diff --git a/testcases/ExB_shear_demo/2D_Z_pinch/GS2_method/fort_01.90 b/demo/ExB_shear/2D_Z_pinch/GS2_method/fort_01.90
similarity index 100%
rename from testcases/ExB_shear_demo/2D_Z_pinch/GS2_method/fort_01.90
rename to demo/ExB_shear/2D_Z_pinch/GS2_method/fort_01.90
diff --git a/demo/ExB_shear/2D_Z_pinch/background_Er/fort_01.90 b/demo/ExB_shear/2D_Z_pinch/background_Er/fort_01.90
new file mode 100644
index 0000000000000000000000000000000000000000..6c7afdd4b280af81cb23e0a4b113a172dd5b6031
--- /dev/null
+++ b/demo/ExB_shear/2D_Z_pinch/background_Er/fort_01.90
@@ -0,0 +1,92 @@
+&BASIC
+ nrun = 1e6
+ dt = 0.025
+ tmax = 200
+ maxruntime = 72000
+ job2load = 0
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 128
+ Lx = 200
+ Ny = 48
+ Ly = 60
+ Nz = 1
+ SG = .f.
+ Nexc = 1
+/
+&GEOMETRY
+ geom = 'z-pinch'
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = 0.5
+ dtsave_3d = 0.5
+ dtsave_5d = 100
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 2 ! number of species
+ mu_x = 1.0
+ mu_y = 1.0
+ N_HD = 4
+ mu_z = 0.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.1
+ beta = 0.0
+ ADIAB_E = .f.
+ tau_i = 1.0
+ ZFrate = 1.0
+ ikxZF = 1
+/
+&CLOSURE
+ hierarchy_closure='truncation'
+ !hierarchy_closure='max_degree'
+ dmax = 2
+ nonlinear_closure='anti_laguerre_aliasing' !(truncation,full_sum,anti_laguerre_aliasing)
+ nmax = -1
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&SPECIES
+ ! electrons
+ name_ = 'electrons'
+ tau_ = 1.0
+ sigma_= 0.023338
+ q_ =-1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .t.
+/
+&INITIAL
+ INIT_OPT = 'phi' !(phi,blob)
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+/
diff --git a/demo/ExB_shear/2D_Z_pinch/control/fort_01.90 b/demo/ExB_shear/2D_Z_pinch/control/fort_01.90
new file mode 100644
index 0000000000000000000000000000000000000000..5899fc021b571093f2888bc11c17d898f07800cf
--- /dev/null
+++ b/demo/ExB_shear/2D_Z_pinch/control/fort_01.90
@@ -0,0 +1,91 @@
+&BASIC
+ nrun = 1e6
+ dt = 0.05
+ tmax = 200
+ maxruntime = 72000
+ job2load = 0
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 128
+ Lx = 200
+ Ny = 48
+ Ly = 60
+ Nz = 1
+ SG = .f.
+ Nexc = 1
+/
+&GEOMETRY
+ geom = 'z-pinch'
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = 0.5
+ dtsave_3d = 0.5
+ dtsave_5d = 100
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 2 ! number of species
+ mu_x = 1.0
+ mu_y = 1.0
+ N_HD = 4
+ mu_z = 0.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.1
+ beta = 0.0
+ ADIAB_E = .f.
+ tau_i = 1.0
+ ExBrate = 0
+/
+&CLOSURE
+ hierarchy_closure='truncation'
+ !hierarchy_closure='max_degree'
+ dmax = 2
+ nonlinear_closure='anti_laguerre_aliasing' !(truncation,full_sum,anti_laguerre_aliasing)
+ nmax = -1
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&SPECIES
+ ! electrons
+ name_ = 'electrons'
+ tau_ = 1.0
+ sigma_= 0.023338
+ q_ =-1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .t.
+/
+&INITIAL
+ INIT_OPT = 'phi' !(phi,blob)
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+/
diff --git a/testcases/ExB_shear_demo/2D_Z_pinch/fort_00.90 b/demo/ExB_shear/2D_Z_pinch/fort_00.90
similarity index 100%
rename from testcases/ExB_shear_demo/2D_Z_pinch/fort_00.90
rename to demo/ExB_shear/2D_Z_pinch/fort_00.90
diff --git a/testcases/ExB_shear_demo/GS2_method/fast_analysis.m b/demo/ExB_shear/GS2_method/fast_analysis.m
similarity index 100%
rename from testcases/ExB_shear_demo/GS2_method/fast_analysis.m
rename to demo/ExB_shear/GS2_method/fast_analysis.m
diff --git a/testcases/ExB_shear_demo/GS2_method/fort_00.90 b/demo/ExB_shear/GS2_method/fort_00.90
similarity index 100%
rename from testcases/ExB_shear_demo/GS2_method/fort_00.90
rename to demo/ExB_shear/GS2_method/fort_00.90
diff --git a/testcases/ExB_shear_demo/background_Er/fast_analysis.m b/demo/ExB_shear/background_Er/fast_analysis.m
similarity index 100%
rename from testcases/ExB_shear_demo/background_Er/fast_analysis.m
rename to demo/ExB_shear/background_Er/fast_analysis.m
diff --git a/testcases/ExB_shear_demo/background_Er/fort.90 b/demo/ExB_shear/background_Er/fort.90
similarity index 100%
rename from testcases/ExB_shear_demo/background_Er/fort.90
rename to demo/ExB_shear/background_Er/fort.90
diff --git a/testcases/ExB_shear_demo/background_Er/fort_00.90 b/demo/ExB_shear/background_Er/fort_00.90
similarity index 100%
rename from testcases/ExB_shear_demo/background_Er/fort_00.90
rename to demo/ExB_shear/background_Er/fort_00.90
diff --git a/demo/Laguerre_aliasing/2D_Z_pinch/Nmax_0/fort_00.90 b/demo/Laguerre_aliasing/2D_Z_pinch/Nmax_0/fort_00.90
new file mode 100644
index 0000000000000000000000000000000000000000..495787124f3c39313bea9ccf7d5566625236a854
--- /dev/null
+++ b/demo/Laguerre_aliasing/2D_Z_pinch/Nmax_0/fort_00.90
@@ -0,0 +1,91 @@
+&BASIC
+ nrun = 1e6
+ dt = 0.02
+ tmax = 500
+ maxruntime = 72000
+ job2load = -1
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 128
+ Lx = 200
+ Ny = 48
+ Ly = 60
+ Nz = 1
+ SG = .f.
+ Nexc = 1
+/
+&GEOMETRY
+ geom = 'z-pinch'
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 2
+ dtsave_5d = 50
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 2 ! number of species
+ mu_x = 1.0
+ mu_y = 0.0
+ N_HD = 4
+ mu_z = 0.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.05
+ beta = 0.0
+ ADIAB_E = .f.
+ tau_i = 1.0
+/
+&CLOSURE
+ !hierarchy_closure='truncation'
+ hierarchy_closure='max_degree'
+ dmax = 2
+ !nonlinear_closure='anti_laguerre_aliasing' !(truncation,full_sum,anti_laguerre_aliasing)
+ nonlinear_closure='truncation'
+ nmax = 0
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&SPECIES
+ ! electrons
+ name_ = 'electrons'
+ tau_ = 1.0
+ sigma_= 0.023338
+ q_ =-1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .t.
+/
+&INITIAL
+ INIT_OPT = 'phi' !(phi,blob)
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+/
diff --git a/demo/Laguerre_aliasing/2D_Z_pinch/anti_Laguerre_aliasing/fort_00.90 b/demo/Laguerre_aliasing/2D_Z_pinch/anti_Laguerre_aliasing/fort_00.90
new file mode 100644
index 0000000000000000000000000000000000000000..79b5231e35d9a595a683c1c4c05f135b43e7edd7
--- /dev/null
+++ b/demo/Laguerre_aliasing/2D_Z_pinch/anti_Laguerre_aliasing/fort_00.90
@@ -0,0 +1,90 @@
+&BASIC
+ nrun = 1e6
+ dt = 0.02
+ tmax = 500
+ maxruntime = 72000
+ job2load = -1
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 128
+ Lx = 200
+ Ny = 48
+ Ly = 60
+ Nz = 1
+ SG = .f.
+ Nexc = 1
+/
+&GEOMETRY
+ geom = 'z-pinch'
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 2
+ dtsave_5d = 50
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 2 ! number of species
+ mu_x = 1.0
+ mu_y = 0.0
+ N_HD = 4
+ mu_z = 0.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.05
+ beta = 0.0
+ ADIAB_E = .f.
+ tau_i = 1.0
+/
+&CLOSURE
+ !hierarchy_closure='truncation'
+ hierarchy_closure='max_degree'
+ dmax = 2
+ nonlinear_closure='anti_laguerre_aliasing' !(truncation,full_sum,anti_laguerre_aliasing)
+ nmax = -1
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&SPECIES
+ ! electrons
+ name_ = 'electrons'
+ tau_ = 1.0
+ sigma_= 0.023338
+ q_ =-1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .t.
+/
+&INITIAL
+ INIT_OPT = 'phi' !(phi,blob)
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+/
diff --git a/demo/Laguerre_aliasing/2D_Z_pinch/fort_00.90 b/demo/Laguerre_aliasing/2D_Z_pinch/fort_00.90
new file mode 100644
index 0000000000000000000000000000000000000000..190c9ffbe3b05f2fbce4bc0bab4d2cb822397499
--- /dev/null
+++ b/demo/Laguerre_aliasing/2D_Z_pinch/fort_00.90
@@ -0,0 +1,90 @@
+&BASIC
+ nrun = 1e6
+ dt = 0.05
+ tmax = 500
+ maxruntime = 72000
+ job2load = -1
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 128
+ Lx = 200
+ Ny = 48
+ Ly = 60
+ Nz = 1
+ SG = .f.
+ Nexc = 1
+/
+&GEOMETRY
+ geom = 'z-pinch'
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = 0.5
+ dtsave_3d = 0.5
+ dtsave_5d = 100
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 2 ! number of species
+ mu_x = 1.0
+ mu_y = 0.0
+ N_HD = 4
+ mu_z = 0.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.05
+ beta = 0.0
+ ADIAB_E = .f.
+ tau_i = 1.0
+/
+&CLOSURE
+ hierarchy_closure='truncation'
+ !hierarchy_closure='max_degree'
+ dmax = 2
+ nonlinear_closure='anti_laguerre_aliasing' !(truncation,full_sum,anti_laguerre_aliasing)
+ nmax = -1
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&SPECIES
+ ! electrons
+ name_ = 'electrons'
+ tau_ = 1.0
+ sigma_= 0.023338
+ q_ =-1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .t.
+/
+&INITIAL
+ INIT_OPT = 'phi' !(phi,blob)
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+/
diff --git a/demo/Laguerre_aliasing/2D_Z_pinch/maximized_sum/fort_00.90 b/demo/Laguerre_aliasing/2D_Z_pinch/maximized_sum/fort_00.90
new file mode 100644
index 0000000000000000000000000000000000000000..a16308273acbe715abde82e3ed416bcc65787632
--- /dev/null
+++ b/demo/Laguerre_aliasing/2D_Z_pinch/maximized_sum/fort_00.90
@@ -0,0 +1,91 @@
+&BASIC
+ nrun = 1e6
+ dt = 0.02
+ tmax = 500
+ maxruntime = 72000
+ job2load = -1
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 128
+ Lx = 200
+ Ny = 48
+ Ly = 60
+ Nz = 1
+ SG = .f.
+ Nexc = 1
+/
+&GEOMETRY
+ geom = 'z-pinch'
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 2
+ dtsave_5d = 50
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 2 ! number of species
+ mu_x = 1.0
+ mu_y = 0.0
+ N_HD = 4
+ mu_z = 0.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.05
+ beta = 0.0
+ ADIAB_E = .f.
+ tau_i = 1.0
+/
+&CLOSURE
+ !hierarchy_closure='truncation'
+ hierarchy_closure='max_degree'
+ dmax = 2
+ !nonlinear_closure='anti_laguerre_aliasing' !(truncation,full_sum,anti_laguerre_aliasing)
+ nonlinear_closure='full_sum'
+ nmax = -1
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&SPECIES
+ ! electrons
+ name_ = 'electrons'
+ tau_ = 1.0
+ sigma_= 0.023338
+ q_ =-1.0
+ k_N_ = 2.0
+ k_T_ = 0.4
+/
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .t.
+/
+&INITIAL
+ INIT_OPT = 'phi' !(phi,blob)
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+/
diff --git a/matlab/compute/compute_fa_2D.m b/matlab/compute/compute_fa_2D.m
index 8d9758e0b27a106faad7bce9a9bce4058ee67f57..f2e9552e97653b21476b4888f0fd77b7aaa31f4f 100644
--- a/matlab/compute/compute_fa_2D.m
+++ b/matlab/compute/compute_fa_2D.m
@@ -1,4 +1,4 @@
-function [SS,XX,FF] = compute_fa_2D(data, options)
+function [SS,XX,FF] = compute_fa_2D(data, species, s, x, T)
%% Compute the dispersion function from the moment hierarchi decomp.
% Normalized Hermite
Hp = @(p,s) polyval(HermitePoly(p),s)./sqrt(2.^p.*factorial(p));
@@ -9,99 +9,90 @@ Lj = @(j,x) polyval(LaguerrePoly(j),x);
FaM = @(s,x) exp(-s.^2-x);
%meshgrid for efficient evaluation
-[SS, XX] = meshgrid(options.SPAR, options.XPERP);
+[SS, XX] = meshgrid(s, x);
-[~, ikx0] = min(abs(data.kx));
-[~, iky0] = min(abs(data.ky));
-kx_ = data.kx; ky_ = data.ky;
-
-switch options.SPECIES
+switch species
case 'e'
- Napj_ = data.Nepj;
- parray = double(data.Pe);
- jarray = double(data.Je);
- case 'i'
- Napj_ = data.Nipj;
- parray = double(data.Pi);
- jarray = double(data.Ji);
-end
+ Napj_ = data.Napjz(2,:,:,:,:);
-switch options.iz
- case 'avg'
- Napj_ = mean(Napj_,5);
- phi_ = mean(data.PHI,3);
- otherwise
- iz = options.iz;
- Napj_ = Napj_(:,:,:,:,iz,:);
- phi_ = data.PHI(:,:,iz);
+ case 'i'
+ Napj_ = data.Napjz(1,:,:,:,:);
end
+parray = double(data.grids.Parray);
+jarray = double(data.grids.Jarray);
+% switch options.iz
+ % case 'avg'
+ options.SHOW_FLUXSURF = 0;
+ options.SHOW_METRICS = 0;
+ options.SHOW_CURVOP = 0;
+ [~, geo_arrays] = plot_metric(data,options);
+ J = geo_arrays.Jacobian;
+ Nz = data.grids.Nz;
+ tmp_ = 0;
+ for iz = 1:Nz
+ tmp_ = tmp_ + J(iz)*Napj_(:,:,:,iz,:);
+ end
+ Napj_ = tmp_/sum(J(iz));
+ % Napj_ = mean(Napj_,4);
+ % Napj_ = Napj_(:,:,:,Nz/2+1,:);
+ % phi_ = mean(data.PHI,3);
+ % otherwise
+ % iz = options.iz;
+ % Napj_ = Napj_(:,:,:,:,iz,:);
+ % phi_ = data.PHI(:,:,iz);
+% end
% Napj_ = squeeze(Napj_);
-frames = options.T;
-for it = 1:numel(options.T)
- [~,frames(it)] = min(abs(options.T(it)-data.Ts5D));
+frames = T;
+for it = 1:numel(T)
+ [~,frames(it)] = min(abs(T(it)-data.Ts3D));
end
frames = unique(frames);
-Napj_ = mean(Napj_(:,:,:,:,frames),5);
+Napj_ = mean(Napj_(:,:,:,:,frames),5);
-% Napj_ = squeeze(Napj_);
+Napj_ = squeeze(Napj_);
Np = numel(parray); Nj = numel(jarray);
-if options.non_adiab
- for ij_ = 1:Nj
- for ikx = 1:data.Nkx
- for iky = 1:data.Nky
- kp_ = sqrt(kx_(ikx)^2 + ky_(iky)^2);
- Napj_(1,ij_,iky,ikx) = Napj_(1,ij_,iky,ikx) + kernel(ij_,kp_)*phi_(iky,ikx);
- end
- end
- end
-end
-
-if options.RMS
- FF = zeros(data.Nky,data.Nkx,numel(options.XPERP),numel(options.SPAR));
+% if options.RMS
+ FF = zeros(numel(x),numel(s));
FAM = FaM(SS,XX);
for ip_ = 1:Np
p_ = parray(ip_);
HH = Hp(p_,SS);
for ij_ = 1:Nj
- j_ = jarray(ij_);
- LL = Lj(j_,XX);
+ j_ = jarray(ij_);
+ LL = Lj(j_,XX);
HLF = HH.*LL.*FAM;
- for ikx = 1:data.Nkx
- for iky = 1:data.Nky
- FF(iky,ikx,:,:) = squeeze(FF(iky,ikx,:,:)) + Napj_(ip_,ij_,iky,ikx)*HLF;
- end
- end
+ FF = FF + Napj_(ip_,ij_)*HLF;
end
end
-else
- FF = zeros(numel(options.XPERP),numel(options.SPAR));
- FAM = FaM(SS,XX);
- for ip_ = 1:Np
- p_ = parray(ip_);
- HH = Hp(p_,SS);
- for ij_ = 1:Nj
- j_ = jarray(ij_);
- LL = Lj(j_,XX);
- FF = FF + squeeze(Napj_(ip_,ij_,ikx0,iky0))*HH.*LL.*FAM;
- end
- end
-end
+% else
+% FF = zeros(numel(options.XPERP),numel(options.SPAR));
+% FAM = FaM(SS,XX);
+% for ip_ = 1:Np
+% p_ = parray(ip_);
+% HH = Hp(p_,SS);
+% for ij_ = 1:Nj
+% j_ = jarray(ij_);
+% LL = Lj(j_,XX);
+% FF = FF + squeeze(Napj_(ip_,ij_,ikx0,iky0))*HH.*LL.*FAM;
+% end
+% end
+% end
FF = (FF.*conj(FF)); %|f_a|^2
% FF = abs(FF); %|f_a|
-if options.RMS
+% if options.RMS
% FF = squeeze(mean(mean(sqrt(FF),1),2)); %sqrt(<|f_a|^2>kx,ky)
- FF = sqrt(squeeze(mean(mean(FF,1),2))); %<|f_a|>kx,ky
-else
- FF = sqrt(squeeze(FF)); %sqrt(<|f_a|>x,y)
-end
+ FF = sqrt(FF); %<|f_a|>kx,ky
+% else
+% FF = sqrt(squeeze(FF)); %sqrt(<|f_a|>x,y)
+% end
-FF = FF./max(max(FF));
-FF = FF';
+% FF = FF./max(max(FF));
+% FF = FF';
% FF = sqrt(FF);
% FF = FF';
end
\ No newline at end of file
diff --git a/matlab/compute/fourier_GENE.m b/matlab/compute/fourier_GENE.m
new file mode 100644
index 0000000000000000000000000000000000000000..2039f29ca9ccad0f446dfbe218642b6a97687fac
--- /dev/null
+++ b/matlab/compute/fourier_GENE.m
@@ -0,0 +1,9 @@
+function [ field_c ] = fourier_GENE( field_r )
+
+%fft, symmetric as we are using real data
+spectrumKxYZ=nx*fft(fieldxyz,[],1);
+field_c=ny*fft(spectrumKxYZ,[],2);
+clear spectrumKxKyZ
+
+end
+
diff --git a/matlab/compute/ifourier_GENE.m b/matlab/compute/ifourier_GENE.m
index 1538c36dfb1cde9ae4803a82e3ebf32b7ecddaea..e05abaa4644297f91490770467a25bb20bd35166 100644
--- a/matlab/compute/ifourier_GENE.m
+++ b/matlab/compute/ifourier_GENE.m
@@ -26,22 +26,6 @@ end
spectrumXKyZ=nx*ifft(spectrumKyKxZ,[],1);
field_r=ny*ifft(spectrumXKyZ,[],2,'symmetric');
clear spectrumKxKyZ
-
-%% Adapted for HeLaZ old representation
-% [nkx,ny,nz]=size(field_c);
-% %extend to whole ky by imposing reality condition
-% nx=2*nkx-1;
-%
-% %note, we need one extra point which we set to zero for the ifft
-% spectrumKxKyZ=zeros(nx,ny,nz);
-% spectrumKxKyZ(1:nkx,:,:)=field_c(:,:,:);
-% spectrumKxKyZ((nkx+1):(nx),1,:)=conj(field_c(nkx:-1:2,1,:));
-% spectrumKxKyZ((nkx+1):(nx),2:ny,:)=conj(field_c(nkx:-1:2,ny:-1:2,:));
-%
-% %inverse fft, symmetric as we are using real data
-% spectrumXKyZ=nx*ifft(spectrumKxKyZ,[],1);
-% field_r=ny*ifft(spectrumXKyZ,[],2,'symmetric');
-% clear spectrumKxKyZ
end
diff --git a/matlab/compute/mode_growth_meter.m b/matlab/compute/mode_growth_meter.m
index ab5736b4f47592164e2158576a322d4c088c1d71..c8998c0a8c22905ed37cf65810a219fa8ccd0fb3 100644
--- a/matlab/compute/mode_growth_meter.m
+++ b/matlab/compute/mode_growth_meter.m
@@ -6,10 +6,16 @@ d = OPTIONS.fftz.flag; % To add spectral evolution of z (useful for 3d zpin
switch OPTIONS.FIELD
case 'Ni00'
FIELD = DATA.Ni00;
- fname = 'N^{00}';
+ fname = 'Ni^{00}';
+ case 'Ne00'
+ FIELD = DATA.Ne00;
+ fname = 'Ne^{00}';
case 'phi'
FIELD = DATA.PHI;
fname = '\phi';
+ case 'T_i'
+ FIELD = DATA.TEMP_I;
+ fname = 'T_i';
end
if numel(size(FIELD)) == 3
field = squeeze(FIELD);
@@ -121,8 +127,13 @@ for i = 1:2
%plot
% subplot(2+d,3,1+3*(i-1))
FIGURE.axes(1+3*(i-1)) = subplot(2+d,3,1+3*(i-1),'parent',FIGURE.fig);
+ if MODES_SELECTOR == 2
[YY,XX] = meshgrid(t,fftshift(k));
pclr = pcolor(XX,YY,abs(plt(fftshift(field,MODES_SELECTOR),1:numel(k))));set(pclr, 'edgecolor','none'); hold on;
+ else
+ [YY,XX] = meshgrid(t,(k));
+ pclr = pcolor(XX,YY,abs(plt((field),1:numel(k))));set(pclr, 'edgecolor','none'); hold on;
+ end
set(gca,'YDir','normal')
% xlim([t(1) t(end)]); %ylim([1e-5 1])
xlabel(['$',kstr,'\rho_s$']); ylabel('$t c_s /R_0$');
@@ -138,10 +149,10 @@ for i = 1:2
semilogy(t,plt(field,ikzf),'--k');
end
%plot the time window where the gr are measured
- plot(t(it1)*[1 1],[1e-10 1],'--k')
- plot(t(it2)*[1 1],[1e-10 1],'--k')
- xlim([t(1) t(end)]); %ylim([1e-5 1])
+ xline(t(it1),'--k')
+ xline(t(it2),'--k')
xlabel('$t c_s /R_0$'); ylabel(['$|',fname,'_{',kstr,'}|$']);
+ axis tight
title('Measure time window')
% subplot(2+d,3,3+3*(i-1))
diff --git a/matlab/load/compile_results_2Da.m b/matlab/load/compile_results_2Da.m
new file mode 100644
index 0000000000000000000000000000000000000000..f89f413bd464f076b155de47693d5eabb401480b
--- /dev/null
+++ b/matlab/load/compile_results_2Da.m
@@ -0,0 +1,37 @@
+function [field, Ts2D] = compile_results_2Da(DIRECTORY,JOBNUMMIN,JOBNUMMAX,fieldname)
+CONTINUE = 1;
+JOBNUM = JOBNUMMIN; JOBFOUND = 0;
+% field
+field = [];
+Ts2D = [];
+ii = 1;
+while(CONTINUE)
+ filename = sprintf([DIRECTORY,'outputs_%.2d.h5'],JOBNUM);
+ % Check presence and jobnummax
+ if (exist(filename, 'file') == 2 && JOBNUM <= JOBNUMMAX)
+ %test if it is corrupted or currently running
+ try
+ openable = ~isempty(h5read(filename,'/data/var2d/time'));
+ catch
+ openable = 0;
+ end
+ if openable
+ % load field %%
+ [ F, T, ~] = load_2Da_data(filename, fieldname);
+ field = cat(4,field,F);
+ Ts2D = cat(1,Ts2D,T);
+ ii = ii + 1;
+ JOBFOUND = JOBFOUND + 1;
+ end
+ elseif (JOBNUM > JOBNUMMAX)
+ CONTINUE = 0;
+ end
+ JOBNUM = JOBNUM + 1;
+end
+
+if(JOBFOUND == 0)
+ disp('no results found, please verify the paths');
+ return;
+end
+
+end
\ No newline at end of file
diff --git a/matlab/load/compile_results_low_mem.m b/matlab/load/compile_results_low_mem.m
index 33fd76b5eb6086530d02faf9553cbc2b7dfddc2f..8ef6048ccd5d717c9c2f64699ddbeb84b77c267f 100644
--- a/matlab/load/compile_results_low_mem.m
+++ b/matlab/load/compile_results_low_mem.m
@@ -29,7 +29,7 @@ while(CONTINUE)
DATA.outfilenames{ii} = filename;
%test if it is corrupted or currently running
try
- openable = ~isempty(h5read(filename,'/data/var3d/time'));
+ openable = ~isempty(h5read(filename,'/data/var0d/time'));
catch
openable = 0;
end
@@ -38,13 +38,25 @@ while(CONTINUE)
fprintf('Loading ID %.2d (%s)\n',JOBNUM,filename);
% loading input parameters
DATA.(sprintf('fort_%.2d',JOBNUM)) = struct();
- DATA.(sprintf('fort_%.2d',JOBNUM)) = read_namelist(fortname);
+ % cp the STDIN.XX from the output file to the directory to load
+ tmpfort = [fortname,'.tmp'];
+ fid = fopen(tmpfort,'wt');
+ input_string = h5read(filename,sprintf('/files/STDIN.%.2d',JOBNUM));
+ fprintf(fid, input_string);
+ fclose(fid);
+ DATA.(sprintf('fort_%.2d',JOBNUM)) = read_namelist(tmpfort);
+ system(['rm ',tmpfort]); % clean it
% Loading from output file
CPUTIME = h5readatt(filename,'/data/input','cpu_time');
DT_SIM = h5readatt(filename,'/data/input/basic','dt');
[Parray, Jarray, kx, ky, z] = load_grid_data(filename);
- W_GAMMA = strcmp(h5readatt(filename,'/data/input/diagnostics','write_gamma'),'y');
- W_HF = strcmp(h5readatt(filename,'/data/input/diagnostics','write_hf' ),'y');
+ try
+ W_GAMMA = strcmp(h5readatt(filename,'/data/input/diagnostics','write_gamma'),'y');
+ W_HF = strcmp(h5readatt(filename,'/data/input/diagnostics','write_hf' ),'y');
+ catch
+ W_GAMMA = strcmp(h5readatt(filename,'/data/input/diag_par','write_gamma'),'y');
+ W_HF = strcmp(h5readatt(filename,'/data/input/diag_par','write_hf' ),'y');
+ end
KIN_E = strcmp(h5readatt(filename,'/data/input/model', 'ADIAB_E' ),'n');
BETA = h5readatt(filename,'/data/input/model','beta');
diff --git a/matlab/load/load_2D_data.m b/matlab/load/load_2D_data.m
index 67da60c9dd1931e73cde73c7520ecb6370a0c153..6ca82e8430e399ec31c1d9feb74d31e3d2203a6e 100644
--- a/matlab/load/load_2D_data.m
+++ b/matlab/load/load_2D_data.m
@@ -1,5 +1,5 @@
function [ data, time, dt ] = load_2D_data( filename, variablename )
-%LOAD_3D_DATA load a 3D variable stored in a hdf5 result file from HeLaZ
+%LOAD_2D_DATA load a 2D variable stored in a hdf5 result file
time = h5read(filename,'/data/var2d/time');
dt = h5readatt(filename,'/data/input/basic','dt');
cstart= h5readatt(filename,'/data/input/basic','start_iframe3d');
diff --git a/matlab/load/load_2Da_data.m b/matlab/load/load_2Da_data.m
new file mode 100644
index 0000000000000000000000000000000000000000..3cdd94bfb0f0db936ee9745c89e8755843deea76
--- /dev/null
+++ b/matlab/load/load_2Da_data.m
@@ -0,0 +1,43 @@
+function [ data, time, dt ] = load_2Da_data( filename, variablename )
+%LOAD_2Da_DATA load a 2D variable stored in a hdf5 result file
+ time = h5read(filename,'/data/var2d/time');
+ dt = h5readatt(filename,'/data/input/basic','dt');
+ cstart= h5readatt(filename,'/data/input/basic','start_iframe2d');
+ Na = h5readatt(filename,'/data/input/model','Na');
+ Np = h5readatt(filename,'/data/input/grid', 'Np');
+ Nj = h5readatt(filename,'/data/input/grid', 'Nj');
+ Nky = h5readatt(filename,'/data/input/grid', 'Nky');
+ Nkx = h5readatt(filename,'/data/input/grid', 'Nkx');
+ Nz = h5readatt(filename,'/data/input/grid', 'Nz');
+
+
+ % Find array size by loading the first output
+ tmp = h5read(filename,['/data/var2d/',variablename,'/', num2str(cstart+1,'%06d')]);
+ try % check if it is complex or real
+ sz = size(tmp.real);
+ cmpx = 1;
+ catch
+ sz = size(tmp);
+ cmpx = 0;
+ end
+ % add a dimension if nz=1 or na=1
+% if Na == 1
+% sz = [1 sz];
+% end
+ if Nz == 1
+ sz = [sz 1];
+ end
+ % add time dimension
+ data = zeros([sz numel(time)]);
+
+ for it = 1:numel(time)
+ tmp = h5read(filename,['/data/var2d/',variablename,'/', num2str(cstart+it,'%06d')]);
+ if cmpx
+ data(:,:,:,it) = reshape(tmp.real,sz) + 1i * reshape(tmp.imaginary,sz);
+ else
+ data(:,:,:,it) = reshape(tmp,sz);
+ end
+ end
+
+end
+
diff --git a/matlab/load/load_multiple_outputs_marconi.m b/matlab/load/load_multiple_outputs_marconi.m
deleted file mode 100644
index 1fdd3b8608236ae4a056034abf7852fc50a814a0..0000000000000000000000000000000000000000
--- a/matlab/load/load_multiple_outputs_marconi.m
+++ /dev/null
@@ -1,6 +0,0 @@
-addpath(genpath('../matlab')) % ... add
-load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/simulation_A/300x150_L_120_P_8_J_4_eta_0.6_nu_1e-01_SGGK_mu_0e+00/')
-load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/simulation_B/300x150_L_120_P_8_J_4_eta_0.6_nu_5e-01_SGGK_mu_0e+00/')
-load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/simulation_A/300x150_L_120_P_8_J_4_eta_0.6_nu_1e-01_PAGK_mu_0e+00/')
-load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/simulation_A/500x500_L_120_P_4_J_2_eta_0.6_nu_1e-01_DGGK_mu_0e+00/')
-load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/simulation_A/500x500_L_120_P_2_J_1_eta_0.6_nu_1e-01_DGGK_mu_0e+00/')
diff --git a/matlab/load/load_params.m b/matlab/load/load_params.m
index 967baf3c4587ab4217c2763ad1c0260becddb13d..85d7c00d0ba3f29c41297abb58c7a6e107cf8b06 100644
--- a/matlab/load/load_params.m
+++ b/matlab/load/load_params.m
@@ -51,12 +51,19 @@ function [DATA] = load_params(DATA,filename)
catch
DATA.inputs.ADIAB_I = 0;
end
- DATA.inputs.W_GAMMA = h5readatt(filename,'/data/input/diagnostics','write_gamma') == 'y';
- DATA.inputs.W_PHI = h5readatt(filename,'/data/input/diagnostics','write_phi') == 'y';
- DATA.inputs.W_NA00 = h5readatt(filename,'/data/input/diagnostics','write_Na00') == 'y';
- DATA.inputs.W_NAPJ = h5readatt(filename,'/data/input/diagnostics','write_Napj') == 'y';
- DATA.inputs.W_SAPJ = h5readatt(filename,'/data/input/diagnostics','write_Sapj') == 'y';
-
+ try
+ DATA.inputs.W_GAMMA = h5readatt(filename,'/data/input/diagnostics','write_gamma') == 'y';
+ DATA.inputs.W_PHI = h5readatt(filename,'/data/input/diagnostics','write_phi') == 'y';
+ DATA.inputs.W_NA00 = h5readatt(filename,'/data/input/diagnostics','write_Na00') == 'y';
+ DATA.inputs.W_NAPJ = h5readatt(filename,'/data/input/diagnostics','write_Napj') == 'y';
+ DATA.inputs.W_SAPJ = h5readatt(filename,'/data/input/diagnostics','write_Sapj') == 'y';
+ catch
+ DATA.inputs.W_GAMMA = h5readatt(filename,'/data/input/diag_par','write_gamma') == 'y';
+ DATA.inputs.W_PHI = h5readatt(filename,'/data/input/diag_par','write_phi') == 'y';
+ DATA.inputs.W_NA00 = h5readatt(filename,'/data/input/diag_par','write_Na00') == 'y';
+ DATA.inputs.W_NAPJ = h5readatt(filename,'/data/input/diag_par','write_Napj') == 'y';
+ DATA.inputs.W_SAPJ = h5readatt(filename,'/data/input/diag_par','write_Sapj') == 'y';
+ end
% Species dependent parameters
DATA.inputs.sigma = zeros(1,DATA.inputs.Na);
DATA.inputs.tau = zeros(1,DATA.inputs.Na);
diff --git a/matlab/load/readFortranNamelist.m b/matlab/load/readFortranNamelist.m
deleted file mode 100644
index 5dbbda9337ba82b2ff2674d9d30573dc51ba30e5..0000000000000000000000000000000000000000
--- a/matlab/load/readFortranNamelist.m
+++ /dev/null
@@ -1,213 +0,0 @@
-function S = read_namelist(filename)
-% S = READ_NAMELIST(FILENAME) returns the struct S containg namelists and
-% variables in the file FILENAME organised in hierachical way:
-%
-% |--VAR1
-% |--VAR2
-% |-- NMLST_A--|...
-% | |--VARNa
-% |
-% | |--VAR1
-% |-- NMLST_B--|--VAR2
-% | |...
-% S --| ... |--VARNb
-% |
-% | |--VAR1
-% |-- NMLST_M--|--VAR2
-% |...
-% |--VARNm
-%
-% Note: The function can read multidimensioal variables as well. The
-% function assumes that there is no more than one namelist section per
-% line. At this time there is no syntax checking functionality so the
-% function will crash in case of errors.
