def __init__(self,hex27=False):
super(mesh, self).__init__()
self.mesh_name='mesh_file'
self.nodecoord_name='nodes_coords_file'
self.material_name='materials_file'
self.nummaterial_name='nummaterial_velocity_file'
self.absname='absorbing_surface_file'
self.freename='free_surface_file'
self.recname='STATIONS'
try:
version_cubit=float(cubit.get_version())
except:
version_cubit=float(cubit.get_version()[0:2])
#
if version_cubit >= 12:
self.face='SHELL4'
else:
self.face='QUAD4'
self.hex='HEX'
self.hex27=hex27
self.edge='BAR2'
self.topo='face_topo'
self.rec='receivers'
if hex27: cubit.cmd('block all except (block 1001 1002 1003 1004 1005 1006) type hex27')
self.block_definition()
self.ngll=5
self.percent_gll=0.172
self.point_wavelength=5
cubit.cmd('compress all')
print 'version hex27'
def prepare_equivalence_new(name_group='lateral'):
length={}
cmd="group 'tmpn' add edge in face in group "+name_group
cubit.cmd(cmd)
ge=cubit.get_id_from_name("tmpn")
e1=cubit.get_group_edges(ge)
lengthmin=1e9
for e in e1:
lengthmin=min(lengthmin,cubit.get_mesh_edge_length(e))
length[e]=lengthmin*.5
cubit.cmd('delete group '+str(ge))
minvalue=min(length.values())
maxvalue=max(length.values())
#
print 'min lentgh: ',minvalue,'max lentgh: ',maxvalue
nbin= int((maxvalue/minvalue)/2.)+1
factor=(maxvalue-minvalue)/nbin
dic_new={}
for k in length.keys():
dic_new[k]=int((length[k]-minvalue)/factor)
inv_length=invert_dict(dic_new)
print inv_length.keys(),factor,minvalue
ks=inv_length.keys()
ks.sort()
for k in range(0,len(inv_length.keys())-1):
inv_length[ks[k]]=inv_length[ks[k]]+inv_length[ks[k+1]]
return factor,minvalue,inv_length
def translate2zero():
ss=cubit.parse_cubit_list('surface','all')
box = cubit.get_total_bounding_box("surface", ss)
xmin=box[0]
ymin=box[3]
cubit.cmd('move surface all x '+str(-1*xmin)+' y '+str(-1*ymin))
return xmin,ymin
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 createSkinCurve2(curves):
circles = ""
for c in curves:
circles += str(c) + " "
cubit.cmd("create surface skin curve %s" % (circles))
surfID = cubit.get_last_id("surface")
return surfID
def free_write(self,freename=None):
# free surface
cubit.cmd('set info off')
cubit.cmd('set echo off')
cubit.cmd('set journal off')
from sets import Set
normal=(0,0,1)
if not freename: freename=self.freename
# writes free surface file
print 'Writing '+freename+'.....'
freehex=open(freename,'w')
# searches block definition with name face_topo
for block,flag in zip(self.block_bc,self.block_bc_flag):
if block == self.topography:
name=cubit.get_exodus_entity_name('block',block)
print ' block name:',name,'id:',block
quads_all=cubit.get_block_faces(block)
print ' number of faces = ',len(quads_all)
dic_quads_all=dict(zip(quads_all,quads_all))
freehex.write('%10i\n' % len(quads_all))
list_hex=cubit.parse_cubit_list('hex','all')
for h in list_hex:
faces=cubit.get_sub_elements('hex',h,2)
for f in faces:
if dic_quads_all.has_key(f):
#print f
nodes=cubit.get_connectivity('Face',f)
nodes_ok=self.normal_check(nodes,normal)
txt='%10i %10i %10i %10i %10i\n' % (h,nodes_ok[0],\
nodes_ok[1],nodes_ok[2],nodes_ok[3])
freehex.write(txt)
freehex.close()
print 'Ok'
cubit.cmd('set info on')
cubit.cmd('set echo on')
def createCombineCurve(curves):
cs = ""
for c in curves:
cs += str(c) + " "
cubit.cmd("create curve combine curve %s" % (cs))
curveID = cubit.get_last_id("curve")
return curveID
def createSpline2(pts):
points = ""
for p in pts:
points += str(p) + " "
cubit.cmd("create curve spline vertex %s" % (points))
splineID = cubit.get_last_id("curve")
return splineID
def seismic_resolution(self,edges,velocity,bins_d=None,bins_u=None,sidelist=None):
"""
dt,edge_dt,freq,edge_freq=seismic_resolution(edges,velocity,bins_d=None,bins_u=None,sidelist=None,ngll=5,np=8)
Given the velocity of a list of edges, seismic_resolution provides the minimum Dt required for the stability condition (and the corrisponding edge).
Furthermore, given the number of gll point in the element (ngll) and the number of GLL point for wavelength, it provide the maximum resolved frequency.
"""
ratiostore=1e10
dtstore=1e10
edgedtstore=-1
edgeratiostore=-1
for edge in edges:
d=self.edge_length(edge)
ratio=(1/2.5)*velocity/d*(self.ngll-1)/self.point_wavelength
dt=.4*d/velocity*self.percent_gll
if dt<dtstore:
dtstore=dt
edgedtstore=edge
if ratio < ratiostore:
ratiostore=ratio
edgeratiostore=edge
try:
for bin_d,bin_u,side in zip(bins_d,bins_u,sidelist):
if ratio >= bin_d and ratio < bin_u:
command = "sideset "+str(side)+" edge "+str(edge)
cubit.cmd(command)
break
except:
pass
return dtstore,edgedtstore,ratiostore,edgeratiostore
def runimport(geometryfile, iproc, filename=None):
import start as start
cubit = start.start_cubit()
cfg = start.start_cfg(filename=filename)
file1 = cfg.output_dir + '/' + geometryfile
cubitcommand = 'open "' + file1 + '" '
cubit.cmd(cubitcommand)
def free_write(self,freename=None):
cubit.cmd('set info off')
cubit.cmd('set echo off')
cubit.cmd('set journal off')
from sets import Set
normal=(0,0,1)
if not freename: freename=self.freename
freehex=open(freename,'w')
print 'Writing '+freename+'.....'
#
#
for block,flag in zip(self.block_bc,self.block_bc_flag):
if block == self.topography:
name=cubit.get_exodus_entity_name('block',block)
print ' block name:',name,'id:',block
quads_all=cubit.get_block_faces(block)
print ' number of faces = ',len(quads_all)
dic_quads_all=dict(zip(quads_all,quads_all))
freehex.write('%10i\n' % len(quads_all))
list_hex=cubit.parse_cubit_list('hex','all')
for h in list_hex:
faces=cubit.get_sub_elements('hex',h,2)
for f in faces:
if dic_quads_all.has_key(f):
#print f
txt=self.create_facenode_string(h,f,normal,cknormal=True)
freehex.write(txt)
freehex.close()
cubit.cmd('set info on')
cubit.cmd('set echo on')
def getAllVolumeIds ():
cubit.cmd ('compress all')
numVolumes = cubit.get_volume_count ()
volumeIds = [x for x in range (1, numVolumes+1)]
return volumeIds
def write(self, path=""):
cubit.cmd("set info off")
cubit.cmd("set echo off")
cubit.cmd("set journal off")
if len(path) != 0:
if path[-1] != "/":
path = path + "/"
# mesh file
self.mesh_write(path + self.mesh_name)
# mesh material
self.material_write(path + self.material_name)
# mesh coordinates
self.nodescoord_write(path + self.nodecoord_name)
# material definitions
self.nummaterial_write(path + self.nummaterial_name)
# free surface: face_top
self.free_write(path + self.freename)
# absorbing surfaces: abs_***
self.abs_write(path + self.absname)
# any other surfaces: ***surface***
self.surface_write(path)
# receivers
if self.receivers:
self.rec_write(path + self.recname)
cubit.cmd("set info on")
cubit.cmd("set echo on")
def write(self,path = ''):
""" Write mesh in specfem2d format """
print 'Writing '+self.recname+'.....'
import os
cubit.cmd('set info off') # Turn off return messages from Cubit commands
cubit.cmd('set echo off') # Turn off echo of Cubit commands
cubit.cmd('set journal off') # Do not save journal file
if len(path) != 0: # If a path is supplied add a / at the end if needed
if path[-1] != '/': path = path+'/'
else:
path = os.getcwd()+'/'
self.mesh_write(path+self.mesh_name) # Write mesh file
self.material_write(path+self.material_name) # Write material file
self.nodescoord_write(path+self.nodecoord_name) # Write nodes coord file
self.free_write(path+self.freename) # Write free surface file (specfem2d needs it even if there is no free surface)
if self.abs_mesh:
self.abs_write(path+self.absname) # Write absorbing surface file
if self.axisymmetric_mesh:
self.axis_write(path+self.axisname) # Write axis on file
if self.pml_layers:
self.pmls_write(path+self.pmlname) # Write axis on file
if self.write_nummaterial_velocity_file:
self.nummaterial_write(path+self.nummaterial_name) # Write nummaterial file
if self.receivers:
self.rec_write(path+self.recname) # If receivers has been set (as nodeset) write receiver file as well
print 'Mesh files has been writen in '+path
cubit.cmd('set info on') # Turn on return messages from Cubit commands
cubit.cmd('set echo on') # Turn on echo of Cubit commands
def __init__(self):
super(mesh, self).__init__()
self.mesh_name = 'mesh_file'
self.axisymmetric_mesh = False # Will be set to true if a group self.pml_boun_name is found
self.topo_mesh = False # Will be set to true if a group self.topo is found
self.abs_mesh = False # Will be set to true if a group self.pml_boun_name or self.abs_boun_name is found
self.pml_layers = False # Will be set to true if a group self.pml_boun_name is found
self.write_nummaterial_velocity_file = False # Will be set to True if 2d blocks have 6 attributes
self.nodecoord_name = 'nodes_coords_file' # Name of nodes coordinates file to create
self.material_name = 'materials_file' # Name of material file to create
self.nummaterial_name = 'nummaterial_velocity_file'
self.absname = 'absorbing_surface_file' # Name of absorbing surface file to create
self.freename = 'free_surface_file' # Name of free surface file to create
self.pmlname = 'elements_cpml_list' # Name of cpml file to create
self.axisname = 'elements_axis' # Name of axial elements file to create and name of the block containing axial edges
self.recname = 'STATIONS'
self.face = 'QUAD9' # Faces' type
self.edge = 'BAR3' # Edges' type
self.topo = 'topo' # Name of the block containing topography edges
self.pml_boun_name = ['pml_x_acoust','pml_z_acoust','pml_xz_acoust','pml_x_elast','pml_z_elast','pml_xz_elast'] # Name of the block containing pml layers elements
self.abs_boun_name = ['abs_bottom','abs_right','abs_top','abs_left'] # Name of the block containing absorbing layer edges
self.abs_boun = [] # block numbers for abs boundaries
self.pml_boun = [] # block numbers for pml boundaries
self.nabs = 4 # Maximum number of absorbing surfaces (4)
self.rec = 'receivers'
self.block_definition() # Import blocks features from Cubit
self.ngll = 5
self.percent_gll = 0.172
self.point_wavelength = 5
cubit.cmd('compress') # Fill the gaps in the numbering of the entities
def cubit_command_check(iproc, command, stop=True):
"""
Run a cubit command, checking if it performs correctly.
