diff --git a/matlab/compute/invert_kxky_to_kykx_gene_results.m b/matlab/compute/invert_kxky_to_kykx_gene_results.m
index 462846b7a85aa00d4f964901258455899898df68..3f320d653472aa52e6583aee1097355680323f1e 100644
--- a/matlab/compute/invert_kxky_to_kykx_gene_results.m
+++ b/matlab/compute/invert_kxky_to_kykx_gene_results.m
@@ -9,19 +9,19 @@ data.TPER_I = rotate(data.TPER_I);
data.TPAR_I = rotate(data.TPAR_I);
data.TEMP_I = rotate(data.TEMP_I);
-data.Ny = data.Nky*2-1;
-data.Nx = data.Nkx;
+data.grids.Ny = data.grids.Nky*2-1;
+data.grids.Nx = data.grids.Nkx;
-if numel(data.kx)>1
- dkx = data.kx(2);
+if numel(data.grids.kx)>1
+ dkx = data.grids.kx(2);
else
dkx = 1;
end
-dky = data.ky(2);
+dky = data.grids.ky(2);
Lx = 2*pi/dkx; Ly = 2*pi/dky;
-x = linspace(-Lx/2,Lx/2,data.Nx+1); x = x(1:end-1);
-y = linspace(-Ly/2,Ly/2,data.Ny+1); y = y(1:end-1);
-data.x = x; data.y = y; data.Lx = Lx; data.Ly = Ly;
+x = linspace(-Lx/2,Lx/2,data.grids.Nx+1); x = x(1:end-1);
+y = linspace(-Ly/2,Ly/2,data.grids.Ny+1); y = y(1:end-1);
+data.grids.x = x; data.grids.y = y; data.grids.Lx = Lx; data.grids.Ly = Ly;
end
diff --git a/matlab/load/compile_results_2D.m b/matlab/load/compile_results_2D.m
new file mode 100644
index 0000000000000000000000000000000000000000..b2ec59459f7093786433df59687a77e403555c2d
--- /dev/null
+++ b/matlab/load/compile_results_2D.m
@@ -0,0 +1,37 @@
+function [field, Ts2D] = compile_results_2D(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_2D_data(filename, fieldname);
+ field = cat(3,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_5Da.m b/matlab/load/compile_results_5Da.m
new file mode 100644
index 0000000000000000000000000000000000000000..914de52aeb7af3d7515a422f3ec87e4212c2e243
--- /dev/null
+++ b/matlab/load/compile_results_5Da.m
@@ -0,0 +1,37 @@
+function [field, Ts5D] = compile_results_5Da(DIRECTORY,JOBNUMMIN,JOBNUMMAX,fieldname)
+CONTINUE = 1;
+JOBNUM = JOBNUMMIN; JOBFOUND = 0;
+% field
+field = [];
+Ts5D = [];
+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/var5d/time'));
+ catch
+ openable = 0;
+ end
+ if openable
+ % load field %%
+ [ F, T, ~] = load_5Da_data(filename, fieldname);
+ field = cat(7,field,F);
+ Ts5D = cat(1,Ts5D,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 cac486ac58f1d3c5863e3f0a75f2853d79fa4000..0c80bd79b489899c6d3289c367cbf1eb921e2066 100644
--- a/matlab/load/compile_results_low_mem.m
+++ b/matlab/load/compile_results_low_mem.m
@@ -1,6 +1,8 @@
function [DATA] = compile_results_low_mem(DATA,DIRECTORY,JOBNUMMIN,JOBNUMMAX)
CONTINUE = 1;
JOBNUM = JOBNUMMIN; JOBFOUND = 0;
+DATA.CODENAME = 'GYAC';
+DATA.folder = DIRECTORY;
DATA.params_evol.TJOB_SE = []; % Start and end times of jobs
DATA.params_evol.NU_EVOL = []; % evolution of parameter nu between jobs
DATA.params_evol.CO_EVOL = []; % evolution of CO
@@ -51,8 +53,8 @@ while(CONTINUE)
[ GGAMMA_R, Ts0D, ~] = load_0D_data(filename, 'gflux_xi');
PGAMMA_R = load_0D_data(filename, 'pflux_xi');
end
- GGAMMA_ = cat(1,GGAMMA_,GGAMMA_R); clear GGAMMA_R
