Add NetCDF Output to DGSWEM - #55

Draft

ashtonvcole wants to merge 147 commits into

foci:masterfrom

ashtonvcole:netcdf

Commits on Apr 7, 2026

Ignore DS_Store
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d142ea0
Initialization of NetCDF output module with skeleton functions

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2bf1432
Split NetCDF into 3 modules: result writing, file creation, and individual file updates

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939fa5c
Working on creating fort.63 file

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2fa7ca5
Working on creating fort.63 file, continued

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764d6c5
Drafted bare-bones wrapper for NetCDF manipulation
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ce0548f
Initial skeleton for fort NetCDFs
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38edcd1
Started fort.63.nc init
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59a2031
Filled in some variable names
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44234fd
NetCDF file closed on initialization
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ad64b0f
Removed close file from init
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9749667
Preliminary fort.63.nc file initialization drafted. Still needs to be tested.
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f005f4d
Defined temporary test program for NetCDF development
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94b7ff9
Set up Meson. Todo: build nctest.
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352884a
Integrated nctest into meson.build, since meson is strict about file names.
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e46533e

Commits on Apr 8, 2026

Fixed typos in meson build and netcdf_file.f90
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489f8de
Removed empty arguments, renamed nctest executable
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507ee3f
Fixed typos in nctest
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d61cd85
Fixed errors in initial netcdf modules
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9e824de
Ignore .wraplock file
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17c23f8

Commits on Apr 16, 2026

Commits on Apr 22, 2026

Moved netcdf tools to separate folder, for now
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8d102d3
Split fort.63.nc into submodule, tested
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cd17cd7
Integrated NetCDF file creation into serial DGSWEM
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08f674f
Initialize fort.63.nc with correct dimensions. Odd behavior where NF90 library reverses dimensions.
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6be2cca

Commits on May 4, 2026

Breaking change: renamed files and modules, drafting inheritance system to reflect ADCIRC conventions
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9130d52
Filled out interface for open/close functions
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ebd7135
Drafted open/close routines
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0e315cd
Introducing dimension and variable information into inherited derived types
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5e34252
New module setup preliminaily works. Todo: id loading/flushing with file open/close
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a0b3255

Commits on May 11, 2026

Set/flush variable and dimension IDs. Removed whitespace for submodule colon syntax.
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b29b662
Workaround for blank -I flag in netcdf dependencies on TACC.
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a2f5fd1
Remove redundant flags
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5f36ced
Updated test script to include metadata IDs, demonstrates that the code works as expected
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081da21
Wrote preliminary mesh writing function with x, y, depth
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d1081d1
Saved intermediate work
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121eb6e

Commits on May 12, 2026

Created initial mesh writing function. Not yet fully compatible with QGIS.
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851c479

Commits on May 13, 2026

Added most metadata. Working on compatibility with QGIS.
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0c6ef33
Documented arrays for multidimensional variable put
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68a7115
Added preliminary step writing function for fort.63.nc
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4b757b4
Tested fort.63 step writing. Seems to work.
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9f124f7

Commits on May 14, 2026

Reorganized NetCDF components in src
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103430e
Output tweak
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6d34143
DGSWEM now writes fort.63 to NetCDF and renders in QGIS. Metadata is not complete.
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7066b22

Commits on May 15, 2026

Finalized core global attrubutes. Deferred ancillary ones.
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1947d46
Wrote fort.64 module
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a2d5e1a
Incorporated fort.64 into DGSWEM, but does not render in QGIS
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48062d9

Commits on May 19, 2026

Enclosing velocity attributes in if blocks for safety
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151ff93
Replaced hyphens with underscores
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1274e41
Adjusted convention metadata
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3fd8031
Fixed ICS codes
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f505697

Commits on May 20, 2026

Commits on May 22, 2026

Renamed formal arguments to correspond with ADCIRC/DGSWEM variables
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f90e63b
Created alias for mesh writing
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5c924af
Made file path optional, set ADCIRC defaults for each type
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22eeb97
Updated fort.64 long names to best fit MDAL heuristic
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21e9133

Commits on May 27, 2026

Added maxele file
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242ddc1
Dropping draft for maxvel.64.nc. DGSWEM does not support it.
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979495a
Added support for parallel I/O in ncdg, but not yet implemeneted
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0bc9a2b

Commits on Jun 8, 2026

Removed MPI args from interface, This can be handled internally.
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7fcf53b
Add preprocessor guard around NetCDF imports
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8f0f41c
Renamed files to enable preprocessor directives
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95fc80a
Added parallel access file init/open
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74fb815

Commits on Jun 9, 2026

Added parallel testing program
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fed1e77

