def computeNonlinearConstraint(x, y):
nlcon = numpy.zeros(len(x))
target_surface = cubit.surface(1)
vertex_on_surface = [False for i in range(0, len(x))]
# First, determine whether the nonlinear constraint is satisfied
for i in range(0, len(x)):
vertex_on_surface[i] = target_surface.point_containment(
[x[i], y[i], 0.])
# Second, determine the magnitude of the nonlinear constraint value
# which is the distance of the point to the closest curve
cid = cubit.get_entities("Curve")
for i in range(0, len(x)):
dist = numpy.zeros(len(cid))
pXYZ = numpy.array([x[i], y[i], 0.])
for c in range(0, 1):
C = cubit.curve(cid[c])
cpXYZ = numpy.array(C.closest_point(pXYZ))
dist[c] = numpy.linalg.norm(cpXYZ - pXYZ)
if vertex_on_surface[i] == True:
# Nonlinear constraint is satisfied
nlcon[i] = -1. * numpy.min(dist)
else:
# Nonlinear constraint not satisfied
nlcon[i] = +1. * numpy.min(dist)
return nlcon
def geom_cubit_solo(configfile):
if not os.path.isfile(configfile):
raise Exception("ERR: CONFIG FILE DON'T EXIST !!!")
# READ CONFIGFILE
cf = ConfigParser.ConfigParser()
cf.optionxform = str
cf.read(configfile)
bathyfile = cf.get('Input', 'bathyfile')
slabfile = cf.get('Input', 'slabfile')
left_extension = cf.getfloat('Parameters',
'left_extension') # (always positive)
right_extension = cf.getfloat('Parameters', 'right_extension')
down_limit = cf.getfloat('Parameters', 'down_limit') # (always positive)
EET_OP = cf.getfloat('Parameters', 'eet_op') # Thickness of the OP Litho
EET_DP = cf.getfloat('Parameters', 'eet_dp') # Thickness of the DP Litho
# backstop_bool=cf.getboolean('Parameters','backstop_bool') # True or False
x_backstop = cf.getfloat('Parameters', 'backstop_distance')
dip_backstop = cf.getfloat('Parameters', 'backstop_angle')
output_path = cf.get('Output', 'output_path')
output_file_prefix = cf.get('Output', 'output_prefix')
output_file_suffix = cf.get('Output', 'output_suffix')
output_pathfile = output_path + '/' + output_file_prefix + '_' + output_file_suffix + '.exo'
dx1 = cf.getfloat('Parameters', 'dx_fine')
dx2 = cf.getfloat('Parameters', 'dx_coarse')
# =======================================================================
# PRIOR DESIGN
# =======================================================================
# Loading the BATHY and SLAB files
XYbathy = np.loadtxt(bathyfile)
XYslab = np.loadtxt(slabfile)
# Creating the bottom of the slab
XslabBot, YslabBot, _ = rcl.shift_thickness(XYslab[:, 0], XYslab[:, 1],
EET_DP)
# Creating the bounding points in a dictionnary
outpts = rcl.make_bounding_points(XYbathy[:, 0], XYbathy[:, 1], XYslab[:,
0],
XYslab[:, 1], EET_OP, EET_DP, down_limit,
left_extension, right_extension)
# Creating the backstop
Xbackstop, Ybackstop = rcl.make_backstop(XYbathy[:, 0],
XYbathy[:, 1],
XYslab[:, 0],
XYslab[:, 1],
x_backstop,
dip_backstop,
dupdown=150)
# Adding the 'Bottom_Litho_DP' point to the Litho_DP Bottom
rcl.add_point_in_list(XslabBot, YslabBot, outpts['vBottom_Litho_DP'])
# Changing the description concept : Bathy & Slab ==> OP & DP
Xop, Yop, Xdp, Ydp = rcl.bathyslab_2_OPDPtop(XYbathy[:, 0], XYbathy[:, 1],
XYslab[:, 0], XYslab[:, 1])
# Adding the limit points of OP & DP
Xop, Yop = rcl.add_point_in_list(Xop, Yop, outpts['vBathy_OP'])
Xdp, Ydp = rcl.add_point_in_list(Xdp, Ydp, outpts['vBathy_DP'])
# PLOT FOR SECURITY
#plt.clf()
#plt.axis('equal')
#plt.plot(XYbathy[:,0],XYbathy[:,1],'+b')
#plt.plot(XYslab[:,0],XYslab[:,1],'r+-')
