Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
# ##### BEGIN GPL LICENSE BLOCK #####
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# ##### END GPL LICENSE BLOCK #####
import bpy
import io
import math
import os
import copy
from math import pi, cos, sin, tan, sqrt
from mathutils import Vector, Matrix
from copy import copy
# -----------------------------------------------------------------------------
# Atom, stick and element data
# This is a list that contains some data of all possible elements. The structure
# is as follows:
#
# 1, "Hydrogen", "H", [0.0,0.0,1.0], 0.32, 0.32, 0.32 , -1 , 1.54 means
#
# No., name, short name, color, radius (used), radius (covalent), radius (atomic),
#
# charge state 1, radius (ionic) 1, charge state 2, radius (ionic) 2, ... all
# charge states for any atom are listed, if existing.
# The list is fixed and cannot be changed ... (see below)
ATOM_CLUSTER_ELEMENTS_DEFAULT = (
( 1, "Hydrogen", "H", ( 1.0, 1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
( 2, "Helium", "He", ( 0.85, 1.0, 1.0), 0.93, 0.93, 0.49 ),
( 3, "Lithium", "Li", ( 0.8, 0.50, 1.0), 1.23, 1.23, 2.05 , 1 , 0.68 ),
( 4, "Beryllium", "Be", ( 0.76, 1.0, 0.0), 0.90, 0.90, 1.40 , 1 , 0.44 , 2 , 0.35 ),
( 5, "Boron", "B", ( 1.0, 0.70, 0.70), 0.82, 0.82, 1.17 , 1 , 0.35 , 3 , 0.23 ),
( 6, "Carbon", "C", ( 0.56, 0.56, 0.56), 0.77, 0.77, 0.91 , -4 , 2.60 , 4 , 0.16 ),
( 7, "Nitrogen", "N", ( 0.18, 0.31, 0.97), 0.75, 0.75, 0.75 , -3 , 1.71 , 1 , 0.25 , 3 , 0.16 , 5 , 0.13 ),
( 8, "Oxygen", "O", ( 1.0, 0.05, 0.05), 0.73, 0.73, 0.65 , -2 , 1.32 , -1 , 1.76 , 1 , 0.22 , 6 , 0.09 ),
( 9, "Fluorine", "F", ( 0.56, 0.87, 0.31), 0.72, 0.72, 0.57 , -1 , 1.33 , 7 , 0.08 ),
(10, "Neon", "Ne", ( 0.70, 0.89, 0.96), 0.71, 0.71, 0.51 , 1 , 1.12 ),
(11, "Sodium", "Na", ( 0.67, 0.36, 0.94), 1.54, 1.54, 2.23 , 1 , 0.97 ),
(12, "Magnesium", "Mg", ( 0.54, 1.0, 0.0), 1.36, 1.36, 1.72 , 1 , 0.82 , 2 , 0.66 ),
(13, "Aluminium", "Al", ( 0.74, 0.65, 0.65), 1.18, 1.18, 1.82 , 3 , 0.51 ),
(14, "Silicon", "Si", ( 0.94, 0.78, 0.62), 1.11, 1.11, 1.46 , -4 , 2.71 , -1 , 3.84 , 1 , 0.65 , 4 , 0.42 ),
(15, "Phosphorus", "P", ( 1.0, 0.50, 0.0), 1.06, 1.06, 1.23 , -3 , 2.12 , 3 , 0.44 , 5 , 0.35 ),
(16, "Sulfur", "S", ( 1.0, 1.0, 0.18), 1.02, 1.02, 1.09 , -2 , 1.84 , 2 , 2.19 , 4 , 0.37 , 6 , 0.30 ),
(17, "Chlorine", "Cl", ( 0.12, 0.94, 0.12), 0.99, 0.99, 0.97 , -1 , 1.81 , 5 , 0.34 , 7 , 0.27 ),
(18, "Argon", "Ar", ( 0.50, 0.81, 0.89), 0.98, 0.98, 0.88 , 1 , 1.54 ),
(19, "Potassium", "K", ( 0.56, 0.25, 0.83), 2.03, 2.03, 2.77 , 1 , 0.81 ),
(20, "Calcium", "Ca", ( 0.23, 1.0, 0.0), 1.74, 1.74, 2.23 , 1 , 1.18 , 2 , 0.99 ),
(21, "Scandium", "Sc", ( 0.90, 0.90, 0.90), 1.44, 1.44, 2.09 , 3 , 0.73 ),
(22, "Titanium", "Ti", ( 0.74, 0.76, 0.78), 1.32, 1.32, 2.00 , 1 , 0.96 , 2 , 0.94 , 3 , 0.76 , 4 , 0.68 ),
(23, "Vanadium", "V", ( 0.65, 0.65, 0.67), 1.22, 1.22, 1.92 , 2 , 0.88 , 3 , 0.74 , 4 , 0.63 , 5 , 0.59 ),
(24, "Chromium", "Cr", ( 0.54, 0.6, 0.78), 1.18, 1.18, 1.85 , 1 , 0.81 , 2 , 0.89 , 3 , 0.63 , 6 , 0.52 ),
(25, "Manganese", "Mn", ( 0.61, 0.47, 0.78), 1.17, 1.17, 1.79 , 2 , 0.80 , 3 , 0.66 , 4 , 0.60 , 7 , 0.46 ),
(26, "Iron", "Fe", ( 0.87, 0.4, 0.2), 1.17, 1.17, 1.72 , 2 , 0.74 , 3 , 0.64 ),
(27, "Cobalt", "Co", ( 0.94, 0.56, 0.62), 1.16, 1.16, 1.67 , 2 , 0.72 , 3 , 0.63 ),
(28, "Nickel", "Ni", ( 0.31, 0.81, 0.31), 1.15, 1.15, 1.62 , 2 , 0.69 ),
(29, "Copper", "Cu", ( 0.78, 0.50, 0.2), 1.17, 1.17, 1.57 , 1 , 0.96 , 2 , 0.72 ),
(30, "Zinc", "Zn", ( 0.49, 0.50, 0.69), 1.25, 1.25, 1.53 , 1 , 0.88 , 2 , 0.74 ),
(31, "Gallium", "Ga", ( 0.76, 0.56, 0.56), 1.26, 1.26, 1.81 , 1 , 0.81 , 3 , 0.62 ),