If the command fails, it writes the result on a file
"error_[processor number]" and stop the meshing process
iproc = process number
command = cubit command
stop = if command fails, stop the meshing process (Default: True)
return status variable (0 ok, -1 fail)
"""
flag = True
er = cubit.get_error_count()
cubit.cmd(command)
print command
ner = cubit.get_error_count()
if ner > er:
text = '"Proc: ' + str(iproc) + ' ERROR ' + str(command) + \
' number of error ' + str(er) + '/' + str(ner) + '"'
cubitcommand = 'comment ' + text
cubit.cmd(cubitcommand)
f = open('error_' + str(iproc) + '.log', 'a')
f.write("CUBIT ERROR: \n" + text)
f.close()
if stop:
raise Exception("CUBIT ERROR: " + text)
flag = False
return flag
def check_lateral_nodes(name_group='lateral'):
cubit.cmd("group 'lateral_nodes' add Node in face in group "+name_group)
ilateral_nodes=cubit.get_id_from_name('lateral_nodes')
lateral_nodes=cubit.get_group_nodes(ilateral_nodes)
cubit.cmd('del group '+str(ilateral_nodes))
print name_group, ' nodes ',len(lateral_nodes)
return len(lateral_nodes)
def createSurfaceCurve2(curves):
cc = ""
for c in curves:
cc += str(c) + " "
cubit.cmd("create surface curve %s" % (cc))
surfID = cubit.get_last_id("surface")
return surfID
def cubit_error_continue(iproc,command,n_er):
"""obsolete"""
er=cubit.get_error_count()
if er >= n_er:
text='"Proc: '+str(iproc)+' ERROR continue '+str(command)+' number of error '+str(er)+' '+str(n_er)+'"'
cubit.cmd('comment '+ text)
print 'error: ',text
return er
def cubit_error_stop(iproc,command,ner):
"""obsolete"""
er=cubit.get_error_count()
if er > ner:
text='"Proc: '+str(iproc)+' ERROR '+str(command)+' number of error '+str(er)+'/'+str(ner)+'"'
cubitcommand = 'comment '+text
cubit.cmd(cubitcommand)
raise NameError, text
def createVolume(surfs):
volID = cubit.get_owning_volume("surface", surfs[-1])
ss = ""
for s in surfs:
ss += str(s) + " "
cubit.cmd("create volume surface %s noheal" % (ss))
#volID = cubit.get_last_id("volume")
return volID
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 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 forcing_write(self,forcname):
""" Write forcing surfaces on file : forcname """
cubit.cmd('set info off') # Turn off return messages from Cubit commands
cubit.cmd('set echo off') # Turn off echo of Cubit commands
cubit.cmd('set journal off') # Do not save journal file
from sets import Set
forceedge = open(forcname,'w')
print 'Writing '+forcname+'.....'
edges_forc = [Set()]*self.nforc # edges_forc[0] will be a Set containing the nodes describing the forcing boundary
# (index 0 : bottom, index 1 : right, index 2 : top, index 3 : left)
nedges_all = 0 # To count the total number of forcing edges
for block,flag in zip(self.block_bc,self.block_bc_flag): # For each 1D block
for iforc in range(0, self.nforc): # iforc = 0,1,2,3 : for each forcing boundaries
if block == self.forcing_boun[iforc]: # If the block considered correspond to the boundary
edges_forc[iforc] = Set(cubit.get_block_edges(block)) # Store each edge on edges_forc
nedges_all = nedges_all+len(edges_forc[iforc]) # add the number of edges to nedges_all
toWritetoFile = [""]*(nedges_all+1)
toWritetoFile[0] = '%10i\n' % nedges_all # Write the total number of forcing edges to the first line of file
#forceedge.write('%10i\n' % nedges_all) # Write the total number of forcing edges to the first line of file
print 'Number of edges', nedges_all
#id_element = 0
indexFile = 1
for block,flag in zip(self.block_mat,self.block_flag): # For each 2D block
quads = cubit.get_block_faces(block) # Import quads id
for quad in quads: # For each quad
#id_element = id_element+1 # id of this quad
edges = Set(cubit.get_sub_elements("face", quad, 1)) # Get the lower dimension entities associated with a higher dimension entities.
# Here it gets the 1D edges associates with the face of id "quad". Store it as a Set
for iforc in range(0,self.nforc): # iforc = 0,1,2,3 : for each forcing boundaries
intersection = edges & edges_forc[iforc] # Contains the edges of the considered quad that is on the forcing boundary considered
if len(intersection) != 0: # If this quad touch the forcing boundary considered
nodes = cubit.get_connectivity('face',quad) # Import the nodes describing the quad
nodes = self.jac_check(list(nodes)) # Check the jacobian of the quad
for e in intersection: # For each edge on the forcing boundary considered
node_edge = cubit.get_connectivity('edge',e) # Import the nodes describing the edge
nodes_ok = []
for i in nodes: # Loop on the nodes of the quad
if i in node_edge: # If this node is belonging to forcing surface
nodes_ok.append(i) # add it to nodes_ok
# forcname contains 1/ element number, 2/ number of nodes that form the acoustic forcing edge
# (which currently must always be equal to two, see comment below),
# 3/ first node on the acforcing surface, 4/ second node on the acforcing surface
# 5/ 1 = IBOTTOME, 2 = IRIGHT, 3 = ITOP, 4 = ILEFT
#txt = '%10i %10i %10i %10i %10i\n' % (id_element,2,nodes_ok[0],nodes_ok[1],iforc+1)
txt = '%10i %10i %10i %10i %10i\n' % (quad,2,nodes_ok[0],nodes_ok[1],iforc+1)
# Write the id of the quad, 2 (number of nodes describing a free surface elements), the nodes and the type of boundary
#print indexFile
toWritetoFile[indexFile] = txt
indexFile = indexFile + 1
#forceedge.write(txt)
forceedge.writelines(toWritetoFile)
forceedge.close()
print 'Ok'
cubit.cmd('set info on') # Turn on return messages from Cubit commands
cubit.cmd('set echo on') # Turn on echo of Cubit commands
def group_timestep(self):
tot = 0.0
if self.dt_hyst is not None:
dtmax = max(self.dt_hyst.values())
dt = self.hyst(self.dt, dtmax, self.dt_hyst)
factor = (dtmax - self.dt) / self.nbin
for i in range(0, self.nbin + 1):
if dt.has_key(i):
txt = 'group "timestep_%.1e_%.1e" add hex ' % (self.dt + factor * i, self.dt + factor * (i + 1))
txt = txt + " ".join(str(hh) for hh in dt[i])
cubit.cmd(txt)
def group_period(self):
tot = 0.0
if self.period_hyst is not None:
pmin = min(self.period_hyst.values())
period = self.hyst(pmin, self.period, self.period_hyst)
factor = (self.period - pmin) / self.nbin
for i in range(0, self.nbin + 1):
if period.has_key(i):
txt = 'group "period_%.1e_%.1e" add hex ' % (pmin + factor * i, pmin + factor * (i + 1))
txt = txt + " ".join(str(hh) for hh in period[i])
cubit.cmd(txt)
def export2SPECFEM3D(path_exporting_mesh_SPECFEM3D='.',hex27=False,cpml=False,cpml_size=False,top_absorbing=False):
sem_mesh=mesh(hex27,cpml,cpml_size,top_absorbing)
#sem_mesh.block_definition()
#print sem_mesh.block_mat
#print sem_mesh.block_flag
#
sem_mesh.write(path=path_exporting_mesh_SPECFEM3D)
print 'END SPECFEM3D exporting process......'
if cpml:
cmd='save as "cpml.cub" overwrite'
cubit.cmd(cmd)
def runsave(geometryfile,iproc,filename=None):
import start as start
cubit = start.start_cubit()
cfg = start.start_cfg(filename=filename)
flag=[0]
ner=cubit.get_error_count()
cubitcommand= 'save as "'+ cfg.output_dir+'/'+geometryfile+ '" overwrite'
cubit.cmd(cubitcommand)
ner2=cubit.get_error_count()
if ner == ner2:
flag=[1]
return flag
def highlight_edgemax(self, low=None, high=None):
if low is None and high is not None:
hexlist = self.show(low, self.max_edge_length, self.edgemax_hyst)
elif low is not None and high is None:
hexlist = self.show(self.min_edge_length, high, self.edgemax_hyst)
if low is not None and high is not None:
hexlist = self.show(low, high, self.edgemax_hyst)
else:
hexlist = self.hex_max_edge_length
command = "highlight hex " + str(hexlist)
command = command.replace("[", " ").replace("]", " ").replace("(", " ").replace(")", " ")
cubit.cmd(command) #
def abs_write(self,absname):
""" Write absorbing surfaces on file : absname """
cubit.cmd('set info off') # Turn off return messages from Cubit commands
cubit.cmd('set echo off') # Turn off echo of Cubit commands
cubit.cmd('set journal off') # Do not save journal file.
from sets import Set
# if not absname: absname = self.absname
absedge = open(absname,'w')
print 'Writing '+absname+'.....'
edges_abs = [Set()]*self.nabs # edges_abs[0] will be a Set containing the nodes describing bottom adsorbing boundary
# (index 0 : bottom, index 1 : right, index 2 : top, index 3 : left)
nedges_all = 0 # To count the total number of absorbing edges
for block,flag in zip(self.block_bc,self.block_bc_flag): # For each 1D block
for iabs in range(0, self.nabs): # iabs = 0,1,2,3 : for each absorbing boundaries
if block == self.abs_boun[iabs]: # If the block considered correspond to the boundary
edges_abs[iabs] = Set(cubit.get_block_edges(block)) # Store each edge on edges_abs
nedges_all = nedges_all+len(edges_abs[iabs]); # add the number of edges to nedges_all
toWritetoFile = [""]*(nedges_all+1)
toWritetoFile[0] = '%10i\n' % nedges_all # Write the total number of absorbing edges to the first line of file
#absedge.write('%10i\n' % nedges_all) # Write the total number of absorbing edges to the first line of file
print 'Number of edges', nedges_all
#id_element = 0
indexFile = 1
for block,flag in zip(self.block_mat,self.block_flag): # For each 2D block
quads = cubit.get_block_faces(block) # Import quads id
for quad in quads: # For each quad
#id_element = id_element+1 # id of this quad
edges = Set(cubit.get_sub_elements("face", quad, 1)) # Get the lower dimension entities associated with a higher dimension entities.
# Here it gets the 1D edges associates with the face of id "quad". Store it as a Set
for iabs in range(0,self.nabs): # iabs = 0,1,2,3 : for each absorbing boundaries
intersection = edges & edges_abs[iabs] # Contains the edges of the considered quad that is on the absorbing boundary considered
if len(intersection) != 0: # If this quad touch the absorbing boundary considered
nodes = cubit.get_connectivity('face',quad) # Import the nodes describing the quad
nodes = self.jac_check(list(nodes)) # Check the jacobian of the quad
for e in intersection: # For each edge on the absorbing boundary considered
node_edge = cubit.get_connectivity('edge',e) # Import the nodes describing the edge
nodes_ok = []
for i in nodes: # Loop on the nodes of the quad
if i in node_edge: # If this node is belonging to absorbing surface
nodes_ok.append(i) # Add it to nodes_ok
#txt = '%10i %10i %10i %10i %10i\n' % (id_element,2,nodes_ok[0],nodes_ok[1],iabs+1)
txt = '%10i %10i %10i %10i %10i\n' % (quad,2,nodes_ok[0],nodes_ok[1],iabs+1)
# Write the id of the quad, 2 (number of nodes describing a free surface elements), the nodes and the type of boundary
toWritetoFile[indexFile] = txt
indexFile = indexFile + 1
#absedge.write(txt)
absedge.writelines(toWritetoFile)
absedge.close()
print 'Ok'
cubit.cmd('set info on') # Turn on return messages from Cubit commands
cubit.cmd('set echo on') # Turn on echo of Cubit commands
print sys.path
cubit.init([""])
# gets version string
cubit_version = cubit.get_version()
print "version: ",cubit_version
# extracts major number
v = cubit_version.split('.')
cubit_version_major = int(v[0])
print "major version number: ",cubit_version_major
# current work directory
cubit.cmd('pwd')
# Creating the volumes
cubit.cmd('reset')
# single volume
cubit.cmd('brick x 134000 y 134000 z 60000')
cubit.cmd('volume 1 move x 67000 y 67000 z -30000')
# two merged volumes
#cubit.cmd('brick x 67000 y 134000 z 60000')
#cubit.cmd('volume 1 move x 33500 y 67000 z -30000')
#cubit.cmd('brick x 67000 y 134000 z 60000')
#cubit.cmd('volume 2 move x 100500 y 67000 z -30000')
#cubit.cmd('merge all')
#### Then you can run cubit2specfem2d.py
#### Author alexis dot bottero at gmail dot com
###########################################################################
import cubit
lx = 50000 #5000
lz = 50000 #500
nPml = 3 # PMLs Thickness (number of elements in pmls)
######################
elementSize = 1000 # Mean element size
#cubit.cmd('cd "/home1/bottero/Desktop/mesh2d"') # Change Cubit working directory
cubit.cmd('reset')
### Create the rectangle :
cubit.cmd('create surface rectangle width ' + str(lx) + ' height ' + str(lz) +
' yplane') # Create a lx*lz rectangle
cubit.cmd('volume 1 move x ' + str(lx / 2.0) + ' z ' +
str(-lz / 2.0)) # To get correct coordinates
### Meshing the surface :
cubit.cmd('surface 1 size ' +
str(elementSize)) # Define the size of an element in surface 1
cubit.cmd('mesh surface 1') # Mesh the surface
### Define blocks and material properties
cubit.cmd('#### DEFINE MATERIAL PROPERTIES #######################')
cubit.cmd(' block 1 face in surface 1')
def MilledLayer(Body_IDs, BB, Alpha, Theta1, Theta2, secmin, Xoffset=.5):
import cubit
import numpy as np
###
### Body_ID: a single volume ID
### BB: bounding box in the form [xmin, xmax, ymin, ymax, zmin, zmax]
### Alpha: lamination angle
### Theta1: thickness of layer 1
### Theta2: thickness of layer 2
### secmin: the cross section after machining
### Xoffset: distance along the x-axis between the center of the bounding box
### and the first interface l1-l2 if specified, in fraction of Theta1
### i.e. 0 -> interface l2-l1 at center
### 1 -> interface l1-l2 at center
### otherwise, the center of BB corresponds to the center of a Layer1
### i.e. Xoffset = .5
###
YL = np.sqrt((BB[1] - BB[0])**2 + (BB[3] - BB[2])**2)
ZL = BB[5] - BB[4]
XC = (BB[0] + BB[1]) / 2.
