mirror of http://GITTEA.DEV/O/O
1305 lines
49 KiB
Python
1305 lines
49 KiB
Python
# ##### BEGIN GPL LICENSE BLOCK #####
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#
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# This program is free software; you can redistribute it and/or
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# modify it under the terms of the GNU General Public License
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# as published by the Free Software Foundation; either version 2
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# of the License, or (at your option) any later version.
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#
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with this program; if not, write to the Free Software Foundation,
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# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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#
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# ##### END GPL LICENSE BLOCK #####
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import bpy
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import io
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import math
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import os
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import copy
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from math import pi, cos, sin, tan, sqrt
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from mathutils import Vector, Matrix
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from copy import copy
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# -----------------------------------------------------------------------------
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# Atom, stick and element data
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# This is a list that contains some data of all possible elements. The structure
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# is as follows:
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#
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# 1, "Hydrogen", "H", [0.0,0.0,1.0], 0.32, 0.32, 0.32 , -1 , 1.54 means
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#
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# No., name, short name, color, radius (used), radius (covalent), radius (atomic),
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#
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# charge state 1, radius (ionic) 1, charge state 2, radius (ionic) 2, ... all
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# charge states for any atom are listed, if existing.
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# The list is fixed and cannot be changed ... (see below)
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ATOM_CLUSTER_ELEMENTS_DEFAULT = (
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( 1, "Hydrogen", "H", ( 1.0, 1.0, 1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
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( 2, "Helium", "He", ( 0.85, 1.0, 1.0, 1.0), 0.93, 0.93, 0.49 ),
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( 3, "Lithium", "Li", ( 0.8, 0.50, 1.0, 1.0), 1.23, 1.23, 2.05 , 1 , 0.68 ),
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( 4, "Beryllium", "Be", ( 0.76, 1.0, 0.0, 1.0), 0.90, 0.90, 1.40 , 1 , 0.44 , 2 , 0.35 ),
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( 5, "Boron", "B", ( 1.0, 0.70, 0.70, 1.0), 0.82, 0.82, 1.17 , 1 , 0.35 , 3 , 0.23 ),
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( 6, "Carbon", "C", ( 0.56, 0.56, 0.56, 1.0), 0.77, 0.77, 0.91 , -4 , 2.60 , 4 , 0.16 ),
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( 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 ),
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( 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 ),
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( 9, "Fluorine", "F", ( 0.56, 0.87, 0.31, 1.0), 0.72, 0.72, 0.57 , -1 , 1.33 , 7 , 0.08 ),
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(10, "Neon", "Ne", ( 0.70, 0.89, 0.96, 1.0), 0.71, 0.71, 0.51 , 1 , 1.12 ),
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(11, "Sodium", "Na", ( 0.67, 0.36, 0.94, 1.0), 1.54, 1.54, 2.23 , 1 , 0.97 ),
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(12, "Magnesium", "Mg", ( 0.54, 1.0, 0.0, 1.0), 1.36, 1.36, 1.72 , 1 , 0.82 , 2 , 0.66 ),
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(13, "Aluminium", "Al", ( 0.74, 0.65, 0.65, 1.0), 1.18, 1.18, 1.82 , 3 , 0.51 ),