(32, "Germanium", "Ge", ( 0.4, 0.56, 0.56), 1.22, 1.22, 1.52 , -4 , 2.72 , 2 , 0.73 , 4 , 0.53 ),
(33, "Arsenic", "As", ( 0.74, 0.50, 0.89), 1.20, 1.20, 1.33 , -3 , 2.22 , 3 , 0.58 , 5 , 0.46 ),
(34, "Selenium", "Se", ( 1.0, 0.63, 0.0), 1.16, 1.16, 1.22 , -2 , 1.91 , -1 , 2.32 , 1 , 0.66 , 4 , 0.50 , 6 , 0.42 ),
(35, "Bromine", "Br", ( 0.65, 0.16, 0.16), 1.14, 1.14, 1.12 , -1 , 1.96 , 5 , 0.47 , 7 , 0.39 ),
(36, "Krypton", "Kr", ( 0.36, 0.72, 0.81), 1.31, 1.31, 1.24 ),
(37, "Rubidium", "Rb", ( 0.43, 0.18, 0.69), 2.16, 2.16, 2.98 , 1 , 1.47 ),
(38, "Strontium", "Sr", ( 0.0, 1.0, 0.0), 1.91, 1.91, 2.45 , 2 , 1.12 ),
(39, "Yttrium", "Y", ( 0.58, 1.0, 1.0), 1.62, 1.62, 2.27 , 3 , 0.89 ),
(40, "Zirconium", "Zr", ( 0.58, 0.87, 0.87), 1.45, 1.45, 2.16 , 1 , 1.09 , 4 , 0.79 ),
(41, "Niobium", "Nb", ( 0.45, 0.76, 0.78), 1.34, 1.34, 2.08 , 1 , 1.00 , 4 , 0.74 , 5 , 0.69 ),
(42, "Molybdenum", "Mo", ( 0.32, 0.70, 0.70), 1.30, 1.30, 2.01 , 1 , 0.93 , 4 , 0.70 , 6 , 0.62 ),
(43, "Technetium", "Tc", ( 0.23, 0.61, 0.61), 1.27, 1.27, 1.95 , 7 , 0.97 ),
(44, "Ruthenium", "Ru", ( 0.14, 0.56, 0.56), 1.25, 1.25, 1.89 , 4 , 0.67 ),
(45, "Rhodium", "Rh", ( 0.03, 0.49, 0.54), 1.25, 1.25, 1.83 , 3 , 0.68 ),
(46, "Palladium", "Pd", ( 0.0, 0.41, 0.52), 1.28, 1.28, 1.79 , 2 , 0.80 , 4 , 0.65 ),
(47, "Silver", "Ag", ( 0.75, 0.75, 0.75), 1.34, 1.34, 1.75 , 1 , 1.26 , 2 , 0.89 ),
(48, "Cadmium", "Cd", ( 1.0, 0.85, 0.56), 1.48, 1.48, 1.71 , 1 , 1.14 , 2 , 0.97 ),
(49, "Indium", "In", ( 0.65, 0.45, 0.45), 1.44, 1.44, 2.00 , 3 , 0.81 ),
(50, "Tin", "Sn", ( 0.4, 0.50, 0.50), 1.41, 1.41, 1.72 , -4 , 2.94 , -1 , 3.70 , 2 , 0.93 , 4 , 0.71 ),
(51, "Antimony", "Sb", ( 0.61, 0.38, 0.70), 1.40, 1.40, 1.53 , -3 , 2.45 , 3 , 0.76 , 5 , 0.62 ),
(52, "Tellurium", "Te", ( 0.83, 0.47, 0.0), 1.36, 1.36, 1.42 , -2 , 2.11 , -1 , 2.50 , 1 , 0.82 , 4 , 0.70 , 6 , 0.56 ),
(53, "Iodine", "I", ( 0.58, 0.0, 0.58), 1.33, 1.33, 1.32 , -1 , 2.20 , 5 , 0.62 , 7 , 0.50 ),
(54, "Xenon", "Xe", ( 0.25, 0.61, 0.69), 1.31, 1.31, 1.24 ),
(55, "Caesium", "Cs", ( 0.34, 0.09, 0.56), 2.35, 2.35, 3.35 , 1 , 1.67 ),
(56, "Barium", "Ba", ( 0.0, 0.78, 0.0), 1.98, 1.98, 2.78 , 1 , 1.53 , 2 , 1.34 ),
(57, "Lanthanum", "La", ( 0.43, 0.83, 1.0), 1.69, 1.69, 2.74 , 1 , 1.39 , 3 , 1.06 ),
(58, "Cerium", "Ce", ( 1.0, 1.0, 0.78), 1.65, 1.65, 2.70 , 1 , 1.27 , 3 , 1.03 , 4 , 0.92 ),
(59, "Praseodymium", "Pr", ( 0.85, 1.0, 0.78), 1.65, 1.65, 2.67 , 3 , 1.01 , 4 , 0.90 ),
(60, "Neodymium", "Nd", ( 0.78, 1.0, 0.78), 1.64, 1.64, 2.64 , 3 , 0.99 ),
(61, "Promethium", "Pm", ( 0.63, 1.0, 0.78), 1.63, 1.63, 2.62 , 3 , 0.97 ),
(62, "Samarium", "Sm", ( 0.56, 1.0, 0.78), 1.62, 1.62, 2.59 , 3 , 0.96 ),
(63, "Europium", "Eu", ( 0.38, 1.0, 0.78), 1.85, 1.85, 2.56 , 2 , 1.09 , 3 , 0.95 ),
(64, "Gadolinium", "Gd", ( 0.27, 1.0, 0.78), 1.61, 1.61, 2.54 , 3 , 0.93 ),
(65, "Terbium", "Tb", ( 0.18, 1.0, 0.78), 1.59, 1.59, 2.51 , 3 , 0.92 , 4 , 0.84 ),
(66, "Dysprosium", "Dy", ( 0.12, 1.0, 0.78), 1.59, 1.59, 2.49 , 3 , 0.90 ),
(67, "Holmium", "Ho", ( 0.0, 1.0, 0.61), 1.58, 1.58, 2.47 , 3 , 0.89 ),
(68, "Erbium", "Er", ( 0.0, 0.90, 0.45), 1.57, 1.57, 2.45 , 3 , 0.88 ),
(69, "Thulium", "Tm", ( 0.0, 0.83, 0.32), 1.56, 1.56, 2.42 , 3 , 0.87 ),
(70, "Ytterbium", "Yb", ( 0.0, 0.74, 0.21), 1.74, 1.74, 2.40 , 2 , 0.93 , 3 , 0.85 ),
(71, "Lutetium", "Lu", ( 0.0, 0.67, 0.14), 1.56, 1.56, 2.25 , 3 , 0.85 ),
(72, "Hafnium", "Hf", ( 0.30, 0.76, 1.0), 1.44, 1.44, 2.16 , 4 , 0.78 ),
(73, "Tantalum", "Ta", ( 0.30, 0.65, 1.0), 1.34, 1.34, 2.09 , 5 , 0.68 ),
(74, "Tungsten", "W", ( 0.12, 0.58, 0.83), 1.30, 1.30, 2.02 , 4 , 0.70 , 6 , 0.62 ),
(75, "Rhenium", "Re", ( 0.14, 0.49, 0.67), 1.28, 1.28, 1.97 , 4 , 0.72 , 7 , 0.56 ),
