def get_uv_curve(list_curve_or):
import math
import numpy as np
klen={}
for curve in list_curve_or:
vertex_list = cubit.get_relatives("curve", curve, "vertex")
coord0=cubit.get_center_point('vertex', vertex_list[0])
coord1=cubit.get_center_point('vertex', vertex_list[1])
klen[curve]=np.array(coord1)-np.array(coord0)
#
l0=list_curve_or[0]
c0=klen[l0]
angles={}
angles[l0]=0
for curve in list_curve_or[1:]:
c1=klen[curve]
angletmp=np.dot(c0,c1)/(np.dot(c0,c0)**.5*np.dot(c1,c1)**.5)
if -1 < angletmp < 1:
angle=math.sin(np.arccos(angletmp))
else:
angle=0.
angles[curve]=angle
a=angles.values()
diff=max(a)-min(a)
ucurve=[]
vcurve=[]
for curve in list_curve_or:
if -diff < angles[curve] < diff:
ucurve.append(curve)
else:
vcurve.append(curve)
#
return ucurve,vcurve
def ordering_surfaces(list_surfaces):
list_z=[]
for s in list_surfaces:
_,_,z=cubit.get_center_point("surface",s)
list_z.append(z)
ord_list_surfaces=[s for s,z in sorted(zip(list_surfaces,list_z),key=lambda x: (x[1]))]
return ord_list_surfaces
def ordering_surfaces(list_surfaces):
list_z=[]
for s in list_surfaces:
_,_,z=cubit.get_center_point("surface",s)
list_z.append(z)
ord_list_surfaces=[s for s,z in sorted(zip(list_surfaces,list_z),key=lambda x: (x[1]))]
return ord_list_surfaces
def select_bottom_curve(lc):
z = []
for l in lc:
center_point = cubit.get_center_point("curve", l)
z.append(center_point[2])
result = zip(z, lc)
result.sort()
return result[0][1]
def select_bottom_curve(lc):
z=[]
for l in lc:
center_point = cubit.get_center_point("curve", l)
z.append(center_point[2])
result=zip(z,lc)
result.sort()
return result[0][1]
def select_bottom_curve(lc):
z=[]
for l in lc:
center_point = cubit.get_center_point("curve", l)
z.append(center_point[2])
result=zip(z,lc)
# takes line number from first entry
curve=0
if len(result) > 0:
result.sort()
curve=result[0][1]
return curve
def define_4side_lateral_surfaces(tres=0.0003, tol=0.000001):
list_vol = cubit.parse_cubit_list("volume", "all")
surf_xmin = []
surf_ymin = []
surf_xmax = []
surf_ymax = []
# min/max of bounding box
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]
zmin_box = cubit.get_total_bounding_box("volume", list_vol)[6]
zmax_box = cubit.get_total_bounding_box("volume", list_vol)[7]
#print('absorbing boundary xmin:' + str(xmin_box) + ' xmax: ' + str(xmax_box))
#print('absorbing boundary ymin:' + str(ymin_box) + ' ymax: ' + str(ymax_box))
#print('absorbing boundary zmin:' + str(zmin_box) + ' zmax: ' + str(zmax_box))
for id_vol in list_vol:
surf_vertical = []
xsurf = []
ysurf = []
lsurf = cubit.get_relatives("volume", id_vol, "surface")
for k in lsurf:
normal = cubit.get_surface_normal(k)
# checks if normal is horizontal (almost 0, i.e., +/- tres)
if normal[2] >= -1 * tres and normal[2] <= tres:
# checks if surface is on minimum/maximum side of the whole model
center_point = cubit.get_center_point("surface", k)
# note: for models with smaller volumes inscribed, we want only the outermost surfaces
# as absorbing ones
#sbox = cubit.get_bounding_box('surface', k)
# xmin of surface box relative to total box xmin
if (abs(center_point[0] - xmin_box) / abs(xmax_box - xmin_box) <= tol) or \
(abs(center_point[0] - xmax_box) / abs(xmax_box - xmin_box) <= tol) or \
(abs(center_point[1] - ymin_box) / abs(ymax_box - ymin_box) <= tol) or \
(abs(center_point[1] - ymax_box) / abs(ymax_box - ymin_box) <= tol):
# adds as vertical surface
surf_vertical.append(k)
xsurf.append(center_point[0])
ysurf.append(center_point[1])
# adds surfaces when on boundary
if len(surf_vertical) > 0:
surf_xmin.append(surf_vertical[xsurf.index(min(xsurf))])
surf_ymin.append(surf_vertical[ysurf.index(min(ysurf))])
surf_xmax.append(surf_vertical[xsurf.index(max(xsurf))])
surf_ymax.append(surf_vertical[ysurf.index(max(ysurf))])
#debug
#print('define_4side_lateral_surfaces: xmin ',surf_xmin)
#print('define_4side_lateral_surfaces: xmax ',surf_xmax)
#print('define_4side_lateral_surfaces: ymin ',surf_ymin)
#print('define_4side_lateral_surfaces: ymax ',surf_ymax)
