def test(xyz):
a = rotate(xyz)
ixyz = '%sx,%sy,%sz' % irotate(a)
a2 = rotate(ixyz)
print(xyz)
print(ixyz)
assert abs(a - a2).max() < 1e-10
def test(xyz):
a = rotate(xyz)
ixyz = '%sx,%sy,%sz' % irotate(a)
a2 = rotate(ixyz)
print(xyz)
print(ixyz)
assert abs(a - a2).max() < 1e-10
def test(xyz):
a = rotate(xyz)
ixyz = '%sx,%sy,%sz' % irotate(a)
a2 = rotate(ixyz)
#print xyz
#print ixyz
#print np.around(a-a2, 5)
assert abs(a-a2).max() < 1e-10
def test(xyz):
a = rotate(xyz)
ixyz = '%sx,%sy,%sz' % irotate(a)
a2 = rotate(ixyz)
print xyz
print ixyz
#print np.around(a-a2, 5)
assert abs(a - a2).max() < 1e-10
def __init__(self, rotations):
self.colormode = 'jmol' # The default colors
self.nselected = 0
self.labels = None
self.axes = rotate(rotations)
self.configured = False
self.frame = None
# XXX
self.colormode = 'jmol'
self.colors = {}
for i, rgb in enumerate(jmol_colors):
self.colors[i] = ('#{0:02X}{1:02X}{2:02X}'.format(*(int(x * 255)
for x in rgb)))
# scaling factors for vectors
self.force_vector_scale = self.config['force_vector_scale']
self.velocity_vector_scale = self.config['velocity_vector_scale']
# buttons
self.b1 = 1 # left
self.b3 = 3 # right
if self.config['swap_mouse']:
self.b1 = 3
self.b3 = 1
def __init__(self, rotations):
self.colormode = 'jmol' # The default colors
self.nselected = 0
self.labels = None
self.axes = rotate(rotations)
self.configured = False
self.frame = None
def __init__(self, vbox, rotations):
self.colormode = 'jmol' # The default colors
self.nselected = 0
self.light_green_markings = 0
self.axes = rotate(rotations)
# this is a hack, in order to be able to toggle menu actions off/on
# without getting into an infinte loop
self.menu_change = 0
self.atoms_to_rotate = None
self.drawing_area = gtk.DrawingArea()
self.drawing_area.set_size_request(450, 450)
self.drawing_area.connect('button_press_event', self.press)
self.drawing_area.connect('button_release_event', self.release)
self.drawing_area.connect('motion-notify-event', self.move)
# Signals used to handle backing pixmap:
self.drawing_area.connect('expose_event', self.expose_event)
self.drawing_area.connect('configure_event', self.configure_event)
self.drawing_area.set_events(gtk.gdk.BUTTON_PRESS_MASK |
gtk.gdk.BUTTON_RELEASE_MASK |
gtk.gdk.BUTTON_MOTION_MASK |
gtk.gdk.POINTER_MOTION_HINT_MASK)
vbox.pack_start(self.drawing_area)
self.drawing_area.show()
self.configured = False
self.frame = None
def __init__(self, vbox, rotations):
self.colormode = 'jmol' # The default colors
self.nselected = 0
self.light_green_markings = 0
self.axes = rotate(rotations)
# this is a hack, in order to be able to toggle menu actions off/on
# without getting into an infinte loop
self.menu_change = 0
self.atoms_to_rotate = None
self.drawing_area = gtk.DrawingArea()
self.drawing_area.set_size_request(450, 450)
self.drawing_area.connect('button_press_event', self.press)
self.drawing_area.connect('button_release_event', self.release)
self.drawing_area.connect('motion-notify-event', self.move)
# Signals used to handle backing pixmap:
self.drawing_area.connect('expose_event', self.expose_event)
self.drawing_area.connect('configure_event', self.configure_event)
self.drawing_area.set_events(gtk.gdk.BUTTON_PRESS_MASK
| gtk.gdk.BUTTON_RELEASE_MASK
| gtk.gdk.BUTTON_MOTION_MASK
| gtk.gdk.POINTER_MOTION_HINT_MASK)
vbox.pack_start(self.drawing_area)
self.drawing_area.show()
