def get_InterpolationData_object(material):
docs_dir = os.path.dirname(os.path.abspath(__file__))
try:
return InterpolationData.from_castep(path=docs_dir, seedname=material)
except FileNotFoundError:
print('{} not found in {}. Fetching remote content.'.format(
material, docs_dir))
return fetch_InterpolationData_object(material)
def setUp(self):
self.seedname = 'quartz'
self.path = os.path.join('data', 'interpolation', 'quartz')
self.data = InterpolationData.from_castep(self.seedname,
path=self.path)
qpts = np.loadtxt(os.path.join('data', 'qgrid_444.txt'))
self.data.calculate_fine_phonons(qpts, asr='reciprocal')
self.dw_path = os.path.join('data', 'dw_factor', 'quartz')
def setUp(self):
self.seedname = 'La2Zr2O7'
phonon_path = 'data'
self.interpolation_path = os.path.join('data', 'interpolation', 'LZO')
self.sqw_path = os.path.join('data', 'sqw_map')
pdata = PhononData.from_castep(self.seedname, path=phonon_path)
self.data = InterpolationData.from_castep(self.seedname,
path=self.interpolation_path)
self.data.calculate_fine_phonons(pdata.qpts, asr='realspace')
self.scattering_lengths = {'La': 8.24, 'Zr': 7.16, 'O': 5.803}
self.ebins = np.arange(0, 100, 1.)
def fetch_InterpolationData_object(material):
base_url = "https://raw.githubusercontent.com/g5t/brille/master/docs/tutorials"
file_to_fetch = material + ".castep_bin"
with tempfile.TemporaryDirectory() as tmp_dir:
r = requests.get(base_url + "/" + file_to_fetch)
if not r.ok:
raise Exception("Fetching {} failed with reason '{}'".format(file_to_fetch, r.reason))
out_path = Path(tmp_dir, file_to_fetch)
open(str(out_path), 'wb').write(r.content)
idata = InterpolationData.from_castep(path=tmp_dir, seedname=material)
return idata
def load_interpolation_data(named):
"""Load a data file from the tests folder."""
b = find_spec('brille')
if b is None:
bdir = '.' # punt! maybe we're in a build directory?
else:
bdir = b.submodule_search_locations[0]
testdir = os.path.join(bdir, '..', 'tests')
if not os.path.exists(testdir):
raise Exception('Could not locate the tests directory')
return InterpolationData(seedname=named, path=testdir)
def load_interpolation_data(named):
"""Load a data file from the repository tests folder
Note that this only works if the package is installed via
python setup.py develop [--user]
which builds the C++ library and installs it inside of the repository
structure with simlinks in the usual package location(s).
"""
test_spec = find_spec('brille')
brilleroot = test_spec.submodule_search_locations[0]
seed = os.path.join(brilleroot, '..', 'tests', named)
return InterpolationData(seed)
def main():
parser = get_parser()
args = parser.parse_args()
etas = np.arange(args.min, args.max + args.step / 100, args.step)
t_init = np.zeros(len(etas), dtype=np.float64)
t_tot = np.zeros(len(etas), dtype=np.float64)
idata = InterpolationData.from_castep(args.seedname)
sfmt = '{:20s}'
tfmt = '{: 3.2f}'
etafmt = '{: 2.2f}'
for i, eta in enumerate(etas):
print(('Results for eta ' + etafmt).format(eta))
# Time Ewald sum initialisation
start = time.time()
idata._dipole_correction_init(eta_scale=eta)
end = time.time()
t_init[i] = end - start
print((sfmt + ': ' + tfmt + ' s').format('Ewald init time', t_init[i]))
# Time per qpt
start = time.time()
for n in range(args.n):
idata._calculate_dipole_correction(np.array([0.5, 0.5, 0.5]))
end = time.time()
t_tot[i] = end - start
print((sfmt + ': ' + tfmt + ' ms\n').format('Ewald time/qpt',
