[[Imported from SVN: r3489]]

[[Imported from SVN: r3413]]

[[Imported from SVN: r3286]]

[[Imported from SVN: r2617]]

[[Imported from SVN: r2524]]

[[Imported from SVN: r2418]]

[[Imported from SVN: r2377]]

[[Imported from SVN: r2376]]

[[Imported from SVN: r2201]]

[[Imported from SVN: r2047]]

[[Imported from SVN: r2046]]

[[Imported from SVN: r2040]]

[[Imported from SVN: r2039]]

- do not hardwire the 3d material parameters
- add method to create a straight initial rod
- remove Neumann damping
- remove anisotropic damping
- do not hardwire the rod material and shape parameters
- use the C++ IPOpt, if requested
- use absolute corrections size for termination
- better determination of the overall convergence rate

[[Imported from SVN: r2018]]

[[Imported from SVN: r1891]]

[[Imported from SVN: r1793]]

[[Imported from SVN: r1773]]

[[Imported from SVN: r1680]]

[[Imported from SVN: r1647]]

[[Imported from SVN: r1639]]

[[Imported from SVN: r1623]]

[[Imported from SVN: r1618]]

[[Imported from SVN: r1617]]

[[Imported from SVN: r1616]]

[[Imported from SVN: r1615]]

[[Imported from SVN: r1613]]

[[Imported from SVN: r1609]]

[[Imported from SVN: r1589]]

[[Imported from SVN: r1562]]

[[Imported from SVN: r1552]]

[[Imported from SVN: r1539]]

[[Imported from SVN: r1538]]

write grid and deformation into a single file;  fix geometric moments of the rod, to really model a quadratic cross-section

[[Imported from SVN: r1537]]

[[Imported from SVN: r1533]]

[[Imported from SVN: r1530]]

[[Imported from SVN: r1076]]

[[Imported from SVN: r1041]]

[[Imported from SVN: r904]]

a first attempt at coupling a 3d object to a 1d object.  Contains the infrastructure to have both hessian matrices in one, but not the actual coupling entries

[[Imported from SVN: r833]]