def generate_2D_Slabs(b):
global view, view_2, struc1, struc2, s1, s2, slabgen1, slabgen2, pressed
pressed = 0
struc1 = slabgen1.get_slabs()[SID1_slide.value].get_sorted_structure()
s1 = build_ase_struc_2d(struc1)
view = nglview.show_ase(s1)
view.add_representation('unitcell')
view.background = 'black'
view.camera = "orthographic"
struc2 = slabgen2.get_slabs()[SID2_slide.value].get_sorted_structure()
s2 = build_ase_struc_2d(struc2)
view_2 = nglview.show_ase(s2)
view_2.add_representation('unitcell')
view_2.background = 'black'
view_2.camera = "orthographic"
with output_1:
output_1.clear_output()
display(view)
display(view_2)
merge_slabs.disabled = False
rep_interface.disabled = False
down_interface.disabled = False
def get_3D_Structures(b):
global view, view_2, struc1, struc2, s1, s2, pressed
pressed = 0
struc1 = a.get_structure_by_material_id(material_1.value)
struc1 = SpacegroupAnalyzer(
struc1).get_conventional_standard_structure()
s1 = build_ase_struc_3d(struc1)
view = nglview.show_ase(s1)
view.add_representation('unitcell')
view.background = 'black'
view.camera = "orthographic"
struc2 = a.get_structure_by_material_id(material_2.value)
struc2 = SpacegroupAnalyzer(
struc2).get_conventional_standard_structure()
s2 = build_ase_struc_3d(struc2)
view_2 = nglview.show_ase(s2)
view_2.add_representation('unitcell')
view_2.background = 'black'
view_2.camera = "orthographic"
with output_1:
output_1.clear_output()
display(view)
display(view_2)
list_interfaces.disabled = False
rep_structures.disabled = False
down_structures.disabled = False
def view_structure(self, snapshot=-1, spacefill=True, show_cell=True):
"""
Args:
snapshot (int): Snapshot of the trajectory one wants
spacefill (bool):
show_cell (bool):
Returns:
view: nglview IPython widget
"""
import nglview
atoms = self.get_structure(snapshot)
picture = nglview.show_ase(atoms)
if spacefill:
picture.add_spacefill(radius_type="vdw", scale=0.5)
picture.remove_ball_and_stick()
else:
picture.add_ball_and_stick()
if show_cell:
if atoms.cell is not None:
picture.add_unitcell()
return picture
def nb_viz(doc, repeat=1, bonds=None):
""" Return an ipywidget for nglview visualisation in
a Jupyter notebook or otherwise.
Parameters:
doc (matador.crystal.Crystal / dict): matador document to show.
Keyword arguments:
repeat (int): number of periodic images to include.
bonds (str): custom bond selection.
"""
import nglview
atoms = doc2ase(doc)
atoms = atoms.repeat((repeat, repeat, repeat))
view = nglview.show_ase(atoms)
view.add_unitcell()
view.remove_ball_and_stick()
view.add_spacefill(radius_type='vdw', scale=0.3)
if bonds is None:
for elements in set(doc['atom_types']):
view.add_ball_and_stick(selection='#{}'.format(elements.upper()))
else:
if not isinstance(bonds, list):
bonds = [bonds]
for bond in bonds:
view.add_ball_and_stick(selection='#{}'.format(bond.upper()))
view.parameters = {'clipDist': 0}
view.camera = 'orthographic'
view.background = '#FFFFFF'
view.center()
return view
def replicate_structures(b):
global view, view_2, s1, s2
s1 = s1.repeat((rep_x1.value, rep_y1.value, rep_z1.value))
s2 = s2.repeat((rep_x2.value, rep_y2.value, rep_z2.value))
view = nglview.show_ase(s1)
view.add_representation('unitcell')
view.background = 'black'
view.camera = "orthographic"
view_2 = nglview.show_ase(s2)
view_2.add_representation('unitcell')
view_2.background = 'black'
view_2.camera = "orthographic"
with output_1:
output_1.clear_output()
display(view)
display(view_2)
def plotConf(self):
""" Plot configuration using nglview """
v = nglview.show_ase(self.conf)
v.add_representation("unitcell")
boxy=widgets.Box([v],layout=self.box_layout)
display(boxy)
def plotEnv(self,myEnvironment):
env_atom_types = np.asarray(self.conf.get_chemical_symbols())[myEnvironment.indeces.astype(int)] #,np.array('C')] #Template[env_number].myindex)]