t_tot[i] * 1000 / args.n))
opt = np.argmin(t_tot)
print('******************************')
print(('Suggested optimum eta is ' + etafmt).format(etas[opt]))
print((sfmt + ': ' + tfmt + ' s').format('init time', t_init[opt]))
print((sfmt + ': ' + tfmt + ' ms\n').format('time/qpt',
t_tot[opt] * 1000 / args.n))
def test_empty_idata_raises_exception(self):
empty_data = InterpolationData.from_castep(self.seedname, self.path)
self.assertRaises(Exception, empty_data._dw_coeff)
base_url = "https://raw.githubusercontent.com/g5t/brille/master/docs/tutorials"
file_to_fetch = material + ".castep_bin"
with tempfile.TemporaryDirectory() as tmp_dir:
r = requests.get(base_url + "/" + file_to_fetch)
if not r.ok:
raise Exception("Fetching {} failed with reason '{}'".format(file_to_fetch, r.reason))
out_path = Path(tmp_dir, file_to_fetch)
open(str(out_path), 'wb').write(r.content)
idata = InterpolationData.from_castep(path=tmp_dir, seedname=material)
return idata
def get_InterpolationData_object(material):
validation_dir = os.path.dirname(os.path.abspath(__file__))
tutorial_dir = str(Path(validation_dir, '..', 'docs', 'tutorials'))
try:
return InterpolationData.from_castep(path=tutorial_dir, seedname=material)
except FileNotFoundError:
print('{} not found in {}. Fetching remote content.'.format(material, tutorial_dir))
return fetch_InterpolationData_object(material)
class PhononEigenvectorRotationValidator(unittest.TestCase):
"""A TestCase object class to validate phonon eigenvector rotation by brille"""
def test_NaCl(self):
# fetch and load the NaCl.castep_bin file from the brille repository
idata = get_InterpolationData_object('NaCl')
# Do not sort the modes on neighbouring trellis vertices to make comparison with Euphonic easier
breu = BrEu(idata, sort=False, trellis=True, max_volume=0.1, parallel=False)
# pick a trellis Q vertex inside the irreducible polyhedron, away from the boundaries:
q_ir = breu.grid.rlu[6:7] # shape = (1,3)
# pull together the pointgroup operations
def setUp(self):
# Create both PhononData and InterpolationData objs for testing
seedname = 'La2Zr2O7'
ppath = 'data'
self.pdata = PhononData.from_castep(seedname, path=ppath)
self.pdata.convert_e_units('1/cm')
ipath = os.path.join('data', 'interpolation', 'LZO')
self.idata = InterpolationData.from_castep(seedname, path=ipath)
self.idata.convert_e_units('1/cm')
self.expected_reordered_freqs = np.array(
[[
65.062447, 65.062447, 70.408176, 76.847761, 76.847761,
85.664054, 109.121893, 109.121893, 117.920003, 119.363588,
128.637195, 128.637195, 155.905812, 155.905812, 160.906969,
170.885818, 172.820917, 174.026075, 178.344487, 183.364621,
183.364621, 199.25343, 199.25343, 222.992334, 225.274444,
231.641854, 253.012884, 265.452117, 270.044891, 272.376357,
272.376357, 275.75891, 299.890562, 299.890562, 315.067652,
315.067652, 319.909059, 338.929562, 338.929562, 339.067304,
340.308461, 349.793091, 376.784786, 391.288446, 391.288446,
396.109935, 408.179774, 408.179774, 410.991152, 421.254131,
456.215732, 456.215732, 503.360953, 532.789756, 532.789756,
545.400861, 548.704226, 552.622463, 552.622463, 557.488238,
560.761581, 560.761581, 618.721858, 734.650232, 739.200593,
739.200593
],
[
62.001197, 62.001197, 67.432601, 70.911126, 70.911126,
87.435181, 109.893289, 109.893289, 110.930712, 114.6143,
129.226412, 129.226412, 150.593502, 150.593502, 148.065107,
165.856823, 168.794942, 167.154743, 169.819174, 187.349434,
