def setUp(self):
seedname = 'La2Zr2O7'
phonon_path = 'data'
self.sqw_path = os.path.join('data', 'sqw_map')
self.sf_path = os.path.join('data', 'structure_factor', 'LZO')
self.data = PhononData.from_castep(seedname, path=phonon_path)
self.scattering_lengths = {'La': 8.24, 'Zr': 7.16, 'O': 5.803}
self.ebins = np.arange(0, 100, 1.)
# PhononData object for DW grid
self.dw_data = PhononData.from_castep('La2Zr2O7-grid',
path=self.sf_path)
def main():
parser = get_parser()
args = parser.parse_args()
# If neither -up nor -down specified, plot both
if not args.up and not args.down:
args.up = True
args.down = True
path, file = os.path.split(args.filename)
seedname = file[:file.rfind('.')]
if file.endswith('.bands'):
data = BandsData.from_castep(seedname, path=path)
else:
data = PhononData.from_castep(seedname, path=path)
data.convert_e_units(args.units)
# Calculate and plot DOS
# Set default DOS bin and broadening width based on whether it's
# electronic or vibrational
if args.b is None:
if file.endswith('.bands'):
bwidth = 0.05*ureg.eV
else:
bwidth = 1.0*(1/ureg.cm)
bwidth.ito(args.units, 'spectroscopy')
else:
bwidth = args.b*ureg[args.units]
if args.w is None:
if file.endswith('.bands'):
gwidth = 0.1*ureg.eV
else:
gwidth = 10.0*(1/ureg.cm)
gwidth.ito(args.units, 'spectroscopy')
else:
gwidth = args.w*ureg[args.units]
if isinstance(data, BandsData):
all_freqs = np.append(data.freqs.magnitude, data.freq_down.magnitude)
else:
all_freqs = data.freqs.magnitude
bwidth = bwidth.magnitude
dos_bins = np.arange(all_freqs.min(), all_freqs.max() + bwidth, bwidth)
data.calculate_dos(dos_bins, gwidth, lorentz=args.lorentz)
if args.grace:
output_grace(data, seedname, mirror=args.mirror, up=args.up,
down=args.down)
else:
fig = plot_dos(data, args.filename, mirror=args.mirror, up=args.up,
down=args.down)
if fig is not None:
import matplotlib.pyplot as plt
# Save or show Matplotlib figure
if args.s:
plt.savefig(args.s)
else:
plt.show()
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 read_castep_gamma_phonons(seed, path='.'):
"""Parse CASTEP phonon data into a casteppy object,
and return eigenvalues and eigenvectors at the gamma point.
"""
try:
from euphonic.data.phonon import PhononData
except ImportError:
raise ImportError("""
Can't use castep phonon interface due to Euphonic not being installed.
Please download and install Euphonic from Github:
HTTPS: https://github.com/pace-neutrons/Euphonic.git
SSH: [email protected]:pace-neutrons/Euphonic.git
and try again.""")
# Parse CASTEP phonon data into casteppy object
try:
pd = PhononData(seed, path=path)
except TypeError:
# This happens in newer versions of Euphonic
pd = PhononData.from_castep(seed, path=path)
# Convert frequencies back to cm-1
pd.convert_e_units('1/cm')
# Get phonon frequencies+modes
evals = np.array(pd.freqs.magnitude)
evecs = np.array(pd.eigenvecs)
# Only grab the gamma point!
gamma_i = None
for i, q in enumerate(pd.qpts):
if np.isclose(q, [0, 0, 0]).all():
gamma_i = i
break
if gamma_i is None:
raise MuonAverageError('Could not find gamma point phonons in CASTEP'
' phonon file')
return evals[gamma_i], evecs[gamma_i]
def test_reorder_freqs(self):
seedname = 'NaH-reorder-test'
path = 'data'
data = PhononData.from_castep(seedname, path=path)
data.convert_e_units('1/cm')
data.reorder_freqs()
freqs = data.freqs.magnitude
reordered_freqs = freqs[np.arange(len(freqs))[:, np.newaxis],
data._mode_map]
expected_reordered_freqs = np.array(
[[
91.847109, 91.847109, 166.053018, 564.508299, 564.508299,
884.068976
],
[
154.825631, 132.031513, 206.21394, 642.513551, 690.303338,
832.120011
],
[
106.414367, 106.414367, 166.512415, 621.498613, 621.498613,
861.71391
],
[
-4.05580000e-02, -4.05580000e-02, 1.23103200e+00,
5.30573108e+02, 5.30573108e+02, 8.90673361e+02
],
[
139.375186, 139.375186, 207.564309, 686.675791, 686.675791,
833.291584
],
[
123.623059, 152.926351, 196.644517, 586.674239, 692.696132,
841.62725
],
[
154.308477, 181.239973, 181.239973, 688.50786, 761.918164,
761.918164
],
[
124.976823, 124.976823, 238.903818, 593.189877, 593.189877,
873.903056
]])
npt.assert_allclose(reordered_freqs, expected_reordered_freqs)
def main():
parser = get_parser()
args = parser.parse_args()
# If neither -up nor -down specified, plot both
if not args.up and not args.down:
args.up = True
args.down = True
# Read data
path, file = os.path.split(args.filename)
seedname = file[:file.rfind('.')]
