Trajectory sampler to ingest multiple IODA files via one route handle

[metdyn]

Description

The trajectory sampler code originally written by @bena-nasa to regrid to flight trajectory is extended to ingest and regrid to multiple IODA file locations. The implementation mainly have followed #2144. The listed items therein, except for the item-8: related to 3D height interpolation, have been finished in this PR.

The important features include:

• Epoch time is tunable by user to determine output freqeuency to netCDF files
• Read in multiple IODA files from one collection and regrid with the route handle therein
• Loc stream is extended from root to distributed MPI processes based on background grids
• Written out to NC files happens at Epoch time only, while each time step the regridded region is accumulated to an intermediate bundle
• A derived type is allocated to handle each individual IODA type (filename, metadata, lon/lat/field)

The drawback is the original aircraft trajectory functionality is disabled, as the code is tuned for IODA files format.

Note:

• I modified MAPL_HistoryGridComp.F90 to read in a table inside a collection

Input:

VERSION: 1

  COLLECTIONS:
  geovals
  ::

  GRID_LABELS:
  ::

  geovals.template:       '%y4%m2%d2_%h2%n2z.nc4',
  geovals.format:         'CFIO',
  geovals.obs_files:     # table start from next line
      DIR/aircraft.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/airs_aqua.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/amsr2_gcom-w1.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/amsua_aqua.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/amsua_metop-b.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/amsua_n15.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/amsua_n18.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/amsua_n19.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/atms_n20.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/atms_npp.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/avhrr3_metop-b.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/avhrr3_n18.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/avhrr3_n19.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/cris-fsr_n20.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/cris-fsr_npp.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/gmi_gpm.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/gps.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/iasi_metop-b.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/mhs_metop-b.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/mhs_n19.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/mls55_aura.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/omi_aura.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/ompsnm_npp.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/satwind.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/scatwind.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/sfc.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/sfcship.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/sondes.%y4%m2%d2T%h2%n2%S2Z.nc4
      DIR/ssmis_f17.%y4%m2%d2T%h2%n2%S2Z.nc4
::
  geovals.obs_file_interval:  '000000 060000'    #  fixed string format:  yymmdd hhmmss
  geovals.Epoch:          060000                 #  fixed integer format:  hhmmss
  geovals.nc_Index:       Location
  geovals.nc_Time:        MetaData/dateTime
  geovals.nc_Longitude:   MetaData/longitude
  geovals.nc_Latitude:    MetaData/latitude

  geovals.regrid_method:  'BILINEAR' ,
  geovals.fields:         'var2', 'Root'
                         'var3', 'Root'
::

Output: *.geovals.20190801_0300z.nc4 etc.

How Has This Been Tested?

Tested regridding the synthetic data from C720 to 29-IODA files spanning 12 hr time period (from 2019-07-31T21Z). Run finishes in 8 min with 6-cores. Previous experience shows when synthetic data runs can succeed through ExtDataDriver.x, the G5NR run can finish without error.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Trivial change (affects only documentation or cleanup)

Checklist:

• I have tested this change with a run of GEOSgcm (if non-trivial)
• I have added one of the required labels (0 diff, 0 diff trivial, 0 diff structural, non 0-diff)
• I have updated the CHANGELOG.md accordingly following the style of Keep a Changelog

[tclune]

A couple of items that need to be addressed immediately (see inline comments). A couple of others that can be addressed later.

[tclune]

The initial description of this PR would probably make a better entry in the CHANGELOG than what is there now.

[mathomp4]

Aww nuts. I think my cleanup from #2346 touched a couple files that @metdyn did when I did an "update branch":

base/Plain_netCDF_Time.F90
gridcomps/History/MAPL_HistoryTrajectoryMod_smod.F90

So, I resolved the conflicts by assuming what @metdyn had is the correct code. This might mean some cleanup was lost, but that's safer.

@metdyn Can you pull your branch and test to make sure everything is still working.

[metdyn]

@metdyn Can you pull your branch and test to make sure everything is still working.
Thank you, @mathomp4. Your merge works for the code, I have built and checked the output netCDF. They look good!

[mathomp4]

Re-approving and I have tested it and seems to be zero-diff (I'm guessing we don't use any of this in regular GCM work)