From 711f9c27d3aa6c0da15fa0cc8afea9af4fb697a6 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Wed, 20 May 2026 14:57:36 -0600 Subject: [PATCH 1/5] initial commit --- .../tech_note/DGVM/CLM50_Tech_Note_DGVM.rst | 24 ++++++++++++++++--- 1 file changed, 21 insertions(+), 3 deletions(-) diff --git a/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst b/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst index 4874ca9943..4057fdff27 100644 --- a/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst +++ b/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst @@ -15,14 +15,32 @@ FATES FATES is the "Functionally Assembled Terrestrial Ecosystem Simulator". It is an external module which can run within a given "Host Land Model" (HLM) like CLM. -FATES was derived from the CLM Ecosystem Demography model (CLM(ED)), which was documented in: - -Fisher, R. A., Muszala, S., Verteinstein, M., Lawrence, P., Xu, C., McDowell, N. G., Knox, R. G., Koven, C., Holm, J., Rogers, B. M., Spessa, A., Lawrence, D., and Bonan, G.: Taking off the training wheels: the properties of a dynamic vegetation model without climate envelopes, CLM4.5(ED), Geosci. Model Dev., 8, 3593-3619, https://doi.org/10.5194/gmd-8-3593-2015, 2015. +FATES was derived from the CLM Ecosystem Demography model (CLM(ED)), which was documented in :ref:`Fisher et al. (2015)`. The Ecosystem Demography ('ED'), concept within FATES is derived from the work of :ref:`Moorcroft et al. (2001)` and is a cohort model of vegetation competition and co-existence, allowing a representation of the biosphere which accounts for the division of the land surface into successional stages, and for competition for light between height structured cohorts of representative trees of various plant functional types. The implementation of the Ecosystem Demography concept within FATES links the surface flux and canopy physiology concepts in CLM with numerous additional developments necessary to accommodate the new model. These include a version of the SPITFIRE (Spread and InTensity of Fire) model of :ref:`Thonicke et al. (2010)`, and an adoption of the concept of `Perfect Plasticity Approximation` approach of :ref:`Purves et al. 2008`, :ref:`Lichstein et al. 2011` and :ref:`Weng et al. 2014`, in accounting for the spatial arrangement of crowns. Novel algorithms accounting for the fragmentation of coarse woody debris into chemical litter streams, for the physiological optimization of canopy thickness, for the accumulation of seeds in the seed bank, for multi-layer multi-PFT radiation transfer, for drought-deciduous and cold-deciduous phenology, for carbon storage allocation, and for tree mortality under carbon stress, are also included. + +FATES Reduced Complexity Modes +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Currently, FATES can be run in several different "reduced complexity modes", where parts of the vegetation model are driven by input data rather than simulated. These modes can be used to facilitate calibration, test features, or run simulations more quickly. These modes are: + +1. **Satellite Phenology** (SP) mode: this mode is designed to run with leaf area index (LAI), stem area index (SAI), and canopy height (HTOP) as input to the model. As such, all processes that are normally used to calculate these values are turned off (e.g., mortality, allocation, etc.) + +2. **No-Competition Mode**: this mode runs with full complexity in terms of processes, but places each FATES PFT on its own patch. As such, PFTs do not compete with one another. + +3. **Fixed Biogeography Mode**: this mode turns off prognostic spatial changes in the distribution of vegetation and instead, the model uses input data to determine which PFTs are present at any given gridcell. The patch area for each PFT is derived from the input CLM surface dataset. However, please note that the PFTs in the FATES parameter file do not always map one-to-one with the CLM PFTs on the surface dataset. See the FATES parameter *fates_hlm_pft_map* on the FATES parameter file for the correct mapping of FATES to CLM PFTs. + +Note that there are different combinations of no-competition and fixed biogeography mode that will result in different behaviors. See the `FATES documentation`_ for these options. + +Scientifically Supported CLM-FATES Configurations +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +We currently scientifally