From 6cbfd8933aa09fcf49e506eaf8f43ece622ce9e7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 6 May 2026 15:49:14 -0600 Subject: [PATCH 01/22] Update first paragraph of bgc spinup section --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 8376c280b1..add5c1ad99 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -6,9 +6,9 @@ Spinup of |version|-BGC-Crop ============================= -To get the |version|-BGC model to a steady state, you first run it from arbitrary initial conditions using the "accelerated decomposition spinup" (``-bgc_spinup on`` in CLM ``configure``, see example below) mode for about 200 simulation years. :numref:`Figure BGC AD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using GSWP3 atmospheric forcing. Generally, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. +To get the |version|-BGC model to a steady state, you start it from arbitrary initial conditions using the "accelerated decomposition spinup" (``CLM_ACCELERATED_SPINUP on`` in CLM ``env_run.xml``, see example below) mode for about 360 simulation years. :numref:`Figure BGC AD spinup plot for 1850` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using CRUJRA atmospheric forcing. Generally, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. -.. _Figure BGC AD spinup plot for 1850 GSWP3: +.. _Figure BGC AD spinup plot for 1850: .. figure:: image3.png From 1859920f3a0a4a76048aad01b203f6983b6351a0 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 6 May 2026 16:41:59 -0600 Subject: [PATCH 02/22] Plans for updating Figure 1.5.3 in the form of comments --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 7 ++++--- doc/source/users_guide/running-special-cases/image3.png | 3 --- 2 files changed, 4 insertions(+), 6 deletions(-) delete mode 100644 doc/source/users_guide/running-special-cases/image3.png diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index add5c1ad99..d800415655 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -8,11 +8,12 @@ To get the |version|-BGC model to a steady state, you start it from arbitrary initial conditions using the "accelerated decomposition spinup" (``CLM_ACCELERATED_SPINUP on`` in CLM ``env_run.xml``, see example below) mode for about 360 simulation years. :numref:`Figure BGC AD spinup plot for 1850` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using CRUJRA atmospheric forcing. Generally, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. -.. _Figure BGC AD spinup plot for 1850: +.. Pick a simulation and create the new figure for the next 3 lines, which I have temporarily commented out: +.. .. _Figure BGC AD spinup plot for 1850: -.. figure:: image3.png +.. .. figure:: AD_spinup.png - BGC AD spinup plot for a year 1850 case with GSWP3 atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl. + BGC AD spinup plot for a year 1850 case with CRUJRA atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. After this you branch from this mode in the "final spinup" (``-bgc_spinup off`` in CLM ``configure``, see example below), and run for several hundred simulation years. :numref:`Figure BGC pAD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC post accelerated decomposition (pAD) case using GSWP3 atmospheric forcing. As before, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. It can be difficult to meet this strict criteria in less than 1000 years and users may want to relax this criteria depending on their application. diff --git a/doc/source/users_guide/running-special-cases/image3.png b/doc/source/users_guide/running-special-cases/image3.png deleted file mode 100644 index 0c11688829..0000000000 --- a/doc/source/users_guide/running-special-cases/image3.png +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:347a4e32e072c6b5d9f87ae7fd36ee3621c8436910691b18f63d9365f853d8de -size 280086 From 98c439670b63bd1c62a080a3d906b61ff5d9c2e8 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 6 May 2026 17:04:58 -0600 Subject: [PATCH 03/22] Include the SASU step and figure placeholder --- ...Spinning-up-the-biogeochemistry-BGC-spinup.rst | 15 ++++++++------- .../users_guide/running-special-cases/image4.png | 3 --- 2 files changed, 8 insertions(+), 10 deletions(-) delete mode 100644 doc/source/users_guide/running-special-cases/image4.png diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index d800415655..8ce74e2041 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -6,22 +6,23 @@ Spinup of |version|-BGC-Crop ============================= -To get the |version|-BGC model to a steady state, you start it from arbitrary initial conditions using the "accelerated decomposition spinup" (``CLM_ACCELERATED_SPINUP on`` in CLM ``env_run.xml``, see example below) mode for about 360 simulation years. :numref:`Figure BGC AD spinup plot for 1850` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using CRUJRA atmospheric forcing. Generally, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. +To get the |version|-BGC model to a steady state, you start it from arbitrary initial conditions using the "accelerated decomposition spinup" (``CLM_ACCELERATED_SPINUP on`` in CLM ``env_run.xml``, see example below) mode for 300-400 simulation years. :numref:`Figure BGC AD spinup plot for 1850` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using CRUJRA atmospheric forcing. Generally, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. -.. Pick a simulation and create the new figure for the next 3 lines, which I have temporarily commented out: -.. .. _Figure BGC AD spinup plot for 1850: +.. _Figure BGC AD spinup plot for 1850: +.. Pick a simulation and create the new figure for the next 2 lines, which I have temporarily commented out: .. .. figure:: AD_spinup.png BGC AD spinup plot for a year 1850 case with CRUJRA atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. -After this you branch from this mode in the "final spinup" (``-bgc_spinup off`` in CLM ``configure``, see example below), and run for several hundred simulation years. :numref:`Figure BGC pAD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC post accelerated decomposition (pAD) case using GSWP3 atmospheric forcing. As before, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. It can be difficult to meet this strict criteria in less than 1000 years and users may want to relax this criteria depending on their application. +After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM ``env_run.xml``, see example below), and run for 300-350 simulation years. :numref:`Figure BGC SASU spinup plot for 1850` shows spinup behavior for an 1850 BGC SASU case using CRUJRA atmospheric forcing. The criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy and need not be met for this step. -.. _Figure BGC pAD spinup plot for 1850 GSWP3: +.. _Figure BGC SASU spinup plot for 1850: -.. figure:: image4.png +.. Pick a simulation and create the new figure for the next 2 lines, which I have temporarily commented out: +.. .. figure:: SASU_spinup.png - BGC pAD spinup plot for a year 1850 case with GSWP3 atmospheric forcing and initialization from the end of the BGC AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl. + BGC SASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. You can also start from a default initial file that is setup as part of the selected compset. :numref:`Figure BGC initialized spinup plot for 1850` shows spinup behavior for an 1850 pAD BGC case that loops over one year of coupler history output for atmospheric forcing (generated from the fully coupled model), initialized with a BGC initial file generated from a GSWP3 atmospheric forcing case. Note that it takes about 10 years for variables such as TLAI (total leaf area index), GPP (gross primary production), and TWS (total water storage) to reach a specified equilibrium state (denoted by the dotted lines) due to the different atmospheric forcing. diff --git a/doc/source/users_guide/running-special-cases/image4.png b/doc/source/users_guide/running-special-cases/image4.png deleted file mode 100644 index 09456b93af..0000000000 --- a/doc/source/users_guide/running-special-cases/image4.png +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:4587fe62aa8c34906e56d13c99749b69d2600f4c770c50781d81faf2480b8842 -size 287344 From d43537d5650bdfb2846690491bd846b5e45c4fd6 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 6 May 2026 17:23:48 -0600 Subject: [PATCH 04/22] Temporary fix to the figure failures; still need new figures though --- .../running-special-cases/AD_spinup_placeholder.png | 3 +++ .../running-special-cases/SASU_spinup_placeholder.png | 3 +++ .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 6 ++---- 3 files changed, 8 insertions(+), 4 deletions(-) create mode 100644 doc/source/users_guide/running-special-cases/AD_spinup_placeholder.png create mode 100644 doc/source/users_guide/running-special-cases/SASU_spinup_placeholder.png diff --git a/doc/source/users_guide/running-special-cases/AD_spinup_placeholder.png b/doc/source/users_guide/running-special-cases/AD_spinup_placeholder.png new file mode 100644 index 0000000000..f0d073565f --- /dev/null +++ b/doc/source/users_guide/running-special-cases/AD_spinup_placeholder.