YC = (BB[2] + BB[3]) / 2.
ZC = (BB[4] + BB[5]) / 2.
Theta = Theta1 + Theta2
if Alpha > 0:
l1 = (BB[0] - XC) * np.cos(np.radians(Alpha)) + (BB[2] - YC) * np.sin(
np.radians(Alpha))
l2 = (BB[1] - XC) * np.cos(np.radians(Alpha)) + (BB[3] - YC) * np.sin(
np.radians(Alpha))
else:
l1 = (BB[0] - XC) * np.cos(np.radians(Alpha)) + (BB[3] - YC) * np.sin(
np.radians(Alpha))
l2 = (BB[1] - XC) * np.cos(np.radians(Alpha)) + (BB[2] - YC) * np.sin(
np.radians(Alpha))
n1 = int(np.ceil(l1 / Theta))
n2 = int(np.ceil(l2 / Theta))
for i in range(n1, n2):
X = XC + i * np.cos(
np.radians(Alpha)) * Theta + Theta1 * (Xoffset - .5)
Y = YC + i * np.sin(np.radians(Alpha)) * Theta
cubit.cmd('create brick X %f Y %f Z %f' % (Theta1, YL, ZL))
tmp_ID = cubit.get_last_id("volume")
cubit.cmd('move volume %i X %f Y %f Z %f' %
(tmp_ID, X, Y, ZL / 2. + secmin[1]))
if not Alpha == 0.:
### cubit doesn't like rotations will 0 angle...
cubit.cmd('create vertex X %f Y %f Z %f' % (X, Y, BB[4]))
v1_ID = cubit.get_last_id("vertex")
cubit.cmd('create vertex X %f Y %f Z %f' % (X, Y, BB[5]))
v2_ID = cubit.get_last_id("vertex")
cubit.cmd('rotate volume %i about vertex %i vertex %i angle %f' %
(tmp_ID, v1_ID, v2_ID, Alpha))
cubit.cmd('delete vertex %i' % v1_ID)
cubit.cmd('delete vertex %i' % v2_ID)
(Body_IDs, tmp_layer) = WebcutTool(Body_IDs, tmp_ID, delete=False)
cmd = "delete volume "
for v in tmp_layer:
cmd += " %i" % v
cubit.cmd(cmd)
cubit.cmd("move volume %i Z %f" %
(tmp_ID, -ZL - secmin[1] + secmin[0]))
(Body_IDs, tmp_layer) = WebcutTool(Body_IDs, tmp_ID, delete=True)
cmd = "delete volume "
for v in tmp_layer:
cmd += " %i" % v
cubit.cmd(cmd)
return (Body_IDs)
def GroupAddVolList(groupname, vol_IDs):
import cubit
cmd = 'group "%s" add volume ' % groupname
for vol in vol_IDs:
cmd += ' %i' % vol
cubit.cmd(cmd)
def PacmanCoinLayeredCreate(R,
lx,
ly,
lz,
alpha,
theta1,
theta2,
thetacrack,
xc=0):
import cubit
import numpy as np
###
### Create Main body
###
OUTSIDE_3D = []
cubit.cmd("Create cylinder height %f radius %f" % (lz, R))
OUTSIDE_3D.append(cubit.get_last_id("volume"))
###
### Create wedge
###
w_ID = []
cubit.cmd("create vertex X %f Y 0 Z %f" % (xc, -lz))
w_ID.append(cubit.get_last_id("vertex"))
X = 1.1 * R * np.cos(np.radians(thetacrack / 2.))
Y = 1.1 * R * np.sin(np.radians(thetacrack / 2.))
cubit.cmd("create vertex X %f Y %f Z %f" % (-X, Y, -lz))
w_ID.append(cubit.get_last_id("vertex"))
cubit.cmd("create vertex X %f Y %f Z %f" % (-X, -Y, -lz))
w_ID.append(cubit.get_last_id("vertex"))
cubit.cmd("create surface vertex %i %i %i" % (w_ID[0], w_ID[1], w_ID[2]))
cubit.cmd("sweep surface %i perpendicular distance %f" %
(cubit.get_last_id("surface"), 2 * lz))
WEDGE = cubit.get_last_id("volume")
###
### remove crack
###
cubit.cmd("subtract volume %i from volume %i" % (WEDGE, OUTSIDE_3D[0]))
###
### Create center coin
###
cubit.cmd("Create cylinder height %f major radius %f minor radius %f" %
(lz, lx, ly))
CYL = cubit.get_last_id("volume")
(OUTSIDE_3D, CYL_ID) = WebcutTool(OUTSIDE_3D, CYL, delete=True)
###
### create layers
###
bb = [-lx, lx, -ly, ly, -2. * lz, 2. * lz]
print('CYL_ID, bb, alpha, theta1, theta2', CYL_ID, bb, alpha, theta1,
theta2)
(LAYER1_3D, LAYER2_3D) = Layer(CYL_ID, bb, alpha, theta1, theta2, 0.)
###
### imprint and merge
###
cubit.cmd("imprint all")
cubit.cmd("merge all")
###
### groups
###
GroupAddVolList("LAYER1_3D", LAYER1_3D)
GroupAddVolList("LAYER2_3D", LAYER2_3D)
GroupAddVolList("OUTSIDE_3D", OUTSIDE_3D)
import cubit
cubit.init([""])
try:
from geocubitlib import boundary_definition
from geocubitlib import cubit2specfem3d
except:
import boundary_definition
import cubit2specfem3d
import os
import sys
cubit.cmd('reset')
cubit.cmd('brick x 134000 y 134000 z 60000')
# This seems to conflict with boundary_definition.py
# ....which leaves the model space at e.g. x=[-67,67] km
cubit.cmd('volume 1 move x 67000 y 67000 z -30000')
# create vertices for discontinuity
cubit.cmd('split curve 9 distance 3000')
cubit.cmd('split curve 10 distance 3000')
cubit.cmd('split curve 11 distance 3000')
cubit.cmd('split curve 12 distance 3000')
# create surface for interface
cubit.cmd('create surface vertex 9 10 12 11')
import sys
import cubit
try:
#cubit.init([""])
cubit.init(["-noecho", "-nojournal"])
except:
pass
version = cubit.get_version()
version_major = int(version.split(".")[0])
version_minor = int(version.split(".")[1])
print("cubit version: ", version)
# allows for elements in multiple block definitions (topo, absorbing faces,..)
cubit.cmd('set duplicate block elements on')
# mesh
#cubit.cmd('open "coffee_cup_with_handle_CUBIT_mesh.cub"')
## block definitions
#
# works with coffee_cup_with_handle_CUBIT_mesh.cub
cubit.cmd('delete block all')
# acoustic volume
if version_major <= 15:
# older cubit versions
cubit.cmd('block 1 hex in volume 2')
else:
# version 16
def mesh_layercake_regularmap(filename=None):
import start as start
mpiflag, iproc, numproc, mpi = start.start_mpi()
from utilities import importgeometry, savemesh, get_v_h_list
from utilities import cubit_command_check, get_cubit_version
#
# numpy = start.start_numpy()
cfg = start.start_cfg(filename=filename)
# from math import sqrt
from sets import Set
version_cubit = get_cubit_version()
list_vol = cubit.parse_cubit_list("volume", "all")
if len(list_vol) != 0:
pass
else:
geometryfile = 'geometry_vol_' + str(iproc) + '.cub'
importgeometry(geometryfile, iproc=iproc)
command = 'composite create curve all'
cubit.cmd(command)
print '###"No valid composites can be created from the specified curves." \
is NOT a critical ERROR.'
#
command = "compress all"
cubit.cmd(command)
list_vol = cubit.parse_cubit_list("volume", "all")
nvol = len(list_vol)
vol = []
for id_vol in list_vol:
p = cubit.get_center_point("volume", id_vol)
vol.append(cubitvolume(id_vol, 1, p[2], 0))
vol.sort(by_z)
#
for id_vol in range(0, nvol):
vol[id_vol].intervalv = cfg.iv_interval[id_vol]
#
#
surf_vertical = []
surf_or = []
# top_surface = 0
# top_surface_add = ''
# bottom_surface = 0
# #
# zmin_box = cubit.get_total_bounding_box("volume", list_vol)[6]
# xmin_box = cubit.get_total_bounding_box("volume", list_vol)[0]
# xmax_box = cubit.get_total_bounding_box("volume", list_vol)[1]
# ymin_box = cubit.get_total_bounding_box("volume", list_vol)[3]
# ymax_box = cubit.get_total_bounding_box("volume", list_vol)[4]
#
#
# interval assignement
surf_or, surf_vertical, list_curve_or, list_curve_vertical, \
bottom, top = get_v_h_list(list_vol, chktop=cfg.chktop)
print 'vertical surfaces: ', surf_vertical
for k in surf_vertical:
command = "surface " + str(k) + " scheme submap"
cubit.cmd(command)
for k in surf_or:
command = "surface " + str(k) + " scheme " + cfg.or_mesh_scheme
cubit.cmd(command)
#
ucurve, vcurve = get_uv_curve(list_curve_or)
schemepave = False
#
ucurve_interval = {}
for k in ucurve:
length = cubit.get_curve_length(k)
interval = int(2 * round(.5 * length / cfg.size, 0))
ucurve_interval[k] = interval
command = "curve " + str(k) + " interval " + str(interval)
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
command = "curve " + str(k) + " scheme equal"
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
if max(ucurve_interval.values()) != min(ucurve_interval.values()):
schemepave = True
print 'mesh scheme is set to pave'
for sk in surf_or:
command = "surface " + str(sk) + " scheme pave"
cubit.cmd(command)
#
vcurve_interval = {}
for k in vcurve:
length = cubit.get_curve_length(k)
interval = int(2 * round(.5 * length / cfg.size, 0))
vcurve_interval[k] = interval
command = "curve " + str(k) + " interval " + str(interval)
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
command = "curve " + str(k) + " scheme equal"
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
if max(vcurve_interval.values()) != min(vcurve_interval.values()):
print 'mesh scheme is set to pave'
schemepave = True
for sk in surf_or:
command = "surface " + str(sk) + " scheme pave"
cubit.cmd(command)
#
for s in surf_vertical:
lcurve = cubit.get_relatives("surface", s, "curve")
interval_store = []
for k in lcurve:
interval_curve = cubit.get_mesh_intervals('curve', k)
if k in list_curve_vertical:
volume_id = cubit.get_owning_volume("curve", k)
for idv in range(0, nvol):
if vol[idv].ID == volume_id:
int_v = vol[idv].intervalv
command = "curve " + str(k) + " interval " + str(int_v)
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
command = "curve " + str(k) + " scheme equal"
cubit.cmd(command)
# cubit_error_stop(iproc,command,ner)
else:
interval_store.append((k, interval_curve))
if len(interval_store) != 0:
interval_min = min([iv[1] for iv in interval_store])
str_interval = [str(iv[0]) for iv in interval_store]
cmd = "curve " + ' '.join(str_interval) + \
" interval " + str(interval_min)
cubit.cmd(cmd)
command = "curve " + \
' '.join(str(iv[0])
for iv in interval_store) + " scheme equal"
cubit.cmd(command)
command = "surface " + str(s) + " scheme submap"
cubit.cmd(command)
# meshing
if cfg.or_mesh_scheme == 'pave' or schemepave:
command = 'mesh surf ' + ' '.join(str(t) for t in top)
status = cubit_command_check(iproc, command, stop=True)
# cubit.cmd(command)
elif cfg.or_mesh_scheme == 'map':
command = 'mesh surf ' + ' '.join(str(t) for t in bottom)
status = cubit_command_check(iproc, command, stop=True)
# cubit.cmd(command)
for id_volume in range(nvol - 1, -1, -1):
command = "mesh vol " + str(vol[id_volume].ID)
status = cubit_command_check(iproc, command, stop=False)
if not status:
for s in surf_vertical:
command_surf = "mesh surf " + str(s)
cubit.cmd(command_surf)
if version_cubit < 16:
command_set_meshvol = '''volume all redistribute nodes on
volume all autosmooth target off
volume all scheme Sweep Vector 0 0 -1
volume all sweep smooth Auto
'''
else:
command_set_meshvol = '''volume all redistribute nodes on
volume all autosmooth target off
volume all scheme Sweep Vector 0 0 -1
'''
status2 = cubit_command_check(iproc,
command_set_meshvol,
stop=False)
status2 = cubit_command_check(iproc, command, stop=False)
if not status2:
_surf = cubit.get_relatives('volume', vol[id_volume].ID,
'surface')
local_o_surf = [x for x in _surf if x in surf_or]
cubit.cmd('volume ' + str(vol[id_volume].ID) +
' redistribute nodes off')
cubit.cmd('volume ' + str(vol[id_volume].ID) +
' scheme Sweep source surface ' +
' '.join(str(x) for x in local_o_surf[0:-1]) +
' target surface ' + str(local_o_surf[-1]))
cubit.cmd('volume ' + str(vol[id_volume].ID) +
' autosmooth_target off')
status = cubit_command_check(iproc, command, stop=True)
#
# smoothing
print iproc, 'untangling...'
