release v2.2.0 "Carbon and Nitrogen in Sync"

CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 title: "SIPNET: Simple Photosynthesis and Evapotranspiration Model"
-version: 2.1.0
+version: 2.2.0
 abstract: >
   SIPNET (Simple Photosynthesis and Evapotranspiration Model) is a process-based
   ecosystem model designed to simulate carbon and water fluxes and (optionally) agricultural management
@@ -56,7 +56,7 @@ keywords:
 preferred-citation:
   type: software
   title: "SIPNET: Simple Photosynthesis and Evapotranspiration Model"
-  version: 2.1.0
+  version: 2.2.0
   url: https://github.com/PecanProject/sipnet
   authors:
     - family-names: Michael

docs/CHANGELOG.md

@@ -19,13 +19,22 @@ sections to include in release notes:
 
 ### Removed
 
-### Git SHA
 -->
 
 ## [Unreleased]
 
 ### Added
 
+### Fixed
+
+### Changed
+
+### Removed
+
+## **SIPNET [2.2.0] - "Carbon and Nitrogen in Sync"**
+
+### Added
+
 - `sipnet-view` tool for visualizing SIPNET output files (#317)
 - `leafon` and `leafoff` events for tracking phenological transitions (#326)
 - `leafon` limited by available carbon and nitrogen; N storage pool; N resorption on `leafoff` (#337)
@@ -34,11 +43,16 @@ sections to include in release notes:
 - New `--debug-log` CLI option to enable debug logging (#352)
 - Ability to create derived columns in `sipnet-view` (#355)
 - New `sipnet-debug-view` tool for visualizing SIPNET debug output files (#359)
-- Plant mortality check with event output on occurrence (#359)
+- Plant mortality check with transfer of remaining carbon and nitrogen to litter and soil pools and a `plantdeath` record in `events.out` (#359)
+- New required nitrogen-cycle parameters `plantStorageNInit` and `leafNResorptionFrac` (#337)
 - Guard against negative mineral N due to volatilization and/or leaching (#375)
 
 ### Fixed
 
+- Corrected plant carbon accounting so the accounting-only carbon delta is not treated as nitrogen-bearing woody biomass (#359).
+- Corrected nitrogen resorption and storage accounting during senescence and negative growth, including the ordering of storage use, fixation, and uptake (#359).
+- Corrected the nitrogen mass-balance sign convention (#359).
+
 ### Changed
 
 - Renamed the CLI option `--file-name` to `--file-prefix` for clarity while keeping `--file-name` as a backward-compatible alias (#320)
@@ -50,9 +64,7 @@ sections to include in release notes:
 - Schema version from restart checkpoint format; model version is sufficient (#338)
 - Resorbed nitrogen from leaf-off events in events.out (this value can be calculated from leaf-off carbon and parameters) (#368)
 
-### Git SHA
-
-## **SIPNET 2.1.0 - "Nitrogen Cycle, Methane, and Restart"**
+## **SIPNET [2.1.0] - "Nitrogen Cycle, Methane, and Restart"**
 
 ### Added
 
@@ -96,10 +108,7 @@ sections to include in release notes:
 - `microbes` option and functionality (#257)
 - 'Notes' line at top of `sipnet.out` header (#267)
 
-### Git SHA
-[TBD]
-
-## **SIPNET 2.0.0 - "SIPNET Overhaul"**
+## **SIPNET [2.0.0] - "SIPNET Overhaul"**
 
 ### Added
 
@@ -147,10 +156,7 @@ sections to include in release notes:
 - Removed `soilWetness` mode (#127)
 - Removed obsolete model params; sipnet now warns on unknown params in the params file (#124)
 
-### Git SHA
-[TBD]
-
-## **SIPNET 1.3.0 - "Event Handler"**
+## **SIPNET [1.3.0] - "Event Handler"**
 
 v1.3.0 represents the initial development of support for agricultural management events.
 
