Skip to content
Snippets Groups Projects
Commit 0675d3c1 authored by moritz.buchhorn's avatar moritz.buchhorn
Browse files

Start molecule viewer functionality

parent 79fbc521
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
04-dft/atom_properties.py 0 → 100644
+ 292
− 0
View file @ 0675d3c1
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 27 11:51:18 2024
@author: benjaminlear
Adapted by M.Buchhorn, thank you Ben!
"""
atom_colors = [
"#000000", # 0 Unknown
"#dddddd", # 1 H
"cyan", # 2 He
"violet", # 3 Li
"#B22222", # 4 Be
"beige", # 5 B
"#444444", # 6 C
"blue", # 7 N
"red", # 8 O
"green", # 9 F
"cyan", # 10 Ne
"#FF1493", # 11 Na
"#A52A2A", # 12 Mg
"#800080", # 13 Al
"#D2691E", # 14 Si
"#228B22", # 15 P
"yellow", # 16 S
"green", # 17 Cl
"cyan", # 18 Ar
"#0000CD", # 19 K
"#8B4513", # 20 Ca
"#8FBC8F", # 21 Sc
"#B8860B", # 22 Ti
"#4682B4", # 23 V
"#B22222", # 24 Cr
"#2E8B57", # 25 Mn
"#FFD700", # 26 Fe
"#DAA520", # 27 Co
"#A52A2A", # 28 Ni
"#4169E1", # 29 Cu
"#708090", # 30 Zn
"#C0C0C0", # 31 Ga
"#808000", # 32 Ge
"#00FF00", # 33 As
"#00CED1", # 34 Se
"#0000FF", # 35 Br
"cyan", # 36 Kr
"#8A2BE2", # 37 Rb
"#8B4513", # 38 Sr
"#9400D3", # 39 Y
"#FF4500", # 40 Zr
"#4682B4", # 41 Nb
"#B22222", # 42 Mo
"#FFD700", # 43 Tc
"#A52A2A", # 44 Ru
"#228B22", # 45 Rh
"#8B4513", # 46 Pd
"#00CED1", # 47 Ag
"#696969", # 48 Cd
"#C0C0C0", # 49 In
"#808000", # 50 Sn
"#228B22", # 51 Sb
"#D2691E", # 52 Te
"#00FF00", # 53 I
"cyan", # 54 Xe
"#8A2BE2", # 55 Cs
"#8B4513", # 56 Ba
"#FF4500", # 57 La
"#FF1493", # 58 Ce
"#9400D3", # 59 Pr
"#4682B4", # 60 Nd
"#DAA520", # 61 Pm
"#B22222", # 62 Sm
"#228B22", # 63 Eu
"#A52A2A", # 64 Gd
"#B8860B", # 65 Tb
"#8FBC8F", # 66 Dy
"#4682B4", # 67 Ho
"#DAA520", # 68 Er
"#B22222", # 69 Tm
"#228B22", # 70 Yb
"#FF4500", # 71 Lu
"#A52A2A", # 72 Hf
"#4682B4", # 73 Ta
"#DAA520", # 74 W
]
atom_symbols = [
"unk", # 0
"H", # 1
"He", # 2
"Li", # 3
"Be", # 4
"B", # 5
"C", # 6
"N", # 7
"O", # 8
"F", # 9
"Ne", # 10
"Na", # 11
"Mg", # 12
"Al", # 13
"Si", # 14
"P", # 15
"S", # 16
"Cl", # 17
"Ar", # 18
"K", # 19
"Ca", # 20
"Sc", # 21
"Ti", # 22
"V", # 23
"Cr", # 24
"Mn", # 25
"Fe", # 26
"Co", # 27
"Ni", # 28
"Cu", # 29
"Zn", # 30
"Ga", # 31
"Ge", # 32
"As", # 33
"Se", # 34
"Br", # 35
"Kr", # 36
"Rb", # 37
"Sr", # 38
"Y", # 39
"Zr", # 40
"Nb", # 41
"Mo", # 42
"Tc", # 43
"Ru", # 44
"Rh", # 45
"Pd", # 46
"Ag", # 47
"Cd", # 48
"In", # 49
"Sn", # 50
"Sb", # 51
"Te", # 52
"I", # 53
"Xe", # 54
"Cs", # 55
"Ba", # 56
"La", # 57
"Ce", # 58
"Pr", # 59
"Nd", # 60
"Pm", # 61
"Sm", # 62
"Eu", # 63
"Gd", # 64
"Tb", # 65
"Dy", # 66
"Ho", # 67
"Er", # 68
"Tm", # 69
"Yb", # 70
"Lu", # 71
"Hf", # 72
"Ta", # 73
"W", # 74
"Re", # 75
"Os", # 76
"Ir", # 77
"Pt", # 78
"Au", # 79
"Hg", # 80
"Tl", # 81
"Pb", # 82
"Bi", # 83
"Po", # 84
"At", # 85
"Rn", # 86
"Fr", # 87
"Ra", # 88
"Ac", # 89
"Th", # 90
"Pa", # 91
"U", # 92
"Np", # 93
"Pu", # 94
"Am", # 95
"Cm", # 96
"Bk", # 97
"Cf", # 98
"Es", # 99
"Fm", # 100
"Md", # 101
"No", # 102
"Lr", # 103
"Rf", # 104
"Db", # 105
"Sg", # 106
"Bh", # 107
"Hs", # 108
"Mt", # 109
"Ds", # 110
"Rg", # 111
"Cn", # 112
"Nh", # 113
"Fl", # 114
"Mc", # 115
"Lv", # 116
"Ts", # 117
