Now, I am wanting to check if it is being read correctly, but I am getting errors in my program. Mostly that atom_types, sigma, epsilon and mass are undeclared identifier. I'm going to have several of these coordinate functions eventually so these variables will be redefined depending on which function is being run. Any help with this is appreciated.
What the error message said. Where are the variables you use on line 45 declared? the compiler has no idea what they are.
Another issue is that the changes you do to them in methane_coords() will have no effect on their values in main(). To fix this, change the parameter types to int& (and double&).