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apply spelling fixes and update formatting a little

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This commit is contained in:
Axel Kohlmeyer
2021-08-31 16:17:03 -04:00
parent ae2f0ef18d
commit c567f33cc1
3 changed files with 15 additions and 14 deletions
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2
doc/src/Howto_structured_data.rst
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@ -115,7 +115,7 @@ data files and obtain a list of dictionaries.
Line Delimited JSON (LD-JSON)
-----------------------------
The JSON format itself is very strict when it comes to delimiters. For continous
The JSON format itself is very strict when it comes to delimiters. For continuous
output/streaming data it is beneficial use the *line delimited JSON* format.
Each line represents one JSON object.

26
doc/src/fix_ttm.rst
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@ -85,20 +85,20 @@ Matter papers: :ref:`(Duffy) <Duffy>` and :ref:`(Rutherford)
a primary knock-on atom (PKA) was initialized with a high velocity to
simulate a radiation event.
The description in this sub-section applies to all 3 of the fixes: fix
ttm, fix ttm/grid, and fix ttm/mod.
The description in this sub-section applies to all 3 fix styles:
*ttm*, *ttm/grid*, and *ttm/mod*.
Fix ttm/grid distributes the regular grid across processors consistent
with the subdomains of atoms owned by each processor, but is otherwise
identical to fix ttm. Note that fix ttm stores a copy of the grid on
each processor, which is fine when the overall grid is reasonably
small. For very large grids you should use fix ttt/grid instead.
Fix *ttm/grid* distributes the regular grid across processors consistent
with the sub-domains of atoms owned by each processor, but is otherwise
identical to fix ttm. Note that fix *ttm* stores a copy of the grid on
each processor, which is acceptable when the overall grid is reasonably
small. For larger grids you should use fix *ttm/grid* instead.
Fix ttm/mod adds options to account for external heat sources (e.g. at
Fix *ttm/mod* adds options to account for external heat sources (e.g. at
a surface) and for specifying parameters that allow the electronic
heat capacity to depend strongly on electronic temperature. It is
more expensive computationally than fix ttm because it treats the
thermal diffusion equation as non-linear. More details on fix ttm/mod
more expensive computationally than fix *ttm* because it treats the
thermal diffusion equation as non-linear. More details on fix *ttm/mod*
are given below.
Heat transfer between the electronic and atomic subsystems is carried
@ -169,11 +169,11 @@ ttm/mod.
periodic boundary conditions in all dimensions. They also require
that the size and shape of the simulation box do not vary
dynamically, e.g. due to use of the :doc:`fix npt <fix_nh>` command.
Likewise, the size/shape of processor subdomains cannot vary due to
Likewise, the size/shape of processor sub-domains cannot vary due to
dynamic load-balancing via use of the :doc:`fix balance
<fix_balance>` command. It is possible however to load balance
before the simulation starts using the :doc:`balance <balance>`
command, so that each processor has a different size subdomain.
command, so that each processor has a different size sub-domain.
Periodic boundary conditions are also used in the heat equation solve
for the electronic subsystem. This varies from the approach of
@ -238,7 +238,7 @@ by this fix.
**Additional details for fix ttm/mod**
Fix ttm/mod uses the heat diffusion equation with possible external
Fix *ttm/mod* uses the heat diffusion equation with possible external
heat sources (e.g. laser heating in ablation simulations):
.. math::

1
doc/utils/sphinx-config/false_positives.txt
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@ -2281,6 +2281,7 @@ normals
Noskov
noslip
noticable
Nout
noutcol
Noutput
noutrow