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Some technical details: the plant is a Russian VVER-1000, a solid and dependable design with a good safety record. It's a pressurized water reactor, pretty similar to the plants in the US, and will produce 1 GW of electricity.

A fun thing about the VVER and similar reactors: they're great for providing a steady chunk of power at a stable cost, but they suck for making nuclear weapons. For producing weapons-grade plutonium, by far the easiest way to go is by making a specialized weapons-production reactor. Commercial power reactors (with a few exceptions, like Chernobyl) just aren't set up for making plutonium that could be used in a nuclear bomb. And because of the international supply and operations chain for these power reactors, it's extra-hard for the country operating them to use them nefariously.

It's counterintuitive, but the export of nuclear power plants may actually help with nuclear arms nonproliferation, by making any attempt to create weapons-production reactors that much easier to spot. After all, why would a small country try to make its own reactor designs when there are cheaper and better designs available on the market already? It would stand out, conspicuously.

One problem here: to have it operated by the locals requires a significant training effort and then it's reinforced by doing it for real.

You're absolutely right about the lack of a direct proliferation problem and the fact that so many people including inexcusably Jimmy Carter when he was President (he was one of Rickover's nuclear engineers) make such a big deal of this non-existent danger says a lot about modern world wide science policy, all bad.

Weapons grade plutonium has to be be bred quickly so that the buildup of the two undesired isotopes is minimized, which required quick fuel exchange, something the RMBK designed used at Chernobyl allows. Taking standard civilian grade plutonium based on the usual infrequent fueling cycles and trying to make a bomb out of it requires refrigeration capable of removing 100kW of waste heat (that's from the plutonium isotope used to power the RTGs used in deep space probes) and results in something that's locomotive sized and that has sub-kiloton yield (we did this as a proof of concept in the late '70s and Jimmy freaked).

That said, while Iran's incompetence at maintaining and expanding their electrical infrastructure means they really do need the power, what's to say they don't use it as an inefficient weapons grade plutonium breeder? It does indeed suck for this purpose, but will they care???

(I suspect they will because the subsequent separation process is so difficult to run in practice (due to how fiercely radioactive what's pulled out of a reactor is) and they're forging ahead on the uranium approach.)

How easy it is to convert the reactor itself , into one that can make weapons grade plutonium? i read somewhere it takes 3 months, is this true.
Is there any doubt remaining that the goal of the Iranian government is to build a nuclear bomb? Is there any doubt that they will use it? Either directly or through a proxy?
Sure there's doubt. They could just be using this as geopolitical maneuvering, plus internal propaganda. Having a credible nuclear program makes Iran's bargaining position much stronger.

As for using it, why would Iran use it? What would they gain from such a thing? One nuclear missile is enough to kill a lot of people, and of course every death is a horrible tragedy, but it's not enough to really seriously hurt another country. Hell, it takes several nuclear missiles just to properly destroy a rail yard.

Iran is being watched carefully enough that, if they used a nuclear bomb (either directly or through a proxy), it would be traced back to them, and the consequences would be dire. Nuclear bombs are far more useful to Iran as bargaining chips than as weapons.

"it's not enough to really seriously hurt another country"

Are you really serious? Have you looked at a map to see how small Israel is? What about the problem that most countries are "one nuclear bomb" size, in that everything having to do with their ruling class is concentrated in one massive city? Which I grant would normally take much more than one fission bomb to destroy, but if the placement and wind directions are good, a lot will be uninhabitable for a while?

London, Paris, Tokyo, Moscow, Seoul (I think), there's lots more. Notably the US and Germany aren't in this category (or so I think for the latter, which is an artifact of the end of WWII).

Israel's big cities aren't, can't be that big nor are their very many of them (more than two that really count???).

There's also the EMP gambit which might be used against us.

As for rail yards, again, are you really serious? They're fantastically harder than civilian buildings.

It's rather surprising given the propaganda on this subject, but the consensus of US intelligence agencies remains that Iran halted its nuclear weapons program in 2003.

http://www.armscontrol.org/issuebriefs/irannie2007

Ignoring everything else about that finding, if you read the fine print you'll note it excludes the enrichment of uranium to weapons grade. Which they certainly seem to be working furiously on.

They don't need any additional work until they've got enough of that stuff. We know from the documents Libya surrendered to us after Saddam was pulled from his spider hole that the Kahn network acquired from the PRC the plans to a 44kT yield uranium implosion device. Plans so detailed they go down to the factory floor level in telling you "using "Loc-tite" of this variety, tighten this bolt to this torque".