cmd = "volume all smooth scheme untangle beta 0.02 cpu 10"
cubit.cmd(cmd)
cmd = "smooth volume all"
cubit.cmd(cmd)
if cfg.smoothing:
print 'smoothing .... ' + str(cfg.smoothing)
cubitcommand = 'surf all smooth scheme laplacian '
cubit.cmd(cubitcommand)
cubitcommand = 'smooth surf all'
cubit.cmd(cubitcommand)
#
cubitcommand = 'vol all smooth scheme laplacian '
cubit.cmd(cubitcommand)
cubitcommand = 'smooth vol all'
cubit.cmd(cubitcommand)
#
#
# vertical refinement
# for nvol = 3
##
# ___________________________ interface 4
##
# vol 2
# ___________________________ interface 3
##
# vol 1
# ___________________________ interface 2
##
# vol 0
# ___________________________ interface 1
##
refinement(nvol, vol, filename=filename)
#
# top layer vertical coarsening
print 'coarsening top layer... ', cfg.coarsening_top_layer
if cfg.coarsening_top_layer:
cubitcommand = 'del mesh vol ' + str(vol[-1].ID) + ' propagate'
cubit.cmd(cubitcommand)
s1 = Set(list_curve_vertical)
command = "group 'list_curve_tmp' add curve " + \
"in vol " + str(vol[-1].ID)
cubit.cmd(command)
group = cubit.get_id_from_name("list_curve_tmp")
list_curve_tmp = cubit.get_group_curves(group)
command = "delete group " + str(group)
cubit.cmd(command)
s2 = Set(list_curve_tmp)
lc = list(s1 & s2)
#
cubitcommand = 'curve ' + \
' '.join(str(x) for x in lc) + ' interval ' + \
str(cfg.actual_vertical_interval_top_layer)
cubit.cmd(cubitcommand)
cubitcommand = 'mesh vol ' + str(vol[-1].ID)
cubit.cmd(cubitcommand)
#
n = cubit.get_sideset_id_list()
if len(n) != 0:
command = "del sideset all"
cubit.cmd(command)
n = cubit.get_block_id_list()
if len(n) != 0:
command = "del block all"
cubit.cmd(command)
#
import boundary_definition
entities = ['face']
print iproc, 'hex block definition...'
boundary_definition.define_bc(entities,
parallel=True,
cpux=cfg.cpux,
cpuy=cfg.cpuy,
cpuxmin=0,
cpuymin=0,
optionsea=False)
# save mesh
print iproc, 'untangling...'
cmd = "volume all smooth scheme untangle beta 0.02 cpu 10"
cubit.cmd(cmd)
cmd = "smooth volume all"
cubit.cmd(cmd)
print iproc, 'saving...'
savemesh(mpiflag, iproc=iproc, filename=filename)
# topography file, data points per lon-increment
inputFile = 'ptopo.mean.utm'
# X coordinate in topography file repeats after line
nstep = 34
#############################################################
# converts xyz to utm
#os.system('./convert_lonlat2utm.pl ptopo.mean.xyz 10 > ptopo.mean.utm ')
# reads in points
print '#reading from file: ', inputFile
cubit.cmd('reset')
cubit.cmd('echo off')
cubit.cmd('Graphics Pause')
# creates point vertices
print '#creating points...'
count = 0
for line in fileinput.input(inputFile):
count = count + 1
#print '# '+str(count)+' point: '+line
lineitems = line.split()
x = lineitems[0]
y = lineitems[1]
z = lineitems[2]
xyz = str(x) + ' ' + str(y) + ' ' + str(z)
#print '#point: ',xyz
def layercake_volume_fromacis_mpiregularmap(filename=None):
import sys
import start as start
#
mpiflag,iproc,numproc,mpi = start.start_mpi()
#
cfg = start.start_cfg(filename=filename)
#
from utilities import geo2utm, savegeometry
#
from math import sqrt
#
try:
mpi.barrier()
except:
pass
#
#
command = "comment '"+"PROC: "+str(iproc)+"/"+str(numproc)+" '"
cubit.cmd(command)
#
#get the limit of the volume considering the cpu
def xwebcut(x):
command='create planar surface with plane xplane offset '+str(x)
cubit.cmd(command)
last_surface=cubit.get_last_id("surface")
command="webcut volume all tool volume in surf "+str(last_surface)
cubit.cmd(command)
command="del surf "+str(last_surface)
cubit.cmd(command)
def ywebcut(x):
command='create planar surface with plane yplane offset '+str(x)
cubit.cmd(command)
last_surface=cubit.get_last_id("surface")
command="webcut volume all tool volume in surf "+str(last_surface)
cubit.cmd(command)
command="del surf "+str(last_surface)
cubit.cmd(command)
def translate2zero():
ss=cubit.parse_cubit_list('surface','all')
box = cubit.get_total_bounding_box("surface", ss)
xmin=box[0]
ymin=box[3]
cubit.cmd('move surface all x '+str(-1*xmin)+' y '+str(-1*ymin))
return xmin,ymin
def translate2original(xmin,ymin):
cubit.cmd('move surface all x '+str(xmin)+' y '+str(ymin))
if mpiflag:
icpux = iproc % cfg.nproc_xi
icpuy = int(iproc / cfg.nproc_xi)
else:
icpuy=int(cfg.id_proc/cfg.nproc_xi)
icpux=cfg.id_proc%cfg.nproc_xi
#
ner=cubit.get_error_count()
#
icurve=0
isurf=0
ivertex=0
#
xlength=(cfg.xmax-cfg.xmin)/float(cfg.cpux) #length of x slide for chunk
ylength=(cfg.ymax-cfg.ymin)/float(cfg.cpuy) #length of y slide for chunk
xmin_cpu=cfg.xmin+(xlength*(icpux))
ymin_cpu=cfg.ymin+(ylength*(icpuy))
xmax_cpu=xmin_cpu+xlength
ymax_cpu=ymin_cpu+ylength
#
#importing the surfaces
for inz in range(cfg.nz-2,-2,-1):
if cfg.bottomflat and inz==-1:
command = "create planar surface with plane zplane offset "+str(cfg.depth_bottom)
cubit.cmd(command)
else:
command = "import cubit '"+cfg.filename[inz]+"'"
cubit.cmd(command)
#translate
xmin,ymin=translate2zero()
print 'translate ...', -xmin,-ymin
xmin_cpu=xmin_cpu-xmin
ymin_cpu=ymin_cpu-ymin
xmax_cpu=xmax_cpu-xmin
ymax_cpu=ymax_cpu-ymin
ss=cubit.parse_cubit_list('surface','all')
box = cubit.get_total_bounding_box("surface", ss)
print 'dimension... ', box
#cutting the surfaces
xwebcut(xmin_cpu)
xwebcut(xmax_cpu)
ywebcut(ymin_cpu)
ywebcut(ymax_cpu)
#
list_surface_all=cubit.parse_cubit_list("surface","all")
#condisidering only the surfaces inside the boundaries
dict_surf={}
for isurf in list_surface_all:
p=cubit.get_center_point("surface",isurf)
if p[0] < xmin_cpu or p[0] > xmax_cpu or p[1] > ymax_cpu or p[1] < ymin_cpu:
command = "del surf "+str(isurf)
cubit.cmd(command)
else:
dict_surf[str(isurf)]=p[2]
z=dict_surf.values()
z.sort()
list_surf=[]
for val in z:
isurf=[k for k, v in dict_surf.iteritems() if v == val][0]
list_surf.append(int(isurf))
#
#lofting the volume
for i,j in zip(list_surf,list_surf[1:]):
ner=cubit.get_error_count()
create_volume(i,j,method=cfg.volumecreation_method)
#cubitcommand= 'create volume loft surface '+ str(i)+' '+str(j)
#cubit.cmd(cubitcommand)
ner2=cubit.get_error_count()
#
translate2original(xmin,ymin)
if ner == ner2:
cubitcommand= 'del surface all'
cubit.cmd(cubitcommand)
#
#
#cubitcommand= 'composite create curve in vol all'
#cubit.cmd(cubitcommand)
list_vol=cubit.parse_cubit_list("volume","all")
if len(list_vol) > 1:
cubitcommand= 'imprint volume all'
cubit.cmd(cubitcommand)
#cubit_error_stop(iproc,cubitcommand,ner)
#
cubitcommand= 'merge all'
cubit.cmd(cubitcommand)
#
savegeometry(iproc,filename=filename)
def translate2original(xmin,ymin):
cubit.cmd('move surface all x '+str(xmin)+' y '+str(ymin))
def main():
import os
import os.path
import numpy as np
import pymef90
import shutil
parser = LCSS.createParser()
options = pymef90.parse(parser, key='configfile')
Geometry = pymef90.parseGroup(parser, options, 'Geometry')
str = repr(Geometry).encode("utf-8")
options.hash = hashlib.sha1(str).hexdigest()
D = options.__dict__
D['dt'] = (options.time_max - options.time_min) / (
options.time_numstep - 1) / options.time_numsubstep
options.__dict__ = pymef90.PrepareJob(Geometry, options.__dict__)
print(options)
scriptpath = os.path.dirname(os.path.abspath(__file__))
###
### Search for the mesh file, and generate it if it is missing
###
archmeshprefix = os.path.join(options.meshdir, options.hash)
if not os.path.isfile(archmeshprefix + '.gen') or options.forcemesh:
if options.dontmesh:
print('Cannot find mesh, exiting')
return -1
else:
print('{0}.gen not found: generating new mesh'.format(
archmeshprefix))
if not os.path.exists(options.meshdir):
os.makedirs(options.meshdir)
ext = os.path.splitext(options.geofile)[-1][1:].lower()
if ext == 'geo':
pymef90.argsWrite(
options.geofile,
os.path.join(options.meshdir, options.hash + '.geo'),
options.__dict__)
os.chdir(options.meshdir)
cmd = 'gmsh -2 -format msh2 -order {order} {hash}.geo'.format(
**options.__dict__)
print("Now running {0}".format(cmd))
os.system(cmd)
cmd = 'gmsh2exo.py --force {hash}.msh {hash}.gen'.format(
**options.__dict__)
print("Now running {0}".format(cmd))
os.system(cmd)
elif ext == 'jou':
pymef90.argsWrite(
options.geofile,
os.path.join(options.meshdir, options.hash + '.jou'),
options.__dict__)
os.chdir(options.meshdir)
journal = open(
os.path.join(options.meshdir, options.hash + '.jou'))
import cubit
cubit.init([''])
for l in journal.readlines():
cubit.cmd(l)
cubit.cmd('set exodus netcdf4 off')
cubit.cmd('set large exodus file on')
cubit.cmd('set journal off')
cubit.cmd(
'export mesh "{0}.gen" dimension 2 overwrite '.format(
os.path.join(options.meshdir, options.hash)))
else:
print(
"unknown geometry file format {0}. Unable to generate mesh"
.format(options.geofile))
else:
print("Found matching mesh at {0}".format(archmeshprefix))
###
### Create computation directory
###
if options.meshonly:
return 0
###
### Write 00_INFO.txt and 00_INFO.json
###
if not os.path.exists(options.workdir):
os.makedirs(options.workdir)
os.chdir(options.workdir)
#pymef90.Dictwritetxt(options.__dict__,'00_INFO.txt',overwrite=False)
pymef90.DictwriteJSON(options.__dict__, '00_INFO.json', overwrite=True)
shutil.copyfile(archmeshprefix + '.gen',
os.path.join(options.workdir, options.prefix + '.gen'))
###
### Prepare vDef yaml options file
####
pymef90.argsWrite(options.yamlfile,
os.path.join(options.workdir, options.prefix + '.yaml'),
options.__dict__)
### Generate heat flux in output file
# find the flux script within the path and pythonpath
for binpath in sys.path + os.getenv('PATH').split(':'):
if os.path.exists(os.path.join(binpath, "LCSS_flux3.py")):
break
cmd = '{0} -i {prefix}.gen -o {prefix}_out.gen --cs 1 2 --force --initialPos {initialPos[0]} {initialPos[1]} {initialPos[2]} --finalPos {finalPos[0]} {finalPos[1]} {finalPos[2]} --r0 {criticalRadius} --Wabs {intensity} --time_min {time_min} --time_max {time_max} --time_numstep {time_numstep}'.format(
os.path.join(binpath, 'LCSS_flux3.py'), **options.__dict__)
print('Now running: {0}'.format(cmd))
os.system(cmd)
### Run the computation
if os.path.isfile(
os.path.join(os.getenv("MEF90_DIR"), "bin",
os.getenv("PETSC_ARCH"), "vDef")):
bin = os.path.join(os.getenv("MEF90_DIR"), "bin",
os.getenv("PETSC_ARCH"), "vDef")
else:
print('Cannot find binary for vDef')
sys.exit(-1)
if options.mpiexec == 'mpirun':
options.mpiexec += ' -machinefile {0}'.format(
os.getenv("PBS_NODEFILE"))
cmd1 = options.mpiexec + ' {0:s} -prefix {prefix:s} -options_file_yaml {prefix:s}.yaml '.format(
bin, **options.__dict__)
if options.extraopts:
cmd1 += options.extraopts
if options.hypre:
cmd1 += ' -disp_pc_type hypre -disp_pc_hypre_type boomeramg -disp_pc_hypre_boomeramg_strong_threshold 0.9 '
if options.ml:
cmd1 += ' -disp_pc_type ml'
#if options.unilateralcontact == 'none':
# cmd1 += ' -disp_snes_type ksponly'
#cmd1 += ' -temp_ksp_monitor_true_residual -temp_ksp_converged_reason'
cmd1 += ' -disp_snes_monitor -disp_ksp_converged_reason'