(76, "Osmium", "Os", ( 0.14, 0.4, 0.58), 1.26, 1.26, 1.92 , 4 , 0.88 , 6 , 0.69 ),
(77, "Iridium", "Ir", ( 0.09, 0.32, 0.52), 1.27, 1.27, 1.87 , 4 , 0.68 ),
(78, "Platinium", "Pt", ( 0.81, 0.81, 0.87), 1.30, 1.30, 1.83 , 2 , 0.80 , 4 , 0.65 ),
(79, "Gold", "Au", ( 1.0, 0.81, 0.13), 1.34, 1.34, 1.79 , 1 , 1.37 , 3 , 0.85 ),
(80, "Mercury", "Hg", ( 0.72, 0.72, 0.81), 1.49, 1.49, 1.76 , 1 , 1.27 , 2 , 1.10 ),
(81, "Thallium", "Tl", ( 0.65, 0.32, 0.30), 1.48, 1.48, 2.08 , 1 , 1.47 , 3 , 0.95 ),
(82, "Lead", "Pb", ( 0.34, 0.34, 0.38), 1.47, 1.47, 1.81 , 2 , 1.20 , 4 , 0.84 ),
(83, "Bismuth", "Bi", ( 0.61, 0.30, 0.70), 1.46, 1.46, 1.63 , 1 , 0.98 , 3 , 0.96 , 5 , 0.74 ),
(84, "Polonium", "Po", ( 0.67, 0.36, 0.0), 1.46, 1.46, 1.53 , 6 , 0.67 ),
(85, "Astatine", "At", ( 0.45, 0.30, 0.27), 1.45, 1.45, 1.43 , -3 , 2.22 , 3 , 0.85 , 5 , 0.46 ),
(86, "Radon", "Rn", ( 0.25, 0.50, 0.58), 1.00, 1.00, 1.34 ),
(87, "Francium", "Fr", ( 0.25, 0.0, 0.4), 1.00, 1.00, 1.00 , 1 , 1.80 ),
(88, "Radium", "Ra", ( 0.0, 0.49, 0.0), 1.00, 1.00, 1.00 , 2 , 1.43 ),
(89, "Actinium", "Ac", ( 0.43, 0.67, 0.98), 1.00, 1.00, 1.00 , 3 , 1.18 ),
(90, "Thorium", "Th", ( 0.0, 0.72, 1.0), 1.65, 1.65, 1.00 , 4 , 1.02 ),
(91, "Protactinium", "Pa", ( 0.0, 0.63, 1.0), 1.00, 1.00, 1.00 , 3 , 1.13 , 4 , 0.98 , 5 , 0.89 ),
(92, "Uranium", "U", ( 0.0, 0.56, 1.0), 1.42, 1.42, 1.00 , 4 , 0.97 , 6 , 0.80 ),
(93, "Neptunium", "Np", ( 0.0, 0.50, 1.0), 1.00, 1.00, 1.00 , 3 , 1.10 , 4 , 0.95 , 7 , 0.71 ),
(94, "Plutonium", "Pu", ( 0.0, 0.41, 1.0), 1.00, 1.00, 1.00 , 3 , 1.08 , 4 , 0.93 ),
(95, "Americium", "Am", ( 0.32, 0.36, 0.94), 1.00, 1.00, 1.00 , 3 , 1.07 , 4 , 0.92 ),
(96, "Curium", "Cm", ( 0.47, 0.36, 0.89), 1.00, 1.00, 1.00 ),
(97, "Berkelium", "Bk", ( 0.54, 0.30, 0.89), 1.00, 1.00, 1.00 ),
(98, "Californium", "Cf", ( 0.63, 0.21, 0.83), 1.00, 1.00, 1.00 ),
(99, "Einsteinium", "Es", ( 0.70, 0.12, 0.83), 1.00, 1.00, 1.00 ),
(100, "Fermium", "Fm", ( 0.70, 0.12, 0.72), 1.00, 1.00, 1.00 ),
(101, "Mendelevium", "Md", ( 0.70, 0.05, 0.65), 1.00, 1.00, 1.00 ),
(102, "Nobelium", "No", ( 0.74, 0.05, 0.52), 1.00, 1.00, 1.00 ),
(103, "Lawrencium", "Lr", ( 0.78, 0.0, 0.4), 1.00, 1.00, 1.00 ),
(104, "Vacancy", "Vac", ( 0.5, 0.5, 0.5), 1.00, 1.00, 1.00),
(105, "Default", "Default", ( 1.0, 1.0, 1.0), 1.00, 1.00, 1.00),
(106, "Stick", "Stick", ( 0.5, 0.5, 0.5), 1.00, 1.00, 1.00),
)
# This list here contains all data of the elements and will be used during
# runtime. It is a list of classes.
# During executing Atomic Blender, the list will be initialized with the fixed
# data from above via the class structure below (CLASS_atom_pdb_Elements). We
# have then one fixed list (above), which will never be changed, and a list of
# classes with same data. The latter can be modified via loading a separate
# custom data file.
ATOM_CLUSTER_ELEMENTS = []
ATOM_CLUSTER_ALL_ATOMS = []
# This is the class, which stores the properties for one element.
class CLASS_atom_cluster_Elements(object):
__slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic')
def __init__(self, number, name, short_name, color, radii, radii_ionic):
self.number = number
self.name = name
self.short_name = short_name
self.color = color
self.radii = radii
self.radii_ionic = radii_ionic
# This is the class, which stores the properties of one atom.
__slots__ = ('location')
def __init__(self, location):
self.location = location
# -----------------------------------------------------------------------------
# Read atom data
def DEF_atom_read_atom_data():
for item in ATOM_CLUSTER_ELEMENTS_DEFAULT:
# All three radii into a list
radii = [item[4],item[5],item[6]]