return surf_xmin, surf_ymin, surf_xmax, surf_ymax
def select_bottom_curve(lc):
z = []
for l in lc:
center_point = cubit.get_center_point("curve", l)
z.append(center_point[2])
result = zip(z, lc)
# takes line number from first entry
curve = 0
if len(result) > 0:
result.sort()
curve = result[0][1]
return curve
def define_4side_lateral_surfaces():
list_vol=cubit.parse_cubit_list("volume","all")
surf_xmin=[]
surf_ymin=[]
surf_xmax=[]
surf_ymax=[]
for id_vol in list_vol:
surf_vertical=[]
xsurf=[]
ysurf=[]
tres=0.3
lsurf=cubit.get_relatives("volume",id_vol,"surface")
for k in lsurf:
normal=cubit.get_surface_normal(k)
center_point = cubit.get_center_point("surface", k)
if normal[2] >= -1*tres and normal[2] <= tres:
surf_vertical.append(k)
xsurf.append(center_point[0])
ysurf.append(center_point[1])
surf_xmin.append(surf_vertical[xsurf.index(min(xsurf))])
surf_ymin.append(surf_vertical[ysurf.index(min(ysurf))])
surf_xmax.append(surf_vertical[xsurf.index(max(xsurf))])
surf_ymax.append(surf_vertical[ysurf.index(max(ysurf))])
return surf_xmin,surf_ymin,surf_xmax,surf_ymax
def define_4side_lateral_surfaces():
list_vol = cubit.parse_cubit_list("volume", "all")
surf_xmin = []
surf_ymin = []
surf_xmax = []
surf_ymax = []
for id_vol in list_vol:
surf_vertical = []
xsurf = []
ysurf = []
tres = 0.3
lsurf = cubit.get_relatives("volume", id_vol, "surface")
for k in lsurf:
normal = cubit.get_surface_normal(k)
center_point = cubit.get_center_point("surface", k)
if normal[2] >= -1 * tres and normal[2] <= tres:
surf_vertical.append(k)
xsurf.append(center_point[0])
ysurf.append(center_point[1])
surf_xmin.append(surf_vertical[xsurf.index(min(xsurf))])
surf_ymin.append(surf_vertical[ysurf.index(min(ysurf))])
surf_xmax.append(surf_vertical[xsurf.index(max(xsurf))])
surf_ymax.append(surf_vertical[ysurf.index(max(ysurf))])
return surf_xmin, surf_ymin, surf_xmax, surf_ymax
def hor_distance(c1,c2):
p1=cubit.get_center_point("curve", c1)
p2=cubit.get_center_point("curve", c2)
d=(p1[0]-p2[0])**2+(p1[1]-p2[1])**2
return d
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 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 saveMesh3D(self):
cubit.cmd("brick x 5000 y 5000 z 5000")
cubit.cmd("create cylinder height 4000 radius 500")
cubit.cmd("subtract body 2 from body 1")
volID = cubit.get_last_id("volume")
self.vol = volID
self.mesh()
nNodes = cubit.get_node_count()
meshFile = open(folder+"mesh3D2.xml", 'w')
meshFile.write('<mesh celltype="tetrahedron" dim="3">\n')
meshFile.write(' <nodes size="%d">\n' % (nNodes))
for x in range(0, nNodes):
coords = cubit.get_nodal_coordinates(x+1)
meshFile.write(' <node id="%d" x="%f" y="%f" z="%f"/>\n' % (x,coords[0],coords[1],coords[2]))
meshFile.write(' </nodes>\n')
nTets = cubit.get_tet_count()
meshFile.write(' <elements size="%d">\n' % (nTets))
for x in range(0, nTets):
nodes = cubit.get_connectivity("tet", x+1)
meshFile.write(' <element id="%d" v0="%d" v1="%d" v2="%d" v3="%d"/>\n' % (x,nodes[0]-1,nodes[1]-1,nodes[2]-1,nodes[3]-1))
meshFile.write(' </elements>\n')
meshFile.write(' <element_data type="fiber_transversely_isotropic">\n')
for x in range(0, nTets):
meshFile.write(' <element id="%d">\n' %(x))
meshFile.write(' <fiber>1.000000,0.000000,0.000000</fiber>\n')
meshFile.write(' </element>\n')
meshFile.write(' </element_data>\n')
meshFile.write(' <boundary celltype="triangle" dim="2">\n')
bsurfs = [10, 11, 12]
ec = 0
for x in range(0, len(bsurfs)):
tris = cubit.get_surface_tris(bsurfs[x])
surf = cubit.surface(bsurfs[x])
for y in range(0, len(tris)):
cp = cubit.get_center_point("tri", tris[y])
norm = surf.normal_at([cp[0],cp[1],cp[2]])
#cubit.cmd("create curve location %f %f %f direction %f %f %f length %f" % (cp[0],cp[1],cp[2],norm[0],norm[1],norm[2],200))
nodes = cubit.get_connectivity("tri", tris[y])
element = [nodes[0]-1, nodes[1]-1, nodes[2]-1]
meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" v2="%d" nx="%f" ny="%f" nz="%f"/>\n' % (ec,1.0,element[0],element[1],element[2],norm[0],norm[1],norm[2]))
ec = ec+1
meshFile.write(' </boundary>\n')