support CLM-FATES run in `carbon-only mode`_, and with either SP or no-competition + fixed biogeography mode. + + Further reading ^^^^^^^^^^^^^^^^^^^^ From 38af48434a735dee44013b3d9f834aa2b8240ed5 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Wed, 20 May 2026 15:03:42 -0600 Subject: [PATCH 2/5] remove CLM5 references --- doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst b/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst index 4057fdff27..e931f811cd 100644 --- a/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst +++ b/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst @@ -6,7 +6,7 @@ Dynamic Global Vegetation and FATES What has changed ^^^^^^^^^^^^^^^^^^^^ -- Deprecation of the dynamic global vegetation model (DGVM): The CLM5.0 model contains the legacy 'CNDV' code, which runs the CLM biogeochemistry model in combination with the LPJ-derived dynamics vegetation model introduced in CLM3. While this capacity has not technically been removed from the model, the DGVM has not been tested in the development of CLM5 and is no longer scientifically supported. +- Deprecation of the dynamic global vegetation model (DGVM): The current CLM model version contains the legacy 'CNDV' code, which runs the CLM biogeochemistry model in combination with the LPJ-derived dynamics vegetation model introduced in CLM3. While this capacity has not technically been removed from the model, the DGVM has not been tested in the development of CLM6 and is no longer scientifically supported. - Introduction of FATES: The Functionally Assembled Terrestrial Ecosystem Simulator (FATES) is the actively developed DGVM for the CLM5. @@ -33,17 +33,15 @@ Currently, FATES can be run in several different "reduced complexity modes", whe 3. **Fixed Biogeography Mode**: this mode turns off prognostic spatial changes in the distribution of vegetation and instead, the model uses input data to determine which PFTs are present at any given gridcell. The patch area for each PFT is derived from the input CLM surface dataset. However, please note that the PFTs in the FATES parameter file do not always map one-to-one with the CLM PFTs on the surface dataset. See the FATES parameter *fates_hlm_pft_map* on the FATES parameter file for the correct mapping of FATES to CLM PFTs. -Note that there are different combinations of no-competition and fixed biogeography mode that will result in different behaviors. See the `FATES documentation`_ for these options. +Note that there are different combinations of no-competition and fixed biogeography mode that will result in different behaviors. See the `FATES namelist documentation `_ for these options. Scientifically Supported CLM-FATES Configurations ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -We currently scientifally support CLM-FATES run in `carbon-only mode`_, and with either SP or no-competition + fixed biogeography mode. +We currently scientifally support CLM-FATES run in `carbon-only mode `_, and with either SP or no-competition + fixed biogeography mode. Further reading ^^^^^^^^^^^^^^^^^^^^ -For more information about FATES, including a Users Guide and Technical Note, please see the `FATES documentation`_. - -.. _FATES documentation: https://fates-users-guide.readthedocs.io/en/latest/index.html +For more information about FATES, including a Users Guide and Technical Note, please see the `FATES documentation `_. From 9b1cdec6539076ad804c51642bdf00c6644a410c Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 28 May 2026 15:42:12 -0600 Subject: [PATCH 3/5] rename files, add paragraphs about ED, add figures --- .../tech_note/DGVM/CLM50_Tech_Note_DGVM.rst | 47 --------------- .../tech_note/FATES/CLM50_Tech_Note_FATES.rst | 60 +++++++++++++++++++ .../FATES/FATES_and_CLM_hierarchy.png | 3 + doc/source/tech_note/FATES/FATES_tiling.png | 3 + doc/source/tech_note/index.rst | 2 +- 5 files changed, 67 insertions(+), 48 deletions(-) delete mode 100644 doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst create mode 100644 doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst create mode 100644 doc/source/tech_note/FATES/FATES_and_CLM_hierarchy.png create mode 100644 doc/source/tech_note/FATES/FATES_tiling.png diff --git a/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst b/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst deleted file mode 100644 index e931f811cd..0000000000 --- a/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst +++ /dev/null @@ -1,47 +0,0 @@ -.. _rst_Dynamic Global Vegetation and FATES: - -Dynamic Global Vegetation and FATES -=================================== - -What has changed -^^^^^^^^^^^^^^^^^^^^ - -- Deprecation of the dynamic global vegetation model (DGVM): The current CLM model version contains the legacy 'CNDV' code, which runs the CLM biogeochemistry model in combination with the LPJ-derived dynamics vegetation model introduced in CLM3. While this capacity has not technically been removed from the model, the DGVM has not been tested in the development of CLM6 and is no longer scientifically supported. - -- Introduction of FATES: The Functionally Assembled Terrestrial Ecosystem Simulator (FATES) is the actively developed DGVM for the CLM5. - -FATES -^^^^^^^^^^^^^^^^^^^^ - -FATES is the "Functionally Assembled Terrestrial Ecosystem Simulator". It is an external module which can run within a given "Host Land Model" (HLM) like CLM. - -FATES was derived from the CLM Ecosystem Demography model (CLM(ED)), which was documented in :ref:`Fisher et al. (2015)`. - -The Ecosystem Demography ('ED'), concept within FATES is derived from the work of :ref:`Moorcroft et al. (2001)` and is a cohort model of vegetation competition and co-existence, allowing a representation of the biosphere which accounts for the division of the land surface into successional stages, and for competition for light between height structured cohorts of representative trees of various plant functional types. - -The implementation of the Ecosystem Demography concept within FATES links the surface flux and canopy physiology concepts in CLM with numerous additional developments necessary to accommodate the new model. These include a version of the SPITFIRE (Spread and InTensity of Fire) model of :ref:`Thonicke et al. (2010)`, and an adoption of the concept of `Perfect Plasticity Approximation` approach of :ref:`Purves et al. 2008`, :ref:`Lichstein et al. 2011` and :ref:`Weng et al. 2014`, in accounting for the spatial arrangement of crowns. Novel algorithms accounting for the fragmentation of coarse woody debris into chemical litter streams, for the physiological optimization of canopy thickness, for the accumulation of seeds in the seed bank, for multi-layer multi-PFT radiation transfer, for drought-deciduous and cold-deciduous phenology, for carbon storage allocation, and for tree mortality under carbon stress, are also included. - - -FATES Reduced Complexity Modes -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Currently, FATES can be run in several different "reduced complexity modes", where parts of the vegetation model are driven by input data rather than simulated. These modes can be used to facilitate calibration, test features, or run simulations more quickly. These modes are: - -1. **Satellite Phenology** (SP) mode: this mode is designed to run with leaf area index (LAI), stem area index (SAI), and canopy height (HTOP) as input to the model. As such, all processes that are normally used to calculate these values are turned off (e.g., mortality, allocation, etc.) - -2. **No-Competition Mode**: this mode runs with full complexity in terms of processes, but places each FATES PFT on its own patch. As such, PFTs do not compete with one another. - -3. **Fixed Biogeography Mode**: this mode turns off prognostic spatial changes in the distribution of vegetation and instead, the model uses input data to determine which PFTs are present at any given gridcell. The patch area for each PFT is derived from the input CLM surface dataset. However, please note that the PFTs in the FATES parameter file do not always map one-to-one with the CLM PFTs on the surface dataset. See the FATES parameter *fates_hlm_pft_map* on the FATES parameter file for the correct mapping of FATES to CLM PFTs. - -Note that there are different combinations of no-competition and fixed biogeography mode that will result in different behaviors. See the `FATES namelist documentation `_ for these options. - -Scientifically Supported CLM-FATES Configurations -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -We currently scientifally support CLM-FATES run in `carbon-only mode `_, and with either SP or no-competition + fixed biogeography mode. - - -Further reading -^^^^^^^^^^^^^^^^^^^^ - -For more information about FATES, including a Users