# The handling of the ionic radii will be done later. So far, it is an
# empty list.
radii_ionic = []
li = CLASS_atom_cluster_Elements(item[0],item[1],item[2],item[3],
radii,radii_ionic)
ATOM_CLUSTER_ELEMENTS.append(li)
# -----------------------------------------------------------------------------
# Routines for shapes
def vec_in_sphere(atom_pos,size, skin):
regular = True
inner = True
inner = False
return (regular, inner)
def vec_in_parabole(atom_pos, height, diameter):
regular = True
inner = True
pz = atom_pos[2] + height/2.0
a = diameter / sqrt(4 * height)
if pz < 0.0:
return (False, False)
if px == 0.0 and py == 0.0:
return (True, True)
if py == 0.0:
y = 0.0
x = a * a * pz / px
z = x * x / (a * a)
else:
y = pz * py * a * a / (px*px + py*py)
x = y * px / py
z = (x*x + y*y) / (a * a)
if( atom_pos.length > sqrt(x*x+y*y+z*z) ):
regular = False
return (regular, inner)
def vec_in_pyramide_square(atom_pos, size, skin):
Please, if possible leave all this! The code documents the
P1 = Vector((-size/2, 0.0, -size/4))
P2 = Vector((0.0, -size/2, -size/4))
P4 = Vector((size/2, 0.0, -size/4))
P5 = Vector((0.0, size/2, -size/4))
P6 = Vector((0.0, 0.0, size/4))
# First face
v11 = P1 - P2
v12 = P1 - P6
n1 = v11.cross(v12)
g1 = -n1 * P1
# Second face
v21 = P6 - P4
v22 = P6 - P5
n2 = v21.cross(v22)
g2 = -n2 * P6
# Third face
v31 = P1 - P5
v32 = P1 - P6
n3 = v32.cross(v31)
g3 = -n3 * P1
# Forth face
v41 = P6 - P2
v42 = P2 - P4
n4 = v41.cross(v42)
g4 = -n4 * P2
# Fith face, base
v51 = P2 - P1
v52 = P2 - P4
n5 = v51.cross(v52)
g5 = -n5 * P2
distance_plane_1 = abs((n1 * atom_pos - g1)/n1.length)
on_plane_1 = (atom_pos - n1 * (distance_plane_1/n1.length)).length
distance_plane_2 = abs((n2 * atom_pos - g2)/n2.length)
on_plane_2 = (atom_pos - n2 * (distance_plane_2/n2.length)).length
distance_plane_3 = abs((n3 * atom_pos - g3)/n3.length)
on_plane_3 = (atom_pos - n3 * (distance_plane_3/n3.length)).length
distance_plane_4 = abs((n4 * atom_pos - g4)/n4.length)
on_plane_4 = (atom_pos - n4 * (distance_plane_4/n4.length)).length
distance_plane_5 = abs((n5 * atom_pos - g5)/n5.length)
on_plane_5 = (atom_pos - n5 * (distance_plane_5/n5.length)).length
regular = True
inner = True
if(atom_pos.length > on_plane_1):
regular = False
if(atom_pos.length > on_plane_2):
regular = False
if(atom_pos.length > on_plane_3):
regular = False
if(atom_pos.length > on_plane_4):
regular = False
if(atom_pos.length > on_plane_5):
regular = False
if skin == 1.0:
return (regular, inner)
size = size * (1.0 - skin)
distance_plane_1 = abs((n1 * atom_pos - g1)/n1.length)
on_plane_1 = (atom_pos - n1 * (distance_plane_1/n1.length)).length
distance_plane_2 = abs((n2 * atom_pos - g2)/n2.length)
on_plane_2 = (atom_pos - n2 * (distance_plane_2/n2.length)).length
distance_plane_3 = abs((n3 * atom_pos - g3)/n3.length)
on_plane_3 = (atom_pos - n3 * (distance_plane_3/n3.length)).length
distance_plane_4 = abs((n4 * atom_pos - g4)/n4.length)
on_plane_4 = (atom_pos - n4 * (distance_plane_4/n4.length)).length
distance_plane_5 = abs((n5 * atom_pos - g5)/n5.length)
on_plane_5 = (atom_pos - n5 * (distance_plane_5/n5.length)).length
inner = False
if(atom_pos.length > on_plane_1):
inner = True
if(atom_pos.length > on_plane_2):
inner = True
if(atom_pos.length > on_plane_3):
inner = True
if(atom_pos.length > on_plane_4):
inner = True
if(atom_pos.length > on_plane_5):
inner = True
return (regular, inner)
def vec_in_pyramide_hex_abc(atom_pos, size, skin):
a = size/2.0
#c = size/2.0*cos((30/360)*2.0*pi)
#s = size/2.0*sin((30/360)*2.0*pi)
s = size * 0.25
#h = 2.0 * (sqrt(6.0)/3.0) * c
h = 1.632993162 * c
Please, if possible leave all this! The code documents the
P1 = Vector((0.0, a, 0.0))
P2 = Vector(( -c, -s, 0.0))
P4 = Vector((0.0, 0.0, h))
C = (P1+P2+P3+P4)/4.0
P1 = P1 - C
P2 = P2 - C
P3 = P3 - C
P4 = P4 - C
# First face
v11 = P1 - P2
v12 = P1 - P4
n1 = v11.cross(v12)
g1 = -n1 * P1
# Second face
v21 = P2 - P3
v22 = P2 - P4
n2 = v21.cross(v22)
g2 = -n2 * P2
# Third face
v31 = P3 - P1
v32 = P3 - P4
n3 = v31.cross(v32)
g3 = -n3 * P3
# Forth face
v41 = P2 - P1
v42 = P2 - P3
n4 = v41.cross(v42)
g4 = -n4 * P1
"""
n1 = Vector(( -h*(a+s), c*h, c*a ))
g1 = -1/2*c*(a*h+s*h)
n2 = Vector(( 0, -2*c*h, 2*c*s ))
g2 = -1/2*c*(a*h+s*h)
n3 = Vector(( h*(a+s), c*h, a*c ))
g3 = -1/2*c*(a*h+s*h)
n4 = Vector(( 0, 0, -2*c*(s+a) ))
g4 = -1/2*h*c*(s+a)
distance_plane_1 = abs((n1 * atom_pos - g1)/n1.length)
on_plane_1 = (atom_pos - n1 * (distance_plane_1/n1.length)).length
distance_plane_2 = abs((n2 * atom_pos - g2)/n2.length)
on_plane_2 = (atom_pos - n2 * (distance_plane_2/n2.length)).length
distance_plane_3 = abs((n3 * atom_pos - g3)/n3.length)
on_plane_3 = (atom_pos - n3 * (distance_plane_3/n3.length)).length
distance_plane_4 = abs((n4 * atom_pos - g4)/n4.length)
on_plane_4 = (atom_pos - n4 * (distance_plane_4/n4.length)).length
regular = True
inner = True
if(atom_pos.length > on_plane_1):
regular = False
if(atom_pos.length > on_plane_2):
regular = False
if(atom_pos.length > on_plane_3):
regular = False
if(atom_pos.length > on_plane_4):
regular = False
if skin == 1.0:
return (regular, inner)
size = size * (1.0 - skin)
a = size/2.0
#c = size/2.0*cos((30/360)*2.0*pi)
c= size * 0.4330127020
#s = size/2.0*sin((30/360)*2.0*pi)
s = size * 0.25
#h = 2.0 * (sqrt(6.0)/3.0) * c
h = 1.632993162 * c
n1 = Vector(( -h*(a+s), c*h, c*a ))
g1 = -1/2*c*(a*h+s*h)
n2 = Vector(( 0, -2*c*h, 2*c*s ))
g2 = -1/2*c*(a*h+s*h)
n3 = Vector(( h*(a+s), c*h, a*c ))
g3 = -1/2*c*(a*h+s*h)
n4 = Vector(( 0, 0, -2*c*(s+a) ))
g4 = -1/2*h*c*(s+a)
distance_plane_1 = abs((n1 * atom_pos - g1)/n1.length)
