ExoCcycleGeo

Calculates net C fluxes from a terrestrial planet's interior to its atmosphere with a coupled geophysical-geochemical, time-evolution box model of outgassing, weathering, and ocean-atmosphere equilibria. Input parameters include planet size (0.5 to 2 Earth masses), detailed chemical coomposition and interior structure, and land coverage and patchiness. The weathering and ocean-atmosphere equilibrium model computes kinetically limited and equilibrium water-rock reactions using the USGS PHREEQC v3 code. The outgassing model scales outgassing from melting, which is computed based on planet size and age (i.e., temperature-pressure profile) and composition using the alphaMELTS implementation of the MELTS code. Currently only the outgassing model is fully benchmarked, so this is the only capability accessible in this repository.

Installation

The installation steps outlined below are valid for Mac OS 10.9+. ExoCcycleGeo could also plausibly run on Windows and Linux, but compilation instructions are not set up and external I/O handling needs to be modified in the source code.

Install R

R is needed to run the geochemistry package CHNOSZ. Go to http://www.r-project.org and follow instructions.

Install CHNOSZ

Open R using either the installed application icon or in a terminal by typing

In R, type the command

install.packages("CHNOSZ")

Install Rcpp and RInside

Rcpp and RInside are libraries that allow R applications to be embedded in C or C++ codes. Go to http://cran.r-project.org/web/packages/Rcpp/index.html and http://cran.r-project.org/web/packages/RInside/index.html, or directly to http://dirk.eddelbuettel.com/code/rcpp to download the respective archives. On Mac, unzip the archives in /Library/Frameworks/R.framework/Resources/library/, so that Rcpp and RInside are two subfolders of library.

Install IPHREEQC

The IPHREEQC library is a module that allows the PHREEQC application to be embedded in C or C++ codes. Go to http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc to download IPHREEQC and follow the default installation instructions (you need admin credentials on your machine):

./configure
make
make install

Install ExoCcycleGeo

Go to https://github.com/MarcNeveu/ExoCcycleGeo. Click the green Clone or download button to the right of the page, then either:

Download ZIP on the bottom right. Unzip ExoCcycleGeo-master.zip. Move the ExoCcycleGeo folder inside to any folder you would like, we will call it Path_to_GitFolder here.
if you are familiar with GitHub, you can clone the directory with your favorite tool (I use Git within the Eclipse developing environment).

The folders within /Path_to_GitFolder/ExoCcycleGeo/ contain:

src: All source code files
Debug: The executable program ExoCcycleGeo
alphaMELTS-1.9: The alphaMELTS code executed by the outgassing subroutine within ExoCcycleGeo
PHREEQC-3.1.2: The PHREEQC code executed by the weathering and ocean-atmosphere equilibrium subroutines within ExoCcycleGeo
Data: Lookup tables. Currently there is only one used for calculated the planet's self-compression.

At this time, and I apologize for the clunkiness, you also need to manually edit three files to change the /Path_to_GitFolder/ from mine (/Users/mneveu/eclipse-workspace/ExoCcycleGeo/ExoCcycleGeo/) to yours (/Path_to_GitFolder/ExoCcycleGeo/):

In alphaMELTS-1.9/run_alphameltsExoC.command at lines 10, 432 (3 instances), and 457 (2 instances)
In alphaMELTS-1.9/ExoC/ExoC_env.txt at l. 6
In alphaMELTS-1.9/ExoCbatch.txt at l. 2.

Running the code

Start the code

To execute the code, I usually open a Terminal window, get to the folder /Path_to_GitFolder/ExoCcycleGeo/Debug which contains the executable by typing

cd /Path_to_GitFolder/ExoCcycleGeo/Debug

and start the execution by typing

./ExoCcycleGeo &

Changing inputs

Planet composition

Outgassing: the composition that controls carbon outgassing in the model is that of the upper mantle, which is set in alphaMELTS-1.9/ExoC/ExoCcycleGeo.melts. To change it, you can either edit the "Initial Composition" lines of this file or create a duplicate, Duplicate.melts, and tell ExoCbatch.txt in the same folder to run Duplicate.melts rather than ExoCcycleGeo.melts. The default composition is that of a mid-ocean ridge basalt (MORB).

