1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338
|
import numpy as np
class DOS:
def __init__(self, energy, weights, info=None, sampling={'type': 'raw'}):
"""
Docstring here
"""
self.energy = np.asarray(energy)
self.weights = np.asarray(weights)
self.sampling = sampling
# Energy format: [e1, e2, ...]
if self.energy.ndim != 1:
msg = ('Incorrect Energy dimensionality. '
'Expected 1 got {}'.format(
self.energy.ndim))
raise ValueError(msg)
# Weights format: [[w1, w2, ...], [w1, w2, ..], ...]
if self.weights.ndim != 2:
msg = ('Incorrect weight dimensionality. '
'Expected 2, got {}'.format(
self.weights.ndim))
raise ValueError(msg)
# Check weight shape matches energy
if self.weights.shape[1] != self.energy.shape[0]:
msg = ('Weight dimensionality does not match energy.'
' Expected {}, got {}'.format(self.energy.shape[0],
self.weights.shape[1]))
raise ValueError(msg)
# One entry for info for each weight
if info is None:
info = [{} for _ in self.weights]
else:
if len(info) != len(weights):
msg = ('Incorrect number of entries in '
'info. Expected {}, got {}'.format(
len(self.weights), len(info)))
raise ValueError(msg)
self.info = np.asarray(info) # Make info np array for slicing purposes
def delta(self, x, x0, width, smearing='Gauss'):
"""Return a delta-function centered at 'x0'."""
if smearing.lower() == 'gauss':
x1 = -((x - x0) / width)**2
return np.exp(x1) / (np.sqrt(np.pi) * width)
else:
msg = 'Requested smearing type not recognized. Got {}'.format(
smearing)
raise ValueError(msg)
def smear(self, energy_grid, width=0.1, smearing='Gauss'):
"""Add Gaussian smearing, to all weights onto an energy grid.
Disabled for width=0.0"""
if width == 0.0:
msg = 'Cannot add 0 width smearing'
raise ValueError(msg)
en0 = self.energy[:, np.newaxis] # Add axis to use NumPy broadcasting
weights_grid = np.dot(self.weights,
self.delta(energy_grid, en0, width,
smearing=smearing))
return weights_grid
def sample(self, grid, width=0.1, smearing='Gauss', gridtype='general'):
"""Sample this DOS on a grid, returning result as a new DOS."""
npts = len(grid)
sampling = {'width': width,
'smearing': smearing,
'npts': npts,
'type': gridtype}
weights_grid = self.smear(grid, width=width, smearing=smearing)
dos_new = DOS(grid, weights_grid,
info=self.info, sampling=sampling)
return dos_new
def sample_grid(self, spacing=None, npts=None, width=0.1,
window=None, smearing='Gauss'):
"""Sample this DOS on a uniform grid, returning result as a new DOS."""
if window is None:
emin, emax = None, None
else:
emin, emax = window
if emin is None:
emin = self.energy.min()
if emax is None:
emax = self.energy.max()
emin -= 5 * width
emax += 5 * width
grid_uniform = DOS._make_uniform_grid(emin, emax, spacing=spacing,
npts=npts, width=width)
return self.sample(grid_uniform, width=width,
smearing=smearing, gridtype='uniform')
@staticmethod
def sample_many(doslist, grid, width=0.1, smearing='Gauss',
gridtype='general'):
"""Take list of DOS objects, and combine into 1, with same grid."""
# Count the total number of weights
n_weights = sum(len(dos.weights) for dos in doslist)
npts = len(grid)
weight_grid = np.zeros((n_weights, npts))
info_new = []
# Do sampling
ii = 0
for dos in doslist:
dos_sample = dos.sample(grid, width=width,
smearing=smearing)
info_new.extend(dos_sample.info)
for w_i in dos_sample.weights:
weight_grid[ii] = w_i
ii += 1
sampling = {'smearing': smearing,
'width': width,
'npts': npts,
'type': gridtype}
return DOS(energy=grid, weights=weight_grid, info=info_new,
sampling=sampling)
@staticmethod
def sample_many_grid(doslist, window=None, spacing=None,
npts=None, width=0.1, smearing='Gauss'):
"""Combine list of DOS objects onto uniform grid.
Takes the lowest and highest energies as grid range, if
no window is specified."""
dosen = [dos.energy for dos in doslist]
# Parse window
if window is None:
emin, emax = None, None
else:
emin, emax = window
if emin is None:
emin = np.min(dosen)
if emax is None:
emax = np.max(dosen)
# Add a little extra to avoid stopping midpeak
emin -= 5 * width
emax += 5 * width
grid_uniform = DOS._make_uniform_grid(emin, emax, spacing=spacing,
npts=npts, width=width)
return DOS.sample_many(doslist, grid_uniform, width=width,
smearing=smearing, gridtype='uniform')
@staticmethod
def join(doslist, atol=1e-08):
"""Join a list of DOS objects into one, without applying sampling.
