Updates for 0.5.3

manual/src/Reference/complex.tex

@@ -0,0 +1,50 @@
+\hypertarget{complex}{%
+\section{Complex}\label{complex}}
+
+Morpho provides complex numbers. The keyword \texttt{im} is used to
+denote the imaginary part of a complex number:
+
+\begin{lstlisting}
+var a=1+5im 
+print a*a
+\end{lstlisting}
+
+Print values on the unit circle in the complex plane:
+
+\begin{lstlisting}
+import constants 
+for (phi in 0..Pi:Pi/5) print exp(im*phi)
+\end{lstlisting}
+
+Get the real and imaginary parts of a complex number:
+
+\begin{lstlisting}
+print real(a) 
+print imag(a) 
+\end{lstlisting}
+
+or alternatively:
+
+\begin{lstlisting}
+print a.real()
+print a.imag() 
+\end{lstlisting}
+
+\hypertarget{angle}{%
+\section{Angle}\label{angle}}
+
+Returns the angle \texttt{phi} associated with the polar representation
+of a complex number \texttt{r*exp(im*phi)}:
+
+\begin{lstlisting}
+print z.angle() 
+\end{lstlisting}
+
+\hypertarget{conj}{%
+\section{Conj}\label{conj}}
+
+Returns the complex conjugate of a number:
+
+\begin{lstlisting}
+print z.conj() 
+\end{lstlisting}

manual/src/Reference/functionals.tex

@@ -166,6 +166,26 @@ \section{GaussCurvature}\label{gausscurvature}}
 The \texttt{GaussCurvature} computes the integrated gaussian curvature
 over a surface.
 
+Note that for surfaces with a boundary, the integrand is correct only
+for the interior points. To compute the geodesic curvature of the
+boundary in that case, you can set the optional flag \texttt{geodesic}
+to \texttt{true} and compute the total on the boundary selection. Here
+is an example for a 2D disk mesh.
+
+\begin{lstlisting}
+var mesh = Mesh("disk.mesh")
+mesh.addgrade(1)
+
+var whole = Selection(mesh, fn(x,y,z) true)
+var bnd = Selection(mesh, boundary=true)
+var interior = whole.difference(bnd)
+
+var gauss = GaussCurvature()
+print gauss.total(mesh, selection=interior) // expect: 0
+gauss.geodesic = true
+print gauss.total(mesh, selection=bnd) // expect: 2*Pi
+\end{lstlisting}
+
 \hypertarget{gradsq}{%
 \section{GradSq}\label{gradsq}}
 
@@ -274,27 +294,35 @@ \section{AreaIntegral}\label{areaintegral}}
 integrand function in the order you supply them to
 \texttt{AreaIntegrand}.
 
-\hypertarget{floryhuggins}{%
-\section{FloryHuggins}\label{floryhuggins}}
+\hypertarget{hydrogel}{%
+\section{Hydrogel}\label{hydrogel}}
 
-The \texttt{FloryHuggins} functional computes the Flory-Huggins mixing
-energy over an element:
+The \texttt{Hydrogel} functional computes the Flory-Rehner energy over
+an element:
 
 \begin{lstlisting}
-a*phi*log(phi) + b*(1-phi)+log(1-phi) + c*phi*(1-phi)
+(a*phi*log(phi) + b*(1-phi)+log(1-phi) + c*phi*(1-phi))*V + 
+d*(log(phiref/phi)/3 - (phiref/phi)^(2/3) + 1)*V0
 \end{lstlisting}
 
-where a, b and c are parameters you can supply. The value of phi is
-calculated from a reference mesh that you provide on initializing the
-Functional:
+The first three terms come from the Flory-Huggins mixing energy, whereas
+the fourth term proportional to d comes from the Flory-Rehner elastic
+energy.
+
+The value of phi is calculated from a reference mesh that you provide on
+initializing the Functional:
 
 \begin{lstlisting}
-var lfh = FloryHuggins(mref)
+var lfh = Hydrogel(mref)
 \end{lstlisting}
 
