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2020-11-20 15:33:46 +00:00
# ##### 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, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
( 2, "Helium", "He", ( 0.85, 1.0, 1.0, 1.0), 0.93, 0.93, 0.49 ),
( 3, "Lithium", "Li", ( 0.8, 0.50, 1.0, 1.0), 1.23, 1.23, 2.05 , 1 , 0.68 ),
( 4, "Beryllium", "Be", ( 0.76, 1.0, 0.0, 1.0), 0.90, 0.90, 1.40 , 1 , 0.44 , 2 , 0.35 ),
( 5, "Boron", "B", ( 1.0, 0.70, 0.70, 1.0), 0.82, 0.82, 1.17 , 1 , 0.35 , 3 , 0.23 ),
( 6, "Carbon", "C", ( 0.56, 0.56, 0.56, 1.0), 0.77, 0.77, 0.91 , -4 , 2.60 , 4 , 0.16 ),
( 7, "Nitrogen", "N", ( 0.18, 0.31, 0.97, 1.0), 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, 1.0), 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, 1.0), 0.72, 0.72, 0.57 , -1 , 1.33 , 7 , 0.08 ),
(10, "Neon", "Ne", ( 0.70, 0.89, 0.96, 1.0), 0.71, 0.71, 0.51 , 1 , 1.12 ),
(11, "Sodium", "Na", ( 0.67, 0.36, 0.94, 1.0), 1.54, 1.54, 2.23 , 1 , 0.97 ),
(12, "Magnesium", "Mg", ( 0.54, 1.0, 0.0, 1.0), 1.36, 1.36, 1.72 , 1 , 0.82 , 2 , 0.66 ),
(13, "Aluminium", "Al", ( 0.74, 0.65, 0.65, 1.0), 1.18, 1.18, 1.82 , 3 , 0.51 ),
(14, "Silicon", "Si", ( 0.94, 0.78, 0.62, 1.0), 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, 1.0), 1.06, 1.06, 1.23 , -3 , 2.12 , 3 , 0.44 , 5 , 0.35 ),
(16, "Sulfur", "S", ( 1.0, 1.0, 0.18, 1.0), 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, 1.0), 0.99, 0.99, 0.97 , -1 , 1.81 , 5 , 0.34 , 7 , 0.27 ),
(18, "Argon", "Ar", ( 0.50, 0.81, 0.89, 1.0), 0.98, 0.98, 0.88 , 1 , 1.54 ),
(19, "Potassium", "K", ( 0.56, 0.25, 0.83, 1.0), 2.03, 2.03, 2.77 , 1 , 0.81 ),
(20, "Calcium", "Ca", ( 0.23, 1.0, 0.0, 1.0), 1.74, 1.74, 2.23 , 1 , 1.18 , 2 , 0.99 ),
(21, "Scandium", "Sc", ( 0.90, 0.90, 0.90, 1.0), 1.44, 1.44, 2.09 , 3 , 0.73 ),
(22, "Titanium", "Ti", ( 0.74, 0.76, 0.78, 1.0), 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, 1.0), 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, 1.0), 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, 1.0), 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, 1.0), 1.17, 1.17, 1.72 , 2 , 0.74 , 3 , 0.64 ),
(27, "Cobalt", "Co", ( 0.94, 0.56, 0.62, 1.0), 1.16, 1.16, 1.67 , 2 , 0.72 , 3 , 0.63 ),
(28, "Nickel", "Ni", ( 0.31, 0.81, 0.31, 1.0), 1.15, 1.15, 1.62 , 2 , 0.69 ),
(29, "Copper", "Cu", ( 0.78, 0.50, 0.2, 1.0), 1.17, 1.17, 1.57 , 1 , 0.96 , 2 , 0.72 ),
(30, "Zinc", "Zn", ( 0.49, 0.50, 0.69, 1.0), 1.25, 1.25, 1.53 , 1 , 0.88 , 2 , 0.74 ),
(31, "Gallium", "Ga", ( 0.76, 0.56, 0.56, 1.0), 1.26, 1.26, 1.81 , 1 , 0.81 , 3 , 0.62 ),
(32, "Germanium", "Ge", ( 0.4, 0.56, 0.56, 1.0), 1.22, 1.22, 1.52 , -4 , 2.72 , 2 , 0.73 , 4 , 0.53 ),
(33, "Arsenic", "As", ( 0.74, 0.50, 0.89, 1.0), 1.20, 1.20, 1.33 , -3 , 2.22 , 3 , 0.58 , 5 , 0.46 ),
(34, "Selenium", "Se", ( 1.0, 0.63, 0.0, 1.0), 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, 1.0), 1.14, 1.14, 1.12 , -1 , 1.96 , 5 , 0.47 , 7 , 0.39 ),
(36, "Krypton", "Kr", ( 0.36, 0.72, 0.81, 1.0), 1.31, 1.31, 1.24 ),
(37, "Rubidium", "Rb", ( 0.43, 0.18, 0.69, 1.0), 2.16, 2.16, 2.98 , 1 , 1.47 ),
