d = dt * (diffusivity * dot(grad(q), grad(p)) - dot(grad(q), u) * p) * dx a = M + 0.5 * d L = action(M - 0.5 * d, t) # Generate code for mass and rhs assembly. lhs, = compile_form(a, "lhs") rhs, = compile_form(L, "rhs") # Set up simulation data structures valuetype = np.float64 nodes, coords, elements, elem_node = read_triangle(opt['mesh']) num_nodes = nodes.size sparsity = op2.Sparsity((nodes, nodes), (elem_node, elem_node), "sparsity") mat = op2.Mat(sparsity, valuetype, "mat") tracer_vals = np.zeros(num_nodes, dtype=valuetype) tracer = op2.Dat(nodes, tracer_vals, valuetype, "tracer") b_vals = np.zeros(num_nodes, dtype=valuetype) b = op2.Dat(nodes, b_vals, valuetype, "b") velocity_vals = np.asarray([1.0, 0.0] * num_nodes, dtype=valuetype) velocity = op2.Dat(nodes ** 2, velocity_vals, valuetype, "velocity")
def main(opt):
# Set up finite element problem
dt = 0.0001
T = FiniteElement("Lagrange", "triangle", 1)
V = VectorElement("Lagrange", "triangle", 1)
p = TrialFunction(T)
q = TestFunction(T)
t = Coefficient(T)
u = Coefficient(V)
a = Coefficient(T)
diffusivity = 0.1
M = p * q * dx
adv_rhs = (q * t + dt * dot(grad(q), u) * t) * dx
d = -dt * diffusivity * dot(grad(q), grad(p)) * dx
diff = M - 0.5 * d
diff_rhs = action(M + 0.5 * d, t)
# Generate code for mass and rhs assembly.
adv, = compile_form(M, "adv")
adv_rhs, = compile_form(adv_rhs, "adv_rhs")
diff, = compile_form(diff, "diff")
diff_rhs, = compile_form(diff_rhs, "diff_rhs")
# Set up simulation data structures
valuetype = np.float64
nodes, vnodes, coords, elements, elem_node, elem_vnode = read_triangle(opt['mesh'])
num_nodes = nodes.size
sparsity = op2.Sparsity((elem_node, elem_node), "sparsity")
if opt['advection']:
adv_mat = op2.Mat(sparsity, valuetype, "adv_mat")
op2.par_loop(adv, elements(3, 3),
adv_mat((elem_node[op2.i[0]], elem_node[op2.i[1]]), op2.INC),
coords(elem_vnode, op2.READ))
if opt['diffusion']:
diff_mat = op2.Mat(sparsity, valuetype, "diff_mat")
op2.par_loop(diff, elements(3, 3),
diff_mat((elem_node[op2.i[0]], elem_node[op2.i[1]]), op2.INC),
coords(elem_vnode, op2.READ))
tracer_vals = np.zeros(num_nodes, dtype=valuetype)
tracer = op2.Dat(nodes, tracer_vals, valuetype, "tracer")
b_vals = np.zeros(num_nodes, dtype=valuetype)
b = op2.Dat(nodes, b_vals, valuetype, "b")
velocity_vals = np.asarray([1.0, 0.0] * num_nodes, dtype=valuetype)
velocity = op2.Dat(vnodes, velocity_vals, valuetype, "velocity")
# Set initial condition
i_cond_code = """void i_cond(double *c, double *t)
{
double A = 0.1; // Normalisation
double D = 0.1; // Diffusivity
double pi = 3.14159265358979;
double x = c[0]-(0.45+%(T)f);
double y = c[1]-0.5;
double r2 = x*x+y*y;
*t = A*(exp(-r2/(4*D*%(T)f))/(4*pi*D*%(T)f));
}
"""
T = 0.01
i_cond = op2.Kernel(i_cond_code % {'T': T}, "i_cond")
op2.par_loop(i_cond, nodes,
coords(op2.IdentityMap, op2.READ),
tracer(op2.IdentityMap, op2.WRITE))
# Assemble and solve
if opt['visualize']:
vis_coords = np.asarray([[x, y, 0.0] for x, y in coords.data_ro], dtype=np.float64)
import viper
v = viper.Viper(x=viper_shape(tracer.data_ro), coordinates=vis_coords, cells=elem_node.values)
