From 1fda930a40c53a5d30079429309058d4f619c59e Mon Sep 17 00:00:00 2001
From: Antoine Cyril David Hoffmann <ahoffman@spcpc606.epfl.ch>
Date: Wed, 11 May 2022 10:01:57 +0200
Subject: [PATCH] scripts update
---
matlab/compute/compute_fa_1D.m | 10 +--
matlab/load/load_pjz_data.m | 16 ++++
matlab/plot/plot_ballooning.m | 33 ++++----
matlab/plot/plot_fa.m | 6 +-
matlab/plot/plot_fa_gene.m | 12 +--
matlab/plot/show_napjz.m | 136 +++++++++++++++++++++++++++++++++
wk/analysis_3D.m | 42 +++++-----
wk/gene_analysis_3D.m | 96 ++---------------------
wk/quick_run.m | 37 ++++-----
9 files changed, 234 insertions(+), 154 deletions(-)
create mode 100644 matlab/load/load_pjz_data.m
create mode 100644 matlab/plot/show_napjz.m
diff --git a/matlab/compute/compute_fa_1D.m b/matlab/compute/compute_fa_1D.m
index d8ab8d74..79fe35d8 100644
--- a/matlab/compute/compute_fa_1D.m
+++ b/matlab/compute/compute_fa_1D.m
@@ -54,7 +54,7 @@ if options.non_adiab
for ikx = 1:data.Nkx
for iky = 1:data.Nky
kp_ = sqrt(kx_(ikx)^2 + ky_(iky)^2);
- Napj_(1,ij_,ikx,iky) = Napj_(1,ij_,ikx,iky) + kernel(ij_,kp_)*phi_(ikx,iky);
+ Napj_(1,ij_,iky,ikx) = Napj_(1,ij_,iky,ikx) + kernel(ij_,kp_)*phi_(iky,ikx);
end
end
end
@@ -63,7 +63,7 @@ end
% x = 0
if options.RMS
- Fs = zeros(data.Nkx,data.Nky,numel(s));
+ Fs = zeros(data.Nky,data.Nkx,numel(s));
FAM = FaM(s,xmin);
for ip_ = 1:Np
p_ = parray(ip_);
@@ -74,7 +74,7 @@ if options.RMS
HLF = HH.*LL.*FAM;
for ikx = 1:data.Nkx
for iky = 1:data.Nky
- Fs(ikx,iky,:) = squeeze(Fs(ikx,iky,:))' + Napj_(ip_,ij_,ikx,iky)*HLF;
+ Fs(iky,ikx,:) = squeeze(Fs(iky,ikx,:))' + Napj_(ip_,ij_,iky,ikx)*HLF;
end
end
end
@@ -95,7 +95,7 @@ end
% s = 0
if options.RMS
- Fx = zeros(data.Nkx,data.Nky,numel(x));
+ Fx = zeros(data.Nky,data.Nkx,numel(x));
FAM = FaM(x,smin);
for ip_ = 1:Np
p_ = parray(ip_);
@@ -106,7 +106,7 @@ if options.RMS
HLF = HH.*LL.*FAM;
for ikx = 1:data.Nkx
for iky = 1:data.Nky
- Fx(ikx,iky,:) = squeeze(Fx(ikx,iky,:))' + Napj_(ip_,ij_,ikx,iky)*HLF;
+ Fx(iky,ikx,:) = squeeze(Fx(iky,ikx,:))' + Napj_(ip_,ij_,iky,ikx)*HLF;
end
end
end
diff --git a/matlab/load/load_pjz_data.m b/matlab/load/load_pjz_data.m
new file mode 100644
index 00000000..81eea09d
--- /dev/null
+++ b/matlab/load/load_pjz_data.m
@@ -0,0 +1,16 @@
+function [ data, time, dt ] = load_pjz_data( filename,variablename,specie)
+ time = h5read(filename,'/data/var3d/time');
+ p = h5read(filename,['/data/grid/coordp_',specie]);
