Preprocessing for PISM

This is a collection of preprocessing routines for input data to be used in PISM for Antarctic ice sheet simulations. The preprocessing provides the steps from downloading the data to making the data PISM-ready, i.e. no other steps in preprocessing should be needed to use the data with PISM.

Initial conditions for PISM include bed topography, ice thickness and ice temperature distribution.

Boundary conditions include ice surface temperature and ice surface mass balance or atmospheric temperature at the snow surface and mass balance at the snow surface. PISM needs ocean melt rates and ice shelf basal temperatures as boundary conditions at the ice shelf base. PISM includes simple ocean models that can provide such data from open ocean properties (i.e. the PICO ocean model).

Structure

Scripts for dataset-specific preprocessing are in the folder with the name of the dataset. They should be run in the order listed below. The grids folder holds scripts for the creation of target grids to which the input data is regridded. The pism_input folder holds general program code. The merging folder holds code to merge single datasets into files that hold all the necessary initial and boundary conditions to drive PISM. Here is the graph:

pism_input
+-- config.py
+-- grids
|   +-- create_cdo_targetgrids.py
+-- bedmap2
|   +-- download_and_extract_to_nc.py
|   +-- remap.py
+-- bedmachine
|   +-- nsidc-download_NSIDC-0756.002_2020-10-12.py
|   +-- move_and_prepare_for_pism.py
|   +-- ready_for_cdo.py
|   +-- remap.py
+-- albmap
|   +-- download_and_rename_variables.py
|   +-- remap.py
|   +-- add_units_fill_bounds_after_regridding.py
+-- basins_icesat_zwally
|   +-- download_and_write_to_netcdf.py
|   +-- remap.py
|   +-- Zwally_basins.gmt (extend to ocean using GMT)
|   +-- unzip_and_extend_to_ocean.old.py (depends on unavailable input file... use Zwally_basins.gmt instead; currently only kept for reference)
+-- racmo_ice2sea
|   +-- merge_and_rename_variables.py
|   +-- remap.py
|   +-- time_mean.py
+-- racmo_wessem
|   +-- merge_and_rename_variables.py
|   +-- remap.py
|   +-- time_mean.py
+-- racmo_era5
|   +-- merge_and_rename_variables.py
|   +-- remap.py
|   +-- time_mean.py
|   +-- monthly_climatology_mean.py
+-- racmo_hadcm3
|   +-- merge_and_rename_variables_c20/a1b.py
+-- racmo_cesm2
|   +-- merge_and_rename_variables.py
|   +-- remap.py
|   +-- time_mean.py
|   +-- cdo_remap.sh
|   +-- cdo_remap_yearly.sh (example for year-wise processing)
|   +-- fill_missing_data.py
|   +-- correct_time_bnds.py
+-- schmidtko
|   +-- download_and_write_to_netcdf.py
|   +-- calculate_potential_temps.py
|   +-- remap.py
|   +-- compute_basin_means.py
|   +-- fill_schmidtko_initmip8km_means_to_basins_on_different_resolution.py 
+-- accum
|   +-- download_and_extract_to_nc.py
|   +-- remap.py
+-- bheatflx_martos
|   +-- download_and_write_to_netcdc.py
|   +-- remap.py
+-- bheatflx_an
|   +-- download_and_extract.py
|   +-- remap.py
+-- bheatflx_minmax
|   +-- download_and_interpolate_to_netcdc.py
+-- bheatflx_purucker
|   +-- download_and_interpolate_to_netcdc.py
+-- bheatflx_shen
|   +-- interpolate_to_netcdc.py
+-- vel_rignot
|   +-- preprocess_netcdf.py
|   +-- remap.py
+-- vel_mouginot17_annual
|   +-- preprocess_netcdf.py
+-- vel_mouginot19
|   +-- preprocess_netcdf.py
|   +-- remap.py
+-- raised
|   +-- convert_to_netcdf.py
|   +-- remap.py
+-- sealevel
|   +--download_specmap_and_rename.py
|   +--convert_ice6g_to_netcdf.py
|   +--download_bintanja_and_convert_to_nc.py
|   +--convert_lambeck_to_netcdf.py
+-- wdc
|   +--convert_tempdata_to_netcdf.py
|   +--convert_accumdatato_netcdf.py
+-- edc
|   +--download_tempdata_and_convert_to_netcdf.py
+-- tillphi_pism
|   +-- extract_and_prepare.py
|   +-- remap.py
+-- initmip
|   +-- preprocess.py (incl. create_anomalies.py)
|   +-- remap.py
|   +-- run_postprocess.sh (make data ISMIP6 compatible; incl. postprocess_ex/ts.py)
+-- larmip
|   +-- preprocess.py (incl. create_anomalies.py)
|   +-- postprocess.py (extract slvol anomalies)
+-- merge_dataset.py
+-- pism_input
    +-- pism_input.py (tools)