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(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 ),
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(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 ),
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(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 ),
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(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 ),
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(18, "Argon", "Ar", ( 0.50, 0.81, 0.89, 1.0), 0.98, 0.98, 0.88 , 1 , 1.54 ),
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(19, "Potassium", "K", ( 0.56, 0.25, 0.83, 1.0), 2.03, 2.03, 2.77 , 1 , 0.81 ),
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(20, "Calcium", "Ca", ( 0.23, 1.0, 0.0, 1.0), 1.74, 1.74, 2.23 , 1 , 1.18 , 2 , 0.99 ),
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(21, "Scandium", "Sc", ( 0.90, 0.90, 0.90, 1.0), 1.44, 1.44, 2.09 , 3 , 0.73 ),
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(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 ),
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(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 ),
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(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 ),
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(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 ),
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(26, "Iron", "Fe", ( 0.87, 0.4, 0.2, 1.0), 1.17, 1.17, 1.72 , 2 , 0.74 , 3 , 0.64 ),
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(27, "Cobalt", "Co", ( 0.94, 0.56, 0.62, 1.0), 1.16, 1.16, 1.67 , 2 , 0.72 , 3 , 0.63 ),
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(28, "Nickel", "Ni", ( 0.31, 0.81, 0.31, 1.0), 1.15, 1.15, 1.62 , 2 , 0.69 ),
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(29, "Copper", "Cu", ( 0.78, 0.50, 0.2, 1.0), 1.17, 1.17, 1.57 , 1 , 0.96 , 2 , 0.72 ),
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(30, "Zinc", "Zn", ( 0.49, 0.50, 0.69, 1.0), 1.25, 1.25, 1.53 , 1 , 0.88 , 2 , 0.74 ),
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(31, "Gallium", "Ga", ( 0.76, 0.56, 0.56, 1.0), 1.26, 1.26, 1.81 , 1 , 0.81 , 3 , 0.62 ),
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(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 ),
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(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 ),
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(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 ),
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(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 ),
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(36, "Krypton", "Kr", ( 0.36, 0.72, 0.81, 1.0), 1.31, 1.31, 1.24 ),
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(37, "Rubidium", "Rb", ( 0.43, 0.18, 0.69, 1.0), 2.16, 2.16, 2.98 , 1 , 1.47 ),
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(38, "Strontium", "Sr", ( 0.0, 1.0, 0.0, 1.0), 1.91, 1.91, 2.45 , 2 , 1.12 ),
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(39, "Yttrium", "Y", ( 0.58, 1.0, 1.0, 1.0), 1.62, 1.62, 2.27 , 3 , 0.89 ),
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(40, "Zirconium", "Zr", ( 0.58, 0.87, 0.87, 1.0), 1.45, 1.45, 2.16 , 1 , 1.09 , 4 , 0.79 ),
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(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 ),
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(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 ),
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(43, "Technetium", "Tc", ( 0.23, 0.61, 0.61, 1.0), 1.27, 1.27, 1.95 , 7 , 0.97 ),
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(44, "Ruthenium", "Ru", ( 0.14, 0.56, 0.56, 1.0), 1.25, 1.25, 1.89 , 4 , 0.67 ),
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(45, "Rhodium", "Rh", ( 0.03, 0.49, 0.54, 1.0), 1.25, 1.25, 1.83 , 3 , 0.68 ),
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(46, "Palladium", "Pd", ( 0.0, 0.41, 0.52, 1.0), 1.28, 1.28, 1.79 , 2 , 0.80 , 4 , 0.65 ),
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(47, "Silver", "Ag", ( 0.75, 0.75, 0.75, 1.0), 1.34, 1.34, 1.75 , 1 , 1.26 , 2 , 0.89 ),
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(48, "Cadmium", "Cd", ( 1.0, 0.85, 0.56, 1.0), 1.48, 1.48, 1.71 , 1 , 1.14 , 2 , 0.97 ),
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(49, "Indium", "In", ( 0.65, 0.45, 0.45, 1.0), 1.44, 1.44, 2.00 , 3 , 0.81 ),
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(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 ),