Ocean-atmosphere equilibrium: the composition that controls ocean-atmosphere equilibrium in the model is set in PHREEQC-3.1.2/io/OceanDiss.txt. At the first time step, it is initiated instead with PHREEQC-3.1.2/io/OceanStart.txt. The default composition is that of Earth's ocean.

Continental weathering: the composition that controls continental weathering in the model is set in PHREEQC-3.1.2/io/ContWeather.txt.

Other inputs

Other inputs that can be modified in Inputs/ExoCcycleGeoInput.txt include:

Simulation time step (default 10 million years, which achieves numerical convergence for the outgassing part of the code);
Simulation start time (default 0.6 billion years (Gyr) after formation, i.e. 4.57-0.6=3.97 Gyr ago);
Simulation end time (default 5 Gyr after formation, i.e. 0.4 Gyr into the future);
Planet mass (default 1 Earth mass, min 0.5 Earth masses, max 2 Earth masses);
Core mass fraction (default 0.325), which sets the mantle thickness, vigor of convection, and ultimately the near-surface pressure-temperature profile;
Rough core and mantle compositions: three 3-digit codes used to identify three materials used to calculate core and mantle radii based on mass from compression equations of state (default codes set to approximate Earth's radius, solid metal inner core, liquid metal outer core, and silicate mantle). Materials and material parameters are provided in Data/Compression_planmat.txt;
Radionuclide abundances: 5 choices of radionuclide abundances: enter 0 for case 3 of Lyubetskaya & Korenaga (2007), 1 for the highest heating case from Turcotte & Schubert (2002) as reported in Table 1 of Kite et al. (2009), 2 for an intermediate heating case from Ringwood (1991) as reported in Table 1 of Kite et al. (2009), 3 for the lowest heating case from Table 2 of Lyubetskaya & Korenaga (2007), other entries default to abundances of McDonough & Sun (1995) as reported in Table 2 of Lyubetskaya & Korenaga (2007) that result in intermediate heating similar to Ringwood (1991);
Rheology (of the mantle rock): enter 0 for the dry olivine rheology of Korenage & Karato (2008), or 1 for their wet olivine rheology. Other entries are not accepted;
Redox state (of the ocean crust): enter 1 for the present-day Earth surface (log fO2 = -0.7 here fO2 is the oxygen fugacity), 2 to set fO2 at the hematite-magnetite (HM) redox buffer, 3 to set fO2 at the fayalite-magnetite-quartz (FMQ) buffer, 4 to set fO2 at the iron-wüstite (IW) buffer;
Mass fraction of carbon in the mantle (default 0.2%);
Mass of the ocean (default 1.4e21 kg, the mass of Earth's ocean);
Areal land fraction (default 29%);
Initial surface temperature (default 288 K);
Initial surface pressure (default 1 bar);
Runoff rate, i.e. rate at which water is delivered from rivers into the ocean (default 0.7 mm/day, i.e., 70 cm/year precipitation with 35% of that rainwater reaching the ocean and the rest evaporated back to the atmosphere before reaching the ocean);
Residence time of water on continents (default 10 years), i.e. continental patchiness;
Initial atmospheric composition (default 280 ppm CO2, 0.0001 ppm CH4, 20% O2, 79% N2, 1% H2O).

Reading outputs

CompoOceanAtm.txt provides the size and composition of the ocean and atmosphere at each time step.
Geotherm.txt provides the pressure, temperature, melt fraction, and density profiles at each time step, from the upper mantle up to the surface.
Outgassing.txt provides geophysical parameters of the planet at each time step.
Output.txt provides reservoirs and fluxes of carbon at each time step.

