gs2crmod 0.11.51 → 0.11.53

metadata

@@ -1,7 +1,8 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.51
+  version: 0.11.53
+  prerelease: 
 platform: ruby
 authors:
 - Edmund Highcock
@@ -9,106 +10,96 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-03 00:00:00.000000000 Z
+date: 2014-07-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9337200 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.14.15
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.14.15
+  version_requirements: *9337200
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9336480 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.1.2
+  version_requirements: *9336480
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf-updated
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9335400 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.6.6.1
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.6.6.1
+  version_requirements: *9335400
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9333560 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - =
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 3.0.1
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
+  version_requirements: *9333560
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9354160 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.12'
+  version_requirements: *9354160
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9350340 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">"
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">"
-      - !ruby/object:Gem::Version
-        version: 1.0.0
+  version_requirements: *9350340
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9347380 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+  version_requirements: *9347380
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: &9260920 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 1.8.4
+        version: '4'
+  type: :development
+  prerelease: false
+  version_requirements: *9260920
 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
@@ -122,7 +113,7 @@ extra_rdoc_files:
 - README.md
 - README.rdoc
 files:
-- ".document"
+- .document
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -175,35 +166,29 @@ files:
 - sync_variables/sync_variables.rb
 - sync_variables_sgk/helper.rb
 - sync_variables_sgk/sync_variables_sgk.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
-- test/slab_itg/dummy
-- test/test_gs2crmod.rb
 homepage: http://gs2crmod.sourceforge.net
 licenses:
 - GSLv3
-metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: 1.9.1
 required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 1.8.11
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
 test_files: []

checksums.yaml

@@ -1,7 +0,0 @@
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-  data.tar.gz: 720329d3734497b4705f8939046a02010be6857f
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-  metadata.gz: a170d96abbc92ffb740b17013c6d3783b39a61256c71d77012a62d7aa2e20ef208a4170cf51443338620d6eee696147188d77405e95c67c43c7d5ce8f9722f62
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data/test/agk_slab_itg_low_kperp.in

@@ -1,212 +0,0 @@
-!==============================================================================
-!  		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/cyclone_low_res.in

