/usr/lib/petscdir/3.7.7/x86_64-linux-gnu-real-debug/bin/petsc_gen_xdmf.py is in libpetsc3.7.7-dbg 3.7.7+dfsg1-2build5.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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import h5py
import numpy as np
import os, sys
class Xdmf:
def __init__(self, filename):
self.filename = filename
self.cellMap = {1 : {1 : 'Polyvertex', 2 : 'Polyline'}, 2 : {3 : 'Triangle', 4 : 'Quadrilateral'}, 3 : {4 : 'Tetrahedron', 8 : 'Hexahedron'}}
self.typeMap = {'scalar' : 'Scalar', 'vector' : 'Vector', 'tensor' : 'Tensor6', 'matrix' : 'Matrix'}
self.typeExt = {2 : {'vector' : ['x', 'y'], 'tensor' : ['xx', 'yy', 'xy']}, 3 : {'vector' : ['x', 'y', 'z'], 'tensor' : ['xx', 'yy', 'zz', 'xy', 'yz', 'xz']}}
return
def writeHeader(self, fp, hdfFilename):
fp.write('''\
<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" [
<!ENTITY HeavyData "%s">
]>
''' % os.path.basename(hdfFilename))
fp.write('\n<Xdmf>\n <Domain Name="domain">\n')
return
def writeCells(self, fp, topologyPath, numCells, numCorners):
fp.write('''\
<DataItem Name="cells"
ItemType="Uniform"
Format="HDF"
NumberType="Float" Precision="8"
Dimensions="%d %d">
&HeavyData;:/%s/cells
</DataItem>
''' % (numCells, numCorners, topologyPath))
return
def writeVertices(self, fp, geometryPath, numVertices, spaceDim):
fp.write('''\
<DataItem Name="vertices"
Format="HDF"
Dimensions="%d %d">
&HeavyData;:/%s/vertices
</DataItem>
<!-- ============================================================ -->
''' % (numVertices, spaceDim, geometryPath))
return
def writeTimeGridHeader(self, fp, time):
fp.write('''\
<Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
<Time TimeType="List">
<DataItem Format="XML" NumberType="Float" Dimensions="%d">
''' % (len(time)))
fp.write(' '.join(map(str, map(float, time))))
fp.write('''
</DataItem>
</Time>
''')
return
def writeSpaceGridHeader(self, fp, numCells, numCorners, cellDim, spaceDim):
fp.write('''\
<Grid Name="domain" GridType="Uniform">
<Topology
TopologyType="%s"
NumberOfElements="%d">
<DataItem Reference="XML">
/Xdmf/Domain/DataItem[@Name="cells"]
</DataItem>
</Topology>
<Geometry GeometryType="%s">
<DataItem Reference="XML">
/Xdmf/Domain/DataItem[@Name="vertices"]
</DataItem>
</Geometry>
''' % (self.cellMap[cellDim][numCorners], numCells, "XYZ" if spaceDim > 2 else "XY"))
return
def writeFieldSingle(self, fp, numSteps, timestep, spaceDim, name, f, domain):
if len(f[1].shape) > 2:
dof = f[1].shape[1]
bs = f[1].shape[2]
elif len(f[1].shape) > 1:
if numSteps > 1:
dof = f[1].shape[1]
bs = 1
else:
dof = f[1].shape[0]
bs = f[1].shape[1]
else:
dof = f[1].shape[0]
bs = 1
fp.write('''\
<Attribute
Name="%s"
Type="%s"
Center="%s">
<DataItem ItemType="HyperSlab"
Dimensions="1 %d %d"
Type="HyperSlab">
<DataItem
Dimensions="3 3"
Format="XML">
%d 0 0
1 1 1
1 %d %d
</DataItem>
<DataItem
DataType="Float" Precision="8"
Dimensions="%d %d %d"
Format="HDF">
&HeavyData;:%s
</DataItem>
</DataItem>
</Attribute>
''' % (f[0], self.typeMap[f[1].attrs['vector_field_type']], domain, dof, bs, timestep, dof, bs, numSteps, dof, bs, name))
return
def writeFieldComponents(self, fp, numSteps, timestep, spaceDim, name, f, domain):
vtype = f[1].attrs['vector_field_type']
if len(f[1].shape) > 2:
dof = f[1].shape[1]
bs = f[1].shape[2]
cdims = '1 %d 1' % dof