-%
-% Example:
-% NMLST = read_namelist('OPTIONS.nam');
-% NMLST.NAM_FRAC.XUNIF_NATURE = 0.1;
-% write_namelist(NMlST, 'MOD_OPTIONS.nam');
-%
-% Written by: Darien Pardinas Diaz (darien.pardinas-diaz@monash.edu)
-% Version: 1.0
-% Date: 16 Dec 2011
-S = struct();
-% Open and read the text file containing the namelists
-fid = fopen(filename,'r');
-c = 0;
-lines = cell(1);
-% Read all the text lines in namelist file
-while ~feof(fid)
- line = fgetl(fid);
- % Remove comments if any on the line
- idx = find(line == '!');
- if ~isempty(idx),
- line = line(1:idx(1)-1);
- end
- if ~isempty(line),
- c = c + 1;
- lines{c} = line;
- end
-end
-fclose(fid);
-i = 0;
-while i < c;
- % Find a record
- i = i + 1;
- line = lines{i};
- idx = find(line == '&');
- if ~isempty(idx), % i.e. a namelist start
- line = line(idx(1) + 1:end);
- % find next space
- idx = find(line == ' ');
- if ~isempty(idx),
- namelst = line(1:idx(1) - 1);
- line = line(idx(1) + 1:end);
- else
- namelst = line;
- line = [];
- end
- nmlst_bdy = [];
- idx = strfind(line,'/');
- % Get the variable specification section
- while isempty(idx) && i < c,
- nmlst_bdy = [nmlst_bdy ' ' line];
- i = i + 1;
- line = lines{i};
- idx = strfind(line,'/');
- end
- if ~isempty(idx) && idx(1) > 1,
- nmlst_bdy = [nmlst_bdy ' ' line];
- end
- % Parse current namelist (set of variables)
- S.(namelst) = parse_namelist(nmlst_bdy);
- end
-end
-function S = parse_namelist(strng)
-% Internal function to parse the body text of a namelist section.
-% Limitations: the following patterns are prohibited inside the literal
-% strings: '.t.' '.f.' '.true.' '.false.' '(:)'
-% Get all .true., .t. and .false., .f. to T and F
-strng = regexprep(strng,'\.true\.' ,'T','ignorecase');
-strng = regexprep(strng,'\.false\.','F','ignorecase');
-strng = regexprep(strng,'\.t\.','T','ignorecase');
-strng = regexprep(strng,'\.f\.','F','ignorecase');
-% Make evaluable the (:) expression in MATLAB if any
-strng = regexprep(strng, '\(:\)', '(1,:)');
-[strng, islit] = parse_literal_strings([strng ' ']);
-% Find the position of all the '='
-eq_idx = find(strng == '=');
-nvars = length(eq_idx);
-arg_start = eq_idx + 1;
-arg_end = zeros(size(eq_idx));
-vars = cell(nvars,1);
-S = struct;
-% Loop through every variable
-for k = 1:nvars,
- i = eq_idx(k) - 1;
- % Move to the left and discard blank spaces
- while strng(i) == ' ', i = i - 1; end
- % Now we are over the variable name or closing parentesis
- j = i;
- if strng(i) == ')',
- while strng(i) ~= '(', i = i - 1; end
- i = i - 1;
- % Move to the left and discard any possible blank spaces
- while strng(i) == ' ', i = i - 1; end
- end
-
- % Now we are over the last character of the variable name
- while strng(i) ~= ' ', i = i - 1; end
-
- if k > 1, arg_end(k - 1) = i; end
- vars{k} = ['S.' strng(i + 1: j)];
-end
-arg_end(end) = length(strng);
-% This variables are used in the eval function to evaluate True/False,
-% so don't remove it!
-T = '.true.';
-F = '.false.';
-% Loop through every variable guess varible type
-for k = 1:nvars,
- arg = strng(arg_start(k):arg_end(k));
- arglit = islit(arg_start(k):arg_end(k))';
-
- % Remove commas in non literal string...
- commas = ~arglit & arg == ',';
- if any(commas)
- arg(commas) = ' ';
- end
-
- if any(arglit),
- % We are parsing a variable that is literal string
- arg = ['{' arg '};'];
- elseif ~isempty(find( arg == 'T' | arg == 'F', 1)),
- % We are parsing a boolean variable
- arg = ['{' arg '};'];
- else
- % We are parsing a numerical array
- arg = ['[' arg '];'];
- end
- % Eval the modified syntax in Matlab
- eval([vars{k} ' = ' arg]);
-end
-function [strng, is_lit] = parse_literal_strings(strng)
-% Parse the literal declarations of strings and change to Matlab syntax
-len = length(strng);
-add_squote = []; % Positions to add a scape single quote on syntax
-rem_dquote = []; % Positions to remove a double quote scape on syntax
-i = 1;
-while i < len,
- if strng(i) == '''', % Opening string with single quote...
- i = i + 1;
- while i < len && strng(i) ~= '''' || strcmp(strng(i:i+1),'''''') ,
- i = i + 1;
- if strcmp(strng(i-1:i),''''''),
- i = i + 1;
- end
- end
- end
- if strng(i) == '"', % Opening string with double quote...
- strng(i) = ''''; % Change to single quote
- i = i + 1;
- while strng(i) ~= '"' || strcmp(strng(i:i+1),'""') && i < len,
- % Check for a possible sigle quote here
- if strng(i) == '''',
- add_squote = [add_squote i];
- end
- i = i + 1;
- if strcmp(strng(i-1:i),'""'),
- rem_dquote = [rem_dquote i-1];
- i = i + 1;
- end
- end
- strng(i) = ''''; % Change to single quote
- end
- i = i + 1;
-end
-for i = 1:length(add_squote);
- strng = [strng(1:add_squote(i)) strng(add_squote(i):end)];
-end
-for i = 1:length(rem_dquote);
- strng = [strng(1:rem_dquote(i)-1) strng(rem_squote(i)+1:end)];
-end
-% Now everything should be in Matlab string syntax
-% Classify syntax as literal or regular expression
-i = 1;
-len = length(strng);
-is_lit = zeros(len,1);
-while i < len,
- if strng(i) == '''', % Opening string with single quote...
- is_lit(i) = 1;
- i = i + 1;
- while i < len && strng(i) ~= '''' || strcmp(strng(i:i+1),''''''),
- is_lit(i) = 1;
- i = i + 1;
- if strcmp(strng(i-1:i),''''''),
- is_lit(i) = 1;
- i = i + 1;
- end
- end
- is_lit(i) = 1;
- end
- i = i + 1;
-end
diff --git a/matlab/load/read_namelist.m b/matlab/load/read_namelist.m
index 3d49e6d0406d2532eaa3fc51ee3f7b2fe84d7631..954dbc9af151a177268b600963ef51968cade8b8 100644
--- a/matlab/load/read_namelist.m
+++ b/matlab/load/read_namelist.m
@@ -40,10 +40,10 @@ while ~feof(fid)
line = fgetl(fid);
% Remove comments if any on the line
idx = find(line == '!');
- if ~isempty(idx),
+ if ~isempty(idx)
line = line(1:idx(1)-1);
end
- if ~isempty(line),
+ if ~isempty(line)
c = c + 1;
lines{c} = line;
end
diff --git a/matlab/plot/Ursula_Meier.m b/matlab/plot/Ursula_Meier.m
new file mode 100644
index 0000000000000000000000000000000000000000..affabdea29979e8a4f585ad3433beb13caf1df26
--- /dev/null
+++ b/matlab/plot/Ursula_Meier.m
@@ -0,0 +1,106 @@
+function [filename] = Ursula_Meier(MOVIE)
+ FPS = 16; BWR = 0; ncolor_level = 128; format = '.gif'; SAT = 0.75;
+ INTERP = 1;
+ if isfield(MOVIE,'FPS')
+ FPS = MOVIE.FPS;
+ end
+ if isfield(MOVIE,'BWR')
+ BWR = MOVIE.BWR;
+ end
+ if isfield(MOVIE,'format')
+ format = MOVIE.format;
+ end
+ if isfield(MOVIE,'SAT')
+ SAT = MOVIE.SAT;
+ end
+ if isfield(MOVIE,'INTERP')
+ INTERP = MOVIE.INTERP;
+ end
+ DELAY = 1/MOVIE.FPS;
+ FILENAME = MOVIE.FILENAME; FIELDNAME = MOVIE.FIELDNAME;
+ X = MOVIE.X; Y = MOVIE.Y; T = MOVIE.T; F = MOVIE.F;
+ XNAME = MOVIE.XNAME; YNAME = MOVIE.YNAME;
+ switch format
+ case '.avi'
+ vidfile = VideoWriter(FILENAME,'Uncompressed AVI');
+ vidfile.FrameRate = FPS;
+ open(vidfile);
+ end
+ % Set colormap boundaries
+ hmax = max(max(max(F(:,:,:))));
+ hmin = min(min(min(F(:,:,:))));
+ if hmax == hmin
+ disp('Warning : h = hmin = hmax = const')
+ else
+ % Setup figure frame
+ fig = figure('Color','white');%,'Position', toplot.DIMENSIONS.*[0.5 0.5 1.0 1]);
+ pcolor(X,Y,F(:,:,1)); % to set up
+ if BWR
+ colormap(bluewhitered)
+ else
+ colormap(gray)
+ end
+ clim(SAT*[-1 1])
+ axis equal
+ axis tight % this ensures that getframe() returns a consistent size
+ if INTERP
+ shading interp;
+ end
+ in = 1;
+ nbytes = fprintf(2,'frame %d/%d',in,numel(F(1,1,:)));
+ for n = 1:numel(T) % loop over selected frames
+ scale = max(max(abs(F(:,:,n)))); % Scaling to normalize
+ pclr = pcolor(X,Y,F(:,:,n)/scale); % frame plot\
+ clim([-1,1]);
+ if INTERP
+ shading interp;
+ end
+ set(pclr, 'edgecolor','none'); %pbaspect(toplot.ASPECT);
+ if BWR
+ colormap(bluewhitered)
+ else
+ colormap(gray)
+ end
+ clim(SAT*[-1 1])
+ title([FIELDNAME,', $t \approx$', sprintf('%.3d',ceil(T(n)))...
+ ,', scaling = ',sprintf('%.1e',scale)]);
+
+ xlabel(XNAME); ylabel(YNAME); %colorbar;
+ axis tight equal
+ drawnow
+ % Capture the plot as an image
+ frame = getframe(fig);
+ switch format
+ case '.gif'
+ im = frame2im(frame);
+ [imind,cm] = rgb2ind(im,ncolor_level);
+ % Write to the GIF File
+ if in == 1
+ imwrite(imind,cm,FILENAME,'gif', 'Loopcount',inf);
+ else
+ imwrite(imind,cm,FILENAME,'gif','WriteMode','append', 'DelayTime',DELAY);
+ end
+ case '.avi'
+ writeVideo(vidfile,frame);
+ otherwise
+ disp('Unknown format');
+ break
+ end
+ % terminal info
+ while nbytes > 0
+ fprintf('\b')
+ nbytes = nbytes - 1;
+ end
+ nbytes = fprintf(2,'frame %d/%d',n,numel(F(1,1,:)));
+ in = in + 1;
+ end
+ disp(' ')
+ switch format
+ case '.gif'
+ disp(['Gif saved @ : ',FILENAME])
+ case '.avi'
+ disp(['Video saved @ : ',FILENAME])
+ close(vidfile);
+ end
+ end
+end
\ No newline at end of file
diff --git a/matlab/plot/cinecita.m b/matlab/plot/cinecita.m
new file mode 100644
index 0000000000000000000000000000000000000000..fcfcdd03609bd2a2667102006d974a1b2d372e22
--- /dev/null
+++ b/matlab/plot/cinecita.m
@@ -0,0 +1,69 @@
+function [ ] = cinecita(DATADIR,J0,J1,fieldname,plan,save)
+
+data = {};
+[data] = compile_results_low_mem(data,DATADIR,J0,J1);
+%% Select the field
+SKIP_COMP = 0; % Turned on only for 2D plots
+OPE_ = 1; % Operation on data
+switch fieldname
+ case 'phi' %ES pot
+ [FIELD,TIME] = compile_results_3D(DATADIR,J0,J1,'phi');
+ ltxname = '\phi';
+ case 'phi_obmp' %ES pot
+ [FIELD,TIME] = compile_results_2D(DATADIR,J0,J1,'phi_obmp');
+ ltxname = '\phi_{z=0}';
+ SKIP_COMP = 1;
+ case '\psi' %EM pot
+ [FIELD,TIME] = compile_results_3D(DATADIR,J0,J1,'psi');
+ ltxname = '\psi';
+ case 'phi_nz' % non-zonal ES pot
+ [FIELD,TIME] = compile_results_3D(DATADIR,J0,J1,'phi');
+ ltxname = '\phi^{NZ}';
+ OPE_ = (KY~=0);
+ case 'vE_y' % y-comp of ExB velocity
+ [FIELD,TIME] = compile_results_3D(DATADIR,J0,J1,'phi');
+ ltxname = 'v_{Ey}';
+ OPE_ = -1i*KX;
+ case 'vE_x' % x-comp of ExB velocity
+ [FIELD,TIME] = compile_results_3D(DATADIR,J0,J1,'phi');
+ ltxname = 'v_{Ex}';
+ OPE_ = -1i*KY;
+ case 'sE_y' % y-comp of ExB shear
+ [FIELD,TIME] = compile_results_3D(DATADIR,J0,J1,'phi');
+ ltxname = 's_{Ey}';
+ OPE_ = KX.^2;
+ case 'sE_x' % x-comp of ExB shear
+ [FIELD,TIME] = compile_results_3D(DATADIR,J0,J1,'phi');
+ ltxname = 's_{Ex}';
+ OPE_ = KY.^2;
+ case 'wz' % ES pot vorticity
+ [FIELD,TIME] = compile_results_3D(DATADIR,J0,J1,'phi');
+ ltxname = '\omega_z';
+ OPE_ = -(KX.^2+KY.^2);
+ otherwise
+ disp('Fieldname not recognized');
+ return
+end
+%% Setup grids
+% [KX, KY] = meshgrid(DATA.grids.kx, DATA.grids.ky);
+Nx = data.grids.Nx; Ny = data.grids.Ny; Nz = data.grids.Nz; Nt = numel(TIME);
+% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Options
+options.INTERP = 0;
+options.POLARPLOT = 0;
+options.BWR = 1; % bluewhitered plot or gray
+options.CLIMAUTO = 1; % adjust the colormap auto
+options.NAME = ltxname;
+options.PLAN = plan;
+options.COMP = 1;
+options.TIME = data.Time(1:1:end);
+data.EPS = 0.1;
+data.a = data.EPS * 2000;
+options.RESOLUTION = 256;
+create_film(data,options,'.gif')
+
+if ~save
+ system(['rm ',FILENAME]);
+end
+
+end
\ No newline at end of file
diff --git a/matlab/plot/cinecita_2D.m b/matlab/plot/cinecita_2D.m
new file mode 100644
index 0000000000000000000000000000000000000000..5a6f0f4f5498ac4f3cf3f5a5748ddd1e4857e5e4
--- /dev/null
+++ b/matlab/plot/cinecita_2D.m
@@ -0,0 +1,136 @@
+function [MOVIE] = cinecita_2D(DATADIR,fieldname,varargin)
+DATADIR = [DATADIR,'/'];
+J0 = 0; J1 = 20; nskip = 1; FOURIER = 0; SAT = 0.75;
+PLAY = 1;
+if numel(varargin) > 0
+ if isfield(varargin{1},'J0')
+ J0 = varargin{1}.J0;
+ end
+ if isfield(varargin{1},'J1')
+ J1 = varargin{1}.J1;
+ end
+ if isfield(varargin{1},'nskip')
+ nskip = varargin{1}.nskip;
+ end
+ if isfield(varargin{1},'FOURIER')
+ FOURIER = varargin{1}.FOURIER;
+ end
+ if isfield(varargin{1},'SAT')
+ SAT = varargin{1}.SAT;
+ end
+ if isfield(varargin{1},'PLAY')
+ PLAY = varargin{1}.PLAY;
+ end
+end
+%
+data = {};
+data = compile_results_low_mem(data,DATADIR,J0,J1);
+data = load_params(data,data.outfilenames{1});
+Nx = data.grids.Nx; Ny = data.grids.Ny; Na = data.inputs.Na;
+[KX,KY] = meshgrid(data.grids.kx,data.grids.ky);
+format = '.gif';
+%% Select the field
+OPE_ = 1; % Operation on data
+Nspec = 0; % Load a specie
+switch fieldname
+case '\phi' %ES pot
+ toload = 'phi';
+ ltxname = '\phi';
+ vname = 'phi';
+case '\phi_{zf}' %ES pot
+ toload = 'phi';
+ OPE_ = KY==0; % Operation on data
+ ltxname = '\phi_{zf}';
+ vname = 'phizf';
+case '\psi' %EM pot
+ toload = 'psi';
+ ltxname = '\psi';
+ vname = 'psi';
+case 'n_i' % ion density
+ toload = 'dens';
+ Nspec = 1;
+ ltxname = 'n_i';
+ vname = 'dens_i';
+case 'n_e' % ion density
+ toload = 'dens';
+ Nspec = 2;
+ ltxname = 'n_e';
+ vname = 'dens_e';
+case 'v_{Ex}' %ES pot
+ toload = 'phi';
+ OPE_ = -1i*KY; % Operation on data
+ ltxname= 'v_{Ex}';
+ vname = 'vEx';
+case 'v_{Ey}' %ES pot
+ toload = 'phi';
+ OPE_ = 1i*KX; % Operation on data
+ ltxname= 'v_{Ey}';
+ vname = 'vEy';
+case '\delta B_x'
+ toload = 'psi';
+ OPE_ = -1i*KY; % Operation on data
+ ltxname = '\delta B_x';
+ vname = 'dBx';
+case '\delta B_y'
+ toload = 'psi';
+ OPE_ = 1i*KX; % Operation on data
+ ltxname = '\delta B_y';
+ vname = 'dBy';
+otherwise
+ toload = fieldname;
+ OPE_ = 1;
+end
+
+if Nspec
+ [FIELD,TIME] = compile_results_2Da(DATADIR,J0,J1,[toload,'_obmp']);
+ FIELD = squeeze(FIELD(Nspec,:,:,:));
+else
+ [FIELD,TIME] = compile_results_2D(DATADIR,J0,J1,[toload,'_obmp']);
+end
+
+TIME = TIME(1:nskip:end); FIELD = FIELD(:,:,1:nskip:end);
+
+switch ~FOURIER
+ case 1 % Real space plot
+ XNAME = '$x$'; YNAME = '$y$'; plane ='xy';
+ [X,Y] = meshgrid(data.grids.x,data.grids.y);
+ INTERP = 1;
+ process = @(x) real(fftshift(ifourier_GENE(x)));
+ shift_x = @(x) x;
+ shift_y = @(x) x;
+ case 0 % Frequencies plot
+ XNAME = '$k_x$'; YNAME = '$k_y$'; plane ='kxky';
+ [X,Y] = meshgrid(data.grids.kx,data.grids.ky);
+ INTERP = 0;
+ process = @(x) abs(fftshift(x,2));
+ shift_x = @(x) fftshift(x,2);
+ shift_y = @(x) fftshift(x,2);
+end
+
+for it = 1:numel(TIME)
+ tmp = squeeze(OPE_.*FIELD(:,:,it));
+ F(:,:,it) = squeeze(process(tmp));
+end
+
+X = shift_x(X);
+Y = shift_y(Y);
+FILENAME = [vname,'_',plane,'_obmp'];
+FILENAME = [DATADIR,FILENAME,format];
+FIELDNAME = ['$',ltxname,'$'];
+MOVIE.F = F;
+MOVIE.X = X;
+MOVIE.Y = Y;
+MOVIE.T = TIME;
+MOVIE.XNAME = XNAME;
+MOVIE.YNAME = YNAME;
+MOVIE.FPS = 16;
+MOVIE.BWR = 0;
+MOVIE.SAT = 0.75;
+MOVIE.FIELDNAME = FIELDNAME;
+MOVIE.FILENAME = FILENAME;
+% Shoot the movie
+if PLAY
+ Ursula_Meier(MOVIE)
+end
+
+end
\ No newline at end of file
diff --git a/matlab/plot/create_film.m b/matlab/plot/create_film.m
index 6becccec8c45ab7c06a95c19e033bbf3d28363c9..ca56570d89752bf52d946ac16a07bc43a0a40f99 100644
--- a/matlab/plot/create_film.m
+++ b/matlab/plot/create_film.m
@@ -1,16 +1,22 @@
function create_film(DATA,OPTIONS,format)
%% Plot options
-FPS = 16; DELAY = 1/FPS;
+FPS = OPTIONS.FPS; DELAY = 1/FPS;
BWR = OPTIONS.BWR; NORMALIZED = 1;
-if ~strcmp(OPTIONS.PLAN,'sx')
- T = DATA.Ts3D;
-else
- T = DATA.Ts5D;
-end
%% Processing
switch OPTIONS.PLAN
case 'RZ'
toplot = poloidal_plot(DATA,OPTIONS);
+ case '3D'
+ OPTIONS.PLAN = 'xy';
+ [~,OPTIONS.COMP] = min(abs(OPTIONS.XYZ(3) - DATA.grids.z));
+ toplot = process_field(DATA,OPTIONS);
+ OPTIONS.PLAN = 'xz';
+ [~,OPTIONS.COMP] = min(abs(OPTIONS.XYZ(2) - DATA.grids.y));
+ toplot_xz = process_field(DATA,OPTIONS);
+ OPTIONS.PLAN = 'yz';
+ [~,OPTIONS.COMP] = min(abs(OPTIONS.XYZ(1) - DATA.grids.x));
+ toplot_yz = process_field(DATA,OPTIONS);
+ OPTIONS.PLAN = '3D';
otherwise
toplot = process_field(DATA,OPTIONS);
end
@@ -20,7 +26,7 @@ XNAME = ['$',toplot.XNAME,'$'];
YNAME = ['$',toplot.YNAME,'$'];
FIELDNAME = ['$',toplot.FIELDNAME,'$'];
FIELD = toplot.FIELD; X = toplot.X; Y = toplot.Y;
-FRAMES = toplot.FRAMES;
+TIME = toplot.TIME;
switch format
case '.avi'
vidfile = VideoWriter(FILENAME,'Uncompressed AVI');
@@ -36,9 +42,22 @@ if hmax == hmin
disp('Warning : h = hmin = hmax = const')
else
% Setup figure frame
-fig = figure('Color','white');%,'Position', toplot.DIMENSIONS.*[0.5 0.5 1.0 1]);
if ~strcmp(OPTIONS.PLAN,'sx')
- pcolor(X,Y,FIELD(:,:,1)); % to set up
+ if ~strcmp(OPTIONS.PLAN,'3D')
+ fig = figure('Color','white');
+ pclr = pcolor(X,Y,FIELD(:,:,1)/scale); % frame plot\
+ set(pclr, 'edgecolor','none'); %pbaspect(toplot.ASPECT);
+ else
+ fig = figure('Color','white','Position', 1024*[0.5 0.5 0.5 1]);
+ s = surface(toplot.X,toplot.Y,OPTIONS.XYZ(3)+0*toplot.X,FIELD(:,:,1)/scale); hold on;
+ s.EdgeColor = 'none';
+ s = surface(toplot_xz.X,OPTIONS.XYZ(2)+0*toplot_xz.X,toplot_xz.Y,toplot_xz.FIELD(:,:,1)./scale);
+ s.EdgeColor = 'none';
+ s = surface(OPTIONS.XYZ(1)+0*toplot_yz.X,toplot_yz.X,toplot_yz.Y,toplot_yz.FIELD(:,:,1)./scale);
+ s.EdgeColor = 'none';
+ zlabel('z');
+ view([1 -1 0.25])
+ end
if BWR
colormap(bluewhitered)
else
@@ -52,30 +71,31 @@ fig = figure('Color','white');%,'Position', toplot.DIMENSIONS.*[0.5 0.5 1.0 1])
shading interp;
end
else
+ fig = figure('Color','white');
contour(toplot.X,toplot.Y,FIELD(:,:,1),128);
end
in = 1;
nbytes = fprintf(2,'frame %d/%d',in,numel(FIELD(1,1,:)));
- for n = 1:numel(FRAMES) % loop over selected frames
+ for n = 1:numel(TIME) % loop over selected frames
scale = max(max(abs(FIELD(:,:,n)))); % Scaling to normalize
if ~strcmp(OPTIONS.PLAN,'sx')
- if NORMALIZED
+ if ~strcmp(OPTIONS.PLAN,'3D')
pclr = pcolor(X,Y,FIELD(:,:,n)/scale); % frame plot\
- caxis([-1,1]);
+ set(pclr, 'edgecolor','none'); %pbaspect(toplot.ASPECT);
else
- pclr = pcolor(X,Y,FIELD(:,:,n)); % frame plot\
- if CONST_CMAP
- caxis([-1,1]*max(abs([hmin hmax]))); % adaptive color map
- else
- caxis([-1,1]*scale); % adaptive color map
- end
- title([FIELDNAME,', $t \approx$', sprintf('%.3d',ceil(T(n)))...
- ,', scale = ',sprintf('%.1e',scale)]);
+ s = surface(toplot.X,toplot.Y,OPTIONS.XYZ(3)+0*toplot.X,FIELD(:,:,n)/scale); hold on;
+ s.EdgeColor = 'none';
+ s = surface(toplot_xz.X,OPTIONS.XYZ(2)+0*toplot_xz.X,toplot_xz.Y,toplot_xz.FIELD(:,:,n)./scale);
+ s.EdgeColor = 'none';
+ s = surface(OPTIONS.XYZ(1)+0*toplot_yz.X,toplot_yz.X,toplot_yz.Y,toplot_yz.FIELD(:,:,n)./scale);
+ s.EdgeColor = 'none';
+ zlabel('z');
+ view([1 -1 0.25])
end
+ clim([-1,1]);
if toplot.INTERP
shading interp;
end
- set(pclr, 'edgecolor','none'); %pbaspect(toplot.ASPECT);
if BWR
colormap(bluewhitered)
else
@@ -87,10 +107,14 @@ fig = figure('Color','white');%,'Position', toplot.DIMENSIONS.*[0.5 0.5 1.0 1])
else % show velocity distr.
contour(toplot.X,toplot.Y,FIELD(:,:,n)/scale,128);
end
- title([FIELDNAME,', $t \approx$', sprintf('%.3d',ceil(T(FRAMES(n))))...
- ,', scaling = ',sprintf('%.1e',scale)]);
-
- xlabel(XNAME); ylabel(YNAME); %colorbar;
+ if ~OPTIONS.RMAXIS
+ title([FIELDNAME,', $t \approx$', sprintf('%.3d',ceil(TIME(n)))...
+ ,', scaling = ',sprintf('%.1e',scale)]);
+ xlabel(XNAME); ylabel(YNAME); %colorbar;
+ else
+ axis off
+ axis tight
+ end
drawnow
% Capture the plot as an image
frame = getframe(fig);
diff --git a/matlab/plot/photomaton.m b/matlab/plot/photomaton.m
index 67b02747b9ca4d0f12ce50d12ff2a476018ecc3e..d563030d9b1ae66ad1ab1cb54ac69dec98bd3b4d 100644
--- a/matlab/plot/photomaton.m
+++ b/matlab/plot/photomaton.m
@@ -4,11 +4,26 @@ function [ FIGURE ] = photomaton( DATA,OPTIONS )
switch OPTIONS.PLAN
case 'RZ'
toplot = poloidal_plot(DATA,OPTIONS);
+ case '3D'
+ OPTIONS.PLAN = 'xy';
+ [~,OPTIONS.COMP] = min(abs(OPTIONS.XYZ(3) - DATA.grids.z));
+ toplot = process_field(DATA,OPTIONS);
+ OPTIONS.PLAN = 'xz';
+ [~,OPTIONS.COMP] = min(abs(OPTIONS.XYZ(2) - DATA.grids.y));
+ toplot_xz = process_field(DATA,OPTIONS);
+ OPTIONS.PLAN = 'yz';
+ [~,OPTIONS.COMP] = min(abs(OPTIONS.XYZ(1) - DATA.grids.x));
+ toplot_yz = process_field(DATA,OPTIONS);
+ OPTIONS.PLAN = '3D';
otherwise
toplot = process_field(DATA,OPTIONS);
end
FNAME = toplot.FILENAME;
FRAMES = toplot.FRAMES;
+if OPTIONS.TAVG
+ toplot.FIELD = mean(toplot.FIELD,3);
+ FRAMES = FRAMES(1);
+end
Nframes= numel(FRAMES);
Nrows = ceil(Nframes/4);
Ncols = ceil(Nframes/Nrows);
@@ -29,17 +44,31 @@ FIGURE.fig = figure; %set(gcf, 'Position', toplot.DIMENSIONS.*[1 1 Ncols Nrows]
end
if ~strcmp(OPTIONS.PLAN,'sx')
tshot = DATA.Ts3D(FRAMES(i_));
- pclr = pcolor(toplot.X,toplot.Y,toplot.FIELD(:,:,i_)./scale); set(pclr, 'edgecolor','none');
- if OPTIONS.AXISEQUAL
- pbaspect(toplot.ASPECT)
- end
- if ~strcmp(OPTIONS.PLAN,'kxky')
- clim([-1,1]*frame_max/scale);
- colormap(bluewhitered);
- if OPTIONS.INTERP
- shading interp;
- end
- end
+ if ~strcmp(OPTIONS.PLAN,'3D')
+ pclr = pcolor(toplot.X,toplot.Y,toplot.FIELD(:,:,i_)./scale); set(pclr, 'edgecolor','none');
+ else
+ % xy plane
+ s = surface(toplot.X,toplot.Y,OPTIONS.XYZ(3)+0*toplot.Y,toplot.FIELD(:,:,i_)./scale); hold on;
+ s.EdgeColor = 'none';
+ % s.FaceAlpha = 0.5;
+ % xz plane
+ s = surface(toplot_xz.X,OPTIONS.XYZ(2)+0*toplot_xz.X,toplot_xz.Y,toplot_xz.FIELD(:,:,i_)./scale);
+ s.EdgeColor = 'none';
+ % s.FaceAlpha = 0.7;
+ % yz plane
+ s = surface(OPTIONS.XYZ(1)+0*toplot_yz.X,toplot_yz.X,toplot_yz.Y,toplot_yz.FIELD(:,:,i_)./scale);
+ s.EdgeColor = 'none';
+ % s.FaceAlpha = 0.7;
+ xlabel('x');
+ ylabel('y');
+ zlabel('z');
+ h = gca;
+ plot3(h.XLim,OPTIONS.XYZ(2)*[1 1],OPTIONS.XYZ(3)*[1 1],'--k','LineWidth',1.)
+ plot3(OPTIONS.XYZ(1)*[1 1],h.YLim,OPTIONS.XYZ(3)*[1 1],'--k','LineWidth',1.)
+ plot3(OPTIONS.XYZ(1)*[1 1],OPTIONS.XYZ(2)*[1 1],h.ZLim,'--k','LineWidth',1.)
+ % zline(OPTIONS.XYZ(3),'-k','LineWidth',1.5)
+ view([1 -1 0.25])
+ end
else
contour(toplot.X,toplot.Y,toplot.FIELD(:,:,i_)./scale,128);
% pclr = pcolor(toplot.X,toplot.Y,toplot.FIELD(:,:,FRAMES(i_))./scale); set(pclr, 'edgecolor','none'); shading interp
@@ -47,12 +76,23 @@ FIGURE.fig = figure; %set(gcf, 'Position', toplot.DIMENSIONS.*[1 1 Ncols Nrows]
end
xlabel(toplot.XNAME); ylabel(toplot.YNAME);
% if i_ > 1; set(gca,'ytick',[]); end;
- title([sprintf('$t c_s/R=%.0f$',tshot),', max = ',sprintf('%.1e',frame_max)]);
+ title([sprintf('$t c_s/R=%5.2f$',tshot),', max = ',sprintf('%.1e',frame_max)]);
if OPTIONS.CLIMAUTO
clim('auto')
end
end
+ if OPTIONS.AXISEQUAL
+ pbaspect(toplot.ASPECT)
+ end
+ if ~strcmp(OPTIONS.PLAN,'kxky')
+ clim([-1,1]*frame_max/scale);
+ colormap(bluewhitered);
+ if OPTIONS.INTERP
+ shading interp;
+ end
+ end
legend(['$',toplot.FIELDNAME,'$']);
+ legend('Location','northeast');
FIGURE.FIGNAME = [FNAME,'_snaps',TNAME];
end
diff --git a/matlab/plot/plot_ballooning.m b/matlab/plot/plot_ballooning.m
index f43866e82dd9cc6cf5cb02dad988bbd859b9f083..aa6565c71b034dbd4be27b87d4be6e42c20b534d 100644
--- a/matlab/plot/plot_ballooning.m
+++ b/matlab/plot/plot_ballooning.m
@@ -6,12 +6,12 @@ function [FIG, b_angle, phib, psib, ky_] = plot_ballooning(DATA,OPTIONS)
[~,ikyarray] = min(abs(DATA.grids.ky - OPTIONS.kymodes));
ikyarray = unique(ikyarray);
dz = DATA.grids.z(2) - DATA.grids.z(1);
- phi_real=real(DATA.PHI(:,:,:,it1));
- phi_imag=imag(DATA.PHI(:,:,:,it1));
+ phi_real=mean(real(DATA.PHI(:,:,:,it0:it1)),4);
+ phi_imag=mean(imag(DATA.PHI(:,:,:,it0:it1)),4);
ncol = 1;
if DATA.inputs.BETA > 0
- psi_real=real(DATA.PSI(:,:,:,it1));
- psi_imag=imag(DATA.PSI(:,:,:,it1));
+ psi_real=mean(real(DATA.PSI(:,:,:,it0:it1)),4);
+ psi_imag=mean(imag(DATA.PSI(:,:,:,it0:it1)),4);
ncol = 2;
end
if OPTIONS.PLOT_KP
@@ -50,12 +50,12 @@ function [FIG, b_angle, phib, psib, ky_] = plot_ballooning(DATA,OPTIONS)
title(['$k_y=',sprintf('%2.2f',DATA.grids.ky(iky)),...
',t_{avg}\in [',sprintf('%1.1f',DATA.Ts3D(it0)),',',sprintf('%1.1f',DATA.Ts3D(it1)),']$']);
% z domain start end point
- for i_ = 2*[1:DATA.grids.Nkx-1]-(DATA.grids.Nkx+1)
- xline(DATA.grids.Npol*(i_),'HandleVisibility','off'); hold on;
- end
- for i_ = 2*[2:DATA.grids.Nkx]-(DATA.grids.Nkx+1)
- xline(DATA.grids.Npol*(i_)-dz/pi,'HandleVisibility','off'); hold on;
- end
+ % for i_ = 2*[1:DATA.grids.Nkx-1]-(DATA.grids.Nkx+1)
+ % xline(DATA.grids.Npol*(i_),'HandleVisibility','off'); hold on;
+ % end
+ % for i_ = 2*[2:DATA.grids.Nkx]-(DATA.grids.Nkx+1)
+ % xline(DATA.grids.Npol*(i_)-dz/pi,'HandleVisibility','off'); hold on;
+ % end
if DATA.inputs.BETA > 0
[psib_real,b_angle] = ballooning_representation(psi_real,DATA.inputs.SHEAR,DATA.grids.Npol,DATA.grids.kx,iky,DATA.grids.ky,DATA.grids.z);
[psib_imag,~] = ballooning_representation(psi_imag,DATA.inputs.SHEAR,DATA.grids.Npol,DATA.grids.kx,iky,DATA.grids.ky,DATA.grids.z);
@@ -71,12 +71,12 @@ function [FIG, b_angle, phib, psib, ky_] = plot_ballooning(DATA,OPTIONS)
legend('real','imag','norm')
% z domain start end point
- for i_ = 2*[1:DATA.grids.Nkx-1]-(DATA.grids.Nkx+1)
- xline(DATA.grids.Npol*(i_),'HandleVisibility','off'); hold on;
- end
- for i_ = 2*[2:DATA.grids.Nkx]-(DATA.grids.Nkx+1)
- xline(DATA.grids.Npol*(i_)-dz/pi,'HandleVisibility','off'); hold on;
- end
+ % for i_ = 2*[1:DATA.grids.Nkx-1]-(DATA.grids.Nkx+1)
+ % xline(DATA.grids.Npol*(i_),'HandleVisibility','off'); hold on;
+ % end
+ % for i_ = 2*[2:DATA.grids.Nkx]-(DATA.grids.Nkx+1)
+ % xline(DATA.grids.Npol*(i_)-dz/pi,'HandleVisibility','off'); hold on;
+ % end
xlabel('$\chi / \pi$')
ylabel('$\psi_B (\chi)$');
title(['$k_y=',sprintf('%2.2f',DATA.grids.ky(iky)),...
