It goes without saying that wars of Religion are so dense and conspicuous in history, that a 6-volume series of books would be required to cover them all in detail. Wars of Religion continue to this day in skirmishes that our media outlets describe as "sectarian violence". Particularly in the middle east, the theological dispute between Sunni and Shia continues to spur unrest and violent clashes in places such as Syria, Iraq, (probably also Egypt recently). Islam, hindu, and christian religious infighting also happens in modern times in the Indian subcontinent and portions of Africa.
So anyways. Wars of Atheism. Where and when? We can say, to first approximation, that there haven't been any. But because I have no agenda, and I am not trying to evangelize something, or be a clever troll, (or an asshole), I will concede a number of minor places where Atheism was the main impetus to the violence and/or persecution.
- The French Revolution. (1789-1799) The bulk of the killing done during the "Reign of Terror" was targeted mostly to monarchs, dukes, duchesses, and tax collectors, and various people associated with the monarchy. I will concede, in the interests of honesty, that some portion of the violence was spurned by atheistic causes. Namely people were targeted on the basis of being connected to the church or part of it.
- Persecution of early Christians by Rome. (approx. 64AD to 310AD) This continued unabated until an edict brought it to a standstill. In this case, the targeted group was being targeted solely due to the fact that they were Christians. With honesty, the perpetrators were not sectarians of any stripe.
- Christian Persecutions in Japan (1597-1637). Christian missionaries were executed by the Shogun in Nagasaki. Various other murders and persecutions totaling over 300 deaths.
It is time to set the record straight.
Russian Civil War. 1917-1923. Civil political clash between Bolsheviks and pro-Tsarist "White Russians". Conflict followed the sacking of the Duma (`parliament`) four or five times.
Chinese Civil War. 1927-1937. Kuomintang (KMT) clashes against Communist insurgency lead by Mao Tse Tung. Neither side of the combatants was Christian, nor even Buddhist for that matter.
Japanese invasion of Manchuria 1931-1932. No Christians here. No sectarian or religious motivation.
Sino-Japanese War 1937-1941. Japanese invasion of mainland China. Rape of Nanking. Etc. Brunt of the fighting was carried out by the military of the KMT, themselves not Christian, Buddhist or otherwise. Japanese motivation for invasion was not motivated by a desire to persecute religious people or to install secular government.
Ukrainian Famine. Golodomor. 1932-1933. Resulted from soviet industrialization schemes and rapid creation of state-run monopolies. Political element also from Stalin. Desire to bring Ukraine under Soviet political control, political despotism, etc. Christians were not targeted. The motivations were not theological in nature. There was no particular targeting of churches or their writings. There was no "sectarian" infighting or the like.
Chinese famine during the Great Leap Forward. 1958 to 1961. Caused by massive failure of centralized government economic planning. Massive failure of state-run monopolies. The central aspect was economic and industrial causes. There was no element of targeting the hearts and minds of the religious, the buddhist, hindu, or otherwise. No element of censorship of religious writing. No targeting of Christians. China did not have a christian population to begin with! It was not the case that only Buddhists were starving in this famine. The people that died in this famine were not of a particular religious or ethnicity, or of a particular theological persuasion. Everyone of every religious persuasion was effected by and suffered from this event. There was no religious targeting.
Russian and Soviet famines 1932-1933. These famines struck rural areas the hardest. The resulted from a deadly combination a Communist scheme of confiscation of grain to sell overseas. This confiscation scheme was being done right in the worst part of the Great Depression. The double-dose of economic failures was catastrophic.
The Purges under Stalin various events between 1921-1930. Wholly motivated by political despotism. The religious were not targeted in particular. The motivation was destruction of any political challengers to the inner portion of the communist party.
World War II itself. 1939-1945. The main combatants in this most violent of times were not religious. The motivations of the various nations involved in this conflict were not to be found in splinters in Church sects, sectarian strife, of theological disputes, or of uprisings by protestants, nor anything of that manner or taste or gist. There was neither a motivation nor an attempt to bring anyone under the heel of a church or of a Pope, nor of a Muslim cleric or whatnot. No particular religion was being spread by the violence. There was no targeting of "apostate" or "pagan" groups or ethnicities. The various wars of Religion throughout history contained all these elements. WWII contained none. World War II was not a religious war.