trinitycrmod 0.3.0 → 0.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 0877712c481a4fec5d91f15adc539a7e1fdb83a8
-  data.tar.gz: 1982d8891a6c0002d8fa0ef9ec7e10b157cc1252
+  metadata.gz: 166e73d674743e9ef9e75198cd3e9919d2ccff40
+  data.tar.gz: acee71bfe6ab75b2f0c3a5ef1ec7b8e3ef622277
 SHA512:
-  metadata.gz: 047fbdde9d918bf6bfb0a3688101c12170c0f3bdbd06aea46d719d74ed357f7f50fd97226e9cebdbf6d9ffd867bf647ebcf729d84f90d8298158bdc43ce70d2a
-  data.tar.gz: 6340ce30b9d2bf792593f84feb303611b86ccd5182cf6258a8bcda4fb72bb5b3d52bd22ea80ed8e5592e422fcb05723d53957d5be88bed1148edf11fb78f6248
+  metadata.gz: 756a2ce534bcc19e6301aaeeaf7412645a3b7bbd6d88c835edfa74284b5c4960c61a75fe9d29a1a4fb97ee28fb3c674af09cabca5c70d9abc5089885dcf9b78e
+  data.tar.gz: 762f3bcaf227624ab4e4a4184b402e2688c13072ac4f0a2d00dccb6630a2d114bcf70f831e9a386fdbe23588f8bb4cdc66c305c287c99b5e7a9589e9cd7de840

data/Rakefile

@@ -21,6 +21,7 @@ Jeweler::Tasks.new do |gem|
   gem.description = %Q{This module allows Trinity, the Multiscale Gyrokinetic Turbulent Transport solver for Fusion Reactors, to harness the power of CodeRunner, a framework for the automated running and analysis of simulations.}
   gem.email = "edmundhighcock@sourceforge.net"
   gem.authors = ["Edmund Highcock"]
+	gem.files.exclude 'test/**/*'
   # dependencies defined in Gemfile
 end
 Jeweler::RubygemsDotOrgTasks.new

data/VERSION

@@ -1 +1 @@
-0.3.0
+0.3.1

data/trinitycrmod.gemspec

@@ -2,11 +2,11 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: trinitycrmod 0.3.0 ruby lib
+# stub: trinitycrmod 0.3.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.3.0"
+  s.version = "0.3.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
@@ -34,15 +34,6 @@ Gem::Specification.new do |s|
     "lib/trinitycrmod/trinity_gs2.rb",
     "sync_variables/helper.rb",
     "sync_variables/sync_variables.rb",
-    "test/gs2_42982/pr08_jet_42982_1d.dat.gz",
-    "test/gs2_42982/pr08_jet_42982_2d.dat.gz",
-    "test/gs2_42982/shot42982_jet.in",
-    "test/gs2_42982/shot42982_jet.trin",
-    "test/gs2_42982_results/v.tgz",
-    "test/helper.rb",
-    "test/ifspppl/test.trin",
-    "test/ifspppl_results/v/id_1.tgz",
-    "test/test_trinitycrmod.rb",
     "trinitycrmod.gemspec"
   ]
   s.homepage = "http://github.com/edmundhighcock/trinitycrmod"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrmod
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.3.1
 platform: ruby
 authors:
 - Edmund Highcock
@@ -133,15 +133,6 @@ files:
 - lib/trinitycrmod/trinity_gs2.rb
 - sync_variables/helper.rb
 - sync_variables/sync_variables.rb
-- test/gs2_42982/pr08_jet_42982_1d.dat.gz
-- test/gs2_42982/pr08_jet_42982_2d.dat.gz
-- test/gs2_42982/shot42982_jet.in
-- test/gs2_42982/shot42982_jet.trin
-- test/gs2_42982_results/v.tgz
-- test/helper.rb
-- test/ifspppl/test.trin
-- test/ifspppl_results/v/id_1.tgz
-- test/test_trinitycrmod.rb
 - trinitycrmod.gemspec
 homepage: http://github.com/edmundhighcock/trinitycrmod
 licenses:

