Write Xdmf

Writing Xdmf

Note code snippets on this page are from version 2 or 1 and need updating for xdmf 3.

Xdmf can be generated in many different manners. Using the low level HDF5 library and print statements is certainly one of them. Utilizing the XDMF API, however, provides some convenient advantages. Suppose we wanted to generate an XDMF dataset of a co-rectilinear mesh with scalar values at each node

from Xdmf import *

d = XdmfDOM() 

root = XdmfRoot()
root.SetDOM(d)
root.SetVersion(2.2) # Change the Version number because we can
root.Build()
# Information
i = XdmfInformation() # Arbitrary Name=Value Facility
i.SetName("SampleLocation")
i.SetValue("4")
root.Insert(i) # XML DOM is used as the keeper of the structure
              # Insert() creates an XML node and inserts it under
              # the parent
# Domain
dm = XdmfDomain()
root.Insert(dm)
# Grid
g = XdmfGrid()
g.SetName("Structured Grid")
# Topology
t = g.GetTopology()
t.SetTopologyType(XDMF_3DCORECTMESH)
t.GetShapeDesc().SetShapeFromString('10 20 30')
# Geometry
geo = g.GetGeometry()
geo.SetGeometryType(XDMF_GEOMETRY_ORIGIN_DXDYDZ)
geo.SetOrigin(1, 2, 3)
geo.SetDxDyDz(0.1, 0.2, 0.3)
dm.Insert(g)
# Attribute
attr = XdmfAttribute()
attr.SetName("Pressure")
attr.SetAttributeCenter(XDMF_ATTRIBUTE_CENTER_NODE);
attr.SetAttributeType(XDMF_ATTRIBUTE_TYPE_SCALAR);
p = attr.GetValues()
p.SetShapeFromString("10 20 30")
p.Generate(0.0, 1.0, 0, p.GetNumberOfElements() - 1)
g.Insert(attr)
# Update XML and Write Values to DataItems
root.Build() # DataItems > 100 values are heavy
print d.Serialize() # prints to stdout 

d.Write('SMesh.xmf') # write to file

Would result in the Light Data XML to be written to the file Smesh.xmf and the Heavy data to be written to Xdmf.h5.

<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf xmlns:xi="http://www.w3.org/2003/XInclude" Version="2.2">
 <Information Name="SampleLocation" Value="4"/>
 <Domain>
   <Grid Name="Structured Grid" GridType="Uniform">
     <Topology TopologyType="3DCORECTMesh" NumberOfElements="10 20 30 "/>
     <Geometry GeometryType="ORIGIN_DXDYDZ">
       <DataItem Dimensions="3 " NumberType="Float" Precision="4" Format="XML">
          1 2 3
       </DataItem>
       <DataItem Dimensions="3 " NumberType="Float" Precision="4" Format="XML">
        0.1 0.2 0.3
       </DataItem>
     </Geometry>
     <Attribute Name="Pressure" AttributeType="Scalar" Center="Cell">
       <DataItem Dimensions="6000 " NumberType="Float" Precision="4" Format="HDF">Xdmf.h5:/Data</DataItem>
     </Attribute>
   </Grid>
 </Domain>
</Xdmf>

Now suppose the HDF5 already existed or we wanted to write the HDF5 files in a specific manner. All XdmfElements have a SetDataXml() method which takes a raw XML string. When the element is built, the XML is blindly copied in and the writing of HeavyData is skipped.

#!/usr/bin/env python

from Xdmf import *

# Example of How to Generate Xdmf
# The Heavy Data for the Attribute is written separately

# Write H5 Data
arr = XdmfArray()
arr.SetNumberType(XDMF_FLOAT64_TYPE)
arr.SetShapeFromString("10 20 30")
arr.Generate(0.0, 1.0, 0, arr.GetNumberOfElements() - 1)
h5 = XdmfHDF()
h5.CopyType(arr)
h5.CopyShape(arr)
h5.Open('XdmfByHand.h5:/Mydata', 'w')
h5.Write(arr)
h5.Close()
# Use XdmfValuesHDF to generate the appropriate
# Xdmf XML from and existing HDF5 dataset
dv = XdmfValuesHDF()
DataXml = dv.DataItemFromHDF('XdmfByHand.h5:/Mydata')
#
# Now build the tree of objects
d = XdmfDOM()

root = XdmfRoot()
root.SetDOM(d)
root.SetVersion(2.2) # Change the Version number because we can
 root.Build()
# Information
i = XdmfInformation() # Arbitrary Name=Value Facility
i.SetName("SampleLocation")
i.SetValue("4")
root.Insert(i) # XML DOM is used as the keeper of the structure
             # Insert() creates an XML node and inserts it under
             # the parent
# Domain
dm = XdmfDomain()
root.Insert(dm)
# Grid
g = XdmfGrid()
g.SetName("Structured Grid")
# Topology
t = g.GetTopology()
t.SetTopologyType(XDMF_3DCORECTMESH)
t.GetShapeDesc().SetShapeFromString('10 20 30')
# Geometry
geo = g.GetGeometry()
geo.SetGeometryType(XDMF_GEOMETRY_ORIGIN_DXDYDZ)
geo.SetOrigin(1, 2, 3)
geo.SetDxDyDz(0.1, 0.2, 0.3)
dm.Insert(g)
# Attribute
attr = XdmfAttribute()
attr.SetName("Pressure")
attr.SetAttributeCenter(XDMF_ATTRIBUTE_CENTER_NODE);
attr.SetAttributeType(XDMF_ATTRIBUTE_TYPE_SCALAR);
# Insert the raw XML
attr.SetDataXml(DataXml)
g.Insert(attr)
# Update XML and Write Values to DataItems
root.Build() # DataItems > 100 values are heavy
print d.Serialize() # prints to stdout 

d.Write('SMesh.xmf') # write to file

This results in identical XML with just the name of the HDF5 dataset changed. ~