def create_mesh():
nx = 3 #how many ellipsoids in x direction
x0 = 3. #spacing of ellipsoids in x
ny = 3 #how many ellipsoids in y direction
y0 = 3. #spacing of ellipsoids in x
nz = 3 #how many ellipsoids in y direction
z0 = 3. #spacing of ellipsoids in x
rx,ry,rz = 0.8,1.2,1#radii of ellipsoids
#create list 'objects' with ellipsoids
objects = []
for i in range(nx):
for j in range(ny):
for k in range(nz):
objects.append( nmesh.ellipsoid([rx,ry,rz], [("shift",[i*x0,j*y0,k*z0])]))
#bounding box
bbox = [[-2,-2,-2],[(nx-1)*x0+2,(ny-1)*y0+2,(nz-1)*z0+2]]
#create the mesh
mesh = nmesh.mesh(objects=objects,a0=0.75,bounding_box=bbox,mesh_bounding_box=True)
#save plot to file
mesh.save("test.nmesh",directory='.')
return mesh
def create_mesh():
nx = 3 #how many ellipsoids in x direction
x0 = 3. #spacing of ellipsoids in x
ny = 3 #how many ellipsoids in y direction
y0 = 3. #spacing of ellipsoids in x
nz = 3 #how many ellipsoids in y direction
z0 = 3. #spacing of ellipsoids in x
rx, ry, rz = 0.8, 1.2, 1 #radii of ellipsoids
#create list 'objects' with ellipsoids
objects = []
for i in range(nx):
for j in range(ny):
for k in range(nz):
objects.append(
nmesh.ellipsoid([rx, ry, rz],
[("shift", [i * x0, j * y0, k * z0])]))
#bounding box
bbox = [[-2, -2, -2],
[(nx - 1) * x0 + 2, (ny - 1) * y0 + 2, (nz - 1) * z0 + 2]]
#create the mesh
mesh = nmesh.mesh(objects=objects,
a0=0.75,
bounding_box=bbox,
mesh_bounding_box=True)
#save plot to file
mesh.save("test.nmesh", directory='.')
return mesh
rings_box = nmesh.box([-16.95, -14.95],
[16.95,14.95])
bbox = [[-half_bbox_dimx,-half_bbox_dimy],[half_bbox_dimx,half_bbox_dimy]]
fix_pts = []
rings = []
voltage_probes = []
for x in range(-1,2):
for y in range(-1,2):
# external ring
R = nmesh.ellipsoid(
[outer_radius, outer_radius],
transform=[("shift",[x*centres_distance, y*centres_distance])]
)
#internal ring
r = nmesh.ellipsoid(
[inner_radius, inner_radius],
transform=[("shift",[x*centres_distance, y*centres_distance])]
)
# take the difference
rings.append(nmesh.difference(R,[r]))
# cut the rings at top and bottom
union_rings = nmesh.union(rings)
rings_array = nmesh.intersect([union_rings,rings_box])
# semiaxis of a rhombus on the diagonals of the array
mat_Py = nmag.MagMaterial(
"Py",
Ms=SI(1e6, "A/m"),
J=SI(13.0e-12, "J/m"),
#Ms=1., #Matteo, very strange: if I use the SI units above,
#J=13., #then I get a wierd magsim-brain failure!
anisotropy_order=2,
anisotropy=test_anisotropy_energy)
sim = nmag.SimulationContext("sphere")
# sim.timestepper_tuning_params=[1e-6,1e-6,2,300] # These are the defaults...
sim.timestepper_tuning_params = [1e-6, 1e-6, 2, 300]
sim.defregion("Py", nm.ellipsoid([3.0, 3.0, 3.0]), mag_mat=mat_Py)
def initial_magnetization_0(coords, mag_type):
return [
0.8 * math.sin(coords[0] / 1.0) * 1e6,
0.8 * math.cos(coords[0] / 1.0) * 1e6, 0.6 * 1e6
]
def initial_magnetization(coords, mag_type):
return [x * (-1.0) for x in coords
] # radially outward-pointing. Will be normalized anyway.
# surface contribution is about +156
from __future__ import division
import nmesh, pylab, timing
#create objects
box = nmesh.box([-2.0,6.0],[2.0,7.0])
ellipsoid = nmesh.ellipsoid ([1.5,1.5])
#create bounding box
bbox =([-3.,-3.],[3.,9.])
#fixed points *to fix points uncomment line below*
fix =([-2.0,6.0],[2.0,7.0],[-2.0,7.0],[2.0,6.0],
[-3.,-3],[-3.,9.],[3.,9.],[3.,-3.])
#density
density = "density=1.0;"
#create empty string
time = []
nodes = []
average_quality=[]
shape=[1]
for shape_elem in shape:
#create quality stacks to plot later
stack1=[]
stack2=[]
stack3=[]
print
"""
** Example: meshing four rings & solving the laplace equation
for a space-dependent resistivity that depends on outer parameters
(Presumably, we will encounter bugs at our first try)
**
"""
##### Creating the mesh #####
# For now, we use a very very simple mesh...
rings = nmesh.union([nmesh.difference(nmesh.ellipsoid([3.0,3.0],
transform=[("shift",[-2.5,0.0])]),
[nmesh.ellipsoid([1.5,1.5],
transform=[("shift",[-2.5,0.0])])]),
nmesh.difference(nmesh.ellipsoid([3.0,3.0],
transform=[("shift",[2.5,0.0])]),
[nmesh.ellipsoid([1.5,1.5],
transform=[("shift",[2.5,0.0])])])])
boxed_rings=nmesh.intersect([rings,nmesh.box([-8.0,-2.5],[8.0,2.5])])
N = 100
density = "density=1.;"
the_mesh = nmesh.mesh(objects = [boxed_rings],
cache_name="rings-mesh",
a0=0.3,
from __future__ import division
import nmesh, pylab, timing, Numeric
#create objects
box = nmesh.box([-2.0, 6.0], [2.0, 7.0])
ellipsoid = nmesh.ellipsoid([1.5, 1.5])
#create bounding box
bbox = ([-3., -3.], [3., 9.])