data/test/gs2_42982/shot42982_jet.in

@@ -1,186 +0,0 @@
-! electrostatic, kinetic electrons
-
-&parameters
- beta = 0.0
- zeff = 1.7
-/
-
-&theta_grid_knobs
- equilibrium_option='eik'
-/
-
-&theta_grid_parameters
- ntheta= 8
- nperiod= 1
-
-! commented out parameters specified via Trinity
-! rhoc = 0.5
-! Rmaj = 5.0
-! R_geo = 5.0
-! qinp = 1.4
-! shat = 0.8
-! akappa = 1.0
-! akappri = 0.0
-! tri = 0.0
-! tripri = 0.0
-! shift = 0.0
-/
-
-&theta_grid_eik_knobs
- itor  = 1
- iflux = 0
- irho  = 2
-
- ppl_eq   = F
- gen_eq   = F
- 
- efit_eq  = F
- local_eq = T
-
- eqfile = 'dskeq.cdf'
- equal_arc = T
- bishop = 4
-! s_hat_input = 0.8
-! beta_prime_input = 0.0
- delrho = 1.e-3
- isym = 0
- writelots = F
-/ 
-
-&collisions_knobs
- collision_model='none'
-/
-
-&hyper_knobs
- hyper_option = 'visc_only'
- const_amp = .false.
- isotropic_shear = .false.
- D_hypervisc = 0.05
-/
-
-&species_knobs
- nspec=          2
-/
-
-&species_parameters_1
- z=   1.0
- mass=   1.0
- dens=   1.0
- temp=   1.0
- tprim=  4.0
- fprim=  0.0
- uprim=  0.0
- vnewk=  0.0
- type='ion'
-/
-
-&dist_fn_species_knobs_1
- fexpr= 0.48
- fexpi= 0.0
- bakdif= 0.02
-/
-
-&species_parameters_2
- z=   -1.0
- mass=   2.2e-4
- dens=   1.0
- temp=   1.0
- tprim=  4.0
- fprim=  0.0
- uprim=  0.0
- vnewk=  0.0
- type='electron'
-/
-
-&dist_fn_species_knobs_2
- fexpr= 0.48
- fexpi= 0.0
- bakdif= 0.02
-/
-
-&dist_fn_knobs
- adiabatic_option="iphi00=2"
- gridfac=   1.0
- boundary_option="linked"
-/
-
-&init_g_knobs
- chop_side = .false.
- phiinit=   1.e-3
- phifrac = 0.1
- zf_init = 0.0
- ginit_option= "noise"
-/
-
-&kt_grids_knobs
- grid_option='box'
-/
-
-&kt_grids_box_parameters
-! (25-1)/3+1 = 9 ky values
- ny = 8
-
-! 2*(40-1)/3 + 1 = 27 kx values
- nx = 8
-
-! dky = 1/y0 = 0.1 => ky: 0 -> 0.8
- y0 = 10.
-
-! default jtwist calculated in kt_grids to
-! make box lengths in x and y equal at
-! outboard midplane
-! jtwist = 5
-/
-
-&le_grids_knobs
- ngauss = 3
- negrid = 6
- vcut= 2.5
-/
-
-&knobs
- wstar_units = .false.
- fphi =   1.0
- fapar =  0.0
- faperp = 0.0
- delt = 0.01
- nstep = 60
-/
-
-&fields_knobs
- field_option='implicit'
-/
-
-&nonlinear_terms_knobs
- nonlinear_mode='on'
- cfl = 0.25
-/
-
-&reinit_knobs
- delt_adj = 2.0
- delt_minimum = 1.e-6
- delt_cushion = 10.0
-/
-
-&layouts_knobs
- layout = 'lxyes'
- local_field_solve = F
-/
-
-&gs2_diagnostics_knobs
- print_flux_line=.false.
- write_nl_flux = .true.
- print_line = F
- write_line = F
- write_final_moments= T
- write_avg_moments = .true.
- write_final_fields=.true.
- write_verr = F
- write_gyx = F
- write_hrate = F
- write_correlation = T
- nwrite=     10
- navg=       40
- omegatinst = 500.0
- save_for_restart = .true.
-/

data/test/gs2_42982/shot42982_jet.trin

@@ -1,57 +0,0 @@
-
-
-
-&geometry
-geo_option = "iterdb"
-geo_file = "../../pr08_jet_42982_2d.dat"
-geo_time = 15.2
-fluxlabel_option = "aminor"
-rad_out = 0.85
-nrad = 5
-use_external_geo = .false.
-write_dbinfo = .true.
-/
-
-&species
-species_option = "iterdb"
-ntspec = 2
-qi = 1.0
-mi = 2.5
-deuterium = 1
-/
-
-&time
-ntstep = 2
-ntdelt = 0.1
-impfac = 1.0
-niter = 1
-errtol = 0.01
-errflr = 0.01
-flrfac = 2.0
-ntdelt_max = 100.0
-/
-
-&fluxes
-flux_option = "gs2"
-vtfac = 2.0
-grad_option = "tigrad"
-fork_flag = .true.
-subfolders = .true.
-/
-
-&physics
-include_neo = .true.
-turb_heat = .false.
-temp_equil = .true.
-/
-
-&sources
-source_option = "iterdb"
-write_pwr_profs = .true.
-include_radiation = .true.
-include_alphas = .true.
-/
-
-&init
-init_option = "iterdb"
-/

