File: cddml-notebook.nb

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(************** Content-type: application/mathematica **************

                    Mathematica-Compatible Notebook

This notebook can be used with any Mathematica-compatible
application, such as Mathematica, MathReader or Publicon. The data
for the notebook starts with the line containing stars above.

To get the notebook into a Mathematica-compatible application, do
one of the following:

* Save the data starting with the line of stars above into a file
  with a name ending in .nb, then open the file inside the
  application;

* Copy the data starting with the line of stars above to the
  clipboard, then use the Paste menu command inside the application.

Data for notebooks contains only printable 7-bit ASCII and can be
sent directly in email or through ftp in text mode.  Newlines can be
CR, LF or CRLF (Unix, Macintosh or MS-DOS style).

NOTE: If you modify the data for this notebook not in a Mathematica-
compatible application, you must delete the line below containing
the word CacheID, otherwise Mathematica-compatible applications may
try to use invalid cache data.

For more information on notebooks and Mathematica-compatible 
applications, contact Wolfram Research:
  web: http://www.wolfram.com
  email: info@wolfram.com
  phone: +1-217-398-0700 (U.S.)

Notebook reader applications are available free of charge from 
Wolfram Research.
*******************************************************************)

(*CacheID: 232*)


(*NotebookFileLineBreakTest
NotebookFileLineBreakTest*)
(*NotebookOptionsPosition[     14720,        468]*)
(*NotebookOutlinePosition[     16078,        512]*)
(*  CellTagsIndexPosition[     15906,        504]*)
(*WindowFrame->Normal*)



Notebook[{
Cell[TextData[{
  StyleBox["cddmathlink",
    FontColor->RGBColor[0.0557107, 0.137819, 0.517113]],
  "\nConvex Hull and Vertex Enumeration by ",
  StyleBox["MathLink",
    FontSlant->"Italic",
    FontColor->RGBColor[0.0146487, 0.461387, 0.0967727]],
  " to ",
  StyleBox["cddlib",
    FontColor->RGBColor[0.517113, 0.0273594, 0.0273594]],
  "\nby Komei Fukuda\nApril 17, 2001"
}], "Title",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell["Connecting  cddmathlink", "Subsection",
  InitializationCell->True,
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell[TextData[{
  "You just put the compiled cddmathlink for your computer in some directory. \
 In this example, the name of the directory is ",
  StyleBox["\"~/Math\".",
    FontFamily->"Courier",
    FontWeight->"Bold"]
}], "Text",
  InitializationCell->True,
  ImageRegion->{{0, 1}, {0, 1}}],

Cell["Off[General::spell1]; Off[General::spell];", "Input",
  InitializationCell->True,
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell["\<\
cddml=
Install[\"~/Math/cddmathlink\"]\
\>", "Input",
  InitializationCell->True,
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \(LinkObject["/Users/fukuda/Math/cddmathlink", 9, 8]\)], "Output"]
}, Open  ]]
}, Open  ]]
}, Closed]],

Cell[CellGroupData[{

Cell["Generating All Vertices ", "Subsection",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell["?AllVertices", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \("AllVertices[m,d+1,A] generates all extreme points (vertices) and \
extreme rays of the convex polyhedron in R^(d+1) given as the solution set to \
an inequality system  A x >= 0 where  A is an m*(d+1) matrix  and  \
x=(1,x1,...,xd).  The output is {{extlist, linearity}, ecdlist} where extlist \
is  the extreme point list and ecdlist is the incidence list.  Each vertex \
(ray) has the first component 1 (0).  If the convex polyhedron is nonempty \
and has no vertices, extlist is a (nonunique) set of generators of the \
polyhedron where those generators in the linearity list are considered as \
linearity space (of points satisfying A (0, x1, x2, ...., xd) = 0)  \
generators."\)], "Print",
  CellTags->"Info3249106863-2654627"],

Cell["\<\
Let's try this function with a 3-dimenstional cube defined by 6 \
inequalities (facets);  
x1  >= 0, x2 >=0, x3 >= 0, 1 - x1 >= 0,   1 - x2 >= 0 and  1 - x3 >= 0.  We \
write these six inequalities  as   A  x  >=  0  and  x=(1, x1, x2, x3).\
\>", \
"Text",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell["\<\
MatrixForm[a={{0,1,0,0},{0,0,1,0},{0,0,0,1},
\t{1,-1,0,0},{1,0,-1,0},{1,0,0,-1}}]\
\>", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    TagBox[
      RowBox[{"(", "\[NoBreak]", GridBox[{
            {"0", "1", "0", "0"},
            {"0", "0", "1", "0"},
            {"0", "0", "0", "1"},
            {"1", \(-1\), "0", "0"},
            {"1", "0", \(-1\), "0"},
            {"1", "0", "0", \(-1\)}
            }], "\[NoBreak]", ")"}],
      Function[ BoxForm`e$, 
        MatrixForm[ BoxForm`e$]]]], "Output"],

