Releases | Open Sustainable Technology

FATES - Reduced Complexity Mode: Fixed Biogeography

This pre-release introduces a reduced complexity mode for FATES. It updates the FATES side to implement the transfer of the PFT area fields into FATES, and prevents plants establishing outside of areas where they are not specified in the surface dataset. The PFTs still compete, hence this is Fixed Biogeography WITH competition

Biosphere - Forest Modeling and Analysis - Fortran
Published by glemieux almost 5 years ago

FATES - Circular dependencies fix, hydro refactor, size/age mortality enhancement

This release includes all updates to the code since the last release at tag sci.1.27.3_api.7.3.0. The major updates include: refactoring FatesInterfaceMod into two separate modules to remove circular dependencies that was holding up a fix for E3SM; the addition of new capability in mortality of cohorts by size and age; a refactor of the hydraulics code that now results in regression tests passing; an update to grass phenology that allows grasses to drop stem in cold and drought conditions, and updates to SPITFIRE resulting in less ignitions, less area burn, and lower fire intensity to more acceptable behavior. This release also initiates the minting of a Zenodo DOI for the repository.
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Biosphere - Forest Modeling and Analysis - Fortran
Published by glemieux almost 5 years ago

FATES - Conversion of modules from public by default to private by default

All modules are now private by default so that developers must now explicitly declare variables/types/procedures to by public as necessary. This change has been adopted to help mitigate potential involuntary or erroneous access to data particularly when importing other modules. Relevant discussion in issue #502 and PR #539.

Biosphere - Forest Modeling and Analysis - Fortran
Published by glemieux almost 6 years ago

FATES - Updates to Root Surface Conductivity and Minimum Stomatal Conductance

This set of changes contains updates to the FATES-HYDRO code that allows for separate specification of the root-to-soil direction of maximum hydraulic conductivity at the root surface. It also makes the calculations of minimum stomatal conductance during photosynthesis more consistent across different contexts. These changes were made by Chonggang Xu.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox almost 6 years ago

FATES - Removed Erroneous Tree LAI/SAI Calls

This set of changes removed unnecessary calls to calculate plant LAI and SAI during the main driver call. These calls also erroneously did not pre-compute crown area, leading to temporarily over-inflated in-crown leaf areas. This addresses issue #540.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox almost 6 years ago

FATES - Refactor of fire code vector indices, fixes to logging

This set of changes contains a set of updates to the fire code, which makes the indexing of litter pools match indexing in relevant non-fire vectors of the code. This set also contains important bug fixes in the logging module.

Note that index changes in the fire code will impact users, in that the values in the parameter files have not changed order for the following variables: fates_FBD, fates_low_moisture_Coeff, fates_low_moisture_Slope, fates_max_decomp, fates_mid_moisture, fates_mid_moisture_Coeff, fates_mid_moisture_Slope, fates_min_moisture and fates_SAV. Specifically, index 1 of the parameters has now been moved to the last position, and the other positions have been moved to lower positions. See differences here: https://github.com/NGEET/fates/pull/523/files#diff-a236898dbb7848d5cfdf2610b0ba32c0R1124

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox almost 6 years ago

FATES - Updated Parameter File

This release contains updates to the fates parameter file. This includes the following changes:

Increased precision of all real numbers from single to double precision
Removal of out-dated "fates-pft_used" parameter
Removal of single element 1d vectors, which are now scalars
fates_seed_rain is now fates_seed_suppl
q10 parameters for frozen (fates_q10_froz) and non-frozen (fates_q10_mr) soils are now exclusively in the fates parameter file
fire parameters have been given a "fire" prefix: fates_fire_FBD, fates_fire_low_moisture_Coeff, fates_fire_low_moisture_Slope, fates_fire_mid_moisture, fates_fire_mid_moisture_Coeff, fates_fire_mid_moisture_Slope, fates_fire_min_moisture, fates_fire_SAV
logging_export_frac has been added which adds an efficiency term to trunk exporting
maximum conductivity for root surfaces (fates_hydr_kmax_rsurf) is now fates_hydr_kmax_rsurf1, and the "out-of-root-direction" on the same surface is now fates_hydr_kmax_rsurf2
parameters have been sorted in alphabetical order
sorting scripts have been debugged and updated

