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As this last method is within a loop (for each species), the matrix is computed outside this loop and is passed to the ```compute_phi``` method, therefore changed.\r\n\r\nOnly the last commit matters, I've branched out of #79 for reducing future complaints of conflicts while remanaging #79 for design purposes.  Also it makes rebasing easy for the ExacT branch.\r\n\r\nThus this is to be merged after #79, 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