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Jaynes left the Navy in 1946 and headed for California. In the summer of 1946 he worked in the W. W. Hansen Laboratories of Physics at Stanford on the design of the first linear electron accelerator.
While he was an Associate Professor at Stanford he also supported himself consulting with Varian Associates, the U. S. Army Corp of Engineers, and the University of California at Livermore. While consulting he wrote a number of reports for both Varian and the U. S. Army. Many of the U. S. Army reports still survive, but are not available for general release; a condition that will change shortly. Two of the reports done for Varian still survive, but are only available from the main Varian corporate library. Varian, at that time, was a young upstart company that could not afford to pay Jaynes in cash, so they paid him in stock. Additionally, Jaynes' records indicate that he continued to buy Varian stock throughout most of this period. At the time of his death this stock constituted about one fourth of Jaynes' total wealth.