@@ -1,236 +0,0 @@
-!==============================================================================
-!  		GS2 INPUT FILE automatically generated by CodeRunner 
-!==============================================================================
-!
-!  GS2 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 0.12.6.0
-!
-!==============================================================================
-
-!==============================
-!GENERAL PARAMETERS  
-!==============================
-&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.
-/
-
-&kt_grids_knobs
- grid_option = "box" ! The general layout of the perpendicular grid.
-/
-
-!==============================
-!  
-!==============================
-&kt_grids_box_parameters
- nx = 8 ! The number of kx modes: the number of kx modes actually simulated (ntheta0) is equal to 2*(nx - 1)/3 + 1, due to the need to prevent aliasing.
- ny = 8 ! The number of ky modes: the number of ky modes actually simulated (naky) is equal to (ny - 1)/3 + 1, due to the need to prevent aliasing.
- jtwist = 1 ! L_x = L_y  jtwist / (2 pi shat)
- y0 = 2.0 ! The length of the box in the y direction (measured in the Larmour radius of species 1)
- x0 = 10.0 ! The length of the box in the x direction (measured in the Larmour radius of species 1) if shat is 0 (ie 1e-6)
-/
-
-!==============================
-!  
-!==============================
-&theta_grid_parameters
- ntheta = 8 ! Number of points along field line (theta) per 2 pi segment
- nperiod = 1 ! Number of 2 pi segments along equilibrium magnetic field.
- eps = 0.18 ! eps=r/R
- epsl = 2.0 ! epsl=2 a/R
- shat = 0.8 ! 
- pk = 1.44 ! pk = 2 a / q R
- shift = 0.0 ! shift = -R q**2 dbeta/drho (>0)
-/
-
-!==============================
-!  
-!==============================
-&theta_grid_knobs
- equilibrium_option = "s-alpha" ! Controls which geometric assumptions are used in the run.
-/
-
-!==============================
-!  
-!==============================
-&theta_grid_salpha_knobs
- model_option = "default" 
-/
-
-!==============================
-!PITCH ANGLE/ENERGY GRID SETUP  
-!==============================
-&le_grids_knobs
- ngauss = 5 ! Number of untrapped pitch-angles moving in one direction along field line.
- negrid = 8 ! Total number of energy grid points
-/
-
-!==============================
-!BOUNDARY CONDITIONS  
-!==============================
-&dist_fn_knobs
- gridfac = 1.0 ! Affects boundary condition at end of theta grid.
- omprimfac = 1.0 
- boundary_option = "linked" ! Sets the boundary condition along the field line (i.e. the boundary conditions at theta = +- pi).
- adiabatic_option = "iphi00=2" ! The form of the adiabatic response (if a species is being modeled as adiabatic).
- g_exb = 0.0 
- nonad_zero = .true. ! If true switches on new parallel boundary condition where h=0 at incoming boundary instead of g=0.
-/
-
-!==============================
-!ALGORITHMIC CHOICES  
-!==============================
-&fields_knobs
- field_option = "implicit" ! Controls which time-advance algorithm is used for the linear terms.
-/
-
-!==============================
-!  
-!==============================
-&knobs
- wstar_units = .false. ! For linear runs only. Evolves each k_y with a different timestep.
- fphi = 1.0 ! Multiplies Phi (electrostatic potential).
- fapar = 0.0 ! Multiplies A_par. Use 1 for finite beta (electromagnetic), 0 otherwise (electrostatic)
- faperp = 0.0 ! Multiplies A_perp. Use 1 for high beta, 0 otherwise. Deprecated: use fbpar instead
- delt = 0.5 ! Time step
- nstep = 50 ! Maximum number of timesteps
-/
-
-!==============================
-!  
-!==============================
-&reinit_knobs
- delt_adj = 2.0 ! When the time step needs to be changed, it is adjusted 
- delt_minimum = 1.0e-06 ! The minimum time step is delt_minimum.
-/
-
-!==============================
-!  
-!==============================
-&layouts_knobs
- layout = "lexys" ! 'yxles', 'lxyes', 'lyxes', 'lexys' Determines the way the grids are laid out in memory.
-/
-
-!==============================
-!COLLISIONS  
-!==============================
-&collisions_knobs
- collision_model = "default" ! Collision model used in the simulation. Options: 'default', 'none', 'lorentz', 'ediffuse'
-/
-
-!==============================
-!NONLINEARITY  
-!==============================
-&nonlinear_terms_knobs
- nonlinear_mode = "off" ! Include nonlinear terms? ('on','off')
- flow_mode = "off" 
- cfl = 0.5 ! The maximum delt < cfl * min(Delta_perp/v_perp)
-/
-
-!==============================
-!EVOLVED SPECIES  
-!==============================
-&species_knobs
- nspec = 1 ! Number of kinetic species evolved.
-/
-
-!==============================
