io_mesh_atomic/xyz_import.py

   1 # SPDX-License-Identifier: GPL-2.0-or-later
   2
   3 import os
   4 import bpy
   5 from math import pi, sqrt
   6 from mathutils import Vector, Matrix
   7
   8 # -----------------------------------------------------------------------------
   9 #                                                  Atom and element data
  10
  11
  12 # This is a list that contains some data of all possible elements. The structure
  13 # is as follows:
  14 #
  15 # 1, "Hydrogen", "H", [0.0,0.0,1.0], 0.32, 0.32, 0.32 , -1 , 1.54   means
  16 #
  17 # No., name, short name, color, radius (used), radius (covalent), radius (atomic),
  18 #
  19 # charge state 1, radius (ionic) 1, charge state 2, radius (ionic) 2, ... all
  20 # charge states for any atom are listed, if existing.
  21 # The list is fixed and cannot be changed ... (see below)
  22
  23 ELEMENTS_DEFAULT = (
  24 ( 1,      "Hydrogen",        "H", (  1.0,   1.0,   1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
  25 ( 2,        "Helium",       "He", ( 0.85,   1.0,   1.0, 1.0), 0.93, 0.93, 0.49 ),
  26 ( 3,       "Lithium",       "Li", (  0.8,  0.50,   1.0, 1.0), 1.23, 1.23, 2.05 ,  1 , 0.68 ),
  27 ( 4,     "Beryllium",       "Be", ( 0.76,   1.0,   0.0, 1.0), 0.90, 0.90, 1.40 ,  1 , 0.44 ,  2 , 0.35 ),
  28 ( 5,         "Boron",        "B", (  1.0,  0.70,  0.70, 1.0), 0.82, 0.82, 1.17 ,  1 , 0.35 ,  3 , 0.23 ),
  29 ( 6,        "Carbon",        "C", ( 0.56,  0.56,  0.56, 1.0), 0.77, 0.77, 0.91 , -4 , 2.60 ,  4 , 0.16 ),
  30 ( 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 ),
  31 ( 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 ),
  32 ( 9,      "Fluorine",        "F", ( 0.56,  0.87,  0.31, 1.0), 0.72, 0.72, 0.57 , -1 , 1.33 ,  7 , 0.08 ),
  33 (10,          "Neon",       "Ne", ( 0.70,  0.89,  0.96, 1.0), 0.71, 0.71, 0.51 ,  1 , 1.12 ),
  34 (11,        "Sodium",       "Na", ( 0.67,  0.36,  0.94, 1.0), 1.54, 1.54, 2.23 ,  1 , 0.97 ),
  35 (12,     "Magnesium",       "Mg", ( 0.54,   1.0,   0.0, 1.0), 1.36, 1.36, 1.72 ,  1 , 0.82 ,  2 , 0.66 ),
  36 (13,     "Aluminium",       "Al", ( 0.74,  0.65,  0.65, 1.0), 1.18, 1.18, 1.82 ,  3 , 0.51 ),
  37 (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 ),
  38 (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 ),
  39 (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 ),
  40 (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 ),
  41 (18,         "Argon",       "Ar", ( 0.50,  0.81,  0.89, 1.0), 0.98, 0.98, 0.88 ,  1 , 1.54 ),
  42 (19,     "Potassium",        "K", ( 0.56,  0.25,  0.83, 1.0), 2.03, 2.03, 2.77 ,  1 , 0.81 ),
  43 (20,       "Calcium",       "Ca", ( 0.23,   1.0,   0.0, 1.0), 1.74, 1.74, 2.23 ,  1 , 1.18 ,  2 , 0.99 ),
