contract_GKCoulomb.m
b3f94e22e87cmaster

contract_GKCoulomb.m
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			function contract_GKCoulomb(resfile)
			% contract_GKCoulomb contracts the (j,n,n) indices, and
			% reorder the rows according to the dataset /Caapj/rows_i.
			% The full GK Coulomb is output in the new dataset in resfile
			% /Caapj/Ciipj_full
			%
			%
			% Input: - absolute result file path


			% Read collisional matrix dimension
			dataset = '/Caapj/Ciipj';
			Pmax = h5readatt(resfile,dataset,'Pmaxi')
			Jmax= h5readatt(resfile,dataset,'Jmaxi')

			% define 1D mapping
			numb = @(pp,jj) (Jmax + 1)*pp + 1 + jj

			% Get rows labels
			rows_4dim= h5read(resfile,'/Caapj/rows_i');
			rows_1d = 1:1:max(rows_4dim(:,1));

			% Get 4dim GK Coulomb
			Ciipj_4dim = h5read(resfile,'/Caapj/Ciipj');

			% Initialize Ciipj_full
			Ciipj_full = zeros(numb(Pmax,Jmax),numb(Pmax,Jmax));

			for irow_1d=1:length(rows_1d)
			idx_of_row = find(rows_4dim(:,1) == irow_1d);
			elements_of_Ciipj_at_idx_of_row = Ciipj_4dim(idx_of_row,:);
			% Contract energy and FLR dimensions
			full_Ciipj_row = sum(elements_of_Ciipj_at_idx_of_row,1);
			Ciipj_full(irow_1d,:) = full_Ciipj_row;
			end

			dim = double(numb(Pmax,Jmax));
			fprintf('Create new dataset "/Caapj/Ciipj_full"')
			h5create(resfile,'/Caapj/Ciipj_full',[dim dim])
			h5write(resfile,'/Caapj/Ciipj_full',Ciipj_full)

			end