[petsc-users] petsc4py - Convert c example code to Python
Nicola Creati
ncreati at inogs.it
Tue Apr 2 03:18:05 CDT 2019
Hello, I have run the two codes using: -pc_type lu -ts_monitor
-snes_monitor -ksp_monitor -ts_max_steps 5. The codes start to diverge
after the first time step:
Python run :
0 TS dt 0.01 time 0.
0 SNES Function norm 2.327405179696e+02
0 KSP Residual norm 1.939100379240e+00
1 KSP Residual norm 1.013760235597e-15
1 SNES Function norm 9.538686413612e-14
1 TS dt 0.01 time 0.01
0 SNES Function norm 8.565210784140e-14
0 KSP Residual norm 1.266678408555e-15
1 KSP Residual norm 2.663404219322e-31
1 SNES Function norm 5.528402779439e-29
2 TS dt 0.01 time 0.02
0 SNES Function norm 5.829656072531e-29
0 KSP Residual norm 3.805606380832e-31
1 KSP Residual norm 3.283104975114e-46
1 SNES Function norm 1.867771204856e-44
3 TS dt 0.01 time 0.03
0 SNES Function norm 1.644541571708e-44
0 KSP Residual norm 1.969573456719e-46
1 KSP Residual norm 1.297976290541e-61
1 SNES Function norm 1.780215821230e-59
4 TS dt 0.01 time 0.04
0 SNES Function norm 1.700894451833e-59
5 TS dt 0.01 time 0.05
ex13.c run:
0 TS dt 0.01 time 0.
0 SNES Function norm 2.327405179696e+02
0 KSP Residual norm 9.158498731719e-01
1 KSP Residual norm 5.129005976821e-16
1 SNES Function norm 1.141297389434e-13
1 TS dt 0.01 time 0.01
0 SNES Function norm 9.158498731719e+01
0 KSP Residual norm 4.156347391374e-01
1 KSP Residual norm 1.996081836894e-16
1 SNES Function norm 3.609761734594e-14
2 TS dt 0.01 time 0.02
0 SNES Function norm 4.156347391374e+01
0 KSP Residual norm 2.203298795311e-01
1 KSP Residual norm 9.047356740098e-17
1 SNES Function norm 3.292648977280e-14
3 TS dt 0.01 time 0.03
0 SNES Function norm 2.203298795311e+01
0 KSP Residual norm 1.367458644503e-01
1 KSP Residual norm 5.055030661919e-17
1 SNES Function norm 1.272304808486e-14
4 TS dt 0.01 time 0.04
0 SNES Function norm 1.367458644503e+01
0 KSP Residual norm 9.695393464180e-02
1 KSP Residual norm 1.918401734795e-17
1 SNES Function norm 1.130247628824e-14
5 TS dt 0.01 time 0.05
I rechecked the Python code against the C one but I did not find the
source of the issue.
# Example 13 petsc TS
import sys, petsc4py
petsc4py.init(sys.argv)
from petsc4py import PETSc
from mpi4py import MPI
import numpy as np
import math
def RHS_func(ts, t, X, xdot, F):
da = ts.getDM()
localU = da.getLocalVec()
da.globalToLocal(X, localU)
mx, my = da.getSizes()
hx, hy = [1.0/(m-1) for m in [mx, my]]
sx = 1.0/(hx*hx)
sy = 1.0/(hy*hy)
uarray = localU.getArray(readonly=1).reshape(8, 8, order='C')
f = F.getArray(readonly=0).reshape(8, 8, order='C')
(xs, xm), (ys, ym) = da.getRanges()
for j in range(ys, ym):
for i in range(xs, xm):
if i == 0 or j == 0 or i == (mx-1) or j == (my-1):
f[i,j] = uarray[i,j]
continue
u = uarray[i,j]
uxx = (-2.0 * u + uarray[i, j-1] + uarray[i, j+1]) * sx
uyy = (-2.0 * u + uarray[i-1, j] + uarray[i+1, j])* sy
f[i, j] = uxx + uyy
F.assemble()
#PETSc.Log.logFlops(11.0*xm*ym)
def Jacobian_func(ts, t, x, xdot, a, A, B):
mx, my = da.getSizes()
hx = 1.0/(mx-1)
hy = 1.0/(my-1)
sx = 1.0/(hx*hx)
sy = 1.0/(hy*hy)
B.setOption(PETSc.Mat.Option.NEW_NONZERO_ALLOCATION_ERR, False)
B.zeroEntries()
(i0, i1), (j0, j1) = da.getRanges()
row = PETSc.Mat.Stencil()
col = PETSc.Mat.Stencil()
for i in range(j0, j1):
for j in range(i0, i1):
row.index = (i,j)
row.field = 0
if i == 0 or j== 0 or i==(my-1) or j==(mx-1):
B.setValueStencil(row, row, 1.0)
else:
for index, value in [
((i-1, j), sx),
((i+1, j), sx),
((i, j-1), sy),
((i, j+1), sy),
((i, j), -2*sx - 2*sy)]:
col.index = index
col.field = 0
B.setValueStencil(row, col, value)
B.assemble()
#B.view()
if A != B: B.assemble()
return PETSc.Mat.Structure.SAME_NONZERO_PATTERN
def make_initial_solution(da, U, c):
mx, my = da.getSizes()
hx = 1.0/(mx-1)
hy = 1.0/(my-1)
(xs, xm), (ys, ym) = da.getRanges()
u = U.getArray(readonly=0).reshape(8, 8, order='C')
for j in range(ys, ym):
y = j*hy
for i in range(xs, xm):
x = i*hx
r = math.sqrt((x-0.5)**2+(y-0.5)**2)
if r < (0.125):
u[i, j] = math.exp(c*r*r*r)
else:
u[i, j] = 0.0
U.assemble()
#U.view()
def monitor(ts, i, t, x):
xx = x[:].tolist()
history.append((i, t, xx))
history = []
nx = 8
ny = 8
da = PETSc.DMDA().create([nx, ny], stencil_type=
PETSc.DA.StencilType.STAR, stencil_width=1, dof=1)
da.setFromOptions()
da.setUp()
u = da.createGlobalVec()
f = u.duplicate()
c = -30.0
ts = PETSc.TS().create()
ts.setDM(da)
ts.setType(ts.Type.BEULER)
ts.setIFunction(RHS_func, f)
da.setMatType('aij')
J = da.createMat()
ts.setIJacobian(Jacobian_func, J, J)
ftime = 1.0
ts.setMaxTime(ftime)
ts.setExactFinalTime(PETSc.TS.ExactFinalTime.STEPOVER)
make_initial_solution(da, u, c)
dt = 0.01
ts.setMonitor(monitor)
ts.setTimeStep(dt)
ts.setFromOptions()
ts.solve(u)
ftime = ts.getSolveTime()
steps = ts.getStepNumber()
Thanks.
Nicola
--
Nicola Creati
Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS www.inogs.it
Dipartimento di Geofisica della Litosfera Geophysics of Lithosphere Department
CARS (Cartography and Remote Sensing) Research Group http://www.inogs.it/Cars/
Borgo Grotta Gigante 42/c 34010 Sgonico - Trieste - ITALY ncreati at ogs.trieste.it
off. +39 040 2140 213
fax. +39 040 327307
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