diff --git a/doc/src/Howto_rheo.rst b/doc/src/Howto_rheo.rst index 4c0f069d92..7c62d09ab1 100644 --- a/doc/src/Howto_rheo.rst +++ b/doc/src/Howto_rheo.rst @@ -4,7 +4,7 @@ Reproducing hydrodynamics and elastic objects (RHEO) The RHEO package is a hybrid implementation of smoothed particle hydrodynamics (SPH) for fluid flow, coupled to the :doc:`BPM package ` 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, 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 @@ -30,7 +30,7 @@ of reproducing kernels). In conjunction to fix rheo, one must specify an instance of :doc:`fix rheo/pressure ` and :doc:`fix rheo/viscosity ` to define a pressure equation of state and viscosity model, respectively. Optionally, one can model -a heat equation with :doc:`fix rheo/thermal `, which also +a heat equation with :doc:`fix rheo/thermal `, which also allows the user to specify equations for a particle's thermal conductivity, 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 @@ -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 ` does not 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 to a surface. Some of these properties (and others) can be accessed using :doc:`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 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 -:doc:`fix rheo/oxidaton ` and bond style -:doc:`rheo/shell `. Essentially, fix rheo/oxidaton creates candidate +:doc:`fix rheo/oxidation ` and bond style +:doc:`rheo/shell `. Essentially, fix rheo/oxidation creates candidate 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 down, the bond will delete itself if particles move too far apart or move away from the diff --git a/doc/src/atom_modify.rst b/doc/src/atom_modify.rst index 0d750f1755..9091626feb 100644 --- a/doc/src/atom_modify.rst +++ b/doc/src/atom_modify.rst @@ -190,7 +190,7 @@ Default 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), 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 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 diff --git a/doc/src/fix_rheo.rst b/doc/src/fix_rheo.rst index d69b52d751..c9bf0a7aa0 100644 --- a/doc/src/fix_rheo.rst +++ b/doc/src/fix_rheo.rst @@ -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 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 -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 with :doc:`fix rheo/oxidation `. Surface detection is not performed on solid bodies. @@ -145,7 +145,7 @@ Restrictions """""""""""" This fix must be used with atom style rheo or rheo/thermal. This fix must -be used in conjuction with :doc:`fix rheo/pressure `. +be used in conjunction with :doc:`fix rheo/pressure `. and :doc:`fix rheo/viscosity `. If the *thermal* setting is used, there must also be an instance of :doc:`fix rheo/thermal `. The fix group must be set to all. diff --git a/doc/src/fix_rheo_pressure.rst b/doc/src/fix_rheo_pressure.rst index e01aebf90f..40d623ae07 100644 --- a/doc/src/fix_rheo_pressure.rst +++ b/doc/src/fix_rheo_pressure.rst @@ -86,7 +86,7 @@ Restrictions 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 -conjuction with :doc:`fix rheo `. The fix group must be +conjunction with :doc:`fix rheo `. The fix group must be 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 diff --git a/doc/src/fix_rheo_thermal.rst b/doc/src/fix_rheo_thermal.rst index e116325091..cf245cbdca 100644 --- a/doc/src/fix_rheo_thermal.rst +++ b/doc/src/fix_rheo_thermal.rst @@ -105,8 +105,8 @@ Restrictions """""""""""" This fix must be used with an atom style that includes temperature, -heatflow, and conductivity such as atom_tyle rheo/thermal This fix -must be used in conjuction with :doc:`fix rheo ` with the +heatflow, and conductivity such as atom_style rheo/thermal This fix +must be used in conjunction with :doc:`fix rheo ` with the *thermal* setting. The fix group must be set to all. Only one instance of fix rheo/pressure can be defined. diff --git a/doc/src/fix_rheo_viscosity.rst b/doc/src/fix_rheo_viscosity.rst index 912de584c2..5eca39dcdd 100644 --- a/doc/src/fix_rheo_viscosity.rst +++ b/doc/src/fix_rheo_viscosity.rst @@ -91,7 +91,7 @@ Restrictions 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 -conjuction with :doc:`fix rheo `. The fix group must be +conjunction with :doc:`fix rheo `. The fix group must be 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 diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index c300cf608d..babe66d27d 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -393,6 +393,7 @@ buf builtin Bulacu Bulatov +Bulkley Bureekaew burlywood Bussi @@ -564,6 +565,7 @@ cond conda Conda Condens +conductivities conf config configfile @@ -1440,6 +1442,7 @@ henrich Henrich Hermitian Herrmann +Hershchel Hertizian hertzian Hertzsch @@ -1831,6 +1834,7 @@ Kspace KSpace KSpaceStyle Kspring +kstyle kT kTequil kth @@ -2271,6 +2275,7 @@ modelled modelling Modelling Modine +modularity moduli mofff MOFFF @@ -2488,6 +2493,7 @@ Neumann Nevent nevery Nevery +Nevins newfile Newns newtype @@ -3067,6 +3073,7 @@ quatw queryargs Queteschiner quickmin +quintic qw qx qy @@ -3078,6 +3085,7 @@ radialscreenedspin radialspin radian radians +radiative radj Rafferty rahman @@ -3181,6 +3189,7 @@ rg Rg Rhaphson Rhe +rheo rheological rheology rhodo @@ -3268,6 +3277,7 @@ rsort rsq rst rstyle +rsurf Rubensson Rubia Rud @@ -3651,6 +3661,7 @@ Telsa tempCorrCoeff templated Templeton +Tencer Tequil ters tersoff @@ -3997,6 +4008,7 @@ Vries Vsevolod Vsmall Vstream +vstyle vtarget vtk VTK