Using xml_grep

[fgygi]

Extracting xml elements from Qbox output is made easier using the xml_grep command. xml_grep is part of the Perl Twig package.

On midway.rcc.uchicago.edu, e.g., you can use module load perl to access the command. A few examples:

Extracting the <etotal> element from the output file gs3.r:

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$ xml_grep etotal gs3.r
<?xml version="1.0" ?>
<xml_grep version="0.9" date="Sat Oct 12 12:17:25 2019">
<file filename="gs3.r">
  <etotal>   -2626.17326085 </etotal>
</file>
</xml_grep>

Extract the <etotal> element with only the text content:

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$ xml_grep --text_only etotal gs3.r 
   -2626.17326085 

Using XPath syntax to extract just atom "O2_110":

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$ xml_grep 'atom[@name="O2_110"]' gs3.r 
<?xml version="1.0" ?>
<xml_grep version="0.9" date="Sat Oct 12 12:23:34 2019">
<file filename="gs3.r">
  <atom name="O2_110" species="oxygen">
    <position> 4.67035000 13.06390000 -3.37325000 </position>
    <velocity> 0.00000000 0.00000000 0.00000000 </velocity>
    <force> 0.00785222 0.00282495 0.00500539 </force>
  </atom>
</file>
</xml_grep>

Extract the position of atom "O2_110", text only:

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$ xml_grep --text_only 'atom[@name="O2_110"]/position' gs3.r 
 4.67035000 13.06390000 -3.37325000