Guide and Technical Note, please see the `FATES documentation `_. diff --git a/doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst b/doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst new file mode 100644 index 0000000000..126661418f --- /dev/null +++ b/doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst @@ -0,0 +1,60 @@ +.. _rst_Ecosystem Demography with FATES: + +Ecosystem Demography with FATES +=================================== + +Ecosystem Demography +^^^^^^^^^^^^^^^^^^^^^^^ + +An important component of representing the land surface is accurately capturing vegetation dynamics and their impact on and interaction with the Earth system. Some models utilize dynamic global vegetation models (DGVMs), which track the fractional cover of plant functional types (PFTs) on a grid cell over time, usually driven by "climate envelopes" which use climate metrics (e.g., temperature and precipitation) to determine where PFTs can grow. However, many DGVMs still do not simulate important processes like mortality, regeneration, and plant competition, which we know are important for accurately capturing vegetation and carbon dynamics (:ref:`Fisher et al. 2015`). + +Ecosystem demography models explicitly represent the size structure and successional state of vegetation, through direct simulation of plant growth, mortality, and regeneration. Thus, important vegetation characteristics such as vegetation canopy height, succession, and even potential biome shifts become emergent properties of the model rather than being prescribed. + +FATES +^^^^^^^^^^^^^^^^^^^^ + +FATES is the "Functionally Assembled Terrestrial Ecosystem Simulator". It is an external module which can run within a given "Host Land Model" (HLM) like CLM. FATES was derived from the CLM Ecosystem Demography model (CLM(ED)), documented in :ref:`Fisher et al. (2015)`. + +FATES is derived from the work of :ref:`Moorcroft et al. (2001)` and is a cohort model of vegetation competition and co-existence, allowing a representation of the biosphere which accounts for the division of the land surface into successional stages, and for competition for light between height structured cohorts of representative trees of various plant functional types. Individual plants within FATES are grouped into "cohorts" of the same size and PFT, and these cohorts compete for light and resources on individual "patches" that represent different disturbance histories (:numref:`fig_FATES_vs_CLM`). This type of ecosystem heterogeneity is in contrast to the default vegetation model in CLM, which uses two (sunlit & shaded) "big leaf" canopies per PFT, each on their own patch, with no representation of within-canopy structural heterogeneity or disturbance history. + +.. _fig_FATES_vs_CLM: + +.. figure:: FATES_tiling.png + + Comparison of grid structure in CLM-FATES and CLM. (a) An example grid of FATES patches showing individual cohorts of plants of different size and PFT. (b) those same FATES patches represented as their age-since-disturbance. (c) the equivalent gridcell in default CLM, showing instead a set of specific PFTs with fixed areas. + +FATES also introduces a new organizational structure to CLM which differs from its default organization. The original hierarchical organization of CLM as described in :ref:`Oleson et al. (2013)` are gridcells which contain land units (e.g. vegetated, lake, urban), which contain columns (e.g., naturally vegetated), which contain PFTs. FATES replaces the PFT level of this hierarchy with patches and cohorts. Thus, gridcells contain land units, which contain columns, which contain patches, which in turn contain some number of cohorts of the same or different PFT (:numref:`fig_FATES_and_CLM_hierarchy`). + +.. _fig_FATES_and_CLM_hierarchy: + +.. figure:: FATES_and_CLM_hierarchy.png + :width: 60% + + Comparison of the organizational hierarchy of default CLM (left) and CLM-FATES (right). + +The implementation of the Ecosystem Demography concept within FATES links the surface flux and canopy physiology concepts in CLM with numerous additional developments necessary to accommodate the new model. These include a version of the SPITFIRE (Spread and InTensity of Fire) model of :ref:`Thonicke et al. (2010)`, and an adoption of the concept of `Perfect Plasticity Approximation` approach of :ref:`Purves et al. 2008`, :ref:`Lichstein et al. 2011` and :ref:`Weng et al. 