Module: CodeRunner::Gs2::GSLMatrices

Included in:
CodeRunner::Gs2
Defined in:
lib/gs2crmod/gsl_data.rb

Instance Method Summary collapse

Instance Method Details

#es_heat_flux_over_ky_over_kx_gsl_matrix(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1205

def es_heat_flux_over_ky_over_kx_gsl_matrix(options)
  raise "The write_fluxes_by_mode flag was not set." unless @write_fluxes_by_mode
  Dir.chdir(@directory) do
    raise "Heat flux spectrum makes no sense for single modes" if @grid_option == "single"
    options.convert_to_index(:t) if options[:t] or options[:t_element]
    options[:t_index] ||= list(:t).keys.max
    #es_heat_by_k index order (in Fortran) is kx, ky, t
    es_heat_narray = netcdf_file.var("es_heat_flux_by_mode").get('start' => [0, 0, 0, options[:t_index] - 1], 'end' => [-1, -1, 0, options[:t_index] - 1])
    es_heat_narray.reshape!(*es_heat_narray.shape.slice(0..1))

    gm =  es_heat_narray.to_gm.move_cols_from_box_order
    if options[:limit]
      for i in 0...gm.shape[0]
        for j in 0...gm.shape[1]
#             j+= extra if
          gm[i, j] = [[gm[i,j], (options[:limit][0] or gm[i,j])].max, (options[:limit][1] or gm[i,j])].min
#             mat[i, j+extra] = gm[i,-j] unless j==0
        end
      end
    end
    return gm
end
end

#growth_rate_over_ky_over_kx_gsl_matrix(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1192

def growth_rate_over_ky_over_kx_gsl_matrix(options)
  if @growth_rate_at_ky_at_kx.nil?
     raise("The CodeRunner variable growth_rate_at_ky_at_kx does not seem to have been calculated for this run. This may result when the environment variable GS2_CALCULATE_ALL is not set when the run was analyzed. Try setting GS2_CALCULATE_ALL and then re-analyze the run using, e.g. from the command line,\n $ coderunner rc 'cgrf\' -j #{@id}")
  end
  array = @growth_rate_at_ky_at_kx.values.map{|h| h.values}
  return GSL::Matrix.alloc(array.flatten, array.size, array[0].size)
end

#phi0_over_x_over_y_gsl_matrix(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1314

def phi0_over_x_over_y_gsl_matrix(options)
Dir.chdir(@directory) do

    #options.convert_to_index(:t) if options[:t] or options[:t_element]
    options.convert_to_index(self, :t) if options[:t] or options[:t_element]
    options[:t_index] ||= list(:t).keys.max
    phi_re_narray = netcdf_file.var("phi0").get('start' => [0, 0, 0, options[:t_index] - 1], 'end' => [0, -1, -1, options[:t_index] - 1])
    phi_re_narray.reshape!(*phi_re_narray.shape.slice(1..2))
    # The narray has index order ky, kx, but we want kx, ky for historical reasons, hence the transpose.
    gm_re = phi_re_narray.to_gm
    phi_im_narray = netcdf_file.var("phi0").get('start' => [1, 0, 0, options[:t_index] - 1], 'end' => [1, -1, -1, options[:t_index] - 1])
    phi_im_narray.reshape!(*phi_im_narray.shape.slice(1..2))
    # The narray has index order ky, kx, but we want kx, ky for historical imasons, hence the transpose.
    gm_im = phi_im_narray.to_gm
    gm = GSL::Matrix::Complex.re_im(gm_re, gm_im)

    ntheta0_temp = gm.shape[1]
    naky_temp = gm.shape[0]



    # Due to a strange GS2 convention, non zonal modes must be divided by 2:
    for i in 1...naky_temp
      for j in 0...ntheta0_temp
        gm[i,j] = gm[i,j]/2.0
      end
    end

    if options[:no_zonal]
      for i in 0...gm.shape[1]
        gm[0,i] = GSL::Complex.alloc([0,0])
      end
    end
    if xres = (options[:xres] or options[:x_resolution])
       if xres < nx
          puts "Warning: xres should be at least nx. Using nx instead of the xres you specified."
          xres = nx
       end
    else
       xres = nx
    end
    if yres = (options[:yres] or options[:y_resolution])
       if yres < ny
          puts "Warning: yres should be at least ny. Using ny instead of the yres you specified."
          yres = ny
       end
    else
       yres = ny
    end

