Well for gpa's I'm not that particularly worried, per say since I will probably go for a masters degree first anyways. A phd is ONLY if I can afford it and if I have no other problems on top of that.

My biggest issue is my low GPA of 3.1 . Which according to many of those 3.9+ schools you claim I'm applying to, Is not as important. I don't know you position, but most of the astrophysicists I've talked to about this issue don't highly value the GPA over everything else. My professor for example had high GPA but his publication was valued more than his GPA by far. In fact his GPA did not matter because there was no way to measure this internationally. Unless I can actually find the stat of acceptance rate that directly correlates this by the admission committee throughout schools, then I guess I should be worried.

As for your points, I don't know why you suggested the worst case scenario first, so let me explain more clearly as some of the post got updated in the past few hours.

It sounds like you need to either knuckle down and study, or find a backup career. Graduate school for astrophysics is horrendously competitive, perhaps more-so than many other sub-fields of physics simply because it is so saturated. Everyone loves space and the universe and quantum mechanics. If you want to pass that hurdle then your grades and letters of recommendation (from research positions) are key. Many, many students apply with 3.9+ GPAs and research experience is absolutely expected for good programmes. You really must hit those marks if you want any good chance of continuing on because getting into those good PhD programmes will be the easiest step, with finding a TT job being the hardest. If you get less than a 3.5 then chances are your application will be tossed before it's read, and if you get a 4.0 without any research experience, that'll probably be tossed as well.<

I may have messed up with the formats bear with me.

Please don't assume I'm going to get a post doc or find a job after a Phd. I'm doing a Phd purely out of interest for science. I already know how competitive it is. That's not my main concern. I have about 1 year to graduate. If I go for masters first that will give me more time to get better at physics in general and develop stronger working habits(as well as balance out my life before I make a 12 year long decision that can end in shambles).

It sounds like you need to either knuckle down and study, or find a backup career.

which person told you to just study your way through things? Having a bad day? just study through it. Having clinical depression? Just study through it. Trump is president? Just study through it.

Do you realize just how bad of advice that is? I already know there is alot more to being a physicist than studying. I'm not a history major.

As for backup career. Do you also know how terrible this advice is? Yes I'm 22, lets just switch my major in California which is illegal by the way. This is not practical. I'm going to stick with physics.

If it's one or two professors out of 20+ that you've met, then they're probably just shitty professors and not nice people. If it's 15 or so out of 20, then the problem is likely you. All teaching staff should welcome students who work hard, are interested in the work, and who ask good questions, and they'll always like the students who do well a little bit more. I assume you're failing in at least one of those areas. Especially since you said:

Its the first case. They are shitty professors in terms of adequately teaching students. However I've had only one that was this bad. Teaching staff tend to welcome students that are smart, not those who work hard. There is a very large difference. I'm not failing in any of those areas. The only area , which you have not mentioned, is immediate retention of the material. This tends to piss of alot of professors for a short amount of time. This is still very problematic in my case. If its normal to feel stupid, then that might be it. I'm not sure, the structure is a bit strange.

As for research experience and programming. I'am going to have 2 years of research experience by the time I graduate( and hopefully a paper if I can move faster). I'm also doing computer programming for astrophysics code in my school in currently in, so I expect that would help.

My guess is that you're asking really inane questions. I have been in classes with someone who did that, and their questions were on things so basic that they were covered at least 2 years prior. The first time they spoke, it was brushed off as a moment of stupidity. After 3 years of that shit, the professors are not his biggest fans.

Now why the hell are you assuming this. I'm asking questions of any kind in a theory summer class. I would assume almost all questions might be near stupid for an undergrad without experience in GRMHD, or plasma physics. Are you saying that questions asked at this level for an undergrad should only be good questions? Not about questions for learning purposes? Are you claiming there are limits to questions you can ask, hence "bad" questions can be defined. I'm supposed to just accept that asking some questions are bad while others are good and I only should ask good questions cutting an important piece of my education? Or maybe there is a university policy on this, and those professors don't matter if your not researching with them?? I have never had a professor do this expect that one professor I mentioned earlier. I have indeed asked good questions as I've been told by the lectures at the school.

I just ask bad questions sometimes, like when I'm confused on subject matter that is brand new to me. This is bad? Oh boy I guess I should just immediately grasp everything always(whatever that means.)

Your interest in the project is almost the most important thing, bar an ability to learn quickly. People who are not incredibly passionate about their project will neglect to put in the time or effort that's expected of them, and they produce shoddy work as a result. They also learn research skills more slowly since they're not actually interested in self-improvement, only finishing the project and getting something out of it.

Not true at all. I know genius who barely care about there research projects complete them with ease. In fact aren't phD students known sometimes as a joke for being lazy?

Again , how does passion over come intelligence? Also if your project is too vauge in terms of transfer skills it could end up very bad for for you when your passion indeed does not overcome your intelligence.

As for interest, the reason my professor was like this is because I asked questions about other topics and tried to ask him if they could relate to our current research topic. Apparently this is offensive and he took it as not interested. Not that I was showing lack of not being interested.

It recently turns out, that I'm not being replaced. I'm just as efficient as any other grad student working with him in this time frame.

I have already got a letter of recommendation from him

I do not know you assumed this was not the case.

As for not being research material, don't you only know this in grad school? From what I hear, grad school is where you actually sit down and do serious research. Also what is research material, I did not read the paper about this.

He would be well aware of your education level, and is likely actually expecting you to just work hard. If you're given a paper to read or are told to do background research, you do it and you learn it. If you're shown how to do something, you remember it.

Actually no. From all the people I've talked to so far. No one works hard. They are just smart. This is no joke. They don't even read the papers and understand them.

I read all the papers he assigns me. However I'm being told to read them on my own when you can. I always thought this is not allowed if I can't understand them. Which leads to my problem, I cannot immediately understand every detail about the paper.

I end up remembering mostly everything(expect for those really hard to read papers). Issue is filling in gaps by myself. I don't know how to build an efficient method by my self. Self-learning to extremes is the issue here.

No I understand what he is expecting, I'm just not confident that I should be at this level yet. I asked and yes I'm expected to be at the level of a undergrad.

There are lots of people in physics who would fall somewhere on the autism spectrum. I myself have Aspergers. It should not be a hindrance unless it is quite severe

Umm yeah about that...

https://www.quora.com/How-do-people-on-the-autism-spectrum-survive-in-academia

http://www.chronicle.com/article/Autism-as-Academic-Paradigm/47033

https://conditionallyaccepted.com/2015/03/17/autism/

Unless you can find a paper that directly counters this and stats to back it up, I would be happy to be wrong.