def getNodesBoundInSelectedVols(target_list):
"""
Return nodes bound in mouse selected CUBIT volumes.
Parameters:
* target_list List of indices of target nodes
Return:
List of indices of nodes bound by the volumes
"""
group_id = cubit.create_new_group()
cubit.silent_cmd("group %i add selection" % (group_id))
volume_ids = cubit.get_group_volumes(group_id)
in_list = []
for v in target_list:
cords = cubit.get_nodal_coordinates(v)
for vol_id in volume_ids:
volume = cubit.volume(vol_id)
body = volume.bodies()[0]
status = body.point_containment(cords)
if status == 1 or status == 2:
in_list.append(v)
break
cubit.delete_group(group_id)
return in_list
def getNodesBoundInSelectedVols(mesh, scale=1e-6):
"""
Return nodes bound in selected CUBIT volumes.
Parameters:
* mesh Associated Tetmesh object created in STEPS
* scale LENGTH scale from the CUBIT gemoetry to real geometry.
e.g. a radius of 10 in CUBIT to a radius of 1 micron in STEPS, scale is 1e-7.
By default the scale is 1e-6, i.e. 1 unit in CUBIT equals 1 micron in STEPS.
Return:
list of STEPS indices of vertex nodes
"""
group_id = cubit.create_new_group()
cubit.silent_cmd("group %i add selection" % (group_id))
volume_ids = cubit.get_group_volumes(group_id)
nverts = mesh.nverts
in_list = []
for v in range(nverts):
cords = mesh.getVertex(v)
cords = [x / scale for x in cords]
for vol_id in volume_ids:
volume = cubit.volume(vol_id)
body = volume.bodies()[0]
status = body.point_containment(cords)
if status == 1 or status == 2:
in_list.append(v)
break
cubit.delete_group(group_id)
return in_list
def pick_hex(self, list_hex=None, volume=None):
if self.cubit_skew > 0:
command = "del group skew_top"
cubit.cmd(command)
command = "group 'skew_top' add quality volume all skew low " + str(
self.cubit_skew)
cubit.silent_cmd(command)
group = cubit.get_id_from_name("skew_top")
self.list_hex = cubit.get_group_hexes(group)
elif list_hex is not None:
self.list_hex = list_hex
elif volume is not None:
command = "group 'hextmp' add hex in volume " + str(volume)
cubit.silent_cmd(command)
group = cubit.get_id_from_name("hextmp")
self.list_hex = cubit.get_group_hexes(group)
command = "del group hextmp"
cubit.silent_cmd(command)
elif self.volume is not None:
command = "group 'hextmp' add hex in volume " + str(self.volume)
cubit.silent_cmd(command)
group = cubit.get_id_from_name("hextmp")
self.list_hex = cubit.get_group_hexes(group)
command = "del group hextmp"
cubit.silent_cmd(command)
elif list_hex is None and self.list_hex is None:
self.list_hex = cubit.parse_cubit_list('hex', 'all')
print 'list_hex: ', len(self.list_hex), ' hexes'
def getNodesBoundInSelectedVols(target_list):
"""
Return nodes bound in selected CUBIT volumes.
Parameters:
* target_list List of indices of target nodes
Return:
List of indices of nodes bound by the volumes
"""
group_id = cubit.create_new_group()
cubit.silent_cmd("group %i add selection" % (group_id))
volume_ids = cubit.get_group_volumes(group_id)
in_list = []
for v in target_list:
cords = cubit.get_nodal_coordinates(v)
for vol_id in volume_ids:
volume = cubit.volume(vol_id)
body = volume.bodies()[0]
status = body.point_containment(cords)
if status == 1 or status == 2:
in_list.append(v)
break
cubit.delete_group(group_id)
return in_list
def pick_hex(self, list_hex=None, volume=None):
if self.cubit_skew > 0:
command = "del group skew_top"
cubit.cmd(command)
command = "group 'skew_top' add quality volume all skew low " + str(self.cubit_skew)
cubit.silent_cmd(command)
group = cubit.get_id_from_name("skew_top")
self.list_hex = cubit.get_group_hexes(group)
elif list_hex is not None:
self.list_hex = list_hex
elif volume is not None:
command = "group 'hextmp' add hex in volume " + str(volume)
cubit.silent_cmd(command)
group = cubit.get_id_from_name("hextmp")
self.list_hex = cubit.get_group_hexes(group)
command = "del group hextmp"
cubit.silent_cmd(command)
elif self.volume is not None:
command = "group 'hextmp' add hex in volume " + str(self.volume)
cubit.silent_cmd(command)
group = cubit.get_id_from_name("hextmp")
self.list_hex = cubit.get_group_hexes(group)
command = "del group hextmp"
cubit.silent_cmd(command)
elif list_hex is None and self.list_hex is None:
self.list_hex = cubit.parse_cubit_list("hex", "all")
print "list_hex: ", len(self.list_hex), " hexes"
def list_2_curve(X,Y,name='',unit='*km'):
Vlist = list_2_listofvertices(X,Y,unit)
finalcmd = "create curve spline from vertex " + str(Vlist[0].id()) + " to " + str(Vlist[-1].id())
cubit.silent_cmd(finalcmd)
C = cubit.curve(cubit.get_last_id('curve'))
if name != '':
C.entity_name(name)
return C
def list_2_listofvertices(X,Y,unit='*km'):
Vlis_out = []
for x,y in zip(X,Y):
komand = "create vertex x { "+str(x)+ unit + "} y { "+str(y) + unit + "}"
cubit.silent_cmd(komand)
v = cubit.vertex(cubit.get_last_id('vertex'))
Vlis_out.append(v)
return Vlis_out
def curver_desc(Cdesc,dx,unit='*km'):
if type(Cdesc) is int:
komand = "curve " + str(Cdesc) + " size {" + str(dx) + unit + "}"
elif type(Cdesc) is str:
komand = "curve " + str(cubit.get_id_from_name(Cdesc)) + " size {" + str(dx) + unit +"}"
print komand
cubit.silent_cmd(komand)
return None
def curver_desc(Cdesc, dx, unit='*km'):
if type(Cdesc) is int:
komand = "curve " + str(Cdesc) + " size {" + str(dx) + unit + "}"
elif type(Cdesc) is str:
komand = "curve " + str(
cubit.get_id_from_name(Cdesc)) + " size {" + str(dx) + unit + "}"