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox almost 6 years ago

FATES - Phenology Refactor

This release contains a refactor of the phenology timing code. These changes are all site-level changes to how leaf drop and leaf flushing is signaled. This includes a combination of code cleaning and some bug fixes.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox almost 6 years ago

FATES - Seed rain bug fix, refactor to dbh resets

This is a minor bug fix release. This adds carbon balance tracking to external seed rain, and refactors a call to reset dbh to occur outside of the parteh structure, thus allowing us to not include its effect in dbh growth diagnostics.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox about 6 years ago

FATES - Consolidation of default parameter file into 12 pfts

This release contains a consolidated default parameter file with 12 pfts. Bug fixes were also implemented to get tests passing with the biodiversity inherent in 12 vs 1 pfts.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox about 6 years ago

FATES - Secondary Forest Tracking and Fixes to External Seed Rain

This release tag contains a feature and a bug fix. Charlie Koven added the ability to discretely track both primary and secondary forest patches, paving the way to a broader expansion of human dimensions interfacing with FATES. Rosie Fisher implemented a fix to correctly account and track external seed input.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox about 6 years ago

FATES - Fixes to leaf area and demotion/promotion. Crown area conservation during fusion

This tag contains a set of changes oriented around achieving stable long-term simulations. This includes a feature addition from Charlie Koven that maintains conservation of crown area during cohort fusion. This also includes a set of fixes: 1) demotion and promotion logic, 2) litter fluxes during demotion termination, 3) ensuring minimum patch areas are being imposed, 4) ensuring that fusion and numerical imprecisions to not generate massive LAI via adjusting target plant sizes and 5) reverting to 30 leaf layers and a 2 layer canopy by default. Fixes were implemented by Ryan Knox, Charlie Koven, Jackie Shuman and Greg Lemieux.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox about 6 years ago

FATES - Carbon Isotope and Updated Photosynthesis Smoothing

This release adds a new feature in tracking carbon isotopes, provided by Liang Wei. Rosie Fisher, Anthony Walker, Alistair Rogers and Jackie Shuman also teamed up on an update to the smoothing function in the photosynthesis scheme. Charlie Koven also provided updated in-line text and descriptions for how the history diagnostics are generated.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox about 6 years ago

FATES - Leaf age discretization within cohort

This release contains a feature that discretizes the leaf biomass pool into age classes within each cohort. This makes use of the vector enabled memory structures in parteh. The discretization (binning) is controlled by the user through the parameter file. vcmax and leaf longevity are now 2d parameter arrays containing the leaf age dimension. Leaf longevity of each bin defines the turnover time governing transfer between bins. This feature was developed by Chonggang Xu, Ryan Knox, Shawn Serbin, Liang Wei, Charlie Koven, Rosie Fisher and the NGEET development team.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox about 6 years ago

FATES - Height based sorting logic and modified static array sizes

This release updates the logic to the cohort sorting logic by using height instead of diameter for cohort order. Along with this, the way ranked promotion and demotion was handled, was updated to allow cohorts of the same height to be treated equally. Static array sizes for maximum cohorts, maximum numbers of canopy layers and maximum number of leaf layers were adjusted to 100, 3 and 20 respectively (from 160, 2 and 40). These changes were mostly implemented by Charlie Koven and Ryan Knox.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox about 6 years ago