dims = '%d %d %d' % (numSteps, dof, bs)
stride = '1 1 1'
size = '1 %d 1' % dof
else:
dof = f[1].shape[0]
bs = f[1].shape[1]
cdims = '%d 1' % dof
dims = '%d %d' % (dof, bs)
stride = '1 1'
size = '%d 1' % dof
for c in range(bs):
ext = self.typeExt[spaceDim][vtype][c]
if len(f[1].shape) > 2: start = '%d 0 %d' % (timestep, c)
else: start = '0 %d' % c
fp.write('''\
<Attribute
Name="%s"
Type="Scalar"
Center="%s">
<DataItem ItemType="HyperSlab"
Dimensions="%s"
Type="HyperSlab">
<DataItem
Dimensions="3 %d"
Format="XML">
%s
%s
%s
</DataItem>
<DataItem
DataType="Float" Precision="8"
Dimensions="%s"
Format="HDF">
&HeavyData;:%s
</DataItem>
</DataItem>
</Attribute>
''' % (f[0]+'_'+ext, domain, cdims, len(f[1].shape), start, stride, size, dims, name))
return
def writeField(self, fp, numSteps, timestep, cellDim, spaceDim, name, f, domain):
ctypes = ['tensor', 'matrix']
if spaceDim == 2 or cellDim != spaceDim: ctypes.append('vector')
if f[1].attrs['vector_field_type'] in ctypes:
self.writeFieldComponents(fp, numSteps, timestep, spaceDim, name, f, domain)
else:
self.writeFieldSingle(fp, numSteps, timestep, spaceDim, name, f, domain)
return
def writeSpaceGridFooter(self, fp):
fp.write(' </Grid>\n')
return
def writeTimeGridFooter(self, fp):
fp.write(' </Grid>\n')
return
def writeFooter(self, fp):
fp.write(' </Domain>\n</Xdmf>\n')
return
def write(self, hdfFilename, topologyPath, numCells, numCorners, cellDim, geometryPath, numVertices, spaceDim, time, vfields, cfields):
useTime = not (len(time) < 2 and time[0] == -1)
with file(self.filename, 'w') as fp:
self.writeHeader(fp, hdfFilename)
self.writeCells(fp, topologyPath, numCells, numCorners)
self.writeVertices(fp, geometryPath, numVertices, spaceDim)
if useTime: self.writeTimeGridHeader(fp, time)
for t in range(len(time)):
self.writeSpaceGridHeader(fp, numCells, numCorners, cellDim, spaceDim)
for vf in vfields: self.writeField(fp, len(time), t, cellDim, spaceDim, '/vertex_fields/'+vf[0], vf, 'Node')
for cf in cfields: self.writeField(fp, len(time), t, cellDim, spaceDim, '/cell_fields/'+cf[0], cf, 'Cell')
self.writeSpaceGridFooter(fp)
if useTime: self.writeTimeGridFooter(fp)
self.writeFooter(fp)
return
def generateXdmf(hdfFilename, xdmfFilename = None):
if xdmfFilename is None:
xdmfFilename = os.path.splitext(hdfFilename)[0] + '.xmf'
# Read mesh
h5 = h5py.File(hdfFilename, 'r')
if 'viz' in h5 and 'geometry' in h5['viz']:
geomPath = 'viz/geometry'
geom = h5['viz']['geometry']
else:
geomPath = 'geometry'
geom = h5['geometry']
if 'viz' in h5 and 'topology' in h5['viz']:
topoPath = 'viz/topology'
topo = h5['viz']['topology']
else:
topoPath = 'topology'
topo = h5['topology']
vertices = geom['vertices']
numVertices = vertices.shape[0]
spaceDim = vertices.shape[1]
cells = topo['cells']
numCells = cells.shape[0]
numCorners = cells.shape[1]
cellDim = topo['cells'].attrs['cell_dim']
if 'time' in h5:
time = np.array(h5['time']).flatten()
else:
time = [-1]
vfields = []
cfields = []
if 'vertex_fields' in h5: vfields = h5['vertex_fields'].items()
if 'cell_fields' in h5: cfields = h5['cell_fields'].items()
# Write Xdmf
Xdmf(xdmfFilename).write(hdfFilename, topoPath, numCells, numCorners, cellDim, geomPath, numVertices, spaceDim, time, vfields, cfields)
h5.close()
return
if __name__ == '__main__':
for f in sys.argv[1:]:
generateXdmf(f)
|