From 7981fef3f37194933d80c22814ccaa448054bd88 Mon Sep 17 00:00:00 2001
From: Sean Bryan <sean.bryan@anu.edu.au>
Date: Mon, 21 Oct 2024 12:42:08 +1100
Subject: [PATCH 1/7] Remove TODO

---
 regrid_aus_05x05_to_005x005.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/regrid_aus_05x05_to_005x005.sh b/regrid_aus_05x05_to_005x005.sh
index ae613ba..acd1c5d 100644
--- a/regrid_aus_05x05_to_005x005.sh
+++ b/regrid_aus_05x05_to_005x005.sh
@@ -120,8 +120,6 @@ modification_attr="${script_name}: Update soil parameter values with fields as u
 echo "Add modification note to global attributes"
 ncatted -h -a modification,global,p,c,"${modification_attr}" ${output_file}
 
-# TODO(Sean): check unit, standard name, long name attributes for appended variables
-
 silt_file=${BIOS_PARAM_DIR}/siltfrac1.nc
 echo "silt_file: ${silt_file}"
 

From eea8da2304e12d4578b64bda3397790cfa1b0038 Mon Sep 17 00:00:00 2001
From: Sean Bryan <sean.bryan@anu.edu.au>
Date: Mon, 21 Oct 2024 12:28:21 +1100
Subject: [PATCH 2/7] Add comment and references for BIOS soil parameters

---
 regrid_aus_05x05_to_005x005.sh | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/regrid_aus_05x05_to_005x005.sh b/regrid_aus_05x05_to_005x005.sh
index acd1c5d..c33f5b3 100644
--- a/regrid_aus_05x05_to_005x005.sh
+++ b/regrid_aus_05x05_to_005x005.sh
@@ -444,6 +444,22 @@ ncks --overwrite --no-alphabetize -x -v c4frac \
 echo "Append c4frac variable to output file"
 ncks -A -v c4frac c4frac.nc ${output_file}
 
+bios_soil_vars_regex='^clay$|^sand$|^ssat$|^bch$|^css$|^hyds$|^sfc$|^sucs$|^rhosoil$|^silt$|^swilt$'
+
+echo "Add provenance information to BIOS soil parameters"
+att_nm='comment'
+var_nm=${bios_soil_vars_regex}
+mode='o'
+att_type='c'
+att_val='Data provided from the Atlas of Australian Soils (digital)'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+att_nm='references'
+var_nm=${bios_soil_vars_regex}
+mode='o'
+att_type='c'
+att_val='https://doi.org/10.25919/5df03e991672d and https://publications.csiro.au/publications/publication/PIlegacy:889'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 echo "Clean up"
 rm clay.nc sand.nc ssat.nc bch.nc css.nc hyds.nc mvg.nc sfc.nc sucs.nc c4frac.nc rhosoil.nc silt.nc swilt.nc
 

From 813e66fb9c1496e252a3d8bebfcd264f36461e67 Mon Sep 17 00:00:00 2001
From: Sean Bryan <sean.bryan@anu.edu.au>
Date: Mon, 21 Oct 2024 14:26:45 +1100
Subject: [PATCH 3/7] Set units and long_name attributes for BIOS variables

---
 regrid_aus_05x05_to_005x005.sh | 200 +++++++++++++++++++++++++++++++++
 1 file changed, 200 insertions(+)

diff --git a/regrid_aus_05x05_to_005x005.sh b/regrid_aus_05x05_to_005x005.sh
index c33f5b3..69de111 100644
--- a/regrid_aus_05x05_to_005x005.sh
+++ b/regrid_aus_05x05_to_005x005.sh
@@ -143,6 +143,22 @@ ncks --overwrite --no-alphabetize -x -v silt \
 echo "Append silt variable to output file"
 ncks -A -v silt silt.nc ${output_file}
 
+echo "Set silt units attribute"
+att_nm='units'
+var_nm='silt'
+mode='o'
+att_type='c'
+att_val='1'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set silt long_name attribute"
+att_nm='long_name'
+var_nm='silt'
+mode='o'
+att_type='c'
+att_val='UM soil texture - silt fraction'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 clay_file=${BIOS_PARAM_DIR}/clayfrac1.nc
 echo "clay_file: ${clay_file}"
 
@@ -166,6 +182,22 @@ ncks --overwrite --no-alphabetize -x -v clay \
 echo "Append clay variable to output file"
 ncks -A -v clay clay.nc ${output_file}
 
