Module: CodeRunner::Gs2::GSLMatrices
- Included in:
- CodeRunner::Gs2
- Defined in:
- lib/gs2crmod/gsl_data.rb
Instance Method Summary collapse
- #es_heat_flux_over_ky_over_kx_gsl_matrix(options) ⇒ Object
- #growth_rate_over_ky_over_kx_gsl_matrix(options) ⇒ Object
- #phi0_over_x_over_y_gsl_matrix(options) ⇒ Object
- #spectrum_over_ky_over_kpar_gsl_matrix(options) ⇒ Object
- #spectrum_over_ky_over_kx_gsl_matrix(options) ⇒ Object
- #transient_amplification_over_ky_over_kx_gsl_matrix(options) ⇒ Object
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 856 def es_heat_flux_over_ky_over_kx_gsl_matrix() Dir.chdir(@directory) do raise "Heat flux spectrum makes no sense for single modes" if @grid_option == "single" .convert_to_index(:t) if [:t] or [:t_element] [: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_by_k").get('start' => [0, 0, 0, [:t_index] - 1], 'end' => [-1, -1, 0, [: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 [:limit] for i in 0...gm.shape[0] for j in 0...gm.shape[1] # j+= extra if gm[i, j] = [[gm[i,j], ([:limit][0] or gm[i,j])].max, ([: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 848 def growth_rate_over_ky_over_kx_gsl_matrix() 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 959 def phi0_over_x_over_y_gsl_matrix() Dir.chdir(@directory) do .convert_to_index(:t) if [:t] or [:t_element] [:t_index] ||= list(:t).keys.max #phi2_by_mode index order (in Fortran) is kx, ky, t phi_re_narray = netcdf_file.var("phi0").get('start' => [0, 0, 0, [:t_index] - 1], 'end' => [0, -1, -1, [:t_index] - 1]) # ep phi_re_narray.shape 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, [:t_index] - 1], 'end' => [1, -1, -1, [: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) # ep gm.shape if [:no_zonal] for i in 0...gm.shape[1] gm[0,i] = GSL::Complex.alloc([0,0]) end end if xres = ([:xres] or [:x_resolution]) mat = GSL::Matrix::Complex.calloc(gm.shape[0], xres) extra = ((xres - gm.shape[1])).floor for i in 0...gm.shape[0] for j in 0...((gm.shape[1] + 1) / 2 ) # j+= extra if mat[i, j] = gm[i,j] mat[i, j+extra] = gm[i,-j] unless j==0 end end gm = mat # gm = mat.vertcat(gm).vertcat(mat) end if yres = ([:yres] or [:y_resolution]) mat = GSL::Matrix::Complex.calloc(yres, gm.shape[1]) extra = ((yres - gm.shape[0])).floor for i in 0...gm.shape[0] for j in 0...gm.shape[1] # j+= extra if mat[i, j] = gm[i,j] # mat[i, j+extra] = gm[i,-j] unless j==0 end end gm = mat # gm = mat.vertcat(gm).vertcat(mat) end # ep gm_re, gm_im # re = GSL::Complex.alloc([1.0, 0.0]) # gm = GSL::Matrix::Complex.calloc(*gm_re.shape) # gm = gm_re * re + gm_im * GSL::Complex.alloc([0.0, 1.0]) # gm_re, gm_im = fourier_transform_gm_matrix_complex_rows(gm_re, gm_im) gm = gm.backward_cols_c2c(true).backward_rows_cc2r(true) if [:limit] for i in 0...gm.shape[0] for j in 0...gm.shape[1] # j+= extra if gm[i, j] = [[gm[i,j], [:limit][0]].max, [:limit][1]].min # mat[i, j+extra] = gm[i,-j] unless j==0 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 912 def spectrum_over_ky_over_kpar_gsl_matrix() Dir.chdir(@directory) do #:re, :theta, :kx, :ky lkx = list(:kx) if [:t_index] or [: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 .convert_to_index(self, :t) end temp = phi_av = (lkx.keys.map do |kx_index| if [:t_index] phi = netcdf_file.var('phi_t').get({'start' => [0,0,kx_index-1,0, [:t_index] - 1], 'end' => [-1,-1,kx_index-1,-1, [:t_index] - 1]}) else phi = netcdf_file.var('phi').get({'start' => [0, 0, kx_index - 1, 0], 'end' => [-1, -1, 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) 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 [:no_kpar0] spectrum[0]=0.0 end spectrum = spectrum.from_box_order #ep spectrum.shape spectrum = spectrum*gvky[ky_element]**2 unless [:phi2_only] gm.set_row(ky_element, spectrum) end if [:no_zonal] gm.row(0).set_all(0.0) end if [: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 878 def spectrum_over_ky_over_kx_gsl_matrix() Dir.chdir(@directory) do raise "Spectrum makes no sense for single modes" if @grid_option == "single" .convert_to_index(:t) if [:t] or [:t_element] [: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, [:t_index] - 1], 'end' => [-1, -1, [:t_index] - 1]) phi_narray.reshape!(*phi_narray.shape.slice(0..1)) gm = phi_narray.to_gm.move_cols_from_box_order if [:times_kx4] or [: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 [:times_kx4] gm[i,j] = gm[i,j] * (vals[j])**2 if [:times_kx2] end end end if [:no_zonal] for i in 0...gm.shape[1] gm[0,i] = 0.0 end end if [: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 852 def transient_amplification_over_ky_over_kx_gsl_matrix() array = @transient_amplification_at_ky_at_kx.values.map{|h| h.values} return GSL::Matrix.alloc(array.flatten, array.size, array[0].size) end |