#plt.plot(XslabBot,YslabBot,'k+-')
#plt.plot(Xbackstop,Ybackstop,'*-y')
#for p in outpts.viewvalues():
# plt.plot(p[0],p[1],'*k')
#plt.plot(Xop,Yop,'b-')
#plt.plot(Xdp,Ydp,'r-')
# =======================================================================
# CUBIT MESHING
# =======================================================================
# Initalisation
cubit.cmd('reset')
cubit.cmd("#{Units('si')}")
# Chargement des courbes
rcl.list_2_curve(Xop, Yop, 'Top_Litho_OP')
rcl.list_2_curve(Xdp, Ydp, 'Top_Litho_limit_DP')
rcl.list_2_curve(XslabBot, YslabBot, 'Bottom_Litho_DP')
rcl.list_2_curve(Xbackstop, Ybackstop, 'Backstop')
# Chargement des Points Isoles
rcl.dico_2_listofvertices(outpts)
## fabrication de "courbes-segments" a partir de vertex
v_Bottom_Litho_OP = cubit.vertex(
cubit.get_id_from_name('vBottom_Litho_OP'))
v_Bathy_DP = rcl.find_extrema(
cubit.curve(cubit.get_id_from_name("Top_Litho_limit_DP")), 'r')
v_Bathy_OP = rcl.find_extrema(
cubit.curve(cubit.get_id_from_name('Top_Litho_OP')), 'l')
v_Bottom_Litho_DP = rcl.find_extrema(
cubit.curve(cubit.get_id_from_name("Bottom_Litho_DP")), 'r')
v_scratch = cubit.vertex(cubit.get_id_from_name('vscratch'))
v_Bottom_Astheno_OP = cubit.vertex(
cubit.get_id_from_name('vBottom_Astheno_OP'))
v_Bottom_Astheno_DP = cubit.vertex(
cubit.get_id_from_name('vBottom_Astheno_DP'))
#
rcl.vertices_2_curve(v_Bottom_Litho_OP, v_Bottom_Astheno_OP,
'Edge_Astheno_OP')
rcl.vertices_2_curve(v_Bottom_Litho_OP, v_scratch, 'Bottom_Litho_OP_PROTO')
rcl.vertices_2_curve(v_Bottom_Litho_OP, v_Bathy_OP, 'Edge_Litho_OP')
rcl.vertices_2_curve(v_Bottom_Astheno_OP, v_Bottom_Astheno_DP,
'Bottom_PROTO')
rcl.vertices_2_curve(v_Bathy_DP, v_Bottom_Litho_DP, 'Edge_Litho_DP')
rcl.vertices_2_curve(v_Bottom_Litho_DP, v_Bottom_Astheno_DP,
'Edge_Astheno_DP')
## Split des courbes
rcl.double_split_desc('Bottom_Litho_OP_PROTO', 'Top_Litho_limit_DP')
rcl.double_split_desc("Bottom_PROTO", "Top_Litho_limit_DP_1")
rcl.double_split_desc("Bottom_PROTO_2", "Bottom_Litho_DP")
rcl.double_split_desc("Backstop", "Top_Litho_limit_DP_2")
rcl.double_split_desc("Top_Litho_OP", "Backstop_1")
rcl.double_split_desc("Top_Litho_limit_DP_2_2", "Top_Litho_OP_2")
if True:
# ## suppression des petits morceaux
rcl.destroy_curve_desc("Top_Litho_limit_DP_1_1")
rcl.destroy_curve_desc("Bottom_Litho_DP_1")
rcl.destroy_curve_desc("Backstop_2")
rcl.destroy_curve_desc("Bottom_Litho_OP_PROTO_2")
rcl.destroy_curve_desc("Backstop_1_1")
# ## renommage des courbes
rcl.rename_curve_desc(7, 'Edge_Litho_OP')
rcl.rename_curve_desc(5, 'Edge_Astheno_OP')
rcl.rename_curve_desc(9, 'Edge_Litho_DP')
rcl.rename_curve_desc(10, 'Edge_Astheno_DP')
rcl.rename_curve_desc("Top_Litho_limit_DP_2_1", 'Contact_OP_DP')
rcl.rename_curve_desc("Top_Litho_limit_DP_2_2_1", 'Contact_Prism_DP')
rcl.rename_curve_desc("Backstop_1_2", 'Contact_Prism_OP')
rcl.rename_curve_desc("Top_Litho_OP_2_1", 'Top_Litho_DP')
rcl.rename_curve_desc("Top_Litho_OP_2_2", 'Top_Prism')
rcl.rename_curve_desc("Top_Litho_OP_1", 'Top_Litho_OP')
rcl.rename_curve_desc("Bottom_PROTO_2_2", 'Bottom_Astheno_DP')
rcl.rename_curve_desc("Bottom_Litho_DP_2", 'Bottom_Litho_DP')
rcl.rename_curve_desc("Bottom_PROTO_1", 'Bottom_Astheno_OP')
rcl.rename_curve_desc("Bottom_Litho_OP_PROTO_1", 'Bottom_Litho_OP')
rcl.rename_curve_desc("Bottom_PROTO_2_1", 'Front_Litho_DP')
rcl.rename_curve_desc("Top_Litho_limit_DP_1_2",
'Astheno_Litho_Contact')
# # creation des surfaces
rcl.create_surface_desc(
