Generalized Permutohedra and type H4 4-uniform polytopes #27760

jplab · 2019-05-02T14:56:33Z

One sort of generalized permutahedra consists in putting the starting point, which is usually taken inside the fundamental chamber, on the boundary of the fundamental chamber.

See https://arxiv.org/abs/1904.11029 for a recent related paper.

This ticket implements the generalized permutahedra and on the way, adds the fifteen H4 4-uniform polytopes.

See https://en.wikipedia.org/wiki/H4_polytope for a list of them.

Many of them are quite large and can only be computed in reasonable time using the backend normaliz.

Depends on #25097

CC: @w-bruns @jplab @mkoeppe @videlec @tscrim

Component: geometry

Keywords: polytopes, non-rational, normaliz, days100

Author: Jean-Philippe Labbé

Branch/Commit: bd1fd21

Reviewer: Frédéric Chapoton

Issue created by migration from https://trac.sagemath.org/ticket/27760

The text was updated successfully, but these errors were encountered:

jplab · 2019-05-02T14:57:02Z

Dependencies: #25097

sagetrac-git · 2019-05-02T15:02:58Z

Branch pushed to git repo; I updated commit sha1. New commits:

`a546fba`	`Added names on top`

sagetrac-git · 2019-05-02T15:02:58Z

Changed commit from 1c7f848 to a546fba

sagetrac-git · 2019-05-02T15:10:49Z

Branch pushed to git repo; I updated commit sha1. New commits:

`91c43a6`	`Made the H4 types regular`

sagetrac-git · 2019-05-02T15:10:49Z

Changed commit from a546fba to 91c43a6

sagetrac-git · 2019-05-03T10:12:13Z

Branch pushed to git repo; I updated commit sha1. New commits:

`57d9b7d`	`Started fixing regularity`
`ef9faa9`	`Fixed the regular construction`

sagetrac-git · 2019-05-03T10:12:13Z

Changed commit from 91c43a6 to ef9faa9

sagetrac-git · 2019-05-03T11:34:46Z

Branch pushed to git repo; I updated commit sha1. New commits:

`8056264`	`Fixed typo in docstring`

sagetrac-git · 2019-05-03T11:34:46Z

Changed commit from ef9faa9 to 8056264

embray · 2019-06-14T14:55:02Z

comment:6

As the Sage-8.8 release milestone is pending, we should delete the sage-8.8 milestone for tickets that are not actively being worked on or that still require significant work to move forward. If you feel that this ticket should be included in the next Sage release at the soonest please set its milestone to the next release milestone (sage-8.9).

sagetrac-git · 2019-07-21T16:05:22Z

Branch pushed to git repo; I updated commit sha1. New commits:

`cce2590`	`Merge branch 'develop' into h4_polytopes`
`0c5b8d9`	`Fix py3 code and tests for Sage8.9beta3`
`d66f7e2`	`pep8`
`a6a5452`	`fixed some doctests`

sagetrac-git · 2019-07-21T16:05:22Z

Changed commit from 8056264 to a6a5452

sagetrac-git · 2019-07-21T16:09:20Z

Changed commit from a6a5452 to 71fbfdf

sagetrac-git · 2019-07-21T16:09:20Z

Branch pushed to git repo; I updated commit sha1. New commits:

`71fbfdf`	`Fixed a test`

jplab · 2019-07-21T16:14:36Z

Changed keywords from polytopes, non-rational, normaliz to polytopes, non-rational, normaliz, days100

fchapoton · 2019-07-21T20:07:53Z

comment:10

apparemment, la doc ne compile pas, voir patchbot

jplab · 2019-07-21T20:13:56Z

comment:11

Replying to @fchapoton:

apparemment, la doc ne compile pas, voir patchbot

Hm, all right. I'm on it!

sagetrac-git · 2019-07-21T20:38:05Z

Branch pushed to git repo; I updated commit sha1. New commits:

`d4260a6`	`trivial doc fix`

sagetrac-git · 2019-07-21T20:38:05Z

Changed commit from 71fbfdf to d4260a6

sagetrac-git · 2019-07-22T09:55:25Z

Branch pushed to git repo; I updated commit sha1. New commits:

`95d6bda`	`fix coding in library`

sagetrac-git · 2019-07-22T09:55:25Z

Changed commit from d4260a6 to 95d6bda

fchapoton · 2019-07-22T20:18:23Z

comment:15

missing the word 'polytope' here, I think:

The runcitruncated 600-cell is a 4-dimensional 4-uniform in the `H_4`

and the same in all the examples.