@@ -89,12 +89,12 @@ function [FIG, b_angle, phib, psib, ky_] = plot_ballooning(DATA,OPTIONS)
subplot(numel(ikyarray),ncol,ncol*(iplot-1)+3)
plot(b_angle/pi, kperpb,'-k'); hold on;
% z domain start end point
- for i_ = 2*[1:DATA.grids.Nkx-1]-(DATA.grids.Nkx+1)
- xline(DATA.grids.Npol*(i_),'HandleVisibility','off'); hold on;
- end
- for i_ = 2*[2:DATA.grids.Nkx]-(DATA.grids.Nkx+1)
- xline(DATA.grids.Npol*(i_)-dz/pi,'HandleVisibility','off'); hold on;
- end
+ % for i_ = 2*[1:DATA.grids.Nkx-1]-(DATA.grids.Nkx+1)
+ % xline(DATA.grids.Npol*(i_),'HandleVisibility','off'); hold on;
+ % end
+ % for i_ = 2*[2:DATA.grids.Nkx]-(DATA.grids.Nkx+1)
+ % xline(DATA.grids.Npol*(i_)-dz/pi,'HandleVisibility','off'); hold on;
+ % end
xlabel('$\chi / \pi$')
ylabel('$k_\perp (\chi)$');
title(['$k_y=',sprintf('%2.2f',DATA.grids.ky(iky)),...
diff --git a/matlab/plot/plot_cosol_mat.m b/matlab/plot/plot_cosol_mat.m
index ff31e4d26519c7a4f4f2870216fdd478d01a2698..3954ced9b260fe2f729e172b68e32cddb4c0a6c4 100644
--- a/matlab/plot/plot_cosol_mat.m
+++ b/matlab/plot/plot_cosol_mat.m
@@ -1,97 +1,103 @@
-% MAT = results.iCa;
-% figure
-% suptitle('FCGK,P=6,J=3');
-% subplot(221)
-% imagesc(log(abs(MAT)));
-% title('log abs')
-% subplot(222)
-% imagesc(imag(MAT)); colormap(bluewhitered)
-% title('imag'); colorbar
-% subplot(223)
-% imagesc(imag(MAT)>0);
-% title('imag$>$0');
-% subplot(224)
-% imagesc(imag(MAT)<0);
-% title('imag$<$0');
-%
-%
- %% SGGK
-P_ = 20; J_ = 10;
-mat_file_name = '/home/ahoffman/HeLaZ/iCa/gk_sugama_P_20_J_10_N_150_kpm_8.0.h5';
-SGGK_self = h5read(mat_file_name,'/00000/Caapj/Ciipj');
-SGGK_ei = h5read(mat_file_name,'/00000/Ceipj/CeipjF')+h5read(mat_file_name,'/00000/Ceipj/CeipjT');
-SGGK_ie = h5read(mat_file_name,'/00000/Ciepj/CiepjF')+h5read(mat_file_name,'/00000/Ciepj/CiepjT');
+%% Coeff trajectory
+% matfilename = 'gk_landau_P10_J5_dk_5e-2_km_2.0_NFLR_12.h5'; JMAX = 5;
+% matfilename = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'; JMAX = 10;
+% matfilename = 'gk_pitchangle_8_P_20_J_10_N_150_kpm_8.0.h5'; JMAX = 10;
+matfilename = 'gk_landau_P16_J9_dk_5e-2_km_2.0_NFLR_8.h5'; JMAX = 10;
+P_ = 10; J_ = P_/2;
+n = 1:((P_+1)*(J_+1));
+for p_ = 0:P_
+ n((0:J_)+p_*(J_+1)+1) = (0:J_)+p_*(JMAX+1);
+end
+mat_file_name = ['/home/ahoffman/gyacomo/iCa/',matfilename];
+kp_a = h5read(mat_file_name,'/coordkperp');
+coeff = kp_a*0;
+gmax = kp_a*0;
+p1 = 0; j1 = 0;
+p2 = 0; j2 = 0;
+for ik = 1:numel(kp_a)
+ matidx = sprintf('%5.5i',ik-1);
+ M_self = h5read(mat_file_name,['/',matidx,'/Caapj/Ciipj']);
+ MAT = M_self(n+1,n+1);
+ ipj1 = n(j1+p1*(J_+1)+1);
+ ipj2 = n(j2+p2*(J_+1)+1);
+ coeff(ik) = MAT(ipj1+1,ipj2+1);
+ gmax(ik) = -max((real(eig(MAT))));
+
+end
+figure
+plot(kp_a,gmax);
+ %% SGGK
+P_ = 10; J_ = 5;
+n = 1:((P_+1)*(J_+1));
+for p_ = 0:P_
+ n((0:J_)+p_*(J_+1)+1) = (0:J_)+p_*(10+1);
+end
+kp = 5.0;
+kp_a = h5read(mat_file_name,'/coordkperp');
+[~,matidx] = min(abs(kp_a-kp));
+matidx = sprintf('%5.5i',matidx);
+mat_file_name = '/home/ahoffman/gyacomo/iCa/gk_sugama_P_20_J_10_N_150_kpm_8.0.h5';
+M_self = h5read(mat_file_name,['/',matidx,'/Caapj/Ciipj']);
figure
-MAT = 1i*SGGK_self; suptitle('SGGK ii,P=20,J=10, k=0');
-% MAT = 1i*SGGK_ei; suptitle('SGGK ei,P=20,J=10');
-% MAT = 1i*SGGK_ie; suptitle('SGGK ie,P=20,J=10');
-subplot(221)
- imagesc(abs(MAT));
- title('log abs')
-subplot(222)
- imagesc(imag(MAT)); colormap(bluewhitered)
- title('imag'); colorbar
-subplot(223)
- imagesc(imag(MAT)>0);
- title('imag$>$0');
-subplot(224)
- imagesc(imag(MAT)<0);
- title('imag$<$0');
+MAT = M_self; %suptitle('SGGK ii,P=20,J=10, k=0');
+imagesc((MAT(n+1,n+1)));
+title('Sugama')
+xlim('tight')
+ylim('tight')
+axis equal
+% clim(1*[-1 1])
+clim auto
+colormap(bluewhitered)
%% PAGK
-P_ = 20; J_ = 10;
-mat_file_name = '/home/ahoffman/HeLaZ/iCa/gk_pitchangle_8_P_20_J_10_N_150_kpm_8.0.h5';
-PAGK_self = h5read(mat_file_name,'/00000/Caapj/Ceepj');
-% PAGK_ei = h5read(mat_file_name,'/00000/Ceipj/CeipjF')+h5read(mat_file_name,'/00000/Ceipj/CeipjT');
-% PAGK_ie = h5read(mat_file_name,'/00000/Ciepj/CiepjF')+h5read(mat_file_name,'/00000/Ciepj/CiepjT');
-
+P_ = 10; J_ = 5;
+n = 1:((P_+1)*(J_+1));
+for p_ = 0:P_
+ n((0:J_)+p_*(J_+1)+1) = (0:J_)+p_*(10+1);
+end
+kp = 1.0;
+kp_a = h5read(mat_file_name,'/coordkperp');
+[~,matidx] = min(abs(kp_a-kp));
+matidx = sprintf('%5.5i',matidx);
+mat_file_name = '/home/ahoffman/gyacomo/iCa/gk_pitchangle_8_P_20_J_10_N_150_kpm_8.0.h5';
+PAGK_self = h5read(mat_file_name,['/',matidx,'/Caapj/Ciipj']);
figure
-MAT = 1i*PAGK_self; suptitle('PAGK ii,P=20,J=10, k=0');
-
-subplot(221)
- imagesc(abs(MAT));
- title('log abs')
-subplot(222)
- imagesc(imag(MAT)); colormap(bluewhitered)
- title('imag'); colorbar
-subplot(223)
- imagesc(imag(MAT)>0);
- title('imag$>$0');
-subplot(224)
- imagesc(imag(MAT)<0);
- title('imag$<$0');
+PA_MAT = PAGK_self;
+ imagesc((PA_MAT(n+1,n+1)));
+ title('Lorentz')
+ xlim('tight')
+ ylim('tight')
+ axis equal
+ % clim(1*[-1 1])
+ clim auto
+ colormap(bluewhitered)
%% FCGK
-P_ = 4; J_ = 2;
-mat_file_name = '/home/ahoffman/gyacomo/iCa/gk_coulomb_NFLR_12_P_4_J_2_N_50_kpm_4.0.h5';
-% mat_file_name = '/home/ahoffman/gyacomo/iCa/LDGK_P6_J3_dk_5e-2_km_2.5_NFLR_20.h5';
-% mat_file_name = '/home/ahoffman/gyacomo/iCa/LDGK_P10_J5_dk_5e-2_km_5_NFLR_12.h5';
-
-kp = 0.0;
+P_ = 10; J_ = 5;
+n = 1:((P_+1)*(J_+1));
+for p_ = 0:P_
+ n((0:J_)+p_*(J_+1)+1) = (0:J_)+p_*(5+1);
+end
+mat_file_name = '/home/ahoffman/gyacomo/iCa/gk_landau_P10_J5_dk_5e-2_km_2.0_NFLR_12.h5';
+kp = 1.0;
kp_a = h5read(mat_file_name,'/coordkperp');
[~,matidx] = min(abs(kp_a-kp));
matidx = sprintf('%5.5i',matidx);
FCGK_self = h5read(mat_file_name,['/',matidx,'/Caapj/Ciipj']);
-FCGK_ei = h5read(mat_file_name,['/',matidx,'/Ceipj/CeipjF'])+h5read(mat_file_name,'/00000/Ceipj/CeipjT');
-FCGK_ie = h5read(mat_file_name,['/',matidx,'/Ciepj/CiepjF'])+h5read(mat_file_name,'/00000/Ciepj/CiepjT');
figure
-MAT = 1i*FCGK_self; suptitle(['FCGK ii,P=6,J=3, k=',num2str(kp),' (',matidx,')']);
+FC_MAT = FCGK_self;
% MAT = 1i*FCGK_ei; suptitle('FCGK ei,P=20,J=10');
% MAT = 1i*FCGK_ie; suptitle('FCGK ie,P=20,J=10');
-subplot(221)
- imagesc(abs(MAT));
- title('log abs')
-subplot(222)
- imagesc(imag(MAT)); colormap(bluewhitered)
- title('imag'); colorbar
-subplot(223)
- imagesc(imag(MAT)>0);
- title('imag$>$0');
-subplot(224)
- imagesc(imag(MAT)<0);
- title('imag$<$0');
+ imagesc((FC_MAT(n+1,n+1)));
+ title('Landau')
+ xlim('tight')
+ ylim('tight')
+ axis equal
+ % clim(1*[-1 1])
+ clim auto
+ colormap(bluewhitered)
%% Eigenvalue spectrum analysis
if 0
@@ -129,16 +135,19 @@ for j_ = 1:numel(mfns)
% kp_a = kp_a(kp_a<=3);
gmax = zeros(size(kp_a));
wmax = zeros(size(kp_a));
+ c44 = zeros(size(kp_a));
for idx_ = 0:numel(kp_a)-1
matidx = sprintf('%5.5i',idx_);
- MAT = h5read(mat_file_name,['/',matidx,'/Caapj/Ciipj']);
- gmax(idx_+1) = max((real(eig(MAT))));
- wmax(idx_+1) = max((imag(eig(MAT))));
+ FC_MAT = h5read(mat_file_name,['/',matidx,'/Caapj/Ciipj']);
+ gmax(idx_+1) = max((real(eig(FC_MAT))));
+ wmax(idx_+1) = max((imag(eig(FC_MAT))));
+ c44 (idx_+1) = FC_MAT(4,4);
end
subplot(121)
plot(kp_a,gmax,'DisplayName',CONAME_A{j_}); hold on;
subplot(122)
- plot(kp_a,wmax,'DisplayName',CONAME_A{j_}); hold on;
+ % plot(kp_a,wmax,'DisplayName',CONAME_A{j_}); hold on;
+ plot(kp_a,c44,'DisplayName',CONAME_A{j_}); hold on;
end
subplot(121)
legend('show'); grid on;
@@ -195,9 +204,9 @@ for j_ = 1:numel(mfns)
kp_a = h5read(mat_file_name,'/coordkperp');
[~,idx_] = min(abs(kp_a-kperp));
matidx = sprintf('%5.5i',idx_);
- MAT = h5read(mat_file_name,['/',matidx,'/Caapj/Ciipj']);
- grow{j_} = real(eig(MAT))*TAU_A(j_);
- puls{j_} = imag(eig(MAT))*TAU_A(j_);
+ FC_MAT = h5read(mat_file_name,['/',matidx,'/Caapj/Ciipj']);
+ grow{j_} = real(eig(FC_MAT))*TAU_A(j_);
+ puls{j_} = imag(eig(FC_MAT))*TAU_A(j_);
end
figure
diff --git a/matlab/plot/plot_isosurf_wip.m b/matlab/plot/plot_isosurf_wip.m
new file mode 100644
index 0000000000000000000000000000000000000000..886c29fa643311a250986760a1197105ab3b7de7
--- /dev/null
+++ b/matlab/plot/plot_isosurf_wip.m
@@ -0,0 +1,20 @@
+options.NAME = ['N_i^{00}'];
+options.PLAN = 'xyz';
+options.TIME = [30];
+TOPLOT = process_field( data, options );
+
+[X,Y,Z] = meshgrid(data.grids.x,data.grids.y,data.grids.z);
+X = smooth3(X,'gaussian',5);
+Y = smooth3(Y,'gaussian',5);
+Z = smooth3(Z,'gaussian',5);
+TOPLOT.FIELD = smooth3(TOPLOT.FIELD,'gaussian',5);
+s = isosurface(X,Y,Z,TOPLOT.FIELD,0);
+s = reducepatch(s,0.1);
+%% figure
+
+figure
+
+p=patch(s);
+set(p,'EdgeColor','none');
+set(p,'FaceColor','r');
+set(p,'FaceAlpha',0.4);
diff --git a/matlab/plot/plot_kernels.m b/matlab/plot/plot_kernels.m
index a02b82cae6367eb22d4012c19859286eec4407cb..2e7f700e9878c13d7766329bfc8f7bf4f915d86b 100644
--- a/matlab/plot/plot_kernels.m
+++ b/matlab/plot/plot_kernels.m
@@ -2,15 +2,15 @@ if 0
%% Kernels
kmax=5;
nmax=6;
-kx = linspace(0,kmax,100);
+kp = linspace(0,kmax,100);
figure
for n_ = 0:nmax
- plot(kx,kernel(n_,kx),'DisplayName',['$\mathcal{K}_{',num2str(n_),'}$']);hold on;
+ plot(kp,kernel(n_,kp),'DisplayName',['$\mathcal{K}_{',num2str(n_),'}$']);hold on;
end
ylim_ = ylim;
-plot(kx(end)*[2/3 2/3],ylim_,'--k','DisplayName','AA');
+plot(kp(end)*[2/3 2/3],ylim_,'--k','DisplayName','AA');
% J0 = besselj(0,kx);
% plot(kx,J0,'-r','DisplayName','$J_0$');
legend('show'); xlabel('k'); title('Kernel functions $\mathcal{K}_n$');
@@ -19,32 +19,32 @@ end
if 0
%% Bessels and approx
-vperp = linspace(0,1.5,4);
+wperp = linspace(0,1.5,4);
nmax1=5;
nmax2=10;
kmax=7;
figure
-for i = 1:4
-subplot(2,2,i)
- v_ = vperp(i);
- kx = linspace(0,kmax,100);
+for id2 = 1:4
+subplot(2,2,id2)
+ v_ = wperp(id2);
+ kp = linspace(0,kmax,100);
- J0 = besselj(0,kx*v_);
- A1 = 1 - kx.^2*v_^2/4;
- K1 = zeros(size(kx));
- K2 = zeros(size(kx));
+ J0 = besselj(0,kp*v_);
+ A1 = 1 - kp.^2*v_^2/4;
+ K1 = zeros(size(kp));
+ K2 = zeros(size(kp));
for n_ = 0:nmax1
- K1 = K1 + kernel(n_,kx).*polyval(LaguerrePoly(n_),v_^2);
+ K1 = K1 + kernel(n_,kp).*polyval(LaguerrePoly(n_),v_^2);
end
for n_ = 0:nmax2
- K2 = K2 + kernel(n_,kx).*polyval(LaguerrePoly(n_),v_^2);
+ K2 = K2 + kernel(n_,kp).*polyval(LaguerrePoly(n_),v_^2);
end
- plot(kx,J0,'-k','DisplayName','$J_0(kv)$'); hold on;
- plot(kx,A1,'-r','DisplayName','$1 - k^2 v^2/4$');
- plot(kx,K1,'--b','DisplayName',['$\sum_{n=0}^{',num2str(nmax1),'}\mathcal K_n(k) L^n(v)$']);
- plot(kx,K2,'-b','DisplayName',['$\sum_{n=0}^{',num2str(nmax2),'}\mathcal K_n(k) L^n(v)$']);
+ plot(kp,J0,'-k','DisplayName','$J_0(kv)$'); hold on;
+ plot(kp,A1,'-r','DisplayName','$1 - k^2 v^2/4$');
+ plot(kp,K1,'--b','DisplayName',['$\sum_{n=0}^{',num2str(nmax1),'}\mathcal K_n(k) L^n(v)$']);
+ plot(kp,K2,'-b','DisplayName',['$\sum_{n=0}^{',num2str(nmax2),'}\mathcal K_n(k) L^n(v)$']);
ylim_ = [-0.5, 1.0];
- plot(kx(end)*[2/3 2/3],ylim_,'--k','DisplayName','AA');
+ plot(kp(end)*[2/3 2/3],ylim_,'--k','DisplayName','AA');
ylim(ylim_); xlabel('$k$')
legend('show'); grid on; title(['$v = ',num2str(v_),'$'])
end
@@ -53,165 +53,223 @@ end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if 0
%% from Sum_n Kn x Ln x Lj to Sum_n Kn Sum_s dnjs x Ls
-vperp = [2];
-kx = linspace(0,10,200);
-Jmax = 15;
-j = 10;
-fig = figure; set(gcf, 'Position', [100, 100, numel(vperp)*300, 250])
-% suptitle(['$J_{max}=',num2str(Jmax),', j=',num2str(j),'$'])
+wperp = [0 0.2 0.4];
+kp = linspace(0,3,50);
+Jmax = 8;
+js = 4;
+fig = figure; set(gcf, 'Position', [100, 100, numel(wperp)*300, 250])
+% suptitle(['$J_{ma}=',num2str(Jmax),', j=',num2str(j),'$'])
Kn = @(x__,y__) kernel(x__,y__);
-for i = 1:numel(vperp)
-subplot(1,numel(vperp),i)
- v_ = vperp(i);
+% dnjs_ = @(n,j,s) dnjs(n,j,s);
+dnjs_ = @(n,j,s) dnjs_GYAC(n+1,j+1,s+1);
+for id2 = 1:numel(wperp)
+subplot(1,numel(wperp),id2)
+ v_ = wperp(id2);
% J0 x Lj
- J0Lj = besselj(0,kx*v_)*polyval(LaguerrePoly(j),v_^2);
+ J0Lj_ = besselj(0,kp*v_)*polyval(LaguerrePoly(js),v_^2);
% Taylor exp of J0
- A1 = (1 - kx.^2*v_^2/4)*polyval(LaguerrePoly(j),v_^2);
+ A1 = (1 - kp.^2*v_^2/4)*polyval(LaguerrePoly(js),v_^2);
% Sum_n^Nmax Kn x Ln x Lj
- KLL = zeros(size(kx));
+ KLL = zeros(size(kp));
for n_ = 0:Jmax
- KLL = KLL + Kn(n_,kx).*polyval(LaguerrePoly(n_),v_^2);
+ KLL = KLL + Kn(n_,kp).*polyval(LaguerrePoly(n_),v_^2);
end
- KLL = KLL.*polyval(LaguerrePoly(j),v_^2);
+ KLL = KLL.*polyval(LaguerrePoly(js),v_^2);
% Sum_n^Nmax Kn Sum_s^Smax dnjs x Ls
- KdL1 = zeros(size(kx));
- for n_ = 0:Jmax-j
+ KdL1_ = zeros(size(kp));
+ for n_ = 0:Jmax-js
tmp_ = 0;
- for s_ = 0:n_+j
- tmp_ = tmp_ + dnjs(n_,j,s_)*polyval(LaguerrePoly(s_),v_^2);
+ for s_ = 0:n_+js
+ tmp_ = tmp_ + dnjs_(n_,js,s_)*polyval(LaguerrePoly(s_),v_^2);
end
- KdL1 = KdL1 + Kn(n_,kx).*tmp_;
+ KdL1_ = KdL1_ + Kn(n_,kp).*tmp_;
end
% Sum_n^Nmax Kn Sum_s^Smax dnjs x Ls
- KdL2 = zeros(size(kx));
+ KdL2_ = zeros(size(kp));
for n_ = 0:Jmax
tmp_ = 0;
- for s_ = 0:min(Jmax,n_+j)
- tmp_ = tmp_ + dnjs(n_,j,s_)*polyval(LaguerrePoly(s_),v_^2);
+ for s_ = 0:min(Jmax,n_+js)
+ tmp_ = tmp_ + dnjs_(n_,js,s_)*polyval(LaguerrePoly(s_),v_^2);
end
- KdL2 = KdL2 + Kn(n_,kx).*tmp_;
+ KdL2_ = KdL2_ + Kn(n_,kp).*tmp_;
end
% plots
- plot(kx,J0Lj,'-k','DisplayName','$J_0 L_j$'); hold on;
- plot(kx,KLL,'-','DisplayName',['$\sum_{n=0}^{J}\mathcal K_n L^n L_j$']);
- plot(kx,KdL1,'-.','DisplayName',['$\sum_{n=0}^{J-j}\mathcal K_n \sum_{s=0}^{n+j} d_{njs} L^s$']);
+ plot(kp,J0Lj_,'-k','DisplayName','$J_0 L_j$');
ylim_ = ylim;
- plot(kx,A1,'-','DisplayName','$(1 - k^2 v^2/4) L_j$'); hold on;
- plot(kx,KdL2,'--','DisplayName',['$\sum_{n=0}^{J}\mathcal K_n \sum_{s=0}^{\min(J,n+j)} d_{njs} L^s$']);
+ plot(kp,KLL,'-','DisplayName',['$\sum_{n=0}^{J}\mathcal K_n L_n L_j$']); hold on;
+ plot(kp,KdL2_,':o','DisplayName',['$\sum_{n=0}^{J}\mathcal K_n \sum_{s=0}^{\min(J,n+j)} d_{njs} L_s$']);
+ plot(kp,J0Lj_,'-k','DisplayName','$J_0 L_j$'); hold on;
+ ylim_ = ylim;
+ plot(kp,A1,':s','DisplayName','$(1 - l_\perp) L_j$'); hold on;
+ plot(kp,KdL1_,':x','MarkerSize',10,...
+ 'DisplayName',['$\sum_{n=0}^{J-j}\mathcal K_n \sum_{s=0}^{n+j} d_{njs} L_s$']);
+ plot(kp,J0Lj_,'-k','DisplayName','$J_0 L_j$'); hold on;
% plot(kx(end)*[2/3 2/3],ylim_,'--k','DisplayName','AA');
ylim(ylim_);
- xlabel('$k_{\perp}$')
- legend('show');
- grid on; title(['$v = ',num2str(v_),'$',' $J_{max}=',num2str(Jmax),', j=',num2str(j),'$'])
+ xlabel('$k_{\perp}\rho_s$')
+ % legend('show');
+ grid on; title(['$w_\perp = ',num2str(v_),'$',' $J_{max}=',num2str(Jmax),', j=',num2str(js),'$'])
end
-FIGNAME = ['/home/ahoffman/Dropbox/Applications/Overleaf/Hermite-Laguerre Z-pinch (HeLaZ Doc.)/figures/J0Lj_approx_J','_',num2str(Jmax),'_j_',num2str(j),'.eps'];
+FIGNAME = ['/home/ahoffman/Dropbox/Applications/Overleaf/Hermite-Laguerre Z-pinch (HeLaZ Doc.)/figures/J0Lj_approx_J','_',num2str(Jmax),'_j_',num2str(js),'.eps'];
% saveas(fig,FIGNAME,'epsc');
end
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-if 1
-%% Convergence analysis
-kx = linspace(0,10,200);
-v_A = linspace(0,1,10);
-J_A = 1:15;
-[YY,XX] = meshgrid(v_A,J_A);
-klimLL = zeros(size(XX));
-klimdL1= zeros(size(XX));
-Kn = @(x__,y__) kernel(x__,y__);
-fig = figure; set(gcf, 'Position', [100, 100, 500, 400]);
-for j = 5
-for ij_ = 1:numel(J_A)
- iv_ = 1;
- for v_ = v_A
- eps = abs(0.01*polyval(LaguerrePoly(j),v_^2));
- Jmax = J_A(ij_);
- % J0 x Lj
- J0Lj = besselj(0,kx*v_)*polyval(LaguerrePoly(j),v_^2);
- % Taylor exp of J0
- A1 = (1 - kx.^2*v_^2/4)*polyval(LaguerrePoly(j),v_^2);
- % Sum_n^Nmax Kn x Ln x Lj
- KLL = zeros(size(kx));
- for n_ = 0:Jmax
- KLL = KLL + Kn(n_,kx).*polyval(LaguerrePoly(n_),v_^2);
- end
- KLL = KLL.*polyval(LaguerrePoly(j),v_^2);
- % Sum_n^Nmax Kn Sum_s^Smax dnjs x Ls
- KdL1 = zeros(size(kx));
- for n_ = 0:Jmax-j
- tmp_ = 0;
- for s_ = 0:n_+j
- tmp_ = tmp_ + dnjs(n_,j,s_)*polyval(LaguerrePoly(s_),v_^2);
- end
- KdL1 = KdL1 + Kn(n_,kx).*tmp_;
- end
- % Sum_n^Nmax Kn Sum_s^Smax dnjs x Ls
- KdL2 = zeros(size(kx));
- for n_ = 0:Jmax
- tmp_ = 0;
- for s_ = 0:min(Jmax,n_+j)
- tmp_ = tmp_ + dnjs(n_,j,s_)*polyval(LaguerrePoly(s_),v_^2);
- end
- KdL2 = KdL2 + Kn(n_,kx).*tmp_;
- end
- % errors
- err_ = abs(J0Lj-KLL);
- idx_ = 1;
- while(err_(idx_)< eps && idx_ < numel(err_))
- idx_ = idx_ + 1;
- end
- klimLL(ij_,iv_) = kx(idx_);
- err_ = abs(J0Lj-KdL1);
- idx_ = 1;
- while(err_(idx_)< eps && idx_ < numel(err_))
- idx_ = idx_ + 1;
- end
- klimdL1(ij_,iv_) = kx(idx_);
- iv_ = iv_ + 1;
- end
-end
-% plot
-% plot(JmaxA,klimLL,'o-'); hold on
-% plot(J_A,klimdL1,'o-'); hold on
-end
-surf(XX,YY,klimdL1)
-xlabel('$J_{max}$'); ylabel('$v_{\perp}$');
-title(['$k$ s.t. $\epsilon=1\%$, $j=',num2str(j),'$'])
-ylim([0,1]); grid on;
-end
if 0
%% Test Lj Ln = sum_s dnjs Ls
-j = 10;
-n = 10;
-smax = n+j;
-vperp = linspace(0,5,20);
-LjLn = zeros(size(vperp));
-dnjsLs = zeros(size(vperp));
-dnjsLs_bin = zeros(size(vperp));
-dnjsLs_stir = zeros(size(vperp));
-
-i=1;
-for x_ = vperp
- LjLn(i) = polyval(LaguerrePoly(j),x_)*polyval(LaguerrePoly(n),x_);
- dnjsLs(i) = 0;
- dnjsLs_bin(i) = 0;
- dnjsLs_stir(i) = 0;
+js = 4;
+n = 4;
+GYAC = 1;
+smax = n+js;
+wperp = linspace(0,5,50);
+LjLn = zeros(size(wperp));
+dnjsLs = zeros(size(wperp));
+dnjsLs_bin = zeros(size(wperp));
+dnjsLs_stir = zeros(size(wperp));
+if GYAC
+ dnjsLs_GYAC = zeros(size(wperp));
+ % Specify the filename
+ filename = '/home/ahoffman/gyacomo/results/dbg/output.txt';
+ % Use the load function to read data from the text file
+ data = load(filename);
+ % Extract columns
+ indices = data(:, 1:3);
+ values = data(:, 4);
+ is_ = unique(indices(:,1));
+ N_ = numel(is_);
+ dnjs_GYAC = zeros(N_,N_,N_);
+ for id2 = 1:numel(values)
+ in_ = indices(id2,1);
+ ij_ = indices(id2,2);
+ is_ = indices(id2,3);
+ dnjs_GYAC(in_,ij_,is_) = values(id2);
+ end
+end
+
+id2=1;
+for x_ = wperp
+ LjLn(id2) = polyval(LaguerrePoly(js),x_)*polyval(LaguerrePoly(n),x_);
+ dnjsLs(id2) = 0;
+ dnjsLs_bin(id2) = 0;
+ dnjsLs_stir(id2) = 0;
for s_ = 0:smax
- dnjsLs(i) = dnjsLs(i) + dnjs(n,j,s_)*polyval(LaguerrePoly(s_),x_);
- dnjsLs_bin(i) = dnjsLs_bin(i) + dnjs_fact(n,j,s_)*polyval(LaguerrePoly(s_),x_);
- dnjsLs_stir(i) = dnjsLs_stir(i) + dnjs_stir(n,j,s_)*polyval(LaguerrePoly(s_),x_);
+ dnjsLs(id2) = dnjsLs(id2) + dnjs(n,js,s_)*polyval(LaguerrePoly(s_),x_);
+ dnjsLs_bin(id2) = dnjsLs_bin(id2) + dnjs_fact(n,js,s_)*polyval(LaguerrePoly(s_),x_);
+ dnjsLs_stir(id2) = dnjsLs_stir(id2) + dnjs_stir(n,js,s_)*polyval(LaguerrePoly(s_),x_);
+ if GYAC
+ dnjsLs_GYAC(id2) = dnjsLs_GYAC(id2) + dnjs_GYAC(n+1,js+1,s_+1)*polyval(LaguerrePoly(s_),x_);
+ end
end
- i = i+1;
+ id2 = id2+1;
end
figure
-plot(vperp,LjLn); hold on;
-plot(vperp,dnjsLs,'d')
-plot(vperp,dnjsLs_bin,'o')
-plot(vperp,dnjsLs_stir/dnjsLs_stir(1),'x')
+plot(wperp,LjLn,'DisplayName',['$L_',num2str(js),' L_',num2str(n),'$']); hold on;
+plot(wperp,dnjsLs,'d','DisplayName',...
+ ['$\sum_{s=0}^{',num2str(smax),'} d^{coeff}_{',num2str(n),',',num2str(js),',s}L_s$'])
+plot(wperp,dnjsLs_bin,'o','DisplayName','$\sum_s d^{fact}_{njs}L_s$')
+plot(wperp,dnjsLs_stir/dnjsLs_stir(1),'x','DisplayName','$\sum_s d^{stir}_{njs}L_s$')
+plot(wperp,dnjsLs_GYAC,'x','DisplayName','$GYAC$')
+xlabel('$w_\perp$');
% We see that starting arround j = 18, n = 0, the stirling formula is the only
% approximation that does not diverge from the target function. However it
% performs badly for non 0 n...
end
-
+if 0
+%%
+ wperp = linspace(0,3,128);
+ kp = linspace(0,3,128);
+ Jmax = 8;
+ js = Jmax/2;[0 2:Jmax];
+ err_KLL = 1:numel(js);
+ err_KdL1 = 1:numel(js);
+ err_KdL2 = 1:numel(js);
+ err_T1 = 1:numel(js);
+ J0Lj = zeros(numel(kp),numel(wperp));
+ KdL1 = zeros(numel(kp),numel(wperp));
+ KdL2 = zeros(numel(kp),numel(wperp));
+ T1 = zeros(numel(kp),numel(wperp));
+ Kn = @(x__,y__) kernel(x__,y__);
+ % dnjs_ = @(n,j,s) dnjs(n,j,s);
+ dnjs_ = @(n,j,s) dnjs_GYAC(n+1,j+1,s+1);
+ for id1 = 1:numel(js)
+ for id2 = 1:numel(wperp)
+ j_ = js(id1);
+ v_ = wperp(id2);
+ % J0 x Lj
+ J0Lj_ = besselj(0,kp*v_)*polyval(LaguerrePoly(j_),v_^2);
+ % Taylor exp of J0
+ T1_ = (1 - kp.^2*v_^2/4)*polyval(LaguerrePoly(j_),v_^2);
+ % Sum_n^Nmax Kn x Ln x Lj
+ KLL = zeros(size(kp));
+ for n_ = 0:Jmax
+ KLL = KLL + Kn(n_,kp).*polyval(LaguerrePoly(n_),v_^2);
+ end
+ KLL = KLL.*polyval(LaguerrePoly(j_),v_^2);
+ % Sum_n^Nmax Kn Sum_s^Smax dnjs x Ls
+ KdL1_ = zeros(size(kp));
+ for n_ = 0:Jmax-j_
+ tmp_ = 0;
+ for s_ = 0:n_+j_
+ tmp_ = tmp_ + dnjs_(n_,j_,s_)*polyval(LaguerrePoly(s_),v_^2);
+ end
+ KdL1_ = KdL1_ + Kn(n_,kp).*tmp_;
+ end
+ % Sum_n^Nmax Kn Sum_s^Smax dnjs x Ls
+ KdL2_ = zeros(size(kp));
+ for n_ = 0:Jmax
+ tmp_ = 0;
+ for s_ = 0:min(Jmax,n_+j_)
+ tmp_ = tmp_ + dnjs_(n_,j_,s_)*polyval(LaguerrePoly(s_),v_^2);
+ end
+ KdL2_ = KdL2_ + Kn(n_,kp).*tmp_;
+ end
+ f_ = @(x) max(x);
+ kp2 = kp.^2+0.001; intJ0Lj = f_(abs(J0Lj_));
+ err_KLL_(id2) = f_(abs(KLL -J0Lj_)./kp2)./f_(intJ0Lj./kp2);
+ err_KdL1_(id2) = f_(abs(KdL1_-J0Lj_)./kp2)./f_(intJ0Lj./kp2);
+ err_KdL2_(id2) = f_(abs(KdL2_-J0Lj_)./kp2)./f_(intJ0Lj./kp2);
+ err_T1_(id2) = f_(abs(T1_ -J0Lj_)./kp2)./f_(intJ0Lj./kp2);
+ J0Lj(:,id2) = J0Lj_;
+ KdL1(:,id2) = KdL1_;
+ KdL2(:,id2) = KdL2_;
+ T1 (:,id2) = T1_;
+ end
+ err_KLL(id1) = sum(err_KLL_)./numel(wperp);
+ err_KdL1(id1) = sum(err_KdL1_)./numel(wperp);
+ err_KdL2(id1) = sum(err_KdL2_)./numel(wperp);
+ err_T1(id1) = sum(err_T1_)./numel(wperp);
+ end
+ clr_ = lines(10);
+ figure
+ plot(js,err_KLL,'-',...