#fixed points *to fix points uncomment line below*
fix = ([-2.0, 6.0], [2.0, 7.0], [-2.0, 7.0], [2.0, 6.0], [-3., -3], [-3., 9.],
[3., 9.], [3., -3.])
#density
density = "density=1.0;"
force = [0, 1, 2, 5, 7, 10, 20, 50, 70, 100]
for e in force:
shape_force = e / 100.0
neigh_force = 1. - shape_force
#create empty string
time = []
nodes = []
average_quality = []
#create quality stacks to plot later
stack1 = []
stack2 = []
stack3 = []
import nmesh
ellipsoid = nmesh.ellipsoid([0.75, 1.25, 1, 0.9])
bbox = [[-1, -1.5, -1.5, -1], [1, 1.5, 1.5, 1]]
mesh = nmesh.mesh(objects=[ellipsoid], bounding_box=bbox, a0=0.5)
mesh.save("simple4d.nmesh")
print "should have saved mesh now"
# create gnuplot plot for manual (in other file not relevant here)
import os, os.path, sys, time
filename = "run_simple4d/simple4d.nmesh"
if not os.path.exists(filename):
print "You need to run simple4d.py first to compute %s" % filename
sys.exit(1)
def gnuplot_2d_points(points, filename):
print "Starting to write %s" % filename,
print time.asctime()
"""Given a list of pairs like
points = [ [x0,y0], [x1,y1], [x2,y2], ..., [xN,yN]]
and a filename, this will create a postscriptfile of name
h_total_Funny[2] += 0.0;
""")
mag.set_default_material(PermAlloy)
mag.set_intensive_parameters(["T","p","H_x","H_y","H_z"])
#mag.defregion("Ball 1",nm.ellipsoid([3.0,3.0,3.0],transform=[("shift",[-3.0,0.0,0.0])]))
print "OK 1"
sys.stdout.flush()
#mag.defregion("Ball 2",nm.ellipsoid([3.0,3.0,3.0],transform=[("shift",[3.0,0.0,0.0])]))
mag.defregion("Ball 2",nm.ellipsoid([2.0,2.0,2.0],transform=[("shift",[3.0,0.0,0.0])]))
# Note: clearly, we DO need a better way to specify geometries. Ideally, I would like to be
# able to write instead:
#
# mag.defregion("Ball 1",nm.shifted([-3,0,0],nm.sphere(3)))
# mag.defregion("Ball 2",nm.shifted([ 3,0,0],nm.sphere(3)))
#
# or alternatively:
#
# sphere = nm.sphere(3)
# mag.defregion("Ball 1",nm.shifted([-3,0,0],sphere))
# mag.defregion("Ball 2",nm.shifted([ 3,0,0],sphere))
mag.set_meshing_parameters(cache_name="two-balls")
import nmesh
def scale_list_of_lists( vec_data, factor ):
"""silly function -- just to change the vector data somehow.
In real life, the simulation would provide this data, obviously."""
v2=[]
for i in range(len(vec_data)):
v2.append(vec_data[i] + Numeric.array([-1,0,0])*factor)
return v2
#create mesh
ellipsoid = nmesh.ellipsoid([1,1,0.5])
bbox = [[-1,-1,-1],[1,1,1]]
mesh = nmesh.mesh(objects=[ellipsoid],bounding_box=bbox,a0=0.5,cache_name="visual_plot_vectorfield")
#visualise
import nmesh.visual
meshinfo=mesh.tolists()
#create some vector field defind on vertices (=nodes)
vec_data = []
points=meshinfo[0][2]
origin = Numeric.array([0,0,0])
for point in points:
vec_data.append(Numeric.array(point) - origin)
#plot the vector field with changing data
# the additional intensive parameters of our model.
#This adds a Zeeman field:
PermAlloy=mag.MagMaterial("Funny",extra_H="""
h_total_Funny[0] += H_x;
h_total_Funny[1] += H_y;
h_total_Funny[2] += H_z;
""")
mag.set_default_material(PermAlloy)
mag.set_intensive_parameters(["T","p","H_x","H_y","H_z"])
mag.defregion("Ball 1",nm.ellipsoid([3.0,3.0,3.0],transform=[("shift",[-3.0,0.0,0.0])]))
print "OK 1"
sys.stdout.flush()
mag.defregion("Ball 2",nm.ellipsoid([3.0,3.0,3.0],transform=[("shift",[3.0,0.0,0.0])]))
# Note: clearly, we DO need a better way to specify geometries. Ideally, I would like to be
# able to write instead:
#
# mag.defregion("Ball 1",nm.shifted([-3,0,0],nm.sphere(3)))
# mag.defregion("Ball 2",nm.shifted([ 3,0,0],nm.sphere(3)))
#
# or alternatively:
#
# sphere = nm.sphere(3)
ocaml.sys_profiling("on")
#get user-specific logger
log = logging.getLogger('user')
#could modify debug level for this logger
log.setLevel(logging.DEBUG)
nfem.set_default_dimension(3)
nfem.set_default_order(1)
##### Creating the mesh #####
# For now, we use a very very simple mesh...
ball = nmesh.ellipsoid([3.0, 3.0, 3.0])
density = "density=1.;"
the_mesh = nmesh.mesh(objects=[ball],
cache_name="bem-ball",
a0=1.0,
bounding_box=[[-5.0, -5.0, -5.0], [5.0, 5.0, 5.0]],
neigh_force_scale=1.,
density=density,
initial_settling_steps=50,
max_relaxation=4,
max_steps=500)
nfem.set_default_mesh(the_mesh)
