diff --git a/wk/p3_geom_scan_analysis.m b/wk/p3_geom_scan_analysis.m
index da097816abe751451d23eee47b426a038cda8c69..f364ab5616f557504e4d7fb015fb9a3fedd702bf 100644
--- a/wk/p3_geom_scan_analysis.m
+++ b/wk/p3_geom_scan_analysis.m
@@ -1,45 +1,108 @@
% Get the current directory (wk)
curdir = pwd;
-partition= '/misc/gyacomo23_outputs/paper_3/';
+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 2
+switch 5
case 1 % delta kappa scan
- scandir = 'DTT_rho85_geom_scan/P2_J1_delta_kappa_scan/';
- % scandir = 'DTT_rho85_geom_scan/P4_J2_delta_kappa_scan/';
- nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0.23;
- nml2 = 'GEOMETRY'; pnam2 = '$\kappa$'; attr2 = 'kappa'; pref2 = 1.53;
+ 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
- % scandir = 'DTT_rho85_geom_scan/P2_J1_PT_sfact_shear_scan/';
- scandir = 'DTT_rho85_geom_scan/P2_J1_NT_sfact_shear_scan/';
- nml1 = 'GEOMETRY'; pnam1 = '$\hat s$'; attr1 = 'shear'; pref1 = 3.63;
- nml2 = 'GEOMETRY'; pnam2 = '$q_0$'; attr2 = 'q0'; pref2 =-2.15;
+ 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
- scandir = 'DTT_rho85_geom_scan/P2_J1_delta_nuDGGK_scan/';
- % scandir = 'DTT_rho85_geom_scan/P4_J2_delta_nuDGGK_scan/';
- % scandir = 'DTT_rho85_geom_scan/P8_J4_delta_nuDGGK_conv_test/';
- % scandir = 'DTT_rho85_geom_scan/P2_J1_delta_nuSGGK_scan/';
- % scandir = 'DTT_rho85_geom_scan/P4_J2_delta_nuSGGK_scan/';
- % scandir = 'DTT_rho85_geom_scan/P8_J4_delta_nuSGGK_conv_test/';
- % scandir = 'DTT_rho85_geom_scan/P4_J2_delta_nuSGGKii_scan/';
- % scandir = 'DTT_rho85_geom_scan/P2_J1_delta_nuLDGK_scan/';
- % scandir = 'DTT_rho85_geom_scan/P4_J2_delta_nuLDGK_scan/';
- nml1 = 'GEOMETRY'; pnam1 = '$\delta$'; attr1 = 'delta'; pref1 = 0.23;
- nml2 = 'MODEL'; pnam2 = '$\nu$'; attr2 = 'nu'; pref2 = 0.5;
+ 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 = 800;
+ 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;
+ 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
-scandir = [partition,scandir];
+scanname= [casename scanname];
+scandir = [partition,scandir,'/'];
% Get a list of all items in the current directory
contents = dir(scandir);
-% give ref value and param names
-REFVAL= 0;
-% normalize to the max
-NORMAL= 0;
-% Get and plot the fluxsurface
-GETFLUXSURFACE = 0;
-
% 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, '.') ...
@@ -53,13 +116,31 @@ for i = 1:length(contents)
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(t_all(end) > 50)
- [fullAvg,sliceAvg,sliceErr] = sliceAverage(Qxi_all+Qxe_all,3);
- Qxavg = [Qxavg fullAvg];
- Qxerr = [Qxerr mean(sliceErr)];
+ 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];
+ Qxavg = [Qxavg nan];
+ Qxerr = [Qxerr nan];
end
end
if GETFLUXSURFACE
@@ -70,10 +151,35 @@ for i = 1:length(contents)
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);
-p2 = unique(para2);
+p1 = unique(para1)/scale1;
+p2 = unique(para2)/scale2;
N1 = numel(p1);
N2 = numel(p2);
@@ -87,8 +193,8 @@ end
Zavg = reshape(Qxavg,sz);
Zerr = reshape(Qxerr,sz);
-XX = reshape(para1,sz);
-YY = reshape(para2,sz);
+XX = reshape(para1/scale1,sz);
+YY = reshape(para2/scale2,sz);
if TRANSPOSE
Zavg = Zavg';
@@ -106,7 +212,7 @@ YY = YY(idx1,idx2);
% compute the
if REFVAL
- if NORMAL
+ if NORM_ALL
Qxname = '$\bar Q_{tot}/\bar Q_{max}[\%]$';
[tmp,iref1] = max(Zavg);
[~, iref2] = max(tmp);
@@ -131,40 +237,63 @@ if REFVAL
Qxref = Zavg(iref1,iref2);
Qrefname = ['$Q_{ref}=$',num2str(Qxref(1,1))];
else
- Qxname = '$\langle Q_{tot} \rangle_t$';
+ 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)
-% contourf(XX(:,1),YY(1,:),Zavg',13); hold on
[xx_,yy_] = meshgrid(XX(:,1),YY(1,:));
if REFVAL
- if NORMAL
- imagesc_custom(xx_,yy_,(Zavg./Qxref)'); hold on
+ if NORM_ALL || NORM_COL || NORM_LIN
+ toplot = (Zavg./Qxref)'
CLIM = [0 1];
else
- imagesc_custom(xx_,yy_,((Zavg-Qxref)./Qxref * 100)'); hold on
+ toplot = ((Zavg-Qxref)./Qxref * 100)';
CLIM = 'auto';
end
else
- imagesc_custom(xx_,yy_,Zavg'); hold on
+ 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(Qxname)
+title(scanname)
colormap(bluewhitered); colorbar; clim(CLIM);
if ~REFVAL
- colormap(hot);
+ colormap(jet);
end
subplot(1,2,2)
+clrs = jet(N2);
for i = 1:N2
errorbar(XX(:,i),Zavg(:,i),Zerr(:,i),...
- 'DisplayName',[pnam2,'=',num2str(para2(1,i))]);
+ 'DisplayName',[pnam2,'=',num2str(p2(i))],...
+ 'Color',clrs(i,:));
hold on;
end
if REFVAL && ~((pref1==999) || (pref2==999))