Doc Cleanup, PDF copies

PythonScripts/GUI/GeoSAM/GeoSams.py

@@ -4,6 +4,7 @@
 # This is the main program for the GeoSAMS GUI
 # 
 # The GUI has 7 tabs
+# -# <b>Math Setup</b>: This frame allows the user to modify the Matlab/Octave startup files.
 # -# <b>Main</b>: Data concerning simulation duration, configutation files in use, and recruitment period
 # -# <b>Growth</b>: Define parameters to compute fishing mortality
 # -# <b>Special Access</b>: Files used to define special areas for fishing management
@@ -12,18 +13,16 @@
 #    location falls within the defined area given by the area defintions in 
 #    Special Access Frame and assigned the area number.
 # -# <b>Sort By Area</b>: Parameters that are used to sort output data and associate with areas of interest
-# -# <b>UKInterpolation</b>: Parameters that are used to interpolate results from survey grid to regional grid
-# -# <b>Math Setup</b>: This frame allows the user to modify the Matlab/Octave startup files.
+# -# <b>Sort By Region</b>: Parameters that are used to sort output data and associate with zones defined by shapefiles
 #
 # The program is started by entering the following command in the root directory of the workspace
 # $ python .\\PythonScripts\\GUI\\GeoSAM\\GeoSams.py [10 8]
 #
-# Where the last three number are optional and used to set limits on:
+# Where the last two number are optional and used to set limits on:
 # - The maximum number of areas of interest that can be defined.
 # - The maximum number of nodes used to specify each area of interest.
-# - The maximum number of years that the simulation can cover, i.e. Stop Year - Start Year + 1
 #
-# When commanded without these values the GUI defaults to 10, 8, and 5. These values can be viewed by 
+# When commanded without these values the GUI defaults to 50 and 8. These values can be viewed by 
 # clicking the <b>SHOW Args</b> Button
 #
 # @section p1p1 SHOW Args
@@ -71,7 +70,6 @@
 
 from MainInputFrame import *
 from GrowthFrame import *
-from InterpolationFrame import *
 from SortByAreaFrame import *
 from SortByRegionFrame import *
 from SpecialAreaFrame import *

PythonScripts/GUI/GeoSAM/SortByRegionFrame.py

@@ -1,15 +1,15 @@
-## @page SortRegion  Sort By Area Frame
-# Assists the user in defining areas of interest to assess accumulated parameters located
-# in these areas of interest.
+## @page SortRegion  Sort By Region Frame
+# Assists the user in viewing accumulated parameters located
+# in zones defined by shapefiles.
 #
-# @section SortRegion p2 Output Parameters
+# @section SortRegionP1 Output Parameters
 #
 # This is a dropbox of the selected output parameters on the main tab. After 
 # a simulation and interpolation have been run, the user would select one of
 # these output, click Run Sort, and the amount of that output in each of the
 # shapefile regions is accumulated by year.
 #
-# @section SortRegion p4 Run Sort
+# @section SortRegionP2 Run Sort
 # This will start the program to check if a region grid value for a given 
 # year is within one of the specified area and if so accumulate the year
 # sum with that value.

SRC/ScallopGrowth.f90

@@ -105,12 +105,6 @@
 !> H_{MN18}(x, \sigma, \omega) = \frac{1}{\omega}\bigg(x\Phi_N(x,0,\sigma^2) + \sigma^2\phi_N(x,0,\sigma^2)\bigg)
 !> @f]
 !>
-!> WAS
-!> @f[
-!> H_{MN18}(x, \sigma, \omega) = \frac{1}{\omega}(x*f+\sigma^2 * f)
-!> @f]
-!> where @f$f = \Phi_N@f$ 
-!>
 !> @subsubsection Gssubsubsec2 Normal Cumulative Distribution Function
 !> @f[
 !> \Phi(x,\mu,\sigma) = \frac{1}{2}(1+Erf(\frac{x-\mu}{\sigma\sqrt{2}}))
@@ -121,8 +115,6 @@
 !> \phi(x,\mu,\sigma) = \frac{1}{\sigma\sqrt{2\pi}}e^{-\frac{(x-\mu)^2}{2\sigma^2}}
 !> @f]
 
-
-!>----------------------------------------------------------------------------------------------------------------
 MODULE Growth_Mod
 use globals
 use Grid_Manager_Mod
@@ -600,12 +592,6 @@ end subroutine increment_mean_std
 !> H_{MN18}(x, \sigma, \omega) = \frac{1}{\omega}[x\Phi_N(x,0,\sigma^2) + \sigma^2\phi_N(x,0,\sigma^2)]
 !> @f]
 !>
-!> WAS
-!> @f[
-!> H_{MN18}(x, \sigma, \omega) = \frac{1}{\omega}(x*f+\sigma^2 * f)
-!> @f]
-!> where @f$f = \Phi_N@f$ 
-!>
 !> @param[in] x - evaluation point
 !> @param[in] sigma - paramaters defined within MN18
 !> @param[in] w  - paramaters defined within MN18

SRC/ScallopMortality.f90

@@ -1,4 +1,3 @@
-!>----------------------------------------------------------------------------------------------------------------
 !> @page page3 Mortality_Mod
 !>
 !> The methods in this class are used to determine the selectiviy and discard of the scallops based on shell

SRC/ScallopRecruit.f90

@@ -1,4 +1,4 @@
-!>---------------------------------------------------------------------------------------------------------------------
+!>
 !> @page page2 Recruit_Mod
 !>
 !> @section Rsec1 Recruitment Class
@@ -8,7 +8,7 @@
 !> - rec_start = a decimal value given as day of the year divided by 365.2425. Typically 0, which would be January 1
 !> - rec_stop = decimal value given as day of the year divided by 365.2425. Typically 100/365.2425, which is April 10th.
 !>
-!>---------------------------------------------------------------------------------------------------------------------
+!>
 module Recruit_Mod
 use globals
 implicit none

docsSIM/Doxyfile

@@ -42,7 +42,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "Scallop Growth Density"
+PROJECT_NAME           = "GeoSAMS Growth"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version