MikeHeiber / Ising_OPV / 29 / 1
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coverage: 71.213% (-7.5%) from 78.698%
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MikeHeiber 
Parameters Class and Testing Update

General:
-added new Parameters class to handle storage and import of all
parameters needed by Ising_OPV
-updated makefile to compile and build new Parameters class
-updated README file output section to have information about the
morphology cross section output files

main:
-removed Input_Params struct and moved all parameters contained by it
into the new Parameters class
-removed usage of TomogramImport_Params and CorrelationCalc_Params
because all of the these different types of parameters are now contained
in the Parameters class
-updated Morphology constructor usage to use the new prefered version
which accepts a Parameters object to define the options
-moved ImportParameters function into the Parameters class

Lattice class:
-added throwing of invalid_argument exception to getSiteCoords when the
input site index is negative

Morphology class:
-commented out all use of the third neighbor interactions because I do
not currently want to support this feature
-added new Parameters object member variable to contain all neccesary
parameters loaded from the input parameter file
-updated constructors to take as input a Parameters object
-updated many analysis functions to longer require passing of parameters
to specify how the calculation is done, and so calculations will be done
using the current values stored by the Parameters member variable
-added new setParameters function that allows users to change the
parameters of the Morphology object without constructing a new object
-corrected bug in calculateAnisotropies where calculation was not being
stopped when the cutoff distance was getting too large
-updated importMorphologyFile to significantly simpify the
implementation and no longer support file formats generated by earlier
versions of Ising_OPV
-removed the CorrelationCalc_Params and TomogramImport_Params structs
and these parameters are not used from the new Parameters object

Parameters class:
-added initial p... (continued)

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Source Files on job 29.1 (OPTIONS="GCC_VERSION=5 && MPI=openmpi && TARGET=test_coverage")