print komand
cubit.silent_cmd(komand)
return None
def dico_2_listofvertices(dico,unit='*km'):
Vlis_out = []
for name , xy in dico.iteritems():
komand = "create vertex x { "+str(xy[0])+ unit + "} y { "+str(xy[1]) + unit + "}"
cubit.silent_cmd(komand)
v = cubit.vertex(cubit.get_last_id('vertex'))
v.entity_name(name)
Vlis_out.append(v)
return Vlis_out
def get_face_connectivity(self,ind):
if self.hex27:
cubit.silent_cmd('group "nf" add Node in face '+str(ind))
group1 = cubit.get_id_from_name("nf")
result=cubit.get_group_nodes(group1)
cubit.cmd('del group '+str(group1))
else:
result=cubit.get_connectivity('face',ind)
return result
def list_2_curve(X, Y, name='', unit='*km'):
Vlist = list_2_listofvertices(X, Y, unit)
finalcmd = "create curve spline from vertex " + str(
Vlist[0].id()) + " to " + str(Vlist[-1].id())
cubit.silent_cmd(finalcmd)
C = cubit.curve(cubit.get_last_id('curve'))
if name != '':
C.entity_name(name)
return C
def get_face_connectivity(self,ind):
if self.hex27:
cubit.silent_cmd('group "nf" add Node in face '+str(ind))
group1 = cubit.get_id_from_name("nf")
result=cubit.get_group_nodes(group1)
cubit.cmd('del group '+str(group1))
else:
result=cubit.get_connectivity('face',ind)
return result
def list_2_listofvertices(X, Y, unit='*km'):
Vlis_out = []
for x, y in zip(X, Y):
komand = "create vertex x { " + str(x) + unit + "} y { " + str(
y) + unit + "}"
cubit.silent_cmd(komand)
v = cubit.vertex(cubit.get_last_id('vertex'))
Vlis_out.append(v)
return Vlis_out
def dico_2_listofvertices(dico, unit='*km'):
Vlis_out = []
for name, xy in dico.iteritems():
komand = "create vertex x { " + str(xy[0]) + unit + "} y { " + str(
xy[1]) + unit + "}"
cubit.silent_cmd(komand)
v = cubit.vertex(cubit.get_last_id('vertex'))
v.entity_name(name)
Vlis_out.append(v)
return Vlis_out
def read_file_2_curve(path,name=''):
Vlist = read_file_2_listofvertices(path)
finalcmd = "create curve spline from vertex " + str(Vlist[0].id()) + " to " + str(Vlist[-1].id())
cubit.silent_cmd(finalcmd)
C = cubit.curve(cubit.get_last_id('curve'))
if name == '':
C.entity_name(os.path.basename(path))
else:
C.entity_name(name)
return C
def get_hex_connectivity(self,ind):
if self.hex27:
cubit.silent_cmd('group "nh" add Node in hex '+str(ind))
group1 = cubit.get_id_from_name("nh")
result=cubit.get_group_nodes(group1)
if len(result) != 27: print 'error hex27'
cubit.cmd('del group '+str(group1))
else:
result=cubit.get_connectivity('hex',ind)
return result
def get_hex_connectivity(self,ind):
if self.hex27:
cubit.silent_cmd('group "nh" add Node in hex '+str(ind))
group1 = cubit.get_id_from_name("nh")
result=cubit.get_group_nodes(group1)
if len(result) != 27: print 'error hex27'
cubit.cmd('del group '+str(group1))
else:
result=cubit.get_connectivity('hex',ind)
return result
def read_file_2_listofvertices(path,unit='*km'):
filein = open(path)
Vlis_out = []
for line in filein:
fields = line.split()
# v = cubit.create_vertex(float(fields[0]),float(fields[1]),0)
komand = "create vertex x { "+str(float(fields[0]))+ unit + "} y { "+str(float(fields[1])) + unit + "}"
cubit.silent_cmd(komand)
v = cubit.vertex(cubit.get_last_id('vertex'))
Vlis_out.append(v)
return Vlis_out
def read_file_2_curve(path, name=''):
Vlist = read_file_2_listofvertices(path)
finalcmd = "create curve spline from vertex " + str(
Vlist[0].id()) + " to " + str(Vlist[-1].id())
cubit.silent_cmd(finalcmd)
C = cubit.curve(cubit.get_last_id('curve'))
if name == '':
C.entity_name(os.path.basename(path))
else:
C.entity_name(name)
return C
def highlightPatch(patch):
"""
Highlight the patch.
Parameters:
* patch ShadowPatch object
Return:
None
"""
cubit.silent_cmd("highlight tri " + toStr(patch.indices))
def highlightComp(comp):
"""
Highlight the compartment.
Parameters:
* comp ShadowComp object
Return:
None
"""
cubit.silent_cmd("highlight tet " + toStr(comp.indices))
def drawPatch(patch):
"""
Draw the patch.
Parameters:
* patch ShadowPatch object
Return:
None
"""
cubit.silent_cmd("draw tri " + toStr(patch.indices))
def drawComp(comp):
"""
Draw the compartment.
Parameters:
* comp ShadowComp object
Return:
None
"""
cubit.silent_cmd("draw tet " + toStr(comp.indices))
def highlightComp(mesh, comp_id):
"""
Highlight the compartment.
Parameters:
* mesh ShadowMesh object
* comp_id ID of the ShadowComp object
Return:
None
"""
cubit.silent_cmd("highlight tet " + toStr(mesh.comps[comp_id].indices))
def highlight_skew(self, low=None, high=None):
if low is None and high is not None:
hexlist = self.show(low, self.max_skewness, self.skew_hyst)
elif low is not None and high is None:
hexlist = self.show(0, high, self.skew_hyst)
if low is not None and high is not None:
hexlist = self.show(low, high, self.skew_hyst)
else:
hexlist = self.hex_min_edge_length
command = "highlight hex " + str(hexlist)
command = command.replace("[", " ").replace("]", " ").replace("(", " ").replace(")", " ")
cubit.silent_cmd(command)
def read_file_2_listofvertices(path, unit='*km'):
filein = open(path)
Vlis_out = []
for line in filein:
fields = line.split()
# v = cubit.create_vertex(float(fields[0]),float(fields[1]),0)
komand = "create vertex x { " + str(float(
fields[0])) + unit + "} y { " + str(float(fields[1])) + unit + "}"
cubit.silent_cmd(komand)
v = cubit.vertex(cubit.get_last_id('vertex'))
Vlis_out.append(v)
return Vlis_out
def highlightPatch(mesh, patch_id):
"""
Highlight the patch.