-Manually set the coefficients and grade to operate on:
+Here, a, b, c, d and phiref are parameters you can supply (they are
+\texttt{nil} by default), V is the current volume and V0 is the
+reference volume of a given element. You also need to supply the initial
+value of phi, labeled as phi0, which is assumed to be the same for all
+the elements. Manually set the coefficients and grade to operate on:
 
 \begin{lstlisting}
-lfh.a = 1; lfh.b = 1; lfh.c = 1;
-lfh.grade = 2
+lfh.a = 1; lfh.b = 1; lfh.c = 1; lfh.d = 1;
+lfh.grade = 2, lfh.phi0 = 0.5, lfh.phiref = 0.1
 \end{lstlisting}

manual/src/Reference/meshslice.tex

@@ -0,0 +1,65 @@
+\hypertarget{meshslice}{%
+\section{Meshslice}\label{meshslice}}
+
+The \texttt{meshslice} module is used to slice a \texttt{Mesh} object
+along a given plane, yielding a new \texttt{Mesh} object of lower
+dimensionality. You can also use \texttt{meshslice} to project
+\texttt{Field} objects onto the new mesh.
+
+To use the module, begin by importing it:
+
+\begin{lstlisting}
+import meshslice 
+\end{lstlisting}
+
+Then construct a \texttt{MeshSlicer} object, passing the mesh you want
+to slice in the constructor:
+
+\begin{lstlisting}
+var slice = MeshSlicer(mesh)
+\end{lstlisting}
+
+You then perform a slice by calling the \texttt{slice} method, passing
+the plane you want to slice through. This method returns a new
+\texttt{Mesh} object comprising the slice. A plane is defined by a point
+that lies on the plane \texttt{pt} and a direction normal to the plan
+\texttt{dirn}:
+
+\begin{lstlisting}
+var slc = slice.slice(pt, dirn)
+\end{lstlisting}
+
+Having performed a slice, you can then project any associated
+\texttt{Field} objects onto the sliced mesh by calling the
+\texttt{slicefield} method:
+
+\begin{lstlisting}
+var phi = Field(mesh, fn (x,y,z) x+y+z)
+var sphi = slice.slicefield(phi)
+\end{lstlisting}
+
+The new field returned by \texttt{slicefield} lives on the sliced mesh.
+You can slice any number of fields.
+
+You can perform multiple slices with the same \texttt{MeshSlicer} simply
+by calling \texttt{slice} again with a different plane.
+
+\hypertarget{slcempty}{%
+\section{SlcEmpty}\label{slcempty}}
+
+This error occurs if you try to use \texttt{slicefield} on a
+\texttt{MeshSlicer} without having performed a slice. For example:
+
+\begin{lstlisting}
+var slice = MeshSlicer(mesh)
+slice.slicefield(phi) // Throws SlcEmpty
+slice.slice([0,0,0],[1,0,0]) 
+\end{lstlisting}
+
+To fix, call \texttt{slice} before \texttt{slicefield}:
+
+\begin{lstlisting}
+var slice = MeshSlicer(mesh)
+slice.slice([0,0,0],[1,0,0]) 
+slice.slicefield(phi) // Now slices correctly 
+\end{lstlisting}

manual/src/Reference/meshtools.tex

@@ -121,8 +121,8 @@ \section{MeshBuilder}\label{meshbuilder}}
 \end{lstlisting}
 
 You can then add vertices, edges, etc. one by one using
-\texttt{addvertex}, \texttt{addedge} and \texttt{addtriangle}. Each of
-these returns an element id:
+\texttt{addvertex}, \texttt{addedge}, \texttt{addface} and
+\texttt{addelement}. Each of these returns an element id:
 
 \begin{lstlisting}
 var id1=build.addvertex(Matrix([0,0,0]))
@@ -137,6 +137,47 @@ \section{MeshBuilder}\label{meshbuilder}}
 var m = build.build()
 \end{lstlisting}
 
