def get_info(self):
symbol = []
x_geo = []
y_geo = []
z_geo = []
color = []
size = []
atoms_colors = blobs.get_colors()
for i in range(self.geometry.natom()):
symbol.append(self.geometry.fsymbol(i))
x_geo.append(int((self.geometry.fx(i) - self.origin[0]) / self.spacing[0]))
y_geo.append(int((self.geometry.fy(i) - self.origin[1]) / self.spacing[1]))
z_geo.append(int((self.geometry.fz(i) - self.origin[2]) / self.spacing[2]))
for atom in atoms_colors:
if self.geometry.fsymbol(i) == atom:
color.append(atoms_colors[atom][0])
size.append(atoms_colors[atom][1] + 15)
mol_dic = {
"sym": symbol,
"x": np.array(x_geo),
"y": np.array(y_geo),
"z": np.array(z_geo),
"color": color,
"size": np.array(size)
}
return mol_dic
def get_info(self):
color = []
size = []
atoms_colors = blobs.get_colors()
for i in range(len(self.geo)):
for atom in atoms_colors:
if self.sym[i] == atom:
color.append(atoms_colors[atom][0])
size.append(atoms_colors[atom][1] + 15)
mol_dic = {"color": color, "size": np.array(size)}
return mol_dic
def plot(self,
size=1,
nframes = 8,
vib = 0,
):
atoms_colors = blobs.get_colors()
bonds = build_bond_list(self.geo)
self.bonds = bonds
fms = []
norm_coord = self.wfn.frequency_analysis['x'][2][:,self.indices].T.reshape(len(self.indices),len(self.geo),3)
self.norm = norm_coord
for frame in range(nframes - 1):
data = []
data.append(go.Scatter3d(x=self.geo[:,0] + self.norm[vib][:,0]/(nframes - frame),
y=self.geo[:,1] + self.norm[vib][:,1]/(nframes - frame),
z=self.geo[:,2] + self.norm[vib][:,2]/(nframes - frame)))
fms.append(go.Frame(data=data))
for i in range(1, len(bonds)):
bond_color_1= atoms_colors[self.sym[bonds[i][0]]][0]
bond_color_2= atoms_colors[self.sym[bonds[i][1]]][0]
midx = (self.geo[bonds[i][0]][0] + self.norm[vib][bonds[i][0],0]/(nframes - frame) + self.geo[bonds[i][1]][0] + self.norm[vib][bonds[i][1],0]/(nframes - frame)) / 2
midy = (self.geo[bonds[i][0]][1] + self.norm[vib][bonds[i][0],1]/(nframes - frame) + self.geo[bonds[i][1]][1] + self.norm[vib][bonds[i][1],1]/(nframes - frame)) / 2
midz = (self.geo[bonds[i][0]][2] + self.norm[vib][bonds[i][0],2]/(nframes - frame) + self.geo[bonds[i][1]][2] + self.norm[vib][bonds[i][1],2]/(nframes - frame)) / 2
bond_x_1 = [self.geo[:,0][bonds[i][0]] + self.norm[vib][bonds[i][0],0]/(nframes - frame), midx]
bond_y_1 = [self.geo[:,1][bonds[i][0]] + self.norm[vib][bonds[i][0],1]/(nframes - frame), midy]
bond_z_1 = [self.geo[:,2][bonds[i][0]] + self.norm[vib][bonds[i][0],2]/(nframes - frame), midz]
bond_x_2 = [self.geo[:,0][bonds[i][1]] + self.norm[vib][bonds[i][1],0]/(nframes - frame), midx]
bond_y_2 = [self.geo[:,1][bonds[i][1]] + self.norm[vib][bonds[i][1],1]/(nframes - frame), midy]
bond_z_2 = [self.geo[:,2][bonds[i][1]] + self.norm[vib][bonds[i][1],2]/(nframes - frame), midz]
data.append(go.Scatter3d(
x=bond_x_1,
y=bond_y_1,
z=bond_z_1,
mode="lines",
line={
"color": bond_color_1,
"width": 7 * size
},
))
data.append(go.Scatter3d(
x=bond_x_2,
y=bond_y_2,
z=bond_z_2,
mode="lines",
line={
"color": bond_color_2,
"width": 7 * size
},
))
fms.reverse()
fms_inv = fms.copy()
fms.reverse()
data = [go.Scatter3d(x=self.geo[:,0] + norm_coord[vib][:,0]/nframes,
y=self.geo[:,1] + norm_coord[vib][:,1]/nframes,
z=self.geo[:,2] + norm_coord[vib][:,2]/nframes,
mode='markers',
marker={"showscale": False,
"color": self.info["color"],
"size": self.info["size"] * size / 1.0,
"showscale": False,
"opacity": 1.0,
"line": {
"width": 2,
"color": "black"
}
})]
for i in range(len(bonds)):
