geometric_object_volume by stevengj · Pull Request #45 · NanoComp/libctl

stevengj · 2019-10-30T01:35:38Z

Adds new geometric_object_volume function to compute the volume of a given object.

Speeds up box_overlap_with_object when the object is entirely contained within the box, by using the analytical volume formula instead of numerical integration in this case.

oskooi · 2019-10-30T01:54:53Z

python/tests/fragment_stats.py is failing:

Using MPI version 3.1, 2 processes
FF....FFFFFFFFF.F.......FFF.F........F....F.................
======================================================================
FAIL: test_1d (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 89, in test_1d
    self._test_1d([])
  File "./tests/fragment_stats.py", line 82, in _test_1d
    cond=300 / sym_factor)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 300.0

======================================================================
FAIL: test_1d_with_overlap (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 104, in test_1d_with_overlap
    self.check_stats(fs, a_eps=300, a_mu=300, nonlin=600, susc=700, cond=600)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 600

======================================================================
FAIL: test_1d_with_partial_fragment (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 117, in test_1d_with_partial_fragment
    self.check_stats(fs, a_eps=260, a_mu=260, nonlin=480, susc=480, cond=480)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 480

======================================================================
FAIL: test_1d_with_pml (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 95, in test_1d_with_pml
    self._test_1d([], pml=[mp.PML(1)])
  File "./tests/fragment_stats.py", line 82, in _test_1d
    cond=300 / sym_factor)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 300.0

======================================================================
FAIL: test_1d_with_symmetry (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 92, in test_1d_with_symmetry
    self._test_1d([mp.Mirror(mp.X)])
  File "./tests/fragment_stats.py", line 82, in _test_1d
    cond=300 / sym_factor)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 150.0

======================================================================
FAIL: test_2d (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 166, in test_2d
    self._test_2d([])
  File "./tests/fragment_stats.py", line 159, in _test_2d
    cond=30000 / sym_factor)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 30000.0

======================================================================
FAIL: test_2d_with_pml_all_sides (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 172, in test_2d_with_pml_all_sides
    self._test_2d([], pml=[mp.PML(1, mp.Y), mp.PML(2, mp.X, mp.Low), mp.PML(3, mp.X, mp.High)])
  File "./tests/fragment_stats.py", line 159, in _test_2d
    cond=30000 / sym_factor)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 30000.0

======================================================================
FAIL: test_2d_with_symmetry (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 169, in test_2d_with_symmetry
    self._test_2d([mp.Mirror(mp.X), mp.Mirror(mp.Y)])
  File "./tests/fragment_stats.py", line 159, in _test_2d
    cond=30000 / sym_factor)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 7500.0

======================================================================
FAIL: test_cyl (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 268, in test_cyl
    self.check_stats(fs, a_eps=90000, a_mu=90000, nonlin=30000, susc=30000, cond=30000)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 30000

----------------------------------------------------------------------
Ran 31 tests in 0.038s

FAILED (failures=9)

Elapsed run time = 0.0442 s
..
======================================================================
FAIL: test_1d (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 89, in test_1d
    self._test_1d([])
  File "./tests/fragment_stats.py", line 82, in _test_1d
    cond=300 / sym_factor)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 300.0

======================================================================
FAIL: test_1d_with_overlap (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 104, in test_1d_with_overlap
    self.check_stats(fs, a_eps=300, a_mu=300, nonlin=600, susc=700, cond=600)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 600

======================================================================
FAIL: test_1d_with_partial_fragment (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 117, in test_1d_with_partial_fragment
    self.check_stats(fs, a_eps=260, a_mu=260, nonlin=480, susc=480, cond=480)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 480

======================================================================
FAIL: test_1d_with_pml (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 95, in test_1d_with_pml
    self._test_1d([], pml=[mp.PML(1)])
  File "./tests/fragment_stats.py", line 82, in _test_1d
    cond=300 / sym_factor)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 300.0

======================================================================
FAIL: test_1d_with_symmetry (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 92, in test_1d_with_symmetry
    self._test_1d([mp.Mirror(mp.X)])
  File "./tests/fragment_stats.py", line 82, in _test_1d
    cond=300 / sym_factor)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 150.0

======================================================================
FAIL: test_2d (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 166, in test_2d
    self._test_2d([])
  File "./tests/fragment_stats.py", line 159, in _test_2d
    cond=30000 / sym_factor)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 30000.0

======================================================================
FAIL: test_2d_with_pml_all_sides (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 172, in test_2d_with_pml_all_sides
    self._test_2d([], pml=[mp.PML(1, mp.Y), mp.PML(2, mp.X, mp.Low), mp.PML(3, mp.X, mp.High)])
  File "./tests/fragment_stats.py", line 159, in _test_2d
    cond=30000 / sym_factor)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 30000.0

======================================================================
FAIL: test_2d_with_symmetry (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 169, in test_2d_with_symmetry
    self._test_2d([mp.Mirror(mp.X), mp.Mirror(mp.Y)])
  File "./tests/fragment_stats.py", line 159, in _test_2d
    cond=30000 / sym_factor)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 7500.0

======================================================================
FAIL: test_cyl (__main__.TestFragmentStats)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./tests/fragment_stats.py", line 268, in test_cyl
    self.check_stats(fs, a_eps=90000, a_mu=90000, nonlin=30000, susc=30000, cond=30000)
  File "./tests/fragment_stats.py", line 25, in check_stats
    self.assertEqual(fragment.num_nonlinear_pixels, nonlin)
AssertionError: 0 != 30000

----------------------------------------------------------------------
Ran 31 tests in 0.040s

FAILED (failures=9)
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[20345,1],1]
  Exit code:    1
--------------------------------------------------------------------------
FAIL tests/fragment_stats.py (exit status: 1)

ChristopherHogan · 2019-11-06T01:37:48Z

utils/geom.c

+	 }
+	 case GEOM BLOCK: {
+          vector3 size = o.subclass.block_data->size;
+          double vol = size.x * size.y * size.z * fabs(matrix3x3_determinant(geometry_lattice.basis) / matrix3x3_determinant(o.subclass.block_data->projection_matrix));


The failing tests are because a size of 0 in any dimension here makes vol equal to 0.

For now, I'll work around this by simply not using the geometric_object_volume optimization in 1d and 2d.

https://build.opensuse.org/request/show/827344 by user badshah400 + dimstar_suse - Update Source URL, moved to https://github.com/NanoComp/libctl. - update to 4.5.0: * New `make_slanted_prism` functions to make a prism with a given sidewall angle (gh#NanoComp/libctl#53). * Defined `LIBCTL_MAJOR_VERSION` etc. in `ctlgeom.h` header file when using stand-alone libctlgeom. * Bugfix in point-in-prism test (gh#NanoComp/libctl#49). * `geom_object_volume` function to get the volume of a 3d object (accelerates `box_overlap_with_object` for objects completely within a box) (gh#NanoComp/libctl#45). * `ctl_printf_callback` so that callers can capture stdout (gh#NanoComp/libctl#39).

stevengj added 4 commits October 2, 2019 18:13

geom_object_volume function

3048dfb

more tests

5848216

some bug fixes

e6f8f4a

more fixes

47ff10a

ChristopherHogan reviewed Nov 6, 2019

View reviewed changes

don't use geom_object_volume in 1d and 2d cases

4a616ae

stevengj merged commit fead47c into master Nov 6, 2019

stevengj deleted the object_vol branch November 6, 2019 02:20

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geometric_object_volume#45

geometric_object_volume#45
stevengj merged 5 commits intomasterfrom
object_vol

stevengj commented Oct 30, 2019

Uh oh!

oskooi commented Oct 30, 2019

Uh oh!

ChristopherHogan Nov 6, 2019

Uh oh!

stevengj Nov 6, 2019

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stevengj commented Oct 30, 2019

Uh oh!

oskooi commented Oct 30, 2019

Uh oh!

ChristopherHogan Nov 6, 2019

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stevengj Nov 6, 2019

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