From ea8013ef32124869b739226101d5019654318f88 Mon Sep 17 00:00:00 2001 From: Michael Levy Date: Thu, 20 Feb 2025 10:20:28 -0700 Subject: [PATCH 1/5] Update iron forcing files This will require updated MARBL and MOM6 tags as well --- param_templates/MOM_input.yaml | 11 +++++++++-- param_templates/json/MOM_input.json | 11 +++++++++-- 2 files changed, 18 insertions(+), 4 deletions(-) diff --git a/param_templates/MOM_input.yaml b/param_templates/MOM_input.yaml index b8509803..70237138 100644 --- a/param_templates/MOM_input.yaml +++ b/param_templates/MOM_input.yaml @@ -329,14 +329,21 @@ Global: datatype: string value: $MARBL_CONFIG == "latest": ecosys_jan_IC_omip_latlon_1x1_180W_c230331.nc - $MARBL_CONFIG == "latest+4p2z": ecosys_jan_IC_omip_latlon_1x1_180W_c231221.nc + $MARBL_CONFIG == "latest+4p2z": ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc MARBL_FESEDFLUX_FILE: description: | "Name of file containing iron sediment flux forcing field for the MARBL tracer package." datatype: string value: - '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2"': fesedflux_total_reduce_oxic_tx2_3v2.c231205.nc + '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2"': fesedflux_2024algo_tx2_3v2.c250220.nc + MARBL_FESEDFLUXRED_FILE: + description: | + "Name of file containing iron reducing sediment flux + forcing field for the MARBL tracer package." + datatype: string + value: + '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2"': fesedfluxRed_2024algo_tx2_3v2.c250220.nc MARBL_FEVENTFLUX_FILE: description: | "Name of file containing iron sediment flux diff --git a/param_templates/json/MOM_input.json b/param_templates/json/MOM_input.json index 773930c0..858151f0 100644 --- a/param_templates/json/MOM_input.json +++ b/param_templates/json/MOM_input.json @@ -232,14 +232,21 @@ "datatype": "string", "value": { "$MARBL_CONFIG == \"latest\"": "ecosys_jan_IC_omip_latlon_1x1_180W_c230331.nc", - "$MARBL_CONFIG == \"latest+4p2z\"": "ecosys_jan_IC_omip_latlon_1x1_180W_c231221.nc" + "$MARBL_CONFIG == \"latest+4p2z\"": "ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc" } }, "MARBL_FESEDFLUX_FILE": { "description": "\"Name of file containing iron sediment flux\n forcing field for the MARBL tracer package.\"\n", "datatype": "string", "value": { - "\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\"": "fesedflux_total_reduce_oxic_tx2_3v2.c231205.nc" + "\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\"": "fesedflux_2024algo_tx2_3v2.c250220.nc" + } + }, + "MARBL_FESEDFLUXRED_FILE": { + "description": "\"Name of file containing iron reducing sediment flux\n forcing field for the MARBL tracer package.\"\n", + "datatype": "string", + "value": { + "\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\"": "fesedfluxRed_2024algo_tx2_3v2.c250220.nc" } }, "MARBL_FEVENTFLUX_FILE": { From 361f5d40ae1a82eb1887f9aaf0cad97ad1f11104 Mon Sep 17 00:00:00 2001 From: Michael Levy Date: Fri, 21 Feb 2025 08:46:59 -0700 Subject: [PATCH 2/5] Update input_data_list --- param_templates/input_data_list.yaml | 9 ++++++--- param_templates/json/input_data_list.json | 11 ++++++++--- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/param_templates/input_data_list.yaml b/param_templates/input_data_list.yaml index a855a75c..d5b5daaf 100644 --- a/param_templates/input_data_list.yaml +++ b/param_templates/input_data_list.yaml @@ -49,11 +49,14 @@ mom.input_data_list: DIAG_COORD_DEF_RHO2: $OCN_GRID == "tx2_3v2": "${INPUTDIR}/ocean_rho2_190917.nc" MARBL_TRACERS_IC_FILE: - $MARBL_CONFIG == "latest": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c230331.nc" - $MARBL_CONFIG == "latest+4p2z": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c231221.nc" + $MARBL_CONFIG == "latest": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc" + $MARBL_CONFIG == "latest+4p2z": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc" MARBL_FESEDFLUX_FILE: '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS': - $OCN_GRID == "tx2_3v2": "${INPUTDIR}/fesedflux_total_reduce_oxic_tx2_3v2.c231205.nc" + $OCN_GRID == "tx2_3v2": "${INPUTDIR}/fesedflux_total_reduce_oxic_tx2_3v2.c250220.nc" + MARBL_FESEDFLUXRED_FILE: + '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS': + $OCN_GRID == "tx2_3v2": "${INPUTDIR}/fesedfluxRed_total_reduce_oxic_tx2_3v2.c250220.nc" MARBL_FEVENTFLUX_FILE: '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS': $OCN_GRID == "tx2_3v2": "${INPUTDIR}/feventflux_5gmol_tx2_3v2.c231205.nc" diff --git a/param_templates/json/input_data_list.json