solver = op2.Solver()
while T < 0.015:
# Advection
if opt['advection']:
b.zero()
op2.par_loop(adv_rhs, elements(3),
b(elem_node[op2.i[0]], op2.INC),
coords(elem_vnode, op2.READ),
tracer(elem_node, op2.READ),
velocity(elem_vnode, op2.READ))
solver.solve(adv_mat, tracer, b)
# Diffusion
if opt['diffusion']:
b.zero()
op2.par_loop(diff_rhs, elements(3),
b(elem_node[op2.i[0]], op2.INC),
coords(elem_vnode, op2.READ),
tracer(elem_node, op2.READ))
solver.solve(diff_mat, tracer, b)
if opt['visualize']:
v.update(viper_shape(tracer.data_ro))
T = T + dt
if opt['print_output'] or opt['test_output']:
analytical_vals = np.zeros(num_nodes, dtype=valuetype)
analytical = op2.Dat(nodes, analytical_vals, valuetype, "analytical")
i_cond = op2.Kernel(i_cond_code % {'T': T}, "i_cond")
op2.par_loop(i_cond, nodes,
coords(op2.IdentityMap, op2.READ),
analytical(op2.IdentityMap, op2.WRITE))
# Print error w.r.t. analytical solution
if opt['print_output']:
print "Expected - computed solution: %s" % tracer.data - analytical.data
if opt['test_output']:
l2norm = dot(t - a, t - a) * dx
l2_kernel, = compile_form(l2norm, "error_norm")
result = op2.Global(1, [0.0])
op2.par_loop(l2_kernel, elements,
result(op2.INC),
coords(elem_vnode,op2.READ),
tracer(elem_node,op2.READ),
analytical(elem_node,op2.READ)
)
with open("adv_diff.%s.out" % os.path.split(opt['mesh'])[-1], "w") as out:
out.write(str(result.data[0]) + "\n")
def run(diffusivity, current_time, dt, endtime, **kwargs):
op2.init(**kwargs)
# Set up finite element problem
T = FiniteElement("Lagrange", "triangle", 1)
V = VectorElement("Lagrange", "triangle", 1)
p = TrialFunction(T)
q = TestFunction(T)
t = Coefficient(T)
u = Coefficient(V)
diffusivity = 0.1
M = p * q * dx
adv_rhs = (q * t + dt * dot(grad(q), u) * t) * dx
d = -dt * diffusivity * dot(grad(q), grad(p)) * dx
diff_matrix = M - 0.5 * d
diff_rhs = action(M + 0.5 * d, t)
# Generate code for mass and rhs assembly.
mass = compile_form(M, "mass")[0]
adv_rhs = compile_form(adv_rhs, "adv_rhs")[0]
diff_matrix = compile_form(diff_matrix, "diff_matrix")[0]
diff_rhs = compile_form(diff_rhs, "diff_rhs")[0]
# Set up simulation data structures
valuetype = np.float64
nodes, coords, elements, elem_node = read_triangle(kwargs['mesh'])
num_nodes = nodes.size
sparsity = op2.Sparsity((elem_node, elem_node), 1, "sparsity")
mat = op2.Mat(sparsity, valuetype, "mat")
tracer_vals = np.asarray([0.0] * num_nodes, dtype=valuetype)
tracer = op2.Dat(nodes, 1, tracer_vals, valuetype, "tracer")
b_vals = np.asarray([0.0] * num_nodes, dtype=valuetype)
b = op2.Dat(nodes, 1, b_vals, valuetype, "b")
velocity_vals = np.asarray([1.0, 0.0] * num_nodes, dtype=valuetype)
velocity = op2.Dat(nodes, 2, velocity_vals, valuetype, "velocity")
# Set initial condition
i_cond_code = """
void i_cond(double *c, double *t)
{
double i_t = 0.01; // Initial time
double A = 0.1; // Normalisation
double D = 0.1; // Diffusivity
double pi = 3.141459265358979;
double x = c[0]-0.5;
double y = c[1]-0.5;
double r = sqrt(x*x+y*y);
if (r<0.25)
*t = A*(exp((-(r*r))/(4*D*i_t))/(4*pi*D*i_t));
else
*t = 0.0;
}
"""
i_cond = op2.Kernel(i_cond_code, "i_cond")
