From 960713be3bd2b13da06f8f78386492df06c24f9d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 5 Feb 2021 17:01:28 -0500 Subject: [PATCH] make recent change to fix ti/spring docs use mathjax --- doc/src/fix_ti_spring.rst | 9 +++++---- doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/doc/src/fix_ti_spring.rst b/doc/src/fix_ti_spring.rst index 303564456e..806619cdb1 100644 --- a/doc/src/fix_ti_spring.rst +++ b/doc/src/fix_ti_spring.rst @@ -135,10 +135,11 @@ system's potential energy as part of :doc:`thermodynamic output This fix computes a global scalar and a global vector quantities which can be accessed by various :doc:`output commands `. The scalar is an energy which is the sum of the spring energy for each -atom, where the per-atom energy is 0.5 \* k \* r\^2. The vector stores -2 values. The first value is the coupling parameter lambda. The -second value is the derivative of lambda with respect to the integer -timestep *s*, i.e. d lambda / ds. In order to obtain d lambda / dt, +atom, where the per-atom energy is :math:`0.5 \cdot k \cdot r^2`. +The vector stores 2 values. The first value is the coupling parameter lambda. +The second value is the derivative of lambda with respect to the integer +timestep *s*, i.e. :math:`\frac{d \lambda}{d s}`. In order to obtain +:math:`\frac{d \lambda}{d t}`, where t is simulation time, this 2nd value needs to be divided by the timestep size (e.g. 0.5 fs). The scalar and vector values calculated by this fix are "extensive". diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index e9ba170ac5..a2f8764aee 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -597,6 +597,7 @@ Dcut de dE De +deallocated decorrelation debye Debye