Did Truman really believe that Hiroshima was a military base?

I think you may not be properly evaluating the context of the diary entry you provide:

I have told [Stimson] to use [the first nuclear bomb] so that military objectives and soldiers and sailors are the target and not women and children. Even if the Japs are savages, ruthless, merciless and fanatic, we as the leader of the world for the common welfare cannot drop this terrible bomb on the old Capitol or the new.

He & I are in accord. The target will be a purely military one and we will issue a warning statement asking the Japs to surrender and save lives.

You are taking this to mean that Truman believed that Hiroshima was a military base and not a city with civilian inhabitants. That is not the meaning I take from it at all.

Kyoto was considered as a target, and Kyoto's military and industrial value was negligible. Kyoto's value was primarily cultural, historical, and psychological. Destroying Kyoto would have been an attempt to break the Japanese politically through sheer terrorization, with very little direct military benefit at all.

The sense I get from this diary entry is that Hiroshima, compared to Kyoto, was a traditional military target.

One could make an analogy to a hypothetical war against (for example) Saudi Arabia. If one launched a nuclear weapon against Saudi Arabia, one would have to choose between traditional targets with military value, and Mecca. Mecca would be a psychological target and not a military one. If Mecca was up for consideration as a target and you rejected it as a target, you might then write in your diary "We chose to go with a military target instead" even if the target you chose had a large civilian population.

Background

Timeline of 1945:

• Feb - firebombing of Dresden
• Feb/Mar - battle of Iwo Jima
• Apr 12 - Truman becomes president.
• May 30 - Groves and Stimson begin to butt heads over targeting Kyoto.
• Jun 16 - committee rejects a demonstration bombing
• Jul 16 - Trinity test
• Jul 25 - Truman's diary entry
• Jul 30 - torpedoing of the Indianapolis
• Aug 6 - Hiroshima bombing

The Allies started out by trying to use precision bombing against Germany, but they found this difficult to do, so they changed to carpet bombing. This set a precedent and put military brass and politicians in a mind-set where there was no longer any real pretense of trying to spare civilian lives. The Battle of Iwo Jima convinced military planners that an invasion of the Japanese homeland would be incredibly costly. Against this backdrop, there was irresistible momentum for using the two available bombs on one or more Japanese cities, and opponents like Szilard were sidelined.

When Truman became president, he knew nothing about the bomb and had to have it explained to him. He was not closely involved in targeting decisions. The main people involved were General Groves and Secretary of War Stimson, who was 77 years old. A committee began discussing targeting on May 30, which was before the Trinity test. At this point, the explosive yield of the bomb was highly uncertain. There was a betting pool (Rhodes, p. 656) among six of the top physicists as to the yield of the Trinity test, with people betting on figures of 0, 0.3, 1.4, 8, 18, and 45 kilotons. This meant that while the targeting decisions were being made initially, there was so little knowledge that nobody could actually project civilian versus military casualties, or the effect to be produced by dropping the bomb in one spot versus another.

The torpedoing of the Indianapolis, with men dying horrible deaths in shark-infested waters, hardened attitudes toward the Japanese. A committee had rejected a demonstration bombing, which was associated with the idea of putting bombs under international control. These hardening attitudes were to some extent vindicated after the Hiroshima bombing, when George Marshall was shocked to find that one bomb hadn't even been sufficient to convince the Japanese to surrender unconditionally (Rhodes, p. 736).

The debate over targeting Kyoto

Before FDR's death, Groves and Stimson began an ongoing battle as to whether to target Kyoto. Stimson wanted to preserve the historic city, for reasons that continue to be debated, while Groves wanted to target it. This battle went on for a long time, so basically any possible debate as to military versus civilian targets never really happened, because it was diverted into this channel. Truman seems to have been involved in the whole targeting discussion only because Stimson kept invoking Truman's support in Stimson's pet cause of not targeting Kyoto.

The criteria used for targeting do not really appear to have included any consideration of Japanese civilian deaths. They were concerned with not killing American POWs (there were none in Hiroshima) and with using targets that had not yet been hit by conventional bombing -- a pristine target would make it easier to determine afterwards what the nuclear bomb's effect had been.

Reading Rhodes, I felt confused about why Stimson didn't want to bomb Kyoto. Wellerstein has an interesting discussion of this, and seems to indicate that historians are puzzled by this as well. Stimson had visited the city during the US occupation of the Phillipines, and may have gone there on his honeymoon. Kyoto had historical and religious significance (Wallerstein, Kelly, Malloy). Kyoto was a tempting military-industrial target (hence Groves's desire to target it), but according to Kelly's analysis Stimson probably wanted to spare the city in order to minimize Japanese anger and resistance, which he believed would be excited by the destruction of a historical and religious site. Malloy seems to agree with this, citing a couple of relevant lines from Groves's autobiography.

Truman's character

There is clear evidence, from after Hiroshima, for a picture of Truman's feelings of guilt, emotional dissembling, and lack of understanding of the technical issues. Oppenheimer and Truman met for the first time on Oct. 25, 1945. My info on this meeting is from Bird and Sherwin, pp. 331-333. Oppenheimer was shocked by Truman's ignorance when Truman claimed that the Russians would "never" be able to build a bomb. Oppenheimer wrung his hands and said, "Mr. President, I feel I have blood on my hands." Truman became very angry about this. This clearly had hit a sore spot. On the one hand, Truman embellished the story later to make himself come out looking tough. On the other hand, he later muttered to himself about having blood on his own hands. The Bird-Sherwin biography quotes contemporaries' opinions of Truman re the nuclear issue on p. 333: that he was "small-minded" and "a simple man." They summarize these common impressions by saying that "Truman's instincts, particularly in the field of nuclear diplomacy, were neither measured not sound--and sadly, certainly were not up to the challenge the country and the world now faced."

A hypothesis about Truman

So I think the basic story here is that the decision was set on track to bomb one or more cities during a period when Truman didn't know about the bomb, and by the time Truman became president, the debate had already been channeled into a decision between Kyoto and other targets. Little was known yet about the yield of the bomb, and Truman understood even less of the technology. He didn't attempt to question the decisions of people who had already been running the bomb project before he heard about it.

Regardless of how passive, uninformed, and uninvolved he was on the targeting issue, he can't possibly have been ignorant of the fact that Hiroshima was a populated city. His diary entries show that he was at least involved and informed enough to have been conscious of the debate about Kyoto. His diary entry shows a cursory moral struggle with the fact that, given the yield measured in the Trinity test, he would clearly be killing something like 100,000 people. This was probably less a real personal struggle than an attempt at test-driving his propaganda for use after the bomb was dropped. His propaganda (and/or self-propagandizing) made use of absurd rationalizations: that Hiroshima was "purely" a military target, and that by targeting Hiroshima rather than Kyoto they were taking some kind of moral high ground.

A more detailed but more uncertain story-line that seems at least plausible to me is the following. This is supported by Kelly and Malloy. Stimson, an experienced imperialist, wanted to spare Kyoto out of cold-blooded calculation regarding the postwar tractability of Japan as a US dependent. Because of this, he made various cynical and specious arguments to Truman, e.g., exaggerating Kyoto's status as a civilian target and Hiroshima's importance as a military target. Truman was incurious and not very smart, and possessed nothing like Stimson's extensive personal experience in Asia. He took the bait and exaggerated the spurious distinction in his own mind in order to self-propagandize and publicly propagandize about US morality. Because the bombing plan had been a long time in the building and had such momentum, it would have taken tremendous moral and intellectual authority, energy, and self-assurance to turn it aside in any significant way. Truman did not have those qualities in such exceptional quantities. However, he did have the moral qualms about mass killing that any non-psychopath would have had, so he needed rationalizations. Stimson gave him one.

In support of this interpretation, it appears that professional historians have also seriously considered the hypothesis that the decision makers were "self-deluded." See Kelly describing Sherry's opinion of Stimson.

Reference

Rhodes, The making of the atomic bomb

Bird and Sherwin, American Prometheus: The trumph and tragedy of J. Robert Oppenheimer

Jason M. Kelly, “Why Did Henry Stimson Spare Kyoto from the Bomb?: Confusion in Postwar Historiography,” Journal of American-East Asian Relations 19 (2012), 183-203

Sean Malloy, “Four Days in May: Henry L. Stimson and the Decision to Use the Atomic Bomb,” The Asia Pacific Journal, Vol. 14-2-09, April 4, 2009.