["Edge_Astheno_DP", "Bottom_Astheno_DP", "Bottom_Litho_DP"])
rcl.create_surface_desc([
"Front_Litho_DP", "Bottom_Litho_DP", "Edge_Litho_DP",
"Top_Litho_DP", "Contact_Prism_DP", "Contact_OP_DP",
"Astheno_Litho_Contact"
])
rcl.create_surface_desc([
"Bottom_Astheno_OP", "Astheno_Litho_Contact", "Bottom_Litho_OP",
"Edge_Astheno_OP"
])
rcl.create_surface_desc([
"Bottom_Litho_OP", "Edge_Litho_OP", "Top_Litho_OP",
"Contact_Prism_OP", "Contact_OP_DP"
])
rcl.create_surface_desc(
["Top_Prism", "Contact_Prism_DP", "Contact_Prism_OP"])
# # renomage des surfaces
cubit.surface(1).entity_name('Astheno_DP')
cubit.surface(2).entity_name('Litho_DP')
cubit.surface(3).entity_name('Astheno_OP')
cubit.surface(4).entity_name('Litho_OP')
cubit.surface(5).entity_name('Prisme')
# Fusion des surfaces
cubit.cmd('delete vertex all')
cubit.cmd('imprint all')
cubit.cmd('merge all')
cubit.cmd('stitch volume all')
rcl.rename_curve_desc(45, 'Astheno_Litho_Contact')
cubit.cmd('surface all scheme trimesh')
cubit.cmd('curve all scheme default')
cubit.cmd('surface all sizing function none')
# nouveau decoupage des courbes
rcl.curver_desc("Contact_Prism_DP", dx1)
rcl.curver_desc("Contact_Prism_OP", dx1)
rcl.curver_desc("Top_Prism", dx1)
rcl.curver_desc("Bottom_Litho_DP", dx2)
rcl.curver_desc("Bottom_Astheno_OP", dx2)
rcl.curver_desc("Front_Litho_DP", dx2)
rcl.curver_desc("Bottom_Astheno_DP", dx2)
rcl.curver_desc("Edge_Astheno_OP", dx2)
rcl.curver_desc("Edge_Litho_OP", dx2)
rcl.curver_desc("Edge_Astheno_DP", dx2)
rcl.curver_desc("Edge_Litho_DP", dx2)
rcl.curver_desc("Contact_OP_DP", dx1)
rcl.curver_start_end_desc("Bottom_Litho_OP", dx1, dx2, 'l')
rcl.curver_start_end_desc("Top_Litho_OP", dx1, dx2, 'l')
rcl.curver_start_end_desc("Top_Litho_DP", dx1, dx2, 'r')
rcl.curver_start_end_desc("Astheno_Litho_Contact", dx1, dx2, 'l')
# fabrication du mesh
cubit.cmd('mesh surface all')
cubit.cmd('surface all smooth scheme condition number beta 1.7 cpu 10')
cubit.cmd('smooth surface all')
cubit.cmd('surface 1 size auto factor 5')
## Fabrication de groupe et de nodeset
for i, s in enumerate(cubit.get_entities("surface")):
S = cubit.surface(s)
cubit.cmd('block ' + str(i + 1) + ' surface ' + S.entity_name())
cubit.cmd('block ' + str(i + 1) + ' name "' + S.entity_name() +
' "')
rcl.create_group_nodeset_desc(
['Astheno_Litho_Contact', 'Contact_OP_DP', 'Contact_Prism_DP'],
"fault_top", 20)
rcl.create_group_nodeset_desc(
['Top_Litho_OP', 'Top_Prism', 'Top_Litho_DP'], "ground_surface",
20)
rcl.create_group_nodeset_desc(['Bottom_Litho_OP'], "bottom_litho_OP",
20)
rcl.create_group_nodeset_desc(['Bottom_Litho_DP'], "bottom_litho_DP",
20)
rcl.create_group_nodeset_desc(['Edge_Litho_OP'], "edge_litho_OP", 20)
rcl.create_group_nodeset_desc(['Edge_Litho_DP'], "edge_litho_DP", 20)
rcl.create_group_nodeset_desc(['Front_Litho_DP'], "front_litho_DP", 20)
rcl.create_group_nodeset_desc(['Contact_Prism_OP'], "contact_prism_OP",
20, ['fault_top'])
print 'ca chie'
rcl.create_group_nodeset_desc(
['Bottom_Astheno_DP', 'Bottom_Astheno_OP'], "bottom_astheno", 20,
['front_litho_DP'])
print 'ca chie 2'
rcl.create_group_nodeset_desc(['Edge_Astheno_DP'], "edge_astheno_DP",
20, ['edge_litho_DP'])
rcl.create_group_nodeset_desc(['Edge_Astheno_OP'], "edge_astheno_OP",
20, ['edge_litho_OP'])
# ecriture fichier final
cubit.cmd('export mesh "' + output_pathfile +
'" dimension 2 overwrite')
return None
def saveMesh2D2(self):