b/param_templates/json/input_data_list.json index a11d65d7..0b4d024e 100644 --- a/param_templates/json/input_data_list.json +++ b/param_templates/json/input_data_list.json @@ -63,12 +63,17 @@ "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/ocean_rho2_190917.nc" }, "MARBL_TRACERS_IC_FILE": { - "$MARBL_CONFIG == \"latest\"": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c230331.nc", - "$MARBL_CONFIG == \"latest+4p2z\"": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c231221.nc" + "$MARBL_CONFIG == \"latest\"": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc", + "$MARBL_CONFIG == \"latest+4p2z\"": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc" }, "MARBL_FESEDFLUX_FILE": { "\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS": { - "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/fesedflux_total_reduce_oxic_tx2_3v2.c231205.nc" + "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/fesedflux_total_reduce_oxic_tx2_3v2.c250220.nc" + } + }, + "MARBL_FESEDFLUXRED_FILE": { + "\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS": { + "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/fesedfluxRed_total_reduce_oxic_tx2_3v2.c250220.nc" } }, "MARBL_FEVENTFLUX_FILE": { From 80b70a2711f01913690a7cddb8641f3936b4bf0d Mon Sep 17 00:00:00 2001 From: Michael Levy Date: Fri, 21 Feb 2025 08:50:16 -0700 Subject: [PATCH 3/5] More updates to input_data_list Also updated the ecosys IC file for 3p1z (since that could potentially be run with variable N:C) --- param_templates/MOM_input.yaml | 2 +- param_templates/input_data_list.yaml | 4 ++-- param_templates/json/MOM_input.json | 2 +- param_templates/json/input_data_list.json | 4 ++-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/param_templates/MOM_input.yaml b/param_templates/MOM_input.yaml index 58874e72..795dca2e 100644 --- a/param_templates/MOM_input.yaml +++ b/param_templates/MOM_input.yaml @@ -330,7 +330,7 @@ Global: for the MARBL tracer package." datatype: string value: - $MARBL_CONFIG == "latest": ecosys_jan_IC_omip_latlon_1x1_180W_c230331.nc + $MARBL_CONFIG == "latest": ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc $MARBL_CONFIG == "latest+4p2z": ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc MARBL_FESEDFLUX_FILE: description: | diff --git a/param_templates/input_data_list.yaml b/param_templates/input_data_list.yaml index d5b5daaf..d3cc10b5 100644 --- a/param_templates/input_data_list.yaml +++ b/param_templates/input_data_list.yaml @@ -53,10 +53,10 @@ mom.input_data_list: $MARBL_CONFIG == "latest+4p2z": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc" MARBL_FESEDFLUX_FILE: '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS': - $OCN_GRID == "tx2_3v2": "${INPUTDIR}/fesedflux_total_reduce_oxic_tx2_3v2.c250220.nc" + $OCN_GRID == "tx2_3v2": "${INPUTDIR}/fesedflux_2024algo_tx2_3v2.c250220.nc" MARBL_FESEDFLUXRED_FILE: '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS': - $OCN_GRID == "tx2_3v2": "${INPUTDIR}/fesedfluxRed_total_reduce_oxic_tx2_3v2.c250220.nc" + $OCN_GRID == "tx2_3v2": "${INPUTDIR}/fesedfluxRed_2024algo_tx2_3v2.c250220.nc" MARBL_FEVENTFLUX_FILE: '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS': $OCN_GRID == "tx2_3v2": "${INPUTDIR}/feventflux_5gmol_tx2_3v2.c231205.nc" diff --git a/param_templates/json/MOM_input.json b/param_templates/json/MOM_input.json index 5637ab25..ef8e7d9b 100644 --- a/param_templates/json/MOM_input.json +++ b/param_templates/json/MOM_input.json @@ -234,7 +234,7 @@ "description": "\"Name of file containing initial conditions\nfor the MARBL tracer package.\"\n", "datatype": "string", "value": { - "$MARBL_CONFIG == \"latest\"": "ecosys_jan_IC_omip_latlon_1x1_180W_c230331.nc", + "$MARBL_CONFIG == \"latest\"": "ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc", "$MARBL_CONFIG == \"latest+4p2z\"": "ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc" } }, diff --git a/param_templates/json/input_data_list.json b/param_templates/json/input_data_list.json index 0b4d024e..1979f0a5 100644 --- a/param_templates/json/input_data_list.json +++ b/param_templates/json/input_data_list.json @@ -68,12 +68,12 @@ }, "MARBL_FESEDFLUX_FILE": { "\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS": { - "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/fesedflux_total_reduce_oxic_tx2_3v2.c250220.nc" + "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/fesedflux_2024algo_tx2_3v2.c250220.nc" } }, "MARBL_FESEDFLUXRED_FILE": { "\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS": { - "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/fesedfluxRed_total_reduce_oxic_tx2_3v2.c250220.nc" + "$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/fesedfluxRed_2024algo_tx2_3v2.c250220.nc" } }, "MARBL_FEVENTFLUX_FILE": { From 