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:991c6fa7d321f0a0e50f38c82f951eb978ba3ae62efe184bc941fcacaf4352c5 +size 316593 diff --git a/doc/source/users_guide/running-special-cases/SASU_spinup_placeholder.png b/doc/source/users_guide/running-special-cases/SASU_spinup_placeholder.png new file mode 100644 index 0000000000..f0d073565f --- /dev/null +++ b/doc/source/users_guide/running-special-cases/SASU_spinup_placeholder.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:991c6fa7d321f0a0e50f38c82f951eb978ba3ae62efe184bc941fcacaf4352c5 +size 316593 diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 8ce74e2041..2d4c9bac33 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -10,8 +10,7 @@ To get the |version|-BGC model to a steady state, you start it from arbitrary in .. _Figure BGC AD spinup plot for 1850: -.. Pick a simulation and create the new figure for the next 2 lines, which I have temporarily commented out: -.. .. figure:: AD_spinup.png +.. figure:: AD_spinup_placeholder.png BGC AD spinup plot for a year 1850 case with CRUJRA atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. @@ -19,8 +18,7 @@ After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM ` .. _Figure BGC SASU spinup plot for 1850: -.. Pick a simulation and create the new figure for the next 2 lines, which I have temporarily commented out: -.. .. figure:: SASU_spinup.png +.. figure:: SASU_spinup_placeholder.png BGC SASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. From df9c7841226679fd793bb6eea676eae7a44b48af Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 6 May 2026 17:43:34 -0600 Subject: [PATCH 05/22] Add the new pSASU step and modify some existing relevant things --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 14 ++++++++------ ...image6.png => initialized_2000_placeholder.png} | 0 ...age5.png => initialized_spinup_placeholder.png} | 0 3 files changed, 8 insertions(+), 6 deletions(-) rename doc/source/users_guide/running-special-cases/{image6.png => initialized_2000_placeholder.png} (100%) rename doc/source/users_guide/running-special-cases/{image5.png => initialized_spinup_placeholder.png} (100%) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 2d4c9bac33..c4893d05d6 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -22,21 +22,23 @@ After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM ` BGC SASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. -You can also start from a default initial file that is setup as part of the selected compset. :numref:`Figure BGC initialized spinup plot for 1850` shows spinup behavior for an 1850 pAD BGC case that loops over one year of coupler history output for atmospheric forcing (generated from the fully coupled model), initialized with a BGC initial file generated from a GSWP3 atmospheric forcing case. Note that it takes about 10 years for variables such as TLAI (total leaf area index), GPP (gross primary production), and TWS (total water storage) to reach a specified equilibrium state (denoted by the dotted lines) due to the different atmospheric forcing. +After this you continue in standard mode for about 160 years. We refer to this as the post-SASU or pSASU phase (``CLM_ACCELERATED_SPINUP off`` in CLM ``env_run.xml``, see example below). :numref:`Figure BGC pSASU spinup plot for 1850` shows spinup behavior for an 1850 BGC pSASU case using CRUJRA atmospheric forcing. As before, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. + +As an alternative to spinning up, you may start from a default initial file that is setup as part of the selected compset. :numref:`Figure BGC initialized spinup plot for 1850` shows spinup behavior for an 1850 pSASU BGC case that loops over one year of coupler history output for atmospheric forcing (generated from the fully coupled model), initialized with a BGC initial file generated from a CRUJRA atmospheric forcing case. Note that it takes about 10 years for variables such as TLAI (total leaf area index), GPP (gross primary production), and TWS (total water storage) to reach a specified equilibrium state (denoted by the dotted lines) due to the different atmospheric forcing. .. _Figure BGC initialized spinup plot for 1850: -.. figure:: image5.png +.. figure:: initialized_spinup_placeholder.png - BGC initialized spinup plot for year 1850. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl. + BGC initialized spinup plot for year 1850. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. -:numref:`Figure BGC initialized spinup plot for 2000 CO2` shows spinup behavior for the same case but also changes CO2 to present-day conditions (379ppmv). Again, it takes about 10 years to reach equilibrium for TLAI, GPP, and TWS. +:numref:`Figure BGC initialized spinup plot for 2000 CO2` shows spinup behavior for the same case but also changes CO2 to present-day conditions (379 ppmv). Again, it takes about 10 years to reach equilibrium for TLAI, GPP, and TWS. .. _Figure BGC initialized spinup plot for 2000 CO2: -.. figure:: image6.png +.. figure:: initialized_2000_placeholder.png - BGC initialized spinup plot for year 2000 CO2. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl. + BGC initialized spinup plot for year 2000 CO2. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. If you use the default initial file and you signficantly change model behavior or atmospheric forcing, and you are concerned about the carbon equilibrium (e.g., TOTECOSYSC, TOTSOMC, TOTVEGC), particularly at high latitudes, then we recommend you put the model back into AD mode to reach a new equilibrium. In this configuration, this will also automatically reseed "dead" plant functional types in the initial file with a bit of leaf carbon to give those plant functional types another chance to grow under the new atmospheric forcing or model conditions. diff --git a/doc/source/users_guide/running-special-cases/image6.png b/doc/source/users_guide/running-special-cases/initialized_2000_placeholder.png similarity index 100% rename from doc/source/users_guide/running-special-cases/image6.png rename to doc/source/users_guide/running-special-cases/initialized_2000_placeholder.png diff --git a/doc/source/users_guide/running-special-cases/image5.png b/doc/source/users_guide/running-special-cases/initialized_spinup_placeholder.png similarity index 100% rename from doc/source/users_guide/running-special-cases/image5.png rename to doc/source/users_guide/running-special-cases/initialized_spinup_placeholder.png From b4d044fb54747522067c763250f44077760c0b59 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 6 May 2026 17:57:17 -0600 Subject: [PATCH 06/22] Add placeholder for pSASU figure --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 6 ++++++ .../running-special-cases/pSASU_spinup_placeholder.png | 3 +++ 2 files changed, 9 insertions(+) create mode 100644 doc/source/users_guide/running-special-cases/pSASU_spinup_placeholder.png diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index c4893d05d6..5230d6c3f3 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -24,6 +24,12 @@ After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM ` After this you continue in standard mode for about 160 years. We refer to this as the post-SASU or pSASU phase (``CLM_ACCELERATED_SPINUP off`` in CLM ``env_run.xml``, see example below). :numref:`Figure BGC pSASU spinup plot for 1850` shows spinup behavior for an 1850 BGC pSASU case using CRUJRA atmospheric forcing. As before, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. +.. _Figure BGC pSASU spinup plot for 1850: + +.. figure:: pSASU_spinup_placeholder.png + + BGC pSASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. + As an alternative to spinning up, you may start from a default initial file that is setup as part of the selected compset. :numref:`Figure BGC initialized spinup plot for 1850` shows spinup behavior for an 1850 pSASU BGC case that loops over one year of coupler history output for atmospheric forcing (generated from the fully coupled model), initialized with a BGC initial file generated from a CRUJRA atmospheric forcing case. Note that it takes about 10 years for variables such as TLAI (total leaf area index), GPP (gross primary production), and TWS (total water storage) to reach a specified equilibrium state (denoted by the dotted lines) due to the different atmospheric forcing. .. _Figure BGC initialized spinup plot for 1850: diff --git a/doc/source/users_guide/running-special-cases/pSASU_spinup_placeholder.png b/doc/source/users_guide/running-special-cases/pSASU_spinup_placeholder.png new file mode 100644 index 0000000000..f0d073565f --- /dev/null +++ b/doc/source/users_guide/running-special-cases/pSASU_spinup_placeholder.