Commits on Jun 17, 2026

Removed debugging print
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0fac33c
Enclosing source code references in conditionals
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1017a08
Initial parallel test program set up
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4336522

Commits on Jun 18, 2026

Fixed nbvv indexing
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2c9ff22
Added additional ifdef guards for NetCDF I/O
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95ec89f
Whitespace tweaks
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e0ae9a0
Introduced NetCDF file creation in prep utility. This is more efficient
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ae3aa96

Commits on Jun 19, 2026

Drafting for PIO
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398de41
Removed mpi netcdf-fortran blocks, along with minor bug fixes
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c5204c8

Commits on Jun 22, 2026

Removed parallel bocks from ncdg submodules
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adb7d6c
Renamed ncdg files to f90 to remove preprocessing
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3b3cf5d
Removed spurious CMPI block from maxele
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876e8f6
Renamed ncdg files in meson build
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ffa6d35
Reworked open to allow struct initialization from opening an existing
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39b6a6d
Renamed init routines to create
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2ceb78c

Commits on Jun 23, 2026

Finished and tested pioutil module
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f92e38d
Minor adjustments
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03468b9

Commits on Jun 24, 2026

Initial PIODG module with open/close functionality
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53646bd
Incorporated PIODG open/close into DGSWEM. Writing not implemented.
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bc0235a
Fixes for piotest
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becc785
Added piodg to piotest
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30061c4

Commits on Jun 25, 2026

Preliminary ncdg_63_write_step, zeta left blank
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5727422

Commits on Jul 1, 2026

Now writes 1 step
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2c9b65e
Writes multiple time steps
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e50e2a0
Added fort.64 parallel write
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d4046c5
Cleaned up comments
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b2bfd30
Added parallel writing for maxele.63.nc
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be3ddc8

Commits on Jul 2, 2026

Commits on Jul 3, 2026

Fixed syncing in test script
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0a6961d
Adjusted NCDG to noclobber by default
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d904eed
Adjusted PIODG to noclobber by default
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8301b9e

Commits on Jul 29, 2026

Read index maps from fort.80
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54c7768
Parallel printing fix
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f80f1cd
Parallel I/O now works
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f1e8d96
Made transposing optional to handle nneg in adcprep
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16fce20

Commits on Aug 3, 2026

Fixed data offset error, caused by padded nodal arrays, eg
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6bbbfa1

Commits on Aug 4, 2026

Moved parallelio init to beginning of program, after read_input
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06343fa
Make nsubdom available for CMPI in general
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cf7b488
Fix to hard coded nsubdom
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f9bb007
Add message_fini to parallelio for I/O processes
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4054ae6
Stop reading fort.80 early if I/O process
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629d72b
Remove unused groups and subcommunicators
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cf7a956
Introduce comm_comp, comm_io to sizes. Assignment in
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1776bfa
Replaced world communicator with computation-specific. Program runs for
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e835bf3
Deallocate PIO global arrays
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a192b09
Patch for excessive writer triggered errors
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9b4746d

Commits on Aug 6, 2026

Reproduce conda env v2
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c96bcf3
Reproduce conda env
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d036660
Begin flag adjustments
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b1301fe
Allow NetCDF flags for output flags
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c54e66e
Add flags for nodal elevation and velocity, untested
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a491398

Commits on Aug 7, 2026

Introduced flags and write interval
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f027901

Commits on Aug 12, 2026

Only create NetCDF files in prep if NOUT flag is 3
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1c59f93
ADCPREP now formally accepts NetCDF flags
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e7aad20
Bug fixes
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c001d47
Merge remote-tracking branch 'upstream/master'
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91fac50
Merge branch 'netcdf'
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4699180
Make NetCDF option boolean
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d806787

Commits on Aug 13, 2026

Commits on Aug 18, 2026

Added inheritance hierarchy in documentation
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c858b21
Rearrange functions and derived types in ncdg
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02e4714
Created intermediate parent types for parallel
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dfbcc23
Deallocate array appropriately
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a630e3f

Commits on Aug 20, 2026

Added support for weather files
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837a03f

Commits on Aug 21, 2026

Changed identifiers from unit numbers to descriptive names
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ab7ec4c
Renamed files to reflect new type names
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275d846
Added bathymetry, tracer incomplete
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22454b7
Added tracer and bathy modules. Tracer not yet active
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c41ea2d

Commits on Aug 25, 2026

Merge with upstream
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4aa6151

Commits on Aug 27, 2026

Moved NetCDF test scripts to test folder
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fd31c01

Commits on Sep 16, 2026

Removed NetCDF dependency from main build
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a6353da
Moved NetCDF variable into preprocessor block
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bee627f