Cell[CellGroupData[{

Cell["{m,d1}=Dimensions[a]", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \({6, 4}\)], "Output"]
}, Open  ]],

Cell[CellGroupData[{

Cell["\<\
{{vertices, linearity}, \
incidences}=AllVertices[m,d1,Flatten[a]]\
\>", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \({{{{1.`, 1.`, 1.`, 0.`}, {1.`, 0.`, 1.`, 0.`}, {1.`, 0.`, 0.`, 
            0.`}, {1.`, 1.`, 0.`, 0.`}, {1.`, 0.`, 0.`, 1.`}, {1.`, 1.`, 0.`, 
            1.`}, {1.`, 0.`, 1.`, 1.`}, {1.`, 1.`, 1.`, 1.`}}, {}}, {{3, 4, 
          5}, {1, 3, 5}, {1, 2, 3}, {2, 3, 4}, {1, 2, 6}, {2, 4, 6}, {1, 5, 
          6}, {4, 5, 6}}}\)], "Output"]
}, Open  ]]
}, Open  ]]
}, Open  ]]
}, Closed]],

Cell[CellGroupData[{

Cell["Generating the Graph Structure", "Subsection",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell["?AllVerticesWithAdjacency", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \("AllVerticesWithAdjacency[m,d+1,A] generates all extreme points \
(vertices) and extreme rays of the convex polyhedron in R^(d+1) given as the \
solution set to an inequality system  A x >= 0 where   A is an m*(d+1) matrix \
 and x=(1,x1,...,xd). The output is {{extlist, linearity}, ecdlist, eadlist, \
icdlist, iadlist} where extlist, ecdlist, eadlist are the extreme point list, \
the incidence list, the adjacency list (of extreme points and rays), and \
icdlist, iadlist are the incidence list, the adjacency list (of \
inequalities).  Each vertex (ray) has the first component 1 (0). If the \
convex polyhedron is nonempty and has no vertices, extlist is a (nonunique) \
set of generators of the polyhedron where those generators in the linearity \
list are considered as linearity space (of points satisfying A (0, x1, x2, \
...., xd) = 0) generators."\)], "Print",
  CellTags->"Info3249106869-2272285"],

Cell[CellGroupData[{

Cell["\<\
{{vertices,linearity},ecd,ead,icd,iad}=
\tAllVerticesWithAdjacency[m,d1,Flatten[a]]\
\>", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \({{{{1.`, 1.`, 1.`, 0.`}, {1.`, 0.`, 1.`, 0.`}, {1.`, 0.`, 0.`, 
            0.`}, {1.`, 1.`, 0.`, 0.`}, {1.`, 0.`, 0.`, 1.`}, {1.`, 1.`, 0.`, 
            1.`}, {1.`, 0.`, 1.`, 1.`}, {1.`, 1.`, 1.`, 1.`}}, {}}, {{3, 4, 
          5}, {1, 3, 5}, {1, 2, 3}, {2, 3, 4}, {1, 2, 6}, {2, 4, 6}, {1, 5, 
          6}, {4, 5, 6}}, {{2, 4, 8}, {1, 3, 7}, {2, 4, 5}, {1, 3, 6}, {3, 6, 
          7}, {4, 5, 8}, {2, 5, 8}, {1, 6, 7}}, {{2, 3, 5, 7}, {3, 4, 5, 
          6}, {1, 2, 3, 4}, {1, 4, 6, 8}, {1, 2, 7, 8}, {5, 6, 7, 
          8}, {}}, {{2, 3, 5, 6}, {1, 3, 4, 6}, {1, 2, 4, 5}, {2, 3, 5, 
          6}, {1, 3, 4, 6}, {1, 2, 4, 5}, {}}}\)], "Output"]
}, Open  ]]
}, Open  ]],

