Last batch of edits

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) <howto_rheo_palermo>` and
 :ref:`(Clemmer) <howto_rheo_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).

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 <Howto_triclinic>` doc page also discusses other
+   invoked.  The :doc:`Howto_triclinic <Howto_triclinic>` doc page also
-   LAMMPS commands which can input/output general triclinic
+   discusses other LAMMPS commands which can input/output general
-   representations of the simulation box and per-atom data.
+   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.

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 <lattice>` command (only when region-ID = NULL)
+* alo,ahi,blo,bhi,clo,chi = multipliers on a1,a2,a3 vectors defined by :doc:`lattice <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*
 

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
+and densities. For an overview of other features available in the RHEO package,
-numerical details, see :ref:`(Palermo) <rheo_palermo>`. For an
+see :doc:`the RHEO howto <Howto_rheo>`.
-overview of other features available in the RHEO package, see
-:doc:`the RHEO howto <Howto_rheo>`.
 
 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
+temporary apparent density and velocity for a solid particle.
-details are the same as those described in
-:ref:`(Palermo) <howto_rheo_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.
 
 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).

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) <rheo_palermo2>`.
-
 
 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.