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Stoney married his cousin, Margaret Sophia, by whom he had had two sons and three daughters. For most of his decades in Dublin, Stoney resided in the Dundrum, Dublin neighbourhood. The street that he lived on was later renamed Stoney Road in his memory. After Stoney died in London, his cremated ashes were buried in Dundrum, Dublin.
One of Stoney's sons, George Gerald Stoney, was a scientist. But a more scientifically notable relative was Stoney's nephew, the Dublin-based physicist George FitzGerald (1851–1901). Stoney and FitzGerald were in regular communication on scientific matters. In addition, on political matters, both Stoney and FitzGearld were active opponents of the Irish Home Rule Movement. In their political opinion, the spirit of Irish Home Rule and later Irish nationalism was contrary to the spirit of science. Stoney resigned from his job as Secretary of Queen's University of Ireland in 1882 in objection to a government decision to introduce "sectarianism" into the system; i.e., Stoney wanted to keep the system non-denominational, but the government acceded to Irish Catholic demands for Catholic institutions.
Craters on Mars and the Moon are named in his honour.
His brother Bindon Blood Stoney was Engineer of Dublin Port is renowned for building a number of the main Dublin bridges, and developing the Quayside, as well as other engineering projects.
Read more about this topic: George Johnstone Stoney