diff --git a/doc/compute_temp_asphere.html b/doc/compute_temp_asphere.html index 3b29b68e74..daaad528a9 100644 --- a/doc/compute_temp_asphere.html +++ b/doc/compute_temp_asphere.html @@ -13,16 +13,29 @@
Syntax:
-compute ID group-ID temp/asphere bias-ID +compute ID group-ID temp/asphere keyword value ...-
bias value = bias-IDuniform or gaussian + bias-ID = ID of a temperature compute that removes a velocity bias + dof value = all or rotate + all = compute temperature of translational and rotational degrees of freedom + rotate = compute temperature of just rotational degrees of freedom ++
Examples:
compute 1 all temp/asphere -compute myTemp mobile temp/asphere tempCOM +compute myTemp mobile temp/asphere bias tempCOM +compute myTemp mobile temp/asphere dof rotate
Description:
@@ -75,15 +88,6 @@ vector are ordered xx, yy, zz, xy, xz, yz. constant for the duration of the run; use the dynamic option of the compute_modify command if this is not the case. -If a bias-ID is specified it must be the ID of a temperature compute -that removes a "bias" velocity from each atom. This allows compute -temp/sphere to compute its thermal temperature after the translational -kinetic energy components have been altered in a prescribed way, -e.g. to remove a velocity profile. Thermostats that use this compute -will work with this bias term. See the doc pages for individual -computes that calculate a temperature and the doc pages for fixes that -perform thermostatting for more details. -
This compute subtracts out translational degrees-of-freedom due to fixes that constrain molecular motion, such as fix shake and fix rigid. This means the @@ -96,6 +100,26 @@ be altered using the extra option of the discussion of different ways to compute temperature and perform thermostatting.
+The keyword/value option pairs are used in the following ways. +
+For the bias keyword, bias-ID refers to the ID of a temperature +compute that removes a "bias" velocity from each atom. This allows +compute temp/sphere to compute its thermal temperature after the +translational kinetic energy components have been altered in a +prescribed way, e.g. to remove a velocity profile. Thermostats that +use this compute will work with this bias term. See the doc pages for +individual computes that calculate a temperature and the doc pages for +fixes that perform thermostatting for more details. +
+For the dof keyword, a setting of all calculates a temperature +that includes both translational and rotational degrees of freedom. A +setting of rotate calculates a temperature that includes only +rotational degrees of freedom. +
+Output info:
This compute calculates a global scalar (the temperature) and a global diff --git a/doc/compute_temp_asphere.txt b/doc/compute_temp_asphere.txt index b22256fbe8..cdd8870981 100755 --- a/doc/compute_temp_asphere.txt +++ b/doc/compute_temp_asphere.txt @@ -10,16 +10,24 @@ compute temp/asphere command :h3 [Syntax:] -compute ID group-ID temp/asphere bias-ID :pre +compute ID group-ID temp/asphere keyword value ... :pre -ID, group-ID are documented in "compute"_compute.html command -temp/asphere = style name of this compute command -bias-ID = ID of a temperature compute that removes a velocity bias (optional) :ul +ID, group-ID are documented in "compute"_compute.html command :ulb,l +temp/asphere = style name of this compute command :l +zero or more keyword/value pairs may be appended :l +keyword = {bias} or {dof} :l + {bias} value = bias-ID{uniform} or {gaussian} + bias-ID = ID of a temperature compute that removes a velocity bias + {dof} value = {all} or {rotate} + all = compute temperature of translational and rotational degrees of freedom + rotate = compute temperature of just rotational degrees of freedom :pre +:ule [Examples:] compute 1 all temp/asphere -compute myTemp mobile temp/asphere tempCOM :pre +compute myTemp mobile temp/asphere bias tempCOM +compute myTemp mobile temp/asphere dof rotate :pre [Description:] @@ -72,15 +80,6 @@ The number of atoms contributing to the temperature is assumed to be constant for the duration of the run; use the {dynamic} option of the "compute_modify"_compute_modify.html command if this is not the case. -If a {bias-ID} is specified it must be the ID of a temperature compute -that removes a "bias" velocity from each atom. This allows compute -temp/sphere to compute its thermal temperature after the translational -kinetic energy components have