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rGOOSEFEM/docs/examples/Mesh/MeshHex8-FineLayer-nodes.py
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MeshHex8-FineLayer-nodes.py
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import h5py
import numpy as np
import GooseFEM as gf
import lxml.etree as etree
# ====================== create fictitious configuration + store to HDF5-file ======================
# create mesh object
mesh = gf.Mesh.Hex8.FineLayer(9,17,27)
# initialize all node sets
nodesets = dict(
nodesFront = np.zeros((mesh.nnode()),dtype='int'),
nodesBack = np.zeros((mesh.nnode()),dtype='int'),
nodesLeft = np.zeros((mesh.nnode()),dtype='int'),
nodesRight = np.zeros((mesh.nnode()),dtype='int'),
nodesBottom = np.zeros((mesh.nnode()),dtype='int'),
nodesTop = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontFace = np.zeros((mesh.nnode()),dtype='int'),
nodesBackFace = np.zeros((mesh.nnode()),dtype='int'),
nodesLeftFace = np.zeros((mesh.nnode()),dtype='int'),
nodesRightFace = np.zeros((mesh.nnode()),dtype='int'),
nodesBottomFace = np.zeros((mesh.nnode()),dtype='int'),
nodesTopFace = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontBottomEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontTopEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontLeftEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontRightEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesBackBottomEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesBackTopEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesBackLeftEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesBackRightEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesBottomLeftEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesBottomRightEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesTopLeftEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesTopRightEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontBottomOpenEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontTopOpenEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontLeftOpenEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontRightOpenEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesBackBottomOpenEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesBackTopOpenEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesBackLeftOpenEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesBackRightOpenEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesBottomLeftOpenEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesBottomRightOpenEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesTopLeftOpenEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesTopRightOpenEdge = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontBottomLeftCorner = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontBottomRightCorner = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontTopLeftCorner = np.zeros((mesh.nnode()),dtype='int'),
nodesFrontTopRightCorner = np.zeros((mesh.nnode()),dtype='int'),
nodesBackBottomLeftCorner = np.zeros((mesh.nnode()),dtype='int'),
nodesBackBottomRightCorner = np.zeros((mesh.nnode()),dtype='int'),
nodesBackTopLeftCorner = np.zeros((mesh.nnode()),dtype='int'),
nodesBackTopRightCorner = np.zeros((mesh.nnode()),dtype='int'),
)
# define node-sets
nodesets['nodesFront' ][mesh.nodesFront() ] = 1
nodesets['nodesBack' ][mesh.nodesBack() ] = 1
nodesets['nodesLeft' ][mesh.nodesLeft() ] = 1
nodesets['nodesRight' ][mesh.nodesRight() ] = 1
nodesets['nodesBottom' ][mesh.nodesBottom() ] = 1
nodesets['nodesTop' ][mesh.nodesTop() ] = 1
nodesets['nodesFrontFace' ][mesh.nodesFrontFace() ] = 1
nodesets['nodesBackFace' ][mesh.nodesBackFace() ] = 1
nodesets['nodesLeftFace' ][mesh.nodesLeftFace() ] = 1
nodesets['nodesRightFace' ][mesh.nodesRightFace() ] = 1
nodesets['nodesBottomFace' ][mesh.nodesBottomFace() ] = 1
nodesets['nodesTopFace' ][mesh.nodesTopFace() ] = 1