op2.par_loop(i_cond, nodes, coords(op2.IdentityMap, op2.READ),
tracer(op2.IdentityMap, op2.WRITE))
zero_dat_code = """
void zero_dat(double *dat)
{
*dat = 0.0;
}
"""
zero_dat = op2.Kernel(zero_dat_code, "zero_dat")
# Assemble and solve
have_advection = True
have_diffusion = True
def timestep_iteration():
# Advection
if have_advection:
tic('advection')
tic('assembly')
mat.zero()
op2.par_loop(
mass, elements(3, 3),
mat((elem_node[op2.i[0]], elem_node[op2.i[1]]), op2.INC),
coords(elem_node, op2.READ))
op2.par_loop(zero_dat, nodes, b(op2.IdentityMap, op2.WRITE))
op2.par_loop(adv_rhs, elements(3), b(elem_node[op2.i[0]], op2.INC),
coords(elem_node, op2.READ),
tracer(elem_node, op2.READ),
velocity(elem_node, op2.READ))
toc('assembly')
tic('solve')
op2.solve(mat, tracer, b)
toc('solve')
toc('advection')
# Diffusion
if have_diffusion:
tic('diffusion')
tic('assembly')
mat.zero()
op2.par_loop(
diff_matrix, elements(3, 3),
mat((elem_node[op2.i[0]], elem_node[op2.i[1]]), op2.INC),
coords(elem_node, op2.READ))
op2.par_loop(zero_dat, nodes, b(op2.IdentityMap, op2.WRITE))
op2.par_loop(diff_rhs, elements(3), b(elem_node[op2.i[0]],
op2.INC),
coords(elem_node, op2.READ),
tracer(elem_node, op2.READ))
toc('assembly')
tic('solve')
op2.solve(mat, tracer, b)
toc('solve')
toc('diffusion')
# Perform 1 iteration to warm up plan cache then reset initial condition
timestep_iteration()
op2.par_loop(i_cond, nodes, coords(op2.IdentityMap, op2.READ),
tracer(op2.IdentityMap, op2.WRITE))
reset()
# Timed iteration
t1 = clock()
while current_time < endtime:
timestep_iteration()
current_time += dt
runtime = clock() - t1
print "/fluidity :: %f" % runtime
summary('profile_pyop2_%s_%s.csv' %
(opt['mesh'].split('/')[-1], opt['backend']))
abs = abs * (-1.0); A[0]+=0.5*abs*0.1 * y[0][0]; z[0][0]+=0.2*(0.5*abs*0.1*y[0][0]); z[1][0]+=0.2*(0.5*abs*0.1*y[0][0]); z[2][0]+=0.2*(0.5*abs*0.1*y[0][0]); z[3][0]+=0.2*(0.5*abs*0.1*y[0][0]); z[4][0]+=0.2*(0.5*abs*0.1*y[0][0]); z[5][0]+=0.2*(0.5*abs*0.1*y[0][0]); }""", "comp_vol") # Set up simulation data structures valuetype = np.float64 nodes, coords, elements, elem_node = read_triangle(mesh_name, layers) # mesh data mesh2d = np.array([3, 3, 1]) mesh1d = np.array([2, 1]) A = np.array([[0, 1], [0]]) # the array of dof values for each element type dofs = np.array([[2, 0], [0, 0], [0, 1]]) dofs_coords = np.array([[2, 0], [0, 0], [0, 0]]) dofs_field = np.array([[0, 0], [0, 0], [0, 1]]) dofs_res = np.array([[1, 0], [0, 0], [0, 0]]) # ALL the nodes, edges amd cells of the 2D mesh nums = np.array([nodes.size, 0, elements.size])
if (area < 0)
area = area * (-1.0);
A[0]+=0.5*area*0.1 * y[0][0];
z[0][0]+=0.2*(0.5*area*0.1*y[0][0]);
z[1][0]+=0.2*(0.5*area*0.1*y[0][0]);
z[2][0]+=0.2*(0.5*area*0.1*y[0][0]);
z[3][0]+=0.2*(0.5*area*0.1*y[0][0]);
z[4][0]+=0.2*(0.5*area*0.1*y[0][0]);
z[5][0]+=0.2*(0.5*area*0.1*y[0][0]);
}""", "comp_vol")
# Set up simulation data structures
valuetype = np.float64
nodes, coords, elements, elem_node = read_triangle(mesh_name, layers)
# mesh data
mesh2d = np.array([3, 3, 1])
mesh1d = np.array([2, 1])
A = np.array([[0, 1], [0]])