2014`, in accounting for the spatial arrangement of crowns. Novel algorithms accounting for the fragmentation of coarse woody debris into chemical litter streams, for the physiological optimization of canopy thickness, for the accumulation of seeds in the seed bank, for multi-layer multi-PFT radiation transfer, for drought-deciduous and cold-deciduous phenology, for carbon storage allocation, and for tree mortality under carbon stress, are also included. + + +FATES Reduced Complexity Modes +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Currently, FATES can be run in several different "reduced complexity modes", where parts of the vegetation model are driven by input data rather than simulated. These modes can be used to facilitate calibration, test features, or run simulations more quickly. These modes are: + +1. **Satellite Phenology** (SP) mode: this mode is designed to run with leaf area index (LAI), stem area index (SAI), and canopy height (HTOP) as input to the model. As such, all processes that are normally used to calculate these values are turned off (e.g., mortality, allocation, etc.) + +2. **No-Competition Mode**: this mode runs with full complexity in terms of processes, but places each FATES PFT on its own patch. As such, PFTs do not compete with one another. + +3. **Fixed Biogeography Mode**: this mode turns off prognostic spatial changes in the distribution of vegetation and instead, the model uses input data to determine which PFTs are present at any given gridcell. The patch area for each PFT is derived from the input CLM surface dataset. However, please note that the PFTs in the FATES parameter file do not always map one-to-one with the CLM PFTs on the surface dataset. See the FATES parameter *fates_hlm_pft_map* on the FATES parameter file for the correct mapping of FATES to CLM PFTs. + +Note that there are different combinations of no-competition and fixed biogeography mode that will result in different behaviors. See the `FATES namelist documentation `_ for these options. + +Scientifically Supported CLM-FATES Configurations +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +We currently scientifally support CLM-FATES run in `carbon-only mode `_, and with either SP or no-competition + fixed biogeography mode. + + +Further reading +^^^^^^^^^^^^^^^^^^^^ + +For more information about FATES, including a Users Guide and Technical Note, please see the `FATES documentation `_. diff --git a/doc/source/tech_note/FATES/FATES_and_CLM_hierarchy.png b/doc/source/tech_note/FATES/FATES_and_CLM_hierarchy.png new file mode 100644 index 0000000000..96634f731e --- /dev/null +++ b/doc/source/tech_note/FATES/FATES_and_CLM_hierarchy.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2c7170ccc816b131b647cb4bbef1505d725725599219ec9c346386e488ade7a4 +size 182139 diff --git a/doc/source/tech_note/FATES/FATES_tiling.png b/doc/source/tech_note/FATES/FATES_tiling.png new file mode 100644 index 0000000000..ad60f3a575 --- /dev/null +++ b/doc/source/tech_note/FATES/FATES_tiling.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6c4eff646cb73012e816b661bafa717b33be408d83de5ba75b5942a2d0f894c9 +size 480743 diff --git a/doc/source/tech_note/index.rst b/doc/source/tech_note/index.rst index 61ccae4361..5082a6d61a 100644 --- a/doc/source/tech_note/index.rst +++ b/doc/source/tech_note/index.rst @@ -44,7 +44,7 @@ CLM Technical Note Methane/CLM50_Tech_Note_Methane.rst Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst Transient_Landcover/CLM50_Tech_Note_Transient_Landcover.rst - DGVM/CLM50_Tech_Note_DGVM.rst + FATES/CLM50_Tech_Note_FATES.rst BVOCs/CLM50_Tech_Note_BVOCs.rst Dust/CLM50_Tech_Note_Dust.rst Hillslope_Hydrology/CLM50_Tech_Note_Hillslope_Hydrology.rst From 196accbb8799a2dcf930b1f6591f101a9716c3a7 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 28 May 2026 16:03:19 -0600 Subject: [PATCH 4/5] add more FATES refs --- .../tech_note/FATES/CLM50_Tech_Note_FATES.rst | 4 ++-- .../References/CLM50_Tech_Note_References.rst | 21 +++++++++++++++++++ 2 files changed, 23 insertions(+), 2 deletions(-) diff --git a/doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst b/doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst index 126661418f..e9be1dd0a5 100644 --- a/doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst +++ b/doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst @@ -13,9 +13,9 @@ Ecosystem demography