on_plane_1 = (atom_pos - n1 * (distance_plane_1/n1.length)).length
distance_plane_2 = abs((n2 * atom_pos - g2)/n2.length)
on_plane_2 = (atom_pos - n2 * (distance_plane_2/n2.length)).length
distance_plane_3 = abs((n3 * atom_pos - g3)/n3.length)
on_plane_3 = (atom_pos - n3 * (distance_plane_3/n3.length)).length
distance_plane_4 = abs((n4 * atom_pos - g4)/n4.length)
on_plane_4 = (atom_pos - n4 * (distance_plane_4/n4.length)).length
inner = False
if(atom_pos.length > on_plane_1):
inner = True
if(atom_pos.length > on_plane_2):
inner = True
if(atom_pos.length > on_plane_3):
inner = True
if(atom_pos.length > on_plane_4):
inner = True
return (regular, inner)
def vec_in_octahedron(atom_pos,size, skin):
regular = True
inner = True
Please, if possible leave all this! The code documents the
P1 = Vector((-size/2, 0.0, 0.0))
P2 = Vector((0.0, -size/2, 0.0))
P3 = Vector((0.0, 0.0, -size/2))
P4 = Vector((size/2, 0.0, 0.0))
P5 = Vector((0.0, size/2, 0.0))
P6 = Vector((0.0, 0.0, size/2))
# First face
v11 = P2 - P1
v12 = P2 - P3
n1 = v11.cross(v12)
g1 = -n1 * P2
# Second face
v21 = P1 - P5
v22 = P1 - P3
n2 = v21.cross(v22)
# Third face
v31 = P1 - P2
v32 = P1 - P6
n3 = v31.cross(v32)
g3 = -n3 * P1
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
# Forth face
v41 = P6 - P2
v42 = P2 - P4
n4 = v41.cross(v42)
g4 = -n4 * P2
# Fith face
v51 = P2 - P3
v52 = P2 - P4
n5 = v51.cross(v52)
g5 = -n5 * P2
# Six face
v61 = P6 - P4
v62 = P6 - P5
n6 = v61.cross(v62)
g6 = -n6 * P6
# Seventh face
v71 = P5 - P4
v72 = P5 - P3
n7 = v71.cross(v72)
g7 = -n7 * P5
# Eigth face
v81 = P1 - P5
v82 = P1 - P6
n8 = v82.cross(v81)
g8 = -n8 * P1
# A much faster way for calculation:
size2 = size * size
size3 = size2 * size
n1 = Vector((-1/4, -1/4, -1/4)) * size2
g1 = -1/8 * size3
n2 = Vector((-1/4, 1/4, -1/4)) * size2
g2 = g1
n3 = Vector((-1/4, -1/4, 1/4)) * size2
g3 = g1
n4 = Vector(( 1/4, -1/4, 1/4)) * size2
g4 = g1
n5 = Vector(( 1/4, -1/4, -1/4)) * size2
g5 = g1
n6 = Vector(( 1/4, 1/4, 1/4)) * size2
g6 = g1
n7 = Vector(( 1/4, 1/4, -1/4)) * size2
g7 = g1
n8 = Vector((-1/4, 1/4, 1/4)) * size2
g8 = g1
distance_plane_1 = abs((n1 * atom_pos - g1)/n1.length)
on_plane_1 = (atom_pos - n1 * (distance_plane_1/n1.length)).length
distance_plane_2 = abs((n2 * atom_pos - g2)/n2.length)
on_plane_2 = (atom_pos - n2 * (distance_plane_2/n2.length)).length
distance_plane_3 = abs((n3 * atom_pos - g3)/n3.length)
on_plane_3 = (atom_pos - n3 * (distance_plane_3/n3.length)).length
distance_plane_4 = abs((n4 * atom_pos - g4)/n4.length)
on_plane_4 = (atom_pos - n4 * (distance_plane_4/n4.length)).length
distance_plane_5 = abs((n5 * atom_pos - g5)/n5.length)
on_plane_5 = (atom_pos - n5 * (distance_plane_5/n5.length)).length
distance_plane_6 = abs((n6 * atom_pos - g6)/n6.length)
on_plane_6 = (atom_pos - n6 * (distance_plane_6/n6.length)).length
distance_plane_7 = abs((n7 * atom_pos - g7)/n7.length)
on_plane_7 = (atom_pos - n7 * (distance_plane_7/n7.length)).length
distance_plane_8 = abs((n8 * atom_pos - g8)/n8.length)
on_plane_8 = (atom_pos - n8 * (distance_plane_8/n8.length)).length
if(atom_pos.length > on_plane_1):
regular = False
if(atom_pos.length > on_plane_2):
regular = False
if(atom_pos.length > on_plane_3):
regular = False
if(atom_pos.length > on_plane_4):
regular = False
if(atom_pos.length > on_plane_5):
regular = False
if(atom_pos.length > on_plane_6):
regular = False
if(atom_pos.length > on_plane_7):
regular = False
if(atom_pos.length > on_plane_8):
regular = False
if skin == 1.0:
return (regular, inner)
size = size * (1.0 - skin)
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
size2 = size * size
size3 = size2 * size
n1 = Vector((-1/4, -1/4, -1/4)) * size2
g1 = -1/8 * size3
n2 = Vector((-1/4, 1/4, -1/4)) * size2
g2 = g1
n3 = Vector((-1/4, -1/4, 1/4)) * size2
g3 = g1
n4 = Vector(( 1/4, -1/4, 1/4)) * size2
g4 = g1
n5 = Vector(( 1/4, -1/4, -1/4)) * size2
g5 = g1
n6 = Vector(( 1/4, 1/4, 1/4)) * size2
g6 = g1
n7 = Vector(( 1/4, 1/4, -1/4)) * size2
g7 = g1
n8 = Vector((-1/4, 1/4, 1/4)) * size2
g8 = g1
distance_plane_1 = abs((n1 * atom_pos - g1)/n1.length)
on_plane_1 = (atom_pos - n1 * (distance_plane_1/n1.length)).length
distance_plane_2 = abs((n2 * atom_pos - g2)/n2.length)
on_plane_2 = (atom_pos - n2 * (distance_plane_2/n2.length)).length
distance_plane_3 = abs((n3 * atom_pos - g3)/n3.length)
on_plane_3 = (atom_pos - n3 * (distance_plane_3/n3.length)).length
distance_plane_4 = abs((n4 * atom_pos - g4)/n4.length)
on_plane_4 = (atom_pos - n4 * (distance_plane_4/n4.length)).length
distance_plane_5 = abs((n5 * atom_pos - g5)/n5.length)
on_plane_5 = (atom_pos - n5 * (distance_plane_5/n5.length)).length
distance_plane_6 = abs((n6 * atom_pos - g6)/n6.length)
on_plane_6 = (atom_pos - n6 * (distance_plane_6/n6.length)).length
distance_plane_7 = abs((n7 * atom_pos - g7)/n7.length)
on_plane_7 = (atom_pos - n7 * (distance_plane_7/n7.length)).length
distance_plane_8 = abs((n8 * atom_pos - g8)/n8.length)
on_plane_8 = (atom_pos - n8 * (distance_plane_8/n8.length)).length
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
inner = False
if(atom_pos.length > on_plane_1):
inner = True
if(atom_pos.length > on_plane_2):
inner = True
if(atom_pos.length > on_plane_3):
inner = True
if(atom_pos.length > on_plane_4):
inner = True
if(atom_pos.length > on_plane_5):
inner = True
if(atom_pos.length > on_plane_6):
inner = True
if(atom_pos.length > on_plane_7):
inner = True
if(atom_pos.length > on_plane_8):
inner = True
return (regular, inner)
def vec_in_truncated_octahedron(atom_pos,size, skin):
