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add support for a region keyword to fix edpd/source and fix tdpd/source

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This commit is contained in:
Axel Kohlmeyer
2023-04-21 17:58:28 -04:00
parent e6e7121445
commit 7c723b4852
31 changed files with 1869 additions and 726 deletions
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46
doc/src/fix_dpd_source.rst
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@ -18,18 +18,21 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* edpd/source or tdpd/source = style name of this fix command
* index (only specified for tdpd/source) = index of chemical species (1 to Nspecies)
* keyword = *sphere* or *cuboid*
* keyword = *sphere* or *cuboid* or *region*
.. parsed-literal::
*sphere* values = cx,cy,cz,radius,source
*sphere* args = cx cy cz radius source
cx,cy,cz = x,y,z center of spherical domain (distance units)
radius = radius of a spherical domain (distance units)
source = heat source or concentration source (flux units, see below)
*cuboid* values = cx,cy,cz,dLx,dLy,dLz,source
cx,cy,cz = x,y,z lower left corner of a cuboid domain (distance units)
*cuboid* values = cx cy cz dLx dLy dLz source
cx,cy,cz = x,y,z center of a cuboid domain (distance units)
dLx,dLy,dLz = x,y,z side length of a cuboid domain (distance units)
source = heat source or concentration source (flux units, see below)
*region* values = region-ID source
region = ID of region for heat or concentration source
source = heat source or concentration source (flux units, see below)
Examples
""""""""
@ -40,6 +43,7 @@ Examples
fix 1 all edpd/source cuboid 0.0 0.0 0.0 20.0 10.0 10.0 -0.01
fix 1 all tdpd/source 1 sphere 5.0 0.0 0.0 5.0 0.01
fix 1 all tdpd/source 2 cuboid 0.0 0.0 0.0 20.0 10.0 10.0 0.01
fix 1 all tdpd/source 1 region lower -0.01
Description
"""""""""""
@ -57,37 +61,45 @@ heat conduction with a source term (see Fig.12 in :ref:`(Li2014) <Li2014b>`)
or diffusion with a source term (see Fig.1 in :ref:`(Li2015) <Li2015b>`), as
an analog of a periodic Poiseuille flow problem.
If the *sphere* keyword is used, the *cx,cy,cz,radius* defines a
spherical domain to apply the source flux to.
If the *sphere* keyword is used, the *cx, cy, cz, radius* values define
a spherical domain to apply the source flux to.
If the *cuboid* keyword is used, the *cx,cy,cz,dLx,dLy,dLz* defines a
cuboid domain to apply the source flux to.
If the *cuboid* keyword is used, the *cx, cy, cz, dLx, dLy, dLz* define
a cuboid domain to apply the source flux to.
If the *region* keyword is used, the *region-ID* selects which
:doc:`region <region>` to apply the source flux to.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
No information of these fixes is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to these fixes. No global or per-atom quantities are stored by
these fixes for access by various :doc:`output commands <Howto_output>`.
No parameter of these fixes can be used with the *start/stop* keywords
of the :doc:`run <run>` command. These fixes are not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the DPD-MESO package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
These fixes are part of the DPD-MESO package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Fix *edpd/source* must be used with the :doc:`pair_style edpd <pair_mesodpd>` command. Fix *tdpd/source* must be used with the
Fix *edpd/source* must be used with the :doc:`pair_style edpd
<pair_mesodpd>` command. Fix *tdpd/source* must be used with the
:doc:`pair_style tdpd <pair_mesodpd>` command.
Related commands
""""""""""""""""
:doc:`pair_style edpd <pair_mesodpd>`, :doc:`pair_style tdpd <pair_mesodpd>`,
:doc:`compute edpd/temp/atom <compute_edpd_temp_atom>`, :doc:`compute tdpd/cc/atom <compute_tdpd_cc_atom>`
:doc:`compute edpd/temp/atom <compute_edpd_temp_atom>`,
:doc:`compute tdpd/cc/atom <compute_tdpd_cc_atom>`
Default
"""""""