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(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 ),
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(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 ),
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(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 ),
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(54, "Xenon", "Xe", ( 0.25, 0.61, 0.69, 1.0), 1.31, 1.31, 1.24 ),
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(55, "Caesium", "Cs", ( 0.34, 0.09, 0.56, 1.0), 2.35, 2.35, 3.35 , 1 , 1.67 ),
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(56, "Barium", "Ba", ( 0.0, 0.78, 0.0, 1.0), 1.98, 1.98, 2.78 , 1 , 1.53 , 2 , 1.34 ),
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(57, "Lanthanum", "La", ( 0.43, 0.83, 1.0, 1.0), 1.69, 1.69, 2.74 , 1 , 1.39 , 3 , 1.06 ),
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(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 ),
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(59, "Praseodymium", "Pr", ( 0.85, 1.0, 0.78, 1.0), 1.65, 1.65, 2.67 , 3 , 1.01 , 4 , 0.90 ),
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(60, "Neodymium", "Nd", ( 0.78, 1.0, 0.78, 1.0), 1.64, 1.64, 2.64 , 3 , 0.99 ),
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(61, "Promethium", "Pm", ( 0.63, 1.0, 0.78, 1.0), 1.63, 1.63, 2.62 , 3 , 0.97 ),
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(62, "Samarium", "Sm", ( 0.56, 1.0, 0.78, 1.0), 1.62, 1.62, 2.59 , 3 , 0.96 ),
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(63, "Europium", "Eu", ( 0.38, 1.0, 0.78, 1.0), 1.85, 1.85, 2.56 , 2 , 1.09 , 3 , 0.95 ),
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(64, "Gadolinium", "Gd", ( 0.27, 1.0, 0.78, 1.0), 1.61, 1.61, 2.54 , 3 , 0.93 ),
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(65, "Terbium", "Tb", ( 0.18, 1.0, 0.78, 1.0), 1.59, 1.59, 2.51 , 3 , 0.92 , 4 , 0.84 ),
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(66, "Dysprosium", "Dy", ( 0.12, 1.0, 0.78, 1.0), 1.59, 1.59, 2.49 , 3 , 0.90 ),
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(67, "Holmium", "Ho", ( 0.0, 1.0, 0.61, 1.0), 1.58, 1.58, 2.47 , 3 , 0.89 ),
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(68, "Erbium", "Er", ( 0.0, 0.90, 0.45, 1.0), 1.57, 1.57, 2.45 , 3 , 0.88 ),
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(69, "Thulium", "Tm", ( 0.0, 0.83, 0.32, 1.0), 1.56, 1.56, 2.42 , 3 , 0.87 ),
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(70, "Ytterbium", "Yb", ( 0.0, 0.74, 0.21, 1.0), 1.74, 1.74, 2.40 , 2 , 0.93 , 3 , 0.85 ),
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(71, "Lutetium", "Lu", ( 0.0, 0.67, 0.14, 1.0), 1.56, 1.56, 2.25 , 3 , 0.85 ),
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(72, "Hafnium", "Hf", ( 0.30, 0.76, 1.0, 1.0), 1.44, 1.44, 2.16 , 4 , 0.78 ),
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(73, "Tantalum", "Ta", ( 0.30, 0.65, 1.0, 1.0), 1.34, 1.34, 2.09 , 5 , 0.68 ),
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(74, "Tungsten", "W", ( 0.12, 0.58, 0.83, 1.0), 1.30, 1.30, 2.02 , 4 , 0.70 , 6 , 0.62 ),
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(75, "Rhenium", "Re", ( 0.14, 0.49, 0.67, 1.0), 1.28, 1.28, 1.97 , 4 , 0.72 , 7 , 0.56 ),
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(76, "Osmium", "Os", ( 0.14, 0.4, 0.58, 1.0), 1.26, 1.26, 1.92 , 4 , 0.88 , 6 , 0.69 ),
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(77, "Iridium", "Ir", ( 0.09, 0.32, 0.52, 1.0), 1.27, 1.27, 1.87 , 4 , 0.68 ),
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(78, "Platinum", "Pt", ( 0.81, 0.81, 0.87, 1.0), 1.30, 1.30, 1.83 , 2 , 0.80 , 4 , 0.65 ),
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(79, "Gold", "Au", ( 1.0, 0.81, 0.13, 1.0), 1.34, 1.34, 1.79 , 1 , 1.37 , 3 , 0.85 ),
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(80, "Mercury", "Hg", ( 0.72, 0.72, 0.81, 1.0), 1.49, 1.49, 1.76 , 1 , 1.27 , 2 , 1.10 ),
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(81, "Thallium", "Tl", ( 0.65, 0.32, 0.30, 1.0), 1.48, 1.48, 2.08 , 1 , 1.47 , 3 , 0.95 ),
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(82, "Lead", "Pb", ( 0.34, 0.34, 0.38, 1.0), 1.47, 1.47, 1.81 , 2 , 1.20 , 4 , 0.84 ),
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(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 ),
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(84, "Polonium", "Po", ( 0.67, 0.36, 0.0, 1.0), 1.46, 1.46, 1.53 , 6 , 0.67 ),
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(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 ),
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(86, "Radon", "Rn", ( 0.25, 0.50, 0.58, 1.0), 1.00, 1.00, 1.34 ),