midx = (self.geo[bonds[i][0]][0] + self.norm[vib][bonds[i][0],0]/(nframes) + self.geo[bonds[i][1]][0] + self.norm[vib][bonds[i][1],0]/(frame)) / 2
midy = (self.geo[bonds[i][0]][1] + self.norm[vib][bonds[i][0],1]/(nframes) + self.geo[bonds[i][1]][1] + self.norm[vib][bonds[i][1],1]/(frame)) / 2
midz = (self.geo[bonds[i][0]][2] + self.norm[vib][bonds[i][0],2]/(nframes) + self.geo[bonds[i][1]][2] + self.norm[vib][bonds[i][1],2]/(frame)) / 2
bond_color_1= atoms_colors[self.sym[bonds[i][0]]][0]
bond_color_2= atoms_colors[self.sym[bonds[i][1]]][0]
bond_x_1 = [self.geo[:,0][bonds[i][0]] + self.norm[vib][bonds[i][0],0]/(frame), midx]
bond_y_1 = [self.geo[:,1][bonds[i][0]] + self.norm[vib][bonds[i][0],1]/(frame), midy]
bond_z_1 = [self.geo[:,2][bonds[i][0]] + self.norm[vib][bonds[i][0],2]/(frame), midz]
bond_x_2 = [self.geo[:,0][bonds[i][1]] + self.norm[vib][bonds[i][1],0]/(frame), midx]
bond_y_2 = [self.geo[:,1][bonds[i][1]] + self.norm[vib][bonds[i][1],1]/(frame), midy]
bond_z_2 = [self.geo[:,2][bonds[i][1]] + self.norm[vib][bonds[i][1],2]/(frame), midz]
# midx = (self.geo[bonds[i][0]][0] + self.geo[bonds[i][1]][0]) / 2
# midy = (self.geo[bonds[i][0]][1] + self.geo[bonds[i][1]][1]) / 2
# midz = (self.geo[bonds[i][0]][2] + self.geo[bonds[i][1]][2]) / 2
# bond_color_1= atoms_colors[self.sym[bonds[i][0]]][0]
# bond_color_2= atoms_colors[self.sym[bonds[i][1]]][0]
# bond_x_1 = [self.geo[bonds[i][0]][0], midx]
# bond_y_1 = [self.geo[bonds[i][0]][1], midy]
# bond_z_1 = [self.geo[bonds[i][0]][2], midz]
# bond_x_2 = [self.geo[bonds[i][1]][0], midx]
# bond_y_2 = [self.geo[bonds[i][1]][1], midy]
# bond_z_2 = [self.geo[bonds[i][1]][2], midz]
data.append(go.Scatter3d(
x=bond_x_1,
y=bond_y_1,
z=bond_z_1,
mode="lines",
line={
"color": bond_color_1,
"width": 7
},
))
data.append(go.Scatter3d(
x=bond_x_2,
y=bond_y_2,
z=bond_z_2,
mode="lines",
line={
"color": bond_color_2,
"width": 7
},
))
fig = go.Figure(data=data,
layout=go.Layout(
scene = {'xaxis': {'range': [self.geo[:,0].min() -2, self.geo[:,0].max() + 2], 'autorange': False},
'yaxis': {'range': [self.geo[:,1].min() -2, self.geo[:,1].max() + 2], 'autorange': False},
'zaxis': {'range': [self.geo[:,2].min() -2, self.geo[:,2].max() + 2], 'autorange': False}},
title=F"Frequency: {self.frequencies[vib].real:.2f} 1/cm",
updatemenus=[dict(
type="buttons",
buttons=[dict(label="Play",
method="animate",
args=[None,{"frame": {"duration": 0, "redraw": True}}]),
{"args": [[None], {"frame": {"duration": 0, "redraw": False},
"mode": "immediate",
"transition": {"duration": 0}}],
"label": "Stop",
"method": "animate"}
])]),
frames = fms + fms_inv + fms + fms_inv + fms + fms_inv + fms + fms_inv + fms + fms_inv
)
#layout = go.layout.Template(layout=go.Layout(title_font=dict(family="Rockwell", size=24)))
fig.update_layout(scene_xaxis_showticklabels=False,
scene_yaxis_showticklabels=False,
scene_zaxis_showticklabels=False,
dragmode="orbit",
width=size * 500,
height=size * 500,
template="plotly_white",
autosize=True,
showlegend=False,
hovermode=False,
xaxis=dict(autorange=True, showgrid=False, ticks='', showticklabels=False),
yaxis=dict(autorange=True, showgrid=False, ticks='', showticklabels=False),
scene={
"xaxis": {
"range": (self.geo[:,0].min() -2, self.geo[:,0].max() + 2),
"showgrid": False,
"zeroline": False,
"showline": False,
"title": "",
"ticks": '',
"showticklabels": False,
"showspikes" : False
},
"yaxis": {
"range": (self.geo[:,1].min() -2, self.geo[:,1].max() + 2),
"showgrid": False,
"zeroline": False,
"showline": False,
