From e828928c5cf3f779282daa7a88141df0b12d3b67 Mon Sep 17 00:00:00 2001
From: Antoine Hoffmann <antoine.hoffmann@epfl.ch>
Date: Thu, 26 Jan 2023 13:40:53 +0100
Subject: [PATCH] script for linear scan
---
wk/CBC_kT_scan_salpha.m | 263 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 263 insertions(+)
create mode 100644 wk/CBC_kT_scan_salpha.m
diff --git a/wk/CBC_kT_scan_salpha.m b/wk/CBC_kT_scan_salpha.m
new file mode 100644
index 00000000..db4aab4b
--- /dev/null
+++ b/wk/CBC_kT_scan_salpha.m
@@ -0,0 +1,263 @@
+gyacomodir = pwd;
+gyacomodir = gyacomodir(1:end-2);
+addpath(genpath([gyacomodir,'matlab'])) % ... add
+addpath(genpath([gyacomodir,'matlab/plot'])) % ... add
+addpath(genpath([gyacomodir,'matlab/compute'])) % ... add
+addpath(genpath([gyacomodir,'matlab/load'])) % ... add% EXECNAME = 'gyacomo_1.0';
+% EXECNAME = 'gyacomo_debug';
+EXECNAME = 'gyacomo';
+CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
+%%
+SIMID = 'p2_CBC_convergence_KT_PJ'; % Name of the simulation
+% SIMID = 'dbg'; % Name of the simulation
+RERUN = 0; % rerun if the data does not exist
+RUN = 0;
+KT_a = [3:0.5:7];
+% KT_a = [3];
+% P_a = [22];
+P_a = [2:2:30];
+% P_a = [2:12];
+J_a = floor(P_a/2);
+% collision setting
+CO = 'DG';
+NU = 0.05;
+GKCO = 0; % gyrokinetic operator
+COLL_KCUT = 1.75;
+% model
+KIN_E = 0; % 1: kinetic electrons, 2: adiabatic electrons
+BETA = 1e-4; % electron plasma beta
+% background gradients setting
+K_N = 2.22; % Density '''
+% Geometry
+% GEOMETRY= 'miller';
+GEOMETRY= 's-alpha';
+SHEAR = 0.8; % magnetic shear
+% time and numerical grid
+DT = 1e-3;
+TMAX = 25;
+kymin = 0.3;
+NY = 2;
+% arrays for the result
+g_ky = zeros(numel(KT_a),numel(P_a),NY/2+1);
+g_avg= g_ky*0;
+g_std= g_ky*0;
+
+j = 1;
+for P = P_a
+i = 1;
+for KT = KT_a
+ %% PHYSICAL PARAMETERS
+ TAU = 1.0; % e/i temperature ratio
+ % SIGMA_E = 0.05196152422706632; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
+ SIGMA_E = 0.0233380; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
+ K_Te = KT; % ele Temperature '''
+ K_Ti = KT; % ion Temperature '''
+ K_Ne = K_N; % ele Density '''
+ K_Ni = K_N; % ion Density gradient drive
+ %% GRID PARAMETERS
+% P = 20;
+ J = floor(P/2);
+ PMAXE = P; % Hermite basis size of electrons
+ JMAXE = J; % Laguerre "
+ PMAXI = P; % " ions
+ JMAXI = J; % "
+ NX = 12; % real space x-gridpoints
+ LX = 2*pi/0.8; % Size of the squared frequency domain
+ LY = 2*pi/kymin; % Size of the squared frequency domain
+ NZ = 24; % number of perpendicular planes (parallel grid)
+ NPOL = 1;
+ SG = 0; % Staggered z grids option
+ NEXC = 1; % To extend Lx if needed (Lx = Nexc/(kymin*shear))
+ %% GEOMETRY
+ % GEOMETRY= 's-alpha';
+ EPS = 0.18; % inverse aspect ratio
+ Q0 = 1.4; % safety factor
+ KAPPA = 1.0; % elongation
+ DELTA = 0.0; % triangularity
+ ZETA = 0.0; % squareness
+ PARALLEL_BC = 'dirichlet'; %'dirichlet','periodic','shearless','disconnected'
+% PARALLEL_BC = 'periodic'; %'dirichlet','periodic','shearless','disconnected'
+ SHIFT_Y = 0.0;
+ %% TIME PARMETERS
+ SPS0D = 1; % Sampling per time unit for 2D arrays
