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#!/bin/env python
#
# Author : Ian Curington
#
# Example to generate a stack of layered prism elements
# Writes a "test20.xmf/h5" files with a 3D unstructured prism grid
# N vertical layers based on triangle plan grid
# containing "pressure" scalar node values,
# uses Compression for connectivity, geometry and attributes.
#
from __future__ import print_function
from Xdmf import *
BaseName = 'test20'
# define simple triangle mesh in horizontal plane
tri_conn = [0,1,6, \
1,2,6, \
2,3,6, \
3,4,6, \
4,5,6, \
5,0,6 ]
ntris = len(tri_conn)/3
tri_coords = [-2, 0, 0, \
-1, 1, 0, \
1, 1, 0, \
2, 0, 0, \
1,-1, 0, \
-1,-1, 0, \
0, 0, 0 ]
ncoords = len(tri_coords)/3
# prism layers, make large enough to trigger hdf5 writing
nlayers = 800
layer_delta = 0.01
"""
Reset an existing .h5 file for truncating all or any existing contents,
by writing small junk array in 'w' mode.
"""
# Write H5 Data
arr = XdmfArray()
#arr.DebugOn()
arr.SetNumberType(XDMF_FLOAT64_TYPE)
arr.SetShapeFromString("2 3")
arr.Generate(0.0, 1.0, 0, arr.GetNumberOfElements() - 1)
h5 = XdmfHDF()
h5.CopyType(arr)
h5.CopyShape(arr)
h5.Open( BaseName + '.h5:/_junk_', 'w')
h5.Write(arr)
h5.Close()
# XDMF init
d = XdmfDOM()
root = XdmfRoot()
root.SetDOM(d)
root.Build()
# Domain
dm = XdmfDomain()
root.Insert(dm)
# Grid
g = XdmfGrid()
g.SetName("Prism Grid")
#g.DebugOn()
# Topology - 3D unstructured grid, prism element type
t = g.GetTopology()
t.SetTopologyType(XDMF_WEDGE)
t.SetNumberOfElements(nlayers * ntris)
#t.DebugOn()
cc = t.GetConnectivity()
cc.SetNumberType(XDMF_INT32_TYPE)
# length of connectivity
nElem = nlayers*ntris*6
cc.SetNumberOfElements(nElem)
cc.SetHeavyDataSetName( BaseName + r'.h5:/Connectivity' )
if nElem > 1000:
cc.SetCompression(9)
c_index = 0
for layer in range(nlayers):
for tri in range(ntris):
cc.SetValueFromInt64( c_index*6+0, tri_conn[3*tri+0]+layer*ncoords )
cc.SetValueFromInt64( c_index*6+1, tri_conn[3*tri+1]+layer*ncoords )
cc.SetValueFromInt64( c_index*6+2, tri_conn[3*tri+2]+layer*ncoords )
cc.SetValueFromInt64( c_index*6+3, tri_conn[3*tri+0]+(layer+1)*ncoords )
cc.SetValueFromInt64( c_index*6+4, tri_conn[3*tri+1]+(layer+1)*ncoords )
cc.SetValueFromInt64( c_index*6+5, tri_conn[3*tri+2]+(layer+1)*ncoords )
c_index = c_index + 1
# Geometry - origin and cell size
geo = g.GetGeometry()
geo.SetGeometryType(XDMF_GEOMETRY_XYZ)
# three explicit corners
ca = geo.GetPoints()
ca.SetNumberType(XDMF_FLOAT32_TYPE)
ca.SetHeavyDataSetName( BaseName + r'.h5:/Coordinates' )
# number of nodes * 3
nElem = (nlayers+1)*ncoords*3
ca.SetNumberOfElements(nElem)
if nElem > 1000:
ca.SetCompression(9)
c_index = 0
for layer in range(nlayers+1):
for node in range(ncoords):
ca.SetValueFromFloat64( c_index*3+0, tri_coords[3*node+0] )
ca.SetValueFromFloat64( c_index*3+1, tri_coords[3*node+1] )
ca.SetValueFromFloat64( c_index*3+2, tri_coords[3*node+2]+layer*layer_delta )
c_index = c_index + 1
dm.Insert(g)
# Attribute - as scalar node data
attr = XdmfAttribute()
attr.SetName("Pressure")
attr.SetAttributeCenter(XDMF_ATTRIBUTE_CENTER_NODE);
attr.SetAttributeType(XDMF_ATTRIBUTE_TYPE_SCALAR);
#attr.DebugOn()
p = attr.GetValues()
p.SetHeavyDataSetName( BaseName + r'.h5:/Pressure')
# number of nodes with values
nElem = (nlayers+1)*ncoords
p.SetNumberOfElements(nElem )
if nElem > 1000:
p.SetCompression(9)
c_index = 0
for layer in range(nlayers+1):
for node in range(ncoords):
value = 10.0 + float(layer) * 2.0
p.SetValueFromFloat64( c_index, value )
c_index = c_index + 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( BaseName + r'.xmf') # write to file
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