/usr/share/pyshared/ase/gui/images.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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import numpy as np
from ase.data import covalent_radii
from ase.atoms import Atoms
from ase.calculators.singlepoint import SinglePointCalculator
from ase.io import read, write, string2index
from ase.constraints import FixAtoms
from ase.gui.defaults import read_defaults
from ase.quaternions import Quaternion
class Images:
def __init__(self, images=None):
if images is not None:
self.initialize(images)
def initialize(self, images, filenames=None, init_magmom=False):
self.natoms = len(images[0])
self.nimages = len(images)
if hasattr(images[0], 'get_shapes'):
self.shapes = images[0].get_shapes()
self.Q = []
else:
self.shapes = None
if filenames is None:
filenames = [None] * self.nimages
self.filenames = filenames
self.P = np.empty((self.nimages, self.natoms, 3))
self.V = np.empty((self.nimages, self.natoms, 3))
self.E = np.empty(self.nimages)
self.K = np.empty(self.nimages)
self.F = np.empty((self.nimages, self.natoms, 3))
self.M = np.empty((self.nimages, self.natoms))
self.T = np.empty((self.nimages, self.natoms), int)
self.A = np.empty((self.nimages, 3, 3))
self.Z = images[0].get_atomic_numbers()
self.pbc = images[0].get_pbc()
self.covalent_radii = covalent_radii
config = read_defaults()
if config['covalent_radii'] is not None:
for data in config['covalent_radii']:
self.covalent_radii[data[0]] = data[1]
warning = False
for i, atoms in enumerate(images):
natomsi = len(atoms)
if (natomsi != self.natoms or
(atoms.get_atomic_numbers() != self.Z).any()):
raise RuntimeError('Can not handle different images with ' +
'different numbers of atoms or different ' +
'kinds of atoms!')
self.P[i] = atoms.get_positions()
self.V[i] = atoms.get_velocities()
if hasattr(self, 'Q'):
for q in atoms.get_quaternions():
self.Q.append(Quaternion(q))
self.A[i] = atoms.get_cell()
if (atoms.get_pbc() != self.pbc).any():
warning = True
try:
self.E[i] = atoms.get_potential_energy()
except RuntimeError:
self.E[i] = np.nan
self.K[i] = atoms.get_kinetic_energy()
try:
self.F[i] = atoms.get_forces(apply_constraint=False)
except RuntimeError:
self.F[i] = np.nan
try:
if init_magmom:
self.M[i] = atoms.get_initial_magnetic_moments()
else:
self.M[i] = atoms.get_magnetic_moments()
except (RuntimeError, AttributeError):
self.M[i] = atoms.get_initial_magnetic_moments()
# added support for tags
try:
self.T[i] = atoms.get_tags()
except RuntimeError:
self.T[i] = 0
if warning:
print('WARNING: Not all images have the same bondary conditions!')
self.selected = np.zeros(self.natoms, bool)
self.selected_ordered = []
self.atoms_to_rotate_0 = np.zeros(self.natoms, bool)
self.visible = np.ones(self.natoms, bool)
self.nselected = 0
self.set_dynamic(constraints = images[0].constraints)
self.repeat = np.ones(3, int)
self.set_radii(0.89)
def prepare_new_atoms(self):
"Marks that the next call to append_atoms should clear the images."
self.next_append_clears = True
def append_atoms(self, atoms, filename=None):
"Append an atoms object to the images already stored."