cubit.cmd("create surface rectangle width 5000 height 5000 zplane")
cubit.cmd("create surface rectangle width 1000 height 1000 zplane")
cubit.cmd("subtract body 2 from body 1")
surfID = cubit.get_last_id("surface")
cubit.cmd("surface all size auto factor 4")
cubit.cmd("surface all scheme TriMesh")
cubit.cmd("mesh surface all")
nNodes = cubit.get_node_count()
meshFile = open(folder+"mesh2D2.xml", 'w')
meshFile.write('<mesh celltype="triangle" dim="2">\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')
tris = cubit.get_surface_tris(surfID)
meshFile.write(' <elements size="%d">\n' % (len(tris)))
for x in range(0, len(tris)):
nd = cubit.get_connectivity("tri", tris[x])
meshFile.write(' <element id="%d" v0="%d" v1="%d" v2="%d"/>\n' % (x,nd[0]-1,nd[1]-1,nd[2]-1))
meshFile.write(' </elements>\n')
meshFile.write(' <element_data type="fiber_transversely_isotropic">\n')
for x in range(0, len(tris)):
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="line" dim="1">\n')
eds = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
ec = 1
surf = cubit.surface(surfID)
for y in range(0, len(eds)):
nodes = cubit.get_connectivity("edge", eds[y])
element = [nodes[0]-1, nodes[1]-1]
#cp = cubit.get_center_point("edge", eds[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))
#ec = ec+1
#meshFile.write(' <element id="%d" marker="%d" v0="%d" v1="%d" nx="%f" ny="%f" nz="%f"/>\n' % (ec,1,element[0],element[1], norm[0], norm[1], norm[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="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.write('<electrophysiology>\n')
meshFile.write(' <stimuli number="1">\n')
bb = cubit.get_bounding_box("surface", surfID)
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" />\n' % (x0,x1,y0,y1))
meshFile.write(' </stimuli>\n')
meshFile.write('</electrophysiology>\n')
meshFile.close()
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()
def makeGeometry(x, y):
status = 0
cubit.cmd("reset")
cubit.cmd('open "circleGeom.trelis"')
cubit.cmd("compress ids")
num_base_vertex = len(cubit.get_entities("vertex"))
x = numpy.array(x)
y = numpy.array(y)
target_surface = cubit.surface(1)
vertex_on_surface = numpy.zeros(len(x), dtype=bool)
for i in range(0, len(x)):
vertex_on_surface[i] = target_surface.point_containment(
[x[i], y[i], 0.])
if vertex_on_surface[i] == True:
cubit.cmd("create vertex " + str(x[i]) + " " + str(y[i]) +
" 0 on surface 1")
nlcon = computeNonlinearConstraint(x, y)
sys.stdout.write("Nonlinear Constraints: ")
sys.stdout.write(str(nlcon))
sys.stdout.write("\n")
sys.stdout.flush()
X = x[vertex_on_surface]
Y = y[vertex_on_surface]
num_active_pins = len(X)
if num_active_pins == 0:
# No pins on board, return with nonlinear constraint values
status = 1
return status, [], [], nlcon
V = cubit.get_list_of_free_ref_entities("vertex")
for i in range(0, len(V)):
cubit.cmd("imprint volume all with vertex " + str(V[i]))
cubit.cmd("delete free vertex all")
cubit.cmd("compress ids")
#for i in range(0,len(V)):
# cubit.cmd("nodeset 1 add vertex " + str(V[i]))
cubit.cmd("surface all size 0.2")
cubit.cmd("mesh surf all")
cubit.cmd("surface all smooth scheme mean ratio cpu 0.1")
cubit.cmd("smooth surf all")
cubit.cmd("compress ids")
V = numpy.zeros(num_active_pins, dtype=int)
#N = numpy.zeros(num_active_pins, dtype=int)
bc_xyz = [[] for i in range(0, num_active_pins)]
cubit.cmd('create group "cf_crease_entities"')
for i in range(0, num_active_pins):
bc_xyz[i] = [X[i], Y[i], 0.]