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:991c6fa7d321f0a0e50f38c82f951eb978ba3ae62efe184bc941fcacaf4352c5 +size 316593 From 0098111102417a054046140c488cd3c0271cfc85 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 12 May 2026 17:38:54 -0600 Subject: [PATCH 07/22] Updates to the bgc spinup section of the User's Guide --- ...ning-up-the-biogeochemistry-BGC-spinup.rst | 99 +++++++++---------- 1 file changed, 48 insertions(+), 51 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 5230d6c3f3..bfe998ecd6 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -28,84 +28,81 @@ After this you continue in standard mode for about 160 years. We refer to this a .. figure:: pSASU_spinup_placeholder.png - BGC pSASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. + BGC pSASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC SASU spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. -As an alternative to spinning up, you may start from a default initial file that is setup as part of the selected compset. :numref:`Figure BGC initialized spinup plot for 1850` shows spinup behavior for an 1850 pSASU BGC case that loops over one year of coupler history output for atmospheric forcing (generated from the fully coupled model), initialized with a BGC initial file generated from a CRUJRA atmospheric forcing case. Note that it takes about 10 years for variables such as TLAI (total leaf area index), GPP (gross primary production), and TWS (total water storage) to reach a specified equilibrium state (denoted by the dotted lines) due to the different atmospheric forcing. +As an alternative to spinning up, one may start from a default initial file that is setup as part of the selected compset. When the simulation's spatial resolution is identical to the initial file's resolution, it may still take 10 or more years for variables such as TLAI (total leaf area index), GPP (gross primary production), and TWS (total water storage) to reach a new equilibrium state due to the different atmospheric forcing. Similarly, it may take 10 or more years for these variables to reach a new equilibrium when switching atmospheric CO2 from 1850 to a present-day value. -.. _Figure BGC initialized spinup plot for 1850: - -.. figure:: initialized_spinup_placeholder.png - - BGC initialized spinup plot for year 1850. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. - -:numref:`Figure BGC initialized spinup plot for 2000 CO2` shows spinup behavior for the same case but also changes CO2 to present-day conditions (379 ppmv). Again, it takes about 10 years to reach equilibrium for TLAI, GPP, and TWS. - -.. _Figure BGC initialized spinup plot for 2000 CO2: - -.. figure:: initialized_2000_placeholder.png - - BGC initialized spinup plot for year 2000 CO2. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. - -If you use the default initial file and you signficantly change model behavior or atmospheric forcing, and you are concerned about the carbon equilibrium (e.g., TOTECOSYSC, TOTSOMC, TOTVEGC), particularly at high latitudes, then we recommend you put the model back into AD mode to reach a new equilibrium. In this configuration, this will also automatically reseed "dead" plant functional types in the initial file with a bit of leaf carbon to give those plant functional types another chance to grow under the new atmospheric forcing or model conditions. - -**1. |version| accelerated-decomposition (AD) spinup** - For the first step of running 200+ years in ``-bgc_spinup on`` mode, you will setup a case, and then edit the values in env_build.xml and env_run.xml so that the right configuration is turned on and the simulation is setup to run for the required length of simulation time. So do the following: - -Example: AD_SPINUP Simulation for |version|-BGC +Example: AD_spinup Simulation for |version|-BGC -------------------------------------------------------- +For the first step of running in ``CLM_ACCELERATED_SPINUP on`` mode, you will setup a case, and then edit the values in env_build.xml and env_run.xml so that the right configuration is turned on and the simulation is setup to run for the required length of simulation time. Try the following: + :: > cd cime/scripts - > ./create_newcase -case BGC_spinup -res f19_g17_gl4 -compset I1850Clm50BgcCropCru - > cd BGC_spinup + > ./create_newcase -case AD_spinup -res f19_g17 -compset I1850Clm60BgcCrop + > cd AD_spinup # Change accelerated spinup mode > ./xmlchange CLM_ACCELERATED_SPINUP="on" # Now setup - > ./case.setup -case + > ./case.setup # Now build > ./case.build - # The following sets RESUBMIT to 3 times in env_run.xml (you could also use an editor) - # The following sets STOP_DATE,STOP_N and STOP_OPTION to Jan/1/0201, 20, "nyears" in env_run.xml (you could also use an editor) - > ./xmlchange RESUBMIT=3,STOP_N=50,STOP_OPTION=nyears,STOP_DATE=02010101 + # The following sets RESUBMIT to 7 times and + # STOP_DATE, STOP_N, and STOP_OPTION to Jan/1/0401, 50, "nyears" in env_run.xml (you could also modify these with an editor) + > ./xmlchange RESUBMIT=7,STOP_N=50,STOP_OPTION=nyears,STOP_DATE=04010101 # Now run normally > ./case.submit -.. note:: This same procedure works for |version|-CN as well. - -Afterwards save the last restart file from this simulation to use in the next step. - -**2. Final spinup for |version|-BGC** - Next save the last restart file from this step and use it as the ``finidat`` file to use for one more spinup for at least 400+ years in normal mode. So do the following: +Save the last restart file from this simulation to use in the next step. -.. _eg-final-clmbgc-spinup: +.. _eg-sasu-spinup: -Example: Final CLMBGC Spinup Simulation for |version|-BGC +Example: SASU_spinup Simulation for |version|-BGC ------------------------------------------------------------------ :: > cd cime/scripts - > ./create_newcase -case BGC_finalspinup -res f19_g17_gl4 -compset I1850Clm50BgcCropCru - > cd BGC_finalspinup - # Now, Copy the last CLM restart file from the earlier case into your run directory - > cp /ptmp/$LOGIN/archive/BGC_spinup/rest/BGC_spinup.clm*.r*.0201-01-01-00000.nc \ - /glade/scratch/$LOGIN/CN_finalspinup/run - # Set the runtype to startup + > ./create_newcase -case SASU_spinup -res f19_g17 -compset I1850Clm60BgcCrop + > cd SASU_spinup + # Copy the last restart files from the AD_spinup case into your run directory + > cp /scratch/archive/AD_spinup/rest/0401-01-01-00000/* /scratch/SASU_spinup/run + # Runtype should already be startup, but this will ensure it > ./xmlchange RUN_TYPE=startup - # And copy the rpointer files for datm and drv from the earlier case - > cp /glade/scratch/$LOGIN/archive/BGC_spinup/rest/rpointer.atm /glade/scratch/$LOGIN/CN_finalspinup/run - # Set the finidat file to the last restart file saved in previous step - > echo ' finidat = "BGC_spinup.clm2.r.0201-01-01-00000.nc"' > user_nl_clm + # Set finidat to the restart file copied in the previous step + > echo ' finidat = "AD_spinup.clm2.r.0401-01-01-00000.nc"' > user_nl_clm # Now setup > ./case.setup > Now build > ./case.build - # The following sets RESUBMIT to 7 times in env_run.xml (you could also use an editor) - # The following sets STOP_N and STOP_OPTION to 50 and "nyears" in env_run.xml (you could also use an editor) - > ./xmlchange RESUBMIT=7,STOP_OPTION=nyears,STOP_N=50 + # The following sets RESUBMIT to 6 times and + # STOP_N to 50 and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) + > ./xmlchange RESUBMIT=6,STOP_OPTION=nyears,STOP_N=50 > Now run as normal > ./case.submit -To assess if the model is spunup, plot trends for CLMBGC variables of interest using .../tools/contrib/SpinupStability.ncl. If you don't meet the equilibrium criteria, you may need to run the simulation longer. Finally save the restart file from the end of this simulation to use as an "finidat" file for future simulations. +Save the last restart file from this step and use it as the ``finidat`` file for the pSASU step. Save the restart file from the end of the pSASU simulation to use as a "finidat" file for future simulations. -.. note:: This same final spinup procedure works for |version|-CN as well. + +Example: pSASU_spinup Simulation for |version|-BGC +------------------------------------------------------------------ +:: + + > cd cime/scripts + > ./create_newcase -case pSASU_spinup -res f19_g17 -compset I1850Clm60BgcCrop + > cd pSASU_spinup + # Copy the last restart files from the SASU_spinup case into your run directory + > cp /scratch/archive/SASU_spinup/rest/0351-01-01-00000/* /scratch/pSASU_spinup/run + # Runtype should already be startup, but this will ensure it + > ./xmlchange RUN_TYPE=startup + # Set finidat to the restart file copied in the previous step + > echo ' finidat = "SASU_spinup.clm2.r.0351-01-01-00000.nc"' > user_nl_clm + # Now setup + > ./case.setup + > Now build + > ./case.build + # The following sets RESUBMIT to 3 times and + # STOP_N to 50 and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) + > ./xmlchange RESUBMIT=3,STOP_OPTION=nyears,STOP_N=50 + > Now run as normal + > ./case.submit From 6c7eaafb4d0e1c123ea15588787d43b9d632296f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 13 May 2026 16:29:32 -0600 Subject: [PATCH 08/22] Add subsection on the SpinupStability.ncl scripts --- ...pinning-up-the-biogeochemistry-BGC-spinup.rst | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index bfe998ecd6..46a2934f7d 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -53,7 +53,19 @@ For the first step of running in ``CLM_ACCELERATED_SPINUP on`` mode, you will se # Now run normally > ./case.submit -Save the last restart file from this simulation to use in the