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add MARBL diags for CMIP7 #355

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add MARBL diags for CMIP7 #355

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7835b12
add and populate cmip7 MARBL_DIAG_MODE
klindsay28 Oct 20, 2026
99f588b
add support for tracer mean_150m and zint_150m diags
klindsay28 Oct 23, 2026
a9899ec
Merge branch 'main' into MARBL_CMIP7_diags
klindsay28 Oct 23, 2026
0fdbe1c
run black on MOM_MARBL_diagnostics.py
klindsay28 Oct 23, 2026
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147 changes: 111 additions & 36 deletions cime_config/MARBL_scripts/MOM_MARBL_diagnostics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ def write_MARBL_diagnostics_file(
# each subsequent diag_mode is a superset of the previous mode; if we have a list of valid modes
# then we can use integer comparison with the .index() function to determine if a variable should
# be included.
valid_diag_modes = ["none", "minimal", "full", "test_suite"]
valid_diag_modes = ["none", "minimal", "cmip7", "full", "test_suite"]
# For now we hard-code the tracers we want included in the output when diag_mode = 'minimal'
# (and for the Jint_100m diagnostics)
# If we expand the minimal set, we may need to change how we track what is included
Expand All @@ -47,8 +47,6 @@ def write_MARBL_diagnostics_file(
"diatChl",
"diazChl",
"coccoChl",
"microzooC",
"mesozooC",
]
Jint_100m_in_minimal_diag_output = ["ALK", "DIC"]

Expand Down Expand Up @@ -99,22 +97,24 @@ def write_MARBL_diagnostics_file(
fout.write(f"SEAICE_DUST_FLUX_CPL : {freq_op}\n")
fout.write(f"ATM_BLACK_CARBON_FLUX_CPL : {freq_op}\n")
fout.write(f"SEAICE_BLACK_CARBON_FLUX_CPL : {freq_op}\n")
fout.write("#\n# temperature and salinity\n#\n")
fout.write(
f"so: {freq_op}\n"
) # so should be included when diag_mode = "minimal"

if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("full"):
fout.write("#\n# temperature and salinity\n#\n")
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
freq_op = "medium_average"
else:
freq_op = "never_average"
fout.write(
f"thetao: {freq_op}\n"
) # thetao should not be included when diag_mode = "minimal"
f"T_mean_150m: {freq_op}\n"
) # T_mean_150m should not be included when diag_mode < "cmip7"

fout.write("#\n# Bottom Flux to Tendency Conversion\n#\n")
fout.write(f"BOT_FLUX_TO_TEND : {freq_op}\n")

if ice_ncat > 0:
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
freq_op = "medium_average"
else:
freq_op = "never_average"
fout.write("#\n# per-category forcings\n#\n")
for m in range(ice_ncat + 1):
fout.write(f"FRACR_CAT_{m+1}: {freq_op}\n")
Expand Down Expand Up @@ -152,7 +152,7 @@ def write_MARBL_diagnostics_file(
freq_op = "never_average"
per_tracer_dict["diags"] = {}
# Tracers themselves and Jint_100m diags have different defaults than the rest
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("full") or (
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7") or (
valid_diag_modes.index(diag_mode) == valid_diag_modes.index("minimal")
and tracer_short_name in tracers_in_minimal_diag_output
):
Expand All @@ -175,7 +175,7 @@ def write_MARBL_diagnostics_file(