if file.endswith('.bands'):
data = BandsData.from_castep(seedname, path=path)
else:
data = PhononData.from_castep(seedname, path=path)
data.convert_e_units(args.units)
# Reorder frequencies if requested
if args.reorder:
data.reorder_freqs()
# Plot
if args.grace:
output_grace(data, seedname, up=args.up, down=args.down)
else:
fig = plot_dispersion(data,
args.filename,
btol=args.btol,
up=args.up,
down=args.down)
if fig is not None:
import matplotlib.pyplot as plt
# Save or show Matplotlib figure
if args.s:
plt.savefig(args.s)
else:
plt.show()
def setUp(self):
seedname = 'La2Zr2O7-grid'
path = os.path.join('data', 'structure_factor', 'LZO')
self.data = PhononData.from_castep(seedname, path=path)
self.dw_path = os.path.join('data', 'dw_factor', 'LZO')
def setUp(self):
# Create trivial function object so attributes can be assigned to it
expctd_data = type('', (), {})()
expctd_data.cell_vec = np.array(
[[0.000000, 2.399500, 2.399500],
[2.399500, 0.000000, 2.399500],
[2.399500, 2.399500, 0.000000]])*ureg('angstrom')
expctd_data.ion_r = np.array([[0.500000, 0.500000, 0.500000],
[0.000000, 0.000000, 0.000000]])
expctd_data.ion_type = np.array(['H', 'Na'])
expctd_data.ion_mass = np.array([1.007940, 22.989770])*ureg('amu')
expctd_data.qpts = np.array([[-0.250000, -0.250000, -0.250000],
[-0.250000, -0.500000, -0.500000]])
expctd_data.weights = np.array([0.125, 0.375])
expctd_data.freqs = np.array(
[[91.847109, 91.847109, 166.053018,
564.508299, 564.508299, 884.068976],
[132.031513, 154.825631, 206.213940,
642.513551, 690.303338, 832.120011]])*ureg('1/cm')
expctd_data.freq_down = np.array([])*ureg('1/cm')
expctd_data.eigenvecs = np.array(
[[[[-0.061613336996 - 0.060761142686*1j,
-0.005526816216 - 0.006379010526*1j,
0.067140153211 + 0.067140153211*1j],
[0.666530886823 - 0.004641603630*1j,
0.064846864124 + 0.004641603630*1j,
-0.731377750947 + 0.000000000000*1j]],
[[-0.043088481348 - 0.041294487960*1j,
0.074981829953 + 0.073187836565*1j,
-0.031893348605 - 0.031893348605*1j],
[0.459604449490 - 0.009771253020*1j,
-0.807028225834 + 0.009771253020*1j,
0.347423776344 + 0.000000000000*1j]],
[[-0.062303354995 - 0.062303354995*1j,
-0.062303354995 - 0.062303354995*1j,
-0.062303354995 - 0.062303354995*1j],
[0.570587344099 - 0.000000000000*1j,
0.570587344099 - 0.000000000000*1j,
0.570587344099 + 0.000000000000*1j]],
[[0.286272749085 + 0.286272749085*1j,
0.286272749085 + 0.286272749085*1j,
-0.572545498170 - 0.572545498170*1j],
[0.052559422840 - 0.000000000000*1j,
0.052559422840 + 0.000000000000*1j,
-0.105118845679 + 0.000000000000*1j]],
[[-0.459591797004 + 0.529611084985*1j,
0.459591797004 - 0.529611084985*1j,
0.000000000000 - 0.000000000000*1j],
[0.006427739587 + 0.090808385909*1j,
-0.006427739587 - 0.090808385909*1j,
0.000000000000 + 0.000000000000*1j]],
[[-0.403466180272 - 0.403466180272*1j,
-0.403466180272 - 0.403466180272*1j,
-0.403466180272 - 0.403466180272*1j],
[-0.088110249616 - 0.000000000000*1j,
-0.088110249616 - 0.000000000000*1j,
-0.088110249616 + 0.000000000000*1j]]],
[[[0.000000000000 + 0.000000000000*1j,
0.031866260273 - 0.031866260273*1j,
-0.031866260273 + 0.031866260273*1j],
[-0.000000000000 - 0.000000000000*1j,
-0.705669244698 + 0.000000000000*1j,
0.705669244698 + 0.000000000000*1j]],
[[-0.001780156891 + 0.001780156891*1j,
-0.012680513033 + 0.012680513033*1j,
-0.012680513033 + 0.012680513033*1j],
[-0.582237273385 + 0.000000000000*1j,
0.574608665929 - 0.000000000000*1j,
0.574608665929 + 0.000000000000*1j]],
[[-0.021184502078 + 0.021184502078*1j,
-0.011544287510 + 0.011544287510*1j,
-0.011544287510 + 0.011544287510*1j],
[0.812686635458 - 0.000000000000*1j,
0.411162853378 + 0.000000000000*1j,
0.411162853378 + 0.000000000000*1j]],
[[0.000000000000 + 0.000000000000*1j,
-0.498983508201 + 0.498983508201*1j,
0.498983508201 - 0.498983508201*1j],
[0.000000000000 + 0.000000000000*1j,
-0.045065697460 - 0.000000000000*1j,
0.045065697460 + 0.000000000000*1j]],
[[0.400389305548 - 0.400389305548*1j,
-0.412005183792 + 0.412005183792*1j,
-0.412005183792 + 0.412005183792*1j],
[0.009657696420 - 0.000000000000*1j,
-0.012050954709 + 0.000000000000*1j,
-0.012050954709 + 0.000000000000*1j]],
[[-0.582440084400 + 0.582440084400*1j,
-0.282767859813 + 0.282767859813*1j,
-0.282767859813 + 0.282767859813*1j],
[-0.021140457173 + 0.000000000000*1j,
-0.024995270201 - 0.000000000000*1j,
-0.024995270201 + 0.000000000000*1j]]]])
self.expctd_data = expctd_data
self.seedname = 'NaH'
self.path = 'data'
data = PhononData.from_castep(self.seedname, path=self.path)
self.data = data
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,
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