N = cubit.parse_cubit_list(
"node", " at " + str(X[i]) + " " + str(Y[i]) + " 0.")
for n in range(0, len(N)):
nodeEdges = cubit.parse_cubit_list("edge", "in node " + str(N[n]))
for e in range(0, len(nodeEdges)):
cubit.cmd("cf_crease_entities add Edge " + str(nodeEdges[e]))
EinC = cubit.parse_cubit_list("edge", " in curve 1")
#for e in range(0,len(EinC)):
# cubit.cmd("cf_crease_entities add Edge " + str(EinC[e]))
VinC = cubit.parse_cubit_list("node", " in curve 1")
for n in range(0, len(VinC)):
nxyz = cubit.get_nodal_coordinates(VinC[n])
bc_xyz.append(list(nxyz))
N = cubit.parse_cubit_list(
"node", " at " + str(nxyz[0]) + " " + str(nxyz[1]) + " 0.")
for n in range(0, len(N)):
nodeEdges = cubit.parse_cubit_list("edge", "in node " + str(N[n]))
for e in range(0, len(nodeEdges)):
if nodeEdges[e] in EinC:
pass
else:
cubit.cmd("cf_crease_entities add Edge " +
str(nodeEdges[e]))
#V = cubit.get_entities("vertex")[num_base_vertex:]
#cubit.cmd('create group "cf_crease_entities"')
#bc_xyz = [[] for i in range(0,len(V))]
#for i in range(0,len(V)):
# #ssID = cubit.get_next_sideset_id()
# bc_xyz[i] = list(cubit.vertex(V[i]).coordinates())
# cubit.parse_cubit_list("vertex", "at " + str(bc_)
# N = cubit.get_vertex_node(V[i])
# nodeEdges = cubit.parse_cubit_list('edge','in node ' + str(N))
# for e in range(0,len(nodeEdges)):
# #cubit.cmd("sideset " + str(ssID) + " add Edge " + str(nodeEdges[e]))
# cubit.cmd("cf_crease_entities add Edge " + str(nodeEdges[e]))
# #cubit.cmd("sideset " + str(ssID) + ' name "node_' + str(N) + '_edges"')
cubit.cmd('save as "mesh.cub" overwrite')
num_elem = len(cubit.get_entities("Face"))
return status, bc_xyz, num_elem, nlcon
def makeGeometry(x, y):
status = 0
cubit.cmd("reset")
cubit.cmd('open "pcb_geom.trelis"')
cubit.cmd("compress ids")
x = numpy.array(x)
y = numpy.array(y)
sys.stdout.write("PIN-X = " + str(x) + "\n")
sys.stdout.flush()
# Test to see if the vertex is contained on the target surface
target_surface = cubit.surface(2) # Target surface is id = 2
vertex_on_surface = numpy.zeros(len(x), dtype=bool)
for i in range(0, len(x)):
vertex_on_surface[i] = target_surface.point_containment(
[x[i], y[i], 0.])
X = x[vertex_on_surface]
Y = y[vertex_on_surface]
# Compute Nonlinear Constraints
nlcon = computeNonlinearConstraint(x, y)
sys.stdout.write("Nonlinear Constraints: ")
sys.stdout.write(str(nlcon))
sys.stdout.write("\n")
sys.stdout.flush()
num_active_pins = len(X)
sys.stdout.write("#" * 10 + "NUMBER OF ACTIVE PINS = " +
str(num_active_pins) + "#" * 10 + "\n")
sys.stdout.flush()
if num_active_pins == 0:
# No pins on board, return with nonlinear constraint values
status = 1
return status, [], [], nlcon
# Delete the target surface -- we don't need it anymore
cubit.cmd("delete vol 2")
cubit.cmd("compress ids")
# Imprint circles on the geometry surface
# Get initial curve ids
C = cubit.get_entities("curve")
for i in range(0, num_active_pins):
cubit.cmd(
"webcut volume all with cylinder radius 2.75 axis z center " +
str(X[i]) + " " + str(Y[i]) + " 0.")