regular = True
inner = True
# The normal octahedron
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
size2 = size * size
size3 = size2 * size
n1 = Vector((-1/4, -1/4, -1/4)) * size2
g1 = -1/8 * size3
n2 = Vector((-1/4, 1/4, -1/4)) * size2
g2 = g1
n3 = Vector((-1/4, -1/4, 1/4)) * size2
g3 = g1
n4 = Vector(( 1/4, -1/4, 1/4)) * size2
g4 = g1
n5 = Vector(( 1/4, -1/4, -1/4)) * size2
g5 = g1
n6 = Vector(( 1/4, 1/4, 1/4)) * size2
g6 = g1
n7 = Vector(( 1/4, 1/4, -1/4)) * size2
g7 = g1
n8 = Vector((-1/4, 1/4, 1/4)) * size2
g8 = g1
distance_plane_1 = abs((n1 * atom_pos - g1)/n1.length)
on_plane_1 = (atom_pos - n1 * (distance_plane_1/n1.length)).length
distance_plane_2 = abs((n2 * atom_pos - g2)/n2.length)
on_plane_2 = (atom_pos - n2 * (distance_plane_2/n2.length)).length
distance_plane_3 = abs((n3 * atom_pos - g3)/n3.length)
on_plane_3 = (atom_pos - n3 * (distance_plane_3/n3.length)).length
distance_plane_4 = abs((n4 * atom_pos - g4)/n4.length)
on_plane_4 = (atom_pos - n4 * (distance_plane_4/n4.length)).length
distance_plane_5 = abs((n5 * atom_pos - g5)/n5.length)
on_plane_5 = (atom_pos - n5 * (distance_plane_5/n5.length)).length
distance_plane_6 = abs((n6 * atom_pos - g6)/n6.length)
on_plane_6 = (atom_pos - n6 * (distance_plane_6/n6.length)).length
distance_plane_7 = abs((n7 * atom_pos - g7)/n7.length)
on_plane_7 = (atom_pos - n7 * (distance_plane_7/n7.length)).length
distance_plane_8 = abs((n8 * atom_pos - g8)/n8.length)
on_plane_8 = (atom_pos - n8 * (distance_plane_8/n8.length)).length
# Here are the 6 additional faces
# pp = (size/2.0) - (sqrt(2.0)/2.0) * ((size/sqrt(2.0))/3.0)
pp = size / 3.0
n_1 = Vector((1.0,0.0,0.0))
n_2 = Vector((-1.0,0.0,0.0))
n_3 = Vector((0.0,1.0,0.0))
n_4 = Vector((0.0,-1.0,0.0))
n_5 = Vector((0.0,0.0,1.0))
n_6 = Vector((0.0,0.0,-1.0))
distance_plane_1b = abs((n_1 * atom_pos + pp)/n_1.length)
on_plane_1b = (atom_pos - n_1 * (distance_plane_1b/n_1.length)).length
distance_plane_2b = abs((n_2 * atom_pos + pp)/n_2.length)
on_plane_2b = (atom_pos - n_2 * (distance_plane_2b/n_2.length)).length
distance_plane_3b = abs((n_3 * atom_pos + pp)/n_3.length)
on_plane_3b = (atom_pos - n_3 * (distance_plane_3b/n_3.length)).length
distance_plane_4b = abs((n_4 * atom_pos + pp)/n_4.length)
on_plane_4b = (atom_pos - n_4 * (distance_plane_4b/n_4.length)).length
distance_plane_5b = abs((n_5 * atom_pos + pp)/n_5.length)
on_plane_5b = (atom_pos - n_5 * (distance_plane_5b/n_5.length)).length
distance_plane_6b = abs((n_6 * atom_pos + pp)/n_6.length)
on_plane_6b = (atom_pos - n_6 * (distance_plane_6b/n_6.length)).length
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
if(atom_pos.length > on_plane_1):
regular = False
if(atom_pos.length > on_plane_2):
regular = False
if(atom_pos.length > on_plane_3):
regular = False
if(atom_pos.length > on_plane_4):
regular = False
if(atom_pos.length > on_plane_5):
regular = False
if(atom_pos.length > on_plane_6):
regular = False
if(atom_pos.length > on_plane_7):
regular = False
if(atom_pos.length > on_plane_8):
regular = False
if(atom_pos.length > on_plane_1b):
regular = False
if(atom_pos.length > on_plane_2b):
regular = False
if(atom_pos.length > on_plane_3b):
regular = False
if(atom_pos.length > on_plane_4b):
regular = False
if(atom_pos.length > on_plane_5b):
regular = False
if(atom_pos.length > on_plane_6b):
regular = False
if skin == 1.0:
return (regular, inner)
size = size * (1.0 - skin)
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
# The normal octahedron
size2 = size * size
size3 = size2 * size
n1 = Vector((-1/4, -1/4, -1/4)) * size2
g1 = -1/8 * size3
n2 = Vector((-1/4, 1/4, -1/4)) * size2
g2 = g1
n3 = Vector((-1/4, -1/4, 1/4)) * size2
g3 = g1
n4 = Vector(( 1/4, -1/4, 1/4)) * size2
g4 = g1
n5 = Vector(( 1/4, -1/4, -1/4)) * size2
g5 = g1
n6 = Vector(( 1/4, 1/4, 1/4)) * size2
g6 = g1
n7 = Vector(( 1/4, 1/4, -1/4)) * size2
g7 = g1
n8 = Vector((-1/4, 1/4, 1/4)) * size2
g8 = g1
distance_plane_1 = abs((n1 * atom_pos - g1)/n1.length)
on_plane_1 = (atom_pos - n1 * (distance_plane_1/n1.length)).length
distance_plane_2 = abs((n2 * atom_pos - g2)/n2.length)
on_plane_2 = (atom_pos - n2 * (distance_plane_2/n2.length)).length
distance_plane_3 = abs((n3 * atom_pos - g3)/n3.length)
on_plane_3 = (atom_pos - n3 * (distance_plane_3/n3.length)).length
distance_plane_4 = abs((n4 * atom_pos - g4)/n4.length)
on_plane_4 = (atom_pos - n4 * (distance_plane_4/n4.length)).length
distance_plane_5 = abs((n5 * atom_pos - g5)/n5.length)
on_plane_5 = (atom_pos - n5 * (distance_plane_5/n5.length)).length
distance_plane_6 = abs((n6 * atom_pos - g6)/n6.length)
on_plane_6 = (atom_pos - n6 * (distance_plane_6/n6.length)).length
distance_plane_7 = abs((n7 * atom_pos - g7)/n7.length)
on_plane_7 = (atom_pos - n7 * (distance_plane_7/n7.length)).length
distance_plane_8 = abs((n8 * atom_pos - g8)/n8.length)
on_plane_8 = (atom_pos - n8 * (distance_plane_8/n8.length)).length
# Here are the 6 additional faces
# pp = (size/2.0) - (sqrt(2.0)/2.0) * ((size/sqrt(2.0))/3.0)
pp = size / 3.0
n_1 = Vector((1.0,0.0,0.0))
n_2 = Vector((-1.0,0.0,0.0))
n_3 = Vector((0.0,1.0,0.0))
n_4 = Vector((0.0,-1.0,0.0))
n_5 = Vector((0.0,0.0,1.0))
n_6 = Vector((0.0,0.0,-1.0))
distance_plane_1b = abs((n_1 * atom_pos + pp)/n_1.length)
on_plane_1b = (atom_pos - n_1 * (distance_plane_1b/n_1.length)).length
distance_plane_2b = abs((n_2 * atom_pos + pp)/n_2.length)
on_plane_2b = (atom_pos - n_2 * (distance_plane_2b/n_2.length)).length
distance_plane_3b = abs((n_3 * atom_pos + pp)/n_3.length)
on_plane_3b = (atom_pos - n_3 * (distance_plane_3b/n_3.length)).length
