io_mesh_atomic/utility_panel.py

   1 # ##### BEGIN GPL LICENSE BLOCK #####
   2 #
   3 #  This program is free software; you can redistribute it and/or
   4 #  modify it under the terms of the GNU General Public License
   5 #  as published by the Free Software Foundation; either version 2
   6 #  of the License, or (at your option) any later version.
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   8 #  This program is distributed in the hope that it will be useful,
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  10 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  11 #  GNU General Public License for more details.
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  13 #  You should have received a copy of the GNU General Public License
  14 #  along with this program; if not, write to the Free Software Foundation,
  15 #  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
  16 #
  17 # ##### END GPL LICENSE BLOCK #####
  18
  19 import os
  20 import bpy
  21 import bmesh
  22 from mathutils import Vector
  23 from math import sqrt
  24 from copy import copy
  25
  26 # -----------------------------------------------------------------------------
  27 #                                                         Atom and element data
  28
  29
  30 # This is a list that contains some data of all possible elements. The structure
  31 # is as follows:
  32 #
  33 # 1, "Hydrogen", "H", [0.0,0.0,1.0], 0.32, 0.32, 0.32 , -1 , 1.54   means
  34 #
  35 # No., name, short name, color, radius (used), radius (covalent), radius (atomic),
  36 #
  37 # charge state 1, radius (ionic) 1, charge state 2, radius (ionic) 2, ... all
  38 # charge states for any atom are listed, if existing.
  39 # The list is fixed and cannot be changed ... (see below)
  40
  41 ELEMENTS_DEFAULT = (
  42 ( 1,      "Hydrogen",        "H", (  1.0,   1.0,   1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
  43 ( 2,        "Helium",       "He", ( 0.85,   1.0,   1.0, 1.0), 0.93, 0.93, 0.49 ),
  44 ( 3,       "Lithium",       "Li", (  0.8,  0.50,   1.0, 1.0), 1.23, 1.23, 2.05 ,  1 , 0.68 ),
  45 ( 4,     "Beryllium",       "Be", ( 0.76,   1.0,   0.0, 1.0), 0.90, 0.90, 1.40 ,  1 , 0.44 ,  2 , 0.35 ),
  46 ( 5,         "Boron",        "B", (  1.0,  0.70,  0.70, 1.0), 0.82, 0.82, 1.17 ,  1 , 0.35 ,  3 , 0.23 ),
  47 ( 6,        "Carbon",        "C", ( 0.56,  0.56,  0.56, 1.0), 0.77, 0.77, 0.91 , -4 , 2.60 ,  4 , 0.16 ),
  48 ( 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 ),
  49 ( 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 ),
  50 ( 9,      "Fluorine",        "F", ( 0.56,  0.87,  0.31, 1.0), 0.72, 0.72, 0.57 , -1 , 1.33 ,  7 , 0.08 ),
  51 (10,          "Neon",       "Ne", ( 0.70,  0.89,  0.96, 1.0), 0.71, 0.71, 0.51 ,  1 , 1.12 ),
  52 (11,        "Sodium",       "Na", ( 0.67,  0.36,  0.94, 1.0), 1.54, 1.54, 2.23 ,  1 , 0.97 ),
  53 (12,     "Magnesium",       "Mg", ( 0.54,   1.0,   0.0, 1.0), 1.36, 1.36, 1.72 ,  1 , 0.82 ,  2 , 0.66 ),
  54 (13,     "Aluminium",       "Al", ( 0.74,  0.65,  0.65, 1.0), 1.18, 1.18, 1.82 ,  3 , 0.51 ),
  55 (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 ),
  56 (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 ),
  57 (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 ),
  58 (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 ),
  59 (18,         "Argon",       "Ar", ( 0.50,  0.81,  0.89, 1.0), 0.98, 0.98, 0.88 ,  1 , 1.54 ),
  60 (19,     "Potassium",        "K", ( 0.56,  0.25,  0.83, 1.0), 2.03, 2.03, 2.77 ,  1 , 0.81 ),
  61 (20,       "Calcium",       "Ca", ( 0.23,   1.0,   0.0, 1.0), 1.74, 1.74, 2.23 ,  1 , 1.18 ,  2 , 0.99 ),
  62 (21,      "Scandium",       "Sc", ( 0.90,  0.90,  0.90, 1.0), 1.44, 1.44, 2.09 ,  3 , 0.73 ),
  63 (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 ),
  64 (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 ),
  65 (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 ),
  66 (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 ),
  67 (26,          "Iron",       "Fe", ( 0.87,   0.4,   0.2, 1.0), 1.17, 1.17, 1.72 ,  2 , 0.74 ,  3 , 0.64 ),
  68 (27,        "Cobalt",       "Co", ( 0.94,  0.56,  0.62, 1.0), 1.16, 1.16, 1.67 ,  2 , 0.72 ,  3 , 0.63 ),
  69 (28,        "Nickel",       "Ni", ( 0.31,  0.81,  0.31, 1.0), 1.15, 1.15, 1.62 ,  2 , 0.69 ),
  70 (29,        "Copper",       "Cu", ( 0.78,  0.50,   0.2, 1.0), 1.17, 1.17, 1.57 ,  1 , 0.96 ,  2 , 0.72 ),
  71 (30,          "Zinc",       "Zn", ( 0.49,  0.50,  0.69, 1.0), 1.25, 1.25, 1.53 ,  1 , 0.88 ,  2 , 0.74 ),
  72 (31,       "Gallium",       "Ga", ( 0.76,  0.56,  0.56, 1.0), 1.26, 1.26, 1.81 ,  1 , 0.81 ,  3 , 0.62 ),
  73 (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 ),
  74 (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 ),
  75 (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 ),
  76 (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 ),
  77 (36,       "Krypton",       "Kr", ( 0.36,  0.72,  0.81, 1.0), 1.31, 1.31, 1.24 ),
  78 (37,      "Rubidium",       "Rb", ( 0.43,  0.18,  0.69, 1.0), 2.16, 2.16, 2.98 ,  1 , 1.47 ),
  79 (38,     "Strontium",       "Sr", (  0.0,   1.0,   0.0, 1.0), 1.91, 1.91, 2.45 ,  2 , 1.12 ),