Parameters:
* mesh ShadowMesh object
* patch_id ID of the ShadowPatch object
Return:
None
"""
cubit.silent_cmd("highlight tri " + toStr(mesh.patches[patch_id].indices))
def create_line(position):
if position:
last_curve_store=cubit.get_last_id("curve")
command='create curve spline '+position
cubit.silent_cmd(command)
last_curve=cubit.get_last_id("curve")
if last_curve != last_curve_store:
return last_curve
else:
return False
else:
return False
def highlight_skew(self, low=None, high=None):
if low is None and high is not None:
hexlist = self.show(low, self.max_skewness, self.skew_hyst)
elif low is not None and high is None:
hexlist = self.show(0, high, self.skew_hyst)
if low is not None and high is not None:
hexlist = self.show(low, high, self.skew_hyst)
else:
hexlist = self.hex_min_edge_length
command = "highlight hex " + str(hexlist)
command = command.replace("[", " ").replace("]", " ").replace(
"(", " ").replace(")", " ")
cubit.silent_cmd(command)
def getSelectedTets():
"""
Return the CUBIT indices of mouse selected tetrahedrons.
Parameters:
None
Return:
cubit_ids
"""
group_id = cubit.create_new_group()
cubit.silent_cmd("group %i add selection" % (group_id))
idxs = cubit.get_group_tets(group_id)
cubit.delete_group(group_id)
return idxs
def getSelectedNodes():
"""
Return the CUBIT indices of the selected vertex nodes.
Parameters:
None
Return:
cubit_ids
"""
group_id = cubit.create_new_group()
cubit.silent_cmd("group %i add selection" % (group_id))
idxs = cubit.get_group_nodes(group_id)
cubit.delete_group(group_id)
return idxs
def getSelectedTris(tri_proxy):
"""
Return the STEPS indices and CUBIT indices of the selected triangles.
Parameters:
* tri_proxy Triangle element proxy generated by STEPS mesh importing function
Return:
(steps_ids, cubit_ids)
"""
group_id = cubit.create_new_group()
cubit.silent_cmd("group %i add selection" % (group_id))
cubit_ids = cubit.get_group_tris(group_id)
steps_ids = [tri_proxy.getSTEPSID(id) for id in cubit_ids]
cubit.delete_group(group_id)
return (steps_ids, cubit_ids)
def curver_start_end(C,dxstrt,dxend,direct='l',unit='*km'):
Vtup = cubit.get_relatives("curve", C.id(), "vertex")
if cubit.vertex(Vtup[1]).coordinates()[0] > cubit.vertex(Vtup[0]).coordinates()[0]:
vr = cubit.vertex(Vtup[1])
vl = cubit.vertex(Vtup[0])
else:
vr = cubit.vertex(Vtup[0])
vl = cubit.vertex(Vtup[1])
if direct == 'l':
vstart = vr
elif direct == 'r':
vstart = vl
komand = "curve " + str(C.id()) + " scheme bias fine size {" + str(dxstrt) + unit + "} coarse size {" + str(dxend) + unit + "} start vertex " + str(vstart.id())
print komand
cubit.silent_cmd(komand)
return None
def create_line_v(ind,n,n2,step,data,unit):
last_curve_store=cubit.get_last_id("curve")
command='create curve spline '
for i in range(0,n):
if i%step == 0:
lon,lat,z=data[n2*i+ind][0],data[n2*i+ind][1],data[n2*i+ind][2]
x,y=geo2utm(lon,lat,unit)
txt=' Position ' + str(x) +' '+ str(y) +' '+ str(z)
command=command+txt
#print command
cubit.silent_cmd(command)
last_curve=cubit.get_last_id("curve")
if last_curve != last_curve_store:
return last_curve
else:
return 0
def getTrisBoundInSelectedVols(mesh, scale=1e-6):
"""
Return triangles bound in selected CUBIT volumes.
Parameters:
* mesh Associated Tetmesh object created in STEPS
* scale LENGTH scale from the CUBIT gemoetry to real geometry.
e.g. a radius of 10 in CUBIT to a radius of 1 micron in STEPS, scale is 1e-7.
By default the scale is 1e-6, i.e. 1 unit in CUBIT equals 1 micron in STEPS.
Return:
list of STEPS indices of triangles
"""
group_id = cubit.create_new_group()
cubit.silent_cmd("group %i add selection" % (group_id))
volume_ids = cubit.get_group_volumes(group_id)
ntris = mesh.ntris
in_list = []
for t in range(ntris):
verts = mesh.getTri(t)
with_in = True
cords = []
for v in verts:
c = mesh.getVertex(v)
c = [x / scale for x in c]
cords.append(c)
for vol_id in volume_ids:
volume = cubit.volume(vol_id)
body = volume.bodies()[0]
within = True
for cord in cords:
status = body.point_containment(cord)
if status == 0:
within = False
break
if within:
in_list.append(t)
break
cubit.delete_group(group_id)
return in_list
def curver_start_end(C, dxstrt, dxend, direct='l', unit='*km'):
Vtup = cubit.get_relatives("curve", C.id(), "vertex")
if cubit.vertex(Vtup[1]).coordinates()[0] > cubit.vertex(
Vtup[0]).coordinates()[0]:
vr = cubit.vertex(Vtup[1])
vl = cubit.vertex(Vtup[0])
else:
vr = cubit.vertex(Vtup[0])
vl = cubit.vertex(Vtup[1])
if direct == 'l':
vstart = vr
elif direct == 'r':
vstart = vl
komand = "curve " + str(C.id()) + " scheme bias fine size {" + str(
dxstrt) + unit + "} coarse size {" + str(
dxend) + unit + "} start vertex " + str(vstart.id())
print komand
cubit.silent_cmd(komand)
return None
def highlightROI(mesh, roi_name):
"""
Highlight elements stored in ROI database with id roi_name.
Parameters:
* mesh ShadowMesh object
* roi_name Name of the ROI
Return:
None
"""
if roi_name not in mesh.rois:
raise Exception(roi_name + " is not in ROI database.")
roi = mesh.rois[roi_name]
idx_str = toStr(roi["Indices"])
if roi["Type"] == ELEM_VERTEX:
cubit.silent_cmd("highlight node " + idx_str)
elif roi["Type"] == ELEM_TET:
cubit.silent_cmd("highlight tet " + idx_str)
elif roi["Type"] == ELEM_TRI:
cubit.silent_cmd("highlight tri " + idx_str)
else:
raise Exception(roi_name + " is undefined element type.")
def getTrisBoundInSelectedVols(target_list):
"""
Return triangles bound in selected CUBIT volumes.
Parameters:
* target_list List of indices of target triangles
Return:
List of indices of triangles bound by the volumes
"""
group_id = cubit.create_new_group()
cubit.silent_cmd("group %i add selection" % (group_id))
volume_ids = cubit.get_group_volumes(group_id)
in_list = []
for t in target_list:
verts = cubit.get_connectivity("tri", t)
with_in = True
cords = []
for v in verts:
c = cubit.get_nodal_coordinates(v)
cords.append(c)
for vol_id in volume_ids:
volume = cubit.volume(vol_id)
body = volume.bodies()[0]
within = True
for cord in cords:
status = body.point_containment(cord)
if status == 0:
within = False
break
if within:
in_list.append(t)
break
cubit.delete_group(group_id)
return in_list
def create_group_nodeset_desc(Clist,grpname,nodesetID=0,grpname_remove=[]):
while nodesetID == 0 or (nodesetID in cubit.get_nodeset_id_list()):
nodesetID = nodesetID +1
for c in Clist:
cubit.silent_cmd('group "' + grpname + '" add node in ' + c)
#Remove some vertice in nodes if specified
print grpname_remove
if len(grpname_remove)!=0:
# Check if group already specified
for grp in grpname_remove:
id_grp=cubit.get_id_from_name(grp)
if id_grp!=0:
cubit.silent_cmd('group "' + grpname + '" remove node in group ' + grp)
# Name the nodesets
cubit.silent_cmd('nodeset ' + str(nodesetID) + ' group ' + grpname)
cubit.silent_cmd('nodeset ' + str(nodesetID) + ' name "' + grpname + '"' )
def getTrisOverlapSelectedVols(target_list):
"""
Return triangles overlap with mouse selected CUBIT volumes.
Parameters:
* target_list List of indices of target triangles
Return:
List of indices of triangles overlap with the volumes
"""
group_id = cubit.create_new_group()
cubit.silent_cmd("group %i add selection" % (group_id))
volume_ids = cubit.get_group_volumes(group_id)
in_list = []
for t in target_list:
verts = cubit.get_connectivity("tri", t)
cords = []
for v in verts:
c = cubit.get_nodal_coordinates(v)
cords.append(c)
for vol_id in volume_ids:
volume = cubit.volume(vol_id)
body = volume.bodies()[0]
within = False
for cord in cords:
status = body.point_containment(cord)
if status == 1:
within = True
break
if within:
in_list.append(t)
break
cubit.delete_group(group_id)
return in_list
def create_group_nodeset_desc(Clist, grpname, nodesetID=0, grpname_remove=[]):
while nodesetID == 0 or (nodesetID in cubit.get_nodeset_id_list()):
nodesetID = nodesetID + 1
for c in Clist:
cubit.silent_cmd('group "' + grpname + '" add node in ' + c)
#Remove some vertice in nodes if specified
print grpname_remove
if len(grpname_remove) != 0:
# Check if group already specified
for grp in grpname_remove:
id_grp = cubit.get_id_from_name(grp)
if id_grp != 0:
cubit.silent_cmd('group "' + grpname +
'" remove node in group ' + grp)
# Name the nodesets
cubit.silent_cmd('nodeset ' + str(nodesetID) + ' group ' + grpname)
cubit.silent_cmd('nodeset ' + str(nodesetID) + ' name "' + grpname + '"')
def collecting_merging(cpuxmin=0,cpuxmax=1,cpuymin=0,cpuymax=1,cpux=1,cpuy=1,cubfiles=False,ckbound_method1=False,ckbound_method2=False,merge_tolerance=None,decimate=False):
import glob
import re
#
rule_st=re.compile("(.+)_[0-9]+\.")
rule_ex=re.compile(".+_[0-9]+\.(.+)")
rule_int=re.compile(".+_([0-9]+)\.")
