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This commit is contained in:
Axel Kohlmeyer
2024-07-03 19:10:37 -04:00
parent b6d11b5902
commit 0fb7493658
7 changed files with 24 additions and 12 deletions
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10
doc/src/Howto_rheo.rst
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@ -4,7 +4,7 @@ Reproducing hydrodynamics and elastic objects (RHEO)
The RHEO package is a hybrid implementation of smoothed particle The RHEO package is a hybrid implementation of smoothed particle
hydrodynamics (SPH) for fluid flow, coupled to the :doc:`BPM package <Howto_bpm>` hydrodynamics (SPH) for fluid flow, coupled to the :doc:`BPM package <Howto_bpm>`
to model solid elements. RHEO combines these methods to enable mesh-free modeling to model solid elements. RHEO combines these methods to enable mesh-free modeling
of multiphase material systems. The SPH solver supports many advanced options of multi-phase material systems. The SPH solver supports many advanced options
including reproducing kernels, particle shifting, free surface identification, including reproducing kernels, particle shifting, free surface identification,
and solid surface reconstruction. To model fluid-solid systems, the status of and solid surface reconstruction. To model fluid-solid systems, the status of
particles can dynamically change between a fluid and solid state, e.g. during particles can dynamically change between a fluid and solid state, e.g. during
@ -30,7 +30,7 @@ of reproducing kernels). In conjunction to fix rheo, one must specify an
instance of :doc:`fix rheo/pressure <fix_rheo_pressure>` and instance of :doc:`fix rheo/pressure <fix_rheo_pressure>` and
:doc:`fix rheo/viscosity <fix_rheo_viscosity>` to define a pressure equation :doc:`fix rheo/viscosity <fix_rheo_viscosity>` to define a pressure equation
of state and viscosity model, respectively. Optionally, one can model of state and viscosity model, respectively. Optionally, one can model
a heat equation with :doc:`fix rheo/thermal <fix_rhe0_thermal>`, which also a heat equation with :doc:`fix rheo/thermal <fix_rheo_thermal>`, which also
allows the user to specify equations for a particle's thermal conductivity, allows the user to specify equations for a particle's thermal conductivity,
specific heat, latent heat, and melting temperature. The ordering of these specific heat, latent heat, and melting temperature. The ordering of these
fixes in an an input script matters. Fix rheo must be defined prior to all fixes in an an input script matters. Fix rheo must be defined prior to all
@ -44,7 +44,7 @@ conductivity. Note that the temperature is always derived from the energy.
This implies the *temperature* attribute of :doc:`the set command <set>` does not This implies the *temperature* attribute of :doc:`the set command <set>` does not
affect particles. Instead, one should use the *sph/e* attribute. affect particles. Instead, one should use the *sph/e* attribute.
The status variable uses bitmasking to track various properties of a particle The status variable uses bit-masking to track various properties of a particle
such as its current state of matter (fluid or solid) and its location relative such as its current state of matter (fluid or solid) and its location relative
to a surface. Some of these properties (and others) can be accessed using to a surface. Some of these properties (and others) can be accessed using
:doc:`compute rheo/property/atom <compute_rheo_property_atom>`. The *status* :doc:`compute rheo/property/atom <compute_rheo_property_atom>`. The *status*
@ -88,8 +88,8 @@ as bonds are created/broken.
The other option for elastic objects is an elastic shell that is nominally much The other option for elastic objects is an elastic shell that is nominally much
thinner than a particle diameter, e.g. a oxide skin which gradually forms over time thinner than a particle diameter, e.g. a oxide skin which gradually forms over time
on the surface of a fluid. Currently, this is implemented using on the surface of a fluid. Currently, this is implemented using
:doc:`fix rheo/oxidaton <fix_rheo_oxidation>` and bond style :doc:`fix rheo/oxidation <fix_rheo_oxidation>` and bond style
:doc:`rheo/shell <bond_rheo_shell>`. Essentially, fix rheo/oxidaton creates candidate :doc:`rheo/shell <bond_rheo_shell>`. Essentially, fix rheo/oxidation creates candidate
bonds of a specified type between surface fluid particles within a specified distance. bonds of a specified type between surface fluid particles within a specified distance.
a newly created rheo/shell bond will then start a timer. While the timer is counting a newly created rheo/shell bond will then start a timer. While the timer is counting
down, the bond will delete itself if particles move too far apart or move away from the down, the bond will delete itself if particles move too far apart or move away from the