##### Making the elements... #####
# This example handles both demag and exchange.
import os,time,sys,math
import nmesh
execfile("../../interface/nsim/linalg_machine.py")
#ocaml.init_hlib("/home/fangohr/build/HLib-1.3/Library/.libs/libhmatrix-1.3.so")
ocaml.init_hlib("/home/tf/HLib-1.3/Library/.libs/libhmatrix-1.3.so")
objects=[nmesh.ellipsoid([3.0,3.0,3.0])
]
mesh = nmesh.mesh(objects=objects,
a0=1.0,
bounding_box=[[-5.0,-5.0,-5.0],[5.0,5.0,5.0]],
cache_name="geometry.mesh",
)
raw_mesh=mesh.raw_mesh
if ocaml.petsc_is_mpi():
print "*** PARALLEL EXECUTION ***"
nr_nodes=ocaml.petsc_mpi_nr_nodes()
nr_points=ocaml.mesh_nr_points(raw_mesh)
z=nr_points/nr_nodes
distrib = [int(round(z*(i+1)))-int(round(z*i)) for i in range(0,nr_nodes)]
slack=nr_points-reduce(lambda x,y:x+y,distrib)
distrib[0] = distrib[0] + slack
print "*** RAW MESH %s *** DISTRIB %s ***" %(repr(raw_mesh),repr(distrib))
import nmesh
box = nmesh.box( [-4,-2],[4,2] )
ellipsoid = nmesh.ellipsoid([3,3])
# create union
union = nmesh.union([box,ellipsoid])
bbox = [[-5,-4],[5,4]]
mesh = nmesh.mesh(objects = [union],bounding_box=bbox)
mesh.save("union.nmesh")
nmesh.visual.plot2d_ps(mesh,"union.ps")
import nmesh
# create a number of objects
one = nmesh.ellipsoid([3.0,3.0])
two = nmesh.ellipsoid([3.0,3.0],transform=[("shift",[7,0])])
three=nmesh.box( [-4.0,-6], [10,-4] )
bbox = [[-5.,-8.],[11.,5.]]
# create mesh of three objects and bounding box
mesh_ex = nmesh.mesh(objects = [one,two,three], bounding_box=bbox,
mesh_bounding_box=True)
# plot mesh
nmesh.visual.plot2d_ps(mesh_ex,"multiobjects.ps")
J=SI(13.0e-12,"J/m"),
#Ms=1., #Matteo, very strange: if I use the SI units above,
#J=13., #then I get a wierd magsim-brain failure!
anisotropy_order=2,
anisotropy=test_anisotropy_energy
)
sim=nmag.SimulationContext("sphere")
# sim.timestepper_tuning_params=[1e-6,1e-6,2,300] # These are the defaults...
sim.timestepper_tuning_params=[1e-6,1e-6,4,300]
sim.set_magnetization([0.0,1.0,0.0])
# ^ just to show we can place set_magnetization() where we want...
sim.defregion("Py", nm.ellipsoid([4.0,4.0,5.0]), mag_mat=mat_Py)
def initial_magnetization(coords,mag_type):
return [0.8*math.sin(coords[0]/1.0)*1e6,
0.8*math.cos(coords[0]/1.0)*1e6,
0.6*1e6
]
sim.generate_mesh(([-30.0,-30.0,-50.0],[30.0,30.0,50.0]), # bounding box
a0=2.0,
max_steps=400,
cache_name="sphere3"
)
#
#sim.set_magnetization(initial_magnetization)
import nmesh
nx = 3 #how many ellipsoids in x direction
x0 = 3. #spacing of ellipsoids in x
ny = 3 #how many ellipsoids in y direction
y0 = 3. #spacing of ellipsoids in x
nz = 3 #how many ellipsoids in y direction
z0 = 3. #spacing of ellipsoids in x
rx,ry,rz = 0.8,1.2,1#radii of ellipsoids
#create list 'objects' with ellipsoids
objects = []
for i in range(nx):
for j in range(ny):
for k in range(nz):
objects.append( nmesh.ellipsoid([rx,ry,rz], [("shift",[i*x0,j*y0,k*z0])]))
#bounding box
bbox = [[-2,-2,-2],[(nx-1)*x0+2,(ny-1)*y0+2,(nz-1)*z0+2]]
#create the mesh
mesh = nmesh.mesh(objects=objects,a0=0.75,bounding_box=bbox)
#save plot to file
mesh.save("ellipsoid_array3d.nmesh")
#create 3d-plot of surfaces and export eps
vis = nmesh.visual.show_bodies_mayavi(mesh)
nmesh.visual.export_visualisation(vis,"ellipsoid_array3d.eps")
import nmesh
ellipsoid = nmesh.ellipsoid([0.75,1.25,1])
# create mesh
bbox = [[-0.75,-1.25,-1],[0.75,1.25,1]]
mesh = nmesh.mesh(objects = [ellipsoid], bounding_box=bbox,a0=0.5)
#create 3d-plot of surfaces and export eps
vis = nmesh.visual.show_bodies_mayavi(mesh)
nmesh.visual.export_visualisation(vis,"simple3d.eps")
#save mesh also as nmesh file
mesh.save('simple3d.nmesh')
import nmesh
nx = 2 #how many ellipsoids in x direction
x0 = 3. #spacing of ellipsoids in x
ny = 3 #how many ellipsoids in y direction
y0 = 3. #spacing of ellipsoids in x
rx, ry = 1, 1.5 #radii of ellipsoids
angle = 45 #orientation of ellipsoids
#create list 'objects' with ellipsoids
objects = []
for i in range(nx):
for j in range(ny):
objects.append( nmesh.ellipsoid([rx,ry], \
[("rotate2d",angle),\
("shift",[i*x0,j*y0])]))
#bounding box
bbox = [[-2, -2], [(nx - 1) * x0 + 2, (ny - 1) * y0 + 2]]
#create the mesh
mesh = nmesh.mesh(objects=objects, a0=0.5, bounding_box=bbox)
#Create post script plot of mesh
nmesh.visual.plot2d_ps(mesh, "ellipsoid_array.ps")
#save plot to file
mesh.save('ellipsoid_array.nmesh')
import nmesh
box1 = nmesh.box([0.0, 0.0], [3.0, 3.0])
box2 = nmesh.box([-1.0, -1.0], [-3.0, -3.0])
circle = nmesh.ellipsoid(length=[1.5, 1.5], transform=[("shift", [-2., 2.])])
