Feat/cmip7 awiesm3 veg hr

CLAUDE.md

@@ -31,6 +31,13 @@ Key features:
 
 ## Development Commands
 
+### Environment Setup
+```bash
+# Load conda environment
+source ~/loadconda.sh
+conda activate pycmor_py312
+```
+
 ### Installation
 
 #### Using pip (traditional)

awi-esm3-veg-hr-variables/README.md

@@ -0,0 +1,186 @@
+# AWI-ESM3-VEG-HR CMIP7 Variable Configuration
+
+CMIP7 CMORization configuration for AWI-ESM3-VEG-HR.
+
+## Model Configuration
+
+Reference runtime: `AWI-ESM3-VEG-HR-CMIP7-Spinup_cont2` (awiesm3-v3.4.1)
+
+### OpenIFS (IFS CY48R1)
+- **Resolution**: TCo319 spectral, L91 vertical levels
+- **Output grid**: 0.25deg regular (1440x720), interpolated via XIOS/FullPos
+- **Time step**: 900 s
+- **Radiation**: ecRad, called every 3 hours
+- **Land surface**: HTESSEL (4-layer soil, snow scheme, Farquhar photosynthesis)
+- **Aerosol**: MACv2-SP simple plumes (no CAMS, no M7)
+- **CO2**: concentration-driven (no prognostic CO2 tracer)
+- **Wave model**: WAM (2-way coupled)
+- **I/O**: XIOS 2.5-ece
+
+### FESOM 2.6
+- **Mesh**: DARS unstructured (~3.1M surface nodes, ~10 km nominal)
+- **Vertical**: 56 z-levels (57 interfaces), linear free surface
+- **Sea ice**: Built-in single-category, mEVP rheology, melt ponds enabled
+- **Diagnostics**: ldiag_cmor=.true. (CMIP scalar diagnostics)
+
+### LPJ-GUESS 4.1.2
+Config from `global.ins` via `run_coupled_4_1_2.ins`:
+- **Fire model**: BLAZE (uses SIMFIRE internally for burned area prediction)
+- **BVOC**: disabled (ifbvoc=0)
+- **Nitrogen cycle**: enabled (ifnlim=1, ifcentury=1)
+- **Land cover**: natural vegetation only (run_landcover=0)
+- **Methane**: disabled (ifmethane=0)
+- **Vegetation mode**: cohort, npatch=15
+- **PFTs**: 12 global + 8 arctic shrub/tundra (~20 active natural PFTs)
+- **CO2**: concentration-driven via OASIS coupling from atmosphere
+- **CMIP output**: extensive monthly + yearly .out files (166 output files defined in `lpjg_output.ins`)
+- **Output format**: plain-text .out files (no XIOS)
+- **Coupling to IFS**: daily via OASIS-MCT (sends LAI, veg type/fraction; receives T, precip, radiation, soil state)
+
+### Coupling (OASIS3-MCT 5.0)
+- **Atm-Ocean**: 2-hourly (7200 s)
+- **Atm-Vegetation**: daily (86400 s)
+- **Runoff mapping**: rnfmap v1.1
+
+### Ice Sheet
+- **No interactive ice sheet model** (no PISM, no Yelmo, no BISICLES)
+- IFS prescribes glaciated areas as grid cells with 10 m water mass equivalent
+- Greenland/Antarctic ice sheets are static boundary conditions
+
+### What this model does NOT have
+- No interactive ice sheet model
+- No prognostic aerosol (no CAMS, no M7 -- only MACv2-SP prescribed plumes)
+- No atmospheric chemistry
+- No interactive ozone (O3 prescribed from climatology, not prognostic)
+- No CO2 tracer (concentration-driven)
+- No ice thickness distribution (single-category sea ice)
+- No icebergs
+- No methane cycle
+- No BVOC emissions
+
+## XIOS XML Configuration (top level)
+
+These files configure the OpenIFS/XIOS output pipeline. XIOS expressions handle unit conversions, deaccumulation, and sign flips at output time so pycmor only needs to add metadata.
+
+| File | Purpose |
+|------|---------|
+| `iodef.xml` | XIOS top-level entry point, references context files |
+| `context_ifs.xml.j2` | IFS XIOS context, includes all `*_def.xml` and `file_def` |
+| `field_def_cmip7.xml` | All CMIP7 field definitions: raw IFS fields + derived expressions |
+| `file_def_oifs_cmip7_spinup.xml.j2` | Output file definitions: fields, frequencies, operations (average/instant/min/max) |
+| `axis_def.xml` | Vertical axes: plev19, plev3 (850/500/250 hPa), model levels |
+| `grid_def.xml` | Grids: regular_sfc, regular_pl, regular_pl3, regular_ml |
+| `domain_def.xml.j2` | Domain definitions for reduced Gaussian to regular grid interpolation |
+
+## FESOM Configuration (top level)
+
+| File | Purpose |
+|------|---------|
+| `namelist.io` | FESOM2 I/O namelist: ocean + sea-ice output variables and frequencies |
+
+## Per-realm Subdirectories
+
+Each subdirectory contains:
+- **CSV files** -- CMIP7 Data Request variables for that realm (from CMIP7_DReq_Software)
+- **YAML file** -- pycmor rules mapping model output to CMOR-compliant files
+- **TODO file** -- implementation status, blockers, research notes, and OIFS source investigation
+
+### Core (CMIP7 mandatory variables)
+
+| Directory | Realm | Model | Rules | Variables | Key notes |
+|-----------|-------|-------|-------|-----------|-----------|
+| `core_atm/` | Atmosphere | OpenIFS | 76 | 45 unique | Monthly/daily/sub-daily (3hr, 6hr, 1hr); surface, plev19, plev3, model levels |
+| `core_land/` | Land | OpenIFS/HTESSEL | 11 | 11 | XIOS-derived + pipeline-computed; 6 variables deferred to lrcs_land |
+| `core_ocean/` | Ocean | FESOM 2.6 | 25 | 25 | Monthly 2D/3D, daily, fx; includes mass transport and zostoga pipelines |
+| `core_seaice/` | Sea Ice | FESOM 2.6 | 9 | 8 unique | Monthly + daily siconc; velocity rotation via vec_autorotate |
+
+### LRCS (additional priority variables)
+
+| Directory | Realm | Model | Rules | Key notes |
+|-----------|-------|-------|-------|-----------|
+| `lrcs_ocean/` | Ocean | FESOM 2.6 | 45 | Decadal, yearly tendencies (6 with FESOM source mods), scalar diagnostics; ~12 blocked by basin masks |
+| `lrcs_seaice/` | Sea Ice | FESOM 2.6 | 40+ | Heat/salt fluxes, tendencies, melt ponds, stress, hemisphere scalars; some blocked by single-category ice |
+| `lrcs_land/` | Land | OIFS/LPJ-GUESS | 6 | 6 deferred variables: 3 from LPJ-GUESS (evspsblsoi, evspsblveg, mrfso), 3 from IFS static fields (sftgif, mrsofc, rootd) |
+| `veg_atm/` | Atmos/Aerosol | OpenIFS + LPJ-GUESS | 27 | 38 variables: 27 implemented (3hr rad/flux, plev6, daily snow, lwp, 7 fire emissions), 11 blocked |
+| `veg_land/` | Land | OpenIFS/HTESSEL + LPJ-GUESS | 58 | 88 variables: 22 IFS (3hr/day/mon hydrology, snow), 36 LPJ-GUESS (N-cycle, fractions, Lut), 30 blocked |
+| `veg_seaice/` | Sea Ice | FESOM 2.6 | 1 | 4 variables: 1 implemented (daily sisnhc from m_snow/a_ice), 3 blocked (2 ITD, 1 missing physics) |
+| `extra_land/` | Land | OpenIFS/HTESSEL + LPJ-GUESS | 13 | 19 variables: 2 fx, 7 LPJ-GUESS (PFT fracs, LAI), 3 IFS hydrology, 1 hourly tas; 6 blocked (irrigation, river, root zone) |
+| `extra_atm/` | Atmos/Aerosol | OpenIFS | 21 | 43 variables: 13 1hr (fluxes, rad, 30S-90S subsets), 2 3hr, 5 daily, 1 monthly gust; 22 blocked (aerosol/chem, crops, heat index, lightning) |
+
+### CAP7 (high-priority additional variables)
+
+| Directory | Realm | Model | Rules | Key notes |
+|-----------|-------|-------|-------|-----------|
+| `cap7_atm/` | Atmosphere | OpenIFS | 58 | 233 variables: 79 already in core/veg/extra/lrcs, 58 new (daily radiation/fluxes/precip, 6hr ml+plev7h, 1hr instant, monthly ml); ~96 blocked (17 COSP, 21 tendencies, 9 aerosol, 5 CO2, 4 reff, ~40 IFS source) |
+| `cap7_ocean/` | Ocean | FESOM 2.6 | 3 | 43 variables: 26 already in core/lrcs, 3 new (daily tossq, monthly volcello, friver); 14 blocked (no icebergs/SF6/geothermal/bigthetao, basin masks, namelist changes for hfx/hfy/3hr stress) |
+| `cap7_seaice/` | Sea Ice | FESOM 2.6 | 9 | 21 variables: 9 already in core/lrcs/veg, 9 new (daily sithick/snd/siu/siv, monthly sieqthick/snw/evspsbl/prra/prsn); 3 blocked (sisali constant, sitempsnic internal, snc single-category) |
+
+## Custom Pipeline Steps
+
+Complex variables that cannot be expressed as XIOS expressions are computed in `../examples/custom_steps.py`.
+
+### Atmosphere pipelines