- PGAMMA_ = cat(1,PGAMMA_,PGAMMA_R); clear PGAMMA_R
+ GGAMMA_ = cat(2,GGAMMA_,GGAMMA_R); clear GGAMMA_R
+ PGAMMA_ = cat(2,PGAMMA_,PGAMMA_R); clear PGAMMA_R
end
if W_HF
@@ -62,7 +64,7 @@ while(CONTINUE)
% old version
[ HFLUX_X, Ts0D, ~] = load_0D_data(filename, 'hflux_xi');
end
- HFLUX_ = cat(1,HFLUX_,HFLUX_X); clear HFLUX_X
+ HFLUX_ = cat(2,HFLUX_,HFLUX_X); clear HFLUX_X
end
Ts0D_ = cat(1,Ts0D_,Ts0D);
diff --git a/matlab/load/load_0D_data.m b/matlab/load/load_0D_data.m
index a4d20bd59a2f8d139eda8e338f57bc6a311db639..c9d75ee1d21e08fdeb79f72e4e4ac2e50cdb1a44 100644
--- a/matlab/load/load_0D_data.m
+++ b/matlab/load/load_0D_data.m
@@ -5,6 +5,6 @@ function [ data, time, dt ] = load_0D_data( filename, variablename )
Na = h5readatt(filename,'/data/input/model','Na');
cstart= h5readatt(filename,'/data/input/basic','start_iframe0d');
data = h5read(filename,['/data/var0d/',variablename]);
-% data = reshape(data,[Na, numel(time)]);
+ data = reshape(data,[Na, numel(time)]);
end
diff --git a/matlab/load/load_2D_data.m b/matlab/load/load_2D_data.m
index b013a63d4be724587abf43b7913cba5421387647..67da60c9dd1931e73cde73c7520ecb6370a0c153 100644
--- a/matlab/load/load_2D_data.m
+++ b/matlab/load/load_2D_data.m
@@ -1,15 +1,28 @@
function [ data, time, dt ] = load_2D_data( filename, variablename )
-%LOAD_2D_DATA load a 2D variable stored in a hdf5 result file from HeLaZ
+%LOAD_3D_DATA load a 3D variable stored in a hdf5 result file from HeLaZ
time = h5read(filename,'/data/var2d/time');
- kx = h5read(filename,'/data/grid/coordkx');
- ky = h5read(filename,'/data/grid/coordky');
- dt = h5readatt(filename,'/data/input','dt');
- cstart= h5readatt(filename,'/data/input','start_iframe2d');
+ dt = h5readatt(filename,'/data/input/basic','dt');
+ cstart= h5readatt(filename,'/data/input/basic','start_iframe3d');
+
+ % 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
+
+ data = zeros(sz);
- data = zeros(numel(kx),numel(ky),numel(time));
for it = 1:numel(time)
tmp = h5read(filename,['/data/var2d/',variablename,'/', num2str(cstart+it,'%06d')]);
- data(:,:,it) = tmp.real + 1i * tmp.imaginary;
+ if cmpx
+ data(:,:,it) = tmp.real + 1i * tmp.imaginary;
+ else
+ data(:,:,it) = tmp;
+ end
end
end
diff --git a/matlab/load/load_5Da_data.m b/matlab/load/load_5Da_data.m
new file mode 100644
index 0000000000000000000000000000000000000000..2077b119d61e69e5eda85b105bd5465bf23241e7
--- /dev/null
+++ b/matlab/load/load_5Da_data.m
@@ -0,0 +1,36 @@
+function [ data, time, dt ] = load_5Da_data( filename, variablename )
+%LOAD_3D_DATA load a 3D variable stored in a hdf5 result file from HeLaZ
+ time = h5read(filename,'/data/var5d/time');
+ dt = h5readatt(filename,'/data/input/basic','dt');
+ cstart= h5readatt(filename,'/data/input/basic','start_iframe3d');
+ 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/var5d/',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 time dimension
+ data = zeros([Na,Np,Nj,Nky,Nkx,Nz,numel(time)]);
+