# Set up dictionary for tracking the Jint_100m_{tracer} freq_ops
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("full") or (
valid_diag_modes.index(diag_mode) == valid_diag_modes.index("minimal")
valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("minimal")
and tracer_short_name in Jint_100m_in_minimal_diag_output
):
Jint_100m_freq_op[tracer_short_name] = "medium_average"
Expand All @@ -186,7 +186,6 @@ def write_MARBL_diagnostics_file(
# 2. Update dictionary for tracers that don't just rely on default diagnostic output
# This is organized per-tracer, and specific blocks are ignored if MARBL is not
# configured to run with that particular tracer
# PO4
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("full"):
freq_op = "medium_average"
low_freq_op = "low_average"
Expand All @@ -195,22 +194,31 @@ def write_MARBL_diagnostics_file(
freq_op = "never_average"
low_freq_op = "never_average"
high_freq_op = "never_average"
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
riv_flux_op = "medium_average"
else:
riv_flux_op = "never_average"
# PO4
if "PO4" in full_diag_dict.keys():
full_diag_dict["PO4"]["diags"]["PO4_RIV_FLUX"] = freq_op
full_diag_dict["PO4"]["diags"]["PO4_RIV_FLUX"] = riv_flux_op
full_diag_dict["PO4"]["diags"]["J_PO4"] = low_freq_op
full_diag_dict["PO4"]["diags"]["Jint_100m_PO4"] = Jint_100m_freq_op["PO4"]
# full_diag_dict['PO4']['diags']['tend_zint_100m_PO4'] = freq_op
full_diag_dict["PO4"]["properties"]["has surface flux"] = True
# NO3
if "NO3" in full_diag_dict.keys():
full_diag_dict["NO3"]["diags"]["NO3_RIV_FLUX"] = freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["NO3"]["diags"]["NO3_SURF"] = "medium_average"
full_diag_dict["NO3"]["diags"]["NO3_RIV_FLUX"] = riv_flux_op
full_diag_dict["NO3"]["diags"]["J_NO3"] = low_freq_op
full_diag_dict["NO3"]["diags"]["Jint_100m_NO3"] = Jint_100m_freq_op["NO3"]
# full_diag_dict['NO3']['diags']['tend_zint_100m_NO3'] = freq_op
full_diag_dict["NO3"]["properties"]["has surface flux"] = True
# SiO3
if "SiO3" in full_diag_dict.keys():
full_diag_dict["SiO3"]["diags"]["SiO3_RIV_FLUX"] = freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["SiO3"]["diags"]["SiO3_SURF"] = "medium_average"
full_diag_dict["SiO3"]["diags"]["SiO3_RIV_FLUX"] = riv_flux_op
full_diag_dict["SiO3"]["diags"]["J_SiO3"] = low_freq_op
full_diag_dict["SiO3"]["diags"]["Jint_100m_SiO3"] = Jint_100m_freq_op[
"SiO3"
Expand All @@ -219,13 +227,17 @@ def write_MARBL_diagnostics_file(
full_diag_dict["SiO3"]["properties"]["has surface flux"] = True
# NH4
if "NH4" in full_diag_dict.keys():
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["NH4"]["diags"]["NH4_SURF"] = "medium_average"
full_diag_dict["NH4"]["diags"]["J_NH4"] = low_freq_op
full_diag_dict["NH4"]["diags"]["Jint_100m_NH4"] = Jint_100m_freq_op["NH4"]
# full_diag_dict['NH4']['diags']['tend_zint_100m_NH4'] = freq_op
full_diag_dict["NH4"]["properties"]["has surface flux"] = True
# Fe
if "Fe" in full_diag_dict.keys():
full_diag_dict["Fe"]["diags"]["Fe_RIV_FLUX"] = freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["Fe"]["diags"]["Fe_SURF"] = "medium_average"