bbox = [[-4, -4], [4, 4]]
#define call back function
def my_fun(piece_nr, iteration_nr, mesh_info):
print "** In callback function: Piece %d, Step %d \n" % \
(piece_nr, iteration_nr)
print "Points = %d\nSimplices = %d\nSurface elements = %d\n" % \
(len(mesh_info[0][2]),len(mesh_info[2][2]),len(mesh_info[4][2]))
#Call callback function every 5 iterations
mesh = nmesh.mesh(objects = [box1,box2,circle], bounding_box=bbox, \
a0=0.5, callback = (my_fun,5))
nmesh.visual.plot2d_ps(mesh, "callback.ps")
import nmesh big = nmesh.ellipsoid([4.0,3.0]) # create a big ellipsoid small = nmesh.ellipsoid([3.0,2.0]) # small ellipsoid diff = nmesh.difference(big,[small])# create difference of ellipsoids bbox = [[-5.,-4.],[5.,4.]] mesh_ex = nmesh.mesh(objects = [diff], a0=0.4, bounding_box=bbox) # plot mesh nmesh.visual.plot2d_ps(mesh_ex,"difference.ps")
nx = 3 #how many ellipsoids in x direction
x0 = 3. #spacing of ellipsoids in x
ny = 3 #how many ellipsoids in y direction
y0 = 3. #spacing of ellipsoids in x
nz = 3 #how many ellipsoids in y direction
z0 = 3. #spacing of ellipsoids in x
rx, ry, rz = 0.8, 1.2, 1 #radii of ellipsoids
#create list 'objects' with ellipsoids
objects = []
for i in range(nx):
for j in range(ny):
for k in range(nz):
objects.append(
nmesh.ellipsoid([rx, ry, rz],
[("shift", [i * x0, j * y0, k * z0])]))
#bounding box
bbox = [[-2, -2, -2], [(nx - 1) * x0 + 2, (ny - 1) * y0 + 2,
(nz - 1) * z0 + 2]]
#create the mesh
mesh = nmesh.mesh(objects=objects, a0=0.75, bounding_box=bbox)
#save plot to file
mesh.save("ellipsoid_array3d.nmesh")
#create 3d-plot of surfaces and export eps
vis = nmesh.visual.show_bodies_mayavi(mesh)
nmesh.visual.export_visualisation(vis, "ellipsoid_array3d.eps")
import nmesh
box = nmesh.box([-4, -2], [4, 2])
ellipsoid = nmesh.ellipsoid([3, 3])
# create union
union = nmesh.union([box, ellipsoid])
bbox = [[-5, -4], [5, 4]]
mesh = nmesh.mesh(objects=[union], bounding_box=bbox)
mesh.save("union.nmesh")
nmesh.visual.plot2d_ps(mesh, "union.ps")
import nmesh ell = nmesh.ellipsoid([3, 2]) # create ellipsoid cone = nmesh.conic([-3, 0], 2, [3, 0], 0) # create cone inters = nmesh.intersect([ell, cone]) # create intersection of objects bbox = [[-5., -4.], [5., 4.]] mesh_ex = nmesh.mesh(objects=[inters], a0=0.4, bounding_box=bbox) nmesh.visual.plot2d_ps(mesh_ex, "intersection.ps")
import nmesh
# create ellipsoid
ell = nmesh.ellipsoid([2.0, 3.0], transform=[("shift", [0, 4])])
bbox = [[-3., 0], [3., 8.]]
# define density string
density = "density=1.0+5*x[1]*x[1]*0.02;"
# create mesh
mesh_ex = nmesh.mesh(objects=[ell],
bounding_box=bbox,
mesh_bounding_box=True,
density=density)
# plot mesh
nmesh.visual.plot2d_ps(mesh_ex, "density1.ps")
import nmesh
nx = 2 #how many ellipsoids in x direction
x0 = 20 #spacing of ellipsoids in x
ny = 2 #how many ellipsoids in y direction
y0 = 20 #spacing of ellipsoids in x
rx, ry = 10.5, 10.5 #radii of ellipsoids
angle = 0 #orientation of ellipsoids
#create list 'objects' with ellipsoids
objects = []
for i in range(nx):
for j in range(ny):
objects.append(
nmesh.ellipsoid([rx, ry], [("rotate2d", angle),
("shift", [i * x0, j * y0])]))
union = nmesh.union(objects)
#bounding box
bbox = [[-15, -15], [(nx - 1) * x0 + 15, (ny - 1) * y0 + 15]]
#create the mesh
mesh = nmesh.mesh(objects=[union], a0=2, bounding_box=bbox)
#save plot to file
nmesh.visual.plot2d_ps(mesh, "mergedspheres.ps")
import nmesh
radius = 4
sphere = nmesh.ellipsoid([radius,radius])
bbox = [[-5.,-5.],[5.,5.]]
