From f8c70b1dfc93a264da00bcb19b827d5ac60dec06 Mon Sep 17 00:00:00 2001 From: Berk Hess Date: Tue, 28 Nov 2017 14:13:00 +0100 Subject: [PATCH] Update documention of Nose-Hoover output The documentation of Nose-Hoover chain variable printing was (long) outdated. Refs #2301 Change-Id: I2ef02e676141000937fedecf096b635ee2e69281 --- docs/manual/algorithms.tex | 9 ++++----- docs/user-guide/mdp-options.rst | 17 ++++++++++++++--- 2 files changed, 18 insertions(+), 8 deletions(-) diff --git a/docs/manual/algorithms.tex b/docs/manual/algorithms.tex index 9fbd45c28f..a12c7f3ffe 100644 --- a/docs/manual/algorithms.tex +++ b/docs/manual/algorithms.tex @@ -1337,12 +1337,11 @@ H = \sum_{i=1}^{N} \frac{\pb_i}{2m_i} + U\left(\rv_1,\rv_2,\ldots,\rv_N\right) + The values and velocities of the Nos{\'e}-Hoover thermostat variables are generally not included in the output, as they take up a fair amount of space and are generally not important for analysis of -simulations, but this can be overridden by defining the environment -variable {\tt GMX_NOSEHOOVER_CHAINS}, which will print the values of all +simulations, but by setting an mdp option the values of all the positions and velocities of all Nos{\'e}-Hoover particles in the -chain to the {\tt .edr} file. Leap-frog simulations currently can only have -Nos{\'e}-Hoover chain lengths of 1, but this will likely be updated in -later version. +chain are written to the {\tt .edr} file. Leap-frog simulations +currently can only have Nos{\'e}-Hoover chain lengths of 1, +but this will likely be updated in later version. As described in the integrator section, for temperature coupling, the temperature that the algorithm attempts to match to the reference diff --git a/docs/user-guide/mdp-options.rst b/docs/user-guide/mdp-options.rst index 3feb1d2737..4284cd77b1 100644 --- a/docs/user-guide/mdp-options.rst +++ b/docs/user-guide/mdp-options.rst @@ -1048,9 +1048,20 @@ Temperature coupling (10) The number of chained Nose-Hoover thermostats for velocity Verlet integrators, the leap-frog :mdp-value:`integrator=md` integrator - only supports 1. Data for the NH chain variables is not printed to - the :ref:`edr` file, but can be using the ``GMX_NOSEHOOVER_CHAINS`` - environment variable + only supports 1. Data for the NH chain variables is not printed + to the :ref:`edr` file by default, but can be turned on with the + :mdp:`print-nose-hoover-chains` option. + +.. mdp:: print-nose-hoover-chain-variables + + .. mdp-value:: no + + Do not store Nose-Hoover chain variables in the energy file. + + .. mdp-value:: yes + + Store all positions and velocities of the Nose-Hoover chain + in the energy file. .. mdp:: tc-grps -- 2.11.4.GIT