General information

The simulation code hosted on this repository derives from the I2ELVIS code family, developed by Taras V. Gerya ([email protected]). Below you will find references on the code, contact options and installation instructions.

Contact

For questions, help and notifications surrounding this code repository please contact Tim Lichtenberg ([email protected]) or Gregor J. Golabek ([email protected]).

References

• Code and fluid dynamics basics

  Gerya, T. (2019). Introduction to numerical geodynamic modelling. Cambridge University Press.

  Gerya, T. V., & Yuen, D. A. (2007). Robust characteristics method for modelling multiphase visco-elasto-plastic thermo-mechanical problems. Physics of the Earth and Planetary Interiors, 163(1-4), 83-105.

  Gerya, T. V., & Yuen, D. A. (2003). Characteristics-based marker-in-cell method with conservative finite-differences schemes for modeling geological flows with strongly variable transport properties. Physics of the Earth and Planetary Interiors, 140(4), 293-318.

• Research applications

  Lichtenberg, T., Schaefer L. K., Nakajima, M., Fischer, R. A. (2023). Geophysical Evolution During Rocky Planet Formation. Protostars and Planets VII, Chapter 25.

  Bonsor, A., Lichtenberg, T., Dra̧żkowska, J., Buchan, A. M. (2023). Rapid formation of exoplanetesimals revealed by white dwarfs. Nature Astronomy, 7, 39–48.

  Lichtenberg, T., Clement, M. S. (2022). Reduced Late Bombardment on Rocky Exoplanets around M Dwarfs. The Astrophysical Journal Letters, 938, L3.

  Lichtenberg, T., Krijt, S. (2021). System-level fractionation of carbon from disk and planetesimal processing. The Astrophysical Journal Letters, 913, L20.

  Lichtenberg, T., Drążkowska, J., Schönbächler, M., Golabek, G. J., Hands, T. O. (2021). Bifurcation of planetary building blocks during Solar System formation. Science, 371, 365–370.

  Lichtenberg, T., Golabek, G. J., Burn, R., Meyer, M. R., Alibert, Y., Gerya, T. V., & Mordasini, C. (2019). A water budget dichotomy of rocky protoplanets from 26 Al-heating. Nature Astronomy, 3(4), 307-313.

  Solferino, G. F., & Golabek, G. J. (2018). Olivine grain growth in partially molten Fe–Ni–S: A proxy for the genesis of pallasite meteorites. Earth and Planetary Science Letters, 504, 38-52.

  Monteux, J., Golabek, G. J., Rubie, D. C., Tobie, G., & Young, E. D. (2018). Water and the interior structure of terrestrial planets and icy bodies. Space Science Reviews, 214(1), 39.

  Hunt, A. C., Cook, D. L., Lichtenberg, T., Reger, P. M., Ek, M., Golabek, G. J., & Schönbächler, M. (2018). Late metal–silicate separation on the IAB parent asteroid: constraints from combined W and Pt isotopes and thermal modelling. Earth and Planetary Science Letters, 482, 490-500.

  Lichtenberg, T., Golabek, G. J., Dullemond, C. P., Schönbächler, M., Gerya, T. V., & Meyer, M. R. (2018). Impact splash chondrule formation during planetesimal recycling. Icarus, 302, 27-43.

  Golabek, G. J., Emsenhuber, A., Jutzi, M., Asphaug, E. I., & Gerya, T. V. (2018). Coupling SPH and thermochemical models of planets: Methodology and example of a Mars-sized body. Icarus, 301, 235-246.

  Lichtenberg, T., Golabek, G. J., Gerya, T. V., & Meyer, M. R. (2016). The effects of short-lived radionuclides and porosity on the early thermo-mechanical evolution of planetesimals. Icarus, 274, 350-365.

  Golabek, G. J., Bourdon, B., & Gerya, T. V. (2014). Numerical models of the thermomechanical evolution of planetesimals: Application to the acapulcoite‐lodranite parent body. Meteoritics & Planetary Science, 49(6), 1083-1099.

  Tkalcec, B. J., Golabek, G. J., & Brenker, F. E. (2013). Solid-state plastic deformation in the dynamic interior of a differentiated asteroid. Nature Geoscience, 6(2), 93-97.

  Lin, J. R., Gerya, T. V., Tackley, P. J., Yuen, D. A., & Golabek, G. J. (2011). Protocore destabilization in planetary embryos formed by cold accretion: Feedbacks from non-Newtonian rheology and energy dissipation. Icarus, 213(1), 24-42.

  Golabek, G. J., Gerya, T. V., Kaus, B. J. P., Ziethe, R., & Tackley, P. J. (2009). Rheological controls on the terrestrial core formation mechanism. Geochemistry, Geophysics, Geosystems, 10(11).

  Lin, J. R., Gerya, T. V., Tackley, P. J., Yuen, D. A., & Golabek, G. J. (2009). Numerical modeling of protocore destabilization during planetary accretion: Methodology and results. Icarus, 204(2), 732-748.

Software requirements

• Intel compilers & MKL library (see below for installation instructions)
• Python 3.x

The code is tested on UNIX systems, such as macOS or Linux distributions.

Minimum working example

1. Clone the code:

   git clone [email protected]:timlichtenberg/i2elvis_planet.git
   

2. Compile code:

   • On ETHZ Euler cluster:

   module load intel
   sh compile.sh
   

   • Local machine (requires Intel compiler, see further down):

   bash compile.sh
   

   • Compilation should produce the executables, including 'in2mart' and 'i2mart'.

3. Run code:

   • On ETHZ Euler:

   sh submitjobs.sh
   

   • Local machine:

   ./in2mart     # generates initial conditions
   ./i2mart      # runs code
   

4. Check output: plot the files using the python script in the 'support_files' folder

   python plot2d.py
   

5. Examine the output in the 'figures' folder, and compare them to the references in the 'support_files/reference_output' folder.

   • main_temp_0002.png:
   
   • main_rho_0002.png:
   

Install Intel compilers (icc) and MKL library

1. Install macOS command line tools (& Xcode via the App Store if you want to use it)

   xcode-select --install
   

2. Download Intel compilers and MKL library:

   • For macOS: install Xcode and the macOS command line tools (otherwise MKL installation will require relinking)
   • At ETH Zurich: https://idesnx.ethz.ch/
   • Otherwise download from official Intel website: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/dpc-compiler.html
     • Download and install 'Intel® oneAPI Base Toolkit' & 'Intel® oneAPI HPC Toolkit'
     • Use the online installer versions
     • Use command line installation only (no installation for Xcode on macOS)
   • In terminal, link to the new icc installation:

      source /opt/intel/bin/compilervars.sh intel64 # (2018 version)
      source /opt/intel/oneapi/setvars.sh # (2020 oneAPI versions)
     

     ('which icc' should show sth alike '/opt/intel/compilers_and_libraries_2018.1.126/mac/bin/intel64/icc' (2018) or '/opt/intel/oneapi/compiler/2021.1.1/mac/bin/intel64/icc' (2020))

3. Try intel/MKL installation by compiling the code in the I2ELVIS directory:

   bash compile.sh