gs2crmod 0.7.0 → 0.7.1

data/VERSION

@@ -1 +1 @@
-0.7.0
+0.7.1

data/gs2crmod.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.7.0"
+  s.version = "0.7.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
@@ -62,6 +62,8 @@ Gem::Specification.new do |s|
     "lib/gs2crmod/species_dependent_namelists.rb",
     "lib/gs2crmod/test_gs2.rb",
     "lib/gs2crmod_extension.rb",
+    "test/agk_slab_itg_low_kperp.in",
+    "test/agk_slab_itg_low_kperp.tgz",
     "test/cyclone_low_res.in",
     "test/cyclone_low_res.tgz",
     "test/helper.rb",

data/test/agk_slab_itg_low_kperp.in

@@ -0,0 +1,212 @@
+!==============================================================================
+!  		AstroGK INPUT FILE automatically generated by CodeRunner 
+!==============================================================================
+!
+!  AstroGK is a gyrokinetic flux tube initial value turbulence code 
+!  which can be used for fusion or astrophysical plasmas.
+!  
+!  	See http://gyrokinetics.sourceforge.net
+!
+!  CodeRunner is a framework for the automated running and analysis 
+!  of large simulations. 
+!
+!  	See http://coderunner.sourceforge.net
+!      by CodeRunner version 0.12.11.0
+!
+!==============================================================================
+
+!==============================
+!  
+!==============================
+&diagnostics
+ print_line = .false. 
+ print_flux_line = .f. 
+ write_linear = .f. 
+  ! write_nonlin not specified --- 
+ write_omega = .false. 
+ write_omavg = .false. 
+  ! write_ascii not specified --- 
+ write_kpar = .true. 
+  ! write_gs not specified --- 
+ write_g = .false. 
+  ! write_gg not specified --- 
+  ! write_vspace_slices not specified --- 
+ write_hrate = .f. 
+  ! write_elsasser not specified --- 
+  ! write_density_velocity not specified --- 
+  ! write_epartot not specified --- 
+ write_final_fields = .false. 
+ write_final_epar = .false. 
+  ! write_final_moments not specified --- 
+  ! write_avg_moments not specified --- 
+  ! write_Epolar not specified --- 
+  ! write_Eshell not specified --- 
+ write_nl_flux = .f. 
+  ! write_full_moments_r not specified --- 
+ nwrite = 4 
+  ! nmovie not specified --- 
+  ! nwrite2 not specified --- 
+  ! nsave not specified --- 
+ navg = 20 
+ omegatol = -0.001 
+ omegatinst = 500.0 
+  ! igomega not specified --- 
+  ! write_lorentzian not specified --- 
+  ! exit_when_converged not specified --- 
+  ! make_movie not specified --- 
+ save_for_restart = .false. 
+  ! write_adapt_hc not specified --- 
+  ! write_verr not specified --- 
+  ! write_vspectrum not specified --- 
+  ! write_kspectrum not specified --- 
+  ! write_init not specified --- 
+  ! write_gkp not specified --- 
+  ! write_hkv not specified --- 
+  ! write_ktrans not specified --- 
+  ! use_qshell not specified --- 
+  ! write_ptrans not specified --- 
+  ! get_wtrans not specified --- 
+  ! get_etrans not specified --- 
+ write_phi_over_time = .false. 
+  ! write_apar_over_time not specified --- 
+  ! write_bpar_over_time not specified --- 
+/
+
+!==============================
+!  
+!==============================
+&layouts_knobs
+ layout = "lexys" ! 'yxles', 'lxyes', 'lyxes', 'lexys' Determines the way the grids are laid out in memory.
+/
+
+!==============================
+!  
+!==============================
+&reinit_knobs
+ delt_adj = 2.0 ! When the time step needs to be changed, it is adjusted 
+ delt_minimum = 5.0e-10 ! The minimum time step is delt_minimum.
+/
+
+!==============================
+!  
+!==============================
+&collisions_knobs
+ collision_model = "none" ! Collision model used in the simulation. Options: 'default', 'none', 'lorentz', 'ediffuse'
+ conserve_momentum = .false. 
+ heating = .false. 
+/
+
+!==============================
+!  
+!==============================
+&dist_fn_knobs
+ test = .false. 
+/
+
+!==============================
+! 1 
+!==============================
+&dist_fn_species_knobs_1
+ fexp = 0.48 
+ bakdif = 0.05 ! Spatial implicitness parameter. Recommended value: 0.05
+/
+
+!==============================
+!  
+!==============================
+&hyper_knobs
+ hyper_option = "visc_only" 
+ const_amp = .true. 
+ include_kpar = .false. 
+ isotropic_shear = .true. 
+ D_hypervisc = 0.01 
+/
+
+!==============================
+!  
+!==============================
+&init_g_knobs
+ ginit_option = "noise" ! Sets the way that the distribution function is initialized.
+ phiinit = 0.1 ! Average amplitude of initial perturbation of each Fourier mode.
+ chop_side = .false. ! Rarely needed. Forces asymmetry into initial condition.
+/
+
+!==============================
+!  
+!==============================
+&kgrids
+ grid_option = "single" 
+ akperp = 0.01 
+ nkpolar = 0 
+/
+
+!==============================
+!  
+!==============================
+&le_grids_knobs
+ ngauss = 8 ! Number of untrapped pitch-angles moving in one direction along field line.
+ negrid = 8 ! Total number of energy grid points
+ ecut = 16.0 
+/
+
+!==============================
+!  
+!==============================
+&nonlinear_terms_knobs
+ nonlinear_mode = "off" ! Include nonlinear terms? ('on','off')
+ cfl = 0.2 ! The maximum delt < cfl * min(Delta_perp/v_perp)
+/
+
+!==============================
+!  
+!==============================
+&parameters
+ beta = 0.0 ! Ratio of particle to magnetic pressure (reference Beta, not total beta):  beta=n_0 T_0 /( B^2 / (8 pi))
+ zeff = 1.0 ! Effective ionic charge.
+ tite = 1.0 ! Ratio of ion to electron temperatures.
+/
+
+!==============================
+!  
+!==============================
+&knobs
+ delt = 0.2 ! Time step
+ nstep = 500 ! Maximum number of timesteps
+ avail_cpu_time = 7200 ! Specify the available wall clock time in seconds. GS2 will exit before this time.
+ use_Phi = .true. 
+ use_Apar = .false. 
+ use_Bpar = .false. 
+/
+
+!==============================
+!  
+!==============================
+&species_knobs
+ nspec = 1 ! Number of kinetic species evolved.
+/
+
+!==============================
+! 1 
+!==============================
+&species_parameters_1
+ z = 1.0 ! Charge
+ mass = 1.0 ! Mass
+ dens = 1.0 ! Density	
+ temp = 1.0 ! Temperature
+ tprim = 100 ! -1/T (dT/drho)
+ fprim = 1.0 ! -1/n (dn/drho)
+ uprim = 0.0 ! ?
+ type = "ion" ! Type of species, e.g. 'ion', 'electron', 'beam'
+ nu = 0 
+ nu_h = 100.0 
+ nexp_h = 6.0 
+/
+
+!==============================
+!  
+!==============================
+&theta_grid
+ z0 = 10.0 
+ ntheta = 20 
+/
+