been altered in a prescribed way, -e.g. to remove a velocity profile. Thermostats that use this compute -will work with this bias term. See the doc pages for individual -computes that calculate a temperature and the doc pages for fixes that -perform thermostatting for more details. - This compute subtracts out translational degrees-of-freedom due to fixes that constrain molecular motion, such as "fix shake"_fix_shake.html and "fix rigid"_fix_rigid.html. This means the @@ -93,6 +92,26 @@ See "this howto section"_Section_howto.html#4_16 of the manual for a discussion of different ways to compute temperature and perform thermostatting. +:line + +The keyword/value option pairs are used in the following ways. + +For the {bias} keyword, {bias-ID} refers to the ID of a temperature +compute that removes a "bias" velocity from each atom. This allows +compute temp/sphere to compute its thermal temperature after the +translational kinetic energy components have been altered in a +prescribed way, e.g. to remove a velocity profile. Thermostats that +use this compute will work with this bias term. See the doc pages for +individual computes that calculate a temperature and the doc pages for +fixes that perform thermostatting for more details. + +For the {dof} keyword, a setting of {all} calculates a temperature +that includes both translational and rotational degrees of freedom. A +setting of {rotate} calculates a temperature that includes only +rotational degrees of freedom. + +:line + [Output info:] This compute calculates a global scalar (the temperature) and a global diff --git a/doc/compute_temp_sphere.html b/doc/compute_temp_sphere.html index 31e73a05f5..23e18d16b5 100644 --- a/doc/compute_temp_sphere.html +++ b/doc/compute_temp_sphere.html @@ -13,16 +13,29 @@
Syntax:
-compute ID group-ID temp/sphere bias-ID +compute ID group-ID temp/sphere keyword value ...-
bias value = bias-IDuniform or gaussian + bias-ID = ID of a temperature compute that removes a velocity bias + dof value = all or rotate + all = compute temperature of translational and rotational degrees of freedom + rotate = compute temperature of just rotational degrees of freedom ++
Examples:
compute 1 all temp/sphere -compute myTemp mobile temp/sphere tempCOM +compute myTemp mobile temp/sphere bias tempCOM +compute myTemp mobile temp/sphere dof rotate
Description:
@@ -66,15 +79,6 @@ the vector are ordered xx, yy, zz, xy, xz, yz. constant for the duration of the run; use the dynamic option of the compute_modify command if this is not the case. -If a bias-ID is specified it must be the ID of a temperature compute -that removes a "bias" velocity from each atom. This allows compute -temp/sphere to compute its thermal temperature after the translational -kinetic energy components have been altered in a prescribed way, -e.g. to remove a velocity profile. Thermostats that use this compute -will work with this bias term. See the doc pages for individual -computes that calculate a temperature and the doc pages for fixes that -perform thermostatting for more details. -
This compute subtracts out translational degrees-of-freedom due to fixes that constrain molecular motion, such as fix shake and fix rigid. This means the @@ -87,6 +91,26 @@ be altered using the extra option of the discussion of different ways to compute temperature and perform thermostatting.
+The keyword/value option pairs are used in the following ways. +
+For the bias keyword, bias-ID refers to the ID of a temperature +compute that removes a "bias" velocity from each atom. This allows +compute temp/sphere to compute its thermal temperature after the +translational kinetic energy components have been altered in a +prescribed way, e.g. to remove a velocity profile. Thermostats that +use this compute will work with this bias term. See the doc pages for +individual computes that calculate a temperature and the doc pages for +fixes that perform thermostatting for more details. +
+For the dof keyword, a setting of all calculates a temperature +that includes both translational and rotational degrees of freedom. A +setting of rotate calculates a temperature that includes only +rotational degrees of freedom. +
+Output info:
This compute calculates a global scalar (the temperature) and a global @@ -116,6 +140,8 @@ particles with radius = 0.0.
compute temp, compute temp/asphere
-Default: none +
Default: +
+The option defaults are no bias and dof = all.