Knee injury due to accident. Deficiency.

I met with an accident on april 2016 . i injured my knee . initially i thought it as a minor injury and allowed it to heal naturally . but 1 year passed the swelling and pain of my knee didn't vanish . i showed to a doctor and he suggested me to go for mri scan . the reports of scan showed negative for ligament tear and it reported of me having chondomalacia grade 3 . when i showed the report back to doctor he told me to go for vitamin d test and the reports suggested that i am suffering from vitamin d deficiency . i was prescribed vit d chewable and a few stretching exercises . but even today the pain and swelling of my knee doesn't seem to decrease . sometimes i find difficult to even walk due to swelling . please suggest me the measures to recover completely .