Subject: [FEniCS-dev] FEniCS book

From: Anders Logg <[email-masked]>
Date: Wed, 11 Jun 2008 14:51:49 +0200

Dear all,

I have talked to Springer about publishing a FEniCS book and they are
very interested. The plan is to have a draft ready in time for the
FEniCS'09 meeting next summer.

The book will summarize the current state of FEniCS, function as a
reference for users, and showcase interesting applications built with
FEniCS.

I therefore invite anyone interested to review the suggested outline
below and give me feedback (either online or offline). Let me know how
and to which extent you would like to contribute to the book. I have
suggested some chapters below, but it's entirely up to the authors to
form their contribution!

The suggested deadline for contributions (title + authors) is
October 1 2008, with a final deadline for the finished chapters
on May 1 2009, after which we will have a review process.

The book will consist of four parts:

  Part 0:
    Introduction  (20-50 pages)
    Tutorial      (20-30 pages)

  Part I: Methodology (10 x 15 pages)

    This part will contain summaries/reviews of published results,
    but could also contain new results.

  Part II: Implementation (10 x 30 pages)

    This part will give a detailed presentation of our packages and
    their design by the package authors, more in the style of
    tutorials than journal papers. Other contributions may include
    discussions of particular aspects not related to a specific
    package like code generation and interface design.

   Part III: Application (10 x 15 pages)

    This part will demonstrate interesting applications where FEniCS
    has been used as the computing platform. It would be very
    interesting to receive contributions from people outside the
    circle of package authors.

Below follows a list of suggested contributions. This is just from the
top of my head so consider the titles/authors a rough initial value
for further iteration.

  Introduction: Logg (+ others?)
  Tutorial: Langtangen

  Methodology:

    Finite element code generation: Alnaes, Logg, Mardal
    Finite element assembly: Logg + others
    Optimal evaluation of finite element variational forms: Kirby, Scott
    Efficient finite element mesh representation: Karpeev, Knepley, Logg?
    Computing finite element basis functions: Kirby, Mardal
    A gallery of finite elements: Kirby? Terrel? Rognes? Mardal? Logg?
    Stabilized Galerkin: Hoffman, Johnson

  Implementation

    DOLFIN: Logg, Wells, Oelgaard
    FErari: Kirby
    FFC: Logg, Oelgaard, Rognes, Wells
    FIAT: Kirby
    Instant: Mardal
    SyFi: Mardal, Alnaes
    UFC: Alnaes, Logg, Mardal, Skavhaug, Langtangen
    UFL: Alnaes, Logg, Mardal
    Unicorn: Hoffman, Jansson
    Viper: Skavhaug

    Generic linear algebra interfaces: Alnaes, Logg, Mardal, Skavhaug, Wells
    A note on build systems: Knepley, Odegard
    Gotran: Skavhaug
    Exterior calculus: Logg, Mardal
    Sieve?

  Application

    Contributions from CBC
    Contributions from KTH
    Contributions from Umeå
    Contributions from Argonne?

    Something on inverse problems: Myklebust, Mardal, Nielsen
    Something on flow problems: Valen-Sendstad, Logg, Mardal
    Something on electro-mechanics: Alnaes, Sundnes
    Something on FSI: Selim

    Other contributors: Narayanan, Schroll, Lines, Ostien, Lindbo,
    Hake, Brown, Nazarov, Lopes, Wilbers, Voigt, Kaasbjerg, etc

  Appendix

    Summary of notation (Logg)
    UFC reference cells
    UFC numbering of mesh entities
    Something about Scons?
    Something about SWIG?

PS: Further discussion of this topic will take place on the fenics-dev
mailing list. So if you are interested in following the discussion,
please sign up at http://www.fenics.org/mailman/listinfo/fenics-dev

-- 
Anders

---

From: [email-masked] (Ridgway Scott)
Date: Wed, 11 Jun 2008 08:17:48 -0500 (CDT)

We will contribute something on non-Newtonian flow and on
non-nested multigrid solvers.

				Ridg

---

From: "Evan Lezar" <[email-masked]>
Date: Wed, 11 Jun 2008 15:23:28 +0200

Sounds like I have picked the right time to start having a look around
here.  This is good news and if I can get something together
pertaining to full-wave computational electromagnetics (perhaps in
collaboration with someone else) I will be more than happy to submit
it.

I look forward to seeing what comes from this.