boundary_dict={}
##
try:
from boundary_definition import check_bc, map_boundary
except:
pass
#
xmin,xmax,ymin,ymax,listfull=map_boundary(cpuxmin,cpuxmax,cpuymin,cpuymax,cpux,cpuy)
#
if cubfiles:
nf,listip,filenames,cubflag=importing_cubfiles(cubfiles)
else:
nf=0
filenames=[]
ip=0
#
if nf > 0:
for ip,filename in zip(listip,filenames):
try:
if ip in listfull:
if cubflag:
cubit.cmd('import cubit "'+filename+'"')
else:
cubit.cmd('import mesh geometry "'+filename+'" block all use nodeset sideset feature_angle 135.00 linear merge')
if decimate: cubit.cmd('refine volume all numsplit 1 bias 1.0 depth 1 ')
boundary=check_bc(ip,xmin,xmax,ymin,ymax,cpux,cpuy,cpuxmin,cpuxmax,cpuymin,cpuymax)
boundary_dict[ip]=boundary
list_vol=list(cubit.parse_cubit_list('volume','all'))
for v in list_vol:
cubit.cmd("disassociate mesh from volume "+str(v))
command = "del vol "+str(v)
cubit.cmd(command)
except:
cubit.cmd('import mesh geometry "'+filename+'" block all use nodeset sideset feature_angle 135.00 linear merge')
if decimate: cubit.cmd('refine volume all numsplit 1 bias 1.0 depth 1 ')
ip=0
boundary=check_bc(ip,xmin,xmax,ymin,ymax,cpux,cpuy,cpuxmin,cpuxmax,cpuymin,cpuymax)
boundary_dict[ip]=boundary
list_vol=list(cubit.parse_cubit_list('volume','all'))
for v in list_vol:
cubit.cmd("disassociate mesh from volume "+str(v))
command = "del vol "+str(v)
cubit.cmd(command)
cubit.cmd('export mesh "tmp_collect_NOmerging.e" dimension 3 block all overwrite')
else:
if decimate: cubit.cmd('refine volume all numsplit 1 bias 1.0 depth 1 ')
boundary=check_bc(ip,xmin,xmax,ymin,ymax,cpux,cpuy,cpuxmin,cpuxmax,cpuymin,cpuymax)
#
#
#print boundary_dict
block_list=cubit.get_block_id_list()
for block in block_list:
ty=cubit.get_block_element_type(block)
if ty == 'HEX8':
cubit.cmd('block '+str(block)+' name "vol'+str(block)+'"')
#
#
print 'chbound',ckbound_method1,ckbound_method2
if ckbound_method1 and not ckbound_method2 and len(filenames) != 1:
#use the equivalence method for groups
if isinstance(merge_tolerance,list):
tol=merge_tolerance[0]
elif merge_tolerance:
tol=merge_tolerance
else:
tol=100000
#
idiag=None
#cubit.cmd('set info off')
#cubit.cmd('set journal off')
#cubit.cmd('set echo off')
ind=0
for ix in range(cpuxmin,cpuxmax):
for iy in range(cpuymin,cpuymax):
ind=ind+1
ip=iy*cpux+ix
print '******************* ',ip, ind,'/',len(listfull)
#
# ileft | ip
# --------------------
# idiag | idown
#
#
if ip not in xmin and ip not in ymin:
ileft=iy*cpux+ix-1
idown=(iy-1)*cpux+ix
idiag=idown-1
elif ip in xmin and ip in ymin:
ileft=ip
idown=ip
idiag=None
elif ip in xmin:
ileft=ip
idown=(iy-1)*cpux+ix
idiag=idown
elif ip in ymin:
ileft=iy*cpux+ix-1
idown=ip
idiag=ileft
#
print ip,ileft,idiag,idown
if ip != idown:
nup=boundary_dict[ip]['nodes_surf_ymin']
ndow=boundary_dict[idown]['nodes_surf_ymax']
merge_node_ck(nup,ndow)
if idiag != idown:
if ip in ymax and ip not in xmin:
nlu=boundary_dict[ip]['node_curve_xminymax'] #node in curve chunck left up... r u
nru=boundary_dict[ileft]['node_curve_xmaxymax']
merge_node(nlu,nru)
if ip in xmax:
nrd=boundary_dict[ip]['node_curve_xmaxymin'] #node in curve chunck left up... r u
nru=boundary_dict[idown]['node_curve_xmaxymax']
merge_node(nrd,nru)
nru=boundary_dict[ip]['node_curve_xminymin'] #node in curve chunck right up... r u
nrd=boundary_dict[idown]['node_curve_xminymax']
nld=boundary_dict[idiag]['node_curve_xmaxymax']
nlu=boundary_dict[ileft]['node_curve_xmaxymin']
merge_node_4(nru,nrd,nld,nlu)
elif ip in xmin:
nlu=boundary_dict[ip]['node_curve_xminymin'] #node in curve chunck right up... r u
nld=boundary_dict[idown]['node_curve_xminymax']
merge_node(nld,nlu)
nru=boundary_dict[ip]['node_curve_xmaxymin'] #node in curve chunck right up... r u
nrd=boundary_dict[idown]['node_curve_xmaxymax']
merge_node(nrd,nru)
#
if ip != ileft:
nright=boundary_dict[ip]['nodes_surf_xmin']
nleft=boundary_dict[ileft]['nodes_surf_xmax']
merge_node_ck(nright,nleft)
#
#
if ip in ymin:
nrd=boundary_dict[ip]['node_curve_xminymin'] #node in curve chunck right down... r u
nld=boundary_dict[ileft]['node_curve_xmaxymin']
merge_node(nrd,nld)
if ip in ymax:
nru=boundary_dict[ip]['node_curve_xminymax'] #node in curve chunck right up... r u
nlu=boundary_dict[ileft]['node_curve_xmaxymax']
merge_node(nlu,nru)
cubit.cmd('set info on')
cubit.cmd('set echo on')
cubit.cmd('set journal on')
#
#
cmd='group "negativejac" add quality hex all Jacobian high'
cubit.cmd(cmd)
group_id_1=cubit.get_id_from_name("negativejac")
n1=cubit.get_group_nodes(group_id_1)
if len(n1) != 0:
print 'error, negative jacobian after the equivalence node command, use --merge2 instead of --equivalence/--merge/--merge1'
elif ckbound_method2 and not ckbound_method1 and len(filenames) != 1:
if isinstance(merge_tolerance,list):
tol=merge_tolerance[0]
elif merge_tolerance:
tol=merge_tolerance
else:
tol=100000
#
idiag=None
for ix in range(cpuxmin,cpuxmax):
for iy in range(cpuymin,cpuymax):
ip=iy*cpux+ix
print '******************* ',ip
#
# ileft | ip
# --------------------
# idiag | idown
#
#
if ip not in xmin and ip not in ymin:
ileft=iy*cpux+ix-1
idown=(iy-1)*cpux+ix
idiag=idown-1
elif ip in xmin and ip in ymin:
ileft=ip
idown=ip
elif ip in xmin:
ileft=ip
idown=(iy-1)*cpux+ix
idiag=idown
elif ip in ymin:
ileft=iy*cpux+ix-1
idown=ip
idiag=ileft
#
#
if ip != idown:
nup=boundary_dict[ip]['nodes_surf_ymin']
ndow=boundary_dict[idown]['nodes_surf_ymax']
for n1,n2 in zip(nup,ndow):
cubit.cmd('equivalence node '+str(n1)+' '+str(n2)+' tolerance '+str(tol))
if idiag != idown:
if ip in ymax and ip not in xmin:
nlu=boundary_dict[ip]['node_curve_xminymax'] #node in curve chunck left up... r u
nru=boundary_dict[ileft]['node_curve_xmaxymax']
for n in zip(nlu,nru):
cubit.cmd('equivalence node '+' '.join(str(x) for x in n)+' tolerance '+str(tol))
nru=boundary_dict[ip]['node_curve_xminymin'] #node in curve chunck right up... r u