"Og", # 118
]
vdw_radii = [
1.70, # 0 Unknown, same as Carbon
1.20, # 1 H
1.40, # 2 He
1.82, # 3 Li
1.53, # 4 Be
1.92, # 5 B
1.70, # 6 C
1.55, # 7 N
1.52, # 8 O
1.47, # 9 F
1.54, # 10 Ne
2.27, # 11 Na
1.73, # 12 Mg
1.84, # 13 Al
2.10, # 14 Si
1.80, # 15 P
1.80, # 16 S
1.75, # 17 Cl
1.88, # 18 Ar
2.75, # 19 K
2.31, # 20 Ca
2.11, # 21 Sc
2.00, # 22 Ti
2.00, # 23 V
2.00, # 24 Cr
2.00, # 25 Mn
2.00, # 26 Fe
2.00, # 27 Co
1.63, # 28 Ni
1.40, # 29 Cu
1.39, # 30 Zn
1.87, # 31 Ga
2.11, # 32 Ge
1.85, # 33 As
1.90, # 34 Se
1.85, # 35 Br
2.02, # 36 Kr
3.03, # 37 Rb
2.49, # 38 Sr
2.19, # 39 Y
2.06, # 40 Zr
2.00, # 41 Nb
2.00, # 42 Mo
2.00, # 43 Tc
2.00, # 44 Ru
2.00, # 45 Rh
2.00, # 46 Pd
1.72, # 47 Ag
1.58, # 48 Cd
1.93, # 49 In
2.17, # 50 Sn
2.00, # 51 Sb
2.06, # 52 Te
1.98, # 53 I
2.16, # 54 Xe
3.43, # 55 Cs
2.68, # 56 Ba
2.50, # 57 La
2.48, # 58 Ce
2.47, # 59 Pr
2.45, # 60 Nd
2.43, # 61 Pm
2.42, # 62 Sm
2.40, # 63 Eu
2.38, # 64 Gd
2.37, # 65 Tb
2.35, # 66 Dy
2.33, # 67 Ho
2.32, # 68 Er
2.30, # 69 Tm
2.28, # 70 Yb
2.27, # 71 Lu
2.16, # 72 Hf
2.09, # 73 Ta
2.02, # 74 W
]
vdw_radii_dict = dict(zip(atom_symbols, vdw_radii))
atom_colors_dict = dict(zip(atom_symbols, atom_colors))
\ No newline at end of file
04-dft/support.py
+ 55
− 2
View file @ 0675d3c1
import numpy as np
import plotly.graph_objects as go
import atom_properties as atomp
class XYZ:
sphere_mode = "ball"
def __init__(self, file: str):
"""
Reads in files with the structure 'element x y z' and returns
......@@ -24,4 +27,54 @@ class XYZ:
@param j: Integer. Index of the second atom.
@return: Float. The bond length between the two atoms.
"""
return np.linalg.norm(self.xyz[i] - self.xyz[j])
\ No newline at end of file
return np.linalg.norm(self.xyz[i] - self.xyz[j])
def make_fibonacci_sphere(self, center, radius=0.1, resolution = 32):
"""Return cartesian coordinates of points evenly distributed
on the surface of a sphere"""
num_points = resolution
indices = np.arange(0, num_points, dtype=float) + 0.5
phi = np.arccos(1 - 2*indices/num_points)
theta = np.pi * (1 + 5**0.5) * indices
x = radius * np.sin(phi) * np.cos(theta) + center[0]
y = radius * np.sin(phi) * np.sin(theta) + center[1]
z = radius * np.cos(phi) + center[2]
return x, y, z
def make_atom_mesh(self, i: int) -> go.Mesh3d:
"""
"""
if self.sphere_mode == "vdw": # check to see if we are going to use the vdw radii
radius = atomp.vdw_radii_dict[self.elements[i]] # if so, then reassign the value
elif self.sphere_mode == "ball":
radius = atomp.vdw_radii_dict[self.elements[i]] * 0.2
print(atomp.vdw_radii_dict[self.elements[i]])
x, y, z = self.make_fibonacci_sphere(self.xyz[i], radius = radius)
atom_trace = go.Mesh3d(
x=x,
y=y,
z=z,
color=atomp.atom_colors_dict[self.elements[i]],
opacity=1,
alphahull=0,
name=f'{self.elements[i]}',
hoverinfo='name', # Only show the name on hover
)
return atom_trace
def get_molecular_viewer(self) -> go.Figure:
"""
Returns a plotly figure with the molecular structure.
"""
fig = go.Figure()
for i in range(len(self.elements)):
fig.add_trace(self.make_atom_mesh(i))
return fig
\ No newline at end of file
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment