diff --git a/doc/src/Howto_rheo.rst b/doc/src/Howto_rheo.rst index 7696fbbae1..3667d88e3a 100644 --- a/doc/src/Howto_rheo.rst +++ b/doc/src/Howto_rheo.rst @@ -15,7 +15,6 @@ details of the system, or develop new capabilities. For instance, the numerics associated with calculating gradients, reproducing kernels, etc. are separated into distinct classes to simplify the development of new integration schemes which can call these calculations. Additional numerical details can be found in -:ref:`(Palermo) ` and :ref:`(Clemmer) `. Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package @@ -107,10 +106,6 @@ criteria for creating/deleting a bond or altering force calculations). ---------- -.. _howto_rheo_palermo: - -**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation. - .. _howto_rheo_clemmer: **(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024). diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 44f569548b..366f86e0a9 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -182,9 +182,9 @@ a simulation box which replicates that unit cell along each of the well as the atoms created by this command with their per-atom information (e.g. coordinates, velocities) are converted (rotated) from general to restricted triclinic form when the two commands are - invoked. The ` doc page also discusses other - LAMMPS commands which can input/output general triclinic - representations of the simulation box and per-atom data. + invoked. The :doc:`Howto_triclinic ` doc page also + discusses other LAMMPS commands which can input/output general + triclinic representations of the simulation box and per-atom data. The *box* style will fill the entire general triclinic box with particles on the lattice, as explained above. diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index 062fa2b360..2c07eb136c 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -13,7 +13,7 @@ Syntax * N = # of atom types to use in this simulation * region-ID = ID of region to use as simulation domain or NULL for general triclinic box -* alo,ahi,blo,bhi,clo,chi = multipliers on a1,a2,a3 vectors defined by :doc"`lattice ` command (only when region-ID = NULL) +* alo,ahi,blo,bhi,clo,chi = multipliers on a1,a2,a3 vectors defined by :doc:`lattice ` command (only when region-ID = NULL) * zero or more keyword/value pairs may be appended * keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom* diff --git a/doc/src/fix_rheo.rst b/doc/src/fix_rheo.rst index c9bf0a7aa0..3c7f8449c7 100644 --- a/doc/src/fix_rheo.rst +++ b/doc/src/fix_rheo.rst @@ -47,10 +47,8 @@ Description .. versionadded:: TBD Perform time integration for RHEO particles, updating positions, velocities, -and densities. For a detailed breakdown of the integration timestep and -numerical details, see :ref:`(Palermo) `. For an -overview of other features available in the RHEO package, see -:doc:`the RHEO howto `. +and densities. For an overview of other features available in the RHEO package, +see :doc:`the RHEO howto `. The type of kernel is specified using *kstyle* and the cutoff is *cut*. Four kernels are currently available. The *quintic* kernel is a standard quintic @@ -73,12 +71,7 @@ and velocity of solid particles are alternatively reconstructed for every fluid-solid interaction to ensure no-slip and pressure-balanced boundaries. This is done by estimating the location of the fluid-solid interface and extrapolating fluid particle properties across the interface to calculate a -temporary apparent density and velocity for a solid particle. The numerical -details are the same as those described in -:ref:`(Palermo) ` except there is an additional -restriction that the reconstructed solid density cannot be less than the -equilibrium density. This prevents fluid particles from sticking to solid -surfaces. +temporary apparent density and velocity for a solid particle. A modified form of Fickian particle shifting can be enabled with the *shift* keyword. This effectively shifts particle positions to generate a @@ -171,10 +164,6 @@ Default ---------- -.. _rheo_palermo: - -**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation. - .. _fix_rheo_hu: **(Hu)** Hu, and Adams J. Comp. Physics, 213, 844-861 (2006). diff --git a/doc/src/fix_rheo_viscosity.rst b/doc/src/fix_rheo_viscosity.rst index 5eca39dcdd..1d78975cde 100644 --- a/doc/src/fix_rheo_viscosity.rst +++ b/doc/src/fix_rheo_viscosity.rst @@ -72,8 +72,6 @@ is assigned. This implies a value of .. math:: \tau_0 = \eta \dot{\gamma}_0 - K \dot{\gamma}_0^N -as further discussed in :ref:`(Palermo) `. - Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" @@ -111,7 +109,3 @@ Default none ---------- - -.. _rheo_palermo2: - -**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, in preparation.