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small doc fixes

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This commit is contained in:
Axel Kohlmeyer
2024-08-13 20:47:46 -04:00
parent 70384d4344
commit 4d1632b9f7
4 changed files with 25 additions and 19 deletions
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7
doc/src/compute_viscosity_cos.rst
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@ -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 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 constant for the duration of the run; use the *dynamic* option of the
:doc:`compute_modify <compute_modify>` command if this is not the case. :doc:`compute_modify <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. be all.
The removal of the cosine-shaped velocity component by this command is 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 <units>`.
Restrictions 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
<Build_package>` page for more info.
Since this compute depends on :doc:`fix accelerate/cos <fix_accelerate_cos>` Since this compute depends on :doc:`fix accelerate/cos <fix_accelerate_cos>`
which can only work for 3d systems, it cannot be used for 2d systems. which can only work for 3d systems, it cannot be used for 2d systems.

31
doc/src/fix_accelerate_cos.rst
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@ -20,7 +20,7 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
fix 1 all accelerate/cos 0.02e-5 fix 1 all accelerate/cos 2.0e-7
Description 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, :math:`x`-component velocity, and :math:`z`-coordinate of a particle,
respectively. respectively.
The velocity amplitude :math:`V` can be calculated with The velocity amplitude :math:`V` can be calculated with :doc:`compute
:doc:`compute viscosity/cos <compute_viscosity_cos>`, viscosity/cos <compute_viscosity_cos>`, which enables viscosity
which enables viscosity calculation with periodic perturbation method, calculation with periodic perturbation method, as described by
as described by :ref:`Hess<Hess2>`. :ref:`Hess<Hess2>`. Because the applied acceleration drives the system
Because the applied acceleration drives the system away from equilibration, away from equilibration, the calculated shear viscosity is lower than
the calculated shear viscosity is lower than the intrinsic viscosity the intrinsic viscosity due to the shear-thinning effect. Extrapolation
due to the shear-thinning effect. to zero acceleration should generally be performed to predict the
Extrapolation to zero acceleration should generally be performed to zero-shear viscosity. As the shear stress decreases, the
predict the zero-shear viscosity. signal-to-noise ratio decreases rapidly, and the simulation time must be
As the shear stress decreases, the signal-noise ratio decreases rapidly, extended accordingly to get converged results.
the simulation time must be extended accordingly to get converged result.
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 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 output commands. No parameter of this fix can be used with the start/stop
keywords of the run command. keywords of the run command.
This fix is not invoked during energy minimization. This fix is not invoked during energy minimization.
Restrictions 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 <Build_package>`
page for more info.
Since this fix depends on the :math:`z`-coordinate of atoms, it cannot be used Since this fix depends on the :math:`z`-coordinate of atoms, it cannot be used
in 2d simulations. in 2d simulations.

2
doc/src/fix_ave_spatial.rst
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@ -1,4 +1,4 @@
Fix ave/spatial command fix ave/spatial command
======================= =======================
.. meta:: .. meta::

4
doc/src/fix_ave_spatial_sphere.rst
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@ -1,5 +1,5 @@
Fix ave/spatial command fix ave/spatial/sphere command
======================= ==============================
.. meta:: .. meta::
:http-equiv=Refresh: 5; url=https://docs.lammps.org/Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere :http-equiv=Refresh: 5; url=https://docs.lammps.org/Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere