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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.Nr = N; % r grid resolution
GRID.Lr = L; % r length
GRID.Nz = N * (1-KREQ0) + KREQ0; % z ''
GRID.Lz = L * (1-KREQ0); % z ''
GRID.kpar = KPAR;
% 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*KR0KH),'_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.initback_moments = 0.0e-5;
INITIAL.initnoise_moments = NOISE0;
INITIAL.iseed = 42;
INITIAL.selfmat_file = '''null''';
INITIAL.eimat_file = '''null''';
INITIAL.iemat_file = '''null''';
if (CO == -3) % Write matrice filename for Full Coulomb DK
cmat_pmaxe = 25;
cmat_jmaxe = 18;
cmat_pmaxi = 25;
cmat_jmaxi = 18;
INITIAL.selfmat_file = ...
['''../../../iCa/self_Coll_GKE_0_GKI_0_ESELF_1_ISELF_1_Pmaxe_',num2str(cmat_pmaxe),...
'_Jmaxe_',num2str(cmat_jmaxe),'_Pmaxi_',num2str(cmat_pmaxi),'_Jmaxi_',...
num2str(cmat_jmaxi),'_pamaxx_10.h5'''];
INITIAL.eimat_file = ...
['''../../../iCa/ei_Coll_GKE_0_GKI_0_ETEST_1_EBACK_1_Pmaxe_',num2str(cmat_pmaxe),...
'_Jmaxe_',num2str(cmat_jmaxe),'_Pmaxi_',num2str(cmat_pmaxi),'_Jmaxi_',...
num2str(cmat_jmaxi),'_pamaxx_10_tau_1.0000_mu_0.0233.h5'''];
INITIAL.iemat_file = ...
['''../../../iCa/ie_Coll_GKE_0_GKI_0_ITEST_1_IBACK_1_Pmaxe_',num2str(cmat_pmaxe),...
'_Jmaxe_',num2str(cmat_jmaxe),'_Pmaxi_',num2str(cmat_pmaxi),'_Jmaxi_',...
num2str(cmat_jmaxi),'_pamaxx_10_tau_1.0000_mu_0.0233.h5'''];
elseif (CO == -2) % Write matrice filename for DK Sugama
cmat_pmaxe = 10;
cmat_jmaxe = 5;
cmat_pmaxi = 10;
cmat_jmaxi = 5;
INITIAL.selfmat_file = ...
['''../../../iCa/self_Coll_GKE_0_GKI_0_ESELF_3_ISELF_3_Pmaxe_',num2str(cmat_pmaxe),...
'_Jmaxe_',num2str(cmat_jmaxe),'_Pmaxi_',num2str(cmat_pmaxi),'_Jmaxi_',...
num2str(cmat_jmaxi),'_JE_12.h5'''];
INITIAL.eimat_file = ...
['''../../../iCa/ei_Coll_GKE_0_GKI_0_ETEST_3_EBACK_3_Pmaxe_',num2str(cmat_pmaxe),...
'_Jmaxe_',num2str(cmat_jmaxe),'_Pmaxi_',num2str(cmat_pmaxi),'_Jmaxi_',...
num2str(cmat_jmaxi),'_JE_12_tau_1.0000_mu_0.0233.h5'''];
INITIAL.iemat_file = ...
['''../../../iCa/ie_Coll_GKE_0_GKI_0_ITEST_3_IBACK_3_Pmaxe_',num2str(cmat_pmaxe),...
'_Jmaxe_',num2str(cmat_jmaxe),'_Pmaxi_',num2str(cmat_pmaxi),'_Jmaxi_',...
num2str(cmat_jmaxi),'_JE_12_tau_1.0000_mu_0.0233.h5'''];
elseif (CO == 2) % Write matrice filename for Sugama GK
cmat_pmaxe = 10;
cmat_jmaxe = 5;
cmat_pmaxi = 10;
cmat_jmaxi = 5;
INITIAL.selfmat_file = ...
['''../../../iCa/self_Coll_GKE_1_GKI_1_ESELF_3_ISELF_3_Pmaxe_',num2str(cmat_pmaxe),...
'_Jmaxe_',num2str(cmat_jmaxe),'_Pmaxi_',num2str(cmat_pmaxi),'_Jmaxi_',...
num2str(cmat_jmaxi),'_JE_12_NFLR_5_'''];
INITIAL.eimat_file = ...
['''../../../iCa/ei_Coll_GKE_1_GKI_1_ETEST_3_EBACK_3_Pmaxe_',num2str(cmat_pmaxe),...
'_Jmaxe_',num2str(cmat_jmaxe),'_Pmaxi_',num2str(cmat_pmaxi),'_Jmaxi_',...
num2str(cmat_jmaxi),'_JE_12_tau_1.0000_mu_0.0233_NFLRe_5_NFLRi_5_'''];
INITIAL.iemat_file = ...
['''../../../iCa/ie_Coll_GKE_1_GKI_1_ITEST_3_IBACK_3_Pmaxe_',num2str(cmat_pmaxe),...
'_Jmaxe_',num2str(cmat_jmaxe),'_Pmaxi_',num2str(cmat_pmaxi),'_Jmaxi_',...
num2str(cmat_jmaxi),'_JE_12_tau_1.0000_mu_0.0233_NFLRe_5_NFLRi_5_'''];
elseif (CO == 3) % 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 = 'FCDK';
elseif(CO == -2); CONAME = 'SGDK';
elseif(CO == -1); CONAME = 'DGDK';
elseif(CO == 0); CONAME = 'LB';
elseif(CO == 1); CONAME = 'DGGK';
elseif(CO == 2); CONAME = 'SGGK';
elseif(CO == 3); CONAME = 'FCGK';
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,'_CLOS_',num2str(CLOS),'_mu_%0.0e'];
degngrad = sprintf(degngrad,[NU,MU]);
if ~NON_LIN; degngrad = ['lin_',degngrad]; end
resolution = [num2str(GRID.Nr),'x',num2str(GRID.Nz/2),'_'];
gridname = ['L_',num2str(L),'_'];
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.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_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;
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
%% 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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