In [18]:

    

# Basic Python modules for http and json encoding/decoding
import urllib2
import json
import pprint
import re
import os
import sys
import xml.etree.ElementTree as ET


    

In [2]:

    

# Environment
path = "/Users/Andi/Development/MICCoM/cli/"
sys.path.append( path )
sys.path.append("/Users/Andi/Development/MG-RAST-Repo/MG-RAST-Tools/tools/lib/")

#os.chdir(path)
os.chdir("..")


    

In [6]:

    

# Path to output data for parser
dataDir = "/Users/Andi/Development/MICCoM/Data/Qbox/Output"


    

In [4]:

    

pwd


    

    
Out[4]:





u'/Users/Andi/Development/Notebooks'

In [5]:

    

sys.path


    

    
Out[5]:





['',
 '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-5.4.1-py2.7.egg',
 '/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip',
 '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7',
 '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin',
 '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac',
 '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages',
 '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk',
 '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old',
 '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload',
 '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages',
 '/Library/Python/2.7/site-packages',
 '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/extensions',
 '/Users/Andi/.ipython',
 '/Users/Andi/Development/MICCoM/cli//',
 '/Users/Andi/Development/MG-RAST-Repo/MG-RAST-Tools/tools/lib/']

In [9]:

    

# Open File - make sure we can read xml structures
import xml.etree.ElementTree as ET
tree = ET.parse(dataDir + '/si2gs.xml')
root = tree.getroot()


    

In [29]:

    

for child in root:
    print child.tag


    

    




description
atomset
wavefunction

In [34]:

    

for child in root:
    print child.tag , child.attrib , child.text , len(child)
    
    if len(child) :
        for c in child:
            print child.tag , c.tag


    

    




description {}   Created 2015-10-07T19:02:36Z by qbox-1.62.3   0
atomset {} 
4
atomset unit_cell
atomset species
atomset atom
atomset atom
wavefunction {'nempty': '0', 'nel': '8', 'nspin': '1', 'ecut': '7.5'} 
15
wavefunction domain
wavefunction reference_domain
wavefunction grid
wavefunction slater_determinant
wavefunction slater_determinant
wavefunction slater_determinant
wavefunction slater_determinant
wavefunction slater_determinant
wavefunction slater_determinant
wavefunction slater_determinant
wavefunction slater_determinant
wavefunction slater_determinant
wavefunction slater_determinant
wavefunction slater_determinant
wavefunction slater_determinant

In [44]:

    

def traverse ( node , parent) :
    
    for i in node :
        print parent.tag , i.tag
        
    for i in node :
        if len(node):
            traverse(i , node)


    

In [45]:

    

for child in root:
    traverse(child , root)


    

    




{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample unit_cell
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample species
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample atom
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample atom
atomset description
atomset symbol
atomset atomic_number
atomset mass
atomset norm_conserving_pseudopotential
species valence_charge
species lmax
species llocal
species nquad
species rquad
species mesh_spacing
species projector
species projector
species projector
norm_conserving_pseudopotential radial_potential
norm_conserving_pseudopotential radial_function
norm_conserving_pseudopotential radial_potential
norm_conserving_pseudopotential radial_function
norm_conserving_pseudopotential radial_potential
norm_conserving_pseudopotential radial_function
atomset position
atomset velocity
atomset position
atomset velocity
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample domain
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample reference_domain
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample grid
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample slater_determinant
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample slater_determinant
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample slater_determinant
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample slater_determinant
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample slater_determinant
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample slater_determinant
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample slater_determinant
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample slater_determinant
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample slater_determinant
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample slater_determinant
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample slater_determinant
{http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0}sample slater_determinant
wavefunction density_matrix
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction density_matrix
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction density_matrix
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction density_matrix
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction density_matrix
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction density_matrix
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction density_matrix
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction density_matrix
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction density_matrix
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction density_matrix
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction density_matrix
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction density_matrix
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function
wavefunction grid_function

In [ ]: