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Demo the Bond Valence Sum calculator.
Example calculation for NaCl and optional customization of bond valence parameters.
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‎cmi_scripts/README.md

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Contents
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--------
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* [calcbvsnacl](./calcbvsnacl) - Calculate bond valence sums for NaCl
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using standard and custom valence parameters.
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* [calcpdfc60](./calcpdfc60) - Calculate and plot a PDF for C60 from a stru
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file. Uses the DebyePDFCalculator from DiffPy-CMI.
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* [calcpdfcds](./calcpdfcds) - Calculate and plot a PDF for CdS wurtzite from
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a cif file. Uses the PDFCalculator module from DiffPy-CMI.
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* [fitCdSeNP](./fitCdSeNP) - Fit the PDF of CdSe nanoparticles using a
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* [fitCdSeNP](./fitCdSeNP) - Fit the PDF of CdSe nanoparticles using a
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non-periodic structure model.
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* [fitCdSeNP](./fitNiPDF) - Fit a Ni neutron PDF using a periodic Ni structure
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similar to Mathematica. To start notebook mode in IPython, run the command
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ipython notebook
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You can then load the .ipynb file directly into your workspace. Alternatively,
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you can run
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you can run
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ipython notebook name_of_notebook.ipynb
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‎cmi_scripts/calcbvsnacl/NaCl.cif