nodesets['nodesFrontBottomEdge' ][mesh.nodesFrontBottomEdge() ] = 1
nodesets['nodesFrontTopEdge' ][mesh.nodesFrontTopEdge() ] = 1
nodesets['nodesFrontLeftEdge' ][mesh.nodesFrontLeftEdge() ] = 1
nodesets['nodesFrontRightEdge' ][mesh.nodesFrontRightEdge() ] = 1
nodesets['nodesBackBottomEdge' ][mesh.nodesBackBottomEdge() ] = 1
nodesets['nodesBackTopEdge' ][mesh.nodesBackTopEdge() ] = 1
nodesets['nodesBackLeftEdge' ][mesh.nodesBackLeftEdge() ] = 1
nodesets['nodesBackRightEdge' ][mesh.nodesBackRightEdge() ] = 1
nodesets['nodesBottomLeftEdge' ][mesh.nodesBottomLeftEdge() ] = 1
nodesets['nodesBottomRightEdge' ][mesh.nodesBottomRightEdge() ] = 1
nodesets['nodesTopLeftEdge' ][mesh.nodesTopLeftEdge() ] = 1
nodesets['nodesTopRightEdge' ][mesh.nodesTopRightEdge() ] = 1
nodesets['nodesFrontBottomOpenEdge' ][mesh.nodesFrontBottomOpenEdge() ] = 1
nodesets['nodesFrontTopOpenEdge' ][mesh.nodesFrontTopOpenEdge() ] = 1
nodesets['nodesFrontLeftOpenEdge' ][mesh.nodesFrontLeftOpenEdge() ] = 1
nodesets['nodesFrontRightOpenEdge' ][mesh.nodesFrontRightOpenEdge() ] = 1
nodesets['nodesBackBottomOpenEdge' ][mesh.nodesBackBottomOpenEdge() ] = 1
nodesets['nodesBackTopOpenEdge' ][mesh.nodesBackTopOpenEdge() ] = 1
nodesets['nodesBackLeftOpenEdge' ][mesh.nodesBackLeftOpenEdge() ] = 1
nodesets['nodesBackRightOpenEdge' ][mesh.nodesBackRightOpenEdge() ] = 1
nodesets['nodesBottomLeftOpenEdge' ][mesh.nodesBottomLeftOpenEdge() ] = 1
nodesets['nodesBottomRightOpenEdge' ][mesh.nodesBottomRightOpenEdge() ] = 1
nodesets['nodesTopLeftOpenEdge' ][mesh.nodesTopLeftOpenEdge() ] = 1
nodesets['nodesTopRightOpenEdge' ][mesh.nodesTopRightOpenEdge() ] = 1
nodesets['nodesFrontBottomLeftCorner' ][mesh.nodesFrontBottomLeftCorner() ] = 1
nodesets['nodesFrontBottomRightCorner'][mesh.nodesFrontBottomRightCorner()] = 1
nodesets['nodesFrontTopLeftCorner' ][mesh.nodesFrontTopLeftCorner() ] = 1
nodesets['nodesFrontTopRightCorner' ][mesh.nodesFrontTopRightCorner() ] = 1
nodesets['nodesBackBottomLeftCorner' ][mesh.nodesBackBottomLeftCorner() ] = 1
nodesets['nodesBackBottomRightCorner' ][mesh.nodesBackBottomRightCorner() ] = 1
nodesets['nodesBackTopLeftCorner' ][mesh.nodesBackTopLeftCorner() ] = 1
nodesets['nodesBackTopRightCorner' ][mesh.nodesBackTopRightCorner() ] = 1
# add DOF-numbers after eliminating periodicity
nodesets['dofsPeriodic'] = mesh.dofsPeriodic()[:,0]
# open data file
name = 'MeshHex8-FineLayer-nodes'
file = h5py.File(name+'.hdf5','w')
# write nodal positions and a dummy connectivity
file['coor'] = mesh.coor()
file['conn'] = np.arange(mesh.nnode())
# write node-sets
for key,value in nodesets.items():
file[key] = value
# ======================================== write XDMF-file =========================================
# get mesh dimensions
dims = dict(
nnode = mesh.nnode(),
ndim = mesh.ndim(),
)
# initialize file
root = etree.fromstring('<Xdmf Version="2.0"></Xdmf>')
domain = etree.SubElement(root, "Domain")
grid = etree.SubElement(domain, "Grid", Name="Nodes")
# add connectivity
conn = etree.SubElement(grid, "Topology", TopologyType="Polyvertex", NumberOfElements='{nnode:d}'.format(**dims), NodesPerElement="1")
data = etree.SubElement(conn, "DataItem", Dimensions='{nnode:d} 1'.format(**dims), Format="HDF")
data.text = "{0:s}.hdf5:/conn".format(name)
# add coordinates
coor = etree.SubElement(grid, "Geometry", GeometryType="XYZ")
data = etree.SubElement(coor, "DataItem", Dimensions='{nnode:d} {ndim:d}'.format(**dims), Format="HDF")
data.text = "{0:s}.hdf5:/coor".format(name)
# add attributes
for key in nodesets:
attr = etree.SubElement(grid, "Attribute", Name=key, AttributeType="Scalar", Center="Node")
data = etree.SubElement(attr, "DataItem", Dimensions='{nnode:d}'.format(**dims), Format="HDF")
data.text = "{name:s}.hdf5:/{key:s}".format(name=name,key=key)
# write to file
open(name+'.xdmf','wb').write(etree.tostring(root, pretty_print=True))
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