Increase array size of material grid by 1 in each dimension

[mawc2019]

The missing +1 in the array size of the material grid is restored in this PR, but some tests in test_adjoint_solver.py fail.

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Merging #2504 (0d73d36) into master (79e8d17) will not change coverage. The diff coverage is 100.00%.

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@@           Coverage Diff           @@
##           master    #2504   +/-   ##
=======================================
  Coverage   73.92%   73.92%           
=======================================
  Files          18       18           
  Lines        5296     5296           
=======================================
  Hits         3915     3915           
  Misses       1381     1381           

Impacted Files	Coverage Δ
python/adjoint/filters.py	79.89% <100.00%> (ø)

[mawc2019]

We need to increase some tolerances in test_adjoint_solver.py.

Python 3.7:

FAIL: test_eigenmode (__main__.TestAdjointSolver)
Verifies that the adjoint gradient for an objective function based
----------------------------------------------------------------------
Traceback (most recent call last):
  File "../../../python/tests/test_adjoint_solver.py", line 592, in test_eigenmode
    self.assertClose(adj_dd, fnd_dd, epsilon=tol)
  File "/home/runner/work/meep/meep/build/meep-1.27.0-beta/python/tests/utils.py", line 30, in assertClose
    self.assertLessEqual(diff_norm, epsilon * np.maximum(x_norm, y_norm), msg)
AssertionError: 2.4692787936065122e-05 not less than or equal to 2.147141650190434e-05 : 

======================================================================
FAIL: test_ldos (__main__.TestAdjointSolver)
Verifies that the adjoint gradient for an objective function based
----------------------------------------------------------------------
Traceback (most recent call last):
  File "../../../python/tests/test_adjoint_solver.py", line 621, in test_ldos
    self.assertClose(adj_dd, fnd_dd, epsilon=tol)
  File "/home/runner/work/meep/meep/build/meep-1.27.0-beta/python/tests/utils.py", line 30, in assertClose
    self.assertLessEqual(diff_norm, epsilon * np.maximum(x_norm, y_norm), msg)
AssertionError: 1.866014771444676e-10 not less than or equal to 7.504694841953264e-11 : 

Python 3.10:

FAIL: test_DFT_fields (__main__.TestAdjointSolver)
Verifies that the adjoint gradient for an objective function based
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/meep/meep/build/meep-1.27.0-beta/_build/sub/python/../../../python/tests/test_adjoint_solver.py", line 551, in test_DFT_fields
    self.assertClose(adj_dd, fnd_dd, epsilon=tol)
  File "/home/runner/work/meep/meep/build/meep-1.27.0-beta/python/tests/utils.py", line 30, in assertClose
    self.assertLessEqual(diff_norm, epsilon * np.maximum(x_norm, y_norm), msg)
AssertionError: 0.00032576555598241895 not less than or equal to 0.00015930181276331502 : 

======================================================================
FAIL: test_eigenmode (__main__.TestAdjointSolver)
Verifies that the adjoint gradient for an objective function based
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/meep/meep/build/meep-1.27.0-beta/_build/sub/python/../../../python/tests/test_adjoint_solver.py", line 592, in test_eigenmode
    self.assertClose(adj_dd, fnd_dd, epsilon=tol)
  File "/home/runner/work/meep/meep/build/meep-1.27.0-beta/python/tests/utils.py", line 30, in assertClose
    self.assertLessEqual(diff_norm, epsilon * np.maximum(x_norm, y_norm), msg)
AssertionError: 6.287598863467803e-05 not less than or equal to 3.214987858228824e-05 : 

======================================================================
FAIL: test_ldos (__main__.TestAdjointSolver)
Verifies that the adjoint gradient for an objective function based
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/meep/meep/build/meep-1.27.0-beta/_build/sub/python/../../../python/tests/test_adjoint_solver.py", line 621, in test_ldos
    self.assertClose(adj_dd, fnd_dd, epsilon=tol)
  File "/home/runner/work/meep/meep/build/meep-1.27.0-beta/python/tests/utils.py", line 30, in assertClose
    self.assertLessEqual(diff_norm, epsilon * np.maximum(x_norm, y_norm), msg)
AssertionError: 2.0344705001442236e-10 not less than or equal to 1.5012644966061473e-10 : 

[mawc2019]

The test in test_unfilter_design also fails due to mismatch of array size.

ValueError: cannot reshape array of size 160000 into shape (401,401)

[stevengj]

A factor of ≈2 increase in the tolerances seems fine.

[oskooi]

Looks like the error tolerances in test_adjoint_solver.py need to be reverted to (close to) what they were in #1769.

[mawc2019]

Looks like the error tolerances in test_adjoint_solver.py need to be reverted to (close to) what they were in https://github.com/NanoComp/meep/pull/1769.

We probably cannot do so because frequency widths are quite different in the two cases. Now there is df = 0.05*fcen, but in #1769 there was df = 0.23*fcen. The values of gradients and hence the tolerances are not comparable between the two cases.

In addition, it seems that +1 is also needed in the expressions of Nr and Nz in test_adjoint_cyl.py.

Nr, Nz = int(design_r * design_region_resolution), int(design_z * design_region_resolution)