+ for it = 1:numel(time)
+ tmp = h5read(filename,['/data/var5d/',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_gene_data.m b/matlab/load/load_gene_data.m
index 8c877d2e5c235a922efaf812d17ec03ce216e05a..196e899617f3ed7af330823bf805d1bb3f7e4c1a 100644
--- a/matlab/load/load_gene_data.m
+++ b/matlab/load/load_gene_data.m
@@ -5,35 +5,35 @@ DATA.namelist = namelist;
DATA.folder = folder;
%% Grid
coofile = 'coord.dat.h5';
-DATA.vp = h5read([folder,coofile],'/coord/vp');
-DATA.Nvp = numel(DATA.vp);
+DATA.grids.vp = h5read([folder,coofile],'/coord/vp');
+DATA.grids.Nvp = numel(DATA.grids.vp);
-DATA.mu = h5read([folder,coofile],'/coord/mu');
-DATA.Nmu = numel(DATA.mu);
+DATA.grids.mu = h5read([folder,coofile],'/coord/mu');
+DATA.grids.Nmu = numel(DATA.grids.mu);
-DATA.kx = h5read([folder,coofile],'/coord/kx');
-DATA.Nkx = numel(DATA.kx);
-DATA.Nx = DATA.Nkx;
+DATA.grids.kx = h5read([folder,coofile],'/coord/kx');
+DATA.grids.Nkx = numel(DATA.grids.kx);
+DATA.grids.Nx = DATA.grids.Nkx;
-DATA.ky = h5read([folder,coofile],'/coord/ky');
-DATA.Nky = numel(DATA.ky);
-DATA.Ny = DATA.Nky*2-1;
+DATA.grids.ky = h5read([folder,coofile],'/coord/ky');
+DATA.grids.Nky = numel(DATA.grids.ky);
+DATA.grids.Ny = DATA.grids.Nky*2-1;
-DATA.z = h5read([folder,coofile],'/coord/z');
-DATA.Nz = numel(DATA.z);
+DATA.grids.z = h5read([folder,coofile],'/coord/z');
+DATA.grids.Nz = numel(DATA.grids.z);
-DATA.paramshort = [num2str(DATA.Nkx),'x',num2str(DATA.Nky),'x',num2str(DATA.Nz),...
- 'x',num2str(DATA.Nvp),'x',num2str(DATA.Nmu)];
-if numel(DATA.kx)>1
- dkx = DATA.kx(2);
+DATA.params_string = [num2str(DATA.grids.Nkx),'x',num2str(DATA.grids.Nky),'x',num2str(DATA.grids.Nz),...
+ 'x',num2str(DATA.grids.Nvp),'x',num2str(DATA.grids.Nmu)];
+if numel(DATA.grids.kx)>1
+ dkx = DATA.grids.kx(2);
else
dkx = 1;
end
-dky = DATA.ky(2);
+dky = DATA.grids.ky(2);
Lx = 2*pi/dkx; Ly = 2*pi/dky;
-x = linspace(-Lx/2,Lx/2,DATA.Nx+1); x = x(1:end-1);
-y = linspace(-Ly/2,Ly/2,DATA.Ny+1); y = y(1:end-1);
-DATA.x = x; DATA.y = y; DATA.Lx = Lx; DATA.Ly = Ly;
+x = linspace(-Lx/2,Lx/2,DATA.grids.Nx+1); x = x(1:end-1);
+y = linspace(-Ly/2,Ly/2,DATA.grids.Ny+1); y = y(1:end-1);
+DATA.grids.x = x; DATA.grids.y = y; DATA.grids.Lx = Lx; DATA.grids.Ly = Ly;
%% Transport
nrgfile = 'nrg.dat.h5';
% nrgfile = 'nrg_1.h5';
@@ -45,10 +45,10 @@ DATA.HFLUX_X = h5read([folder,nrgfile],'/nrgions/Q_es');
phifile = 'field.dat.h5';
% phifile = 'field_1.h5';
DATA.Ts3D = h5read([folder,phifile],'/field/time');
-DATA.DENS_I = zeros(DATA.Nkx,DATA.Nky,DATA.Nz,numel(DATA.Ts3D));
-DATA.TPER_I = zeros(DATA.Nkx,DATA.Nky,DATA.Nz,numel(DATA.Ts3D));
-DATA.TPAR_I = zeros(DATA.Nkx,DATA.Nky,DATA.Nz,numel(DATA.Ts3D));
-DATA.PHI = zeros(DATA.Nkx,DATA.Nky,DATA.Nz,numel(DATA.Ts3D));
+DATA.DENS_I = zeros(DATA.grids.Nkx,DATA.grids.Nky,DATA.grids.Nz,numel(DATA.Ts3D));
+DATA.TPER_I = zeros(DATA.grids.Nkx,DATA.grids.Nky,DATA.grids.Nz,numel(DATA.Ts3D));
+DATA.TPAR_I = zeros(DATA.grids.Nkx,DATA.grids.Nky,DATA.grids.Nz,numel(DATA.Ts3D));
