Remove default value constituent overwrite

[peverwhee]

Tag name (required for release branches): sima0_04_001
Originator(s): peverwhee

Description (include the issue title, and the keyword ['closes', 'fixes', 'resolves'] followed by the issue number): Removes the behavior in read_data that overwrites constituent values that aren't found on the snapshot file with the default value. @boulderdaze ran into this problem - it was overwriting the constituents she had initialized in the init phase.

Also removes some diagnostic variables from the Hack shallow snapshot test output - closes #375

Describe any changes made to build system: none

Describe any changes made to the namelist: none

List any changes to the defaults for the input datasets (e.g. boundary datasets): none

List all files eliminated and why: none

List all files added and what they do: none

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

M cime_config/testdefs/testmods_dirs/cam/outfrq_hack_shallow_derecho/user_nl_cam

• remove diagnostic variables that do not have history_out_field calls in the source code (scheme not part of test SDF)

M src/data/write_init_files.py

• remove the "if (has_default)" block (instead, do nothing because the constituent object routines will have already initialized the constituent to the default.

M test/unit/python/sample_files/write_init_files/physics_inputs_*.F90

• fix tests to match new output

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:
SMS_Ln2.ne3pg3_ne3pg3_mg37.FPHYStest.derecho_gnu.cam-outfrq_hack_shallow_derecho (Overall: DIFF)

• this PR established new baseline due to change in test name (+ removed history fields)
• confirmed that the non-reproducible output issue has been resolved.

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

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

[jimmielin]

Thanks @peverwhee!

[nusbaume]

Looks good! Just had one regression test update request.

[nusbaume]

Thanks @peverwhee!