def extract_bottom_curves(surf_xmin,surf_ymin,surf_xmax,surf_ymax):
curve_xmin=[]
curve_ymin=[]
curve_xmax=[]
curve_ymax=[]
from sets import Set #UPGRADE.... the sets module is deprecated after python 2.6
for s in surf_xmin:
lcs=cubit.get_relatives("surface",s,"curve")
for lc in lcs:
curve_xmin.append(lc)
for s in surf_xmax:
lcs=cubit.get_relatives("surface",s,"curve")
for lc in lcs:
curve_xmax.append(lc)
for s in surf_ymin:
lcs=cubit.get_relatives("surface",s,"curve")
for lc in lcs:
curve_ymin.append(lc)
for s in surf_ymax:
lcs=cubit.get_relatives("surface",s,"curve")
for lc in lcs:
curve_ymax.append(lc)
curve_xmin=list(Set(curve_xmin))
curve_ymin=list(Set(curve_ymin))
curve_xmax=list(Set(curve_xmax))
curve_ymax=list(Set(curve_ymax))
curve_bottom_xmin=select_bottom_curve(curve_xmin)
curve_bottom_ymin=select_bottom_curve(curve_ymin)
curve_bottom_xmax=select_bottom_curve(curve_xmax)
curve_bottom_ymax=select_bottom_curve(curve_ymax)
#
return curve_bottom_xmin,curve_bottom_ymin,curve_bottom_xmax,curve_bottom_ymax
def extract_bottom_curves(surf_xmin, surf_ymin, surf_xmax, surf_ymax):
curve_xmin = []
curve_ymin = []
curve_xmax = []
curve_ymax = []
from sets import Set #UPGRADE.... the sets module is deprecated after python 2.6
for s in surf_xmin:
lcs = cubit.get_relatives("surface", s, "curve")
for lc in lcs:
curve_xmin.append(lc)
for s in surf_xmax:
lcs = cubit.get_relatives("surface", s, "curve")
for lc in lcs:
curve_xmax.append(lc)
for s in surf_ymin:
lcs = cubit.get_relatives("surface", s, "curve")
for lc in lcs:
curve_ymin.append(lc)
for s in surf_ymax:
lcs = cubit.get_relatives("surface", s, "curve")
for lc in lcs:
curve_ymax.append(lc)
curve_xmin = list(Set(curve_xmin))
curve_ymin = list(Set(curve_ymin))
curve_xmax = list(Set(curve_xmax))
curve_ymax = list(Set(curve_ymax))
curve_bottom_xmin = select_bottom_curve(curve_xmin)
curve_bottom_ymin = select_bottom_curve(curve_ymin)
curve_bottom_xmax = select_bottom_curve(curve_xmax)
curve_bottom_ymax = select_bottom_curve(curve_ymax)
#
return curve_bottom_xmin, curve_bottom_ymin, curve_bottom_xmax, curve_bottom_ymax
def create_volume(surf1,surf2,method='loft'):
if method == 'loft':
cmd='create volume loft surface '+str(surf1)+' '+str(surf2)
cubit.cmd(cmd)
else:
lcurve1=cubit.get_relatives("surface",surf1,"curve")
lcurve2=cubit.get_relatives("surface",surf2,"curve")
couples=coupling_curve(lcurve1,lcurve2)
is_start=cubit.get_last_id('surface')+1
for cs in couples:
cmd='create surface skin curve '+str(cs[1])+' '+str(cs[0])
cubit.cmd(cmd)
is_stop=cubit.get_last_id('surface')
cmd="create volume surface "+str(surf1)+' '+str(surf2)+' '+str(is_start)+' to '+str(is_stop)+" heal keep"
cubit.cmd(cmd)
def create_volume(surf1,surf2,method='loft'):
if method == 'loft':
cmd='create volume loft surface '+str(surf1)+' '+str(surf2)
cubit.cmd(cmd)
else:
lcurve1=cubit.get_relatives("surface",surf1,"curve")
lcurve2=cubit.get_relatives("surface",surf2,"curve")
couples=coupling_curve(lcurve1,lcurve2)
is_start=cubit.get_last_id('surface')+1
for cs in couples:
cmd='create surface skin curve '+str(cs[1])+' '+str(cs[0])
cubit.cmd(cmd)
is_stop=cubit.get_last_id('surface')
cmd="create volume surface "+str(surf1)+' '+str(surf2)+' '+str(is_start)+' to '+str(is_stop)+" heal"