+DATA.PHI = zeros(DATA.grids.Nkx,DATA.grids.Nky,DATA.grids.Nz,numel(DATA.Ts3D));
momfile = 'mom_ions.dat.h5';
% momfile = 'mom_ions_1.h5';
diff --git a/matlab/plot/show_moments_spectrum.m b/matlab/plot/show_moments_spectrum.m
index 02291c8e2e11b50772b0763ae61e5f833c4ecb39..d4d71fccd12d133015d88c0d4da74ccce9fb0964 100644
--- a/matlab/plot/show_moments_spectrum.m
+++ b/matlab/plot/show_moments_spectrum.m
@@ -6,98 +6,83 @@ 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
-% compress = @(x,ia) log(sum(abs(squeeze(x(ia,:,:,:))),3));
- compress = @(x,ia) log(sum(abs(squeeze(x(:,:,:,:))),3));
+ logname = 'log';
+ compress = @(x,ia) squeeze(log(sum(abs(x(ia,:,:,:,:)),4)));
+% compress = @(x,ia) log(sum(abs(squeeze(x(:,:,:,:))),3));
else
-% compress = @(x,ia) sum(abs(squeeze(x(ia,:,:,:))),3);
- compress = @(x,ia) sum(abs(squeeze(x(:,:,:,:))),3);
+ logname = '';
+ compress = @(x,ia) squeeze(sum(abs(x(ia,:,:,:,:)),4));
+% compress = @(x,ia) sum(abs(squeeze(x(:,:,:,:))),3);
end
for ia = 1:DATA.inputs.Na
% Napjz = sum(abs(squeeze(DATA.Napjz(ia,:,:,:,:))),3);
- Napjz =compress(DATA.Napjz);
+ Napjz =compress(DATA.Napjz,ia);
subplot(double(DATA.inputs.Na),1,double(ia))
- if OPTIONS.P2J
- plotname = ['$\langle\sum_k |N_',species_name{ia},'^{pj}|\rangle_{p+2j=const}$'];
- [JJ,PP] = meshgrid(Ja,Pa);
- P2J = PP + 2*JJ;
- % form an axis of velocity ordered moments
- p2j = unique(P2J); yname = '$p+2j$';
- % weights to average
- weights = zeros(size(p2j));
- % space time of moments amplitude wrt to p+2j degree
- Na_ST = zeros(numel(p2j),numel(Time_));
- % 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(p2j-(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(p2j)
- Na_ST(ip2j,:) = Na_ST(ip2j,:)/weights(ip2j);
- end
- ticks_labels = {};
- else % We just order our moments w.r.t. to the convention ..
- % (0,0) (1,0) (2,0) (0,1) (3,0) (1,1) (4,0) (2,1) (0,2) etc.
- plotname = '$\langle\sum_k |N_i^{pj}|^2\rangle_z$';
- Nmoments = numel(Napjz(:,:,1)); % total number of moments
- HL_deg = zeros(Nmoments,2); % list of degrees, first column Hermite, second Laguerre
- im = 2;
- deg = 1; % the zero degree is always here first place
- ticks_labels = cell(10,1);
- ticks_labels{1} = '(0,0)';
- while(im<=Nmoments)
- FOUND = 1;
- while(FOUND) % As we find a pair matching the degree we retry
- FOUND = 0;
- for ij = 1:DATA.grids.Nj
- for ip = 1:DATA.grids.Np
- if((ip-1)+2*(ij-1) == deg)
- % Check if the pair is already added
- check_ = HL_deg == [DATA.grids.Parray(ip) DATA.grids.Jarray(ij)];
- check_ = sum(check_(:,1) .* check_(:,2));
- if ~check_ % if not add it
- HL_deg(im,1) = DATA.grids.Parray(ip);
- HL_deg(im,2) = DATA.grids.Jarray(ij);
- ticks_labels{im} = ['(',num2str(DATA.grids.Parray(ip)),',',num2str(DATA.grids.Jarray(ij)),')'];
- im = im + 1; FOUND = 1;
- end
- end
+ plotname = [logname,'$\langle\sum_k |N_',species_name{ia},'^{pj}|\rangle_{p+2j=const}$'];
+ %We order the moments (0,0) (1,0) (2,0) (0,1) (3,0) (1,1) (4,0) (2,1) (0,2) etc.