-!SPECIES PARAMETERS 1 
-!==============================
-&species_parameters_1
- z = 1.0 ! Charge
- mass = 1.0 ! Mass
- dens = 1.0 ! Density	
- temp = 1.0 ! Temperature
- tprim = 6.9 ! -1/T (dT/drho)
- fprim = 2.2 ! -1/n (dn/drho)
- uprim = 0.0 ! ?
- vnewk = 0.01 ! collisionality parameter
- type = "ion" ! Type of species, e.g. 'ion', 'electron', 'beam'
-/
-
-!==============================
-! 1 
-!==============================
-&dist_fn_species_knobs_1
- fexpr = 0.45 ! Temporal implicitness parameter. Recommended value: 0.48
- bakdif = 0.05 ! Spatial implicitness parameter. Recommended value: 0.05
-/
-
-!==============================
-!INITIAL CONDITIONS  
-!==============================
-&init_g_knobs
- chop_side = .false. ! Rarely needed. Forces asymmetry into initial condition.
- phiinit = 0.001 ! Average amplitude of initial perturbation of each Fourier mode.
- restart_file = "v_nstep_50_delt_0.5_nwrite_1_nsave_100_nonlinear_mode_off_g_exb_0.0_y0_2.0_nonad_zero_.true._jtwist_1_id_16.nc" ! Base of filenames with restart data.
- ginit_option = "noise" ! Sets the way that the distribution function is initialized.
- restart_dir = "nc" 
-/
-
-!==============================
-!DIAGNOSTICS  
-!==============================
-&gs2_diagnostics_knobs
- print_flux_line = .F. ! Instantaneous fluxes output to screen
- write_nl_flux = .true. ! Write nonlinear fluxes as a function of time.
- print_line = .false. ! Estimated frequencies and growth rates to the screen/stdout
- write_verr = .true. ! Write velocity space diagnostics to '.lpc' and '.verr' files
-  ! write_g not specified --- Write the distribution function to the '.dist' (NetCDF?)
- write_line = .false. ! If (write_ascii = T) write estimated frequencies and growth rates to the output file
-  ! write_gyx not specified --- Write dist fn at a given physical spacial point to a file
- write_hrate = .false. ! Write heating rate, collisonal entropy generation etc to '.heat'
-  ! write_final_epar not specified --- If (write_ascii = T) E_parallel(theta) written to runname.eigenfunc
- write_avg_moments = .T. ! Write flux surface averaged low-order moments of g to runname.out.nc and runname.moments (if write_ascii = T)
-  ! write_lorentzian not specified --- Frequency Sweep Data
- write_omega = .false. ! If (write_ascii = T) instantaneous omega to output file. Very heavy output
- write_omavg = .false. ! If (write_ascii = T) time-averaged growth rate and frequency to the output file.
- write_eigenfunc = .true. ! If (write_ascii = T) Normalized phi written to runname.eigenfunc
- write_final_fields = .true. ! If (write_ascii = T) Phi(theta) written to '.fields'
- write_final_moments = .true. ! write final n, T
-  ! write_parity not specified --- Writes parities in dist fn and particle fluxes
- nsave = 100 ! Write restart files every nsave timesteps
- nwrite = 1 ! Output diagnostic data every nwrite
- navg = 10 ! Any time averages performed over navg
- omegatol = -0.001 ! The convergence has to be better than one part in 1/omegatol
- omegatinst = 500.0 ! Recommended value: 500.
- save_for_restart = .false. ! Write restart files.
-  ! write_flux_line not specified --- 
-  ! write_ascii not specified --- 
-  ! write_kpar not specified --- 
-  ! write_gs not specified --- 
-  ! write_gg not specified --- 
-  ! write_lpoly not specified --- 
-  ! write_fields not specified --- 
-  ! write_final_antot not specified --- 
-  ! write_cerr not specified --- 
-  ! write_max_verr not specified --- 
-  ! nmovie not specified --- 
-  ! igomega not specified --- 
-  ! exit_when_converged not specified --- 
-  ! write_full_moments_notgc not specified --- 
-  ! write_cross_phase not specified --- 
-  ! dump_check1 not specified --- 
-  ! dump_check2 not specified --- 
-  ! dump_fields_periodically not specified --- 
-  ! make_movie not specified --- 
- write_phi_over_time = .true. ! Write entire Phi field to NetCDF file every nwrite.
-  ! write_apar_over_time not specified --- Write entire A_parallel field to NetCDF file every nwrite.
-  ! write_bpar_over_time not specified --- Write entire B_parallel field to NetCDF file every nwrite.
-  ! write_symmetry not specified --- Test the symmetry properties of the GK eqn.
-  ! save_distfn not specified --- Save dist_fn with lots of detail.
-  ! write_correlation_extend not specified --- Extend domain of correlation function calculation.
-  ! nwrite_mult not specified --- Large datasets written every nwrite_mult * nwrite timesteps.
-  ! write_correlation not specified --- Write parallel correlation.
-  ! write_moments not specified --- 
-  ! write_final_db not specified --- Write final delta B.
-/
-

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