Markdown-based manuscripts with pandoc-scholar

A lot of time is wasted on formatting for journals that completely reformat the article to their liking in the final stage anyway. Let’s avoid that.

The ‘pandoc-scholar’ software provides a set of generalized templates that automatically creates nice academic manuscript files in a huge set of formats simultaneously. This allows you to write the manuscript in plain text markdown, and then distribute to colleagues or submit to journal in any required format. The key insight to this approach is Do not waste effort fiddling with the format. The manuscript file contains all the content, and journals can worry about formatting details. Any changes that are absolutely required for submission should be applied manually to the output file just before submission.

I have customized and extended this approach by developing my own pandoc-scholar-template. This is presented in the form of a manuscript that describes the markdown-to-manuscript capabilities it demonstrates. * The current version of the pandoc-scholar-template manuscript can be found here, presented in both html and pdf formats.

Equilibrium Algorithms Manuscript Outlines

Below I include rough outlines for a pair of companion papers in preparation describing our new computational equilibrium algorithms.

The problem [[lab-book-post]]

• modeling equilibrium assemblages is generally very slow, holding back planetary understanding
• especially problematic in Monte Carlo applications (e.g. exoplanet studies, MCS for igneous suite inference)
• Existing tools are often too slow, not sufficiently robust, or rely on special conditions (e.g. melt-present)
  • MELTS
  • THERMOCALC
  • THERIAK
  • PerpleX (inaccessible composition space)
  • Hephestos
• Many tools are locked to specific thermodynamic database making comparison difficult (e.g. MELTS, THERMOCALC, Hephestos)

Paper 1

• title: ‘Urgently seeking equilibrium: I. Rapid and robust phase saturation calaculations with the Metastable eXchange EQuilibrium ALgorithm (MEXQAL)’
• MEXQAL phase saturation algorithm
• Equilibrium of individual phases with environment
• motivate BOTH papers 1 and 2
• optimized algorithm underlying full equilibration algorithm (described in paper 2)
• Metastable Equilibrium phase properties obtained for imposed environmental conditions
• Consider simple vs Complex phases
• Geological Benchmarks [[lab-book-post]]
  • simple to complex phases
  • robust convergence
  • fast results
  • compare w/ existing tools??
  • Objective C implementation likely required
• Miscibility gaps and exsolution [[lab-book-post]]
  • employs simplified deCapitani algorithm
• Miscibility gaps for complex phases [[lab-book-post]]
  • w/ structural transition (like Cpx)
  • include in paper 1 if possible
  • special case of phase with identical endmembers should be possible
  • 3 phase triangle
• Gap finder algorithm? [[lab-book-post]]
  • Do we need a method to trace miscibility gaps?
  • Find exteremum of concavity of Gibbs surface
  • Use simulated annealing or MCMC to explore/map-out concave down regions of composition space
  • Then run MEXQAL to trace boundary edges
  • comment on calibration opportunities
• application demos:
  • exsovled Fe-rich liquid phase vs SiO2 rich
  • Feldspar geo-thermometer
  • cpx 3 phase triangle?

Paper 2

• title: Urgently seeking equilibrium: II. Computing phase assemblages with confidence using the sunken hull method
• Equilibrate full assemblage w/ sunken hull method
• Especially subsolidus assemblages
• Robust fallback for optimized MELTS algorithm
• use MEXQAL finds equil state for individual phases
• Sunken Hull Algorithm
• demonstrate efficacy
• Benchmark speed
• Show utility on subsolidus assemblages (MELTS & Stixrude databases)
• application to pyrolite, MORB, etc