+echo "Set clay units attribute"
+att_nm='units'
+var_nm='clay'
+mode='o'
+att_type='c'
+att_val='1'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set clay long_name attribute"
+att_nm='long_name'
+var_nm='clay'
+mode='o'
+att_type='c'
+att_val='UM soil texture - clay fraction'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 echo "Create sand file"
 ncks --overwrite --no-alphabetize silt.nc sand.nc
 ncks -A -v clay clay.nc sand.nc
@@ -181,6 +213,22 @@ ncks --overwrite --no-alphabetize -x -v sand \
 echo "Append sand variable to output file"
 ncks -A -v sand sand.nc ${output_file}
 
+echo "Set sand units attribute"
+att_nm='units'
+var_nm='sand'
+mode='o'
+att_type='c'
+att_val='1'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set sand long_name attribute"
+att_nm='long_name'
+var_nm='sand'
+mode='o'
+att_type='c'
+att_val='UM soil texture - sand fraction'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 css_file=${BIOS_PARAM_DIR}/csoil1.nc
 echo "css_file: ${css_file}"
 
@@ -204,6 +252,22 @@ ncks --overwrite --no-alphabetize -x -v css \
 echo "Append css variable to output file"
 ncks -A -v css css.nc ${output_file}
 
+echo "Set css units attribute"
+att_nm='units'
+var_nm='css'
+mode='o'
+att_type='c'
+att_val='J/kg/K'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set css long_name attribute"
+att_nm='long_name'
+var_nm='css'
+mode='o'
+att_type='c'
+att_val='Soil specific heat capacity'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 sfc_file=${BIOS_PARAM_DIR}/wvol1fc_m3m3.nc
 echo "sfc_file: ${sfc_file}"
 
@@ -227,6 +291,22 @@ ncks --overwrite --no-alphabetize -x -v sfc \
 echo "Append sfc variable to output file"
 ncks -A -v sfc sfc.nc ${output_file}
 
+echo "Set sfc units attribute"
+att_nm='units'
+var_nm='sfc'
+mode='o'
+att_type='c'
+att_val='m3 m-3'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set sfc long_name attribute"
+att_nm='long_name'
+var_nm='sfc'
+mode='o'
+att_type='c'
+att_val='VOL SMC AT CRIT PT'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 rhosoil_file=${BIOS_PARAM_DIR}/bulkdens1_kgm3.nc
 echo "rhosoil_file: ${rhosoil_file}"
 
@@ -250,6 +330,22 @@ ncks --overwrite --no-alphabetize -x -v rhosoil \
 echo "Append rhosoil variable to output file"
 ncks -A -v rhosoil rhosoil.nc ${output_file}
 
+echo "Set rhosoil units attribute"
+att_nm='units'
+var_nm='rhosoil'
+mode='o'
+att_type='c'
+att_val='kg/m^3'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set rhosoil long_name attribute"
+att_nm='long_name'
+var_nm='rhosoil'
+mode='o'
+att_type='c'
+att_val='SOIL BULK DENSITY'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 bch_file=${BIOS_PARAM_DIR}/b1.nc
 echo "bch_file: ${bch_file}"
 
@@ -278,6 +374,22 @@ ncks --overwrite --no-alphabetize -x -v bch \
 echo "Append bch variable to output file"
 ncks -A -v bch bch.nc ${output_file}
 
+echo "Set bch units attribute"
+att_nm='units'
+var_nm='bch'
+mode='o'
+att_type='c'
+att_val='1'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set bch long_name attribute"
+att_nm='long_name'
+var_nm='bch'
+mode='o'
+att_type='c'
+att_val='CLAPP-HORNBERGER B COEFFICIENT'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 hyds_file=${BIOS_PARAM_DIR}/hyk1sat_ms.nc
 echo "hyds_file: ${hyds_file}"
 
@@ -306,6 +418,22 @@ ncks --overwrite --no-alphabetize -x -v hyds \
 echo "Append hyds variable to output file"
 ncks -A -v hyds hyds.nc ${output_file}
 
+echo "Set hyds units attribute"
+att_nm='units'
+var_nm='hyds'
+mode='o'
+att_type='c'
+att_val='m/s'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set hyds long_name attribute"
+att_nm='long_name'
+var_nm='hyds'
+mode='o'
+att_type='c'
+att_val='SAT SOIL CONDUCTIVITY'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 ssat_file=${BIOS_PARAM_DIR}/wvol1sat_m3m3.nc
 echo "ssat_file: ${ssat_file}"
 
@@ -334,6 +462,22 @@ ncks --overwrite --no-alphabetize -x -v ssat \
 echo "Append ssat variable to output file"
 ncks -A -v ssat ssat.nc ${output_file}
 