data/test/test_gs2crmod.rb

@@ -135,4 +135,35 @@ class TestAnalysis < Test::Unit::TestCase
 	end
 end
 
+AGK_SLAB_ITG_LOW_KPERP_FOLDER = 'test/agk_slab_itg_low_kperp'
 
+if ENV['AGK_EXEC']
+	class TestAstrogkSubmission < Test::Unit::TestCase
+		def setup
+			CodeRunner.setup_run_class('gs2', modlet: 'astrogk')
+			CodeRunner::Gs2::Astrogk.make_new_defaults_file('test_gs2crmod_astrogk', 'test/agk_slab_itg_low_kperp.in')
+			FileUtils.mv('test_gs2crmod_astrogk_defaults.rb', CodeRunner::Gs2::Astrogk.rcp.user_defaults_location + '/.')
+			FileUtils.makedirs(tfolder)
+		end
+		def tfolder
+			AGK_SLAB_ITG_LOW_KPERP_FOLDER
+		end
+		def teardown
+			FileUtils.rm(CodeRunner::Gs2::Astrogk.rcp.user_defaults_location + '/' + 'test_gs2crmod_astrogk_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 agk_slab_itg_low_kperp.tgz agk_slab_itg_low_kperp/" unless FileTest.exist?('agk_slab_itg_low_kperp.tgz')}
+			FileUtils.rm_r(tfolder)
+		end
+		def test_submission
+			CodeRunner.submit(C: 'gs2', X: ENV['AGK_EXEC'], D: 'test_gs2crmod_astrogk', n: '4', Y: tfolder, m: 'astrogk')
+			
+			CodeRunner.status(Y: tfolder)
+		end
+	end
+else
+	puts "\n************************************\nWarning: agk submission tests not run. Please specify the evironment variable AGK_EXEC (the path to the agk executable) if you wish to test submission.\n************************************\n"
+	sleep 0.1
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.7.0
+  version: 0.7.1
   prerelease: 
 platform: ruby
 authors:
@@ -148,6 +148,8 @@ files:
 - lib/gs2crmod/species_dependent_namelists.rb
 - lib/gs2crmod/test_gs2.rb
 - lib/gs2crmod_extension.rb
+- test/agk_slab_itg_low_kperp.in
+- test/agk_slab_itg_low_kperp.tgz
 - test/cyclone_low_res.in
 - test/cyclone_low_res.tgz
 - test/helper.rb