data/test/helper.rb

@@ -1,18 +0,0 @@
-require 'rubygems'
-require 'bundler'
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
-require 'test/unit'
-require 'shoulda'
-
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
-$LOAD_PATH.unshift(File.dirname(__FILE__))
-require 'coderunner'
-
-class Test::Unit::TestCase
-end

data/test/ifspppl/test.trin

@@ -1,57 +0,0 @@
-
-
-
-&geometry
-geo_option = "iterdb"
-geo_file = "../../../ifspppl/2d.dat"
-geo_time = 15.2
-fluxlabel_option = "aminor"
-rad_out = 0.85
-nrad = 9
-use_external_geo = .false.
-write_dbinfo = .true.
-/
-
-&species
-species_option = "iterdb"
-ntspec = 2
-qi = 1.0
-mi = 2.5
-deuterium = 1
-tritium = 2
-/
-
-&time
-ntstep = 200
-ntdelt = 0.1
-impfac = 1.0
-niter = 1
-errtol = 0.01
-errflr = 0.01
-flrfac = 2.0
-ntdelt_max = 100.0
-/
-
-&fluxes
-flux_option = "ifspppl"
-vtfac = 2.0
-grad_option = "tgrads"
-fork_flag = .false.
-/
-
-&physics
-include_neo = .true.
-turb_heat = .false.
-temp_equil = .true.
-/
-
-&sources
-source_option = "iterdb"
-write_pwr_profs = .true.
-include_radiation = .true.
-include_alphas = .true.
-/
-
-&init
-init_option = "iterdb"
-/

