From 16dd89c641dc804f6d39e5c87bd9eacd20fae9eb Mon Sep 17 00:00:00 2001 From: Stephen Sanderson Date: Sat, 23 Apr 2022 10:30:44 +1000 Subject: [PATCH] Added qualifier to assertions + note about inhomogeneous rigid systems --- doc/src/compute_temp_profile.rst | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index 7ccf403eb9..1be82efbdd 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -138,7 +138,12 @@ needed, the subtracted degrees-of-freedom can be altered using the bin. As a result, the bin degrees-of-freedom summed over all bins exactly equals the degrees-of-freedom used in the scalar temperature calculation, :math:`\Sigma N_{DOF_i} = N_{DOF}` and the corresponding relation for temperature - is also satisfied :math:`\Sigma N_{DOF_i} T_i = N_{DOF} T` + is also satisfied :math:`\Sigma N_{DOF_i} T_i = N_{DOF} T`, so long as + all bins contain more degrees of freedom than the number of constraints per bin. + Note that as degrees-of-freedom subtracted due to fixes that contstrain + molecular motion are distributed equally between bins, the reported + temperature within a bin may not be accurate for systems containing + inhomogeneously distributed rigid molecules. See the :doc:`Howto thermostat ` doc page for a discussion of different ways to compute temperature and perform