06bbe7bb3675ad9ef8d36acf1e8b99dc9613874d Mon Sep 17 00:00:00 2001 From: Michael Levy Date: Mon, 16 Jun 2025 15:09:53 -0600 Subject: [PATCH 4/5] Add DEPTH_EDGES to fesedflux The DEPTH variable needs the edges attribute, and these changes were also needed for the fesedfluxRed file --- param_templates/MOM_input.yaml | 4 ++-- param_templates/json/MOM_input.json | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/param_templates/MOM_input.yaml b/param_templates/MOM_input.yaml index bcb9b628..3a412aef 100644 --- a/param_templates/MOM_input.yaml +++ b/param_templates/MOM_input.yaml @@ -338,14 +338,14 @@ Global: forcing field for the MARBL tracer package." datatype: string value: - '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2"': fesedflux_2024algo_tx2_3v2.c250220.nc + '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2"': fesedflux_2024algo_tx2_3v2.c250616.nc MARBL_FESEDFLUXRED_FILE: description: | "Name of file containing iron reducing sediment flux forcing field for the MARBL tracer package." datatype: string value: - '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2"': fesedfluxRed_2024algo_tx2_3v2.c250220.nc + '"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2"': fesedfluxRed_2024algo_tx2_3v2.c250616.nc MARBL_FEVENTFLUX_FILE: description: | "Name of file containing iron sediment flux diff --git a/param_templates/json/MOM_input.json b/param_templates/json/MOM_input.json index 5af64ad6..4cce3bcc 100644 --- a/param_templates/json/MOM_input.json +++ b/param_templates/json/MOM_input.json @@ -242,14 +242,14 @@ "description": "\"Name of file containing iron sediment flux\n forcing field for the MARBL tracer package.\"\n", "datatype": "string", "value": { - "\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\"": "fesedflux_2024algo_tx2_3v2.c250220.nc" + "\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\"": "fesedflux_2024algo_tx2_3v2.c250616.nc" } }, "MARBL_FESEDFLUXRED_FILE": { "description": "\"Name of file containing iron reducing sediment flux\n forcing field for the MARBL tracer package.\"\n", "datatype": "string", "value": { - "\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\"": "fesedfluxRed_2024algo_tx2_3v2.c250220.nc" + "\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\"": "fesedfluxRed_2024algo_tx2_3v2.c250616.nc" } }, "MARBL_FEVENTFLUX_FILE": { From 2fc3694b5f0c2067c6769b88e48f98213f9eb69e Mon Sep 17 00:00:00 2001 From: Michael Levy Date: Fri, 27 Jun 2025 10:14:20 -0600 Subject: [PATCH 5/5] Update IC files Enforce autotroph consistency (if any of an autotroph's tracers are zero, they all should be zero) to cocco tracers; also include the new nitrogen tracer in the consistency check. --- param_templates/MOM_input.yaml | 4 ++-- param_templates/json/MOM_input.json | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/param_templates/MOM_input.yaml b/param_templates/MOM_input.yaml index 3a412aef..7929bc58 100644 --- a/param_templates/MOM_input.yaml +++ b/param_templates/MOM_input.yaml @@ -330,8 +330,8 @@ Global: for the MARBL tracer package." datatype: string value: - $MARBL_CONFIG == "latest": ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc - $MARBL_CONFIG == "latest+4p2z": ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc + $MARBL_CONFIG == "latest": ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc + $MARBL_CONFIG == "latest+4p2z": ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc MARBL_FESEDFLUX_FILE: description: | "Name of file containing iron sediment flux diff --git a/param_templates/json/MOM_input.json b/param_templates/json/MOM_input.json index 4cce3bcc..0de879d3 100644 --- a/param_templates/json/MOM_input.json +++ b/param_templates/json/MOM_input.json @@ -234,8 +234,8 @@ "description": "\"Name of file containing initial conditions\nfor the MARBL tracer package.\"\n", "datatype": "string", "value": { - "$MARBL_CONFIG == \"latest\"": "ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc", - "$MARBL_CONFIG == \"latest+4p2z\"": "ecosys_jan_IC_omip_latlon_1x1_180W_c250116.nc" + "$MARBL_CONFIG == \"latest\"": "ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc", + "$MARBL_CONFIG == \"latest+4p2z\"": "ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc" } }, "MARBL_FESEDFLUX_FILE": {