full_diag_dict["Fe"]["diags"]["Fe_RIV_FLUX"] = riv_flux_op
full_diag_dict["Fe"]["diags"]["J_Fe"] = low_freq_op
full_diag_dict["Fe"]["diags"]["Jint_100m_Fe"] = Jint_100m_freq_op["Fe"]
# full_diag_dict['Fe']['diags']['tend_zint_100m_Fe'] = freq_op
Expand All @@ -241,28 +253,38 @@ def write_MARBL_diagnostics_file(
full_diag_dict["O2"]["diags"]["STF_O2"] = "medium_average, high_average"
else:
full_diag_dict["O2"]["diags"]["STF_O2"] = "never_average"
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["O2"]["diags"][
"O2_SURF"
] = "medium_average, high_average"
full_diag_dict["O2"]["diags"]["Jint_100m_O2"] = Jint_100m_freq_op["O2"]
# full_diag_dict['O2']['diags']['tend_zint_100m_O2'] = freq_op
full_diag_dict["O2"]["properties"]["include budget terms"] = True
full_diag_dict["O2"]["properties"]["has surface flux"] = True
# DIC
if "DIC" in full_diag_dict.keys():
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["DIC"]["diags"]["DIC_SURF"] = "medium_average"
full_diag_dict["DIC"]["diags"]["DIC_zint"] = "medium_average"
else:
full_diag_dict["DIC"]["diags"]["DIC_zint"] = freq_op
# STF_SALT_DIC is special case
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("minimal"):
full_diag_dict["DIC"]["diags"]["STF_SALT_DIC"] = "medium_average"
full_diag_dict["DIC"]["diags"]["DIC_RIV_FLUX"] = freq_op
full_diag_dict["DIC"]["diags"]["DIC_RIV_FLUX"] = riv_flux_op
full_diag_dict["DIC"]["diags"]["J_DIC"] = freq_op
full_diag_dict["DIC"]["diags"]["Jint_100m_DIC"] = Jint_100m_freq_op["DIC"]
# full_diag_dict['DIC']['diags']['tend_zint_100m_DIC'] = freq_op
full_diag_dict["DIC"]["properties"]["include budget terms"] = True
full_diag_dict["DIC"]["properties"]["has surface flux"] = True
# DIC_ALT_CO2
if "DIC_ALT_CO2" in full_diag_dict.keys():
full_diag_dict["DIC_ALT_CO2"]["diags"]["DIC_ALT_CO2_RIV_FLUX"] = freq_op
# full_diag_dict["DIC_ALT_CO2"]["diags"]["DIC_ALT_CO2_RIV_FLUX"] = riv_flux_op
full_diag_dict["DIC_ALT_CO2"]["diags"]["J_DIC_ALT_CO2"] = freq_op
full_diag_dict["DIC_ALT_CO2"]["diags"]["Jint_100m_DIC_ALT_CO2"] = (
Jint_100m_freq_op["DIC_ALT_CO2"]
)
full_diag_dict["DIC_ALT_CO2"]["diags"]["DIC_ALT_CO2_zint"] = freq_op
# full_diag_dict['DIC_ALT_CO2']['diags']['tend_zint_100m_DIC_ALT_CO2'] = freq_op
full_diag_dict["DIC_ALT_CO2"]["properties"]["include budget terms"] = True
full_diag_dict["DIC_ALT_CO2"]["properties"]["has surface flux"] = True
Expand All @@ -271,15 +293,15 @@ def write_MARBL_diagnostics_file(
# STF_SALT_ALK is special case
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("minimal"):
full_diag_dict["ALK"]["diags"]["STF_SALT_ALK"] = "medium_average"
full_diag_dict["ALK"]["diags"]["ALK_RIV_FLUX"] = freq_op
full_diag_dict["ALK"]["diags"]["ALK_RIV_FLUX"] = riv_flux_op
full_diag_dict["ALK"]["diags"]["STF_ALK"] = freq_op
full_diag_dict["ALK"]["diags"]["J_ALK"] = low_freq_op
full_diag_dict["ALK"]["diags"]["Jint_100m_ALK"] = Jint_100m_freq_op["ALK"]
# full_diag_dict['ALK']['diags']['tend_zint_100m_ALK'] = freq_op
full_diag_dict["ALK"]["properties"]["has surface flux"] = True
# ALK_ALT_CO2
if "ALK_ALT_CO2" in full_diag_dict.keys():