distance_plane_4b = abs((n_4 * atom_pos + pp)/n_4.length)
on_plane_4b = (atom_pos - n_4 * (distance_plane_4b/n_4.length)).length
distance_plane_5b = abs((n_5 * atom_pos + pp)/n_5.length)
on_plane_5b = (atom_pos - n_5 * (distance_plane_5b/n_5.length)).length
distance_plane_6b = abs((n_6 * atom_pos + pp)/n_6.length)
on_plane_6b = (atom_pos - n_6 * (distance_plane_6b/n_6.length)).length
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
inner = False
if(atom_pos.length > on_plane_1):
inner = True
if(atom_pos.length > on_plane_2):
inner = True
if(atom_pos.length > on_plane_3):
inner = True
if(atom_pos.length > on_plane_4):
inner = True
if(atom_pos.length > on_plane_5):
inner = True
if(atom_pos.length > on_plane_6):
inner = True
if(atom_pos.length > on_plane_7):
inner = True
if(atom_pos.length > on_plane_8):
inner = True
if(atom_pos.length > on_plane_1b):
inner = True
if(atom_pos.length > on_plane_2b):
inner = True
if(atom_pos.length > on_plane_3b):
inner = True
if(atom_pos.length > on_plane_4b):
inner = True
if(atom_pos.length > on_plane_5b):
inner = True
if(atom_pos.length > on_plane_6b):
inner = True
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
return (regular, inner)
# -----------------------------------------------------------------------------
# Routines for lattices
def create_hexagonal_abcabc_lattice(ctype, size, skin, lattice):
atom_number_total = 0
atom_number_drawn = 0
y_displ = 0
z_displ = 0
"""
e = (1/sqrt(2.0)) * lattice
f = sqrt(3.0/4.0) * e
df1 = (e/2.0) * tan((30.0/360.0)*2.0*pi)
df2 = (e/2.0) / cos((30.0/360.0)*2.0*pi)
g = sqrt(2.0/3.0) * e
"""
e = 0.7071067810 * lattice
f = 0.8660254038 * e
df1 = 0.2886751348 * e
df2 = 0.5773502690 * e
g = 0.8164965810 * e
if ctype == "parabolid_abc":
# size = height, skin = diameter
number_x = int(skin/(2*e))+4
number_y = int(skin/(2*f))+4
number_z = int(size/(2*g))
else:
number_x = int(size/(2*e))+4
number_y = int(size/(2*f))+4
number_z = int(size/(2*g))+1+4
for k in range(-number_z,number_z+1):
for j in range(-number_y,number_y+1):
for i in range(-number_x,number_x+1):
atom = Vector((float(i)*e,float(j)*f,float(k)*g))
if y_displ == 1:
if z_displ == 1:
else:
atom[0] -= e/2.0
if z_displ == 1:
atom[0] -= e/2.0
atom[1] += df1
if z_displ == 2:
atom[0] += 0.0
atom[1] += df2
if ctype == "sphere_hex_abc":
message = vec_in_sphere(atom, size, skin)
elif ctype == "pyramide_hex_abc":
# size = height, skin = diameter
message = vec_in_pyramide_hex_abc(atom, size, skin)
elif ctype == "parabolid_abc":
if message[0] == True and message[1] == True:
atom_add = CLASS_atom_cluster_atom(atom)
ATOM_CLUSTER_ALL_ATOMS.append(atom_add)
atom_number_total += 1
atom_number_drawn += 1
if message[0] == True and message[1] == False:
if y_displ == 1:
y_displ = 0
else:
y_displ = 1
y_displ = 0
if z_displ == 0:
z_displ = 1
elif z_displ == 1:
z_displ = 2
else:
z_displ = 0
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
return (atom_number_total, atom_number_drawn)
def create_hexagonal_abab_lattice(ctype, size, skin, lattice):
atom_number_total = 0
atom_number_drawn = 0
y_displ = "even"
z_displ = "even"
"""
e = (1/sqrt(2.0)) * lattice
f = sqrt(3.0/4.0) * e
df = (e/2.0) * tan((30.0/360.0)*2*pi)
g = sqrt(2.0/3.0) * e
"""
e = 0.7071067814 * lattice
f = 0.8660254038 * e
df = 0.2886751348 * e
g = 0.8164965810 * e
if ctype == "parabolid_ab":
# size = height, skin = diameter
number_x = int(skin/(2*e))+4
number_y = int(skin/(2*f))+4
number_z = int(size/(2*g))
else:
number_x = int(size/(2*e))+4
number_y = int(size/(2*f))+4
number_z = int(size/(2*g))+1+4
for k in range(-number_z,number_z+1):
for j in range(-number_y,number_y+1):
for i in range(-number_x,number_x+1):
atom = Vector((float(i)*e,float(j)*f,float(k)*g))
if "odd" in y_displ:
if "odd" in z_displ:
else:
atom[0] -= e/2.0
if "odd" in z_displ:
atom[0] -= e/2.0
atom[1] += df
if ctype == "sphere_hex_ab":
message = vec_in_sphere(atom, size, skin)
elif ctype == "parabolid_ab":
# size = height, skin = diameter
message = vec_in_parabole(atom, size, skin)
if message[0] == True and message[1] == True:
atom_add = CLASS_atom_cluster_atom(atom)
ATOM_CLUSTER_ALL_ATOMS.append(atom_add)
atom_number_total += 1
atom_number_drawn += 1
if message[0] == True and message[1] == False:
if "even" in y_displ:
y_displ = "odd"
else:
y_displ = "even"
y_displ = "even"
if "even" in z_displ:
z_displ = "odd"
else:
z_displ = "even"
return (atom_number_total, atom_number_drawn)
def create_square_lattice(ctype, size, skin, lattice):
atom_number_total = 0
atom_number_drawn = 0
if ctype == "parabolid_square":
# size = height, skin = diameter
number_k = int(size/(2.0*lattice))
number_j = int(skin/(2.0*lattice)) + 5
number_i = int(skin/(2.0*lattice)) + 5
else:
number_k = int(size/(2.0*lattice))
number_j = int(size/(2.0*lattice))
for j in range(-number_j,number_j+1):
for i in range(-number_i,number_i+1):
atom = Vector((float(i),float(j),float(k))) * lattice
if ctype == "sphere_square":
message = vec_in_sphere(atom, size, skin)
elif ctype == "pyramide_square":
message = vec_in_pyramide_square(atom, size, skin)
elif ctype == "parabolid_square":
# size = height, skin = diameter
elif ctype == "octahedron":
message = vec_in_octahedron(atom, size, skin)
elif ctype == "truncated_octahedron":
message = vec_in_truncated_octahedron(atom,size, skin)
if message[0] == True and message[1] == True:
atom_add = CLASS_atom_cluster_atom(atom)
ATOM_CLUSTER_ALL_ATOMS.append(atom_add)
atom_number_total += 1
atom_number_drawn += 1
if message[0] == True and message[1] == False:
return (atom_number_total, atom_number_drawn)