Requires all energies to be identical"""
# Test if energies are the same
eneq = all(np.allclose(doslist[0].energy, dos.energy, atol=atol)
for dos in doslist)
if not eneq:
msg = 'Energies must the the same in all DOS objects.'
raise ValueError(msg)
energy = doslist[0].energy # Just use the first energy
weights = []
info = []
for dos in doslist:
for info_i, w_i in zip(dos.info, dos.weights):
weights.append(w_i)
info.append(info_i)
return DOS(energy, weights, info=info)
@staticmethod
def _make_uniform_grid(emin, emax, spacing=None, npts=None, width=0.1):
if spacing and npts:
msg = ('spacing and npts cannot both be defined'
' at the same time.')
raise ValueError(msg)
if not spacing and not npts:
# Default behavior
spacing = 0.2 * width
# Now either spacing or npts is defined
if npts:
grid_uniform = np.linspace(emin, emax, npts)
else:
grid_uniform = np.arange(emin, emax, spacing)
return grid_uniform
def plot(self,
# We need to grab init keywords
ax=None,
emin=None, emax=None,
ymin=None, ymax=None, ylabel=None,
*plotargs, **plotkwargs):
pdp = DOSPlot(self, ax=None,
emin=None, emax=None,
ymin=None, ymax=None, ylabel=None)
return pdp.plot(*plotargs, **plotkwargs)
def sum(self):
"""Return the sum of all weights in this DOS as a new DOS."""
weights_sum = self.weights.sum(0)[np.newaxis]
# Find shared (key, value) pairs
# dict(set.intersection(*(set(d.items()) for d in info)))
all_kv = []
for d in self.info:
kv_pairs = set()
for key, value in d.items():
try:
kv_pairs.add((key, value))
except TypeError:
# Unhashable type, skip it
pass
all_kv.append(kv_pairs)
if all_kv:
info_new = [dict(set.intersection(*all_kv))]
else:
# We didn't find any shared (key, value) pairs
# This prevents set.intersection from blowing up
info_new = None
return DOS(energy=self.energy, weights=weights_sum,
info=info_new, sampling=self.sampling)
def pick(self, **kwargs):
"""Pick key/value pairs using logical AND
i.e., all conditions from kwargs must be met"""
idx = [i for i, d in enumerate(self.info)
if all(d.get(key) == value
for key, value in kwargs.items())]
return self[idx]
def split(self, key):
"""Find all unique instances of key in info"""
unique = np.unique([info.get(key) for info in self.info
if info.get(key, None) is not None])
dos_lst = []
for value in unique:
# Use **{key: value} instead of key=value,
# as key=value will literally look up "key" in info.
dos_lst.append(self.pick(**{key: value}))
return dos_lst
def __getitem__(self, i):
if isinstance(i, int):
n_weights = len(self.weights)
if i < -n_weights or i >= n_weights:
raise IndexError('Index out of range.')
indices = np.arange(len(self.weights))[i]
if len(indices.shape) == 0:
indices = indices[np.newaxis]
return DOS(energy=self.energy,
weights=self.weights[indices],
info=self.info[indices],
sampling=self.sampling)
class DOSPlot:
def __init__(self, dos, ax=None,
emin=None, emax=None,
ymin=None, ymax=None, ylabel=None):
self.dos = dos
self.ax = ax
if self.ax is None:
self.ax = self.prepare_plot(ax, emin, emax,
ymin=ymin, ymax=ymax,
ylabel=ylabel)
def plot(self, filename=None, show=None, colors=None,
labels=None, show_legend=True, loc='best', **plotkwargs):
ax = self.ax
for ii, w_i in enumerate(self.dos.weights):
# We can add smater labeling later
kwargs = {}
if colors is not None:
kwargs['color'] = colors[ii]
# We could possibly have some better label logic here
if labels is not None:
kwargs['label'] = labels[ii]
else:
kwargs['label'] = self.dos.info[ii]
kwargs.update(plotkwargs)
ax.plot(self.dos.energy, w_i,
**kwargs)
self.finish_plot(filename, show, show_legend, loc)
return ax
def prepare_plot(self, ax=None, emin=None, emax=None,
ymin=None, ymax=None,
ylabel=None, xlabel=None):
import matplotlib.pyplot as plt
if ax is None:
ax = plt.figure().add_subplot(111)
ylabel = ylabel if ylabel is not None else 'DOS'
xlabel = xlabel if xlabel is not None else 'Energy [eV]'
ax.axis(xmin=emin, xmax=emax, ymin=ymin, ymax=ymax)
ax.set_ylabel(ylabel)
self.ax = ax
return ax
def finish_plot(self, filename, show, show_legend, loc):
import matplotlib.pyplot as plt
if show_legend:
leg = plt.legend(loc=loc)
leg.get_frame().set_alpha(1)
if filename:
plt.savefig(filename)
if show is None:
show = not filename
if show:
plt.show()
|