Install:
copy all files in a directory in Matlab (i.e. work), keeping the directory structure as on the cd

Start program:
cd to the casa directory, and type 'casa' in the command window. Change spinup years etc in 'defineConstants'


Changes:

- many, many small ones, but most importantly:
- each gridcell consist of a woody and herbaceous fraction, with different turnover times
- no more loops: see below

% avoiding loops: when one has to check, for example, that an array does
% not contain values that are zero, it is easiest to do it like this:

array = rand(10000,1);  % create an array of 10000 rows by 1 column array with random values

[x,y] = size(array);
for i=1:x
    if array(i,1) == 0 
        array(i,1) = 1;
    end
end

% the problem is that this is slow in matlab (and IDL as well), so there are ways around it

io = (array == 0);        % this returns an array (io) with ones where there are zero values in 'array'
array(io) = 1;            % replace the zeros in these locations with ones

% or even shorter:

array(array==0) = 1;

% this does make a big difference in processortime: let's do it 100 times:
tic
for i=1:100
	for i=1:x
        if array(i,1) == 0 
            array(i,1) = 1;
        end
	end
end
disp(['with loop: ',num2str(toc),' seconds'])

tic
for i=1:100
    array(array==0) = 1;
end
disp(['without loop: ',num2str(toc),' seconds'])

% this gives on my computer:
% with loop: 2.032 seconds
% without loop: 0.016 seconds