187.349434, 202.003734, 202.003734, 221.329787, 231.797486,
228.999412, 259.308314, 264.453017, 279.078288, 270.15176,
270.15176, 278.861064, 300.349651, 300.349651, 311.929653,
311.929653, 318.251662, 334.967743, 334.967743, 340.747776,
338.357732, 356.048074, 372.658152, 395.526156, 395.526156,
398.356528, 406.398552, 406.398552, 407.216469, 421.122741,
460.527859, 460.527859, 486.346855, 533.694179, 533.694179,
544.93361, 549.252501, 550.733812, 550.733812, 558.006939,
559.641583, 559.641583, 591.170512, 739.589673, 738.563124,
738.563124
],
[
55.889266, 55.889266, 64.492348, 66.375741, 66.375741,
88.940906, 109.388591, 109.388591, 100.956751, 109.379914,
130.017598, 130.017598, 145.579207, 145.579207, 134.563651,
161.166842, 164.427227, 159.401681, 161.563336, 190.735683,
190.735683, 205.550607, 205.550607, 219.351563, 238.204625,
226.878861, 265.686284, 263.148071, 287.722953, 267.983859,
267.983859, 281.041577, 299.480498, 299.480498, 308.176127,
308.176127, 318.101514, 332.930623, 332.930623, 344.002317,
335.480119, 361.930637, 368.350971, 399.050499, 399.050499,
399.241143, 404.639113, 404.639113, 400.809087, 420.335936,
465.504468, 465.504468, 470.205579, 534.544778, 534.544778,
544.501022, 549.755212, 548.80696, 548.80696, 556.193672,
558.101279, 558.101279, 565.776342, 741.372005, 737.860626,
737.860626
],
[
46.935517, 46.935517, 61.690137, 63.177342, 63.177342,
90.180632, 107.721223, 107.721223, 86.944159, 104.159787,
130.879196, 130.879196, 141.295304, 141.295304, 122.536218,
157.146893, 160.037586, 151.613374, 153.750028, 193.160653,
193.160653, 209.882364, 209.882364, 215.936117, 244.178665,
225.432553, 272.052764, 261.655838, 295.533954, 265.906764,
265.906764, 282.006965, 295.142911, 295.142911, 307.16826,
307.16826, 319.295877, 332.071847, 332.071847, 348.814514,
332.065989, 367.152249, 364.288189, 400.773283, 400.773283,
399.790407, 404.068253, 404.068253, 387.165977, 418.829125,
470.716023, 470.716023, 460.278318, 535.223077, 535.223077,
544.111882, 550.193478, 547.016352, 547.016352, 552.362689,
556.261571, 556.261571, 543.678775, 740.965394, 737.162508,
737.162508
],
[
36.367201, 36.367201, 59.168434, 60.36167, 60.36167,
91.154677, 105.37576, 105.37576, 68.755044, 99.446481,
131.658334, 131.658334, 138.017877, 138.017877, 113.14576,
153.975056, 156.016054, 144.576942, 146.47047, 194.581347,
194.581347, 214.716315, 214.716315, 210.473211, 249.235088,
224.769091, 278.102009, 260.171794, 302.032435, 263.72796,
263.72796, 282.018114, 289.408098, 289.408098, 308.097577,
308.097577, 321.241146, 331.659808, 331.659808, 353.492915,
328.675778, 371.468173, 362.406897, 399.901709, 399.901709,
399.179346, 405.625572, 405.625572, 368.236337, 416.52493,
475.665346, 475.665346, 458.944007, 535.667484, 535.667484,
543.78033, 550.551048, 545.494533, 545.494533, 547.179463,
554.338811, 554.338811, 524.846465, 739.380608, 736.536495,
736.536495
],
[
24.785718, 24.785718, 57.117299, 57.830885, 57.830885,
91.859898, 103.047316, 103.047316, 47.456331, 95.691927,
132.248074, 132.248074, 135.79383, 135.79383, 106.389552,
151.718169, 152.772977, 138.984268, 139.88209, 195.244028,
195.244028, 219.466615, 219.466615, 203.707835, 252.993107,
224.615517, 283.248783, 258.912028, 306.841458, 261.246129,
261.246129, 281.584343, 284.696598, 284.696598, 309.37963,
309.37963, 323.205545, 331.373295, 331.373295, 353.088149,
326.000428, 374.686778, 367.331006, 398.738183, 398.738183,
