MikeHeiber / Ising_OPV / 19 / 1
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LAST BUILD BRANCH: bugfix_tortuosity_histograms
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MikeHeiber 
Code Cleanup and Testing Update

-updated documentation

main:
-refactored MPI collection of results to use Utils functions for
gathering vectors
-added use of new MPI_gatherValues function to gather individual metrics
from each processor into a single vector on proc0
-removed output of end-to-end path data
-updated output of depth dependent data to only produce interfacial
volume fraction for the whole morphology instead of separate metrics for
each site type
-updated analysis fle output to use vector analysis template functions
in Utils
-renamed Correlation_cutoff_distance to
Extended_correlation_cutoff_distance to be more descriptive about how
the parameter is used

Morphology class:
-updated depth dependent interfacial volume ratio to be calculated for
the whole morphology instead of for each site type
-update tortuosity data to use a double vector instead of a float vector
to be more consistent with other data outputs
-commented out the old, unused calculateEnergyChange function
-renamed Correlation_cutoff_distance to
Extended_correlation_cutoff_distance to be more descriptive about how
the parameter is used
-updated calculateInterfacialVolumeFraction function to use
isNearInterface function to simplify the implementation and re-use
existing code

Utils
-added new MPI_gatherValues function to gather a variable value from all
processors into a vector on proc0
-added template function vector_median and vector_which_median to
calculate the median and data elements closest to the median for generic
data vectors

tests:
-added Morphology class tests for the depth dependent analysis metrics
-added Morphology class tests comparing the results from two two
different tortuosity methods
-added Utils tests for the new vector_median and vector_which_median
functions

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