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gyacomo/wk/compile_cosolver_mat.m
fd5937d3df0fgather_output

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compile_cosolver_mat.m
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addpath(genpath('../matlab')) % ... add
%% Grid configuration
N = 200; % Frequency gridpoints (Nkr = N/2)
L = 120; % Size of the squared frequency domain
dk = 2.*pi/L;
kmax = N/2*dk;
kr = dk*(0:N/2);
kz = dk*(0:N/2);
[KZ, KR]= meshgrid(kz,kr);
KPERP = sqrt(KR.^2 + KZ.^2);
kperp = reshape(KPERP,[1,numel(kr)^2]);
kperp = uniquetol(kperp,1e-14);
Nperp = numel(kperp);
%% Model
% ! 0 = nothing
% ! 1 = coulomb
% ! 2 = pitch-angle (with constant coll.freq.)
% ! 3 = sugama
% ! 4 = pitch-angle with veloty dependent coll. freq.
% ! 5 = improved sugama
% ! 6 = Hirschman-Sigmar Clarke
% ! 7 = Abel (only for like species)
% ! 8 = conserving momentun pitch-angle operator (with veloty dependent coll. freq.)
% ! 9 = GK coulomb polarization term
CO = 3;
GK = 1;
P = 10;
J = 5;
M_FLR= 0; %to increase the NFLR
if 0
%% plot the kperp distribution
figure
plot(kperp)
end
% %% Check if the differences btw kperp is larger than naming precision
%%
%% We compute only on a kperp grid with dk space from 0 to kperpmax
kperpmax = sqrt(2) * kmax;
kperp = unique([0:dk:kperpmax,kperpmax]);
%% Naming
if CO == 1; CONAME = 'FC'; end;
if CO == 2; CONAME = 'PA'; end;
if CO == 3; CONAME = 'SG'; end;
% matfilename = ['../iCa/',CONAME,'_P_',num2str(P),'_J_',num2str(J),...
% '_N_',num2str(N),'_dk_',num2str(dk),'_MFLR_',num2str(M_FLR),'.h5'];
matfilename = '../iCa/gk_sugama_P_10_J_5.h5';
n_ = 0;
for k_ = kperp
disp(['-Writing matrices for kperp = ',num2str(k_)])
%% Script to run COSOlver in order to create needed collision matrices
COSOlver_path = '../../Documents/MoliSolver/COSOlver/';
COSOLVER.pmaxe = P;
COSOLVER.jmaxe = J;
COSOLVER.pmaxi = P;
COSOLVER.jmaxi = J;
COSOLVER.kperp = k_;
COSOLVER.neFLR = min(ceil((2/3*kperpmax)^2),max(5,ceil(COSOLVER.kperp^2)))+M_FLR; % rule of thumb for sum truncation
COSOLVER.niFLR = min(ceil((2/3*kperpmax)^2),max(5,ceil(COSOLVER.kperp^2)))+M_FLR;
COSOLVER.idxT4max = 40;
COSOLVER.neFLRs = 0; % ... only for GK abel
COSOLVER.npeFLR = 0; % ... only for GK abel
COSOLVER.niFLRs = 0; % ... only for GK abel
COSOLVER.npiFLR = 0; % ... only for GK abel
COSOLVER.gk = GK;
COSOLVER.co = CO;
k_string = sprintf('%0.4f',k_);
n_string = sprintf('%0.5d',n_);
self_mat_file_name = ['../iCa/self_Coll_GKE_',num2str(COSOLVER.gk),'_GKI_',num2str(COSOLVER.gk),...
'_ESELF_',num2str(COSOLVER.co),'_ISELF_',num2str(COSOLVER.co),...
'_Pmaxe_',num2str(COSOLVER.pmaxe),'_Jmaxe_',num2str(COSOLVER.jmaxe),...
'_Pmaxi_',num2str(COSOLVER.pmaxi),'_Jmaxi_',num2str(COSOLVER.jmaxi),...
'_JE_12',...