(38, "Strontium", "Sr", ( 0.0, 1.0, 0.0, 1.0), 1.91, 1.91, 2.45 , 2 , 1.12 ),
(39, "Yttrium", "Y", ( 0.58, 1.0, 1.0, 1.0), 1.62, 1.62, 2.27 , 3 , 0.89 ),
(40, "Zirconium", "Zr", ( 0.58, 0.87, 0.87, 1.0), 1.45, 1.45, 2.16 , 1 , 1.09 , 4 , 0.79 ),
(41, "Niobium", "Nb", ( 0.45, 0.76, 0.78, 1.0), 1.34, 1.34, 2.08 , 1 , 1.00 , 4 , 0.74 , 5 , 0.69 ),
(42, "Molybdenum", "Mo", ( 0.32, 0.70, 0.70, 1.0), 1.30, 1.30, 2.01 , 1 , 0.93 , 4 , 0.70 , 6 , 0.62 ),
(43, "Technetium", "Tc", ( 0.23, 0.61, 0.61, 1.0), 1.27, 1.27, 1.95 , 7 , 0.97 ),
(44, "Ruthenium", "Ru", ( 0.14, 0.56, 0.56, 1.0), 1.25, 1.25, 1.89 , 4 , 0.67 ),
(45, "Rhodium", "Rh", ( 0.03, 0.49, 0.54, 1.0), 1.25, 1.25, 1.83 , 3 , 0.68 ),
(46, "Palladium", "Pd", ( 0.0, 0.41, 0.52, 1.0), 1.28, 1.28, 1.79 , 2 , 0.80 , 4 , 0.65 ),
(47, "Silver", "Ag", ( 0.75, 0.75, 0.75, 1.0), 1.34, 1.34, 1.75 , 1 , 1.26 , 2 , 0.89 ),
(48, "Cadmium", "Cd", ( 1.0, 0.85, 0.56, 1.0), 1.48, 1.48, 1.71 , 1 , 1.14 , 2 , 0.97 ),
(49, "Indium", "In", ( 0.65, 0.45, 0.45, 1.0), 1.44, 1.44, 2.00 , 3 , 0.81 ),
(50, "Tin", "Sn", ( 0.4, 0.50, 0.50, 1.0), 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, 1.0), 1.40, 1.40, 1.53 , -3 , 2.45 , 3 , 0.76 , 5 , 0.62 ),
(52, "Tellurium", "Te", ( 0.83, 0.47, 0.0, 1.0), 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, 1.0), 1.33, 1.33, 1.32 , -1 , 2.20 , 5 , 0.62 , 7 , 0.50 ),
(54, "Xenon", "Xe", ( 0.25, 0.61, 0.69, 1.0), 1.31, 1.31, 1.24 ),
(55, "Caesium", "Cs", ( 0.34, 0.09, 0.56, 1.0), 2.35, 2.35, 3.35 , 1 , 1.67 ),
(56, "Barium", "Ba", ( 0.0, 0.78, 0.0, 1.0), 1.98, 1.98, 2.78 , 1 , 1.53 , 2 , 1.34 ),
(57, "Lanthanum", "La", ( 0.43, 0.83, 1.0, 1.0), 1.69, 1.69, 2.74 , 1 , 1.39 , 3 , 1.06 ),
(58, "Cerium", "Ce", ( 1.0, 1.0, 0.78, 1.0), 1.65, 1.65, 2.70 , 1 , 1.27 , 3 , 1.03 , 4 , 0.92 ),
(59, "Praseodymium", "Pr", ( 0.85, 1.0, 0.78, 1.0), 1.65, 1.65, 2.67 , 3 , 1.01 , 4 , 0.90 ),
(60, "Neodymium", "Nd", ( 0.78, 1.0, 0.78, 1.0), 1.64, 1.64, 2.64 , 3 , 0.99 ),
(61, "Promethium", "Pm", ( 0.63, 1.0, 0.78, 1.0), 1.63, 1.63, 2.62 , 3 , 0.97 ),
(62, "Samarium", "Sm", ( 0.56, 1.0, 0.78, 1.0), 1.62, 1.62, 2.59 , 3 , 0.96 ),
(63, "Europium", "Eu", ( 0.38, 1.0, 0.78, 1.0), 1.85, 1.85, 2.56 , 2 , 1.09 , 3 , 0.95 ),
(64, "Gadolinium", "Gd", ( 0.27, 1.0, 0.78, 1.0), 1.61, 1.61, 2.54 , 3 , 0.93 ),
(65, "Terbium", "Tb", ( 0.18, 1.0, 0.78, 1.0), 1.59, 1.59, 2.51 , 3 , 0.92 , 4 , 0.84 ),
(66, "Dysprosium", "Dy", ( 0.12, 1.0, 0.78, 1.0), 1.59, 1.59, 2.49 , 3 , 0.90 ),
(67, "Holmium", "Ho", ( 0.0, 1.0, 0.61, 1.0), 1.58, 1.58, 2.47 , 3 , 0.89 ),
(68, "Erbium", "Er", ( 0.0, 0.90, 0.45, 1.0), 1.57, 1.57, 2.45 , 3 , 0.88 ),
(69, "Thulium", "Tm", ( 0.0, 0.83, 0.32, 1.0), 1.56, 1.56, 2.42 , 3 , 0.87 ),
(70, "Ytterbium", "Yb", ( 0.0, 0.74, 0.21, 1.0), 1.74, 1.74, 2.40 , 2 , 0.93 , 3 , 0.85 ),
(71, "Lutetium", "Lu", ( 0.0, 0.67, 0.14, 1.0), 1.56, 1.56, 2.25 , 3 , 0.85 ),
(72, "Hafnium", "Hf", ( 0.30, 0.76, 1.0, 1.0), 1.44, 1.44, 2.16 , 4 , 0.78 ),
(73, "Tantalum", "Ta", ( 0.30, 0.65, 1.0, 1.0), 1.34, 1.34, 2.09 , 5 , 0.68 ),
(74, "Tungsten", "W", ( 0.12, 0.58, 0.83, 1.0), 1.30, 1.30, 2.02 , 4 , 0.70 , 6 , 0.62 ),