FATES - Ecosystem dynamics compatible FATES-HYDRO

This release provides the core functionality that enables FATES-HYDRO to work with a dynamic ecosystem. This functionality accounts for the fate of water in dying plants, growing plants, and newly recruited plants. This release also has added in a first pass at restart capabilities with FATES-HYDRO, although initial testing shows restarts with dynamic FATES-HYDRO is incomplete. Also note, that while FATES-HYDRO has shown stable and publication worthy results thus far, this is still considered unsupported, "beta level" code. Those using it should consider it still under development as of this release, and should consult with Chonggang Xu and Bradley Christoffersen. Authors are Chonggang Xu, Bradley Christoffersen and Ryan Knox, with consultation from Yilin Fang, Junyan Ding and others on the FATES development team.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox over 6 years ago

FATES - Fixes to fire mortality diagnostics, patch disturbance area checks and trimming

This release adds a modest set of feature changes and several small bug fixes. The small feature additions improve the way that mortality is calculated for fire, by saving these diagnostics to a tracking array. The bug fixes are as follows: 1) Many site level diagnostics were not being saved in restarts, thereby the first day following a restart was contributing bogus information to the diagnostics, 2) the net assimilation budget had not been correctly calculating night-time respiration for trimming calculations (the prognostic carbon balance was not affected) , and 3) in very rare cases, patches with nearly zero sizes were creating problems during patch generation and creating problems during carbon balance checks, so checks were implemented. Contributions from Jackie Shuman, Charlie Koven, Ryan Knox, and others.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox over 6 years ago

FATES - Remove Lasslop wind effects on fire Rate of Spread

This release contains contributions from Jackie Shuman. Per her pull request:
Within SFMain remove the conditional clause that reduces fire rate of spread for high wind speeds. Within parameter files removed the parameter for fire_wind_max that triggers the conditional.
This showed an improvement in mode simulated fire behavior in past work (Lasslop et al 2014), but current research demonstrates there is not a clear link between high winds and a reducing effect on rate of spread. Andela et al 2018 ESSDD https://doi.org/10.5194/essd-2018-89
This PR acts to remove this Lasslop et al (2014) reducing effect, and revert back to original Thonicke ROS wind effect.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox over 6 years ago

FATES - Provisions for Coastal Grasses

This tag contains key changes that enable simulation of a coastal salt marsh. Key features are 1) an allowance that when maximum height/dbh reached, all the carbons goes to the bstore for grasses; 2) when plant dies, bstore goes to reproduction for grasses; 3) recruitment only happens at the growing seasons so that the newly developed cohorts are viable; 4) add a new capability to simulate the impact of salinity and sulphide through btran; and 5) a
new parameter file for Spartina.
These changes were developed by Joel Rowland and Chonggang Xu, with help from Rosie Fisher, Charlie Koven and Ryan Knox.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox over 6 years ago

FATES - Hydro, Recruitment and Radiation Refactors

This tag contains mostly updates, bug fixes and refactors. Chongang Xu and Yilin Fang submitted updates to FATES-hydro related to parameters and commenting. This also included a pass through the code to remove calls to the dble() intrinsic (replaced by real(,r8)). Charlie Koven added a diagnostic that tracks recruitment across size classes. Ryan Knox refactored the restart system to bypass the saving of 3D arrays, dimensioned by pft x canopy-layer x leaf-layer.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox over 6 years ago

FATES - PARTEH v1

The Plant Allocation Reactive Transport Extensible Hypotheses (PARTEH) software infrastructure has been added. This module allows FATES to accommodate plants with much greater flexibility in how they are represented (nutrients, multiple discrete spaces for state variables, etc).