+ 'DisplayName','$\sum_{n=0}^{J}\mathcal K_n L_n L_j$'); hold on
+ plot(js,err_KdL1,':x',...
+ 'DisplayName','$\sum_{n=0}^{J-j}\mathcal K_n \sum_{s=0}^{n+j} d_{njs} L_s$',...
+ 'Color',clr_(5,:)); hold on
+ plot(js,err_KdL2,':o',...
+ 'DisplayName','$\sum_{n=0}^{J}\mathcal K_n \sum_{s=0}^{\min(J,n+j)} d_{njs} L_s$',...
+ 'Color',clr_(2,:)); hold on
+ plot(js,err_T1,':s',...
+ 'DisplayName','$(1 - l_\perp) L_j$',...
+ 'Color',clr_(4,:)); hold on
+ set(gca,'YScale','log');
+ xlabel('$j$'); ylabel('$\varepsilon_J$')
+ if 1
+ %%
+ figure
+ nc = 25
+ subplot(131)
+ contourf(kp,wperp,J0Lj',nc); xlabel('$l_{\perp a}$'); ylabel('$w_{\perp a}$')
+ clim_ = clim;
+ subplot(132)
+ contourf(kp,wperp,KdL1', nc); xlabel('$l_{\perp a}$'); ylabel('$w_{\perp a}$')
+ clim(clim_);
+ % subplot(132)
+ subplot(133)
+ contourf(kp,wperp,KdL2', nc); xlabel('$l_{\perp a}$'); ylabel('$w_{\perp a}$')
+ % contourf(kp,wperp,T1 ,20); xlabel('$k_\perp$'); ylabel('$w_\perp$')
+ clim(clim_);
+ end
+end
diff --git a/matlab/plot/plot_metric.m b/matlab/plot/plot_metric.m
index 1267999b25d0121511e955858f9b6b53c6509e4f..9a88d3b5dae77018ff8478197e9bd7e90b43ef9b 100644
--- a/matlab/plot/plot_metric.m
+++ b/matlab/plot/plot_metric.m
@@ -96,9 +96,14 @@ if NPLOT > 0
end
end
%outputs
-arrays = squeeze(geo_arrays(:,:));
+% arrays = squeeze(geo_arrays(:,:));
R = [geo_arrays(:,12);geo_arrays(1,12)];
Z = [geo_arrays(:,13);geo_arrays(1,13)];
+
+for i_ = 1:numel(names)
+ namae = names{i_};
+ arrays.(namae) = geo_arrays(:,i_);
+end
try
if ~options.SHOWFIG
close
diff --git a/matlab/plot/plot_radial_transport_and_spacetime.m b/matlab/plot/plot_radial_transport_and_spacetime.m
index 8fdcbc3d2cb4250cb560cd2de67a429ea9032e70..a33d3612a46247dd21d15ac9e292f418a18fbbe8 100644
--- a/matlab/plot/plot_radial_transport_and_spacetime.m
+++ b/matlab/plot/plot_radial_transport_and_spacetime.m
@@ -56,7 +56,8 @@ mvm = @(x) movmean(x,OPTIONS.NMVA);
grid on; set(gca,'xticklabel',[]);
title({DATA.param_title,...
['$\Gamma^{\infty} = $',num2str(Gx_infty_avg),'$, Q^{\infty} = $',num2str(Qx_infty_avg)]});
-%% radial shear radial profile
+ axis tight
+ %% radial shear radial profile
% computation
Ns3D = numel(DATA.Ts3D);
[KX, KY] = meshgrid(DATA.grids.kx, DATA.grids.ky);
@@ -68,18 +69,33 @@ mvm = @(x) movmean(x,OPTIONS.NMVA);
OPTIONS.NAME = OPTIONS.ST_FIELD;
OPTIONS.PLAN = 'xy';
OPTIONS.COMP = 'avg';
+ OPTIONS.TAVG = 0;
OPTIONS.TIME = DATA.Ts3D;
OPTIONS.POLARPLOT = 0;
- toplot = process_field(DATA,OPTIONS);
- f2plot = toplot.FIELD;
+ try
+ if DATA.fort_00.DIAGNOSTICS.dtsave_2d > 0
+ opt_.PLAY = 0;
+ [MOVIE] = cinecita_2D(DATA.dir,OPTIONS.ST_FIELD,opt_);
+ f2plot = MOVIE.F;
+ TIME = MOVIE.T;
+ else
+ toplot = process_field(DATA,OPTIONS);
+ f2plot = toplot.FIELD;
+ TIME = DATA.Ts3D(toplot.FRAMES);
+ end
+ catch
+ toplot = process_field(DATA,OPTIONS);
+ f2plot = toplot.FIELD;
+ TIME = DATA.Ts3D(toplot.FRAMES);
+ end
dframe = ite3D - its3D;
- clim = max(max(max(abs(plt(f2plot(:,:,:))))));
+ clim_ = max(max(max(abs(plt(f2plot(:,:,:))))));
FIGURE.ax3 = subplot(2,1,2,'parent',FIGURE.fig);
- [TY,TX] = meshgrid(DATA.grids.x,DATA.Ts3D(toplot.FRAMES));
+ [TY,TX] = meshgrid(DATA.grids.x,TIME);
pclr = pcolor(TX,TY,squeeze(plt(f2plot))');
set(pclr, 'edgecolor','none');
legend(['$\langle ',OPTIONS.ST_FIELD,' \rangle_{y,z}$']) %colorbar;
- caxis(clim*[-1 1]);
+ clim(clim_*[-1 1]);
cmap = bluewhitered(256);
colormap(cmap)
xlabel('$t c_s/R$'), ylabel('$x/\rho_s$');
diff --git a/matlab/plot/show_moments_spectrum.m b/matlab/plot/show_moments_spectrum.m
index ab9d3aea55bd247e410291c6560aa38f823805d4..f193f118b32725c1187cee06d4fe97f8b1bf215e 100644
--- a/matlab/plot/show_moments_spectrum.m
+++ b/matlab/plot/show_moments_spectrum.m
@@ -6,16 +6,8 @@ Ja = DATA.grids.Jarray;
Time_ = DATA.Ts3D;
FIGURE.fig = figure; FIGURE.FIGNAME = ['mom_spectrum_',DATA.params_string];
% set(gcf, 'Position', [100 50 1000 400])
-if OPTIONS.ST == 0
- OPTIONS.LOGSCALE = 0;
-end
-if OPTIONS.LOGSCALE
- logname = 'log';
- compress = @(x,ia) log(sum(abs((x(ia,:,:,:,:))),4));
-else
- logname = '';
- compress = @(x,ia) sum(abs((x(ia,:,:,:,:))),4);
-end
+logname = '';
+compress = @(x,ia) sum(abs((x(ia,:,:,:,:))),4);
for ia = 1:DATA.inputs.Na
Napjz = compress(DATA.Napjz,ia);
Napjz = reshape(Napjz,DATA.grids.Np,DATA.grids.Nj,numel(DATA.Ts3D));
@@ -71,8 +63,10 @@ for ia = 1:DATA.inputs.Na
% plots
% scaling
if OPTIONS.TAVG_2D
- nt_half = ceil(numel(Time_)/2);
- Napjz_tavg = mean(Napjz(:,:,nt_half:end),3);
+ t0 = OPTIONS.TWINDOW(1); t1 = OPTIONS.TWINDOW(2);
+ [~,it0] = min(abs(DATA.Ts3D-t0));
+ [~,it1] = min(abs(DATA.Ts3D-t1));
+ Napjz_tavg = mean(Napjz(:,:,it0:it1),3);
x_ = DATA.grids.Parray;
y_ = DATA.grids.Jarray;
if OPTIONS.TAVG_2D_CTR
@@ -84,7 +78,7 @@ for ia = 1:DATA.inputs.Na
xlabel('$p$'); ylabel('$j$');
end
clb = colorbar; colormap(jet);
- clb.Label.String = '$\log\langle E(p,j) \rangle_t$';
+ clb.Label.String = '$\langle E(p,j) \rangle_t$';
clb.TickLabelInterpreter = 'latex';
clb.Label.Interpreter = 'latex';
clb.Label.FontSize= 18;
@@ -95,7 +89,7 @@ for ia = 1:DATA.inputs.Na
plt = @(x,i) reshape(x(i,:),numel(p2j),numel(Time_));
end
Nlabelmax = 15;
- nskip = floor(numel(p2j)/Nlabelmax);
+ nskip = max(1,floor(numel(p2j)/Nlabelmax));
if OPTIONS.ST
imagesc(Time_,p2j,plt(Na_ST,1:numel(p2j)));
set(gca,'YDir','normal')
@@ -105,10 +99,13 @@ for ia = 1:DATA.inputs.Na
yticklabels(ticks_labels(1:nskip:end))
end
if OPTIONS.FILTER
- caxis([0 0.2]);
- title('Relative fluctuation from the average');
+ clim([0 0.2]);
+ title('Relative fluctuation from the average');
end
colorbar
+ if OPTIONS.LOGSCALE
+ set(gca,'ColorScale','log');
+ end
else
colors_ = jet(numel(p2j));
for i = 1:numel(p2j)
@@ -120,6 +117,7 @@ for ia = 1:DATA.inputs.Na
end
end
top_title(DATA.paramshort)
+ title(plotname)
end
diff --git a/matlab/plot/tight_layout_generator.m b/matlab/plot/tight_layout_generator.m
new file mode 100644
index 0000000000000000000000000000000000000000..f85c09ea5da8cb84dd92c719614570d0a22ecdf7
--- /dev/null
+++ b/matlab/plot/tight_layout_generator.m
@@ -0,0 +1,11 @@
+function [] = tight_layout_generator(m,n)
+% Generate a layout with tight subplots
+% m = 3; % number lines
+% n = 3; % number of columns
+figure
+t = tiledlayout(m,n,'TileSpacing','Compact','Padding','Compact');
+for i = 1:(m*n)
+nexttile
+end
+
+end
diff --git a/matlab/process_field.m b/matlab/process_field.m
index 9390b1b2cd33e40186f458a292373df32dad64bd..9ead884c631372d4790cf003240b3e5aebbad2df 100644
--- a/matlab/process_field.m
+++ b/matlab/process_field.m
@@ -8,45 +8,44 @@ for i = 1:numel(OPTIONS.TIME)
[~,FRAMES(i)] =min(abs(OPTIONS.TIME(i)-DATA.Ts3D));
end
FRAMES = unique(FRAMES);
+TIME = DATA.Ts3D(FRAMES);
%% Setup the plot geometry
[KX, KY] = meshgrid(DATA.grids.kx, DATA.grids.ky);
directions = {'y','x','z'};
Nx = DATA.grids.Nx; Ny = DATA.grids.Ny; Nz = DATA.grids.Nz; Nt = numel(FRAMES);
-POLARPLOT = OPTIONS.POLARPLOT;
LTXNAME = OPTIONS.NAME;
+SKIP_COMP = 0; % Turned on only for kin. distr. func. plot;
+Z = 0;
switch OPTIONS.PLAN
case 'xy'
- XNAME = '$x$'; YNAME = '$y$';
+ XNAME = '$x/\rho_s$'; YNAME = '$y/\rho_s$';
[X,Y] = meshgrid(DATA.grids.x,DATA.grids.y);
REALP = 1; COMPDIM = 3; POLARPLOT = 0; SCALE = 1;
case 'xz'
- XNAME = '$x$'; YNAME = '$z$';
+ XNAME = '$x/\rho_s$'; YNAME = '$z/L_\parallel$';
[Y,X] = meshgrid(DATA.grids.z,DATA.grids.x);
- REALP = 1; COMPDIM = 1; SCALE = 0;
+ REALP = 1; COMPDIM = 1; SCALE = 0; POLARPLOT = 0;
case 'yz'
- XNAME = '$y$'; YNAME = '$z$';
+ XNAME = '$y/\rho_s$'; YNAME = '$z/L_\parallel$';
[Y,X] = meshgrid(DATA.grids.z,DATA.grids.y);
- REALP = 1; COMPDIM = 2; SCALE = 0;
+ REALP = 1; COMPDIM = 2; POLARPLOT = 0; SCALE = 0;
case 'kxky'
- XNAME = '$k_x$'; YNAME = '$k_y$';
+ XNAME = '$k_x\rho_s$'; YNAME = '$k_y\rho_s$';
[X,Y] = meshgrid(DATA.grids.kx,DATA.grids.ky);
REALP = 0; COMPDIM = 3; POLARPLOT = 0; SCALE = 1;
case 'kxz'
- XNAME = '$k_x$'; YNAME = '$z$';
+ XNAME = '$k_x\rho_s$'; YNAME = '$z/L_\parallel$';
[Y,X] = meshgrid(DATA.grids.z,DATA.grids.kx);
REALP = 0; COMPDIM = 1; POLARPLOT = 0; SCALE = 0;
case 'kyz'
- XNAME = '$k_y$'; YNAME = '$z$';
+ XNAME = '$k_y\rho_s$'; YNAME = '$z/L_\parallel$';
[Y,X] = meshgrid(DATA.grids.z,DATA.grids.ky);
REALP = 0; COMPDIM = 2; POLARPLOT = 0; SCALE = 0;
- case 'sx'
- XNAME = '$v_\parallel$'; YNAME = '$\mu$';
- [Y,X] = meshgrid(OPTIONS.XPERP,OPTIONS.SPAR);
- REALP = 1; COMPDIM = 3; POLARPLOT = 0; SCALE = 0;
- for i = 1:numel(OPTIONS.TIME)
- [~,FRAMES(i)] =min(abs(OPTIONS.TIME(i)-DATA.Ts5D));
- end
- FRAMES = unique(FRAMES); Nt = numel(FRAMES);
+ case 'xyz'
+ XNAME = '$x/\rho_s$'; YNAME = '$y/\rho_s$';
+ [X,Y] = meshgrid(DATA.grids.x,DATA.grids.y);
+ REALP = 1; COMPDIM = 3; POLARPLOT = 0; SCALE = 1;
+ SKIP_COMP = 1; OPTIONS.COMP = 3;
end
Xmax_ = max(max(abs(X))); Ymax_ = max(max(abs(Y)));
Lmin_ = min([Xmax_,Ymax_]);
@@ -73,29 +72,6 @@ else
FIELD = zeros(sz(1),sz(2),Nt);
end
%% Process the field to plot
-% short term writing --
-% b_e = DATA.sigma_e*sqrt(2*DATA.tau_e)*sqrt(KX.^2+KY.^2);
-% adiab_e = kernel(0,b_e);
-% pol_e = kernel(0,b_e).^2;
-% for n = 1:DATA.Jmaxe
-% adiab_e = adiab_e + kernel(n,b_e).^2;
-% pol_e = pol_e + kernel(n,b_e).^2;
-% end
-% adiab_e = DATA.q_e/DATA.tau_e .* adiab_e;
-% pol_e = DATA.q_e^2/DATA.tau_e * (1 - pol_e);
-%
-% b_i = DATA.sigma_i*sqrt(2*DATA.tau_i)*sqrt(KX.^2+KY.^2);
-% adiab_i = kernel(0,b_i);
-% pol_i = kernel(0,b_i).^2;
-% for n = 1:DATA.Jmaxi
-% adiab_i = adiab_i + kernel(n,b_i).^2;
-% pol_i = pol_i + kernel(n,b_i).^2;
-% end
-% pol_i = DATA.q_i^2/DATA.tau_i * (1 - pol_i);
-% adiab_i = DATA.q_i/DATA.tau_i .* adiab_i;
-% poisson_op = (pol_i + pol_e);
-adiab_e =0; adiab_i =0; poisson_op=1;
-SKIP_COMP = 0; % Turned on only for kin. distr. func. plot
% --
switch OPTIONS.COMP
case 'avg'
@@ -112,18 +88,18 @@ switch OPTIONS.COMP
i = OPTIONS.COMP;
compr = @(x) x(i,:,:);
if REALP
- COMPNAME = sprintf(['y=','%2.1f'],DATA.grids.x(i));
+ COMPNAME = sprintf(['y=','%2.1f'],DATA.grids.y(i));
else
- COMPNAME = sprintf(['k_y=','%2.1f'],DATA.grids.kx(i));
+ COMPNAME = sprintf(['k_y=','%2.1f'],DATA.grids.ky(i));
end
FIELDNAME = [LTXNAME,'(',COMPNAME,')'];
case 2
i = OPTIONS.COMP;
compr = @(x) x(:,i,:);
if REALP
- COMPNAME = sprintf(['x=','%2.1f'],DATA.grids.y(i));
+ COMPNAME = sprintf(['x=','%2.1f'],DATA.grids.x(i));
else
- COMPNAME = sprintf(['k_x=','%2.1f'],DATA.grids.ky(i));
+ COMPNAME = sprintf(['k_x=','%2.1f'],DATA.grids.kx(i));
end
FIELDNAME = [LTXNAME,'(',COMPNAME,')'];
case 3
@@ -188,6 +164,10 @@ switch OPTIONS.NAME
NAME = 'sx';
FLD_ = DATA.PHI(:,:,:,FRAMES);
OPE_ = KY.^2;
+ case 'w_{Ez}' % x-comp of ExB shear
+ NAME = 'wEz';
+ FLD_ = DATA.PHI(:,:,:,FRAMES);
+ OPE_ = (KX.^2+KY.^2).*(abs(KX)<=2).*(abs(KY)<=2);
case '\omega_z' % ES pot vorticity
NAME = 'vorticity';
FLD_ = DATA.PHI(:,:,:,FRAMES);
@@ -206,11 +186,11 @@ switch OPTIONS.NAME
OPE_ = 1;
case 'n_i' % ion density
NAME = 'ni';
- FLD_ = DATA.DENS_I(:,:,:,FRAMES) - adiab_i.* DATA.PHI(:,:,:,FRAMES);
+ FLD_ = DATA.DENS_I(:,:,:,FRAMES);
OPE_ = 1;
case 'n_e' % electron density
NAME = 'ne';
- FLD_ = DATA.DENS_E(:,:,:,FRAMES) - adiab_e.* DATA.PHI(:,:,:,FRAMES);
+ FLD_ = DATA.DENS_E(:,:,:,FRAMES);
OPE_ = 1;
case 'k^2n_e' % electron vorticity
NAME = 'k2ne';
@@ -219,12 +199,24 @@ switch OPTIONS.NAME
case 'n_i-n_e' % polarisation
NAME = 'pol';
OPE_ = 1;
- FLD_ = ((DATA.DENS_I(:,:,:,FRAMES)- adiab_i.* DATA.PHI(:,:,:,FRAMES))...
- -(DATA.DENS_E(:,:,:,FRAMES)- adiab_e.* DATA.PHI(:,:,:,FRAMES)));
+ FLD_ = DATA.DENS_I(:,:,:,FRAMES)...
+ -DATA.DENS_E(:,:,:,FRAMES);
+ case 'u_i' % ion density
+ NAME = 'ui';
+ FLD_ = DATA.UPAR_I(:,:,:,FRAMES);
+ OPE_ = 1;
+ case 'u_e' % electron density
+ NAME = 'ue';
+ FLD_ = DATA.UPAR_E(:,:,:,FRAMES);
+ OPE_ = 1;
case 'T_i' % ion temperature
NAME = 'Ti';
FLD_ = DATA.TEMP_I(:,:,:,FRAMES);
OPE_ = 1;
+ case 'T_e' % ion temperature
+ NAME = 'Te';
+ FLD_ = DATA.TEMP_E(:,:,:,FRAMES);
+ OPE_ = 1;
case 'G_x' % ion particle flux
NAME = 'Gx';
FLD_ = 0.*DATA.PHI(:,:,:,FRAMES);
@@ -238,24 +230,55 @@ switch OPTIONS.NAME
% tmp(:,:,iz) = abs(fftshift((squeeze(fft2(gx_,DATA.grids.Ny,DATA.grids.Nx))),2));
tmp(:,:,iz) = abs((squeeze(fft2(gx_,DATA.grids.Ny,DATA.grids.Nx))));
end
- FLD_(:,:,it)= squeeze(compr(tmp(1:DATA.grids.Nky,1:DATA.grids.Nkx,:)));
- end
- case 'Q_x' % ion heat flux
- NAME = 'Qx';
- % FLD_ = 0.*DATA.PHI(:,:,:,FRAMES);
+ FLD_(:,:,:,it)= squeeze((tmp(1:DATA.grids.Nky,1:DATA.grids.Nkx,:)));
+ end
+ case 'n_i T_i' % ion heat flux
+ NAME = 'niTi';
+ FLD_ = 0.*DATA.PHI(:,:,:,FRAMES);
OPE_ = 1;
for it = 1:numel(FRAMES)
- tmp = zeros(DATA.grids.Ny,DATA.grids.Nx,Nz);
+ qx_c = zeros(DATA.grids.Ny,DATA.grids.Nx,Nz);
for iz = 1:DATA.grids.Nz
- vx_ = real((ifourier_GENE(-1i*KY.*(DATA.PHI (:,:,iz,FRAMES(it))))));
- ni_ = real((ifourier_GENE( DATA.DENS_I(:,:,iz,FRAMES(it)))));
- Ti_ = real((ifourier_GENE( DATA.TEMP_I(:,:,iz,FRAMES(it)))));
- qx_ = vx_.*ni_.*Ti_;
-% tmp(:,:,iz) = abs(fftshift((squeeze(fft2(gx_,DATA.grids.Ny,DATA.grids.Nx))),2));
- tmp(:,:,iz) = abs((squeeze(fft2(qx_,DATA.grids.Ny,DATA.grids.Nx))));
+ ni_ = real((ifourier_GENE( DATA.DENS_I(:,:,iz,FRAMES(it)))));
+ Ti_ = real((ifourier_GENE( DATA.TEMP_I(:,:,iz,FRAMES(it)))));
+ cx_r = ni_.*Ti_;
+ cx_ = fft(cx_r,[],1);
+ cx_c(:,:,iz) = fft(cx_ ,[],2);
end
- FLD_(:,:,:,it)= squeeze(tmp(1:DATA.grids.Nky,1:DATA.grids.Nkx,:));
- end
+ FLD_(:,:,:,it)= squeeze(cx_c(1:DATA.grids.Nky,1:DATA.grids.Nkx,:))./numel(qx_c);
+ end
+ case 'Q_{xi}' % ion heat flux
+ NAME = 'Qxi';
+ FLD_ = 0.*DATA.PHI(:,:,:,FRAMES);
+ OPE_ = 1;
+ for it = 1:numel(FRAMES)
+ qx_c = zeros(DATA.grids.Ny,DATA.grids.Nx,Nz);
+ for iz = 1:DATA.grids.Nz
+ vx_ = real((ifourier_GENE(-1i*KY.*(DATA.PHI (:,:,iz,FRAMES(it))))));
+ ni_ = real((ifourier_GENE( DATA.DENS_I(:,:,iz,FRAMES(it)))));
+ Ti_ = real((ifourier_GENE( DATA.TEMP_I(:,:,iz,FRAMES(it)))));
+ qx_r = vx_.*ni_.*Ti_;
+ qx_ = fft(qx_r,[],1);
+ qx_c(:,:,iz) = fft(qx_ ,[],2);
+ end
+ FLD_(:,:,:,it)= squeeze(qx_c(1:DATA.grids.Nky,1:DATA.grids.Nkx,:))./numel(qx_c);
+ end
+ case 'Q_{xe}' % electron heat flux
+ NAME = 'Qxe';
+ FLD_ = 0.*DATA.PHI(:,:,:,FRAMES);
+ OPE_ = 1;
+ for it = 1:numel(FRAMES)
+ qx_c = zeros(DATA.grids.Ny,DATA.grids.Nx,Nz);
+ for iz = 1:DATA.grids.Nz
+ vx_ = real((ifourier_GENE(-1i*KY.*(DATA.PHI (:,:,iz,FRAMES(it))))));
+ ne_ = real((ifourier_GENE( DATA.DENS_E(:,:,iz,FRAMES(it)))));
+ Te_ = real((ifourier_GENE( DATA.TEMP_E(:,:,iz,FRAMES(it)))));
+ qx_r = vx_.*ne_.*Te_;
+ qx_ = fft(qx_r,[],1);
+ qx_c(:,:,iz) = fft(qx_ ,[],2);
+ end
+ FLD_(:,:,:,it)= squeeze(qx_c(1:DATA.grids.Nky,1:DATA.grids.Nkx,:))./numel(qx_c);
+ end
case 'f_i'
SKIP_COMP = 1;
shift_x = @(x) x; shift_y = @(y) y;
@@ -284,29 +307,34 @@ switch OPTIONS.NAME
end
% Process the field according to the 2D plane and the space (real/cpx)
if ~SKIP_COMP
-if COMPDIM == 3
- for it = 1:numel(FRAMES)
- tmp = squeeze(compr(OPE_.*FLD_(:,:,:,it)));
- FIELD(:,:,it) = squeeze(process(tmp));
- end
-else
- if REALP
- tmp = zeros(Ny,Nx,Nz);
+ if COMPDIM == 3
+ for it = 1:numel(FRAMES)
+ tmp = squeeze(compr(OPE_.*FLD_(:,:,:,it)));
+ FIELD(:,:,it) = squeeze(process(tmp));
+ end
else
- tmp = zeros(DATA.grids.Nky,DATA.grids.Nkx,Nz);
- end
- for it = 1:numel(FRAMES)
- for iz = 1:numel(DATA.grids.z)
- tmp(:,:,iz) = squeeze(process(OPE_.*FLD_(:,:,iz,it)));
+ if REALP
+ tmp = zeros(Ny,Nx,Nz);
+ else
+ tmp = zeros(DATA.grids.Nky,DATA.grids.Nkx,Nz);
end
- FIELD(:,:,it) = squeeze(compr(tmp));
- end
-end
+ for it = 1:numel(FRAMES)
+ for iz = 1:numel(DATA.grids.z)
+ tmp(:,:,iz) = squeeze(process(OPE_.*FLD_(:,:,iz,it)));
+ end
+ FIELD(:,:,it) = squeeze(compr(tmp));
+ end
+ end
+else
+ clear FIELD;
+ FIELD = squeeze(process(FLD_));
end
TOPLOT.FIELD = FIELD;
+TOPLOT.TIME = TIME;
TOPLOT.FRAMES = FRAMES;
TOPLOT.X = shift_x(X);
TOPLOT.Y = shift_y(Y);
+TOPLOT.Z = Z;
TOPLOT.FIELDNAME = FIELDNAME;
TOPLOT.XNAME = XNAME;
TOPLOT.YNAME = YNAME;
@@ -315,5 +343,6 @@ TOPLOT.DIMENSIONS= DIMENSIONS;
TOPLOT.ASPECT = ASPECT;
TOPLOT.FRAMES = FRAMES;
TOPLOT.INTERP = INTERP;
+
end
diff --git a/matlab/read_flux_out_XX.m b/matlab/read_flux_out_XX.m
index 2c7737ea4c28c895ca065fcae4df59af0b02c592..22f4ce581ac07712ec5492602e0ff5f354c28395 100644
--- a/matlab/read_flux_out_XX.m
+++ b/matlab/read_flux_out_XX.m
@@ -1,4 +1,4 @@
-function [t_all, Pxi_all, Qxi_all, Pxe_all, Qxe_all] = read_flux_out_XX(folderPath,PLOT)
+function [out] = read_flux_out_XX(folderPath,PLOT)
% Check if the prompt_string is provided as an argument
if nargin < 1
% If not provided, prompt the user for input
@@ -90,4 +90,11 @@ function [t_all, Pxi_all, Qxi_all, Pxe_all, Qxe_all] = read_flux_out_XX(folderPa
legend('show');
title('Radial heat flux')
end
+
+
+ out.t = t_all;
+ out.Pxi = Pxi_all;
+ out.Qxi = Qxi_all;
+ out.Pxe = Pxe_all;
+ out.Qxe = Qxe_all;
end
diff --git a/src/coeff_mod.F90 b/src/coeff_mod.F90
index 3c4c9125a19bfb7103e6050140f4850558bb715e..9739766ce2f727db1bac0fc445abd99484458646 100644
--- a/src/coeff_mod.F90
+++ b/src/coeff_mod.F90
@@ -1,7 +1,9 @@
MODULE coeff
-! this module contains routines to compute normalization coefficients and velocity integrals
-!
+! this module contains routines to compute the Laguerre-Laguerre products coefficients
+! dnjs for the nonlinear term. ALL2L(n,j,s,0) = dnjs
+! Lpjl(p,j,l) returns the l-th coefficient of the j-th order associated Laguerre_{p-1/2} poynomial
+ ! the canonical basis (p=0) writes L_j(x) = sum_{l=0}^j c_l x^l
USE PREC_CONST
use BASIC
diff --git a/src/initial_mod.F90 b/src/initial_mod.F90
index a744d64ee3fd253ae3ab52d8dad7af984cb4e9da..94eaedb74026ce00db61b6bb5869b109be7a44b0 100644
--- a/src/initial_mod.F90
+++ b/src/initial_mod.F90
@@ -289,8 +289,8 @@ CONTAINS
USE fields, ONLY: moments
USE prec_const, ONLY: xp
USE model, ONLY: LINEARITY
- USE grid, ONLY: total_nkx, local_nkx_offset, local_nky, local_nky_offset,&
- kxarray_full, kyarray_full, kx_max, kx_min, ky_max
+ USE grid, ONLY: total_nkx, local_nkx_offset, local_nky, local_nky_offset, iky0,&
+ kxarray_full, kyarray_full, kx_max, kx_min, ky_max, deltakx, deltaky
IMPLICIT NONE
INTEGER :: ikx,iky, im, I_, J_
REAL(xp):: maxkx, minkx, maxky, kx_, ky_, A_
@@ -314,19 +314,16 @@ CONTAINS
IF(I_ .LT. 0) THEN
I_ = I_ + total_nkx
ENDIF
- I_ = I_ + 1 ! array indices start at 1
- J_ = J_ + 1
! Check the validity of the modes
- kx_ = kxarray_full(I_)
- ky_ = kyarray_full(J_)
+ kx_ = I_*deltakx
+ ky_ = J_*deltaky
IF( ((kx_ .GE. minkx) .AND. (kx_ .LE. maxkx)) .AND. &
((ky_ .GE. 0._xp) .AND. (ky_ .LE. maxky)) ) THEN
! Init the mode
DO ikx=1,total_nkx
DO iky=1,local_nky
- IF ( (ikx+local_nkx_offset .EQ. I_) .AND. &
- (iky+local_nky_offset .EQ. J_) ) THEN
- ! WRITE(*,'(A10,F4.2,A,F4.2,A,F4.2)') '-init (kx=',kx_,',ky=',ky_,') at Amp=',A_
+ IF ( (kxarray_full(ikx+local_nkx_offset) .EQ. kx_) .AND. &
+ (kyarray_full(iky+local_nky_offset) .EQ. ky_) ) THEN
WRITE(*,'(A,F5.3,A,F5.3,A,G9.2)') '-init (kx=',kx_,',ky=',ky_,') with Amp= ',A_
moments(:,:,:,iky,ikx,:,:) = A_
ENDIF
diff --git a/src/model_mod.F90 b/src/model_mod.F90
index 81ebdbe7494f15083d894913421ed1ef707d8554..7edf6e87ebaebf62ab330bd3003edbbe494bc1d6 100644
--- a/src/model_mod.F90
+++ b/src/model_mod.F90
@@ -4,7 +4,6 @@ MODULE model
IMPLICIT NONE
PRIVATE
! INPUTS
- INTEGER, PUBLIC, PROTECTED :: KERN = 0 ! Kernel model
CHARACTER(len=16), &
PUBLIC, PROTECTED ::LINEARITY= 'linear' ! To turn on non linear bracket term
REAL(xp), PUBLIC, PROTECTED :: mu_x = 0._xp ! spatial x-Hyperdiffusivity coefficient (for num. stability)
@@ -39,6 +38,11 @@ MODULE model
LOGICAL, PUBLIC, PROTECTED :: FORCE_SYMMETRY = .false.
! Add or remove the ExB nonlinear correction (Mcmillan 2019)
LOGICAL, PUBLIC, PROTECTED :: ExB_NL_CORRECTION = .true.