#cubit.cmd("create curve arc radius 2.75 center location " + str(X[i]) + " " + str(Y[i]) + " 0 normal 0 0 1 start angle 0 stop angle 360 ")
cubit.cmd("imprint all")
cubit.cmd("merge all")
cubit.cmd("stitch volume all")
cubit.cmd("compress ids")
#CF = cubit.get_list_of_free_ref_entities("curve")
#for i in range(0,len(CF)):
# cubit.cmd("partition create surface all curve " + str(CF[i]))
#cubit.cmd("delete free curve all")
cubit.cmd("compress ids")
# Mesh the pin surfaces first
S = cubit.get_entities("surface")
for i in range(0, len(S)):
if cubit.surface(S[i]).area() <= (1.1 * numpy.pi * (2.75**2)):
cubit.cmd("surface " + str(S[i]) + " size 4")
cubit.cmd("surface " + str(S[i]) + " scheme circle")
cubit.cmd("mesh surface " + str(S[i]))
else:
board_surf_id = S[i]
# Now mesh the board
cubit.cmd("surface " + str(board_surf_id) + " size 10")
cubit.cmd("mesh surface " + str(board_surf_id))
# Smooth the surface mesh
cubit.cmd("surface all smooth scheme mean ratio cpu 0.1")
cubit.cmd("smooth surf all")
# Set the BC edges to be creased to C^0
cubit.cmd('create group "cf_crease_entities"')
S_BC = cubit.get_entities("surface")
for i in range(0, len(S_BC)):
if S_BC[i] == board_surf_id:
pass
else:
surf_edges = cubit.parse_cubit_list("edge",
"in surface " + str(S_BC[i]))
for e in range(0, len(surf_edges)):
cubit.cmd("group 2 add edge " + str(surf_edges[e]))
### Prepare function return ###
num_elem = len(cubit.get_entities("Face"))
# Package the pin locations for function return
bc_xyz = []
for i in range(0, len(X)):
bc_xyz.append([X[i], Y[i], 0.])
# Save the cubit file
cubit.cmd('save as "mesh.cub" overwrite')
return status, bc_xyz, num_elem, nlcon
def geom_cubit_main(configfile):
if not os.path.isfile(configfile) :
raise Exception("ERR: CONFIG FILE DON'T EXIST !!!")
# READ CONFIGFILE
cf = ConfigParser.ConfigParser()
cf.read(configfile)
experience_name = cf.get('Input','experience_name')
bathyfile = cf.get('Input','bathyfile')
slabfile = cf.get('Input','slabfile')
left_extension=cf.getfloat('Parameters','left_extension') # (always positive)
right_extension=cf.getfloat('Parameters','right_extension')
down_limit=cf.getfloat('Parameters','down_limit') # (always positive)
EET_OP=cf.getfloat('Parameters','EET_OP') # Thickness of the OP Litho
EET_DP=cf.getfloat('Parameters','EET_DP') # Thickness of the DP Litho
backstop_bool=cf.getboolean('Parameters','backstop_bool') # True or False
x_backstop=cf.getfloat('Parameters','x_backstop')
dip_backstop=cf.getfloat('Parameters','dip_backstop')
output_path=cf.get('Output','output_path')
output_file_prefix=cf.get('Output','output_file_prefix')
output_pathfile = output_path + '/' + output_file_prefix + '_' + experience_name + '.exo'
# =======================================================================
# PRIOR DESIGN
# =======================================================================
# Loading the BATHY and SLAB files
XYbathy = np.loadtxt(bathyfile)
XYslab = np.loadtxt(slabfile)
# Creating the bottom of the slab
XslabBot,YslabBot,_ = gcl.shift_thickness(XYslab[:,0],XYslab[:,1],EET_DP)
# Creating the bounding points in a dictionnary
outpts = gcl.make_bounding_points(XYbathy[:,0],XYbathy[:,1],XYslab[:,0],XYslab[:,1],EET_OP,EET_DP,down_limit,left_extension,right_extension)