cubit.cmd(cmd)
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 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 fixCurves(self):
small = self.root.radius/100
cvs = cubit.get_relatives("volume", self.vol, "curve")
for x in range(0, len(cvs)):
type1 = cubit.get_curve_type(cvs[x])
virtual1 = cubit.is_virtual("curve", cvs[x])
if type1 == "Ellipse curve" or type1 == "Arc curve" or virtual1 or type1 == "Spline curve":
vts1 = cubit.get_relatives("curve", cvs[x], "vertex")
for y in range(0, len(cvs)):
type2 = cubit.get_curve_type(cvs[y])
virtual2 = cubit.is_virtual("curve", cvs[y])
vts2 = cubit.get_relatives("curve", cvs[y], "vertex")
equal = False
arcEli = type2 == "Ellipse curve" or type2 == "Arc curve" or type2 == "Spline curve"
equal = type1 == type2 or virtual2 or (virtual1 and arcEli)
if equal and x != y and len(vts1) > 1 and len(vts2) > 1:
if vts1[0] == vts2[0] or vts1[0] == vts2[1] or vts1[1] == vts2[0] or vts1[1] == vts2[1]:
cubit.set_modified()
geo.compositeCurve(cvs[x], cvs[y])
if cubit.is_modified():
return True
return False
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 curver_start_end(C,dxstrt,dxend,direct='l',unit='*km'):
Vtup = cubit.get_relatives("curve", C.id(), "vertex")
if cubit.vertex(Vtup[1]).coordinates()[0] > cubit.vertex(Vtup[0]).coordinates()[0]:
vr = cubit.vertex(Vtup[1])
vl = cubit.vertex(Vtup[0])
else:
vr = cubit.vertex(Vtup[0])
vl = cubit.vertex(Vtup[1])
if direct == 'l':
vstart = vr
elif direct == 'r':
vstart = vl
komand = "curve " + str(C.id()) + " scheme bias fine size {" + str(dxstrt) + unit + "} coarse size {" + str(dxend) + unit + "} start vertex " + str(vstart.id())
print komand
cubit.silent_cmd(komand)
return None
def define_absorbing_surf_sphere():
try:
cubit.cmd('comment')
except:
try:
import cubit
cubit.init([""])
except:
print 'error importing cubit'
import sys
sys.exit()
surf = []
list_surf = cubit.parse_cubit_list("surface", "all")
for s in list_surf:
v = cubit.get_relatives('surface', s, 'volume')
if len(v) == 1:
surf.append(s)
return surf
def define_absorbing_surf_sphere():
try:
cubit.cmd('comment')
except:
try:
import cubit
cubit.init([""])
except:
print 'error importing cubit'
import sys
sys.exit()
surf=[]
list_surf=cubit.parse_cubit_list("surface","all")
for s in list_surf:
v=cubit.get_relatives('surface',s,'volume')
if len(v) == 1:
surf.append(s)
return surf
def curver_start_end(C, dxstrt, dxend, direct='l', unit='*km'):
Vtup = cubit.get_relatives("curve", C.id(), "vertex")
if cubit.vertex(Vtup[1]).coordinates()[0] > cubit.vertex(
Vtup[0]).coordinates()[0]:
vr = cubit.vertex(Vtup[1])
vl = cubit.vertex(Vtup[0])
else:
vr = cubit.vertex(Vtup[0])
vl = cubit.vertex(Vtup[1])
if direct == 'l':
vstart = vr
elif direct == 'r':
vstart = vl
komand = "curve " + str(C.id()) + " scheme bias fine size {" + str(
dxstrt) + unit + "} coarse size {" + str(
dxend) + unit + "} start vertex " + str(vstart.id())
print komand
cubit.silent_cmd(komand)
return None
def boundary(self):
boundary = []
surfs = cubit.get_relatives("volume", self.vol, "surface")
for x in range(6, len(surfs)):
tris = cubit.get_surface_tris(surfs[x])
for y in range(0, len(tris)):
nodes = cubit.get_connectivity("tri", tris[y])
