Hardly had he taken up his work when the civil war broke out, and for four trying years the university had a hard struggle, handicapped as it was by loss of professors and students, but with reduced resources it braved the storm and continued the work of the institution in all departments. In 1862 the first class was graduated from the college, and in November of the same year, after four years of successful labor, spent in organizing the work of the university. Chancellor Hoyt died. He was succeeded in 1863 by William Chauvenet, who, a year or so before, had been appointed professor of mathematics and astronomy. Chancellor Chauvenet was a classmate of his predecessor at Yale College and a mathematician of national and even of international reputation. He was for some years professor of mathematics at the United States Naval Academy, both at Philadelphia and at Annapolis, and great credit is due to him for his part in organizing that institution, which has always enjoyed such a high scientific position. His textbook on trigonometry is still the standard work in most colleges of this country. For seven years he held the chancellorship, and during his administration a steady growth was maintained. On his death he was succeeded, in 1872, by the Rev. Wm. G. Eliot, the president of the board of directors since the incorporation, both of which positions he continued to hold until his death in 1887.
In 1867 the law school was organized and equipped, and some of the ablest lawyers and judges of the city became members of the faculty. Two years later, in reorganizing the scientific department, courses of study leading to degrees in civil and mechanical engineering and in chemistry were established in this department; in 1870 these courses were lengthened from three to four years, and in 1871 a course of study in mining and metallurgy was added.
And so, finally, we find the work of the scientific department carried on in conjunction with the work of the college, and these two departments soon became grouped together, as the undergraduate department. This union gave final form to the general scheme of the university—a department offering work in arts and science, around which center preparatory and professional schools. Thus, in but a little more than a decade, the university had been organized and the various departments brought into due coordination, leaving the way clear for rapid expansion in the directions which were best adapted to the demands of the times.
In 1878 a new building was provided for the academy, thus separating it completely from the college, and in 1880 the Manual Training School was organized as a third preparatory department. It was the first school of its kind in the country, and its organization is due to Professor Calvin M. Woodward, who was, and still is, professor of mathematics and applied science in the university.