@@ -165,10 +171,7 @@ v1.3.0 represents the initial development of support for agricultural management
 - Update Doxyfile
 - Add `make help`.
 
-### Git SHA
-8ff893e61d69d0374bdf0fa14d156fd621c40eb4
-
-## **SIPNET 1.2.1 - "Add LICENSE and minor fixes"**
+## **SIPNET [1.2.1] - "Add LICENSE and minor fixes"**
 
 ### Added
 
@@ -180,10 +183,7 @@ v1.3.0 represents the initial development of support for agricultural management
 - Minor fixes prior to agricultural management implementation.
 - Bug fix for output formatting (identified by @Qianyuxuan).
 
-### Git SHA
-0c77ce863ac61113740c759dbe502a74e2d64edf
-
-## **SIPNET 1.2.0 - "fAPAR assimilation"**
+## **SIPNET [1.2.0] - "fAPAR assimilation"**
 
 ### Added
 
@@ -193,10 +193,7 @@ v1.3.0 represents the initial development of support for agricultural management
 
 Zobitz, J.M., David J.P. Moore, Tristan Quaife, Bobby H. Braswell, Andrew Bergeson, Jeremy A. Anthony, and Russell K. Monson. 2014. “Joint Data Assimilation of Satellite Reflectance and Net Ecosystem Exchange Data Constrains Ecosystem Carbon Fluxes at a High-Elevation Subalpine Forest.” Agricultural and Forest Meteorology 195–196 (September):73–88. https://doi.org/10.1016/j.agrformet.2014.04.011.
 
-### Git SHA
-97a225956775035506f573a29c7022de8d7d269d
-
-## **SIPNET 1.1.0 - "Roots and Microbes"**
+## **SIPNET [1.1.0] - "Roots and Microbes"**
 
 **Moore et al. (2008)**
 
@@ -215,7 +212,7 @@ Moore, David J.P., Jia Hu, William J. Sacks, David S. Schimel, and Russell K. Mo
 
 Zobitz, J. M., D. J. P. Moore, W. J. Sacks, R. K. Monson, D. R. Bowling, and D. S. Schimel. 2008. “Integration of Process-Based Soil Respiration Models with Whole-Ecosystem CO2 Measurements.” Ecosystems 11 (2): 250–69. https://doi.org/10.1007/s10021-007-9120-1.
 
-## **SIPNET 1.0.0 - "SIPNET First Release"**
+## **SIPNET [1.0.0] - "SIPNET First Release"**
 
 The first release of SIPNET reflected a series of improvements over the original SIPNET model (Braswell et al., 2005).
 The model was developed by Bill Sacks and Dave Moore, with contributions from John Zobitz. The model was parameterized using data from the Harvard Forest flux tower using MCMC (Sacks et al., 2006).
@@ -238,9 +235,6 @@ The model was designed to simulate the carbon and water cycles of a forest ecosy
 - Shut down photosynthesis and foliar respiration when soil temperature < threshold.
 - Partition autotrophic and heterotrophic respiration.
 
-### Git SHA
-47d6546e245384dbda7e981a3bc8b729d4f756fc
-
 ### Publications
 
 Braswell, Bobby H., William J. Sacks, Ernst Linder, and David S. Schimel. 2005. “Estimating Diurnal to Annual Ecosystem Parameters by Synthesis of a Carbon Flux Model with Eddy Covariance Net Ecosystem Exchange Observations.” Global Change Biology 11 (2): 335–55. https://doi.org/10.1111/j.1365-2486.2005.00897.x.
@@ -251,3 +245,13 @@ Sacks, William J., David S. Schimel, Russell K. Monson, and Bobby H. Braswell. 2
 