This is a minor feature release, as the science changes are small. This is a major API change because this release breaks compatibility with previous versions of the host model API.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox over 6 years ago

FATES - Case changes to debug flags

Changes in this release were small. The case of debug flags were changed to lowercase from uppercase. These changes were identified and requested by Erik Kluzek to aid in future compatibility with CESM.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox over 6 years ago

FATES - Fire fluxes updates/fixes for leaves/sapwood

This release includes fixes to the fire flux routine for live plants. The fire flux for live plants was updated to remove leaves according to the fraction of the crown scorched by fire. Consumption of branches would burn sapwood and remove stemwood, and will be addressed in a separate issue with separate fluxes. These changes also included more verbose naming of variables. The equation was also updated to remove the minimum evaluation, as the fraction_crown_burned term already has a check on it to confirm it is not greater than 1 within the fire routine.
Contributors: Jacquelyn Shuman

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox over 6 years ago

FATES - Sapwood allometry house cleaning

This release does not add new features, but mostly does house-cleaning for sapwood allometry. The updates include an update to the parameter latosa_int and latosa_slp, to be inverted and more verbose: sa_per_la_int and sa_per_la_slp. Also, the slope term was updated to respond to increases in height (not diameter). A sapwood area was also output from the function, to aid in hydraulics calculations.
Updates to the parameter file require updates to the default parameter files in E3SM and CTSM used in testing (hence the minor API change).

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox over 6 years ago

FATES - Variable SLA Profile and Wood CN Ratio

This release adds two features. Marlies Kovenock added the capacity to have variable SLA throughout the canopy depth, increasing as a function of integrated leaf area. Charlie Koven added a dedicated wood CN ratio parameter that effects sapwood respiration rates.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox almost 7 years ago

FATES - Bug fixes - demotion/promotion precision, growth, seed-decay

This tag contains mostly bug fixes, but also changes that may considered feature improvements. A bug fix was applied to the calculation of target sapwood in allometry. A bug fix was applied to the orderering of allometric targets during and after re-calculation of dbh. A bug fix was applied to a double counting of seed-decay flux (which has improved error magnitude on carbon balance diagnostics). Various updates to comments and in-code documentation, inlcluding a re-defining of intra-cellular co2 concentrations to inter-cellular. Bug fixes were applied to an incorrectly defined constant which was a 4-byte real in an intrinsice expecting 8-byte reals. Finally, the promotion/demotion scheme was refactored to allow higher precisions, and an area correction scheme was re-ordered to move area out of the largest patch instead of the oldest.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox almost 7 years ago

FATES - Variable Soil Depths and Expanded History Dimensions

This release contains a change to the interface with E3SM/CTSM. Please ensure that the corresponding API change has been issued in the version of those drivers.

Two changes are contained in this release. Firstly, new history dimensions (age x pft) and (size x age x pft) have been added, along with corresponding new history variables. New history variables are also available to help with lidar comparisons. Thanks Charlie Koven. Secondly, the host land-models CTSM and E3SM now have the capacity to have variable depths of coils at the column (equivalent to fates site) level, and FATES now allocates soil depths accordingly. To facilitate this, a modest refactor of rooting depth functions has been started.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox almost 7 years ago

FATES - FATES Hydro

This release contains the beta version of plant hydraulics by Christoffersen and Xu et al.. Plant hydraulics has been tested an developed at key sites, but limited testing has been performed globally and will be developed in later releases. Hydraulics also has limited support during growth, and some features need to be added to address the flux of water bound in dying vegetation back into the ecosystem and water-balances on newly recruited plants.

The API tag was incremented to denote a new parameter was added, and thus parameter files must now include the scalar: fates_hydr_kmax_rsurf.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox almost 7 years ago

FATES - Bug fix - Stomatal conductance scaling

This release is a bug fix on the calculation of stomatal conductance, and how it is scaled from leaf layer to cohort. Fixes also correct gpp and dark respiration calculations in isolated cases of un-ful leaf layers.
This is a result changing release.

Biosphere - Forest Modeling and Analysis - Fortran
Published by rgknox almost 7 years ago

FATES - Bug fixes - pointer-pointers , respiration and memory leaks

This release includes three bug fixes.
Patch and cohort pointers to sites that pointed to spread terms were being forgotten during calls to calculate crown areas, and thus the site pointer was removed. Respiration accumulation was added to restarts. A memory leak was fixed during cohort termination.