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improve fix indent documentation

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Axel Kohlmeyer
2024-07-06 09:55:22 -04:00
parent fdf9ffee73
commit f34b6dacaf
1 changed files with 21 additions and 18 deletions
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doc/src/fix_indent.rst
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@ -68,10 +68,10 @@ material or as an obstacle in a flow. Alternatively, it can be used as a
constraining wall around a simulation; see the discussion of the
*side* keyword below.
The *gstyle* geometry of the indenter can either be a sphere, a
cylinder, a cone, or a plane.
The *gstyle* keyword selects the geometry of the indenter and it can
either have the value of *sphere*, *cylinder*, *cone*, or *plane*\ .
A spherical indenter exerts a force of magnitude
A spherical indenter (*gstyle* = *sphere*) exerts a force of magnitude
.. math::
@ -82,13 +82,16 @@ distance from the atom to the center of the indenter, and *R* is the
radius of the indenter. The force is repulsive and F(r) = 0 for *r* >
*R*\ .
A cylindrical indenter exerts the same force, except that *r* is the
distance from the atom to the center axis of the cylinder. The
cylinder extends infinitely along its axis.
A cylindrical indenter (*gstyle* = *cylinder*) follows the same formula
for the force as a sphere, except that *r* is defined the distance
from the atom to the center axis of the cylinder. The cylinder extends
infinitely along its axis.
A conical indenter is similar to a cylindrical indenter except that it
has a finite length (between *lo* and *hi*), and that two different
radii (one at each end, *radlo* and *radhi*) can be defined.
.. versionadded:: 17April2024
A conical indenter (*gstyle* = *cone*) is similar to a cylindrical indenter
except that it has a finite length (between *lo* and *hi*), and that two
different radii (one at each end, *radlo* and *radhi*) can be defined.
Spherical, cylindrical, and conical indenters account for periodic
boundaries in two ways. First, the center point of a spherical
@ -101,15 +104,15 @@ or axis accounts for periodic boundaries. Both of these mean that an
indenter can effectively move through and straddle one or more
periodic boundaries.
A planar indenter is really an axis-aligned infinite-extent wall
exerting the same force on atoms in the system, where *R* is the
position of the plane and *r-R* is the distance from the plane. If
the *side* parameter of the plane is specified as *lo* then it will
indent from the lo end of the simulation box, meaning that atoms with
a coordinate less than the plane's current position will be pushed
towards the hi end of the box and atoms with a coordinate higher than
the plane's current position will feel no force. Vice versa if *side*
is specified as *hi*\ .
A planar indenter (*gstyle* = *plane*) behaves like an axis-aligned
infinite-extent wall with the same force expression on atoms in the
system as before, but where *R* is the position of the plane and *r-R*
is the distance of an from the plane. If the *side* parameter of the
plane is specified as *lo* then it will indent from the lo end of the
simulation box, meaning that atoms with a coordinate less than the
plane's current position will be pushed towards the hi end of the box
and atoms with a coordinate higher than the plane's current position
will feel no force. Vice versa if *side* is specified as *hi*\ .
Any of the 4 quantities defining a spherical indenter's geometry can
be specified as an equal-style :doc:`variable <variable>`, namely *x*,