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#------------------------------------------------------------------------------
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#$Date: 2010-01-30 13:59:17 +0000 (Sat, 30 Jan 2010) $
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#$Revision: 966 $
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#$URL: svn://cod.ibt.lt/cod/cif/1/1000041.cif $
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#------------------------------------------------------------------------------
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#
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# This file is available in the Crystallography Open Database (COD),
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# http://www.crystallography.net/
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#
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# All data on this site have been placed in the public domain by the
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# contributors.
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#
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data_1000041
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_chemical_name_systematic 'Sodium chloride'
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_chemical_formula_structural 'Na Cl'
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_chemical_formula_sum 'Cl Na'
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_publ_section_title
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;
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Accuracy of an automatic diffractometer. measurement of the sodium
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chloride structure factors
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;
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loop_
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_publ_author_name
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'Abrahams, S C'
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'Bernstein, J L'
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_journal_name_full 'Acta Crystallographica (1,1948-23,1967)'
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_journal_coden_ASTM ACCRA9
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_journal_volume 18
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_journal_year 1965
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_journal_page_first 926
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_journal_page_last 932
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_cell_length_a 5.62
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_cell_length_b 5.62
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_cell_length_c 5.62
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_cell_angle_alpha 90
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_cell_angle_beta 90
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_cell_angle_gamma 90
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_cell_volume 177.5
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_cell_formula_units_Z 4
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_symmetry_space_group_name_H-M 'F m -3 m'
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_symmetry_Int_Tables_number 225
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_symmetry_cell_setting cubic
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loop_
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_symmetry_equiv_pos_as_xyz
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'x,y,z'
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'y,z,x'
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'z,x,y'
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'x,z,y'
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'y,x,z'
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'z,y,x'
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'x,-y,-z'
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'y,-z,-x'
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'z,-x,-y'
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'x,-z,-y'
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'y,-x,-z'
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'z,-y,-x'
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'-x,y,-z'
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'-y,z,-x'
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'-z,x,-y'
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'-x,z,-y'
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'-y,x,-z'
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'-z,y,-x'
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'-x,-y,z'
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'-y,-z,x'
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'-z,-x,y'
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'-x,-z,y'
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'-y,-x,z'
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'-z,-y,x'
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'-x,-y,-z'
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'-y,-z,-x'
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'-z,-x,-y'
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'-x,-z,-y'
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'-y,-x,-z'
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'-z,-y,-x'
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'-x,y,z'
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'-y,z,x'
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'-z,x,y'
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'-x,z,y'
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'-y,x,z'
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'-z,y,x'
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'x,-y,z'
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'y,-z,x'
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'z,-x,y'
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'x,-z,y'
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'y,-x,z'
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'z,-y,x'
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'x,y,-z'
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'y,z,-x'
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'z,x,-y'
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'x,z,-y'
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'y,x,-z'
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'z,y,-x'
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'x,1/2+y,1/2+z'
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'1/2+x,y,1/2+z'
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'1/2+x,1/2+y,z'
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'y,1/2+z,1/2+x'
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'1/2+y,z,1/2+x'
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'1/2+y,1/2+z,x'
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'z,1/2+x,1/2+y'
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'1/2+z,x,1/2+y'
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'1/2+z,1/2+x,y'
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'x,1/2+z,1/2+y'
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'1/2+x,z,1/2+y'
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'1/2+x,1/2+z,y'
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'y,1/2+x,1/2+z'
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'1/2+y,x,1/2+z'
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'1/2+y,1/2+x,z'
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'z,1/2+y,1/2+x'
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'1/2+z,y,1/2+x'
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'1/2+z,1/2+y,x'
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'x,1/2-y,1/2-z'
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'1/2+x,-y,1/2-z'
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'1/2+x,1/2-y,-z'
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'y,1/2-z,1/2-x'
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'1/2+y,-z,1/2-x'
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'1/2+y,1/2-z,-x'
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'z,1/2-x,1/2-y'
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'1/2+z,-x,1/2-y'
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'1/2+z,1/2-x,-y'
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'x,1/2-z,1/2-y'
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'1/2+x,-z,1/2-y'
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'1/2+x,1/2-z,-y'
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'y,1/2-x,1/2-z'
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'1/2+y,-x,1/2-z'
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'1/2+y,1/2-x,-z'
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'z,1/2-y,1/2-x'
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'1/2+z,-y,1/2-x'
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'1/2+z,1/2-y,-x'
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'-x,1/2+y,1/2-z'
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'1/2-x,y,1/2-z'
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'1/2-x,1/2+y,-z'
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'-y,1/2+z,1/2-x'
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'1/2-y,z,1/2-x'
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'1/2-y,1/2+z,-x'
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'-z,1/2+x,1/2-y'
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'1/2-z,x,1/2-y'
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'1/2-z,1/2+x,-y'
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'-x,1/2+z,1/2-y'
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'1/2-x,z,1/2-y'
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'1/2-x,1/2+z,-y'
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'-y,1/2+x,1/2-z'
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'1/2-y,x,1/2-z'
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'1/2-y,1/2+x,-z'
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'-z,1/2+y,1/2-x'
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'1/2-z,y,1/2-x'
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'1/2-z,1/2+y,-x'
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'-x,1/2-y,1/2+z'
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'1/2-x,-y,1/2+z'
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'1/2-x,1/2-y,z'
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'-y,1/2-z,1/2+x'
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'1/2-y,-z,1/2+x'
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'1/2-y,1/2-z,x'
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'-z,1/2-x,1/2+y'
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'1/2-z,-x,1/2+y'
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'1/2-z,1/2-x,y'
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'-x,1/2-z,1/2+y'
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'1/2-x,-z,1/2+y'
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'1/2-x,1/2-z,y'
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'-y,1/2-x,1/2+z'
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'1/2-y,-x,1/2+z'
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'1/2-y,1/2-x,z'
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'-z,1/2-y,1/2+x'
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'1/2-z,-y,1/2+x'
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'1/2-z,1/2-y,x'
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'-x,1/2-y,1/2-z'
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'1/2-x,-y,1/2-z'
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'1/2-x,1/2-y,-z'
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'-y,1/2-z,1/2-x'
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'1/2-y,-z,1/2-x'
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'1/2-y,1/2-z,-x'
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'-z,1/2-x,1/2-y'
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'1/2-z,-x,1/2-y'
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'1/2-z,1/2-x,-y'
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'-x,1/2-z,1/2-y'
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'1/2-x,-z,1/2-y'
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'1/2-x,1/2-z,-y'
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'-y,1/2-x,1/2-z'
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'1/2-y,-x,1/2-z'
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'1/2-y,1/2-x,-z'
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'-z,1/2-y,1/2-x'
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'1/2-z,-y,1/2-x'
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'1/2-z,1/2-y,-x'
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'-x,1/2+y,1/2+z'
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'1/2-x,y,1/2+z'
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'1/2-x,1/2+y,z'
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'-y,1/2+z,1/2+x'
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'1/2-y,z,1/2+x'
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'1/2-y,1/2+z,x'
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'-z,1/2+x,1/2+y'
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'1/2-z,x,1/2+y'
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'1/2-z,1/2+x,y'
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'-x,1/2+z,1/2+y'
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'1/2-x,z,1/2+y'
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'1/2-x,1/2+z,y'
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'-y,1/2+x,1/2+z'
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'1/2-y,x,1/2+z'
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'1/2-y,1/2+x,z'
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'-z,1/2+y,1/2+x'
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'1/2-z,y,1/2+x'
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'1/2-z,1/2+y,x'
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'x,1/2-y,1/2+z'
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'1/2+x,-y,1/2+z'
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'1/2+x,1/2-y,z'
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'y,1/2-z,1/2+x'
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'1/2+y,-z,1/2+x'
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'1/2+y,1/2-z,x'
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'z,1/2-x,1/2+y'
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'1/2+z,-x,1/2+y'
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'1/2+z,1/2-x,y'
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'x,1/2-z,1/2+y'
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'1/2+x,-z,1/2+y'
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'1/2+x,1/2-z,y'
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'y,1/2-x,1/2+z'
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'1/2+y,-x,1/2+z'
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'1/2+y,1/2-x,z'
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'z,1/2-y,1/2+x'
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'1/2+z,-y,1/2+x'
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'1/2+z,1/2-y,x'
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'x,1/2+y,1/2-z'
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'1/2+x,y,1/2-z'
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'1/2+x,1/2+y,-z'
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'y,1/2+z,1/2-x'
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'1/2+y,z,1/2-x'
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'1/2+y,1/2+z,-x'
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'z,1/2+x,1/2-y'
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'1/2+z,x,1/2-y'
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'1/2+z,1/2+x,-y'
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'x,1/2+z,1/2-y'
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'1/2+x,z,1/2-y'
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'1/2+x,1/2+z,-y'
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'y,1/2+x,1/2-z'
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'1/2+y,x,1/2-z'
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'1/2+y,1/2+x,-z'
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'z,1/2+y,1/2-x'
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'1/2+z,y,1/2-x'
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'1/2+z,1/2+y,-x'
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loop_
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_atom_type_symbol
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_atom_type_oxidation_number
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Na1+ 1.000
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Cl1- -1.000
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loop_
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_atom_site_label
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_atom_site_type_symbol
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_atom_site_symmetry_multiplicity
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_atom_site_Wyckoff_symbol
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_atom_site_fract_x
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_atom_site_fract_y
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_atom_site_fract_z
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_atom_site_occupancy
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_atom_site_attached_hydrogens
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_atom_site_calc_flag
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Na1 Na1+ 4 a 0. 0. 0. 1. 0 d
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Cl1 Cl1- 4 b 0.5 0.5 0.5 1. 0 d
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_refine_ls_R_factor_all 0.022
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_cod_database_code 1000041

