reorder_cosolver_resfile.m
b3f94e22e87cllechot

reorder_cosolver_resfile.m
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			function reorder_cosolver_resfile(resfile)
			% reorder_cosolver_resfile reorder the collisional matric stored in resfile
			% (only for ion-ion for the time being) when calculated using mpi_balanced.

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

			fprintf(['Reorder rows of ', resfile,'\n']);

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

			% Get rows labels
			rows_mpi_balanced= h5read(resfile,'/Caapj/rows_i');

			% Read collisional matrix
			Ciipj_mpi_balanced = h5read(resfile,'/Caapj/Ciipj');

			% reorder collisional matrix by ordering rows.

			new_Ciipj = zeros(numb(Pmax,Jmax),numb(Pmax,Jmax));

			for irow=1:length(rows_mpi_balanced)
			row_tmp = rows_mpi_balanced(irow);
			new_Ciipj(row_tmp,:) = Ciipj_mpi_balanced(irow,:);
			end


			% Write reordered matrix in h5 resfile
			dim = double(numb(Pmax,Jmax));
			fprintf('Create new dataset "/Caapj/Ciipj_ordered"')
			h5create(resfile,'/Caapj/Ciipj_ordered',[dim dim])
			h5write(resfile,'/Caapj/Ciipj_ordered',new_Ciipj)

			% Plot before and after results
			%figure; pcolor(Ciipj_mpi_balanced); title('Before')
			%figure; pcolor(new_Ciipj); title('After')

			end