full_diag_dict["ALK_ALT_CO2"]["diags"]["ALK_ALT_CO2_RIV_FLUX"] = freq_op
# full_diag_dict["ALK_ALT_CO2"]["diags"]["ALK_ALT_CO2_RIV_FLUX"] = riv_flux_op
full_diag_dict["ALK_ALT_CO2"]["diags"]["STF_ALK_ALT_CO2"] = freq_op
full_diag_dict["ALK_ALT_CO2"]["diags"]["J_ALK_ALT_CO2"] = low_freq_op
full_diag_dict["ALK_ALT_CO2"]["diags"]["Jint_100m_ALK_ALT_CO2"] = (
Expand All @@ -289,7 +311,11 @@ def write_MARBL_diagnostics_file(
full_diag_dict["ALK_ALT_CO2"]["properties"]["has surface flux"] = True
# DOC
if "DOC" in full_diag_dict.keys():
full_diag_dict["DOC"]["diags"]["DOC_RIV_FLUX"] = freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["DOC"]["diags"]["DOC_zint"] = "medium_average"
else:
full_diag_dict["DOC"]["diags"]["DOC_zint"] = freq_op
full_diag_dict["DOC"]["diags"]["DOC_RIV_FLUX"] = riv_flux_op
full_diag_dict["DOC"]["diags"]["Jint_100m_DOC"] = Jint_100m_freq_op["DOC"]
# full_diag_dict['DOC']['diags']['tend_zint_100m_DOC'] = freq_op
full_diag_dict["DOC"]["properties"]["include budget terms"] = True
Expand All @@ -298,23 +324,49 @@ def write_MARBL_diagnostics_file(
] = False # this should be True if EBM is off
# DON
if "DON" in full_diag_dict.keys():
full_diag_dict["DON"]["diags"]["DON_RIV_FLUX"] = freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["DON"]["diags"]["DON_zint"] = "low_average"
else:
full_diag_dict["DON"]["diags"]["DON_zint"] = freq_op
full_diag_dict["DON"]["diags"]["DON_RIV_FLUX"] = riv_flux_op
full_diag_dict["DON"]["properties"]["has surface flux"] = True
# DOP
if "DOP" in full_diag_dict.keys():
full_diag_dict["DOP"]["diags"]["DOP_RIV_FLUX"] = freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["DOP"]["diags"]["DOP_zint"] = "low_average"
else:
full_diag_dict["DOP"]["diags"]["DOP_zint"] = freq_op
full_diag_dict["DOP"]["diags"]["DOP_RIV_FLUX"] = riv_flux_op
full_diag_dict["DOP"]["properties"]["has surface flux"] = True
# DOPr
if "DOPr" in full_diag_dict.keys():
full_diag_dict["DOPr"]["diags"]["DOPr_RIV_FLUX"] = freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["DOPr"]["diags"]["DOPr_zint"] = "low_average"
full_diag_dict["DOPr"]["diags"]["Jint_DOPr"] = "low_average"
else:
full_diag_dict["DOPr"]["diags"]["DOPr_zint"] = freq_op
full_diag_dict["DOPr"]["diags"]["Jint_DOPr"] = freq_op
full_diag_dict["DOPr"]["diags"]["DOPr_RIV_FLUX"] = riv_flux_op
full_diag_dict["DOPr"]["properties"]["has surface flux"] = True
# DONr
if "DONr" in full_diag_dict.keys():
full_diag_dict["DONr"]["diags"]["DONr_RIV_FLUX"] = freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["DONr"]["diags"]["DONr_zint"] = "low_average"
full_diag_dict["DONr"]["diags"]["Jint_DONr"] = "low_average"
else:
full_diag_dict["DONr"]["diags"]["DONr_zint"] = freq_op
full_diag_dict["DONr"]["diags"]["Jint_DONr"] = freq_op
full_diag_dict["DONr"]["diags"]["DONr_RIV_FLUX"] = riv_flux_op
full_diag_dict["DONr"]["properties"]["has surface flux"] = True
# DOCr
if "DOCr" in full_diag_dict.keys():
full_diag_dict["DOCr"]["diags"]["DOCr_RIV_FLUX"] = freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["DOCr"]["diags"]["DOCr_zint"] = "medium_average"