‎cmi_scripts/calcbvsnacl/README.md

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# Calculate bond valence sums for NaCl
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This example shows how to evaluate bond valence sums using the `diffpy.srreal`
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module in DiffPy-CMI. BVS calculator uses a standard set of bond valence
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parameters obtained from a lookup table. Bond valence parameters can be
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set to custom values. Multiple BVS calculator objects can be created,
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where each one has separate lookup table and optionally different valence
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parameters.

‎cmi_scripts/calcbvsnacl/calcbvs.py

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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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'''Calculation of bond valence sums using diffpy.srreal module included in
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DiffPy-CMI.
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'''
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from diffpy.Structure import loadStructure
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from diffpy.srreal.bvscalculator import BVSCalculator
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# load crystal structure data from a CIF file
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nacl = loadStructure('NaCl.cif')
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# create bond valence sum calculator object
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bvsc = BVSCalculator()
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# calculate BVS and print the expected and actual valences
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vsim = bvsc(nacl)
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print 'Calculate bond valence sums for NaCl "bvsc(nacl)"'
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print 'expected "bvsc.valences":\n ', bvsc.valences
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print 'calculated "bvsc.value":\n ' , vsim
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print 'difference "bvsc.bvdiff":\n ', bvsc.bvdiff
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print 'root mean square difference "bvsc.bvrmsdiff":', bvsc.bvrmsdiff
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print
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# create new BVS calculator with a custom bond valence parameters
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bvsc2 = BVSCalculator()
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# Use alternate value for the Na+ Cl- bond valence parameters from
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# http://www.iucr.org/__data/assets/file/0018/59004/bvparm2011.cif
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# These parameters have 6A cutoff.
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bvsc2.bvparamtable.setCustom('Na', +1, 'Cl', -1, Ro=1.6833, B=0.608)
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bvsc2.rmax = 6
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print "BVS in NaCl with alternate parameters:\n ", bvsc2(nacl)
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print
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# Lookup table of bond valence parameters can be used as separate object.
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from diffpy.srreal.bvparameterstable import BVParametersTable
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table = BVParametersTable()
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bp = table.lookup('Na+', 'Cl-')
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bp2 = table.lookup('Na', +1, 'Br', -1)
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print "Standard lookup of bond valence parameters:"
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print " ", bp
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print " ", bp2
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print
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print "Handling of unknown or invalid ion pairs:"
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print " table.lookup('A+', 'X-'):", table.lookup('A+', 'X-')
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print " table.lookup('A+', 'X-') == table.none():", (
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table.lookup('A+', 'X-') == table.none())

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