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gyacomo/matlab/setup.m
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setup.m
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%% ________________________________________________________________________
SIMDIR = ['../results/',SIMID,'/'];
% Grid parameters
GRID.pmaxe = PMAXE; % Electron Hermite moments
GRID.jmaxe = JMAXE; % Electron Laguerre moments
GRID.pmaxi = PMAXI; % Ion Hermite moments
GRID.jmaxi = JMAXI; % Ion Laguerre moments
GRID.Nx = N; % x grid resolution
GRID.Lx = L; % x length
GRID.Ny = N * (1-KXEQ0) + KXEQ0; % y ''
GRID.Ly = L * (1-KXEQ0); % y ''
GRID.Nz = Nz; % z resolution
GRID.q0 = q0; % q factor
% Model parameters
MODEL.CO = CO; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
MODEL.CLOS = CLOS;
MODEL.NL_CLOS = NL_CLOS;
if NON_LIN; MODEL.NON_LIN = '.true.'; else; MODEL.NON_LIN = '.false.';end;
MODEL.mu = MU;
MODEL.mu_p = MU_P;
MODEL.mu_j = MU_J;
MODEL.nu = NU; % hyper diffusive coefficient nu for HW
% temperature ratio T_a/T_e
MODEL.tau_e = TAU;
MODEL.tau_i = TAU;
% mass ratio sqrt(m_a/m_i)
MODEL.sigma_e = 0.0233380;
MODEL.sigma_i = 1.0;
% charge q_a/e
MODEL.q_e =-1.0;
MODEL.q_i = 1.0;
if MODEL.q_e == 0; SIMID = [SIMID,'_i']; end;
% gradients L_perp/L_x
MODEL.eta_n = ETAN; % source term kappa for HW
MODEL.eta_T = ETAT; % Temperature
MODEL.eta_B = ETAB; % Magnetic
MODEL.lambdaD = LAMBDAD;
% if A0KH ~= 0; SIMID = [SIMID,'_Nz_',num2str(L/2/pi*KX0KH),'_A_',num2str(A0KH)]; end;
% Time integration and intialization parameters
TIME_INTEGRATION.numerical_scheme = '''RK4''';
if (INIT_PHI); INITIAL.init_noisy_phi = '.true.'; else; INITIAL.init_noisy_phi = '.false.';end;
INITIAL.INIT_ZF = INIT_ZF;
if (WIPE_TURB); INITIAL.wipe_turb = '.true.'; else; INITIAL.wipe_turb = '.false.';end;
if (INIT_BLOB); INITIAL.init_blob = '.true.'; else; INITIAL.init_blob = '.false.';end;
INITIAL.init_background = (INIT_ZF>0)*ZF_AMP;
INITIAL.init_noiselvl = NOISE0;
INITIAL.iseed = 42;
INITIAL.mat_file = '''null''';
if (abs(CO) == 2) %Sugama operator
INITIAL.mat_file = ['''../../../iCa/gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'''];
elseif (abs(CO) == 3) %pitch angle operator
INITIAL.mat_file = ['''../../../iCa/gk_pitchangle_8_P_20_J_10_N_150_kpm_8.0.h5'''];
elseif (CO == 4) % Full Coulomb GK
disp('Warning, FCGK not implemented yet')
elseif (CO == -1) % DGDK
disp('Warning, DGDK not debugged')
end
% Naming and creating input file
if (CO == -3); CONAME = 'PADK';
elseif(CO == -2); CONAME = 'SGDK';
elseif(CO == -1); CONAME = 'DGDK';
elseif(CO == 0); CONAME = 'LBDK';
elseif(CO == 1); CONAME = 'DGGK';
elseif(CO == 2); CONAME = 'SGGK';
elseif(CO == 3); CONAME = 'PAGK';
end
if (CLOS == 0); CLOSNAME = 'Trunc.';
elseif(CLOS == 1); CLOSNAME = 'Clos. 1';
elseif(CLOS == 2); CLOSNAME = 'Clos. 2';
end
if (PMAXE == PMAXI) && (JMAXE == JMAXI)
degngrad = ['P_',num2str(PMAXE),'_J_',num2str(JMAXE)];
else
degngrad = ['Pe_',num2str(PMAXE),'_Je_',num2str(JMAXE),...