+echo "Set ssat units attribute"
+att_nm='units'
+var_nm='ssat'
+mode='o'
+att_type='c'
+att_val='1'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set ssat long_name attribute"
+att_nm='long_name'
+var_nm='ssat'
+mode='o'
+att_type='c'
+att_val='VOL SMC AT SATURATION'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 swilt_file=${BIOS_PARAM_DIR}/wvol1w_m3m3.nc
 echo "swilt_file: ${swilt_file}"
 
@@ -362,6 +506,22 @@ ncks --overwrite --no-alphabetize -x -v swilt \
 echo "Append swilt variable to output file"
 ncks -A -v swilt swilt.nc ${output_file}
 
+echo "Set swilt units attribute"
+att_nm='units'
+var_nm='swilt'
+mode='o'
+att_type='c'
+att_val='1'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set swilt long_name attribute"
+att_nm='long_name'
+var_nm='swilt'
+mode='o'
+att_type='c'
+att_val='VOL SMC AT WILTING'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 sucs_file=${BIOS_PARAM_DIR}/psie1_m.nc
 echo "sucs_file: ${sucs_file}"
 
@@ -395,6 +555,22 @@ ncks --overwrite --no-alphabetize -x -v sucs \
 echo "Append sucs variable to output file"
 ncks -A -v sucs sucs.nc ${output_file}
 
+echo "Set sucs units attribute"
+att_nm='units'
+var_nm='sucs'
+mode='o'
+att_type='c'
+att_val='m'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set sucs long_name attribute"
+att_nm='long_name'
+var_nm='sucs'
+mode='o'
+att_type='c'
+att_val='SATURATED SOIL WATER SUCTION'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 mvg_file=${BIOS_PARAM_DIR}/nvis5pre1750grp.nc
 echo "mvg_file: ${mvg_file}"
 
@@ -421,6 +597,14 @@ ncks --overwrite --no-alphabetize -x -v mvg \
 echo "Append mvg variable to output file"
 ncks -A -v mvg mvg.nc ${output_file}
 
+echo "Set mvg long_name attribute"
+att_nm='long_name'
+var_nm='mvg'
+mode='o'
+att_type='c'
+att_val='NVIS major vegetation group (v5.0)'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 c4frac_file=${BIOS_PARAM_DIR}/c4_grass_frac_cov.nc
 echo "c4frac_file: ${c4frac_file}"
 
@@ -444,6 +628,22 @@ ncks --overwrite --no-alphabetize -x -v c4frac \
 echo "Append c4frac variable to output file"
 ncks -A -v c4frac c4frac.nc ${output_file}
 
+echo "Set c4frac units attribute"
+att_nm='units'
+var_nm='c4frac'
+mode='o'
+att_type='c'
+att_val='1'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set c4frac long_name attribute"
+att_nm='long_name'
+var_nm='c4frac'
+mode='o'
+att_type='c'
+att_val='Fractional cover of C4 grass'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 bios_soil_vars_regex='^clay$|^sand$|^ssat$|^bch$|^css$|^hyds$|^sfc$|^sucs$|^rhosoil$|^silt$|^swilt$'
 
 echo "Add provenance information to BIOS soil parameters"

From e8764c01f5aa2f593de934dda1131a34ca59c90d Mon Sep 17 00:00:00 2001
From: Sean Bryan <sean.bryan@anu.edu.au>
Date: Tue, 22 Oct 2024 11:33:11 +1100
Subject: [PATCH 4/7] Set sfc units to 1

---
 regrid_aus_05x05_to_005x005.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/regrid_aus_05x05_to_005x005.sh b/regrid_aus_05x05_to_005x005.sh
index 69de111..c0c5f30 100644
--- a/regrid_aus_05x05_to_005x005.sh
+++ b/regrid_aus_05x05_to_005x005.sh
@@ -296,7 +296,7 @@ att_nm='units'
 var_nm='sfc'
 mode='o'
 att_type='c'
-att_val='m3 m-3'
+att_val='1'
 ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
 
 echo "Set sfc long_name attribute"

From 98eeacb905a1af9321bc532ee96ff79db1578560 Mon Sep 17 00:00:00 2001
From: Sean Bryan <sean.bryan@anu.edu.au>
Date: Tue, 22 Oct 2024 11:36:57 +1100
Subject: [PATCH 5/7] Use upper case for long_name description

