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improve typesetting, record version change, a few more k_B changes

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This commit is contained in:
Axel Kohlmeyer
2022-08-23 00:51:36 -04:00
parent 007f7fbbfb
commit 54c928dbce
2 changed files with 26 additions and 17 deletions
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39
doc/src/fix_ave_chunk.rst
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@ -71,23 +71,26 @@ Examples
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
**NOTE:**
.. versionchanged: 31 May 2016
If you are trying to replace a deprecated fix ave/spatial command
with the newer, more flexible fix ave/chunk and :doc:`compute chunk/atom <compute_chunk_atom>` commands, you simply need to split
the fix ave/spatial arguments across the two new commands. For
example, this command:
.. note::
.. code-block:: LAMMPS
If you are trying to replace a deprecated fix ave/spatial command
with the newer, more flexible fix ave/chunk and :doc:`compute
chunk/atom <compute_chunk_atom>` commands, you simply need to split
the fix ave/spatial arguments across the two new commands. For
example, this command:
fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
.. code-block:: LAMMPS
could be replaced by:
fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
.. code-block:: LAMMPS
could be replaced by:
compute cc1 flow chunk/atom bin/1d y 0.0 1.0
fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile
.. code-block:: LAMMPS
compute cc1 flow chunk/atom bin/1d y 0.0 1.0
fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile
Description
"""""""""""
@ -236,10 +239,16 @@ bins, the volume is the bin volume. Otherwise it is the volume of the
entire simulation box.
The *temp* value means the temperature is computed for each chunk, by
the formula KE = DOF/2 k T, where KE = total kinetic energy of the
chunk of atoms (sum of 1/2 m v\^2), DOF = the total number of degrees
of freedom for all atoms in the chunk, k = Boltzmann constant, and T =
temperature.
the formula
.. math::
\text{KE} = \frac{\text{DOF}}{2} k_B T,
where KE = total kinetic energy of the chunk of atoms (sum of
:math:`\frac{1}{2} m v^2`), DOF = the total number of degrees of freedom
for all atoms in the chunk, :math:`k_B` = Boltzmann constant, and
:math:`T` = temperature.
The DOF is calculated as N\*adof + cdof, where N = number of atoms in
the chunk, adof = degrees of freedom per atom, and cdof = degrees of

4
doc/src/fix_eos_table_rx.rst
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@ -45,13 +45,13 @@ computed according to the following relation:
.. math::
U_{i} = \displaystyle\sum_{j=1}^{m} c_{i,j}(u_{j} + \Delta H_{f,j}) + \frac{3k_{b}T}{2} + Nk_{b}T \\
U_{i} = \displaystyle\sum_{j=1}^{m} c_{i,j}(u_{j} + \Delta H_{f,j}) + \frac{3k_{B}T}{2} + Nk_{B}T \\
where *m* is the number of species, :math:`c_{i,j}` is the
concentration of species *j* in particle *i*, :math:`u_j` is the
internal energy of species j, :math:`\Delta H_{f,j} is the heat of
formation of species *j*, N is the number of molecules represented
by the coarse-grained particle, :math:`k_b` is the Boltzmann constant,
by the coarse-grained particle, :math:`k_B` is the Boltzmann constant,
and *T* is the temperature of the system. Additionally, it is
possible to modify the concentration-dependent particle internal
energy relation by adding an energy correction, temperature-dependent