VIPER, XANES, XAFMASS

It does not need special installation, just unpack it to any suitable folder and use it. The archive also has documentation and examples. To use the examples easier, it is recommended to associate the project files *.vpj with VIPER and *.xpj with XANES dactyloscope. This would enable a quick project opening by mouse double-click. Observe then some example projects and follow the instructions appearing in a message box.

Analysis Programs

VIPER - Visual Processing in EXAFS Researches

The software program is designed to process XAFS-data while allowing maximum visual control, and includes the following parts:

  • Several glitch- and step-corrections on the absorptance curve with simultaneous observation of the EXAFS curve. Before this, glitches are detected on the derivative level of the first ionization chamber current.
  • Energy calibration with optional constant-E or constant-theta shift.
  • Deconvolution of absorption coefficient with a monochromator resolution curve and/or core-hole lifetime deconvolution.
  • The extraction of EXAFS-part, χ(k). Three methods for the construction of the atomic-like absorption are realized: (i) by a spline drawn through the knots which is varied so as to minimize the low-r EXAFS FT part; (ii) by a smoothing spline and (iii) by a Bayesian smoothing curve. The last two can take into account a priori information about the atomic-like absorption (edge shape, multi-electron contribution, etc.). χ(k) extraction can be verified simultaneously by use of a Fourier-transform. χ(k) or χ(E) can be corrected by user-defined functions f(k) or f(E) in order to correct, for example, the fluorescence self-absorption. The function f(E) may, alternatively,  refer to the theoretical tables of absorption coefficients incorporated into the program. The self-absorption correcting formula can be easily generated by specifying the chemical composition. Errors of χ(k) are calculated in various ways in order to validate the spectrum extension.
  • Fast Fourier analysis, k-weighting, several windowing functions, phase and amplitude corrections. Decomposition into amplitude and phase and subsequent calculation of the EXAFS amplitude and phase.
  • Fitting procedures for the first few coordination shells:
  1. By ordinary EXAFS formula. A user-defined (cumulant) extension is possible by specifying an additional phase and an additional exponent with any number of varied parameters. Multiple-edge refinement is possible.
  2. Using the radial distribution function RDF(r) specified by a user-defined formula, parameters of which can then be varied. Multiple-edge refinement is possible.
  3. Using the oscillatory potential U(r) of the absorber-scatterer pair. The potential U(r) is set by a user-defined formula, parameters of which are then varied. U(r) may consist of many wells. Both classical and quantum approaches can be used.

All fit parameters can be fixed and constrained or related to the homogeneous parameters of the other shells (wells) by user-defined functions. Fitting is done either in k- or in r-space. Scattering amplitudes and phases must be calculated by other programs (FEFF format is recognized) or can be extracted by VIPER from a reference spectrum. The parameters and results of fitting can be saved in (and then a model can be loaded from) a database. Advanced error analysis is developed and applied. Statistical χ2- and F- tests can be performed on request from a user.

At all times, all curves and their changes under processing are visual. Several parameters can quickly be changed by mouse dragging. Data file structure is tunable and flexible, no previous conversion needed in order to load multiple column files from different EXAFS stations. Several data files (also of different formats) can be loaded and processed simultaneously; data files can then be added. During the processing, selected spectra can be summed up, which is especially convenient for fluorescence spectra. A project file can be stored (and then opened) with all the individual parameters of chi extraction for every spectrum. All the curves (μ, χ, FT, BFT) can be stored by a single shot, which is important if tens of data files are currently loaded.

Download screenshoots

Documentation: pdf-file (2169k).
Examples: provided in a separate zip-file as VIPER Project files (*.vpj). These files can be associated with VIPER (then you can double-click on them to open), or they can be opened from the VIPER 'Load data' dialog box. Open them all one-by-one and read the instructions.
Hardware/Software Issues: Windows NT/2000/XP, 95/98/ME
Input Data Format: ASCII text files. User should specify the file header and how to interpret and use the columns of data (or functions of these columns). Once described, the data formats are then recognized automatically.

XANES dactyloscope - a program for quick and rigorous XANES analysis

Features:

The program is designed for analysis of XANES-data ('fingerprints') with maximum visual control and includes the following steps:

  • Energy calibration.
  • Deconvolution of absorption coefficient with a monochromator resolution curve and/or core-hole lifetime deconvolution.
  • Transformation to a new equidistant grid.
  • Pre-edge background subtraction (a polynomial with chosen powers).
  • Correction by a user-defined function or fluorescence self-absorption correction for thick or thin samples.
  • Normalization to unity.
  • Base line subtraction for analysis of pre-edge peaks.
  • Principal component analysis or target transformation.
  • Fitting by a user-defined formula (usually, alinear combination fitting).
  • Calculation of average, RMS and difference spectra.

Download screenshoots

Documentation: pdf-file
Examples: provided in a separate zip-file as XANDa Project files (*.xpj). These files can be associated with XANDa (then you can double-click on them to open), or can be opened from the XANDa 'Load project' dialog box.
Hardware/Software Issues: Windows NT/2000/XP, 95/98/ME
Input Data Format: ASCII text files. User should specify the file header and how to interpret and use the columns of data (or functions of these columns). Once described, the data formats are then recognized automatically.

Utility Program

XAFSmass - a program for calculation of X-ray absorption

A program for calculating the mass of XAFS samples. Notice that you typically do not need the calculated values at exactly the edge position, but rather at an energy somewhere above it. The list of edges does not force you to use those exact energies. The energy field can always be edited manually.

  • Calculation of mass and absorption step for powder samples.
  • Calculation of thickness and absorption step for samples with known density.
  • Calculation of gas pressure for ionization chambers.
  • Calculation of an unknown elemental concentration.
  • Calculation of two unknown elemental concentrations.
  • Finding the scattering factors f''

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Ray Tracing programs

xrt (XRayTracer) - a Python program for X-ray tracing

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