PIO reader class cleanup (#408)

Tag name (required for release branches):
Originator(s): nusbaume

Description (include the issue title, and the keyword ['closes',
'fixes', 'resolves'] followed by the issue number):

This PR does several things:

1. Modifies the "get_var" methods to expect allocatables and not
pointers, which is needed for ESCOMP/atmospheric_physics#265

2. Adds optional "start" and "count" variables to the "get_var" method,
in preparation for variable subsetting. However, for now these variables
are both no-ops.

3. Cleanup the code by creating a new "get_dim_sizes" subroutine, which
noticeably reduces the amount of duplicated code.

Addresses #406 

Describe any changes made to build system: N/A

Describe any changes made to the namelist: N/A

List any changes to the defaults for the input datasets (e.g. boundary
datasets): N/A

List all files eliminated and why:  N/A

List all files added and what they do: N/A

List all existing files that have been modified, and describe the
changes:
(Helpful git command: `git diff --name-status
development...<your_branch_name>`)

M  .gitmodules
M  src/physics/ncar_ccpp
- Update atmospheric_physics external to use new abstract NetCDF file
reader interface.

M src/physics/utils/pio_reader.F90
- Implement the three different changes listed above in the
"Description"

 M test/unit/fortran/src/pio_reader/test_pio_reader.pf
- Update the pio_reader unit tests so that they work with the new file
reader interfaces.

If there are new failures (compared to the
`test/existing-test-failures.txt` file),
have them OK'd by the gatekeeper, note them here, and add them to the
file.
If there are baseline differences, include the test and the reason for
the
diff. What is the nature of the change? Roundoff?

derecho/intel/aux_sima:  ALL PASS

derecho/gnu/aux_sima:  ALL PASS

If this changes climate describe any run(s) done to evaluate the new
climate in enough detail that it(they) could be reproduced:

CAM-SIMA date used for the baseline comparison tests if different than
latest:

Author: nusbaume

.gitmodules

@@ -20,7 +20,7 @@
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
 	url           = https://github.com/ESCOMP/atmospheric_physics
-	fxtag         = 754a0c28631655289765e99f747c1d96a6d882f4
+	fxtag         = 178c1833d72a4027c6162a6c11b52bbbdcb272b6
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "rrtmgp-data"]
@@ -119,4 +119,3 @@
 	fxtag         = v0.1.4
 	fxrequired    = ToplevelRequired
 	fxDONOTUSEurl = https://github.com/NCAR/CUPiD.git
-