398.433921, 407.157219, 407.157219, 349.637392, 413.438689,
479.806857, 479.806857, 463.608166, 535.889622, 535.889622,
543.524255, 550.815232, 544.325882, 544.325882, 541.757933,
552.630089, 552.630089, 508.677347, 737.533584, 736.042236,
736.042236
],
[
12.555025, 12.555025, 55.757043, 55.972359, 55.972359,
92.288749, 101.380298, 101.380298, 24.214202, 93.270077,
132.593517, 132.593517, 134.540163, 134.540163, 102.211134,
150.378051, 150.665566, 135.38769, 134.747421, 195.473725,
195.473725, 223.210107, 223.210107, 197.85154, 255.276828,
224.659659, 286.758828, 258.068085, 309.776254, 258.846604,
258.846604, 281.147316, 281.874849, 281.874849, 310.385381,
310.385381, 324.609898, 331.158402, 331.158402, 351.072968,
324.818103, 376.67194, 374.186388, 397.950964, 397.950964,
397.878833, 408.114477, 408.114477, 336.37863, 410.112489,
482.591747, 482.591747, 471.735469, 535.964134, 535.964134,
543.361599, 550.977172, 543.571634, 543.571634, 537.566668,
551.451065, 551.451065, 494.626062, 736.133131, 735.72609,
735.72609
],
[
-0.019621, -0.019621, 55.277927, 55.277927, 55.277927,
92.432911, 100.780857, 100.780857, -0.019621, 92.432911,
132.696363, 132.696363, 134.147102, 134.147102, 100.780857,
149.934817, 149.934817, 134.147102, 132.696363, 195.519690,
195.519690, 224.698049, 224.698049, 195.519690, 256.039866,
224.698049, 288.011070, 257.771213, 310.763767, 257.771213,
257.771213, 280.972846, 280.972846, 280.972846, 310.763767,
310.763767, 325.114540, 331.073494, 331.073494, 350.234619,
325.114540, 377.342620, 377.342620, 397.677533, 397.677533,
397.677533, 408.435923, 408.435923, 331.073494, 408.435923,
483.578389, 483.578389, 480.948578, 535.976810, 535.976810,
543.305729, 551.031712, 543.305729, 543.305729, 535.976810,
551.031712, 551.031712, 483.578389, 735.617369, 735.617369,
735.617369
],
[
12.555025, 12.555025, 55.757043, 55.972359, 55.972359,
92.288749, 101.380298, 101.380298, 24.214202, 93.270077,
132.593517, 132.593517, 134.540163, 134.540163, 102.211134,
150.378051, 150.665566, 135.38769, 134.747421, 195.473725,
195.473725, 223.210107, 223.210107, 197.85154, 255.276828,
224.659659, 286.758828, 258.068085, 309.776254, 258.846604,
258.846604, 281.147316, 281.874849, 281.874849, 310.385381,
310.385381, 324.609898, 331.158402, 331.158402, 351.072968,
324.818103, 376.67194, 374.186388, 397.950964, 397.950964,
397.878833, 408.114477, 408.114477, 336.37863, 410.112489,
482.591747, 482.591747, 471.735469, 535.964134, 535.964134,
543.361599, 550.977172, 543.571634, 543.571634, 537.566668,
551.451065, 551.451065, 494.626062, 736.133131, 735.72609,
735.72609
],
[
24.785718, 24.785718, 57.117299, 57.830885, 57.830885,
91.859898, 103.047316, 103.047316, 47.456331, 95.691927,
132.248074, 132.248074, 135.79383, 135.79383, 106.389552,
151.718169, 152.772977, 138.984268, 139.88209, 195.244028,
195.244028, 219.466615, 219.466615, 203.707835, 252.993107,
224.615517, 283.248783, 258.912028, 306.841458, 261.246129,
261.246129, 281.584343, 284.696598, 284.696598, 309.37963,
309.37963, 323.205545, 331.373295, 331.373295, 353.088149,
326.000428, 374.686778, 367.331006, 398.738183, 398.738183,
398.433921, 407.157219, 407.157219, 349.637392, 413.438689,
479.806857, 479.806857, 463.608166, 535.889622, 535.889622,
543.524255, 550.815232, 544.325882, 544.325882, 541.757933,
552.630089, 552.630089, 508.677347, 737.533584, 736.042236,
736.042236
]])
