user_guide:tutorials:latest:apps_topaz

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 — user_guide:tutorials:latest:apps_topaz [2020/01/22 09:02] (current) Line 1: Line 1: + ===== 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'',​ + + <​code>​ + 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<​Int>​ >'',​ or ''​Array<​ Array<​Int>​ >'':​ + + + > # $s = new SimplicialComplex(INPUT_FACES=>​[new Set(0), new Set(0,1), new Set(1,​2,​3)]);​ + >$s = new SimplicialComplex(INPUT_FACES=>​[,​[0,​1],​[1,​2,​3]]);​ + ​ + {{ :​tutorial:​small_complex.png?​400|}} As you can see, redundancies are allowed -- ''​''​ 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 + + + > $s->​VISUAL;​ + ​ + For more information on visualizing simplicial complex, see the section below. + + {{:​tutorial:​face_lattice.png?​200 |}}''​polymake''​ can compute the Hasse diagram of a simplicial complex (watch out, this gets really large for large complexes!). To print all the faces of the complex together with their rank in the face lattice, do this: + + + > print$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:​ + + + > $s->​VISUAL_FACE_LATTICE;​ + ​ + === Using clients === + + There are several clients that construct common simplicial complexes (for a comprehensive list, see the [[https://​polymake.org/​release_docs/​latest/​topaz.html|topaz documentation]]). An example is the torus client: + + + >$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 $t->​MANIFOLD;​ + 1 + > print$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 $bs->​SPHERE;​ + 1 + + ​ + === Triangulating polytopes === + + The triangulation of a polytope is a simplicial complex, too. The ''​TRIANGULATION''​ gets stored in a property of the polytope. We use the ''​cube''​ client from the ''​polytope''​ application to demonstrate:​ + + + >$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,​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 [[https://​polymake.org/​release_docs/​latest/​topaz.html|topaz documentation]] for a comprehensive list. + + ==== Visualization ==== + + Visualization of simplicial complexes uses the ''​VISUAL''​ property. Check out + + + > help '​objects/​SimplicialComplex/​methods/​Visualization/​VISUAL';​ + ​ + {{ :​tutorial:​ball_triang.png?​300|}} 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. + + + > $bs->​VISUAL;​ + ​ + You should give the ''​explode''​ feature of jReality a try -- it gives a good (and pretty!) overview of the object. You can find it in the left slot of the jReality interface. + + {{:​tutorial:​ball//​triang//​pink.png?​250 |}} ''​topaz''​ may also visualize distinguished subcomplexes or just sets of faces with different decorations (colors, styles, etc.). For example, to highlight the fourth facet of ''​$bs''​ in pink, do this: + + + > $a = new Array<​Set<​Int>>​(1);​$a-> = $bs->​FACETS->​;​ + >$bs->​VISUAL->​FACES($a,​ FacetColor => '​pink'​);​ + ​ + The same can be used for the visualization of the face lattice. As an example, we have a look at a ''​morse matching''​ of the Klein bottle with its associated critical faces. In order to see the arrowheads in the picture clearly, you ought to use graphviz or svg to vizualize it. + + + >$k =  klein_bottle();​ + > graphviz($k->​VISUAL_FACE_LATTICE->​MORSE_MATCHING->​FACES($k->​MORSE_MATCHING->​CRITICAL_FACES));​ + ​ + {{ :​tutorial:​kb//​mm//​faces.gif?​400|}} 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;​ + ​ + 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. + + {{ :​tutorial:​cube_graph.png?​600 |}} + + 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: + + <​code>​ + tikz(\$s->​VISUAL_FACE_LATTICE,​ File=>"/​path/​to/​file.tikz"​);​ +
• user_guide/tutorials/latest/apps_topaz.txt