Re-expose Voxelshape to user

doc/templates/api-template.html

@@ -42,7 +42,7 @@ <h3>Basics</h3>
     <li class="pure-menu-item"><a href="#" class="pure-menu-link api-section-link" onclick="openSection(event, 'mesh')">Mesh size and geometry</a></li>
     <li class="pure-menu-item"><a href="#" class="pure-menu-link api-section-link" onclick="openSection(event, 'shapes')">Shapes</a></li>
     <li class="pure-menu-item"><a href="#" class="pure-menu-link api-section-link" onclick="openSection(event, 'regions')">Material regions</a></li>
-    <li class="pure-menu-item"><a href="#" class="pure-menu-link api-section-link" onclick="openSection(event, 'initial')">Initial Magnetization</a></li>
+    <li class="pure-menu-item"><a href="#" class="pure-menu-link api-section-link" onclick="openSection(event, 'initial')">Initial magnetization</a></li>
     <li class="pure-menu-item"><a href="#" class="pure-menu-link api-section-link" onclick="openSection(event, 'parameters')">Material parameters</a></li>
     <li class="pure-menu-item"><a href="#" class="pure-menu-link api-section-link" onclick="openSection(event, 'excitation')">Excitation</a></li>
     <li class="pure-menu-item"><a href="#" class="pure-menu-link api-section-link" onclick="openSection(event, 'outputquantities')">Output quantities</a></li>

doc/templates/examples-template.html

@@ -222,7 +222,7 @@ <h2 id="ex_SP4">Getting started with Standard Problem #4</h2>
 
 Note: these are 3D geometries seen from above. The displayed cell filling is averaged along the thickness (notable in ellipse and layers example). Black means empty space, white is filled.
 
-<hr/><h2 id="ex_initmag">Initial Magnetization</h2>
+<hr/><h2 id="ex_initmag">Initial magnetization</h2>
 Some initial magnetization functions are provided, as well as transformations similar to those on Shapes. See the Config <a href="http://mumax.github.io/api.html">API</a>.
 
 {{.Example `
@@ -280,7 +280,7 @@ <h2 id="ex_SP4">Getting started with Standard Problem #4</h2>
 The magnetization can also be set in separate regions, see below.
 
 
-<hr/><h2 id="ex_cheese">Interlude: Rotating Cheese</h2>
+<hr/><h2 id="ex_cheese">Interlude: rotating cheese</h2>
 
 In this example we define a geometry that looks like a slice of cheese and have it rotate in time.
 
@@ -317,7 +317,7 @@ <h2 id="ex_SP4">Getting started with Standard Problem #4</h2>
 {{.Output}}
 
 
-<hr/><h2 id="ex_regions">Regions: Space-dependent Parameters</h2>
+<hr/><h2 id="ex_regions">Regions: space-dependent parameters</h2>
 
 <p>Space-dependent parameters are defined using material <i>regions</i>. Regions are numbered 0-255 and represent different materials. Each cell can belong to only one region. At the start of a simulation all cells have region number 0.</p>
 
@@ -429,7 +429,7 @@ <h2 id="ex_SP4">Getting started with Standard Problem #4</h2>
 {{.Output}}
 
 
-<hr/><h2 id="ex_PMA">PMA Racetrack</h2>
+<hr/><h2 id="ex_PMA">PMA racetrack</h2>
 In this example we drive a domain wall in PMA material by spin-transfer torque.  We set up a post-step function that makes the simulation box "follow" the domain wall. Like this, only a small number of cells is needed to simulate an infinitely long magnetic wire.
 
 {{.Example `
@@ -463,7 +463,7 @@ <h2 id="ex_SP4">Getting started with Standard Problem #4</h2>
 Since we center on the domain wall we can not see that it is actually moving, but the domain wall breakdown is visible.
 
 
-<hr/><h2 id="ex_Py">Py Racetrack</h2>
+<hr/><h2 id="ex_Py">Py racetrack</h2>
 
 In this example we drive a vortex wall in Permalloy by spin-transfer torque. The simulation box "follows" the domain wall. By removing surface charges at the left and right ends, we mimic an infintely long wire.
 

engine/shape.go

@@ -30,6 +30,7 @@ func init() {
 	DeclFunc("Universe", Universe, "Entire space")
 	DeclFunc("Cell", Cell, "Single cell with given integer index (i, j, k)")
 	DeclFunc("ImageShape", ImageShape, "Use black/white image as shape")
+	DeclFunc("VoxelShape", VoxelShape, "Use slice (ScalarMask containing 0s and 1s) of rectangular cells (with size defined by last 3 arguments) as a 3D object")
 	DeclFunc("GrainRoughness", GrainRoughness, "Grainy surface with different heights per grain "+
 		"with a typical grain size (first argument), minimal height (second argument), and maximal "+
 		"height (third argument). The last argument is a seed for the random number generator.")

test/voxelshape.mx3

@@ -0,0 +1,42 @@
+Nx := 64
+Ny := 64
+Nz := 32
+cs := 5e-9
+
+SetGridSize(Nx, Ny, Nz)
+SetCellSize(cs, cs, cs)
+
+d := 100e-9
+mask := NewScalarMask(Nx, Ny, Nz)
+for i := 0; i < Nx; i++ {
+	for j := 0; j < Ny; j++ {
+		for k := 0; k < Nz; k++ {
+			r := index2coord(i, j, k)
+			x2 := pow(r.X(), 2)
+			y2 := pow(r.Y(), 2)
+			z2 := pow(r.Z(), 2)
+			if pow((x2+y2+z2), 0.5) < d/2 {
+				mask.Set(0, i, j, k, 1)
+			}
+		}
+	}
+}
+
+geomfrommask := VoxelShape(mask, 5e-9, 5e-9, 5e-9)
+SetGeom(geomfrommask)
+
+m.setInShape(geomfrommask, Uniform(1, 0, 0)) // Setup for checks: set m in VoxelShape
+
+// Sphere shape should equal the created VoxelShape 
+SetGeom(Ellipsoid(d, d, d))
+ExpectV("Same shape m_avg", m.Average(), Vector(1, 0, 0), 0)
+
+// Bigger than VoxelShape: random magnetization gets included
+SetGeom(Ellipsoid(d, d, 3*d/2))
+ExpectV("Too large m_avg", m.Average(), Vector(0.6658, -0.00345, 0.00593), 1e-5)
+print(m.Average())
+
+// Change cell size to see if voxels scale along
+SetCellSize(cs/2, cs/2, cs)
+SetGeom(geomfrommask)
+ExpectV("New cellsize m_avg", m.Average(), Vector(0.25808, -0.00174, 0.00508), 1e-5)