How is JCPOA compliance monitored? [closed]

Question

JCPOA compliance is monitored by the IAEA.

IAEA inspectors spend around 3000 man-days a year in Iran.

The Iranian leadership declared military sites off-limits to the inspectors. Prior to the signing of the agreement, at least one of these sites was known to include a nuclear research facility.

Given this, how does the IAEA confirm compliance with the JCPOA at these sites?

Note: It appears that the IAEA entered into a self-certification agreement with the Iranian authorities for the Parchin complex, at which nuclear testing was known to be being performed. Perhaps this is the compliance-checking mechanism used?

Answer 1

No sites were agreed as "off limits." There is no clause in the agreement saying that any are. When negotiating the deal, there was, of course, noise and bluster, mostly from politicians looking to score points with their bases about that, but there was never any kind of site that was declared to be off limits, and Iran never refused access to any sites requested by the IAEA. After Trump took office, and they made noise about wanting unfettered access to all their military sites, without any evidence that there was reason to suspect nuclear activity, of course Iran pushed back, as any sovereign nation would. If Iran demanded access to US military sites, nuclear and not, we'd laugh at such a request.

There were sites that were agreed that the IAEA would have unfettered access to, and agreements for a process for them to get access to other sites, if they showed cause to investigate.

The agreement allows for a "long-term IAEA presence in Iran" to monitor materials and nuclear development that wouldn't be used in weapons. Inspectors will have continuous monitoring capabilities at known nuclear facilities like Fordow fuel enrichment plant and the Natanz enrichment facility. For other areas in the country, including military sites where there is suspected nuclear activity, IAEA inspectors will have to request access.

If inspectors have concerns that Iran is developing its nuclear capabilities at any of the non-official nuclear sites, they are allowed to request access "for the sole reason to verify the absence of undeclared nuclear materials and activities or activities inconsistent with" the agreement. They must also inform Iran of the basis for their concerns.

Iran, in response, can propose alternatives to inspection that might satisfy the IAEA's concerns, the deal says. But if they can't come to an agreement to satisfy the inspectors within 14 days of the original request for access, the issue goes to a joint commission that consists of representatives from the P5+1 powers (the U.S., China, Russia, France, the United Kingdom and Germany), Iran, and the European High Representative for Foreign Affairs. They have another seven days to reach an agreement that must be supported at least five of the eight members. If they decide inspectors should get access, Iran has three days to provide it.

CBS News: Obama says inspectors get access to "any" site in Iran. Is it true?

The thing is, even if Iran had months of time, they couldn't hide a nuclear program. The equipment and infrastructure are too heavy-duty to be thrown into a truck and hauled away, and you're dealing with material that leaves traces for hundreds of thousands of years.

In the agreement, Iran gave access that was more intrusive than any nation had ever agreed to before, and they lived up to their end of the agreement.

It said the Vienna-based U.N. nuclear watchdog was able to carry out all so-called complementary access inspections needed to verify Iran’s compliance with the deal.

“Timely and proactive cooperation by Iran in providing such access facilitates implementation of the Additional Protocol and enhances confidence,” said the report, which was distributed to IAEA member states.

“The production rate (of enriched uranium) is constant. There is no change whatsoever,” a senior diplomat added.

Reuters - Iran is complying with nuclear deal restrictions: IAEA report

Answer 2

No the IAEA did not enter a "self-certification agreement with the Iranian authorities" regarding Parchin if that's what this confusing question is about. Instead

The diplomats, who have knowledge of the deal, said that while the IAEA inspectors will not be next to the Iranian technicians when they take samples, they will be at Parchin overseeing the process. Cameras will record the process.

I don't know if IEAE has requested to inspect the SPND (aka Organization of Defensive Innovation and Research) headquarters, which seems to be another prong of your question. But the IAEA document you link on that does not allege any fissile material stored there. The US has imposed unilateral sanctions against SPND though in March 2019. I see no mention in that latter article of IAEA (e.g. having requested access but having been denied to SPND). And the reason why SPND isn't so hot for IAEA might be that the information is not of present relevance, as an article in The Atlantic (on the 2018 revelations of Netanyahu on the topic) suggests:

In his presentation last week, Netanyahu cited a secret Iranian nuclear program called Project Amad (which the IAEA had reported on in 2011). The project had been shuttered, he claimed, but “today, in 2018, this work is carried out by SPND, that’s an organization inside Iran’s Defense Ministry.” The implication is that Iran’s nuclear-weapons project continues; all that has changed is its name. But Netanyahu offered no evidence of that. And in the materials his aides distributed to journalists, the present tense was removed.

Similarly, Bolton has repeatedly declared—despite the IAEA’s findings and without proof—that Iran is still actively seeking nuclear weapons. Last September, he said, “Iran’s program continues unhindered.” This March, he spoke about Iran’s “continued effort to get deliverable nuclear weapons.” Which helps explain why the Trump administration keeps suggesting the same thing. After Netanyahu’s presentation, the White House issued a statement declaring that “Iran has a robust, clandestine nuclear-weapons program.” It later changed “has” to “had,” but Trump himself keeps using the present tense. Asked about Netanyahu’s presentation, he declared, “I’ve been saying it’s happening. They’re not sitting back idly.”

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The edited/long version of the question is basically a case of "no true Scotsman". The point of all inspection regimes is to make something (much) less likely to happen. That's the point of reducing Iran's stockpile of enriched materials, reducing their centrifuges etc. If you want to be 100% sure they're not making anything, occupy and/or annihilate them.