self.configured = False
self.config = None
self.frame = None
def __init__(self, rotations):
self.colormode = 'jmol' # The default colors
self.nselected = 0
self.labels = None
self.axes = rotate(rotations)
self.configured = False
self.frame = None
# XXX
self.colormode = 'jmol'
self.colors = {}
for i, rgb in enumerate(jmol_colors):
self.colors[i] = ('#{0:02X}{1:02X}{2:02X}'.format(*(int(x * 255)
for x in rgb)))
def __init__(self, rotations):
self.colormode = 'jmol' # The default colors
self.nselected = 0
self.labels = None
self.axes = rotate(rotations)
self.configured = False
self.frame = None
# XXX
self.colormode = 'jmol'
self.colors = {}
for i, rgb in enumerate(jmol_colors):
self.colors[i] = ('#{0:02X}{1:02X}{2:02X}'
.format(*(int(x * 255) for x in rgb)))
def calculate_plotting_offset(self, rotation, scale, maxwidth):
# from ase.visualize.plot and ase.io.utils
R = np.dot(self.atoms.get_positions(), rotate(rotation))
radii = covalent_radii[self.atoms.numbers]
X1 = (R - radii[:, None]).min(0)
X2 = (R + radii[:, None]).max(0)
if show_unit_cell == 2:
X1 = np.minimum(X1, cell_vertices.min(0))
X2 = np.maximum(X2, cell_vertices.max(0))
M = (X1 + X2) / 2
S = 1.05 * (X2 - X1)
w = scale * S[0]
if w > maxwidth:
w = maxwidth
scale = w / S[0]
h = scale * S[1]
offset = np.array([scale * M[0] - w / 2, scale * M[1] - h / 2, 0])
return offset
def __init__(self, vbox, rotations):
self.colors = [None] * (len(jmol_colors) + 1)
self.nselected = 0
self.rotation = rotate(rotations)
self.drawing_area = gtk.DrawingArea()
self.drawing_area.set_size_request(450, 450)
self.drawing_area.connect('button_press_event', self.press)
self.drawing_area.connect('button_release_event', self.release)
self.drawing_area.connect('motion-notify-event', self.move)
# Signals used to handle backing pixmap:
self.drawing_area.connect('expose_event', self.expose_event)
self.drawing_area.connect('configure_event', self.configure_event)
self.drawing_area.set_events(gtk.gdk.BUTTON_PRESS_MASK |
gtk.gdk.BUTTON_RELEASE_MASK |
gtk.gdk.BUTTON_MOTION_MASK |
gtk.gdk.POINTER_MOTION_HINT_MASK)
vbox.pack_start(self.drawing_area)
self.drawing_area.show()
self.configured = False
self.frame = None
def set_view(self, menuitem):
plane_rotation = menuitem.get_name()
if plane_rotation == 'xyPlane':
self.axes = rotate('0.0x,0.0y,0.0z')
elif plane_rotation == 'yzPlane':
self.axes = rotate('-90.0x,-90.0y,0.0z')
elif plane_rotation == 'zxPlane':
self.axes = rotate('90.0x,0.0y,90.0z')
elif plane_rotation == 'yxPlane':
self.axes = rotate('180.0x,0.0y,90.0z')
elif plane_rotation == 'zyPlane':
self.axes = rotate('0.0x,90.0y,0.0z')
elif plane_rotation == 'xzPlane':
self.axes = rotate('-90.0x,0.0y,0.0z')
else:
if plane_rotation == 'a1a2Plane':
i, j = 0, 1
elif plane_rotation == 'a2a3Plane':
i, j = 1, 2
elif plane_rotation == 'a3a1Plane':
i, j = 2, 0
elif plane_rotation == 'a2a1Plane':
i, j = 1, 0
elif plane_rotation == 'a3a2Plane':
i, j = 2, 1
elif plane_rotation == 'a1a3Plane':
i, j = 0, 2
x1 = self.images.A[self.frame, i]
x2 = self.images.A[self.frame, j]
norm = np.linalg.norm
x1 = x1 / norm(x1)
x2 = x2 - x1 * np.dot(x1, x2)
x2 /= norm(x2)
x3 = np.cross(x1, x2)
self.axes = np.array([x1, x2, x3]).T
self.set_coordinates()
def set_view(self, menuitem):
plane_rotation = menuitem.get_name()
if plane_rotation == 'xyPlane':
self.axes = rotate('0.0x,0.0y,0.0z')
elif plane_rotation == 'yzPlane':