Cell[TextData[{
  "The graph structure is output as the adjacency  list  ",
  StyleBox["ead. ",
    FontFamily->"Courier",
    FontWeight->"Bold"],
  "For example, the first list {2, 4 ,8} represents the neighbour vertices of \
the first vertex 1.  The adjacency of input is given by\nthe list  ",
  StyleBox["iad.",
    FontFamily->"Courier",
    FontWeight->"Bold"]
}], "Text",
  ImageRegion->{{0, 1}, {0, 1}}]
}, Closed]],

Cell[CellGroupData[{

Cell["Convex Hull (Facet Generation)", "Subsection",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell["?AllFacets", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \("AllFacets[n,d+1,G] generates all facet inequalities of the convex \
polyhedron in R^(d+1) generated by points and rays given in the rows of an \
n*(d+1) matrix G.  Each point (ray) must have 1 (0) in the first coordinate.  \
The output is {{faclist, equalities}, icdlist} where faclist is  the facet  \
list and icdlist is the incidence list.  If the convex polyhedron is not \
full-dimensional, extlist is a (nonunique) set of inequalities of the \
polyhedron where those inequalities in the equalities list are considered as \
equalities."\)], "Print",
  CellTags->"Info3249106877-5554290"],

Cell["\<\
We have computed all the vertices of a 3-cube.  Let's try the \
reverse operation.  First check the size of the list of vertics.   It should \
reconstruct the facets we have started with.\
\>", "Text",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell["{n, d1}=Dimensions[vertices]", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \({8, 4}\)], "Output"]
}, Open  ]],

Cell[CellGroupData[{

Cell["\<\

{{facets,equalities}, fincidences}= AllFacets[n,d1,Flatten[vertices]]\
\>", \
"Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \({{{{0.`, 0.`, 0.`, 1.`}, {0.`, 1.`, 0.`, 0.`}, {0.`, 0.`, 1.`, 
            0.`}, {1.`, 0.`, 0.`, \(-1.`\)}, {1.`, 0.`, \(-1.`\), 
            0.`}, {1.`, \(-1.`\), 0.`, 0.`}}, {}}, {{1, 2, 3, 4}, {2, 3, 5, 
          7}, {3, 4, 5, 6}, {5, 6, 7, 8}, {1, 2, 7, 8}, {1, 4, 6, 
          8}}}\)], "Output"]
}, Open  ]],

Cell[TextData[{
  "We can compute how the facets are connected by using ",
  StyleBox["AllFacetsWithAdjacency",
    FontWeight->"Bold"],
  " function."
}], "Text",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell["\<\

{{facets,equalities}, icd,iad, ecd,ead}= 
\tAllFacetsWithAdjacency[n,d1,Flatten[vertices]]\
\>", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \({{{{0.`, 0.`, 0.`, 1.`}, {0.`, 1.`, 0.`, 0.`}, {0.`, 0.`, 1.`, 
            0.`}, {1.`, 0.`, 0.`, \(-1.`\)}, {1.`, 0.`, \(-1.`\), 
            0.`}, {1.`, \(-1.`\), 0.`, 0.`}}, {}}, {{1, 2, 3, 4}, {2, 3, 5, 
          7}, {3, 4, 5, 6}, {5, 6, 7, 8}, {1, 2, 7, 8}, {1, 4, 6, 8}}, {{2, 
          3, 5, 6}, {1, 3, 4, 5}, {1, 2, 4, 6}, {2, 3, 5, 6}, {1, 2, 4, 
          6}, {1, 3, 4, 5}}, {{1, 5, 6}, {1, 2, 5}, {1, 2, 3}, {1, 3, 6}, {2, 
          3, 4}, {3, 4, 6}, {2, 4, 5}, {4, 5, 6}}, {{2, 4, 8}, {1, 3, 7}, {2, 
          4, 5}, {1, 3, 6}, {3, 6, 7}, {4, 5, 8}, {2, 5, 8}, {1, 6, 
          7}}}\)], "Output"]
}, Open  ]]
}, Open  ]],

Cell[CellGroupData[{

Cell["\<\
If you want to compute an inequality description of the \
one-dimensional cone in R^3 with a vertex at origin and containing the \
direction (1,1,1), you must set up the input (generator) data as:\
\>", "Text",\

  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell["coneGenerators={{1,0,0,0},{0,1,1,1}}", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \({{1, 0, 0, 0}, {0, 1, 1, 1}}\)], "Output"]
}, Open  ]],

