gryfxcrmod 0.0.0 → 0.1.0

data/sync_mediawiki/helper.rb

@@ -0,0 +1,18 @@
+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/sync_mediawiki/sync_mediawiki.rb

@@ -0,0 +1,7 @@
+require 'helper'
+CodeRunner.setup_run_class('gryfx')
+
+raise "curl failed" unless system %[curl 'http://sourceforge.net/apps/mediawiki/gyrokinetics/index.php?title=Gryfx_Input_Parameters&action=edit' | sed 's/&amp;/\&/g' | sed 's/&quot;/"/g' | sed 's/&gt;/>/g' | sed 's/&lt;/</g'  | sed 's/&nbsp;/ /g' > gryfx_mediawiki.txt]
+CodeRunner::Gryfx.read_mediawiki_documentation('gryfx_mediawiki.txt')
+CodeRunner::Gryfx.write_mediawiki_documentation('gryfx_mediawiki.txt')
+system 'kwrite gryfx_mediawiki.txt' or system '/Applications/TextEdit.app/Contents/MacOS/TextEdit gryfx_mediawiki.txt' 

data/sync_variables/helper.rb

@@ -0,0 +1,18 @@
+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/sync_variables/sync_variables.rb

@@ -0,0 +1,27 @@
+require 'helper'
+CodeRunner.setup_run_class('gryfx')
+
+###################################################################################
+# Code to analyse the source code to look for new input variables... very imperfect
+################################################################################
+
+CodeRunner::Gryfx.synchronise_variables_from_input_file('test/cyclone_miller_ke.in')
+#CodeRunner::Gryfx.update_defaults_from_source_code(ENV['GRYFX_SOURCE'])
+
+
+############################################################
+#  Attempt to copy help from equivalent variables in GS2
+###########################################################
+
+CodeRunner.setup_run_class('gs2')
+
+CodeRunner::Gryfx.rcp.namelists.each do |namelist, namelist_hash|
+	namelist_hash[:variables].each do |var, varhash|
+		if CodeRunner::Gs2.rcp.namelists[namelist] and CodeRunner::Gs2.rcp.namelists[namelist][:variables][var]
+			varhash[:help] = CodeRunner::Gs2.rcp.namelists[namelist][:variables][var][:help]
+			varhash[:description] = CodeRunner::Gs2.rcp.namelists[namelist][:variables][var][:description]
+			CodeRunner::Gryfx.save_namelists
+		end
+	end
+end
+