2
doc/src/atom_modify.rst
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@ -190,7 +190,7 @@ Default
By default, *id* is yes. By default, atomic systems (no bond topology By default, *id* is yes. By default, atomic systems (no bond topology
info) do not use a map. For molecular systems (with bond topology info) do not use a map. For molecular systems (with bond topology
info), the default is to use a map of either *array* or *hash* style info), the default is to use a map of either *array* or *hash* style
depending on the size of the sustem, as explained above for the *map depending on the size of the system, as explained above for the *map
yes* keyword/value option. By default, a *first* group is not yes* keyword/value option. By default, a *first* group is not
defined. By default, sorting is enabled with a frequency of 1000 and defined. By default, sorting is enabled with a frequency of 1000 and
a binsize of 0.0, which means the neighbor cutoff will be used to set a binsize of 0.0, which means the neighbor cutoff will be used to set

4
doc/src/fix_rheo.rst
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@ -90,7 +90,7 @@ In systems with free surfaces, the *surface/detection* keyword can be used
to classify the location of particles as being within the bulk fluid, on a to classify the location of particles as being within the bulk fluid, on a
free surface, or isolated from other particles in a splash or droplet. free surface, or isolated from other particles in a splash or droplet.
Shifting is then disabled in the normal direction away from the free surface Shifting is then disabled in the normal direction away from the free surface
to prevent particles from difusing away. Surface detection can also be used to prevent particles from diffusing away. Surface detection can also be used
to control surface-nucleated effects like oxidation when used in combination to control surface-nucleated effects like oxidation when used in combination
with :doc:`fix rheo/oxidation <fix_rheo_oxidation>`. Surface detection is not with :doc:`fix rheo/oxidation <fix_rheo_oxidation>`. Surface detection is not
performed on solid bodies. performed on solid bodies.
@ -145,7 +145,7 @@ Restrictions
"""""""""""" """"""""""""
This fix must be used with atom style rheo or rheo/thermal. This fix must This fix must be used with atom style rheo or rheo/thermal. This fix must
be used in conjuction with :doc:`fix rheo/pressure <fix_rheo_pressure>`. be used in conjunction with :doc:`fix rheo/pressure <fix_rheo_pressure>`.
and :doc:`fix rheo/viscosity <fix_rheo_viscosity>`. If the *thermal* setting and :doc:`fix rheo/viscosity <fix_rheo_viscosity>`. If the *thermal* setting
is used, there must also be an instance of is used, there must also be an instance of
:doc:`fix rheo/thermal <fix_rheo_thermal>`. The fix group must be set to all. :doc:`fix rheo/thermal <fix_rheo_thermal>`. The fix group must be set to all.

2
doc/src/fix_rheo_pressure.rst
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@ -86,7 +86,7 @@ Restrictions
This fix must be used with an atom style that includes density This fix must be used with an atom style that includes density
such as atom_style rheo or rheo/thermal. This fix must be used in such as atom_style rheo or rheo/thermal. This fix must be used in
conjuction with :doc:`fix rheo <fix_rheo>`. The fix group must be conjunction with :doc:`fix rheo <fix_rheo>`. The fix group must be
set to all. Only one instance of fix rheo/pressure can be defined. set to all. Only one instance of fix rheo/pressure can be defined.
This fix is part of the RHEO package. It is only enabled if This fix is part of the RHEO package. It is only enabled if

