s

===== Introduction to topaz ===== This tutorial tries to give the user a first idea about the features of the ''%%topaz%%'' application of ''%%polymake%%''. We take a look at a variety of small examples. First, we have to make ''%%topaz%%'' the current application. For this you can either start ''%%polymake%%'' with the option ''%%-A topaz%%'',


polymake -A topaz

or, if you've already started ''%%polymake%%'', type


> application 'topaz';

in the ''%%polymake%%'' shell. ==== Simplicial complexes ==== The most important object of the ''%%topaz%%'' application is the simplicial complex. There are several ways of obtaining one. === From faces === For example, you can specify some faces of the complex. You can pass them as an ''%%Array< Set >%%'', or ''%%Array< Array >%%'':


> # $s = new SimplicialComplex(INPUT_FACES=>[new Set(0), new Set(0,1), new Set(1,2,3)]);
> $s = new SimplicialComplex(INPUT_FACES=>[[0],[0,1],[1,2,3]]);

As you can see, redundancies are allowed -- ''%%[0]%%'' is not a facet of the complex, and thus not necessary for encoding ''%%$s%%''. You can compute the inclusion maximal faces like this:


> print $s->FACETS;
{0 1}
{1 2 3}

You can also pass the ''%%FACETS%%'' to the constructor, but be aware that in that case the vertices must be numbered increasingly starting with ''%%0%%'' and redundancies are prohibited. Take a look at your complex using


> $s->VISUAL;

Explode

Automatic explosion

Exploding speed

Transparency

depthWrite

Rotation

x-axis

y-axis

z-axis

Rotation speed

Display

Objects

Camera

SVG

For more information on visualizing simplicial complex, see the section below. ''%%polymake%%'' can compute the Hasse diagram of a simplicial complex (watch out, this gets really large for large complexes!). To print all the faces of the complex together with their rank in the face lattice, do this:


> print $s->HASSE_DIAGRAM->DECORATION;
({-1} 4)
({0 1} 2)
({1 2 3} 3)
({0} 1)
({1} 1)
({1 2} 2)
({1 3} 2)
({2 3} 2)
({} 0)
({2} 1)
({3} 1)

The first entry of each pair denotes the face, the second is the rank. The ''%%{-1}%%''-node is a dummy representing the whole complex. the ''%%{}%%''-node is the empty face. If you want to look at a pretty graph representation, try the visualization:


> $s->VISUAL_FACE_LATTICE;

{{ tutorials:release:4.7:apps_topaz:output_0.svg }} === Using clients === There are several clients that construct common simplicial complexes (for a comprehensive list, see the [[documentation:latest:topaz|topaz documentation]]). An example is the torus client:


> $t = torus();

Of course, ''%%polymake%%'' can compute the reduced integer homology groups of a simplicial complex, so we can convice ourselves this is a torus:


> print $t->MANIFOLD;
true
> print $t->HOMOLOGY;
({} 0)
({} 2)
({} 1)

The ''%%i%%''-th line represents the $i$-th homology module. The curly braces contain torsion coefficients with multiplicity, the second pair entry denotes the Betti number. The empty curly braces indicate that ''%%$t%%'' is torsion-free. You can see a non-empty torsion group here (using the ''%%rows_numbered%%'' client for a pretty print with the corresponding dimensions):


> print rows_numbered( real_projective_plane()->HOMOLOGY );
0:{} 0
1:{(2 1)} 0
2:{} 0

As expected, the first homology group has torsion coefficient ''%%2%%'' with multiplicity ''%%1%%'' and all Betti numbers are zero. === As boundary complex === If your complex is a pseudo-manifold, you can obtain a new complex from its boundary. For example, this produces a triangulation of the $2$-sphere:


> $bs = simplex(3)->BOUNDARY;
> print $bs->SPHERE;
true

=== Triangulating polytopes === The triangulation of a polytope is a simplicial complex, too. The ''%%TRIANGULATION%%'' gets stored in a property of the polytope. We use the ''%%cube%%'' client from the ''%%polytope%%'' application to demonstrate:


> $c = polytope::cube(3);
> $tc = $c->TRIANGULATION;
> print $tc->FACETS;
{0 1 2 4}
{1 2 3 4}
{1 3 4 5}
{2 3 4 6}
{3 4 5 6}
{3 5 6 7}

==== Geometric realizations ==== The ''%%topaz%%'' application is primarily designed to deal with abstract simplicial complexes that do not come with coordinates for an embedding in euclidean space. There is a special object subtype named ''%%GeometricSimplicialComplex%%'' that has extra properties for dealing with coodinates. You can pass the coordinates to the constructor. Take care to choose an embedding without crossings!