    # Next, pad with 0's:
    padded = GSL::Matrix::Complex.calloc(yres, xres)
    # Zonal modes first:
    for ix in 0...((ntheta0_temp+1)/2)
        padded[0, ix] = gm[0, ix]
    end
    for ix in ((ntheta0_temp+1)/2)...ntheta0_temp
        padded[0, ix+xres-ntheta0_temp] = gm[0, ix]
    end
    # Now include the non-zonal modes in the padded matrix mat:
    for iy in 1...naky_temp
        for ix in 0...((ntheta0_temp + 1)/2)
           padded[iy, ix] = gm[iy, ix]
        end
        for ix in ((ntheta0_temp+1)/2)...ntheta0_temp
           padded[iy, ix+xres-ntheta0_temp] = gm[iy, ix]
        end
        padded[yres-iy, 0] = gm[iy,0].conj
        for ix in 1...xres
           padded[yres-iy, ix] = padded[iy, xres-ix].conj
        end
    end
    gm = padded

    gm = gm.backward_cols_c2c(false).backward_rows_c2c(false)
    # At this point, gm should be purely real (within machine precision), but let's check to be sure:
    should_be_zero = gm.imag.abs.max
    if should_be_zero > 1.0e-10
       puts "should_be_zero = #{should_be_zero}"
       raise "Something went wrong - reconstructed phi is not purely real."
    end

    gm = gm.real

    if options[:limit]
      for i in 0...gm.shape[0]
        for j in 0...gm.shape[1]
          gm[i, j] = [[gm[i,j], options[:limit][0]].max, options[:limit][1]].min
        end
      end
    end

    return gm
end
end

#spectrum_over_ky_over_kpar_gsl_matrix(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1264

def spectrum_over_ky_over_kpar_gsl_matrix(options)
Dir.chdir(@directory) do

    #:re, :theta, :kx, :ky
    lkx = list(:kx)

    if options[:t_index] or options[:t]
      #extra option required is t_index
      raise CRFatal.new("write_phi_over_time is not enabled so this function won't work") unless @write_phi_over_time
      options.convert_to_index(self, :t)
    end
     phi_av = (lkx.keys.map do |kx_index|
      if options[:t_index]
        phi =  netcdf_file.var('phi_t').get({'start' => [0,0,kx_index-1,0, options[:t_index] - 1], 'end' => [-1,-2,kx_index-1,-1, options[:t_index] - 1]})
      else
        phi = netcdf_file.var('phi').get({'start' => [0, 0, kx_index - 1, 0], 'end' => [-1, -2, kx_index-1, -1]})
      end
      #ep phi.shape
      phi.reshape(*phi.shape.values_at(0,1,3))
    end).sum / lkx.size

    phi_t = phi_av.to_a #.map{|arr| arr.transpose}.transpose.map{|a| a.transpose}
    #ep 'phi_t', phi_t.size, phi_t[0].size, phi_t[0][0].size
    gvky = gsl_vector('ky')
    gm = GSL::Matrix.alloc(gvky.size, gsl_vector('theta').size-1)
    for ky_element in 0...gm.shape[0]
      #p phi_t[ky_element].transpose[0]
      spectrum = GSL::Vector::Complex.alloc(phi_t[ky_element]).forward.square
      if options[:no_kpar0]
        spectrum[0]=0.0
      end
      #ep spectrum.size
      spectrum = spectrum.from_box_order
      #ep spectrum.shape
      spectrum = spectrum*gvky[ky_element]**2 unless options[:phi2_only]
      #ep gm.size
      #ep spectrum.size
      gm.set_row(ky_element, spectrum)
    end
    if options[:no_zonal]
      gm.row(0).set_all(0.0)
    end
    if options[:log]
      gm = gm.log
    end

    return gm
end
end

#spectrum_over_ky_over_kx_gsl_matrix(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1229

def spectrum_over_ky_over_kx_gsl_matrix(options)
Dir.chdir(@directory) do
    raise "Spectrum makes no sense for single modes" if @grid_option == "single"
    options.convert_to_index(:t) if options[:t] or options[:t_element]
    options[:t_index] ||= list(:t).keys.max
    #phi2_by_mode index order (in Fortran) is kx, ky, t
    phi_narray = netcdf_file.var("phi2_by_mode").get('start' => [0, 0, options[:t_index] - 1], 'end' => [-1, -1, options[:t_index] - 1])
    phi_narray.reshape!(*phi_narray.shape.slice(0..1))

    gm =  phi_narray.to_gm.move_cols_from_box_order
    if options[:times_kx4] or options[:times_kx2]
#         puts 'normalising'
      vals = list(:kx).values.sort
      for i in 0...gm.shape[0]
        for j in 0...gm.shape[1]
#             p vals[j]
          gm[i,j] =  gm[i,j] * (vals[j])**4 if options[:times_kx4]
          gm[i,j] =  gm[i,j] * (vals[j])**2 if options[:times_kx2]
        end
      end
    end
    if options[:no_zonal]

      for i in 0...gm.shape[1]
        gm[0,i] = 0.0
      end
    end
    if options[:log]
      gm = gm.log
    end

    return gm
end
end

#transient_amplification_over_ky_over_kx_gsl_matrix(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1200

def transient_amplification_over_ky_over_kx_gsl_matrix(options)
    array = @transient_amplification_at_ky_at_kx.values.map{|h| h.values}
    return GSL::Matrix.alloc(array.flatten, array.size, array[0].size)
end