+ CHARACTER(len=16), &
+ PUBLIC, PROTECTED :: KN_MODEL = 'std' ! Kernel model
+ INTEGER, PUBLIC, PROTECTED :: ORDER = 1 ! order for Taylor expansion
+ INTEGER, PUBLIC, PROTECTED :: ORDER_NUM = 2 ! numerator order for Pade approx
+ INTEGER, PUBLIC, PROTECTED :: ORDER_DEN = 4 ! denominator order for Pade approx
! Module's routines
PUBLIC :: model_readinputs, model_outputinputs
@@ -52,11 +56,11 @@ CONTAINS
USE prec_const, ONLY: xp
IMPLICIT NONE
- NAMELIST /MODEL/ KERN, LINEARITY, RM_LD_T_EQ, FORCE_SYMMETRY, MHD_PD, &
+ NAMELIST /MODEL/ LINEARITY, RM_LD_T_EQ, FORCE_SYMMETRY, MHD_PD, &
Na, ADIAB_E, ADIAB_I, q_i, tau_i, &
mu_x, mu_y, N_HD, HDz_h, mu_z, mu_p, mu_j, HYP_V, &
nu, k_gB, k_cB, lambdaD, beta, ExBrate, ExB_NL_CORRECTION,&
- ikxZF, ZFrate, ZF_ONLY
+ ikxZF, ZFrate, ZF_ONLY, KN_MODEL, ORDER, ORDER_NUM, ORDER_DEN
READ(lu_in,model)
@@ -96,7 +100,6 @@ CONTAINS
CHARACTER(len=256) :: str
WRITE(str,'(a)') '/data/input/model'
CALL creatd(fid, 0,(/0/),TRIM(str),'Model Input')
- CALL attach(fid, TRIM(str), "KERN", KERN)
CALL attach(fid, TRIM(str), "LINEARITY", LINEARITY)
CALL attach(fid, TRIM(str),"RM_LD_T_EQ",RM_LD_T_EQ)
CALL attach(fid, TRIM(str), "mu_x", mu_x)
@@ -120,6 +123,10 @@ CONTAINS
CALL attach(fid, TRIM(str), "ADIAB_E", ADIAB_E)
CALL attach(fid, TRIM(str), "ADIAB_I", ADIAB_I)
CALL attach(fid, TRIM(str), "tau_i", tau_i)
+ CALL attach(fid, TRIM(str),"kern model",KN_MODEL)
+ CALL attach(fid, TRIM(str), "order den",ORDER_DEN)
+ CALL attach(fid, TRIM(str), "order num",ORDER_NUM)
+ CALL attach(fid, TRIM(str), "order", ORDER)
END SUBROUTINE model_outputinputs
END MODULE model
diff --git a/src/nonlinear_mod.F90 b/src/nonlinear_mod.F90
index c11fa8f8422c98b2726d56399645652cf496d016..7b8fb4308df6015832cb7c77caa521821caa413c 100644
--- a/src/nonlinear_mod.F90
+++ b/src/nonlinear_mod.F90
@@ -94,6 +94,7 @@ SUBROUTINE compute_nonlinear
ENDIF
! Second convolution terms
G_cmpx = 0._xp ! initialization of the sum
+ ! We set smax as min(n+j,Jmax) for safety reason but nmaxarray may prevent it as well (see anti-Laguerre-aliasing truncation)
smax = MIN( jarray(ini)+jarray(iji), jmax );
s1:DO is = 1, smax+1 ! sum truncation on number of moments
isi = is + ngj/2
diff --git a/src/numerics_mod.F90 b/src/numerics_mod.F90
index 62f242199ff654f81ec877bf498c3a6edf393283..357f092c1bdd1222e59aa38b6b6b13f4ca6ace2e 100644
--- a/src/numerics_mod.F90
+++ b/src/numerics_mod.F90
@@ -77,31 +77,80 @@ SUBROUTINE evaluate_kernels
USE grid, ONLY : local_na, local_nj,ngj, local_nkx, local_nky, local_nz, ngz, jarray, kp2array,&
nzgrid
USE species, ONLY : sigma2_tau_o2
+ USE model, ONLY : KN_MODEL, ORDER, ORDER_NUM, ORDER_DEN
IMPLICIT NONE
INTEGER :: j_int, ia, eo, ikx, iky, iz, ij
REAL(xp) :: j_xp, y_, factj, sigma_i
sigma_i = 1._xp ! trivial singe sigma_a = sqrt(m_a/m_i)
-DO ia = 1,local_na
- DO eo = 1,nzgrid
- DO ikx = 1,local_nkx
- DO iky = 1,local_nky
- DO iz = 1,local_nz + ngz
- DO ij = 1,local_nj + ngj
- j_int = jarray(ij)
- j_xp = REAL(j_int,xp)
- y_ = sigma2_tau_o2(ia) * kp2array(iky,ikx,iz,eo)
- IF(j_int .LT. 0) THEN !ghosts values
- kernel(ia,ij,iky,ikx,iz,eo) = 0._xp
- ELSE
- factj = REAL(GAMMA(j_xp+1._xp),xp)
- kernel(ia,ij,iky,ikx,iz,eo) = y_**j_int*EXP(-y_)/factj
- ENDIF
+ SELECT CASE (KN_MODEL)
+ CASE('taylor') ! developped with Leonhard Driever
+ ! Kernels based on the ORDER_NUM order Taylor series of J0
+ WRITE (*,*) 'Kernel approximation uses Taylor series with ', ORDER, ' powers of k'
+ DO ia = 1,local_na
+ DO eo = 1,nzgrid
+ DO ikx = 1,local_nkx
+ DO iky = 1,local_nky
+ DO iz = 1,local_nz + ngz
+ DO ij = 1,local_nj + ngj
+ y_ = sigma2_tau_o2(ia) * kp2array(iky,ikx,iz,eo)
+ j_int = jarray(ij)
+ IF (j_int > ORDER .OR. j_int < 0) THEN
+ kernel(ia,ij,ikx,iky,iz,eo) = 0._xp
+ ELSE
+ kernel(ia,ij,ikx,iky,iz,eo) = taylor_kernel_n(ORDER, j_int, y_)
+ ENDIF
+ ENDDO
+ ENDDO
ENDDO
ENDDO
ENDDO
ENDDO
- ENDDO
+ CASE ('pade')
+ ! Kernels based on the ORDER_NUM / ORDER_DEN Pade approximation of the kernels
+ WRITE (*,*) 'Kernel approximation uses ', ORDER_NUM ,'/', ORDER_DEN, ' Pade approximation'
+ DO ia = 1,local_na
+ DO eo = 1,nzgrid
+ DO ikx = 1,local_nkx
+ DO iky = 1,local_nky
+ DO iz = 1,local_nz + ngz
+ DO ij = 1,local_nj + ngj
+ y_ = sigma2_tau_o2(ia) * kp2array(iky,ikx,iz,eo)
+ j_int = jarray(ij)
+ IF (j_int > ORDER_NUM .OR. j_int < 0) THEN
+ kernel(ia,ij,ikx,iky,iz,eo) = 0._xp
+ ELSE
+ kernel(ia,ij,ikx,iky,iz,eo) = pade_kernel_n(j_int, y_,ORDER_NUM,ORDER_DEN)
+ ENDIF
+ ENDDO
+ ENDDO
+ ENDDO
+ ENDDO
+ ENDDO
+ ENDDO
+ CASE DEFAULT
+ DO ia = 1,local_na
+ DO eo = 1,nzgrid
+ DO ikx = 1,local_nkx
+ DO iky = 1,local_nky
+ DO iz = 1,local_nz + ngz
+ DO ij = 1,local_nj + ngj
+ j_int = jarray(ij)
+ j_xp = REAL(j_int,xp)
+ y_ = sigma2_tau_o2(ia) * kp2array(iky,ikx,iz,eo)
+ IF(j_int .LT. 0) THEN !ghosts values
+ kernel(ia,ij,iky,ikx,iz,eo) = 0._xp
+ ELSE
+ factj = REAL(GAMMA(j_xp+1._xp),xp)
+ kernel(ia,ij,iky,ikx,iz,eo) = y_**j_int*EXP(-y_)/factj
+ ENDIF
+ ENDDO
+ ENDDO
+ ENDDO
+ ENDDO
+ ENDDO
+ ENDDO
+ END SELECT
! !! Correction term for the evaluation of the heat flux
! HF_phi_correction_operator(:,:,:) = &
@@ -117,7 +166,6 @@ DO ia = 1,local_na
! - (j_xp+1.0_xp) * Kernel(ia,ij+1,:,:,:,1) &
! - j_xp * Kernel(ia,ij-1,:,:,:,1))
! ENDDO
-ENDDO
END SUBROUTINE evaluate_kernels
!******************************************************************************!
@@ -324,4 +372,123 @@ SUBROUTINE compute_lin_coeff
ENDDO
END SUBROUTINE compute_lin_coeff
+
+!******************************************************************************!
+!!!!!!! Auxilliary kernel functions/subroutines (developped with Leonhard Driever)
+!******************************************************************************!
+REAL(xp) FUNCTION taylor_kernel_n(order, n, y)
+ IMPLICIT NONE
+ INTEGER, INTENT(IN) :: order
+ INTEGER, INTENT(IN) :: n
+ REAL(xp), INTENT(IN) :: y
+ REAL(xp) :: sum_variable
+ INTEGER :: m
+ REAL(xp) :: m_dp, n_dp
+
+ n_dp = REAL(n, xp)
+ sum_variable = 0._xp
+
+ DO m = n, order
+ m_dp = REAL(m, xp)
+ sum_variable = sum_variable + (-1._xp)**(m - n) * y**m / (GAMMA(n_dp + 1._xp) * GAMMA(m_dp - n_dp + 1._xp)) ! Denominator of m C n
+ END DO
+ taylor_kernel_n = sum_variable
+END FUNCTION taylor_kernel_n
+
+
+REAL(xp) FUNCTION pade_kernel_n(n, y, N_NUM, N_DEN)
+ IMPLICIT NONE
+ INTEGER, INTENT(IN) :: n, N_NUM, N_DEN
+ REAL(xp), INTENT(IN) :: y
+ REAL(xp) :: pade_numerator_coeffs(N_NUM + 1), pade_denominator_coeffs(N_NUM + 1)
+ REAL(xp) :: numerator_sum
+ REAL(xp) :: denominator_sum
+ INTEGER :: m
+ ! If N_NUM == 0, then the approximation should be the same as the Taylor approx. of N_NUM:
+ IF (N_NUM == 0) THEN
+ pade_kernel_n = taylor_kernel_n(N_NUM, n, y)
+ ELSE
+ CALL find_pade_coefficients(pade_numerator_coeffs, pade_denominator_coeffs, n, N_NUM, N_DEN)
+ numerator_sum = 0
+ denominator_sum = 0
+ DO m = 0, N_NUM
+ numerator_sum = numerator_sum + pade_numerator_coeffs(m + 1) * y ** m
+ END DO
+ DO m = 0, N_NUM
+ denominator_sum = denominator_sum + pade_denominator_coeffs(m + 1) * y ** m
+ END DO
+ pade_kernel_n = numerator_sum / denominator_sum
+ END IF
+END FUNCTION pade_kernel_n
+
+
+SUBROUTINE find_pade_coefficients(pade_num_coeffs, pade_denom_coeffs, n, N_NUM, N_DEN)
+ IMPLICIT NONE
+#ifdef SINGLE_PRECISION
+ EXTERNAL :: SGESV ! Use DGESV rather than SGESV for double precision
+#else
+ EXTERNAL :: DGESV ! Use DGESV rather than SGESV for double precision
+#endif
+ INTEGER, INTENT (IN) :: n, N_NUM, N_DEN ! index of the considered Kernel
+ REAL(xp), INTENT(OUT) :: pade_num_coeffs(N_NUM + 1), pade_denom_coeffs(N_NUM + 1) ! OUT rather than INOUT to make sure no information is retained from previous Kernel computations
+
+ REAL(xp) :: taylor_kernel_coeffs(N_NUM + N_NUM + 1), denom_matrix(N_NUM, N_NUM)
+ INTEGER :: m, j
+ REAL(xp) :: m_dp, n_dp
+ INTEGER :: return_code ! for DGESV
+ REAL(xp) :: pivot(N_NUM) ! for DGESV
+
+ n_dp = REAL(n, xp)
+
+ ! First find the kernel Taylor expansion coefficients
+ DO m = 0, N_NUM + N_NUM ! m here counts the order of the derivatives
+ m_dp = REAL(m, xp)
+
+ IF (m < n) THEN
+ taylor_kernel_coeffs(m + 1) = 0
+ ELSE
+ taylor_kernel_coeffs(m + 1) = (-1)**(n + m) / (GAMMA(n_dp + 1._xp) * GAMMA(m_dp - n_dp + 1._xp))
+ END IF
+ END DO
+
+ ! Next construct the denominator solving matrix
+ DO m = 1, N_NUM
+ DO j = 1, N_NUM
+ IF (N_NUM + m - j < 0) THEN
+ denom_matrix(m, j) = 0
+ ELSE
+ denom_matrix(m, j) = taylor_kernel_coeffs(N_NUM + m - j + 1)
+ END IF
+ END DO
+ END DO
+
+ ! Then solve for the denominator coefficients, setting the first one to 1
+ !!!! SOLVER NOT YET IMPLEMENTED!!!!
+ pade_denom_coeffs(1) = 1
+ pade_denom_coeffs(2:) = - taylor_kernel_coeffs(N_NUM + 2 : N_NUM + N_NUM + 1) ! First acts as RHS vector for equation, is then transformed to solution by DGESV
+#ifdef SINGLE_PRECISION
+ CALL SGESV(N_NUM, 1, denom_matrix, N_NUM, pivot, pade_denom_coeffs(2:), N_NUM, return_code) ! LAPACK solver for matrix equation. Note that denom_matrix is now no longer as expected
+#else
+ CALL DGESV(N_NUM, 1, denom_matrix, N_NUM, pivot, pade_denom_coeffs(2:), N_NUM, return_code) ! LAPACK solver for matrix equation. Note that denom_matrix is now no longer as expected
+#endif
+
+
+ ! Print an error message in case there was a problem with the solver
+ IF (return_code /= 0) THEN
+ WRITE (*,*) 'An error occurred in the solving for the Pade denominator coefficients. The error code is: ', return_code
+ END IF
+
+ ! Finally compute the numerator coefficients
+ DO m = 1, N_NUM + 1
+ pade_num_coeffs(m) = 0 ! As the array is not automatically filled with zeros
+ DO j = 1, m
+ !num_matrix(m, j) = taylor_kernel_coeffs(m - j + 1)
+ pade_num_coeffs(m) = pade_num_coeffs(m) + pade_denom_coeffs(j) * taylor_kernel_coeffs(m - j + 1)
+ END DO
+ END DO
+
+END SUBROUTINE find_pade_coefficients
+!******************************************************************************!
+
+
END MODULE numerics
diff --git a/src/solve_EM_fields.F90 b/src/solve_EM_fields.F90
index d28a4aca89bd83c3e024baa31cc9e580e563d9a6..dfbc9d2dedfa97ca32b572316832535855cf0fec 100644
--- a/src/solve_EM_fields.F90
+++ b/src/solve_EM_fields.F90
@@ -69,10 +69,7 @@ CONTAINS
!!!!!!!!!!!!!!! adiabatic ion model
! Candy et al. 2007, rho_i = -q_i/tau_i phi
IF (ADIAB_I) THEN
- DO iz = 1,local_nz
- izi = iz+ngz/2
- rho(iz) = rho(iz) - 0*q_i/tau_i * phi(iky,ikx,izi)
- ENDDO
+ ! No ion contribution
ENDIF
!!!!!!!!!!!!!!! Inverting the poisson equation
diff --git a/src/species_mod.F90 b/src/species_mod.F90
index 2d86e0601d40fb81ea8843927a1757a225afdb0c..43c8557bbb2176aaccd4874f8a0de76b11e6834b 100644
--- a/src/species_mod.F90
+++ b/src/species_mod.F90
@@ -10,6 +10,7 @@ MODULE species
REAL(xp) :: q_ ! Charge
REAL(xp) :: k_N_ ! density drive (L_ref/L_Ni)
REAL(xp) :: k_T_ ! temperature drive (L_ref/L_Ti)
+ REAL(xp) :: mu_ ! species-wise hyperdiffusion (not tested)
!! Arrays to store all species features
CHARACTER(len=32),&
ALLOCATABLE, DIMENSION(:), PUBLIC, PROTECTED :: name ! name of the species
@@ -19,6 +20,7 @@ MODULE species
REAL(xp), ALLOCATABLE, DIMENSION(:), PUBLIC, PROTECTED :: k_N ! density drive (L_ref/L_Ni)
REAL(xp), ALLOCATABLE, DIMENSION(:), PUBLIC, PROTECTED :: k_T ! temperature drive (L_ref/L_Ti)
REAL(xp), ALLOCATABLE, DIMENSION(:,:),PUBLIC, PROTECTED :: nu_ab ! Collision frequency tensor
+ REAL(xp), ALLOCATABLE, DIMENSION(:), PUBLIC, PROTECTED :: mu ! Hyperdiffusion
!! Auxiliary variables to store precomputation
REAL(xp), ALLOCATABLE, DIMENSION(:),PUBLIC, PROTECTED :: tau_q ! factor of the magnetic moment coupling
REAL(xp), ALLOCATABLE, DIMENSION(:),PUBLIC, PROTECTED :: q_tau ! charge/temp ratio
@@ -43,7 +45,7 @@ CONTAINS
INTEGER :: ia,ib
! expected namelist in the input file
NAMELIST /SPECIES/ &
- name_, tau_, sigma_, q_, k_N_, k_T_
+ name_, tau_, sigma_, q_, k_N_, k_T_, mu_
! allocate the arrays of species parameters
CALL species_allocate
! loop over the species namelists in the input file
@@ -56,6 +58,7 @@ CONTAINS
q_ = 1._xp
k_N_ = 2.22_xp
k_T_ = 6.96_xp
+ mu_ = 0._xp
! read input
READ(lu_in,species)
! place values found in the arrays
@@ -66,6 +69,7 @@ CONTAINS
k_N(ia) = k_N_
k_T(ia) = k_T_
tau_q(ia) = tau_/q_
+ mu(ia) = mu_
! precompute factors
q_tau(ia) = q_/tau_
sqrtTau_q(ia) = sqrt(tau_)/q_
@@ -130,6 +134,7 @@ CONTAINS
CALL attach(fid, TRIM(str), "q", q(ia))
CALL attach(fid, TRIM(str), "k_N", k_N(ia))
CALL attach(fid, TRIM(str), "k_T", k_T(ia))
+ CALL attach(fid, TRIM(str), "mu", mu(ia))
ENDDO
END SUBROUTINE species_outputinputs
@@ -144,6 +149,7 @@ CONTAINS
ALLOCATE( q(Na))
ALLOCATE( k_N(Na))
ALLOCATE( k_T(Na))
+ ALLOCATE( mu(Na))
ALLOCATE( tau_q(Na))
ALLOCATE( q_tau(Na))
ALLOCATE( sqrtTau_q(Na))
diff --git a/testcases/ITG_zpinch/3D/fort_00.90 b/testcases/ITG_zpinch/3D/fort_00.90
new file mode 100644
index 0000000000000000000000000000000000000000..d6255d0b0adb301845994752276cbcb0c4646089
--- /dev/null
+++ b/testcases/ITG_zpinch/3D/fort_00.90
@@ -0,0 +1,104 @@
+&BASIC
+ nrun = 99999999
+ dt = 0.01
+ tmax = 500
+ maxruntime = 72000
+ job2load = -1
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 128
+ Lx = 80
+ Ny = 64
+ Ly = 80
+ Nz = 24
+ SG = .t.
+ Nexc = 1
+/
+&GEOMETRY
+ geom = 'Z-pinch'
+ q0 = 0.0
+ shear = 0.0
+ eps = 0.0
+ kappa = 1.0
+ s_kappa= 0.0
+ delta = 0.0
+ s_delta= 0.0
+ zeta = 0.0
+ s_zeta = 0.0
+ parallel_bc = 'shearless'
+ shift_y= 0.0
+ Npol = 1
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 0.5
+ dtsave_5d = 50
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 1 ! number of species
+ mu_x = 1.0
+ mu_y = 1.0
+ N_HD = 4
+ mu_z = 1.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.05
+ beta = 0.0
+ ADIAB_E = .t.
+/
+&CLOSURE
+ !hierarchy_closure='truncation'
+ hierarchy_closure='max_degree'
+ dmax = 2
+ nonlinear_closure='anti_laguerre_aliasing' !(truncation,full_sum,anti_laguerre_aliasing)
+ nmax = 1
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 0.0
+ k_T_ = 6.96
+/
+&SPECIES
+ ! electrons
+ name_ = 'electrons'
+ tau_ = 1.0
+ sigma_= 0.023338
+ q_ =-1.0
+ k_N_ = 1.6
+ k_T_ = 0.4
+/
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .f.
+ INTERSPECIES = .true.
+ mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
+/
+&INITIAL
+ INIT_OPT = 'blob' !(phi,blob)
+ ACT_ON_MODES = 'donothing'
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+/
diff --git a/testcases/ITG_zpinch/NO_SG/fort_00.90 b/testcases/ITG_zpinch/NO_SG/fort_00.90
new file mode 100644
index 0000000000000000000000000000000000000000..381ace207c4e3c115a4066627e74a2ad529a10fb
--- /dev/null
+++ b/testcases/ITG_zpinch/NO_SG/fort_00.90
@@ -0,0 +1,103 @@
+&BASIC
+ nrun = 99999999
+ dt = 0.02
+ tmax = 100
+ maxruntime = 72000
+ job2load = -1
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 64
+ Lx = 80
+ Ny = 48
+ Ly = 80
+ Nz = 16
+ SG = .f.
+ Nexc = 1
+/
+&GEOMETRY
+ geom = 'Z-pinch'
+ q0 = 0.0
+ shear = 0.0
+ eps = 0.0
+ kappa = 1.0
+ s_kappa= 0.0
+ delta = 0.0
+ s_delta= 0.0
+ zeta = 0.0
+ s_zeta = 0.0
+ parallel_bc = 'shearless'
+ shift_y= 0.0
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 0.5
+ dtsave_5d = 50
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 1 ! number of species
+ mu_x = 0.0
+ mu_y = 0.0
+ N_HD = 4
+ mu_z = 0.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.05
+ beta = 0.0
+ ADIAB_E = .t.
+/
+&CLOSURE
+ !hierarchy_closure='truncation'
+ hierarchy_closure='max_degree'
+ dmax = 2
+ nonlinear_closure='anti_laguerre_aliasing' !(truncation,full_sum,anti_laguerre_aliasing)
+ nmax = -1
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 0.0
+ k_T_ = 4.0
+/
+&SPECIES
+ ! electrons
+ name_ = 'electrons'
+ tau_ = 1.0
+ sigma_= 0.023338
+ q_ =-1.0
+ k_N_ = 1.6
+ k_T_ = 0.4
+/
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .t.
+ INTERSPECIES = .true.
+ mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
+/
+&INITIAL
+ INIT_OPT = 'phi' !(phi,blob)
+ ACT_ON_MODES = 'donothing'
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+/
diff --git a/testcases/ITG_zpinch/PAR_DIFF/fort_00.90 b/testcases/ITG_zpinch/PAR_DIFF/fort_00.90
new file mode 100644
index 0000000000000000000000000000000000000000..30fdace3f704b6418134cc0d8df9c2992bef1716
--- /dev/null
+++ b/testcases/ITG_zpinch/PAR_DIFF/fort_00.90
@@ -0,0 +1,103 @@
+&BASIC
+ nrun = 99999999
+ dt = 0.02
+ tmax = 100
+ maxruntime = 72000
+ job2load = -1
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 64
+ Lx = 80
+ Ny = 48
+ Ly = 80
+ Nz = 16
+ SG = .f.
+ Nexc = 1
+/
+&GEOMETRY
+ geom = 'Z-pinch'
+ q0 = 0.0
+ shear = 0.0
+ eps = 0.0
+ kappa = 1.0
+ s_kappa= 0.0
+ delta = 0.0
+ s_delta= 0.0
+ zeta = 0.0
+ s_zeta = 0.0
+ parallel_bc = 'shearless'
+ shift_y= 0.0
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 0.5
+ dtsave_5d = 50
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 1 ! number of species
+ mu_x = 0.0
+ mu_y = 0.0
+ N_HD = 4
+ mu_z = 0.2
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.05
+ beta = 0.0
+ ADIAB_E = .t.
+/
+&CLOSURE
+ !hierarchy_closure='truncation'
+ hierarchy_closure='max_degree'
+ dmax = 2
+ nonlinear_closure='anti_laguerre_aliasing' !(truncation,full_sum,anti_laguerre_aliasing)
+ nmax = -1
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 0.0
+ k_T_ = 4.0
+/
+&SPECIES
+ ! electrons
+ name_ = 'electrons'
+ tau_ = 1.0
+ sigma_= 0.023338
+ q_ =-1.0
+ k_N_ = 1.6
+ k_T_ = 0.4
+/
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .t.
+ INTERSPECIES = .true.
+ mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
+/
+&INITIAL
+ INIT_OPT = 'phi' !(phi,blob)
+ ACT_ON_MODES = 'donothing'
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+/
diff --git a/testcases/ITG_zpinch/fort.90 b/testcases/ITG_zpinch/fort.90
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/testcases/ITG_zpinch/fort_00.90 b/testcases/ITG_zpinch/fort_00.90
index 87253b73dd8669e3481ffc76c1e920fd59f5d150..522164900fc4152cfd9b103684cec6ee97433096 100644
--- a/testcases/ITG_zpinch/fort_00.90
+++ b/testcases/ITG_zpinch/fort_00.90
@@ -1,19 +1,19 @@
&BASIC
nrun = 99999999
dt = 0.01
- tmax = 250
+ tmax = 500
maxruntime = 72000
job2load = -1
/
&GRID
pmax = 2
jmax = 1
- Nx = 64
- Lx = 120
- Ny = 48
- Ly = 120
- Nz = 16
- SG = .f.
+ Nx = 128
+ Lx = 80
+ Ny = 64
+ Ly = 80
+ Nz = 1
+ SG = .t.
Nexc = 1
/
&GEOMETRY
@@ -34,8 +34,8 @@
dtsave_0d = 1
dtsave_1d = -1
dtsave_2d = -1
- dtsave_3d = 1
- dtsave_5d = 10
+ dtsave_3d = 0.5
+ dtsave_5d = 50
write_doubleprecision = .f.
write_gamma = .t.
write_hf = .t.
@@ -49,8 +49,8 @@
&MODEL
LINEARITY = 'nonlinear'
Na = 1 ! number of species
- mu_x = 0.0
- mu_y = 0.0
+ mu_x = 1.0
+ mu_y = 1.0
N_HD = 4
mu_z = 0.0
HYP_V = 'hypcoll'
@@ -59,14 +59,13 @@
nu = 0.05
beta = 0.0
ADIAB_E = .t.
- tau_e = 1.0
/
&CLOSURE
!hierarchy_closure='truncation'
hierarchy_closure='max_degree'
dmax = 2
nonlinear_closure='anti_laguerre_aliasing' !(truncation,full_sum,anti_laguerre_aliasing)
- nmax = -1
+ nmax = 1
/
&SPECIES
! ions
@@ -75,7 +74,7 @@
sigma_= 1.0
q_ = 1.0
k_N_ = 0.0
- k_T_ = 4.0
+ k_T_ = 6.96
/
&SPECIES
! electrons
@@ -88,7 +87,7 @@
/
&COLLISION
collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
- GK_CO = .t.
+ GK_CO = .f.
INTERSPECIES = .true.
mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
/
diff --git a/testcases/ITG_zpinch/fort_01.90 b/testcases/ITG_zpinch/fort_01.90
new file mode 100644
index 0000000000000000000000000000000000000000..3f22e004be173a628ab9e2e72f95ef8eda9446d1
--- /dev/null
+++ b/testcases/ITG_zpinch/fort_01.90
@@ -0,0 +1,103 @@
+&BASIC
+ nrun = 99999999
+ dt = 0.01
+ tmax = 1000
+ maxruntime = 72000
+ job2load = 0
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 128
+ Lx = 80
+ Ny = 64
+ Ly = 80
+ Nz = 16
+ SG = .t.
+ Nexc = 1
+/
+&GEOMETRY
+ geom = 'Z-pinch'
+ q0 = 0.0
+ shear = 0.0
+ eps = 0.0
+ kappa = 1.0
+ s_kappa= 0.0
+ delta = 0.0
+ s_delta= 0.0
+ zeta = 0.0
+ s_zeta = 0.0
+ parallel_bc = 'shearless'
+ shift_y= 0.0
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 0.5
+ dtsave_5d = 50
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 1 ! number of species
+ mu_x = 1.0
+ mu_y = 1.0
+ N_HD = 4
+ mu_z = 0.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.05
+ beta = 0.0
+ ADIAB_E = .t.
+/
+&CLOSURE
+ !hierarchy_closure='truncation'
+ hierarchy_closure='max_degree'
+ dmax = 2
+ nonlinear_closure='anti_laguerre_aliasing' !(truncation,full_sum,anti_laguerre_aliasing)
+ nmax = 1
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 0.0
+ k_T_ = 6.96
+/
+&SPECIES
+ ! electrons
+ name_ = 'electrons'
+ tau_ = 1.0
+ sigma_= 0.023338
+ q_ =-1.0
+ k_N_ = 1.6
+ k_T_ = 0.4
+/
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .f.
+ INTERSPECIES = .true.
+ mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
+/
+&INITIAL
+ INIT_OPT = 'blob' !(phi,blob)
+ ACT_ON_MODES = 'donothing'
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+/
diff --git a/testcases/Rosenbluth_Hinton_test/fort_00.90 b/testcases/Rosenbluth_Hinton_test/fort_00.90
new file mode 100644
index 0000000000000000000000000000000000000000..bc86583eef35435c1298ac6ad684f9aaa7c8bfed
--- /dev/null
+++ b/testcases/Rosenbluth_Hinton_test/fort_00.90
@@ -0,0 +1,101 @@
+&BASIC
+ nrun = 99999999
+ dt = 0.025
+ tmax = 25
+ maxruntime = 72000
+ job2load = -1
+/
+&GRID
+ pmax = 32
+ jmax = 0
+ Nx = 2
+ Lx = 120
+ Ny = 2
+ Ly = 120
+ Nz = 24
+ SG = .f.
+ Nexc = 0
+/
+&GEOMETRY
+ geom = 's-alpha'
+ !geom = 'miller'
+ q0 = 1.4
+ shear = 0.0
+ eps = 0.1
+ kappa = 1.0
+ s_kappa= 0.0
+ delta = 0.0
+ s_delta= 0.0
+ zeta = 0.0
+ s_zeta = 0.0
+ parallel_bc = 'dirichlet'
+ shift_y= 0.0
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 0.1
+ dtsave_5d = 20
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'linear'
+ Na = 1 ! number of species
+ mu_x = 0.0
+ mu_y = 0.0
+ N_HD = 4
+ mu_z = 0.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.01
+ beta = 0.0
+ ADIAB_E = .t.
+/
+&CLOSURE
+ hierarchy_closure='truncation'
+ dmax = -1
+ nonlinear_closure='truncation'
+ nmax = 0
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 0
+ k_T_ = 0
+/
+
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .f.
+ INTERSPECIES = .true.
+ mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
+/
+&INITIAL
+ INIT_OPT = 'mom00'
+ !INIT_OPT = 'mom00_mode'
+ init_background = 1.0
+ init_noiselvl = 0
+ iseed = 42
+ Nmodes = 1
+/
+&MODE
+ I_ = 1
+ J_ = 0
+ amp_ = 1.0
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+/
diff --git a/testcases/cyclone_example/Z_pinch/fort_00.90 b/testcases/cyclone_example/Z_pinch/fort_00.90
new file mode 100644
index 0000000000000000000000000000000000000000..96c03136dd6b2778c54337686dfa9457e0050baf
--- /dev/null
+++ b/testcases/cyclone_example/Z_pinch/fort_00.90
@@ -0,0 +1,96 @@
+&BASIC
+ nrun = 99999999
+ dt = 0.01
+ tmax = 50
+ maxruntime = 72000
+ job2load = -1
+/
+&GRID
+ pmax = 4
+ jmax = 1
+ Nx = 64
+ Lx = 120
+ Ny = 48
+ Ly = 120
+ Nz = 16
+ SG = .f.
+ Nexc = 0
+/
+&GEOMETRY
+ geom = 'Z-pinch'
+ !geom = 'miller'
+ q0 = 100!1.4
+ shear = 0.0!0.8
+ eps = 0.001!0.18
+ kappa = 1.0
+ s_kappa= 0.0
+ delta = 0.0
+ s_delta= 0.0
+ zeta = 0.0
+ s_zeta = 0.0
+ parallel_bc = 'dirichlet'
+ shift_y= 0.0
+/
+&DIAGNOSTICS
+ dtsave_0d = 0.1
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 1
+ dtsave_5d = 20
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 1 ! number of species
+ mu_x = 0.0
+ mu_y = 0.0
+ N_HD = 4
+ mu_z = 1.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.05
+ beta = 0.0
+ ADIAB_E = .t.
+/
+&CLOSURE
+ hierarchy_closure='truncation'
+ dmax = -1
+ nonlinear_closure='truncation'
+ nmax = 0
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 2.22
+ k_T_ = 6.96
+/
+
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .f.
+ INTERSPECIES = .true.
+ mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
+/
+&INITIAL
+ INIT_OPT = 'blob'
+ ACT_ON_MODES = 'donothing'
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+ !numerical_scheme = 'SSP_RK3'
+/
diff --git a/testcases/cyclone_example/Z_pinch_limit/fort_00.90 b/testcases/cyclone_example/Z_pinch_limit/fort_00.90
new file mode 100644
index 0000000000000000000000000000000000000000..a555316f0a3503c4e6ec430e7cb5ca90c4fad25e
--- /dev/null
+++ b/testcases/cyclone_example/Z_pinch_limit/fort_00.90
@@ -0,0 +1,96 @@
+&BASIC
+ nrun = 99999999
+ dt = 0.01
+ tmax = 0.1
+ maxruntime = 72000
+ job2load = -1
+/
+&GRID
+ pmax = 4
+ jmax = 1
+ Nx = 64
+ Lx = 120
+ Ny = 48
+ Ly = 120
+ Nz = 16
+ SG = .f.
+ Nexc = 0
+/
+&GEOMETRY
+ !geom = 's-alpha'
+ geom = 'miller'
+ q0 = 1000!1.4
+ shear = 0.0!0.8
+ eps = 0.001!0.18
+ kappa = 1.0
+ s_kappa= 0.0
+ delta = 0.0
+ s_delta= 0.0
+ zeta = 0.0
+ s_zeta = 0.0
+ parallel_bc = 'dirichlet'
+ shift_y= 0.0
+/
+&DIAGNOSTICS
+ dtsave_0d = 0.1
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 1
+ dtsave_5d = 20
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 1 ! number of species
+ mu_x = 0.0
+ mu_y = 0.0
+ N_HD = 4
+ mu_z = 1.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 0.05
+ beta = 0.0
+ ADIAB_E = .t.
+/
+&CLOSURE
+ hierarchy_closure='truncation'
+ dmax = -1
+ nonlinear_closure='truncation'
+ nmax = 0
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 2.22
+ k_T_ = 6.96
+/
+
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .f.
+ INTERSPECIES = .true.
+ mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
+/
+&INITIAL
+ INIT_OPT = 'blob'
+ ACT_ON_MODES = 'donothing'
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ numerical_scheme = 'RK4'
+ !numerical_scheme = 'SSP_RK3'
+/
diff --git a/testcases/cyclone_example/fort_00.90 b/testcases/cyclone_example/fort_00.90
index ce02b619f0d1394c95dc6ecde45bdf99934531b2..abeb5052a73822c2351f43a623f63c2bd25f27b6 100644
--- a/testcases/cyclone_example/fort_00.90
+++ b/testcases/cyclone_example/fort_00.90
@@ -1,7 +1,7 @@
&BASIC
nrun = 99999999
dt = 0.01
- tmax = 5
+ tmax = 50
maxruntime = 72000
job2load = -1
/
@@ -53,7 +53,7 @@
mu_x = 0.0
mu_y = 0.0
N_HD = 4
- mu_z = 1.0
+ mu_z = 2.0
HYP_V = 'hypcoll'
mu_p = 0.0
mu_j = 0.0
@@ -79,7 +79,7 @@
&COLLISION
collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
- GK_CO = .f.
+ GK_CO = .t.