print("Now running: {0}".format(cmd1))
os.system(cmd1)
if options.postprocess:
cmd = 'ml visit; visit -cli -nowin -s {0} --output {1}.png {1}_out.gen;'.format(
os.path.join(binpath, "LCSS_PNG.py"), options.prefix)
print('now running: {0}'.format(cmd))
os.system(cmd)
cmd = 'ml visit; visit -cli -nowin -s {0} --output {1}_disp.png --displacementScaling 1 {1}_out.gen;'.format(
os.path.join(binpath, "LCSS_PNG.py"), options.prefix)
print('now running: {0}'.format(cmd))
os.system(cmd)
def layercake_volume_ascii_regulargrid_mpiregularmap(filename=None,verticalsandwich=False,onlysurface=False):
import sys
import start as start
#
mpiflag,iproc,numproc,mpi = start.start_mpi()
#
numpy = start.start_numpy()
cfg = start.start_cfg(filename=filename)
from utilities import geo2utm, savegeometry,savesurf,cubit_command_check
from math import sqrt
#
try:
mpi.barrier()
except:
pass
#
#
command = "comment '"+"PROC: "+str(iproc)+"/"+str(numproc)+" '"
cubit_command_check(iproc,command,stop=True)
if verticalsandwich: cubit.cmd("comment 'Starting Vertical Sandwich'")
#
#get icpuy,icpux values
if mpiflag:
icpux = iproc % cfg.nproc_xi
icpuy = int(iproc / cfg.nproc_xi)
else:
icpuy=int(cfg.id_proc/cfg.nproc_xi)
icpux=cfg.id_proc%cfg.nproc_xi
#
if cfg.geometry_format == 'ascii':
#for the original surfaces
#number of points in the files that describe the topography
import local_volume
if cfg.localdir_is_globaldir:
if iproc == 0 or not mpiflag:
coordx_0,coordy_0,elev_0,nx_0,ny_0=local_volume.read_grid(filename)
print 'end of reading grd files '+str(nx_0*ny_0)+ ' points'
else:
pass
if iproc == 0 or not mpiflag:
coordx=mpi.bcast(coordx_0)
else:
coordx=mpi.bcast()
if iproc == 0 or not mpiflag:
coordy=mpi.bcast(coordy_0)
else:
coordy=mpi.bcast()
if iproc == 0 or not mpiflag:
elev=mpi.bcast(elev_0)
else:
elev=mpi.bcast()
if iproc == 0 or not mpiflag:
nx=mpi.bcast(nx_0)
else:
nx=mpi.bcast()
if iproc == 0 or not mpiflag:
ny=mpi.bcast(ny_0)
else:
ny=mpi.bcast()
else:
coordx,coordy,elev,nx,ny=local_volume.read_grid(filename)
print str(iproc)+ ' end of receving grd files '
nx_segment=int(nx/cfg.nproc_xi)+1
ny_segment=int(ny/cfg.nproc_eta)+1
elif cfg.geometry_format=='regmesh': # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
if cfg.depth_bottom != cfg.zdepth[0]:
if iproc == 0: print 'the bottom of the block is at different depth than depth[0] in the configuration file'
nx= cfg.nproc_xi+1
ny= cfg.nproc_eta+1
nx_segment=2
ny_segment=2
#if iproc == 0: print nx,ny,cfg.cpux,cfg.cpuy
xp=(cfg.xmax-cfg.xmin)/float((nx-1))
yp=(cfg.ymax-cfg.ymin)/float((ny-1))
#
if verticalsandwich:
elev=numpy.zeros([nx,ny,cfg.nxvol],float)
else:
elev=numpy.zeros([nx,ny,cfg.nz],float)
coordx=numpy.zeros([nx,ny],float)
coordy=numpy.zeros([nx,ny],float)
#
#
xlength=(cfg.xmax-cfg.xmin)/float(cfg.nproc_xi) #length of x slide for chunk
ylength=(cfg.ymax-cfg.ymin)/float(cfg.nproc_eta) #length of y slide for chunk
nelem_chunk_x=1
nelem_chunk_y=1
ivxtot=nelem_chunk_x+1
ivytot=nelem_chunk_y+1
xstep=xlength #distance between vertex on x
ystep=ylength
if verticalsandwich:
for i in range(0,cfg.nxvol):
elev[:,:,i] = cfg.xwidth[i]
else:
for i in range(0,cfg.nz):
elev[:,:,i] = cfg.zdepth[i]
icoord=0
for iy in range(0,ny):
for ix in range(0,nx):
icoord=icoord+1
coordx[ix,iy]=cfg.xmin+xlength*(ix)
coordy[ix,iy]=cfg.ymin+ylength*(iy)
#print coordx,coordy,nx,ny
#
print 'end of building grid '+str(iproc)
print 'number of point: ', len(coordx)*len(coordy)
#
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
#for each processor
#
nxmin_cpu=(nx_segment-1)*(icpux)
nymin_cpu=(ny_segment-1)*(icpuy)
nxmax_cpu=min(nx-1,(nx_segment-1)*(icpux+1))
nymax_cpu=min(ny-1,(ny_segment-1)*(icpuy+1))
#if iproc == 0:
# print nx_segment,ny_segment,nx,ny
# print icpux,icpuy,nxmin_cpu,nxmax_cpu
# print icpux,icpuy,nymin_cpu,nymax_cpu
# print coordx[0,0],coordx[nx-1,ny-1]
# print coordy[0,0],coordy[nx-1,ny-1]
#
#
icurve=0
isurf=0
ivertex=0
#
#create vertex
if verticalsandwich:
nlayer=cfg.nxvol
else:
nlayer=cfg.nz
for inz in range(0,nlayer):
if cfg.sea and inz==cfg.nz-1: #sea layer
sealevel=True
bathymetry=False
elif cfg.sea and inz==cfg.nz-2: #bathymetry layer
sealevel=False
bathymetry=True
else:
sealevel=False
bathymetry=False
print sealevel,bathymetry
if cfg.bottomflat and inz == 0: #bottom layer
#
if cfg.geometry_format == 'ascii' and not verticalsandwich:
lv=cubit.get_last_id("vertex")
x_current,y_current=(coordx[nxmin_cpu,nymin_cpu],coordy[nxmin_cpu,nymin_cpu])
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=(coordx[nxmin_cpu,nymax_cpu],coordy[nxmin_cpu,nymax_cpu])
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=(coordx[nxmax_cpu,nymax_cpu],coordy[nxmax_cpu,nymax_cpu])
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=(coordx[nxmax_cpu,nymin_cpu],coordy[nxmax_cpu,nymin_cpu])
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
lv2=cubit.get_last_id("vertex")
cubitcommand= 'create surface vertex '+str(lv+1)+' to '+str(lv2)
cubit.cmd(cubitcommand)
#
isurf = isurf + 1
else:
lv=cubit.get_last_id("vertex")
x_current,y_current=geo2utm(coordx[nxmin_cpu,nymin_cpu],coordy[nxmin_cpu,nymin_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmin_cpu,nymax_cpu],coordy[nxmin_cpu,nymax_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
if verticalsandwich:
x_current,y_current=geo2utm(coordx[nxmin_cpu,nymax_cpu],coordy[nxmin_cpu,nymax_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( 0 )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmin_cpu,nymin_cpu],coordy[nxmin_cpu,nymin_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( 0 )
cubit.cmd(cubitcommand)
else:
x_current,y_current=geo2utm(coordx[nxmax_cpu,nymax_cpu],coordy[nxmax_cpu,nymax_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmax_cpu,nymin_cpu],coordy[nxmax_cpu,nymin_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
lv2=cubit.get_last_id("vertex")
cubitcommand= 'create surface vertex '+str(lv+1)+' to '+str(lv2)
cubit.cmd(cubitcommand)
#
isurf = isurf + 1
else:
if cfg.geometry_format == 'regmesh':
if verticalsandwich:
zvertex=cfg.xwidth[inz]
lv=cubit.get_last_id("vertex")
x_current,y_current=geo2utm(coordx[nxmax_cpu,nymin_cpu],coordy[nxmax_cpu,nymin_cpu],'utm')
x_current = x_current + zvertex;
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmax_cpu,nymax_cpu],coordy[nxmax_cpu,nymax_cpu],'utm')
x_current = x_current + zvertex;
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( cfg.depth_bottom )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmax_cpu,nymax_cpu],coordy[nxmax_cpu,nymax_cpu],'utm')
x_current = x_current + zvertex;
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( 0 )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmax_cpu,nymin_cpu],coordy[nxmax_cpu,nymin_cpu],'utm')
x_current = x_current + zvertex;
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( 0 )
cubit.cmd(cubitcommand)
else:
zvertex=cfg.zdepth[inz]
lv=cubit.get_last_id("vertex")
x_current,y_current=geo2utm(coordx[nxmin_cpu,nymin_cpu],coordy[nxmin_cpu,nymin_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( zvertex )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmin_cpu,nymax_cpu],coordy[nxmin_cpu,nymax_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( zvertex )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmax_cpu,nymax_cpu],coordy[nxmax_cpu,nymax_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( zvertex )
cubit.cmd(cubitcommand)
#
x_current,y_current=geo2utm(coordx[nxmax_cpu,nymin_cpu],coordy[nxmax_cpu,nymin_cpu],'utm')
cubitcommand= 'create vertex '+ str( x_current )+ ' ' + str( y_current) +' '+ str( zvertex )
cubit.cmd(cubitcommand)
#
cubitcommand= 'create surface vertex '+str(lv+1)+' '+str(lv+2)+' '+str(lv+3)+' '+str(lv+4)
cubit.cmd(cubitcommand)
#
isurf = isurf + 1
elif cfg.geometry_format == 'ascii':
vertex=[]
for iy in range(nymin_cpu,nymax_cpu+1):
ivx=0
for ix in range(nxmin_cpu,nxmax_cpu+1):
zvertex=elev[ix,iy,inz]
#zvertex=adjust_sea_layers(zvertex,sealevel,bathymetry,cfg)
x_current,y_current=(coordx[ix,iy],coordy[ix,iy])
#
vertex.append(' Position '+ str( x_current ) +' '+ str( y_current )+' '+ str( zvertex ) )
#
print 'proc',iproc, 'vertex list created....',len(vertex)
n=max(nx,ny)
uline=[]
vline=[]
iv=0
cubit.cmd("set info off")
cubit.cmd("set echo off")
cubit.cmd("set journal off")
for iy in range(0,nymax_cpu-nymin_cpu+1):
positionx=''
for ix in range(0,nxmax_cpu-nxmin_cpu+1):
positionx=positionx+vertex[iv]
iv=iv+1
command='create curve spline '+positionx
cubit.cmd(command)
#print command
uline.append( cubit.get_last_id("curve") )
for ix in range(0,nxmax_cpu-nxmin_cpu+1):
positiony=''
for iy in range(0,nymax_cpu-nymin_cpu+1):
positiony=positiony+vertex[ix+iy*(nxmax_cpu-nxmin_cpu+1)]
command='create curve spline '+positiony
cubit.cmd(command)
#print command
vline.append( cubit.get_last_id("curve") )
#
cubit.cmd("set info "+cfg.cubit_info)
cubit.cmd("set echo "+cfg.echo_info)
cubit.cmd("set journal "+cfg.jou_info)
#
#
print 'proc',iproc, 'lines created....',len(uline),'*',len(vline)
umax=max(uline)
umin=min(uline)
vmax=max(vline)
vmin=min(vline)
ner=cubit.get_error_count()
cubitcommand= 'create surface net u curve '+ str( umin )+' to '+str( umax )+ ' v curve '+ str( vmin )+ ' to '+str( vmax )+' heal'
cubit.cmd(cubitcommand)
ner2=cubit.get_error_count()
if ner == ner2:
command = "del curve all"
cubit.cmd(command)
isurf=isurf+1
#
else:
raise NameError, 'error, check geometry_format, it should be ascii or regmesh' #
#
cubitcommand= 'del vertex all'
cubit.cmd(cubitcommand)
if cfg.save_surface_cubit:
savegeometry(iproc=iproc,surf=True,filename=filename)
#
#
#!create volume
if not onlysurface:
if nlayer == 1:
nsurface=2
else:
nsurface=nlayer
for inz in range(1,nsurface):
ner=cubit.get_error_count()
create_volume(inz,inz+1,method=cfg.volumecreation_method)
ner2=cubit.get_error_count()
if ner == ner2 and not cfg.debug_geometry:
#cubitcommand= 'del surface 1 to '+ str( cfg.nz )
cubitcommand= 'del surface all'
cubit.cmd(cubitcommand)
list_vol=cubit.parse_cubit_list("volume","all")
for v in list_vol:
sv=cubit.get_relatives("volume",v,"surface")
if len(sv) <=1: cubit.cmd("del vol "+str(v))
list_vol=cubit.parse_cubit_list("volume","all")
if len(list_vol) > 1:
cubitcommand= 'imprint volume all'
cubit.cmd(cubitcommand)
cubitcommand= 'merge all'
cubit.cmd(cubitcommand)
#ner=cubit.get_error_count()
#cubitcommand= 'composite create curve in vol all'
#cubit.cmd(cubitcommand)
savegeometry(iproc,filename=filename)
#if cfg.geological_imprint:
# curvesname=[cfg.outlinebasin_curve,cfg.transition_curve,cfg.faulttrace_curve]
# outdir=cfg.working_dir
# imprint_topography_with_geological_outline(curvesname,outdir)
#
#
cubit.cmd("set info "+cfg.cubit_info)
cubit.cmd("set echo "+cfg.echo_info)
cubit.cmd("set journal "+cfg.jou_info)
def define_absorbing_surf_nopar():
"""
define the absorbing surfaces for a layered topological box where boundary surfaces are not parallel to the axis.
