Reference volume from MRC or PDB file

To address a numba-related incompatibility on Crusher, the code was adjusted so that either a PDB or MRC file can be provided as the reference. If the latter, the density array is simply loaded rather than computed from a coordinates file using skopi, which depends on numba. The relevant entry in the toml file has been changed from pdb_path to ref_path. This was tested on Cori GPU as follows:

srun -n 1 -G 1 python -m spinifel --default-settings=cgpu_mpi.toml --mode=mpi

with the chk_convergence flag set to true.

@yoon82, is there a Crusher-specific toml file? I wasn't sure which toml files should use an MRC rather than a PDB file; for now, I've only updated the cgpu_mpi.toml to use the former.