notebooks
Starting to revamp for inclusion of tmat

need: check convergence
depends on: movie code
Maybe working
Include ipynotbook for good measure
Made some critical fixes in movie making
Add new notebook, fix calculation of number of plot rows
New configs
Set get_eigen to False, as was originally intended

But never implemented.
New visualization for scatter

Plot size as 1/Energy and color ~ Energy
Hack to select a particular seed structure based on runcopy
Visualization scales with number of states for tmat

Allows compatibility between alanine and ntl9
Merge pull request #11 from mpharrigan/inttmat_patch1

Inttmat patch1
Change this default
Changes to make subdivision work for tmat
Merge pull request #12 from mpharrigan/inttmat

Inttmat