The old version kept was too big, and kept a useless row of zeros around.
Removing this row should lead to a tiny increase in efficiency.  More importantly,
it gets us closer to the CosseratEnergyLocalStiffness class again, which
is scheduled to replace MixedCosseratEnergy eventually.

This is an important step towards making the 'mixed' Cosserat code more like
the regular one.  The mid-term goal is to merge the two implementations, because
there is way too much code duplication here.

[[Imported from SVN: r10101]]

'Mixed' means that the spaces for deformations and microrotations can
be chosen separately.

At this point there hasn't been a lot of testing yet.  In particular,
parallelizing the assembly is currently not supported.

[[Imported from SVN: r9852]]

[[Imported from SVN: r9785]]

The CosseratStrain object is a 3x3 matrix, where the last column
is (0,0,1)^T.  This special structure allows to use specially tuned
matrix methods (e.g., the determinant), which I intent to do in the
future.

[[Imported from SVN: r9752]]

This move more than halfs the size of this file, and makes it *much* easier
to understand.  If we ever need the gradient code we can still recover it
from the 2.3-2 branch.

[[Imported from SVN: r9650]]

It used to be a compile-term error, but now that we have ADOL-C support
the missing gradient is not a problem anymore.

[[Imported from SVN: r9516]]

This patch brings it back.

[[Imported from SVN: r9477]]

[[Imported from SVN: r9402]]

The only exception is the material parameters.  ADOL-C (for which
we are doing this), doesn't need to have them in a special type.

[[Imported from SVN: r9401]]

Saves us one call to sqrt().

[[Imported from SVN: r9400]]

[[Imported from SVN: r9389]]

[[Imported from SVN: r9388]]

[[Imported from SVN: r9387]]

[[Imported from SVN: r9308]]

[[Imported from SVN: r9290]]

    
Very surprisingly, it appears to work...

[[Imported from SVN: r9286]]

[[Imported from SVN: r9285]]

    
I still do not really understand it, but I believe it is
correct nevertheless.

[[Imported from SVN: r9282]]

[[Imported from SVN: r8627]]

There were two issues fixed by this patch:

a) The bending energy only involves the third director.
   One must look at it as a function in S^2, not as
   a subset of coefficients of a function to SO(3).
   This means that we have to use a different projection
   in one place.
b) A certain subset of the coefficients (see the code)
   must always be zero, because they are parts of
   3-vectors which are known to be perpendicular to (0,0,1).
   For some strange reason they aren't.  I now hardwire
   them to be 0 anyway.  This makes my test pass.
   Maybe one day I'll find the true reason :-)

[[Imported from SVN: r8626]]

of Neumann boundary forces.  But I am not sure and I want to
postpone the issue.  Therefore this patch adds a cpp warning.

[[Imported from SVN: r8625]]

Don't use a loop with 4 iteration to clear an array,
if the array has only length 3.

Boy, this did take a while to find...

[[Imported from SVN: r8593]]

[[Imported from SVN: r8572]]

[[Imported from SVN: r8571]]

[[Imported from SVN: r8570]]

[[Imported from SVN: r8569]]

Because trace(sym(A)) == trace(A)

[[Imported from SVN: r8568]]

[[Imported from SVN: r8567]]

[[Imported from SVN: r8566]]

[[Imported from SVN: r8565]]

[[Imported from SVN: r8409]]

implement the remaining curvature and bending terms for the energy gradient.  These are not working yet, though.

[[Imported from SVN: r8408]]

So far, the long form of the quadratic bending energy has been
implemented and tested, and it appears to do the right thing.

This is a snapshot commit.  The code remains out-commented until
it is finished.

[[Imported from SVN: r8403]]

[[Imported from SVN: r8364]]

we know the function value when calling evaluateDerivative.  So let's give that value to the method, to prevent it from recomputing it

[[Imported from SVN: r8363]]

Use the long form for the quadratic energy stiffness.  I tested it: when kappa=1 is does the same as the short form

[[Imported from SVN: r8308]]

[[Imported from SVN: r8307]]

to set the shear correction factor.

[[Imported from SVN: r8290]]