# Creating the backstop
Xbackstop,Ybackstop = gcl.make_backstop(XYbathy[:,0],XYbathy[:,1],XYslab[:,0],XYslab[:,1],x_backstop,dip_backstop,dupdown=150)
# Adding the 'Bottom_Litho_DP' point to the Litho_DP Bottom
gcl.add_point_in_list(XslabBot,YslabBot,outpts['vBottom_Litho_DP'])
# Changing the description concept : Bathy & Slab ==> OP & DP
Xop,Yop,Xdp,Ydp = gcl.bathyslab_2_OPDPtop(XYbathy[:,0],XYbathy[:,1],XYslab[:,0],XYslab[:,1])
# Adding the limit points of OP & DP
Xop,Yop = gcl.add_point_in_list(Xop,Yop,outpts['vBathy_OP'])
Xdp,Ydp = gcl.add_point_in_list(Xdp,Ydp,outpts['vBathy_DP'])
# PLOT FOR SECURITY
#plt.clf()
#plt.axis('equal')
#plt.plot(XYbathy[:,0],XYbathy[:,1],'+b')
#plt.plot(XYslab[:,0],XYslab[:,1],'r+-')
#plt.plot(XslabBot,YslabBot,'k+-')
#plt.plot(Xbackstop,Ybackstop,'*-y')
#for p in outpts.viewvalues():
# plt.plot(p[0],p[1],'*k')
#plt.plot(Xop,Yop,'b-')
#plt.plot(Xdp,Ydp,'r-')
# =======================================================================
# CUBIT MESHING
# =======================================================================
# Initalisation
cubit.cmd('reset')
cubit.cmd("#{Units('si')}")
# Chargement des courbes
gcl.list_2_curve(Xop,Yop,'Top_Litho_OP')
gcl.list_2_curve(Xdp,Ydp,'Top_Litho_limit_DP')
gcl.list_2_curve(XslabBot,YslabBot,'Bottom_Litho_DP')
gcl.list_2_curve(Xbackstop,Ybackstop,'Backstop')
# Chargement des Points Isolés
gcl.dico_2_listofvertices(outpts)
## fabrication de "courbes-segments" a partir de vertex
v_Bottom_Litho_OP = cubit.vertex(cubit.get_id_from_name('vBottom_Litho_OP'))
v_Bathy_DP = gcl.find_extrema(cubit.curve(cubit.get_id_from_name("Top_Litho_limit_DP")),'r')
v_Bathy_OP = gcl.find_extrema(cubit.curve(cubit.get_id_from_name('Top_Litho_OP')),'l')
v_Bottom_Litho_DP = gcl.find_extrema(cubit.curve(cubit.get_id_from_name("Bottom_Litho_DP")),'r')
v_scratch = cubit.vertex(cubit.get_id_from_name('vscratch'))
v_Bottom_Astheno_OP = cubit.vertex(cubit.get_id_from_name('vBottom_Astheno_OP'))
v_Bottom_Astheno_DP = cubit.vertex(cubit.get_id_from_name('vBottom_Astheno_DP'))
#
gcl.vertices_2_curve(v_Bottom_Litho_OP,v_Bottom_Astheno_OP,'Edge_Astheno_OP')
gcl.vertices_2_curve(v_Bottom_Litho_OP,v_scratch,'Bottom_Litho_OP_PROTO')
gcl.vertices_2_curve(v_Bottom_Litho_OP,v_Bathy_OP,'Edge_Litho_OP')
gcl.vertices_2_curve(v_Bottom_Astheno_OP,v_Bottom_Astheno_DP,'Bottom_PROTO')
gcl.vertices_2_curve(v_Bathy_DP,v_Bottom_Litho_DP,'Edge_Litho_DP')
gcl.vertices_2_curve(v_Bottom_Litho_DP,v_Bottom_Astheno_DP,'Edge_Astheno_DP')
## Split des courbes
gcl.double_split_desc(2,6)
gcl.double_split_desc(8,11)
gcl.double_split_desc(16,3)
gcl.double_split_desc(4,12)
gcl.double_split_desc(1,23)
gcl.double_split_desc(26,28)
## suppression des petits morceaux
gcl.destroy_curve(cubit.curve(14))
gcl.destroy_curve(cubit.curve(24))
gcl.destroy_curve(cubit.curve(17))
gcl.destroy_curve(cubit.curve(21))
gcl.destroy_curve(cubit.curve(29))
## renommage des courbes
gcl.rename_curve_desc(7,'Edge_Litho_OP')
gcl.rename_curve_desc(5,'Edge_Astheno_OP')
gcl.rename_curve_desc(9,'Edge_Litho_DP')
gcl.rename_curve_desc(10,'Edge_Astheno_DP')
gcl.rename_curve_desc(25,'Contact_OP_DP')
gcl.rename_curve_desc(31,'Contact_Prism_DP')
gcl.rename_curve_desc(30,'Contact_Prism_OP')
gcl.rename_curve_desc(32,'Top_Litho_DP')