env_atom_types = np.append(env_atom_types,np.asarray(self.conf.get_chemical_symbols())[myEnvironment.myindex])
env_positions = np.vstack((myEnvironment.delta*10,np.array([0,0,0]) ) )
env = ase.Atoms(env_atom_types,env_positions)
v = nglview.show_ase(env)
boxy=widgets.Box([v],layout=self.box_layout)
display(boxy)
def __init__(self, atoms, xsize=500, ysize=500):
import nglview
import nglview.color
from ipywidgets import Dropdown, FloatSlider, IntSlider, HBox, VBox
self.atoms = atoms
if isinstance(atoms[0], Atoms):
# Assume this is a trajectory or struct list
self.view = nglview.show_asetraj(atoms, default=False)
self.frm = IntSlider(value=0, min=0, max=len(atoms) - 1)
self.frm.observe(self._update_frame)
self.struct = atoms[0]
else:
# Assume this is just a single structure
self.view = nglview.show_ase(atoms, default=False)
self.struct = atoms
self.frm = None
self.colors = {}
self.view._remote_call('setSize', target='Widget',
args=['%dpx' % (xsize,), '%dpx' % (ysize,)])
self.view.add_unitcell()
self.view.add_spacefill()
self.view.camera = 'orthographic'
self.view.parameters = { "clipDist": 0 }
self.view.center()
self.asel = Dropdown(options=['All'] +
list(set(self.struct.get_chemical_symbols())),
value='All', description='Show')
self.csel = Dropdown(options=nglview.color.COLOR_SCHEMES,
value='element', description='Color scheme')
self.rad = FloatSlider(value=0.5, min=0.0, max=1.5, step=0.01,
description='Ball size')
self.asel.observe(self._select_atom)
self.csel.observe(self._update_repr)
self.rad.observe(self._update_repr)
self.view.update_spacefill(radiusType='covalent',
radiusScale=0.5,
color_scheme=self.csel.value,
color_scale='rainbow')
wdg = [self.asel, self.csel, self.rad]
if self.frm:
wdg.append(self.frm)
self.gui = HBox([self.view, VBox(wdg)])
# Make useful shortcuts for the user of the class
self.gui.view = self.view
self.gui.control_box = self.gui.children[1]
self.gui.custom_colors = self.custom_colors
def replicate_interface(b):
global view_3, s3
s3 = s3.repeat((rep_x3.value, rep_y3.value, rep_z3.value))
view_3 = nglview.show_ase(s3)
view_3.add_representation('unitcell')
view_3.background = 'black'
view_3.camera = "orthographic"
with output_1:
output_1.clear_output()
display(view_3)
def merge_2D_slabs(b):
global view, view_2, struc1, struc2, s1, s2, slabgen1, slabgen2, s3, view_3, pressed
pressed = 1
a1_tmp = (s2.cell.lengths()[0] / (s1.cell.lengths()[0]))
a2_tmp = (s2.cell.lengths()[1] / (s1.cell.lengths()[1]))
a1 = 1
b1 = 1
a2 = 1
b2 = 1
if (a1_tmp >= 1):
a1 = int(np.round(a1))
else:
b1 = int(np.round(1 / a1))
if (a2_tmp >= 1):
a2 = int(np.round(a1))
else:
b2 = int(np.round(1 / a1))
s1 = s1.repeat((a1, a2, 1))
s2 = s2.repeat((b1, b2, 1))
if (substrate_slide.value == 1):
cell_final = s1.cell.copy()
fix_val = 0
else:
cell_final = s2.cell.copy()
fix_val = 1
vac = gap_slide.value / 2
s1.center(vacuum=vac, axis=2)
s2.center(vacuum=vac, axis=2)
s3, s1_strain, s2_strain = stack(s1,
s2,
axis=2,
fix=0,
cell=cell_final,
maxstrain=None,
distance=None,
output_strained=True)
strain1 = np.sqrt(((s1_strain.cell - s1.cell).sum(axis=0)**2).sum())
strain2 = np.sqrt(((s2_strain.cell - s2.cell).sum(axis=0)**2).sum())
view_3 = nglview.show_ase(s3)
view_3.add_representation('unitcell')
view_3.background = 'black'
view_3.camera = "orthographic"
with output_1:
output_1.clear_output()
print("Strain on cell of Material 1 is", strain1)
print("Strain on cell of Material 2 is", strain2)
display(view_3)
def _plot3d_ase(
self,
spacefill=True,
show_cell=True,
camera="perspective",
particle_size=0.5,
background="white",
color_scheme="element",
show_axes=True,
):
"""
Possible color schemes:
" ", "picking", "random", "uniform", "atomindex", "residueindex",
"chainindex", "modelindex", "sstruc", "element", "resname", "bfactor",
"hydrophobicity", "value", "volume", "occupancy"
Returns:
"""
try: # If the graphical packages are not available, the GUI will not work.
