7. GSAS-II Data Storage Modules

These modules are used to provide a place to find constants that are used in various locations.

7.1. GSASIIdata: Ramachandran Parameters

At present this module defines one dict, ramachandranDist, which contains arrays for All and specific amino acids.

7.2. ElementTable: Periodic Table Data

Element table data for building periodic table with valences & JMOL colors. Need these in case we go back to this periodic table coloring scheme.

Defines list ElTable which contains all defined oxidation states for each element, the location in the table, an element name, a color, a size and a second color.

7.3. FormFactors: Scattering Data

Contains atomic scattering factors from “New Analytical Scattering Factor Functions for Free Atoms and Ions for Free Atoms and Ions”, D. Waasmaier & A. Kirfel, Acta Cryst. (1995). A51, 416-413.

Also, tabulated coefficients for calculation of Compton Cross Section as a function of sin(theta)/lambda from “Analytic Approximations to Incoherently Scattered X-Ray Intensities”, H. H. M. Balyuzi, Acta Cryst. (1975). A31, 600.

7.4. ImageCalibrants: Calibration Standards

GSASII powder calibrants in dictionary ImageCalibrants.Calibrants containing substances commonly used for powder calibrations for image data.

Each entry in ImageCalibrants consists of:

 'key':([Bravais num,],[space group,],[(a,b,c,alpha,beta,gamma),],no. lines skipped,(dmin,pixLimit,cutOff),(absent list))

* See below for Bravais num assignments.
* The space group may be an empty string.
* The absent list is optional; it gives indices of lines that have no intensity despite being allowed - see the Si example below; counting begins at zero

As an example:

'LaB6  SRM660a':([2,],['',][(4.1569162,4.1569162,4.1569162,90,90,90),],0,(1.0,10,10.)),

For calibrants that are mixtures, the “Bravais num” and “(a,b,…)” values are repeated, as in this case:

'LaB6 & CeO2':([2,0],['',''] [(4.1569,4.1569,4.1569,90,90,90),(5.4117,5.4117,5.4117,90,90,90)], 0, (1.0,2,1.)),

Note that Si has reflections (the 4th, 11th,…) that are not extinct by symmetry but still have zero intensity. These are supplied in the final list:

'Si':([0,],['F d 3 m'],[(5.4311946,5.4311946,5.4311946,90,90,90),],0,(1.,10,10.),(3,10,13,20,23,26,33,35,40,43)),
Note, the Bravais numbers are:
  • 0 F cubic

  • 1 I cubic

  • 2 P cubic

  • 3 R hexagonal (trigonal not rhombohedral)

  • 4 P hexagonal

  • 5 I tetragonal

  • 6 P tetragonal

  • 7 F orthorhombic

  • 8 I orthorhombic

  • 9 C orthorhombic

  • 10 P orthorhombic

  • 11 C monoclinic

  • 12 P monoclinic

  • 13 P triclinic

7.4.1. User-Defined Calibrants

To expand this list with locally needed additions, do not modify this ImageCalibrants.py file, because you may lose these changes during a software update. Instead duplicate the format of this file in a file named UserCalibrants.py and there define the material(s) you want:

  'LaB6 skip 2 lines':([2,],['',],[(4.1569162,4.1569162,4.1569162,90,90,90),],2,(1.0,10,10),()),

New key values will be added to the list of options. If a key is duplicated, the information in UserCalibrants.py will override the entry in this (the ImageCalibrants.py file).

7.5. atmdata: Table of atomic data

The entries here are:

XrayFF: a dict of form factor coefficients

AtmSize: atom Sizes, bond radii, angle radii, H-bond radii

AtmBlens: atom masses & neutron scattering length (b,b’), sig(incoh) @ 1A

MagFF: neutron magnetic form factor coeff: M for j<0> & N for j<2>


Exponential scattering factor curve coeficients, Cromer and Waber(1971) Int. Tables Vol. IV. Delta f’ and delta f” terms calcd via D.T. Cromer & D.A. Liberman (1981), Acta Cryst. A37, 267-268. Atomic weights from CRC 56th Edition

Electron scattering factor curve coefficients from International Tables for Crystallography, Vol. C, Ch 4. Sect. 4.3.2.

Neutron scattering lengths & abs. cross sections from H. Rauch & W. Waschowski, Neutron Data Booklet, 2003. X-ray <j0> & <j2> coeff. from Intl. Tables for Cryst, Vol. C 5-d <j0> & <j2> from Kobayashi K, Nagao T, Ito M. Acta Crystallogr A67, 473-480 (2011)

Neutron anomalous coeff (LS) from fitting Lynn & Seeger, At. Data & Nuc. Data Tables, 44, 191-207(1990)

O2- x-ray scattering factor from Tokonami (1965) Acta Cryst 19, 486

At wts from 14th ed Nuclides & Isotopes, 1989 GE Co.

Orbital form factors from fitting Table 2.2D in International Tables for x-ray Crystallography Vol IV by Cromer & Waber (1974)

7.6. defaultIparms: Table of instrument parameters

Defines some default instrument parameters. Format for each is a list of strings finished with a ‘ ‘. Begin with ‘#GSAS-II…’ as the reader routine checks this. Each line can be comprised of a block of ‘;’ delimited name:value pairs. All instrument parameters must be included; even those = 0. Use a GSAS-II instprm file as a source for the entries.

For a new entry:

Append a useful name to defaultIparms_lbl.

Append the list of lines to defaultIparms.

defaultIparm_lbl: defines a list of labels.

defaultIparms: defines a list of multiple strings with values for each set of defaults.