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rGOOSEFEM/docs/examples/Mesh/MeshTri3-Regular_paraview.py
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MeshTri3-Regular_paraview.py
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# ========================================= load libraries =========================================
import GooseFEM as gf
import numpy as np
import h5py
# ========================================== define mesh ===========================================
mesh = gf.Mesh.Tri3.Regular(4,5)
coor = mesh.coor()
conn = mesh.conn()
# ======================================== write HDF5=file =========================================
# set file-name base
name = 'MeshTri3-Regular_paraview'
# open data file
f = h5py.File('{name:s}.hdf5'.format(name=name),'w')
# write particle positions, and a dummy connectivity
f.create_dataset('/coor',data=coor)
f.create_dataset('/conn',data=conn)
# create a sample deformation: simple shear
for inc,gamma in enumerate(np.linspace(0,1,100)):
# - initialize displacement (should be 3-d for ParaView)
U = np.zeros((mesh.nnode(),3),dtype='float64')
# - set
U[:,0] += gamma * coor[:,1]
# - store
f.create_dataset('/disp/%d'%inc,data=U)
# ======================================== write XDMF-file =========================================
# --------------------------------- format of the main structure ----------------------------------
xmf = '''<?xml version="1.0" ?>
<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>
<Xdmf Version="2.0">
<Domain>
<Grid Name="TimeSeries" GridType="Collection" CollectionType="Temporal">
{series:s}
</Grid>
</Domain>
</Xdmf>
'''
# ----------------------------- format of an increment in time-series ------------------------------
grid = '''<Grid Name="Increment = {inc:d}">
<Time Value="{inc:d}"/>
<Topology TopologyType="Triangle" NumberOfElements="{nelem:d}">
<DataItem Dimensions="{nelem:d} {nne:d}" Format="HDF">
{name:s}.hdf5:/conn
</DataItem>
</Topology>
<Geometry GeometryType="XY">
<DataItem Dimensions="{nnode:d} {ndim:d}" Format="HDF">
{name:s}.hdf5:/coor
</DataItem>
</Geometry>
<Attribute Name="Displacement" AttributeType="Vector" Center="Node">
<DataItem Dimensions="{nnode:d} 3" NumberType="Float" Precision="8" Format="HDF">
{name:s}.hdf5:/disp/{inc:d}
</DataItem>
</Attribute>
</Grid>
'''
# ------------------------------------------- write file -------------------------------------------
# initialize string that will contain the full time series
txt = ''
# loop over all increments, append the time series
for inc in range(100):
txt += grid.format(
name = name,
inc = inc,
nnode = mesh.nnode(),
ndim = mesh.ndim(),
nelem = mesh.nelem(),
nne = mesh.nne()
)
# write xmf-file, fix the indentation
fname = '{name:s}.xmf'.format(name=name)
open(fname,'w').write(xmf.format(series=' '+txt.replace('\n','\n ')))
# ======================================== print node=sets =========================================
np.set_printoptions(linewidth=200)
print('nodesBottomEdge =', mesh.nodesBottomEdge())
print('nodesTopEdge =', mesh.nodesTopEdge())
print('nodesLeftEdge =', mesh.nodesLeftEdge())
print('nodesRightEdge =', mesh.nodesRightEdge())
print('nodesLeftBottomCorner =', mesh.nodesLeftBottomCorner())
print('nodesRightBottomCorner =', mesh.nodesRightBottomCorner())
print('nodesRightTopCorner =', mesh.nodesRightTopCorner())
print('nodesLeftTopCorner =', mesh.nodesLeftTopCorner())
print('nodesPeriodic =')
print(mesh.nodesPeriodic())
print('nodesOrigin =')
print(mesh.nodesOrigin())
# check uniqueness of tied nodes
ties = mesh.nodesPeriodic()[:,1]
if len(np.unique(ties)) != len(ties):
raise IOError('Nodal ties not unique')
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