  44 (21,      "Scandium",       "Sc", ( 0.90,  0.90,  0.90, 1.0), 1.44, 1.44, 2.09 ,  3 , 0.73 ),
  45 (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 ),
  46 (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 ),
  47 (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 ),
  48 (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 ),
  49 (26,          "Iron",       "Fe", ( 0.87,   0.4,   0.2, 1.0), 1.17, 1.17, 1.72 ,  2 , 0.74 ,  3 , 0.64 ),
  50 (27,        "Cobalt",       "Co", ( 0.94,  0.56,  0.62, 1.0), 1.16, 1.16, 1.67 ,  2 , 0.72 ,  3 , 0.63 ),
  51 (28,        "Nickel",       "Ni", ( 0.31,  0.81,  0.31, 1.0), 1.15, 1.15, 1.62 ,  2 , 0.69 ),
  52 (29,        "Copper",       "Cu", ( 0.78,  0.50,   0.2, 1.0), 1.17, 1.17, 1.57 ,  1 , 0.96 ,  2 , 0.72 ),
  53 (30,          "Zinc",       "Zn", ( 0.49,  0.50,  0.69, 1.0), 1.25, 1.25, 1.53 ,  1 , 0.88 ,  2 , 0.74 ),
  54 (31,       "Gallium",       "Ga", ( 0.76,  0.56,  0.56, 1.0), 1.26, 1.26, 1.81 ,  1 , 0.81 ,  3 , 0.62 ),
  55 (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 ),
  56 (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 ),
  57 (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 ),
  58 (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 ),
  59 (36,       "Krypton",       "Kr", ( 0.36,  0.72,  0.81, 1.0), 1.31, 1.31, 1.24 ),
  60 (37,      "Rubidium",       "Rb", ( 0.43,  0.18,  0.69, 1.0), 2.16, 2.16, 2.98 ,  1 , 1.47 ),
  61 (38,     "Strontium",       "Sr", (  0.0,   1.0,   0.0, 1.0), 1.91, 1.91, 2.45 ,  2 , 1.12 ),
  62 (39,       "Yttrium",        "Y", ( 0.58,   1.0,   1.0, 1.0), 1.62, 1.62, 2.27 ,  3 , 0.89 ),
  63 (40,     "Zirconium",       "Zr", ( 0.58,  0.87,  0.87, 1.0), 1.45, 1.45, 2.16 ,  1 , 1.09 ,  4 , 0.79 ),
  64 (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 ),
  65 (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 ),
  66 (43,    "Technetium",       "Tc", ( 0.23,  0.61,  0.61, 1.0), 1.27, 1.27, 1.95 ,  7 , 0.97 ),
  67 (44,     "Ruthenium",       "Ru", ( 0.14,  0.56,  0.56, 1.0), 1.25, 1.25, 1.89 ,  4 , 0.67 ),
  68 (45,       "Rhodium",       "Rh", ( 0.03,  0.49,  0.54, 1.0), 1.25, 1.25, 1.83 ,  3 , 0.68 ),
  69 (46,     "Palladium",       "Pd", (  0.0,  0.41,  0.52, 1.0), 1.28, 1.28, 1.79 ,  2 , 0.80 ,  4 , 0.65 ),
  70 (47,        "Silver",       "Ag", ( 0.75,  0.75,  0.75, 1.0), 1.34, 1.34, 1.75 ,  1 , 1.26 ,  2 , 0.89 ),
  71 (48,       "Cadmium",       "Cd", (  1.0,  0.85,  0.56, 1.0), 1.48, 1.48, 1.71 ,  1 , 1.14 ,  2 , 0.97 ),
  72 (49,        "Indium",       "In", ( 0.65,  0.45,  0.45, 1.0), 1.44, 1.44, 2.00 ,  3 , 0.81 ),
  73 (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 ),
  74 (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 ),
  75 (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 ),
  76 (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 ),
  77 (54,         "Xenon",       "Xe", ( 0.25,  0.61,  0.69, 1.0), 1.31, 1.31, 1.24 ),
  78 (55,       "Caesium",       "Cs", ( 0.34,  0.09,  0.56, 1.0), 2.35, 2.35, 3.35 ,  1 , 1.67 ),
  79 (56,        "Barium",       "Ba", (  0.0,  0.78,   0.0, 1.0), 1.98, 1.98, 2.78 ,  1 , 1.53 ,  2 , 1.34 ),
  80 (57,     "Lanthanum",       "La", ( 0.43,  0.83,   1.0, 1.0), 1.69, 1.69, 2.74 ,  1 , 1.39 ,  3 , 1.06 ),
  81 (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 ),
  82 (59,  "Praseodymium",       "Pr", ( 0.85,   1.0,  0.78, 1.0), 1.65, 1.65, 2.67 ,  3 , 1.01 ,  4 , 0.90 ),
  83 (60,     "Neodymium",       "Nd", ( 0.78,   1.0,  0.78, 1.0), 1.64, 1.64, 2.64 ,  3 , 0.99 ),
  84 (61,    "Promethium",       "Pm", ( 0.63,   1.0,  0.78, 1.0), 1.63, 1.63, 2.62 ,  3 , 0.97 ),
  85 (62,      "Samarium",       "Sm", ( 0.56,   1.0,  0.78, 1.0), 1.62, 1.62, 2.59 ,  3 , 0.96 ),
  86 (63,      "Europium",       "Eu", ( 0.38,   1.0,  0.78, 1.0), 1.85, 1.85, 2.56 ,  2 , 1.09 ,  3 , 0.95 ),
  87 (64,    "Gadolinium",       "Gd", ( 0.27,   1.0,  0.78, 1.0), 1.61, 1.61, 2.54 ,  3 , 0.93 ),
  88 (65,       "Terbium",       "Tb", ( 0.18,   1.0,  0.78, 1.0), 1.59, 1.59, 2.51 ,  3 , 0.92 ,  4 , 0.84 ),
  89 (66,    "Dysprosium",       "Dy", ( 0.12,   1.0,  0.78, 1.0), 1.59, 1.59, 2.49 ,  3 , 0.90 ),
  90 (67,       "Holmium",       "Ho", (  0.0,   1.0,  0.61, 1.0), 1.58, 1.58, 2.47 ,  3 , 0.89 ),
  91 (68,        "Erbium",       "Er", (  0.0,  0.90,  0.45, 1.0), 1.57, 1.57, 2.45 ,  3 , 0.88 ),
  92 (69,       "Thulium",       "Tm", (  0.0,  0.83,  0.32, 1.0), 1.56, 1.56, 2.42 ,  3 , 0.87 ),
  93 (70,     "Ytterbium",       "Yb", (  0.0,  0.74,  0.21, 1.0), 1.74, 1.74, 2.40 ,  2 , 0.93 ,  3 , 0.85 ),
  94 (71,      "Lutetium",       "Lu", (  0.0,  0.67,  0.14, 1.0), 1.56, 1.56, 2.25 ,  3 , 0.85 ),
  95 (72,       "Hafnium",       "Hf", ( 0.30,  0.76,   1.0, 1.0), 1.44, 1.44, 2.16 ,  4 , 0.78 ),
  96 (73,      "Tantalum",       "Ta", ( 0.30,  0.65,   1.0, 1.0), 1.34, 1.34, 2.09 ,  5 , 0.68 ),
  97 (74,      "Tungsten",        "W", ( 0.12,  0.58,  0.83, 1.0), 1.30, 1.30, 2.02 ,  4 , 0.70 ,  6 , 0.62 ),
  98 (75,       "Rhenium",       "Re", ( 0.14,  0.49,  0.67, 1.0), 1.28, 1.28, 1.97 ,  4 , 0.72 ,  7 , 0.56 ),
  99 (76,        "Osmium",       "Os", ( 0.14,   0.4,  0.58, 1.0), 1.26, 1.26, 1.92 ,  4 , 0.88 ,  6 , 0.69 ),
 100 (77,       "Iridium",       "Ir", ( 0.09,  0.32,  0.52, 1.0), 1.27, 1.27, 1.87 ,  4 , 0.68 ),
 101 (78,      "Platinum",       "Pt", ( 0.81,  0.81,  0.87, 1.0), 1.30, 1.30, 1.83 ,  2 , 0.80 ,  4 , 0.65 ),