  80 (39,       "Yttrium",        "Y", ( 0.58,   1.0,   1.0, 1.0), 1.62, 1.62, 2.27 ,  3 , 0.89 ),
  81 (40,     "Zirconium",       "Zr", ( 0.58,  0.87,  0.87, 1.0), 1.45, 1.45, 2.16 ,  1 , 1.09 ,  4 , 0.79 ),
  82 (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 ),
  83 (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 ),
  84 (43,    "Technetium",       "Tc", ( 0.23,  0.61,  0.61, 1.0), 1.27, 1.27, 1.95 ,  7 , 0.97 ),
  85 (44,     "Ruthenium",       "Ru", ( 0.14,  0.56,  0.56, 1.0), 1.25, 1.25, 1.89 ,  4 , 0.67 ),
  86 (45,       "Rhodium",       "Rh", ( 0.03,  0.49,  0.54, 1.0), 1.25, 1.25, 1.83 ,  3 , 0.68 ),
  87 (46,     "Palladium",       "Pd", (  0.0,  0.41,  0.52, 1.0), 1.28, 1.28, 1.79 ,  2 , 0.80 ,  4 , 0.65 ),
  88 (47,        "Silver",       "Ag", ( 0.75,  0.75,  0.75, 1.0), 1.34, 1.34, 1.75 ,  1 , 1.26 ,  2 , 0.89 ),
  89 (48,       "Cadmium",       "Cd", (  1.0,  0.85,  0.56, 1.0), 1.48, 1.48, 1.71 ,  1 , 1.14 ,  2 , 0.97 ),
  90 (49,        "Indium",       "In", ( 0.65,  0.45,  0.45, 1.0), 1.44, 1.44, 2.00 ,  3 , 0.81 ),
  91 (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 ),
  92 (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 ),
  93 (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 ),
  94 (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 ),
  95 (54,         "Xenon",       "Xe", ( 0.25,  0.61,  0.69, 1.0), 1.31, 1.31, 1.24 ),
  96 (55,       "Caesium",       "Cs", ( 0.34,  0.09,  0.56, 1.0), 2.35, 2.35, 3.35 ,  1 , 1.67 ),
  97 (56,        "Barium",       "Ba", (  0.0,  0.78,   0.0, 1.0), 1.98, 1.98, 2.78 ,  1 , 1.53 ,  2 , 1.34 ),
  98 (57,     "Lanthanum",       "La", ( 0.43,  0.83,   1.0, 1.0), 1.69, 1.69, 2.74 ,  1 , 1.39 ,  3 , 1.06 ),
  99 (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 ),
 100 (59,  "Praseodymium",       "Pr", ( 0.85,   1.0,  0.78, 1.0), 1.65, 1.65, 2.67 ,  3 , 1.01 ,  4 , 0.90 ),
 101 (60,     "Neodymium",       "Nd", ( 0.78,   1.0,  0.78, 1.0), 1.64, 1.64, 2.64 ,  3 , 0.99 ),
 102 (61,    "Promethium",       "Pm", ( 0.63,   1.0,  0.78, 1.0), 1.63, 1.63, 2.62 ,  3 , 0.97 ),
 103 (62,      "Samarium",       "Sm", ( 0.56,   1.0,  0.78, 1.0), 1.62, 1.62, 2.59 ,  3 , 0.96 ),
 104 (63,      "Europium",       "Eu", ( 0.38,   1.0,  0.78, 1.0), 1.85, 1.85, 2.56 ,  2 , 1.09 ,  3 , 0.95 ),
 105 (64,    "Gadolinium",       "Gd", ( 0.27,   1.0,  0.78, 1.0), 1.61, 1.61, 2.54 ,  3 , 0.93 ),
 106 (65,       "Terbium",       "Tb", ( 0.18,   1.0,  0.78, 1.0), 1.59, 1.59, 2.51 ,  3 , 0.92 ,  4 , 0.84 ),
 107 (66,    "Dysprosium",       "Dy", ( 0.12,   1.0,  0.78, 1.0), 1.59, 1.59, 2.49 ,  3 , 0.90 ),
 108 (67,       "Holmium",       "Ho", (  0.0,   1.0,  0.61, 1.0), 1.58, 1.58, 2.47 ,  3 , 0.89 ),
 109 (68,        "Erbium",       "Er", (  0.0,  0.90,  0.45, 1.0), 1.57, 1.57, 2.45 ,  3 , 0.88 ),
 110 (69,       "Thulium",       "Tm", (  0.0,  0.83,  0.32, 1.0), 1.56, 1.56, 2.42 ,  3 , 0.87 ),
 111 (70,     "Ytterbium",       "Yb", (  0.0,  0.74,  0.21, 1.0), 1.74, 1.74, 2.40 ,  2 , 0.93 ,  3 , 0.85 ),
 112 (71,      "Lutetium",       "Lu", (  0.0,  0.67,  0.14, 1.0), 1.56, 1.56, 2.25 ,  3 , 0.85 ),
 113 (72,       "Hafnium",       "Hf", ( 0.30,  0.76,   1.0, 1.0), 1.44, 1.44, 2.16 ,  4 , 0.78 ),
 114 (73,      "Tantalum",       "Ta", ( 0.30,  0.65,   1.0, 1.0), 1.34, 1.34, 2.09 ,  5 , 0.68 ),
 115 (74,      "Tungsten",        "W", ( 0.12,  0.58,  0.83, 1.0), 1.30, 1.30, 2.02 ,  4 , 0.70 ,  6 , 0.62 ),
 116 (75,       "Rhenium",       "Re", ( 0.14,  0.49,  0.67, 1.0), 1.28, 1.28, 1.97 ,  4 , 0.72 ,  7 , 0.56 ),
 117 (76,        "Osmium",       "Os", ( 0.14,   0.4,  0.58, 1.0), 1.26, 1.26, 1.92 ,  4 , 0.88 ,  6 , 0.69 ),
 118 (77,       "Iridium",       "Ir", ( 0.09,  0.32,  0.52, 1.0), 1.27, 1.27, 1.87 ,  4 , 0.68 ),
 119 (78,      "Platinum",       "Pt", ( 0.81,  0.81,  0.87, 1.0), 1.30, 1.30, 1.83 ,  2 , 0.80 ,  4 , 0.65 ),
 120 (79,          "Gold",       "Au", (  1.0,  0.81,  0.13, 1.0), 1.34, 1.34, 1.79 ,  1 , 1.37 ,  3 , 0.85 ),
 121 (80,       "Mercury",       "Hg", ( 0.72,  0.72,  0.81, 1.0), 1.49, 1.49, 1.76 ,  1 , 1.27 ,  2 , 1.10 ),
 122 (81,      "Thallium",       "Tl", ( 0.65,  0.32,  0.30, 1.0), 1.48, 1.48, 2.08 ,  1 , 1.47 ,  3 , 0.95 ),
 123 (82,          "Lead",       "Pb", ( 0.34,  0.34,  0.38, 1.0), 1.47, 1.47, 1.81 ,  2 , 1.20 ,  4 , 0.84 ),
 124 (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 ),
 125 (84,      "Polonium",       "Po", ( 0.67,  0.36,   0.0, 1.0), 1.46, 1.46, 1.53 ,  6 , 0.67 ),
 126 (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 ),
 127 (86,         "Radon",       "Rn", ( 0.25,  0.50,  0.58, 1.0), 1.00, 1.00, 1.34 ),
 128 (87,      "Francium",       "Fr", ( 0.25,   0.0,   0.4, 1.0), 1.00, 1.00, 1.00 ,  1 , 1.80 ),
 129 (88,        "Radium",       "Ra", (  0.0,  0.49,   0.0, 1.0), 1.00, 1.00, 1.00 ,  2 , 1.43 ),
 130 (89,      "Actinium",       "Ac", ( 0.43,  0.67,  0.98, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.18 ),
 131 (90,       "Thorium",       "Th", (  0.0,  0.72,   1.0, 1.0), 1.65, 1.65, 1.00 ,  4 , 1.02 ),
 132 (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 ),
 133 (92,       "Uranium",        "U", (  0.0,  0.56,   1.0, 1.0), 1.42, 1.42, 1.00 ,  4 , 0.97 ,  6 , 0.80 ),
 134 (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 ),