Evan

On Wed, Jun 11, 2008 at 2:51 PM, Anders Logg <[email-masked]> wrote:
> _______________________________________________
> FEniCS-dev mailing list
> [email-masked]
> http://www.fenics.org/mailman/listinfo/fenics-dev
>

---

From: "Matthew Knepley" <[email-masked]>
Date: Wed, 11 Jun 2008 08:28:51 -0500

I would also be willing to write something on the Sieve idea for
handling meshes.
It should include the content of Anders paper, and Rob might be willing to talk
about extending the idea into handling computational (equation) graphs as well.

   Matt

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which
their experiments lead.
-- Norbert Wiener

---

From: "Johan Hoffman" <[email-masked]>
Date: Wed, 11 Jun 2008 16:36:58 +0200 (MEST)

Anders,

Sounds like a very good idea! Below is some input on the plan:

Part I: Our group could add material on mesh refinement, ALE technology
including mesh smoothing, parallel computing (including mesh refinement),
adaptivity and a posteriori error estimation.

Part II: We could contribute to the DOLFIN chapter.

Part III: Here we could contribute with a number of industry/research
examples. What is the difference between "Contributions X" and "Something
X" ?

/Johan

---

From: Anders Logg <[email-masked]>
Date: Thu, 12 Jun 2008 10:13:37 +0200

> examples. What is the difference between "Contributions X" and "Something

No difference. It's just that I happened to list some contributions
that have been suggested to me already. There may very well be
overlapping contributions. So "Something on flow problems" does not
exclude other contributions related to flow problems!

-- 
Anders

---

From: "Johan Hoffman" <[email-masked]>
Date: Thu, 12 Jun 2008 10:31:27 +0200 (MEST)

> exclude other contributions related to flow problems!

Ok, I see.

/Johan

---

From: Anders Logg <[email-masked]>
Date: Thu, 12 Jun 2008 12:29:43 +0200

Thanks for all comments regarding the book. I'm looking forward to
your receiving your contributions. 

I will send out a reminder again before the deadline for submissions
in October.

After that, I will prepare a detailed table of contents and provide
all authors with LaTeX templates for the chapters. I'm also planning
to prepare a summary of suggested notation to have a (somewhat)
uniform presentation throughout the book.

-- 
Anders

---

From: 'Anders Logg' <[email-masked]>
Date: Thu, 12 Jun 2008 21:11:55 +0200

Sounds good!

-- 
Anders

On Thu, Jun 12, 2008 at 09:06:36PM +0200, Achim Schroll wrote:
> I can contribute with a note on "automatic calibration of depositional
> models using DOLFIN".
> 
> Best regards, Achim
> 
> Achim Schroll [ simula . research laboratory ] 
> computational geoscience - turning rocks into knowledge.
> 
> -----Ursprungligt meddelande-----
> Från: [email-masked] [mailto:[email-masked]] För Anders Logg
> Skickat: den 11 juni 2008 14:52
> Till: Discussion of FEniCS development; [email-masked]
> Kopia: Martin Peters
> Ämne: FEniCS book
> 
> 
> Dear all,
> 
> I have talked to Springer about publishing a FEniCS book and they are very
> interested. The plan is to have a draft ready in time for the FEniCS'09
> meeting next summer.
> 
> The book will summarize the current state of FEniCS, function as a reference
> for users, and showcase interesting applications built with FEniCS.
> 
> I therefore invite anyone interested to review the suggested outline below
> and give me feedback (either online or offline). Let me know how and to
> which extent you would like to contribute to the book. I have suggested some
> chapters below, but it's entirely up to the authors to form their
> contribution!
> 
> The suggested deadline for contributions (title + authors) is October 1
> 2008, with a final deadline for the finished chapters on May 1 2009, after
> which we will have a review process.
> 
> Below follows a list of suggested contributions. This is just from the top
> of my head so consider the titles/authors a rough initial value for further
> iteration.
> 
> mailing list. So if you are interested in following the discussion, please
> sign up at http://www.fenics.org/mailman/listinfo/fenics-dev
>

---

From: [email-masked]
Date: Wed, 18 Jun 2008 22:33:38 +0100

I hope i've something to submit by that date.
Is Boussinesq type equations for Surface Waves a good topic for the 
Application part?
I've done some  study/work  for that subject, 
and I want, in the next two months,  to implement a  DOLFIN solver for some of 
that equations.  
-- 
Nuno David Lopes
Wed Jun 18 22:26:51 WEST 2008

---

From: Anders Logg <[email-masked]>
Date: Fri, 20 Jun 2008 22:42:07 +0200

> and I want, in the next two months,  to implement a  DOLFIN solver for some of 

Yes, please submit an abstract before the deadline and I'd be happy to
consider it for inclusion.

-- 
Anders