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(87, "Francium", "Fr", ( 0.25, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 , 1 , 1.80 ),
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(88, "Radium", "Ra", ( 0.0, 0.49, 0.0, 1.0), 1.00, 1.00, 1.00 , 2 , 1.43 ),
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(89, "Actinium", "Ac", ( 0.43, 0.67, 0.98, 1.0), 1.00, 1.00, 1.00 , 3 , 1.18 ),
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(90, "Thorium", "Th", ( 0.0, 0.72, 1.0, 1.0), 1.65, 1.65, 1.00 , 4 , 1.02 ),
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(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 ),
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(92, "Uranium", "U", ( 0.0, 0.56, 1.0, 1.0), 1.42, 1.42, 1.00 , 4 , 0.97 , 6 , 0.80 ),
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(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 ),
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(94, "Plutonium", "Pu", ( 0.0, 0.41, 1.0, 1.0), 1.00, 1.00, 1.00 , 3 , 1.08 , 4 , 0.93 ),
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(95, "Americium", "Am", ( 0.32, 0.36, 0.94, 1.0), 1.00, 1.00, 1.00 , 3 , 1.07 , 4 , 0.92 ),
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(96, "Curium", "Cm", ( 0.47, 0.36, 0.89, 1.0), 1.00, 1.00, 1.00 ),
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(97, "Berkelium", "Bk", ( 0.54, 0.30, 0.89, 1.0), 1.00, 1.00, 1.00 ),
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(98, "Californium", "Cf", ( 0.63, 0.21, 0.83, 1.0), 1.00, 1.00, 1.00 ),
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(99, "Einsteinium", "Es", ( 0.70, 0.12, 0.83, 1.0), 1.00, 1.00, 1.00 ),
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(100, "Fermium", "Fm", ( 0.70, 0.12, 0.72, 1.0), 1.00, 1.00, 1.00 ),
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(101, "Mendelevium", "Md", ( 0.70, 0.05, 0.65, 1.0), 1.00, 1.00, 1.00 ),
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(102, "Nobelium", "No", ( 0.74, 0.05, 0.52, 1.0), 1.00, 1.00, 1.00 ),
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(103, "Lawrencium", "Lr", ( 0.78, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 ),
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(104, "Vacancy", "Vac", ( 0.5, 0.5, 0.5, 1.0), 1.00, 1.00, 1.00),
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(105, "Default", "Default", ( 1.0, 1.0, 1.0, 1.0), 1.00, 1.00, 1.00),
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(106, "Stick", "Stick", ( 0.5, 0.5, 0.5, 1.0), 1.00, 1.00, 1.00),
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)
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# This list here contains all data of the elements and will be used during
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# runtime. It is a list of classes.
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# During executing Atomic Blender, the list will be initialized with the fixed
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# data from above via the class structure below (CLASS_atom_pdb_Elements). We
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# have then one fixed list (above), which will never be changed, and a list of
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# classes with same data. The latter can be modified via loading a separate
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# custom data file.
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ATOM_CLUSTER_ELEMENTS = []
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ATOM_CLUSTER_ALL_ATOMS = []
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# This is the class, which stores the properties for one element.
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class CLASS_atom_cluster_Elements(object):
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__slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic')
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def __init__(self, number, name, short_name, color, radii, radii_ionic):
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self.number = number
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self.name = name
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self.short_name = short_name
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self.color = color
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self.radii = radii
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self.radii_ionic = radii_ionic
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# This is the class, which stores the properties of one atom.