data/test/cyclone_miller_ke.in

@@ -0,0 +1,200 @@
+!-------------------LINEAR CYCLONE ITG CASE-----------------------
+! Widely used benchmark case.  Original study published
+! in Phys. Plasmas Vol. 7, p. 969 (Dimits et al.)
+! Can compare linear.out file with linear.test, which
+! is included in this directory.
+!-----------------------------------------------------------------
+
+&collisions_knobs
+ collision_model='none'
+/
+!
+!&hyper_knobs
+! hyper_option = 'visc_only'
+! const_amp = .false.
+! isotropic_shear = .false.
+! D_hypervisc = 0.1
+!/
+
+&theta_grid_parameters
+
+ ntheta = 12
+ nperiod = 1
+
+ rhoc = 0.54
+ eps = 0.18
+ shat = 0.8
+ qinp = 1.4
+ Rmaj = 1.0
+ R_geo = 3.0
+ shift = 0.0
+ akappa = 1.0
+ akappri = 0.0
+ tri = 0.0
+ tripri = 0.0
+ drhodpsi = 1.0
+ epsl = 2.0
+ kxfac = 1.0
+/
+&parameters
+ !beta = 0.0
+ !zeff = 1.0
+/
+&theta_grid_eik_knobs
+ !itor = 1
+ !iflux = 0
+ irho = 2
+ equilibrium_type = "miller"
+
+ !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
+/
+&fields_knobs
+ !field_option='implicit'
+/
+&gs2_diagnostics_knobs
+ !print_flux_line = T
+ !write_nl_flux = T
+ !print_line = F
+ !write_line = F
+ !write_omega = F
+ !write_final_fields = T
+ !write_g = F
+ !write_verr = T
+ nwrite=     10
+ navg=       40000
+ nsave = 20
+ !omegatinst = 500.0
+ !save_for_restart = .true.
+ !omegatol = -1.0e-3
+/
+!&le_grids_knobs
+! ngauss = 5
+! negrid = 12
+! vcut= 2.5
+!/
+
+&dist_fn_knobs
+ !adiabatic_option="iphi00=2"
+ !gridfac=   1.0
+ !boundary_option="linked"
+ g_exb = 0.0
+/
+
+&kt_grids_knobs
+ !grid_option='box'
+/
+&kt_grids_box_parameters
+ ! naky = (ny-1)/3 + 1
+ ny = 8
+ ! nakx = 2*(nx-1)/3 + 1
+ nx = 8 
+ ! ky_min = 1/y0
+ y0 = 20
+ x0 = 20
+ jtwist = 5
+/
+&init_g_knobs
+ !chop_side = F
+ !phiinit=   1.e-3
+ !restart_file = "nc/cyclone_miller_ke.nc"
+ !ginit_option= "noise"
+/
+
+&knobs
+! fphi =   1.0
+! fapar =  0.0
+  !faperp = 0.0
+!  delt = 0.05
+  dt = 0.02 
+  maxdt = 0.02
+  nstep = 1000
+/
+&species_knobs
+ nspec=          1
+/
+&species_parameters_1
+ z=   1.0
+ mass=   1.0
+ dens=   1.0
+ temp=   1.0
+ tprim=  6.9
+ fprim=  2.2
+ uprim=  0.0
+ vnewk=  0.0
+ type='ion'
+/
+&dist_fn_species_knobs_1
+ !fexpr= 0.45
+ !bakdif= 0.05
+/
+&species_parameters_2
+ z=     -1.0
+ mass=   2.7e-4
+ dens=   1.0
+ temp=   1.0
+ tprim=  2.3
+ fprim=  0.733
+ uprim=  0.0
+ vnewk=  0.0
+ type='electron'
+/
+&dist_fn_species_knobs_2
+ !fexpr= 0.45
+ !bakdif= 0.05
+/
+&theta_grid_knobs
+ !equilibrium_option='eik'
+/
+&nonlinear_terms_knobs
+ nonlinear_mode='off'
+ cfl = 0.1
+/
+&reinit_knobs
+ !delt_adj = 2.0
+ !delt_minimum = 1.e-4
+/
+&layouts_knobs
+! layout = 'lxyes'
+! local_field_solve = F
+/
+
+&gryfx_knobs
+  inlpm = 2
+  dnlpm = 1.0
+  hyper = "off"
+  nu_hyper = 1.0
+  p_hyper = 2
+  init_amp = 1.0e-5
+  scan_type = "outputs"
+  scan_number = 1
+  zero_restart_avg = "off"
+  no_zderiv_covering = "off"
+  write_omega = 'off'
+  write_phi = "off"
+  restart = "off"
+  no_omegad = "off"
+  const_curv = "off"
+  varenna = "off"
+  nlpm = "off"
+  smagorinsky = "off"
+  init = "density"
+  debug = "on"
+  s_alpha = "on"  
+  fluxfile = "./scan/output/linearflux"
+  stopfile = "linear.stop"
+  restartfile = "restart/linear.bin"  
+/
+
+

data/test/test_gryfxcrmod.rb

@@ -5,5 +5,59 @@ class TestGryfxcrmod < Test::Unit::TestCase
 		CodeRunner.setup_run_class('gryfx')
 	end
 	def test_basics
+		assert_equal("gryfx", CodeRunner::Gryfx.rcp.code)
+	end
+end
+
+
+if ENV['GRYFX_EXEC']
+	class TestSubmission < Test::Unit::TestCase
+		def setup
+			CodeRunner.setup_run_class('gryfx')
+			CodeRunner::Gryfx.make_new_defaults_file('test_gryfxcrmod', 'test/cyclone_miller_ke.in')
+			FileUtils.mv('test_gryfxcrmod_defaults.rb', CodeRunner::Gryfx.rcp.user_defaults_location + '/.')
+			FileUtils.makedirs(tfolder)
+		end
+		def tfolder
+			'test/cyclone_miller_ke'
+		end
+		def teardown
+			FileUtils.rm(CodeRunner::Gryfx.rcp.user_defaults_location + '/' + 'test_gryfxcrmod_defaults.rb')
+			FileUtils.rm(tfolder + '/.CODE_RUNNER_TEMP_RUN_LIST_CACHE')
+			FileUtils.rm(tfolder + '/v/id_1/.code_runner_run_data')
+			FileUtils.rm(tfolder + '/v/id_1/code_runner_results.rb')
+			## Don't uncomment the line below unless you *really* know what you are doing! Replacing the test archive will break many of the tests
+			Dir.chdir('test'){system "tar -czf cyclone_miller_ke.tgz cyclone_miller_ke/" unless FileTest.exist?('cyclone_miller_ke.tgz')}
+			FileUtils.rm_r(tfolder)
+		end
+		def test_submission
+			CodeRunner.submit(T: false, C: 'gryfx', X: ENV['GRYFX_EXEC'], D: 'test_gryfxcrmod', n: '1', Y: tfolder, p: '{}')
+			CodeRunner::Gryfx.diff_input_files(tfolder + '/v/id_1/v_id_1.in', 'test/cyclone_miller_ke.in')
+			CodeRunner.status(Y: tfolder)
+		end
+	end
+else
+	puts "\n************************************\nWarning: submission tests not run. Please specify the evironment variable GRYFX_EXEC (the path to the gs2 executable) if you wish to test submission.\n************************************\n"
+	sleep 0.1
+end
+
+class TestAnalysis < Test::Unit::TestCase
+	def setup
+		Dir.chdir('test'){assert(system "tar -xzf cyclone_miller_ke.tgz")}
+		@runner = CodeRunner.fetch_runner(Y: tfolder)
+		@run = @runner.run_list[1]
+	end
+	def test_analysis
+		CodeRunner.status(Y: tfolder)
+		assert_equal(1, @runner.run_list.size)
+		#assert_equal(0.13066732664774272, @runner.run_list[1].max_growth_rate)
+		#assert_equal(0.13066732664774272, @runner.run_list[1].growth_rate_at_ky[0.5])
+		#assert_equal(:Complete, @runner.run_list[1].status)
+	end
+	def tfolder
+		'test/cyclone_miller_ke'
+	end
+	def teardown
+		FileUtils.rm_rf(tfolder)
 	end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gryfxcrmod
 version: !ruby/object:Gem::Version
-  version: 0.0.0
+  version: 0.1.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-09 00:00:00.000000000 Z
+date: 2013-08-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -27,6 +27,38 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.13.0
+- !ruby/object:Gem::Dependency
+  name: gs2crmod
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.9.9
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.9.9
+- !ruby/object:Gem::Dependency
+  name: ruby-netcdf
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.6.6
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.6.6
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
@@ -43,6 +75,22 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: shoulda-context
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.5
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.5
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
@@ -108,8 +156,16 @@ files:
 - VERSION
 - gryfxcrmod.gemspec
 - lib/gryfxcrmod.rb
+- lib/gryfxcrmod/deleted_variables.rb
 - lib/gryfxcrmod/gryfx.rb
+- lib/gryfxcrmod/namelist_tools.rb
 - lib/gryfxcrmod/namelists.rb
+- sync_mediawiki/helper.rb
+- sync_mediawiki/sync_mediawiki.rb
+- sync_variables/helper.rb
+- sync_variables/sync_variables.rb
+- test/cyclone_miller_ke.in
+- test/cyclone_miller_ke.tgz
 - test/helper.rb
 - test/test_gryfxcrmod.rb
 homepage: http://github.com/edmundhighcock/gryfxcrmod
@@ -127,7 +183,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 3372535012813393564
+      hash: -2691510310459698350
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: