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import errno
import os
import sys
import time
from math import sin, cos, radians, atan2, degrees
from contextlib import contextmanager
try:
from math import gcd
except ImportError:
from fractions import gcd
import numpy as np
from ase.data import chemical_symbols
__all__ = ['exec_', 'basestring', 'import_module', 'seterr', 'plural',
'devnull', 'gcd', 'convert_string_to_fd', 'Lock',
'opencew', 'OpenLock', 'hill', 'rotate', 'irotate', 'givens',
'hsv2rgb', 'hsv']
# Python 2+3 compatibility stuff:
if sys.version_info[0] == 3:
import builtins
exec_ = getattr(builtins, 'exec')
basestring = str
from io import StringIO
else:
def exec_(code, dct):
exec('exec code in dct')
basestring = basestring
from StringIO import StringIO
StringIO # appease pyflakes
if sys.version_info >= (2, 7):
from importlib import import_module
else:
# Python 2.6:
def import_module(name):
module = __import__(name)
for part in name.split('.')[1:]:
module = getattr(module, part)
return module
@contextmanager
def seterr(**kwargs):
"""Set how floating-point errors are handled.
See np.seterr() for more details.
"""
old = np.seterr(**kwargs)
yield
np.seterr(**old)
def plural(n, word):
if n == 1:
return '1 ' + word
return '%d %ss' % (n, word)
class DevNull:
encoding = 'UTF-8'
def write(self, string):
pass
def flush(self):
pass
def seek(self, offset, whence=0):
return 0
def tell(self):
return 0
def close(self):
pass
def isatty(self):
return False
devnull = DevNull()
def convert_string_to_fd(name, world=None):
"""Create a file-descriptor for text output.
Will open a file for writing with given name. Use None for no output and
'-' for sys.stdout.
"""
if world is None:
from ase.parallel import world
if name is None or world.rank != 0:
return devnull
if name == '-':
return sys.stdout
if isinstance(name, basestring):
return open(name, 'w')
return name # we assume name is already a file-descriptor
# Only Windows has O_BINARY:
CEW_FLAGS = os.O_CREAT | os.O_EXCL | os.O_WRONLY | getattr(os, 'O_BINARY', 0)
def opencew(filename, world=None):
"""Create and open filename exclusively for writing.
If master cpu gets exclusive write access to filename, a file
descriptor is returned (a dummy file descriptor is returned on the
slaves). If the master cpu does not get write access, None is
returned on all processors."""
if world is None:
from ase.parallel import world
if world.rank == 0:
try:
fd = os.open(filename, CEW_FLAGS)
except OSError as ex:
error = ex.errno
else:
error = 0
fd = os.fdopen(fd, 'wb')
else:
error = 0
fd = devnull
# Syncronize:
error = world.sum(error)
if error == errno.EEXIST:
return None
if error:
raise OSError(error, 'Error', filename)
return fd
class Lock:
def __init__(self, name='lock', world=None):
self.name = name
if world is None:
from ase.parallel import world
self.world = world
def acquire(self):
while True:
fd = opencew(self.name, self.world)
if fd is not None:
break
time.sleep(1.0)
def release(self):
self.world.barrier()
if self.world.rank == 0:
os.remove(self.name)
def __enter__(self):
self.acquire()
def __exit__(self, type, value, tb):
self.release()
class OpenLock:
def acquire(self):
pass
def release(self):
pass
def __enter__(self):
pass
def __exit__(self, type, value, tb):
pass
def hill(numbers):
"""Convert list of atomic numbers to a chemical formula as a string.
Elements are alphabetically ordered with C and H first."""
if isinstance(numbers, dict):
count = dict(numbers)
else:
count = {}
for Z in numbers:
symb = chemical_symbols[Z]
count[symb] = count.get(symb, 0) + 1
result = [(s, count.pop(s)) for s in 'CH' if s in count]
result += [(s, count[s]) for s in sorted(count)]
return ''.join('{0}{1}'.format(symbol, n) if n > 1 else symbol
for symbol, n in result)
def rotate(rotations, rotation=np.identity(3)):
"""Convert string of format '50x,-10y,120z' to a rotation matrix.
Note that the order of rotation matters, i.e. '50x,40z' is different
from '40z,50x'.
"""
if rotations == '':
return rotation.copy()
for i, a in [('xyz'.index(s[-1]), radians(float(s[:-1])))
for s in rotations.split(',')]:
s = sin(a)
c = cos(a)
if i == 0:
rotation = np.dot(rotation, [(1, 0, 0),
(0, c, s),
(0, -s, c)])
elif i == 1:
rotation = np.dot(rotation, [(c, 0, -s),
(0, 1, 0),
(s, 0, c)])
else:
rotation = np.dot(rotation, [(c, s, 0),
(-s, c, 0),
(0, 0, 1)])
return rotation
def givens(a, b):
"""Solve the equation system::
[ c s] [a] [r]
[ ] . [ ] = [ ]
[-s c] [b] [0]
"""
sgn = np.sign
if b == 0:
c = sgn(a)
s = 0
r = abs(a)
elif abs(b) >= abs(a):
cot = a / b
u = sgn(b) * (1 + cot**2)**0.5
s = 1. / u
c = s * cot
r = b * u
else:
tan = b / a
u = sgn(a) * (1 + tan**2)**0.5
c = 1. / u
s = c * tan
r = a * u
return c, s, r
def irotate(rotation, initial=np.identity(3)):
"""Determine x, y, z rotation angles from rotation matrix."""
a = np.dot(initial, rotation)
cx, sx, rx = givens(a[2, 2], a[1, 2])
cy, sy, ry = givens(rx, a[0, 2])
cz, sz, rz = givens(cx * a[1, 1] - sx * a[2, 1],
cy * a[0, 1] - sy * (sx * a[1, 1] + cx * a[2, 1]))
x = degrees(atan2(sx, cx))
y = degrees(atan2(-sy, cy))
z = degrees(atan2(sz, cz))
return x, y, z
def hsv2rgb(h, s, v):
"""http://en.wikipedia.org/wiki/HSL_and_HSV
h (hue) in [0, 360[
s (saturation) in [0, 1]
v (value) in [0, 1]
return rgb in range [0, 1]
"""
if v == 0:
return 0, 0, 0
if s == 0:
return v, v, v
i, f = divmod(h / 60., 1)
p = v * (1 - s)
q = v * (1 - s * f)
t = v * (1 - s * (1 - f))
if i == 0:
return v, t, p
elif i == 1:
return q, v, p
elif i == 2:
return p, v, t
elif i == 3:
return p, q, v
elif i == 4:
return t, p, v
elif i == 5:
return v, p, q
else:
raise RuntimeError('h must be in [0, 360]')
def hsv(array, s=.9, v=.9):
array = (array + array.min()) * 359. / (array.max() - array.min())
result = np.empty((len(array.flat), 3))
for rgb, h in zip(result, array.flat):
rgb[:] = hsv2rgb(h, s, v)
return np.reshape(result, array.shape + (3,))
# This code does the same, but requires pylab
# def cmap(array, name='hsv'):
# import pylab
# a = (array + array.min()) / array.ptp()
# rgba = getattr(pylab.cm, name)(a)
# return rgba[:-1] # return rgb only (not alpha)
def longsum(x):
"""128-bit floating point sum."""
return float(np.asarray(x, dtype=np.longdouble).sum())
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