assert len(atoms) == self.natoms
if self.next_append_clears:
i = 0
else:
i = self.nimages
for name in ('P', 'V', 'E', 'K', 'F', 'M', 'A', 'T'):
a = getattr(self, name)
newa = np.empty( (i+1,) + a.shape[1:], a.dtype )
if not self.next_append_clears:
newa[:-1] = a
setattr(self, name, newa)
self.next_append_clears = False
self.P[i] = atoms.get_positions()
self.V[i] = atoms.get_velocities()
self.A[i] = atoms.get_cell()
try:
self.E[i] = atoms.get_potential_energy()
except RuntimeError:
self.E[i] = np.nan
self.K[i] = atoms.get_kinetic_energy()
try:
self.F[i] = atoms.get_forces(apply_constraint=False)
except RuntimeError:
self.F[i] = np.nan
try:
self.M[i] = atoms.get_magnetic_moments()
except (RuntimeError, AttributeError):
self.M[i] = np.nan
try:
self.T[i] = atoms.get_tags()
except AttributeError:
if i == 0:
self.T[i] = 0
else:
self.T[i] = self.T[i-1]
self.nimages = i + 1
self.filenames.append(filename)
self.set_dynamic()
return self.nimages
def set_radii(self, scale):
if self.shapes == None:
self.r = self.covalent_radii[self.Z] * scale
else:
self.r = np.sqrt(np.sum(self.shapes**2, axis=1)) * scale
def read(self, filenames, index=-1, filetype=None):
images = []
names = []
for filename in filenames:
i = read(filename, index,filetype)
if not isinstance(i, list):
i = [i]
images.extend(i)
names.extend([filename] * len(i))
self.initialize(images, names)
def import_atoms(self, filename, cur_frame):
if filename:
filename = filename[0]
old_a = self.get_atoms(cur_frame)
imp_a = read(filename, -1)
new_a = old_a + imp_a
self.initialize([new_a], [filename])
def repeat_images(self, repeat):
n = self.repeat.prod()
repeat = np.array(repeat)
self.repeat = repeat
N = repeat.prod()
natoms = self.natoms // n
P = np.empty((self.nimages, natoms * N, 3))
V = np.empty((self.nimages, natoms * N, 3))
M = np.empty((self.nimages, natoms * N))
T = np.empty((self.nimages, natoms * N), int)
F = np.empty((self.nimages, natoms * N, 3))
Z = np.empty(natoms * N, int)
r = np.empty(natoms * N)
dynamic = np.empty(natoms * N, bool)
a0 = 0
for i0 in range(repeat[0]):
for i1 in range(repeat[1]):
for i2 in range(repeat[2]):
a1 = a0 + natoms
for i in range(self.nimages):
P[i, a0:a1] = (self.P[i, :natoms] +
np.dot((i0, i1, i2), self.A[i]))
V[:, a0:a1] = self.V[:, :natoms]
F[:, a0:a1] = self.F[:, :natoms]
M[:, a0:a1] = self.M[:, :natoms]
T[:, a0:a1] = self.T[:, :natoms]
Z[a0:a1] = self.Z[:natoms]
r[a0:a1] = self.r[:natoms]
dynamic[a0:a1] = self.dynamic[:natoms]
a0 = a1
self.P = P
self.V = V
self.F = F
self.Z = Z
self.T = T
self.M = M
self.r = r
self.dynamic = dynamic
self.natoms = natoms * N
self.selected = np.zeros(natoms * N, bool)
self.atoms_to_rotate_0 = np.zeros(self.natoms, bool)
self.visible = np.ones(natoms * N, bool)
self.nselected = 0
def center(self):
""" center each image in the existing unit cell, keeping the cell constant. """
c = self.A.sum(axis=1) / 2.0 - self.P.mean(axis=1)
self.P += c[:, np.newaxis, :]
def graph(self, expr):
""" routine to create the data in ag graphs, defined by the string expr. """
import ase.units as units
code = compile(expr + ',', 'atoms.py', 'eval')
n = self.nimages
def d(n1, n2):
return sqrt(((R[n1] - R[n2])**2).sum())
def a(n1, n2, n3):
v1 = R[n1]-R[n2]
v2 = R[n3]-R[n2]
arg = np.vdot(v1,v2)/(sqrt((v1**2).sum()*(v2**2).sum()))
if arg > 1.0: arg = 1.0
if arg < -1.0: arg = -1.0
return 180.0*np.arccos(arg)/np.pi
def dih(n1, n2, n3, n4):
# vector 0->1, 1->2, 2->3 and their normalized cross products:
a = R[n2]-R[n1]
b = R[n3]-R[n2]
c = R[n4]-R[n3]
bxa = np.cross(b,a)
bxa /= np.sqrt(np.vdot(bxa,bxa))
cxb = np.cross(c,b)
cxb /= np.sqrt(np.vdot(cxb,cxb))
angle = np.vdot(bxa,cxb)
# check for numerical trouble due to finite precision:
if angle < -1: angle = -1
if angle > 1: angle = 1
angle = np.arccos(angle)
if (np.vdot(bxa,c)) > 0: angle = 2*np.pi-angle
return angle*180.0/np.pi
# get number of mobile atoms for temperature calculation
ndynamic = 0