Cell[CellGroupData[{

Cell["\<\
{{cfacets,cequalities}, cfincidences}= 
\tAllFacets[2,4,Flatten[coneGenerators]]\
\>", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \({{{{1.`, 0.`, 0.`, 0.`}, {0.`, 1.`, 0.`, 0.`}, {0.`, \(-1.`\), 1.`, 
            0.`}, {0.`, \(-1.`\), 0.`, 1.`}}, {3, 4}}, {{2}, {1}, {1, 2}, {1, 
          2}}}\)], "Output"]
}, Open  ]],

Cell["\<\
Since the equalities list contains 3 and 4, of the four output \
inequalities , the third and the forth must be considered as equalities.  It \
is important to note that this cone can have infinitely many different \
minimal inequality descriptions, since it is not full-dimensional.\
\>", \
"Text",
  ImageRegion->{{0, 1}, {0, 1}}]
}, Open  ]]
}, Closed]],

Cell[CellGroupData[{

Cell["A Larger Example (Random 0/1 Polytopes)", "Subsection",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell["\<\
Let's compute the convex hull of 0/1 points in R^d.  First generate \
0/1 points.  Below each point with the first component 0 is considered as a \
direction that must be included in the convex hull.\
\>", "Text",
  ImageRegion->{{0, 1}, {0, 1}},
  FontSize->13],

Cell["n=30; d1=8;", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell["\<\
points=Table[Prepend[Table[Random[Integer,{0,1}],{d1-1}],0],{n}]\
\>\
", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \({{0, 0, 1, 1, 0, 1, 1, 1}, {0, 1, 0, 0, 1, 1, 0, 0}, {0, 1, 0, 1, 0, 0, 
        0, 0}, {0, 0, 0, 0, 1, 1, 1, 1}, {0, 0, 1, 1, 0, 1, 1, 1}, {0, 1, 0, 
        1, 0, 1, 1, 1}, {0, 0, 1, 1, 0, 0, 0, 0}, {0, 1, 0, 0, 1, 1, 0, 
        1}, {0, 0, 0, 0, 1, 0, 1, 1}, {0, 0, 1, 0, 0, 0, 1, 1}, {0, 0, 1, 0, 
        0, 0, 1, 0}, {0, 0, 0, 0, 1, 0, 1, 0}, {0, 0, 0, 0, 0, 1, 0, 0}, {0, 
        0, 0, 0, 1, 0, 0, 0}, {0, 1, 0, 0, 1, 1, 0, 1}, {0, 0, 0, 1, 1, 1, 0, 
        0}, {0, 0, 1, 1, 1, 0, 0, 1}, {0, 1, 1, 0, 0, 1, 1, 0}, {0, 0, 1, 1, 
        0, 0, 0, 1}, {0, 1, 0, 1, 1, 0, 1, 0}, {0, 1, 1, 1, 0, 1, 0, 1}, {0, 
        1, 1, 1, 1, 0, 1, 1}, {0, 0, 0, 0, 1, 0, 0, 1}, {0, 1, 1, 0, 0, 0, 1, 
        1}, {0, 0, 1, 0, 1, 1, 0, 1}, {0, 1, 0, 0, 0, 1, 1, 1}, {0, 1, 0, 0, 
        0, 1, 1, 1}, {0, 0, 0, 1, 0, 0, 0, 1}, {0, 0, 1, 0, 1, 1, 0, 0}, {0, 
        0, 0, 0, 1, 0, 1, 1}}\)], "Output"]
}, Open  ]],

Cell[CellGroupData[{

Cell["Dimensions[points]", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \({30, 8}\)], "Output"]
}, Open  ]],

Cell["\<\

{CPUtime, {{facets,equalities}, inc}}= 
\tTiming[AllFacets[n,d1,Flatten[points]]];\
\>", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell["{CPUtime,Length[facets]}", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \({0.`\ Second, 33}\)], "Output"]
}, Open  ]],

Cell["\<\
Usually facets of 0/1 polytopes are very pretty and their \
coefficients are small integers.\
\>", "Text",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[CellGroupData[{

Cell["Take[facets,5]", "Input",
  ImageRegion->{{0, 1}, {0, 1}}],

Cell[BoxData[
    \({{0.`, 0.`, 0.`, 1.`, 0.`, 0.`, 0.`, 0.`}, {0.`, \(-1.`\), 0.`, 1.`, 
        0.`, 1.`, 0.`, 1.`}, {0.`, \(-1.`\), \(-1.`\), 1.`, 0.`, 1.`, 1.`, 
        1.`}, {0.`, 0.`, 0.`, 0.`, 0.`, 0.`, 0.`, 1.`}, {0.`, 0.`, 1.`, 0.`, 
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