"title": "",
"ticks": '',
"showticklabels": False,
"showspikes": False
},
"zaxis": {
"range": (self.geo[:,2].min() -2, self.geo[:,2].max() + 2),
"showgrid": False,
"zeroline": False,
"showline": False,
"title": "",
"ticks": '',
"showticklabels": False,
"showspikes": False
}
})
fig.show(config={'scrollZoom': False})
def plot(self,
cube_file,
iso=0.03,
cube_type="density",
colorscale="Blues",
size=1,
plot_geometry=True,
plot_bonds=True):
atoms_colors = blobs.get_colors()
cube, meta = cube_to_array(cube_file)
self.meta = meta
X, Y, Z = np.mgrid[:cube.shape[0], :cube.shape[1], :cube.shape[2]]
data = []
vol_data = go.Isosurface(x=X.flatten(),
y=Y.flatten(),
z=Z.flatten(),
value=cube.flatten(),
showscale=False,
surface_count=2,
isomax=iso,
isomin=iso,
opacity=0.2,
colorscale=colorscale)
data.append(vol_data)
if cube_type == "orbital":
vol_data_neg = go.Isosurface(x=X.flatten(),
y=Y.flatten(),
z=Z.flatten(),
value=cube.flatten(),
showscale=False,
isomin=-1 * iso,
isomax=-1 * iso,
opacity=0.2,
colorscale="Reds")
data.append(vol_data_neg)
if plot_geometry == True:
geo_data = go.Scatter3d(x=self.info["x"],
y=self.info["y"],
z=self.info["z"],
mode="markers",
marker={
"showscale": False,
"color": self.info["color"],
"size": self.info["size"] * size / 1.0,
"showscale": False,
"opacity": 1.0,
"line": {
"width": 10,
"color": "black"
}
})
data.append(geo_data)
fig = go.Figure(data=data)
if plot_bonds == True:
bonds = build_bond_list(self.geometry.geometry().np)
for i in range(len(bonds)):
midx = (self.info["x"][bonds[i][0]] + self.info["x"][bonds[i][1]]) / 2
midy = (self.info["y"][bonds[i][0]] + self.info["y"][bonds[i][1]]) / 2
midz = (self.info["z"][bonds[i][0]] + self.info["z"][bonds[i][1]]) / 2
bond_color_1= atoms_colors[self.info["sym"][bonds[i][0]]][0]
bond_color_2= atoms_colors[self.info["sym"][bonds[i][1]]][0]
bond_x_1 = [self.info["x"][bonds[i][0]], midx]
bond_y_1 = [self.info["y"][bonds[i][0]], midy]
bond_z_1 = [self.info["z"][bonds[i][0]], midz]
bond_x_2 = [self.info["x"][bonds[i][1]], midx]
bond_y_2 = [self.info["y"][bonds[i][1]], midy]
bond_z_2 = [self.info["z"][bonds[i][1]], midz]
fig.add_trace(
go.Scatter3d(
x=bond_x_1,
y=bond_y_1,
z=bond_z_1,
mode="lines",
line={
"color": bond_color_1,
"width": 7 * size
},
))
fig.add_trace(
go.Scatter3d(
x=bond_x_2,
y=bond_y_2,
z=bond_z_2,
mode="lines",
line={
"color": bond_color_2,
"width": 7 * size
},
))
layout = go.layout.Template(layout=go.Layout(title_font=dict(family="Rockwell", size=24)))
fig.update_layout(scene_xaxis_showticklabels=False,
scene_yaxis_showticklabels=False,
scene_zaxis_showticklabels=False,
dragmode="orbit",
width=size * 500,
height=size * 500,
template="plotly_white",
autosize=True,
showlegend=False,
hovermode=False,
xaxis=dict(autorange=True, showgrid=False, ticks='', showticklabels=False),
yaxis=dict(autorange=True, showgrid=False, ticks='', showticklabels=False),
scene={
"xaxis": {
"autorange": True,
"showgrid": False,
"zeroline": False,
"showline": False,
"title": "",
"ticks": '',
"showticklabels": False,
"showbackground": False,
"showspikes" : False
},
"yaxis": {
"autorange": True,
"showgrid": False,
"zeroline": False,
"showline": False,
"title": "",
"ticks": '',
"showticklabels": False,
"showbackground": False,
"showspikes": False
},
"zaxis": {
"autorange": True,
"showgrid": False,
"zeroline": False,
"showline": False,
"title": "",
"ticks": '',
"showbackground": False,
"showticklabels": False,
"showspikes": False
}
})
fig.show(config={'scrollZoom': False})