Chucui,
it is clearly suspicious that you don't use any of your ConstraintMatrix
objects in the assembly loops.
Instead of calling
system_matrix.add(local_dof_indices[i],
local_dof_indices[j],
local_matrix(i, j));
you should use
constraints.distribute_local_to_global(local_matrix, local_dof_indices,
system_matrix)
In case that you also have inhomogeneous boundary conditions, this is in
general not sufficient
and you should asemble the respective right hand sides in the same loop you
construct the matrix.
Then, call
constraints.distribute_local_to_global(cell_matrix, cell_rhs,
local_dof_indices, system_matrix, system_rhs);
The error you are getting is only slightly related to using periodic
boundary conditions. By saying
DoFTools::make_sparsity_pattern(dof_handler, dsp, constraints, false);
you are telling the sparsity pattern (or the matrix) that you will never
write to the constraint entries.
This assumption is true, when you use
constraints.distribute_local_to_global, but not when you copy the matrix
entries manually
(without taking the constraints into account at all).
Best,
Daniel
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