Here, you could remove the []

sum([adjusted_col[j]**2 for j in range(n) if j != i])

apart from that, ready to go..

sagetrac-git · 2019-07-23T06:36:15Z

Changed commit from 95d6bda to 5971228

vbraun · 2019-07-29T13:03:21Z

comment:23

**********************************************************************
File "src/sage/geometry/polyhedron/library.py", line 2324, in sage.geometry.polyhedron.library.Polytopes.generalized_permutahedron
Failed example:
    perm_b3 = polytopes.generalized_permutahedron(['B',3]); perm_b3
Expected:
    A 3-dimensional polyhedron in (Number Field in a with defining polynomial x^2 - 2 with a = 1.414213562373095?)^3 defined as the convex hull of 48 vertices
    A 3-dimensional polyhedron in AA^3 defined as the convex hull of 48 vertices
Got:
    A 3-dimensional polyhedron in (Number Field in a with defining polynomial x^2 - 2 with a = 1.414213562373095?)^3 defined as the convex hull of 48 vertices
**********************************************************************
1 item had failures:
   1 of  21 in sage.geometry.polyhedron.library.Polytopes.generalized_permutahedron
    [240 tests, 1 failure, 156.68 s]
----------------------------------------------------------------------
sage -t --long src/sage/geometry/polyhedron/library.py  # 1 doctest failed
----------------------------------------------------------------------

jplab · 2019-08-21T12:37:40Z

comment:24

Replying to @vbraun:

**********************************************************************
File "src/sage/geometry/polyhedron/library.py", line 2324, in sage.geometry.polyhedron.library.Polytopes.generalized_permutahedron
Failed example:
    perm_b3 = polytopes.generalized_permutahedron(['B',3]); perm_b3
Expected:
    A 3-dimensional polyhedron in (Number Field in a with defining polynomial x^2 - 2 with a = 1.414213562373095?)^3 defined as the convex hull of 48 vertices
    A 3-dimensional polyhedron in AA^3 defined as the convex hull of 48 vertices
Got:
    A 3-dimensional polyhedron in (Number Field in a with defining polynomial x^2 - 2 with a = 1.414213562373095?)^3 defined as the convex hull of 48 vertices
**********************************************************************
1 item had failures:
   1 of  21 in sage.geometry.polyhedron.library.Polytopes.generalized_permutahedron
    [240 tests, 1 failure, 156.68 s]
----------------------------------------------------------------------
sage -t --long src/sage/geometry/polyhedron/library.py  # 1 doctest failed
----------------------------------------------------------------------

I have trouble figuring out how this failure occurred.

The expected block is not as the attached branch would predict. Namely, the second line is absent. I merged the last version of develop into this ticket and made a test on my machine and I got:

jplabbe@blackbomb:~/sage/src/sage/geometry/polyhedron$ sage -t library.py 
Using --optional=4ti2,bliss,build,dochtml,e_antic,gfortran,latte_int,lidia,lrslib,memlimit,ninja_build,normaliz,pynormaliz,python2,sage,topcom
Doctesting 1 file.
sage -t library.py
    [305 tests, 77.99 s]
----------------------------------------------------------------------
All tests passed!
----------------------------------------------------------------------
Total time for all tests: 78.1 seconds
    cpu time: 78.0 seconds
    cumulative wall time: 78.0 seconds

I get 305 tests in total. Would it be possible to get more feedback on how this failing doctest occurred? (which optional packages were used?)

sagetrac-git · 2019-08-21T12:41:09Z

Changed commit from a1ad959 to cc1a6ab

sagetrac-git · 2019-08-21T12:41:09Z

Branch pushed to git repo; I updated commit sha1. New commits:

`cc1a6ab`	`Merge branch 'develop' into h4_polytopes`

jplab · 2019-08-21T12:45:15Z

comment:27

Let's have another run of bots to see if the problem still occurs. This failure is strange.

fchapoton · 2019-08-22T10:08:45Z

comment:28

patchbot reports another failure

sagetrac-git · 2019-08-22T10:49:37Z

Branch pushed to git repo; I updated commit sha1. New commits:

`b67e0c5`	`Added missing not tested tag`

sagetrac-git · 2019-08-22T10:49:37Z

Changed commit from cc1a6ab to b67e0c5

jplab · 2019-08-22T10:50:38Z

comment:30

Found it.

