def test_read_auto_col_one_line(tmpdir):
he_col = (' He 2.0 0.00000000 0.00000000 0.00000000' +
' 4.00260325\n')
f = ef.tmpf(tmpdir, he_col)
elem, xyz, vec, com = fileio.read_auto(f)
assert np.all(elem == ['He'])
assert np.allclose(xyz, np.zeros((1, 3)))
def test_read_auto_col_one_line(tmpdir):
he_col = (' He 2.0 0.00000000 0.00000000 0.00000000' +
' 4.00260325\n')
f = ef.tmpf(tmpdir, he_col)
elem, xyz, vec, com = fileio.read_auto(f)
assert np.all(elem == ['He'])
assert np.allclose(xyz, np.zeros((1, 3)))
def test_read_auto_zmt_one_line(tmpdir):
f = ef.tmpf(tmpdir, 'He\n')
elem, xyz, vec, com = fileio.read_auto(f)
assert np.all(elem == ['He'])
assert np.allclose(xyz, np.zeros((1, 3)))
def test_read_auto_only_comment(tmpdir):
f = ef.tmpf(tmpdir, 'comment line\n')
with pytest.raises(IOError, match=r'cannot have comment with single .*'):
elem, xyz, vec, com = fileio.read_auto(f, hascom=True)
def test_read_auto_only_comment(tmpdir):
f = ef.tmpf(tmpdir, 'comment line\n')
with pytest.raises(IOError, match=r'cannot have comment with single .*'):
elem, xyz, vec, com = fileio.read_auto(f, hascom=True)
def test_read_auto_traj(tmpdir):
f = ef.tmpf(tmpdir, ef.traj_time)
elem, xyz, vec, com = fileio.read_auto(f)
assert np.all(elem == 5*['X'])
assert np.allclose(xyz, eg.ch4[1], atol=1e-4)
def test_read_auto_zmt(tmpdir):
f = ef.tmpf(tmpdir, ef.zmt_nocom)
elem, xyz, vec, com = fileio.read_auto(f)
assert np.all(elem == eg.ch4[0])
assert np.allclose(xyz, eg.ch4_zmt[1], atol=1e-6)
def test_read_auto_col(tmpdir):
f = ef.tmpf(tmpdir, ef.col_nocom)
elem, xyz, vec, com = fileio.read_auto(f)
assert np.all(elem == eg.ch4[0])
assert np.allclose(xyz, eg.ch4[1])
def test_read_auto_traj_one_line_comment(tmpdir):
f = ef.tmpf(tmpdir, ef.traj_com)
elem, xyz, vec, com = fileio.read_auto(f, hascom=True)
assert np.all(elem == 5*['X'])
assert np.allclose(xyz, eg.ch4[1], atol=1e-4)
assert com == 'comment line'
def test_read_auto_gdat(tmpdir):
f = ef.tmpf(tmpdir, ef.gdat_bohr)
elem, xyz, vec, com = fileio.read_auto(f)
assert np.all(elem == eg.ch4[0])
assert np.allclose(xyz, eg.ch4[1])
def test_read_auto_col(tmpdir):
f = ef.tmpf(tmpdir, ef.col_nocom)
elem, xyz, vec, com = fileio.read_auto(f)
assert np.all(elem == eg.ch4[0])
assert np.allclose(xyz, eg.ch4[1])
def test_read_auto_unrecognized_one_line_comment(tmpdir):
f = ef.tmpf(tmpdir, 'comment line\n123 abc 456 def\n')
with pytest.raises(IOError, match=r'single line input in unrecognized .*'):
elem, xyz, vec, com = fileio.read_auto(f, hascom=True)
def test_read_auto_traj_one_line_comment(tmpdir):
f = ef.tmpf(tmpdir, ef.traj_com)
elem, xyz, vec, com = fileio.read_auto(f, hascom=True)
assert np.all(elem == 5 * ['X'])
assert np.allclose(xyz, eg.ch4[1], atol=1e-4)
assert com == 'comment line'
