diff --git a/docs/source/CLM50_Tech_Note_References.rst b/docs/source/CLM50_Tech_Note_References.rst index 2e1f49e..b05e71f 100644 --- a/docs/source/CLM50_Tech_Note_References.rst +++ b/docs/source/CLM50_Tech_Note_References.rst @@ -112,6 +112,21 @@ Variability in leaf and litter optical properties: implications for BRDF model inversions using AVHRR, MODIS, and MISR. Remote Sens. Environ. 63:243-257. +.. _Asneretal2004: + +|br| + +Asner, G. P., Keller, M., Pereira, J. R., Zweede, J. C., and Silva, J. N. M. 2004. +Canopy damage and recovery after selective logging in amazonia: field and satellite +studies, Ecological Applications, 14, 280-298, 10.1890/01-6019. + +.. _Asneretal2005: + +|br| + +Asner, G. P., Knapp, D. E., Broadbent, E. N., Oliveira, P. J. C., Keller, M., and Silva, J. N. 2005. +Selective Logging in the Brazilian Amazon, Science, 310, 480. + .. _AxelssonAxelsson1986: |br| @@ -631,6 +646,12 @@ Drewniak, B., Song, J., Prell, J., Kotamarthi, V.R., and Jacob, R. 2013. Modeling agriculture in the Community Land Model. Geosci. Model Dev. 6:495-515. DOI:10.5194/gmd-6-495-2013. +.. _dykstraetal2002: + +|br| + +Dykstra, D. P. 2002. Reduced impact logging: concepts and issues, Applying Reduced Impact Logging to Advance Sustainable Forest Management, 23-39. + .. _Dunfieldetal1993: |br| @@ -680,6 +701,12 @@ Nobel, C.B. Osmond, and H. Zeigler (editors) Encyclopedia of Plant Physiology. Vol. 12B. Physiological Plant Ecology. II. Water Relations and Carbon Assimilation. Springer-Verlag, New York. +.. _feldpauschetal2005: + +|br| + +Feldpausch, T. R., Jirka, S., Passos, C. A. M., Jasper, F., and Riha, S. J. 2005. When big trees fall: Damage and carbon export by reduced impact logging in southern Amazonia, Forest Ecology and Management, 219, 199-215, https://doi.org/10.1016/j.foreco.2005.09.0035. + .. _Ferrari1999: |br| @@ -1755,6 +1782,12 @@ carbon and nitrogen dynamics in estimating net primary productivity for potential vegetation in North America. Global Biogeochem. Cycles 6:101-124. +.. _macphersonetal2012: + +|br| + +Macpherson, A. J., Carter, D. R., Schulze, M. D., Vidal, E., and Lentini, M. W. 2012. The sustainability of timber production from Eastern Amazonian forests, Land Use Policy, 29, 339-350, https://doi.org/10.1016/j.landusepol.2011.07.004. + .. _Medlynetal2011: |br| @@ -2091,6 +2124,12 @@ New York, 480 pp. Pelletier, J. D., P. D. Broxton, P. Hazenberg, X. Zeng, P. A. Troch, G. Y. Niu, Z. Williams, M. A. Brunke, and D. Gochis, 2016: A gridded global data set of soil, intact regolith, and sedimentary deposit thicknesses for regional and global land surface modeling. J. Adv. Mod. Earth Sys. 8:41-65. +.. _pereirajretal2002: + +|br| + +Pereira Jr, R., Zweede, J., Asner, G. P., and Keller, M. 2002. Forest canopy damage and recovery in reduced-impact and conventional selective logging in eastern Para, Brazil, Forest Ecology and Management, 168, 77-89, http://dx.doi.org/10.1016/S0378-1127(01)00732-0. + .. _peterson1986: |br| @@ -2194,6 +2233,12 @@ millennial-scale deglaciation simulations. Geophys. Res. Lett. ** Purves, D.W. et al., 2008. Predicting and understanding forest dynamics using a simple tractable model. Proceedings of the National Academy of Sciences 105.44, pp. 17018-17022. +.. _putzetal2008: + +|br| + +Putz, F. E., Sist, P., Fredericksen, T., and Dykstra, D., 2008. Reduced-impact logging: Challenges and opportunities, Forest Ecology and Management, 256, 1427-1433, https://doi.org/10.1016/j.foreco.2008.03.036. + .. _Qianetal2006: |br| diff --git a/docs/source/fates_tech_note.rst b/docs/source/fates_tech_note.rst index 13b5444..90e9ce6 100644 --- a/docs/source/fates_tech_note.rst +++ b/docs/source/fates_tech_note.rst @@ -3192,4 +3192,168 @@ within the area affected by fire is a function of the ratio between | s}` | parameter | | | +-----------------+-----------------+-----------------+-----------------+ +Wood Harvest (The selective logging module) +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +Over half of all tropical forests have been cleared or logged, and almost half of standing +old-growth tropical forests are designated by national forest services for timber production +(:ref:`Sist et al., 