nrd=boundary_dict[idown]['node_curve_xminymax']
nld=boundary_dict[idiag]['node_curve_xmaxymax']
nlu=boundary_dict[ileft]['node_curve_xmaxymin']
for n in zip(nru,nrd,nlu,nld):
cubit.cmd('equivalence node '+' '.join(str(x) for x in n)+' tolerance '+str(tol))
elif ip in xmin:
nru=boundary_dict[ip]['node_curve_xminymin'] #node in curve chunck right up... r u
nrd=boundary_dict[idown]['node_curve_xminymax']
for n in zip(nru,nrd):
cubit.cmd('equivalence node '+' '.join(str(x) for x in n)+' tolerance '+str(tol))
#
#
if ip != ileft:
nright=boundary_dict[ip]['nodes_surf_xmin']
nleft=boundary_dict[ileft]['nodes_surf_xmax']
for n1,n2 in zip(nleft,nright):
cubit.cmd('equivalence node '+str(n1)+' '+str(n2)+' tolerance '+str(tol))
#
#
if ip in ymin:
nrd=boundary_dict[ip]['node_curve_xminymin'] #node in curve chunck right down... r u
nld=boundary_dict[ileft]['node_curve_xmaxymin']
for n in zip(nrd,nld):
cubit.cmd('equivalence node '+' '.join(str(x) for x in n)+' tolerance '+str(tol))
if ip in ymax:
nru=boundary_dict[ip]['node_curve_xminymax'] #node in curve chunck right up... r u
nlu=boundary_dict[ileft]['node_curve_xmaxymax']
for n in zip(nru,nlu):
cubit.cmd('equivalence node '+' '.join(str(x) for x in n)+' tolerance '+str(tol))
#
#
cmd='topology check coincident node face all tolerance '+str(tol*2)+' nodraw brief result group "checkcoinc"'
cubit.silent_cmd(cmd)
group_id_1=cubit.get_id_from_name("checkcoinc")
if group_id_1 != 0:
n1=cubit.get_group_nodes(group_id_1)
if len(n1) != 0:
print 'error, coincident nodes after the equivalence node command, check the tolerance'
import sys
sys.exit()
cmd='group "negativejac" add quality hex all Jacobian high'
cubit.cmd(cmd)
group_id_1=cubit.get_id_from_name("negativejac")
n1=cubit.get_group_nodes(group_id_1)
if len(n1) != 0:
print 'error, negative jacobian after the equivalence node command, check the mesh'
elif ckbound_method1 and ckbound_method2 and len(filenames) != 1:
block_list=cubit.get_block_id_list()
i=-1
for block in block_list:
ty=cubit.get_block_element_type(block)
if ty == 'HEX8':
i=i+1
if isinstance(merge_tolerance,list):
try:
tol=merge_tolerance[i]
except:
tol=merge_tolerance[-1]
elif merge_tolerance:
tol=merge_tolerance
else:
tol=1
cmd='topology check coincident node face in hex in block '+str(block)+' tolerance '+str(tol)+' nodraw brief result group "b'+str(block)+'"'
cubit.cmd(cmd)
print cmd
cmd='equivalence node in group b'+str(block)+' tolerance '+str(tol)
cubit.cmd(cmd)
print cmd
if isinstance(merge_tolerance,list):
tol=max(merge_tolerance)
elif merge_tolerance:
tol=merge_tolerance
else:
tol=1
#
#
cmd='topology check coincident node face all tolerance '+str(tol)+' nodraw brief result group "checkcoinc"'
cubit.silent_cmd(cmd)
group_id_1=cubit.get_id_from_name("checkcoinc")
if group_id_1 != 0:
n1=cubit.get_group_nodes(group_id_1)
if len(n1) != 0:
print 'error, coincident nodes after the equivalence node command, check the tolerance'
import sys
sys.exit()
cmd='group "negativejac" add quality hex all Jacobian high'
cubit.silent_cmd(cmd)
group_id_1=cubit.get_id_from_name("negativejac")
n1=cubit.get_group_nodes(group_id_1)
if len(n1) != 0:
print 'error, negative jacobian after the equivalence node command, use --merge instead of --equivalence'
def collect(cpuxmin=0,
cpuxmax=1,
cpuymin=0,
cpuymax=1,
cpux=1,
cpuy=1,
cubfiles=False,
ckbound_method1=False,
ckbound_method2=False,
merge_tolerance=None,
curverefining=False,
outfilename='totalmesh_merged',
qlog=False,
export2SPECFEM3D=False,
listblock=None,
listflag=None,
outdir='.',
add_sea=False,
decimate=False,
cpml=False,
cpml_size=False,
top_absorbing=False,
hex27=False):
#
cubit.cmd('set journal error off')
cubit.cmd('set verbose error off')
collecting_merging(cpuxmin,
cpuxmax,
cpuymin,
cpuymax,
cpux,
cpuy,
cubfiles=cubfiles,
ckbound_method1=ckbound_method1,
ckbound_method2=ckbound_method2,
merge_tolerance=merge_tolerance,
decimate=decimate)
cubit.cmd('set journal error on')
cubit.cmd('set verbose error on')
#
if curverefining:
block = 1001 #topography
refine_closecurve(block, curverefining, acis=True)
#
#
if add_sea:
block = 1001
add_sea_layer(block=block)
outdir2 = '/'.join(x for x in outfilename.split('/')[:-1])
if outdir2 == '':
outdir2 = outdir + '/'
else:
outdir2 = outdir + '/' + outdir2 + '/'
import os
try:
os.makedirs(outdir2)
except OSError:
pass
cubit.cmd('compress all')
command = "export mesh '" + outdir2 + outfilename + ".e' block all overwrite xml '" + outdir2 + outfilename + ".xml'"
cubit.cmd(command)
f = open(outdir2 + 'blocks.dat', 'w')
blocks = cubit.get_block_id_list()
#
for block in blocks:
name = cubit.get_exodus_entity_name('block', block)
element_count = cubit.get_exodus_element_count(block, "block")
nattrib = cubit.get_block_attribute_count(block)
attr = [
cubit.get_block_attribute_value(block, x)
for x in range(0, nattrib)
]
ty = cubit.get_block_element_type(block)
f.write(
str(block) + ' ; ' + name + ' ; nattr ' + str(nattrib) + ' ; ' +
' '.join(str(x) for x in attr) + ' ; ' + ty + ' ' +
str(element_count) + '\n')
f.close()
#
#
cubit.cmd('set info echo journ off')
cmd = 'del group all'
cubit.silent_cmd(cmd)
cubit.cmd('set info echo journ on')
#
command = "save as '" + outdir2 + outfilename + ".cub' overwrite"
cubit.cmd(command)
#
print 'end meshing'
#
#
if qlog:
print '\n\nQUALITY CHECK.... ***************\n\n'
import quality_log
tq = open(outdir2 + outfilename + '.quality', 'w')
max_skewness, min_length = quality_log.quality_log(tq)
#
#
#
if export2SPECFEM3D:
e2SEM(files=False,
listblock=listblock,
listflag=listflag,
outdir=outdir,
cpml=cpml,
cpml_size=cpml_size,
top_absorbing=top_absorbing,
hex27=hex27)
for id in volumeIds:
overLapping = cubit.get_overlapping_volumes ([id, volIdCutter])
for vol in overLapping:
if vol != volIdCutter:
searchVolumes.append (vol)
# Report
print "Found " + str (len (searchVolumes)) + " intersecting volumes."
