Troubles in Doctoral Studies Currently I am on the second year of my PhD. I started more than a year back and I doing phd in basic science and I am not from basic science. 
My problems are: 

I don't cope with the ideology people have in my work station. So, I ended up having issues with them. 
I lack quiet a bit of knowledge on the subject area. 
I lack communication with my supervisor. 
Now, I supervisor wants me to quit but I don't. I still want to try even if it's just getting harder and stressful. 
I am an open person and have strong personality. I like to make changes about me and on my surroundings. 

I don't really know what to do, since if I loose the position now I will be into more trouble. Since I don't have any safety net. 

I also will not be able to prolong my residence permit in Europe also if loose the position, which is also a reason that I don't want to quit now. 

I am passionate about everything that I do. I have enough will power as well, but being with my supervisor is getting too hard. My study mentor have suggested me to sick for another supervisor but to keep the position I have to find someone from the department. Hopefully there is a possibility there.

Unfortunately, my supervisor is highly known scientist and he told me that he will write everything on my reference letter, which means it will be much harder to find something later. 

Please let me know what you all think about it.
While @user18244 suggested a viable option, I would argue that switching fields may not be worth the effort, as the poster may run into similar issues regardless of which field s/he studies. 

Problems that I can glean from the post:

1. Amateur with lack of direction wasting an expert's time: OP is coming at a PhD level into an unfamiliar subject area. I can see how this might seem annoying to a highly known scientist who is serious about his work and his students, expecting them to be as focused and dedicated to the field as he is. This may contribute to the resentment i.e., "Why don't you quit, that way you would stop wasting my time and yours?"

2. Staying in the country as the main and only reason for pursuing PhD: Despite being "passionate about everything", lack of coherent reason for pursuing advanced study in this particular area, except for unrelated practical reasons such as visa status and desire to remain in a particular geographic area. This alone does not usually cut it as valid rationale for pursuing advanced study for most academics. 

3. Personality/cultural issues: As OP suggests, "I...have strong personality. I like to make changes about me and on my surroundings." As a student, you are naturally in an inferior position in relation to the faculty. A student's first and foremost role is to be a humble, dedicated, agreeable, adaptable and quick learner who causes minimum problems for the faculty (read: takes the least amount of time to advise and direct, and in return performs the highest quality work s/he is capable of). When a student's assertive personality causes them to fail to meet this expectation, this may earn the student a 'reputation' for being a "loose cannon" who is out of control and creates more problems than s/he solves. This is not a position you want to find yourself in. 

Given the above assumptions, I would recommend the following strategy:

1. Carefully consider how your personality may be causing some of the issues you are describing. Try to find the problem with yourself first, and only then turn to others (better yet, stop with yourself, for now). If you feel that you could possibly express your strong personality a little less strongly when this does not seem helpful in your interactions, try to think objectively about such situations and see how you can change your attitudes, responses, opinions, etc. in ways that would eliminate this as a possible cause of disagreement and discomfort on the part of your supervisor. 

2. Fix the communication. Focus on developing the following qualities: humility, respect, patience, and politeness. This will go far with communication with any professional colleagues, and academic faculty are no exception. This is difficult, but one place to start may be to have a conversation with your advisor with the main goal of asking questions and listening, not talking. Be honest and say that you are struggling, but are passionate about this field and give specific examples of topics or theories that interest you (hint: there should be some alignment there with your professor's interests!). Ask for feedback on what strategies you could apply to be more successful in your studies. Ask for guidance, direction, and advice on how to communicate better, study better, and work better so that you could succeed and catch up to your peers. Do NOT argue with anything you hear, but thank the advisor for their time and effort in giving you their feedback. If they say "I think your best strategy is not to waste my time and quit your studies ASAP", ask "I appreciate this, but IF there was just 1% or 5% chance that I could succeed against the odds, what do you think I should start doing immediately to make this happen?" You want to turn the conversation from a diagnosis of current situation to a prescription for how to remedy the situation toward a better future state. Good Luck!

3. Prioritize your studies above all else. This is difficult, but necessary if you truly want to catch up to your peers and "grow" in the eyes of your professor. Study hard and study all the time. A favorite show on TV? Nope, you have a paper to write or book to read. Great weather outside for a picnic? Walk for 30 min, then go back to your homework. A friend's birthday party? Show up for 1 hr, then head to computer lab to do more data analysis or whatever you need do there for your professor. During the first 3 years of grad school I have often sat in the office late (very late!) getting home after midnight, only to return back to work next morning at 8am. My reward was a reputation of a very hard working and reliable member of the research team, who could finish the tasks that were given to him with quality and on time. Achieve THIS, and it is 100% guarantee that your advisor's opinion of you will change for the positive. Good luck!