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The evaluation of Teller's Super project at the 1946 meeting was guardedly optimistic, but the participants were aware of major technical uncertainties and potential difficulties with the Super design. In discussing the conclusions reached at the meeting J. Carson Mark has written, "The estimates available of the behavior of the various steps and links in the sort of device considered were rather qualitative and open to question in detail. The main question of whether there was a specific design of that type which would work well was not answered." Studies prior to 1946 had established that the net balance of energy gains over losses in the Super bomb was marginal; there was no large margin of design flexibility for which a successful detonation could be guaranteed. According to Mark,

As it was, the studies of this question had merely sufficed to show that the problem was very difficult indeed; that the mechanisms by which energy would be created in the system and uselessly lost from it were comparable; and that because of the great complexity and variety of processes which were important, it would require one of the most difficult and extensive mathematical analyses which had ever been contemplated to resolve the question — with no certainty that even such an attempt could succeed in being conclusive.

The uncertainties regarding the ignition and sustenance of fusion reactions in the Super bomb design as developed by Teller's group during the war years were still present in late 1949 and early 1950. Nevertheless, this was the hydrogen bomb design that Teller lobbied for in Washington and that formed the basis of President Truman's decision early in 1950 to accelerate work on the fusion bomb.

The two main questions about the Super design were (1) whether it would be possible to ignite some of the deuterium to get the thermonuclear reactions started, and (2) whether a thermonulcear reaction in the liquid deuterium, once started, would be self-sustaining or, alternatively, would slow down and fizzle away if the rate that energy is lost from the reacting regions exceeded that produced by the reactions. The ignition of the Super would require a gun-type atomic bomb trigger in which two subcritical masses of fissionable uranium would be rapidly united to form a supercritical explosive mass, as in the Hiroshima bomb. The ignition problem was difficult. The unusually high temperatures required for ignition would require a trigger A-bomb that would need to have a yield, reach temperatures, and use a quantity of fissionable material substantially in excess of the bombs in the arsenal in 1950. Even under the most favorable circumstances, the deuterium could not be ignited directly. It was thought that a small amount of tritium could be used to help initiate deuterium-burning in the region initially heated by the fission bomb.

The first a major difficulty for the Super, the problem of ignition, was attacked by Ulam on his own initiative but in collaboration with Cornelius Everett, a mathematical colleague of Ulam's at the University of Wisconsin who had come to Los Alamos after the war at Ulam's invitation. These calculations followed in detail the initial evolution of the nuclear reactions in tritium and deuterium and included an estimate of the heating of the unburnt nuclear fuel by the hot reacting regions with allowances made for the energy lost due to expansion and radiation. The Ulam-Everett calculation was tedius and exacting. While each step of the computation was understood, the complex interplay among the many components involved made the whole calculation extremely difficult. The exchange of energy between electrons and radiation. Ulam's first problem at Los Alamos, was just one part of this monumental calculation. For several months Ulam and Everett worked in concentrated effort from four to six hours a day. Since each step in the calculation depended on the previous work, it was necessary to complete each stage virtually without error; fortunately, freedom from error was one of Everett's specialties. It is hard to imagine today that these calculations were performed with slide rules and old-fashioned manually operated mechanical desk calculators. Ulam and Everett had to make many approximations and educated guesses in order for a solution to be possible at all. By this time Ulam had clearly mastered the physical intuition and judgment needed to make sensible estimates. When the calculation was finished, however, their conclusion was negative. The deuterium could not be ignited without spectacular amounts of tritum, amounts sufficient to make the entire Super project impractical and uneconomical. Within a few months the conclusions of the Ulam-Everett calculation were confirmed by von Neumann using an early electronic computer at Princeton.

The second uncertainty in the design of the Super was the question of the propagation of the deuterium-burning region throughout the entire amount of liquid deuterium. Would the fusion reaction be self-sustaining assuming that the ignition difficulty could somehow be overcome? This fundamental problem was solved by Ulam in collaboration with the brilliant physicist Enrico Fermi. Again using slide rules and desk calculators — and great care in making the appropriate physical approximations — they reached another negative conclusion; the heat lost form the deuterium burning region was too great to sustain the reaction. In discussing the conclusions of the Ulam-Fermi calculations, Fermi noted cautiously that "if the cross-sections for the nuclear reactions could somehow be two or three times larger than what was measured and assumed, the reaction could behave more successfully." In fact the cross-sections (which characterize the rate that the reactions can occur) used by both Teller's group and by Ulam and Fermi in 1950 were larger and therefore more otpimistic than the more accurate cross-sections obtained experimentally by James Tuck in the following year. In recent years the Ulam-Everett calcualtion has been redone in a much more refined manner using modern computers that have confirmed the marginal character of the self-sustaining propagation.

Within months of president Truman's directive to expedite the development of a thermonuclear bomb, the two basic assumptions of Teller's Super model were shown by Ulam and his colleagues to be incorrect. A crash program had begun on a project that was fundamentally flawed and which had never been seriously tested prior to Ulam's work. According to Hans Bethe, Teller "was blamed at Los Alamos for leading the Laboratory, and indeed the whole country, into an adventurous program on the basis of calculations which he himself must have known to have been very incomplete." The energy released by the deuterium reaction would be lost before adjacent regions could be ignited since, in Ulam's explanation, "the hydrodynamical disassembly proceeded faster than the buildup and maintenance of the reaction." Teller, who had worked on the Super during the war years and who later became a one-man political action committee urging a crash program for its construction, was distraught and practically undone by the Ulam-Everett-Fermi conclusions. Teller has written that "Ulam's work indicated that we were on the wrong track, that the hydrogen bomb design we thought would work best would not work at all."

The crisis of disappointment following these developments was quite stunningly resolved by Ulam in February, 1951, when he suggested a means of compressing the deuterium sufficiently to allow both ignition and self-sustaining propagation. According to Hans Bethe, director of the theoretical division at Los Alamos during the war, Ulam's idea was to use "the propagation of [a] mechanical shock" (compression) wave from a fission explosion to induce a strong compression in the thermonuclear fuel, which would subsequently explode with great violence. The advantages of compression in helping to make thermonuclear reactions more efficient had been discussed even as early as the April 1946 meeting, but were never taken seriously since the compression required was far greater than could be achieved with chemical explosions. When Ulam told Teller of his idea of using a fission bomb to compress the deuterium just prior to its ignition, Teller immediately perceived the value of the idea. However, Teller suggested that the implosion could be achieved more conveniently by the action of radiation, with a so-called "radiation implosion," rather than with the mechanical shock proposed by Ulam (which would also have worked). The new idea for the hydrogen bomb, known euphemistically as the "Teller-Ulam device," was rapidly accepted by Los Alamos scientists and government officials. Since first proposed by Ulam, the coupling of a primary fission explosion with a secondary fusion explosion by means of implosion has been a standard feature of thermonuclear bombs.