2015`). Disturbances that result from logging are known to +cause forest degradation at the same magnitude as deforestation each year in terms of both +geographic extent and intensity, with widespread collateral damage to remaining trees, +vegetation and soils, leading to disturbance to water, energy, and carbon cycling, as well as +ecosystem integrity (:ref:`Keller et al., 2004 `; :ref:`Asner et al., 2004 `). + +The selective logging module in FATES mimics the ecological, biophysical, +and biogeochemical processes following a logging event. The module +(1) specifies the timing and areal extent of a logging event; +(2) calculates the fractions of trees that are damaged by direct felling, collateral damage, +and infrastructure damage, and adds these size-specific plant mortality types to FATES; +(3) splits the logged patch into disturbed and intact new patches; +(4) applies the calculated survivorship to cohorts in the disturbed patch; +and (5) transports harvested logs off-site by adding the remaining necromass +from damaged trees into coarse woody debris and litter pool. + +Logging practices +----------------- + +The logging module struture and parameterization is based on detailed field and remote +sensing studies (:ref:`Putz et al., 2008`; :ref:`Asner et al., 2004 `; +:ref:`Pereira Jr et al., 2002 `; :ref:`Asner et al., 2005 `; +:ref:`Feldpausch et al., 2005 `). Logging infrastructure including roads, +skids, trails, and log decks are represented (Figure 1.17.1). The construction of log decks used +to store logs prior to road transport leads to large canopy openings but their contribution +to landscape-level gap dynamics is small. In contrast, the canopy gaps caused by tree felling +are small but their coverage is spatially extensive at the landscape scale. Variations in logging +practices significantly affect the level of disturbance to tropical forest following logging +(:ref:`Pereira Jr et al., 2002 `; :ref:`Macpherson et al., 2012 `; +:ref:`Dykstra, 2002 `; :ref:`Putz et al., 2008 `. + +Logging operations in the tropics are often carried out with little planning, and typically use +heavy machinery to access the forests accompanied by construction of excessive roads and skid trails, +leading to unnecessary tree fall and compaction of the soil. We refer to these typical operations as +conventional logging (CL). In contrast, reduced impact logging (RIL) is a practice with extensive +pre-harvest planning,where trees are inventoried and mapped out for the most efficient and +cost-effective harvest and seed trees are deliberately left on site to facilitate faster recovery. +Through planning, the construction of skid trails and roads, soil compaction and disturbance +can be minimized. Vines connecting trees are cut and tree-fall directions are controlled to +reduce damages to surrounding trees. Reduced impact logging results in consistently less disturbance +to forests than conventional logging +(:ref:`Pereira Jr et al. 2002 `; :ref:`Putz et al. 2008 `). + +.. figure:: images/Logging_figure1.png + +Mortality associated with logging +--------------------------------- + +The FATES logging module was designed to represent a range of logging practices in field operations +at a landscape level. Once logging events are activated, we define three types of mortality +associated with logging practices: direct-felling mortality (:math:`lmort_{direct}`), +collateral mortality (:math:`lmort _{collateral}`), and mechanical mortality (:math:`lmort_{mechanical}`). +The direct felling mortality represents the fraction of trees selected for harvesting that are greater +or equal to a diameter threshold (this threshold is defined by the diameter at breast height (DBH) = 1.3 m +denoted as :math:`DBH_{min}`); collateral mortality denotes the fraction of adjacent trees +that killed by felling of the harvested trees; and the mechanical mortality represents the +fraction of trees killed by construction of log decks, skid trails and roads for accessing +the harvested trees, as well as storing and transporting logs offsite (Figure 1.17.1a). +In a logging operation, the loggers typically avoid large trees when they build log decks, skids, +and trails