diff --git a/doc/src/compute_viscosity_cos.rst b/doc/src/compute_viscosity_cos.rst index 1bf9bc2588..87cfec56cf 100644 --- a/doc/src/compute_viscosity_cos.rst +++ b/doc/src/compute_viscosity_cos.rst @@ -96,7 +96,7 @@ ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. 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 :doc:`compute_modify ` command if this is not the case. -However, in order to get meaningful result, the group ID of this compute should +However, in order to get meaningful results, the group ID of this compute should be all. The removal of the cosine-shaped velocity component by this command is @@ -145,7 +145,10 @@ The seventh element of vector value will be in velocity :doc:`units `. Restrictions """""""""""" -This command is only available when LAMMPS was built with the MISC package. +This compute is part of the MISC package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` page for more info. + Since this compute depends on :doc:`fix accelerate/cos ` which can only work for 3d systems, it cannot be used for 2d systems. diff --git a/doc/src/fix_accelerate_cos.rst b/doc/src/fix_accelerate_cos.rst index 0b31a88915..c5a02f3bf8 100644 --- a/doc/src/fix_accelerate_cos.rst +++ b/doc/src/fix_accelerate_cos.rst @@ -20,7 +20,7 @@ Examples .. code-block:: LAMMPS - fix 1 all accelerate/cos 0.02e-5 + fix 1 all accelerate/cos 2.0e-7 Description """"""""""" @@ -57,19 +57,18 @@ where :math:`m_i`, :math:`v_{i,x}`, and :math:`z_i` are the mass, :math:`x`-component velocity, and :math:`z`-coordinate of a particle, respectively. -The velocity amplitude :math:`V` can be calculated with -:doc:`compute viscosity/cos `, -which enables viscosity calculation with periodic perturbation method, -as described by :ref:`Hess`. -Because the applied acceleration drives the system away from equilibration, -the calculated shear viscosity is lower than the intrinsic viscosity -due to the shear-thinning effect. -Extrapolation to zero acceleration should generally be performed to -predict the zero-shear viscosity. -As the shear stress decreases, the signal-noise ratio decreases rapidly, -the simulation time must be extended accordingly to get converged result. +The velocity amplitude :math:`V` can be calculated with :doc:`compute +viscosity/cos `, which enables viscosity +calculation with periodic perturbation method, as described by +:ref:`Hess`. Because the applied acceleration drives the system +away from equilibration, the calculated shear viscosity is lower than +the intrinsic viscosity due to the shear-thinning effect. Extrapolation +to zero acceleration should generally be performed to predict the +zero-shear viscosity. As the shear stress decreases, the +signal-to-noise ratio decreases rapidly, and the simulation time must be +extended accordingly to get converged results. -In order to get meaningful result, the group ID of this fix should be all. +In order to get meaningful results, the group ID of this fix should be all. ---------- @@ -81,12 +80,16 @@ None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. + This fix is not invoked during energy minimization. Restrictions """""""""""" -This command is only available when LAMMPS was built with the MISC package. +This fix is part of the MISC package. It is only enabled if LAMMPS was +built with that package. See the :doc:`Build package ` +page for more info. + Since this fix depends on the :math:`z`-coordinate of atoms, it cannot be used in 2d simulations. diff --git a/doc/src/fix_ave_spatial.rst b/doc/src/fix_ave_spatial.rst index 14c1518fd9..1e596e3ee2 100644 --- a/doc/src/fix_ave_spatial.rst +++ b/doc/src/fix_ave_spatial.rst @@ -1,4 +1,4 @@ -Fix ave/spatial command +fix ave/spatial command ======================= .. meta:: diff --git a/doc/src/fix_ave_spatial_sphere.rst b/doc/src/fix_ave_spatial_sphere.rst index c83b7c7f27..470bd49797 100644 --- a/doc/src/fix_ave_spatial_sphere.rst +++ b/doc/src/fix_ave_spatial_sphere.rst @@ -1,5 +1,5 @@ -Fix ave/spatial command -======================= +fix ave/spatial/sphere command +============================== .. meta:: :http-equiv=Refresh: 5; url=https://docs.lammps.org/Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere