gs2crmod 0.11.86 → 0.11.87
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- data/.document +0 -0
- data/Gemfile +0 -0
- data/LICENSE.txt +0 -0
- data/README.md +0 -0
- data/README.rdoc +0 -0
- data/Rakefile +0 -0
- data/VERSION +1 -1
- data/ext/extconf.rb +0 -0
- data/ext/gs2crmod_ext.c +0 -0
- data/gs2crmod.gemspec +2 -2
- data/include/gs2crmod_ext.h +0 -0
- data/lib/gs2crmod/astrogk/astrogk.rb +0 -0
- data/lib/gs2crmod/astrogk/calculations.rb +0 -0
- data/lib/gs2crmod/astrogk/check_convergence.rb +0 -0
- data/lib/gs2crmod/astrogk/deleted_variables.rb +0 -0
- data/lib/gs2crmod/astrogk/graphs.rb +0 -0
- data/lib/gs2crmod/astrogk/gsl_data.rb +0 -0
- data/lib/gs2crmod/astrogk/gsl_tools.rb +0 -0
- data/lib/gs2crmod/astrogk/ingen.rb +0 -0
- data/lib/gs2crmod/astrogk/input_file_tools.rb +0 -0
- data/lib/gs2crmod/astrogk/namelist_tools.rb +0 -0
- data/lib/gs2crmod/astrogk/namelists.rb +0 -0
- data/lib/gs2crmod/astrogk/properties.rb +0 -0
- data/lib/gs2crmod/astrogk/species_dependent_namelists.rb +0 -0
- data/lib/gs2crmod/astrogk/test_gs2.rb +0 -0
- data/lib/gs2crmod/astrogk.rb +0 -0
- data/lib/gs2crmod/calculations.rb +0 -0
- data/lib/gs2crmod/check_convergence.rb +0 -0
- data/lib/gs2crmod/cyclone_defaults.rb +0 -0
- data/lib/gs2crmod/deleted_variables.rb +0 -0
- data/lib/gs2crmod/graphs.rb +3 -3
- data/lib/gs2crmod/graphs_rdoc.rb +0 -0
- data/lib/gs2crmod/gs2.rb +3 -1
- data/lib/gs2crmod/gsl_data.rb +14 -18
- data/lib/gs2crmod/gsl_data_3d.rb +0 -0
- data/lib/gs2crmod/gsl_tools.rb +0 -0
- data/lib/gs2crmod/ingen.rb +0 -0
- data/lib/gs2crmod/namelists.rb +0 -0
- data/lib/gs2crmod/properties.rb +0 -0
- data/lib/gs2crmod/read_netcdf.rb +0 -0
- data/lib/gs2crmod/species_dependent_namelists.rb +0 -0
- data/lib/gs2crmod/spectrogk/deleted_variables.rb +0 -0
- data/lib/gs2crmod/spectrogk/namelists.rb +0 -0
- data/lib/gs2crmod/spectrogk.rb +0 -0
- data/lib/gs2crmod/test_gs2.rb +0 -0
- data/lib/gs2crmod.rb +0 -0
- data/lib/gs2crmod_extension.rb +0 -0
- data/sync_mediawiki/helper.rb +0 -0
- data/sync_mediawiki/sync_mediawiki.rb +0 -0
- data/sync_variables/copy_help.rb +0 -0
- data/sync_variables/helper.rb +0 -0
- data/sync_variables/sync_variables.rb +0 -0
- data/sync_variables_sgk/helper.rb +0 -0
- data/sync_variables_sgk/sync_variables_sgk.rb +0 -0
- metadata +2 -2
data/.document
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data/Gemfile
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data/LICENSE.txt
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data/README.md
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data/README.rdoc
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data/Rakefile
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data/VERSION
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@@ -1 +1 @@
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1
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-
0.11.
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1
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+
0.11.87
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data/ext/extconf.rb
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data/ext/gs2crmod_ext.c
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data/gs2crmod.gemspec
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@@ -5,11 +5,11 @@
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Gem::Specification.new do |s|
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s.name = "gs2crmod"
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-
s.version = "0.11.