p1 = cubit.get_nodal_coordinates(nodes[0])
p2 = cubit.get_nodal_coordinates(nodes[1])
p3 = cubit.get_nodal_coordinates(nodes[2])
u_0 = [p2[0]-p1[0],p2[1]-p1[1],p2[2]-p1[2]]
u_1 = [p3[0]-p1[0],p3[1]-p1[1],p3[2]-p1[2]]
u1 = geo2.crossProduct(u_0, u_1)
u1 = geo2.getVector4_3(u1)
geo2.normalizeVector(u1)
# if y == 0:
# center_point = cubit.get_center_point("tri", tris[y])
# cubit.cmd("create curve location %f %f %f direction %f %f %f length %f" %(center_point[0],center_point[1],center_point[2],u1[0],u1[1],u1[2],self.root.radius))
element = [nodes[0]-1, nodes[1]-1, nodes[2]-1, u1[0], u1[1], u1[2]]
boundary.append(element)
return boundary
def saveMeshPoisson(self):
nNodes = cubit.get_node_count()
nTets = cubit.get_tet_count()
meshFile = open(folder+"meshPoisson.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(' <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="1.0" />\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.close()
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 get_ordered_node_surf(lsurface, icurve):
if not isinstance(lsurface, str):
lsurf = list2str(lsurface)
#
if not isinstance(icurve, str):
icurvestr = str(icurve)
# initializes
orient_nodes_surf = []
nodes_curve = []
#
#get the nodes on a surface, I don't use the method get_surface_nodes since it has different behavior in cubit12.2 and cubit13.2+
k = cubit.get_id_from_name('sl')
if k != 0:
cubit.cmd('del group sl')
else:
print 'initializing group sl'
cubit.cmd("group 'sl' add node in surf " + lsurf)
group1 = cubit.get_id_from_name("sl")
nodes_ls = list(cubit.get_group_nodes(group1))
nnode = len(nodes_ls)
#
#get the nodes on curves
orient = []
k = cubit.get_id_from_name('n1')
if k != 0:
cubit.cmd('del group n1')
else:
print 'initializing group n1'
cubit.cmd("group 'n1' add node in curve " + icurvestr)
x = cubit.get_bounding_box('curve', icurve)
# checks if anything to do
if len(x) == 0:
return nodes_curve, orient_nodes_surf
# gets nodes
if x[2] > x[5]:
idx = 0
else:
idx = 1
group1 = cubit.get_id_from_name("n1")
nodes1 = list(cubit.get_group_nodes(group1))
for n in nodes1:
v = cubit.get_nodal_coordinates(n)
orient.append(v[idx])
result = zip(orient, nodes1)
result.sort()
nodes2 = [c[1] for c in result]
for n in nodes2:
try:
nodes_ls.remove(n)
except:
pass
orient_nodes_surf = orient_nodes_surf + nodes2
#
while len(orient_nodes_surf) < nnode:
cubit.cmd('del group n1')
cubit.cmd("group 'n1' add node in edge in node " +
str(nodes2).replace('[', ' ').replace(']', ' '))
group1 = cubit.get_id_from_name("n1")
nodes1 = list(cubit.get_group_nodes(group1))
orient = []
nd = []
for n in nodes1:
if n in nodes_ls:
v = cubit.get_nodal_coordinates(n)
orient.append(v[idx])
nd.append(n)
result = zip(orient, nd)
result.sort()
nodes2 = [c[1] for c in result]
for n in nodes2:
try:
nodes_ls.remove(n)
except:
pass
orient_nodes_surf = orient_nodes_surf + nodes2
#get the vertical curve
curve_vertical = []
for s in lsurface:
lcs = cubit.get_relatives("surface", s, "curve")
for l in lcs:
x = cubit.get_bounding_box('curve', l)
length = [(x[2], 1), (x[5], 2), (x[8], 3)]
length.sort()
if length[-1][1] == 3:
curve_vertical.append(l)
#
kcurve = list2str(curve_vertical)
k = cubit.get_id_from_name('curve_vertical')
if k != 0:
cubit.cmd('del group curve_vertical')
else:
print 'initializing group curve_vertical'
cubit.cmd("group 'curve_vertical' add node in curve " + kcurve)
group1 = cubit.get_id_from_name('curve_vertical')
nodes_curve = list(cubit.get_group_nodes(group1))
for n in nodes_curve:
try:
orient_nodes_surf.remove(n)
except:
pass
#
return nodes_curve, orient_nodes_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_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_ascii_regulargrid_mpiregularmap(filename=None,
verticalsandwich=False,
onlysurface=False):
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, cubit_command_check
#
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 as lvolume
if cfg.localdir_is_globaldir:
if iproc == 0 or not mpiflag:
coordx_0, coordy_0, elev_0, nx_0, ny_0 = lvolume.read_grid(
filename)
print 'end 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 = lvolume.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)
#
#
# length of x slide for chunk
xlength = (cfg.xmax - cfg.xmin) / float(cfg.nproc_xi)
# length of y slide for chunk
ylength = (cfg.ymax - cfg.ymin) / float(cfg.nproc_eta)
# 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
elif cfg.topflat and inz == nlayer - 1:
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_top)
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_top)
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_top)
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_top)
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:
print "top_flat is not a valid option for sandwich"
else:
print inz, 'layer'
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):
for ix in range(nxmin_cpu, nxmax_cpu + 1):
zvertex = elev[ix, iy, inz]
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)
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 ValueError('error creating the surface')
#
else:
raise ValueError(
'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:
if cfg.volumecreation_method != 'loft':
ner = cubit.get_error_count()
create_volume(inz, inz + 1, method='loft')
ner2 = cubit.get_error_count()
if ner != ner2:
print 'ERROR creating volume'
break
else:
print 'ERROR creating volume'
break
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)
import os
import sys
#Domain parameters
Lx = 250
Ly = 200
depth = 50
Cx = Lx / 2
Cy = Ly / 2
mesh_size = 2.5
cubit.cmd('brick x ' + str(Lx) + ' y ' + str(Ly) + ' z ' + str(depth))
cubit.cmd('volume 1 move x ' + str(Lx / 2) + ' y ' + str(Ly / 2) + ' z ' +
str(-depth / 2))
id_intern = cubit.get_last_id("volume")
s = cubit.get_relatives("volume", id_intern, "surface")
print s
side_xmin = []
side_xmax = []
side_ymin = []
side_ymax = []
side_zmin = []
side_xmax.append(s[5])
side_xmin.append(s[3])
side_ymax.append(s[4])
side_ymin.append(s[2])
side_zmin.append(s[1])
surf_id = s[0]
#meshing
cubit.cmd('volume all size ' + str(mesh_size))
# torre means tower, here pile
id_torre_surf_orig = [i for i in range(nt)]
id_torre_surf = [i for i in range(4 * nt)]
#each pile is divided into 4 surfaces after imprint and merge with 4 soil layers
id_layer0 = [i for i in range(nt + 1)]
id_layer1 = [i for i in range(nt + 1)]
id_layer2 = [i for i in range(nt + 1)]
