def test_uni_from_cubes_rotate_and_write(self):
self.assertEquals(self.uni.field.shape[0], 2)
self.assertEquals(len(self.uni.field.field_values), 2)
rot = self.uni.field.rotate(0, 1, np.pi / 4)
self.assertEquals(rot.shape[0], 2)
f = Cube.from_universe(self.uni, 1)
self.assertEquals(len(f), 874)
def test_uni_from_cubes_rotate_and_write(self):
self.assertEqual(self.uni.field.shape[0], 2)
self.assertEqual(len(self.uni.field.field_values), 2)
rot = self.uni.field.rotate(0, 1, np.pi / 4)
self.assertEqual(rot.shape[0], 2)
f = Cube.from_universe(self.uni, 1)
self.assertEqual(len(f), 874)
def write_cube(self, file_name='output', field_number=0):
"""
Write to a file in cube format for a single 3D scalar field in universe object.
.. code-block:: python
uni.add_molecular_orbitals() # Default around (H**O-5, LUMO+7)
uni.write_cube('cubefile', 0) # write to cubefile.cube for H**O-5
Args:
file_name (str): name of the output file without file extension
field_number (int): number of the single field starting with 0
Returns:
None
"""
import os
from exatomic.interfaces.cube import Cube
if os.path.isfile(file_name+'.cube'):
raise FileExistsError('File '+file_name+'.cube '+'exists.')
cube_edi = Cube.from_universe(self,field_number)
cube_edi.write(file_name+'.cube')
def setUp(self):
self.lg = Cube(resource('mol-carbon-dz-1.cube'))
self.sm1 = Cube(resource('adf-lu-35.cube'))
self.sm2 = Cube(resource('adf-lu-36.cube'))
self.uni = uni_from_cubes(staticdir() + '/cube/', ext='*lu*cube')
class TestCube(TestCase):
"""Tests cube reading and writing."""
def setUp(self):
self.lg = Cube(resource('mol-carbon-dz-1.cube'))
self.sm1 = Cube(resource('adf-lu-35.cube'))
self.sm2 = Cube(resource('adf-lu-36.cube'))
self.uni = uni_from_cubes(staticdir() + '/cube/', ext='*lu*cube')
def test_parse_atom(self):
self.lg.parse_atom()
self.sm1.parse_atom()
self.sm2.parse_atom()
self.assertEquals(self.lg.atom.shape[0], 1)
self.assertEquals(self.sm1.atom.shape[0], 1)
self.assertEquals(self.sm2.atom.shape[0], 1)
def test_parse_field(self):
self.lg.parse_field()
self.sm1.parse_field()
self.sm2.parse_field()
self.assertEquals(self.lg.field.shape[0], 1)
self.assertEquals(self.sm1.field.shape[0], 1)
self.assertEquals(self.sm2.field.shape[0], 1)
self.assertEquals(self.lg.field.field_values[0].shape[0], 132651)
self.assertEquals(self.sm1.field.field_values[0].shape[0], 4913)
self.assertEquals(self.sm2.field.field_values[0].shape[0], 4913)
def test_to_universe(self):
lg = self.lg.to_universe()
sm1 = self.sm1.to_universe()
sm2 = self.sm2.to_universe()
for uni in [lg, sm1, sm2]:
for attr in ['atom', 'field']:
self.assertTrue(hasattr(uni, attr))
def test_uni_from_cubes_rotate_and_write(self):
self.assertEquals(self.uni.field.shape[0], 2)
self.assertEquals(len(self.uni.field.field_values), 2)
rot = self.uni.field.rotate(0, 1, np.pi / 4)
self.assertEquals(rot.shape[0], 2)
f = Cube.from_universe(self.uni, 1)
self.assertEquals(len(f), 874)
def setUp(self):
self.lg = Cube(resource('mol-carbon-dz-1.cube'))
self.sm1 = Cube(resource('adf-lu-35.cube'))
self.sm2 = Cube(resource('adf-lu-36.cube'))
self.uni = uni_from_cubes(staticdir() + '/cube/', ext='*lu*cube')
class TestCube(TestCase):
"""Tests cube reading and writing."""
def setUp(self):
self.lg = Cube(resource('mol-carbon-dz-1.cube'))
self.sm1 = Cube(resource('adf-lu-35.cube'))
self.sm2 = Cube(resource('adf-lu-36.cube'))
self.uni = uni_from_cubes(staticdir() + '/cube/', ext='*lu*cube')
def test_parse_atom(self):
self.lg.parse_atom()
self.sm1.parse_atom()
self.sm2.parse_atom()
self.assertEqual(self.lg.atom.shape[0], 1)
self.assertEqual(self.sm1.atom.shape[0], 1)
self.assertEqual(self.sm2.atom.shape[0], 1)
def test_parse_field(self):
self.lg.parse_field()
self.sm1.parse_field()
self.sm2.parse_field()
self.assertEqual(self.lg.field.shape[0], 1)
self.assertEqual(self.sm1.field.shape[0], 1)
self.assertEqual(self.sm2.field.shape[0], 1)
self.assertEqual(self.lg.field.field_values[0].shape[0], 132651)
self.assertEqual(self.sm1.field.field_values[0].shape[0], 4913)
self.assertEqual(self.sm2.field.field_values[0].shape[0], 4913)
def test_to_universe(self):
lg = self.lg.to_universe()
sm1 = self.sm1.to_universe()
sm2 = self.sm2.to_universe()
for uni in [lg, sm1, sm2]:
for attr in ['atom', 'field']:
self.assertTrue(hasattr(uni, attr))
def test_uni_from_cubes_rotate_and_write(self):
self.assertEqual(self.uni.field.shape[0], 2)
self.assertEqual(len(self.uni.field.field_values), 2)
rot = self.uni.field.rotate(0, 1, np.pi / 4)
self.assertEqual(rot.shape[0], 2)
f = Cube.from_universe(self.uni, 1)
self.assertEqual(len(f), 874)