Trajectory continuation with NFsim

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What steps will reproduce the problem?
1. Run a simulation with the attached file (TLBR, split over two nfsim runs).
2. You will notice that the observable entries for the last point in the first 
half don't match exactly the observable entries at the start of the second 
half.  One fewer R site is free and one more R site is bound.  This corresponds 
to creation of half a bond! 

Not sure where the problem is, but somehow the configuration isn't being 
restored perfectly.

Original issue reported on code.google.com by jrfae...@gmail.com on 24 Jul 2012 at 2:52

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Original comment by jrfae...@gmail.com on 24 Jul 2012 at 2:53

Attachments:

• PS_tlbr.bngl

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Other issues with trajectory continuation in NFsim:

1) NFsim doesn't recognize t_start. Currently, simulate_nf() calculates 
t_end-t_start and passes this to NFsim, so simulations run from 0 to 
(t_end-t_start).

2) NFsim doesn't recognize 'continue' argument. Thus, GDAT files are 
overwritten in continuation simulations unless 'suffix' argument is used to 
modify the name of the output file.

Original comment by lh64@cornell.edu on 28 May 2013 at 10:42