next step. +While this simulation progresses, use SpinupStability_BGC_v11.ncl to assess whether the simulation is approaching equilibrium. When the simulation ends, save the last restart file for use in the SASU_spinup step. + +Using the SpinupStability.ncl scripts +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +In CLM's /tools/contrib directory there are three versions of this .ncl script: +- SpinupStability_BGC_v11.ncl for Bgc and BgcCrop compsets run on 2D lat/lon grids. +- SpinupStability_BGC_v12_SE.ncl for Bgc, BgcCrop, or Fates compsets run on certain spectral element grids (currently ne120, ne30, ne16). +- SpinupStability_SP_v10.ncl for Sp compsets run on 2D lat/lon grids. + +To run one of these scripts on derecho, one loads ncl (module load ncl) and submits with `ncl SpinupStability_BGC_v11`, for example. Before running one needs to confirm a few easy settings appearing near the top of each script. + +One of the settings that may not be intuitive at first glance is `annual_hist`. By default the phases AD_spinup and SASU_spinup generate annual history, so set this to "True", while pSASU generates monthly history, so set this to "False". .. _eg-sasu-spinup: @@ -84,7 +96,7 @@ Save the last restart file from this step and use it as the ``finidat`` file for Example: pSASU_spinup Simulation for |version|-BGC ------------------------------------------------------------------- +-------------------------------------------------- :: > cd cime/scripts From 214f3c665a763df2b82938d93fbe1e3e8f017554 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 13 May 2026 16:54:24 -0600 Subject: [PATCH 09/22] Replace placeholder figures with the new figures --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 46a2934f7d..1ed28806f5 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -10,7 +10,7 @@ To get the |version|-BGC model to a steady state, you start it from arbitrary in .. _Figure BGC AD spinup plot for 1850: -.. figure:: AD_spinup_placeholder.png +.. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_AD_Spinup-0.jpg BGC AD spinup plot for a year 1850 case with CRUJRA atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. @@ -18,7 +18,7 @@ After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM ` .. _Figure BGC SASU spinup plot for 1850: -.. figure:: SASU_spinup_placeholder.png +.. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_SASU_Spinup-0.jpg BGC SASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. @@ -26,7 +26,7 @@ After this you continue in standard mode for about 160 years. We refer to this a .. _Figure BGC pSASU spinup plot for 1850: -.. figure:: pSASU_spinup_placeholder.png +.. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_pSASU_Spinup-0.jpg BGC pSASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC SASU spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. @@ -59,6 +59,7 @@ Using the SpinupStability.ncl scripts ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ In CLM's /tools/contrib directory there are three versions of this .ncl script: + - SpinupStability_BGC_v11.ncl for Bgc and BgcCrop compsets run on 2D lat/lon grids. - SpinupStability_BGC_v12_SE.ncl for Bgc, BgcCrop, or Fates compsets run on certain spectral element grids (currently ne120, ne30, ne16). - SpinupStability_SP_v10.ncl for Sp compsets run on 2D lat/lon grids. From 89fcb467a1461c83b97ad225c2f23f66044727a5 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 13 May 2026 17:16:44 -0600 Subject: [PATCH 10/22] Remove old .png files and add new .png files --- .../running-special-cases/AD_spinup_placeholder.png | 3 --- .../running-special-cases/SASU_spinup_placeholder.png | 3 --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 8 ++++---- ...ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_AD_Spinup-0.png | 3 +++ ...sm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_SASU_Spinup-0.png | 3 +++ ...m5.4.CMIP7_ciso_ctsm5.3.075_f09_124_pSASU_Spinup-0.png | 3 +++ .../initialized_2000_placeholder.png | 3 --- .../initialized_spinup_placeholder.png | 3 --- .../running-special-cases/pSASU_spinup_placeholder.png | 3 --- 9 files changed, 13 insertions(+), 19 deletions(-) delete mode 100644 doc/source/users_guide/running-special-cases/AD_spinup_placeholder.png delete mode 100644 doc/source/users_guide/running-special-cases/SASU_spinup_placeholder.png create mode 100644 doc/source/users_guide/running-special-cases/ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_AD_Spinup-0.png create mode 100644 doc/source/users_guide/running-special-cases/ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_SASU_Spinup-0.png create mode 100644 doc/source/users_guide/running-special-cases/ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_pSASU_Spinup-0.png delete mode 100644 doc/source/users_guide/running-special-cases/initialized_2000_placeholder.png delete mode 100644 doc/source/users_guide/running-special-cases/initialized_spinup_placeholder.png delete mode 100644 doc/source/users_guide/running-special-cases/pSASU_spinup_placeholder.png diff --git a/doc/source/users_guide/running-special-cases/AD_spinup_placeholder.png b/doc/source/users_guide/running-special-cases/AD_spinup_placeholder.png deleted file mode 100644 index f0d073565f..0000000000 --- a/doc/source/users_guide/running-special-cases/AD_spinup_placeholder.png +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:991c6fa7d321f0a0e50f38c82f951eb978ba3ae62efe184bc941fcacaf4352c5 -size 316593 diff --git a/doc/source/users_guide/running-special-cases/SASU_spinup_placeholder.png b/doc/source/users_guide/running-special-cases/SASU_spinup_placeholder.png deleted file mode 100644 index f0d073565f..0000000000 --- a/doc/source/users_guide/running-special-cases/SASU_spinup_placeholder.png +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:991c6fa7d321f0a0e50f38c82f951eb978ba3ae62efe184bc941fcacaf4352c5 -size 316593 diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 1ed28806f5..37d1513137 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -10,7 +10,7 @@ To get the |version|-BGC model to a steady state, you start it from arbitrary in .. _Figure BGC AD spinup plot for 1850: -.. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_AD_Spinup-0.jpg +.. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_AD_Spinup-0.png BGC AD spinup plot for a year 1850 case with CRUJRA atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. @@ -18,7 +18,7 @@ After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM ` .. _Figure BGC SASU spinup plot for 1850: -.. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_SASU_Spinup-0.jpg +.. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_SASU_Spinup-0.png BGC SASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. @@ -26,7 +26,7 @@ After this you continue in standard mode for about 160 years. We refer to this a .. _Figure BGC pSASU spinup plot for 1850: -.. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_pSASU_Spinup-0.jpg +.. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_pSASU_Spinup-0.png BGC pSASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC SASU spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. @@ -64,7 +64,7 @@ In CLM's /tools/contrib directory there are three versions of this .ncl script: - SpinupStability_BGC_v12_SE.ncl for Bgc, BgcCrop, or Fates compsets run on certain spectral element grids (currently ne120, ne30, ne16). - SpinupStability_SP_v10.ncl for Sp compsets run on 2D lat/lon grids. -To run one of these scripts on derecho, one loads ncl (module load ncl) and submits with `ncl SpinupStability_BGC_v11`, for example. Before running one needs to confirm a few easy settings appearing near the top of each script. +To run one of these scripts on derecho, one loads ncl (module load ncl) and submits with `ncl SpinupStability_BGC_v11.ncl`, for example. Before running one needs to confirm a few easy settings appearing near the top of each script. One of the settings that may not be intuitive at first glance is `annual_hist`. By default the phases AD_spinup and SASU_spinup generate annual history, so set this to "True", while pSASU generates monthly history, so set this to "False". diff --git a/doc/source/users_guide/running-special-cases/ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_AD_Spinup-0.png b/doc/source/users_guide/running-special-cases/ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_AD_Spinup-0.png new file mode 100644 index 0000000000..0db353da62 --- /dev/null +++ b/doc/source/users_guide/running-special-cases/ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_AD_Spinup-0.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5019303d5d02530c1ad6a58512ee956072e8c793774bceecbc84041c7d7fa95d +size 67505 diff --git a/doc/source/users_guide/running-special-cases/ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_SASU_Spinup-0.png b/doc/source/users_guide/running-special-cases/ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_SASU_Spinup-0.png new file mode 100644 index 0000000000..d7e5787054 --- /dev/null +++ b/doc/source/users_guide/running-special-cases/ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_SASU_Spinup-0.