 135 (94,     "Plutonium",       "Pu", (  0.0,  0.41,   1.0, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.08 ,  4 , 0.93 ),
 136 (95,     "Americium",       "Am", ( 0.32,  0.36,  0.94, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.07 ,  4 , 0.92 ),
 137 (96,        "Curium",       "Cm", ( 0.47,  0.36,  0.89, 1.0), 1.00, 1.00, 1.00 ),
 138 (97,     "Berkelium",       "Bk", ( 0.54,  0.30,  0.89, 1.0), 1.00, 1.00, 1.00 ),
 139 (98,   "Californium",       "Cf", ( 0.63,  0.21,  0.83, 1.0), 1.00, 1.00, 1.00 ),
 140 (99,   "Einsteinium",       "Es", ( 0.70,  0.12,  0.83, 1.0), 1.00, 1.00, 1.00 ),
 141 (100,       "Fermium",       "Fm", ( 0.70,  0.12, 0.72, 1.0), 1.00, 1.00, 1.00 ),
 142 (101,   "Mendelevium",       "Md", ( 0.70,  0.05, 0.65, 1.0), 1.00, 1.00, 1.00 ),
 143 (102,      "Nobelium",       "No", ( 0.74,  0.05, 0.52, 1.0), 1.00, 1.00, 1.00 ),
 144 (103,    "Lawrencium",       "Lr", ( 0.78,   0.0,  0.4, 1.0), 1.00, 1.00, 1.00 ),
 145 (104,       "Vacancy",      "Vac", (  0.5,   0.5,  0.5, 1.0), 1.00, 1.00, 1.00),
 146 (105,       "Default",  "Default", (  1.0,   1.0,  1.0, 1.0), 1.00, 1.00, 1.00),
 147 (106,         "Stick",    "Stick", (  0.5,   0.5,  0.5, 1.0), 1.00, 1.00, 1.00),
 148 )
 149
 150 # The list 'ELEMENTS' contains all data of the elements and will be used during
 151 # runtime. The list will be initialized with the fixed
 152 # data from above via the class below (ElementProp). One fixed list (above),
 153 # which cannot be changed, and a list of classes with same data (ELEMENTS) exist.
 154 # The list 'ELEMENTS' can be modified by e.g. loading a separate custom
 155 # data file.
 156 ELEMENTS = []
 157
 158
 159 # This is the class, which stores the properties for one element.
 160 class ElementProp(object):
 161     __slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic')
 162     def __init__(self, number, name, short_name, color, radii, radii_ionic):
 163         self.number = number
 164         self.name = name
 165         self.short_name = short_name
 166         self.color = color
 167         self.radii = radii
 168         self.radii_ionic = radii_ionic
 169
 170
 171 # This function measures the distance between two selected objects.
 172 def distance():
 173
 174     # In the 'EDIT' mode
 175     if bpy.context.mode == 'EDIT_MESH':
 176
 177         atom = bpy.context.edit_object
 178         bm = bmesh.from_edit_mesh(atom.data)
 179         locations = []
 180
 181         for v in bm.verts:
 182             if v.select:
 183                 locations.append(atom.matrix_world @ v.co)
 184
 185         if len(locations) > 1:
 186             location1 = locations[0]
 187             location2 = locations[1]
 188         else:
 189             return "N.A"
 190     # In the 'OBJECT' mode
 191     else:
 192
 193         if len(bpy.context.selected_objects) > 1:
 194             location1 = bpy.context.selected_objects[0].location
 195             location2 = bpy.context.selected_objects[1].location
 196         else:
 197             return "N.A."
 198
 199     dv = location2 - location1
 200     dist = str(dv.length)
 201     pos = str.find(dist, ".")
 202     dist = dist[:pos+4]
 203     dist = dist + " A"
 204
 205     return dist
 206
 207
 208 def choose_objects(action_type,
 209                    who,
 210                    radius_all,
 211                    radius_pm,
 212                    radius_type,
 213                    radius_type_ionic,
 214                    sticks_all):
 215
 216     # For selected objects of all selected layers
 217     if who == "ALL_IN_LAYER":
 218         # Determine all selected layers.
 219         layers = []
 220         for i, layer in enumerate(bpy.context.scene.layers):
 221             if layer == True:
 222                 layers.append(i)
 223
 224         # Put all objects, which are in the layers, into a list.
 225         change_objects_all = []
 226         for atom in bpy.context.scene.objects:
 227             for layer in layers:
 228                 if atom.layers[layer] == True:
 229                     change_objects_all.append(atom)
 230     # For selected objects of the visible layer
 231     elif who == "ALL_ACTIVE":
 232         change_objects_all = []
 233         # Note all selected objects first.
 234         for atom in bpy.context.selected_objects:
 235             change_objects_all.append(atom)
 236
 237     # This is very important now: If there are dupliverts structures, note
 238     # only the parents and NOT the children! Otherwise the double work is
 239     # done or the system can even crash if objects are deleted. - The
 240     # chidlren are accessed anyways (see below).
 241     change_objects = []
 242     for atom in change_objects_all:
 243         if atom.parent != None:
 244             FLAG = False
 245             for atom2 in change_objects:
 246                 if atom2 == atom.parent:
 247                    FLAG = True
 248             if FLAG == False:
 249                 change_objects.append(atom)
 250         else:
 251             change_objects.append(atom)
 252
 253     # And now, consider all objects, which are in the list 'change_objects'.
 254     for atom in change_objects:
 255         if len(atom.children) != 0:
 256             for atom_child in atom.children:
 257                 if atom_child.type in {'SURFACE', 'MESH', 'META'}:
 258                     modify_objects(action_type,
 259                                    atom_child,
 260                                    radius_all,
 261                                    radius_pm,
 262                                    radius_type,
 263                                    radius_type_ionic,
 264                                    sticks_all)
 265         else:
 266             if atom.type in {'SURFACE', 'MESH', 'META'}:
 267                 modify_objects(action_type,
 268                                atom,
 269                                radius_all,
 270                                radius_pm,
 271                                radius_type,
 272                                radius_type_ionic,
 273                                sticks_all)
 274
 275
 276 # Modifying the radius of a selected atom or stick
 277 def modify_objects(action_type,
 278                    atom,
 279                    radius_all,
 280                    radius_pm,
 281                    radius_type,
 282                    radius_type_ionic,
 283                    sticks_all):
 284
 285     # Modify atom radius (in pm)
 286     if action_type == "ATOM_RADIUS_PM" and "STICK" not in atom.name.upper():
 287         if radius_pm[0] in atom.name:
 288             atom.scale = (radius_pm[1]/100,) * 3
 289
 290     # Modify atom radius (all selected)
 291     if action_type == "ATOM_RADIUS_ALL" and "STICK" not in atom.name.upper():
 292         atom.scale *= radius_all
 293
 294     # Modify atom radius (type, van der Waals, atomic or ionic)
 295     if action_type == "ATOM_RADIUS_TYPE" and "STICK" not in atom.name.upper():
 296         for element in ELEMENTS:
 297             if element.name in atom.name:
 298                 # For ionic radii
 299                 if radius_type == '3':
 300                     charge_states = element.radii_ionic[::2]
 301                     charge_radii =  element.radii_ionic[1::2]
 302                     charge_state_chosen = int(radius_type_ionic) - 4
 303
 304                     find = (lambda searchList, elem:
 305                             [[i for i, x in enumerate(searchList) if x == e]
 306                             for e in elem])
 307                     index = find(charge_states,[charge_state_chosen])[0]
 308
 309                     # Is there a charge state?
 310                     if index != []:
 311                         atom.scale = (charge_radii[index[0]],) * 3
 312
 313                 # For atomic and van der Waals radii.
 314                 else:
 315                     atom.scale = (element.radii[int(radius_type)],) * 3
 316
 317     # Modify atom sticks
 318     if (action_type == "STICKS_RADIUS_ALL" and 'STICK' in atom.name.upper() and
 319                                     ('CUP'      in atom.name.upper() or
 320                                      'CYLINDER' in atom.name.upper())):
 321
 322         # For dupliverts structures only: Make the cylinder or cup visible
 323         # first, otherwise one cannot go into EDIT mode. Note that 'atom' here
 324         # is in fact a 'stick' (cylinder or cup).
 325         # First, identify if it is a normal cylinder object or a dupliverts
 326         # structure. The identifier for a dupliverts structure is the parent's
 327         # name, which includes "_sticks_mesh"
 328         if "_sticks_mesh" in atom.parent.name:
 329             atom.hide_set(False)
 330
 331         bpy.context.view_layer.objects.active = atom
 332         bpy.ops.object.mode_set(mode='EDIT', toggle=False)
 333         bm = bmesh.from_edit_mesh(atom.data)
 334
 335         locations = []
 336         for v in bm.verts:
 337             locations.append(v.co)
 338
 339         center = Vector((0.0,0.0,0.0))
 340         center = sum([location for location in locations], center)/len(locations)
 341
 342         radius = sum([(loc[0]-center[0])**2+(loc[1]-center[1])**2
 343                      for loc in locations], 0)
 344         radius_new = radius * sticks_all
 345
 346         for v in bm.verts:
 347             v.co[0] = ((v.co[0] - center[0]) / radius) * radius_new + center[0]
 348             v.co[1] = ((v.co[1] - center[1]) / radius) * radius_new + center[1]
 349
 350         bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
 351         # Hide again the representative stick (cylinder or cup) if it is a
 352         # dupliverts structure.
 353         if "_sticks_mesh" in atom.parent.name:
 354             atom.hide_set(True)
 355
 356         bpy.context.view_layer.objects.active = None
 357
 358     # Replace atom objects
 359     if action_type == "ATOM_REPLACE_OBJ" and "STICK" not in atom.name.upper():
 360
 361         scn = bpy.context.scene.atom_blend
 362
 363         new_material = draw_obj_material(scn.replace_objs_material,
 364                                          atom.active_material)
 365
 366         # Special object (like halo, etc.)
 367         if scn.replace_objs_special != '0':
 368             new_atom = draw_obj_special(scn.replace_objs_special, atom)
 369         # Standard geometrical objects
 370         else:
 371             # If the atom shape shall not be changed, then:
 372             if scn.replace_objs == '0':
 373                 atom.active_material = new_material
 374                 #return {'FINISHED'}
 375             # If the atom shape shall change, then:
 376             else:
 377                 new_atom = draw_obj(scn.replace_objs, atom, new_material)
 378
 379     # Default shapes and colors for atoms
 380     if action_type == "ATOM_DEFAULT_OBJ" and "STICK" not in atom.name.upper():
 381
 382         scn = bpy.context.scene.atom_blend
 383
 384         # Create new material
 385         new_material = bpy.data.materials.new("tmp")
 386         # Create new object (NURBS sphere = '1b')
 387         new_atom = draw_obj('1b', atom, new_material)
 388         new_atom.active_material = new_material
 389         new_material = draw_obj_material('0', new_material)
 390
 391         # Change size and color of the new object
 392         for element in ELEMENTS:
 393             if element.name in new_atom.name:
 394                 new_atom.scale = (element.radii[0],) * 3
 395                 new_atom.active_material.diffuse_color = element.color
 396                 new_atom.name = element.name + "_ball"
 397                 new_atom.active_material.name = element.name
 398                 break
 399
 400
 401 # Separating atoms from a dupliverts structure.
 402 def separate_atoms(scn):
 403
 404     # Get the mesh.
 405     mesh = bpy.context.edit_object
 406
 407     # Do nothing if it is not a dupliverts structure.
 408     if not mesh.instance_type == "VERTS":
 409        return {'FINISHED'}
 410
 411     # This is the name of the mesh
 412     mesh_name = mesh.name
 413     # Get the collection
 414     coll = mesh.users_collection[0]
 415
 416     # Get the coordinates of the selected vertices (atoms)
 417     bm = bmesh.from_edit_mesh(mesh.data)
 418     locations = []
 419     for v in bm.verts:
 420         if v.select:
 421             locations.append(mesh.matrix_world @ v.co)
 422
 423     # Free memory
 424     bm.free()
 425     del(bm)
 426
 427     # Delete already the selected vertices
 428     bpy.ops.mesh.delete(type='VERT')
 429
 430     # Find the representative ball within the collection.
 431     for obj in coll.objects:
 432         if obj.parent != None:
 433             if obj.parent.name == mesh_name:
 434                 break
 435
 436     # Create balls and put them at the places where the vertices (atoms) have
 437     # been before.
 438     for location in locations:
 439         obj_dupli = obj.copy()
 440         obj_dupli.data = obj.data.copy()
 441         obj_dupli.parent = None
 442         coll.objects.link(obj_dupli)
 443         obj_dupli.location = location
 444         obj_dupli.name = obj.name + "_sep"
 445         # Do not hide the object!