meshFile.write('</mesh>\n')
meshFile.write('<poisson>\n')
meshFile.write(' <neumann>\n')
meshFile.write(' <node id="1" marker="1" value="0.5" />\n')
meshFile.write(' </neumann>\n')
meshFile.write('</poisson>\n')
#meshFile.write('<electrophysiology>\n')
#meshFile.write(' <stimuli number="1">\n')
#bb = cubit.get_bounding_box("volume", self.vol)
#x0 = bb[0]
#x1 = 0.8*x0 + 0.2*bb[1]
#y0 = bb[3]
#y1 = 0.8*y0 + 0.2*bb[4]
#z0 = bb[6]
#z1 = 0.8*z0 + 0.2*bb[7]
#meshFile.write(' <stim start="0.00" duration="4.00" value="-35.7140" x0="%f" x1="%f" y0="%f" y1="%f" z0="%f" z1="%f" />\n' % (x0,x1,y0,y1,z0,z1))
#meshFile.write(' </stimuli>\n')
#meshFile.write('</electrophysiology>\n')
meshFile.close()
def saveMesh(self):
nNodes = cubit.get_node_count()
nTets = cubit.get_tet_count()
meshFile = open(folder+"Cubo.xml", 'w')
meshFile.write('<mesh celltype="tetrahedron" dim="3">\n')
meshFile.write(' <nodes size="%d">\n' % (nNodes))
for x in range(0, nNodes):
coords = cubit.get_nodal_coordinates(x+1)
meshFile.write(' <node id="%d" x="%f" y="%f" z="%f"/>\n' % (x,coords[0],coords[1],coords[2]))
meshFile.write(' </nodes>\n')
meshFile.write(' <elements size="%d">\n' % (nTets))
for x in range(0, nTets):
nodes = cubit.get_connectivity("tet", x+1)
meshFile.write(' <element id="%d" v0="%d" v1="%d" v2="%d" v3="%d"/>\n' % (x,nodes[0]-1,nodes[1]-1,nodes[2]-1,nodes[3]-1))
meshFile.write(' </elements>\n')
meshFile.write(' <element_data type="fiber_transversely_isotropic">\n')
for x in range(0, nTets):
meshFile.write(' <element id="%d">\n' %(x))
meshFile.write(' <fiber>1.000000,0.000000,0.000000</fiber>\n')
meshFile.write(' </element>\n')
meshFile.write(' </element_data>\n')
meshFile.write(' <boundary celltype="triangle" dim="2">\n')
bsurfs = cubit.get_relatives("volume", self.vol, "surface")
ec = 0
for x in range(0, len(bsurfs)):
#for x in range(6, len(bsurfs)):
#if x is not 16 and x is not 14:
tris = cubit.get_surface_tris(bsurfs[x])
surf = cubit.surface(bsurfs[x])
for y in range(0, len(tris)):
cp = cubit.get_center_point("tri", tris[y])
norm = surf.normal_at([cp[0],cp[1],cp[2]])
#cubit.cmd("create curve location %f %f %f direction %f %f %f length %f" % (cp[0],cp[1],cp[2],norm[0],norm[1],norm[2],200))
nodes = cubit.get_connectivity("tri", tris[y])
element = [nodes[0]-1, nodes[1]-1, nodes[2]-1]
meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" v2="%d" nx="%f" ny="%f" nz="%f"/>\n' % (ec,1.0,element[0],element[1],element[2],norm[0],norm[1],norm[2]))
ec = ec+1
meshFile.write(' </boundary>\n')
#meshFile.write(' <boundary celltype="triangle" dim="2">\n')
#surfs = cubit.get_relatives("volume", self.vol, "surface")
#ec = 0
#for x in range(0, 2):
# tris = cubit.get_surface_tris(surfs[x])
# for y in range(0, len(tris)):
# nodes = cubit.get_connectivity("tri", tris[y])
# element = [nodes[0]-1, nodes[1]-1, nodes[2]-1]
# ec = ec+1
# meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" v2="%d"/>\n' % (ec,x,element[0],element[1],element[2]))
#meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" v2="%d"/>\n' % (ec+1,2,element[0],element[1],element[2]))
#meshFile.write(' </boundary>\n')
meshFile.write('</mesh>\n')
meshFile.write('<poisson>\n')
meshFile.write(' <neumann>\n')
#meshFile.write(' <node id="0" marker="0" value="-1.0" />\n')
meshFile.write(' <node id="1" marker="1" value="0.05"/>\n')
meshFile.write(' </neumann>\n')
#meshFile.write(' <dirichlet>\n')
#meshFile.write(' <node id="2" marker="2" value="0.0" />\n')
#meshFile.write(' </dirichlet>\n')
meshFile.write('</poisson>\n')
#meshFile.write('<electrophysiology>\n')
#meshFile.write(' <stimuli number="1">\n')
#bb = cubit.get_bounding_box("volume", self.vol)
#x0 = bb[0]
#x1 = 0.8*x0 + 0.2*bb[1]
#y0 = bb[3]
#y1 = 0.8*y0 + 0.2*bb[4]
#z0 = bb[6]
#z1 = 0.8*z0 + 0.2*bb[7]
#meshFile.write(' <stim start="0.00" duration="4.00" value="-35.7140" x0="%f" x1="%f" y0="%f" y1="%f" z0="%f" z1="%f" />\n' % (x0,x1,y0,y1,z0,z1))
#meshFile.write(' </stimuli>\n')
#meshFile.write('</electrophysiology>\n')
meshFile.close()
print "Convert mesh to Specfem-format..."
