Some regrid notes

Author: zmoon

04-regrid.md

@@ -3,22 +3,126 @@ title: Regrid
 subtitle: Tools for regridding MPAS-A output to regular lat-lon grids
 ---
 
-# pyremap
+# Options
+
+## pyremap
 
 [pyremap](https://mpas-dev.github.io/pyremap/main/remapper/index.html)
 simplifies the process of regridding MPAS data to other grids.
-It helps you compute weights (using ESMF or MOAB) and apply them,
+It helps you compute weights (using `ESMF_RegridWeightGen` or the MOAB CLI[^mbcli])
+and apply them,
 and works with global and limited-area meshes.
 
-# Global
+## NCO
+
+[NCO](https://nco.sourceforge.net/) [ncremap](https://nco.sourceforge.net/nco.html#ncremap-netCDF-Remapper)
+provides many facilities for regridding.
+
+- Use `ncremap` to generate weights
+  with `ESMF_RegridWeightGen` ("ERWG"),
+  the TempestRemap CLI[^trcli],
+  the MOAB CLI[^mbcli], or internal routines[^nco-internal]
+  - ERWG and MOAB can use multiple processors with `--mpi_nbr=<n>`
+- To apply weights:
+  - `ncks -m map.nc --rgr`
+  - `ncremap -P mpasa -m map.nc in.nc out.nc`
+    - `-P mpasa` (not always necessary) was added in NCO v5.2.6 (2024-06-20)
+  - `ncremap --pdq=Time,nVertLevels,nIsoLevelsT,nIsoLevelsZ,nCells -m map.nc in.nc out.nc`
+
+[^trcli]:
+    `GenerateOverlapMesh` (overlay the source and destination meshes and compute intersections),
+    `GenerateOfflineMap` (generate weights)
+
+[^mbcli]:
+    `mbconvert` (to the MOAB native format), `mbpart` (partition into pieces for parallel processing),
+    `mbtempest` (generate weights using the TempestRemap library)
+
+[^nco-internal]:
+    `-a nco_con` (first-order conservative),
+    `-a nco_idw` (inverse distance weighting, can extrapolate)
+
+### Examples
+
+```bash
+# Automatically generate a 1-degree target grid
+# Generate weights with TempestRemap conservative monotone algorithm
+ncremap -m map.nc -s mpas_source_grid.nc -g target_grid.nc -G latlon=180,360 -a traave
+
+# Apply weights
+ncremap -P mpasa -m map.nc in.nc out.nc
+```
+
+### Notes
+
+> In practice, it may make sense to use the default "conservative" algorithm when performing conservative regridding,
+> and the "renormalized" algorithm when performing other regridding such as bilinear interpolation or nearest-neighbor.
+> Another consideration is whether the fields being regridded are fluxes or state variables.
+> For example, temperature (unlike heat) and concentrations (amount per unit volume)
+> are not physically conserved quantities under areal-regridding
+> so it often makes sense to interpolate them in a non-conservative fashion, to preserve their fine-scale structure.
+> Few researchers can digest the unphysical values of temperature
+> that the "conservative" option will produce in regions rife with missing values.
+> A counter-example is fluxes, which should be physically conserved under areal-regridding.
+> One should consider both the type of field and its conservation properties when choosing a regridding strategy.
+>
+> -- NCO doc, Section 3.26 Regridding
+
+Renormalization is specified using `--rnr=<threshold>` where the threshold ranges from 0 to 1
+and indicates the fraction of given destination cell covered by valid (data not missing) source cells.
+Cell-times where the threshold is met preserve the mean, while others are set to missing.
+[](#pyremap) supports renormalization as well (example uses 0.01).
+
+It may be possible to use NCO RRG mode to generate weights for limited-area meshes,
+but it is more involved than using pyremap.
+However, you can use NCO to _apply_ pyremap-generated weights.
+
+It is also possible to use [TempestRemap](https://github.com/ClimateGlobalChange/tempestremap)
+or [MOAB](https://sigma.mcs.anl.gov/category/moab/) directly instead of through NCO.
+
+## CDO
+
+(convert_mpas)=
+
+## convert_mpas
+
+[convert_mpas](https://github.com/mgduda/convert_mpas)[^cm] provides a simple way
+to convert to a 0.5°x0.5° regular lat-lon grid (or other rectangular lat-lon grids).
+
+[^cm]:
+    Provided by the MPAS-A lead developer,
+    and used in [the official virtual tutorial](https://www2.mmm.ucar.edu/projects/mpas/tutorial/Virtual2025/).
+
+### Examples
+
+```bash
+# Default 0.5-degree global, one file
+convert_mpas x1.10242.init.nc diag.2017-09-20_12.00.00.nc
+```
+
+```bash
+# 2-degree global, all diag files
+convert_mpas x1.10242.init.nc diag.*.nc nlat=90 nlon=180
+```
+
+```bash
+# CONUS rectangle, all diag files
+echo "startlat=25
+endlat=50
+nlat=25
+startlon=-125
+endlon=-66
+nlon=59
+" > target_domain
+
+convert_mpas x1.10242.init.nc diag.*.nc
+```
 
-For global files, commonly used regridding tools should work
-(i.e., they have implemented support for MPAS meshes):
+# Recommendations
 
-- NCO `ncremap`
-- CDO
-- TempestRemap
+[](#convert_mpas) for a quick remap, e.g. for checking your data with tools like ncview
 
-# Limited-area
+Otherwise:
 
-- Kelly has a tool that allows CDO to work with limited-area meshes.
+- [](#pyremap) for generating weights
+  - Generate both conservative and bilinear weights to be used for different variables
+- [](#pyremap) for applying weights