models explicitly represent the size structure and successi FATES ^^^^^^^^^^^^^^^^^^^^ -FATES is the "Functionally Assembled Terrestrial Ecosystem Simulator". It is an external module which can run within a given "Host Land Model" (HLM) like CLM. FATES was derived from the CLM Ecosystem Demography model (CLM(ED)), documented in :ref:`Fisher et al. (2015)`. +FATES is the "Functionally Assembled Terrestrial Ecosystem Simulator". It is an external module which can run within a given "Host Land Model" (HLM) like CLM. FATES was derived from the CLM Ecosystem Demography model (CLM(ED)). FATES is documented in :ref:`Fisher et al. (2015)`, and has since been further developed and evaluated across a range of ecosystems and configurations (e.g., :ref:`Koven et al., 2020`; :ref:`Buotte et al., 2021`; :ref:`Needham et al., 2022`; :ref:`Shuman et al., 2024`) -FATES is derived from the work of :ref:`Moorcroft et al. (2001)` and is a cohort model of vegetation competition and co-existence, allowing a representation of the biosphere which accounts for the division of the land surface into successional stages, and for competition for light between height structured cohorts of representative trees of various plant functional types. Individual plants within FATES are grouped into "cohorts" of the same size and PFT, and these cohorts compete for light and resources on individual "patches" that represent different disturbance histories (:numref:`fig_FATES_vs_CLM`). This type of ecosystem heterogeneity is in contrast to the default vegetation model in CLM, which uses two (sunlit & shaded) "big leaf" canopies per PFT, each on their own patch, with no representation of within-canopy structural heterogeneity or disturbance history. +FATES is derived from the work of :ref:`Moorcroft et al. (2001)` and is a cohort model of vegetation competition and co-existence, allowing a representation of the biosphere which accounts for the division of the land surface into successional stages, and for competition for light between height structured cohorts of representative trees of various plant functional types. Individual plants within FATES are grouped into "cohorts" of the same size and PFT, and these cohorts compete for light and resources on individual "patches" that represent different disturbance histories (:numref:`fig_FATES_vs_CLM`). This type of ecosystem heterogeneity is in contrast to the default vegetation model in CLM, which uses two (sunlit & shaded) "big leaf" canopies per PFT, each on their own patch, with no representation of within-canopy structural heterogeneity or disturbance history. Recent work comparing the parametric sensitivity of default CLM and CLM-FATES highlights key structural differences between the two approaches (`Foster et al., 2026`). .. _fig_FATES_vs_CLM: diff --git a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst index e2ec10855f..24eb8f05c6 100644 --- a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst +++ b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst @@ -192,6 +192,11 @@ Brzostek, E. R., J. B. Fisher, and R. P. Phillips, 2014. Modeling the carbon cos Bugmann, H., and Solomon, A.M. 2000. Explaining forest composition and biomass across multiple biogeographical regions. Ecol. Appl. 10:95-114. +.. _Buotteetal2021: + +Buotte, P. C., Koven, C. D., Xu, C., Shuman, J. K., Goulden, M. L., Levis, S., Katz, J., Ding, J., Ma, W., Robbins, Z., and Kueppers, L. M. 2021. Capturing functional strategies and compositional dynamics in vegetation demographic models, Biogeosciences, 18, 4473–4490, DOI:10.5194/bg-18-4473-2021. + + .. _Busing2005: Busing, R.T. 2005. Tree mortality, canopy turnover, and woody detritus in old cove forests of the southern Appalachians. Ecology 86:73-84. @@ -452,6 +457,10 @@ Flatau, P.J., Walko, R.L., and Cotton, W.R. 1992. Polynomial fits to saturation Foley, J.A. et al., 1996. An integrated biosphere model of land surface processes, terrestrial carbon balance, and vegetation dynamics. Global Biogeochemical Cycles 10.4, pp. 603-628. +.. _Fosteretal2026: + +Foster, A.C., Hawkins, L.R., Kennedy, D., Bonan, G.B., Fisher, R.A., Needham, J.F, Knox, R.G., Koven, C.D., Wieder, W.R., Dagon, K., and Lawrence, D.M. 2026. Contrasting parametric sensitivities in two global vegetation models using parameter perturbation ensembles. Journal of Advances in Modeling Earth Systems. 