os.system('mkdir -p MESH')
## fault surfaces (up/down)
Au = [cubit.get_id_from_name("fault1")]
Ad = [cubit.get_id_from_name("fault2")]
### Obtain the id of boundaries
# I define the original sphere surface as spheresurf. After webcut, CUBIT renames the new-cutted surface by adding @A, @B ...
SpheresurfID = [cubit.get_id_from_name("spheresurf@A")]
# Find the surface ID for the free surface
freesur_tolerance = 3e3
FreesurfID = []
list_surf = cubit.parse_cubit_list("surface", "all")
for k in list_surf:
center_point = cubit.get_center_point("surface", k)
if abs(center_point[2]) <= freesur_tolerance:
FreesurfID.append(k)
print SpheresurfID, FreesurfID
# define blocks
Vol_num = cubit.get_volume_count()
for i in range(Vol_num):
cubit.cmd('block {0} hex in vol {0}'.format(i + 1))
cubit.cmd('block 1000 face in surface ' +
str(list(SpheresurfID)).replace("[", " ").replace("]", " "))
cubit.cmd('block 1000 name "face_semisphere"')
cubit.cmd('block 1001 face in surface ' +
str(list(FreesurfID)).replace("[", " ").replace("]", " "))
cubit.cmd('block 1001 name "face_topo"')
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 mesh_layercake_regularmap(filename=None):
import sys,os
import start as start
mpiflag,iproc,numproc,mpi = start.start_mpi()
from utilities import importgeometry,savemesh,get_v_h_list,cubit_command_check
#
numpy = start.start_numpy()
cfg = start.start_cfg(filename=filename)
from math import sqrt
from sets import Set
#
class cubitvolume:
def __init__(self,ID,intervalv,centerpoint,dimension):
self.ID=ID
self.intervalv=intervalv
self.centerpoint=centerpoint
self.dim=dimension
def __repr__(self):
msg="(vol:%3i, vertical interval: %4i, centerpoint: %8.2f)" % (self.ID, self.intervalv,self.centerpoint)
return msg
#
def by_z(x,y):
return cmp(x.centerpoint,y.centerpoint)
#
#
#
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])
command = "curve "+' '.join(str(iv[0]) for iv in interval_store)+" interval "+str(interval_min)
cubit.cmd(command)
#cubit_error_stop(iproc,command,ner)
command = "curve "+' '.join(str(iv[0]) for iv in interval_store)+" scheme equal"
cubit.cmd(command)
#cubit_error_stop(iproc,command,ner)
command = "surface "+str(s)+" scheme submap"
cubit.cmd(command)
#cubit_error_stop(iproc,command,ner)
#
#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)
command_set_meshvol='volume all redistribute nodes on\nvolume all autosmooth target off\nvolume all scheme Sweep Vector 0 0 -1\nvolume all sweep smooth Auto\n'
status=cubit_command_check(iproc,command_set_meshvol,stop=False)
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:
from sets import Set
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)
def define_parallel_absorbing_surf():
"""
define the absorbing surfaces for a layered topological box where boundary are surfaces parallel to the axis.
it returns absorbing_surf,absorbing_surf_xmin,absorbing_surf_xmax,absorbing_surf_ymin,absorbing_surf_ymax,absorbing_surf_bottom,topo_surf
where
absorbing_surf is the list of all the absorbing boundary surf
absorbing_surf_xmin is the list of the absorbing boundary surfaces that correnspond to x=xmin
...