(75, "Rhenium", "Re", ( 0.14, 0.49, 0.67, 1.0), 1.28, 1.28, 1.97 , 4 , 0.72 , 7 , 0.56 ),
(76, "Osmium", "Os", ( 0.14, 0.4, 0.58, 1.0), 1.26, 1.26, 1.92 , 4 , 0.88 , 6 , 0.69 ),
(77, "Iridium", "Ir", ( 0.09, 0.32, 0.52, 1.0), 1.27, 1.27, 1.87 , 4 , 0.68 ),
(78, "Platinum", "Pt", ( 0.81, 0.81, 0.87, 1.0), 1.30, 1.30, 1.83 , 2 , 0.80 , 4 , 0.65 ),
(79, "Gold", "Au", ( 1.0, 0.81, 0.13, 1.0), 1.34, 1.34, 1.79 , 1 , 1.37 , 3 , 0.85 ),
(80, "Mercury", "Hg", ( 0.72, 0.72, 0.81, 1.0), 1.49, 1.49, 1.76 , 1 , 1.27 , 2 , 1.10 ),
(81, "Thallium", "Tl", ( 0.65, 0.32, 0.30, 1.0), 1.48, 1.48, 2.08 , 1 , 1.47 , 3 , 0.95 ),
(82, "Lead", "Pb", ( 0.34, 0.34, 0.38, 1.0), 1.47, 1.47, 1.81 , 2 , 1.20 , 4 , 0.84 ),
(83, "Bismuth", "Bi", ( 0.61, 0.30, 0.70, 1.0), 1.46, 1.46, 1.63 , 1 , 0.98 , 3 , 0.96 , 5 , 0.74 ),
(84, "Polonium", "Po", ( 0.67, 0.36, 0.0, 1.0), 1.46, 1.46, 1.53 , 6 , 0.67 ),
(85, "Astatine", "At", ( 0.45, 0.30, 0.27, 1.0), 1.45, 1.45, 1.43 , -3 , 2.22 , 3 , 0.85 , 5 , 0.46 ),
(86, "Radon", "Rn", ( 0.25, 0.50, 0.58, 1.0), 1.00, 1.00, 1.34 ),
(87, "Francium", "Fr", ( 0.25, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 , 1 , 1.80 ),
(88, "Radium", "Ra", ( 0.0, 0.49, 0.0, 1.0), 1.00, 1.00, 1.00 , 2 , 1.43 ),
(89, "Actinium", "Ac", ( 0.43, 0.67, 0.98, 1.0), 1.00, 1.00, 1.00 , 3 , 1.18 ),
(90, "Thorium", "Th", ( 0.0, 0.72, 1.0, 1.0), 1.65, 1.65, 1.00 , 4 , 1.02 ),
(91, "Protactinium", "Pa", ( 0.0, 0.63, 1.0, 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, 1.0), 1.42, 1.42, 1.00 , 4 , 0.97 , 6 , 0.80 ),
(93, "Neptunium", "Np", ( 0.0, 0.50, 1.0, 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, 1.0), 1.00, 1.00, 1.00 , 3 , 1.08 , 4 , 0.93 ),
(95, "Americium", "Am", ( 0.32, 0.36, 0.94, 1.0), 1.00, 1.00, 1.00 , 3 , 1.07 , 4 , 0.92 ),
(96, "Curium", "Cm", ( 0.47, 0.36, 0.89, 1.0), 1.00, 1.00, 1.00 ),
(97, "Berkelium", "Bk", ( 0.54, 0.30, 0.89, 1.0), 1.00, 1.00, 1.00 ),
(98, "Californium", "Cf", ( 0.63, 0.21, 0.83, 1.0), 1.00, 1.00, 1.00 ),
(99, "Einsteinium", "Es", ( 0.70, 0.12, 0.83, 1.0), 1.00, 1.00, 1.00 ),
(100, "Fermium", "Fm", ( 0.70, 0.12, 0.72, 1.0), 1.00, 1.00, 1.00 ),
(101, "Mendelevium", "Md", ( 0.70, 0.05, 0.65, 1.0), 1.00, 1.00, 1.00 ),
(102, "Nobelium", "No", ( 0.74, 0.05, 0.52, 1.0), 1.00, 1.00, 1.00 ),
(103, "Lawrencium", "Lr", ( 0.78, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 ),
(104, "Vacancy", "Vac", ( 0.5, 0.5, 0.5, 1.0), 1.00, 1.00, 1.00),
(105, "Default", "Default", ( 1.0, 1.0, 1.0, 1.0), 1.00, 1.00, 1.00),
(106, "Stick", "Stick", ( 0.5, 0.5, 0.5, 1.0), 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.
class CLASS_atom_cluster_atom(object):
__slots__ = ('location')
def __init__(self, location):
self.location = location
# -----------------------------------------------------------------------------
# Read atom data
def DEF_atom_read_atom_data():
del ATOM_CLUSTER_ELEMENTS[:]
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
if atom_pos.length > size/2.0:
regular = False
if atom_pos.length < (size/2.0)*(1-skin):
inner = False
return (regular, inner)
def vec_in_parabole(atom_pos, height, diameter):
regular = True
