#These KNOWN ISSUES belong to work by Gygli and Pleiss

#'Simulation Foundry: scalable and FAIR molecular modelling'

# This code is released under a GNU GPL license
# https://www.gnu.org/licenses/gpl-3.0.html

# This is free software; you are free to change and redistribute it.
# There is NO WARRANTY, to the extent permitted by law.

# Gudrun Gygli October 19 gudrungygli@gmail.com
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# Read the manual for the Simulation Foundry before using it!
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This is a short list of errors we have encountered while using the 

Simulation Foundry - it is probably not complete, 
but can help to eliminate some common mistakes

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known errors produced if files are missing:

If a file is missing/empty and averaging_diffusion_CML.py tries to work with it, the following errors are produced (for my user, gug)

/home/gug/.local/lib/python2.7/site-packages/numpy/core/_methods.py:140: RuntimeWarning: Degrees of freedom <= 0 for slice
  keepdims=keepdims)
/home/gug/.local/lib/python2.7/site-packages/numpy/core/_methods.py:110: RuntimeWarning: invalid value encountered in true_divide
  arrmean, rcount, out=arrmean, casting='unsafe', subok=False)
/home/gug/.local/lib/python2.7/site-packages/numpy/core/_methods.py:132: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/home/gug/.local/lib/python2.7/site-packages/numpy/core/fromnumeric.py:2920: RuntimeWarning: Mean of empty slice.
  out=out, **kwargs)
/home/gug/.local/lib/python2.7/site-packages/numpy/core/_methods.py:85: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
[]

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LATEX error with "
 bad adaptive filter value

!pdfTeX error: pdflatex: libpng: internal error"

means one of your pngs is broken - fix it and run again

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errors:

/home/jka/Documents/Workflows/glyceline_EQ20ns_MD50ns/ANALYSIS_V1.5/scripts/ANALYSIS.morecomplexfunctions: line 382: ((: R<=: syntax error: operand expected (error token is "<=")
working on supercomputer homer

means that your parameters (replicates, temperatures etc) are not working - e.g. replicates 1 instead of 1 1 in INPUT etc

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