gcl.rename_curve_desc(33,'Top_Prism')
gcl.rename_curve_desc(27,'Top_Litho_OP')
gcl.rename_curve_desc(20,'Bottom_Astheno_DP')
gcl.rename_curve_desc(22,'Bottom_Litho_DP')
gcl.rename_curve_desc(15,'Bottom_Astheno_OP')
gcl.rename_curve_desc(13,'Bottom_Litho_OP')
gcl.rename_curve_desc(19,'Front_Litho_DP')
gcl.rename_curve_desc(18,'Astheno_Litho_Contact')
# creation des surfaces
gcl.create_surface_desc([10,20,22])
gcl.create_surface_desc([19,18,25,31,32,9,22])
gcl.create_surface_desc([13,18,15,5])
gcl.create_surface_desc([13,7,27,30,25])
gcl.create_surface_desc([30,31,33])
# renomage des surfaces
cubit.surface(1).entity_name('Astheno_DP')
cubit.surface(2).entity_name('Litho_DP')
cubit.surface(3).entity_name('Astheno_OP')
cubit.surface(4).entity_name('Litho_OP')
cubit.surface(5).entity_name('Prisme')
# Fusion des surfaces
cubit.cmd('delete vertex all')
cubit.cmd('imprint all')
cubit.cmd('merge all')
cubit.cmd('stitch volume all')
cubit.cmd('surface all scheme trimesh')
cubit.cmd('curve all scheme default')
cubit.cmd('surface all sizing function none')
# nouveau decoupage des courbes
dx1 = 4.0
dx2 = 25.0
dx3 = 8
b1=1.1
gcl.curver_desc("Contact_Prism_DP",dx1)
gcl.curver_desc("Contact_Prism_OP",dx1)
gcl.curver_desc("Top_Prism",dx1)
gcl.curver_desc("Bottom_Litho_DP",dx2)
gcl.curver_desc("Bottom_Astheno_OP",dx2)
gcl.curver_desc("Front_Litho_DP",dx2)
gcl.curver_desc("Bottom_Astheno_DP",dx2)
gcl.curver_desc("Edge_Astheno_OP",dx2)
gcl.curver_desc("Edge_Litho_OP",dx2)
gcl.curver_desc("Edge_Astheno_DP",dx2)
gcl.curver_desc("Edge_Litho_DP",dx2)
gcl.curver_desc("Contact_OP_DP",dx1)
gcl.curver_start_end_desc("Bottom_Litho_OP",dx1,dx2,'l')
gcl.curver_start_end_desc("Top_Litho_OP",dx1,dx2,'l')
gcl.curver_start_end_desc("Top_Litho_DP",dx1,dx2,'r')
gcl.curver_start_end_desc("Astheno_Litho_Contact",dx1,dx2,'l')
# fabrication du mesh
cubit.cmd('mesh surface all')
cubit.cmd('surface all smooth scheme condition number beta 1.7 cpu 10')
cubit.cmd('smooth surface all')
cubit.cmd('surface 1 size auto factor 5')
## Fabrication de groupe et de nodeset
for i,s in enumerate(cubit.get_entities("surface")):
S = cubit.surface(s)
cubit.cmd('block ' + str(i+1) + ' surface ' + S.entity_name())
cubit.cmd('block ' + str(i+1) + ' name "' + S.entity_name() + ' "' )
gcl.create_group_nodeset_desc(['Astheno_Litho_Contact','Contact_OP_DP','Contact_Prism_DP'],"fault_top",20)
gcl.create_group_nodeset_desc(['Top_Litho_OP','Top_Prism','Top_Litho_DP'],"ground_surface",20)
gcl.create_group_nodeset_desc(['Bottom_Litho_OP'],"bottom_litho_OP",20)
gcl.create_group_nodeset_desc(['Bottom_Litho_DP'],"bottom_litho_DP",20)
gcl.create_group_nodeset_desc(['Bottom_Astheno_DP','Bottom_Astheno_OP'],"bottom_astheno",20)
gcl.create_group_nodeset_desc(['Edge_Litho_OP'],"edge_litho_OP",20)
gcl.create_group_nodeset_desc(['Edge_Litho_DP'],"edge_litho_DP",20)
gcl.create_group_nodeset_desc(['Edge_Astheno_OP'],"edge_astheno_OP",20)
gcl.create_group_nodeset_desc(['Edge_Astheno_DP'],"edge_astheno_DP",20)
gcl.create_group_nodeset_desc(['Front_Litho_DP'],"front_litho_DP",20)
gcl.create_group_nodeset_desc(['Contact_Prism_OP'],"contact_prism_OP",20)
# ecriture fichier final
cubit.cmd('export mesh "' + output_pathfile + '" dimension 2 overwrite')
return None