for dyn in self.dynamic:
if dyn: ndynamic += 1
S = self.selected
D = self.dynamic[:, np.newaxis]
E = self.E
s = 0.0
data = []
for i in range(n):
R = self.P[i]
V = self.V[i]
F = self.F[i]
A = self.A[i]
M = self.M[i]
f = ((F * D)**2).sum(1)**.5
fmax = max(f)
fave = f.mean()
epot = E[i]
ekin = self.K[i]
e = epot + ekin
T = 2.0 * ekin / (3.0 * ndynamic * units.kB)
data = eval(code)
if i == 0:
m = len(data)
xy = np.empty((m, n))
xy[:, i] = data
if i + 1 < n:
s += sqrt(((self.P[i + 1] - R)**2).sum())
return xy
def set_dynamic(self, constraints = None):
self.dynamic = np.ones(self.natoms, bool)
if constraints is not None:
for con in constraints:
if isinstance(con,FixAtoms):
self.dynamic[con.index] = False
def write(self, filename, rotations='', show_unit_cell=False, bbox=None, **kwargs):
indices = range(self.nimages)
p = filename.rfind('@')
if p != -1:
try:
slice = string2index(filename[p + 1:])
except ValueError:
pass
else:
indices = indices[slice]
filename = filename[:p]
if isinstance(indices, int):
indices = [indices]
images = [self.get_atoms(i) for i in indices]
if len(filename) > 4 and filename[-4:] in ['.eps', '.png', '.pov']:
write(filename, images,
rotation=rotations, show_unit_cell=show_unit_cell,
bbox=bbox, **kwargs)
else:
write(filename, images, **kwargs)
def get_atoms(self, frame):
atoms = Atoms(positions=self.P[frame],
numbers=self.Z,
magmoms=self.M[0],
tags=self.T[frame],
cell=self.A[frame],
pbc=self.pbc)
if not np.isnan(self.V).any():
atoms.set_velocities(self.V[frame])
# check for constrained atoms and add them accordingly:
if not self.dynamic.all():
atoms.set_constraint(FixAtoms(mask=1-self.dynamic))
atoms.set_calculator(SinglePointCalculator(self.E[frame],
self.F[frame],
None, None, atoms))
return atoms
def delete(self, i):
self.nimages -= 1
P = np.empty((self.nimages, self.natoms, 3))
V = np.empty((self.nimages, self.natoms, 3))
F = np.empty((self.nimages, self.natoms, 3))
A = np.empty((self.nimages, 3, 3))
E = np.empty(self.nimages)
P[:i] = self.P[:i]
P[i:] = self.P[i + 1:]
self.P = P
V[:i] = self.V[:i]
V[i:] = self.V[i + 1:]
self.V = V
F[:i] = self.F[:i]
F[i:] = self.F[i + 1:]
self.F = F
A[:i] = self.A[:i]
A[i:] = self.A[i + 1:]
self.A = A
E[:i] = self.E[:i]
E[i:] = self.E[i + 1:]
self.E = E
del self.filenames[i]
def aneb(self):
n = self.nimages
assert n % 5 == 0
levels = n // 5
n = self.nimages = 2 * levels + 3
P = np.empty((self.nimages, self.natoms, 3))
V = np.empty((self.nimages, self.natoms, 3))
F = np.empty((self.nimages, self.natoms, 3))
E = np.empty(self.nimages)
for L in range(levels):
P[L] = self.P[L * 5]
P[n - L - 1] = self.P[L * 5 + 4]
V[L] = self.V[L * 5]
V[n - L - 1] = self.V[L * 5 + 4]
F[L] = self.F[L * 5]
F[n - L - 1] = self.F[L * 5 + 4]
E[L] = self.E[L * 5]
E[n - L - 1] = self.E[L * 5 + 4]
for i in range(3):
P[levels + i] = self.P[levels * 5 - 4 + i]
V[levels + i] = self.V[levels * 5 - 4 + i]
F[levels + i] = self.F[levels * 5 - 4 + i]
E[levels + i] = self.E[levels * 5 - 4 + i]
self.P = P
self.V = V
self.F = F
self.E = E
def interpolate(self, m):
assert self.nimages == 2
self.nimages = 2 + m
P = np.empty((self.nimages, self.natoms, 3))
V = np.empty((self.nimages, self.natoms, 3))
F = np.empty((self.nimages, self.natoms, 3))
A = np.empty((self.nimages, 3, 3))
E = np.empty(self.nimages)
P[0] = self.P[0]
V[0] = self.V[0]
F[0] = self.F[0]
A[0] = self.A[0]
E[0] = self.E[0]
for i in range(1, m + 1):
x = i / (m + 1.0)
y = 1 - x
P[i] = y * self.P[0] + x * self.P[1]
V[i] = y * self.V[0] + x * self.V[1]
F[i] = y * self.F[0] + x * self.F[1]
A[i] = y * self.A[0] + x * self.A[1]
E[i] = y * self.E[0] + x * self.E[1]
P[-1] = self.P[1]
V[-1] = self.V[1]
F[-1] = self.F[1]
A[-1] = self.A[1]
E[-1] = self.E[1]
self.P = P
self.V = V
self.F = F
self.A = A
self.E = E
self.filenames[1:1] = [None] * m
if __name__ == '__main__':
import os
os.system('python gui.py')
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