> $s = new GeometricSimplicialComplex(INPUT_FACES=>[[0],[0,1],[1,2,3]], COORDINATES=>[[1,0],[1,1],[0,2],[2,2]]);

Some clients produce complexes with geometric realization...


> $b = ball(3);
> # print a dense representation of the sparse matrix
> print dense( $b->COORDINATES );
0 0 0
1 0 0
0 1 0
0 0 1

...some others provide the option ''%%geometric_realization%%'' so you can decide whether to invest the extra computing time.


> $bs = barycentric_subdivision($b,geometric_realization=>1);

Again, see the [[documentation:latest:topaz|topaz documentation]] for a comprehensive list. ==== Visualization ==== Visualization of simplicial complexes uses the ''%%VISUAL%%'' property. Check out


> help 'objects/SimplicialComplex/methods/Visualization/VISUAL';
VISUAL(Options) -> Visual::SimplicialComplex

 Visualizes the complex.

 If __G_DIM__ < 4, the __GRAPH__ and the facets
 are visualized using the __COORDINATES__.

 Otherwise, the spring embedder and the __GRAPH__ are used to
 produce coordinates for the visualization.

 If __JavaView__ is used to visualize the complex, all faces of
 one facet build a geometry in the jvx-file, so you may use
 __Method -> Effect -> Explode Group of Geometries__ in the JavaView menu.

Options: 
  __mixed_graph__ => Bool use the __MIXED_GRAPH__ for the spring embedder
  __seed__ => Int random seed value for the string embedder

Options:  Attributes modifying the appearance of filled polygons.
  __FacetColor__ => Color filling color of the polygon
  __FacetTransparency__ => Float transparency factor of the polygon between 0 (opaque) and 1 (completely translucent)
  __FacetStyle__ => String if set to "hidden", the inner area of the polygon is not rendered
  __EdgeColor__ => Color color of the boundary lines
  __EdgeThickness__ => Float scaling factor for the thickness of the boundary lines
  __EdgeStyle__ => String if set to "hidden", the boundary lines are not rendered
  __Title__ => String the name of the drawing
  __Name__ => String the name of this visual object in the drawing
  __Hidden__ => Bool if set to true, the visual object is not rendered
    (useful for interactive visualization programs allowing for switching details on and off)
  __PointLabels__ => String if set to "hidden", no point labels are displayed
  __VertexLabels__ => String alias for PointLabels
  __PointColor__ => Flexible color of the spheres or rectangles representing the points
  __VertexColor__ => Flexible alias for PointColor
  __PointThickness__ => Flexible scaling factor for the size of the spheres or rectangles representing the points
  __VertexThickness__ => Flexible alias for PointThickness
  __PointBorderColor__ => Flexible color of the border line of rectangles representing the points
  __VertexBorderColor__ => Flexible alias for PointBorderColor
  __PointBorderThickness__ => Flexible scaling factor for the thickness of the border line of rectangles representing the points
  __VertexBorderThickness__ => Flexible alias for PointBorderThickness
  __PointStyle__ => Flexible if set to "hidden", neither point nor its label is rendered
  __VertexStyle__ => Flexible alias for PointStyle
  __ViewPoint__ => Vector ViewPoint for Sketch visualization
  __ViewDirection__ => Vector ViewDirection for Sketch visualization
  __ViewUp__ => Vector ViewUp for Sketch visualization
  __Scale__ => Float scale for Sketch visualization
  __LabelAlignment__ => Flexible Defines the alignment of the vertex labels: left, right or center