+You can specify the dimension of the \texttt{Mesh} explicitly when
+initializing the \texttt{MeshBuilder}:
+
+\begin{lstlisting}
+var mb = MeshBuilder(dimension=2)
+\end{lstlisting}
+
+or implicitly when adding the first vertex:
+
+\begin{lstlisting}
+var mb = MeshBuilder() 
+mb.addvertex([0,1]) // A 2D mesh
+\end{lstlisting}
+
+\hypertarget{mshblddimincnstnt}{%
+\section{MshBldDimIncnstnt}\label{mshblddimincnstnt}}
+
+This error is produced if you try to add a vertex that is inconsistent
+with the mesh dimension, e.g.~
+
+\begin{lstlisting}
+var mb = MeshBuilder(dimension=2) 
+mb.addvertex([1,0,0]) // Throws an error! 
+\end{lstlisting}
+
+To fix this ensure all vertices have the correct dimension.
+
+\hypertarget{mshblddimunknwn}{%
+\section{MshBldDimUnknwn}\label{mshblddimunknwn}}
+
+This error is produced if you try to add an element to a
+\texttt{MeshBuilder} object but haven't yet specified the dimension (at
+initialization) or by adding a vertex.
+
+\begin{lstlisting}
+var mb = MeshBuiler() 
+mb.addedge([0,1]) // No vertices have been added 
+\end{lstlisting}
+
+To fix this add the vertices first.
+
 \hypertarget{meshrefiner}{%
 \section{MeshRefiner}\label{meshrefiner}}
 

manual/src/Reference/plot.tex

@@ -94,6 +94,6 @@ \section{Plotfield}\label{plotfield}}
   \texttt{default} - Color \texttt{Mesh} elements by the corresponding
   value of the \texttt{Field}.
 \item
-  \texttt{interpolated} - Interpolate \texttt{Field} quantities onto
+  \texttt{interpolate} - Interpolate \texttt{Field} quantities onto
   higher elements.
 \end{itemize}

manual/src/manual.lyx

@@ -164,7 +164,7 @@ figs-within-sections
 \begin_inset Newline newline
 \end_inset
 
-Version 0.5.2
+Version 0.5.3
 \end_layout
 
 \begin_layout Standard
@@ -4178,6 +4178,16 @@ filename "Reference/array.tex"
 \end_inset
 
 
+\end_layout
+
+\begin_layout Standard
+\begin_inset CommandInset include
+LatexCommand input
+filename "Reference/complex.tex"
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Standard

morpho5/build.h

@@ -4,6 +4,12 @@
  *  @brief Define constants that choose how Morpho is built
  */
 
+/* **********************************************************************
+ * Version
+ * ********************************************************************** */
+
+#define MORPHO_VERSIONSTRING "0.5.3"
+
 /* **********************************************************************
  * Paths and file system
  * ********************************************************************** */

morpho5/docs/index.rst

@@ -59,6 +59,7 @@ Morpho
    optimize
    plot
    povray
+   vtk
 
 .. toctree::
    :caption: Error messages

morpho5/interface/cli.c

@@ -208,11 +208,11 @@ void cli_help (lineditor *edit, char *query, error *err, bool avail) {
 void cli(clioptions opt) {
     #ifdef MORPHO_LONG_BANNER
         printf(BLU " ___   ___ \n" RESET);
-        printf(BLU "(" CYN " @ " GRY"\\Y/" CYN " @ " BLU ") " RESET "  |  morpho 0.5.2  | \U0001F44B Type 'help' or '?' for help\n");
+        printf(BLU "(" CYN " @ " GRY"\\Y/" CYN " @ " BLU ") " RESET "  |  morpho " MORPHO_VERSIONSTRING "  | \U0001F44B Type 'help' or '?' for help\n");
         printf(BLU " \\" CYN"__" GRY"+|+" CYN"__" BLU"/  " RESET "  |  Documentation: https://morpho-lang.readthedocs.io/en/latest/ \n");
         printf(BLU"  {" CYN"_" BLU "/ \\" CYN "_" BLU"}   " RESET "  |  Code: https://github.com/Morpho-lang/morpho \n\n");
     #else
-        printf("\U0001F98B morpho 0.5.2  | \U0001F44B Type 'help' or '?' for help\n");
+        printf("\U0001F98B morpho " MORPHO_VERSIONSTRING "  | \U0001F44B Type 'help' or '?' for help\n");
     #endif
     // Original ASCII art source - https://www.asciiart.eu/animals/insects/butterflies
     cli_file=NULL;