18, e2025MS005590. DOI:10.1029/2025MS005590. + .. _Friedl,etal2002: Friedl, M.A., McIver, D.K., Hodges, J.C.F., Zhang, X.Y., Muchoney, D., Strahler, A.H., Woodcock, C.E., Gopal, S., Schneider, A., Cooper, A., Baccini, A., Gao, F., and Schaaf, C. 2002. Global land cover mapping from MODIS: algorithms and early results. Remote Sens. Environ. 83:287-302. @@ -744,6 +753,10 @@ Koven, C.D. et al. 2015. Permafrost carbon-climate feedback is sensitive to deep Koven, C.D., G. Hugelius, D.M. Lawrence, and W.R. Wieder, 2017: Higher climatological temperature sensitivity of soil carbon in cold than warm climates. Nature Clim. Change, 7, doi:10.1038/nclimate3421. +.. _Kovenetal2020: + +Koven, C. D., Knox, R. G., Fisher, R. A., Chambers, J. Q., Christoffersen, B. O., Davies, S. J., Detto, M., Dietze, M. C., Faybishenko, B., Holm, J., Huang, M., Kovenock, M., Kueppers, L. M., Lemieux, G., Massoud, E., McDowell, N. G., Muller-Landau, H. C., Needham, J. F., Norby, R. J., Powell, T., Rogers, A., Serbin, S. P., Shuman, J. K., Swann, A. L. S., Varadharajan, C., Walker, A. P., Wright, S. J., and Xu, C. 2020. Benchmarking and parameter sensitivity of physiological and vegetation dynamics using the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) at Barro Colorado Island, Panama, Biogeosciences, 17, 3017–3044, DOI:10.5194/bg-17-3017-2020. + .. _kucharik1998: Kucharik, C.J., J.M. Norman, and S.T. Gower, 1998. Measurements of branch area and adjusting leaf area index indirect measurements. Agricultural and Forest Meteorology 91.1, pp. 69-88. @@ -1049,6 +1062,10 @@ Moorcroft, P.R., G.C. Hurtt, and S.W. Pacala, 2001. A method for scaling vegetat Myneni, R.B., et al. 2002. Global products of vegetation leaf area and fraction absorbed PAR from year one of MODIS data. Remote Sens. Environ. 83:214-231. +.. _Needhametal2022: + +Needham, J. F., Johnson, D. J., Anderson-Teixeira, K. J., Bourg, N., Bunyavejchewin, S., Butt, N., Cao, M., Cárdenas, D., Chang-Yang, C.-H., Chen, Y.-Y., Chuyong, G., Dattaraja, H. S., Davies, S. J., Duque, A., Ewango, C. E. N., Fernando, E. S., Fisher, R., Fletcher, C. D., Foster, R., ... McMahon, S. M. 2022. Demographic composition, not demographic diversity, predicts biomass and turnover across temperate and tropical forests. Global Change Biology, 28, 2895–2909. DOI:10.1111/gcb.16100 + .. _Neffetal2005: Neff, J.C., Harden, J.W. and Gleixner, G. 2005. Fire effects on soil organic matter content, composition, and nutrients in boreal interior Alaska. Canadian Journal of Forest Research-Revue Canadienne De Recherche Forestiere 35:2178-2187. @@ -1405,6 +1422,10 @@ Shi, M., J. B. Fisher, E. R. Brzostek, and R. P. Phillips, 2016: Carbon cost of Shiklomanov, I.A. 2000. Appraisal and assessment of world water resources. Water International 25:11-32. +.. _Shumanetal2024: + +Shuman, J. K., Fisher, R. A., Koven, C., Knox, R., Kueppers, L., and Xu, C. 2024. Dynamic ecosystem assembly and escaping the “fire trap” in the tropics: insights from FATES_15.0.0, Geosci. Model Dev., 17, 4643–4671, DOI:10.5194/gmd-17-4643-2024. + .. _Siebertetal2005: Siebert, S., Döll, P., Hoogeveen, J., Faures, J.M., Frenken, K., Feick, S., 2005. Development and validation of the global map of irrigation areas. Hydrol Earth Syst Sc 9:535–547 From e3e77a60c3492354d4df8aac3202ab9c401c8834 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 28 May 2026 16:10:31 -0600 Subject: [PATCH 5/5] add cn text --- doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst b/doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst index e9be1dd0a5..dcc4cd3fd7 100644 --- a/doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst +++ b/doc/source/tech_note/FATES/CLM50_Tech_Note_FATES.rst @@ -51,7 +51,7 @@ Note that there are different combinations of no-competition and fixed biogeogra Scientifically Supported CLM-FATES Configurations ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -We currently scientifally support CLM-FATES run in `carbon-only mode `_, and with either SP or no-competition + fixed biogeography mode. +We currently scientifally support CLM-FATES run in `carbon-only mode `_, and with either SP or no-competition + fixed biogeography mode. Carbon and nitrogen capabilities are currently enabled, but are still being scientifically tested. C-N mode can be turned on using the CLM namelist variable ``fates_parteh_mode = 2``, as opposed to the default ``fates_parteh_mode = 1``. Further reading