Demeter Programmer's Guide: Middleware for Feff and Ifeffit

Then, spent as they were from all their toil, they set out food, the bounty of
Ceres, drenched in sea-salt, Ceres' utensils too, her mills and troughs, and
bend to parch with fire the grain they had salvaged, grind it fine on stone.

                                             Virgil, The Aeneid, 1:209-213

DEMETER is the goddess of grain and agriculture

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Contents

• 1. Introduction
  • 1.1. The technology behind Demeter
  • 1.2. Some vocabulary
• 2. The basics of data processing
  • 2.1. μ(E) data files
  • 2.2. χ(k) data files
  • 2.3. Column data files
  • 2.4. Athena project files
  • 2.5. Multichannel data files
  • 2.6. Special data types
  • 2.7. Handling arbitrary data
  • 2.8. Plotting and basic data processing
• 3. Processing μ(E) data
  • 3.1. Aligning data
  • 3.2. Merging data
  • 3.3. Deglitching data
  • 3.4. Truncating data
  • 3.5. Adding artificial nose to data
  • 3.6. Smoothing data
  • 3.7. Convolving data
  • 3.8. Deconvolving data
  • 3.9. Rebinning data
  • 3.10. Processing dispersive XAS data
• 4. High level actions of the object model
  • 4.1. Command disposal and command templates
  • 4.2. Demeter's templating system
  • 4.3. Mode object
  • 4.4. Plot object
  • 4.5. Config object
  • 4.6. Other high level object methods
• 5. Analysis of XANES data
  • 5.1. Linear Combination Fitting
  • 5.2. Peak Fitting
  • 5.3. Principle Components Analysis
  • 5.4. Difference spectra
• 6. Atoms
  • 6.1. Input crystal data
  • 6.2. Object methods
  • 6.3. Other methods
  • 6.4. Output
• 7. Feff
  • 7.1. Input data for Feff
  • 7.2. Computng potentials
  • 7.3. The path finder
  • 7.4. Path interpretation
• 8. Scattering paths
  • 8.1. Calculating individual scattering paths
  • 8.2. Semantic path descriptions
  • 8.3. Path parameters
  • 8.4. Plotting individual paths
  • 8.5. Running Feff outside of Demeter
• 9. Guess/Def/Set Parameters
  • 9.1. Simplified interface
  • 9.2. Parameter types
  • 9.3. Reporting on and annotating GDS parameters
• 10. Fitting EXAFS data
  • 10.1. Setting up a fit
  • 10.2. Sanity checks
  • 10.3. After a fit
  • 10.4. The non-statistical happiness metric
• 11. Using perl to structure a fit
  • 11.1. Using perl's control structures
  • 11.2. Cloning Demeter objects
• 12. Local guess parameters and the characteristic value
• 13. Path-like objects
  • 13.1. VPath object
  • 13.2. FSPath object
  • 13.3. FPath object
  • 13.4. SSPath object
  • 13.5. MSPath object
  • 13.6. ThreeBody object
  • 13.7. Forward object
  • 13.8. Structural units
• 14. User interfaces
  • 14.1. Command line interface
  • 14.2. Graphical interface
  • 14.3. Web interface
  • 14.4. Plotting backends
• 15. Output formats
  • 15.1. Single object column data files
  • 15.2. Fit result column data files
  • 15.3. Multiple object column data files
  • 15.4. Athena project files
  • 15.5. Serialization files
  • 15.6. Log files
  • 15.7. Project files
  • 15.8. Atoms and feff I/O
  • 15.9. Scripts
• 16. Full examples
  • 16.1. Methyltin chloride
  • 16.2. Silver/gold alloy
  • 16.3. Uranyl ion in solution
  • 16.4. Histogram

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DEMETER is copyright © 2009-2016 Bruce Ravel – This document is copyright © 2016 Bruce Ravel

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