 446         obj_dupli.hide_set(False)
 447
 448
 449     bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
 450     bpy.context.view_layer.objects.active = mesh
 451
 452
 453 # Prepare a new material
 454 def draw_obj_material(material_type, material):
 455
 456     if material_type == '0': # Unchanged
 457         material_new = material
 458     if material_type == '1': # Normal
 459         material_new = bpy.data.materials.new(material.name + "_normal")
 460     if material_type == '2': # Transparent
 461         material_new = bpy.data.materials.new(material.name + "_transparent")
 462         material_new.metallic = 0.8
 463         material_new.specular_intensity = 0.5
 464         material_new.roughness = 0.3
 465         material_new.blend_method = 'OPAQUE'
 466         material_new.show_transparent_back = False
 467         # Some properties for cycles
 468         material_new.use_nodes = True
 469         mat_P_BSDF = material_new.node_tree.nodes['Principled BSDF']
 470         mat_P_BSDF.inputs['Metallic'].default_value = 0.1
 471         mat_P_BSDF.inputs['Roughness'].default_value = 0.2
 472         mat_P_BSDF.inputs['Transmission'].default_value = 0.9
 473         mat_P_BSDF.inputs['IOR'].default_value = 0.8
 474     if material_type == '3': # Reflecting
 475         material_new = bpy.data.materials.new(material.name + "_reflecting")
 476         material_new.metallic = 0.5
 477         material_new.specular_intensity = 0.5
 478         material_new.roughness = 0.0
 479         material_new.blend_method = 'OPAQUE'
 480         # Some properties for cycles
 481         material_new.use_nodes = True
 482         mat_P_BSDF = material_new.node_tree.nodes['Principled BSDF']
 483         mat_P_BSDF.inputs['Metallic'].default_value = 0.95
 484         mat_P_BSDF.inputs['Roughness'].default_value = 0.1
 485         mat_P_BSDF.inputs['Transmission'].default_value = 0.0
 486         mat_P_BSDF.inputs['IOR'].default_value = 1.0
 487     if material_type == '4': # Transparent + reflecting
 488         material_new = bpy.data.materials.new(material.name + "_trans+refl")
 489         material_new.metallic = 0.3
 490         material_new.specular_intensity = 0.5
 491         material_new.roughness = 0.3
 492         material_new.blend_method = 'OPAQUE'
 493         material_new.show_transparent_back = False
 494         # Some properties for cycles
 495         material_new.use_nodes = True
 496         mat_P_BSDF = material_new.node_tree.nodes['Principled BSDF']
 497         mat_P_BSDF.inputs['Metallic'].default_value = 0.5
 498         mat_P_BSDF.inputs['Roughness'].default_value = 0.2
 499         mat_P_BSDF.inputs['Transmission'].default_value = 0.5
 500         mat_P_BSDF.inputs['IOR'].default_value = 0.8
 501
 502     # Always, when the material is changed, a new name is created. Note that
 503     # this makes sense: Imagine, an other object uses the same material as the
 504     # selected one. After changing the material of the selected object the old
 505     # material should certainly not change and remain the same.
 506     if material_type in {'1','2','3','4'}:
 507         if "_repl" in material.name:
 508             pos = material.name.rfind("_repl")
 509             if material.name[pos+5:].isdigit():
 510                 counter = int(material.name[pos+5:])
 511                 material_new.name = material.name[:pos]+"_repl"+str(counter+1)
 512             else:
 513                 material_new.name = material.name+"_repl1"
 514         else:
 515             material_new.name = material.name+"_repl1"
 516         material_new.diffuse_color = material.diffuse_color
 517
 518     return material_new
 519
 520
 521 # Get the collection of an object.
 522 def get_collection_object(obj):
 523
 524     coll_all = obj.users_collection
 525     if len(coll_all) > 0:
 526         coll = coll_all[0]
 527     else:
 528         coll = bpy.context.scene.collection
 529
 530     return coll
 531
 532
 533 # Draw an object (e.g. cube, sphere, cylinder, ...)
 534 def draw_obj(atom_shape, atom, new_material):
 535
 536     # No change
 537     if atom_shape == '0':
 538         return None
 539
 540     if atom_shape == '1a': #Sphere mesh
 541         bpy.ops.mesh.primitive_uv_sphere_add(
 542             segments=32,
 543             ring_count=32,
 544             radius=1,
 545             align='WORLD',
 546             enter_editmode=False,
 547             location=atom.location,
 548             rotation=(0, 0, 0))
 549     if atom_shape == '1b': #Sphere NURBS
 550         bpy.ops.surface.primitive_nurbs_surface_sphere_add(
 551             align='WORLD',
 552             enter_editmode=False,
 553             location=atom.location,
 554             rotation=(0.0, 0.0, 0.0))
 555     if atom_shape == '2': #Cube
 556         bpy.ops.mesh.primitive_cube_add(
 557             align='WORLD',
 558             enter_editmode=False,
 559             location=atom.location,
 560             rotation=(0.0, 0.0, 0.0))
 561     if atom_shape == '3': #Plane
 562         bpy.ops.mesh.primitive_plane_add(
 563             align='WORLD',
 564             enter_editmode=False,
 565             location=atom.location,
 566             rotation=(0.0, 0.0, 0.0))
 567     if atom_shape == '4a': #Circle
 568         bpy.ops.mesh.primitive_circle_add(
 569             vertices=32,
 570             radius=1,
 571             fill_type='NOTHING',
 572             align='WORLD',
 573             enter_editmode=False,
 574             location=atom.location,
 575             rotation=(0, 0, 0))
 576     if atom_shape == '4b': #Circle NURBS
 577         bpy.ops.surface.primitive_nurbs_surface_circle_add(
 578             align='WORLD',
 579             enter_editmode=False,
 580             location=atom.location,
 581             rotation=(0, 0, 0))
 582     if atom_shape in {'5a','5b','5c','5d','5e'}: #Icosphere
 583         index = {'5a':1,'5b':2,'5c':3,'5d':4,'5e':5}
 584         bpy.ops.mesh.primitive_ico_sphere_add(
 585             subdivisions=int(index[atom_shape]),
 586             radius=1,
 587             align='WORLD',
 588             enter_editmode=False,
 589             location=atom.location,
 590             rotation=(0, 0, 0))
 591     if atom_shape == '6a': #Cylinder
 592         bpy.ops.mesh.primitive_cylinder_add(
 593             vertices=32,
 594             radius=1,
 595             depth=2,
 596             end_fill_type='NGON',
 597             align='WORLD',
 598             enter_editmode=False,
 599             location=atom.location,
 600             rotation=(0, 0, 0))
 601     if atom_shape == '6b': #Cylinder NURBS
 602         bpy.ops.surface.primitive_nurbs_surface_cylinder_add(
 603             align='WORLD',
 604             enter_editmode=False,
 605             location=atom.location,
 606             rotation=(0, 0, 0))
 607     if atom_shape == '7': #Cone
 608         bpy.ops.mesh.primitive_cone_add(
 609             vertices=32,
 610             radius1=1,
 611             radius2=0,
 612             depth=2,
 613             end_fill_type='NGON',
 614             align='WORLD',
 615             enter_editmode=False,
 616             location=atom.location,
 617             rotation=(0, 0, 0))
 618     if atom_shape == '8a': #Torus
 619         bpy.ops.mesh.primitive_torus_add(
 620             rotation=(0, 0, 0),
 621             location=atom.location,
 622             align='WORLD',
 623             major_radius=1,
 624             minor_radius=0.25,
 625             major_segments=48,
 626             minor_segments=12,
 627             abso_major_rad=1,
 628             abso_minor_rad=0.5)
 629     if atom_shape == '8b': #Torus NURBS
 630         bpy.ops.surface.primitive_nurbs_surface_torus_add(
 631             align='WORLD',
 632             enter_editmode=False,
 633             location=atom.location,
 634             rotation=(0, 0, 0))
 635
 636     new_atom = bpy.context.view_layer.objects.active
 637     new_atom.scale = atom.scale + Vector((0.0,0.0,0.0))
 638     new_atom.name = atom.name
 639     new_atom.select_set(True)
 640
 641     new_atom.active_material = new_material
 642
 643     # If it is the representative object of a duplivert structure then
 644     # transfer the parent and hide the new object.