it returns absorbing_surf,topo_surf
where
absorbing_surf is the list of all the absorbing boundary surf
"""
try:
cubit.cmd('comment')
except:
try:
import cubit
cubit.init([""])
except:
print 'error importing cubit'
import sys
sys.exit()
from sets import Set
def product(*args, **kwds):
# product('ABCD', 'xy') --> Ax Ay Bx By Cx Cy Dx Dy
# product(range(2), repeat=3) --> 000 001 010 011 100 101 110 111
pools = map(tuple, args) * kwds.get('repeat', 1)
result = [[]]
for pool in pools:
result = [x + [y] for x in result for y in pool]
return result
absorbing_surf = []
absorbing_surf_xmin = []
absorbing_surf_xmax = []
absorbing_surf_ymin = []
absorbing_surf_ymax = []
absorbing_surf_bottom = []
top_surf = []
list_vol = cubit.parse_cubit_list("volume", "all")
init_n_vol = len(list_vol)
zmax_box = cubit.get_total_bounding_box("volume", list_vol)[7]
zmin_box = cubit.get_total_bounding_box(
"volume", list_vol
)[6] #it is the z_min of the box ... box= xmin,xmax,d,ymin,ymax,d,zmin...
xmin_box = cubit.get_total_bounding_box("volume", list_vol)[0]
xmax_box = cubit.get_total_bounding_box("volume", list_vol)[1]
ymin_box = cubit.get_total_bounding_box("volume", list_vol)[3]
ymax_box = cubit.get_total_bounding_box("volume", list_vol)[4]
list_surf = cubit.parse_cubit_list("surface", "all")
lv = []
for k in list_surf:
sbox = cubit.get_bounding_box('surface', k)
dzmax = abs((sbox[7] - zmax_box) / zmax_box)
dzmin = abs((sbox[6] - zmin_box) / zmin_box)
normal = cubit.get_surface_normal(k)
zn = normal[2]
if dzmax <= 0.001 and zn > 0.7:
top_surf.append(k)
list_vertex = cubit.get_relatives('surface', k, 'vertex')
for v in list_vertex:
valence = cubit.get_valence(v)
if valence <= 4: #valence 3 is a corner, 4 is a vertex between 2 volumes, > 4 is a vertex not in the boundaries
lv.append(v)
elif dzmin <= 0.001 and zn < -0.7:
absorbing_surf.append(k)
lp = []
combs = product(lv, lv)
for comb in combs:
v1 = comb[0]
v2 = comb[1]
c = Set(cubit.get_relatives("vertex", v1, "curve")) & Set(
cubit.get_relatives("vertex", v2, "curve"))
if len(c) == 1:
p = cubit.get_center_point("curve", list(c)[0])
lp.append(p)
for k in list_surf:
center_point = cubit.get_center_point("surface", k)
for p in lp:
if abs((center_point[0] - p[0]) / p[0]) <= 0.005 and abs(
(center_point[1] - p[1]) / p[1]) <= 0.005:
absorbing_surf.append(k)
break
return absorbing_surf, top_surf
#!/usr/bin/env python
import cubit
cubit.init([""])
import os
import sys
# Creating the volumes
cubit.cmd('reset')
cubit.cmd('brick x 134000 y 134000 z 60000')
cubit.cmd('volume 1 move x 67000 y 67000 z -30000')
# Meshing the volumes
elementsize = 3750.0
cubit.cmd('volume 1 size '+str(elementsize))
cubit.cmd('mesh volume 1')
#
# GEOCUBIT
#
# adds path to geocubit (if not setup yet)
sys.path.append('../../CUBIT_GEOCUBIT/')
print "path: "
print sys.path
print ""
def surface_regular_grid(isurface=0, cfgname=None):
"""
create an acis surface from a regular lon/lat/z grid
"""
from utilities import geo2utm
import start as start
#
#
cfg = start.start_cfg(cfgname)
numpy = start.start_numpy()
#
def create_line_u(ind, n, 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[i + ind][0], data[i + ind][1], data[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 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
#
#
cubit.cmd("reset")
#
#
#
nu = cfg.num_x[isurface]
nv = cfg.num_y[isurface]
ustep = cfg.xstep[isurface]
vstep = cfg.ystep[isurface]
unit = cfg.unit2[isurface]
#
#
data = numpy.loadtxt(cfg.surface_name[isurface])
if len(data) > 100:
command = "set echo off"
cubit.cmd(command)
command = "set journal off"
cubit.cmd(command)
#
u_curve = []
v_curve = []
#
for iv in range(0, nv):
if iv % vstep == 0.:
u = create_line_u(iv * (nu), nu, ustep, data, unit)
u_curve.append(u)
for iu in range(0, nu):
if iu % ustep == 0.:
v = create_line_v(iu, nv, nu, ustep, data, unit)
v_curve.append(v)
#
umax = max(u_curve)
umin = min(u_curve)
vmax = max(v_curve)
vmin = min(v_curve)
cubitcommand = 'create surface net u curve ' + \
str(umin) + ' to ' + str(umax) + ' v curve ' + \
str(vmin) + ' to ' + str(vmax) + ' heal'
cubit.cmd(cubitcommand)
command = "del curve all"
cubit.cmd(command)
suff = cfg.surface_name[isurface].split('/')
command = "save as '" + cfg.working_dir + \
"/surf_" + suff[-1] + ".cub' overwrite"
cubit.cmd(command)
#
#
#
cubit.cmd("set info " + cfg.cubit_info)
cubit.cmd("set echo " + cfg.echo_info)
cubit.cmd("set journal " + cfg.jou_info)
def save_geometry(export_path):
cubit.cmd("set attribute on")
cubit.cmd("export acis '" + export_path + ".sat' overwrite")
def surface_skin(isurface=0, cfgname=None):
"""
create an acis surface interpolating no-intersecting lines
"""
import start as start
#
#
cubit = start.start_cubit()
cfg = start.start_cfg(cfgname)
#
def define_next_line(directionx, directiony, n, data):
ndata = len(data)
command = ''
ind = n
try:
record = data[ind]
except:
return False, False
try:
x, y, z = map(float, record.split())
except:
return False, False
txt = ' Position ' + record
command = command + txt
x_store, y_store, z_store = x, y, z
icount = 1
while True:
ind += 1
if ind >= ndata:
return ind, command
record = data[ind]
try:
x, y, z = map(float, record.split())
except:
return ind, command
dx, dy = x - x_store, y - y_store
if directionx == 0 and dy / abs(dy) * directiony >= 0:
txt = ' Position ' + record
command = command + txt
icount += 1
x_store, y_store, z_store = x, y, z
elif directiony == 0 and dx / abs(dx) == directionx:
txt = ' Position ' + record
command = command + txt
icount += 1
x_store, y_store, z_store = x, y, z
else:
if icount == 1:
x, y, z = x_store + 1e-4 * directionx, y_store + 1e-4 * \
directiony, z_store
txt = ' Position ' + str(x) + ' ' + str(y) + ' ' + str(z)
command = command + txt
return ind, command
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
command = "reset"
cubit.cmd(command)
#
position = True
#
try:
grdfile = open(cfg.surface_name[isurface], 'r')
except:
raise NameError('No such file or directory: ' +
str(cfg.surface_name[isurface]))
directionx = cfg.directionx[isurface]
directiony = cfg.directiony[isurface]
step = cfg.step[isurface]
position = True
curveskin = []
data = grdfile.read().split('\n')
n = 0
#
#
command = "set echo off"
cubit.cmd(command)
command = "set journal off"
cubit.cmd(command)
command = "set info off"
cubit.cmd(command)
#
while position:
index, position = define_next_line(directionx, directiony, n, data)
if n % step == 0:
curve = create_line(position)
if curve:
curveskin.append(curve)
elif n % step != 0 and not position:
curve = create_line(position)
if curve:
curveskin.append(curve)
n = index
umax = max(curveskin)
umin = min(curveskin)
print('create surface skin curve ' + str(umin) + ' to ' + str(umax))
cubitcommand = 'create surface skin curve ' + \
str(umin) + ' to ' + str(umax)
cubit.cmd(cubitcommand)
command = "del curve all"
cubit.cmd(command)
last_surface = cubit.get_last_id("surface")
command = "regularize surf " + str(last_surface)
cubit.cmd(command)
#
suff = cfg.surface_name[isurface].split('/')
command = "save as '" + cfg.working_dir + \
"/surf_" + suff[-1] + ".cub' overwrite"
cubit.cmd(command)
#
#
#
cubit.cmd("set info " + cfg.cubit_info)
cubit.cmd("set echo " + cfg.echo_info)
cubit.cmd("set journal " + cfg.jou_info)
def define_top_bottom_absorbing_surf(zmin_box, zmax_box):
"""
absorbing_surf_bottom is the list of the absorbing boundary surfaces that correspond to z=zmin
"""
try:
cubit.cmd('comment')
except:
try:
import cubit
cubit.init([""])
except:
print 'error importing cubit'
import sys
sys.exit()
absorbing_surf_bottom = []
top_surf = []
list_vol = cubit.parse_cubit_list("volume", "all")
init_n_vol = len(list_vol)
# TO DO : Make zmin_box work properly.
# zmax_box=cubit.get_total_bounding_box("volume",list_vol)[7]
# zmin_box=cubit.get_total_bounding_box("volume",list_vol)[6] #it is the z_min of the box ... box= xmin,xmax,d,ymin,ymax,d,zmin...
xmin_box = cubit.get_total_bounding_box("volume", list_vol)[0]
xmax_box = cubit.get_total_bounding_box("volume", list_vol)[1]
ymin_box = cubit.get_total_bounding_box("volume", list_vol)[3]
ymax_box = cubit.get_total_bounding_box("volume", list_vol)[4]
list_surf = cubit.parse_cubit_list("surface", "all")
print '##boundary box: '
print '## x min: ' + str(xmin_box)
print '## y min: ' + str(ymin_box)
print '## z min: ' + str(zmin_box)
print '## x max: ' + str(xmax_box)
print '## y max: ' + str(ymax_box)
print '## z max: ' + str(zmax_box)
#box lengths
x_len = abs(xmax_box - xmin_box)
y_len = abs(ymax_box - ymin_box)
z_len = abs(zmax_box - zmin_box)
print '##boundary box: '
print '## x length: ' + str(x_len)
print '## y length: ' + str(y_len)
print '## z length: ' + str(z_len)
# tolerance parameters
absorbing_surface_distance_tolerance = 0.005
topographic_surface_distance_tolerance = 0.001
topographic_surface_normal_tolerance = 0.2
for k in list_surf:
center_point = cubit.get_center_point("surface", k)
if abs((center_point[2] - zmin_box) /
z_len) <= absorbing_surface_distance_tolerance:
print 'center_point[2]' + str(center_point[2])
print 'kz:' + str(k)
absorbing_surf_bottom.append(k)
else:
sbox = cubit.get_bounding_box('surface', k)
dz = abs((sbox[7] - zmax_box) / z_len)
normal = cubit.get_surface_normal(k)
zn = normal[2]
dn = abs(zn - 1)
if dz <= topographic_surface_distance_tolerance and dn < topographic_surface_normal_tolerance:
top_surf.append(k)
return absorbing_surf_bottom, top_surf
def PacmanCreate(lx, ly, lz, thetacrack):
import cubit
import numpy as np
###
### Create Main body
###
cubit.cmd("Create cylinder height %f major radius %f minor radius %f" %
(lz, lx, ly))
CYL = cubit.get_last_id("volume")
###
### Create wedge
###
w_ID = []
cubit.cmd("create vertex X 0 Y 0 Z %f" % (-lz))
w_ID.append(cubit.get_last_id("vertex"))
X = 1.1 * np.max(lx, ly) * np.cos(np.radians(thetacrack / 2.))