+ j = h5read(filename,['/data/grid/coordj_',specie]);
+ z = h5read(filename,'/data/grid/coordz');
+ dt = h5readatt(filename,'/data/input','dt');
+ cstart= h5readatt(filename,'/data/input','start_iframe3d');
+
+ data = zeros(numel(p),numel(j),numel(z),numel(time));
+ for it = 1:numel(time)
+ tmp = h5read(filename,['/data/var3d/',variablename,'/', num2str(cstart+it,'%06d')]);
+ data(:,:,:,it) = tmp;
+ end
+
+end
+
diff --git a/matlab/plot/plot_ballooning.m b/matlab/plot/plot_ballooning.m
index f209aea5..49d59248 100644
--- a/matlab/plot/plot_ballooning.m
+++ b/matlab/plot/plot_ballooning.m
@@ -1,30 +1,30 @@
function [FIG] = plot_ballooning(data,options)
-
+ FIG.fig = figure; iplot = 1;
[~,it] = min(abs(data.Ts3D - options.time_2_plot));
+ [~,ikyarray] = min(abs(data.ky - options.kymodes));
phi_real=(real(data.PHI(:,:,:,it)));
phi_imag=(imag(data.PHI(:,:,:,it)));
% Apply baollooning tranform
- for iky=2
+ for iky=ikyarray
dims = size(phi_real);
- phib_real = zeros( dims(1)*dims(3) ,1);
+ phib_real = zeros( dims(2)*dims(3) ,1);
phib_imag= phib_real;
b_angle = phib_real;
- midpoint = floor((dims(1)*dims(3) )/2)+1;
- for ip =1: dims(1)
- start_ = (ip -1)*dims(3) +1;
- end_ = ip*dims(3);
- phib_real(start_:end_) = phi_real(ip,iky,:);
- phib_imag(start_:end_) = phi_imag(ip,iky, :);
+ for ikx =1: dims(2)
+ start_ = (ikx -1)*dims(3) +1;
+ end_ = ikx*dims(3);
+ phib_real(start_:end_) = phi_real(iky,ikx,:);
+ phib_imag(start_:end_) = phi_imag(iky,ikx,:);
end
% Define ballooning angle
Nkx = numel(data.kx)-1; coordz = data.z;
idx = -Nkx:1:Nkx;
- for ip =1: dims(1)
+ for ikx =1: dims(2)
for iz=1:dims(3)
- ii = dims(3)*(ip -1) + iz;
- b_angle(ii) =coordz(iz) + 2*pi*idx(ip);
+ ii = dims(3)*(ikx -1) + iz;
+ b_angle(ii) =coordz(iz) + 2*pi*idx(ikx);
end
end
@@ -40,14 +40,15 @@ function [FIG] = plot_ballooning(data,options)
phib_real_norm = real( phib_norm);%phib_real(:)/phib_real(idxLFS);
phib_imag_norm = imag( phib_norm);%phib_imag(:)/ phib_imag(idxLFS);
-
- FIG.fig = figure; hold all;
- plot(b_angle/pi, phib_real_norm,'-b');
+ subplot(numel(ikyarray),1,iplot)
+ plot(b_angle/pi, phib_real_norm,'-b'); hold on;
plot(b_angle/pi, phib_imag_norm ,'-r');
plot(b_angle/pi, sqrt(phib_real_norm .^2 + phib_imag_norm.^2),'-k');
legend('real','imag','norm')
xlabel('$\chi / \pi$')
ylabel('$\phi_B (\chi)$');
- title(['HeLaZ ballooning, t=',num2str(data.Ts3D(it))]);
+ title(['ky=',sprintf('%1.1f',data.ky(iky)),...