 ### Changed
 - Renamed n2oFlux output column to n2o and converted from flux (rate) to timestep-integrated amount.
+
+[Unreleased]: https://github.com/PecanProject/sipnet/compare/v2.1.0...HEAD
+[2.2.0]: `https://github.com/PecanProject/sipnet/compare/v2.1.0...v2.2.0`
+[2.1.0]: https://github.com/PecanProject/sipnet/compare/v2.0.0...v2.1.0
+[2.0.0]: https://github.com/PecanProject/sipnet/compare/v1.3.0...v2.0.0
+[1.3.0]: https://github.com/PecanProject/sipnet/compare/v1.2.1...v1.3.0
+[1.2.1]: https://github.com/PecanProject/sipnet/compare/v1.2.0...v1.2.1
+[1.2.0]: https://github.com/PecanProject/sipnet/compare/v1.1.0...v1.2.0
+[1.1.0]: https://github.com/PecanProject/sipnet/compare/v1.0.0...v1.1.0
+[1.0.0]: https://github.com/PecanProject/sipnet/releases/tag/v1.0.0

docs/Doxyfile

@@ -48,7 +48,7 @@ PROJECT_NAME           = SIPNET
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 2.1.0
+PROJECT_NUMBER         = 2.2.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

docs/parameters.md

@@ -107,6 +107,7 @@ Run-time parameters can change from one run to the next, or when the model is st
 | $N_{\text{org, litter},0}$        | litterOrgNInit | Initial litter organic nitrogen content                                  | $\text{g N} \cdot \text{m}^{-2}$                                    |                                                                                          |
 | $N_{\text{org, soil},0}$          | soilOrgNInit   | Initial soil organic nitrogen content                                    | $\text{g N} \cdot \text{m}^{-2}$                                    |                                                                                          |
 | $N_{\text{min, soil},0}$          | mineralNInit   | Initial mineral nitrogen content                                         | $\text{g N} \cdot \text{m}^{-2}$                                    | Single mineral N pool used by soil and litter N fluxes                                   |
+| $N_{\text{plant,storage},0}$      | plantStorageNInit | Initial plant nitrogen storage pool                                   | $\text{g N} \cdot \text{m}^{-2}$                                    | Use 0 unless initial storage pool is known or estimated                                          |
 | $f_{\text{fine root},0}$          | fineRootFrac   | Fraction of `plantWoodInit` allocated to initial fine root carbon pool   | unitless                                                            |                                                                                          |
 | $f_{\text{coarse root},0}$        | coarseRootFrac | Fraction of `plantWoodInit` allocated to initial coarse root carbon pool | unitless                                                            |                                                                                          |
 | $W_{\text{snow},0}$               | snowInit       | Initial snow water equivalent                                            | cm water equivalent                                                 |                                                                                          |
@@ -207,6 +208,7 @@ Run-time parameters support mineral nitrogen losses through volatilization and l
 | ---------------------- | -------------------- | ------------------------------------------------------------------------------------------------------------------------------------ | ----------------- | -------------------------------- |
 | $K_\text{vol}$         | nVolatilizationFrac  | Nitrogen volatilization rate constant that determines the maximum rate of N volatilization as a proportion of available $N_\text{min}$ | $\text{day}^{-1}$ | \eqref{eq:n_vol}                 |
 | $f^N_{\text{leach}}$   | nLeachingFrac        | Fraction of $N_\text{min}$ available to be leached, applied after scaling by $\phi = \min(F^W_\text{drainage}/W_\text{WHC}, 1)$      | $\text{day}^{-1}$  | \eqref{eq:n_leach}               |
+| $f^N_{\text{resorb}}$ | leafNResorptionFrac | Fraction of senescing leaf nitrogen transferred to the plant nitrogen storage pool | unitless |  |
 
 ### Moisture-Related Parameters
 

src/sipnet/version.h

@@ -1,7 +1,7 @@
 #ifndef SIPNET_VERSION_H
 #define SIPNET_VERSION_H
 
-#define NUMERIC_VERSION "2.1.0"
+#define NUMERIC_VERSION "2.2.0"
 
 // To enable, compile with `-DGIT_HASH="<your revision here>"`
 #ifdef GIT_HASH