init commit for working ancil suite emulator, but without ants_src

ancillaries/JULES/ants_lct_inputs/ancil_lct-app.conf

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+[ants_decomposition]
+x_split=10
+y_split=10

ancillaries/JULES/ants_lct_inputs/ancil_lct_postproc_c4-app.conf

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+[ants_decomposition]
+x_split=10
+y_split=10
+
+[ants_regridding_horizontal]
+scheme=Linear

ancillaries/JULES/ants_lct_inputs/grid.nl

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+&grid
+delta_lambda_targ=0.11,
+delta_phi_targ=0.11,
+global=.false.,
+igrid_targ=6,
+inwsw=1,
+lambda_origin_targ=107.01,
+lambda_pole=180.0,
+phi_origin_targ=-46.58,
+phi_pole=90.0,
+points_lambda_targ=490,
+points_phi_targ=386,
+rotated=.false.,
+/

ancillaries/JULES/run_ancil_lct.sh

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+#!/bin/bash
+#PBS -q normal
+#PBS -l ncpus=1
+#PBS -l mem=4GB
+#PBS -l walltime=01:00:00
+#PBS -l storage=gdata/hh5+gdata/access+gdata/rp23
+#PBS -l wd
+#PBS -l jobfs=1GB
+#PBS -P rp23
+
+module purge
+module use /g/data/access/ngm/modules
+module load ants/1.1.0  # as used by Siyuan's code, also works with the RAS-based code
+# module load ants/0.18  # as used in RAS
+
+ANTS_SRC_PATH=/g/data/rp23/experiments/2024-10-10_LWG_workingbee/mjl561/ants_src/ants_1p1
+ANCIL_MASTER=/g/data/access/TIDS/UM/ancil/atmos/master
+INPUT_PATH=/g/data/rp23/experiments/2024-10-10_LWG_workingbee/mjl561/ants_lct_inputs
+ANCIL_TARGET_PATH=/g/data/rp23/experiments/2024-10-10_LWG_workingbee/mjl561/outputs_1p1
+
+# check if the output directory exists
+if [ ! -d ${ANCIL_TARGET_PATH} ]; then
+    mkdir -p ${ANCIL_TARGET_PATH}
+fi
+
+# based on RAS (u-bu503) app/ancil_lct/rose-app.conf
+source=${ANCIL_MASTER}/vegetation/cover/cci/v3/vegetation_fraction.nc
+target_grid=${INPUT_PATH}/grid.nl
+transformpath=/g/data/access/TIDS/UM/ancil/data/transforms/cci2jules_ra1.json
+output_vegfrac=${ANCIL_TARGET_PATH}/qrparm.veg.frac_cci_pre_c4
+output_lsm=${ANCIL_TARGET_PATH}
+ANTS_CONFIG=${INPUT_PATH}/ancil_lct-app.conf
+
+python ${ANTS_SRC_PATH}/ancil_lct.py ${source} \
+         --target-grid ${target_grid} --transform-path ${transformpath} \
+         -o ${output_vegfrac} --landseamask-output ${output_lsm}       \
+         --ants-config ${ANTS_CONFIG}
+
+# based on RAS app/ancil_lct_postproc_c4/rose-app.conf
+ANCIL_CONFIG=${INPUT_PATH}/ancil_lct_postproc_c4-app.conf
+source=${ANCIL_TARGET_PATH}/qrparm.veg.frac_cci_pre_c4.nc
+target_lsm=${ANCIL_TARGET_PATH}/qrparm.mask
+output=${ANCIL_TARGET_PATH}/qrparm.veg.frac_cci
+c4source=${ANCIL_MASTER}/vegetation/cover/cci/v3/c4_percent_1d.nc
+# c4source=/g/data/dp9/mjl561/au_ancils_source/Oceania_CSIRO_ISLSCP_C4_percent_300m.nc # high res version by Luigi
+
+python ${ANTS_SRC_PATH}/ancil_general_regrid.py --ants-config ${ANCIL_CONFIG} \
+       ${c4source} --target-lsm ${target_lsm} -o ${ANCIL_TARGET_PATH}/c4_percent_1d.nc
+
+python ${ANTS_SRC_PATH}/ancil_lct_postproc_c4.py \
+       ${source} --islscpiic4 ${ANCIL_TARGET_PATH}/c4_percent_1d.nc -o ${output}

ancillaries/JULES/run_ancil_lct_README.md

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+author: mathew lipson [email protected]
+
+# Purpose
+This script emulates the rose/cycl suites that generate ancillaries 
+(e.g. vegetation fraction and land-sea mask) required to run JULES offline or 
+with the UM. It is based on RAS suite (u-bu503) but uses ants/1.1.0 per 
+Siyuan's offline code.
+
+# Usage
+from the command line: `qsub run_ancil_lct.sh`
+this uses 1 cpu and takes ~ 2 mins to process this example domain
+
+The domain is defined in `./ants_lct_inputs/grid.nl` using the same format as in the RAS.
+By default the lsm mask is defined from the land cover source, however an alternative lsm
+can be provided as an ancil_lct.py argument (not yet tested).
+
+Other ANTS configuration inputs are defined in `./ants_lct_<app-name>-app.conf`, for example
+the ants x/y decomposition and regridding schemes.
+
+# Method
+
+Uses a variety of methods and ants functionality, including
+`ants.analysis.make_consistent_with_lsm`
+`ants.regrid.GeneralRegridScheme` with a linear horizontal scheme
+
+Outputs are placed by default into `./outputs_1p1` (configurable).
+Following the ancillary generation suites, outputs are saved in both UM (no extension) and .nc formats.
+Some files are not required at all by current versions of JULES (e.g. `qrparm.landfrac`).
+Some files are only required as an intermediatory step (e.g. `qrparm.veg.frac_cci_pre_c4`, `c4_percent_1d.nc`)
+
+The final files important for JULES are `qrparm.mask` and `qrparm.veg.frac_cci`
+
+# Other notes
+
+## Siyuans offline JULES ancillary suite
+svn co https://code.metoffice.gov.uk/svn/roses-u/b/x/0/3/8/nci-gadi
+
+## The land-atmos Regional Ancillary Suite (RAS)
+svn co https://code.metoffice.gov.uk/svn/roses-u/b/u/5/0/3/trunk
+
+# The RAS uses ANTS 1.0 branch: 
+https://code.metoffice.gov.uk/svn/ancil/ants/branches/dev/claudiosanchez/r13230_RAS_ANTS_1p0
+
+# Siyuans ancil suite uses ANTS 1.1 branch:
+https://code.metoffice.gov.uk/svn/ancil/ants/branches/dev/martinbest/r13910_ancil_ants_JULES_vn1.1.0/