self.axes = rotate('-90.0x,-90.0y,0.0z')
elif plane_rotation == 'zxPlane':
self.axes = rotate('90.0x,0.0y,90.0z')
elif plane_rotation == 'yxPlane':
self.axes = rotate('180.0x,0.0y,90.0z')
elif plane_rotation == 'zyPlane':
self.axes = rotate('0.0x,90.0y,0.0z')
elif plane_rotation == 'xzPlane':
self.axes = rotate('-90.0x,0.0y,0.0z')
else:
if plane_rotation == 'a1a2Plane':
i, j = 0, 1
elif plane_rotation == 'a2a3Plane':
i, j = 1, 2
elif plane_rotation == 'a3a1Plane':
i, j = 2, 0
elif plane_rotation == 'a2a1Plane':
i, j = 1, 0
elif plane_rotation == 'a3a2Plane':
i, j = 2, 1
elif plane_rotation == 'a1a3Plane':
i, j = 0, 2
x1 = self.images.A[self.frame, i]
x2 = self.images.A[self.frame, j]
norm = np.linalg.norm
x1 = x1 / norm(x1)
x2 = x2 - x1 * np.dot(x1, x2)
x2 /= norm(x2)
x3 = np.cross(x1, x2)
self.axes = np.array([x1, x2, x3]).T
self.set_coordinates()
def set_view(self, key):
if key == 'Z':
self.axes = rotate('0.0x,0.0y,0.0z')
elif key == 'X':
self.axes = rotate('-90.0x,-90.0y,0.0z')
elif key == 'Y':
self.axes = rotate('90.0x,0.0y,90.0z')
elif key == 'Alt+Z':
self.axes = rotate('180.0x,0.0y,90.0z')
elif key == 'Alt+X':
self.axes = rotate('0.0x,90.0y,0.0z')
elif key == 'Alt+Y':
self.axes = rotate('-90.0x,0.0y,0.0z')
else:
if key == '3':
i, j = 0, 1
elif key == '1':
i, j = 1, 2
elif key == '2':
i, j = 2, 0
elif key == 'Alt+3':
i, j = 1, 0
elif key == 'Alt+1':
i, j = 2, 1
elif key == 'Alt+2':
i, j = 0, 2
A = complete_cell(self.atoms.cell)
x1 = A[i]
x2 = A[j]
norm = np.linalg.norm
x1 = x1 / norm(x1)
x2 = x2 - x1 * np.dot(x1, x2)
x2 /= norm(x2)
x3 = np.cross(x1, x2)
self.axes = np.array([x1, x2, x3]).T
self.set_frame()
def set_view(self, key):
if key == 'Z':
self.axes = rotate('0.0x,0.0y,0.0z')
elif key == 'X':
self.axes = rotate('-90.0x,-90.0y,0.0z')
elif key == 'Y':
self.axes = rotate('90.0x,0.0y,90.0z')
elif key == 'Alt+Z':
self.axes = rotate('180.0x,0.0y,90.0z')
elif key == 'Alt+X':
self.axes = rotate('0.0x,90.0y,0.0z')
elif key == 'Alt+Y':
self.axes = rotate('-90.0x,0.0y,0.0z')
else:
if key == '3':
i, j = 0, 1
elif key == '1':
i, j = 1, 2
elif key == '2':
i, j = 2, 0
elif key == 'Alt+3':
i, j = 1, 0
elif key == 'Alt+1':
i, j = 2, 1
elif key == 'Alt+2':
i, j = 0, 2
A = complete_cell(self.atoms.cell)
x1 = A[i]
x2 = A[j]
norm = np.linalg.norm
x1 = x1 / norm(x1)
x2 = x2 - x1 * np.dot(x1, x2)
x2 /= norm(x2)
x3 = np.cross(x1, x2)
self.axes = np.array([x1, x2, x3]).T
self.set_frame()
def __init__(self, atoms, rotation='', show_unit_cell=2,
radii=None, bbox=None, colors=None, scale=20,
maxwidth=500, extra_offset=(0., 0.)):
self.numbers = atoms.get_atomic_numbers()
self.colors = colors
if colors is None:
self.colors = jmol_colors[self.numbers]
if radii is None:
radii = covalent_radii[self.numbers]
elif isinstance(radii, float):
radii = covalent_radii[self.numbers] * radii
else:
radii = np.array(radii)
natoms = len(atoms)
if isinstance(rotation, basestring):
rotation = rotate(rotation)
cell = atoms.get_cell()
disp = atoms.get_celldisp().flatten()
if show_unit_cell > 0:
L, T, D = cell_to_lines(self, cell)
cell_vertices = np.empty((2, 2, 2, 3))
for c1 in range(2):
for c2 in range(2):
for c3 in range(2):
cell_vertices[c1, c2, c3] = np.dot([c1, c2, c3],
cell) + disp
cell_vertices.shape = (8, 3)
cell_vertices = np.dot(cell_vertices, rotation)
else:
L = np.empty((0, 3))
T = None
D = None
cell_vertices = None
