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 = 'gyacomo23_sp';
CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%
SIMID = 'p2_linear_new'; % Name of the simulation
RERUN = 0; % rerun if the data does not exist
RUN = 0;
NU = 1e-3;
K_T= 6.96;
P_a = 2:2:40;
J_a = 2:2:40;
% collision setting
CO = 'DG';
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 = 1e-2;
TMAX = 30;
kymin = 0.3;
NY = 2;
% arrays for the result
g_ky = zeros(numel(P_a),numel(J_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);
PMAX = P; % Hermite basis size
JMAX = J; % Laguerre "
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
DTSAVE0D = 1; % Sampling per time unit for 0D arrays
DTSAVE2D = -1; % Sampling per time unit for 2D arrays
DTSAVE3D = 2; % Sampling per time unit for 3D arrays
DTSAVE5D = 100; % Sampling per time unit for 5D arrays
JOB2LOAD = -1; % Start a new simulation serie
%% 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
NA = 1;
ADIAB_E = (NA==1);
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;
HYP_V = 'none';
HRCY_CLOS = 'truncation'; % Closure model for higher order moments
DMAX = -1;
NLIN_CLOS = 'truncation'; % Nonlinear closure model for higher order moments
NMAX = 0;
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_ = {};
try
data_ = compile_results_low_mem(data_,LOCALDIR,00,00);
Ntime = numel(data_.Ts0D);
catch
data_.outfilenames = [];
end
if RUN && (RERUN || isempty(data_.outfilenames) || Ntime < 10)
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 2 ',gyacomodir,'bin/',EXECNAME,' 1 2 1 0; cd ../../../wk'])
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
try
data_ = compile_results_low_mem(data_,LOCALDIR,00,00);
[data_.PHI, data_.Ts3D] = compile_results_3D(LOCALDIR,00,00,'phi');
if numel(data_.Ts3D)>10
if numel(data_.Ts3D)>10
% Load results after trying to run
filename = [SIMID,'/',PARAMS,'/'];
LOCALDIR = [gyacomodir,'results/',filename,'/'];
data_ = compile_results_low_mem(data_,LOCALDIR,00,00);
[data_.PHI, data_.Ts3D] = compile_results_3D(LOCALDIR,00,00,'phi');
% 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 = double(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_.grids.ky(ikmax)); disp(msg);
end
end
catch
g_ky(i,j,:) = 0;
g_std(i,j,:) = 0;
end
i = i + 1;
end
j = j + 1;
end
if 0
%% Check time evolution
figure;
to_measure = log(field_t);
plot(data_.Ts3D,to_measure); hold on
plot(data_.Ts3D(it1:it2),to_measure(it1:it2),'--');
end
%% take max growth rate among z coordinate
y_ = g_ky(:,:,2);
e_ = g_std(:,:,2);
%%
if(numel(J_a)>1 && numel(P_a)>1)
%% Save metadata
pmin = num2str(min(P_a)); pmax = num2str(max(P_a));
jmin = num2str(min(J_a)); jmax = num2str(max(J_a));
filename = [num2str(NX),'x',num2str(NZ),'_ky_',num2str(kymin),...
'_P_',pmin,'_',pmax,...
'_J_',jmin,'_',jmax,'_',CONAME,'_',num2str(NU),'_kT_',num2str(K_T),'.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.s2name = '$P$';
metadata.s2 = P_a;
metadata.s1name = '$J$';
metadata.s1 = J_a;
metadata.dname = '$\gamma c_s/R$';
metadata.data = y_;
metadata.err = e_;
save([SIMDIR,filename],'-struct','metadata');
disp(['saved in ',SIMDIR,filename]);
clear metadata tosave
end