# Find overlapping ids.
overlap_tets = []
# Save to temp file.
saveTmpFile ()
for id in searchVolumes:
openTmpFile ()
print "Finding tets in volume: " + str (id),
tet_list = cubit.get_volume_tets (id)
temp = es.getTetsOverlapPassedVols (tet_list, [volIdCutter])
overlap_tets.extend (temp)
removeTmpFile ()
cubit.silent_cmd ('set duplicate block elements on')
cubit.silent_cmd ('block 100 tet ' + es.toStr (overlap_tets))
cubit.silent_cmd ('block 100 name "kernel"')
cubit.silent_cmd ('set large exodus file on')
cubit.silent_cmd ('export mesh "' + kernelWritePath + '/kernelMesh.ex2" block 100 overwrite')
def rename_curve(C, newname):
# C is a object
command = 'curve ' + str(C.id()) + ' rename "' + newname + '"'
cubit.silent_cmd(command)
return None
def destroy_curve(Cin):
# C is a object
command = 'delete curve ' + str(Cin.id())
cubit.silent_cmd(command)
return None
def rename_curve(C,newname):
# C is a object
command = 'curve ' + str(C.id()) + ' rename "' + newname + '"'
cubit.silent_cmd(command)
return None
def collect_new(cpuxmin=0,cpuxmax=1,cpuymin=0,cpuymax=1,cpux=1,cpuy=1,cubfiles=False,ckbound_method1=False,ckbound_method2=False,merge_tolerance=None,curverefining=False,outfilename='totalmesh_merged',qlog=False,export2SPECFEM3D=False,listblock=None,listflag=None,outdir='.',add_sea=False,decimate=False,cpml=False,cpml_size=False,top_absorbing=False,hex27=False,save_cubfile=True,check_merging=False):
#
cubit.cmd('set info off')
cubit.cmd('set echo off')
cubit.cmd('set journal off')
#cubit.cmd('set error off')
version_cubit=get_cubit_version()
if decimate:
if version_cubit >= 14.0:
raise VersionException('check cubit version, decimate capability has been tested only with cubit <= 12.2')
if version_cubit <= 12.2:
collecting_merging(cpuxmin,cpuxmax,cpuymin,cpuymax,cpux,cpuy,cubfiles=cubfiles,ckbound_method1=ckbound_method1,ckbound_method2=ckbound_method2,merge_tolerance=merge_tolerance,decimate=decimate)
elif version_cubit >= 14:
collecting_merging_new(cpuxmin,cpuxmax+1,cpuymin,cpuymax+1,cpux,cpuy,cubfiles=cubfiles,check_merging=check_merging)
else:
raise VersionException('check cubit version, parallel capability of geocubit is working with cubit/trelis 14+ (or cubit 12.2)')
cubit.cmd('set info on')
cubit.cmd('set echo on')
cubit.cmd('set journal on')
#cubit.cmd('set error on')
#
if curverefining:
if version_cubit <= 12.2:
block=1001 #topography
refine_closecurve(block,curverefining,acis=True)
else:
raise VersionException('check cubit version, refine curve capability has been tested only with cubit <= 12.2')
#
#
if add_sea:
if version_cubit <= 12.2:
block=1001
add_sea_layer(block=block)
else:
raise VersionException('check cubit version, sea capability has been tested only with cubit <= 12.2')
outdir2='/'.join(x for x in outfilename.split('/')[:-1])
if outdir2 == '':
outdir2=outdir+'/'
else:
outdir2=outdir+'/'+outdir2+'/'
import os
try:
os.makedirs(outdir2)
except OSError:
pass
cubit.cmd('compress all')
command="export mesh '"+outdir2+outfilename+".e' block all overwrite xml '"+outdir2+outfilename+".xml'"
cubit.cmd(command)
f=open(outdir2+'blocks.dat','w')
blocks=cubit.get_block_id_list()
#
for block in blocks:
name=cubit.get_exodus_entity_name('block',block)
element_count = cubit.get_exodus_element_count(block, "block")
nattrib=cubit.get_block_attribute_count(block)
attr=[cubit.get_block_attribute_value(block,x) for x in range(0,nattrib)]
ty=cubit.get_block_element_type(block)
f.write(str(block)+' ; '+name+' ; nattr '+str(nattrib)+' ; '+' '.join(str(x) for x in attr)+' ; '+ty+' '+str(element_count)+'\n')
f.close()
#
#
cubit.cmd('set info echo journ off')
cmd='del group all'
cubit.silent_cmd(cmd)
cubit.cmd('set info echo journ on')
#
#
print 'end meshing'
#
#
if qlog:
print '\n\nQUALITY CHECK.... ***************\n\n'
import quality_log
tq=open(outdir2+outfilename+'.quality','w')
max_skewness,min_length=quality_log.quality_log(tq)
#
#
#
if export2SPECFEM3D:
e2SEM(files=False,listblock=listblock,listflag=listflag,outdir=outdir,cpml=cpml,cpml_size=cpml_size,top_absorbing=top_absorbing,hex27=hex27)
if save_cubfile:
vol_blocks=[x for x in blocks if x <=1000]
cubit.cmd("create mesh geometry block "+' '.join(str(x) for x in vol_blocks)+" feature_angle 135.0")
command = "save as '"+outdir2+outfilename+".cub' overwrite"
print command
cubit.cmd(command)
def destroy_curve(Cin):
# C is a object
command = 'delete curve ' + str(Cin.id())