Y = 1.1 * np.max(lx, ly) * np.sin(np.radians(thetacrack / 2.))
cubit.cmd("create vertex X %f Y %f Z %f" % (-X, Y, -lz))
w_ID.append(cubit.get_last_id("vertex"))
cubit.cmd("create vertex X %f Y %f Z %f" % (-X, -Y, -lz))
w_ID.append(cubit.get_last_id("vertex"))
cubit.cmd("create surface vertex %i %i %i" % (w_ID[0], w_ID[1], w_ID[2]))
cubit.cmd("sweep surface %i perpendicular distance %f" %
(cubit.get_last_id("surface"), 2 * lz))
WEDGE = cubit.get_last_id("volume")
###
### remove crack
###
cubit.cmd("subtract volume %i from volume %i" % (WEDGE, CYL))
###
### Return the ID of the cylinder
###
return CYL
def plane(cfg):
from utilities import geo2utm
import start as start
#
#
cubit = start.start_cubit()
#
#
command = "reset"
cubit.cmd(command)
#
#
for p in [cfg.x1, cfg.x2, cfg.x3, cfg.x4]:
x_current, y_current = geo2utm(p[0], p[1], cfg.unit)
cubitcommand = 'create vertex ' + \
str(x_current) + ' ' + str(y_current) + ' ' + str(p[2])
cubit.cmd(cubitcommand)
#
cubitcommand = 'create surface vertex 1 2 3 4'
cubit.cmd(cubitcommand)
command = "del vertex all"
cubit.cmd(command)
command = "save as 'plane.cub' overwrite"
cubit.cmd(command)
#
#
#
cubit.cmd("set info " + cfg.cubit_info)
cubit.cmd("set echo " + cfg.echo_info)
cubit.cmd("set journal " + cfg.jou_info)
def refine_inside_curve(curves, ntimes=1, depth=1, block=1, surface=False):
sflag = surface
if not isinstance(curves, list):
if isinstance(curves, str):
curves = map(int, curves.split())
else:
curves = [curves]
for curve in curves:
cubit.cmd('del group ntop')
if not surface:
cubit.cmd("group 'ntop' add node in face in block " + str(block))
else:
cubit.cmd("group 'ntop' add node in face in surface " + str(sflag))
group1 = cubit.get_id_from_name("ntop")
nodes = list(cubit.get_group_nodes(group1))
ni = get_nodes_inside_curve(nodes, curve)
if ntimes > 1:
cmd = 'del group hex_ref'
cubit.cmd(cmd)
command = "group 'hex_ref' add hex propagate face in node " +\
' '.join(str(x) for x in ni) + "times " + str(ntimes)
cubit.cmd(command)
# id_group = cubit.get_id_from_name('hex_ref')
cmd = 'refine hex in group "hex_ref" numsplit 1 bias 1 depth ' + \
str(depth) + ' smooth'
cubit.cmd(cmd)
else:
command = 'refine node ' + \
" ".join(str(x) for x in ni) + \
' numsplit 1 bias 1.0 depth ' + str(depth) + ' smooth'
cubit.cmd(command)
#
#
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 refining'
os.system('mkdir -p '+ SEMoutput)
os.system('mkdir -p '+ CUBIToutput)
import cubit
try:
#cubit.init([""])
cubit.init(["-noecho","-nojournal"])
except:
pass
version = cubit.get_version()
version_major = int(version.split(".")[0])
version_minor = int(version.split(".")[1])
print "cubit version: ",version
cubit.cmd('reset')
cubit.cmd('brick x 134000 y 134000 z 60000')
# This seems to conflict with boundary_definition.py
# ....which leaves the model space at e.g. x=[-67,67] km
cubit.cmd('volume 1 move x 67000 y 67000 z -30000')
# create vertices for discontinuity
cubit.cmd('split curve 9 distance 3000')
cubit.cmd('split curve 10 distance 3000')
cubit.cmd('split curve 11 distance 3000')
cubit.cmd('split curve 12 distance 3000')
# create surface for interface
cubit.cmd('create surface vertex 9 10 12 11')
def curve2poly(line):
curve = int(line)
cubit.cmd('curve ' + str(curve) + ' size auto factor 1')
cubit.cmd('mesh curve ' + str(curve))
n = cubit.get_curve_nodes(curve)
orientnode = []
vertex_list = cubit.get_relatives("curve", curve, "vertex")
if len(vertex_list) != 0:
startnode = cubit.get_vertex_node(vertex_list[0])
cubit.cmd('del group pgon')
cubit.cmd("group 'pgon' add edge in node " + str(startnode))
group1 = cubit.get_id_from_name("pgon")
edges = list(cubit.get_group_edges(group1))
edgestart = edges[0]
else:
startnode = n[0]
cubit.cmd('del group pgon')
cubit.cmd("group 'pgon' add edge in node " + str(startnode))
group1 = cubit.get_id_from_name("pgon")
edges = list(cubit.get_group_edges(group1))
edgestart = edges[0]
begin = startnode
orientnode.append(begin)
node_id_list = list(cubit.get_connectivity("edge", edgestart))
node_id_list.remove(startnode)
startnode = node_id_list[0]
orientnode.append(startnode)
stopflag = False
while startnode != begin and not stopflag:
cubit.cmd('del group pgon')
cubit.cmd("group 'pgon' add edge in node " + str(startnode))
group1 = cubit.get_id_from_name("pgon")
edges = list(cubit.get_group_edges(group1))
if len(edges) != 1:
edges.remove(edgestart)
edgestart = edges[0]
node_id_list = list(cubit.get_connectivity("edge", edgestart))
node_id_list.remove(startnode)
orientnode.append(node_id_list[0])
startnode = node_id_list[0]
else:
stopflag = True
vx = []
vy = []
for n in orientnode:
v = cubit.get_nodal_coordinates(n)
vx.append(v[0])
vy.append(v[1])
return vx, vy, orientnode
def cohgen(exodusIn, fileOutPrefix):
"""
This function operates within Cubit. It imports an exodus mesh of
polycrystalline geometry with the void meshed, generates a skin of zero
thickness cohesive elements surrounding individual crystals, and exports
a valid ABAQUS mesh.
"""
# Provide the installation path of Cubit
sys.path.append('~/Software/Cubit-15.3-Lin64/bin')
# sys.path.append('/Applications/Cubit-15.3/Cubit.app/Contents/MacOS/')
import cubit as cb
# Start cubit
cb.init(['cubit', '-nojournal'])
# Import model while creating geometry
fileIn = "'" + exodusIn + ".e'"
print fileIn
cb.cmd("import mesh geometry %s feature_angle 135.00 merge" % fileIn)
# Get volumes and separate into blocks
# Compress volume id's and sort by volume (likely void volume is largest)
cb.cmd('compress all sort')
# cb.cmd('label volume id')
# cb.cmd('label volume name id')
# Remove pre-established element blocks
cb.cmd('del block all')
vols = cb.get_volume_count()
print "Number of volumes: %s" % vols
# Check if volumes sorted properly (largest last)
firstvol = cb.volume(1)
lastvol = cb.volume(vols)
firstvol_vol = firstvol.volume()
lastvol_vol = lastvol.volume()
# Set volume number containing matrix material
# Proper sort should set last (assuming it is the largest individual volume)
# One case, it left the matrix material as volume 1
# Could be other cases requiring a more generic fix (check cuibt file manually)
if firstvol_vol > lastvol_vol:
matrix_vol_num = 1
elif firstvol_vol < lastvol_vol:
matrix_vol_num = vols
# Assign each grain its own element block and name.
grain_list = []
for cv in range(1, vols + 1):
cb.cmd("block %s add volume %s" % (repr(cv + 1), repr(cv)))
if cv == matrix_vol_num:
cb.cmd("block %s name 'Matrix'" % repr(cv + 1))
else:
cb.cmd("block %s name 'Grain_%s'" % (repr(cv + 1), repr(cv)))
grain_list.append('Grain_%s' % repr(cv))
cb.cmd('disassociate mesh from Volume all')
# cb.cmd('delete volume all')
# Pillow each grain to skin with 0 thickness hexes for cohesive elements
el_blocks = cb.get_block_count()
# Note, indexing skips last element block (presumed binder)
for block in range(2, el_blocks + 1):
if block == matrix_vol_num + 1:
pass
else:
cb.cmd("pillow hex in block %s distance 0 no_smooth" % repr(block))
cb.cmd('block 1 add hex not block_assigned')
cb.cmd("block 1 name 'Coh_El'")
# Get bounding box for removing cohesive elements on the domain boundary
# cb.get_bounding_box('entity',id) returns a vector with the following info:
#(min_x, max_x, range_x, min_y, max_y, range_y, min_z, max_z, range_z, diag)
bbox = cb.get_bounding_box("volume", matrix_vol_num)
cb.cmd('delete hex in block 1 with X_Coord == %s' % repr(bbox[0]))
cb.cmd('delete hex in block 1 with X_Coord == %s' % repr(bbox[1]))
cb.cmd('delete hex in block 1 with Y_Coord == %s' % repr(bbox[3]))
cb.cmd('delete hex in block 1 with Y_Coord == %s' % repr(bbox[4]))
cb.cmd('delete hex in block 1 with Z_Coord == %s' % repr(bbox[6]))
cb.cmd('delete hex in block 1 with Z_Coord == %s' % repr(bbox[7]))
# Reassign domain nodesets since pillowing and removing domain hexes messes this up
cb.cmd('delete nodeset all')
cb.cmd('delete sideset all')
cb.cmd('nodeset 1 add node with X_Coord == %s' % repr(bbox[0]))
cb.cmd('nodeset 2 add node with X_Coord == %s' % repr(bbox[1]))
cb.cmd('nodeset 3 add node with Y_Coord == %s' % repr(bbox[3]))
cb.cmd('nodeset 4 add node with Y_Coord == %s' % repr(bbox[4]))
cb.cmd('nodeset 5 add node with Z_Coord == %s' % repr(bbox[6]))
cb.cmd('nodeset 6 add node with Z_Coord == %s' % repr(bbox[7]))
cb.cmd('nodeset 7 add node in nodeset 1 to 6')
cb.cmd('nodeset 8 add node in hex in block 1') # Interface nodes
cb.cmd('nodeset 1 name "negXNodes"')
cb.cmd('nodeset 2 name "posXNodes"')
cb.cmd('nodeset 3 name "negYNodes"')
cb.cmd('nodeset 4 name "posYNodes"')
cb.cmd('nodeset 5 name "negZNodes"')
cb.cmd('nodeset 6 name "posZNodes"')
cb.cmd('nodeset 7 name "allBoundaryNodes"')
cb.cmd('nodeset 8 name "matIntNodes"')