# the array of dof values for each element type
dofs = np.array([[2, 0], [0, 0], [0, 1]])
dofs_coords = np.array([[2, 0], [0, 0], [0, 0]])
dofs_field = np.array([[0, 0], [0, 0], [0, 1]])
dofs_res = np.array([[1, 0], [0, 0], [0, 0]])
# ALL the nodes, edges amd cells of the 2D mesh
nums = np.array([nodes.size, 0, elements.size])
d = dt * (diffusivity * dot(grad(q), grad(p)) - dot(grad(q), u) * p) * dx a = M + 0.5 * d L = action(M - 0.5 * d, t) # Generate code for mass and rhs assembly. lhs, = compile_form(a, "lhs") rhs, = compile_form(L, "rhs") # Set up simulation data structures valuetype = np.float64 nodes, vnodes, coords, elements, elem_node, elem_vnode = read_triangle(opt["mesh"]) num_nodes = nodes.size sparsity = op2.Sparsity((elem_node, elem_node), "sparsity") mat = op2.Mat(sparsity, valuetype, "mat") tracer_vals = np.zeros(num_nodes, dtype=valuetype) tracer = op2.Dat(nodes, tracer_vals, valuetype, "tracer") b_vals = np.zeros(num_nodes, dtype=valuetype) b = op2.Dat(nodes, b_vals, valuetype, "b") velocity_vals = np.asarray([1.0, 0.0] * num_nodes, dtype=valuetype) velocity = op2.Dat(vnodes, velocity_vals, valuetype, "velocity") # Set initial condition
def run(diffusivity, current_time, dt, endtime, **kwargs):
op2.init(**kwargs)
# Set up finite element problem
T = FiniteElement("Lagrange", "triangle", 1)
V = VectorElement("Lagrange", "triangle", 1)
p = TrialFunction(T)
q = TestFunction(T)
t = Coefficient(T)
u = Coefficient(V)
diffusivity = 0.1
M = p * q * dx
adv_rhs = (q * t + dt * dot(grad(q), u) * t) * dx
d = -dt * diffusivity * dot(grad(q), grad(p)) * dx
diff_matrix = M - 0.5 * d
diff_rhs = action(M + 0.5 * d, t)
# Generate code for mass and rhs assembly.
mass = compile_form(M, "mass")[0]
adv_rhs = compile_form(adv_rhs, "adv_rhs")[0]
diff_matrix = compile_form(diff_matrix, "diff_matrix")[0]
diff_rhs = compile_form(diff_rhs, "diff_rhs")[0]
# Set up simulation data structures
valuetype = np.float64
nodes, coords, elements, elem_node = read_triangle(kwargs["mesh"])
num_nodes = nodes.size
sparsity = op2.Sparsity((elem_node, elem_node), 1, "sparsity")
mat = op2.Mat(sparsity, valuetype, "mat")
tracer_vals = np.asarray([0.0] * num_nodes, dtype=valuetype)
tracer = op2.Dat(nodes, 1, tracer_vals, valuetype, "tracer")
b_vals = np.asarray([0.0] * num_nodes, dtype=valuetype)
b = op2.Dat(nodes, 1, b_vals, valuetype, "b")
velocity_vals = np.asarray([1.0, 0.0] * num_nodes, dtype=valuetype)
velocity = op2.Dat(nodes, 2, velocity_vals, valuetype, "velocity")
# Set initial condition
i_cond_code = """
void i_cond(double *c, double *t)
{
double i_t = 0.01; // Initial time
double A = 0.1; // Normalisation
double D = 0.1; // Diffusivity
double pi = 3.141459265358979;
double x = c[0]-0.5;
double y = c[1]-0.5;
double r = sqrt(x*x+y*y);
if (r<0.25)
*t = A*(exp((-(r*r))/(4*D*i_t))/(4*pi*D*i_t));
else
*t = 0.0;
}
"""
i_cond = op2.Kernel(i_cond_code, "i_cond")
op2.par_loop(i_cond, nodes, coords(op2.IdentityMap, op2.READ), tracer(op2.IdentityMap, op2.WRITE))
zero_dat_code = """
void zero_dat(double *dat)
{
*dat = 0.0;
}
"""
zero_dat = op2.Kernel(zero_dat_code, "zero_dat")