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class CLASS_atom_cluster_atom(object):
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__slots__ = ('location')
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def __init__(self, location):
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self.location = location
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# -----------------------------------------------------------------------------
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# Read atom data
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def DEF_atom_read_atom_data():
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del ATOM_CLUSTER_ELEMENTS[:]
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for item in ATOM_CLUSTER_ELEMENTS_DEFAULT:
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# All three radii into a list
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radii = [item[4],item[5],item[6]]
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# The handling of the ionic radii will be done later. So far, it is an
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# empty list.
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radii_ionic = []
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li = CLASS_atom_cluster_Elements(item[0],item[1],item[2],item[3],
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radii,radii_ionic)
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ATOM_CLUSTER_ELEMENTS.append(li)
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# -----------------------------------------------------------------------------
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# Routines for shapes
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def vec_in_sphere(atom_pos,size, skin):
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regular = True
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inner = True
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if atom_pos.length > size/2.0:
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regular = False
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if atom_pos.length < (size/2.0)*(1-skin):
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inner = False
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return (regular, inner)
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def vec_in_parabole(atom_pos, height, diameter):
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regular = True
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inner = True
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px = atom_pos[0]
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py = atom_pos[1]
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pz = atom_pos[2] + height/2.0
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a = diameter / sqrt(4 * height)
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if pz < 0.0:
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return (False, False)
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if px == 0.0 and py == 0.0:
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return (True, True)
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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
|
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# leave the code as is.
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#
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# To do:
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#
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# 1. Unlimited cluster size
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# 2. Skin effect
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def create_icosahedron(size, lattice):
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natot = int(1 + (10*size*size+15*size+11)*size/3)
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x = list(range(natot+1))
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y = list(range(natot+1))
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z = list(range(natot+1))
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xs = list(range(12+1))
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ys = list(range(12+1))
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zs = list(range(12+1))
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xa = [[[ [] for i in range(12+1)] for j in range(12+1)] for k in range(20+1)]
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ya = [[[ [] for i in range(12+1)] for j in range(12+1)] for k in range(20+1)]
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za = [[[ [] for i in range(12+1)] for j in range(12+1)] for k in range(20+1)]
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naret = [[ [] for i in range(12+1)] for j in range(12+1)]
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nfacet = [[[ [] for i in range(12+1)] for j in range(12+1)] for k in range(12+1)]
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rac2 = sqrt(2.0)
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rac5 = sqrt(5.0)
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tdef = (rac5+1.0)/2.0
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rapp = sqrt(2.0*(1.0-tdef/(tdef*tdef+1.0)))
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nats = 2 * (5*size*size+1)
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nat = 13
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epsi = 0.01
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x[1] = 0.0
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y[1] = 0.0
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z[1] = 0.0
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for i in range(2, 5+1):
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z[i] = 0.0
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y[i+4] = 0.0
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x[i+8] = 0.0
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for i in range(2, 3+1):
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x[i] = tdef
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x[i+2] = -tdef
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x[i+4] = 1.0
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x[i+6] = -1.0
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y[i+8] = tdef
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y[i+10] = -tdef
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for i in range(2, 4+1, 2):
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y[i] = 1.0
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y[i+1] = -1.0
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z[i+4] = tdef
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z[i+5] = -tdef
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z[i+8] = 1.0
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z[i+9] = -1.0
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xdef = rac2 / sqrt(tdef * tdef + 1)
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for i in range(2, 13+1):
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x[i] = x[i] * xdef / 2.0
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y[i] = y[i] * xdef / 2.0
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z[i] = z[i] * xdef / 2.0
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if size > 1:
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for n in range (2, size+1):
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ifacet = 0
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iaret = 0
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inatf = 0
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for i in range(1, 12+1):
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for j in range(1, 12+1):
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naret[i][j] = 0
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for k in range (1, 12+1):
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nfacet[i][j][k] = 0
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nl1 = 6
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nl2 = 8
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nl3 = 9