INTERSPECIES = .true.
mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
/
diff --git a/wk/Ch7_HF_analysis.m b/wk/Ch7_HF_analysis.m
new file mode 100644
index 0000000000000000000000000000000000000000..750ec4b91f6f3a950b95b72ff7f7e2d61ba75ca1
--- /dev/null
+++ b/wk/Ch7_HF_analysis.m
@@ -0,0 +1,45 @@
+PARTITION = '/misc/gyacomo23_outputs/paper_3/';
+switch 3
+case 1
+ SIM_SET_NAME = 'Multi-scale';
+ E_FLUX = 1;
+ FOLDER = 'DIIID_fullphys_rho95_geom_scan/multi_scale/multi_scale_3x2x768x192x24';
+ % FOLDER = 'DIIID_fullphys_rho95_geom_scan/multi_scale/multi_scale_5x2x768x192x24';
+case 2
+ SIM_SET_NAME = 'Ion-scale';
+ E_FLUX = 1;
+ FOLDER = 'DIIID_fullphys_rho95_geom_scan/ion_scale/ion_scale_5x2x256x64x32_tau_1_RN_0';
+case 3
+ SIM_SET_NAME = 'Adiab. e.';
+ E_FLUX = 0;
+ FOLDER = 'DIIID_adiab_e_rho95_geom_scan/5x2x256x64x32_tau_1_RN_0/';
+case 4
+ SIM_SET_NAME = 'Adiab. e.';
+ E_FLUX = 0;
+ FOLDER = 'DIIID_adiab_e_rho95_geom_scan/5x2x256x64x32_tau_1_RN_0/';
+end
+
+GEOM = {'NT','0T','PT'};
+COLO = {'b','k','r'};
+figure
+for i = 1:3
+ OPTION = GEOM{i};
+ datadir = [PARTITION,FOLDER,'/',OPTION];
+ out = read_flux_out_XX(datadir,0);
+
+ [ts, is] = sort(out.t);
+ Pxis = out.Pxi(is);
+ Qxis = out.Qxi(is);
+
+ if E_FLUX
+ Pxes = out.Pxe(is);
+ Qxes = out.Qxe(is);
+ subplot(211)
+ plot(ts,Qxes,COLO{i}); hold on;
+ subplot(212)
+ title(SIM_SET_NAME)
+ end
+ plot(ts,Qxis,COLO{i}); hold on;
+end
+title(SIM_SET_NAME)
+
diff --git a/wk/HEL_lin_solver.m b/wk/HEL_GM_eig_solver.m
similarity index 82%
rename from wk/HEL_lin_solver.m
rename to wk/HEL_GM_eig_solver.m
index 752fb87f5e8c45cd9aff50f6f19cc2df5f8a8f92..457f4417847a408aead1211f6273028cd603cc04 100644
--- a/wk/HEL_lin_solver.m
+++ b/wk/HEL_GM_eig_solver.m
@@ -1,24 +1,33 @@
% We formulate the linear system as dN/dt + A*N = 0
+% parameters
+q = 1; % Safety factor
+Jxyz = 1; % Jacobian
+hatB = 1; % normalized B field
+dzlnB = 0; % B parallel derivative
+ddz = 0; % parallel derivative operator
+tau = 0.001; % ion-electron temperature ratio
+IVAN = 0; % flag for Ivanov scaling
+kT = 7; % scaled temperature gradient
+chi = 0.16; % scaled collisionality
+kx_a = 0;linspace(-2.0,2.0,256); % radial fourier grid
+ky_a = linspace(0.01,5,256); % binormal fourier grid
+
+% translate into parameters in GM formulation
+RN = 0;
+RT = kT*2*q/tau;
+NU = chi*3/2/tau/(4-IVAN*2.25);
+MU = 0.0;
-q = 1;
-Jxyz = 1; hatB = 1; dzlnB = 0;
-ddz = 0;
-tau = 0.001;
-IVAN = 1;
%ordering
O1_n = 1;
O1_u = 1-IVAN;
O1_Tpar = 1-IVAN;
O1_Tper = 1-IVAN;
-RN = 0;
-RT = 1*2*q/tau;
-NU = 0.1*3/2/tau/(4-IVAN*2.25);
-MU = 0.0;
-
-kx_a = 0;linspace(-2.0,2.0,256);
-ky_a = linspace(0.01,3.5,256);
+% array of most unstable growth rates and corresponding frequencies
g_a = zeros(numel(kx_a),numel(ky_a)); w_a = g_a;
+
+% Evaluation of the matrices and solver
for i = 1:numel(kx_a)
for j = 1:numel(ky_a)
kx = kx_a(i);
@@ -116,26 +125,8 @@ for j = 1:numel(ky_a)
CDG(4,3) =-2/3*sqrt(2)*K0*(K0-2*K1*O1_Tper);
CDG(4,4) = 4/3*(K0-2*K1*O1_Tper)^2 + 2*tau*(K0-K1)^2*lperp*O1_Tper;
CDG(4,5) =-2/3*q/tau*(K0-K1)*(3*tau*K0^2*lperp-K0*K1*(4+3*tau*lperp)+K1^2*(8+3*tau*lperp));
- if 1
- C = NU*(CLB + CDG);
- else %to check
- C = zeros(4,5);
- C(1,1) = -2/3*tau*lperp*(4*tau*lperp);
- C(1,3) = -2/3*tau*lperp*(sqrt(2)-2*sqrt(2)*tau*lperp);
- C(1,4) = -2/3*tau*lperp*(1-tau*lperp);
- C(1,5) = -2/3*tau*lperp*(5*q*lperp - 11*q*tau*lperp^2);
- C(2,2) = -(1+2*tau*lperp);
- C(3,1) = -2/3*(sqrt(2)*tau*lperp);
- C(3,3) = -2/3*(2+5*tau*lperp);
- C(3,4) = -2/3*(sqrt(2)-4*sqrt(2)*tau*lperp);
- C(3,5) = -2/3*(2*sqrt(2)*q*lperp+8*sqrt(2)*q*tau*lperp^2);
- C(4,1) = -2/3*(tau*lperp - tau^2*lperp^2);
- C(4,3) = -2/3*(sqrt(2)*4*sqrt(2)*tau*lperp);
- C(4,4) = -2/3*(1+12*tau*lperp);
- C(4,5) = -2/3*(2*q*lperp+9*q*tau*lperp^2);
- C = NU*C;
+ C = NU*(CLB + CDG);
- end
% Numerical diffusion
Diff = MU*lperp^2*eye(4);
@@ -166,7 +157,11 @@ for j = 1:numel(ky_a)
gamma =-real(lambda);
omega = imag(lambda);
[g_a(i,j),idx] = max(gamma);
- % w_a(i,j) = omega(idx);
+ % gsorted = sort(gamma);
+ % g_a(i,j) = gsorted(1);
+ w_a(i,j) = omega(idx);
+ % wsorted = sort(omega);
+ % g_a(i,j) = wsorted(1);
w_a(i,j) = max(omega);
end
end
diff --git a/wk/fast_analysis.m b/wk/fast_analysis.m
index 215a920d5753933fa524a6cdb26377480ee81713..4e0e5814654e347f9d832e3af220307ef7567f15 100644
--- a/wk/fast_analysis.m
+++ b/wk/fast_analysis.m
@@ -7,7 +7,7 @@ default_plots_options
% Partition of the computer where the data have to be searched
% PARTITION='/Users/ahoffmann/gyacomo/results/paper_3/';
PARTITION='/misc/gyacomo23_outputs/paper_3/';
-% PARTITION = '';
+% PARTITION = '../results/paper_3/';
%% Paper 3
% resdir = 'DTT_rho85/3x2x192x48x32';
% resdir = 'DTT_rho85/3x2x192x48x32_NT';
@@ -17,88 +17,168 @@ PARTITION='/misc/gyacomo23_outputs/paper_3/';
% resdir = 'LM_DIIID_rho95/3x2x512x92x32';
% resdir = 'DIIID_LM_rho90/3x2x256x128x32';
% resdir = 'DTT_rho85_geom_scan/P8_J4_delta_nuDGGK_conv_test/delta_-0.3_nu_0.9';
-resdir = 'NT_DIIID_Austin2019_rho95/3x2x256x64x32';
-% resdir = '../testcases/cyclone_example';
+% resdir = 'NT_DIIID_Austin2019_rho95/3x2x256x64x32';
+
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_2500/largerbox_moremodes';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_2500/PT/3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_2500/NT/3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_2500/VNT/3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_2500/VPT/3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_2500/CIRC/3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_2500/ELONG/3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_2500/PT/lin_3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_2500/NT/lin_3x2x128x32x32';
+
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/huge';
+
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_1000/PT/3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_1000/NT/3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_1000/PT/lin_3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_1000/NT/lin_3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_750/PT/lin_3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_750/NT/lin_3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_250/PT/lin_3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/RT_250/NT/lin_3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-3/huge';
+
+% resdir = 'DIIID_rho95_cold_ions_tau1e-2/PT/3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e-2/NT/3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e0/PT/3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e0/PT/5x3x192x48x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e0/NT/3x2x128x32x32';
+% resdir = 'DIIID_rho95_cold_ions_tau1e0/NT/5x3x192x48x32';
+% resdir = 'DTT_rho85_cold_ions_tau1e-3/NT/3x2x128x32x32';
+% % resdir = '../testcases/cyclone_example';
% resdir = '../testcases/CBC_ExBshear/std';
% resdir = '../results/paper_3/HM_DTT_rho98/3x2x128x64x64';
- %%
-J0 = 00; J1 = 10;
-% Load basic info (grids and time traces)
+% resdir = 'DIIID_cold_ions_rho95_geom_scan/3x2x192x48x32_RT_1000_eps_q0_scan/NT/eps_0.35_q0_4.0';
+% resdir = 'DTT_rho85_geom_scan/P2_J1_PT_sfact_shear_scan/shear_2.7_q0_-2.9';
+% PARTITION = ''; resdir ='../results/HEL_CBC/tau_1e-3_kT_3500/128x32x24';
+% PARTITION = ''; resdir ='../results/HEL_CBC/tau_1e-3_kT_3500/256x64x24';
+% PARTITION = ''; resdir ='../results/HEL_CBC/tau_1e-3_colless';
+% PARTITION = ''; resdir ='../results/HEL_CBC/tau_1e-3_kT_2000/lin_128x32x24';
+% PARTITION = ''; resdir ='../results/HEL_CBC/tau_1e-3_kT_2000/128x32x24';
+% PARTITION = ''; resdir ='../results/HEL_CBC/CBC_21/128x32x24';
+% PARTITION = ''; resdir ='../results/HEL_CBC/192x48x24';
+% PARTITION = ''; resdir ='../testcases/Ivanov_2020';
+% PARTITION = ''; resdir ='../testcases/Hasegawa_Wakatani';
+% resdir = 'HEL_CBC/256x92x24_max_trunc';
+
+% resdir ='HEL_CBC/192x48x24';
+% resdir ='HEL_CBC/256x92x24'3;
+% resdir ='HEL_CBC/256x256x32/k_N__0.0_k_T__1750';
+
+PARTITION = '/misc/gyacomo23_outputs/paper_3/DIIID_rho_95_Tstudy/';
+% resdir = 'multi_scale_3x2x512x128x24';
+% resdir = 'multi_scale_3x2x512x128x24_larger_box';
+% resdir = 'multi_scale_3x2x768x192x24/continue_with_gradN_and_tau';
+% resdir = 'multi_scale/multi_scale_5x2x768x192x24/PT';
+% resdir = 'NT';
+% resdir = 'electron_scale_3x2x256x64x24';
+% resdir = 'electron_scale_3x2x128x64x24';
+% resdir = 'ion_scale_3x2x192x48x32_larger_box';
+% resdir = 'ion_scale_3x2x256x64x32'; % PT and NT also
+% resdir = 'ion_scale/ion_scale_5x2x256x64x32_tau_1_RN_0/NT';
+% resdir = 'adiab_e/5x2x256x64x32_tau_1_RN_0/NT';
+
+resdir = 'multi_scale/multi_scale_3x2x768x192x24/NT';
+% resdir = 'multi_scale/multi_scale_3x2x512x128x24_larger_box/NT';
+% resdir = 'multi_scale/multi_scale_3x2x768x192x24/continue_with_gradN_and_tau';
+% resdir = 'ion_scale/ion_scale_5x2x256x64x32_tau_1_RN_0/NT';
+% resdir = 'adiab_e/5x2x256x64x32_tau_1_RN_0/0T';
+% resdir = 'hot_electrons/hot_electrons_256x64x24/0T';
+
+
+
+% PARTITION = '/misc/gyacomo23_outputs/paper_3/';
+% resdir = 'DIIID_HEL_rho95/PT';
+
DATADIR = [PARTITION,resdir,'/'];
+%%
+J0 = 00; J1 = 20;
+
+% Load basic info (grids and time traces)
data = {};
data = compile_results_low_mem(data,DATADIR,J0,J1);
-
+[data.Na00, data.Ts3D] = compile_results_3Da(DATADIR,J0,J1,'Na00');
+data.Ni00 = reshape(data.Na00(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+try
+data.Ne00 = reshape(data.Na00(2,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+catch
+end
+[data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
+if 1
+ %%
+[data.TEMP, data.Ts3D] = compile_results_3Da(data.folder,J0,J1,'temp');
+% [data.UPAR, data.Ts3D] = compile_results_3Da(data.folder,J0,J1,'upar');
+[data.DENS, data.Ts3D] = compile_results_3Da(data.folder,J0,J1,'dens');
+data.TEMP_I = reshape(data.TEMP(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+% data.UPAR_I = reshape(data.UPAR(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+data.DENS_I = reshape(data.DENS(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+data.Ni00 = reshape(data.Na00(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+if data.inputs.Na > 1
+ data.TEMP_E = reshape(data.TEMP(2,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+ data.DENS_E = reshape(data.DENS(2,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+ data.Ne00 = reshape(data.Na00(2,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+end
+end
if 1
%% Plot transport and phi radial profile
-[data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
+% [data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
% [data.PSI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'psi');
-options.TAVG_0 = 100;
-options.TAVG_1 = 1000;
+options.TAVG_0 = data.Ts3D(end)/2;
+options.TAVG_1 = data.Ts3D(end);
options.NCUT = 5; % Number of cuts for averaging and error estimation
options.NMVA = 1; % Moving average for time traces
% options.ST_FIELD = '\Gamma_x'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
+% options.ST_FIELD = 'n_e'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
+% options.ST_FIELD = 'u_i'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
+% options.ST_FIELD = 'T_i'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
+% options.ST_FIELD = 'n_i T_i'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
options.ST_FIELD = '\phi'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
+% options.ST_FIELD = 'Q_{xi}'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
+% options.ST_FIELD = 'G_x'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
+% options.ST_FIELD = 'w_{Ez}'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
+% options.ST_FIELD = 'v_{Ey}'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
+% options.ST_FIELD = 'N_i^{00}'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
options.INTERP = 0;
options.RESOLUTION = 256;
plot_radial_transport_and_spacetime(data,options);
end
-if 0
-%% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Options
-[data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
-[data.Na00, data.Ts3D] = compile_results_3Da(DATADIR,J0,J1,'Na00');
-data.Ni00 = reshape(data.Na00(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
-options.INTERP = 1;
-options.POLARPLOT = 0;
-options.BWR = 0; % bluewhitered plot or gray
-options.CLIMAUTO = 1; % adjust the colormap auto
-% options.NAME = '\phi';
-% options.NAME = '\phi^{NZ}';
-% options.NAME = '\omega_z';
-options.NAME = 'N_i^{00}';
-% options.NAME = 's_{Ey}';
-% options.NAME = 'n_i^{NZ}';
-% options.NAME = 'Q_x';
-% options.NAME = 'n_i';
-% options.NAME = 'n_i-n_e';
-options.PLAN = 'kxky';
-% options.NAME = 'f_i';
-% options.PLAN = 'sx';
-options.COMP = 'avg';
-% options.TIME = data.Ts5D(end-30:end);
-options.TIME = data.Ts3D(1:1:end);
-% options.TIME = [0:1500];
-data.EPS = 0.1;
-data.a = data.EPS * 2000;
-options.RESOLUTION = 256;
-create_film(data,options,'.gif')
-end
-
-if 0
-%% field snapshots
+if 1
+%% 2D field snapshots
% Options
-[data.Na00, data.Ts3D] = compile_results_3Da(data.folder,J0,J1,'Na00');
-[data.PHI, data.Ts3D] = compile_results_3D(data.folder,J0,J1,'phi');
-data.Ni00 = reshape(data.Na00(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
-
options.INTERP = 0;
options.POLARPLOT = 0;
options.AXISEQUAL = 0;
options.NORMALIZE = 0;
options.LOGSCALE = 0;
options.CLIMAUTO = 1;
-options.NAME = 'N_i^{00}';
-% options.NAME = 's_{Ey}';
+options.TAVG = 1;
+% options.NAME = ['N_e^{00}'];
+% options.NAME = 'n_e';
+% % options.NAME = 'u_i';
+% options.NAME = 'T_i';
+% options.NAME = 'Q_{xe}';
+options.NAME = 'v_{Ey}';
+% options.NAME = 'w_{Ez}';
+% options.NAME = '\omega_z';
% options.NAME = '\phi';
-options.PLAN = 'yz';
-options.COMP = 'avg';
-options.TIME = [50 100];
-% options.TIME = data.Ts3D(1:2:end);
+% options.NAME = 'n_i-n_e';
+loc =11;
+[~,i_] = min(abs(loc - data.grids.y));
+options.COMP =i_;
+% options.PLAN = '3D';
+options.PLAN = 'xy'; options.COMP =floor(data.grids.Nz/2)+1;
+% options.PLAN = 'yz'; options.COMP ='avg';
+% options.COMP ='avg';
+options.XYZ =[-11 20 0];
+options.TIME = [90:150];
options.RESOLUTION = 256;
fig = photomaton(data,options);
-colormap(gray)
+% colormap(gray)
clim('auto')
% save_figure(data,fig)
end
@@ -107,42 +187,147 @@ if 0
profiler(data)
end
-if 0
+if 1
+%% Mode evolution
+% [data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
+% [data.Na00, data.Ts3D] = compile_results_3Da(DATADIR,J0,J1,'Na00');
+% data.Ni00 = reshape(data.Na00(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+% data.Ne00 = reshape(data.Na00(2,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+
+options.NORMALIZED = 0;
+options.TIME = data.Ts3D;
+options.KX_TW = [0.1 2.5]; %kx Growth rate time window
+options.KY_TW = [0.1 2.5]; %ky Growth rate time window
+options.NMA = 1;
+options.NMODES = 64;
+options.iz = 'avg'; % avg or index
+options.ik = 1; % sum, max or index
+options.fftz.flag = 0;
+options.FIELD = 'Ni00';
+% options.FIELD = 'phi';
+% options.FIELD = 'T_i';
+options.GOK2 = 0;
+options.SHOWFIG = 1;
+[fig, wkykx, ekykx] = mode_growth_meter(data,options);
+%%
+kx = (1:data.grids.Nx/2)'*2*pi/data.fort_00.GRID.Lx;
+ky = (1:data.grids.Ny/2)'*2*pi/data.fort_00.GRID.Ly;
+gkxky = real(wkykx(2:end,1:data.grids.Nx/2))';
+gkxky(isnan(gkxky)) =0;
+gkxky(isinf(gkxky)) =0;
+% gkxky(gkxky<0) =0;
+% gkxky = imgaussfilt(gkxky,1);
+%
+wkxky = imag(wkykx(2:end,1:data.grids.Nx/2))';
+wkxky(isnan(wkxky)) =0;
+wkxky(isinf(wkxky)) =0;
+% wkxky(wkxky<0) =0;
+% wkxky = imgaussfilt(wkxky,1.5);
+%
+figure;
+subplot(121)
+ contourf(kx,ky,gkxky',10)
+ % clim(0.5*[0 1]);
+ % colormap(bluewhitered); colorbar;
+ xlim([0.025 1]);
+ xlabel('$k_x\rho_s$'); ylabel('$k_y\rho_s$')
+subplot(122)
+ contourf(kx,ky,wkxky',10)
+ % clim(1*[0 1]);
+ % colormap(bluewhitered); colorbar
+ xlim([0.025 1]);
+ xlabel('$k_x\rho_s$'); ylabel('$k_y\rho_s$')
+% save_figure(data,fig,'.png')
+end
+
+if 1
%% Hermite-Laguerre spectrum
-[data.Napjz, data.Ts3D] = compile_results_3Da(DATADIR,J0,J1,'Napjz');
+[data.Napjz, data.Ts3D] = compile_results_3Da(DATADIR,0,10,'Napjz');
% [data.Napjz, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'Nipjz');
-options.ST = 0;
+options.ST = 1;
options.NORMALIZED = 0;
-options.LOGSCALE = 1;
+options.LOGSCALE = 0;
options.FILTER = 0; %filter the 50% time-average of the spectrum from
options.TAVG_2D = 0; %Show a 2D plot of the modes, 50% time averaged
options.TAVG_2D_CTR= 0; %make it contour plot
+options.TWINDOW = [6 20];
fig = show_moments_spectrum(data,options);
end
-if 0
-%% Mode evolution
-[data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
-[data.Na00, data.Ts3D] = compile_results_3Da(DATADIR,J0,J1,'Na00');
-data.Ni00 = reshape(data.Na00(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+if (0 && NZ>4)
+%% Ballooning plot
+% [data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
+if data.inputs.BETA > 0
+[data.PSI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'psi');
+end
+options.time_2_plot = [25 100];
+options.kymodes = 1.5;
+options.normalized = 1;
+options.PLOT_KP = 0;
+% options.field = 'phi';
+options.SHOWFIG = 1;
+[fig, chi, phib, psib, ~] = plot_ballooning(data,options);
+end
-options.NORMALIZED = 0;
-options.TIME = data.Ts3D;
-options.KX_TW = [ 0 20]; %kx Growth rate time window
-options.KY_TW = [ 0 50]; %ky Growth rate time window
-options.NMA = 1;
-options.NMODES = 50;
-options.iz = 'avg'; % avg or index
-options.ik = 9; % sum, max or index
-options.fftz.flag = 0;
-% options.FIELD = 'Ni00';
-options.FIELD = 'phi';
-options.GOK2 = 0;
-fig = mode_growth_meter(data,options);
-% save_figure(data,fig,'.png')
+if 1
+%% 1D spectral plot
+options.TIME = [30 80]; % averaging time window
+% options.NAME = ['N_i^{00}'];
+% options.NAME = 'n_i';
+% options.NAME = 'T_i';
+% options.NAME = 'Q_{xi}';
+% options.NAME = 's_{Ey}';
+options.NAME = '\psi';
+options.NORMALIZE = 0;
+[fig] = plot_spectrum(data,options);
end
+if 0
+%% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Options
+% [data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
+% [data.PSI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'psi');
+% [data.Na00, data.Ts3D] = compile_results_3Da(DATADIR,J0,J1,'Na00');
+% data.Ni00 = reshape(data.Na00(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+% data.Ne00 = reshape(data.Na00(2,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+% [data.DENS, data.Ts3D] = compile_results_3Da(DATADIR,J0,J1,'dens');
+% data.DENS_I = reshape(data.DENS(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+% [data.TEMP, data.Ts3D] = compile_results_3Da(DATADIR,J0,J1,'temp');
+% data.TEMP_I = reshape(data.TEMP(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+options.INTERP = 0;
+options.POLARPLOT = 0;
+options.BWR = 1; % bluewhitered plot or gray
+options.CLIMAUTO = 0; % adjust the colormap auto
+% options.NAME = '\phi';
+% options.NAME = 'w_{Ez}';
+% options.NAME = '\psi';
+options.NAME = 'T_i';
+% options.NAME = '\phi^{NZ}';
+% options.NAME = ['N_e^{00}'];
+% options.NAME = ['N_i^{00}'];
+options.PLAN = 'xy';
+% options.PLAN = '3D';
+% options.XYZ =[-11 20 0];
+% options.COMP = 'avg';
+options.COMP = floor(data.grids.Nz/2+1);
+options.TIME = data.Ts3D(1:1:end);
+% options.TIME = [0:1500];
+data.EPS = 0.1;
+data.a = data.EPS * 2000;
+options.RESOLUTION = 256;
+options.FPS = 12;
+options.RMAXIS = 0;
+create_film(data,options,'.gif');
+end
+
+if 0
+%% Metric infos
+options.SHOW_FLUXSURF = 1;
+options.SHOW_METRICS = 1;
+[fig, geo_arrays] = plot_metric(data,options);
+end
+
if 0
%% Study singular values
[data.SV_ky_pj, data.Ts2D] = compile_results_2D(DATADIR,J0,J1,'sv_ky_pj');
diff --git a/wk/lin_run_script.m b/wk/lin_run_script.m
index f872fc8767ddeeb77a2475406efafb4050956861..7e0eb7271fab42b84a51e3fea2c12c986b5eee4b 100644
--- a/wk/lin_run_script.m
+++ b/wk/lin_run_script.m
@@ -27,15 +27,17 @@ EXECNAME = 'gyacomo23_dp'; % double precision
% run lin_DTT_HM_rho98
% run lin_DIIID_LM_rho90
% run lin_DIIID_LM_rho95
+% run lin_DIIID_LM_rho95_HEL
% run lin_JET_rho97
% run lin_Entropy
% run lin_ITG
% run lin_KBM
% run lin_RHT
-rho = 0.95; TRIANG = 'NT'; READPROF = 0;
-prof_folder = ['parameters/profiles/DIIID_Austin_et_al_2019/',TRIANG,'/'];
+% run lin_Ivanov
+rho = 0.95; TRIANG = 'NT'; READPROF = 1;
+% prof_folder = ['parameters/profiles/DIIID_Austin_et_al_2019/',TRIANG,'/'];
% prof_folder = ['parameters/profiles/DIIID_Oak_Nelson/',TRIANG,'/'];
-% prof_folder = ['parameters/profiles/DIIID_Oak_Nelson_high_density/',TRIANG,'/'];
+prof_folder = ['parameters/profiles/DIIID_Oak_Nelson_high_density/',TRIANG,'/'];
run lin_DIIID_data
% run lin_STEP_EC_HD_psi71
% run lin_STEP_EC_HD_psi49
@@ -43,47 +45,31 @@ if 1
% Plot the profiles
plot_params_vs_rho(geom,prof_folder,rho,0.5,1.1,Lref,mref,Bref,READPROF);
end
+% SIMID = ['rho_scan_DIIID_AUSTIN_2019/3x2x192x96x32/rho',num2str(rho)];
%% Change parameters
-% EXBRATE = 0.0; % Background ExB shear flow
-% K_Ti = 5.3;
-% NU = 0.001;
-CO = 'LD';
-GKCO = 1;
-kymin= 0.3; LY = 2*pi/kymin;
+% GEOMETRY = 's-alpha';
+DELTA =0.0;
+K_Ni = 0; K_Ne = 0;
+% DELTA = 0.0;
+% DELTA = 0.2;
+S_DELTA = DELTA/2;
+LY = 2*pi/0.25;
+TMAX = 20;
NY = 2;
-NX = 4;
-NZ = 32;
-PMAX = 2;
-JMAX = PMAX/2;
-DT = 20e-4;
-EXBRATE = 0;
-% EPS = 0.25;
-% KAPPA = 1.0;
-S_DELTA = min(2.0,S_DELTA);
-% DELTA = -DELTA;
-% PT parameters
-% TAU = 5.45;
-% K_Ne = 0; %vs 2.79
-% K_Ni = 0;
-% K_Te = 9.6455;%vs 17.3
-% K_Ti = 3.3640;%vs 5.15
-% BETA = 7.9e-4;
-% NU = 0.1;
-MU_X = 0.0; MU_Y = 0.0;
-SIGMA_E = 0.04;
-TMAX = 1;
-% DTSAVE0D = 200*DT;
-DTSAVE3D = 0.1;
-%%-------------------------------------------------------------------------
+DT = 0.01;
+TAU = 1; NU = 0.05;
+% TAU = 1e-3; K_Ti = K_Ti/2/TAU; NU = 3*NU/8/TAU; ADIAB_E = 1; NA = 1;
+% MU_X = 1; MU_Y = 1;
%% RUN
setup
+system(['cp ../results/',SIMID,'/',PARAMS,'/fort_00.90 ../results/',SIMID,'/.']);
% system(['rm fort*.90']);
% Run linear simulation
if RUN
MVIN =['cd ../results/',SIMID,'/',PARAMS,'/;'];
% RUN =['time ',mpirun,' -np 2 ',gyacomodir,'bin/',EXECNAME,' 1 2 1 0;'];
- RUN =['time ',mpirun,' -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 2 2 0;'];
- % RUN =['time ',mpirun,' -np 6 ',gyacomodir,'bin/',EXECNAME,' 3 2 1 0;'];
+ RUN =['time ',mpirun,' -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 4 1 0;'];
+ % RUN =['time ',mpirun,' -np 4 ',gyacomodir,'bin/',EXECNAME,' 2 2 1 0;'];
% RUN =['time ',mpirun,' -np 8 ',gyacomodir,'bin/',EXECNAME,' 2 2 2 0;'];
% RUN =['time ',mpirun,' -np 1 ',gyacomodir,'bin/',EXECNAME,' 1 1 1 0;'];
% RUN = ['./../../../bin/gyacomo23_sp 0;'];
@@ -102,15 +88,15 @@ data = {}; % Initialize data as an empty cell array
% load grids, inputs, and time traces
data = compile_results_low_mem(data,LOCALDIR,J0,J1);
-if 0 % Activate or not
+if 1 % Activate or not
%% plot mode evolution and growth rates
% Load phi
[data.PHI, data.Ts3D] = compile_results_3D(LOCALDIR,J0,J1,'phi');
options.NORMALIZED = 0;
options.TIME = data.Ts3D;
% Time window to measure the growth of kx/ky modes
-options.KY_TW = [0.5 1.0]*data.Ts3D(end);
-options.KX_TW = [0.5 1.0]*data.Ts3D(end);
+options.KY_TW = [0.25 1.0]*data.Ts3D(end);
+options.KX_TW = [0.25 1.0]*data.Ts3D(end);
options.NMA = 1; % Set NMA option to 1
options.NMODES = 999; % Set how much modes we study
options.iz = 'avg'; % Compressing z
@@ -118,8 +104,38 @@ options.ik = 1; %
options.GOK2 = 0; % plot gamma/k^2
options.fftz.flag = 0; % Set fftz.flag option to 0
options.FIELD = 'phi';
-options.SHOWFIG = 1;
-[fig, kykx, wkykx, ekykx] = mode_growth_meter(data,options); % Call the function mode_growth_meter with data and options as input arguments, and store the result in fig
+options.SHOWFIG = 1;
+[fig, wkykx, ekykx] = mode_growth_meter(data,options);
+% %%
+% kx = (1:data.grids.Nx/2)'*2*pi/data.fort_00.GRID.Lx;
+ky = (1:data.grids.Ny/2)'*2*pi/data.fort_00.GRID.Ly;
+gkxky = real(wkykx(2:end,1:data.grids.Nx/2))';
+gkxky(isnan(gkxky)) =0;
+gkxky(isinf(gkxky)) =0;
+figure; plot(ky,gkxky(1,:));
+% gkxky(gkxky<0) =0;
+% % gkxky = imgaussfilt(gkxky,1);
+% %
+% wkxky = imag(wkykx(2:end,1:data.grids.Nx/2))';
+% wkxky(isnan(wkxky)) =0;
+% wkxky(isinf(wkxky)) =0;
+% % wkxky(wkxky<0) =0;
+% % wkxky = imgaussfilt(wkxky,1.5);
+% %
+% figure;
+% subplot(121)
+% contourf(kx,ky,gkxky',10)
+% % clim(0.5*[0 1]);
+% % colormap(bluewhitered); colorbar;
+% xlim([0.025 1]);
+% xlabel('$k_x\rho_s$'); ylabel('$k_y\rho_s$')
+% subplot(122)
+% contourf(kx,ky,wkxky',10)
+% % clim(1*[0 1]);
+% % colormap(bluewhitered); colorbar
+% xlim([0.025 1]);
+% xlabel('$k_x\rho_s$'); ylabel('$k_y\rho_s$')
+% % save_figure(data,fig,'.png')
end
if (0 && NZ>4)
@@ -144,13 +160,13 @@ ikx = 2; iky = 1; t0 = 1; t1 = data.Ts3D(end);
[~, it0] = min(abs(t0-data.Ts3D));[~, it1] = min(abs(t1-data.Ts3D));
plt = @(x) squeeze(mean(real(x(iky,ikx,:,it0:it1)),3))./squeeze(mean(real(x(iky,ikx,:,it0)),3));
t_ = data.Ts3D(it0:it1);
-% TH = 1.635*EPS^1.5 + 0.5*EPS^2+0.35*EPS^2.5; theory = 1/(1+Q0^2*TH/EPS^2);
+TH = 1.635*EPS^1.5 + 0.5*EPS^2+0.36*EPS^2.5; theory = 1/(1+Q0^2*TH/EPS^2);
clr_ = lines(20);
figure
-plot(t_, plt(data.PHI)); hold on;
+plot(t_, -plt(data.PHI)); hold on;
plot(t_,0.5* exp(-t_*NU)+theory,'--k');
plot([t_(1) t_(end)],theory*[1 1],'-k');
-plot([t_(1) t_(end)],mean(plt(data.PHI))*[1 1],'-g');
+plot([t_(1) t_(end)],-mean(plt(data.PHI))*[1 1],'-g');
xlabel('$t$'); ylabel('$\phi_z(t)/\phi_z(0)$')
title(sprintf('$k_x=$%2.2f, $k_y=$%2.2f',data.grids.kx(ikx),data.grids.ky(iky)))
end
@@ -160,7 +176,7 @@ if 0
plot_metric(data);
end
-if 1
+if 0
%% Compiled plot for lin EM analysis
[data.PHI, data.Ts3D] = compile_results_3D(LOCALDIR,J0,J1,'phi');
if data.inputs.BETA > 0
@@ -185,16 +201,22 @@ if 1
options.FIELD = 'phi';
options.SHOWFIG = 0;
[~, chi, phib, psib, ~] = plot_ballooning(data,options);
- [~, kykx, wkykx, ekykx] = mode_growth_meter(data,options); % Call the function mode_growth_meter with data and options as input arguments, and store the result in fig
+ [fig, wkykx, ekykx] = mode_growth_meter(data,options);
+ kx = (1:data.grids.Nx/2)'*2*pi/data.fort_00.GRID.Lx;
+ ky = (1:data.grids.Ny/2)'*2*pi/data.fort_00.GRID.Ly;
[~,~,R,Z] = plot_metric(data,options);
figure;
subplot(3,2,1); plot(chi,real(phib),'-b'); hold on;
plot(chi,imag(phib),'-r'); xlabel('$\chi$'); ylabel('$\phi$')
subplot(3,2,3); plot(chi,real(psib),'-b'); hold on;
plot(chi,imag(psib),'-r'); xlabel('$\chi$'); ylabel('$\psi$')
- subplot(3,2,5); plot(squeeze(kykx(:,1)),squeeze(real(wkykx(:,1))),'o--'); hold on;
- plot(squeeze(kykx(:,1)),squeeze(imag(wkykx(:,1))),'o--');
- xlabel('$k_y\rho_s$'); ylabel('$\gamma,\omega$');
+ subplot(3,2,5); errorbar(ky,squeeze(real(wkykx(2:end,1))),...
+ squeeze(real(ekykx(2:end,1))),...
+ 'ok--','MarkerSize',8,'LineWidth',1.5); hold on;
+ errorbar(ky,squeeze(imag(wkykx(2:end,1))),...
+ squeeze(imag(ekykx(2:end,1))),...
+ '*k--','MarkerSize',8,'LineWidth',1.5);
+ xlabel('$k_y\rho_s$'); ylabel('$\gamma (o),\,\omega (*)$');
R = R*geom.R0; Z = Z*geom.R0;
subplot(1,2,2); plot(R,Z,'-k'); xlabel('$R$'); ylabel('$Z$');
axis equal
diff --git a/wk/lin_scan_script.m b/wk/lin_scan_script.m
index bf36d44d2d156a2c46e53834f47edaa055c7b349..3883f0e9b4fff3be942ca2dc74e8f14c0b89dbbc 100644
--- a/wk/lin_scan_script.m
+++ b/wk/lin_scan_script.m
@@ -28,24 +28,29 @@ EXECNAME = 'gyacomo23_dp'; % double precision
% run lin_Entropy
% run lin_ITG
% run lin_RHT
-rho = 0.95; TRIANG = 'NT'; READPROF = 1;
+rho = 0.95; TRIANG = 'PT'; READPROF = 1;
% prof_folder = ['parameters/profiles/DIIID_Austin_et_al_2019/',TRIANG,'/'];
% prof_folder = ['parameters/profiles/DIIID_Oak_Nelson/',TRIANG,'/'];
prof_folder = ['parameters/profiles/DIIID_Oak_Nelson_high_density/',TRIANG,'/'];
run lin_DIIID_data
%% Change parameters
-NU = 1;
-TAU = 1;
+% NU = 1;
+% TAU = 1;
NY = 2;
EXBRATE = 0;
+S_DELTA = min(2.0,S_DELTA);
SIGMA_E = 0.023;
+NEXC = 0;
+LX = 120;
%% Scan parameters
SIMID = [SIMID,'_scan'];
P_a = [2 4];
% P_a = 2;
-ky_a = [0.01 0.02 0.05 0.1 0.2 0.5 1.0 2.0 5.0 10.0];
-CO = 'LD';
+ky_a = [0.01 0.02 0.05 0.1 0.2 0.5 1.0 2.0 5.0 10.0];
+% ky_a = 4.0;
+dt_a = logspace(-2,-3,numel(ky_a));
+CO = 'DG';
%% Scan loop
% arrays for the result
g_ky = zeros(numel(ky_a),numel(P_a));
@@ -58,10 +63,10 @@ for PMAX = P_a
i = 1;
for ky = ky_a
LY = 2*pi/ky;
- DT = 2e-4;%/(1+log(ky/0.05));%min(1e-2,1e-3/ky);
- TMAX = 20;%min(10,1.5/ky);
- DTSAVE0D = 0.1;
- DTSAVE3D = 0.01;
+ DT = dt_a(i);%1e-3;%/(1+log(ky/0.05));%min(1e-2,1e-3/ky);
+ TMAX = DT*10000;%2;%min(10,1.5/ky);
+ DTSAVE0D = 100*DT;
+ DTSAVE3D = 10*DT;
%% RUN
setup
% naming
@@ -94,21 +99,27 @@ for PMAX = P_a
data_ = compile_results_low_mem(data_,LOCALDIR,00,00);
[data_.PHI, data_.Ts3D] = compile_results_3D(LOCALDIR,00,00,'phi');
-
- % linear growth rate (adapted for 2D zpinch and fluxtube)
- options.TRANGE = [0.5 1]*data_.Ts3D(end);
- options.NPLOTS = 0; % 1 for only growth rate and error, 2 for omega local evolution, 3 for plot according to z
- options.GOK = 0; %plot 0: gamma 1: gamma/k 2: gamma^2/k^3
-
- [~,it1] = min(abs(data_.Ts3D-0.5*data_.Ts3D(end))); % start of the measurement time window
- [~,it2] = min(abs(data_.Ts3D-1.0*data_.Ts3D(end))); % end of ...