 645     if atom.parent != None:
 646         new_atom.parent = atom.parent
 647         new_atom.hide_set(True)
 648
 649     # Note the collection where the old object was placed into.
 650     coll_old_atom = get_collection_object(atom)
 651
 652     # Note the collection where the new object was placed into.
 653     coll_new_atom_past = get_collection_object(new_atom)
 654
 655     # If it is not the same collection then ...
 656     if coll_new_atom_past != coll_old_atom:
 657         # Put the new object into the collection of the old object and ...
 658         coll_old_atom.objects.link(new_atom)
 659         # ... unlink the new atom from its original collection.
 660         coll_new_atom_past.objects.unlink(new_atom)
 661
 662     # If necessary, remove the childrens of the old object.
 663     for child in atom.children:
 664         bpy.ops.object.select_all(action='DESELECT')
 665         child.hide_set(True)
 666         child.select_set(True)
 667         child.parent = None
 668         coll_child = get_collection_object(child)
 669         coll_child.objects.unlink(child)
 670         bpy.ops.object.delete()
 671         del(child)
 672
 673     # Deselect everything
 674     bpy.ops.object.select_all(action='DESELECT')
 675     # Make the old atom visible.
 676     atom.hide_set(True)
 677     # Select the old atom.
 678     atom.select_set(True)
 679     # Remove the parent if necessary.
 680     atom.parent = None
 681     # Unlink the old object from the collection.
 682     coll_old_atom.objects.unlink(atom)
 683     # Delete the old atom
 684     bpy.ops.object.delete()
 685     del(atom)
 686
 687     #if "_F2+_center" or "_F+_center" or "_F0_center" in coll_old_atom:
 688     #    print("Delete the collection")
 689
 690     return new_atom
 691
 692
 693 # Draw a special object (e.g. halo, etc. ...)
 694 def draw_obj_special(atom_shape, atom):
 695
 696     # Note the collection where 'atom' is placed into.
 697     coll_atom = get_collection_object(atom)
 698
 699     # Now, create a collection for the new objects
 700     coll_new = atom.name
 701     # Create the new collection and ...
 702     coll_new = bpy.data.collections.new(coll_new)
 703     # ... link it to the collection, which contains 'atom'.
 704     coll_atom.children.link(coll_new)
 705
 706
 707     # F2+ center
 708     if atom_shape == '1':
 709         # Create first a cube
 710         bpy.ops.mesh.primitive_cube_add(align='WORLD',
 711                                         enter_editmode=False,
 712                                         location=atom.location,
 713                                         rotation=(0.0, 0.0, 0.0))
 714         cube = bpy.context.view_layer.objects.active
 715         cube.scale = atom.scale + Vector((0.0,0.0,0.0))
 716         cube.name = atom.name + "_F2+_vac"
 717         cube.select_set(True)
 718         # New material for this cube
 719         material_cube = bpy.data.materials.new(atom.name + "_F2+_vac")
 720         material_cube.diffuse_color = [0.8, 0.0, 0.0, 1.0]
 721         material_cube.metallic = 0.8
 722         material_cube.specular_intensity = 0.5
 723         material_cube.roughness = 0.3
 724         material_cube.blend_method = 'OPAQUE'
 725         material_cube.show_transparent_back = True
 726         # Some properties for cycles
 727         material_cube.use_nodes = True
 728         mat_P_BSDF = material_cube.node_tree.nodes['Principled BSDF']
 729         mat_P_BSDF.inputs['Metallic'].default_value = 0.1
 730         mat_P_BSDF.inputs['Roughness'].default_value = 0.2
 731         mat_P_BSDF.inputs['Transmission'].default_value = 0.9
 732         mat_P_BSDF.inputs['IOR'].default_value = 0.8
 733         cube.active_material = material_cube
 734         # Put a nice point lamp inside the defect
 735         lamp_data = bpy.data.lights.new(name=atom.name + "_F2+_lamp",
 736                                         type="POINT")
 737         lamp_data.distance = atom.scale[0] * 2.0
 738         lamp_data.energy = 1.0
 739         lamp_data.color = (0.8, 0.8, 0.8)
 740         lamp = bpy.data.objects.new(atom.name + "_F2+_lamp", lamp_data)
 741         lamp.location = Vector((0.0, 0.0, 0.0))
 742         bpy.context.collection.objects.link(lamp)
 743         lamp.parent = cube
 744         # Some properties for cycles
 745         lamp.data.use_nodes = True
 746         lmp_P_BSDF = lamp.data.node_tree.nodes['Emission']
 747         lmp_P_BSDF.inputs['Strength'].default_value = 2000
 748         # The new 'atom' is the F2+ defect
 749         new_atom = cube
 750
 751         # Note the collection where all the new objects were placed into.
 752         # We use only one object, the cube
 753         coll_ori = get_collection_object(cube)
 754
 755         # If it is not the same collection then ...
 756         if coll_ori != coll_new:
 757             # Put all new objects into the new collection and ...
 758             coll_new.objects.link(cube)
 759             coll_new.objects.link(lamp)
 760             # ... unlink them from their original collection.