import nglview
except ImportError:
raise ImportError(
"The package nglview needs to be installed for the plot3d() function!"
)
# Always visualize the parent basis
parent_basis = self._ref_atoms.get_parent_basis()
view = nglview.show_ase(parent_basis)
if spacefill:
view.add_spacefill(radius_type="vdw",
color_scheme=color_scheme,
radius=particle_size)
# view.add_spacefill(radius=1.0)
view.remove_ball_and_stick()
else:
view.add_ball_and_stick()
if show_cell:
if parent_basis.cell is not None:
if all(np.max(parent_basis.cell, axis=0) > 1e-2):
view.add_unitcell()
if show_axes:
view.shape.add_arrow([-2, -2, -2], [2, -2, -2], [1, 0, 0], 0.5)
view.shape.add_arrow([-2, -2, -2], [-2, 2, -2], [0, 1, 0], 0.5)
view.shape.add_arrow([-2, -2, -2], [-2, -2, 2], [0, 0, 1], 0.5)
if camera != "perspective" and camera != "orthographic":
print("Only perspective or orthographic is permitted")
return None
view.camera = camera
view.background = background
return view
def show_atoms(atoms, dis=True):
import nglview
v = nglview.show_ase(atoms)
v.clear_representations()
v.add_unitcell()
v.add_spacefill(radius_type='vdw',
radius_scale=0.5,
roughness=1,
metalness=0)
v.parameters = dict(clipDist=-100, sampleLevel=2)
v.control.spin([1, 0, 0], 3.14 * 1.5)
if dis:
display(v)
else:
return v
def __init__(self, atoms, xsize=500, ysize=500):
import nglview
from ipywidgets import Dropdown, FloatSlider, IntSlider, HBox, VBox
self.atoms = atoms
if isinstance(atoms[0], Atoms):
# Assume this is a trajectory or struct list
self.view = nglview.show_asetraj(atoms)
self.frm = IntSlider(value=0, min=0, max=len(atoms) - 1)
self.frm.observe(self._update_frame)
self.struct = atoms[0]
else:
# Assume this is just a single structure
self.view = nglview.show_ase(atoms)
self.struct = atoms
self.frm = None
self.colors = {}
self.view._remote_call('setSize', target='Widget',
args=['%dpx' % (xsize,), '%dpx' % (ysize,)])
self.view.add_unitcell()
self.view.add_spacefill()
self.view.camera = 'orthographic'
self.view.update_spacefill(radiusType='covalent', scale=0.7)
self.view.center()
self.asel = Dropdown(options=['All'] +
list(set(self.struct.get_chemical_symbols())),
value='All', description='Show')
self.rad = FloatSlider(value=0.8, min=0.0, max=1.5, step=0.01,
description='Ball size')
self.asel.observe(self._select_atom)
self.rad.observe(self._update_repr)
wdg = [self.asel, self.rad]
if self.frm:
wdg.append(self.frm)
self.gui = HBox([self.view, VBox(wdg)])
# Make useful shortcuts for the user of the class
self.gui.view = self.view
self.gui.control_box = self.gui.children[1]
self.gui.custom_colors = self.custom_colors
def ase_view(s, gui=False):
view=nv.show_ase(s, gui=gui)
view.clear_representations()
view.add_ball_and_stick(aspectRatio=4)
return view
def test_show_ase():
from ase import Atom, Atoms
dimer = Atoms([Atom('X', (0, 0, 0)),
Atom('X', (0, 0, 1))])
dimer.set_positions([(1, 2, 3), (4, 5, 6.2)])
nv.show_ase(dimer)
def test_show_ase():
from ase import Atom, Atoms
dimer = Atoms([Atom('X', (0, 0, 0)), Atom('X', (0, 0, 1))])
dimer.set_positions([(1, 2, 3), (4, 5, 6.2)])
nv.show_ase(dimer)
def get_nglview(nsys):
"""
Retern a nglview object via ase_atoms.
