Source code for ase.utils

import os
import sys
import time
from math import sin, cos, radians, atan2, degrees
from contextlib import contextmanager

import numpy as np

from ase.data import chemical_symbols


# Python 2+3 compatibility stuff:
if sys.version_info[0] == 3:
    import builtins
    exec_ = getattr(builtins, 'exec')
    basestring = str
else:
    def exec_(code, dct):
        exec('exec code in dct')
    basestring = basestring
    

@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:
    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()


# Only Windows has O_BINARY:
CEW_FLAGS = os.O_CREAT | os.O_EXCL | os.O_WRONLY | getattr(os, 'O_BINARY', 0)


[docs]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: ok = 0 else: ok = 1 fd = os.fdopen(fd, 'wb') else: ok = 0 fd = devnull # Syncronize: if world.sum(ok) == 0: return None else: 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 prnt(*args, **kwargs): """Python 3 style print function.""" fd = kwargs.pop('file', sys.stdout) fd.write( kwargs.pop('sep', ' ').join(str(arg) for arg in args) + kwargs.pop('end', '\n')) if kwargs.pop('flush', False): fd.flush() if kwargs: raise TypeError('%r is an invalid keyword argument for this function' % kwargs.keys()[0])
[docs]def gcd(a, b): """Greatest common divisor of a and b.""" while a != 0: a, b = b % a, a return b
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) ON_POSIX = 'posix' in sys.builtin_module_names try: from subprocess import Popen except ImportError: from os import popen3 else: def popen3(cmd): from subprocess import PIPE p = Popen(cmd, shell=True, close_fds=ON_POSIX, stdin=PIPE, stdout=PIPE, stderr=PIPE) return p.stdin, p.stdout, p.stderr