TODO

for 221 spe, why do you have so many separate sdf files?! this should be able to go into a single one since all same coordinates

 script modifications
  1. timeAvg
     * make timeAvg able to take command line inputs, rename 
     * print out the tag, level of theory being analyzed
  2. remove adir dependency from all scripts. Input file should be in relevant directory already.
  3. remove the wdir variables! instead use os.path.dirname(file)
  4. remove any global variables outside functions.
  5. make sure that blank return matches number of expected returns, e.g. return (None, None)


  x. when it can't find an output file, it just quits. have it bypass and write warning
     ===== Div_1 =====
     No output.dat file found in directory of /data12/cmf/limvt/qm_AlkEthOH/pipeline/4_diverse-D/OPT2/Div_1/1

 clean up
  1. argument names
  2. docstrings
  3. import modules
  4. warning can't open file --> include return line after
  5. Length of python lines for purple stop signal

 write some kind of fucking instructions manual
  - actually, update docstrings and description for each script
  - then combine these into one document, 'documentation.md' or something

 figure out why slurm skips jobs?
 is numConfs supposed to stay constant before and after SPE calcns?
 how much of the ancillary SDF files should we keep? delete the *1* files?