+ Nmoments = numel(Napjz(:,:,1)); % total number of moments
+ HL_deg = zeros(Nmoments,2); % list of degrees, first column Hermite, second Laguerre
+ im = 2;
+ deg = 1; % the zero degree is always here first place
+ ticks_labels = cell(10,1);
+ ticks_labels{1} = '(0,0)';
+ while(im<=Nmoments)
+ FOUND = 1;
+ while(FOUND) % As we find a pair matching the degree we retry
+ FOUND = 0;
+ for ij = 1:DATA.grids.Nj
+ for ip = 1:DATA.grids.Np
+ if((ip-1)+2*(ij-1) == deg)
+ % Check if the pair is already added
+ check_ = HL_deg == [DATA.grids.Parray(ip) DATA.grids.Jarray(ij)];
+ check_ = sum(check_(:,1) .* check_(:,2));
+ if ~check_ % if not add it
+ HL_deg(im,1) = DATA.grids.Parray(ip);
+ HL_deg(im,2) = DATA.grids.Jarray(ij);
+ ticks_labels{im} = ['(',num2str(DATA.grids.Parray(ip)),',',num2str(DATA.grids.Jarray(ij)),')'];
+ im = im + 1; FOUND = 1;
end
end
+ end
end
- % No pair found anymore, increase the degree
- deg = deg + 1;
- end
-
- % form an axis of velocity ordered moments
- p2j = 1:Nmoments; yname = '$(P,J)$';
- % space time of moments amplitude wrt to p+2j degree
- Na_ST = zeros(Nmoments,numel(Time_));
- for i_ = 1:Nmoments
- Na_ST(i_,:) = Napjz((HL_deg(i_,1)/DATA.grids.deltap)+1,HL_deg(i_,2)+1,:);
end
- end
+ % No pair found anymore, increase the degree
+ deg = deg + 1;
+ end
+ % form an axis of velocity ordered moments
+ p2j = 1:Nmoments; yname = '$(P,J)$';
+ % space time of moments amplitude wrt to p+2j degree
+ Na_ST = zeros(Nmoments,numel(Time_));
+ for i_ = 1:Nmoments
+ Na_ST(i_,:) = Napjz((HL_deg(i_,1)/DATA.grids.deltap)+1,HL_deg(i_,2)+1,:);
+ end
% plots
% scaling
if OPTIONS.NORMALIZED
- plt = @(x,i) x(i,:)./max(x(i,:));
+ plt = @(x,i) squeeze(x(i,:)./max(x(i,:)));
else
- plt = @(x,i) x;
- end
-
- imagesc(Time_,p2j,plt(Na_ST,1:numel(p2j)));
- set(gca,'YDir','normal')
- xlabel('$t$'); ylabel(yname);
- if ~isempty(ticks_labels)
- yticks(p2j);
- yticklabels(ticks_labels)
+ plt = @(x,i) squeeze(x(i,:));
end
+ if OPTIONS.ST
+ imagesc(Time_,p2j,plt(Na_ST,1:numel(p2j)));
+ set(gca,'YDir','normal')
+ xlabel('$t$'); ylabel(yname);
+ if ~isempty(ticks_labels)
+ yticks(p2j);
+ yticklabels(ticks_labels)
+ end
+ else
+ colors_ = jet(numel(p2j));
+ for i = 1:numel(p2j)
+ semilogy(Time_,plt(Na_ST,i),...
+ 'DisplayName',ticks_labels{i},...
+ 'color',colors_(i,:)); hold on;
+ end
title(plotname)
-
end
suptitle(DATA.paramshort)
diff --git a/matlab/profiler.m b/matlab/profiler.m
index 5056f61e4e709e2f65f094e9dd41484c57c8bfb0..43a3713a1c24cdb63d077c38b9d0e56dc72311fb 100644
--- a/matlab/profiler.m
+++ b/matlab/profiler.m
@@ -24,7 +24,8 @@ for i = 1:numel(data.outfilenames)
STETC = [ STETC; h5read(outfilename,'/profiler/Tc_step')];
TS0TC = [ TS0TC; h5read(outfilename,'/profiler/time')];
end
-
+CPUTI = CPUTI(end);
+DTSIM = mean(DTSIM);
N_T = 12;
missing_Tc = STETC - RHSTC - ADVTC - GHOTC - CLOTC ...