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5b12cbf832a022eb6390eb3c75b0fe97dd47b2704206d282e2c2c65b30420855 +size 72370 diff --git a/doc/source/users_guide/running-special-cases/ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_pSASU_Spinup-0.png b/doc/source/users_guide/running-special-cases/ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_pSASU_Spinup-0.png new file mode 100644 index 0000000000..f41afe0036 --- /dev/null +++ b/doc/source/users_guide/running-special-cases/ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_pSASU_Spinup-0.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5b1eae04e80108750a2f7770ba151f419196dd5ddb51dd9a11d9c3e5c8170c56 +size 62444 diff --git a/doc/source/users_guide/running-special-cases/initialized_2000_placeholder.png b/doc/source/users_guide/running-special-cases/initialized_2000_placeholder.png deleted file mode 100644 index 949acde48d..0000000000 --- a/doc/source/users_guide/running-special-cases/initialized_2000_placeholder.png +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:65a5121d47597ae3d508a8bda8989708c928e3f0b9e183009dfc4bcd661ad4b6 -size 311278 diff --git a/doc/source/users_guide/running-special-cases/initialized_spinup_placeholder.png b/doc/source/users_guide/running-special-cases/initialized_spinup_placeholder.png deleted file mode 100644 index f0d073565f..0000000000 --- a/doc/source/users_guide/running-special-cases/initialized_spinup_placeholder.png +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:991c6fa7d321f0a0e50f38c82f951eb978ba3ae62efe184bc941fcacaf4352c5 -size 316593 diff --git a/doc/source/users_guide/running-special-cases/pSASU_spinup_placeholder.png b/doc/source/users_guide/running-special-cases/pSASU_spinup_placeholder.png deleted file mode 100644 index f0d073565f..0000000000 --- a/doc/source/users_guide/running-special-cases/pSASU_spinup_placeholder.png +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:991c6fa7d321f0a0e50f38c82f951eb978ba3ae62efe184bc941fcacaf4352c5 -size 316593 From 2150db16280f16b590bcc5fe1d4194b3e79e5c55 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 13 May 2026 17:48:38 -0600 Subject: [PATCH 11/22] Refer to prev. section for useful info and update some quote marks --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 37d1513137..bf4fe5ed51 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -6,7 +6,7 @@ Spinup of |version|-BGC-Crop ============================= -To get the |version|-BGC model to a steady state, you start it from arbitrary initial conditions using the "accelerated decomposition spinup" (``CLM_ACCELERATED_SPINUP on`` in CLM ``env_run.xml``, see example below) mode for 300-400 simulation years. :numref:`Figure BGC AD spinup plot for 1850` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using CRUJRA atmospheric forcing. Generally, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. +To get the |version|-BGC model to a steady state, you start it from arbitrary initial conditions using the "accelerated decomposition spinup" (``CLM_ACCELERATED_SPINUP on`` in CLM `env_run.xml`, see example below) mode for 300-400 simulation years. :numref:`Figure BGC AD spinup plot for 1850` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using CRUJRA atmospheric forcing. Generally, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. .. _Figure BGC AD spinup plot for 1850: @@ -14,7 +14,7 @@ To get the |version|-BGC model to a steady state, you start it from arbitrary in BGC AD spinup plot for a year 1850 case with CRUJRA atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. -After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM ``env_run.xml``, see example below), and run for 300-350 simulation years. :numref:`Figure BGC SASU spinup plot for 1850` shows spinup behavior for an 1850 BGC SASU case using CRUJRA atmospheric forcing. The criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy and need not be met for this step. +After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM `env_run.xml`, see example below), and run for 300-350 simulation years. :numref:`Figure BGC SASU spinup plot for 1850` shows spinup behavior for an 1850 BGC SASU case using CRUJRA atmospheric forcing. The criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy and need not be met for this step. .. _Figure BGC SASU spinup plot for 1850: @@ -22,7 +22,7 @@ After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM ` BGC SASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. -After this you continue in standard mode for about 160 years. We refer to this as the post-SASU or pSASU phase (``CLM_ACCELERATED_SPINUP off`` in CLM ``env_run.xml``, see example below). :numref:`Figure BGC pSASU spinup plot for 1850` shows spinup behavior for an 1850 BGC pSASU case using CRUJRA atmospheric forcing. As before, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. +After this you continue in standard mode for about 160 years. We refer to this as the post-SASU or pSASU phase (``CLM_ACCELERATED_SPINUP off`` in CLM `env_run.xml`, see example below). :numref:`Figure BGC pSASU spinup plot for 1850` shows spinup behavior for an 1850 BGC pSASU case using CRUJRA atmospheric forcing. As before, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. .. _Figure BGC pSASU spinup plot for 1850: @@ -62,11 +62,11 @@ In CLM's /tools/contrib directory there are three versions of this .ncl script: - SpinupStability_BGC_v11.ncl for Bgc and BgcCrop compsets run on 2D lat/lon grids. - SpinupStability_BGC_v12_SE.ncl for Bgc, BgcCrop, or Fates compsets run on certain spectral element grids (currently ne120, ne30, ne16). -- SpinupStability_SP_v10.ncl for Sp compsets run on 2D lat/lon grids. +- SpinupStability_SP_v10.ncl for Sp compsets run on 2D lat/lon grids. See section :numref:`spinning-up-sp` for helpful pointers about this script that may also apply to the BGC versions. -To run one of these scripts on derecho, one loads ncl (module load ncl) and submits with `ncl SpinupStability_BGC_v11.ncl`, for example. Before running one needs to confirm a few easy settings appearing near the top of each script. +To run one of these scripts on derecho, one loads ncl (module load ncl) and submits with ``ncl SpinupStability_BGC_v11.ncl``, for example. Before running one needs to confirm a few easy settings appearing near the top of each script. -One of the settings that may not be intuitive at first glance is `annual_hist`. By default the phases AD_spinup and SASU_spinup generate annual history, so set this to "True", while pSASU generates monthly history, so set this to "False". +One of the settings that may not be intuitive at first glance is ``annual_hist``. By default the phases AD_spinup and SASU_spinup generate annual history, so set this to "True", while pSASU generates monthly history, so set this to "False". .. _eg-sasu-spinup: From 3ad82f4c073db36d447acf95027f3e6f43c0df0c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 14 May 2026 16:51:20 -0600 Subject: [PATCH 12/22] Remove the version number and change BGC to BGC-Crop throughout --- ...ning-up-the-biogeochemistry-BGC-spinup.rst | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index bf4fe5ed51..e5153bf0d3 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -3,36 +3,36 @@ .. _spinning-up-clm-bgc: ============================= - Spinup of |version|-BGC-Crop + Spinup of CLM-BGC-Crop ============================= -To get the |version|-BGC model to a steady state, you start it from arbitrary initial conditions using the "accelerated decomposition spinup" (``CLM_ACCELERATED_SPINUP on`` in CLM `env_run.xml`, see example below) mode for 300-400 simulation years. :numref:`Figure BGC AD spinup plot for 1850` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using CRUJRA atmospheric forcing. Generally, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. +To get the CLM-BGC-Crop model to a steady state, you start it from arbitrary initial conditions using the "accelerated decomposition spinup" (``CLM_ACCELERATED_SPINUP on`` in CLM `env_run.xml`, see example below) mode for 300-400 simulation years. :numref:`Figure BGC-Crop AD spinup plot for 1850` shows spinup behavior for an 1850 BGC-Crop accelerated decomposition (AD) case using CRUJRA atmospheric forcing. Generally, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. -.. _Figure BGC AD spinup plot for 1850: +.. _Figure BGC-Crop AD spinup plot for 1850: .. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_AD_Spinup-0.png - BGC AD spinup plot for a year 1850 case with CRUJRA atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. + BGC-Crop AD spinup plot for a year 1850 case with CRUJRA atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. -After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM `env_run.xml`, see example below), and run for 300-350 simulation years. :numref:`Figure BGC SASU spinup plot for 1850` shows spinup behavior for an 1850 BGC SASU case using CRUJRA atmospheric forcing. The criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy and need not be met for this step. +After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM `env_run.xml`, see example below), and run for 300-350 simulation years. :numref:`Figure BGC-Crop SASU spinup plot for 1850` shows spinup behavior for an 1850 BGC-Crop SASU case using CRUJRA atmospheric forcing. The criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy and need not be met for this step. -.. _Figure BGC SASU spinup plot for 1850: +.. _Figure BGC-Crop SASU spinup plot for 1850: .. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_SASU_Spinup-0.png - BGC SASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. + BGC-Crop SASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC-Crop AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. -After this you continue in standard mode for about 160 years. We refer to this as the post-SASU or pSASU phase (``CLM_ACCELERATED_SPINUP off`` in CLM `env_run.xml`, see example below). :numref:`Figure BGC pSASU spinup plot for 1850` shows spinup behavior for an 1850 BGC pSASU case using CRUJRA atmospheric forcing. As before, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. +After this you continue in standard mode for about 160 years. We refer to this as the post-SASU or pSASU phase (``CLM_ACCELERATED_SPINUP off`` in CLM `env_run.xml`, see example below). :numref:`Figure BGC-Crop pSASU spinup plot for 1850` shows spinup behavior for an 1850 BGC-Crop pSASU case using CRUJRA atmospheric forcing. As before, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. -.. _Figure BGC pSASU spinup plot for 1850: +.. _Figure BGC-Crop pSASU spinup plot for 1850: .. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_pSASU_Spinup-0.png - BGC pSASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC SASU spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. + BGC-Crop pSASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC-Crop SASU spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. As an alternative to spinning up, one may start from a default initial file that is setup as part of the selected compset. When the simulation's spatial resolution is identical to the initial file's resolution, it may still take 10 or more years for variables such as TLAI (total leaf area index), GPP (gross primary production), and TWS (total water storage) to reach a new equilibrium state due to the different atmospheric forcing. Similarly, it may take 10 or more years for these variables to reach a new equilibrium when switching atmospheric CO2 from 1850 to a present-day value. -Example: AD_spinup Simulation for |version|-BGC +Example: AD_spinup Simulation for CLM-BGC-Crop -------------------------------------------------------- For the first step of running in ``CLM_ACCELERATED_SPINUP on`` mode, you will setup a case, and then edit the values in env_build.xml and env_run.xml so that the right configuration is turned on and the simulation is setup to run for the required length of simulation time. Try the following: @@ -62,7 +62,7 @@ In CLM's /tools/contrib directory there are three versions of this .ncl script: - SpinupStability_BGC_v11.ncl for Bgc and BgcCrop compsets run on 2D lat/lon grids. - SpinupStability_BGC_v12_SE.ncl for Bgc, BgcCrop, or Fates compsets run on certain spectral element grids (currently ne120, ne30, ne16). -- SpinupStability_SP_v10.ncl for Sp compsets run on 2D lat/lon grids. See section :numref:`spinning-up-sp` for helpful pointers about this script that may also apply to the BGC versions. +- SpinupStability_SP_v10.ncl for Sp compsets run on 2D lat/lon grids. See section :numref:`spinning-up-sp` for helpful pointers about this script that may also apply to the BGC-Crop versions. To run one of these scripts on derecho, one loads ncl (module load ncl) and submits with ``ncl SpinupStability_BGC_v11.ncl``, for example. Before running one needs to confirm a few easy settings appearing near the top of each script. @@ -70,7 +70,7 @@ One of the settings that may not be intuitive at first glance is ``annual_hist`` .. _eg-sasu-spinup: -Example: SASU_spinup Simulation for |version|-BGC +Example: SASU_spinup Simulation for CLM-BGC-Crop ------------------------------------------------------------------ :: @@ -96,7 +96,7 @@ Example: SASU_spinup Simulation for |version|-BGC Save the last restart file from this step and use it as the ``finidat`` file for the pSASU step. Save the restart file from the end of the pSASU simulation to use as a "finidat" file for future simulations. -Example: pSASU_spinup Simulation for |version|-BGC +Example: pSASU_spinup Simulation for CLM-BGC-Crop -------------------------------------------------- :: From fb5cd44ebff224a7323a9d83d7fa4387bc3891e7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 14 May 2026 17:01:02 -0600 Subject: [PATCH 13/22] Replace pSASU with "normal mode" except in shorthand, eg for case names --- ...nning-up-the-biogeochemistry-BGC-spinup.rst | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index e5153bf0d3..711fae8458 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -22,13 +22,13 @@ After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM ` BGC-Crop SASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC-Crop AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. -After this you continue in standard mode for about 160 years. We refer to this as the post-SASU or pSASU phase (``CLM_ACCELERATED_SPINUP off`` in CLM `env_run.xml`, see example below). :numref:`Figure BGC-Crop pSASU spinup plot for 1850` shows spinup behavior for an 1850 BGC-Crop pSASU case using CRUJRA atmospheric forcing. As before, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. +After this you continue in standard mode for about 160 years. We refer to this phase as post-SASU, pSASU, or normal mode (``CLM_ACCELERATED_SPINUP off`` in CLM `env_run.xml`, see example below). :numref:`Figure BGC-Crop normal mode plot for 1850` shows spinup behavior for an 1850 BGC-Crop normal mode case using CRUJRA atmospheric forcing. As before, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. -.. _Figure BGC-Crop pSASU spinup plot for 1850: +.. _Figure BGC-Crop normal mode spinup plot for 1850: .. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_pSASU_Spinup-0.png - BGC-Crop pSASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC-Crop SASU spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. + BGC-Crop normal mode plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC-Crop SASU spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. As an alternative to spinning up, one may start from a default initial file that is setup as part of the selected compset. When the simulation's spatial resolution is identical to the initial file's resolution, it may still take 10 or more years for variables such as TLAI (total leaf area index), GPP (gross primary production), and TWS (total water storage) to reach a new equilibrium state due to the different atmospheric forcing. Similarly, it may take 10 or more years for these variables to reach a new equilibrium when switching atmospheric CO2 from 1850 to a present-day value. @@ -50,7 +50,7 @@ For the first step of running in ``CLM_ACCELERATED_SPINUP on`` mode, you will se # The following sets RESUBMIT to 7 times and # STOP_DATE, STOP_N, and STOP_OPTION to Jan/1/0401, 50, "nyears" in env_run.xml (you could also modify these with an editor) > ./xmlchange RESUBMIT=7,STOP_N=50,STOP_OPTION=nyears,STOP_DATE=04010101 - # Now run normally + # Now run > ./case.submit While this simulation progresses, use SpinupStability_BGC_v11.ncl to assess whether the simulation is approaching equilibrium. When the simulation ends, save the last restart file for use in the SASU_spinup step. @@ -66,7 +66,7 @@ In CLM's /tools/contrib directory there are three versions of this .ncl script: To run one of these scripts on derecho, one loads ncl (module load ncl) and submits with ``ncl SpinupStability_BGC_v11.ncl``, for example. Before running one needs to confirm a few easy settings appearing near the top of each script. -One of the settings that may not be intuitive at first glance is ``annual_hist``. By default the phases AD_spinup and SASU_spinup generate annual history, so set this to "True", while pSASU generates monthly history, so set this to "False". +One of the settings that may not be intuitive at first glance is ``annual_hist``. By default the phases AD_spinup and SASU_spinup generate annual history, so set this to "True", while normal mode generates monthly history, so set this to "False". .. _eg-sasu-spinup: @@ -90,13 +90,13 @@ Example: SASU_spinup Simulation for CLM-BGC-Crop # The following sets RESUBMIT to 6 times and # STOP_N to 50 and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) > ./xmlchange RESUBMIT=6,STOP_OPTION=nyears,STOP_N=50 - > Now run as normal + > Now run > ./case.submit -Save the last restart file from this step and use it as the ``finidat`` file for the pSASU step. Save the restart file from the end of the pSASU simulation to use as a "finidat" file for future simulations. +Save the last restart file from this step and use it as the ``finidat`` file for the normal mode simulation. Save the restart file from the end of the normal mode simulation to use as a "finidat" file for future simulations. -Example: pSASU_spinup Simulation for CLM-BGC-Crop +Example: Normal