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_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")
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[0] - xmin_box) /
x_len) <= absorbing_surface_distance_tolerance:
absorbing_surf_xmin.append(k)
elif abs((center_point[0] - xmax_box) /
x_len) <= absorbing_surface_distance_tolerance:
absorbing_surf_xmax.append(k)
elif abs((center_point[1] - ymin_box) /
y_len) <= absorbing_surface_distance_tolerance:
absorbing_surf_ymin.append(k)
elif abs((center_point[1] - ymax_box) /
y_len) <= absorbing_surface_distance_tolerance:
absorbing_surf_ymax.append(k)
elif 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_xmin, absorbing_surf_xmax, absorbing_surf_ymin, absorbing_surf_ymax, absorbing_surf_bottom, top_surf
def get_v_h_list(vol_id_list, chktop=False):
"""return the lists of the cubit ID of vertical/horizontal surface and vertical/horizontal curves
where v/h is defined by the distance of the z normal component from the axis direction
the parameter cfg.tres is the threshold as for example if
-tres <= normal[2] <= tres
then the surface is vertical
#
usage: surf_or,surf_vertical,list_curve_or,list_curve_vertical,bottom,top = get_v_h_list(list_vol,chktop=False)
"""
#
tres = 0.3
try:
nvol = len(vol_id_list)
except:
nvol = 1
vol_id_list = [vol_id_list]
surf_vertical = []
surf_or = []
list_curve_vertical = []
list_curve_or = []
#
#
for id_vol in vol_id_list:
lsurf = cubit.get_relatives("volume", id_vol, "surface")
for k in lsurf:
normal = cubit.get_surface_normal(k)
center_point = cubit.get_center_point("surface", k)
if -1 * tres <= normal[2] <= tres:
surf_vertical.append(k)
lcurve = cubit.get_relatives("surface", k, "curve")
list_curve_vertical = list_curve_vertical + list(lcurve)
else:
surf_or.append(k)
lcurve = cubit.get_relatives("surface", k, "curve")
list_curve_or = list_curve_or + list(lcurve)
for x in list_curve_or:
try:
list_curve_vertical.remove(x)
except:
pass
#find the top and the bottom surfaces
k = surf_or[0]
center_point = cubit.get_center_point("surface", k)[2]
center_point_top = center_point
center_point_bottom = center_point
top = k
bottom = k
for k in surf_or[1:]:
center_point = cubit.get_center_point("surface", k)[2]
if center_point > center_point_top:
center_point_top = center_point
top = k
elif center_point < center_point_bottom:
center_point_bottom = center_point
bottom = k
#check that a top surface exists
#it assume that the z coord of the center point
if chktop:
k = lsurf[0]
vertical_centerpoint_top = cubit.get_center_point("surface", k)[2]
vertical_zmax_box_top = cubit.get_bounding_box('surface', k)[7]
normal_top = cubit.get_surface_normal(k)
top = k
for k in lsurf:
vertical_centerpoint = cubit.get_center_point("surface", k)[2]
vertical_zmax_box = cubit.get_bounding_box('surface', k)[7]
normal = cubit.get_surface_normal(k)
check = (vertical_centerpoint >= vertical_centerpoint_top) and (
vertical_zmax_box >= vertical_zmax_box_top) and (normal >=
normal_top)
if check:
top = k
if top in surf_vertical:
surf_vertical.remove(top)
if top not in surf_or:
surf_or.append(top)
#if more than one surf is on the top, I get all the surfaces that are in touch with top surface but not the vertical surfaces
surftop = list(cubit.get_adjacent_surfaces(
"surface", top)) #top is included in the list
for s in surf_vertical:
try:
surftop.remove(s)
except:
pass
top = surftop
#check that all the surf are Horizontal or vertical
surf_all = surf_vertical + surf_or
if len(surf_all) != len(lsurf):
print 'not all the surf are horizontal or vertical, check the normals'
print 'list of surfaces: ', surf_all
print 'list of vertical surface', surf_vertical
print 'list of horizontal surface', surf_or
bottom = [bottom]
return surf_or, surf_vertical, list_curve_or, list_curve_vertical, bottom, top
def define_surf(ip=0,
cpuxmin=0,
cpuxmax=1,
cpuymin=0,
cpuymax=1,
cpux=1,
cpuy=1):
"""
define the absorbing surfaces for a layered topological box where boundary are surfaces parallel to the axis.
it returns absorbing_surf,absorbing_surf_xmin,absorbing_surf_xmax,absorbing_surf_ymin,absorbing_surf_ymax,absorbing_surf_bottom,topo_surf
where
absorbing_surf is the list of all the absorbing boundary surf
absorbing_surf_xmin is the list of the absorbing boundary surfaces that correnspond to x=xmin
...
absorbing_surf_bottom is the list of the absorbing boundary surfaces that correspond to z=zmin
"""
from utilities import get_v_h_list
#
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
# for compatibility with python2.5
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 = []
xmin = []
xmax = []
ymin = []
ymax = []
#
top_surf = []
bottom_surf = []
list_vol = cubit.parse_cubit_list("volume", "all")
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")
absorbing_surface_distance_tolerance = 0.001
topographic_surface_distance_tolerance = 0.1
topographic_surface_normal_tolerance = 0.4
lv = []
for k in list_surf:
sbox = cubit.get_bounding_box('surface', k)
if zmax_box == 0 and sbox[7] == 0:
dzmax = 0
elif zmax_box == 0 or sbox[7] == 0:
dzmax = abs(sbox[7] - zmax_box)
else:
dzmax = abs(sbox[7] - zmax_box) / max(abs(sbox[7]), abs(zmax_box))
if zmin_box == 0 and sbox[6] == 0:
dzmin = 0
elif zmin_box == 0 or sbox[6] == 0:
dzmin = abs(sbox[6] - zmin_box)
else:
dzmin = abs(sbox[6] - zmin_box) / max(abs(sbox[6]), abs(zmin_box))
