gs2crmod 0.12.9 → 0.12.10

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data/lib/gs2crmod/gs2.rb CHANGED
@@ -100,51 +100,51 @@ eval(%[
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  @results = [
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  :converged,
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  :decaying,
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+ :es_heat_flux_stav_error,
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+ :es_heat_flux_stav_std_dev,
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+ :es_mom_flux_stav_error,
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+ :es_mom_flux_stav_std_dev,
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+ :es_part_flux_stav_error,
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+ :es_part_flux_stav_std_dev,
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+ :es_heat_flux_stav,
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+ :es_mom_flux_stav,
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+ :es_part_flux_stav,
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+ :frequency_at_ky_at_kx,
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+ :fastest_growing_mode,
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+ :freq_of_max_growth_rate,
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+ :gamma_r,
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+ :gamma_i,
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  :growth_rates,
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- :real_frequencies,
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  :growth_rates_by_ky, # deprecated
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  :growth_rates_by_kx, # deprecated
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  :growth_rate_at_ky,
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  :growth_rate_at_kx,
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  :growth_rate_at_ky_at_kx,
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- :frequency_at_ky_at_kx,
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- :real_frequencies_by_ky,
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- :max_growth_rate,
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- :fastest_growing_mode,
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- :freq_of_max_growth_rate,
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- :ky,
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- :gamma_r,
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- :gamma_i,
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- :run_time,
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  :hflux_tot_stav,
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- :phi2_tot_stav,
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- :saturation_time_index,
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- :es_heat_flux_stav,
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- :es_mom_flux_stav,
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- :es_part_flux_stav,
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  :hflux_tot_stav_error,
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  :hflux_tot_stav_std_dev,
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- :es_heat_flux_stav_error,
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- :es_heat_flux_stav_std_dev,
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- :es_mom_flux_stav_error,
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- :es_mom_flux_stav_std_dev,
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- :es_part_flux_stav_error,
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- :es_part_flux_stav_std_dev,
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- :saturated,
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- :shot_time,
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- :spectrum_check,
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+ :ky,
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  :ky_spectrum_peak_idx,
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  :ky_spectrum_peak_ky,
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  :ky_spectrum_peak_phi2,
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  :kx_spectrum_peak_kx,
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  :kx_spectrum_peak_phi2,
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+ :max_growth_rate,
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+ :max_transient_amplification_index_at_ky,
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+ :phi2_tot_stav,
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  :par_mom_flux_stav,
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  :perp_mom_flux_stav,
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  :phi2_zonal,
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+ :run_time,
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+ :real_frequencies,
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+ :real_frequencies_by_ky,
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+ :saturation_time_index,
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+ :saturated,
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+ :shot_time,
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+ :spectrum_check,
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  :transient_amplification_at_kx,
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  :transient_amplification_at_ky,
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  :transient_amplification_at_ky_at_kx,
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- :max_transient_amplification_index_at_ky,
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  :transient_es_heat_flux_amplification_at_species_at_kx,
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  :transient_es_heat_flux_amplification_at_species_at_ky,
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  :transient_es_heat_flux_amplification_at_species_at_ky_at_kx,
@@ -238,12 +238,9 @@ end
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  def calculate_results
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  return if ENV['CODE_RUNNER_NO_ANALYSIS'] =~ /true/
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-
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  eputs "Analysing run"
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  if @nonlinear_mode == "off"
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-
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- calculate_growth_rates_and_frequencies
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  calculate_transient_amplifications
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  elsif @nonlinear_mode == "on"
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  calculate_saturation_time_index
@@ -259,7 +256,6 @@ def calculate_results
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  @real_frequencies ||={}
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  end
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-
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  # Try to read the runtime in minutes from the GS2 standard out.
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  def get_run_time
@@ -281,7 +277,6 @@ end
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  # ncdump([:hflux, :phi])
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  # ncdump([:hflux, :phi], :dims)
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-
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  def ncdump(names=nil, values=nil, extension = '.out.nc')
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  names = [names] unless !names or names.class == Array
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  names.map!{|name| name.to_s} if names
@@ -1323,16 +1318,14 @@ class Hash
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  # puts self
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  def convert_to_index(run, *names)
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- if self[:strongest_non_zonal_mode]
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- ky_element, kx_element = run.gsl_matrix('spectrum_over_ky_over_kx', no_zonal: true).max_index
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- p self[:kx_index] = kx_element + 1
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- p self[:ky_index] = ky_element + 1
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- self[:strongest_non_zonal_mode] = false
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- end
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+ if self[:strongest_non_zonal_mode]
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+ ky_element, kx_element = run.gsl_matrix('spectrum_over_ky_over_kx', no_zonal: true).max_index
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+ p self[:kx_index] = kx_element + 1
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+ p self[:ky_index] = ky_element + 1
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+ self[:strongest_non_zonal_mode] = false
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+ end
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  raise "No names specified" if names.size == 0
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-
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- # ep run
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  names.each do |name|
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  if name == :kx
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  if lkx = self[:lagrangian_kx]
@@ -1343,10 +1336,8 @@ class Hash
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  end
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  end
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- #ep 'name', name
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  self[:ky_index] = 1 if name == :ky and run.grid_option == "single"
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  self[:kx_index] = 1 if name == :kx and run.grid_option == "single"
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- # ep run.list(name)
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  self[name + :_index] ||= run.list(name).key(self[name]) || (raise ("#{name} not specified"))
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  end
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