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8
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+
s.version = "0.11.87"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
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-
s.date = "2015-
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s.date = "2015-02-12"
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s.description = "GS2 is a gyrokinetic flux tube initial value turbulence code which can be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated running and analysis of large simulations. This module allows GS2 (and its sister code AstroGK) to harness the power of the CodeRunner framework."
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s.email = "edmundhighcock@sourceforge.net"
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s.extensions = ["ext/extconf.rb"]
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data/include/gs2crmod_ext.h
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data/lib/gs2crmod/astrogk.rb
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data/lib/gs2crmod/graphs.rb
CHANGED
@@ -58,7 +58,7 @@ def auto_axiskits(name, options)
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'es_mom_flux_over_time' => ["#{species_type((options[:species_index] or 1)).capitalize} Momentum Flux", '', 1],
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'es_part_flux_over_time' => ["#{species_type((options[:species_index] or 1)).capitalize} Particle Flux", '', 1],
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'zonal_spectrum' => ["Zonal spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
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-
'
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+
'zf_velocity_over_x' => ['Zonal Flow Velocity', "", 1],
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'mean_flow_velocity_over_x' => ['Mean Flow Velocity', "", 1]
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}
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return hash[name]
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@@ -2419,7 +2419,7 @@ module GraphKits
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end
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end
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-
def
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+
def zf_velocity_vs_x_graphkit(options={})
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case options[:command]
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when :help
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return "zonal_flow_velocity_vs_x: Graph of the zonal flow velocity kxfac*IFT(i k_x phi). kxfac = (qinp/rhoc)*grho(rhoc)."
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@@ -2427,7 +2427,7 @@ module GraphKits
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return [:t, :t_index, :theta_index, :kxfac, :add_mean_flow]
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else
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options[:ky_index]=0
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2430
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-
kit = GraphKit.autocreate({x: axiskit('x', options), y: axiskit("
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2430
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+
kit = GraphKit.autocreate({x: axiskit('x', options), y: axiskit("zf_velocity_over_x", options)})
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if options[:add_mean_flow]
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kit.data[0].y.data += mean_flow_velocity_over_x_gsl_vector(options)
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end
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data/lib/gs2crmod/graphs_rdoc.rb
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data/lib/gs2crmod/gs2.rb
CHANGED
@@ -1252,7 +1252,7 @@ folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file
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def latex_graphs
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#will have a different set of graphs to look at depending on whether linear or nonlinear
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if @nonlinear_mode == "off"
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-
#make up a list of graphs that are to be included. The order of the arguments is [code to generate graphkit, LaTeX description
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+
#make up a list of graphs that are to be included. The order of the arguments is [code to generate graphkit, LaTeX description]
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graphs = [
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#[(kit = phi2_by_mode_vs_time({kx_index:1, ky_index:1}); kit.xlabel=%[TEST]; kit.gp.term = "post eps color enhanced size 3.5in,2.33in"; kit.gp.output = "test.eps"; kit), "This is a test graph written into a \LaTeX file. \n\n \\myfigure{test.eps}"]
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[(kit = phi2tot_vs_time_graphkit; kit.data[0].title=""; kit.gp.logscale="y"; kit.file_name = "phi2tot.eps"; kit), "Total $\\phi^2$ versus time."],
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@@ -1277,6 +1277,8 @@ folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file
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[(kit = es_mom_flux_vs_time_graphkit(species_index:1); kit.file_name = "es_mom_flux_1_vs_time.eps"; kit), "Momentum flux for species 1 as a function of time."],
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if @nspec > 1 then [(kit = es_mom_flux_vs_time_graphkit(species_index:2); kit.file_name = "es_mom_flux_2_vs_time.eps"; kit), "Momentum flux for species 2 as a function of time."] end,
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[(kit = zonal_spectrum_graphkit; kit.gp.logscale="y"; kit.file_name = "zonal_spectrum.eps"; kit), "Zonal spectrum at the final time step."],
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+
if @write_eigenfunc == ".true." then [(kit = zf_velocity_vs_x_graphkit(theta_index:get_list_of(:theta).length/2); kit.file_name = "zonal_flow_velocity_vs_x.eps"; kit), "Zonal flow velocity avg over time versus x."] end,
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+
if @write_eigenfunc == ".true." and @g_exb then [(kit = zf_velocity_vs_x_graphkit(theta_index:get_list_of(:theta).length/2, add_mean_flow:true); kit.file_name = "zonal_flow_velocity_vs_x_with_mean_flow.eps"; kit), "Zonal flow velocity with mean flow added avg over time versus x."] end,
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].compact
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end
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data/lib/gs2crmod/gsl_data.rb
CHANGED
@@ -1037,16 +1037,23 @@ module GSLVectors
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1038
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#This function returns the zonal flow velocity as a function of x (the radial coordinate).
