Opened 10 years ago
Closed 9 years ago
#11608 closed enhancement (fixed)
RDF/CDF eigenvalues: symmetric matrices, multiplicities
Reported by: | rbeezer | Owned by: | jason, was |
---|---|---|---|
Priority: | minor | Milestone: | sage-5.1 |
Component: | linear algebra | Keywords: | sd40.5 |
Cc: | jason | Merged in: | sage-5.1.beta4 |
Authors: | Rob Beezer | Reviewers: | Volker Braun |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description (last modified by )
As the summary says, this patch improves eigenvalues of matrices with double-precision floating-point entries.
- Uses SciPy's
eigh
routine for symmetric and Hermitian matrices. - Allows grouping of "equal" eigenvalues, based on a tolerance parameter.
Apply:
Attachments (2)
Change History (19)
comment:1 Changed 10 years ago by
- Description modified (diff)
- Status changed from new to needs_review
comment:2 Changed 9 years ago by
- Cc jason added
comment:3 Changed 9 years ago by
- Status changed from needs_review to needs_work
- Work issues set to rebase
comment:4 Changed 9 years ago by
- Description modified (diff)
- Status changed from needs_work to needs_review
- Work issues rebase deleted
comment:5 Changed 9 years ago by
it's kind of weird that one coerces a complex matrix into real symmetric, but then treats it as a Hermitian one... Surely with real symmetric matrices there might be better options, no?
comment:6 Changed 9 years ago by
Despite the name, scipy.linalg.eigh
will call lapack syevr
/ heevr
depending on whether the field is real / complex.
comment:7 Changed 9 years ago by
The algorithm='symmetric'
keyword is meant to allow the routine accomodate both base rings (RDF/CDF) while also allowing a user to specify that a matrix is known to be symmetric. In this case, the conversion from CDF to RDF is made by the routine and then the SciPy behavior that Volker notes will take place.
Any suggestions on making the docstring clearer? Maybe saying "then applies the algorithm for Hermitian matrices" should be stated differently?
comment:8 follow-up: ↓ 9 Changed 9 years ago by
- Reviewers set to Volker Braun
- Status changed from needs_review to needs_work
On Fedora 16 x86_64, I get
sage -t devel/sage-main/sage/matrix/matrix_double_dense.pyx ********************************************************************** File "/home/vbraun/opt/sage-5.0.rc0/devel/sage-main/sage/matrix/matrix_double_dense.pyx", line 1570: sage: A.eigenvalues(algorithm='symmetric', tol=1.0e-20) Expected: [(-2.0, 1), (-2.0, 2), (-2.0, 1), (1.0, 1), (1.0, 1), (1.0, 1), (1.0, 1), (1.0, 1), (3.0, 1)] Got: [(-2.0, 1), (-2.0, 2), (-2.0, 1), (1.0, 1), (1.0, 1), (1.0, 2), (1.0, 1), (3.0, 1)]
ATLAS is from Fedora, CPU is a Sandy-Bridge i7 quad-core.
Minor nitpicks while we are at it:
- Can you return a tuple (=immutable) instead of a list?
- the symmetric docstring, how about: "converts
self
to a real matrix and applies the algorithm for Hermitian matrices". Note: technically you convert (explicit), not coerce (implicit). - in the hermitian docstring, how about: "uses the :meth:
~scipy.linalg.eigh
method from SciPy, which applies only to real symmetric or complex Hermitian matrices. Since...". This would make it clear that thesyevr
implementation is used if possible. - the ".. warning::" block is not indented, so it is not typeset correctly.
comment:9 in reply to: ↑ 8 Changed 9 years ago by
Replying to vbraun:
On Fedora 16 x86_64, I get...
Thanks, I'll increase the tolerance and that should work better across platforms. You'd think I'd get the hang of this numerical stuff...
Minor nitpicks while we are at it:
- Can you return a tuple (=immutable) instead of a list?
I'm not opposed, but other eigenvalue routines return mutable objects. I'd prefer to do one grand change across all matrix types, on a single-purpose ticket of its own.
sage: A = matrix(QQ, [[1]]) sage: ev=A.eigenvalues() sage: type(ev) <class 'sage.structure.sequence.Sequence_generic'> sage: ev[0]=5 sage: ev [5]
- the symmetric docstring, how about: "converts
self
to a real matrix and applies the algorithm for Hermitian matrices". Note: technically you convert (explicit), not coerce (implicit).- in the hermitian docstring, how about: "uses the :meth:
~scipy.linalg.eigh
method from SciPy, which applies only to real symmetric or complex Hermitian matrices. Since...". This would make it clear that thesyevr
implementation is used if possible.- the ".. warning::" block is not indented, so it is not typeset correctly.
Thanks for the nits. I'll make some changes right now.
Rob
comment:10 Changed 9 years ago by
- Description modified (diff)
- Status changed from needs_work to needs_review
"Update" patch:
- Removes the
10^-20
tolerance doctest. Not really needed and will only cause trouble. (It was suppose to illustrate how a very small tolerance would split up "equal" eigenvalues.) - Adjusts documentation according to suggestions above.
- Includes new pointers to routines to check symmetric and Hermitian properties.
- No code changes.
Rob
comment:11 follow-up: ↓ 12 Changed 9 years ago by
- Status changed from needs_review to positive_review
Looks great!
comment:12 in reply to: ↑ 11 Changed 9 years ago by
Replying to vbraun:
Looks great!
Thanks, Volker!
This was built on various 5.0-beta's, so I just double-checked that it applies, tests and builds on 5.0-rc0.
Rob
comment:13 Changed 9 years ago by
- Milestone changed from sage-5.0 to sage-5.1
comment:14 Changed 9 years ago by
- Status changed from positive_review to needs_work
The warning
in the docstring is misformatted, see http://sagemath.org/doc/developer/conventions.html#documentation-strings
Changed 9 years ago by
comment:15 Changed 9 years ago by
- Description modified (diff)
- Status changed from needs_work to positive_review
I thought this was OK and I just triple-checked, and I think it is OK. One change: made "warning" all capital letters, this is the only change to the v2 version of the update patch.
The HTML documentation renders the warning blocks as they should. I'm going to move this back to positive review.
Jeroen - please let me know if I am really missing something here. Thanks.
Rob
comment:16 Changed 9 years ago by
- Keywords sd40.5 added
Yes, it looks okay now. I don't remember what precisely was wrong before.
comment:17 Changed 9 years ago by
- Merged in set to sage-5.1.beta4
- Resolution set to fixed
- Status changed from positive_review to closed
Patch does not apply to 5.0.beta7 (see patchbot logs)