 761             coll_ori.objects.unlink(cube)
 762             coll_ori.objects.unlink(lamp)
 763
 764         coll_new.name = atom.name + "_F2+_center"
 765
 766         if atom.parent != None:
 767             cube.parent = atom.parent
 768             cube.hide_set(True)
 769             lamp.hide_set(True)
 770
 771     # F+ center
 772     if atom_shape == '2':
 773         # Create first a cube
 774         bpy.ops.mesh.primitive_cube_add(align='WORLD',
 775                                         enter_editmode=False,
 776                                         location=atom.location,
 777                                         rotation=(0.0, 0.0, 0.0))
 778         cube = bpy.context.view_layer.objects.active
 779         cube.scale = atom.scale + Vector((0.0,0.0,0.0))
 780         cube.name = atom.name + "_F+_vac"
 781         cube.select_set(True)
 782         # New material for this cube
 783         material_cube = bpy.data.materials.new(atom.name + "_F+_vac")
 784         material_cube.diffuse_color = [0.0, 0.0, 0.8, 1.0]
 785         material_cube.metallic = 0.8
 786         material_cube.specular_intensity = 0.5
 787         material_cube.roughness = 0.3
 788         material_cube.blend_method = 'OPAQUE'
 789         material_cube.show_transparent_back = True
 790         # Some properties for cycles
 791         material_cube.use_nodes = True
 792         mat_P_BSDF = material_cube.node_tree.nodes['Principled BSDF']
 793         mat_P_BSDF.inputs['Metallic'].default_value = 0.1
 794         mat_P_BSDF.inputs['Roughness'].default_value = 0.2
 795         mat_P_BSDF.inputs['Transmission'].default_value = 0.9
 796         mat_P_BSDF.inputs['IOR'].default_value = 0.8
 797         cube.active_material = material_cube
 798         # Create now an electron
 799         scale = atom.scale / 10.0
 800         bpy.ops.surface.primitive_nurbs_surface_sphere_add(
 801                                         align='WORLD',
 802                                         enter_editmode=False,
 803                                         location=(0.0, 0.0, 0.0),
 804                                         rotation=(0.0, 0.0, 0.0))
 805         electron = bpy.context.view_layer.objects.active
 806         electron.scale = scale
 807         electron.name = atom.name + "_F+_electron"
 808         electron.parent = cube
 809         # New material for the electron
 810         material_electron = bpy.data.materials.new(atom.name + "_F+-center")
 811         material_electron.diffuse_color = [0.0, 0.0, 0.8, 1.0]
 812         material_electron.metallic = 0.8
 813         material_electron.specular_intensity = 0.5
 814         material_electron.roughness = 0.3
 815         material_electron.blend_method = 'OPAQUE'
 816         material_electron.show_transparent_back = False
 817         electron.active_material = material_electron
 818         # Put a nice point lamp inside the electron
 819         lamp_data = bpy.data.lights.new(name=atom.name + "_F+_lamp",
 820                                         type="POINT")
 821         lamp_data.distance = atom.scale[0] * 2.0
 822         lamp_data.energy = 1.0
 823         lamp_data.color = (0.8, 0.8, 0.8)
 824         lamp = bpy.data.objects.new(atom.name + "_F+_lamp", lamp_data)
 825         lamp.location = Vector((scale[0]*1.5, 0.0, 0.0))
 826         bpy.context.collection.objects.link(lamp)
 827         lamp.parent = cube
 828         # Some properties for cycles
 829         lamp.data.use_nodes = True
 830         lmp_P_BSDF = lamp.data.node_tree.nodes['Emission']
 831         lmp_P_BSDF.inputs['Strength'].default_value = 2000
 832         # The new 'atom' is the F+ defect complex + lamp
 833         new_atom = cube
 834
 835         # Note the collection where all the new objects were placed into.
 836         # We use only one object, the cube
 837         coll_ori = get_collection_object(cube)
 838
 839         # If it is not the same collection then ...
 840         if coll_ori != coll_new:
 841             # Put all new objects into the new collection and ...
 842             coll_new.objects.link(cube)
 843             coll_new.objects.link(electron)
 844             coll_new.objects.link(lamp)
 845             # ... unlink them from their original collection.
 846             coll_ori.objects.unlink(cube)
 847             coll_ori.objects.unlink(electron)
 848             coll_ori.objects.unlink(lamp)
 849
 850         coll_new.name = atom.name + "_F+_center"
 851
 852         if atom.parent != None:
 853             cube.parent = atom.parent
 854             cube.hide_set(True)
 855             electron.hide_set(True)
 856             lamp.hide_set(True)
 857
 858     # F0 center
 859     if atom_shape == '3':
 860         # Create first a cube
 861         bpy.ops.mesh.primitive_cube_add(align='WORLD',
 862                                         enter_editmode=False,
 863                                         location=atom.location,
 864                                         rotation=(0.0, 0.0, 0.0))
 865         cube = bpy.context.view_layer.objects.active
 866         cube.scale = atom.scale + Vector((0.0,0.0,0.0))
 867         cube.name = atom.name + "_F0_vac"
 868         cube.select_set(True)
 869         # New material for this cube
 870         material_cube = bpy.data.materials.new(atom.name + "_F0_vac")
 871         material_cube.diffuse_color = [0.8, 0.8, 0.8, 1.0]
 872         material_cube.metallic = 0.8
 873         material_cube.specular_intensity = 0.5
 874         material_cube.roughness = 0.83
 875         material_cube.blend_method = 'OPAQUE'
 876         material_cube.show_transparent_back = True
 877         # Some properties for cycles
 878         material_cube.use_nodes = True
 879         mat_P_BSDF = material_cube.node_tree.nodes['Principled BSDF']
 880         mat_P_BSDF.inputs['Metallic'].default_value = 0.1
 881         mat_P_BSDF.inputs['Roughness'].default_value = 0.2
 882         mat_P_BSDF.inputs['Transmission'].default_value = 0.9
 883         mat_P_BSDF.inputs['IOR'].default_value = 0.8
 884         cube.active_material = material_cube
 885         # Create now two electrons
 886         scale = atom.scale / 10.0
 887         bpy.ops.surface.primitive_nurbs_surface_sphere_add(
 888                                         align='WORLD',
 889                                         enter_editmode=False,
 890                                         location=(scale[0]*1.5,0.0,0.0),
 891                                         rotation=(0.0, 0.0, 0.0))
 892         electron1 = bpy.context.view_layer.objects.active
 893         electron1.scale = scale
 894         electron1.name = atom.name + "_F0_electron1"
 895         electron1.parent = cube
 896         bpy.ops.surface.primitive_nurbs_surface_sphere_add(
 897                                         align='WORLD',
 898                                         enter_editmode=False,
 899                                         location=(-scale[0]*1.5,0.0,0.0),
 900                                         rotation=(0.0, 0.0, 0.0))
 901         electron2 = bpy.context.view_layer.objects.active
 902         electron2.scale = scale
 903         electron2.name = atom.name + "_F0_electron2"
 904         electron2.parent = cube
 905         # New material for the electrons
 906         material_electron = bpy.data.materials.new(atom.name + "_F0-center")
 907         material_electron.diffuse_color = [0.0, 0.0, 0.8, 1.0]
 908         material_electron.metallic = 0.8
 909         material_electron.specular_intensity = 0.5
 910         material_electron.roughness = 0.3
 911         material_electron.blend_method = 'OPAQUE'
 912         material_electron.show_transparent_back = False
 913         electron1.active_material = material_electron
 914         electron2.active_material = material_electron
 915         # Put two nice point lamps inside the electrons
 916         lamp1_data = bpy.data.lights.new(name=atom.name + "_F0_lamp1",
 917                                          type="POINT")
 918         lamp1_data.distance = atom.scale[0] * 2.0
 919         lamp1_data.energy = 1.0
 920         lamp1_data.color = (0.8, 0.8, 0.8)
 921         lamp1 = bpy.data.objects.new(atom.name + "_F0_lamp", lamp1_data)
 922         lamp1.location = Vector((scale[0]*1.5, 0.0, 0.0))
 923         bpy.context.collection.objects.link(lamp1)
 924         lamp1.parent = cube
 925         lamp2_data = bpy.data.lights.new(name=atom.name + "_F0_lamp2",
 926                                          type="POINT")
 927         lamp2_data.distance = atom.scale[0] * 2.0
 928         lamp2_data.energy = 1.0
 929         lamp2_data.color = (0.8, 0.8, 0.8)
 930         lamp2 = bpy.data.objects.new(atom.name + "_F0_lamp", lamp2_data)
 931         lamp2.location = Vector((-scale[0]*1.5, 0.0, 0.0))
 932         bpy.context.collection.objects.link(lamp2)
 933         lamp2.parent = cube
 934         # Some properties for cycles
 935         lamp1.data.use_nodes = True
 936         lamp2.data.use_nodes = True
 937         lmp1_P_BSDF = lamp1.data.node_tree.nodes['Emission']
 938         lmp2_P_BSDF = lamp1.data.node_tree.nodes['Emission']
 939         lmp1_P_BSDF.inputs['Strength'].default_value = 200
 940         lmp2_P_BSDF.inputs['Strength'].default_value = 200
 941         # The new 'atom' is the F0 defect complex + lamps
 942         new_atom = cube
 943
 944         # Note the collection where all the new objects were placed into.