mode simulation for CLM-BGC-Crop -------------------------------------------------- :: @@ -116,6 +116,6 @@ Example: pSASU_spinup Simulation for CLM-BGC-Crop # The following sets RESUBMIT to 3 times and # STOP_N to 50 and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) > ./xmlchange RESUBMIT=3,STOP_OPTION=nyears,STOP_N=50 - > Now run as normal + > Now run > ./case.submit From 4b6ecf1ade78e5628023ab10e3be64a88ffc08f1 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 14 May 2026 17:09:17 -0600 Subject: [PATCH 14/22] Adding ./xmlchange MOSART_MODE=NULL --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 711fae8458..4a9318d4a5 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -50,6 +50,8 @@ For the first step of running in ``CLM_ACCELERATED_SPINUP on`` mode, you will se # The following sets RESUBMIT to 7 times and # STOP_DATE, STOP_N, and STOP_OPTION to Jan/1/0401, 50, "nyears" in env_run.xml (you could also modify these with an editor) > ./xmlchange RESUBMIT=7,STOP_N=50,STOP_OPTION=nyears,STOP_DATE=04010101 + # The following makes sure that we run with MOSART off + > ./xmlchange MOSART_MODE=NULL # Now run > ./case.submit @@ -90,6 +92,8 @@ Example: SASU_spinup Simulation for CLM-BGC-Crop # The following sets RESUBMIT to 6 times and # STOP_N to 50 and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) > ./xmlchange RESUBMIT=6,STOP_OPTION=nyears,STOP_N=50 + # The following makes sure that we run with MOSART off + > ./xmlchange MOSART_MODE=NULL > Now run > ./case.submit @@ -116,6 +120,8 @@ Example: Normal mode simulation for CLM-BGC-Crop # The following sets RESUBMIT to 3 times and # STOP_N to 50 and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) > ./xmlchange RESUBMIT=3,STOP_OPTION=nyears,STOP_N=50 + # The following makes sure that we run with MOSART off + > ./xmlchange MOSART_MODE=NULL > Now run > ./case.submit From 5d0baeaf8c76c9d59e4a8b2e6606425e6e9d1b9d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 14 May 2026 17:19:40 -0600 Subject: [PATCH 15/22] Add --run-unsupported to the create_newcases --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 4a9318d4a5..9f5b977fda 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -39,7 +39,7 @@ For the first step of running in ``CLM_ACCELERATED_SPINUP on`` mode, you will se :: > cd cime/scripts - > ./create_newcase -case AD_spinup -res f19_g17 -compset I1850Clm60BgcCrop + > ./create_newcase -case AD_spinup -res f19_g17 -compset I1850Clm60BgcCrop --run-unsupported > cd AD_spinup # Change accelerated spinup mode > ./xmlchange CLM_ACCELERATED_SPINUP="on" @@ -77,7 +77,7 @@ Example: SASU_spinup Simulation for CLM-BGC-Crop :: > cd cime/scripts - > ./create_newcase -case SASU_spinup -res f19_g17 -compset I1850Clm60BgcCrop + > ./create_newcase -case SASU_spinup -res f19_g17 -compset I1850Clm60BgcCrop --run-unsupported > cd SASU_spinup # Copy the last restart files from the AD_spinup case into your run directory > cp /scratch/archive/AD_spinup/rest/0401-01-01-00000/* /scratch/SASU_spinup/run @@ -105,7 +105,7 @@ Example: Normal mode simulation for CLM-BGC-Crop :: > cd cime/scripts - > ./create_newcase -case pSASU_spinup -res f19_g17 -compset I1850Clm60BgcCrop + > ./create_newcase -case pSASU_spinup -res f19_g17 -compset I1850Clm60BgcCrop --run-unsupported > cd pSASU_spinup # Copy the last restart files from the SASU_spinup case into your run directory > cp /scratch/archive/SASU_spinup/rest/0351-01-01-00000/* /scratch/pSASU_spinup/run From be155229de85c64a3efdc6c0b5170b4e3480932f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 14 May 2026 16:28:30 -0700 Subject: [PATCH 16/22] Update doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst Add double quotes around module load ncl Co-authored-by: Keith Oleson --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index bf4fe5ed51..7668833717 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -64,7 +64,7 @@ In CLM's /tools/contrib directory there are three versions of this .ncl script: - SpinupStability_BGC_v12_SE.ncl for Bgc, BgcCrop, or Fates compsets run on certain spectral element grids (currently ne120, ne30, ne16). - SpinupStability_SP_v10.ncl for Sp compsets run on 2D lat/lon grids. See section :numref:`spinning-up-sp` for helpful pointers about this script that may also apply to the BGC versions. -To run one of these scripts on derecho, one loads ncl (module load ncl) and submits with ``ncl SpinupStability_BGC_v11.ncl``, for example. Before running one needs to confirm a few easy settings appearing near the top of each script. +To run one of these scripts on derecho, one loads ncl (``module load ncl``) and submits with ``ncl SpinupStability_BGC_v11.ncl``, for example. Before running one needs to confirm a few easy settings appearing near the top of each script. One of the settings that may not be intuitive at first glance is ``annual_hist``. By default the phases AD_spinup and SASU_spinup generate annual history, so set this to "True", while pSASU generates monthly history, so set this to "False". From bb1ce4474587e3006c8fcc616bf3643fe2b2ebef Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 14 May 2026 17:38:33 -0600 Subject: [PATCH 17/22] Clarify the location of the /archive and /run directories --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 9f5b977fda..7f1dcfd068 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -80,7 +80,8 @@ Example: SASU_spinup Simulation for CLM-BGC-Crop > ./create_newcase -case SASU_spinup -res f19_g17 -compset I1850Clm60BgcCrop --run-unsupported > cd SASU_spinup # Copy the last restart files from the AD_spinup case into your run directory - > cp /scratch/archive/AD_spinup/rest/0401-01-01-00000/* /scratch/SASU_spinup/run + # On NSF-NCAR's derecho computer, cd to /glade/derecho/scratch/$USER + > cp archive/AD_spinup/rest/0401-01-01-00000/* SASU_spinup/run # Runtype should already be startup, but this will ensure it > ./xmlchange RUN_TYPE=startup # Set finidat to the restart file copied in the previous step @@ -108,7 +109,8 @@ Example: Normal mode simulation for CLM-BGC-Crop > ./create_newcase -case pSASU_spinup -res f19_g17 -compset I1850Clm60BgcCrop --run-unsupported > cd pSASU_spinup # Copy the last restart files from the SASU_spinup case into your run directory - > cp /scratch/archive/SASU_spinup/rest/0351-01-01-00000/* /scratch/pSASU_spinup/run + # On NSF-NCAR's derecho computer, cd to /glade/derecho/scratch/$USER + > cp archive/SASU_spinup/rest/0351-01-01-00000/* pSASU_spinup/run # Runtype should already be startup, but this will ensure it > ./xmlchange RUN_TYPE=startup # Set finidat to the restart file copied in the previous step From fe4ce58eab1654c493923ec8277dfd6a23592d59 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 14 May 2026 17:47:47 -0600 Subject: [PATCH 18/22] Add CLM_ACCELERATED_SPINUP to sasu and off cases and correct setup order --- ...Spinning-up-the-biogeochemistry-BGC-spinup.rst | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 7f1dcfd068..964aa28c60 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -43,9 +43,8 @@ For the first step of running in ``CLM_ACCELERATED_SPINUP on`` mode, you will se > cd AD_spinup # Change accelerated spinup mode > ./xmlchange CLM_ACCELERATED_SPINUP="on" - # Now setup + # Now setup and build > ./case.setup - # Now build > ./case.build # The following sets RESUBMIT to 7 times and # STOP_DATE, STOP_N, and STOP_OPTION to Jan/1/0401, 50, "nyears" in env_run.xml (you could also modify these with an editor) @@ -79,6 +78,10 @@ Example: SASU_spinup Simulation for CLM-BGC-Crop > cd cime/scripts > ./create_newcase -case SASU_spinup -res f19_g17 -compset I1850Clm60BgcCrop --run-unsupported > cd SASU_spinup + # Change accelerated spinup mode + > ./xmlchange CLM_ACCELERATED_SPINUP="sasu" + > Now setup + > ./case.setup # Copy the last restart files from the AD_spinup case into your run directory # On NSF-NCAR's derecho computer, cd to /glade/derecho/scratch/$USER > cp archive/AD_spinup/rest/0401-01-01-00000/* SASU_spinup/run @@ -86,8 +89,6 @@ Example: SASU_spinup Simulation for CLM-BGC-Crop > ./xmlchange RUN_TYPE=startup # Set finidat to the restart file copied in the previous step > echo ' finidat = "AD_spinup.clm2.r.0401-01-01-00000.nc"' > user_nl_clm - # Now setup - > ./case.setup > Now build > ./case.build # The following sets RESUBMIT to 6 times and @@ -108,6 +109,10 @@ Example: Normal mode simulation for CLM-BGC-Crop > cd cime/scripts > ./create_newcase -case pSASU_spinup -res f19_g17 -compset I1850Clm60BgcCrop --run-unsupported > cd pSASU_spinup + # Change accelerated spinup mode + > ./xmlchange CLM_ACCELERATED_SPINUP="off" + > Now setup + > ./case.setup # Copy the last restart files from the SASU_spinup case into your run directory # On NSF-NCAR's derecho computer, cd to /glade/derecho/scratch/$USER > cp archive/SASU_spinup/rest/0351-01-01-00000/* pSASU_spinup/run @@ -115,8 +120,6 @@ Example: Normal mode simulation for CLM-BGC-Crop > ./xmlchange RUN_TYPE=startup # Set finidat to the restart file copied in the previous step > echo ' finidat = "SASU_spinup.clm2.r.0351-01-01-00000.nc"' > user_nl_clm - # Now setup - > ./case.setup > Now build > ./case.build # The following sets RESUBMIT to 3 