4
doc/src/fix_rheo_thermal.rst
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@ -105,8 +105,8 @@ Restrictions
"""""""""""" """"""""""""
This fix must be used with an atom style that includes temperature, This fix must be used with an atom style that includes temperature,
heatflow, and conductivity such as atom_tyle rheo/thermal This fix heatflow, and conductivity such as atom_style rheo/thermal This fix
must be used in conjuction with :doc:`fix rheo <fix_rheo>` with the must be used in conjunction with :doc:`fix rheo <fix_rheo>` with the
*thermal* setting. The fix group must be set to all. Only one *thermal* setting. The fix group must be set to all. Only one
instance of fix rheo/pressure can be defined. instance of fix rheo/pressure can be defined.

2
doc/src/fix_rheo_viscosity.rst
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@ -91,7 +91,7 @@ Restrictions
This fix must be used with an atom style that includes viscosity This fix must be used with an atom style that includes viscosity
such as atom_style rheo or rheo/thermal. This fix must be used in such as atom_style rheo or rheo/thermal. This fix must be used in
conjuction with :doc:`fix rheo <fix_rheo>`. The fix group must be conjunction with :doc:`fix rheo <fix_rheo>`. The fix group must be
set to all. Only one instance of fix rheo/viscosity can be defined. set to all. Only one instance of fix rheo/viscosity can be defined.
This fix is part of the RHEO package. It is only enabled if This fix is part of the RHEO package. It is only enabled if

12
doc/utils/sphinx-config/false_positives.txt
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@ -393,6 +393,7 @@ buf
builtin builtin
Bulacu Bulacu
Bulatov Bulatov
Bulkley
Bureekaew Bureekaew
burlywood burlywood
Bussi Bussi
@ -564,6 +565,7 @@ cond
conda conda
Conda Conda
Condens Condens
conductivities
conf conf
config config
configfile configfile
@ -1440,6 +1442,7 @@ henrich
Henrich Henrich
Hermitian Hermitian
Herrmann Herrmann
Hershchel
Hertizian Hertizian
hertzian hertzian
Hertzsch Hertzsch
@ -1831,6 +1834,7 @@ Kspace
KSpace KSpace
KSpaceStyle KSpaceStyle
Kspring Kspring
kstyle
kT kT
kTequil kTequil
kth kth
@ -2271,6 +2275,7 @@ modelled
modelling modelling
Modelling Modelling
Modine Modine
modularity
moduli moduli
mofff mofff
MOFFF MOFFF
@ -2488,6 +2493,7 @@ Neumann
Nevent Nevent
nevery nevery
Nevery Nevery
Nevins
newfile newfile
Newns Newns
newtype newtype
@ -3067,6 +3073,7 @@ quatw
queryargs queryargs
Queteschiner Queteschiner
quickmin quickmin
quintic
qw qw
qx qx
qy qy
@ -3078,6 +3085,7 @@ radialscreenedspin
radialspin radialspin
radian radian
radians radians
radiative
radj radj
Rafferty Rafferty
rahman rahman
@ -3181,6 +3189,7 @@ rg
Rg Rg
Rhaphson Rhaphson
Rhe Rhe
rheo
rheological rheological
rheology rheology
rhodo rhodo
@ -3268,6 +3277,7 @@ rsort
rsq rsq
rst rst
rstyle rstyle
rsurf
Rubensson Rubensson
Rubia Rubia
Rud Rud
@ -3651,6 +3661,7 @@ Telsa
tempCorrCoeff tempCorrCoeff
templated templated
Templeton Templeton
Tencer
Tequil Tequil
ters ters
tersoff tersoff
@ -3997,6 +4008,7 @@ Vries
Vsevolod Vsevolod
Vsmall Vsmall
Vstream Vstream
vstyle
vtarget vtarget
vtk vtk
VTK VTK