Data archive and R notebook visualization toolkit for "Titan's Refractory Core Evolution: Implications for Organics in its Subsurface Ocean"

This repository contains: Condensed data ("titan_data.zip") to reproduce the figures in the manuscript "Titan's Refractory Core Evolution: Implications for Organics in its Subsurface Ocean" by K. E. Miller et al., related to interior evolution, i.e., phase assemblage for Cases A, B and C, and extracted and retained elemental masses over Titan's thermal evolution. The "data_manifest.csv" documents what each file is. A R notebook ("Titan_interior_evolution_visualization_toolkit.Rmd") that uses the uncompressed "titan_data" folder, placed in the same path, to faciliate plotting all the relevant figures. This notebook has been coded for ease of use, to plot figures identical or similar to those for interior phase assemblages, element extraction and retention as in the manuscript. Compressed raw output Project files from the Rcrust program ("Rcrust_data_files.zip"), for Cases A, B, and C, originally known as "Titan_100CI_DEW19_713_20230914_Extract100_v1", "Titan_case8_DEW19_713_20230914_Extract100_v7", and "Titan_case11_DEW19_713_20230914_Extract100_v2" respectively. These can be used to check the original model outcomes, used for subsequent analyses of the phase assemblage, and extracted and retained elements. Rcrust/Perple_X thermodynamic data file, solution model file, option file, and used 64-bit Windows meemum executable, all compressed into "Rcrust_data_files.zip" These are used by Rcrust/Perple_X to reproduce the models. Perple_X is suite of programs that perform Gibbs free energy minimization (among other things) to predict stable phase equilibria with thermodynamics, for geologic settings. Perple_X can be found here: Relevant references are: Connolly, J.A.D., 2009. The geodynamic equation of state: What and how. Geochemistry, Geophysics, Geosystems 10, Q10014. https://doi.org/10.1029/2009GC002540Connolly, J.A.D., 2005. Computation of phase equilibria by linear programming: A tool for geodynamic modeling and its application to subduction zone decarbonation. Earth and Planetary Science Letters 236, 524–541. https://doi.org/10.1016/j.epsl.2005.04.033Connolly, J.A.D., Galvez, M.E., 2018. Electrolytic fluid speciation by Gibbs energy minimization and implications for subduction zone mass transfer. Earth and Planetary Science Letters 501, 90–102. https://doi.org/10.1016/j.epsl.2018.08.024 Rcrust is a wrapper program for Perple_X, to facilitate pressure-temperature pathway modeling with phase (e.g., fluid, melt, mineral) fractionation. Rcrust can be found here: https://www.sun.ac.za/english/faculty/science/earthsciences/Pages/Rcrust-3.aspx Relevant references are: Mayne, M.J., Moyen, J.-F., Stevens, G., Kaislaniemi, L., 2016. Rcrust: a tool for calculating path-dependent open system processes and application to melt loss. Journal of Metamorphic Geology 34, 663–682. https://doi.org/10.1111/jmg.12199 Mayne, M.J., Stevens, G., Moyen, J.-F., Johnson, T., 2019. Performing process-oriented investigations involving mass transfer using Rcrust: a new phase equilibrium modelling tool. Geological Society, London, Special Publications 491, SP491-2018–85. https://doi.org/10.1144/SP491-2018-85本代码仓库包含以下内容： 1. 精简数据集（"titan_data.zip"）：用于复现K. E. Miller等人发表的论文《土卫六难熔核演化：对其次表层海洋有机物的启示》中的相关图表，该数据集围绕土卫六内部演化展开，涵盖A、B、C三种情形下的相组合，以及土卫六热演化过程中提取与留存的元素质量。文件"data_manifest.csv"用于说明各文件的具体内容。 2. R Markdown交互式脚本文件（"Titan_interior_evolution_visualization_toolkit.Rmd"）：需将解压后的"titan_data"文件夹置于同一目录下，用于便捷生成所有相关图表。本脚本兼顾易用性设计，可复现或生成与论文中内部相组合、元素提取与留存相关的一致或相似图表。 3. Rcrust（Perple_X的封装程序）生成的压缩原始输出项目文件（"Rcrust_data_files.zip"），对应A、B、C三种情形，原始文件名分别为"Titan_100CI_DEW19_713_20230914_Extract100_v1"、"Titan_case8_DEW19_713_20230914_Extract100_v7"以及"Titan_case11_DEW19_713_20230914_Extract100_v2"。该文件可用于验证原始模型结果，以供后续开展相组合以及元素提取与留存相关分析。 此外，"Rcrust_data_files.zip"中还包含Rcrust/Perple_X热力学数据文件、溶液模型文件、配置选项文件，以及所用的64位Windows平台meemum可执行程序，供Rcrust/Perple_X复现模型时使用。 Perple_X（地质热力学相平衡计算程序套件）是一套可在地质场景中使用的热力学计算程序，核心功能为通过吉布斯自由能最小化等方法，基于热力学原理预测稳定相平衡。Perple_X的获取地址如下： 相关参考文献如下： 1. Connolly, J.A.D., 2009. 地球动力学状态方程：原理与实现. 地球化学、地球物理学、地球系统学, 10卷, Q10014. https://doi.org/10.1029/2009GC002540 2. Connolly, J.A.D., 2005. 基于线性规划的相平衡计算：地球动力学建模工具及其在俯冲带脱碳中的应用. 地球与行星科学通讯, 236卷, 524–541页. https://doi.org/10.1016/j.epsl.2005.04.033 3. Connolly, J.A.D., Galvez, M.E., 2018. 基于吉布斯自由能最小化的电解流体物种分析及其对俯冲带物质迁移的启示. 地球与行星科学通讯, 501卷, 90–102页. https://doi.org/10.1016/j.epsl.2018.08.024 Rcrust是Perple_X的封装程序，用于便捷开展包含相（如流体、熔体、矿物）分异的温压路径模拟。Rcrust的获取地址如下：https://www.sun.ac.za/english/faculty/science/earthsciences/Pages/Rcrust-3.aspx 相关参考文献如下： 1. Mayne, M.J., Moyen, J.-F., Stevens, G., Kaislaniemi, L., 2016. Rcrust：一种路径依赖开放系统过程计算工具及其在熔体损失研究中的应用. 变质地质学报, 34卷, 663–682页. https://doi.org/10.1111/jmg.12199 2. Mayne, M.J., Stevens, G., Moyen, J.-F., Johnson, T., 2019. 基于Rcrust开展涉及物质迁移的过程导向研究：一款新型相平衡模拟工具. 伦敦地质学会特刊, 491卷, SP491-2018–85. https://doi.org/10.1144/SP491-2018-85