cubit.silent_cmd(command)
return None
def collect_old(cpuxmin=0,cpuxmax=1,cpuymin=0,cpuymax=1,cpux=1,cpuy=1,cubfiles=False,ckbound_method1=False,ckbound_method2=False,merge_tolerance=None,curverefining=False,outfilename='totalmesh_merged',qlog=False,export2SPECFEM3D=False,listblock=None,listflag=None,outdir='.',add_sea=False,decimate=False,cpml=False,cpml_size=False,top_absorbing=False,hex27=False):
#
cubit.cmd('set journal error off')
cubit.cmd('set verbose error off')
collecting_merging(cpuxmin,cpuxmax,cpuymin,cpuymax,cpux,cpuy,cubfiles=cubfiles,ckbound_method1=ckbound_method1,ckbound_method2=ckbound_method2,merge_tolerance=merge_tolerance,decimate=decimate)
cubit.cmd('set journal error on')
cubit.cmd('set verbose error on')
#
if curverefining:
block=1001 #topography
refine_closecurve(block,curverefining,acis=True)
#
#
if add_sea:
block=1001
add_sea_layer(block=block)
outdir2='/'.join(x for x in outfilename.split('/')[:-1])
if outdir2 == '':
outdir2=outdir+'/'
else:
outdir2=outdir+'/'+outdir2+'/'
import os
try:
os.makedirs(outdir2)
except OSError:
pass
cubit.cmd('compress all')
command="export mesh '"+outdir2+outfilename+".e' block all overwrite xml '"+outdir2+outfilename+".xml'"
cubit.cmd(command)
f=open(outdir2+'blocks.dat','w')
blocks=cubit.get_block_id_list()
#
for block in blocks:
name=cubit.get_exodus_entity_name('block',block)
element_count = cubit.get_exodus_element_count(block, "block")
nattrib=cubit.get_block_attribute_count(block)
attr=[cubit.get_block_attribute_value(block,x) for x in range(0,nattrib)]
ty=cubit.get_block_element_type(block)
f.write(str(block)+' ; '+name+' ; nattr '+str(nattrib)+' ; '+' '.join(str(x) for x in attr)+' ; '+ty+' '+str(element_count)+'\n')
f.close()
#
#
cubit.cmd('set info echo journ off')
cmd='del group all'
cubit.silent_cmd(cmd)
cubit.cmd('set info echo journ on')
#
command = "save as '"+outdir2+outfilename+".cub' overwrite"
cubit.cmd(command)
#
print 'end meshing'
#
#
if qlog:
print '\n\nQUALITY CHECK.... ***************\n\n'
import quality_log
tq=open(outdir2+outfilename+'.quality','w')
max_skewness,min_length=quality_log.quality_log(tq)
#
#
#
if export2SPECFEM3D:
e2SEM(files=False,listblock=listblock,listflag=listflag,outdir=outdir,cpml=cpml,cpml_size=cpml_size,top_absorbing=top_absorbing,hex27=hex27)
def save_elements_nodes(name,quads_fault_u,quads_fault_d):
fault_file = open(name,'w')
txt =''
list_hex=cubit.parse_cubit_list('hex','all')
txt='%10i %10i\n' % (len(quads_fault_u),len(quads_fault_d))
fault_file.write(txt)
dic_quads_fault_u = dict(zip(quads_fault_u,quads_fault_u))
dic_quads_fault_d = dict(zip(quads_fault_d,quads_fault_d))
# FAULT SIDE DOWN
# fault_file.write('upsurface')
for h in list_hex:
faces = cubit.get_sub_elements('hex',h,2)
for f in faces:
if dic_quads_fault_d.has_key(f):
cubit.silent_cmd('group "nf" add Node in face '+str(f))
group1 = cubit.get_id_from_name("nf")
nodes = cubit.get_group_nodes(group1)
cubit.silent_cmd('del group '+ str(group1))
# nodes=cubit.get_connectivity('Face',f)
# print 'h,fault nodes side down :',h,nodes[0],nodes[1],nodes[2],nodes[3]
# txt='%10i %10i %10i %10i %10i\n' % (h,nodes[0],\
# nodes[1],nodes[2],nodes[3])
ngnod2d = len(nodes)
if ngnod2d == 9:
#kangchen added txt='%10i %10i %10i %10i %10i\n' % (h,nodes[0],\
# nodes[1],nodes[2],nodes[3])
txt='%10i %10i %10i %10i %10i %10i %10i %10i %10i %10i\n' % (h,nodes[0],\
nodes[1],nodes[2],nodes[3],nodes[4],nodes[5],nodes[6],nodes[7],nodes[8])
else:
txt='%10i %10i %10i %10i %10i \n' % (h,nodes[0],\
nodes[1],nodes[2],nodes[3])
fault_file.write(txt)
# FAULT SIDE UP
# fault_file.write('downsurface')
for h in list_hex:
faces = cubit.get_sub_elements('hex',h,2)
for f in faces:
if dic_quads_fault_u.has_key(f):
cubit.silent_cmd('group "nf" add Node in face '+str(f))
group1 = cubit.get_id_from_name("nf")
nodes = cubit.get_group_nodes(group1)
cubit.cmd('del group '+ str(group1))
ngnod2d=len(nodes)
if ngnod2d == 9:
# nodes=cubit.get_connectivity('Face',f)
# print 'h,fault nodes side up :',h,nodes[0],nodes[1],nodes[2],nodes[3]
#kangchen added txt='%10i %10i %10i %10i %10i\n' % (h,nodes[0],\
# nodes[1],nodes[2],nodes[3])
txt='%10i %10i %10i %10i %10i %10i %10i %10i %10i %10i\n' % (h,nodes[0],\
nodes[1],nodes[2],nodes[3],nodes[4],nodes[5],nodes[6],nodes[7],nodes[8])
else:
txt='%10i %10i %10i %10i %10i \n' % (h,nodes[0],\
nodes[1],nodes[2],nodes[3])
fault_file.write(txt)
fault_file.close()