Data sources

Surface elevation

Albmap

5km resolution, NetCDF files of Antarctica gathered from various data sources and interpolated, when necessary, onto the same grid using polar stereographic projection

Documentation: http://websrv.cs.umt.edu/isis/index.php/Present_Day_Antarctica

Citation:

• Bamber, J. L., Gomez-Dans, J. L., & Griggs, J. A. (2009). A new 1 km digital elevation model of the Antarctic derived from combined satellite radar and laser data-Part 1: Data and methods. The Cryosphere, 3(1), 101.

• Griggs, J. A., & Bamber, J. L. (2009). A new 1 km digital elevation model of Antarctica derived from combined radar and laser data-Part 2: Validation and error estimates. The Cryosphere, 3(1), 113.

Bedmap2

Dataset describing surface elevation, ice-thickness and the sea floor and subglacial bed elevation of the Antarctic south of 60◦ S. Dataset was derived using data from a variety of sources, including many substantial surveys completed since the original Bedmap compilation (Bedmap1) in 2001. The Bedmap2 ice thickness grid is made from 25 million measurements, over two orders of magnitude more than were used in Bedmap1.

Documentation: https://www.bas.ac.uk/project/bedmap-2/

Citation:

• Fretwell, P., Pritchard, H. D., Vaughan, D. G., Bamber, J. L., Barrand, N. E., Bell, R., Bianchi, C., Bingham, R. G., Blankenship, D. D., Casassa, G., Catania, G., Callens, D., Conway, H., Cook, A. J., Corr, H. F. J., Damaske, D., Damm, V., Ferraccioli, F., Forsberg, R., Fujita, S., Gim, Y., Gogineni, P., Griggs, J. A., Hindmarsh, R. C. A., Holmlund, P., Holt, J. W., Jacobel, R. W., Jenkins, A., Jokat, W., Jordan, T., King, E. C., Kohler, J., Krabill, W., Riger-Kusk, M., Langley, K. A., Leitchenkov, G., Leuschen, C., Luyendyk, B. P., Matsuoka, K., Mouginot, J., Nitsche, F. O., Nogi, Y., Nost, O. A., Popov, S. V., Rignot, E., Rippin, D. M., Rivera, A., Roberts, J., Ross, N., Siegert, M. J., Smith, A. M., Steinhage, D., Studinger, M., Sun, B., Tinto, B. K., Welch, B. C., Wilson, D., Young, D. A., Xiangbin, C., and Zirizzotti, A.: Bedmap2: improved ice bed, surface and thickness datasets for Antarctica, The Cryosphere, 7, 375-393, doi:10.5194/tc-7-375-2013, 2013.

Bedrock topography

Bedmap2

Dataset describing surface elevation, ice-thickness and the sea floor and subglacial bed elevation of the Antarctic south of 60◦ S. Dataset was derived using data from a variety of sources, including many substantial surveys completed since the original Bedmap compilation (Bedmap1) in 2001. The Bedmap2 ice thickness grid is made from 25 million measurements, over two orders of magnitude more than were used in Bedmap1.

Documentation: https://www.bas.ac.uk/project/bedmap-2/

Citation:

• Fretwell, P., Pritchard, H. D., Vaughan, D. G., Bamber, J. L., Barrand, N. E., Bell, R., Bianchi, C., Bingham, R. G., Blankenship, D. D., Casassa, G., Catania, G., Callens, D., Conway, H., Cook, A. J., Corr, H. F. J., Damaske, D., Damm, V., Ferraccioli, F., Forsberg, R., Fujita, S., Gim, Y., Gogineni, P., Griggs, J. A., Hindmarsh, R. C. A., Holmlund, P., Holt, J. W., Jacobel, R. W., Jenkins, A., Jokat, W., Jordan, T., King, E. C., Kohler, J., Krabill, W., Riger-Kusk, M., Langley, K. A., Leitchenkov, G., Leuschen, C., Luyendyk, B. P., Matsuoka, K., Mouginot, J., Nitsche, F. O., Nogi, Y., Nost, O. A., Popov, S. V., Rignot, E., Rippin, D. M., Rivera, A., Roberts, J., Ross, N., Siegert, M. J., Smith, A. M., Steinhage, D., Studinger, M., Sun, B., Tinto, B. K., Welch, B. C., Wilson, D., Young, D. A., Xiangbin, C., and Zirizzotti, A.: Bedmap2: improved ice bed, surface and thickness datasets for Antarctica, The Cryosphere, 7, 375-393, doi:10.5194/tc-7-375-2013, 2013.

BedMachine Antarctica

Dataset based on mass conservation (currently version 2, dated 2020-07-15), available from the National Snow & Ice Data Center at https://nsidc.org/data/nsidc-0756 (data set ID NSIDC-0756).

Website: https://sites.uci.edu/morlighem/bedmachine-antarctica/

Citation:

• Morlighem, M., E. Rignot, T. Binder, D. D. Blankenship, R. Drews, G. Eagles, O. Eisen, F. Ferraccioli, R. Forsberg, P. Fretwell, V. Goel, J. S. Greenbaum, H. Gudmundsson, J. Guo, V. Helm, C. Hofstede, I. Howat, A. Humbert, W. Jokat, N. B. Karlsson, W. Lee, K. Matsuoka, R. Millan, J. Mouginot, J. Paden, F. Pattyn, J. L. Roberts, S. Rosier, A. Ruppel, H. Seroussi, E. C. Smith, D. Steinhage, B. Sun, M. R. van den Broeke, T. van Ommen, M. van Wessem, and D. A. Young. 2020. Deep glacial troughs and stabilizing ridges unveiled beneath the margins of the Antarctic ice sheet, Nature Geoscience. 13. 132-137. https://doi.org/10.1038/s41561-019-0510-8

Accumulation

Arthern et al.

Antarctic surface accumulation map on the same grid, with the same projection and in the same file formats as bedmap2.

Documentation: https://secure.antarctica.ac.uk/data/bedmap2/resources/Arthern_accumulation/Arthern_accumulation_bedmap2_grid_readme.rtf

Citation:

• Arthern, R. J., D. P. Winebrenner, and D. G. Vaughan (2006), Antarctic snow accumulation mapped using polarization of 4.3-cm wavelength microwave emission, J. Geophys. Res., 111, D06107, doi:10.1029/2004JD005667.

Albmap

5km resolution, NetCDF files of Antarctica gathered from various data sources and interpolated, when necessary, onto the same grid using polar stereographic projection

Documentation: http://websrv.cs.umt.edu/isis/index.php/Present_Day_Antarctica

Citation:

• Vaughan, D. G., Bamber, J. L., Giovinetto, M., Russell, J., & Cooper, A. P. R. (1999). Reassessment of net surface mass balance in Antarctica. Journal of climate, 12(4), 933-946.

