Checking in code and initial sample data.


git-svn-id: https://simtk.org/svn/checkensemble@1 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Should be more useable now.


git-svn-id: https://simtk.org/svn/checkensemble@2 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Updated checkdist.py to handle different observables.


git-svn-id: https://simtk.org/svn/checkensemble@3 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Bug fixes for generalization of the temperature test code.


git-svn-id: https://simtk.org/svn/checkensemble@4 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Remove the dependence on pymbar by adding the needed functions, and simplifying them.


git-svn-id: https://simtk.org/svn/checkensemble@5 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Updated of the output.


git-svn-id: https://simtk.org/svn/checkensemble@6 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Changing the figures.


git-svn-id: https://simtk.org/svn/checkensemble@7 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Removed pymbar dependence for good this time.


git-svn-id: https://simtk.org/svn/checkensemble@8 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Updated the various files, and added the harmonic test and the harmonic_pressure test


git-svn-id: https://simtk.org/svn/checkensemble@9 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Adding a bunch or graphs and output files, plus the updated files.  It is now possible to vary most of the parameters from the command line.


git-svn-id: https://simtk.org/svn/checkensemble@10 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Allowed specification of random seed, and regerated the runs with -s 12345


git-svn-id: https://simtk.org/svn/checkensemble@11 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Forgot to add this graph.


git-svn-id: https://simtk.org/svn/checkensemble@12 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Added ability to look at multidimensional harmonic oscillators.


git-svn-id: https://simtk.org/svn/checkensemble@13 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Updated the code to properly allow bootstrap sampling for the analytical codes.


git-svn-id: https://simtk.org/svn/checkensemble@14 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Some minor bugfixes.


git-svn-id: https://simtk.org/svn/checkensemble@15 3b6020e3-42ab-0410-be60-f0e2a992d8c5
g is not the correlation time, but the statistical inefficiency,
2*tau+1


git-svn-id: https://simtk.org/svn/checkensemble@16 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Fixed typo with taking the max with numpy.max(N0,N1), instead of numpy.max([N0,N1])


git-svn-id: https://simtk.org/svn/checkensemble@17 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Removed pdb note


git-svn-id: https://simtk.org/svn/checkensemble@18 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Added option to either scale or subsample to use the statistical efficiency.


git-svn-id: https://simtk.org/svn/checkensemble@19 3b6020e3-42ab-0410-be60-f0e2a992d8c5
Added some comments, made things more clear.


git-svn-id: https://simtk.org/svn/checkensemble@20 3b6020e3-42ab-0410-be60-f0e2a992d8c5