Options:  Attributes modifying the appearance of graphs
  __Coord__ => Matrix 2-d or 3-d coordinates of the nodes.
    If not specified, a random embedding is generated using a pseudo-physical spring model
  __NodeColor__ => Flexible alias for PointColor
  __NodeThickness__ => Flexible alias for PointThickness
  __NodeBorderColor__ => Flexible alias for PointBorderColor
  __NodeBorderThickness__ => Flexible alias for PointBorderThickness
  __NodeStyle__ => Flexible alias for PointStyle
  __NodeLabels__ => String alias for PointLabels
  __ArrowStyle__ => Flexible How to draw directed edges: 0 (like undirected), 1 (with an arrow pointing towards the edge),
    or -1 (with an arrow pointing against the edge).  Default is 1 for directed graphs and lattices.
  __EdgeColor__ => Flexible color of the lines representing the edges
  __EdgeThickness__ => Flexible scaling factor for the thickness of the lines representing the edges
  __EdgeLabels__ => EdgeMap textual labels to be placed along the edges
  __EdgeStyle__ => Flexible if set to "hidden", neither the edge nor its label is rendered
  __Title__ => String the name of the drawing
  __Name__ => String the name of this visual object in the drawing
  __Hidden__ => Bool if set to true, the visual object is not rendered
    (useful for interactive visualization programs allowing for switching details on and off)
  __PointLabels__ => String if set to "hidden", no point labels are displayed
  __VertexLabels__ => String alias for PointLabels
  __PointColor__ => Flexible color of the spheres or rectangles representing the points
  __VertexColor__ => Flexible alias for PointColor
  __PointThickness__ => Flexible scaling factor for the size of the spheres or rectangles representing the points
  __VertexThickness__ => Flexible alias for PointThickness
  __PointBorderColor__ => Flexible color of the border line of rectangles representing the points
  __VertexBorderColor__ => Flexible alias for PointBorderColor
  __PointBorderThickness__ => Flexible scaling factor for the thickness of the border line of rectangles representing the points
  __VertexBorderThickness__ => Flexible alias for PointBorderThickness
  __PointStyle__ => Flexible if set to "hidden", neither point nor its label is rendered
  __VertexStyle__ => Flexible alias for PointStyle
  __ViewPoint__ => Vector ViewPoint for Sketch visualization
  __ViewDirection__ => Vector ViewDirection for Sketch visualization
  __ViewUp__ => Vector ViewUp for Sketch visualization
  __Scale__ => Float scale for Sketch visualization
  __LabelAlignment__ => Flexible Defines the alignment of the vertex labels: left, right or center

Returns Visual::SimplicialComplex

{{:tutorials:release:4.7:apps_topaz:ball_triang.png}} for a list of available options and this [[visual_tutorial|tutorial]] for a general intro to visualization in polymake. If your complex is of dimension three or lower, you can visualize a geometric realization together with the ''%%GRAPH%%'' of the complex using the ''%%VISUAL%%'' property. Note that if your complex is not a ''%%GeometricSimplicialComplex%%'', ''%%polymake%%'' will use the spring embedder to find an embedding of the graph of the complex, which is not guaranteed to result in an intersection-free visualization.


> $bs->VISUAL;

Explode

Automatic explosion

Exploding speed

Transparency

depthWrite

Rotation

x-axis

y-axis

z-axis

Rotation speed

Display

Objects

Camera

SVG

You should give the ''%%explode%%'' feature of jReality a try -- it gives a good (and pretty!) overview of the object. You can find it in the left slot of the jReality interface. {{:tutorials:release:4.7:apps_topaz:ball_triang_pink.png}} ''%%topaz%%'' may also visualize distinguished subcomplexes or just sets of faces with different decorations (colors, styles, etc.). For example, to highlight the fourth facet of ''%%$bs%%'' in pink, do this:


> $a = new Array>(1); $a->[0] = $bs->FACETS->[4];
> $bs->VISUAL->FACES($a, FacetColor => 'pink');

Explode

Automatic explosion

Exploding speed

Transparency

depthWrite

Rotation

x-axis

y-axis

z-axis

Rotation speed

Display

Objects

Camera

SVG

The same can be used for the visualization of the face lattice. As an example, we have a look at a ''%%morse matching%%'' of the Klein bottle with its associated critical faces. In order to see the arrowheads in the picture clearly, you ought to use graphviz or svg to vizualize it.


> $k =  klein_bottle();
> svg($k->VISUAL_FACE_LATTICE->MORSE_MATCHING->FACES($k->MORSE_MATCHING->CRITICAL_FACES));

{{ tutorials:release:4.7:apps_topaz:output_1.svg }} {{:tutorials:release:4.7:apps_topaz:kb_mm_faces.gif}} Here the matching of faces is denoted by reversed red arrows and the critical faces are marked red. Check that the graph remains acyclic. For higher dimensional complexes that cannot be visualized in 3D, you can still have a look at the graphs while ignoring any specified coordinates by using ''%%VISUAL_GRAPH%%'', ''%%VISUAL_DUAL_GRAPH%%'', or ''%%VISUAL_MIXED_GRAPH%%''. An easy example:


> polytope::cube(3)->TRIANGULATION->VISUAL_MIXED_GRAPH;

GRAPH of

Explode

Automatic explosion

Exploding speed

Transparency

depthWrite

Rotation

x-axis

y-axis

z-axis

Rotation speed

Display

Objects

Camera

SVG

shows the primal and dual graph of the polytope together with an edge between a primal and a dual node iff the primal node represents a vertex of the corresponding facet of the dual node. {{:tutorials:release:4.7:apps_topaz:cube_graph.png}} Visualization of the ''%%HASSE_DIAGRAM%%'' is possible via ''%%VISUAL_FACE_LATTICE%%''. It renders the graph in a .pdf file. You can even pipe the tikz code to whatever location using the ''%%tikz%%'' client:


tikz($s->VISUAL_FACE_LATTICE, File=>"/path/to/file.tikz");