diff --git a/wk/analysis_gene.m b/wk/analysis_gene.m
index b3aa355a68f1fb929cdf35527a539bf252465c4b..a968d3db896445b50f2370645eb044d329366f29 100644
--- a/wk/analysis_gene.m
+++ b/wk/analysis_gene.m
@@ -47,14 +47,14 @@ addpath(genpath([gyacomodir,'matlab/load'])) % ... add
%Paper 2
% folder = '/misc/gene_results/CBC/KT_6.96_64x32x32x24x12_Nexc_5/';
% folder = '/misc/gene_results/CBC/KT_6.96_128x64x24x8x4_Nexc_5_00/';
-% folder = '/misc/gene_results/CBC/KT_6.96_128x64x24x16x8_Nexc_5_00/';
+folder = '/misc/gene_results/CBC/KT_6.96_128x64x24x16x8_Nexc_5_00/';
% folder = '/misc/gene_results/CBC/KT_6.96_128x64x24x32x16_Nexc_5_00/';
% folder = '/misc/gene_results/CBC/KT_6.96_128x64x24x32x16_Nexc_5_01/';
% folder = '/misc/gene_results/CBC/KT_5.3_128x64x24x32x16_Nexc_5_00/';
% folder = '/misc/gene_results/CBC/KT_5.3_128x64x24x32x16_Nexc_5_01/';
% folder = '/misc/gene_results/CBC/new_sim/KT_5.3_128x64x24x16x8_Nexc_5/';
-folder = '/misc/gene_results/CBC/new_sim/KT_5.3_128x64x24x8x4_Nexc_5/';
+% folder = '/misc/gene_results/CBC/new_sim/KT_5.3_128x64x24x8x4_Nexc_5/';
% folder = '/misc/gene_results/CBC/new_sim/KT_6.96_128x64x24x8x4_Nexc_5_smallvbox/';
% folder = '/misc/gene_results/CBC/new_sim/KT_6.96_128x64x24x16x8_Nexc_5_largexbox/';
% folder = '/misc/gene_results/CBC/KT_5.3_128x64x24x16x8_Muz_0.02/';
@@ -69,10 +69,12 @@ folder = '/misc/gene_results/CBC/new_sim/KT_5.3_128x64x24x8x4_Nexc_5/';
gene_data = load_gene_data(folder);
gene_data.FIGDIR = folder;
gene_data = invert_kxky_to_kykx_gene_results(gene_data);
-gene_data.Pmaxi = gene_data.Nvp-1;
-gene_data.Jmaxi = gene_data.Nmu-1;
+gene_data.grids.Np = gene_data.grids.Nvp-1;
+gene_data.grids.Nj = gene_data.grids.Nmu-1;
gene_data.CODENAME = 'GENE';
-
+gene_data.inputs = gene_data.grids;
+gene_data.inputs.Na = 1;
+gene_data.paramshort = gene_data.params_string;
%% Dashboard (Compilation of main plots of the sim)
dashboard(gene_data);
@@ -86,7 +88,7 @@ options.ST_FIELD = '\phi'; % chose your field to plot in spacetime diag
options.INTERP = 1;
options.NCUT = 4; % Number of cuts for averaging and error estimation
options.RESOLUTION = 256;
-fig = plot_radial_transport_and_spacetime(gene_data,options,'GENE');
+fig = plot_radial_transport_and_spacetime(gene_data,options);
save_figure(gene_data,fig,'.png')
end
diff --git a/wk/benchmark and scan scripts/Ajay_scan_CH4_lin_ITG.m b/wk/benchmark and scan scripts/old/Ajay_scan_CH4_lin_ITG.m
similarity index 100%
rename from wk/benchmark and scan scripts/Ajay_scan_CH4_lin_ITG.m
rename to wk/benchmark and scan scripts/old/Ajay_scan_CH4_lin_ITG.m
diff --git a/wk/benchmark and scan scripts/CBC_P_J_scan.m b/wk/benchmark and scan scripts/old/CBC_P_J_scan.m
similarity index 100%
rename from wk/benchmark and scan scripts/CBC_P_J_scan.m
rename to wk/benchmark and scan scripts/old/CBC_P_J_scan.m
diff --git a/wk/benchmark and scan scripts/CBC_hypcoll_PJ_scan.m b/wk/benchmark and scan scripts/old/CBC_hypcoll_PJ_scan.m
similarity index 100%
rename from wk/benchmark and scan scripts/CBC_hypcoll_PJ_scan.m
rename to wk/benchmark and scan scripts/old/CBC_hypcoll_PJ_scan.m
diff --git a/wk/benchmark and scan scripts/CBC_kT_PJ_scan.m b/wk/benchmark and scan scripts/old/CBC_kT_PJ_scan.m
similarity index 100%
rename from wk/benchmark and scan scripts/CBC_kT_PJ_scan.m
rename to wk/benchmark and scan scripts/old/CBC_kT_PJ_scan.m