# Define nodesets for periodic boundary conditions. For universal application
# to implicit and explicit analyses, corners, edges, and faces cannot contain
# duplicate nodes (restriction for implicit only). Therefore, new specific
# nodesets are defined in a way to eleminate this duplicate definition problem.
# Redefine Faces for PBC's
cb.cmd('nodeset 101 add node in nodeset 1')
cb.cmd('nodeset 102 add node in nodeset 2')
cb.cmd('nodeset 103 add node in nodeset 3')
cb.cmd('nodeset 104 add node in nodeset 4')
cb.cmd('nodeset 105 add node in nodeset 5')
cb.cmd('nodeset 106 add node in nodeset 6')
cb.cmd('nodeset 101 name "PBCnXF"')
cb.cmd('nodeset 102 name "PBCpXF"')
cb.cmd('nodeset 103 name "PBCnYF"')
cb.cmd('nodeset 104 name "PBCpYF"')
cb.cmd('nodeset 105 name "PBCnZF"')
cb.cmd('nodeset 106 name "PBCpZF"')
# Define Edges for PBC's
cb.cmd(
'nodeset 1001 add node with X_Coord == {x:s} and with Y_Coord == {y:s}'
.format(x=repr(bbox[0]), y=repr(bbox[3])))
cb.cmd('nodeset 1001 name "PBCnXnYE"')
cb.cmd(
'nodeset 1002 add node with X_Coord == {x:s} and with Y_Coord == {y:s}'
.format(x=repr(bbox[0]), y=repr(bbox[4])))
cb.cmd('nodeset 1002 name "PBCnXpYE"')
cb.cmd(
'nodeset 1003 add node with X_Coord == {x:s} and with Y_Coord == {y:s}'
.format(x=repr(bbox[1]), y=repr(bbox[3])))
cb.cmd('nodeset 1003 name "PBCpXnYE"')
cb.cmd(
'nodeset 1004 add node with X_Coord == {x:s} and with Y_Coord == {y:s}'
.format(x=repr(bbox[1]), y=repr(bbox[4])))
cb.cmd('nodeset 1004 name "PBCpXpYE"')
cb.cmd(
'nodeset 1005 add node with Y_Coord == {y:s} and with Z_Coord == {z:s}'
.format(y=repr(bbox[3]), z=repr(bbox[6])))
cb.cmd('nodeset 1005 name "PBCnYnZE"')
cb.cmd(
'nodeset 1006 add node with Y_Coord == {y:s} and with Z_Coord == {z:s}'
.format(y=repr(bbox[3]), z=repr(bbox[7])))
cb.cmd('nodeset 1006 name "PBCnYpZE"')
cb.cmd(
'nodeset 1007 add node with Y_Coord == {y:s} and with Z_Coord == {z:s}'
.format(y=repr(bbox[4]), z=repr(bbox[6])))
cb.cmd('nodeset 1007 name "PBCpYnZE"')
cb.cmd(
'nodeset 1008 add node with Y_Coord == {y:s} and with Z_Coord == {z:s}'
.format(y=repr(bbox[4]), z=repr(bbox[7])))
cb.cmd('nodeset 1008 name "PBCpYpZE"')
cb.cmd(
'nodeset 1009 add node with X_Coord == {x:s} and with Z_Coord == {z:s}'
.format(x=repr(bbox[0]), z=repr(bbox[6])))
cb.cmd('nodeset 1009 name "PBCnXnZE"')
cb.cmd(
'nodeset 1010 add node with X_Coord == {x:s} and with Z_Coord == {z:s}'
.format(x=repr(bbox[0]), z=repr(bbox[7])))
cb.cmd('nodeset 1010 name "PBCnXpZE"')
cb.cmd(
'nodeset 1011 add node with X_Coord == {x:s} and with Z_Coord == {z:s}'
.format(x=repr(bbox[1]), z=repr(bbox[6])))
cb.cmd('nodeset 1011 name "PBCpXnZE"')
cb.cmd(
'nodeset 1012 add node with X_Coord == {x:s} and with Z_Coord == {z:s}'
.format(x=repr(bbox[1]), z=repr(bbox[7])))
cb.cmd('nodeset 1012 name "PBCpXpZE"')
# Remove nodes in edge sets from face sets
for nn in range(101, 107):
cb.cmd('nodeset {num:s} remove node in nodeset 1001 to 1012'.format(
num=repr(nn)))
# Define Corners for PBC's
cb.cmd(
'nodeset 10001 add node with X_Coord == {x:s} and with Y_Coord == {y:s} and with Z_Coord == {z:s}'
.format(x=repr(bbox[0]), y=repr(bbox[3]), z=repr(bbox[6])))
cb.cmd('nodeset 10001 name "PBCnXnYnZC"')
cb.cmd(
'nodeset 10002 add node with X_Coord == {x:s} and with Y_Coord == {y:s} and with Z_Coord == {z:s}'
.format(x=repr(bbox[0]), y=repr(bbox[3]), z=repr(bbox[7])))
cb.cmd('nodeset 10002 name "PBCnXnYpZC"')
cb.cmd(
'nodeset 10003 add node with X_Coord == {x:s} and with Y_Coord == {y:s} and with Z_Coord == {z:s}'
.format(x=repr(bbox[0]), y=repr(bbox[4]), z=repr(bbox[6])))
cb.cmd('nodeset 10003 name "PBCnXpYnZC"')
cb.cmd(
'nodeset 10004 add node with X_Coord == {x:s} and with Y_Coord == {y:s} and with Z_Coord == {z:s}'
.format(x=repr(bbox[0]), y=repr(bbox[4]), z=repr(bbox[7])))
cb.cmd('nodeset 10004 name "PBCnXpYpZC"')
cb.cmd(
'nodeset 10005 add node with X_Coord == {x:s} and with Y_Coord == {y:s} and with Z_Coord == {z:s}'
.format(x=repr(bbox[1]), y=repr(bbox[3]), z=repr(bbox[6])))
cb.cmd('nodeset 10005 name "PBCpXnYnZC"')
cb.cmd(
'nodeset 10006 add node with X_Coord == {x:s} and with Y_Coord == {y:s} and with Z_Coord == {z:s}'
.format(x=repr(bbox[1]), y=repr(bbox[3]), z=repr(bbox[7])))
cb.cmd('nodeset 10006 name "PBCpXnYpZC"')
cb.cmd(
'nodeset 10007 add node with X_Coord == {x:s} and with Y_Coord == {y:s} and with Z_Coord == {z:s}'
.format(x=repr(bbox[1]), y=repr(bbox[4]), z=repr(bbox[6])))
cb.cmd('nodeset 10007 name "PBCpXpYnZC"')
cb.cmd(
'nodeset 10008 add node with X_Coord == {x:s} and with Y_Coord == {y:s} and with Z_Coord == {z:s}'
.format(x=repr(bbox[1]), y=repr(bbox[4]), z=repr(bbox[7])))
cb.cmd('nodeset 10008 name "PBCpXpYpZC"')
# Remove nodes in corner sets from edge sets
for nn in range(1001, 1013):
cb.cmd('nodeset {num:s} remove node in nodeset 10001 to 10008'.format(
num=repr(nn)))
# Export abaqus file
absFileOutPrefix = os.path.abspath(fileOutPrefix)
cb.cmd("set Abaqus precision 4")
cb.cmd(
'export abaqus "%s.inp" block all nodeset all dimension 3 overwrite' %
absFileOutPrefix)
cb.cmd('save as "%s.cub" overwrite' % absFileOutPrefix)
return absFileOutPrefix, grain_list
import boundary_definition
import cubit2specfem3d
# time stamp
print("#" + time.strftime("%a, %d %b %Y %H:%M:%S", time.localtime()))
# working directory
cwd = os.getcwd()
print("#current working directory: " + str(cwd))
if cwd[len(cwd)-14:len(cwd)] != "Mount_StHelens":
print("")
print("#please run this script from example directory: SPECFEM3D/example/Mount_StHelens/")
print("")
cubit.cmd('version')
cubit.cmd('reset')
print("running meshing script...")
print("")
print("note: this script uses topography surface in ACIS format")
print(" meshing will take around 15 min")
print("")
# uses developer commands
cubit.cmd('set developer commands on')
cubit.cmd('set import mesh tolerance 1')
#############################################################
#
# 0. step: loading topography surface
def mesh_cpml(list_vol,
remesh=True,
refinement=None,
top_surf=None,
size=None):
from utilities import list2str
top_surf = list2str(top_surf)
if remesh:
cubit.cmd('reset vol all')
cubit.cmf('set dev on')
cubit.cmd('imprint vol all')
cubit.cmd('merge vol all')
cubit.cmd('vol all size ' + str(size))
cubit.cmd('mesh vol all')
try:
for refdepth in refinement:
cubit.cmd('refine surf ' + top_surf +
' numsplit 1 bias 1 depth ' + str(refdepth))
except:
print 'DEBUG: error in refinement cpml'
xmin = xmin - size
xmax = xmax + size
ymin = ymin - size
ymax = ymax + size
zmin = zmin - size
zmin = zmax - size
txt = "group 'vol_xmin' add vol in surf with X_coord < " + str(xmin)
cubit.cmd(txt)
txt = "group 'vol_xmax' add vol in surf with X_coord > " + str(xmax)
cubit.cmd(txt)
txt = "group 'vol_ymin' add vol in surf with Y_coord < " + str(ymin)
cubit.cmd(txt)
txt = "group 'vol_ymax' add vol in surf with Y_coord > " + str(ymax)
cubit.cmd(txt)
txt = "group 'vol_zmin' add vol in surf with Z_coord < " + str(zmin)
cubit.cmd(txt)
def Layer(Body_IDs, BB, Alpha, Theta1, Theta2, Xoffset=.5):
import cubit
import numpy as np
###
### Body_ID: a single volume ID
### BB: bounding box in the form [xmin, xmax, ymin, ymax, zmin, zmax]
### Alpha: lamination angle
### Theta1: thickness of layer 1
### Theta2: thickness of layer 2
### Xoffset: distance along the x-axis between the center of the bounding box
### and the first interface l1-l2 if specified, in fraction of Theta1
### i.e. 0 -> interface l2-l1 at center
### 1 -> interface l1-l2 at center
### otherwise, the center of BB corresponds to the center of a Layer1
### i.e. Xoffset = .5
###
YL = np.sqrt((BB[1] - BB[0])**2 + (BB[3] - BB[2])**2)
XC = (BB[0] + BB[1]) / 2.
YC = (BB[2] + BB[3]) / 2.
ZC = (BB[4] + BB[5]) / 2.
Theta = Theta1 + Theta2
if Alpha > 0:
l1 = (BB[0] - XC) * np.cos(np.radians(Alpha)) + (BB[2] - YC) * np.sin(
np.radians(Alpha))
l2 = (BB[1] - XC) * np.cos(np.radians(Alpha)) + (BB[3] - YC) * np.sin(
np.radians(Alpha))
else:
l1 = (BB[0] - XC) * np.cos(np.radians(Alpha)) + (BB[3] - YC) * np.sin(
np.radians(Alpha))
l2 = (BB[1] - XC) * np.cos(np.radians(Alpha)) + (BB[2] - YC) * np.sin(
np.radians(Alpha))
n1 = int(np.ceil(l1 / Theta)) - 1
n2 = int(np.ceil(l2 / Theta)) + 1
LAYER1_IDs = Body_IDs[:]
LAYER2_IDs = []
###
### offset layers
###
for i in range(n1, n2):
X = XC + i * np.cos(np.radians(Alpha)) * Theta
Y = YC + i * np.sin(np.radians(Alpha)) * Theta
cubit.cmd('create brick X %f Y %f Z %f' % (Theta1, YL, BB[5] - BB[4]))
tmp_ID = cubit.get_last_id("volume")
cubit.cmd('move volume %i X %f Y %f Z %f' % (tmp_ID, X + Theta1 *
(.5 - Xoffset), Y, ZC))
if not Alpha == 0.:
### cubit doesn't like rotations will 0 angle...
cubit.cmd('create vertex X %f Y %f Z %f' % (X, Y, BB[4]))
v1_ID = cubit.get_last_id("vertex")
cubit.cmd('create vertex X %f Y %f Z %f' % (X, Y, BB[5]))
v2_ID = cubit.get_last_id("vertex")
cubit.cmd('rotate volume %i about vertex %i vertex %i angle %f' %
(tmp_ID, v1_ID, v2_ID, Alpha))
cubit.cmd('delete vertex %i' % v1_ID)
cubit.cmd('delete vertex %i' % v2_ID)
(LAYER1_IDs, tmp_layer) = WebcutTool2(LAYER1_IDs, tmp_ID, delete=True)
for l in tmp_layer:
LAYER2_IDs.append(l)
return (LAYER1_IDs, LAYER2_IDs)
#!/usr/bin/env python
from __future__ import print_function
import cubit
import boundary_definition
import cubit2specfem3d
import os
import sys
# two volumes separating 134000x134000x60000 block horizontally
cubit.cmd('reset')
cubit.cmd('brick x 67000 y 134000 z 60000')
cubit.cmd('volume 1 move x 33500 y 67000 z -30000')
cubit.cmd('brick x 67000 y 134000 z 60000')
cubit.cmd('volume 2 move x 100500 y 67000 z -30000')
cubit.cmd('merge all')
# Meshing the volumes
elementsize = 3750.0
cubit.cmd('volume 1 size ' + str(elementsize))
cubit.cmd('volume 2 size ' + str(elementsize))
cubit.cmd('mesh volume 1 2')
#### End of meshing
###### This is boundary_definition.py of GEOCUBIT
#..... which extracts the bounding faces and defines them into blocks
boundary_definition.entities = ['face']
boundary_definition.define_bc(boundary_definition.entities, parallel=True)
def collecting_cpml(ip,
size=None,
cpuxmin=0,
cpuxmax=1,
cpuymin=0,
cpuymax=1,
cpux=1,
cpuy=1,
cubfiles=False,
decimate=False,
layers=2):
import glob
import re
from utilities import list2str
#
if not size:
print 'cpml size must be specified'
return
boundary_dict = {}
##
try:
from boundary_definition import check_bc, map_boundary, define_surf
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 ')
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
if decimate:
cubit.cmd(
'export mesh "decimated_before_cmpl.e" dimension 3 block all overwrite'
)
else:
if decimate:
cubit.cmd('refine volume all numsplit 1 bias 1.0 depth 1 ')
cubit.cmd(
'export mesh "decimated_before_cmpl.e" dimension 3 block all overwrite'
)
#
#
#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) + '"')
list_vol = list(cubit.parse_cubit_list('volume', 'all'))
create_pml(xmin=xmin,
xmax=xmax,
ymax=ymax,
ymin=ymin,
zmin=zmin,
zmax=zmax,
size=size,
layers=layers,
vol=list_vol)