# Assemble and solve
have_advection = True
have_diffusion = True
def timestep_iteration():
# Advection
if have_advection:
tic("advection")
tic("assembly")
mat.zero()
op2.par_loop(
mass,
elements(3, 3),
mat((elem_node[op2.i[0]], elem_node[op2.i[1]]), op2.INC),
coords(elem_node, op2.READ),
)
op2.par_loop(zero_dat, nodes, b(op2.IdentityMap, op2.WRITE))
op2.par_loop(
adv_rhs,
elements(3),
b(elem_node[op2.i[0]], op2.INC),
coords(elem_node, op2.READ),
tracer(elem_node, op2.READ),
velocity(elem_node, op2.READ),
)
toc("assembly")
tic("solve")
op2.solve(mat, tracer, b)
toc("solve")
toc("advection")
# Diffusion
if have_diffusion:
tic("diffusion")
tic("assembly")
mat.zero()
op2.par_loop(
diff_matrix,
elements(3, 3),
mat((elem_node[op2.i[0]], elem_node[op2.i[1]]), op2.INC),
coords(elem_node, op2.READ),
)
op2.par_loop(zero_dat, nodes, b(op2.IdentityMap, op2.WRITE))
op2.par_loop(
diff_rhs,
elements(3),
b(elem_node[op2.i[0]], op2.INC),
coords(elem_node, op2.READ),
tracer(elem_node, op2.READ),
)
toc("assembly")
tic("solve")
op2.solve(mat, tracer, b)
toc("solve")
toc("diffusion")
# Perform 1 iteration to warm up plan cache then reset initial condition
timestep_iteration()
op2.par_loop(i_cond, nodes, coords(op2.IdentityMap, op2.READ), tracer(op2.IdentityMap, op2.WRITE))
reset()
# Timed iteration
t1 = clock()
while current_time < endtime:
timestep_iteration()
current_time += dt
runtime = clock() - t1
print "/fluidity :: %f" % runtime
summary("profile_pyop2_%s_%s.csv" % (opt["mesh"].split("/")[-1], opt["backend"]))
def main(opt):
# Set up finite element identity problem
E = FiniteElement("Lagrange", "triangle", 1)
v = TestFunction(E)
u = TrialFunction(E)
f = Coefficient(E)
a = v * u * dx
L = v * f * dx
# Generate code for mass and rhs assembly.
mass, = compile_form(a, "mass")
rhs, = compile_form(L, "rhs")
# Set up simulation data structures
valuetype = np.float64
nodes, coords, elements, elem_node = read_triangle(opt['mesh'])
sparsity = op2.Sparsity((nodes, nodes), (elem_node, elem_node), "sparsity")
mat = op2.Mat(sparsity, valuetype, "mat")
b = op2.Dat(nodes, np.zeros(nodes.size, dtype=valuetype), valuetype, "b")
x = op2.Dat(nodes, np.zeros(nodes.size, dtype=valuetype), valuetype, "x")
# Set up initial condition
f_vals = np.array([2 * X + 4 * Y for X, Y in coords.data], dtype=valuetype)
f = op2.Dat(nodes, f_vals, valuetype, "f")
# Assemble and solve
op2.par_loop(mass, elements,
mat(op2.INC, (elem_node[op2.i[0]], elem_node[op2.i[1]])),
coords(op2.READ, elem_node, flatten=True))
op2.par_loop(rhs, elements,
b(op2.INC, elem_node[op2.i[0]]),
coords(op2.READ, elem_node, flatten=True),
f(op2.READ, elem_node))
solver = op2.Solver()
solver.solve(mat, x, b)
# Print solution (if necessary)
if opt['print_output']:
print "Expected solution: %s" % f.data
print "Computed solution: %s" % x.data
# Save output (if necessary)
if opt['return_output']:
return f.data, x.data
if opt['save_output']:
from cPickle import dump, HIGHEST_PROTOCOL
import gzip
out = gzip.open("mass2d_triangle.out.gz", "wb")
dump((f.data, x.data, b.data, mat.array), out, HIGHEST_PROTOCOL)
out.close()