by knocking down relatively small trees as it is not economical to knock down large trees. +Therefore, we implemented another DBH threshold, :math:`DBH_{max_{infra}}`, so that only a fraction +of trees :math:`<=DBH_{max_{infra}}` (called mechanical damage fraction) are removed for +building infrastructure (:ref:`Feldpausch et al., 2005 `). + +Patch dynamics following logging disturbance +-------------------------------------------- + +To capture the disturbance mechanisms and degree of damage associated with logging practices +at the landscape level, we apply the mortality types following a workflow designed to correspond to +field operations. In FATES, as illustrated in Figure 1.17.2., individual trees of all plant functional types (PFTs) +in one patch are grouped into cohorts of similar-sized trees, whose size and population sizes evolve in time +through processes of recruitment, growth, and mortality. For the purpose of reporting and visualizing the model state, +these cohorts are binned into a set of 13 fixed size classes in terms of the diameter at the breast height (DBH) +(i.e., 0 - 5, 5 - 10, 10 - 15, 15 - 20, 20 - 30 , 30 - 40, 40 - 50, 50 - 60, 60 - 70, 70 - 80, 80 - 90, +90 - 100, and :math:`<=100 cm`). Cohorts are further organized into canopy and understory layers, +which are subject to different light conditions (Figure 1.17.2a). When logging activities occur, +the canopy trees and a portion of big understory trees lose their crown coverage through direct felling +for harvesting logs, or as a result of collateral and mechanical damages ((Figure 1.17.2b). The fractions of +(only the) canopy trees affected by the three mortality mechanisms are then summed up to specify the areal +percentages of an old (undisturbed) and a new (disturbed) patch caused by logging in the patch fission process +(Figure 1.17.2c). After patch fission, the canopy layer over the disturbed patch is removed, +while that over the undisturbed patch stays untouched (Figure 1.17.2d). In the undisturbed patch, the survivorship of +understory trees is calculated using an understory death fraction consistent with whose default value corresponds +to that used for natural disturbance (i.e., 0.5598). To differentiate logging from natural disturbance, +a slightly elevated, logging-specific understory death fraction is applied in the disturbed patch instead at the +time of the logging event. Based on data from field surveys over logged forest plots in southern Amazon +(:ref:`Feldpausch et al., 2005 `), understory death fraction corresponding to logging +is now set to be 0.65 as the default, but can be modified via the FATES parameter file (Figure 1.17.2e). +Therefore, the logging operations will change the forest from the undisturbed state shown in Figure 1.17.2a +to a disturbed state in Figure 1.17.2f in the logging module. It is worth mentioning that the newly generated +patches are tracked according to age since disturbance and will be merged with other patches of similar +canopy structure following the patch fusion processes in FATES in later time steps of a simulation, +pending the inclusion of separate land-use fractions for managed and unmanaged forest. + +.. figure:: images/Logging_figure2.png + +Flow of necromass following logging disturbance +----------------------------------------------- + +Logging operations affect forest structure and composition, and also carbon cycling +(:ref:`Palace et al., 2008 `) by modifying the live biomass pools and flow of +necromass (Figure 1.17.3). Following a logging event, the logged trunk products from the harvested trees +are transported off-site (as an added carbon pool for resource management in the model), while their branches +enter the coarse woody debris (CWD) pool, and their leaves and fine roots enter the litter pool. Similarly, +trunks and branches of the dead trees caused by collateral and mechanical damages also become CWD, while their +leaves and fine roots become litter. Specifically, the densities of dead trees as a result of direct felling, +collateral, and mechanical damages in a cohort are calculated as follows: + +.. math:: D_{direct} = lmort_{direct} * n/A +.. math:: D_{collateral} = lmort_{collateral} * n/A +.. math:: D_{mechanical} = lmort_{mechanical} * n/A + +where :math:`A` stands for the area of the patch being logged, and :math:`n` is the number of individuals +in the cohort where the mortality types apply (i.e., as specified by the size thresholds, :math:`DBH_{min}` +and :math:`DBH_{max_{infra}}`). For each cohort, we denote :math:`D_{indirect} = D_{collateral} + D_{mechanical}` +and :math:`D_{total} = D_{direct} + D_{indirect}`, respectively. + +.. figure:: images/Logging_figure3.png + +Leaf litter (:math:`Litter_{leaf}, [kg C]`) and root litter (:math:`Litter_{root}, [kg C]`) at the cohort level +are then calculated as: + +.. math:: Litter_{leaf} = D_{total} * B_{leaf} * A +.. math:: D_{leaf} = D_{total} * (B_{root} + B_{store}) * A + +where :math:`B_{leaf}`, :math:`B_{root}`, :math:`B_{store}` are live biomass in leaves and fine roots, and stored +biomass in the labile carbon reserve in all individual trees in the cohort of interest. + +Following the existing CWD structure in FATES (:ref:`Fisher et al., 2015 `), CWD in the logging module +is first separated into two categories: above-ground CWD and below-ground CWD. Within each category, four size classes +are tracked based on their source, following :ref:`Thonicke et al. (2010)`: trunks, large branches, +small branches and twigs. Above-ground CWD from trunks (:math:`CWD_{trunk_{agb}}, [kg C]`) and large branches/small +branches/twig (:math:`CWD_{branch_{agb}}, [kg C]`) are calculated as follows: + +.. math:: CWD_{trunk_{agb}} = D_{indiect} * AGB_{stem} * f_{trunk} * A +.. math:: CWD_{branch_{agb}} = D_{total} * AGB_{stem} * f_{branch} * A + +where :math:`AGB_{stem}` is the amount of above ground stem biomass in the cohort, :math:`f_{trunk}` and :math:`f_{branch}` +represent the fraction of trunks and large branches/small branches/twig. Similarly, the below-ground CWD from +trunks (:math:`CWD_{trunk_{bg}}, [kg C]`) and branches/twig (:math:`CWD_{branch_{bg}}, [kg C]`) are calculated as follows: + +.. math:: CWD_{trunk_{bg}} = D_{total} * B_{root_{bg}} * f_{trunk} * A +.. math:: CWD_{branch_{bg}} = D_{total} * B_{root_{bg}} * f_{branch} * A + +where :math:`B_{croot} [kg C]` is the amount of coarse root biomass in the cohort. Site-level total litter and CWD inputs +can then be obtained by integrating the corresponding pools over all the cohorts in the site. To ensure mass conservation, + +.. math:: \delta_B= \delta_{Litter} + \delta_{CWD} + trunk_{product} + +where :math:`\delta_B` is total loss of biomass due to logging, :math:`\delta_{litter}` and :math:`\delta_{CWD}` are the +increments in litter and CWD pools, and :math:`trunk_{product}` represents harvested logs shipped offsite. + +Following the logging event, the forest structure and composition in terms of cohort distributions, as well as the live +biomass and necromass pools are updated. Following this logging event update to forest structure, the native processes +simulating physiology, growth and competition for resources in and between cohorts resume. Since the canopy layer is +removed in the disturbed patch, the existing understory trees are promoted to the canopy layer, but, in general, +the canopy is incompletely filled in by these newly-promoted trees, and thus the canopy does not fully close. +Therefore, more light can penetrate and reach the understory layer in the disturbed patch, leading to increases +in light-demanding species in the early stage of regeneration, followed by a succession process in which shade +tolerant species dominate gradually. diff --git a/docs/source/images/Logging_figure1.png b/docs/source/images/Logging_figure1.png new file mode 100644 index 0000000..0d60e58 Binary files /dev/null and b/docs/source/images/Logging_figure1.png differ diff --git a/docs/source/images/Logging_figure2.png b/docs/source/images/Logging_figure2.png new file mode 100644 index 0000000..908da02 Binary files /dev/null and b/docs/source/images/Logging_figure2.png differ diff --git a/docs/source/images/Logging_figure3.png b/docs/source/images/Logging_figure3.png new file mode 100644 index 0000000..6cbc366 Binary files /dev/null and b/docs/source/images/Logging_figure3.png differ