+- **sfcWind**: sqrt(u10^2 + v10^2) from 10u + 10v
+- **hurs**: Magnus formula from 2t + 2d
+- **huss**: Tetens formula from 2d + sp
+- **clwvi**: tclw + tciw (liquid + ice water path)
+
+### Land pipelines
+- **snc**: snow cover saturation curve from sd (threshold 15mm water equiv)
+- **areacella**: spherical grid cell area from lat/lon coordinates
+- **slthick**: constant HTESSEL soil layer thicknesses [0.07, 0.21, 0.72, 1.89] m
+
+### LPJ-GUESS loaders and fire emission pipelines
+- **load_lpjguess_monthly**: custom loader for LPJ-GUESS plain-text .out files (Lon/Lat/Year/Jan..Dec)
+- **load_lpjguess_yearly**: loader for yearly .out files (Lon/Lat/Year/Total)
+- **load_lpjguess_yearly_lut**: loader for yearly Lut .out files (Lon/Lat/Year/psl/crp/pst/urb)
+- **load_lpjguess_monthly_lut**: loader for monthly Lut .out files (Lon/Lat/Year/Mth/psl/crp/pst/urb)
+- **compute_fire_emission**: converts fFireAll (kgC/m2/s) to species emissions using Andreae (2019) savanna/grassland emission factors (BC, CH4, CO, DMS, OA, SO2, NMVOC)
+
+### Land hydrology/snow custom steps
+- **compute_temporal_diff**: temporal differencing for dgw, dsn, dsw, dcw, dslw (daily storage changes)
+- **compute_mrtws**: terrestrial water storage summation (soil + snow + skin reservoir)
+- **compute_snd**: physical snow depth from SWE and snow density (sd*1000/rsn)
+- **compute_mrsow**: total soil wetness ratio (weighted mean swvl / porosity)
+- **sum_lpjguess_monthly_files**: load and sum multiple LPJ-GUESS .out files (for c3PftFrac)
+- **select_southern_hemisphere**: lat subset for 30S-90S regional variables (orog, tas)
+
+### CAP7 atmosphere custom steps
+- **compute_rtmt**: net downward radiative flux at model top (rsdt - rsut + rlds - rlus)
+- **extract_single_plevel**: extract single pressure level from multi-level dataset (ta@700hPa, wap@500hPa)
+
+### CAP7 sea ice custom steps
+- **compute_snd_from_msnow**: snow depth on ice from m_snow/a_ice (unused after h_snow switched to daily)
+
+### Ocean pipelines
+- **zostoga**: global thermosteric sea level via gsw/TEOS-10
+- **mass transport** (umo/vmo/wmo): Boussinesq approximation (velocity x rho_0 x cell area)
+- **bottom/surface extract**: tob, sob from 3D fields; uos, vos from daily 3D
+- **vertical integration**: scint, phcint, opottempmint, somint
+- **fx pipelines**: areacello, deptho, sftof, thkcello, masscello, volcello from mesh
+
+### Sea ice pipelines
+- **siconc/simpconc**: fraction to percent conversion
+- **sispeed**: sqrt(uice^2 + vice^2)
+- **sihc/sisnhc**: heat content from ice/snow thickness + thermodynamic constants
+- **sisnhc (daily)**: derived from daily m_snow/a_ice (h_snow not available daily)
+- **sistressave/sistressmax**: stress invariants from sigma tensor components
+- **sitempbot**: freezing temperature from SSS
+- **sifb**: freeboard from ice/snow thickness and density ratios
+- **ice mass transport**: uice/vice x m_ice
+- **hemisphere integrals**: sisnmass N/S from m_snow x cell_area
+
+### FESOM2 source code modifications
+Six new diagnostic outputs added to `gen_modules_cmor_diag.F90`:
+- opottemptend, opottempdiff, opottemprmadvect (temperature tendencies)
+- osalttend, osaltdiff, osaltrmadvect (salinity tendencies)
+- rsdoabsorb (shortwave absorption by ocean layer)
+
+## Summary of Implementation Status
+
+| Realm | Core done | Core total | LRCS done | LRCS total | Blocked |
+|-------|-----------|------------|-----------|------------|---------|
+| Atmosphere | 76 | 76 | -- | -- | 3 items need runtime verification |
+| Land | 11 | 17 | 0 | 6 | 3 need OIFS source changes, 3 derivable offline |
+| Ocean | 25 | 27 | 45 | ~80 | ~12 need basin masks, ~8 need online diag |
+| Sea Ice | 9 | 9 | 40+ | ~70 | ITD/age/ridge tracers not enabled |

