diff --git a/PythonScripts/GUI/GeoSAM/InterpolationFrame.py b/PythonScripts/DEPRECATE/InterpolationFrame.py similarity index 100% rename from PythonScripts/GUI/GeoSAM/InterpolationFrame.py rename to PythonScripts/DEPRECATE/InterpolationFrame.py diff --git a/PythonScripts/GUI/GeoSAM/GeoSams.py b/PythonScripts/GUI/GeoSAM/GeoSams.py index 070c943..120e612 100644 --- a/PythonScripts/GUI/GeoSAM/GeoSams.py +++ b/PythonScripts/GUI/GeoSAM/GeoSams.py @@ -4,6 +4,7 @@ # This is the main program for the GeoSAMS GUI # # The GUI has 7 tabs +# -# Math Setup: This frame allows the user to modify the Matlab/Octave startup files. # -# Main: Data concerning simulation duration, configutation files in use, and recruitment period # -# Growth: Define parameters to compute fishing mortality # -# Special Access: 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. # -# Sort By Area: Parameters that are used to sort output data and associate with areas of interest -# -# UKInterpolation: Parameters that are used to interpolate results from survey grid to regional grid -# -# Math Setup: This frame allows the user to modify the Matlab/Octave startup files. +# -# Sort By Region: 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 SHOW Args 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 * diff --git a/PythonScripts/GUI/GeoSAM/SortByRegionFrame.py b/PythonScripts/GUI/GeoSAM/SortByRegionFrame.py index 09fd0c3..916c07c 100644 --- a/PythonScripts/GUI/GeoSAM/SortByRegionFrame.py +++ b/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. diff --git a/SRC/ScallopGrowth.f90 b/SRC/ScallopGrowth.f90 index a1c965d..703e706 100644 --- a/SRC/ScallopGrowth.f90 +++ b/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 diff --git a/SRC/ScallopMortality.f90 b/SRC/ScallopMortality.f90 index 6e63baa..c7f5640 100644 --- a/SRC/ScallopMortality.f90 +++ b/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 diff --git a/SRC/ScallopRecruit.f90 b/SRC/ScallopRecruit.f90 index db56ead..76cc429 100644 --- a/SRC/ScallopRecruit.f90 +++ b/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 diff --git a/docs/GeoSAMS-GUI.docx b/docs/GeoSAMS-GUI.docx new file mode 100644 index 0000000..36391ad Binary files /dev/null and b/docs/GeoSAMS-GUI.docx differ diff --git a/docs/GeoSAMS-GUI.pdf b/docs/GeoSAMS-GUI.pdf index 078b0a0..b294b8d 100644 Binary files a/docs/GeoSAMS-GUI.pdf and b/docs/GeoSAMS-GUI.pdf differ diff --git a/docs/GeoSAMS-Growth.docx b/docs/GeoSAMS-Growth.docx new file mode 100644 index 0000000..7ce107e Binary files /dev/null and b/docs/GeoSAMS-Growth.docx differ diff --git a/docs/GeoSAMS-Growth.pdf b/docs/GeoSAMS-Growth.pdf index 7921b16..3303420 100644 Binary files a/docs/GeoSAMS-Growth.pdf and b/docs/GeoSAMS-Growth.pdf differ diff --git a/docs/GeoSamsStartup.docx b/docs/GeoSamsStartup.docx index ac43a8a..81f9032 100644 Binary files a/docs/GeoSamsStartup.docx and b/docs/GeoSamsStartup.docx differ diff --git a/docsSIM/Doxyfile b/docsSIM/Doxyfile index fee70c9..fcae689 100644 --- a/docsSIM/Doxyfile +++ b/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