Modifying the source code

Install gcc

In Mac OS 10.8+, the default compiler clang has replaced the compiler gcc, which can lead to compatibility issues between Mac versions. For example, if compiled on Mac OS 10.15 Catalina, the code cannot be excuted on Mac OS 10.13 High Sierra and older versions. This issue can be resolved by reinstalling gcc and manually compiling the code with it. Go to http://hpc.sourceforge.net and follow the instructions there to download and install gcc. Once installed, you might need to break the symbolic link between the command gcc and clang by typing:

alias gcc=/usr/local/bin/gcc

Compiling and linking instructions

If you wish to modify the code, set up your compiler and linker so that all the relevant flags are added. My compiling and linking commands (executed in a Terminal window from within the ExoCcycleGeo/Debug folder) look like this:

gcc -I/Library/Frameworks/R.framework/Versions/4.1/Resources/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RInside/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -O0 -g3 -Wall -c -fmessage-length=0 -o src/ExoCcycleGeo.o ../src/ExoCcycleGeo.c
gcc -L/Library/Frameworks/R.framework/Versions/4.1/Resources/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -o ExoCcycleGeo src/ExoCcycleGeo.o /usr/local/lib/libiphreeqc-3.7.3.dylib /usr/local/lib/libiphreeqc.dylib -lR

You might need to specify the full path to gcc (e.g. /usr/local/bin/gcc) rather than simply the gcc alias.

Your include directories might be more simply found at -I/usr/include.

Email me if you have any issues.

References

Antoshechkina, P. M., and P. D. Asimow (2010), alphaMELTS 3.0 and the MAGMA website: educational and research tools for studying the petrology and geochemistry of plate margins, Abstract ED41B-0644 presented at 2010 Fall Meeting, AGU, San Francisco, Calif., 13-17 Dec.

Antoshechkina, P. M., P. D. Asimow, E. H. Hauri, and P. I. Luffi (2010), Effect of water on mantle melting and magma differentiation, as modeled using alphaMELTS 3.0, Abstract V53C-2264 presented at 2010 Fall Meeting, AGU, San Francisco, Calif., 13-17 Dec.

Asimow, P.D., and M.S. Ghiorso (1998), Algorithmic modifications extending MELTS to calculate subsolidus phase relations, American Mineralogist, 83 (9-10), 1127-1132.

Ghiorso, M.S., and R.O. Sack (1995), Chemical Mass-Transfer in Magmatic Processes IV. A Revised and Internally Consistent Thermodynamic Model for the Interpolation and Extrapolation of Liquid-Solid Equilibria in Magmatic Systems at Elevated-Temperatures and Pressures, Contributions to Mineralogy and Petrology, 119 (2-3), 197-212.

Ghiorso, M.S., M.M. Hirschmann, P.W. Reiners, and V.C. Kress (2002), The pMELTS: A revision of MELTS for improved calculation of phase relations and major element partitioning related to partial melting of the mantle to 3 GPa, Geochemistry Geophysics Geosystems, 3(5), art. no. 1030, doi:10.1029/2001GC000217.

Parkhurst, D.L. and Appelo, C.A.J., 2013. Description of input and examples for PHREEQC version 3: a computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations (No. 6-A43). US Geological Survey.

Smith, P. M., and P. D. Asimow (2005), Adiabat_1ph: A new public front-end to the MELTS, pMELTS, and pHMELTS models, Geochem. Geophys. Geosyst., 6, art. no. Q02004, doi:10.1029/2004GC000816.

Thompson, R. N., A. J. V. Riches, P. M. Antoshechkina, D. G. Pearson, G. M. Nowell, C. J. Ottley, A. P. Dickin, V. L. Hards, A.-K. Nguno and V. Niku-Paavola (2007), Origin of CFB magmatism: Multi-tiered intracrustal picrite-rhyolite magmatic plumbing at Spitzkoppe, western Namibia, during early-Cretaceous Etendeka magmatism, J. Petrol., 48, 1119-1154.

MarcNeveu / ExoCcycleGeo