# -----------------------------------------------------------------------------
# Routine for the icosahedron
# Note that the icosahedron needs a special treatment since it requires a
# non-common crystal lattice. The faces are (111) facets and the geometry
# is five-fold. So far, a max size of 8217 atoms can be chosen.
# More details about icosahedron shaped clusters can be found in:
#
# 1. C. Mottet, G. Tréglia, B. Legrand, Surface Science 383 (1997) L719-L727
# 2. C. R. Henry, Surface Science Reports 31 (1998) 231-325
# The following code is a translation from an existing Fortran code into Python.
# The Fortran code has been created by Christine Mottet and translated by me
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
# Although a couple of code lines are non-typical for Python, it is best to
# leave the code as is.
#
# To do:
#
# 1. Unlimited cluster size
# 2. Skin effect
def create_icosahedron(size, lattice):
natot = int(1 + (10*size*size+15*size+11)*size/3)
x = list(range(natot+1))
y = list(range(natot+1))
z = list(range(natot+1))
xs = list(range(12+1))
ys = list(range(12+1))
zs = list(range(12+1))
xa = [[[ [] for i in range(12+1)] for j in range(12+1)] for k in range(20+1)]
ya = [[[ [] for i in range(12+1)] for j in range(12+1)] for k in range(20+1)]
za = [[[ [] for i in range(12+1)] for j in range(12+1)] for k in range(20+1)]
naret = [[ [] for i in range(12+1)] for j in range(12+1)]
nfacet = [[[ [] for i in range(12+1)] for j in range(12+1)] for k in range(12+1)]
rac2 = sqrt(2.0)
rac5 = sqrt(5.0)
tdef = (rac5+1.0)/2.0
rapp = sqrt(2.0*(1.0-tdef/(tdef*tdef+1.0)))
nats = 2 * (5*size*size+1)
nat = 13
epsi = 0.01
x[1] = 0.0
y[1] = 0.0
z[1] = 0.0
for i in range(2, 5+1):
z[i] = 0.0
y[i+4] = 0.0
x[i+8] = 0.0
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
for i in range(2, 3+1):
x[i] = tdef
x[i+2] = -tdef
x[i+4] = 1.0
x[i+6] = -1.0
y[i+8] = tdef
y[i+10] = -tdef
for i in range(2, 4+1, 2):
y[i] = 1.0
y[i+1] = -1.0
z[i+4] = tdef
z[i+5] = -tdef
z[i+8] = 1.0
z[i+9] = -1.0
xdef = rac2 / sqrt(tdef * tdef + 1)
for i in range(2, 13+1):
x[i] = x[i] * xdef / 2.0
y[i] = y[i] * xdef / 2.0
z[i] = z[i] * xdef / 2.0
if size > 1:
for n in range (2, size+1):
ifacet = 0
iaret = 0
inatf = 0
for i in range(1, 12+1):
for j in range(1, 12+1):
naret[i][j] = 0
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
nfacet[i][j][k] = 0
nl1 = 6
nl2 = 8
nl3 = 9
k1 = 0
k2 = 0
k3 = 0
k12 = 0
for i in range(1, 12+1):
nat += 1
xs[i] = n * x[i+1]
ys[i] = n * y[i+1]
zs[i] = n * z[i+1]
x[nat] = xs[i]
y[nat] = ys[i]
z[nat] = zs[i]
k1 += 1
for i in range(1, 12+1):
for j in range(2, 12+1):
if j <= i:
continue
xij = xs[j] - xs[i]
yij = ys[j] - ys[i]
zij = zs[j] - zs[i]
xij2 = xij * xij
yij2 = yij * yij
zij2 = zij * zij
dij2 = xij2 + yij2 + zij2
dssn = n * rapp / rac2
dssn2 = dssn * dssn
diffij = abs(dij2-dssn2)
if diffij >= epsi:
continue
xjk = xs[k] - xs[j]
yjk = ys[k] - ys[j]
zjk = zs[k] - zs[j]
xjk2 = xjk * xjk
yjk2 = yjk * yjk
zjk2 = zjk * zjk
djk2 = xjk2 + yjk2 + zjk2
diffjk = abs(djk2-dssn2)
if diffjk >= epsi:
continue
xik = xs[k] - xs[i]
yik = ys[k] - ys[i]
zik = zs[k] - zs[i]
xik2 = xik * xik
yik2 = yik * yik
zik2 = zik * zik
dik2 = xik2 + yik2 + zik2
diffik = abs(dik2-dssn2)
if diffik >= epsi:
continue
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
if nfacet[i][j][k] != 0:
continue
ifacet += 1
nfacet[i][j][k] = ifacet
if naret[i][j] == 0:
iaret += 1
naret[i][j] = iaret
for l in range(1,n-1+1):
nat += 1
xa[i][j][l] = xs[i]+l*(xs[j]-xs[i]) / n
ya[i][j][l] = ys[i]+l*(ys[j]-ys[i]) / n
za[i][j][l] = zs[i]+l*(zs[j]-zs[i]) / n
x[nat] = xa[i][j][l]
y[nat] = ya[i][j][l]
z[nat] = za[i][j][l]
if naret[i][k] == 0:
iaret += 1
naret[i][k] = iaret
for l in range(1, n-1+1):
nat += 1
xa[i][k][l] = xs[i]+l*(xs[k]-xs[i]) / n
ya[i][k][l] = ys[i]+l*(ys[k]-ys[i]) / n
za[i][k][l] = zs[i]+l*(zs[k]-zs[i]) / n
x[nat] = xa[i][k][l]
y[nat] = ya[i][k][l]
z[nat] = za[i][k][l]
if naret[j][k] == 0:
iaret += 1
naret[j][k] = iaret
for l in range(1, n-1+1):
nat += 1
xa[j][k][l] = xs[j]+l*(xs[k]-xs[j]) / n
ya[j][k][l] = ys[j]+l*(ys[k]-ys[j]) / n
za[j][k][l] = zs[j]+l*(zs[k]-zs[j]) / n
x[nat] = xa[j][k][l]
y[nat] = ya[j][k][l]
z[nat] = za[j][k][l]
for l in range(2, n-1+1):
for ll in range(1, l-1+1):
xf = xa[i][j][l]+ll*(xa[i][k][l]-xa[i][j][l]) / l
yf = ya[i][j][l]+ll*(ya[i][k][l]-ya[i][j][l]) / l
zf = za[i][j][l]+ll*(za[i][k][l]-za[i][j][l]) / l
nat += 1
inatf += 1
x[nat] = xf
y[nat] = yf
z[nat] = zf
k3 += 1
atom_number_total = 0
atom_number_drawn = 0
for i in range (1,natot+1):