},ij} See `hoomd.hpmc.integrate` for the full expression which includes diff --git a/hoomd/md/external/wall.py b/hoomd/md/external/wall.py index 3714bdd523..33926ccca4 100644 --- a/hoomd/md/external/wall.py +++ b/hoomd/md/external/wall.py @@ -6,7 +6,7 @@ .. math:: - U_\mathrm{wall} = \sum_{i=0}^{\mathrm{N_{particles}-1}} + U_\mathrm{wall} = \sum_{i=0}^{{N_\mathrm{particles}-1}} \sum_{w \in walls} U_w(d_i), where :math:`d_i` is the signed distance between particle :math:`i` and the wall diff --git a/hoomd/md/pair/__init__.py b/hoomd/md/pair/__init__.py index bcec25731b..ee09159bce 100644 --- a/hoomd/md/pair/__init__.py +++ b/hoomd/md/pair/__init__.py @@ -6,7 +6,7 @@ .. math:: - U_\mathrm{pair,total} = \frac{1}{2} \sum_{i=0}^\mathrm{N_{particles}-1} + U_\mathrm{pair,total} = \frac{1}{2} \sum_{i=0}^{N_\mathrm{particles}-1} \sum_{j \ne i, (i,j) \notin \mathrm{exclusions}} U_\mathrm{pair}(r_{ij}) diff --git a/hoomd/md/pair/aniso.py b/hoomd/md/pair/aniso.py index b0f6c08253..3a6d1e5c62 100644 --- a/hoomd/md/pair/aniso.py +++ b/hoomd/md/pair/aniso.py @@ -6,7 +6,7 @@ .. math:: - U_\mathrm{pair,total} = \frac{1}{2} \sum_{i=0}^\mathrm{N_{particles}-1} + U_\mathrm{pair,total} = \frac{1}{2} \sum_{i=0}^{N_\mathrm{particles}-1} \sum_{j \ne i, (i,j) \notin \mathrm{exclusions}} U_\mathrm{pair}(r_{ij}, \mathbf{q}_i, \mathbf{q}_j) From 406c6870317e1f8b470174a42f72190ab4210b1d Mon Sep 17 00:00:00 2001 From: janbridley Date: Fri, 3 Oct 2025 13:28:59 -0400 Subject: [PATCH 5/7] Fix style --- hoomd/hpmc/external/external.py | 2 +- hoomd/hpmc/pair/pair.py | 4 ++-- hoomd/md/integrate.py | 2 +- hoomd/md/many_body.py | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/hoomd/hpmc/external/external.py b/hoomd/hpmc/external/external.py index 5dc43bbb9a..2d2e0de6cb 100644 --- a/hoomd/hpmc/external/external.py +++ b/hoomd/hpmc/external/external.py @@ -76,7 +76,7 @@ def energy(self): .. math:: - U = \\sum_{i=0}^{N_\mathrm{particles}-1} + U = \\sum_{i=0}^{N_\\mathrm{particles}-1} U_{\\mathrm{external},i} See `hoomd.hpmc.integrate` for the full expression which includes diff --git a/hoomd/hpmc/pair/pair.py b/hoomd/hpmc/pair/pair.py index 0aad7e64b5..600ed956e7 100644 --- a/hoomd/hpmc/pair/pair.py +++ b/hoomd/hpmc/pair/pair.py @@ -83,8 +83,8 @@ def energy(self): .. math:: - U = \\sum_{i=0}^{N_\mathrm{particles}-1} - \\sum_{j=i+1}^{N_\mathrm{particles}-1} + U = \\sum_{i=0}^{N_\\mathrm{particles}-1} + \\sum_{j=i+1}^{N_\\mathrm{particles}-1} U_{\\mathrm{pair},ij} See `hoomd.hpmc.integrate` for the full expression which includes diff --git a/hoomd/md/integrate.py b/hoomd/md/integrate.py index ed4a95c18a..63231bb120 100644 --- a/hoomd/md/integrate.py +++ b/hoomd/md/integrate.py @@ -379,7 +379,7 @@ def linear_momentum(self): .. math:: - \\vec{p} = \\sum_{i=0}^\\mathrm{N_particles-1} m_i \\vec{v}_i + \\vec{p} = \\sum_{i=0}^{N_\\mathrm{particles}-1} m_i \\vec{v}_i """ v = self._cpp_obj.computeLinearMomentum() return (v.x, v.y, v.z) diff --git a/hoomd/md/many_body.py b/hoomd/md/many_body.py index 3f085468ca..f740268861 100644 --- a/hoomd/md/many_body.py +++ b/hoomd/md/many_body.py @@ -6,7 +6,7 @@ .. math:: - U_\mathrm{many-body} = \frac{1}{2} \sum_{i=0}^\mathrm{N_particles-1} + U_\mathrm{many-body} = \frac{1}{2} \sum_{i=0}^{N_\\mathrm{particles}-1} \sum_{j \ne i} \sum_{j \ne k} U(\vec{r}_{ij}, \vec{r}_{ik}) From 3c00306e128e3618856b4bdc79f4845b4fcf4104 Mon Sep 17 00:00:00 2001 From: janbridley Date: Fri, 3 Oct 2025 13:29:58 -0400 Subject: [PATCH 6/7] Fix typo --- hoomd/md/many_body.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hoomd/md/many_body.py b/hoomd/md/many_body.py index f740268861..c735e8c652 100644 --- a/hoomd/md/many_body.py +++ b/hoomd/md/many_body.py @@ -6,7 +6,7 @@ .. math:: - U_\mathrm{many-body} = \frac{1}{2} \sum_{i=0}^{N_\\mathrm{particles}-1} + U_\mathrm{many-body} = \frac{1}{2} \sum_{i=0}^{N_\mathrm{particles}-1} \sum_{j \ne i} \sum_{j \ne k} U(\vec{r}_{ij}, \vec{r}_{ik}) From 542cf51d9faae2cb69766a246b0f2466dd930d57 Mon Sep 17 00:00:00 2001 From: Jenna Bradley <55467578+janbridley@users.noreply.github.com> Date: Fri, 3 Oct 2025 13:30:55 -0400 Subject: [PATCH 7/7] Update hoomd/md/external/wall.py --- hoomd/md/external/wall.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hoomd/md/external/wall.py b/hoomd/md/external/wall.py index 33926ccca4..9cddf0518d 100644 --- a/hoomd/md/external/wall.py +++ b/hoomd/md/external/wall.py @@ -6,7 +6,7 @@ .. math:: - U_\mathrm{wall} = \sum_{i=0}^{{N_\mathrm{particles}-1}} + U_\mathrm{wall} = \sum_{i=0}^{N_\mathrm{particles}-1} \sum_{w \in walls} U_w(d_i), where :math:`d_i` is the signed distance between particle :math:`i` and the wall