Added Python modules and scripts, still haven't figured out how to add documentation cleanly



git-svn-id: https://simtk.org/svn/forcebalance@1 e93b7d5b-8bb4-0410-82c6-a20ae092c748
Added a bunch of documentation files (individual files in dirs can be added with svn add --depth=empmty directory)



git-svn-id: https://simtk.org/svn/forcebalance@2 e93b7d5b-8bb4-0410-82c6-a20ae092c748
I did a git clone of the SVN repo so they should be synced now

git-svn-id: https://simtk.org/svn/forcebalance@3 e93b7d5b-8bb4-0410-82c6-a20ae092c748
Added a script and updated the logo

git-svn-id: https://simtk.org/svn/forcebalance@4 e93b7d5b-8bb4-0410-82c6-a20ae092c748
Not quite sure what I did. :P
Not quite sure what I did. :P

git-svn-id: https://simtk.org/svn/forcebalance@5 e93b7d5b-8bb4-0410-82c6-a20ae092c748
Many changes
Removed storage of mvals, pvals, mvals0 in force field
Implemented read-in of mvals and pvals
Implemented checkpoint files

git-svn-id: https://simtk.org/svn/forcebalance@6 e93b7d5b-8bb4-0410-82c6-a20ae092c748
Many changes
Removed storage of mvals, pvals, mvals0 in force field
Implemented read-in of mvals and pvals
Implemented checkpoint files
Added test case 1: water 12-mer, two different fitting simulations,
several different run options
Greatly improved the documentation, new navigation tabs added
Merge branch 'master' of leeping:/home/leeping/git/forcebalance
Commit for editing on laptop
Modified printcool_dictionary to omit printing of None values
Modified parser.py in a major way (comments are now strings that can be accessed)
Added MakeInputFile.py, a script to create input files
Currently working on the OptionIndex portion of the documentation.
Added test case 1: water 12-mer, two different fitting simulations,
several different run options

git-svn-id: https://simtk.org/svn/forcebalance@7 e93b7d5b-8bb4-0410-82c6-a20ae092c748
Greatly improved the documentation, new navigation tabs added

git-svn-id: https://simtk.org/svn/forcebalance@8 e93b7d5b-8bb4-0410-82c6-a20ae092c748
Still working on making things installable
Even more documentation
Merge branch 'master' of leeping:/home/leeping/git/forcebalance

Conflicts:
	MANIFEST.in
	doc/add-tabs.py
	doc/mainpage.py
	forcebalance/parser.py
	test/001_water12_tip4p/01_bfgs_from_start.in
	test/001_water12_tip4p/02a_bfgs_writechk.in
	test/001_water12_tip4p/02b_bfgs_readchk.in
	test/001_water12_tip4p/02c_bfgs_readmvals.in
	test/001_water12_tip4p/03a_test_grad.in
	test/001_water12_tip4p/03b_test_hess.in
	test/001_water12_tip4p/04a_cg.in
	test/001_water12_tip4p/04b_simplex.in
	test/001_water12_tip4p/result/water.itp
Still working on making things installable

git-svn-id: https://simtk.org/svn/forcebalance@9 e93b7d5b-8bb4-0410-82c6-a20ae092c748