# periodicity on x-axis
mesh_ex = nmesh.mesh(objects = [sphere], bounding_box=bbox,
mesh_bounding_box=True,periodic=[True,False])
nmesh.visual.plot2d_ps(mesh_ex,"periodic.ps")
mesh_ex.save('periodic.nmesh')
import os,time,sys,math
import nmesh
execfile("../interface/nsim/linalg_machine.py")
clock_time0=time.time()
objects=[nmesh.ellipsoid([3.0,3.0],[("shift",[0,0])]),
]
mesh = nmesh.mesh(objects=objects,
# a0=0.5,
a0=0.25,
bounding_box=[[-5.0,-5.0],[5.0,5.0]],
cache_name="linalg_machine_test.mesh",
)
raw_mesh=mesh.raw_mesh
print "MESH: ",raw_mesh
elem_T=ocaml.make_element("T",[],2,1)
mwe_T=ocaml.make_mwe("T",raw_mesh,[(1,elem_T)],[])
mwe_Laplace_T=ocaml.mwe_sibling(mwe_T,"Laplace_T","Laplace_T/T",[("T","Laplace_T")])
mwe_dT=ocaml.mwe_sibling(mwe_T,"dT","dT/T",[("T","dT")])
def plot_T(name,field,dof_name="T"):
ocaml.plot_scalar_field(field,dof_name,name,
[(1.0,[0.0,0.0,0.0]),(3.0,[1.0,1.0,1.0])],
1, # plot order=1
import nmesh
ellipsoid = nmesh.ellipsoid([1.25,0.75])
bbox = [[-1.25,-0.75],[1.25,0.75]]
mesh = nmesh.mesh(objects = [ellipsoid], bounding_box=bbox,a0=0.5)
mesh.save("simplemesh.nmesh")
meshinfo = mesh.tolists()
import nmesh
cigar = nmesh.ellipsoid([4, 2])
bbox = [[-5, -5], [5, 5]]
mesh = nmesh.mesh(objects=[cigar], bounding_box=bbox, mesh_bounding_box=True)
mesh.save("tutorial2.nmesh")
nmesh.visual.plot2d_ps(mesh, "tutorial2.ps")
#J=13.,
anisotropy_order=2,
anisotropy=test_anisotropy_energy
)
sim=nmag.SimulationContext("sphere")
# sim.timestepper_tuning_params=[1e-6,1e-6,2,300] # These are the defaults...
sim.timestepper_tuning_params=[1e-6,1e-6,4,300]
#sim.set_magnetization([0.0,1.0,0.0])
# ^ just to show we can place set_magnetization() where we want...
sim.defregion("Py", nm.ellipsoid([20.0,20.0,5.0]), mag_mat=mat_Py)
def initial_magnetization(coords,mag_type):
#return [1,0,0]
return [0.8*math.sin(coords[2]/5.0*6.28)*1e6,
0.8*math.cos(coords[2]/5.0*6.28)*1e6,
1e6
]
sim.set_magnetization(initial_magnetization)
sim.generate_mesh(([-25.0,-25.0,-25.0],[25.0,25.0,25.0]), # bounding box
a0=2.0,
max_steps=200,
cache_name="sphere3"
)
print
"""
** Example: meshing four rings & solving the laplace equation
for a space-dependent resistivity that depends on outer parameters
(Presumably, we will encounter bugs at our first try)
**
"""
##### Creating the mesh #####
# For now, we use a very very simple mesh...
rings = nmesh.union([
nmesh.difference(
nmesh.ellipsoid([3.0, 3.0], transform=[("shift", [-2.5, 0.0])]),
[nmesh.ellipsoid([1.0, 1.0], transform=[("shift", [-2.5, 0.0])])]),
nmesh.difference(
nmesh.ellipsoid([3.0, 3.0], transform=[("shift", [2.5, 0.0])]),
[nmesh.ellipsoid([1.0, 1.0], transform=[("shift", [2.5, 0.0])])])
])
boxed_rings = nmesh.intersect([rings, nmesh.box([-8.0, -2.5], [8.0, 2.5])])
N = 100
density = "density=1.;"
the_mesh = nmesh.mesh(
objects=[boxed_rings],
cache_name="rings-mesh",
a0=0.508,
import nmesh ell = nmesh.ellipsoid([3,2]) # create ellipsoid cone = nmesh.conic([-3,0],2,[3,0],0) # create cone inters = nmesh.intersect([ell, cone]) # create intersection of objects bbox = [[-5.,-4.],[5.,4.]] mesh_ex = nmesh.mesh(objects = [inters], a0=0.4, bounding_box=bbox) nmesh.visual.plot2d_ps(mesh_ex,"intersection.ps")
)
mat_Fe = nmag.MagMaterial("Fe",
Ms=SI(1.7e6,"A/m"),
J=SI(2.07e-11,"J/m")
)
sim=nmag.SimulationContext("sphere")
# sim.timestepper_tuning_params=[1e-6,1e-6,2,300] # These are the defaults...
sim.timestepper_tuning_params=[1e-6,1e-6,4,300]
sim.set_magnetization([0.0,1.0,0.0])
# ^ just to show we can place set_magnetization() where we want...
sim.defregion("Py", nmesh.ellipsoid([2.0,2.0,2.0],transform=[('shift',[5,0,0])]), mag_mat=mat_Py)
sim.defregion("Fe", nmesh.ellipsoid([2.0,2.0,2.0]), mag_mat=mat_Fe)
def initial_magnetization(coords,mag_type):
if mag_type == "m_Fe":
return [1,0,0]
else:
return [0.8*math.sin(coords[0]/3.0)*1e6,
0.8*math.cos(coords[0]/3.0)*1e6,
0.6*1e6
]
sim.generate_mesh(([-2.5,-2.5,-2.5],[7.5,2.5,2.5]), # bounding box
a0=1.0,
max_steps=1200,
"""Compounds outer_skin() with order_mesh() to obtain a cross-section
of the outer skin of an ellipsoid.