full_diag_dict["DOCr"]["diags"]["Jint_DOCr"] = "low_average"
else:
full_diag_dict["DOCr"]["diags"]["DOCr_zint"] = freq_op
full_diag_dict["DOCr"]["diags"]["Jint_DOCr"] = freq_op
full_diag_dict["DOCr"]["diags"]["DOCr_RIV_FLUX"] = riv_flux_op
full_diag_dict["DOCr"]["diags"]["Jint_100m_DOCr"] = Jint_100m_freq_op[
"DOCr"
]
Expand Down Expand Up @@ -371,6 +423,10 @@ def write_MARBL_diagnostics_file(
full_diag_dict["ABIO_DIC"]["properties"]["has surface flux"] = True
# DI14C
if "ABIO_DI14C" in full_diag_dict.keys():
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict["ABIO_DI14C"]["diags"][
"ABIO_DI14C_SURF"
] = "medium_average"
# full_diag_dict['ABIO_DI14C']['diags']['J_ABIO_DI14C'] = freq_op
full_diag_dict["ABIO_DI14C"]["diags"]["STF_ABIO_DI14C"] = freq_op
full_diag_dict["ABIO_DI14C"]["diags"]["Jint_ABIO_DI14C"] = freq_op
Expand All @@ -382,19 +438,28 @@ def write_MARBL_diagnostics_file(
for autotroph_name in autotroph_list:
tracer_short_name = autotroph_name + "C"
if tracer_short_name in full_diag_dict.keys():
full_diag_dict[tracer_short_name]["diags"][
"%s_zint_100m" % tracer_short_name
] = high_freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict[tracer_short_name]["diags"][
"%s_SURF" % tracer_short_name
] = "high_average, medium_average"
full_diag_dict[tracer_short_name]["diags"][
"%s_zint_100m" % tracer_short_name
] = "medium_average"
tracer_short_name = autotroph_name + "CaCO3"
if tracer_short_name in full_diag_dict.keys():
full_diag_dict[tracer_short_name]["diags"][
"%s_zint_100m" % tracer_short_name
] = high_freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict[tracer_short_name]["diags"][
"%s_SURF" % tracer_short_name
] = "medium_average"
full_diag_dict[tracer_short_name]["diags"][
"%s_zint_100m" % tracer_short_name
] = "medium_average"
tracer_short_name = autotroph_name + "Chl"
if tracer_short_name in full_diag_dict.keys():
full_diag_dict[tracer_short_name]["diags"][
"%s_SURF" % tracer_short_name
] = high_freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict[tracer_short_name]["diags"][
"%s_SURF" % tracer_short_name
] = "high_average, medium_average"

# 4. Per-zooplankton diagnostics
for zooplankton_name in zooplankton_list:
Expand All @@ -403,6 +468,13 @@ def write_MARBL_diagnostics_file(
full_diag_dict[tracer_short_name]["diags"][
"%s_zint_100m" % tracer_short_name
] = high_freq_op
if valid_diag_modes.index(diag_mode) >= valid_diag_modes.index("cmip7"):
full_diag_dict[tracer_short_name]["diags"][
"%s_SURF" % tracer_short_name
] = "medium_average"
full_diag_dict[tracer_short_name]["diags"][
"%s_zint_150m" % tracer_short_name
] = "medium_average"

# 5. Write tracer-specific diagnostics to file
for tracer_short_name in full_diag_dict.keys():
Expand Down Expand Up @@ -496,6 +568,9 @@ def _2D_varcheck(varname):
or varname.endswith("_FLUX_CPL")
or varname.endswith("_RIV_FLUX")
or varname.endswith("_SURF")
or varname.endswith("_zint")
or varname.endswith("_zint_100m")
or varname.endswith("_zint_150m")
or varname.endswith("_mean_150m")
or "_CAT_" in varname
)
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