Hi Kun-Dar, Reply below.
2009/7/7 Kun-Dar Li <[email protected]>: > Hello all, > > I ran FiPy under RedHat 5 to solve 4th-order PDE with anisotropic diffusion > coefficient and periodic boundary in 2D model. During the first few steps, > it shows: > > ----------------------------------------------------------------------------------------------------------------------------------------------------------- > /usr/lib/python2.4/site-packages/numpy/core/ma.py:609: UserWarning: > Cannot automatically convert masked array to numeric because data > is masked in one or more locations. > warnings.warn("Cannot automatically convert masked array to "\ > /usr/lib/python2.4/site-packages/FiPy-2.0.2-py2.4.egg/fipy/solvers/pysparse/pysparseSolver.py:51: Just a warning, don't worry about it. > DeprecationWarning: 'iterations' should be used instead of > 'steps' Again, just a warning about an argument name change, don't worry about it. > Solver.__init__(self, *args, **kwargs) > regularapatite.py:115: DeprecationWarning: 'Viewer' should be used > instead of 'make' > viewer = fipy.viewers.make(vars = var, limits = {'datamin': 0., > 'datamax': 1.}) Again, just a warning. To get rid of these just update your script based on the message so, "make" can be changed to "Viewer", but not really important. > regularapatite.py:136: MaximumIterationWarning: Iterations: 15001. > Relative error: 5.96005 The solver is not converging. This is bad. First off, try using the LU solver on a small problem to make sure things are working. Once you are sure thing are working you can figure out which iterative solver to use for bigger systems. > eqch.solve(var, solver = solver, dt = dt) > step 0 dt 0.5 > regularapatite.py:136: StagnatedSolverWarning: The solver stagnated. > Iterations: 1. Relative error: nan > eqch.solve(var, solver = solver, dt = dt) > step 1 dt 0.5 > step 2 dt 0.5 > step 3 dt 0.5 > > --------------------------------------------------------------------------------------------------------------------- > I guessed there are four errors. But, I'm not sure how to fix it. Can > someone explain me what's the meanings about these messages? Or, I can not > solve the anisotropic diffusion coefficient under periodic boundary? You should be able to. This is something we have never tried, so I cannot be sure. There are certainly a lot of complications with boundary conditions and anisotropy, but shouldn't be for periodic boundaries. > Thank > you so much for any help. > > -- Daniel Wheeler