inner = True
px = atom_pos[0]
py = atom_pos[1]
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
mathemetical way of cutting a pyramide with square base.
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
"""
# A much faster way for calculation:
size2 = size * size
size3 = size2 * size
n1 = Vector((-1/4, -1/4, 1/4)) * size2
g1 = -1/16 * 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(( 0.0, 0.0, -1/2)) * size2
g5 = -1/8 * size3
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)
size2 = size * size
size3 = size2 * size
n1 = Vector((-1/4, -1/4, 1/4)) * size2
g1 = -1/16 * 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(( 0.0, 0.0, -1/2)) * size2
g5 = -1/8 * size3
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)
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
"""
Please, if possible leave all this! The code documents the
mathemetical way of cutting a tetraeder.
P1 = Vector((0.0, a, 0.0))
P2 = Vector(( -c, -s, 0.0))
P3 = 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
mathemetical way of cutting an octahedron.
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)
g2 = -n2 * P1
# Third face
v31 = P1 - P2
v32 = P1 - P6
n3 = v31.cross(v32)
g3 = -n3 * P1
# 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)
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
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
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
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)
# 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
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
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:
atom[0] += e/2.0
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":
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:
atom_number_total += 1
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
print("Atom positions calculated")
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:
atom[0] += e/2.0
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:
atom_number_total += 1
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"
print("Atom positions calculated")
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))
number_i = int(size/(2.0*lattice))
for k in range(-number_k,number_k+1):
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
message = vec_in_parabole(atom, size, skin)
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:
atom_number_total += 1
print("Atom positions calculated")
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
# (Clemens Barth).
# 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
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
for k in range (1, 12+1):
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
for k in range(3, 12+1):
if k <= j:
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
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):
atom = Vector((x[i],y[i],z[i])) * lattice
atom_add = CLASS_atom_cluster_atom(atom)
ATOM_CLUSTER_ALL_ATOMS.append(atom_add)
atom_number_total += 1
atom_number_drawn += 1
return (atom_number_total, atom_number_drawn)