this was due to the indexing, you were putting the temporary data into "nn{n1,n} = F1{n1}", thus at the second run of "n" a new column would be added to "nn" and it would result in the same number of rows as "n=1".
The solution is to allocate a new cell at each loop.
S = load('CCSD.mat');
F = fieldnames(S);
for n = 1:numel(F)
F1 = fieldnames(S.(F{n}));
F11{n} = F1;
% allocate the variables
nn = cell(numel(F1),1);
PArea = cell(numel(F1),1);
for n1 = 1:numel(F1)
t = S.(F{n}).(F1{n1}).cc.t;
nn{n1} = F1{n1};
output{n1} = cumtrapz(t);
NF = @(p,q) max(output{n1}(t<=q)) - min(output{n1}(t>=p));
PArea{n1} = NF(5, 6);
end
cumulat{n} = [nn, PArea];
end
cumulat
cumulat{1,2}
