def configure_event(self, drawing_area, event):
if self.configured:
w = self.width
h = self.height
else:
self.config = read_defaults()
self.colormap = self.drawing_area.get_colormap()
self.foreground_gc = self.drawing_area.window.new_gc(
self.colormap.alloc_color(self.config['gui_foreground_color']))
self.background_gc = self.drawing_area.window.new_gc(
self.colormap.alloc_color(self.config['gui_background_color']))
self.red = self.drawing_area.window.new_gc(
self.colormap.alloc_color(62345, 0, 0), line_width=2)
self.green = self.drawing_area.window.new_gc(
self.colormap.alloc_color(0, 54456, 0), line_width=2)
self.blue = self.drawing_area.window.new_gc(
self.colormap.alloc_color(0, 0, 54456), line_width=2)
self.selected_gc = self.drawing_area.window.new_gc(
self.colormap.alloc_color(0, 16456, 0),
line_width=3)
x, y, self.width, self.height = drawing_area.get_allocation()
self.pixmap = gtk.gdk.Pixmap(drawing_area.window,
self.width, self.height)
if self.configured:
self.scale *= sqrt(1.0 * self.width * self.height / (w * h))
self.draw()
self.configured = True
def configure_event(self, drawing_area, event):
if self.configured:
w = self.width
h = self.height
else:
self.config = read_defaults()
self.colormap = self.drawing_area.get_colormap()
self.foreground_gc = self.drawing_area.window.new_gc(
self.colormap.alloc_color(self.config['gui_foreground_color']))
self.background_gc = self.drawing_area.window.new_gc(
self.colormap.alloc_color(self.config['gui_background_color']))
self.red = self.drawing_area.window.new_gc(
self.colormap.alloc_color(62345, 0, 0), line_width=2)
self.green = self.drawing_area.window.new_gc(
self.colormap.alloc_color(0, 54456, 0), line_width=2)
self.blue = self.drawing_area.window.new_gc(
self.colormap.alloc_color(0, 0, 54456), line_width=2)
self.selected_gc = self.drawing_area.window.new_gc(
self.colormap.alloc_color(0, 16456, 0), line_width=3)
x, y, self.width, self.height = drawing_area.get_allocation()
self.pixmap = gtk.gdk.Pixmap(drawing_area.window, self.width,
self.height)
if self.configured:
self.scale *= sqrt(1.0 * self.width * self.height / (w * h))
self.draw()
self.configured = True
def __init__(self, images=None):
self.covalent_radii = covalent_radii.copy()
self.config = read_defaults()
self.atom_scale = self.config['radii_scale']
if images is None:
images = [Atoms()]
self.initialize(images)
def __init__(self, images=None, rotations='', show_bonds=False, expr=None):
if not isinstance(images, Images):
images = Images(images)
self.images = images
self.observers = []
self.config = read_defaults()
if show_bonds:
self.config['show_bonds'] = True
menu = self.get_menu_data()
self.window = ui.ASEGUIWindow(close=self.exit,
menu=menu,
config=self.config,
scroll=self.scroll,
scroll_event=self.scroll_event,
press=self.press,
move=self.move,
release=self.release,
resize=self.resize)
View.__init__(self, rotations)
Status.__init__(self)
self.subprocesses = [] # list of external processes
self.movie_window = None
self.vulnerable_windows = []
self.simulation = {} # Used by modules on Calculate menu.
self.module_state = {} # Used by modules to store their state.
self.arrowkey_mode = self.ARROWKEY_SCAN
self.move_atoms_mask = None
self.set_frame(len(self.images) - 1, focus=True)
# Used to move the structure with the mouse
self.prev_pos = None
self.last_scroll_time = time()
self.orig_scale = self.scale
if len(self.images) > 1:
self.movie()
if expr is None:
expr = self.config['gui_graphs_string']
if expr is not None and expr != '' and len(self.images) > 1:
self.plot_graphs(expr=expr, ignore_if_nan=True)
def __init__(self,
images=None,
rotations='',
show_unit_cell=True,
show_bonds=False):
# Try to change into directory of file you are viewing
try:
os.chdir(os.path.split(sys.argv[1])[0])
# This will fail sometimes (e.g. for starting a new session)
except:
pass
if not images:
images = Images()
images.initialize([Atoms()])
self.images = images
self.config = read_defaults()
menu = self.get_menu_data(show_unit_cell, show_bonds)
self.window = ui.ASEGUIWindow(close=self.exit,
menu=menu,
config=self.config,
scroll=self.scroll,
scroll_event=self.scroll_event,
press=self.press,
move=self.move,
release=self.release,
resize=self.resize)
View.__init__(self, rotations)
Status.__init__(self)
self.graphs = [] # list of matplotlib processes
self.graph_wref = [] # list of weakrefs to Graph objects
self.movie_window = None
self.vulnerable_windows = []
self.simulation = {} # Used by modules on Calculate menu.