Author: James Kenny Last modified: $Date$
"""
import nmesh
ellipsoid = nmesh.ellipsoid([1.5,2.5,2])
# create mesh
bbox = [[-1.5,-2.5,-2],[1.5,2.5,2]]
mesh = nmesh.mesh(objects = [ellipsoid], bounding_box=bbox,a0=0.5)
# now extract the outer layer of cells and order the mesh in the y-axis
# to see an outer skin with only elements containing at least 2 surface
# points, the user should uncomment the end of the 2nd following line
mesh_info = mesh.tolists()
mesh_info = nmesh.visual.outer_skin(mesh_info)#, condition='>=2')
# visualise with in2circ as a solid and order it in the y-axis
v = nmesh.visual.solid_in2circ(mesh_info, order=1)
#nmag.set_log_level('debug')
intensive_param_by_name={"H_x":0.1,"H_y":0.0,"H_z":0.0}
# very slightly pulling in x-direction
mat_Py = nmag.MagMaterial("Py",
Ms=SI(1e6,"A/m"),
exchange_coupling=SI(13.0e-12,"J/m"),
)
sim=nmag.SimulationContext("sphere")
# sim.timestepper_tuning_params=[1e-6,1e-6,2,300] # These are the defaults...
sim.timestepper_tuning_params=[1e-6,1e-6,2,300]
sim.defregion("Py", nm.ellipsoid([3.0,3.0,3.0]), mag_mat=mat_Py)
def initial_magnetization(coords,mag_type):
return [0.8*math.sin(coords[0]/1.0)*1e6,
0.8*math.cos(coords[0]/1.0)*1e6,
0.6*1e6
]
sim.generate_mesh(([-5.0,-5.0,-5.0],[5.0,5.0,5.0]), # bounding box
a0=0.7,
max_steps=450,
cache_name="sphere"
)
#sim.set_magnetization([1.0,0.0,0.0])
#sim.set_magnetization([0.0,1.0,0.0])
J=13.0,
anisotropy_order=2,
anisotropy=test_anisotropy_energy)
mat_Fe = nmag.MagMaterial("Fe", Ms=SI(1.7e6, "A/m"), J=SI(2.07e-11, "J/m"))
sim = nmag.SimulationContext("sphere")
# sim.timestepper_tuning_params=[1e-6,1e-6,2,300] # These are the defaults...
sim.timestepper_tuning_params = [1e-6, 1e-6, 4, 300]
sim.set_magnetization([0.0, 1.0, 0.0])
# ^ just to show we can place set_magnetization() where we want...
sim.defregion("Py",
nmesh.ellipsoid([2.0, 2.0, 2.0],
transform=[('shift', [5, 0, 0])]),
mag_mat=mat_Py)
sim.defregion("Fe", nmesh.ellipsoid([2.0, 2.0, 2.0]), mag_mat=mat_Fe)
def initial_magnetization(coords, mag_type):
if mag_type == "m_Fe":
return [1, 0, 0]
else:
return [
0.8 * math.sin(coords[0] / 3.0) * 1e6,
0.8 * math.cos(coords[0] / 3.0) * 1e6, 0.6 * 1e6
]
sim.generate_mesh(
# This example handles both demag and exchange.
import os, time, sys, math
import nmesh
execfile("../../interface/nsim/linalg_machine.py")
#ocaml.init_hlib("/home/fangohr/build/HLib-1.3/Library/.libs/libhmatrix-1.3.so")
ocaml.init_hlib("/home/tf/HLib-1.3/Library/.libs/libhmatrix-1.3.so")
objects = [nmesh.ellipsoid([3.0, 3.0, 3.0])]
mesh = nmesh.mesh(
objects=objects,
a0=1.0,
bounding_box=[[-5.0, -5.0, -5.0], [5.0, 5.0, 5.0]],
cache_name="geometry.mesh",
)
raw_mesh = mesh.raw_mesh
if ocaml.petsc_is_mpi():
print "*** PARALLEL EXECUTION ***"
nr_nodes = ocaml.petsc_mpi_nr_nodes()
nr_points = ocaml.mesh_nr_points(raw_mesh)
z = nr_points / nr_nodes
distrib = [
int(round(z * (i + 1))) - int(round(z * i))
for i in range(0, nr_nodes)
]
slack = nr_points - reduce(lambda x, y: x + y, distrib)
"""Compounds outer_skin() with order_mesh() to obtain a cross-section of the outer skin of an ellipsoid. Author: James Kenny Last modified: $Date$ """ import nmesh ellipsoid = nmesh.ellipsoid([1.5, 2.5, 2]) # create mesh bbox = [[-1.5, -2.5, -2], [1.5, 2.5, 2]] mesh = nmesh.mesh(objects=[ellipsoid], bounding_box=bbox, a0=0.5) # now extract the outer layer of cells and order the mesh in the y-axis # to see an outer skin with only elements containing at least 2 surface # points, the user should uncomment the end of the 2nd following line mesh_info = mesh.tolists() mesh_info = nmesh.visual.outer_skin(mesh_info) #, condition='>=2') # visualise with in2circ as a solid and order it in the y-axis v = nmesh.visual.solid_in2circ(mesh_info, order=1)
ocaml.sys_profiling("on")
#get user-specific logger
log=logging.getLogger('user')
#could modify debug level for this logger
log.setLevel(logging.DEBUG)
nfem.set_default_dimension(3)
nfem.set_default_order(1)
##### Creating the mesh #####
# For now, we use a very very simple mesh...
ball = nmesh.ellipsoid([3.0,3.0,3.0])
density = "density=1.;"
the_mesh = nmesh.mesh(objects = [ball],
cache_name="bem-ball",
a0=1.0,
bounding_box=[[-5.0,-5.0,-5.0],[5.0,5.0,5.0]],
neigh_force_scale = 1.,
density = density,
initial_settling_steps = 50,
max_relaxation = 4,
max_steps=500
)
nfem.set_default_mesh(the_mesh)
nfem.set_default_dimension(2)
nfem.set_default_order(1)
# Simulation parameters
sigma0=1.0
print
"""