+ ',t=',sprintf('%1.1f',data.Ts3D(it))]);
+ iplot = iplot + 1;
end
end
diff --git a/matlab/plot/plot_fa.m b/matlab/plot/plot_fa.m
index ab93497e..00a2ca2f 100644
--- a/matlab/plot/plot_fa.m
+++ b/matlab/plot/plot_fa.m
@@ -26,13 +26,15 @@ if OPTIONS.ONED
end
else
- [SS,XX,FFa] = compute_fa_2D(DATA, OPTIONS);
+ [SS,XX,FFa] = compute_fa_2D(DATA, OPTIONS); sz = size(SS);
[~,it] = min(abs(OPTIONS.T-DATA.Ts5D));
switch OPTIONS.PLT_FCT
case 'contour'
- contour(SS,XX,FFa',128);
+ contour(SS,XX,FFa',sum(sz)/2);
case 'pcolor'
pclr = pcolor(SS,XX,FFa'); set(pclr, 'edgecolor','none'); shading interp
+ case 'contourf'
+ contourf(SS,XX,FFa',sum(sz)/2);
end
xlabel('$v_\parallel$'); ylabel('$\mu$');
legend(['$\langle |f_',OPTIONS.SPECIE,'|^2\rangle_{xy}^{1/2}$',zcomp])
diff --git a/matlab/plot/plot_fa_gene.m b/matlab/plot/plot_fa_gene.m
index 5a228a1f..997cfe1f 100644
--- a/matlab/plot/plot_fa_gene.m
+++ b/matlab/plot/plot_fa_gene.m
@@ -5,8 +5,8 @@ specie = OPTIONS.specie;
PLT_FCT= OPTIONS.PLT_FCT;
file = 'coord.dat.h5';
-vp = h5read([folder,file],'/coord/vp');
-mu = h5read([folder,file],'/coord/mu');
+vp = h5read([folder,file],'/coord/vp'); nvp = numel(vp);
+mu = h5read([folder,file],'/coord/mu'); nmu = numel(mu);
z = h5read([folder,file],'/coord/z');
[XX,SS] = meshgrid(mu,vp);
@@ -68,9 +68,9 @@ switch specie
FFa = abs(FFa)./max(max(abs(FFa)));
switch PLT_FCT
case 'contour'
- contour(SS,XX,FFa,128);
+ contour(SS,XX,FFa);
case 'contourf'
- pclr = contourf(SS,XX,FFa,128); set(pclr, 'edgecolor','none')
+ pclr = contourf(SS,XX,FFa);
case 'pcolor'
pclr = pcolor(SS,XX,FFa); set(pclr, 'edgecolor','none'); shading interp
end
@@ -80,9 +80,9 @@ switch specie
FFa = abs(FFa)./max(max(abs(FFa)));
switch PLT_FCT
case 'contour'
- contour(SS,XX,FFa,128);
+ contour(SS,XX,FFa,(nvp+nmu)/2);
case 'contourf'
- pclr = contourf(SS,XX,FFa,128); set(pclr, 'edgecolor','none')
+ pclr = contourf(SS,XX,FFa,(nvp+nmu)/2);
case 'pcolor'
pclr = pcolor(SS,XX,FFa); set(pclr, 'edgecolor','none'); shading interp
end
diff --git a/matlab/plot/show_napjz.m b/matlab/plot/show_napjz.m
new file mode 100644
index 00000000..e521b944
--- /dev/null
+++ b/matlab/plot/show_napjz.m
@@ -0,0 +1,136 @@
+function [ FIGURE ] = show_napjz( DATA, OPTIONS )
+fname = DATA.outfilenames{OPTIONS.JOBNUM+1};
+switch OPTIONS.specie
+ case 'i'
+ Pa = DATA.Pi;
+ Ja = DATA.Ji;
+ Napjz = load_pjz_data(fname,'Nipjz','i');
+ name = 'N_i^{pj}';
+ FIGURE.FIGNAME = ['Nipj_spectrum_',DATA.PARAMS];
+ case 'e'
+ Pa = DATA.Pe;
+ Ja = DATA.Je;
+ Napjz = load_pjz_data(fname,'Nipjz','i');
+ name = 'N_e^{pj}';
+ FIGURE.FIGNAME = ['Nepj_spectrum_',DATA.PARAMS];
+end
+
+switch OPTIONS.compz
+ case 'avg'
+ Napjz = squeeze(mean(Napjz,3));
+ otherwise
+ Napjz = squeeze(Napjz(:,:,OPTIONS.compz));
+end
+
+FIGURE.fig = figure;
+set(gcf, 'Position', [100 50 1000 400])
+
+switch OPTIONS.PLOT_TYPE
+ case 'space-time'
+ [JJ,PP] = meshgrid(Ja,Pa);
+ P2Ja = PP + 2*JJ;
+ % form an axis of velocity ordered moments
+ p2ja = unique(P2Ja);
+ % weights to average
+ weights = zeros(size(p2ja));
+ % space time of moments amplitude wrt to p+2j degree
+ Na_ST = zeros(numel(p2ja),numel(DATA.Ts5D));
+ % fill the st diagramm by averaging every p+2j=n moments together