 102 (79,          "Gold",       "Au", (  1.0,  0.81,  0.13, 1.0), 1.34, 1.34, 1.79 ,  1 , 1.37 ,  3 , 0.85 ),
 103 (80,       "Mercury",       "Hg", ( 0.72,  0.72,  0.81, 1.0), 1.49, 1.49, 1.76 ,  1 , 1.27 ,  2 , 1.10 ),
 104 (81,      "Thallium",       "Tl", ( 0.65,  0.32,  0.30, 1.0), 1.48, 1.48, 2.08 ,  1 , 1.47 ,  3 , 0.95 ),
 105 (82,          "Lead",       "Pb", ( 0.34,  0.34,  0.38, 1.0), 1.47, 1.47, 1.81 ,  2 , 1.20 ,  4 , 0.84 ),
 106 (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 ),
 107 (84,      "Polonium",       "Po", ( 0.67,  0.36,   0.0, 1.0), 1.46, 1.46, 1.53 ,  6 , 0.67 ),
 108 (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 ),
 109 (86,         "Radon",       "Rn", ( 0.25,  0.50,  0.58, 1.0), 1.00, 1.00, 1.34 ),
 110 (87,      "Francium",       "Fr", ( 0.25,   0.0,   0.4, 1.0), 1.00, 1.00, 1.00 ,  1 , 1.80 ),
 111 (88,        "Radium",       "Ra", (  0.0,  0.49,   0.0, 1.0), 1.00, 1.00, 1.00 ,  2 , 1.43 ),
 112 (89,      "Actinium",       "Ac", ( 0.43,  0.67,  0.98, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.18 ),
 113 (90,       "Thorium",       "Th", (  0.0,  0.72,   1.0, 1.0), 1.65, 1.65, 1.00 ,  4 , 1.02 ),
 114 (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 ),
 115 (92,       "Uranium",        "U", (  0.0,  0.56,   1.0, 1.0), 1.42, 1.42, 1.00 ,  4 , 0.97 ,  6 , 0.80 ),
 116 (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 ),
 117 (94,     "Plutonium",       "Pu", (  0.0,  0.41,   1.0, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.08 ,  4 , 0.93 ),
 118 (95,     "Americium",       "Am", ( 0.32,  0.36,  0.94, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.07 ,  4 , 0.92 ),
 119 (96,        "Curium",       "Cm", ( 0.47,  0.36,  0.89, 1.0), 1.00, 1.00, 1.00 ),
 120 (97,     "Berkelium",       "Bk", ( 0.54,  0.30,  0.89, 1.0), 1.00, 1.00, 1.00 ),
 121 (98,   "Californium",       "Cf", ( 0.63,  0.21,  0.83, 1.0), 1.00, 1.00, 1.00 ),
 122 (99,   "Einsteinium",       "Es", ( 0.70,  0.12,  0.83, 1.0), 1.00, 1.00, 1.00 ),
 123 (100,       "Fermium",       "Fm", ( 0.70,  0.12, 0.72, 1.0), 1.00, 1.00, 1.00 ),
 124 (101,   "Mendelevium",       "Md", ( 0.70,  0.05, 0.65, 1.0), 1.00, 1.00, 1.00 ),
 125 (102,      "Nobelium",       "No", ( 0.74,  0.05, 0.52, 1.0), 1.00, 1.00, 1.00 ),
 126 (103,    "Lawrencium",       "Lr", ( 0.78,   0.0,  0.4, 1.0), 1.00, 1.00, 1.00 ),
 127 (104,       "Vacancy",      "Vac", (  0.5,   0.5,  0.5, 1.0), 1.00, 1.00, 1.00),
 128 (105,       "Default",  "Default", (  1.0,   1.0,  1.0, 1.0), 1.00, 1.00, 1.00),
 129 (106,         "Stick",    "Stick", (  0.5,   0.5,  0.5, 1.0), 1.00, 1.00, 1.00),
 130 )
 131
 132 # This list here contains all data of the elements and will be used during
 133 # runtime. It is a list of classes.