data/test/test_trinitycrmod.rb

@@ -1,128 +0,0 @@
-require 'helper'
-
-class TestTrinitycrmodIFSPPPL < Test::Unit::TestCase
-  def setup
-    @runner = CodeRunner.fetch_runner(Y: 'test/ifspppl', C: 'trinity', X: '/dev/null')
-  end
-  def teardown
-    FileUtils.rm('test/ifspppl/.code_runner_script_defaults.rb')
-    FileUtils.rm('test/ifspppl/.CODE_RUNNER_TEMP_RUN_LIST_CACHE')
-  end
-  def test_basics
-    assert_equal(@runner.run_class, CodeRunner::Trinity)
-  end
-  def test_submit
-    @runner.run_class.make_new_defaults_file("rake_test", "test/ifspppl/test.trin")
-    FileUtils.mv('rake_test_defaults.rb', @runner.run_class.rcp.user_defaults_location)
-    CodeRunner.submit(Y: 'test/ifspppl', T: true, D: 'rake_test')
-		base_hash = @runner.run_class.parse_input_file('test/ifspppl/test.trin')
-		test_hash = @runner.run_class.parse_input_file('test/ifspppl/v/id_1/v_id_1_t.trin')
-		assert_equal(base_hash, test_hash)
-    FileUtils.rm(@runner.run_class.rcp.user_defaults_location + '/rake_test_defaults.rb')
-    FileUtils.rm('test/ifspppl/rake_test_defaults.rb')
-		FileUtils.rm_r('test/ifspppl/v')
-  end
-end
-
-class TestTrinitycrmodGs2 < Test::Unit::TestCase
-	def setup
-		CodeRunner.setup_run_class('trinity')
-		Dir.chdir('test/gs2_42982'){
-			CodeRunner::Trinity.use_new_defaults_file_with_gs2('rake_test_gs2_42982', 'shot42982_jet.trin', 'shot42982_jet.in')
-		}
-    @runner = CodeRunner.fetch_runner(Y: 'test/gs2_42982', C: 'trinity', X: '/dev/null')
-		system("gunzip test/gs2_42982/pr08_jet_42982_1d.dat.gz -c > test/gs2_42982/pr08_jet_42982_1d.dat")
-		system("gunzip test/gs2_42982/pr08_jet_42982_2d.dat.gz -c > test/gs2_42982/pr08_jet_42982_2d.dat")
-	end
-	def test_submit
-		if ENV['TRINITY_EXEC']
-			CodeRunner.submit(Y: 'test/gs2_42982', X: ENV['TRINITY_EXEC'], n: '8')
-		else
-			CodeRunner.submit(Y: 'test/gs2_42982', T: true, X: '/dev/null', n: '8')
-		end
-		@runner.use_component = :component
-		@runner.recalc_all = true
-		@runner.update
-		CodeRunner.status(Y: 'test/gs2_42982', h: :component, A: true)
-	end
-	def teardown 
-    FileUtils.rm(@runner.run_class.rcp.user_defaults_location + '/rake_test_gs2_42982_defaults.rb')
-    FileUtils.rm('test/gs2_42982/rake_test_gs2_42982_defaults.rb')
-    FileUtils.rm('test/gs2_42982/pr08_jet_42982_1d.dat')
-    FileUtils.rm('test/gs2_42982/pr08_jet_42982_2d.dat')
-    FileUtils.rm('test/gs2_42982/.CODE_RUNNER_TEMP_RUN_LIST_CACHE')
-		if ENV['TRINITY_EXEC'] and not FileTest.exist?('test/gs2_42982_results/v.tgz')
-			Dir.chdir('test/gs2_42982'){system("tar -czf v.tgz v/")}
-			FileUtils.mv('test/gs2_42982/v.tgz', 'test/gs2_42982_results/.')
-		end
-		FileUtils.rm_r('test/gs2_42982/v/')
-	end
-end
-
-class TestTrinitycrmodGs2Analysis < Test::Unit::TestCase
-	def setup
-		Dir.chdir('test/gs2_42982_results/'){system "tar -xzf v.tgz"}
-    @runner = CodeRunner.fetch_runner(Y: 'test/gs2_42982_results', C: 'trinity', A: true)
-	end
-	def test_analysis
-		CodeRunner.status(Y: 'test/gs2_42982_results')
-		CodeRunner.status(Y: 'test/gs2_42982_results', h: :component)
-	end
-	def teardown
-		FileUtils.rm_r('test/gs2_42982_results/v')
-    FileUtils.rm('test/gs2_42982_results/.code_runner_script_defaults.rb')
-    FileUtils.rm('test/gs2_42982_results/.CODE_RUNNER_TEMP_RUN_LIST_CACHE')
-	end
-end
-
-class TestTrinitycrmodIFSPPPLAnalysis < Test::Unit::TestCase
-  def setup
-    #@runner = CodeRunner.fetch_runner(Y: 'test/ifspppl_results', C: 'trinity', X: '/dev/null')
-		Dir.chdir('test/ifspppl_results/v'){str = "tar -xzf id_1.tgz";system str}
-    @runner = CodeRunner.fetch_runner(Y: 'test/ifspppl_results', C: 'trinity', X: ENV['HOME'] + '/Code/trinity/trunk/trinity', A: true)
-    #@runner.run_class.make_new_defaults_file("rake_test", "test/ifspppl/test.trin")
-    #FileUtils.mv('rake_test_defaults.rb', @runner.run_class.rcp.user_defaults_location)
-    #CodeRunner.submit(Y: 'test/ifspppl_results', D: 'rake_test', n: '1')
-  end
-  def test_analysis
-    CodeRunner.status(Y: 'test/ifspppl_results')
-    assert_equal(@runner.run_list.size, 1)
-    assert_equal(@runner.run_list[1].fusionQ, 0.075658439797815016)
-		list_t = @runner.run_list[1].list(:t)
-		assert_equal(201, list_t.size)
-		assert_equal(0.04375, list_t[10])
-    FileUtils.rm('test/ifspppl_results/.CODE_RUNNER_TEMP_RUN_LIST_CACHE')
-  end
-	def test_graphs
-	  kit = @runner.run_list[1].graphkit('ion_temp_prof', {t_index: 2})
-		#kit.gnuplot
-		assert_equal(kit.data[0].class, GraphKit::DataKit)
-		assert_equal(kit.data[0].x.data[0], 0.05)
-	  kit = @runner.run_list[1].graphkit('ion_hflux_gb_prof', {t_index: 2})
-		#kit.gnuplot
-		assert_equal(kit.data[0].class, GraphKit::DataKit)
-		assert_equal(8,kit.data[0].y.data.size)
-		assert_equal(kit.data[0].y.data[0], 0.001944)
-	  kit = @runner.run_list[1].graphkit('ion_pwr_prof', {t_index: 2})
-		assert_equal(8,kit.data[0].y.data.size)
-		assert_equal(kit.data[0].y.data[0], 0.2412)
-		#kit.gnuplot
-	end
-
-	def test_average_graphs
-	  kit = @runner.run_list[1].graphkit('ion_hflux_gb_prof', {t_index: 2})
-		#kit.gnuplot
-		assert_equal(kit.data[0].class, GraphKit::DataKit)
-		assert_equal(kit.data[0].y.data[0], 0.001944)
-	  kit = @runner.run_list[1].graphkit('ion_hflux_gb_prof', {t_index: 1})
-		#kit.gnuplot
-		assert_equal(kit.data[0].class, GraphKit::DataKit)
-		assert_equal(kit.data[0].y.data[0], 0.001975)
-	  kit = @runner.run_list[1].graphkit('ion_hflux_gb_prof', {t_index: 2, time_average: -1})
-		assert_equal([0.001975, 0.001944].sum/2.0, kit.data[0].y.data[0])
-	end
-  def teardown
-    FileUtils.rm('test/ifspppl_results/.code_runner_script_defaults.rb')
-    FileUtils.rm_r('test/ifspppl_results/v/id_1/')
-  end
-end