+ for ip = 1:numel(Pa)
+ for ij = 1:numel(Ja)
+ [~,ip2j] = min(abs(p2ja-(Pa(ip)+2*Ja(ij))));
+ Na_ST(ip2j,:) = Na_ST(ip2j,:) + transpose(squeeze(Napjz(ip,ij,:)));
+ weights(ip2j) = weights(ip2j) + 1;
+ end
+ end
+ % doing the average
+ for ip2j = 1:numel(p2ja)
+ Na_ST(ip2j,:) = Na_ST(ip2j,:)/weights(ip2j);
+ end
+ % plots
+ if OPTIONS.NORMALIZED
+ plt = @(x,ip2j) x(ip2j,:)./max(x(ip2j,:));
+ else
+ plt = @(x,ip2j) x;
+ end
+ imagesc(DATA.Ts5D,p2ja,plt(Na_ST,1:numel(p2ja)));
+ set(gca,'YDir','normal')
+ xlabel('$t$'); ylabel('$p+2j$')
+ title('$\langle\sum_k |',name,'|\rangle_{p+2j=const}$')
+ if DATA.K_E
+ subplot(2,1,2)
+ imagesc(DATA.Ts5D,p2je,plt(Ne_ST,1:numel(p2ja)));
+ set(gca,'YDir','normal')
+ xlabel('$t$'); ylabel('$p+2j$')
+ title('$\langle\sum_k |N_e^{pj}|\rangle_{p+2j=const}$')
+ suptitle(DATA.param_title);
+ end
+
+ case 'Tavg-1D'
+ t0 = OPTIONS.TIME(1);
+ t1 = OPTIONS.TIME(end);
+ [~,it0] = min(abs(t0-DATA.Ts5D));
+ [~,it1] = min(abs(t1-DATA.Ts5D));
+ Napjz = mean(Napjz(:,:,it0:it1),3);
+ if DATA.K_E
+ Napjz = mean(Napjz(:,:,it0:it1),3);
+ end
+ if numel(OPTIONS.TIME) == 1
+ TITLE=['$t=',num2str(OPTIONS.TIME),'$'];
+ else
+ TITLE=['$t\in[',num2str(t0),',',num2str(t1),']$'];
+ end
+ Napjz = squeeze(Napjz);
+
+ ymini = min(Napjz); ymaxi = max(Napjz);
+
+ if DATA.K_E
+ Napjz = squeeze(Napjz);
+ ymine = min(Napjz); ymaxe = max(Napjz);
+ ymax = max([ymaxi ymaxe]);
+ ymin = min([ymini ymine]);
+ end
+ if DATA.K_E
+ subplot(121)
+ end
+ if ~OPTIONS.P2J
+ for ij = 1:numel(Ja)
+ name = ['$j=',num2str(Ja(ij)),'$'];
+ semilogy(Pa,Napjz(:,ij),'o-','DisplayName',name); hold on;
+ end
+ xlabel('$p$');
+ else
+ for ij = 1:numel(Ja)
+ name = ['$j=',num2str(Ja(ij)),'$'];
+ semilogy(Pa+2*Ja(ij),Napjz(:,ij),'o-','DisplayName',name); hold on;
+ end
+ xlabel('$p+2j$')
+ end
+ ylabel(['$\sum_{kx,ky}|N_i^{pj}|$']);
+ legend('show');
+ title([TITLE,' He-La ion spectrum']);
+
+ if DATA.K_E
+ subplot(122)
+ if ~OPTIONS.P2J
+ for ij = 1:numel(Ja)
+ name = ['$j=',num2str(Ja(ij)),'$'];
+ semilogy(Pa,Napjz(:,ij),'o-','DisplayName',name); hold on;
+ end
+ xlabel('p');
+ else
+ for ij = 1:numel(Ja)
+ name = ['$j=',num2str(Ja(ij)),'$'];
+ semilogy(Pa+2*Ja(ij),Napjz(:,ij),'o-','DisplayName',name); hold on;
+ end
+ xlabel('$p+2j$')
+ end
+ ylabel(['$\sum_{kx,ky}|N_e^{pj}|$']);
+ legend('show');
+ title([TITLE,' He-La elec. spectrum']);
+ end
+
+end
+
+end
+
diff --git a/wk/analysis_3D.m b/wk/analysis_3D.m
index 34dbcadc..f8ea45ee 100644
--- a/wk/analysis_3D.m
+++ b/wk/analysis_3D.m
@@ -40,20 +40,20 @@ end
if 0
%% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Options
-options.INTERP = 1;
+options.INTERP = 0;
options.POLARPLOT = 0;
-options.NAME = '\phi';
-% options.NAME = 'N_i^{00}';
+% options.NAME = '\phi';
+options.NAME = 'N_i^{00}';
% options.NAME = 'v_y';
% options.NAME = 'n_i^{NZ}';
% options.NAME = '\Gamma_x';
% options.NAME = 'n_i';
-options.PLAN = 'xy';
+options.PLAN = 'kxky';
% options.NAME = 'f_e';
% options.PLAN = 'sx';
-options.COMP = 'avg';
+options.COMP = 9;
% options.TIME = dat.Ts5D;
-options.TIME = 00:1:250;
+options.TIME = 200:1:600;
data.EPS = 0.1;
data.a = data.EPS * 2000;
create_film(data,options,'.gif')