'_NFLR_',num2str(COSOLVER.neFLR),...
'_kperp_',k_string,'.h5'];
ei_mat_file_name = ['../iCa/ei_Coll_GKE_',num2str(COSOLVER.gk),'_GKI_',num2str(COSOLVER.gk),...
'_ETEST_',num2str(COSOLVER.co),'_EBACK_',num2str(COSOLVER.co),...
'_Pmaxe_',num2str(COSOLVER.pmaxe),'_Jmaxe_',num2str(COSOLVER.jmaxe),...
'_Pmaxi_',num2str(COSOLVER.pmaxi),'_Jmaxi_',num2str(COSOLVER.jmaxi),...
'_JE_12_tau_1.0000_mu_0.0233',...
'_NFLRe_',num2str(COSOLVER.neFLR),'_NFLRi_',num2str(COSOLVER.neFLR)...
'_kperp_',k_string,'.h5'];
ie_mat_file_name = ['../iCa/ie_Coll_GKE_',num2str(COSOLVER.gk),'_GKI_',num2str(COSOLVER.gk),...
'_ITEST_',num2str(COSOLVER.co),'_IBACK_',num2str(COSOLVER.co),...
'_Pmaxe_',num2str(COSOLVER.pmaxe),'_Jmaxe_',num2str(COSOLVER.jmaxe),...
'_Pmaxi_',num2str(COSOLVER.pmaxi),'_Jmaxi_',num2str(COSOLVER.jmaxi),...
'_JE_12_tau_1.0000_mu_0.0233',...
'_NFLRe_',num2str(COSOLVER.neFLR),'_NFLRi_',num2str(COSOLVER.neFLR)...
'_kperp_',k_string,'.h5'];
%% Load self matrix
C_self = h5read(self_mat_file_name,'/Caapj/Ceepj');
sz_ = size(C_self);
% Write it in the compiled file
h5create(matfilename,['/',n_string,'/Caapj/Ceepj'],sz_)
h5write (matfilename,['/',n_string,'/Caapj/Ceepj'],C_self)
h5create(matfilename,['/',n_string,'/Caapj/Ciipj'],sz_)
h5write (matfilename,['/',n_string,'/Caapj/Ciipj'],C_self)
%% Load ei matrices
% Field
C_eiF = h5read(ei_mat_file_name,'/Ceipj/CeipjF');
sz_ = size(C_eiF);
h5create(matfilename,['/',n_string,'/Ceipj/CeipjF'],sz_)
h5write (matfilename,['/',n_string,'/Ceipj/CeipjF'],C_eiF)
% Test
C_eiT = h5read(ei_mat_file_name,'/Ceipj/CeipjT');
sz_ = size(C_eiT);
h5create(matfilename,['/',n_string,'/Ceipj/CeipjT'],sz_)
h5write (matfilename,['/',n_string,'/Ceipj/CeipjT'],C_eiT)
%% Load ie matrices
% Field
C_ieF = h5read(ie_mat_file_name,'/Ciepj/CiepjF');
sz_ = size(C_ieF);
h5create(matfilename,['/',n_string,'/Ciepj/CiepjF'],sz_)
h5write (matfilename,['/',n_string,'/Ciepj/CiepjF'],C_ieF)
% Test
C_ieT = h5read(ie_mat_file_name,'/Ciepj/CiepjT');
sz_ = size(C_eiT);
h5create(matfilename,['/',n_string,'/Ciepj/CiepjT'],sz_)
h5write (matfilename,['/',n_string,'/Ciepj/CiepjT'],C_ieT)
%% Copy fort.90 input file and put grid params
if(k_ == 0)
h5create(matfilename,'/coordkperp',numel(kperp));
h5write (matfilename,'/coordkperp',kperp);
h5create(matfilename,'/dims_e',2);
h5write (matfilename,'/dims_e',[P,J]);
h5create(matfilename,'/dims_i',2);
h5write (matfilename,'/dims_i',[P,J]);
end
n_ = n_ + 1;
end
disp(['File saved @ :',matfilename])
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