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k1 = 0
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k2 = 0
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k3 = 0
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k12 = 0
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for i in range(1, 12+1):
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nat += 1
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xs[i] = n * x[i+1]
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ys[i] = n * y[i+1]
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zs[i] = n * z[i+1]
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x[nat] = xs[i]
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y[nat] = ys[i]
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z[nat] = zs[i]
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k1 += 1
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for i in range(1, 12+1):
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for j in range(2, 12+1):
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if j <= i:
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continue
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xij = xs[j] - xs[i]
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yij = ys[j] - ys[i]
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zij = zs[j] - zs[i]
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xij2 = xij * xij
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yij2 = yij * yij
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zij2 = zij * zij
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dij2 = xij2 + yij2 + zij2
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dssn = n * rapp / rac2
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dssn2 = dssn * dssn
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diffij = abs(dij2-dssn2)
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if diffij >= epsi:
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continue
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for k in range(3, 12+1):
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if k <= j:
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continue
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xjk = xs[k] - xs[j]
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yjk = ys[k] - ys[j]
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zjk = zs[k] - zs[j]
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xjk2 = xjk * xjk
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yjk2 = yjk * yjk
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zjk2 = zjk * zjk
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djk2 = xjk2 + yjk2 + zjk2
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diffjk = abs(djk2-dssn2)
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if diffjk >= epsi:
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continue
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xik = xs[k] - xs[i]
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yik = ys[k] - ys[i]
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zik = zs[k] - zs[i]
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xik2 = xik * xik
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yik2 = yik * yik
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zik2 = zik * zik
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dik2 = xik2 + yik2 + zik2
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diffik = abs(dik2-dssn2)
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if diffik >= epsi:
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continue
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if nfacet[i][j][k] != 0:
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continue
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ifacet += 1
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nfacet[i][j][k] = ifacet
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if naret[i][j] == 0:
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iaret += 1
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naret[i][j] = iaret
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for l in range(1,n-1+1):
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nat += 1
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xa[i][j][l] = xs[i]+l*(xs[j]-xs[i]) / n
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ya[i][j][l] = ys[i]+l*(ys[j]-ys[i]) / n
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za[i][j][l] = zs[i]+l*(zs[j]-zs[i]) / n
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x[nat] = xa[i][j][l]
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y[nat] = ya[i][j][l]
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z[nat] = za[i][j][l]
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if naret[i][k] == 0:
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iaret += 1
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naret[i][k] = iaret
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for l in range(1, n-1+1):
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nat += 1
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xa[i][k][l] = xs[i]+l*(xs[k]-xs[i]) / n
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ya[i][k][l] = ys[i]+l*(ys[k]-ys[i]) / n
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za[i][k][l] = zs[i]+l*(zs[k]-zs[i]) / n
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x[nat] = xa[i][k][l]
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y[nat] = ya[i][k][l]
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z[nat] = za[i][k][l]
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if naret[j][k] == 0:
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iaret += 1
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naret[j][k] = iaret
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for l in range(1, n-1+1):
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nat += 1
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xa[j][k][l] = xs[j]+l*(xs[k]-xs[j]) / n
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ya[j][k][l] = ys[j]+l*(ys[k]-ys[j]) / n
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za[j][k][l] = zs[j]+l*(zs[k]-zs[j]) / n
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x[nat] = xa[j][k][l]
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y[nat] = ya[j][k][l]
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z[nat] = za[j][k][l]
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for l in range(2, n-1+1):
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for ll in range(1, l-1+1):
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xf = xa[i][j][l]+ll*(xa[i][k][l]-xa[i][j][l]) / l
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yf = ya[i][j][l]+ll*(ya[i][k][l]-ya[i][j][l]) / l
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zf = za[i][j][l]+ll*(za[i][k][l]-za[i][j][l]) / l
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nat += 1
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inatf += 1
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x[nat] = xf
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y[nat] = yf
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z[nat] = zf
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k3 += 1
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atom_number_total = 0
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atom_number_drawn = 0
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for i in range (1,natot+1):
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atom = Vector((x[i],y[i],z[i])) * lattice
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atom_add = CLASS_atom_cluster_atom(atom)
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ATOM_CLUSTER_ALL_ATOMS.append(atom_add)
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atom_number_total += 1
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atom_number_drawn += 1
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return (atom_number_total, atom_number_drawn)
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