- [wkykx,ekykx] = compute_growth_rates(data_.PHI(:,:,:,it1:it2),data_.Ts3D(it1:it2));
+ options.NORMALIZED = 0;
+ options.TIME = data_.Ts3D;
+ % Time window to measure the growth of kx/ky modes
+ options.KY_TW = [0.7 1.0]*data_.Ts3D(end);
+ options.KX_TW = [0.7 1.0]*data_.Ts3D(end);
+ options.NMA = 1; % Set NMA option to 1
+ options.NMODES = 999; % Set how much modes we study
+ options.iz = 'avg'; % Compressing z
+ options.ik = 1; %
+ options.GOK2 = 0; % plot gamma/k^2
+ options.fftz.flag = 0; % Set fftz.flag option to 0
+ options.FIELD = 'phi';
+ options.SHOWFIG = 0;
+ [fig, wkykx, ekykx] = mode_growth_meter(data_,options);
+ % [wkykx,ekykx] = compute_growth_rates(data_.PHI(:,:,:,it1:it2),data_.Ts3D(it1:it2));
g_ky (i,j) = real(wkykx(2,1));
g_std(i,j) = real(ekykx(2,1));
w_ky (i,j) = imag(wkykx(2,1));
w_std(i,j) = imag(ekykx(2,1));
[gmax, ikmax] = max(g_ky(i,j));
-
+
msg = sprintf('gmax = %2.2f, kmax = %2.2f',gmax,data_.grids.ky(ikmax)); disp(msg);
end
i = i + 1;
diff --git a/wk/load_metadata_scan.m b/wk/load_metadata_scan.m
index a9df5c95be4a524979dbae0448bf4f1f2461c3c2..89db4acbe3035dde9e6d5f3226eba85105138ded 100644
--- a/wk/load_metadata_scan.m
+++ b/wk/load_metadata_scan.m
@@ -11,7 +11,7 @@ addpath(genpath([gyacomodir,'matlab/load'])) % ... add% EXECNAME = 'gyacomo_1.0'
% datafname = 'lin_DIIID_Oak_Nelson_high_density_NT_scan/6x32_ky_0.01_10_P_2_8_kN_1.0883_LDGK_0.0080915_be_0.0015991.mat';
% rho = 0.95
% datagname = 'lin_DIIID_Oak_Nelson_high_density_PT_scan/6x32_ky_0.01_10_P_2_8_kN_0.62888_LDGK_0.0046858_be_0.0048708.mat';
-datafname = 'lin_DIIID_Oak_Nelson_high_density_NT_scan/6x32_ky_0.01_10_P_2_8_kN_1.6989_LDGK_0.0167_be_0.00075879.mat';
+datafname = 'lin_DIIID_Oak_Nelson_high_density_PT_scan/6x32_ky_0.01_10_P_2_4_kN_0.62888_DGGK_0.0046858_be_0.0048708.mat';
%% Chose if we filter gamma>0.05
FILTERGAMMA = 1;
diff --git a/wk/old scripts/p3_geom_scan_analysis.m b/wk/old scripts/p3_geom_scan_analysis.m
new file mode 100644
index 0000000000000000000000000000000000000000..1c63315622f6a2a84a842307f9f66e86d04c9a7f
--- /dev/null
+++ b/wk/old scripts/p3_geom_scan_analysis.m
@@ -0,0 +1,306 @@
+% Get the current directory (wk)
+curdir = pwd;
+NCONTOUR = 0;
+% give ref value and param names
+REFVAL= 0;
+% normalize to the max all data
+NORM_ALL= 0;
+% normalize to the max each line
+NORM_LIN= 0;
+% normalize to the max each column
+NORM_COL= 0;
+% Get and plot the fluxsurface
+GETFLUXSURFACE = 0;
+
+% partition= '../results/paper_3/';
+% Get the scan directory
+switch 6
+ case 1 % delta kappa scan
+ casename = 'DTT rho85';
+ partition= '/misc/gyacomo23_outputs/paper_3/DTT_rho85_geom_scan/';
+ scandir = 'P2_J1_delta_kappa_scan'; scanname= '(2,1)';
+ % scandir = 'P4_J2_delta_kappa_scan'; scanname= '(4,2)';
+ nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0.23; scale1 =1.0;
+ nml2 = 'GEOMETRY'; pnam2 = '$\kappa$'; attr2 = 'kappa'; pref2 = 1.53; scale2 =1.0;
+ t1 = 50; t2 = 150;
+ case 2 % shear safety factor scan
+ casename = 'DTT rho85';
+ partition= '/misc/gyacomo23_outputs/paper_3/DTT_rho85_geom_scan/';
+ scandir = 'P2_J1_PT_sfact_shear_scan'; scanname= '(2,1)';
+ % scandir = 'P2_J1_NT_sfact_shear_scan'; scanname= '(2,1)';
+ nml1 = 'GEOMETRY'; pnam1 = '$\hat s$'; attr1 = 'shear'; pref1 = 3.63; scale1 =1.0;
+ nml2 = 'GEOMETRY'; pnam2 = '$q_0$'; attr2 = 'q0'; pref2 =-2.15; scale2 =1.0;
+ t1 = 50; t2 = 150;
+ case 3
+ casename = 'DTT rho85';
+ partition= '/misc/gyacomo23_outputs/paper_3/DTT_rho85_geom_scan/';
+ % scandir = 'P2_J1_delta_nuDGGK_scan'; scanname= 'DG (2,1)';
+ % scandir = 'P4_J2_delta_nuDGGK_scan'; scanname= 'DG (4,2)';
+ % scandir = 'P8_J4_delta_nuDGGK_conv_test'; scanname= 'DG (8,4)';
+ % scandir = 'P2_J1_delta_nuSGGK_scan'; scanname= 'SG (2,1)';
+ % scandir = 'P4_J2_delta_nuSGGK_scan'; scanname= 'SG (4,2)';
+ % scandir = 'P8_J4_delta_nuSGGK_conv_test'; scanname= 'SG (8,4)';
+ % scandir = 'P4_J2_delta_nuSGGKii_scan'; scanname= 'SGii (4,2)';
+ scandir = 'P2_J1_delta_nuLDGK_scan'; scanname= 'LD (2,1)';
+ % scandir = 'P4_J2_delta_nuLDGK_scan'; scanname= 'LD (4,2)';
+ nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0.23; scale1 =1.0;
+ nml2 = 'MODEL'; pnam2 = '$\nu$'; attr2 = 'nu'; pref2 = 0.5; scale2 =1.0;
+ t1 = 50; t2 = 150;
+ case 4 % shear delta scan
+ casename = 'DIIID rho95';
+ partition= '/misc/gyacomo23_outputs/paper_3/DIIID_cold_ions_rho95_geom_scan/';
+ scandir = '3x2x192x48x32_RT_2500_delta_shear_scan'; scanname= 'CI DG RT 2500';
+ % scandir = '3x2x256x64x48_delta_shear_scan';
+ nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0; scale1 =1.0;
+ nml2 = 'GEOMETRY'; pnam2 = '$\hat s$'; attr2 = 'shear'; pref2 = 0.8; scale2 =1.0;
+ t1 = 50; t2 = 150;
+ case 5 % delta K_T tau=1
+ casename = 'DIIID rho95 $\tau=1$';
+ partition= '/misc/gyacomo23_outputs/paper_3/DIIID_tau_1_rho95_geom_scan/';
+ scandir = '3x2x192x48x32_delta_RT_scan'; scanname= '(2,1)';
+ % scandir = '5x3x192x48x32_delta_RT_scan'; scanname= '(4,2)';
+ % scandir = 'delta_RT_scan_PJ_21'; scanname= '(2,1)';
+ nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0; scale1 =1.0;
+ nml2 = 'SPECIES'; pnam2 = '$R_0/L_T\times T_i/T_e$'; attr2 = 'K_T_'; pref2 = 0.8; scale2 =1.0;
+ t1 = 200; t2 = 500;
+ case 6 % delta K_T cold ions
+ casename = 'DIIID rho95 $\tau=10^{-3}$';
+ partition= '/misc/gyacomo23_outputs/paper_3/DIIID_cold_ions_rho95_geom_scan/';
+ scandir = '3x2x192x48x32_delta_RT_scan'; scanname= '(2,1)';
+ nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0; scale1 =1.0;
+ nml2 = 'SPECIES'; pnam2 = '$R_0/L_T\times T_i/T_e$'; attr2 = 'K_T_'; pref2 = 0.8; scale2 =1e3/2;
+ t1 = 200; t2 = 480;
+ case 7 % delta s_delta
+ casename = 'DIIID rho95 $\tau=10^{-3}$';
+ partition= '/misc/gyacomo23_outputs/paper_3/DIIID_cold_ions_rho95_geom_scan/';
+ scandir = '3x2x192x48x32_RT_1000_delta_sdelta_scan'; scanname= 'RT=1000 (2,1)';
+ % scandir = '';
+ nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0; scale1 =1.0;
+ nml2 = 'GEOMETRY'; pnam2 = '$s_\delta$'; attr2 = 's_delta'; pref2 = 0.8; scale2 =1.0;
+ t1 = 200; t2 = 295;
+ case 8 % eps q0
+ casename = 'DIIID rho95 $\tau=10^{-3}$';
+ partition= '/misc/gyacomo23_outputs/paper_3/DIIID_cold_ions_rho95_geom_scan/';
+ scandir = '3x2x192x48x32_RT_1000_eps_q0_scan/PT'; scanname= 'PT, RT=1000 (2,1)';
+ % scandir = '3x2x192x48x32_RT_1000_eps_q0_scan/NT'; scanname= 'NT, RT=1000 (2,1)';
+ % scandir = '';
+ nml1 = 'GEOMETRY'; pnam1 = '$\epsilon$'; attr1 = 'eps'; pref1 = 0; scale1 =1.0;
+ nml2 = 'GEOMETRY'; pnam2 = '$q_0$'; attr2 = 'q0'; pref2 = 0; scale2 =1.0;
+ t1 = 200; t2 = 400;
+ case 9 % CBC Dimits shift
+ casename = 'HEL CBC';
+ partition= '/misc/gyacomo23_outputs/paper_3/HEL_CBC/';
+ scandir = '128x32x24'; scanname= 'CBC HEL';
+ nml1 = 'SPECIES'; pnam1 = '$R_T$'; attr1 = 'k_T_'; pref1 = 0; scale1 =1.0;
+ nml2 = 'SPECIES'; pnam2 = '$R_N$'; attr2 = 'k_N_'; pref2 = 0; scale2 =1.0;
+ t1 = 1000; t2 = 2000;
+end
+scanname= [casename scanname];
+scandir = [partition,scandir,'/'];
+% Get a list of all items in the current directory
+contents = dir(scandir);
+
+% Iterate through the contents
+Qxavg = []; Qxerr = []; para1 = []; para2 = []; R = []; Z = [];
+Qxt = struct();
+for i = 1:length(contents)
+ % Check if the item is a directory and not '.' or '..'
+ if contents(i).isdir && ~strcmp(contents(i).name, '.') ...
+ && ~strcmp(contents(i).name, '..')
+ % Get and display the name of the subdirectory
+ subdir = [scandir,contents(i).name];
+ disp(['Subdirectory: ' contents(i).name]);
+ % Get parameters
+ param = read_namelist([subdir,'/fort_00.90']);
+ para1 = [para1 param.(nml1).(attr1)];
+ para2 = [para2 param.(nml2).(attr2)];
+ % Now you are in the subdirectory. You can perform operations here.
+ [t_all, Pxi_all, Qxi_all, Pxe_all, Qxe_all] = read_flux_out_XX(subdir);
+ if(numel(Qxe_all) > 1)
+ Qxtot = Qxi_all+Qxe_all;
+ else
+ Qxtot = Qxi_all;
+ end
+ Qxt.(['dat_',num2str(i)]) = struct();
+ Qxt.(['dat_',num2str(i)]).Qx = Qxtot;
+ Qxt.(['dat_',num2str(i)]).t = t_all;
+ Qxt.(['dat_',num2str(i)]).name = contents(i).name;
+ if(numel(t_all) > 1)
+ disp(num2str(t_all(end)))
+ [~,it1] = min(abs(t_all-t1));
+ [~,it2] = min(abs(t_all-t2));
+ steady_slice = it1:it2;
+ if(t_all(end) >= t2)
+ [fullAvg,sliceAvg,sliceErr] = sliceAverage(Qxtot(steady_slice),3);
+ Qxavg = [Qxavg fullAvg];
+ Qxerr = [Qxerr mean(sliceErr)];
+ else
+ Qxavg = [Qxavg nan];
+ Qxerr = [Qxerr nan];
+ end
+ else
+ Qxavg = [Qxavg nan];
+ Qxerr = [Qxerr nan];
+ end
+ end
+ if GETFLUXSURFACE
+ data = load([subdir,'/RZ.txt']);
+ R_ = data(:, 1);
+ Z_ = data(:, 2);
+ R_ = [R_;R_(1)]'; Z_ = [Z_;Z_(1)]';
+ R = [R ; R_]; Z = [Z ; Z_];
+ end
+
+end
+if 0
+%% plot time traces
+attr = fieldnames(Qxt);
+Nsim = numel(attr);
+figure
+% compute growth at the begining
+tw = [10 40];
+gr = 1:Nsim; err = 1:Nsim;
+for i = 1:1:Nsim
+ tmp_ = Qxt.(attr{i});
+ t = tmp_.t;
+ y = tmp_.Qx;
+ plot(t,y,'DisplayName',tmp_.name); hold on;
+ [~,it1] = min(abs(t-tw(1)));
+ [~,it2] = min(abs(t-tw(2)));
+ [gr_, err_] = compute_growth(t(it1:it2),y(it1:it2));
+ gr(i) = gr_; err(i) = err_;
+end
+%%
+toplot = real(reshape(gr,sz))';
+toplot = toplot(idx1,idx2);
+
+figure
+imagesc_custom(xx_,yy_,toplot); hold on
+end
+%% reshaping, sorting and plotting
+p1 = unique(para1)/scale1;
+p2 = unique(para2)/scale2;
+N1 = numel(p1);
+N2 = numel(p2);
+
+if para1(1) == para1(2)
+ sz = [N2 N1];
+ TRANSPOSE = 1;
+else
+ sz = [N1 N2];
+ TRANSPOSE = 0;
+end
+
+Zavg = reshape(Qxavg,sz);
+Zerr = reshape(Qxerr,sz);
+XX = reshape(para1/scale1,sz);
+YY = reshape(para2/scale2,sz);
+
+if TRANSPOSE
+ Zavg = Zavg';
+ Zerr = Zerr';
+ XX = XX';
+ YY = YY';
+end
+
+[~,idx1] = sort(XX(:,1));
+[~,idx2] = sort(YY(1,:));
+Zavg = Zavg(idx1,idx2);
+Zerr = Zerr(idx1,idx2);
+XX = XX(idx1,idx2);
+YY = YY(idx1,idx2);
+
+% compute the
+if REFVAL
+ if NORM_ALL
+ Qxname = '$\bar Q_{tot}/\bar Q_{max}[\%]$';
+ [tmp,iref1] = max(Zavg);
+ [~, iref2] = max(tmp);
+ iref1 = iref1(iref2);
+ else
+ Qxname = '$\langle (Q_{tot}-Q_{ref})/Q_{ref} \rangle_t[\%]$';
+ if pref1 ~= 999
+ [~,iref1] = min(abs(XX(:,1)-pref1));
+ else
+ iref1 = 1:N1;
+ end
+ if pref2 ~= 999
+ [~,iref2] = min(abs(YY(1,:)-pref2));
+ else
+ iref2 = 1:N2;
+ end
+ end
+ iref1 = ones(N1,1).*iref1;
+ iref2 = ones(N2,1).*iref2;
+ xref = XX(iref1,iref2);
+ yref = YY(iref1,iref2);
+ Qxref = Zavg(iref1,iref2);
+ Qrefname = ['$Q_{ref}=$',num2str(Qxref(1,1))];
+else
+ Qref = 1;
+ if NORM_LIN
+ Qxname = '$\bar Q_{tot}/\bar Q_{max}[\%]$, per line';
+ for il = 1:sz(1)
+ maxline = max(Zavg(:,il));
+ Zavg(:,il) = Zavg(:,il)./maxline;
+ Zerr(:,il) = Zerr(:,il)./maxline;
+ end
+ elseif NORM_COL
+ Qxname = '$\bar Q_{tot}/\bar Q_{max}[\%]$, per column';
+ for ic = 1:sz(2)
+ maxcol = max(Zavg(ic,:));
+ Zavg(ic,:) = Zavg(ic,:)./maxcol;
+ Zerr(ic,:) = Zerr(ic,:)./maxcol;
+ end
+ else
+ Qxname = '$\langle Q_{tot} \rangle_t$';
+ end
+end
+
+% Figure
+figure
+subplot(1,2,1)
+[xx_,yy_] = meshgrid(XX(:,1),YY(1,:));
+if REFVAL
+ if NORM_ALL || NORM_COL || NORM_LIN
+ toplot = (Zavg./Qxref)'
+ CLIM = [0 1];
+ else
+ toplot = ((Zavg-Qxref)./Qxref * 100)';
+ CLIM = 'auto';
+ end
+else
+ toplot = Zavg';
+ CLIM = 'auto';
+end
+if NCONTOUR <= 0
+ imagesc_custom(xx_,yy_,toplot); hold on
+else
+ contourf(XX(:,1),YY(1,:),Zavg',NCONTOUR); hold on
+end
+if REFVAL && ~((pref1==999) || (pref2==999))
+ plot(xref(1,1),yref(1,1),'xk','MarkerSize',14,'DisplayName',Qrefname)
+ legend('show')
+end
+xlabel(pnam1); ylabel(pnam2);
+title(scanname)
+colormap(bluewhitered); colorbar; clim(CLIM);
+if ~REFVAL
+ colormap(jet);
+end
+subplot(1,2,2)
+clrs = jet(N2);
+for i = 1:N2
+ errorbar(XX(:,i),Zavg(:,i),Zerr(:,i),...
+ 'DisplayName',[pnam2,'=',num2str(p2(i))],...
+ 'Color',clrs(i,:));
+ hold on;
+end
+if REFVAL && ~((pref1==999) || (pref2==999))
+ plot(xref(1,1),0,'xk','MarkerSize',14,'DisplayName',Qrefname)
+end
+grid on
+xlabel(pnam1); ylabel('$\langle Q_{tot} \rangle_t$');
+legend('show','Location','northwest');
+title([param.COLLISION.collision_model{1}, ...
+ ', $(P,J)=(',num2str(param.GRID.pmax),',',num2str(param.GRID.jmax),')$'])
diff --git a/wk/p3_geom_scan_analysis.m b/wk/p3_geom_scan_analysis.m
index 0ae2554962bbe6fe28fa0ce57bb36140f3c165a3..d81207835636db7190a19f13bcbfc7d9d95f7581 100644
--- a/wk/p3_geom_scan_analysis.m
+++ b/wk/p3_geom_scan_analysis.m
@@ -14,87 +14,38 @@ GETFLUXSURFACE = 0;
% partition= '../results/paper_3/';
% Get the scan directory
-switch 6
- case 1 % delta kappa scan
- casename = 'DTT rho85';
- partition= '/misc/gyacomo23_outputs/paper_3/DTT_rho85_geom_scan/';
- scandir = 'P2_J1_delta_kappa_scan'; scanname= '(2,1)';
- % scandir = 'P4_J2_delta_kappa_scan'; scanname= '(4,2)';
- nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0.23; scale1 =1.0;
- nml2 = 'GEOMETRY'; pnam2 = '$\kappa$'; attr2 = 'kappa'; pref2 = 1.53; scale2 =1.0;
- t1 = 50; t2 = 150;
- case 2 % shear safety factor scan
- casename = 'DTT rho85';
- partition= '/misc/gyacomo23_outputs/paper_3/DTT_rho85_geom_scan/';
- scandir = 'P2_J1_PT_sfact_shear_scan'; scanname= '(2,1)';
- % scandir = 'P2_J1_NT_sfact_shear_scan'; scanname= '(2,1)';
- nml1 = 'GEOMETRY'; pnam1 = '$\hat s$'; attr1 = 'shear'; pref1 = 3.63; scale1 =1.0;
- nml2 = 'GEOMETRY'; pnam2 = '$q_0$'; attr2 = 'q0'; pref2 =-2.15; scale2 =1.0;
- t1 = 50; t2 = 150;
- case 3
- casename = 'DTT rho85';
- partition= '/misc/gyacomo23_outputs/paper_3/DTT_rho85_geom_scan/';
- % scandir = 'P2_J1_delta_nuDGGK_scan'; scanname= 'DG (2,1)';
- % scandir = 'P4_J2_delta_nuDGGK_scan'; scanname= 'DG (4,2)';
- % scandir = 'P8_J4_delta_nuDGGK_conv_test'; scanname= 'DG (8,4)';
- % scandir = 'P2_J1_delta_nuSGGK_scan'; scanname= 'SG (2,1)';
- % scandir = 'P4_J2_delta_nuSGGK_scan'; scanname= 'SG (4,2)';
- % scandir = 'P8_J4_delta_nuSGGK_conv_test'; scanname= 'SG (8,4)';
- % scandir = 'P4_J2_delta_nuSGGKii_scan'; scanname= 'SGii (4,2)';
- scandir = 'P2_J1_delta_nuLDGK_scan'; scanname= 'LD (2,1)';
- % scandir = 'P4_J2_delta_nuLDGK_scan'; scanname= 'LD (4,2)';
- nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0.23; scale1 =1.0;
- nml2 = 'MODEL'; pnam2 = '$\nu$'; attr2 = 'nu'; pref2 = 0.5; scale2 =1.0;
- t1 = 50; t2 = 150;
- case 4 % shear delta scan
- casename = 'DIIID rho95';
- partition= '/misc/gyacomo23_outputs/paper_3/DIIID_cold_ions_rho95_geom_scan/';
- scandir = '3x2x192x48x32_RT_2500_delta_shear_scan'; scanname= 'CI DG RT 2500';
- % scandir = '3x2x256x64x48_delta_shear_scan';
- nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0; scale1 =1.0;
- nml2 = 'GEOMETRY'; pnam2 = '$\hat s$'; attr2 = 'shear'; pref2 = 0.8; scale2 =1.0;
- t1 = 50; t2 = 150;
- case 5 % delta K_T tau=1
+switch 2
+ case 1 % delta K_T tau=1
casename = 'DIIID rho95 $\tau=1$';
partition= '../results/paper_3/DIIID_tau_1_rho95_geom_scan/';
- % scandir = '3x2x192x48x32_delta_RT_scan'; scanname= '(2,1)';
+ % % scandir = '3x2x192x48x32_nu_0.05_delta_RT_scan'; scanname= '(2,1)';
+ % scandir = '3x2x192x48x32_nu_0.1_delta_RT_scan'; scanname= '(2,1)';
+ % scandir = '3x2x192x48x24_nu_0.1_delta_RT_scan'; scanname= '(2,1)';
+ % scandir = '3x2x192x48x32_nu_1.0_delta_RT_scan'; scanname= '(2,1)';
scandir = '2_1_delta_RT_scan'; scanname= '(2,1)';
- % scandir = '5x3x192x48x32_delta_RT_scan'; scanname= '(4,2)';
+ % scandir = '5x3x192x48x32_nu_0.05_delta_RT_scan'; scanname= '(4,2)';
+ scandir = '5x3x192x48x32_nu_1.0_delta_RT_scan'; scanname= '(4,2)';
+ % scandir = '5x3x192x48x32_delta_RT_scan'; scanname= '(2,1)';
% scandir = 'delta_RT_scan_PJ_21'; scanname= '(2,1)';
nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0; scale1 =1.0;
- nml2 = 'SPECIES'; pnam2 = '$R_0/L_T\times T_i/T_e$'; attr2 = 'K_T_'; pref2 = 0.8; scale2 =1.0;
- t1 = 200; t2 = 500;
- case 6 % delta K_T cold ions
+ nml2 = 'SPECIES'; pnam2 = '$R_0/L_T\times T_i/T_e$'; attr2 = 'K_T_'; pref2 = 5; scale2 =1.0;
+ t1 = 300; t2 = 500; zfactor = 1;
+ case 2 % delta K_T cold ions
casename = 'DIIID rho95 $\tau=10^{-3}$';
- partition= '../results/paper_3/DIIID_cold_ions_rho95_geom_scan/';
- scandir = '3x2x192x48x32_delta_RT_scan'; scanname= '(2,1)';
- nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0; scale1 =1.0;
- nml2 = 'SPECIES'; pnam2 = '$R_0/L_T\times T_i/T_e$'; attr2 = 'K_T_'; pref2 = 0.8; scale2 =1e3/2;
- t1 = 150; t2 = 280;
- case 7 % delta s_delta
- casename = 'DIIID rho95 $\tau=10^{-3}$';
- partition= '/misc/gyacomo23_outputs/paper_3/DIIID_cold_ions_rho95_geom_scan/';
- scandir = '3x2x192x48x32_RT_1000_delta_sdelta_scan'; scanname= 'RT=1000 (2,1)';
- % scandir = '';
+ partition= '/misc/gyacomo23_outputs/paper_3/DIIID_cold_ions_rho95_geom_scan/';
+ % scandir = '3x2x192x48x32_nu_0_delta_RT_scan'; scanname= '(2,1)';
+ scandir = '3x2x192x48x32_nu_0.05_delta_RT_scan'; scanname= '(2,1)';
+ nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0; scale1 =1;
+ nml2 = 'SPECIES'; pnam2 = '$\kappa_T$'; attr2 = 'K_T_'; pref2 = 5; scale2 =500;
+ t1 = 80; t2 = 400; zfactor = 2;
+ case 3 % delta K_T HEL, better resolution
+ casename = 'DIIID rho95 $\tau=1$';
+ % partition= '/misc/gyacomo23_outputs/paper_3/geom_scan_DIIID_HEL/NU_50/';
+ partition= '/misc/gyacomo23_outputs/paper_3/geom_scan_DIIID_HEL/NU_20/';
+ scandir = '.'; scanname= 'CBC HEL';
nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0; scale1 =1.0;
- nml2 = 'GEOMETRY'; pnam2 = '$s_\delta$'; attr2 = 's_delta'; pref2 = 0.8; scale2 =1.0;
- t1 = 200; t2 = 295;
- case 8 % eps q0
- casename = 'DIIID rho95 $\tau=10^{-3}$';
- partition= '/misc/gyacomo23_outputs/paper_3/DIIID_cold_ions_rho95_geom_scan/';
- scandir = '3x2x192x48x32_RT_1000_eps_q0_scan/PT'; scanname= 'PT, RT=1000 (2,1)';
- % scandir = '3x2x192x48x32_RT_1000_eps_q0_scan/NT'; scanname= 'NT, RT=1000 (2,1)';
- % scandir = '';
- nml1 = 'GEOMETRY'; pnam1 = '$\epsilon$'; attr1 = 'eps'; pref1 = 0; scale1 =1.0;
- nml2 = 'GEOMETRY'; pnam2 = '$q_0$'; attr2 = 'q0'; pref2 = 0; scale2 =1.0;
- t1 = 200; t2 = 400;
- case 9 % CBC Dimits shift
- casename = 'HEL CBC';
- partition= '/misc/gyacomo23_outputs/paper_3/HEL_CBC/';
- scandir = '128x32x24'; scanname= 'CBC HEL';
- nml1 = 'SPECIES'; pnam1 = '$R_T$'; attr1 = 'k_T_'; pref1 = 0; scale1 =1.0;
- nml2 = 'SPECIES'; pnam2 = '$R_N$'; attr2 = 'k_N_'; pref2 = 0; scale2 =1.0;
- t1 = 1000; t2 = 2000;
+ nml2 = 'SPECIES'; pnam2 = '$R_0/L_T\times T_i/T_e$'; attr2 = 'K_T_'; pref2 = 5; scale2 =500;
+ t1 = 100; t2 = 150; zfactor = 1;
end
scanname= [casename scanname];
scandir = [partition,scandir,'/'];
@@ -116,11 +67,16 @@ for i = 1:length(contents)
para1 = [para1 param.(nml1).(attr1)];
para2 = [para2 param.(nml2).(attr2)];
% Now you are in the subdirectory. You can perform operations here.
- [t_all, Pxi_all, Qxi_all, Pxe_all, Qxe_all] = read_flux_out_XX(subdir);
+ out = read_flux_out_XX(subdir);
+ t_all = out.t;
+ Pxi_all = out.Pxi;
+ Qxi_all = out.Qxi;
+ Pxe_all = out.Pxe;
+ Qxe_all = out.Qxe;
if(numel(Qxe_all) > 1)
- Qxtot = Qxi_all+Qxe_all;
+ Qxtot = zfactor*(Qxi_all+Qxe_all);
else
- Qxtot = Qxi_all;
+ Qxtot = zfactor*(Qxi_all);
end
Qxt.(['dat_',num2str(i)]) = struct();
Qxt.(['dat_',num2str(i)]).Qx = Qxtot;
@@ -140,7 +96,7 @@ for i = 1:length(contents)
Qxerr = [Qxerr nan];
end
else
- Qxavg = [Qxavg nan];
+ Qxavg = [Qxavg nan];
Qxerr = [Qxerr nan];
end
end
@@ -159,7 +115,7 @@ attr = fieldnames(Qxt);
Nsim = numel(attr);
figure
% compute growth at the begining
-tw = [10 40];
+tw = [5 20];
gr = 1:Nsim; err = 1:Nsim;
for i = 1:1:Nsim
tmp_ = Qxt.(attr{i});
@@ -277,7 +233,7 @@ end
if NCONTOUR <= 0
imagesc_custom(xx_,yy_,toplot); hold on
else
- contourf(XX(:,1),YY(1,:),Zavg',NCONTOUR); hold on
+ contour(XX(:,1),YY(1,:),Zavg'); hold on
end
if REFVAL && ~((pref1==999) || (pref2==999))
plot(xref(1,1),yref(1,1),'xk','MarkerSize',14,'DisplayName',Qrefname)
@@ -305,3 +261,40 @@ xlabel(pnam1); ylabel('$\langle Q_{tot} \rangle_t$');
legend('show','Location','northwest');
title([param.COLLISION.collision_model{1}, ...
', $(P,J)=(',num2str(param.GRID.pmax),',',num2str(param.GRID.jmax),')$'])
+
+if 0
+%% plot minimum
+idxmax = 1:numel(Zavg(1,:));
+idxmin = 1:numel(Zavg(1,:));
+xmax = 1:numel(Zavg(1,:));
+xmin = 1:numel(Zavg(1,:));
+ymax = 1:numel(Zavg(1,:));
+ymin = 1:numel(Zavg(1,:));
+err = 1:numel(Zavg(1,:));
+
+x = linspace(min(p1),max(p1),128);
+for i=1:numel(Zavg(1,:))
+ [fit, dat] = polyfit(p1,Zavg(:,i)+0*Zerr(:,i),2);
+ [ymax(i),idx] = min(polyval(fit,x));
+ xmax(i) = x(idx);
+ [fit, dat] = polyfit(p1,Zavg(:,i)-0*Zerr(:,i),2);
+ [ymin(i),idx] = min(polyval(fit,x));
+ xmin(i) = x(idx);
+
+ [zmin,idx] = min(Zavg(:,i));
+ % err(i) = abs(zmin-Zavg(idx+1,i))/abs(zmin)+abs(zmin-Zavg(idx-1,i))/abs(zmin);
+end
+err = min(err,1);
+xavg = 0.5*(xmax+xmin);
+xerr = 0.5*abs(xmax-xmin);
+
+fit = polyfit(p2,xavg,1);
+y = linspace(min(p2),max(p2),128);
+
+figure
+plot(xavg+xerr,p2); hold on
+plot(xavg-xerr,p2); hold on
+plot(polyval(fit,y),y)
+plot(polyval(fit,y),y)
+plot(polyval(fit,y),y)
+end
\ No newline at end of file
diff --git a/wk/parallel_scaling.m b/wk/parallel_scaling.m
index ed35a92c497eedd0683c4d59d9a1d50616a051cb..5df3ebe177b84e9856bb87daadc5ea557ab760d8 100644
--- a/wk/parallel_scaling.m
+++ b/wk/parallel_scaling.m
@@ -1,11 +1,12 @@
-DIR = '/misc/gyacomo23_outputs/scaling/strong/17x9x256x256x32/'; scaling='strong';
+% DIR = '/misc/gyacomo23_outputs/scaling/strong/17x9x256x256x32/'; scaling='strong';
% DIR = '/misc/gyacomo23_outputs/scaling/strong/9x5x768x192x32/'; scaling='strong';
-% DIR = '/misc/gyacomo23_outputs/scaling/strong/3x2x768x192x32/'; scaling='strong';
+DIR = '/misc/gyacomo23_outputs/scaling/strong/3x2x768x192x32/'; scaling='strong';
% DIR = '/misc/gyacomo23_outputs/scaling/weak/Np_5x2x128x64x32/'; scaling='weak';
% DIR = '/misc/gyacomo23_outputs/scaling/weak/Ny_3x2x768x8x32/'; scaling='weak';
% DIR = '/misc/gyacomo23_outputs/scaling/weak/Nz_3x2x768x32x8/'; scaling='weak';
% DIR = '/misc/gyacomo23_outputs/scaling/weak/Nz_5x2x128x64x8/'; scaling='weak';
-% DIR = '/misc/gyacomo23_outputs/scaling/weak/Npyz_4x2x32x16x16/'; scaling='weak';
+% DIR = '/misc/gyacomo23_outputs/scaling/weak/Npyz_4x2x32x16x8/'; scaling='weak';
+% DIR = '/misc/gyacomo23_outputs/scaling/weak/Npyz_8x2x32x32x4/'; scaling='weak';
% Get a list of all items in the current directory
contents = dir(DIR);
@@ -76,31 +77,52 @@ Rt_ref = Rt_avg(Np_tot==1);
Np_ref = 1;
MaxN = max(Np_tot);
Np1Nz1 = logical((Np==1).*(Nz==1));
-Np2Nz1 = logical((Np==2).*(Nz==1));
Np1Nz2 = logical((Np==1).*(Nz==2));
Np1Nz4 = logical((Np==1).*(Nz==4));
+Np2Nz1 = logical((Np==2).*(Nz==1));
+Np2Nz2 = logical((Np==2).*(Nz==2));
+Np2Nz4 = logical((Np==2).*(Nz==4));
+Np4Nz1 = logical((Np==4).*(Nz==1));
+Np4Nz2 = logical((Np==4).*(Nz==2));
+Np4Nz4 = logical((Np==4).*(Nz==4));
%%
-figure; hold on;
+figure; hold on; msz = 8;
xlabel('Number of cores');
+clr_ = lines(3);
switch scaling
case 'strong'
- plot(Np_tot(Np1Nz1),Rt_ref./Rt_avg(Np1Nz1),...