diff --git a/wk/benchmark and scan scripts/CBC_kT_nu_scan.m b/wk/benchmark and scan scripts/old/CBC_kT_nu_scan.m
similarity index 100%
rename from wk/benchmark and scan scripts/CBC_kT_nu_scan.m
rename to wk/benchmark and scan scripts/old/CBC_kT_nu_scan.m
diff --git a/wk/benchmark and scan scripts/CBC_nu_PJ_scan.m b/wk/benchmark and scan scripts/old/CBC_nu_PJ_scan.m
similarity index 100%
rename from wk/benchmark and scan scripts/CBC_nu_PJ_scan.m
rename to wk/benchmark and scan scripts/old/CBC_nu_PJ_scan.m
diff --git a/wk/benchmark and scan scripts/lin_3D_Zpinch.m b/wk/benchmark and scan scripts/old/lin_3D_Zpinch.m
similarity index 100%
rename from wk/benchmark and scan scripts/lin_3D_Zpinch.m
rename to wk/benchmark and scan scripts/old/lin_3D_Zpinch.m
diff --git a/wk/benchmark and scan scripts/lin_ETPY.m b/wk/benchmark and scan scripts/old/lin_ETPY.m
similarity index 100%
rename from wk/benchmark and scan scripts/lin_ETPY.m
rename to wk/benchmark and scan scripts/old/lin_ETPY.m
diff --git a/wk/benchmark and scan scripts/lin_ITG.m b/wk/benchmark and scan scripts/old/lin_ITG.m
similarity index 100%
rename from wk/benchmark and scan scripts/lin_ITG.m
rename to wk/benchmark and scan scripts/old/lin_ITG.m
diff --git a/wk/benchmark and scan scripts/lin_KBM.m b/wk/benchmark and scan scripts/old/lin_KBM.m
similarity index 100%
rename from wk/benchmark and scan scripts/lin_KBM.m
rename to wk/benchmark and scan scripts/old/lin_KBM.m
diff --git a/wk/benchmark and scan scripts/lin_MTM.m b/wk/benchmark and scan scripts/old/lin_MTM.m
similarity index 100%
rename from wk/benchmark and scan scripts/lin_MTM.m
rename to wk/benchmark and scan scripts/old/lin_MTM.m
diff --git a/wk/benchmark and scan scripts/lin_RHT.m b/wk/benchmark and scan scripts/old/lin_RHT.m
similarity index 100%
rename from wk/benchmark and scan scripts/lin_RHT.m
rename to wk/benchmark and scan scripts/old/lin_RHT.m
diff --git a/wk/benchmark and scan scripts/lin_TEM.m b/wk/benchmark and scan scripts/old/lin_TEM.m
similarity index 100%
rename from wk/benchmark and scan scripts/lin_TEM.m
rename to wk/benchmark and scan scripts/old/lin_TEM.m
diff --git a/wk/dashboard.m b/wk/dashboard.m
index 6c4f65b69c028cad173114e510fddc2d97595a24..7937ef7697747be45643c452e5f694f558542d07 100644
--- a/wk/dashboard.m
+++ b/wk/dashboard.m
@@ -22,7 +22,7 @@ options.ST_FIELD = '\phi'; % chose your field to plot in spacetime diag
options.INTERP = 1;
options.NCUT = 4; % Number of cuts for averaging and error estimation
options.RESOLUTION = 256;
-PLOT = plot_radial_transport_and_spacetime(DATA,options,'GENE');
+PLOT = plot_radial_transport_and_spacetime(DATA,options);
% Put on full fig
axcp = copyobj(PLOT.ax1,full_fig);
set(axcp,'Position',get(axes(1),'position'));delete(axes(1));
diff --git a/wk/fast_analysis.m b/wk/fast_analysis.m
index 6f3841cca6ad5f997056f69ce15c059a3f5fc1f6..af8a6e41f1a863aead95f9067732c1288ca0119e 100644
--- a/wk/fast_analysis.m
+++ b/wk/fast_analysis.m
@@ -18,14 +18,25 @@ PARTITION = '/home/ahoffman/gyacomo/';
% resdir = 'paper_2_GYAC23/precision_study/test_3x2x128x64x24_sp_muz_2.0';
% resdir = 'paper_2_GYAC23/precision_study/3x2x128x64x24_sp_clos_1';
-%%
-% resdir = 'paper_2_GYAC23/collisionless/kT_5.3/5x3x128x64x24_dp_muz_2.0';
-% resdir = 'paper_2_GYAC23/collisionless/kT_5.3/5x3x128x64x24_dp_muz_2.0_full_NL';
+%%
% resdir = 'paper_2_GYAC23/collisionless/kT_5.3/5x3x128x64x24_dp_muz_2.0_muxy_0';
