# ##### 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)