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_linear'; % Name of the simulation
RERUN = 0; % rerun if the data does not exist
RUN = 0;
P_a = [2:20];
J_a = [2:15];
% P_a = [18:22];
% J_a = [2:6];
% collision setting
CO = 'DG';
HYP_V = 'dvpar4';
NU = 0.02;
K_T = 6.96;
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
DT0 = 5e-3;
TMAX = 25;
kymin = 0.3;
NY = 2;
% arrays for the result
g_ky = zeros(numel(J_a),numel(P_a),NY/2+1);
g_avg= g_ky*0;
g_std= g_ky*0;
% Naming of the collision operator
if GKCO
CONAME = [CO,'GK'];
else
CONAME = [CO,'DK'];
end
j = 1;
for P = P_a
i = 1;
for J = J_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 = K_T; % ele Temperature '''
K_Ti = K_T; % ion Temperature '''
K_Ne = K_N; % ele Density '''
K_Ni = K_N; % ion Density gradient drive
%% GRID PARAMETERS
DT = DT0/sqrt(J);
PMAXE = P; % Hermite basis size of electrons
JMAXE = J; % Laguerre "
PMAXI = P; % " ions
JMAXI = J; % "
NX = 8; % 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 = 0;
W_GAMMA = 1; W_HF = 1;
W_PHI = 1; W_NA00 = 1;
W_DENS = 0; W_TEMP = 1;
W_NAPJ = 0; 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 = 1.0; %
MU_P = 0.0; %
MU_J = 0.0; %
LAMBDAD = 0.0;
NOISE0 = 1.0e-5; % Init noise amplitude
BCKGD0 = 0.0; % Init background
k_gB = 1.0;
k_cB = 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
if ~isempty(data_.NU_EVOL)
if numel(data_.Ts3D)>10
% 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
[~,it1] = min(abs(data_.Ts3D-0.7*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 = 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);
end
end
i = i + 1;
end
j = j + 1;
end
%% take max growth rate among z coordinate
y_ = g_ky(:,:,2);
e_ = g_std(:,:,2);
if 0
%% Check time evolution
figure;
field = squeeze(sum(abs(data_.PHI),3)); field_t = squeeze(field(2,1,:)); to_measure = log(field_t);
plot(data_.Ts3D,to_measure); hold on
plot(data_.Ts3D(it1:it2),to_measure(it1:it2),'--');
end
if 0
%% Pcolor of the peak
figure;
[XX_,YY_] = meshgrid(J_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
%%
if(numel(J_a)>1 && numel(P_a)>1)
%% Save metadata
jmin = num2str(min(J_a)); jmax = num2str(max(J_a));
pmin = num2str(min(P_a)); pmax = num2str(max(P_a));
filename = [num2str(NX),'x',num2str(NZ),'_ky_',num2str(kymin),...
'_J_',jmin,'_',jmax,...
'_P_',pmin,'_',pmax,'_kT_',num2str(K_T),'_',CONAME,'_',num2str(NU),'.mat'];
metadata.name = filename;
metadata.kymin = kymin;
metadata.title = ['$\nu_{',CONAME,'}=$',num2str(NU),', $\kappa_T=$',num2str(K_T),', $\kappa_N=$',num2str(K_N),', $k_y=$',num2str(kymin)];
metadata.par = [num2str(NX),'x1x',num2str(NZ)];
metadata.nscan = 2;
metadata.s1name = '$J$';
metadata.s1 = J_a;
metadata.s2name = '$P$';
metadata.s2 = P_a;
metadata.dname = '$\gamma c_s/R$';
metadata.data = y_;
metadata.err = e_;
% metadata.input_file = h5read([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
end