I had a rough first year in undergrad— what now? I think I'm off to a poor start to my undergraduate career.

Some context: my major is Materials Science and Nanoengineering at the University of California, San Diego. I'm on the BS/MS track for 2020. My GPA for my first year is a 3.2, which I think is quite bad in regards to my prospects of getting into a good PhD programme. My research advisor even told me that I need a 3.5 to have any hope at all of getting into a top tier PhD programme for my area of discipline. I need to know how I can make myself as competitive as possible for top PhD programmes in materials science.

In regards to clubs and activities, I'm involved in three places. I do research in the bioengineering department, where I focus on fabricating biosensors to read genetic errors. I am a candidate for three project teams' leadership positions in AIChE (American Institute of Chemical Engineers) and NETS (Nano Engineering and Technology Society), for the solar energy, piezo energy, and wave energy teams. And lastly, I am a central member of the UCSD Wushu Team, which I do entirely for physical and mental health (it's done wonders for both anxiety and depression).

I will take my first upper division classes this September, where I've that they are both harder and easier than lower divs to get good grades (B+ and up). I've gotten to know most of my professors via AIChE and NETS. I tend to stay in touch with every professor I talk to, either personally, or via email/LinkedIn.

Have I put myself in a bad situation? Am I overreacting? Where do I go from here to optimise myself for a strong PhD programme? I need all the advice I can get.
Although this question may be out-of-bounds for this site... Well, "obviously", you'd want to do better in the future. True, screw-ups are not a plus, but, well, it's already on your record, so what can you do other than try to do better in the future. To give up on your ambitions would be nonsensical: if you don't try at all, sure, you won't fail, but you also cannot possibly succeed.

From my own perspective, it is very clear that many talented, motivated people in late teens and early twenties do screw up. (Not to mention older people too!) Obviously not a good thing, but, yes, quasi-ironically, people who've been through mistakes are sometimes (!) wiser and more effective than people who've magically avoided all mistakes.