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Title: Addressing numerical challenges in introducing a reactive transport code into a land surface model: A biogeochemical modeling proof-of-concept with CLM-PFLOTRAN 1.0: Modeling Archive

This Modeling Archive is in support of an NGEE Arctic discussion paper under review and available at doi:10.5194/gmd-9-927-2016. The purpose is to document the simulations to allow verification, reproducibility, and follow-up studies. This dataset contains shell scripts to create the CLM-PFLOTRAN cases, specific input files for PFLOTRAN and CLM, outputs, and python scripts to make the figures using the outputs in the publication. Through these results, we demonstrate that CLM-PFLOTRAN can approximately reproduce CLM results in selected cases for the Arctic, temperate and tropic sites. In addition, the new framework facilitates mechanistic representations of soil biogeochemistry processes in the land surface model.
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Publication Date:
DOE Contract Number:
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Research Org(s):
Next Generation Ecosystems Experiment - Arctic, Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (US)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
54 Environmental Sciences; ngee; ngee arctic; nonnegativity; reactive transport model; soil biogeochemistry
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  1. This Modeling Archive is in support of an NGEE Arctic discussion paper under review and available at Vast carbon stocks stored in permafrost soils of Arctic tundra are under risk of release to atmosphere under warming climate. Ice--wedge polygons in the low-gradient polygonal tundramore » create a complex mosaic of microtopographic features. The microtopography plays a critical role in regulating the fine scale variability in thermal and hydrological regimes in the polygonal tundra landscape underlain by continuous permafrost. Modeling of thermal regimes of this sensitive ecosystem is essential for understanding the landscape behaviour under current as well as changing climate. We present here an end-to-end effort for high resolution numerical modeling of thermal hydrology at real-world field sites, utilizing the best available data to characterize and parameterize the models. We develop approaches to model the thermal hydrology of polygonal tundra and apply them at four study sites at Barrow, Alaska spanning across low to transitional to high-centered polygon and representative of broad polygonal tundra landscape. A multi--phase subsurface thermal hydrology model (PFLOTRAN) was developed and applied to study the thermal regimes at four sites. Using high resolution LiDAR DEM, microtopographic features of the landscape were characterized and represented in the high resolution model mesh. Best available soil data from field observations and literature was utilized to represent the complex hetogeneous subsurface in the numerical model. This data collection provides the complete set of input files, forcing data sets and computational meshes for simulations using PFLOTRAN for four sites at Barrow Environmental Observatory. It also document the complete computational workflow for this modeling study to allow verification, reproducibility and follow up studies. « less
  2. This Modeling Archive is in support of an NGEE Arctic manuscript under review. A new subgrid model was implemented in the Advanced Terrestrial Simulator (ATS) to capture micro-topography effects on surface flow. A comparison of the fine-scale simulations on seven individual ice-wedge polygons and amore » cluster of polygons was made between the results of the subgrid model and no-subgrid model. Our finding confirms that the effects of small-scale spatial heterogeneities can be captured in the coarsened models. The dataset contains meshes, inputfiles, subgrid parameters used in the simulations. Python scripts for post-processing and files for geometric analyses are also included. « less
  3. The intercomparison of Radiation Codes in Climate Models (ICRCCM) study was launched under the auspices of the World Meteorological Organization and with the support of the U.S. Department of Energy to document differences in results obtained with various radiation codes and radiation parameterizations in generalmore » circulation models (GCMs). ICRCCM produced benchmark, longwave, line-by-line (LBL) fluxes that may be compared against each other and against models of lower spectral resolution. During ICRCCM, infrared fluxes and cooling rates for several standard model atmospheres with varying concentrations of water vapor, carbon dioxide, and ozone were calculated with LBL methods at resolutions of 0.01 cm-1 or higher. For comparison with other models, values were summed for the IR spectrum and given at intervals of 5 or 10 cm-1. This archive contains fluxes for ICRCCM-prescribed clear-sky cases. Radiative flux and cooling-rate profiles are given for specified atmospheric profiles for temperature, water vapor, and ozone-mixing ratios. The archive contains 328 files, including spectral summaries, formatted data files, and a variety of programs (i.e., C-shell scripts, FORTRAN codes, and IDL programs) to read, reformat, and display data. Collectively, these files require approximately 59 MB of disk space. « less
  4. Data were collected to improve understanding of the Arctic troposphere, and to provide researchers with a focused case-study period for future observational and modeling studies pertaining to Arctic atmospheric processes.
  5. Cloud ice water concentration is one of the most important, yet poorly observed, cloud properties. Developing physical parameterizations used in general circulation models through single-column modeling is one of the key foci of the ARM program. In addition to the vertical profiles of temperature, watermore » vapor and condensed water at the model grids, large-scale horizontal advective tendencies of these variables are also required as forcing terms in the single-column models. Observed horizontal advection of condensed water has not been available because the radar/lidar/radiometer observations at the ARM site are single-point measurement, therefore, do not provide horizontal distribution of condensed water. The intention of this product is to provide large-scale distribution of cloud ice water by merging available surface and satellite measurements. The satellite cloud ice water algorithm uses ARM ground-based measurements as baseline, produces datasets for 3-D cloud ice water distributions in a 10 deg x 10 deg area near ARM site. The approach of the study is to expand a (surface) point measurement to an (satellite) areal measurement. That is, this study takes the advantage of the high quality cloud measurements at the point of ARM site. We use the cloud characteristics derived from the point measurement to guide/constrain satellite retrieval, then use the satellite algorithm to derive the cloud ice water distributions within an area, i.e., 10 deg x 10 deg centered at ARM site. « less