** Example: meshing half ring and compute current density for contacts at either side.
This is for possible collaboration with Uni Hamburg. **
"""
##### Creating the mesh #####
ring = nmesh.difference(nmesh.ellipsoid([4.0,4.0]),[nmesh.ellipsoid([2.5,2.5])])
halfring=nmesh.intersect([ring,nmesh.box([-4.0,-0.0],[4.0,4.0])])
the_mesh = nmesh.mesh(objects = [halfring],
cache_name="halfring",
a0=0.2,
bounding_box=[[-4.0,-4],[4.0,4.0]],
neigh_force_scale = 1.,
initial_settling_steps = 50,
max_relaxation = 4,
max_steps=400
)
nfem.set_default_mesh(the_mesh)
import nmesh
nx = 2 #how many ellipsoids in x direction
x0 = 3. #spacing of ellipsoids in x
ny = 3 #how many ellipsoids in y direction
y0 = 3. #spacing of ellipsoids in x
rx,ry = 1,1.5 #radii of ellipsoids
angle = 45 #orientation of ellipsoids
#create list 'objects' with ellipsoids
objects = []
for i in range(nx):
for j in range(ny):
objects.append( nmesh.ellipsoid([rx,ry], \
[("rotate2d",angle),\
("shift",[i*x0,j*y0])]))
#bounding box
bbox = [[-2,-2],[(nx-1)*x0+2,(ny-1)*y0+2]]
#create the mesh
mesh = nmesh.mesh(objects=objects,a0=0.5,bounding_box=bbox)
#Create post script plot of mesh
nmesh.visual.plot2d_ps(mesh,"ellipsoid_array.ps")
#save plot to file
mesh.save('ellipsoid_array.nmesh')
"""
** Example: meshing four rings & solving the laplace equation
for a space-dependent resistivity that depends on outer parameters
(Presumably, we will encounter bugs at our first try)
**
"""
##### Creating the mesh #####
# For now, we use a very very simple mesh...
rings = nmesh.union(
[
nmesh.difference(
nmesh.ellipsoid([3.0, 3.0], transform=[("shift", [-2.5, 0.0])]),
[nmesh.ellipsoid([1.0, 1.0], transform=[("shift", [-2.5, 0.0])])],
),
nmesh.difference(
nmesh.ellipsoid([3.0, 3.0], transform=[("shift", [2.5, 0.0])]),
[nmesh.ellipsoid([1.0, 1.0], transform=[("shift", [2.5, 0.0])])],
),
]
)
boxed_rings = nmesh.intersect([rings, nmesh.box([-8.0, -2.5], [8.0, 2.5])])
N = 100
density = "density=1.;"
the_mesh = nmesh.mesh(
import nmesh
box = nmesh.box([0.0,0.0], [1.0,1.0], \
transform=[("rotate2d",45), \
("shift",[-1.0,-2.0]), \
("scale",[1.5,1.5])])
# create ellipsoid
ell = nmesh.ellipsoid([1.0,2.0], \
transform=[("rotate2d",45), \
("shift",[1.0,1.0]),])
rod = 0.5
bbox = [[-3., -3.], [4., 4.]]
# create mesh
mesh = nmesh.mesh(objects=[box, ell], a0=rod, bounding_box=bbox)
# plot mesh
nmesh.visual.plot2d_ps(mesh, "transformations.ps")
m=[0.0,1.0,0.0]
return m[dof_name_indices[1][0]]
# Note that we can easily also use the 3d differential operators for
# the 2d problems...
diffop_laplace=nfem.diffop("-<d/dxj rho_M||d/dxj phi_M>, j:3")
diffop_div_M=nfem.diffop("<rho_M||d/dxj M(j)>, j:3")
diffop_grad_phi=nfem.diffop("<H(j)||d/dxj phi_M>, j:3")
##### Creating the mesh #####
# For now, we use a very very simple mesh...
double_disc_2d = nmesh.union([nmesh.ellipsoid([3.0,3.0], transform=[("shift",[-1.0,0.0])]),
nmesh.ellipsoid([3.0,3.0], transform=[("shift",[1.0,0.0])])])
double_disc_3d = nmesh.union([nmesh.conic([-1.0,0.0,thickness2d*0.5],3.0,[-1.0,0.0,-thickness2d*0.5],3.0),
nmesh.conic([ 1.0,0.0,thickness2d*0.5],3.0,[ 1.0,0.0,-thickness2d*0.5],3.0)])
density = "density=1.;"
mesh_2d = nmesh.mesh(objects = [double_disc_2d],
cache_name="double-disc-2d",
a0=0.4,
bounding_box=[[-5.0,-5.0],[5.0,5.0]],
neigh_force_scale = 1.,
density = density,
initial_settling_steps = 50,
nfem.set_default_dimension(2)
nfem.set_default_order(1)
# Simulation parameters
sigma0 = 1.0
print
"""