self.module_state = {} # Used by modules to store their state.
self.arrowkey_mode = self.ARROWKEY_SCAN
self.move_atoms_mask = None
def __init__(self, images=None,
rotations='',
show_unit_cell=True,
show_bonds=False):
# Try to change into directory of file you are viewing
try:
os.chdir(os.path.split(sys.argv[1])[0])
# This will fail sometimes (e.g. for starting a new session)
except:
pass
if not images:
images = Images()
images.initialize([Atoms()])
self.images = images
self.config = read_defaults()
menu = self.get_menu_data(show_unit_cell, show_bonds)
self.window = ui.ASEGUIWindow(self.exit, menu, self.config,
self.scroll,
self.scroll_event,
self.press, self.move, self.release,
self.resize)
View.__init__(self, rotations)
Status.__init__(self)
self.graphs = [] # list of matplotlib processes
self.graph_wref = [] # list of weakrefs to Graph objects
self.movie_window = None
self.vulnerable_windows = []
self.simulation = {} # Used by modules on Calculate menu.
self.module_state = {} # Used by modules to store their state.
self.moving = False
self.move_atoms_mask = None
def initialize(self, images, filenames=None, init_magmom=False):
self.natoms = len(images[0])
self.nimages = len(images)
if filenames is None:
filenames = [None] * self.nimages
self.filenames = filenames
if hasattr(images[0], 'get_shapes'):
self.Q = np.empty((self.nimages, self.natoms, 4))
self.shapes = images[0].get_shapes()
import os as os
if os.path.exists('shapes'):
shapesfile = open('shapes')
lines = shapesfile.readlines()
shapesfile.close()
if '#{type:(shape_x,shape_y,shape_z), .....,}' in lines[0]:
shape = eval(lines[1])
shapes = []
for an in images[0].get_atomic_numbers():
shapes.append(shape[an])
self.shapes = np.array(shapes)
else:
print 'shape file has wrong format'
else:
print 'no shapesfile found: default shapes were used!'
else:
self.shapes = None
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.D = np.empty((self.nimages, 3))
self.Z = images[0].get_atomic_numbers()
self.q = np.empty((self.nimages, self.natoms))
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'):
self.Q[i] = atoms.get_quaternions()
self.A[i] = atoms.get_cell()
self.D[i] = atoms.get_celldisp().reshape((3, ))
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()
self.q[i] = atoms.get_initial_charges()
# 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(config['radii_scale'])
def initialize(self, images, filenames=None, init_magmom=False):
self.natoms = len(images[0])
self.nimages = len(images)
if filenames is None:
filenames = [None] * self.nimages
self.filenames = filenames
if hasattr(images[0], 'get_shapes'):
self.Q = np.empty((self.nimages, self.natoms, 4))
self.shapes = images[0].get_shapes()
import os as os
if os.path.exists('shapes'):
shapesfile = open('shapes')
lines = shapesfile.readlines()
shapesfile.close()
if '#{type:(shape_x,shape_y,shape_z), .....,}' in lines[0]:
shape = eval(lines[1])
shapes=[]
for an in images[0].get_atomic_numbers():
shapes.append(shape[an])
self.shapes = np.array(shapes)
else:
print 'shape file has wrong format'
else:
print 'no shapesfile found: default shapes were used!'
else:
self.shapes = None
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.D = np.empty((self.nimages, 3))
self.Z = images[0].get_atomic_numbers()
self.q = np.empty((self.nimages, self.natoms))
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'):
self.Q[i] = atoms.get_quaternions()
self.A[i] = atoms.get_cell()
self.D[i] = atoms.get_celldisp().reshape((3,))
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()
self.q[i] = atoms.get_initial_charges()
# 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(config['radii_scale'])
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(config['radii_scale'])
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(config['radii_scale'])
def __init__(self, images=None):
self.covalent_radii = covalent_radii.copy()
self.config = read_defaults()
self.atom_scale = self.config['radii_scale']
if images is not None:
self.initialize(images)