id_layer3 = [i for i in range(1)]
#sheet body are volume, though surface-like
for n in range(0, nt, 1):
fid2.write("%04.1f\n" % (xr + dx * n))
id_torre[n], id_torre_surf_orig[n], id_curv = add_beam(
xr + dx * n, hr - n * dh, lr)
c = cubit.get_relatives("volume", id_torre[n], "curve")
bordo[n] = c[2]
cmd = 'imprint volume ' + str(id_base0) + ' ' + str(id_base1) + ' ' + str(
id_base2) + ' ' + str(id_base3) + ' with ' + str(id_torre[n])
cubit.cmd(cmd)
cmd = 'merge volume ' + str(id_base0) + ' ' + str(id_base1) + ' ' + str(
id_base2) + ' ' + str(id_base3) + ' ' + str(id_torre[n])
cubit.cmd(cmd)
p = cubit.get_relatives("volume", id_torre[n], "surface")
id_torre_surf[4 * n] = p[0]
id_torre_surf[4 * n + 1] = p[1]
id_torre_surf[4 * n + 2] = p[2]
id_torre_surf[4 * n + 3] = p[3]
cmd = 'surf ' + str(id_torre_surf[4 * n]) + ' ' + str(
id_torre_surf[4 * n + 1]) + ' ' + str(
id_torre_surf[4 * n + 2]) + ' ' + str(
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_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
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 genSons(self, branch):
ipr = self.points[branch.initialPoint]
fpr = self.points[branch.finalPoint]
fp = self.points[branch.son1.finalPoint]
fp2 = self.points[branch.son2.finalPoint]
lenght = geo.distance(ipr, fpr)
t=(lenght-branch.radius)/lenght
ref = [(1-t)*ipr[0]+t*fpr[0],((1-t)*ipr[1]+t*fpr[1]),((1-t)*ipr[2]+t*fpr[2])]
t2=(lenght+branch.radius)/lenght
ref2 = [(1-t2)*ipr[0]+t2*fpr[0],((1-t2)*ipr[1]+t2*fpr[1]),((1-t2)*ipr[2]+t2*fpr[2])]
u_0 = [fp[0]-fpr[0],fp[1]-fpr[1],fp[2]-fpr[2]]
u_1 = [fp2[0]-fpr[0],fp2[1]-fpr[1],fp2[2]-fpr[2]]
u_2 = [ref[0]-fp2[0],ref[1]-fp2[1],ref[2]-fp2[2]]
u1 = geo2.crossProduct(u_0, u_1)
u1 = geo2.getVector4_3(u1)
geo2.normalizeVector(u1)
u2 = geo2.crossProduct(u_0, u_2)
u2 = geo2.getVector4_3(u2)
geo2.normalizeVector(u2)
coords = geo2.rotateByAxis(geo2.getVector4_3(ref), geo2.getVector4_3(fpr), u1, -90)
vAux1 = geo.createVertex(coords[0],coords[1],coords[2])
vAP = geo.createVertex(ref2[0],ref2[1],ref2[2])
#
circleAux = geo.createCircleNormal2(branch.finalPoint+1,vAux1,vAux1,branch.radius,branch.index)
v1 = geo.createVertexOnCurveFraction(circleAux, 0.25)
v2 = geo.createVertexOnCurveFraction(circleAux, 0.75)
geo.deleteCurve(circleAux)
arc1 = geo.createCircleNormal2(branch.finalPoint+1, v1, v2, branch.radius, branch.index)
arc2 = geo.createCircleNormal2(branch.finalPoint+1, v2, v1, branch.radius, branch.index)
vts1 = cubit.get_relatives("curve", arc1, "vertex")
vts2 = cubit.get_relatives("curve", arc2, "vertex")
l1 = geo.createLine(vts1[0], vts1[1])
#l2 = geo.createLine(vts2[0], vts2[1])
t=(lenght-branch.radius*1)/lenght
u_3 = [cubit.vertex(vts1[0]).coordinates()[0]-cubit.vertex(vts1[1]).coordinates()[0],cubit.vertex(vts1[0]).coordinates()[1]-cubit.vertex(vts1[1]).coordinates()[1],cubit.vertex(vts1[0]).coordinates()[2]-cubit.vertex(vts1[1]).coordinates()[2]]
u3 = geo2.getVector4_3(u_3)
geo2.normalizeVector(u3)
refE1 = [(1-t)*ipr[0]+t*fpr[0],((1-t)*ipr[1]+t*fpr[1]),((1-t)*ipr[2]+t*fpr[2])]
coords = geo2.rotateByAxis(geo2.getVector4_3(refE1), geo2.getVector4_3(fpr), u3, 90)
vE = geo.createVertex(coords[0],coords[1],coords[2])
mid = geo.createVertexOnCurveFraction(l1, 0.5)