"""
import nglview as nv
return nv.show_ase(nsys.to_ase_atoms())
# interact(f, x=10);
# +
# import nglview as np
# from nglview.datafiles import ASE_Traj
# ASE_Traj
# +
# import MDAnalysis as mda
import nglview as nv
from nglview.datafiles import PDB, XTC
# u = mda.Universe(PDB, XTC)
# protein = u.select_atoms('protein')
# +
# w = nv.ASEStructure(atoms)
# nv.ASEStructure?
# w
# -
nv.__version__
nv.show_ase(atoms)
nv.demo()
def visualize_MO(self, index, particle_size=0.5, show_bonds=True):
'''
Visualize the MO identified by its index.
**Arguments**
index index of the MO, as listed by print_MO()
particle_size
size of the atoms for visualization, lower value if orbital is too small to see
show_bonds connect atoms or not
**Notes**
This function should always be accompanied with the following commands (in a separate cell)
view[1].update_surface(isolevel=1, color='blue', opacity=.3)
view[2].update_surface(isolevel=-1, color='red', opacity=.3)
This makes sure that the bonding and non-bonding MO's are plotted and makes them transparent
'''
n_MO = self.get('output/structure/dft/scf_density').shape[0]
assert index >= 0 and index < n_MO
assert len(
self.get('output/structure/numbers')
) < 50 # check whether structure does not become too large for interactive calculation of cube file
# print orbital information
occ_alpha = int(
self.get('output/structure/dft/n_alpha_electrons') > index)
occ_beta = int(
self.get('output/structure/dft/n_beta_electrons') > index)
if self.get('output/structure/dft/beta_orbital_e') is None:
orbital_energy = self.get(
'output/structure/dft/alpha_orbital_e')[index]
print("Orbital energy = {:>10.5f} \t Occ. = {}".format(
orbital_energy, occ_alpha + occ_beta))
else:
orbital_energy = [
self.get('output/structure/dft/alpha_orbital_e')[index],
self.get('output/structure/dft/beta_orbital_e')[index]
]
print(
"Orbital energies (alpha,beta) = {:>10.5f},{:>10.5f} \t Occ. = {},{}"
.format(orbital_energy[0], orbital_energy[1], occ_alpha,
occ_beta))
# make cube file
path = self.path + '_hdf5/' + self.name + '/input'
out = subprocess.check_output(
"ml load Gaussian/g16_E.01-intel-2019a;module use /apps/gent/CO7/haswell-ib/modules/all; cubegen 1 MO={} {}.fchk {}.cube"
.format(index + 1, path, path),
stderr=subprocess.STDOUT,
universal_newlines=True,
shell=True,
)
# visualize cube file
try:
import nglview
except ImportError:
raise ImportError(
"The animate_nma_mode() function requires the package nglview to be installed"
)
atom_numbers = []
atom_positions = []
with open('{}.cube'.format(path), 'r') as f:
for i in range(2):
f.readline()
n_atoms = int(f.readline().split()[0][1:])
for i in range(3):
f.readline()
for n in range(n_atoms):
line = f.readline().split()
atom_numbers.append(int(line[0]))
atom_positions.append(
np.array([float(m) for m in line[2:]]) / angstrom)
structure = Atoms(numbers=np.array(atom_numbers),
positions=atom_positions)
view = nglview.show_ase(structure)
if not show_bonds:
view.add_spacefill(radius_type='vdw',
scale=0.5,
radius=particle_size)
view.remove_ball_and_stick()
else:
view.add_ball_and_stick()
view.add_component('{}.cube'.format(path))
view.add_component('{}.cube'.format(path))
return view
def atom_view(self):
return nv.show_ase(self.atoms) #, gui=True)