@@ -62,7 +62,7 @@ end
if 0
%% 2D snapshots
% Options
-options.INTERP = 0;
+options.INTERP = 1;
options.POLARPLOT = 0;
options.AXISEQUAL = 1;
options.NAME = '\phi';
@@ -71,12 +71,12 @@ options.NAME = '\phi';
% options.NAME = 'T_i';
% options.NAME = '\Gamma_x';
% options.NAME = 'k^2n_e';
-options.PLAN = 'xy';
+options.PLAN = 'xz';
% options.NAME = 'f_e';
% options.PLAN = 'sx';
-options.COMP = 1;
-options.TIME = [150];
-data.a = data.EPS * 1000;
+options.COMP = 'avg';
+options.TIME = [260:265];
+data.a = data.EPS * 2e3;
fig = photomaton(data,options);
save_figure(data,fig)
end
@@ -85,8 +85,8 @@ if 0
%% 3D plot on the geometry
options.INTERP = 1;
options.NAME = 'n_i';
-options.PLANES = 1;
-options.TIME = [100 200];
+options.PLANES = [1:2:12];
+options.TIME = [60];
options.PLT_MTOPO = 1;
data.rho_o_R = 2e-3; % Sound larmor radius over Machine size ratio
fig = show_geometry(data,options);
@@ -100,8 +100,8 @@ if 0
options.SPAR = gene_data.vp';
options.XPERP = gene_data.mu';
options.Z = 'avg';
-options.T = 200;
-options.PLT_FCT = 'pcolor';
+options.T = 340;
+options.PLT_FCT = 'contour';
options.ONED = 0;
options.non_adiab = 1;
options.SPECIE = 'i';
@@ -113,10 +113,16 @@ end
if 0
%% Hermite-Laguerre spectrum
% options.TIME = 'avg';
-options.P2J = 1;
-options.ST = 0;
+options.P2J = 1;
+options.ST = 0;
+options.PLOT_TYPE = 'space-time';
options.NORMALIZED = 0;
-fig = show_moments_spectrum(data,options);
+options.JOBNUM = 03;
+options.TIME = [200 500];
+options.specie = 'i';
+options.compz = 'avg';
+% fig = show_moments_spectrum(data,options);
+fig = show_napjz(data,options);
save_figure(data,fig)
end
diff --git a/wk/gene_analysis_3D.m b/wk/gene_analysis_3D.m
index 7479f55e..5716569d 100644
--- a/wk/gene_analysis_3D.m
+++ b/wk/gene_analysis_3D.m
@@ -7,7 +7,6 @@ folder = '/misc/gene_results/shearless_cyclone/s_alpha_output_1.0/';
% folder = '/misc/gene_results/HP_fig_2b_mu_5e-2/';
% folder = '/misc/gene_results/HP_fig_2c_mu_5e-2/';
gene_data = load_gene_data(folder);
-% gene_data = rotate_c_plane_nxnky_to_nkxny(gene_data);
gene_data = invert_kxky_to_kykx_gene_results(gene_data);
if 1
%% Space time diagramm (fig 11 Ivanov 2020)
@@ -23,100 +22,19 @@ end
if 0
%% 2D snapshots
% Options
-options.INTERP = 1;
-options.POLARPLOT = 0;
-options.AXISEQUAL = 1;
-options.NAME = '\phi';
-% options.NAME = 'n_i';
-% options.NAME = 'T_i';
-% options.NAME = '\Gamma_x';
-% options.NAME = 'k^2n_e';
-options.PLAN = 'xz';
-% options.NAME ='f_e';
-% options.PLAN = 'sx';
-options.COMP = 'avg';
-options.TIME = [100 300 900];
-gene_data.a = data.EPS * 2000;
-fig = photomaton(gene_data,options);
-save_figure(gene_data,fig)
-end
-
-if 0
-%% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Options
options.INTERP = 0;
options.POLARPLOT = 0;
-options.NAME = '\phi';
-% options.NAME = 'v_y';
-% options.NAME = 'n_i^{NZ}';
-% options.NAME = '\Gamma_x';
-% options.NAME = 'n_i';
-options.PLAN = 'xy';
-% options.NAME = 'f_e';
-% options.PLAN = 'sx';
-options.COMP = 'avg';
-options.TIME = 000:200;
-gene_data.a = data.EPS * 2000;
-create_film(gene_data,options,'.gif')
-end
-
-if 0
-%% Geometry
-names = {'$g^{xx}$','$g^{xy}$','$g^{xz}$','$g^{yy}$','$g^{yz}$','$g^{zz}$',...
