Purpose: Use XPath to address data in xml files.
XSLT
XPath is a language for finding information in an XML document. It is designed to address parts of an xml file, such as elements or attributes, and to get their assigned content.
Select Data
This very minimal template can select any data from the source file with the help of xpath.
<?xml version="1.0" encoding="UTF-8"?> <xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0"> <xsl:template match="/"> <xsl:value-of select="xpath"/> </xsl:template> </xsl:stylesheet>
The important part, which is used to specify the content to be extracted from the xml file, is the following,
... <xsl:value-of select="xpath"/> ...
where xpath stands for an expression like /parent_element/child1/child2/../@attribute.
The template is applied with xsltproc
xsltproc template.xsl input.xml
A short reference of the syntax can be found here.
EXERCISE
Extract the k-point grid, the title, and the name of the first speciesfile from an exciting input.xml file,.
Node Sets
<?xml version="1.0" encoding="UTF-8"?> <xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0"> <xsl:template match="/"> <xsl:for-each select="/input/structure/species"> <xsl:value-of select="@speciesfile"/> <xsl:text> </xsl:text> </xsl:for-each> </xsl:template> </xsl:stylesheet>
EXERCISE
Transform the atomic positions of an input.xml to a simple text file. You may try to mimic your favorite chemical file format if you have one!
Python
Python has one of the nicest XML modules, called lxml. The following example parses an exciting input, selects the atomic positions, and after applying a transformation it writes the changed content back to a new file.
from lxml import etree as ET fileobj=open("input.xml","r") doc = ET.parse(fileobj) #Get instance of root element: root = doc.getroot() #Get list of elements named "atom": atoms = doc.xpath('//atom') #Loop over all "atom" elements and set a new "coord" attribute: for atom in atoms: x, y, z = atom.get('coord').split() print [float(x) , float(y) , float(z)] atom.set('coord', str(float(x) + 0.5) +" " +str(float(y) + 0.5) +" " +str(float(z) + 0.5) ) #Write changes to inputgen.xml: fileobj2=open("inputgen.xml","w") fileobj2.write(ET.tostring(root, pretty_print=True, xml_declaration=True, encoding='UTF-8'))
EXERCISE:
Take the script and add code to change the scale attribute of the crystal element.