It was a missing tag from fixing comment 19. Should be good to go now...

fchapoton · 2019-08-23T06:35:48Z

comment:31

Adding tags on the results of doctests make no sense.

This does not fix the patchbot failure.

jplab · 2019-08-23T08:44:34Z

comment:32

Replying to @fchapoton:

Adding tags on the results of doctests make no sense.

This does not fix the patchbot failure.

That's what I thought at first too!

But then, that's the only way I can make sense of seeing

Expected:
    A 3-dimensional polyhedron in (Number Field in a with defining polynomial x^2 - 2 with a = 1.414213562373095?)^3 defined as the convex hull of 48 vertices
    A 3-dimensional polyhedron in AA^3 defined as the convex hull of 48 vertices

which are two distinct consecutive outputs of test, the second of which is not tested. I was thinking that it might preparse the string and remove the not tested things and thus the expected block would now consist of two lines.

Otherwise, I have no clue how come the expected block would consist of two lines, it is simply not as the source entails!?

Puzzled.

jplab · 2019-08-23T08:49:57Z

comment:33

Replying to @fchapoton:

Adding tags on the results of doctests make no sense.

This does not fix the patchbot failure.

From the patch bot shortog, the following information is a bit obscure:

Expected:
    There are 7 tests in sage/combinat/finite_state_machine.py that are not being run
    There are 3 unexpected tests being run in sage/doctest/parsing.py
    There are 1 unexpected tests being run in sage/doctest/reporting.py
    There are 3 tests in sage/rings/invariants/invariant_theory.py that are not being run
Got:
    There are 7 tests in sage/combinat/finite_state_machine.py that are not being run
    There are 3 unexpected tests being run in sage/doctest/parsing.py
    There are 1 unexpected tests being run in sage/doctest/reporting.py
    There are 1 unexpected tests being run in sage/geometry/polyhedron/library.py
    There are 3 tests in sage/rings/invariants/invariant_theory.py that are not being run
**********************************************************************

I guess it is the same test that causes a problem, but I have no output to inspect. Also, I am curious, what is an "unexpected test"? It's the first time I see such a thing.

sagetrac-git · 2019-08-23T09:05:26Z

Changed commit from b67e0c5 to cc1a6ab

sagetrac-git · 2019-08-23T09:05:26Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

jplab · 2019-08-23T09:06:34Z

comment:35

Replying to @sagetrac-git:

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

I removed the unless tag on the doctest result...

fchapoton · 2019-08-23T19:58:09Z

comment:36

Apparemment, ce qui pose problème est le fait que l'annotation contienne "64-bits".

sagetrac-git · 2019-08-23T19:58:43Z

Branch pushed to git repo; I updated commit sha1. New commits:

`bd1fd21`	`fix details`

sagetrac-git · 2019-08-23T19:58:43Z

Changed commit from cc1a6ab to bd1fd21

fchapoton · 2019-08-24T08:10:50Z

comment:38

ok, let us try again

jplab · 2019-08-26T10:13:05Z

comment:39

Replying to @fchapoton:

Apparemment, ce qui pose problème est le fait que l'annotation contienne "64-bits".

Wow. I see. Good to know. It looks like it's passing the test now at least.

vbraun · 2019-08-26T22:15:05Z

Changed branch from public/uniform_H4_polytopes to bd1fd21

jplab added this to the sage-8.8 milestone May 2, 2019

jplab added c: geometry labels May 2, 2019

embray removed this from the sage-8.8 milestone Jun 14, 2019

jplab added the s: needs review label Jul 21, 2019

jplab added this to the sage-8.9 milestone Jul 21, 2019

vbraun added s: needs work and removed s: positive review labels Jul 29, 2019

jplab added s: needs review and removed s: needs work labels Aug 21, 2019

fchapoton added s: positive review and removed s: needs review labels Aug 24, 2019

vbraun removed the s: positive review label Aug 26, 2019

vbraun closed this as completed in 8f76f4d Aug 26, 2019

jplab mentioned this issue Oct 31, 2019

Add the classical construction of the 120-cell #28429

Closed

Generalized Permutohedra and type H4 4-uniform polytopes #27760

Generalized Permutohedra and type H4 4-uniform polytopes #27760

Comments

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