normal = cubit.get_surface_normal(k)
zn = normal[2]
if dzmax <= topographic_surface_distance_tolerance and zn > topographic_surface_normal_tolerance:
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 < -1 + topographic_surface_normal_tolerance:
bottom_surf.append(k)
if len(top_surf) == 0: #assuming that one topo surface need to be selected
_, _, _, _, _, top_surf = get_v_h_list(list_vol, chktop=False)
lp = []
labelp = []
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])
labelp.append(list(c)[0])
labelps = Set(labelp)
for c in labelps:
p = cubit.get_center_point("curve", c)
lp.append(p)
for k in list_surf:
center_point = cubit.get_center_point("surface", k)
for p in lp:
try:
if abs((center_point[0] - p[0]) /
p[0]) <= absorbing_surface_distance_tolerance and abs(
(center_point[1] - p[1]) /
p[1]) <= absorbing_surface_distance_tolerance:
absorbing_surf.append(k)
break
except:
if -1 <= center_point[0] <= 1 and -1 <= center_point[1] <= 1:
absorbing_surf.append(k)
break
#
four_side = True
if four_side:
xmintmp, ymintmp, xmaxtmp, ymaxtmp = define_4side_lateral_surfaces()
xmin = list(Set(xmintmp) - Set(xmaxtmp))
xmax = list(Set(xmaxtmp) - Set(xmintmp))
ymin = list(Set(ymintmp) - Set(ymaxtmp))
ymax = list(Set(ymaxtmp) - Set(ymintmp))
abs_xmintmp, abs_xmaxtmp, abs_ymintmp, abs_ymaxtmp = lateral_boundary_are_absorbing(
ip, cpuxmin, cpuxmax, cpuymin, cpuymax, cpux, cpuy)
abs_xmin = list(Set(abs_xmintmp) - Set(abs_xmaxtmp))
abs_xmax = list(Set(abs_xmaxtmp) - Set(abs_xmintmp))
abs_ymin = list(Set(abs_ymintmp) - Set(abs_ymaxtmp))
abs_ymax = list(Set(abs_ymaxtmp) - Set(abs_ymintmp))
return absorbing_surf, abs_xmin, abs_xmax, abs_ymin, abs_ymax, top_surf, bottom_surf, xmin, ymin, xmax, ymax
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 define_surf(ip=0,cpuxmin=0,cpuxmax=1,cpuymin=0,cpuymax=1,cpux=1,cpuy=1):
"""
define the absorbing surfaces for a layered topological box where boundary are surfaces parallel to the axis.
it returns absorbing_surf,absorbing_surf_xmin,absorbing_surf_xmax,absorbing_surf_ymin,absorbing_surf_ymax,absorbing_surf_bottom,topo_surf
where
absorbing_surf is the list of all the absorbing boundary surf
absorbing_surf_xmin is the list of the absorbing boundary surfaces that correnspond to x=xmin
...
absorbing_surf_bottom is the list of the absorbing boundary surfaces that correspond to z=zmin
"""
from utilities import get_v_h_list
#
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
# for compatibility with python2.5
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=[]
xmin=[]
xmax=[]
ymin=[]
ymax=[]
#
top_surf=[]
bottom_surf=[]
list_vol=cubit.parse_cubit_list("volume","all")
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")
absorbing_surface_distance_tolerance=0.001
topographic_surface_distance_tolerance=0.1
topographic_surface_normal_tolerance=0.4
lv=[]
for k in list_surf:
sbox=cubit.get_bounding_box('surface',k)
if zmax_box == 0 and sbox[7] == 0:
dzmax=0
elif zmax_box == 0 or sbox[7] == 0:
dzmax=abs(sbox[7] - zmax_box)
else:
dzmax=abs(sbox[7] - zmax_box)/max(abs(sbox[7]),abs(zmax_box))
if zmin_box == 0 and sbox[6] == 0:
dzmin=0
elif zmin_box == 0 or sbox[6] == 0:
dzmin=abs(sbox[6] - zmin_box)
else:
dzmin=abs(sbox[6] - zmin_box)/max(abs(sbox[6]),abs(zmin_box))
normal=cubit.get_surface_normal(k)
zn=normal[2]
if dzmax <= topographic_surface_distance_tolerance and zn > topographic_surface_normal_tolerance:
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 < -1+topographic_surface_normal_tolerance:
bottom_surf.append(k)
if len(top_surf) ==0: #assuming that one topo surface need to be selected
_,_,_,_,_,top_surf=get_v_h_list(list_vol,chktop=False)
lp=[]
labelp=[]
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])
labelp.append(list(c)[0])
labelps=Set(labelp)
for c in labelps:
p=cubit.get_center_point("curve",c)
lp.append(p)
for k in list_surf:
center_point = cubit.get_center_point("surface", k)
for p in lp:
try:
if abs((center_point[0] - p[0])/p[0]) <= absorbing_surface_distance_tolerance and abs((center_point[1] - p[1])/p[1]) <= absorbing_surface_distance_tolerance:
absorbing_surf.append(k)
break
except:
if -1 <= center_point[0] <= 1 and -1 <= center_point[1] <= 1:
absorbing_surf.append(k)
break
#
four_side=True
if four_side:
xmintmp,ymintmp,xmaxtmp,ymaxtmp=define_4side_lateral_surfaces()
xmin=list(Set(xmintmp)-Set(xmaxtmp))
xmax=list(Set(xmaxtmp)-Set(xmintmp))
ymin=list(Set(ymintmp)-Set(ymaxtmp))
ymax=list(Set(ymaxtmp)-Set(ymintmp))
abs_xmintmp,abs_xmaxtmp,abs_ymintmp,abs_ymaxtmp=lateral_boundary_are_absorbing(ip,cpuxmin,cpuxmax,cpuymin,cpuymax,cpux,cpuy)
abs_xmin=list(Set(abs_xmintmp)-Set(abs_xmaxtmp))
abs_xmax=list(Set(abs_xmaxtmp)-Set(abs_xmintmp))
abs_ymin=list(Set(abs_ymintmp)-Set(abs_ymaxtmp))
abs_ymax=list(Set(abs_ymaxtmp)-Set(abs_ymintmp))
return absorbing_surf,abs_xmin,abs_xmax,abs_ymin,abs_ymax,top_surf,bottom_surf,xmin,ymin,xmax,ymax
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
## fault surfaces (up/down)
Au = [cubit.get_id_from_name("fault1")]
Ad = [cubit.get_id_from_name("fault2")]
# FOR THE BULK (Seismic wave propagation part for SPECFEM3D)
entities = ['face']
xmin, xmax, ymin, ymax, bottom, topo = absorbing_boundary.define_parallel_absorbing_surf(
)
# The above function is expected to obtain the correct topo and bottom surfaces, but for curved fault this function may fail (I don't know why).