+% resdir = 'paper_2_GYAC23/collisionless/kT_5.3/5x3x128x64x24_dp_SG';
+% resdir = 'paper_2_GYAC23/collisionless/kT_5.3/5x3x128x64x24_dp_muz_2.0_full_NL';
+% resdir = 'paper_2_GYAC23/collisionless/kT_5.3/7x4x128x64x24_dp';
+% resdir = 'paper_2_GYAC23/collisionless/kT_5.3/9x5x128x64x24_dp';
+% resdir = 'paper_2_GYAC23/collisionless/kT_5.3/11x6x128x64x24_dp';
+% resdir = 'paper_2_GYAC23/collisionless/CBC/5x3x128x64x24_dp';
+% resdir = 'paper_2_GYAC23/collisionless/CBC/7x4x128x64x24_dp';
+% resdir = 'paper_2_GYAC23/collisionless/CBC/9x5x128x64x24_dp';
+% resdir = 'paper_2_GYAC23/collisionless/CBC/11x6x128x64x24_dp';
+% resdir = 'paper_2_GYAC23/collisionless/CBC/9x5x192x96x32_dp';
%% testcases
-resdir = 'testcases/zpinch_example';
+% resdir = 'testcases/zpinch_example';
% resdir = 'testcases/cyclone_example';
+resdir = 'testcases/DLRA_zpinch/base_case';
+% resdir = 'testcases/DLRA_zpinch/nsv_filter_2';
+% resdir = 'testcases/DLRA_zpinch/nsv_filter_6';
%%
J0 = 00; J1 = 10;
@@ -35,7 +46,7 @@ DATADIR = [PARTITION,resdir,'/'];
data = {};
data = compile_results_low_mem(data,DATADIR,J0,J1);
-if 0
+if 1
%% Plot transport and phi radial profile
[data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
@@ -49,10 +60,11 @@ options.INTERP = 0;
options.RESOLUTION = 256;
fig = plot_radial_transport_and_spacetime(data,options);
end
+
if 0
%% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Options
-options.INTERP = 0;
+options.INTERP = 1;
options.POLARPLOT = 0;
options.NAME = '\phi';
% options.NAME = '\omega_z';
@@ -67,28 +79,45 @@ options.PLAN = 'xy';
% options.PLAN = 'sx';
options.COMP = 'avg';
% options.TIME = data.Ts5D(end-30:end);
-% options.TIME = data.Ts3D;
-options.TIME = [0:1500];
+options.TIME = data.Ts3D;
+% options.TIME = [0:1500];
data.EPS = 0.1;
data.a = data.EPS * 2000;
options.RESOLUTION = 256;
create_film(data,options,'.gif')
end
+if 0
+%% fields snapshots
+% Options
+[data.Na00, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'Na00');
+
+data.Ni00 = reshape(squeeze(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.NAME = 'N_i^{00}';
+% options.NAME = '\phi';
+options.PLAN = 'xy';
+options.COMP = 'avg';
+options.TIME = [800 900 1000];
+options.RESOLUTION = 256;
+fig = photomaton(data,options);
+% save_figure(data,fig)
+end
if 0
%% Performance profiler
profiler(data)
end
-if 1
+if 0
%% Hermite-Laguerre spectrum
[data.Napjz, data.Ts3D] = compile_results_3Da(DATADIR,J0,J1,'Napjz');
-% data.Nipjz = log(data.Nipjz);
-% options.TIME = 'avg';
-options.P2J = 0;
-options.ST = 1;
+% [data.Napjz, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'Nipjz');
+options.ST = 0;
options.NORMALIZED = 0;
-options.TIME = [500:800];
+options.LOGSCALE = 1;
fig = show_moments_spectrum(data,options);
% fig = show_napjz(data,options);
% save_figure(data,fig,'.png');
@@ -109,4 +138,19 @@ options.ik = 1; % sum, max or index
options.fftz.flag = 0;
fig = mode_growth_meter(data,options);
% save_figure(data,fig,'.png')
+end
+
+
+if 0
+%% Study singular values
+[data.SV_ky_pj, data.Ts2D] = compile_results_2D(DATADIR,J0,J1,'sv_ky_pj');
+nSV = data.grids.Np * data.grids.Nj;
+colors_ = jet(nSV);
+figure
+for i = 1:nSV
+ sv = squeeze(data.SV_ky_pj(i,:));
+ semilogy(data.Ts2D,sv,...
+ 'color',colors_(i,:),'DisplayName',['SV ',num2str(i)]);hold on
+end
+legend('show');
end
\ No newline at end of file