mostly doc page edits

doc/src/region.rst

@@ -11,7 +11,7 @@ Syntax
    region ID style args keyword arg ...
 
 * ID = user-assigned name for the region
-* style = *delete* or *block* or *cone* or *cylinder* or *plane* or *prism* or *sphere* or *union* or *intersect*
+* style = *delete* or *block* or *cone* or *cylinder* or *ellipsoid* or *plane* or *prism* or *sphere* or *union* or *intersect*
 
   .. parsed-literal::
 
@@ -64,7 +64,7 @@ Syntax
          *lattice* = the geometry is defined in lattice units
          *box* = the geometry is defined in simulation box units
        *move* args = v_x v_y v_z
-         v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time
+         v_x,v_y,v_z = equal-style variables for x,y,z displacement of region over time (distance units)
        *rotate* args = v_theta Px Py Pz Rx Ry Rz
          v_theta = equal-style variable for rotaton of region over time (in radians)
          Px,Py,Pz = origin for axis of rotation (distance units)
@@ -162,9 +162,11 @@ Thus the third example above specifies a cylinder with its axis in the
 y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
 extending in the y-direction from -5.0 to the upper box boundary.
 
-For style *ellipsoid*, an axis-alligned ellipsoid is defined. The ellipsoid has
-its center at (x,y,z) and is defined by 3 axis-aligned vectors given by
-A = (a,0,0); B = (0,b,0); C = (0,0,c).
+For style *ellipsoid*, an axis-aligned ellipsoid is defined. The
+ellipsoid has its center at (x,y,z) and is defined by 3 axis-aligned
+vectors given by A = (a,0,0); B = (0,b,0); C = (0,0,c).  Note that
+although the ellipsoid is specified as axis-aligned it can be rotated
+via the optional *rotate* keyword.
 
 For style *plane*, a plane is defined which contain the point
 (px,py,pz) and has a normal vector (nx,ny,nz).  The normal vector does
@@ -192,16 +194,21 @@ since if the maximum tilt factor is 5 (as in this example), then
 configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
 geometrically equivalent.
 
-The *radius* value for style *sphere* and *cylinder* as well as
-the parameters a, b, c for style *ellipsoid* can be specified
-as an equal-style :doc:`variable <variable>`.  If the value is a
-variable, it should be specified as v_name, where name is the variable
-name.  In this case, the variable will be evaluated each timestep, and
-its value used to determine the radius of the region. For style *sphere*
-and *ellipsoid* also the x-, y-, and z- coordinate of the center of the sphere/ellipsoid
-and for style *cylinder* the two center positions c1 and c2 for the location of
-the cylinder axes can be a variable with the same kind of effect and
-requirements than for the radius.
+For style *sphere*, a sphere is defined with its center at (x,y,z)
+and with radius as its radius.
+
+The *radius* value for styles *sphere* and *cylinder*, and the
+parameters a,b,c for style *ellipsoid*, can each be specified as an
+equal-style :doc:`variable <variable>`.  Likewise, for style *sphere*
+and *ellipsoid* the x-, y-, and z- coordinates of the center of the
+sphere/ellipsoid can be specified as an equal-style variable.  And for
+style *cylinder* the two center positions c1 and c2 for the location
+of the cylinder axes can be specified as a equal-style variable.
+
+If the value is a variable, it should be specified as v_name, where
+name is the variable name.  In this case, the variable will be
+evaluated each timestep, and its value used to determine the radius of
+the region.
 
 Equal-style variables can specify formulas with various mathematical
 functions, and include :doc:`thermo_style <thermo_style>` command
@@ -259,6 +266,9 @@ define the lattice spacings which are used as follows:
   to lo and hi.  The spacings in the two radial dimensions are applied
   to c1 and c2.  The cylinder radius is scaled by the lattice
   spacing in the dimension corresponding to c1.
+* For style *ellipsoid*, the lattice spacing in dimensions x,y,z are
+  applied to the ellipsoid center x,y,z.  The spacing in dimensions
+  x,y,z are applied to the ellipsoid radii a,b,c respectively.
 * For style *plane*, the lattice spacing in dimension x is applied to
   px and nx, similarly the spacings in dimensions y,z are applied to
   py/ny and pz/nz.

src/region_ellipsoid.cpp

@@ -460,6 +460,7 @@ void RegEllipsoid::variable_check()
   }
 }
 
+// ------------------------------------------------------------------
 // David Eberly, Geometric Tools, Redmond WA 98052
 // Copyright (c) 1998-2021
 // Based on https://www.geometrictools.com/Documentation/DistancePointEllipseEllipsoid.pdf
@@ -467,10 +468,11 @@ void RegEllipsoid::variable_check()
 // https://www.boost.org/LICENSE_1_0.txt
 // https://www.geometrictools.com/License/Boost/LICENSE_1_0.txt
 // Version: 4.0.2021.08.01
+// ------------------------------------------------------------------
 
 /* ----------------------------------------------------------------------
- *    functions for the 2D case
- *    ------------------------------------------------------------------------- */
+   functions for the 2D case
+------------------------------------------------------------------------- */
 
 double RegEllipsoid::GetRoot2D(double r0, double z0, double z1, double g)
 {
@@ -543,8 +545,8 @@ double RegEllipsoid::DistancePointEllipse(double e0, double e1, double y0, doubl
 }
 
 /* ----------------------------------------------------------------------
- *    functions for the 3D case
- * ------------------------------------------------------------------------- */
+   functions for the 3D case
+------------------------------------------------------------------------- */
 
 double RegEllipsoid::GetRoot3D(double r0, double r1, double z0, double z1, double z2, double g)
 {
@@ -647,4 +649,3 @@ double RegEllipsoid::DistancePointEllipsoid(double e0, double e1, double e2, dou
   }
   return distance;
 }
-