eli = geo.createEllipseFull(vts1[0], vE, mid)
eli1 = geo.splitCurve2(eli, vts1[0], vts1[1])
eli2 = eli1-1
e1 = geo.createEllipse(vts1[0], vAP, branch.finalPoint+1)
e2 = geo.createEllipse(vts1[1], vAP, branch.finalPoint+1)
e3 = geo.createCombineCurve([e1,e2])
#e3 = geo.createSpline(vts1[0], vAP, vts1[1])
circleI = branch.circleF
uaux = cubit.vertex(v1).coordinates()
uaux2 = cubit.vertex(v2).coordinates()
u = [uaux2[0]-uaux[0],uaux2[1]-uaux[1],uaux2[2]-uaux[2]]
u = geo2.getVector4_3(u)
geo2.normalizeVector(u)
ip = self.points[branch.son1.initialPoint]
fp = self.points[branch.son1.finalPoint]
fps = self.points[branch.son1.son1.finalPoint]
lenght = geo.distance(ip, fp)
t=(lenght-branch.son1.radius)/lenght
ref = [(1-t)*ip[0]+t*fp[0],((1-t)*ip[1]+t*fp[1]),((1-t)*ip[2]+t*fp[2])]
arcsf1 = self.genArc2(branch.son1, branch.son1.finalPoint+1,ref,u1,branch.son1.radius,1)
branch.son1.circleI = circleI
branch.son1.circleF = arcsf1[2]
branch.son1.link = arcsf1[2]
branch.son1.tube = Tube([arc1,e3], arcsf1)
branch.son1.tube.line = l1
ip = self.points[branch.son2.initialPoint]
fp = self.points[branch.son2.finalPoint]
fps = self.points[branch.son2.son1.finalPoint]
lenght = geo.distance(ip, fp)
t=(lenght-branch.son2.radius)/lenght
ref = [(1-t)*ip[0]+t*fp[0],((1-t)*ip[1]+t*fp[1]),((1-t)*ip[2]+t*fp[2])]
arcsf2 = self.genArc2(branch.son2, branch.son2.finalPoint+1,ref,u1,branch.son2.radius,2)
branch.son2.circleI = circleI
branch.son2.circleF = arcsf2[2]
branch.son2.link = arcsf2[2]
branch.son2.tube = Tube([arc2,e3], arcsf2)
branch.son2.tube.line = l1
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()
def get_ordered_node_surf(lsurface,icurve):
if not isinstance(lsurface,str):
lsurf=list2str(lsurface)
#
if not isinstance(icurve,str):
icurvestr=str(icurve)
orient_nodes_surf=[]
#
#get the nodes on a surface, I don't use the method get_surface_nodes since it has different behavior in cubit12.2 and cubit13.2+
k=cubit.get_id_from_name('sl')
if k!=0:
cubit.cmd('del group sl')
else:
print 'initializing group sl'
cubit.cmd("group 'sl' add node in surf "+lsurf)
group1 = cubit.get_id_from_name("sl")
nodes_ls =list(cubit.get_group_nodes(group1))
nnode=len(nodes_ls)
#
#get the nodes on curves
orient=[]
k=cubit.get_id_from_name('n1')
if k!=0:
cubit.cmd('del group n1')
else:
print 'initializing group n1'
cubit.cmd("group 'n1' add node in curve "+icurvestr)
x=cubit.get_bounding_box('curve', icurve)
if x[2]>x[5]:
idx=0
else:
idx=1
group1 = cubit.get_id_from_name("n1")
nodes1 = list(cubit.get_group_nodes(group1))
for n in nodes1:
v = cubit.get_nodal_coordinates(n)
orient.append(v[idx])
result=zip(orient,nodes1)
result.sort()
nodes2=[c[1] for c in result]
for n in nodes2:
try:
nodes_ls.remove(n)
except:
pass
orient_nodes_surf=orient_nodes_surf+nodes2
#
while len(orient_nodes_surf) < nnode:
cubit.cmd('del group n1')
cubit.cmd("group 'n1' add node in edge in node "+str(nodes2).replace('[',' ').replace(']',' '))
group1 = cubit.get_id_from_name("n1")
nodes1 = list(cubit.get_group_nodes(group1))
orient=[]
nd=[]
for n in nodes1:
if n in nodes_ls:
v = cubit.get_nodal_coordinates(n)
orient.append(v[idx])
nd.append(n)
result=zip(orient,nd)
result.sort()
nodes2=[c[1] for c in result]