Surface mass balance

RACMO2.1

HadCM3_c20_I2S_precip_Y.nc contains precipitation in mm/yr for 1980-1999 over Antarctica from RACMO2 run forced with HadCM3 data. HadCM3_c20_I2S_t2m_Y.nc contains temperature in Kelvin for 1980-1999 over Antarctica from RACMO2 run forced with HadCM3 data. (ANT55/HAD)

Citation:

• Ligtenberg, S. R. M., van de Berg, W. J., van den Broeke, M. R., Rae, J. G. L. & van Meijgaard, E. (2013). Future surface mass balance of the Antarctic Ice Sheet and its influence on sea level change, simulated by a regional atmospheric climate model. Clim. Dynam. 41, 867–884

Note: Data was given for use in this paper:

• Frieler Katja; Clark Peter U.; He Feng; Buizert Christo; Reese Ronja; Ligtenberg Stefan R. M.; van den Broeke Michiel R.; Winkelmann Ricarda & Levermann Anders Consistent evidence of increasing Antarctic accumulation with warming. Nature Clim. Change, 2015, 5, 348-352

RACMO2.3p2

The latest RACMO2.3p2 data (ANT27/2) forced by ERA-Interim provide yearly mean air temperature (t2m) and surface mass balance (smb) for the years 1979-2016.

Download link: https://www.projects.science.uu.nl/iceclimate/publications/data/2018/vwessem2018_tc/RACMO_Yearly/

Website: https://www.projects.science.uu.nl/iceclimate/models/antarctica.php

Citation:

• Van Wessem, Jan Melchior, Willem Jan Van De Berg, Brice PY Noël, Erik Van Meijgaard, Charles Amory, Gerit Birnbaum, Constantijn L. Jakobs et al. "Modelling the climate and surface mass balance of polar ice sheets using racmo2: Part 2: Antarctica (1979-2016)." Cryosphere 12, no. 4 (2018): 1479-1498.

RACMO2.3p2 data (ANT27/2) forced by HadCM3 climate model provide yearly mean air temperature (tskin) and surface mass balance (smb) for the historical period 1980-1999 and the A1B projection period 2000-2200.

RACMO2.3p2 data (ANT27/2) forced by CESM2 climate model provide monthly mean air temperature (tskin) and surface mass balance (smb) for the historical period 1950-2014 and the SSP5-8.5 projection period 2015-2100.

Citation: not yet published, contact J.M.vanWessem[at]uu.nl

Mean annual temperature

Albmap

5km resolution, NetCDF files of Antarctica gathered from various data sources and interpolated, when necessary, onto the same grid using polar stereographic projection

Documentation: http://websrv.cs.umt.edu/isis/index.php/Present_Day_Antarctica

Citation:

• Comiso, J. C. (2000). Variability and trends in Antarctic surface temperatures from in situ and satellite infrared measurements. Journal of Climate, 13(10), 1674-1696.

Geothermal flux

Overview white paper: https://www.scar.org/scar-news/serce-news/scar-serce-ghf

Albmap

5km resolution, NetCDF files of Antarctica gathered from various data sources and interpolated, when necessary, onto the same grid using polar stereographic projection

Documentation: http://websrv.cs.umt.edu/isis/index.php/Present_Day_Antarctica

Citation:

• Shapiro, N. M., & Ritzwoller, M. H. (2004). Inferring surface heat flux distributions guided by a global seismic model: particular application to Antarctica. Earth and Planetary Science Letters, 223(1), 213-224.

• Maule, C. F., Purucker, M. E., Olsen, N., & Mosegaard, K. (2005). Heat flux anomalies in Antarctica revealed by satellite magnetic data. Science, 309(5733), 464-467.

Martos et al.

Documentation: https://doi.pangaea.de/10.1594/PANGAEA.882503

Citation:

• Martos, Y. M., Catalán, M., Jordan, T. A., Golynsky, A., Golynsky, D., Eagles, G., & Vaughan, D. G. (2017). Heat flux distribution of Antarctica unveiled. Geophysical Research Letters, 44(22).