- '$B_0$','$\partial_x B_0$','$\partial_y B_0$','$\partial_z B_0$',...
- '$J$','$R$','$\phi$','$Z$','$\partial_R x$','$\partial_Z x$'};
-figure;
-subplot(311)
- for i = 1:6
- plot(gene_data.z, gene_data.geo_arrays(:,i),'DisplayName',names{i}); hold on;
- end
- xlim([min(gene_data.z),max(gene_data.z)]); legend('show'); title('GENE geometry');
-
-subplot(312)
- for i = 7:10
- plot(gene_data.z, gene_data.geo_arrays(:,i),'DisplayName',names{i}); hold on;
- end
- xlim([min(gene_data.z),max(gene_data.z)]); legend('show');
-
-subplot(313)
- for i = 11:16
- plot(gene_data.z, gene_data.geo_arrays(:,i),'DisplayName',names{i}); hold on;
- end
- xlim([min(gene_data.z),max(gene_data.z)]); legend('show');
-
-end
-% folder = '/misc/gene_results/HP_fig_2b_mu_5e-2/';
-folder = '/misc/gene_results/shearless_cyclone/s_alpha_output_1.0/';
-% folder = '/misc/gene_results/cyclone/s_alpha_output_1.0/';
-gene_data = load_gene_data(folder);
-gene_data = rotate_c_plane_nxnky_to_nkxny(gene_data);
-if 1
-%% Space time diagramm (fig 11 Ivanov 2020)
-TAVG_0 = 0.8*gene_data.Ts3D(end); TAVG_1 = gene_data.Ts3D(end); % Averaging times duration
-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 = '\phi'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
-options.INTERP = 1;
-fig = plot_radial_transport_and_spacetime(gene_data,options);
-% save_figure(data,fig)
-end
-
-if 0
-%% 2D snapshots
-% Options
-options.INTERP = 1;
-options.POLARPLOT = 0;
options.AXISEQUAL = 1;
-options.NAME = '\phi';
-% options.NAME = 'n_i';
+% options.NAME = 'Q_x';
+options.NAME = 'n_i';
% options.NAME = 'T_i';
% options.NAME = '\Gamma_x';
% options.NAME = 'k^2n_e';
-options.PLAN = 'xz';
+options.PLAN = 'xy';
% options.NAME ='f_e';
% options.PLAN = 'sx';
options.COMP = 'avg';
-options.TIME = [100 300 900];
+options.TIME = [200];
gene_data.a = data.EPS * 2000;
fig = photomaton(gene_data,options);
save_figure(gene_data,fig)
@@ -132,11 +50,11 @@ options.NAME = '\phi';
% options.NAME = 'n_i^{NZ}';
% options.NAME = '\Gamma_x';
% options.NAME = 'n_i';
-options.PLAN = 'xy';
+options.PLAN = 'kxky';
% options.NAME = 'f_e';
% options.PLAN = 'sx';
options.COMP = 'avg';
-options.TIME = 000:170;
+options.TIME = 000:700;
gene_data.a = data.EPS * 2000;
create_film(gene_data,options,'.gif')
end
@@ -175,7 +93,7 @@ options.PLT_FCT = 'pcolor';
options.folder = folder;
options.Z = 'avg';
options.FIELD = '<f_>';
-options.ONED = 0;
+options.ONED = 1;
% options.FIELD = 'Q_es';
plot_fa_gene(options);
end
diff --git a/wk/quick_run.m b/wk/quick_run.m
index e7525829..b3f5829b 100644
--- a/wk/quick_run.m
+++ b/wk/quick_run.m
@@ -13,33 +13,33 @@ EXECNAME = 'helaz3.12';
CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
-NU = 0.1; % Collision frequency
+NU = 0.0; % Collision frequency
TAU = 1.0; % e/i temperature ratio
-K_N = 1.9;%2.22; % Density gradient drive
