MikeHeiber / Ising_OPV / 31

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Parameters and Testing Update

General:
-updated documentation
-updated travis yml file to change the compiler and mpi configuration of
the code coverage test to make it faster
-added new parameters to the parameter file to designate when users want
to import morphology files or a tomogram dataset
-reorganized sections of the parameter file
-updated default parameter file with addition explanation of the
parameters
-updated README with latest information about how to run Ising_OPV to
create and import morphologies

main:
-removed usage of command line arguments to specify when users want to
import morphologies or tomogram datasets and moved this functionality to
the parameter file
-moved imort enable variables to the Parameters class
-updated behavior so that when importing morphologies, the output data
analysis and morphology files overwrite the original files in the
working directory

Lattice class:
-updated extractSublattice function to throw different exceptions when
the inputs are not valid

Morphology class:
-corrected bugs in importMorphologyFile function

Parameters class:
-added parameters to handle enabling the import of morphology files and
tomogram datasets
-added checkParameters function that performs basic checks on the
validity of all parameters
-updated importParameters function to work with format of latest
parameter file version

tests:
-readded morphology file export and import tests

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1821 of 2353 relevant lines covered (77.39%)

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