Purucker et al.

Documentation: https://core2.gsfc.nasa.gov/research/purucker/heatflux_updates.html

Citation:

• Purucker, M. E.: Geothermal heat flux data set based on low res- olution observations collected by the CHAMP satellite between 2000 and 2010, and produced from the MF-6 model following the technique described in Fox Maule et al. (2005), 2013

An et al.

Documentation: http://www.seismolab.org/model/antarctica/lithosphere/#an1-hf

Citation:

• An, M., Wiens, D.A., Zhao, Y., Feng, M., Nyblade, A., Kanao, M., Li, Y., Maggi, A. and Lévêque, J.J., 2015. Temperature, lithosphere‐asthenosphere boundary, and heat flux beneath the Antarctic Plate inferred from seismic velocities. Journal of Geophysical Research: Solid Earth, 120(12), pp.8720-8742.

Shen et al.

Documentation: https://sites.google.com/view/weisen/research-products?authuser=0

Citation:

• Shen, W., Wiens, D., Lloyd, A. and Nyblade, A., 2020. A Geothermal heat flux map of Antarctica empirically constrained by seismic structure. Geophysical Research Letters, https://doi.org/10.1029/2020GL086955

Loesing & Ebbing

Documentation: https://doi.pangaea.de/10.1594/PANGAEA.930237

Citation:

• Loesing, M.; Ebbing, J. (2021): Predicting Geothermal Heat Flow in Antarctica With a Machine Learning Approach. Journal of Geophysical Research: Solid Earth, 126(6), https://doi.org/10.1029/2020JB021499

Southern Ocean

Schmidtko et al.

Citation:

• Schmidtko, Sunke, Heywood, Karen J., Thompson, Andrew F. and Aoki, Shigeru (2014) Multidecadal warming of Antarctic waters Science, 346 (6214). pp. 1227-1231.

Drainage regions

Zwally et al. / ICESat

Documentation: https://earth.gsfc.nasa.gov/cryo/data/polar-altimetry/antarctic-and-greenland-drainage-systems

Citation:

• Zwally, H. Jay, Mario B. Giovinetto, Matthew A. Beckley, and Jack L. Saba, 2012, Antarctic and Greenland Drainage Systems, GSFC Cryospheric Sciences Laboratory at http://icesat4.gsfc.nasa.gov/cryo_data/ant_grn_drainage_systems.php.

Surface Velocity

Rignot et al. (2017)

Citation:

• Rignot, E., J. Mouginot, and B. Scheuchl. 2017. MEaSUREs InSAR-Based Antarctica Ice Velocity Map, Version 2. [Indicate subset used]. Boulder, Colorado USA. NASA National Snow and Ice Data Center Distributed Active Archive Center. doi: http://dx.doi.org/10.5067/D7GK8F5J8M8R. [Date Accessed].

More infos: http://nsidc.org/data/nsidc-0484

Mouginot et al. (2017) (annual)

Citation:

• Mouginot, J., E. Rignot, B. Scheuchl, and R. Millan. 2017. Comprehensive Annual Ice Sheet Velocity Mapping Using Landsat-8, Sentinel-1, and RADARSAT-2 Data, Remote Sensing. 9. Art. #364. https://doi.org/10.3390/rs9040364

More infos: https://nsidc.org/data/NSIDC-0720/

Mouginot et al. (2019)

Citation:

• Mouginot, J., E. Rignot, and B. Scheuchl. 2019. MEaSUREs Phase-Based Antarctica Ice Velocity Map, Version 1. [Indicate subset used]. doi: https://doi.org/10.5067/PZ3NJ5RXRH10. [Date Accessed].

More infos: https://nsidc.org/data/NSIDC-0754/

Grounding line

RAISED

Citation:

• Bentley, Michael J., et al. "A community-based geological reconstruction of Antarctic Ice Sheet deglaciation since the Last Glacial Maximum." Quaternary Science Reviews 100 (2014): 1-9.