Alex Wellerstein, "The Kyoto misconception," http://blog.nuclearsecrecy.com/2014/08/08/kyoto-misconception/

I think we may be operating from a misconception, that the diary entry concerning that the 'target will be a purely military one' and that the statement that 'Hiroshima, a military base' imply Truman did not understand the presence of a city.

The target selection process had been going on for some time. A lot of documents are available and the discussion on narrowing down the city to be bombed can be read National Security Archive-George Washington University. This defines Hiroshima

"This is an important army depot and port of embarkation in the middle of an urban industrial area. It is a good radar target and it is such a size that a large part of the city could be extensively damaged."

(emphasis mine) This was dated May 12 1945. Hiroshima was one of two AA rated targets, the other being Kyoto(a city of 1,000,000 at the time). Hiroshima was selected for its military value. From the wiki (and I know there are many different casualty estimates):

directly killing an estimated 70,000 people, including 20,000 Japanese combatants

and this entry from Yale Law School discusses the military significance of Hiroshima:

Hiroshima was a city of considerable military importance. It contained the 2nd Army Headquarters, which commanded the defense of all of southern Japan. The city was a communications center, a storage point, and an assembly area for troops. To quote a Japanese report, "Probably more than a thousand times since the beginning of the war did the Hiroshima citizens see off with cries of 'Banzai' the troops leaving from the harbor."

So the military effect is established. There were military casualties. The military base existed.

I don't see a problem characterizing Hiroshima, in the radio address of Aug 9, as a military base. (on a side note, if you ask someone in the military where they were stationed, a typical reply might be 'San Diego' for instance-not 'Naval Base San Diego') In the radio address I doubt there was any thought that the public would have any idea where or what Hiroshima was. The term 'a military base' is just descriptive.

Concerning the possibility of Truman being deceived concerning the nature of this target let's take a look at this quote from the page on the target selection:

a large part of the city could be extensively damaged.

It seems to me this portion of text says a lot. It acknowledges the presence of the city, but seems to show a lack of understanding concerning the power of the weapon they are about to unleash. A 'large part', 'could be',and 'extensively damaged' all express uncertainty at the range,the outcome, and the amount of damage.

If we look at the first part of the above mentioned diary article, it discusses the information concerning the weapon test.

An experiment in the New Mexico desert was startling — to put it mildly. Thirteen pounds of the explosive caused the complete disintegration of a steel tower 60 feet high, created a crater 6 feet deep and 1200 feet in diameter, knocked over a steel tower 1/2 mile away and knocked men down 10,000 yards away.

A crater 1200 feet in diameter. A crater this size would destroy a few city blocks, but 1/2 mile away it just knocked over a test structure. This test is what they keep mentioning in later references.

The Truman library has a lot of documents, concerning tests, target selection, ect. The last couple pages of one document has some related reports from after the bomb was dropped, both of which express surprise at the results, and compare to the first test (emphasis mine):

letter from Admiral Edwards to Admiral Leahy, 6 Aug

"visible effects greater than any test"

letter from Stimson to Truman, also 6 Aug

..."first reports indicate complete success which was even more conspicuous than the first test.

There is no doubt that there were military objectives at Hiroshima. I don't think there were any illusions that there would be no civilian casualties. But it appears from the documents, that they were in no way expecting to completely destroy an entire city (possibly 'extensive' damage), and that they were all surprised by the results (since they kept comparing results to the earlier test detonation, which was minor in comparison).

So concerning the 'purely military' nature of the target. The target was the military facility at Hiroshima; the expectation was its destruction; and they understood there would be collateral damage(I hate that term),but not its vast extent . This was the 'purely military' aspect of the selection of this target. If he did not desire a military target, Kyoto with its population of 1,000,000 would have likely been selected (the other AA rated target),to not minimize but to maximize civilian casualties, and the horror of this moment in history would have been (if possible) greater yet.

(I hope this somewhat clears up the last half of the answer. My goal was to show that the massive casualties may have been unexpected, since the individuals involved all kept thinking and comparing to the original test. This, combined with the fact that they rejected targets which contained more civilians, shows the consideration which makes this target 'military' in nature. Its not that the target would cause only military casualties, but that the reason for the selection of this target over others was due to its military nature.)