# Here I try to obtain the topo and bottom surface automaticly in case the above function fails.
# If this part also doesn't work well (such as the topography has more than one surfaces), please setup bottom=[surface_list] and topo=[surface_list] manually.
list_surf = cubit.parse_cubit_list("surface", "all")
center_depth = []
for k in list_surf:
center_depth.append(cubit.get_center_point("surface", k)[2])
bottom = numpy.asarray(list_surf)[numpy.argwhere(
center_depth == numpy.amin(center_depth))[:, 0]].tolist()
topo = numpy.asarray(list_surf)[numpy.argwhere(
center_depth == numpy.amax(center_depth))[:, 0]].tolist()
#bottom = [surface_list]
#topo = [surface_list]
if (len(bottom) == 0 or len(topo) == 0):
print "Fail in obtaining the topo and bottom surfaces."
print "Please change setup topo and bottom surfaces manually."
exit()
print "Xmin surface list: ", xmin
print "Xmax surface list: ", xmax
print "Ymin surface list: ", ymin
print "Ymax surface list: ", ymax
print "Bott surface list: ", bottom
def define_absorbing_surf():
"""
define the absorbing surfaces for a layered topological box where boundary are surfaces parallel to the axis.
it returns absorbing_surf,absorbing_surf_xmin,absorbing_surf_xmax,absorbing_surf_ymin,absorbing_surf_ymax,absorbing_surf_bottom,topo_surf
where
absorbing_surf is the list of all the absorbing boundary surf
absorbing_surf_xmin is the list of the absorbing boundary surfaces that correnspond to x=xmin
...
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=[]
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")
# for k in list_surf:
# center_point = cubit.get_center_point("surface", k)
# if abs((center_point[0] - xmin_box)/xmin_box) <= 0.005:
# absorbing_surf_xmin.append(k)
# absorbing_surf.append(k)
# elif abs((center_point[0] - xmax_box)/xmax_box) <= 0.005:
# absorbing_surf_xmax.append(k)
# absorbing_surf.append(k)
# elif abs((center_point[1] - ymin_box)/ymin_box) <= 0.005:
# absorbing_surf_ymin.append(k)
# absorbing_surf.append(k)
# elif abs((center_point[1] - ymax_box)/ymax_box) <= 0.005:
# absorbing_surf_ymax.append(k)
# absorbing_surf.append(k)
# elif abs((center_point[2] - zmin_box)/zmin_box) <= 0.005:
# absorbing_surf_bottom.append(k)
# absorbing_surf.append(k)
# else:
# sbox=cubit.get_bounding_box('surface',k)
# dz=abs((sbox[7] - zmax_box)/zmax_box)
# normal=cubit.get_surface_normal(k)
# zn=normal[2]
# dn=abs(zn-1)
# if dz <= 0.001 and dn < 0.2:
# top_surf.append(k)
#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[0] - xmin_box)/x_len) <= absorbing_surface_distance_tolerance:
absorbing_surf_xmin.append(k)
absorbing_surf.append(k)
elif abs((center_point[0] - xmax_box)/x_len) <= absorbing_surface_distance_tolerance:
absorbing_surf_xmax.append(k)
absorbing_surf.append(k)
elif abs((center_point[1] - ymin_box)/y_len) <= absorbing_surface_distance_tolerance:
absorbing_surf_ymin.append(k)
absorbing_surf.append(k)
elif abs((center_point[1] - ymax_box)/y_len) <= absorbing_surface_distance_tolerance:
absorbing_surf_ymax.append(k)
absorbing_surf.append(k)
elif abs((center_point[2] - zmin_box)/z_len) <= absorbing_surface_distance_tolerance:
absorbing_surf_bottom.append(k)
absorbing_surf.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,absorbing_surf_xmin,absorbing_surf_xmax,absorbing_surf_ymin,absorbing_surf_ymax,absorbing_surf_bottom,top_surf
def hor_distance(c1, c2):
p1 = cubit.get_center_point("curve", c1)
p2 = cubit.get_center_point("curve", c2)
d = (p1[0] - p2[0])**2 + (p1[1] - p2[1])**2
return d
def get_v_h_list(vol_id_list, chktop=False):
"""
return the lists of the cubit ID of vertical/horizontal
surface and vertical/horizontal curves
where v/h is defined by the distance of the z normal component from
the axis direction the parameter cfg.tres is the threshold as
for example if
-tres <= normal[2] <= tres
then the surface is vertical
