Merge pull request #4148 from jtclemm/small-patches

Small patches for various commands

doc/src/Howto_bpm.rst

@@ -15,7 +15,8 @@ orientation for rotational models. This produces a stress-free initial
 state. Furthermore, bonds are allowed to break under large strains,
 producing fracture. The examples/bpm directory has sample input scripts
 for simulations of the fragmentation of an impacted plate and the
-pouring of extended, elastic bodies.
+pouring of extended, elastic bodies. See :ref:`(Clemmer) <howto-Clemmer>`
+for more general information on the approach and the LAMMPS implementation.
 
 ----------
 
@@ -150,3 +151,9 @@ the following are currently compatible with BPM bond styles:
    interactions, one will need to switch between different *special_bonds*
    settings in the input script. An example is found in
    ``examples/bpm/impact``.
+
+----------
+
+.. _howto-Clemmer:
+
+**(Clemmer)** Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).

doc/src/fix_deform_pressure.rst

@@ -29,10 +29,12 @@ Syntax
            NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
 
        *xy*, *xz*, *yz* args = style value
-         style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure*
+         style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure* or *erate/rescale*
            *pressure* values = target gain
              target = target pressure (pressure units)
              gain = proportional gain constant (1/(time * pressure) or 1/time units)
+           *erate/rescale* value = R
+             R = engineering shear strain rate (1/time units)
            NOTE: All other styles are documented by the :doc:`fix deform <fix_deform>` command
 
        *box* = style value
@@ -159,6 +161,21 @@ details of a simulation and testing different values is
 recommended. One can also apply a maximum limit to the magnitude of
 the applied strain using the :ref:`max/rate <deform_max_rate>` option.
 
+The *erate/rescale* style operates similarly to the *erate* style with
+a specified strain rate in units of 1/time. The difference is that
+the change in the tilt factor will depend on the current length of
+the box perpendicular to the shear direction, L, instead of the
+original length, L0. The tilt factor T as a function of time will
+change as
+
+.. parsed-literal::
+
+   T(t) = T(t-1) + L\*erate\* \Delta t
+
+where T(t-1) is the tilt factor on the previous timestep and :math:`\Delta t`
+is the timestep size. This option may be useful in scenarios where
+L changes in time.
+
 ----------
 
 The *box* parameter provides an additional control over the *x*, *y*,

doc/src/fix_nonaffine_displacement.rst

@@ -8,7 +8,7 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group nonaffine/displacement style args reference/style nstep
+   fix ID group nonaffine/displacement style args reference/style nstep keyword values
 
 * ID, group are documented in :doc:`fix <fix>` command
 * nonaffine/displacement = style name of this fix command
@@ -32,6 +32,13 @@ Syntax
        *update* = update the reference frame every *nstep* timesteps
        *offset* = update the reference frame *nstep* timesteps before calculating the nonaffine displacement
 
+* zero or more keyword/value pairs may be appended
+
+  .. parsed-literal::
+
+       *z/min* values = zmin
+         zmin = minimum coordination number to calculate D2min
+
 Examples
 """"""""
 
@@ -76,6 +83,12 @@ is the identity tensor. This calculation is only performed on timesteps that
 are a multiple of *nevery* (including timestep zero). Data accessed before
 this occurs will simply be zeroed.
 
+For particles with low coordination numbers, calculations of :math:`D^2_\mathrm{min}`
+may not be accurate. An optional minimum coordination number can be defined using
+the *z/min* keyword. If any particle has fewer than the specified number of particles
+in the cutoff distance or in contact, the above calculations will be skipped and the
+corresponding peratom array entries will be zero.
+
 The *integrated* style simply integrates the velocity of particles
 every timestep to calculate a displacement. This style only works if
 used in conjunction with another fix that deforms the box and displaces