times and From 8b2222d426fab34018735dd2de1d91a3e34c431f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 14 May 2026 17:52:45 -0600 Subject: [PATCH 19/22] Change some > to # to indicate comments --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 964aa28c60..403d2febd5 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -80,7 +80,7 @@ Example: SASU_spinup Simulation for CLM-BGC-Crop > cd SASU_spinup # Change accelerated spinup mode > ./xmlchange CLM_ACCELERATED_SPINUP="sasu" - > Now setup + # Now setup > ./case.setup # Copy the last restart files from the AD_spinup case into your run directory # On NSF-NCAR's derecho computer, cd to /glade/derecho/scratch/$USER @@ -89,14 +89,14 @@ Example: SASU_spinup Simulation for CLM-BGC-Crop > ./xmlchange RUN_TYPE=startup # Set finidat to the restart file copied in the previous step > echo ' finidat = "AD_spinup.clm2.r.0401-01-01-00000.nc"' > user_nl_clm - > Now build + # Now build > ./case.build # The following sets RESUBMIT to 6 times and # STOP_N to 50 and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) > ./xmlchange RESUBMIT=6,STOP_OPTION=nyears,STOP_N=50 # The following makes sure that we run with MOSART off > ./xmlchange MOSART_MODE=NULL - > Now run + # Now run > ./case.submit Save the last restart file from this step and use it as the ``finidat`` file for the normal mode simulation. Save the restart file from the end of the normal mode simulation to use as a "finidat" file for future simulations. @@ -111,7 +111,7 @@ Example: Normal mode simulation for CLM-BGC-Crop > cd pSASU_spinup # Change accelerated spinup mode > ./xmlchange CLM_ACCELERATED_SPINUP="off" - > Now setup + # Now setup > ./case.setup # Copy the last restart files from the SASU_spinup case into your run directory # On NSF-NCAR's derecho computer, cd to /glade/derecho/scratch/$USER @@ -120,13 +120,13 @@ Example: Normal mode simulation for CLM-BGC-Crop > ./xmlchange RUN_TYPE=startup # Set finidat to the restart file copied in the previous step > echo ' finidat = "SASU_spinup.clm2.r.0351-01-01-00000.nc"' > user_nl_clm - > Now build + # Now build > ./case.build # The following sets RESUBMIT to 3 times and # STOP_N to 50 and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) > ./xmlchange RESUBMIT=3,STOP_OPTION=nyears,STOP_N=50 # The following makes sure that we run with MOSART off > ./xmlchange MOSART_MODE=NULL - > Now run + # Now run > ./case.submit From 19cebdd1dfc487c3266830d1e90699140415191d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 14 May 2026 17:54:07 -0600 Subject: [PATCH 20/22] Change 160 yrs to 200 for consistency with the example --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 403d2febd5..e4037c86af 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -22,7 +22,7 @@ After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM ` BGC-Crop SASU spinup plot for a year 1850 case with CRUJRA atmospheric forcing and initialization from the end of the BGC-Crop AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability_BGC_v11.ncl. -After this you continue in standard mode for about 160 years. We refer to this phase as post-SASU, pSASU, or normal mode (``CLM_ACCELERATED_SPINUP off`` in CLM `env_run.xml`, see example below). :numref:`Figure BGC-Crop normal mode plot for 1850` shows spinup behavior for an 1850 BGC-Crop normal mode case using CRUJRA atmospheric forcing. As before, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. +After this you continue in standard mode for 200 years. We refer to this phase as post-SASU, pSASU, or normal mode (``CLM_ACCELERATED_SPINUP off`` in CLM `env_run.xml`, see example below). :numref:`Figure BGC-Crop normal mode plot for 1850` shows spinup behavior for an 1850 BGC-Crop normal mode case using CRUJRA atmospheric forcing. As before, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. .. _Figure BGC-Crop normal mode spinup plot for 1850: From 2bc4a2856d0be181a4d7c3a503ee721a49586a08 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 14 May 2026 18:01:37 -0600 Subject: [PATCH 21/22] Correct a figure reference --- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index f7e95554d0..8667372dbc 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -24,7 +24,7 @@ After this you continue in "SASU" mode (``CLM_ACCELERATED_SPINUP sasu`` in CLM ` After this you continue in standard mode for 200 years. We refer to this phase as post-SASU, pSASU, or normal mode (``CLM_ACCELERATED_SPINUP off`` in CLM `env_run.xml`, see example below). :numref:`Figure BGC-Crop normal mode plot for 1850` shows spinup behavior for an 1850 BGC-Crop normal mode case using CRUJRA atmospheric forcing. As before, the criterion that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. -.. _Figure BGC-Crop normal mode spinup plot for 1850: +.. _Figure BGC-Crop normal mode plot for 1850: .. figure:: ctsm5.4.CMIP7_ciso_ctsm5.3.075_f09_124_pSASU_Spinup-0.png From a3ecfbf49ec8c555187e78546a62f60b91a59330 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 18 May 2026 16:37:46 -0600 Subject: [PATCH 22/22] Update the examples to ensure that they work smoothly --- ...ning-up-the-biogeochemistry-BGC-spinup.rst | 38 ++++++++----------- 1 file changed, 16 insertions(+), 22 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 8667372dbc..4372c946f0 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -43,14 +43,14 @@ For the first step of running in ``CLM_ACCELERATED_SPINUP on`` mode, you will se > cd AD_spinup # Change accelerated spinup mode > ./xmlchange CLM_ACCELERATED_SPINUP="on" - # Now setup and build + # Now setup > ./case.setup - > ./case.build - # The following sets RESUBMIT to 7 times and - # STOP_DATE, STOP_N, and STOP_OPTION to Jan/1/0401, 50, "nyears" in env_run.xml (you could also modify these with an editor) - > ./xmlchange RESUBMIT=7,STOP_N=50,STOP_OPTION=nyears,STOP_DATE=04010101 - # The following makes sure that we run with MOSART off + # The following makes sure we run with MOSART off > ./xmlchange MOSART_MODE=NULL + # Now build + > ./case.build + # The following sets RESUBMIT to 7 times, STOP_N to 50, and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) + > ./xmlchange RESUBMIT=7,STOP_N=50,STOP_OPTION=nyears # Now run > ./case.submit @@ -78,24 +78,21 @@ Example: SASU_spinup Simulation for CLM-BGC-Crop > cd cime/scripts > ./create_newcase -case SASU_spinup -res f19_g17 -compset I1850Clm60BgcCrop --run-unsupported > cd SASU_spinup - # Change accelerated spinup mode - > ./xmlchange CLM_ACCELERATED_SPINUP="sasu" + # Change accelerated spinup mode, turn off coldstart, and change runtype to hybrid to allow use of a finidat + > ./xmlchange CLM_ACCELERATED_SPINUP="sasu",CLM_FORCE_COLDSTART=off,RUN_TYPE=hybrid # Now setup > ./case.setup # Copy the last restart files from the AD_spinup case into your run directory # On NSF-NCAR's derecho computer, cd to /glade/derecho/scratch/$USER > cp archive/AD_spinup/rest/0401-01-01-00000/* SASU_spinup/run - # Runtype should already be startup, but this will ensure it - > ./xmlchange RUN_TYPE=startup # Set finidat to the restart file copied in the previous step > echo ' finidat = "AD_spinup.clm2.r.0401-01-01-00000.nc"' > user_nl_clm + # The following makes sure we run with MOSART off + > ./xmlchange MOSART_MODE=NULL # Now build > ./case.build - # The following sets RESUBMIT to 6 times and - # STOP_N to 50 and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) + # The following sets RESUBMIT to 6 times, STOP_N to 50, and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) > ./xmlchange RESUBMIT=6,STOP_OPTION=nyears,STOP_N=50 - # The following makes sure that we run with MOSART off - > ./xmlchange MOSART_MODE=NULL # Now run > ./case.submit @@ -109,24 +106,21 @@ Example: Normal mode simulation for CLM-BGC-Crop > cd cime/scripts > ./create_newcase -case pSASU_spinup -res f19_g17 -compset I1850Clm60BgcCrop --run-unsupported > cd pSASU_spinup - # Change accelerated spinup mode - > ./xmlchange CLM_ACCELERATED_SPINUP="off" + # Change accelerated spinup mode, turn off coldstart, and change runtype to hybrid to allow use of a finidat + > ./xmlchange CLM_ACCELERATED_SPINUP="off",CLM_FORCE_COLDSTART=off,RUN_TYPE=hybrid # Now setup > ./case.setup # Copy the last restart files from the SASU_spinup case into your run directory # On NSF-NCAR's derecho computer, cd to /glade/derecho/scratch/$USER > cp archive/SASU_spinup/rest/0351-01-01-00000/* pSASU_spinup/run - # Runtype should already be startup, but this will ensure it - > ./xmlchange RUN_TYPE=startup # Set finidat to the restart file copied in the previous step > echo ' finidat = "SASU_spinup.clm2.r.0351-01-01-00000.nc"' > user_nl_clm + # The following makes sure we run with MOSART off + > ./xmlchange MOSART_MODE=NULL # Now build > ./case.build - # The following sets RESUBMIT to 3 times and - # STOP_N to 50 and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) + # The following sets RESUBMIT to 3 times, STOP_N to 50, and STOP_OPTION to "nyears" in env_run.xml (you could also modify these with an editor) > ./xmlchange RESUBMIT=3,STOP_OPTION=nyears,STOP_N=50 - # The following makes sure that we run with MOSART off - > ./xmlchange MOSART_MODE=NULL # Now run > ./case.submit