for n in nodes2:
try:
nodes_ls.remove(n)
except:
pass
orient_nodes_surf=orient_nodes_surf+nodes2
#get the vertical curve
curve_vertical=[]
for s in lsurface:
lcs=cubit.get_relatives("surface",s,"curve")
for l in lcs:
x=cubit.get_bounding_box('curve', l)
length=[(x[2],1),(x[5],2),(x[8],3)]
length.sort()
if length[-1][1] == 3:
curve_vertical.append(l)
#
kcurve=list2str(curve_vertical)
k=cubit.get_id_from_name('curve_vertical')
if k!=0:
cubit.cmd('del group curve_vertical')
else:
print 'initializing group curve_vertical'
cubit.cmd("group 'curve_vertical' add node in curve "+kcurve)
group1 = cubit.get_id_from_name('curve_vertical')
nodes_curve = list(cubit.get_group_nodes(group1))
for n in nodes_curve:
try:
orient_nodes_surf.remove(n)
except:
pass
#
return nodes_curve,orient_nodes_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:
_ = 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
xmax = cubit.get_total_bounding_box('volume', cubit.get_entities('volume'))[1]
ymin = cubit.get_total_bounding_box('volume', cubit.get_entities('volume'))[3]
ymax = cubit.get_total_bounding_box('volume', cubit.get_entities('volume'))[4]
zmin = cubit.get_total_bounding_box('volume', cubit.get_entities('volume'))[6]
zmax = cubit.get_total_bounding_box('volume', cubit.get_entities('volume'))[7]
cubit.cmd('webcut volume all with cylinder radius 20.0 axis z center 0,0,0')
cubit.cmd('webcut volume all with cylinder radius 2.0 axis z center 0,0,0')
cubit.cmd('webcut volume all with cylinder radius 1.8 axis z center 0,0,0')
for icurve in cubit.get_entities('curve'):
l = cubit.get_curve_length(icurve)
r1 = 2 * math.pi * 1.8
r2 = 2 * math.pi * 2.0
r3 = 2 * math.pi * 20.0
if cubit.get_relatives('curve', icurve, 'volume') > 36:
if np.abs(l - r1) < 0.01 or np.abs(l - r2) < 0.01 or np.abs(l -
r3) < 0.01:
cubit.cmd('curve %i interval 6' % icurve)
for ivol in cubit.get_entities('volume'):
for icurve in cubit.get_relatives('volume', ivol, 'curve'):
v = [
cubit.vertex(ivertex)
for ivertex in cubit.get_relatives('curve', icurve, 'vertex')
]
if len(v) == 2:
x0, y0, z0 = v[0].coordinates()
x1, y1, z1 = v[1].coordinates()
if np.abs(x0 - x1) < 0.01 and np.abs(y0 - y1) < 0.01:
z = 0.5 * (z0 + z1)
cubit.cmd("Graphics Pause")
(OUTSIDE_3D,
GRAINS_3D) = pymef90.PacmanCoinCrystalCreate(R, r, lz, thetac, xc, ngrains)
cubit.cmd("Display")
###
### imprint and merge
###
#for i in range(len(GRAINS_3D)):
# cubit.cmd("imprint volume in OUTSIDE_3D with volume in Grain%i" % (i-1))
cubit.cmd("imprint all")
cubit.cmd("merge all")
###
### find edges of the domain and create nodesets
###
allcurves = []
allcurves.extend(cubit.get_relatives("volume", OUTSIDE_3D, "curve"))
for grain in GRAINS_3D:
for vol in grain:
allcurves.extend(cubit.get_relatives("volume", vol, "curve"))
alledges = [
c for c in allcurves if len(cubit.get_relatives("curve", c, "volume")) == 1
]
for e in alledges:
cubit.cmd('group "ALLEDGES" add curve %i' % e)
cubit.cmd("nodeset 1 curve with z_min>0 in ALLEDGES")
cubit.cmd("delete ALLEDGES")
cubit.cmd("nodeset 1 remove curve with z_min>0 and x_max=%f" % R)
cubit.cmd("nodeset 2 curve with z_min>0 and x_max=%f" % R)
###
### create element blocks
###
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)
