Refactor functions that take struct volume *state

This commit refactored some funtions that took the entire simulation state
(struct volume *state) by alternatively only passing in what was needed.
However, this can be difficult since some functions depend on so many members
of struct volume *state/world.
Merge branch 'master' of https://github.com/mcellteam/mcell
More refactoring of functions taking state/world.

- Refactoring functions so that they don't require the entire
  state/world passed to them
- Renamed some variables for consistency
- Put related variables in a single struct