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#This is v_ZF = kxfac*IFT(i k_x phi_imag), where kxfac = (qinp/rhoc)*grho(rhoc).
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-
def
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+
def zf_velocity_over_x_gsl_vector(options)
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Dir.chdir(@directory) do
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raise CRFatal.new("Need to specify a theta_index.") unless options[:theta_index]
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raise CRFatal.new("Need either qinp or pk and epsl specified in order to calculate kxfac.
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If using numerical equil use the option :kxfac to override calculation.") unless @qinp or (@pk and @epsl or options[:kxfac])
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-
phi = gsl_vector_complex('phi_zonal', options)
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kx = gsl_vector(:kx).to_box_order
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_x = gsl_vector(:x)
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grho = gsl_vector('grho')[options[:theta_index]]
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+
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+
phi = GSL::Vector.alloc(kx.size)
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+
for it in 0...gsl_vector(:t).size
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+
options[:t_index] = it
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+
phi += gsl_vector_complex('phi_zonal', options)
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+
end
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+
phi /= gsl_vector(:t).size
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+
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if @qinp
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kxfac = (@qinp/@rhoc)*grho
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elsif @pk and @epsl
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@@ -1164,25 +1171,14 @@ module GSLVectorComplexes
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#and time index if write_phi_over_time was enabled during the simulation
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def phi_zonal_gsl_vector_complex(options)
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Dir.chdir(@directory) do
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-
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#extra option required is t_index
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-
raise CRFatal.new("write_phi_over_time is not enabled so this function won't work") unless @write_phi_over_time
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-
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+
raise CRFatal.new("write_eigenfunc is not enabled so this function won't work") unless @write_eigenfunc
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options.convert_to_index(self, :t)
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-
a = netcdf_file.var('
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-
'start' => [0,
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-
'end' => [-1
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+
a = netcdf_file.var('phi0').get({
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+
'start' => [0,0,0, options[:t_index] - 1],
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+
'end' => [-1,-1,0, options[:t_index] - 1]
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})
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-
vector = GSL::Vector::Complex.alloc(GSL::Vector.alloc(a[0,0
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+
vector = GSL::Vector::Complex.alloc(GSL::Vector.alloc(a[0,0..-1,0,0]), GSL::Vector.alloc(a[1,0..-1,0,0]))
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return vector
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-
else
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-
a = netcdf_file.var('phi').get({
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-
'start' => [0, options[:theta_index], 0, 0],
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-
'end' => [-1, options[:theta_index], -1, 0]
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-
})
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-
vector = GSL::Vector::Complex.alloc(GSL::Vector.alloc(a[0,0,0..-1,0]), GSL::Vector.alloc(a[1,0,0..-1,0]))
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-
return vector
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-
end
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end
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end
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data/lib/gs2crmod/gsl_data_3d.rb
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data/lib/gs2crmod/gsl_tools.rb
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data/lib/gs2crmod/ingen.rb
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data/lib/gs2crmod/namelists.rb
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data/lib/gs2crmod/properties.rb
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data/lib/gs2crmod/read_netcdf.rb
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data/lib/gs2crmod/spectrogk.rb
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data/lib/gs2crmod/test_gs2.rb
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data/lib/gs2crmod.rb
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data/lib/gs2crmod_extension.rb
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data/sync_mediawiki/helper.rb
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data/sync_variables/copy_help.rb
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data/sync_variables/helper.rb
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metadata
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@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: gs2crmod
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version: !ruby/object:Gem::Version
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-
version: 0.11.
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+
version: 0.11.87
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prerelease:
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platform: ruby
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authors:
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@@ -10,7 +10,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2015-
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+
date: 2015-02-12 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: coderunner
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