From 8a535a457e41228d9ed15aa62394ce571f249fff Mon Sep 17 00:00:00 2001 From: Wei-Tse Hsu Date: Wed, 24 Apr 2024 16:48:16 +0800 Subject: [PATCH] Added sphinxcontrib-pseudocode to docs/requirements.txt --- docs/requirements.txt | 2 +- docs/theory.rst | 8 +++++--- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index eed0dac8..356d74bf 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -11,4 +11,4 @@ seaborn matplotlib pyemma pymbar==4.0.1 - +sphinxcontrib-pseudocode diff --git a/docs/theory.rst b/docs/theory.rst index c3cf730f..db1fe293 100644 --- a/docs/theory.rst +++ b/docs/theory.rst @@ -207,12 +207,14 @@ As detailed in Algorithm 1 below. \end{algorithm} - 3. Correction schemes ===================== +For weight-updating REXEE simulations, we experimented a few correction schemes that aim to improve the convergence of the alchemical weights. +These correction schemes include weight combination schemes (enabled by setting :code:`w_combine: True` in the input YAML file) and histogram correction schemes +(enabled by setting :code:`hist_corr: True` in the input YAML file). While there has not been evidence showing that these correction schemes could improve the +weight convergence in REXEE simulations (as discussed in our paper), we still provide these options for users to experiment with. +In the following sections, we elaborate on the details of these correction schemes. -3.1. Weight correction -----------------------