#
usage: surf_or,surf_vertical,list_curve_or,
list_curve_vertical,bottom,top = get_v_h_list(list_vol,chktop=False)
"""
#
tres = 0.3
try:
_ = len(vol_id_list)
except:
vol_id_list = [vol_id_list]
surf_vertical = []
surf_or = []
list_curve_vertical = []
list_curve_or = []
#
#
for id_vol in vol_id_list:
lsurf = cubit.get_relatives("volume", id_vol, "surface")
for k in lsurf:
normal = cubit.get_surface_normal(k)
center_point = cubit.get_center_point("surface", k)
if -1 * tres <= normal[2] <= tres:
surf_vertical.append(k)
lcurve = cubit.get_relatives("surface", k, "curve")
list_curve_vertical = list_curve_vertical + list(lcurve)
else:
surf_or.append(k)
lcurve = cubit.get_relatives("surface", k, "curve")
list_curve_or = list_curve_or + list(lcurve)
for x in list_curve_or:
try:
list_curve_vertical.remove(x)
except:
pass
# find the top and the bottom surfaces
k = surf_or[0]
center_point = cubit.get_center_point("surface", k)[2]
center_point_top = center_point
center_point_bottom = center_point
top = k
bottom = k
for k in surf_or[1:]:
center_point = cubit.get_center_point("surface", k)[2]
if center_point > center_point_top:
center_point_top = center_point
top = k
elif center_point < center_point_bottom:
center_point_bottom = center_point
bottom = k
# check that a top surface exists
# it assume that the z coord of the center point
if chktop:
k = lsurf[0]
vertical_centerpoint_top = cubit.get_center_point("surface", k)[2]
vertical_zmax_box_top = cubit.get_bounding_box('surface', k)[7]
normal_top = cubit.get_surface_normal(k)
top = k
for k in lsurf:
vertical_centerpoint = cubit.get_center_point("surface", k)[2]
vertical_zmax_box = cubit.get_bounding_box('surface', k)[7]
normal = cubit.get_surface_normal(k)
check = (vertical_centerpoint >= vertical_centerpoint_top) and (
vertical_zmax_box >= vertical_zmax_box_top) and (
normal >= normal_top)
if check:
top = k
if top in surf_vertical:
surf_vertical.remove(top)
if top not in surf_or:
surf_or.append(top)
# if more than one surf is on the top, I get all the surfaces that are in
# touch with top surface but not the vertical surfaces
surftop = list(cubit.get_adjacent_surfaces(
"surface", top)) # top is included in the list
for s in surf_vertical:
try:
surftop.remove(s)
except:
pass
top = surftop
# check that all the surf are Horizontal or vertical
surf_all = surf_vertical + surf_or
if len(surf_all) != len(lsurf):
print 'not all the surf are horizontal or vertical, check the normals'
print 'list of surfaces: ', surf_all
print 'list of vertical surface', surf_vertical
print 'list of horizontal surface', surf_or
bottom = [bottom]
return surf_or, surf_vertical, list_curve_or, \
list_curve_vertical, bottom, top
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
cubit.cmd('sideset 1 add surface %i' % isurf) # N
if np.abs(y0 - ymax) < 0.1:
cubit.cmd('sideset 2 add surface %i' % isurf) # S
if c0[0] == 1 or c0[0] == -1:
if np.abs(x0 - xmin) < 0.1:
cubit.cmd('sideset 3 add surface %i' % isurf) # E
if np.abs(x0 - xmax) < 0.1:
cubit.cmd('sideset 4 add surface %i' % isurf) # W
if c0[2] == 1 or c0[2] == -1:
if np.abs(z0 - zmin) < 0.1:
cubit.cmd('sideset 5 add surface %i' % isurf) # lower
if np.abs(z0 - zmax) < 0.1:
isWell = False
ovol = cubit.get_owning_volume('surface', isurf)
if np.sum((np.array([0, 0]) -
np.array(cubit.get_center_point('volume', ovol)[0:2]))**
2)**0.5 < 0.1:
if np.abs(cubit.get_surface_area(isurf) -
(math.pi * 1.8**2)) < 0.01:
print ovol
isWell = True
if isWell:
cubit.cmd('sideset 7 add surface %i' % (isurf)) # injection
else:
cubit.cmd('sideset 6 add surface %i' % isurf) # upper
hex_ids = np.zeros([0, 3], dtype='int')
hex_xyzs = np.zeros([0, 3], dtype='float')
hex_types = np.zeros([0, 1], dtype='float')
iblock = 0
for ivol in range(1, cubit.get_volume_count() + 1):
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
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)
