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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 = NX; % x grid resolution
GRID.Lx = LX; % x length
GRID.Ny = NY; % y ''
GRID.Ly = LY; % y ''
GRID.Nz = NZ; % z resolution
GRID.q0 = Q0; % q factor
GRID.shear = SHEAR; % shear
GRID.eps = EPS; % inverse aspect ratio
if SG; GRID.SG = '.true.'; else; GRID.SG = '.false.';end;
% Model parameters
MODEL.CLOS = CLOS;
MODEL.NL_CLOS = NL_CLOS;
MODEL.LINEARITY = ['''',LINEARITY,''''];
MODEL.KIN_E = KIN_E;
if KIN_E; MODEL.KIN_E = '.true.'; else; MODEL.KIN_E = '.false.';end;
MODEL.mu_x = MU_X;
MODEL.mu_y = MU_Y;
MODEL.mu_z = 0;
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 = SIGMA_E;
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.K_n = K_N; % source term kappa for HW
MODEL.K_T = K_T; % Temperature
MODEL.K_E = K_E; % Electric
MODEL.GradB = GRADB; % Magnetic gradient
MODEL.CurvB = CURVB; % Magnetic curvature
MODEL.lambdaD = LAMBDAD;
% Collision parameters
COLL.collision_model = ['''',CO,''''];
if (GKCO); COLL.gyrokin_CO = '.true.'; else; COLL.gyrokin_CO = '.false.';end;
if (ABCO); COLL.interspecies = '.true.'; else; COLL.interspecies = '.false.';end;
COLL.mat_file = '''null''';
switch CO
case 'SG'
COLL.mat_file = '''../../../iCa/gk_sugama_P_20_J_10_N_150_kpm_8.0.h5''';
case 'LR'
COLL.mat_file = '''../../../iCa/gk_pitchangle_8_P_20_J_10_N_150_kpm_8.0.h5''';
case 'LD'
COLL.mat_file = '''../../../iCa/gk_coulomb_NFLR_12_P_4_J_2_N_75_kpm_6.0.h5''';
end
% Time integration and intialization parameters
TIME_INTEGRATION.numerical_scheme = '''RK4''';
INITIAL.INIT_OPT = ['''',INIT_OPT,''''];
INITIAL.ACT_ON_MODES = ['''',ACT_ON_MODES,''''];
INITIAL.init_background = BCKGD0;
INITIAL.init_noiselvl = NOISE0;
INITIAL.iseed = 42;
% Naming and creating input file
CONAME = CO;
if GKCO
CONAME = [CONAME,'GK'];
else
CONAME = [CONAME,'DK'];
end
if ~ABCO
CONAME = [CONAME,'aa'];
end
if (CLOS == 0); CLOSNAME = 'Trunc.';
elseif(CLOS == 1); CLOSNAME = 'Clos. 1';
elseif(CLOS == 2); CLOSNAME = 'Clos. 2';
end
% Hermite-Laguerre degrees naming
if (PMAXE == PMAXI) && (JMAXE == JMAXI)
HLdeg_ = ['_',num2str(PMAXE+1),'x',num2str(JMAXE+1)];
else
HLdeg_ = ['_Pe_',num2str(PMAXE+1),'_Je_',num2str(JMAXE+1),...
'_Pi_',num2str(PMAXI+1),'_Ji_',num2str(JMAXI+1)];
end
% temp. dens. drives
drives_ = [];
if abs(K_N) > 0; drives_ = [drives_,'_kN_',num2str(K_N)]; end;
if abs(K_T) > 0; drives_ = [drives_,'_kT_',num2str(K_T)]; end;
% collision
coll_ = ['_nu_%0.0e_',CONAME];
coll_ = sprintf(coll_,NU);
% nonlinear
lin_ = [];
if ~LINEARITY; lin_ = '_lin'; end
adiabe_ = [];
if ~KIN_E; adiabe_ = '_adiabe'; end
% resolution and boxsize
res_ = [num2str(GRID.Nx),'x',num2str(GRID.Ny)];
if (LX ~= LY)
geo_ = ['_Lx_',num2str(LX),'_Ly_',num2str(LY)];
else
geo_ = ['_L_',num2str(LX)];
end
if (NZ > 1) %3D case
res_ = [res_,'x',num2str(NZ)];
if abs(Q0) > 0
geo_ = [geo_,'_q0_',num2str(Q0)];
end
if abs(EPS) > 0
geo_ = [geo_,'_e_',num2str(EPS)];
end
if abs(SHEAR) > 0
geo_ = [geo_,'_s_',num2str(SHEAR)];
end
end
% put everything together in the param character chain
u_ = '_'; % underscore variable
PARAMS = [res_,HLdeg_,geo_,drives_,coll_,lin_,adiabe_];
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
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);
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_HF; OUTPUTS.write_hf = '.true.'; else; OUTPUTS.write_hf = '.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.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,COLL,INITIAL,TIME_INTEGRATION,BASIC);
nproc = 1;
MAKE = 'cd ..; make; cd wk';
% system(MAKE);
%%
disp(['Set up ',SIMID]);
disp([res_,geo_,HLdeg_]);
if JOB2LOAD>=0
disp(['- restarting from JOBNUM = ',num2str(JOB2LOAD)]); else
disp(['- starting from T = 0']);
end
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