 945         # We use only one object, the cube
 946         coll_ori = get_collection_object(cube)
 947
 948         # If it is not the same collection then ...
 949         if coll_ori != coll_new:
 950             # Put all new objects into the collection of 'atom' and ...
 951             coll_new.objects.link(cube)
 952             coll_new.objects.link(electron1)
 953             coll_new.objects.link(electron2)
 954             coll_new.objects.link(lamp1)
 955             coll_new.objects.link(lamp2)
 956             # ... unlink them from their original collection.
 957             coll_ori.objects.unlink(cube)
 958             coll_ori.objects.unlink(electron1)
 959             coll_ori.objects.unlink(electron2)
 960             coll_ori.objects.unlink(lamp1)
 961             coll_ori.objects.unlink(lamp2)
 962
 963         coll_new.name = atom.name + "_F0_center"
 964
 965         if atom.parent != None:
 966             cube.parent = atom.parent
 967             cube.hide_set(True)
 968             electron1.hide_set(True)
 969             electron2.hide_set(True)
 970             lamp1.hide_set(True)
 971             lamp2.hide_set(True)
 972
 973     # Deselect everything
 974     bpy.ops.object.select_all(action='DESELECT')
 975     # Make the old atom visible.
 976     atom.hide_set(True)
 977     # Select the old atom.
 978     atom.select_set(True)
 979     # Remove the parent if necessary.
 980     atom.parent = None
 981     # Unlink the old object from the collection.
 982     coll_atom.objects.unlink(atom)
 983     # Delete the old atom
 984     bpy.ops.object.delete()
 985     del(atom)
 986
 987     return new_atom
 988
 989
 990 # Initialization of the list 'ELEMENTS'.
 991 def read_elements():
 992
 993     del ELEMENTS[:]
 994
 995     for item in ELEMENTS_DEFAULT:
 996
 997         # All three radii into a list
 998         radii = [item[4],item[5],item[6]]
 999         # The handling of the ionic radii will be done later. So far, it is an
1000         # empty list.
1001         radii_ionic = item[7:]
1002
1003         li = ElementProp(item[0],item[1],item[2],item[3],
1004                                      radii,radii_ionic)
1005         ELEMENTS.append(li)
1006
1007
1008 # Custom data file: changing color and radii by using the list 'ELEMENTS'.
1009 def custom_datafile_change_atom_props():
1010
1011     for atom in bpy.context.selected_objects:
1012         if len(atom.children) != 0:
1013             child = atom.children[0]
1014             if child.type in {'SURFACE', 'MESH', 'META'}:
1015                 for element in ELEMENTS:
1016                     if element.name in atom.name:
1017                         child.scale = (element.radii[0],) * 3
1018                         child.active_material.diffuse_color = element.color
1019         else:
1020             if atom.type in {'SURFACE', 'MESH', 'META'}:
1021                 for element in ELEMENTS:
1022                     if element.name in atom.name:
1023                         atom.scale = (element.radii[0],) * 3
1024                         atom.active_material.diffuse_color = element.color
1025
1026
1027 # Reading a custom data file and modifying the list 'ELEMENTS'.
1028 def custom_datafile(path_datafile):
1029
1030     if path_datafile == "":
1031         return False
1032
1033     path_datafile = bpy.path.abspath(path_datafile)
1034
1035     if os.path.isfile(path_datafile) == False:
1036         return False
1037
1038     # The whole list gets deleted! We build it new.
1039     del ELEMENTS[:]
1040
1041     # Read the data file, which contains all data
1042     # (atom name, radii, colors, etc.)
1043     data_file_p = open(path_datafile, "r")
1044
1045     for line in data_file_p:
1046
1047         if "Atom" in line:
1048
1049             line = data_file_p.readline()
1050             # Number
1051             line = data_file_p.readline()
1052             number = line[19:-1]
1053             # Name
1054             line = data_file_p.readline()
1055             name = line[19:-1]
1056             # Short name
1057             line = data_file_p.readline()
1058             short_name = line[19:-1]
1059             # Color
1060             line = data_file_p.readline()
1061             color_value = line[19:-1].split(',')
1062             color = [float(color_value[0]),
1063                      float(color_value[1]),
1064                      float(color_value[2]),
1065                      float(color_value[3])]
1066             # Used radius
1067             line = data_file_p.readline()
1068             radius_used = float(line[19:-1])
1069             # Atomic radius
1070             line = data_file_p.readline()
1071             radius_atomic = float(line[19:-1])
1072             # Van der Waals radius
1073             line = data_file_p.readline()
1074             radius_vdW = float(line[19:-1])
1075             radii = [radius_used,radius_atomic,radius_vdW]
1076             radii_ionic = []
1077
1078             element = ElementProp(number,name,short_name,color,
1079                                               radii, radii_ionic)
1080
1081             ELEMENTS.append(element)
1082
1083     data_file_p.close()
1084
1085     return True