nlines = len(L)
positions = np.empty((natoms + nlines, 3))
R = atoms.get_positions()
positions[:natoms] = R
positions[natoms:] = L
r2 = radii**2
for n in range(nlines):
d = D[T[n]]
if ((((R - L[n] - d)**2).sum(1) < r2) &
(((R - L[n] + d)**2).sum(1) < r2)).any():
T[n] = -1
positions = np.dot(positions, rotation)
R = positions[:natoms]
if bbox is None:
X1 = (R - radii[:, None]).min(0)
X2 = (R + radii[:, None]).max(0)
if show_unit_cell == 2:
X1 = np.minimum(X1, cell_vertices.min(0))
X2 = np.maximum(X2, cell_vertices.max(0))
M = (X1 + X2) / 2
S = 1.05 * (X2 - X1)
w = scale * S[0]
if w > maxwidth:
w = maxwidth
scale = w / S[0]
h = scale * S[1]
offset = np.array([scale * M[0] - w / 2, scale * M[1] - h / 2, 0])
else:
w = (bbox[2] - bbox[0]) * scale
h = (bbox[3] - bbox[1]) * scale
offset = np.array([bbox[0], bbox[1], 0]) * scale
offset[0] = offset[0] - extra_offset[0]
offset[1] = offset[1] - extra_offset[1]
self.w = w + extra_offset[0]
self.h = h + extra_offset[1]
positions *= scale
positions -= offset
if nlines > 0:
D = np.dot(D, rotation)[:, :2] * scale
if cell_vertices is not None:
cell_vertices *= scale
cell_vertices -= offset
cell = np.dot(cell, rotation)
cell *= scale
self.cell = cell
self.positions = positions
self.D = D
self.T = T
self.cell_vertices = cell_vertices
self.natoms = natoms
self.d = 2 * scale * radii
# extension for partial occupancies
self.frac_occ = False
self.tags = None
self.occs = None
try:
self.occs = atoms.info['occupancy']
self.tags = atoms.get_tags()
self.frac_occ = True
except KeyError:
pass
def change(self, adjustment):
if self.update:
x, y, z = [float(a.value) for a in self.rotate]
self.gui.axes = rotate('%fx,%fy,%fz' % (x, y, z))
self.gui.set_coordinates()
return True
def __init__(self, atoms,
rotation='', show_unit_cell=False, radii=None,
bbox=None, colors=None, scale=20):
self.numbers = atoms.get_atomic_numbers()
self.colors = colors
if colors is None:
self.colors = jmol_colors[self.numbers]
if radii is None:
radii = covalent_radii[self.numbers]
elif type(radii) is float:
radii = covalent_radii[self.numbers] * radii
else:
radii = np.array(radii)
natoms = len(atoms)
if isinstance(rotation, str):
rotation = rotate(rotation)
A = atoms.get_cell()
if show_unit_cell > 0:
L, T, D = self.cell_to_lines(A)
C = np.empty((2, 2, 2, 3))
for c1 in range(2):
for c2 in range(2):
for c3 in range(2):
C[c1, c2, c3] = np.dot([c1, c2, c3], A)
C.shape = (8, 3)
C = np.dot(C, rotation) # Unit cell vertices
else:
L = np.empty((0, 3))
T = None
D = None
C = None
nlines = len(L)
X = np.empty((natoms + nlines, 3))
R = atoms.get_positions()
X[:natoms] = R
X[natoms:] = L
r2 = radii**2
for n in range(nlines):
d = D[T[n]]
if ((((R - L[n] - d)**2).sum(1) < r2) &
(((R - L[n] + d)**2).sum(1) < r2)).any():
T[n] = -1
X = np.dot(X, rotation)
R = X[:natoms]
if bbox is None:
X1 = (R - radii[:, None]).min(0)
X2 = (R + radii[:, None]).max(0)
if show_unit_cell == 2:
X1 = np.minimum(X1, C.min(0))
X2 = np.maximum(X2, C.max(0))
M = (X1 + X2) / 2
S = 1.05 * (X2 - X1)
w = scale * S[0]
if w > 500:
w = 500
scale = w / S[0]
h = scale * S[1]
offset = np.array([scale * M[0] - w / 2, scale * M[1] - h / 2, 0])
else:
w = (bbox[2] - bbox[0]) * scale
h = (bbox[3] - bbox[1]) * scale
offset = np.array([bbox[0], bbox[1], 0]) * scale
self.w = w
self.h = h
X *= scale
X -= offset
if nlines > 0:
D = np.dot(D, rotation)[:, :2] * scale
if C is not None:
C *= scale
C -= offset
A = np.dot(A, rotation)
A *= scale
self.A = A
self.X = X
self.D = D
self.T = T
self.C = C
self.natoms = natoms
self.d = 2 * scale * radii
def reset_view(self, menuitem):
self.axes = rotate('0.0x,0.0y,0.0z')
self.set_coordinates()
self.focus(self)
def change(self):
x, y, z = [float(a.value) for a in self.rotate]
self.gui.axes = rotate('%fx,%fy,%fz' % (x, y, z))
self.gui.set_frame()
def reset_view(self, menuitem):
self.axes = rotate('0.0x,0.0y,0.0z')
self.set_coordinates()
self.focus(self)
def change(self, adjustment):
if self.update:
x, y, z = [float(a.value) for a in self.rotate]
self.gui.axes = rotate('%fx,%fy,%fz' % (x, y, z))
self.gui.set_coordinates()
return True
def generate_writer_variables(writer,
atoms,
rotation='',
show_unit_cell=0,
radii=None,
bbox=None,
colors=None,
scale=20,
maxwidth=500,
extra_offset=(0., 0.)):
writer.numbers = atoms.get_atomic_numbers()
writer.colors = colors
if colors is None:
writer.colors = jmol_colors[writer.numbers]
if radii is None:
radii = covalent_radii[writer.numbers]
elif isinstance(radii, float):
radii = covalent_radii[writer.numbers] * radii
else:
radii = np.array(radii)
natoms = len(atoms)
if isinstance(rotation, basestring):
rotation = rotate(rotation)
cell = atoms.get_cell()
disp = atoms.get_celldisp().flatten()
if show_unit_cell > 0:
L, T, D = cell_to_lines(writer, cell)
cell_vertices = np.empty((2, 2, 2, 3))
for c1 in range(2):
for c2 in range(2):
for c3 in range(2):
cell_vertices[c1, c2,
c3] = np.dot([c1, c2, c3], cell) + disp
cell_vertices.shape = (8, 3)
cell_vertices = np.dot(cell_vertices, rotation)
else:
L = np.empty((0, 3))
T = None
D = None
cell_vertices = None
nlines = len(L)
positions = np.empty((natoms + nlines, 3))
R = atoms.get_positions()
positions[:natoms] = R
positions[natoms:] = L
r2 = radii**2
for n in range(nlines):
d = D[T[n]]
if ((((R - L[n] - d)**2).sum(1) < r2) &
(((R - L[n] + d)**2).sum(1) < r2)).any():
T[n] = -1
positions = np.dot(positions, rotation)
R = positions[:natoms]
if bbox is None:
X1 = (R - radii[:, None]).min(0)
X2 = (R + radii[:, None]).max(0)
if show_unit_cell == 2:
X1 = np.minimum(X1, cell_vertices.min(0))
X2 = np.maximum(X2, cell_vertices.max(0))
M = (X1 + X2) / 2
S = 1.05 * (X2 - X1)
w = scale * S[0]
if w > maxwidth:
w = maxwidth
scale = w / S[0]
h = scale * S[1]
offset = np.array([scale * M[0] - w / 2, scale * M[1] - h / 2, 0])
else:
w = (bbox[2] - bbox[0]) * scale
h = (bbox[3] - bbox[1]) * scale
offset = np.array([bbox[0], bbox[1], 0]) * scale
offset[0] = offset[0] - extra_offset[0]
offset[1] = offset[1] - extra_offset[1]
writer.w = w + extra_offset[0]
writer.h = h + extra_offset[1]
positions *= scale
positions -= offset
if nlines > 0:
D = np.dot(D, rotation)[:, :2] * scale
if cell_vertices is not None:
cell_vertices *= scale
cell_vertices -= offset
cell = np.dot(cell, rotation)
cell *= scale
writer.cell = cell
writer.positions = positions
writer.D = D
writer.T = T
writer.cell_vertices = cell_vertices
writer.natoms = natoms
writer.d = 2 * scale * radii
def change(self):
x, y, z = [float(a.value) for a in self.rotate]
self.gui.axes = rotate('%fx,%fy,%fz' % (x, y, z))
self.gui.set_frame()
def reset_view(self, menuitem):
self.axes = rotate('0.0x,0.0y,0.0z')
self.set_frame()
self.focus(self)
def reset_view(self, menuitem):
self.axes = rotate('0.0x,0.0y,0.0z')
self.set_frame()
self.focus(self)