---
 regrid_aus_05x05_to_005x005.sh | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/regrid_aus_05x05_to_005x005.sh b/regrid_aus_05x05_to_005x005.sh
index c0c5f30..e06c9e0 100644
--- a/regrid_aus_05x05_to_005x005.sh
+++ b/regrid_aus_05x05_to_005x005.sh
@@ -156,7 +156,7 @@ att_nm='long_name'
 var_nm='silt'
 mode='o'
 att_type='c'
-att_val='UM soil texture - silt fraction'
+att_val='UM SOIL TEXTURE - SILT FRACTION'
 ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
 
 clay_file=${BIOS_PARAM_DIR}/clayfrac1.nc
@@ -195,7 +195,7 @@ att_nm='long_name'
 var_nm='clay'
 mode='o'
 att_type='c'
-att_val='UM soil texture - clay fraction'
+att_val='UM SOIL TEXTURE - CLAY FRACTION'
 ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
 
 echo "Create sand file"
@@ -226,7 +226,7 @@ att_nm='long_name'
 var_nm='sand'
 mode='o'
 att_type='c'
-att_val='UM soil texture - sand fraction'
+att_val='UM SOIL TEXTURE - SAND FRACTION'
 ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
 
 css_file=${BIOS_PARAM_DIR}/csoil1.nc
@@ -265,7 +265,7 @@ att_nm='long_name'
 var_nm='css'
 mode='o'
 att_type='c'
-att_val='Soil specific heat capacity'
+att_val='SOIL SPECIFIC HEAT CAPACITY'
 ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
 
 sfc_file=${BIOS_PARAM_DIR}/wvol1fc_m3m3.nc
@@ -602,7 +602,7 @@ att_nm='long_name'
 var_nm='mvg'
 mode='o'
 att_type='c'
-att_val='NVIS major vegetation group (v5.0)'
+att_val='NVIS MAJOR VEGETATION GROUP (V5.0)'
 ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
 
 c4frac_file=${BIOS_PARAM_DIR}/c4_grass_frac_cov.nc
@@ -641,7 +641,7 @@ att_nm='long_name'
 var_nm='c4frac'
 mode='o'
 att_type='c'
-att_val='Fractional cover of C4 grass'
+att_val='FRACTIONAL COVER OF C4 GRASS'
 ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
 
 bios_soil_vars_regex='^clay$|^sand$|^ssat$|^bch$|^css$|^hyds$|^sfc$|^sucs$|^rhosoil$|^silt$|^swilt$'

From 855970f92c718e87e391b0e6bd797fc3fb78844a Mon Sep 17 00:00:00 2001
From: Sean Bryan <sean.bryan@anu.edu.au>
Date: Tue, 22 Oct 2024 11:42:41 +1100
Subject: [PATCH 6/7] Add comment and references to mvg

---
 regrid_aus_05x05_to_005x005.sh | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/regrid_aus_05x05_to_005x005.sh b/regrid_aus_05x05_to_005x005.sh
index e06c9e0..7478284 100644
--- a/regrid_aus_05x05_to_005x005.sh
+++ b/regrid_aus_05x05_to_005x005.sh
@@ -605,6 +605,22 @@ att_type='c'
 att_val='NVIS MAJOR VEGETATION GROUP (V5.0)'
 ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
 
+echo "Set mvg comment attribute"
+att_nm='comment'
+var_nm='mvg'
+mode='o'
+att_type='c'
+att_val='Data provided from National Vegetation Information System (NVIS)'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
+echo "Set mvg references attribute"
+att_nm='references'
+var_nm='mvg'
+mode='o'
+att_type='c'
+att_val='https://www.dcceew.gov.au/environment/land/native-vegetation/national-vegetation-information-system/data-products#mvg5'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 c4frac_file=${BIOS_PARAM_DIR}/c4_grass_frac_cov.nc
 echo "c4frac_file: ${c4frac_file}"
 

From aad786c0ad2f2940b51ca40240916e98e5315557 Mon Sep 17 00:00:00 2001
From: Sean Bryan <sean.bryan@anu.edu.au>
Date: Tue, 19 Nov 2024 11:11:51 +1100
Subject: [PATCH 7/7] Set c4frac references attribute

---
 regrid_aus_05x05_to_005x005.sh | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/regrid_aus_05x05_to_005x005.sh b/regrid_aus_05x05_to_005x005.sh
index 7478284..4a5ff70 100644
--- a/regrid_aus_05x05_to_005x005.sh
+++ b/regrid_aus_05x05_to_005x005.sh
@@ -660,6 +660,14 @@ att_type='c'
 att_val='FRACTIONAL COVER OF C4 GRASS'
 ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
 
+echo "Set c4frac references attribute"
+att_nm='references'
+var_nm='c4frac'
+mode='o'
+att_type='c'
+att_val='https://doi.org/10.5194/bg-10-2011-2013 following https://doi.org/10.1007/BF00379569'
+ncatted -h -a "${att_nm}","${var_nm}","${mode}","${att_type}","${att_val}" ${output_file}
+
 bios_soil_vars_regex='^clay$|^sand$|^ssat$|^bch$|^css$|^hyds$|^sfc$|^sucs$|^rhosoil$|^silt$|^swilt$'
 
 echo "Add provenance information to BIOS soil parameters"