- 'o','DisplayName','$N_{pp}=1, N_{pz}=1$');
- plot(Np_tot(Np2Nz1),Rt_ref./Rt_avg(Np2Nz1), ...
- 'o','DisplayName','$N_{pp}=2, N_{pz}=1$');
- plot(Np_tot(Np1Nz2),Rt_ref./Rt_avg(Np1Nz2), ...
- 'o','DisplayName','$N_{pp}=1, N_{pz}=2$');
- plot(Np_tot(Np1Nz4),Rt_ref./Rt_avg(Np1Nz4), ...
- 'o','DisplayName','$N_{pp}=1, N_{pz}=4$');
- plot(1:MaxN,(1:MaxN)/Np_ref,'--k','DisplayName','Ideal');
+ plot(Np_tot(Np1Nz1),Rt_ref./Rt_avg(Np1Nz1),'o', ...
+ 'Color',clr_(1,:),'DisplayName','$N_{pp}=1, N_{pz}=1$','MarkerSize',msz);
+ plot(Np_tot(Np1Nz2),Rt_ref./Rt_avg(Np1Nz2),'o',...
+ 'Color',clr_(2,:),'DisplayName','$N_{pp}=1, N_{pz}=2$','MarkerSize',msz);
+ plot(Np_tot(Np1Nz4),Rt_ref./Rt_avg(Np1Nz4),'o', ...
+ 'Color',clr_(3,:),'DisplayName','$N_{pp}=1, N_{pz}=4$','MarkerSize',msz);
+ plot(Np_tot(Np2Nz1),Rt_ref./Rt_avg(Np2Nz1),'x', ...
+ 'Color',clr_(1,:),'DisplayName','$N_{pp}=2, N_{pz}=1$','MarkerSize',msz);
+ plot(Np_tot(Np2Nz2),Rt_ref./Rt_avg(Np2Nz2),'x', ...
+ 'Color',clr_(2,:),'DisplayName','$N_{pp}=2, N_{pz}=2$','MarkerSize',msz);
+ plot(Np_tot(Np2Nz4),Rt_ref./Rt_avg(Np2Nz4),'x', ...
+ 'Color',clr_(3,:),'DisplayName','$N_{pp}=2, N_{pz}=4$','MarkerSize',msz);
+ plot(Np_tot(Np4Nz1),Rt_ref./Rt_avg(Np4Nz1),'+', ...
+ 'Color',clr_(1,:),'DisplayName','$N_{pp}=4, N_{pz}=1$','MarkerSize',msz);
+ plot(Np_tot(Np4Nz2),Rt_ref./Rt_avg(Np4Nz2),'+', ...
+ 'Color',clr_(2,:),'DisplayName','$N_{pp}=4, N_{pz}=2$','MarkerSize',msz);
+ plot(Np_tot(Np4Nz4),Rt_ref./Rt_avg(Np4Nz4),'+', ...
+ 'Color',clr_(3,:),'DisplayName','$N_{pp}=4, N_{pz}=4$','MarkerSize',msz);
+ plot(Np_tot,Rt_ref./Rt_avg,...
+ '.k','DisplayName','Strong scaling');
+ plot([1 1000],[1 1000],'--k','DisplayName','Ideal');
+ axis equal
set(gca,'XScale','log'); set(gca,'YScale','log');
ylabel('Speedup');
% title('Strong scaling speedup')
case 'weak'
hold on;
- filt = logical((Np==2).*(Ny>=1).*(Nz>=1));
- plot(Np_tot(filt),Rt_ref./Rt_avg(filt),...
- 'o','DisplayName','Effective');
+ % for n = [1 2 4 8 12]
+ filt = logical((Np>=1).*(Ny>=1).*(Nz>=1));
+ plot(Np_tot(filt),Rt_ref./Rt_avg(filt),...
+ 'o','DisplayName','Effective');
+ % end
plot(1:MaxN,ones(1,MaxN),'--k','DisplayName','Ideal');
ylim([0 1]);
set(gca,'XScale','log')
diff --git a/wk/parameters/lin_DIIID_LM_rho95.m b/wk/parameters/lin_DIIID_LM_rho95.m
index 2bd5ba9b2f383bfb8a885ecb30666f6b79194743..17c6cbf8552518eb05c6cbd2b62d9671e59d0730 100644
--- a/wk/parameters/lin_DIIID_LM_rho95.m
+++ b/wk/parameters/lin_DIIID_LM_rho95.m
@@ -96,4 +96,5 @@ BCKGD0 = 0.0e-5; % Initial background
k_gB = 1.0; % Magnetic gradient strength
k_cB = 1.0; % Magnetic curvature strength
COLL_KCUT = 1; % Cutoff for collision operator
-ADIAB_I = 0; % adiabatic ion model
\ No newline at end of file
+ADIAB_I = 0; % adiabatic ion model
+EXBRATE = 0;
\ No newline at end of file
diff --git a/wk/parameters/lin_DIIID_LM_rho95_HEL.m b/wk/parameters/lin_DIIID_LM_rho95_HEL.m
new file mode 100644
index 0000000000000000000000000000000000000000..cbd940901c56c65a2f11ccf80320324342097e03
--- /dev/null
+++ b/wk/parameters/lin_DIIID_LM_rho95_HEL.m
@@ -0,0 +1,100 @@
+%% Reference values
+% See Neiser et al. 2019 Gyrokinetic GENE simulations of DIII-D near-edge L-mode plasmas
+%% Set simulation parameters
+SIMID = 'lin_DIIID_HM_rho90'; % Name of the simulation
+%% Set up physical parameters
+CLUSTER.TIME = '99:00:00'; % Allocation time hh:mm:ss
+NU = 50; %(0.00235 in GENE)
+TAU = 0.001; % i/e temperature ratio
+K_Ne = 0; % ele Density '''
+K_Te = 0; % ele Temperature '''
+K_Ni = 0; % ion Density gradient drive
+K_Ti = 5.2256/2/TAU; % ion Temperature '''
+SIGMA_E = 0.0233380/sqrt(2); % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
+NA = 1; % number of kinetic species
+ADIAB_E = (NA==1); % adiabatic electron model
+BETA = 0; % electron plasma beta in prct
+MHD_PD = 1;
+%% Set up grid parameters
+P = 2;
+J = P/2;%P/2;
+PMAX = P; % Hermite basis size
+JMAX = J; % Laguerre basis size
+NX = 8; % real space x-gridpoints
+NY = 2; % real space y-gridpoints
+LX = 2*pi/0.1; % Size of the squared frequency domain in x direction
+LY = 2*pi/0.3; % Size of the squared frequency domain in y direction
+NZ = 32; % number of perpendicular planes (parallel grid)
+SG = 0; % Staggered z grids option
+NEXC = 1; % To extend Lx if needed (Lx = Nexc/(kymin*shear))
+
+%% GEOMETRY
+% GEOMETRY= 's-alpha';
+GEOMETRY= 'miller';
+Q0 = 4.8; % safety factor
+SHEAR = 2.55; % magnetic shear
+EPS = 0.3; % inverse aspect ratio
+KAPPA = 1.57; % elongation
+S_KAPPA = 0.48;
+DELTA = 0.2; % triangularity
+S_DELTA = 0.1;
+ZETA = 0.0; % squareness
+S_ZETA = 0.0;
+PARALLEL_BC = 'dirichlet'; % Boundary condition for parallel direction ('dirichlet','periodic','shearless','disconnected')
+SHIFT_Y = 0.0; % Shift in the periodic BC in z
+NPOL = 1; % Number of poloidal turns
+PB_PHASE = 0;
+%% TIME PARAMETERS
+TMAX = 15; % Maximal time unit
+DT = 1e-2; % Time step
+DTSAVE0D = 0.5; % Sampling time for 0D arrays
+DTSAVE2D = -1; % Sampling time for 2D arrays
+DTSAVE3D = 0.5; % Sampling time for 3D arrays
+DTSAVE5D = 100; % Sampling time for 5D arrays
+JOB2LOAD = -1; % Start a new simulation serie
+
+%% OPTIONS
+LINEARITY = 'linear'; % activate non-linearity (is cancelled if KXEQ0 = 1)
+CO = 'DG'; % Collision operator (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
+GKCO = 1; % Gyrokinetic operator
+ABCO = 1; % INTERSPECIES collisions
+INIT_ZF = 0; % Initialize zero-field quantities
+HRCY_CLOS = 'truncation'; % Closure model for higher order moments
+DMAX = -1;
+NLIN_CLOS = 'truncation'; % Nonlinear closure model for higher order moments
+NMAX = 0;
+KERN = 0; % Kernel model (0 : GK)
+INIT_OPT = 'phi'; % Start simulation with a noisy mom00/phi/allmom
+NUMERICAL_SCHEME = 'RK4'; % Numerical integration scheme (RK2,SSPx_RK2,RK3,SSP_RK3,SSPx_RK3,IMEX_SSP2,ARK2,RK4,DOPRI5)
+
+%% OUTPUTS
+W_DOUBLE = 1; % Output flag for double moments
+W_GAMMA = 1; % Output flag for gamma (Gyrokinetic Energy)
+W_HF = 1; % Output flag for high-frequency potential energy
+W_PHI = 1; % Output flag for potential
+W_NA00 = 1; % Output flag for nalpha00 (density of species alpha)
+W_DENS = 1; % Output flag for total density
+W_TEMP = 1; % Output flag for temperature
+W_NAPJ = 1; % Output flag for nalphaparallel (parallel momentum of species alpha)
+W_SAPJ = 0; % Output flag for saparallel (parallel current of species alpha)
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% UNUSED PARAMETERS
+% These parameters are usually not to play with in linear runs
+MU = 0.0; % Hyperdiffusivity coefficient
+MU_X = MU; % Hyperdiffusivity coefficient in x direction
+MU_Y = MU; % Hyperdiffusivity coefficient in y direction
+N_HD = 4; % Degree of spatial-hyperdiffusivity
+MU_Z = 5.0; % Hyperdiffusivity coefficient in z direction
+HYP_V = 'hypcoll'; % Kinetic-hyperdiffusivity model
+MU_P = 0.0; % Hyperdiffusivity coefficient for Hermite
+MU_J = 0.0; % Hyperdiffusivity coefficient for Laguerre
+LAMBDAD = 0.0; % Lambda Debye
+NOISE0 = 1.0e-5; % Initial noise amplitude
+BCKGD0 = 0.0e-5; % Initial background
+k_gB = 1.0; % Magnetic gradient strength
+k_cB = 1.0; % Magnetic curvature strength
+COLL_KCUT = 1; % Cutoff for collision operator
+ADIAB_I = 0; % adiabatic ion model
+EXBRATE = 0;
\ No newline at end of file
diff --git a/wk/parameters/lin_ITG.m b/wk/parameters/lin_ITG.m
index 07d85ebc3aa01595ebd7e924280e8eaf25d875c9..d1c06b664d3094daa98e7e1c8e4c327e342cf16f 100644
--- a/wk/parameters/lin_ITG.m
+++ b/wk/parameters/lin_ITG.m
@@ -15,10 +15,8 @@ ADIAB_E = (NA==1); % adiabatic electron model
BETA = 0.0; % electron plasma beta
EXBRATE = 0.0; % Background ExB shear flow
%% Set up grid parameters
-P = 4;
-J = 2;%P/2;
-PMAX = P; % Hermite basis size
-JMAX = J; % Laguerre basis size
+PMAX = 4; % Hermite basis size
+JMAX = 2; % Laguerre basis size
NX = 8; % real space x-gridpoints
NY = 12; % real space y-gridpoints
LX = 2*pi/0.05; % Size of the squared frequency domain in x direction
diff --git a/wk/parameters/lin_Ivanov.m b/wk/parameters/lin_Ivanov.m
index 80dccb8e179b3b7fae17dc3faa49e3eef211c83d..a578f0bc8ec6a04a2ea32e0cd771d7dd45ab8f1b 100644
--- a/wk/parameters/lin_Ivanov.m
+++ b/wk/parameters/lin_Ivanov.m
@@ -3,12 +3,12 @@ SIMID = 'lin_Ivanov'; % Name of the simulation
%% Set up physical parameters
CLUSTER.TIME = '99:00:00'; % Allocation time hh:mm:ss
-TAU = 0.001; % e/i temperature ratio
-NU = 1.0*3/2/TAU/4; % Collision frequency
+TAU = 1e-3; % e/i temperature ratio
+NU = 0.1*3/8/TAU; % Collision frequency
K_Ne = 0*2.22; % ele Density
K_Te = 0*6.96; % ele Temperature
K_Ni = 0*2.22; % ion Density gradient drive
-K_Ti = 1.0*2/TAU+0*5*TAU; % ion Temperature
+K_Ti = 1*2/TAU; % ion Temperature
SIGMA_E = 0.0233380; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
NA = 1; % number of kinetic species
ADIAB_E = (NA==1); % adiabatic electron model
@@ -96,7 +96,10 @@ BCKGD0 = 0.0; % Initial background
k_gB = 1.0; % Magnetic gradient strength
k_cB = 1.0; % Magnetic curvature strength
COLL_KCUT = 1.0; % Cutoff for collision operator
-PB_PHASE = 0.0;
+S_KAPPA = 0.0;
+S_DELTA = 0.0;
+S_ZETA = 0.0;
+PB_PHASE= 0;
ADIAB_I = 0;
MHD_PD = 0;
EXBRATE = 0;
\ No newline at end of file
diff --git a/wk/parameters/lin_RHT.m b/wk/parameters/lin_RHT.m
index 72137f75d6cb2f219d7ce3bf3bd81ecc77aea40e..0f39498d342d28c11b63c43d64e70132d1f07e0a 100644
--- a/wk/parameters/lin_RHT.m
+++ b/wk/parameters/lin_RHT.m
@@ -15,15 +15,15 @@ ADIAB_E = (NA==1); % adiabatic electron model
BETA = 0.0; % electron plasma beta
EXBRATE = 0.0; % Background ExB shear flow
%% Set up grid parameters
-P = 4;
-J = 2;%P/2;
+P = 256;
+J = 16;%P/2;
PMAX = P; % Hermite basis size
JMAX = J; % Laguerre basis size
NX = 2; % real space x-gridpoints
NY = 2; % real space y-gridpoints
LX = 2*pi/0.05; % Size of the squared frequency domain in x direction
LY = 2*pi/0.01; % Size of the squared frequency domain in y direction
-NZ = 8; % number of perpendicular planes (parallel grid)
+NZ = 24; % number of perpendicular planes (parallel grid)
SG = 0; % Staggered z grids option
NEXC = 1; % To extend Lx if needed (Lx = Nexc/(kymin*shear))
@@ -42,7 +42,7 @@ NPOL = 1; % Number of poloidal turns
%% TIME PARAMETERS
TMAX = 50; % Maximal time unit
-DT = 1e-3; % Time step
+DT = 5e-3; % Time step
DTSAVE0D = 1; % Sampling time for 0D arrays
DTSAVE2D = -1; % Sampling time for 2D arrays
DTSAVE3D = 0.1; % Sampling time for 3D arrays
diff --git a/wk/particle_trajectory.m b/wk/particle_trajectory.m
new file mode 100644
index 0000000000000000000000000000000000000000..62da611a8b43f50d5b00184918e8d22416b0b2ed
--- /dev/null
+++ b/wk/particle_trajectory.m
@@ -0,0 +1,36 @@
+R = 1;
+a = 0.05;
+d = 0.02;
+Wc= 80;
+
+
+figure
+
+% Magnetic field line
+Bx = @(R,th) R*cos(th);
+By = @(R,th) R*sin(th);
+Bz = @(R,th) 0*(th);
+
+thB = linspace(0,2*pi,128);
+plot3(Bx(R,thB),By(R,thB),Bz(R,thB)); hold on;
+
+% Particle trochoid
+Tx = @(R,th) a*cos(th).*cos(Wc*th);
+Ty = @(R,th) a*sin(th).*cos(Wc*th);
+Tz = @(R,th) a*sin(Wc*th)+d*th;
+
+thP = linspace(0,2.5*pi,2048);
+Xp = Bx(R,thP)+Tx(R,thP);
+Yp = By(R,thP)+Ty(R,thP);
+Zp = Bz(R,thP)+Tz(R,thP);
+plot3(Xp,Yp,Zp)
+plot3(Xp(1),Yp(1),Zp(1),'xk','MarkerSize',10)
+plot3(Xp(end),Yp(end),Zp(end),'ok','MarkerSize',8,'MarkerFaceColor','k')
+
+
+% finish the plot
+axis equal
+xlim(1.2*R*[-1 1])
+ylim(1.2*R*[-1 1])
+zlim(0.25*[-1 1])
+axis off
\ No newline at end of file
diff --git a/wk/plot_params_vs_rho.m b/wk/plot_params_vs_rho.m
index 0b3d64860fbba428210049054fa658e9b577785f..0f12e391a80a4bc72a373a40bc098cdb4bec93ae 100644
--- a/wk/plot_params_vs_rho.m
+++ b/wk/plot_params_vs_rho.m
@@ -3,6 +3,7 @@ function [ ] = plot_params_vs_rho(geom,prof_folder,rho,rho_min,rho_max,Lref,mref
if FROMPROFILE
% profiles = read_DIIID_profile([prof_folder,'/profiles.txt']);
[params,profiles] = get_param_from_profiles(prof_folder,rho,Lref,mref,Bref,FROMPROFILE);
+ rho_a = profiles.ne.x;
m_e = 9.11e-31;
sigma = sqrt(m_e/mref);
TAU_a = profiles.ti.y./profiles.te.y;
@@ -42,12 +43,15 @@ if FROMPROFILE
else
rho_a = linspace(rho_min,rho_max,100);
- NU_a = zeros(size(rho_a));
- BETA_a = zeros(size(rho_a));
- K_Ne_a = zeros(size(rho_a));
- K_Ti_a = zeros(size(rho_a));
- K_Te_a = zeros(size(rho_a));
-
+ NU_a = zeros(size(rho_a));
+ BETA_a = zeros(size(rho_a));
+ K_Ne_a = zeros(size(rho_a));
+ K_Ti_a = zeros(size(rho_a));
+ K_Te_a = zeros(size(rho_a));
+ Kappa_a = zeros(size(rho_a));
+ Delta_a = zeros(size(rho_a));
+ Zeta_a = zeros(size(rho_a));
+ geom_a = cell(size(rho_a));
for i = 1:numel(rho_a)
rho_ = rho_a(i);
[params,profiles] = get_param_from_profiles(prof_folder,rho_,Lref,mref,Bref,FROMPROFILE);
@@ -56,6 +60,12 @@ else
K_Ne_a(i) = params.K_Ne;
K_Ti_a(i) = params.K_Ti;
K_Te_a(i) = params.K_Te;
+
+ geom_ = get_miller_GENE_py(prof_folder,rho_);
+ Kappa_a(i) = geom_.kappa;
+ Delta_a(i) = geom_.delta;
+ Zeta_a(i) = geom_.zeta;
+ geom_a{i} = geom_;
end
figure
subplot(231)
@@ -88,8 +98,15 @@ else
grid on
end
subplot(133)
- [R,Z] = plot_miller(geom,rho,32,0);
- plot(R,Z,'-b');
+ [R,Z] = plot_miller(geom,rho,128,0);
+ plot(R,Z,'-b'); hold on
+ % rhos = linspace(0.09,0.99,6);
+ % for i = 1:numel(rhos)
+ % rho_ = rhos(i);
+ % geom_ = get_miller_GENE_py(prof_folder,rho_);
+ % [R,Z] = plot_miller(geom_,rho_,128,0);
+ % plot(R,Z,'-k');
+ % end
xlabel('R [m]');
ylabel('Z [m]');
axis tight
diff --git a/wk/plot_spectrum.m b/wk/plot_spectrum.m
new file mode 100644
index 0000000000000000000000000000000000000000..264f3a72b3acb75aaf3e96e22353b17192cf3b6f
--- /dev/null
+++ b/wk/plot_spectrum.m
@@ -0,0 +1,45 @@
+function [FIGURE] = plot_spectrum(data,options)
+
+
+options.INTERP = 0;
+options.POLARPLOT = 0;
+options.AXISEQUAL = 1;
+options.LOGSCALE = 0;
+options.CLIMAUTO = 1;
+options.PLAN = 'kxky'; options.COMP = data.grids.Nz/2+1;
+options.RESOLUTION = 256;
+options.BWR = 0; % bluewhitered plot or gray
+options.COMP = 'avg';
+[toplot] = process_field(data,options);
+
+% Time averaging
+fkykx = squeeze(mean(abs(toplot.FIELD(:,:,:)),3));
+
+FNAME = toplot.FILENAME;
+
+
+kx = toplot.X(1,:);
+Nkx = numel(kx);
+kx = toplot.X(1,Nkx/2:end);
+fkx = squeeze(fkykx(1,Nkx/2:end));
+ky = toplot.Y(:,data.grids.Nkx/2+1);
+fky = squeeze(fkykx(:,data.grids.Nkx/2+1));
+
+FIGURE.fig = figure;
+subplot(121)
+ scale = max(fkx)*options.NORMALIZE + 1*(1-options.NORMALIZE);
+ plot(kx,fkx./scale)
+ xlabel(toplot.XNAME)
+ ylabel(['$|',toplot.FIELDNAME,'|$'])
+
+
+subplot(122)
+ scale = max(fky)*options.NORMALIZE + 1*(1-options.NORMALIZE);
+ plot(ky,fky./scale)
+ xlabel(toplot.YNAME)
+ ylabel(['$|',toplot.FIELDNAME,'|$'])
+
+
+FIGURE.FIGNAME = [FNAME,'_spectrum'];
+
+end
\ No newline at end of file
diff --git a/wk/plot_toroidal_fluxtube_geom.m b/wk/plot_toroidal_fluxtube_geom.m
index b6aa8e4e1a8a7c0a381a08da32cd94842ca0fd65..f38037a99451e2dc7b3820340302ef82fd143510 100644
--- a/wk/plot_toroidal_fluxtube_geom.m
+++ b/wk/plot_toroidal_fluxtube_geom.m
@@ -1,3 +1,8 @@
+%% This script is made for illustrating different magnetic geometry
+% it is not bugfree but work pretty well for illustration purpose of the
+% magnetic flux surface of a tokamak and for the particle trajectory in it.
+% ! The particle trajectory is not correct (does not work for Z-pinch for
+% ! example) but is good enough for illustation.
gyacomodir = pwd; gyacomodir = gyacomodir(1:end-2); % get code directory
addpath(genpath([gyacomodir,'matlab'])) % ... add
addpath(genpath([gyacomodir,'matlab/plot'])) % ... add
@@ -8,27 +13,31 @@ default_plots_options
Nx = 128;
Ny = 128;
-Nturns = 1;
-Nz = 128;
-x = linspace(-60,60,Nx)*0.001;
+Nz = 64;
+Nturns = 1.0;
+lr = 0.05; %larmor radius
+Wc = 750; %~cyclotron freq
+vd = 0.25; %~drift velocty
+Gx = linspace(-60,60,Nx)*0.001;
y = linspace(-60,60,Ny)*0.001;
FIELD = ones(Nx,Ny,Nz);
z = linspace(-Nturns*pi,Nturns*pi,Nz);
-N_field_lines = 2;
+N_field_lines = 10;
N_magn_flux_surf = 1;
openangle = pi/3;
-phi0 = openangle/2; phi1= 2*pi-openangle/2;
+% phi0 = openangle/2; phi1= 2*pi-openangle/2;
+phi0 = 0; phi1= 2*pi-1.3;
PLT_FTUBE = 0;
PLT_BASIS = 0;
PLT_DATA = 0;
R0 = 1; % Torus major radius
Z0 = 0;
xpoint = 0;
-select = 3;
+select = 1;
switch select
case 1
- % CBC
- rho = 0.3; drho = 0.1;% Torus minor radius
+ % Z-pinch
+ rho = 0.50; drho = 0.1;% Torus minor radius
eps = 0.3;
q0 = 1.4; % Flux tube safety factor
shear = 0.8;
@@ -78,36 +87,20 @@ switch select
zeta = 0.1;
s_zeta = 0.0;
case 5
- % Fake x-point DIII-D
- N_magn_flux_surf = 2;
- phi0 = 0; phi1= pi/48;
- N_field_lines = 0;
- rho = 0.40; drho = 0.1;% Torus minor radius
- eps = 0.3;
- q0 = 4.8; % Flux tube safety factor
- shear = 2.5;
- kappa = 1.0;
- s_kappa= 0.0;
- delta = 0.0;
- s_delta= 0.0;
- zeta = 0.0;
- s_zeta = 0.0;
- xpoint = 0.5;
- case 6
% play with DIII-D edge
rho = 0.90; drho = 0.1;% Torus minor radius
eps = 0.3;
- q0 = 1.0; % Flux tube safety factor
- Nturns = max(1,q0);
+ q0 = 1.8; % Flux tube safety factor
+ % Nturns = max(1,q0);
shear = 2.5;
- kappa = 0.5;
+ kappa = 1.5;
s_kappa= 1.0;
- delta = 0.0;
+ delta = 0.3;
s_delta= 0.0;
- zeta =-1.0;
+ zeta = 0.0;
s_zeta = 0.0;
end
-
+% Nturns = 1/q0;
Nptor = 64;
% Toroidal angle for the flux surf
% phi = linspace(0+openangle/2, 2*pi-openangle/2, Nptor);
@@ -115,20 +108,23 @@ phi = linspace(phi0,phi1, Nptor);
theta = linspace(-pi, pi, Nptor) ; % Poloidal angle
[p, t] = meshgrid(phi, theta);
Tgeom = 1;
-
DIMENSIONS = [600 600 1200 600];
rho = rho*eps; drho = drho*eps;
+iota = 1/q0;
% field line coordinates
Xfl = @(z) (R0+rho*cos(z+asin(delta*sin(z)))).*cos(q0*z);
Yfl = @(z) (R0+rho*cos(z+asin(delta*sin(z)))).*sin(q0*z);
Zfl = @(z) Z0+kappa*rho*sin(z+zeta*sin(2*z)+xpoint*cos(2*z));
Rvec= @(z) [Xfl(z); Yfl(z); Zfl(z)];
% xvec shearless
-xX = @(z) (Xfl(z)-R0*cos(q0*z))./sqrt((Xfl(z)-R0*cos(q0*z)).^2+(Yfl(z)-R0*sin(q0*z)).^2+Zfl(z).^2);
-xY = @(z) (Yfl(z)-R0*sin(q0*z))./sqrt((Xfl(z)-R0*cos(q0*z)).^2+(Yfl(z)-R0*sin(q0*z)).^2+Zfl(z).^2);
-xZ = @(z) Zfl(z)./sqrt((Xfl(z)-R0*cos(q0*z)).^2+(Yfl(z)-R0*sin(q0*z)).^2+Zfl(z).^2);
+% xX = @(z) (Xfl(z)-R0*cos(q0*z))./sqrt((Xfl(z)-R0*cos(q0*z)).^2+(Yfl(z)-R0*sin(q0*z)).^2+Zfl(z).^2);
+% xY = @(z) (Yfl(z)-R0*sin(q0*z))./sqrt((Xfl(z)-R0*cos(q0*z)).^2+(Yfl(z)-R0*sin(q0*z)).^2+Zfl(z).^2);
+% xZ = @(z) Zfl(z)./sqrt((Xfl(z)-R0*cos(q0*z)).^2+(Yfl(z)-R0*sin(q0*z)).^2+Zfl(z).^2);
+xX = @(z) cos(z+asin(delta*sin(z))).*cos(q0*z)./sqrt(cos(z+asin(delta*sin(z))).^2+kappa^2*sin(z+zeta*sin(2*z)).^2);
+xY = @(z) cos(z+asin(delta*sin(z))).*sin(q0*z)./sqrt(cos(z+asin(delta*sin(z))).^2+kappa^2*sin(z+zeta*sin(2*z)).^2);
+xZ = @(z) kappa*sin(z+zeta*sin(2*z))./sqrt(cos(z+asin(delta*sin(z))).^2+kappa^2*sin(z+zeta*sin(2*z)).^2);
xvec= @(z) [xX(z); xY(z); xZ(z)];
-% bvec
+% bvec shearless
bX = @(z) Tgeom*(rho*cos(z).*cos(q0*z) - q0*Yfl(z))./sqrt(Tgeom*(rho*cos(z).*cos(q0*z) - q0*Yfl(z)).^2+(rho*cos(z).*sin(q0*z) + q0*Xfl(z)).^2+(rho*cos(z)).^2);
bY = @(z) (rho*cos(z).*sin(q0*z) + q0*Xfl(z))./sqrt(Tgeom*(rho*cos(z).*cos(q0*z) - q0*Yfl(z)).^2+(rho*cos(z).*sin(q0*z) + q0*Xfl(z)).^2+(rho*cos(z)).^2);
bZ = @(z) rho*cos(z)./sqrt(Tgeom*(rho*cos(z).*cos(q0*z) - q0*Yfl(z)).^2+(rho*cos(z).*sin(q0*z) + q0*Xfl(z)).^2+(rho*cos(z)).^2);
@@ -141,13 +137,6 @@ yvec= @(z) [yX(z); yY(z); yZ(z)];
scale = 0.10;
-% Plot plane result
-OPTIONS.POLARPLOT = 0;
-OPTIONS.PLAN = 'xy';
-rhostar = 0.1;
-[X,Y] = meshgrid(x,y);
-max_ = 0;
-
figure; set(gcf, 'Position', DIMENSIONS)
%plot magnetic geometry
@@ -171,7 +160,8 @@ figure; set(gcf, 'Position', DIMENSIONS)
end
%plot field lines
if N_field_lines > 0
- theta = linspace(-Nturns*pi, Nturns*pi, Nturns*256) ; % Poloidal angle
+ % theta = linspace(-Nturns*pi, Nturns*pi, 1024) ; % Poloidal angle
+ theta = linspace(0, Nturns*2*pi, 1024) ; % Poloidal angle
vecfl = Rvec(theta);
plot3(vecfl(1,:),vecfl(2,:),vecfl(3,:),'-b'); hold on;
% Multiple field lines
@@ -179,17 +169,22 @@ figure; set(gcf, 'Position', DIMENSIONS)
for ifl = 1:N_field_lines-1
% rotation for multiple field lines
t = q0*pi*ifl;
- x_ = [x_ cos(t)*vecfl(1,:) - sin(t)*vecfl(2,:)];
- y_ = [y_ sin(t)*vecfl(1,:) + cos(t)*vecfl(2,:)];
- z_ = [z_ vecfl(3,:)];
+ % x_ = [x_ cos(t)*vecfl(1,:) - sin(t)*vecfl(2,:)];
+ % y_ = [y_ sin(t)*vecfl(1,:) + cos(t)*vecfl(2,:)];
+ % z_ = [z_ vecfl(3,:)];
+ x_ = cos(t)*vecfl(1,:) - sin(t)*vecfl(2,:);
+ y_ = sin(t)*vecfl(1,:) + cos(t)*vecfl(2,:);
+ z_ = vecfl(3,:);
+ % plot3(x_,y_,z_,'-','color',[1.0 0.6 0.6]*0.8); hold on;
+ plot3(x_,y_,z_,'-','color',[0.0 0.5 1.0]*0.8,'LineWidth',1); hold on;
end
- plot3(x_,y_,z_,'-','color',[1.0 0.6 0.6]*0.8); hold on;
+ %plot3(x_,y_,z_,'-','color',[1.0 0.6 0.6]*0.8); hold on;
end
%plot fluxe tube
if PLT_FTUBE
theta = linspace(-Nturns*pi, Nturns*pi, 64) ; % Poloidal angle
%store the shifts in an order (top left to bottom right)
- s_x = rhostar*[x(1) x(end) x(1) x(end)];
+ s_x = rhostar*[Gx(1) Gx(end) Gx(1) Gx(end)];
s_y = rhostar*[y(1) y(1) y(end) y(end)];
for i_ = 1:4
vx_ = Xfl(theta) + s_x(i_)*xX(theta) + s_y(i_)*yX(theta);
@@ -206,19 +201,49 @@ figure; set(gcf, 'Position', DIMENSIONS)
quiver3(Xfl(theta),Yfl(theta),Zfl(theta),scale*yX(theta),scale*yY(theta),scale*yZ(theta),0,'g');
quiver3(Xfl(theta),Yfl(theta),Zfl(theta),scale*bX(theta),scale*bY(theta),scale*bZ(theta),0,'b');
end
- xlabel('X');ylabel('Y');zlabel('Z');
- %Plot time dependent data
- if PLT_DATA
- for iz = 1:Nz
- z_ = z(iz);
- Xp = Xfl(z_) + X*xX(z_) + Y*yX(z_);
- Yp = Yfl(z_) + X*xY(z_) + Y*yY(z_);
- Zp = Zfl(z_) + X*xZ(z_) + Y*yZ(z_);
- s=surface(Xp,Yp,Zp,FIELD(:,:,iz)/max(max(max(abs(FIELD)))));
- s.EdgeColor = 'none';
- colormap(bluewhitered);
+ % Particle trajectory
+ if 1
+ % Particle gyration
+ Gx = @(z) lr*cos(z).*cos(Wc*z);
+ Gy = @(z) lr*sin(z).*cos(Wc*z);
+ Gz = @(z) lr*sin(Wc*z);
+ % This is the "real" helicoidal trajectory
+ theta = linspace(0, Nturns*2*pi, 10000) ; % Poloidal angle
+ dtheta = theta(2)-theta(1);
+ dX = 0*theta; dY = dX; dZ = dX; % init drifts
+ for i = 2:numel(theta)
+ th_old = theta(i-1);
+ th_ = theta(i);
+ % find magnetic displacement vector
+ bx_= Xfl(th_)-Xfl(th_old);
+ by_= Yfl(th_)-Yfl(th_old);
+ bz_= Zfl(th_)-Zfl(th_old);
+ % find binormal
+ yx_= xY(th_).*bz_ - xZ(th_).*by_;
+ yy_= xZ(th_).*bx_ - xX(th_).*bz_;
+ yz_= xX(th_).*by_ - xY(th_).*bx_;
+ % normalize
+ yx_=yx_/sqrt(yx_^2+yy_^2+yz_^2);
+ yy_=yy_/sqrt(yx_^2+yy_^2+yz_^2);
+ yz_=yz_/sqrt(yx_^2+yy_^2+yz_^2);
+ % add drift
+ dX(i) = dX(i-1) - vd*yx_*dtheta;
+ dY(i) = dY(i-1) - vd*yy_*dtheta;
+ dZ(i) = dZ(i-1) - vd*yz_*dtheta;
end
+ % add gyration
+ dX = dX + Gx(theta);
+ dY = dY + Gy(theta);
+ dZ = dZ + Gz(theta);
+ % add fieldline
+ Tx = Xfl(theta)+dX;
+ Ty = Yfl(theta)+dY;
+ Tz = Zfl(theta)+dZ;
+ plot3(Tx,Ty,Tz,'-r','LineWidth',1.2); hold on;
+ plot3(Tx(1),Ty(1),Tz(1),'xk','MarkerSize',10); hold on;
+ plot3(Tx(end),Ty(end),Tz(end),'ok','MarkerSize',8,'MarkerFaceColor','k'); hold on;
end
+ xlabel('X');ylabel('Y');zlabel('Z');
%
axis equal
view([1,-2,1])