Vertices downloaded and converted to csv as publication supplement from https://ars.els-cdn.com/content/image/1-s2.0-S0277379114002546-mmc1.xlsx.

Temperature forcing

EDC

Citation:

• Jouzel, J., Masson-Delmotte, V., Cattani, O., Dreyfus, G., Falourd, S., Hoffmann, G., ... & Fischer, H. (2007). Orbital and millennial Antarctic climate variability over the past 800,000 years. science, 317(5839), 793-796.

Anomaly over the last 800kyr provided as difference from the average of the last 1000 years, downloaded from ftp://ftp.ncdc.noaa.gov/pub/data/paleo/icecore/antarctica/epica_domec/edc3deuttemp2007.txt

WDC

Citation:

• Cuffey, K.M., G.D. Clow, E.J. Steig, C. Buizert, T.J. Fudge, M. Koutnik, E.D. Waddington, R.B. Alley, and J.P. Severinghaus (2016). Deglacial temperature history of West Antarctica. Proc. Natl. Acad. Sci. 113(50): 14249-14254. doi:10.1073/pnas.1609132113.

Download .txt data from <http://www.usap-dc.org/view/dataset/600377 and calculate anomaly to year 0 BP over the last 67kyr>.

Accumulation forcing

WDC

Citation:

• Fudge, T. J., et al. "Variable relationship between accumulation and temperature in West Antarctica for the past 31,000 years." Geophysical Research Letters 43.8 (2016): 3795-3803.

Download .xls file from http://www.usap-dc.org/view/dataset/601004 and convert sheet "50year" to .csv.

Sea level forcing

ICE-6G

Citation:

• Stuhne, G. R., and W. R. Peltier. "Reconciling the ICE‐6G_C reconstruction of glacial chronology with ice sheet dynamics: The cases of Greenland and Antarctica." Journal of Geophysical Research: Earth Surface 120.9 (2015): 1841-1865.

Anomaly over last 122kyr. Data not public (contact Dick Peltier).

SPECMAP

Citation:

• Imbrie, J. D., and A. McIntyre. "SPECMAP time scale developed by Imbrie et al., 1984 based on normalized planktonic records (normalized O-18 vs. time, specmap. 017)." Earth System Science Data (2006).

Anomaly over last 405kyr, data extracted from Albmap dataset.

Bintanja & Van de Wal

Citation:

• Bintanja, R., & Van de Wal, R. S. W. (2008). North American ice-sheet dynamics and the onset of 100,000-year glacial cycles. Nature, 454(7206), 869.

Anomaly data over last 3,000kyr downloaded from ftp://ftp.ncdc.noaa.gov/pub/data/paleo/contributions_by_author/bintanja2008/bintanja2008.txt.

Lambeck et al.

Citation:

• Lambeck, K., Rouby, H., Purcell, A., Sun, Y., & Sambridge, M. (2014). Sea level and global ice volumes from the Last Glacial Maximum to the Holocene. Proceedings of the National Academy of Sciences, 111(43), 15296-15303.

Anomaly data over 35kyr extracted from Table 3 in PDF supplement http://www.pnas.org/content/suppl/2014/10/08/1411762111.DCSupplemental.

Model intercomparisons

InitMIP

Wiki: http://www.climate-cryosphere.org/wiki/index.php?title=InitMIP-Antarctica

Larmip

Wiki: https://www.pik-potsdam.de/research/earth-system-analysis/models/larmip

Abumip

Wiki: http://www.climate-cryosphere.org/wiki/index.php?title=ABUMIP-Antarctica

ISMIP6

Wiki: https://www.climate-cryosphere.org/wiki/index.php?title=ISMIP6-Projections-Antarctica

License

pism-ais is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 2 of the License, or (at your option) any later version.

psim-ais is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You find a copy of the GNU General Public License along with pism-ais in the file LICENSE.txt;