** Example: meshing half ring and compute current density for contacts at either side.
This is for possible collaboration with Uni Hamburg. **
"""
##### Creating the mesh #####
ring = nmesh.difference(
nmesh.ellipsoid([4.0, 4.0]), [nmesh.ellipsoid([2.5, 2.5])])
halfring = nmesh.intersect([ring, nmesh.box([-4.0, -0.0], [4.0, 4.0])])
the_mesh = nmesh.mesh(
objects=[halfring],
cache_name="halfring",
a0=0.2,
bounding_box=[[-4.0, -4], [4.0, 4.0]],
neigh_force_scale=1.,
initial_settling_steps=50,
max_relaxation=4,
max_steps=400)
nfem.set_default_mesh(the_mesh)
import nmesh ellipsoid = nmesh.ellipsoid([1.25,0.75]) bbox = [[-1.25,-0.75],[1.25,0.75]] #Define all parameters, for example in string: myconf = """ [nmesh-2D] a0 : 1.0 shape_force_scale : 0.1 volume_force_scale : 0.0 neigh_force_scale : 1.0 irrel_elem_force_scale : 0.0 thresh_add : 0.6 thresh_del : 1.6 initial_settling_steps : 200 sliver_correction : 1.0 max_relaxation : 3.0 topology_threshold : 0.2 max_relaxation : 3.0 topology_threshold : 0.2 time_step_scale : 0.1 tolerated_rel_move : 0.002 max_steps : 2000 """ #Then create MeshingParameters object mp = nmesh.MeshingParameters(string=myconf) #and use MeshingParameter object when computing the mesh:
import nmesh cigar = nmesh.ellipsoid( [4,2] ) bbox = [[-5,-5],[5,5]] mesh = nmesh.mesh(objects=[cigar], bounding_box=bbox, a0=0.5, mesh_bounding_box=True) nmesh.visual.plot2d_ps( mesh, "tutorial3.ps")
""")
mag.set_default_material(PermAlloy)
mag.set_intensive_parameters(["T", "p", "H_x", "H_y", "H_z"])
#mag.defregion("Ball 1",nm.ellipsoid([3.0,3.0,3.0],transform=[("shift",[-3.0,0.0,0.0])]))
print "OK 1"
sys.stdout.flush()
#mag.defregion("Ball 2",nm.ellipsoid([3.0,3.0,3.0],transform=[("shift",[3.0,0.0,0.0])]))
mag.defregion(
"Ball 2",
nm.ellipsoid([2.0, 2.0, 2.0], transform=[("shift", [3.0, 0.0, 0.0])]))
# Note: clearly, we DO need a better way to specify geometries. Ideally, I would like to be
# able to write instead:
#
# mag.defregion("Ball 1",nm.shifted([-3,0,0],nm.sphere(3)))
# mag.defregion("Ball 2",nm.shifted([ 3,0,0],nm.sphere(3)))
#
# or alternatively:
#
# sphere = nm.sphere(3)
# mag.defregion("Ball 1",nm.shifted([-3,0,0],sphere))
# mag.defregion("Ball 2",nm.shifted([ 3,0,0],sphere))
mag.set_meshing_parameters(cache_name="two-balls")
# plan. There is a problematic issue with the dof name resolution of
# the EOM LHS! FIXME!
# Notes:
#
# (1) It is somewhat problematic/annoying that the first script does
# not really make clear when a name is a MWE name and when it is a
# field/vector name. Corrected that for this example.
import os, time, sys, math
import nmesh
execfile("../../interface/nsim/linalg_machine.py")
objects = [
nmesh.difference(nmesh.ellipsoid([3.0, 3.0], [("shift", [0, 0])]),
[nmesh.ellipsoid([2.5, 2.5], [("shift", [0, 0])])])
]
mesh = nmesh.mesh(
objects=objects,
a0=0.25,
bounding_box=[[-5.0, -5.0], [5.0, 5.0]],
cache_name="geometry.mesh",
)
raw_mesh = mesh.raw_mesh
if ocaml.petsc_is_mpi():
print "*** PARALLEL EXECUTION ***"
nr_nodes = ocaml.petsc_mpi_nr_nodes()
rings_box = nmesh.box([-17, -15],
[17,15])
bbox = [[-half_bbox_dimx,-half_bbox_dimy],[half_bbox_dimx,half_bbox_dimy]]
fix_pts = []
rings = []
voltage_probes = []
for x in range(-1,2):
for y in range(-1,2):
# external ring
R = nmesh.ellipsoid(
[outer_radius, outer_radius],
transform=[("shift",[x*centres_distance, y*centres_distance])]
)
#internal ring
r = nmesh.ellipsoid(
[inner_radius, inner_radius],
transform=[("shift",[x*centres_distance, y*centres_distance])]
)
# take the difference
rings.append(nmesh.difference(R,[r]))
# cut the rings at top and bottom
union_rings = nmesh.union(rings)
rings_array = nmesh.intersect([union_rings,rings_box])
# semiaxis of a rhombus on the diagonals of the array
# A parallelizable demo script implementing a reaction/diffusion system
# ("burning sparkler")
import os,time,sys,math
import nmesh
execfile("../interface/nsim/linalg_machine.py")
objects=[nmesh.difference(nmesh.ellipsoid([3.0,3.0],[("shift",[0,0])]),
[nmesh.ellipsoid([2.5,2.5],[("shift",[0,0])])])
]
mesh = nmesh.mesh(objects=objects,
a0=0.25,
bounding_box=[[-5.0,-5.0],[5.0,5.0]],
cache_name="linalg_machine_rd.mesh",
)
raw_mesh=mesh.raw_mesh
if ocaml.petsc_is_mpi():
print "*** PARALLEL EXECUTION ***"
nr_nodes=ocaml.petsc_mpi_nr_nodes()
nr_points=ocaml.mesh_nr_points(raw_mesh)
z=nr_points/nr_nodes
distrib = [int(round(z*(i+1)))-int(round(z*i)) for i in range(0,nr_nodes)]
slack=nr_points-reduce(lambda x,y:x+y,distrib)
distrib[0] = distrib[0] + slack
print "*** RAW MESH %s *** DISTRIB %s ***" %(repr(raw_mesh),repr(distrib))
ocaml.mesh_set_vertex_distribution(raw_mesh,distrib)
import nmesh
ellipse = nmesh.ellipsoid([1])
bbox = [[-2],[2]]
mesh = nmesh.mesh(objects = [ellipse], bounding_box=bbox, a0 = 0.5,
mesh_bounding_box=True)
mesh.save("simple1d.nmesh")