From dbdb1085129323f97729c57a94ac4327e1dcd892 Mon Sep 17 00:00:00 2001 From: Pablo Piaggi Date: Thu, 10 Dec 2020 15:18:48 -0500 Subject: [PATCH 1/3] update temp/csvr manual --- doc/src/fix_temp_csvr.rst | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index 8faa6035cf..c5ca2ed5eb 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -124,6 +124,19 @@ temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. +An important feature of these thermostats is that they have an +associated effective energy that is a contant of the motion. +The effective energy is the total energy (kinetic + potential) plus +the accumulated kinetic energy changes due to the thermostat. The +latter quantity is the global scalar computed by these fixes. This +feature is useful to check the integration of the equations of motion +against discretization errors. In other words, the conservation of +the effective energy can be used to choose an appropriate integration +:doc:`timestep `. This is similar to the usual paradigm of +checking the conservation of the total energy in the microcanonical +ensemble. + + ---------- Restart, fix_modify, output, run start/stop, minimize info @@ -153,7 +166,7 @@ These fixes are not invoked during :doc:`energy minimization `. These fixes compute a global scalar which can be accessed by various :doc:`output commands `. The scalar is the cumulative -energy change due to the fix. The scalar value calculated by this fix +kinetic energy change due to the fix. The scalar value calculated by this fix is "extensive". Restrictions From 65d1594474fabfcbdf4fee7c297b9a9242e6a7a1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 14 Dec 2020 08:39:27 -0500 Subject: [PATCH 2/3] Fix typo and adjust grammar --- doc/src/fix_temp_csvr.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index c5ca2ed5eb..ea023c4e24 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -125,7 +125,7 @@ removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. An important feature of these thermostats is that they have an -associated effective energy that is a contant of the motion. +associated effective energy that is a constant of motion. The effective energy is the total energy (kinetic + potential) plus the accumulated kinetic energy changes due to the thermostat. The latter quantity is the global scalar computed by these fixes. This From 40d260dcc6bbdbea23c9268065e3e5920d6d097e Mon Sep 17 00:00:00 2001 From: PabloPiaggi Date: Mon, 14 Dec 2020 18:45:46 -0500 Subject: [PATCH 3/3] Remove word kinetic --- doc/src/fix_temp_csvr.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_temp_csvr.rst b/doc/src/fix_temp_csvr.rst index ea023c4e24..5e6074bc66 100644 --- a/doc/src/fix_temp_csvr.rst +++ b/doc/src/fix_temp_csvr.rst @@ -166,7 +166,7 @@ These fixes are not invoked during :doc:`energy minimization `. These fixes compute a global scalar which can be accessed by various :doc:`output commands `. The scalar is the cumulative -kinetic energy change due to the fix. The scalar value calculated by this fix +energy change due to the fix. The scalar value calculated by this fix is "extensive". Restrictions