+ SPS2D = -1; % Sampling per time unit for 2D arrays
+ SPS3D = 1; % Sampling per time unit for 2D arrays
+ SPS5D = 1/2; % Sampling per time unit for 5D arrays
+ SPSCP = 0; % Sampling per time unit for checkpoints
+ JOB2LOAD= -1;
+ %% OPTIONS
+ LINEARITY = 'linear'; % activate non-linearity (is cancelled if KXEQ0 = 1)
+ % Collision operator
+ ABCO = 1; % interspecies collisions
+ INIT_ZF = 0; ZF_AMP = 0.0;
+ CLOS = 0; % Closure model (0: =0 truncation, 1: v^Nmax 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
+ NUMERICAL_SCHEME = 'RK4'; % RK2,SSPx_RK2,RK3,SSP_RK3,SSPx_RK3,IMEX_SSP2,ARK2,RK4,DOPRI5
+ %% OUTPUTS
+ W_DOUBLE = 1;
+ W_GAMMA = 1; W_HF = 1;
+ W_PHI = 1; W_NA00 = 1;
+ W_DENS = 1; W_TEMP = 1;
+ W_NAPJ = 1; W_SAPJ = 0;
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ % unused
+ HD_CO = 0.0; % Hyper diffusivity cutoff ratio
+ MU = 0.0; % Hyperdiffusivity coefficient
+ INIT_BLOB = 0; WIPE_TURB = 0; ACT_ON_MODES = 0;
+ MU_X = MU; %
+ MU_Y = MU; %
+ N_HD = 4;
+ MU_Z = 0.2; %
+ MU_P = 0.0; %
+ MU_J = 0.0; %
+ LAMBDAD = 0.0;
+ NOISE0 = 1.0e-5; % Init noise amplitude
+ BCKGD0 = 0.0; % Init background
+ GRADB = 1.0;
+ CURVB = 1.0;
+ %% RUN
+ setup
+ % naming
+ filename = [SIMID,'/',PARAMS,'/'];
+ LOCALDIR = [gyacomodir,'results/',filename,'/'];
+ % check if data exist to run if no data
+ data_ = compile_results(LOCALDIR,0,0); %Compile the results from first output found to JOBNUMMAX if existing
+ if RUN && (RERUN || isempty(data_.NU_EVOL) || numel(data_.Ts3D)<10)
+ system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 2 2 0; cd ../../../wk'])
+% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',gyacomodir,'bin/',EXECNAME,' 3 2 1 0; cd ../../../wk'])
+ end
+
+ % Load results after trying to run
+ filename = [SIMID,'/',PARAMS,'/'];
+ LOCALDIR = [gyacomodir,'results/',filename,'/'];
+
+ data_ = compile_results(LOCALDIR,0,0); %Compile the results from first output found to JOBNUMMAX if existing
+
+ % 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 ...
+ field = 0;
+ field_t = 0;
+ for ik = 2:NY/2+1
+ field = squeeze(sum(abs(data_.PHI),3)); % take the sum over z
+ field_t = squeeze(field(ik,1,:)); % take the kx =0, ky = ky mode only
+ to_measure = log(field_t(it1:it2));
+ tw = data_.Ts3D(it1:it2);
+% gr = polyfit(tw,to_measure,1);
+ gr = fit(tw,to_measure,'poly1');
+ err= confint(gr);
+ g_ky(i,j,ik) = gr.p1;
+ g_std(i,j,ik) = abs(err(2,1)-err(1,1))/2;
+ end
+ [gmax, ikmax] = max(g_ky(i,j,:));
+
+ msg = sprintf('gmax = %2.2f, kmax = %2.2f',gmax,data_.ky(ikmax)); disp(msg);
+
+
+ i = i + 1;
+end
+j = j + 1;
+end
+
+if 0
+%% Check time evolution
+figure;
+plot(data_.Ts3D,to_measure); hold on
+plot(data_.Ts3D(it1:it2),to_measure(it1:it2),'--');
+end
+
+if 1
+%% Study of the peak growth rate
+figure
+
+y_ = g_ky;
+e_ = 0.05;
+
+% filter growth rate with less than 0.05 value
+y_ = y_.*(y_-e_>0);
+e_ = e_ .* (y_>0);
+
+[y_,idx_] = max(g_ky,[],3);
+for i = 1:numel(idx_)
+ e_ = g_std(:,:,idx_(i));
+end
+
+colors_ = jet(numel(KT_a));
+subplot(121)
+for i = 1:numel(KT_a)
+% errorbar(P_a,y_(i,:),e_(i,:),...