'_Pi_',num2str(PMAXI),'_Ji_',num2str(JMAXI)];
end
degngrad = [degngrad,'_eta_',num2str(ETAB/ETAN),'_nu_%0.0e_',...
CONAME,'_mu_%0.0e'];
degngrad = sprintf(degngrad,[NU,MU]);
if ~NON_LIN; degngrad = ['lin_',degngrad]; end
if (Nz == 1)
resolution = [num2str(GRID.Nx),'x',num2str(GRID.Ny/2),'_'];
gridname = ['L_',num2str(L),'_'];
else
resolution = [num2str(GRID.Nx),'x',num2str(GRID.Ny/2),'x',num2str(GRID.Nz),'_'];
gridname = ['L_',num2str(L),'_q_',num2str(q),'_'];
end
if (exist('PREFIX','var') == 0); PREFIX = []; end;
if (exist('SUFFIX','var') == 0); SUFFIX = []; end;
PARAMS = [PREFIX,resolution,gridname,degngrad,SUFFIX];
BASIC.RESDIR = [SIMDIR,PARAMS,'/'];
BASIC.MISCDIR = ['/misc/HeLaZ_outputs/',SIMDIR(4:end),PARAMS,'/'];
BASIC.PARAMS = PARAMS;
BASIC.SIMID = SIMID;
BASIC.nrun = 1e8;
BASIC.dt = DT;
BASIC.tmax = TMAX; %time normalized to 1/omega_pe
BASIC.maxruntime = str2num(CLUSTER.TIME(1:2))*3600 ...
+ str2num(CLUSTER.TIME(4:5))*60 ...
+ str2num(CLUSTER.TIME(7:8));
% Outputs parameters
if RESTART; BASIC.RESTART = '.true.'; else; BASIC.RESTART = '.false.';end;
OUTPUTS.nsave_0d = floor(1.0/SPS0D/DT);
OUTPUTS.nsave_1d = -1;
OUTPUTS.nsave_2d = floor(1.0/SPS2D/DT);
OUTPUTS.nsave_3d = floor(1.0/SPS3D/DT);
OUTPUTS.nsave_5d = floor(1.0/SPS5D/DT);
OUTPUTS.nsave_cp = floor(1.0/SPSCP/DT);
if W_DOUBLE; OUTPUTS.write_doubleprecision = '.true.'; else; OUTPUTS.write_doubleprecision = '.false.';end;
if W_GAMMA; OUTPUTS.write_gamma = '.true.'; else; OUTPUTS.write_gamma = '.false.';end;
if W_PHI; OUTPUTS.write_phi = '.true.'; else; OUTPUTS.write_phi = '.false.';end;
if W_NA00; OUTPUTS.write_Na00 = '.true.'; else; OUTPUTS.write_Na00 = '.false.';end;
if W_NAPJ; OUTPUTS.write_Napj = '.true.'; else; OUTPUTS.write_Napj = '.false.';end;
if W_SAPJ; OUTPUTS.write_Sapj = '.true.'; else; OUTPUTS.write_Sapj = '.false.';end;
if W_DENS; OUTPUTS.write_dens = '.true.'; else; OUTPUTS.write_dens = '.false.';end;
if W_TEMP; OUTPUTS.write_temp = '.true.'; else; OUTPUTS.write_temp = '.false.';end;
OUTPUTS.resfile0 = '''outputs''';
OUTPUTS.rstfile0 = '''checkpoint''';
OUTPUTS.job2load = JOB2LOAD;
%% Create directories
if ~exist(SIMDIR, 'dir')
mkdir(SIMDIR)
end
if ~exist(BASIC.RESDIR, 'dir')
mkdir(BASIC.RESDIR)
end
if ~exist(BASIC.MISCDIR, 'dir')
mkdir(BASIC.MISCDIR)
end
%% Compile and WRITE input file
INPUT = write_fort90(OUTPUTS,GRID,MODEL,INITIAL,TIME_INTEGRATION,BASIC);
nproc = 1;
MAKE = 'cd ..; make; cd wk';
system(MAKE);
%%
disp(['Set up ',SIMID]);
disp([resolution,gridname,degngrad]);
if RESTART
disp(['- restarting from JOBNUM = ',num2str(JOB2LOAD)]); else
disp(['- starting from T = 0']);
end
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