def test_read_auto_zmt_one_line_comment(tmpdir):
f = ef.tmpf(tmpdir, 'comment line\nHe\n')
elem, xyz, vec, com = fileio.read_auto(f, hascom=True)
assert np.all(elem == ['He'])
assert np.allclose(xyz, np.zeros((1, 3)))
assert com == 'comment line'
def test_read_auto_zmt_one_line(tmpdir):
f = ef.tmpf(tmpdir, 'He\n')
elem, xyz, vec, com = fileio.read_auto(f)
assert np.all(elem == ['He'])
assert np.allclose(xyz, np.zeros((1, 3)))
def test_read_auto_zmt(tmpdir):
f = ef.tmpf(tmpdir, ef.zmt_nocom)
elem, xyz, vec, com = fileio.read_auto(f)
assert np.all(elem == eg.ch4[0])
assert np.allclose(xyz, eg.ch4_zmt[1], atol=1e-6)
def test_read_auto_zmt_one_line_comment(tmpdir):
f = ef.tmpf(tmpdir, 'comment line\nHe\n')
elem, xyz, vec, com = fileio.read_auto(f, hascom=True)
assert np.all(elem == ['He'])
assert np.allclose(xyz, np.zeros((1, 3)))
assert com == 'comment line'
def test_read_auto_zmt_comment(tmpdir):
f = ef.tmpf(tmpdir, ef.zmt_com)
elem, xyz, vec, com = fileio.read_auto(f, hascom=True)
assert np.all(elem == eg.ch4[0])
assert np.allclose(xyz, eg.ch4_zmt[1], atol=1e-6)
assert com == 'comment line'
def test_read_auto_unrecognized_one_line_comment(tmpdir):
f = ef.tmpf(tmpdir, 'comment line\n123 abc 456 def\n')
with pytest.raises(IOError, match=r'single line input in unrecognized .*'):
elem, xyz, vec, com = fileio.read_auto(f, hascom=True)
def test_read_auto_traj(tmpdir):
f = ef.tmpf(tmpdir, ef.traj_time)
elem, xyz, vec, com = fileio.read_auto(f)
assert np.all(elem == 5 * ['X'])
assert np.allclose(xyz, eg.ch4[1], atol=1e-4)
def test_read_auto_gdat(tmpdir):
f = ef.tmpf(tmpdir, ef.gdat_bohr)
elem, xyz, vec, com = fileio.read_auto(f)
assert np.all(elem == eg.ch4[0])
assert np.allclose(xyz, eg.ch4[1])
def test_read_auto_unrecognized_multi_lines(tmpdir):
f = ef.tmpf(tmpdir, 'abc 123 def 456\nabc def 123 456\n123 456 abc def\n')
with pytest.raises(IOError, match=r'unrecognized file format'):
elem, xyz, vec, com = fileio.read_auto(f)
def test_read_auto_zmt_comment(tmpdir):
f = ef.tmpf(tmpdir, ef.zmt_com)
elem, xyz, vec, com = fileio.read_auto(f, hascom=True)
assert np.all(elem == eg.ch4[0])
assert np.allclose(xyz, eg.ch4_zmt[1], atol=1e-6)
assert com == 'comment line'
def test_read_auto_end_of_file(tmpdir):
f = ef.tmpf(tmpdir, '')
with pytest.raises(IOError, match=r'end of file'):
elem, xyz, vec, com = fileio.read_auto(f)
def test_read_auto_unrecognized_multi_lines(tmpdir):
f = ef.tmpf(tmpdir, 'abc 123 def 456\nabc def 123 456\n123 456 abc def\n')
with pytest.raises(IOError, match=r'unrecognized file format'):
elem, xyz, vec, com = fileio.read_auto(f)
def test_read_auto_end_of_file(tmpdir):
f = ef.tmpf(tmpdir, '')
with pytest.raises(IOError, match=r'end of file'):
elem, xyz, vec, com = fileio.read_auto(f)