+% 'LineWidth',1.2,...
+% 'DisplayName',['$\nu=$',num2str(KT_a(i))],...
+% 'color',colors_(i,:));
+ plot(P_a,y_(i,:),'s-',...
+ 'LineWidth',2.0,...
+ 'DisplayName',['$\kappa_T=$',num2str(KT_a(i))],...
+ 'color',colors_(i,:));
+ hold on;
+end
+title(['$\nu_{',CO,'}=$',num2str(NU),', $\kappa_N=$',num2str(K_N),', $k_y=$',num2str(kymin)]);
+legend('show'); xlabel('$P$, $J=P/2$'); ylabel('$\gamma$');
+
+colors_ = jet(numel(P_a));
+subplot(122)
+for j = 1:numel(P_a)
+% errorbar(KT_a,y_(:,j),e_(:,j),...
+% 'LineWidth',1.2,...
+% 'DisplayName',['(',num2str(P_a(j)),',',num2str(J_a(j)),')'],...
+% 'color',colors_(j,:));
+ plot(KT_a,y_(:,j),'s-',...
+ 'LineWidth',2.0,...
+ 'DisplayName',['(',num2str(P_a(j)),',',num2str(J_a(j)),')'],...
+ 'color',colors_(j,:));
+ hold on;
+end
+title(['$\nu_{',CO,'}=$',num2str(NU),', $\kappa_N=$',num2str(K_N),', $k_y=$',num2str(kymin)]);
+legend('show'); xlabel('$\kappa_T$'); ylabel('$\gamma$');
+end
+
+if 0
+%% Pcolor of the peak
+figure;
+[XX_,YY_] = meshgrid(KT_a,P_a);
+% pclr=pcolor(XX_,YY_,y_'); set(pclr,'EdgeColor','none'); axis ij;
+pclr=imagesc_custom(XX_,YY_,y_'.*(y_>0)');
+title(['$\nu_{',data.CO,'}=$',num2str(data.NU),', $\kappa_N=$',num2str(K_N),', $k_y=$',num2str(kymin)]);
+xlabel('$\kappa_T$'); ylabel('$P$, $J=P/2$');
+colormap(bluewhitered)
+clb=colorbar;
+clb.Label.String = '$\gamma c_s/R$';
+clb.Label.Interpreter = 'latex';
+clb.Label.FontSize= 18;
+end
+%%
+%% Save metadata
+ktmin = num2str(min(KT_a)); ktmax = num2str(max(KT_a));
+ pmin = num2str(min(P_a)); pmax = num2str(max(P_a));
+filename = [num2str(NX),'x',num2str(NZ),'_ky_',num2str(kymin),...
+ '_kT_',ktmin,'_',ktmax,'_',...
+ '_P_',pmin,'_',pmax,'_',data_.CO,'_',num2str(NU),'.mat'];
+metadata.name = filename;
+metadata.kymin = kymin;
+metadata.title = ['$\nu_{',data_.CO,'}=$',num2str(NU),', $\kappa_N=$',num2str(K_N),', $k_y=$',num2str(kymin)];
+metadata.par = data_.PARAMS;
+metadata.nscan = 2;
+metadata.s1name = '$\kappa_T$';
+metadata.s1 = KT_a;
+metadata.s2name = '$P$, $J=P/2$';
+metadata.s2 = P_a;
+metadata.dname = '$\gamma c_s/R$';
+metadata.data = y_;
+metadata.err = e_;
+metadata.input_file = h5read([data_.localdir,'/outputs_00.h5'],'/files/STDIN.00');
+metadata.date = date;
+% tosave.data = metadata;
+save([SIMDIR,filename],'-struct','metadata');
+disp(['saved in ',SIMDIR,filename]);
+clear metadata tosave
\ No newline at end of file
--
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