awi-esm3-veg-hr-variables/axis_def.xml

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+<axis_definition>
+  <!-- Definition of model levels axes -->
+  <axis_group id="ml_axes" unit="-" positive="up" >
+    <axis id="model_levels" long_name="vertical model levels" />
+    <axis id="model_levels_zoom" long_name="vertical model levels zoom" axis_ref="model_levels" >
+      <zoom_axis index="(0,10)[0 1 2 3 4 23 24 25 26 78 79]" />
+    </axis>
+  </axis_group>
+
+  <!-- Definition of pressure levels axes -->
+  <axis_group id="pl_axes" unit="Pa" positive="up" >
+    <axis id="pressure_levels" long_name="vertical pressure levels" n_glo="19" value="(0,18)[100000.0 92500.0 85000.0 70000.0 60000.0 50000.0 40000.0 30000.0 25000.0 20000.0 15000.0 10000.0 7000.0 5000.0 3000.0 2000.0 1000.0 500.0 100.0]" />    <!--<axis id="pressure_levels" long_name="vertical pressure levels" n_glo="39" value="(0,38)[100000.0 92500.0 85000.0 70000.0 60000.0 50000.0 40000.0 30000.0 25000.0 20000.0 17000.0 15000.0 13000.0 11500.0 10000.0 9000.0 8000.0 7000.0 5000.0 3000.0 2000.0 1500.0 1000.0 700.0 500.0 300.0 200.0 150.0 100.0 70.0 50.0 40.0 30.0 20.0 15.0 10.0 7.0 5.0 3.0]" />-->
+    <axis id="pressure_levels_zoom" long_name="vertical pressure levels zoom" axis_ref="pressure_levels" >
+      <zoom_axis index="(0,2)[10 11 12]" />
+    </axis>
+    <axis id="pressure_levels_3" long_name="vertical pressure levels plev3" n_glo="3" value="(0,2)[85000.0 50000.0 25000.0]" />
+    <axis id="pressure_levels_6" long_name="vertical pressure levels plev6 lower troposphere" n_glo="6" value="(0,5)[95000.0 90000.0 85000.0 80000.0 75000.0 70000.0]" />
+    <axis id="pressure_levels_7h" long_name="vertical pressure levels plev7h" n_glo="7" value="(0,6)[100000.0 92500.0 85000.0 70000.0 50000.0 25000.0 10000.0]" />
+  </axis_group>
+
+  <!-- Definition of theta levels axes -->
+  <axis_group id="th_axes" unit="K" positive="up" >
+    <axis id="theta_levels" long_name="vertical theta (potential temperature) levels" n_glo="3" value="(0,2)[300 320 360]" />
+    <axis id="theta_levels_zoom" long_name="vertical theta (potential temperature) levels zoom" axis_ref="theta_levels" >
+      <zoom_axis index="(0,1)[0 2]" />
+    </axis>
+  </axis_group>
+
+  <!-- Definition of PV levels axes -->
+  <axis_group id="pv_axes" unit="PVU" positive="up" >
+    <axis id="pv_levels" long_name="vertical potential vorticity (PV) levels" n_glo="2" value="(0,1)[2.e-6 3.e-6]" />
+    <axis id="pv_levels_zoom" long_name="vertical potential vorticity (PV) levels zoom" axis_ref="pv_levels" >
+      <!-- <zoom_axis begin="1" n="1" /> -->
+      <zoom_axis index="(0,0)[1]" />
+    </axis>
+  </axis_group>
+</axis_definition>