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use np.testing.assert_almost_equal to compare numpy arrays #201

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Merged
amcadmus merged 1 commit into from
Sep 14, 2021
Merged

use np.testing.assert_almost_equal to compare numpy arrays #201

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55 changes: 21 additions & 34 deletions tests/comp_sys.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,28 +35,22 @@ def test_nframs(self):
def test_cell(self):
self.assertEqual(self.system_1.get_nframes(),
self.system_2.get_nframes())
for ff in range(self.system_1.get_nframes()) :
for ii in range(3) :
for jj in range(3) :
self.assertAlmostEqual(self.system_1.data['cells'][ff][ii][jj],
self.system_2.data['cells'][ff][ii][jj],
places = self.places,
msg = 'cell[%d][%d][%d] failed' % (ff,ii,jj))
np.testing.assert_almost_equal(self.system_1.data['cells'],
self.system_2.data['cells'],
decimal = self.places,
err_msg = 'cell failed')

def test_coord(self):
self.assertEqual(self.system_1.get_nframes(),
self.system_2.get_nframes())
# think about direct coord
tmp_cell = self.system_1.data['cells']
tmp_cell = np.reshape(tmp_cell, [-1, 3])
tmp_cell_norm = np.reshape(np.linalg.norm(tmp_cell, axis = 1), [-1, 3])
for ff in range(self.system_1.get_nframes()) :
for ii in range(sum(self.system_1.data['atom_numbs'])) :
for jj in range(3) :
self.assertAlmostEqual(self.system_1.data['coords'][ff][ii][jj] / tmp_cell_norm[ff][jj],
self.system_2.data['coords'][ff][ii][jj] / tmp_cell_norm[ff][jj],
places = self.places,
msg = 'coord[%d][%d][%d] failed' % (ff,ii,jj))
tmp_cell_norm = np.reshape(np.linalg.norm(tmp_cell, axis = 1), [-1, 1, 3])
np.testing.assert_almost_equal(self.system_1.data['coords'] / tmp_cell_norm,
self.system_2.data['coords'] / tmp_cell_norm,
decimal = self.places,
err_msg = 'coord failed')

def test_nopbc(self):
self.assertEqual(self.system_1.nopbc, self.system_2.nopbc)
Expand All @@ -66,22 +60,18 @@ class CompLabeledSys (CompSys) :
def test_energy(self) :
self.assertEqual(self.system_1.get_nframes(),
self.system_2.get_nframes())
for ff in range(self.system_1.get_nframes()) :
self.assertAlmostEqual(self.system_1.data['energies'][ff],
self.system_2.data['energies'][ff],
places = self.e_places,
msg = 'energies[%d] failed' % (ff))
np.testing.assert_almost_equal(self.system_1.data['energies'],
self.system_2.data['energies'],
decimal = self.e_places,
err_msg = 'energies failed')

def test_force(self) :
self.assertEqual(self.system_1.get_nframes(),
self.system_2.get_nframes())
for ff in range(self.system_1.get_nframes()) :
for ii in range(self.system_1.data['forces'].shape[1]) :
for jj in range(3) :
self.assertAlmostEqual(self.system_1.data['forces'][ff][ii][jj],
self.system_2.data['forces'][ff][ii][jj],
places = self.f_places,
msg = 'forces[%d][%d][%d] failed' % (ff,ii,jj))
np.testing.assert_almost_equal(self.system_1.data['forces'],
self.system_2.data['forces'],
decimal = self.f_places,
err_msg = 'forces failed')

def test_virial(self) :
self.assertEqual(self.system_1.get_nframes(),
Expand All @@ -92,13 +82,10 @@ def test_virial(self) :
if not 'virials' in self.system_1:
self.assertFalse('virials' in self.system_2)
return
for ff in range(self.system_1.get_nframes()) :
for ii in range(3) :
for jj in range(3) :
self.assertAlmostEqual(self.system_1['virials'][ff][ii][jj],
self.system_2['virials'][ff][ii][jj],
places = self.v_places,
msg = 'virials[%d][%d][%d] failed' % (ff,ii,jj))
np.testing.assert_almost_equal(self.system_1['virials'],
self.system_2['virials'],
decimal = self.v_places,
err_msg = 'virials failed')


class MultiSystems:
Expand Down