-K_T = 0.25*K_N; % Temperature '''
+K_N = 2.22; % Density gradient drive
+K_T = 6.96; % Temperature '''
K_E = 0.0; % Electrostat '''
SIGMA_E = 0.0233380; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
-KIN_E = 1; % 1: kinetic electrons, 2: adiabatic electrons
+KIN_E = 0; % 1: kinetic electrons, 2: adiabatic electrons
%% GRID PARAMETERS
-PMAXE = 4; % Hermite basis size of electrons
-JMAXE = 2; % Laguerre "
-PMAXI = 4; % " ions
-JMAXI = 2; % "
-NX = 32; % real space x-gridpoints
-NY = 32; % '' y-gridpoints
+PMAXE = 8; % Hermite basis size of electrons
+JMAXE = 4; % Laguerre "
+PMAXI = 8; % " ions
+JMAXI = 4; % "
+NX = 1; % real space x-gridpoints
+NY = 20; % '' y-gridpoints
LX = 120; % Size of the squared frequency domain
LY = 120; % Size of the squared frequency domain
-NZ = 1; % number of perpendicular planes (parallel grid)
+NZ = 16; % number of perpendicular planes (parallel grid)
NPOL = 1;
SG = 0; % Staggered z grids option
%% GEOMETRY
GEOMETRY= 'Z-pinch'; % Z-pinch overwrites q0, shear and eps
% GEOMETRY= 's-alpha';
-Q0 = 2.5; % safety factor
+Q0 = 1.4; % safety factor
SHEAR = 0.0; % magnetic shear (Not implemented yet)
EPS = 0.18; % inverse aspect ratio
%% TIME PARMETERS
-TMAX = 25; % Maximal time unit
+TMAX = 50; % Maximal time unit
DT = 2e-2; % Time step
SPS0D = 1; % Sampling per time unit for 2D arrays
SPS2D = 0; % Sampling per time unit for 2D arrays
@@ -49,14 +49,14 @@ SPSCP = 0; % Sampling per time unit for checkpoints
JOB2LOAD= -1;
%% OPTIONS
SIMID = 'quick_run'; % Name of the simulation
-LINEARITY = 'nonlinear'; % activate non-linearity (is cancelled if KXEQ0 = 1)
+LINEARITY = 'linear'; % activate non-linearity (is cancelled if KXEQ0 = 1)
% Collision operator
% (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
-CO = 'SG';
+CO = 'DG';
GKCO = 1; % gyrokinetic operator
ABCO = 1; % interspecies collisions
INIT_ZF = 0; ZF_AMP = 0.0;
-CLOS = 0; % Closure model (0: =0 truncation, 1: gyrofluid closure (p+2j<=Pmax))s
+CLOS = 1; % Closure model (0: =0 truncation, 1: gyrofluid closure (p+2j<=Pmax))s
NL_CLOS = 0; % nonlinear closure model (-2:nmax=jmax; -1:nmax=jmax-j; >=0:nmax=NL_CLOS)
KERN = 0; % Kernel model (0 : GK)
INIT_OPT= 'phi'; % Start simulation with a noisy mom00/phi/allmom
@@ -75,7 +75,7 @@ MU = 0.0; % Hyperdiffusivity coefficient
INIT_BLOB = 0; WIPE_TURB = 0; ACT_ON_MODES = 0;
MU_X = MU; %
MU_Y = MU; %
-MU_Z = 0.0; %
+MU_Z = 0.2; %
MU_P = 0.0; %
MU_J = 0.0; %
LAMBDAD = 0.0;
@@ -114,12 +114,13 @@ end
if 0
%% Ballooning plot
options.time_2_plot = data.Ts3D(end);
+options.kymodes = [0.2 0.5 0.7];
options.normalized = 1;
options.field = 'phi';
fig = plot_ballooning(data,options);
end
-if 1
+if 0
%% linear growth rate for 3D Zpinch (kz fourier transform)
trange = [0.5 1]*data.Ts3D(end);
options.keq0 = 1; % chose to plot planes at k=0 or max
--
GitLab