 134 # During executing Atomic Blender, the list will be initialized with the fixed
 135 # data from above via the class structure below (ElementProp). We
 136 # have then one fixed list (above), which will never be changed, and a list of
 137 # classes with same data. The latter can be modified via loading a separate
 138 # custom data file for instance.
 139 ELEMENTS = []
 140
 141 # This is the list, which contains all atoms of all frames! Each item is a
 142 # list which contains the atoms of a single frame. It is a list of
 143 # 'AtomProp'.
 144 ALL_FRAMES = []
 145
 146 # A list of ALL balls which are put into the scene
 147 STRUCTURE = []
 148
 149
 150 # This is the class, which stores the properties for one element.
 151 class ElementProp(object):
 152     __slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic')
 153     def __init__(self, number, name, short_name, color, radii, radii_ionic):
 154         self.number = number
 155         self.name = name
 156         self.short_name = short_name
 157         self.color = color
 158         self.radii = radii
 159         self.radii_ionic = radii_ionic
 160
 161 # This is the class, which stores the properties of one atom.
 162 class AtomProp(object):
 163     __slots__ = ('element', 'name', 'location', 'radius', 'color', 'material')
 164     def __init__(self, element, name, location, radius, color, material):
 165         self.element = element
 166         self.name = name
 167         self.location = location
 168         self.radius = radius
 169         self.color = color
 170         self.material = material
 171
 172
 173 # -----------------------------------------------------------------------------
 174 #                                                           Some basic routines
 175
 176 def read_elements():
 177
 178     del ELEMENTS[:]
 179
 180     for item in ELEMENTS_DEFAULT:
 181
 182         # All three radii into a list
 183         radii = [item[4],item[5],item[6]]
 184         # The handling of the ionic radii will be done later. So far, it is an
 185         # empty list.
 186         radii_ionic = []
 187
 188         li = ElementProp(item[0],item[1],item[2],item[3],
 189                                      radii,radii_ionic)
 190         ELEMENTS.append(li)
 191
 192
 193 # filepath_pdb: path to pdb file
 194 # radiustype  : '0' default
 195 #               '1' atomic radii
 196 #               '2' van der Waals
 197 def read_xyz_file(filepath_xyz,radiustype):
 198
 199     number_frames = 0
 200     total_number_atoms = 0
 201
 202     # Open the file ...
 203     filepath_xyz_p = open(filepath_xyz, "r")
 204
 205     #Go through the whole file.
 206     FLAG = False
 207     for line in filepath_xyz_p:
 208
 209         # ... the loop is broken here (EOF) ...
 210         if line == "":
 211             continue
 212
 213         split_list = line.rsplit()
 214
 215         if len(split_list) == 1:
 216             number_atoms = int(split_list[0])
 217             FLAG = True
 218
 219         if FLAG == True:
 220
 221             line = filepath_xyz_p.readline()
 222             line = line.rstrip()
 223
 224             all_atoms= []
 225             for i in range(number_atoms):
 226
 227
 228                 # This is a guarantee that only the total number of atoms of the
 229                 # first frame is used. Condition is, so far, that the number of
 230                 # atoms in a xyz file is constant. However, sometimes the number
 231                 # may increase (or decrease). If it decreases, the addon crashes.
 232                 # If it increases, only the tot number of atoms of the first frame
 233                 # is used.
 234                 # By time, I will allow varying atom numbers ... but this takes
 235                 # some time ...
 236                 if number_frames != 0:
 237                     if i >= total_number_atoms:
 238                         break
 239
 240
 241                 line = filepath_xyz_p.readline()
 242                 line = line.rstrip()
 243                 split_list = line.rsplit()
 244                 short_name = str(split_list[0])
 245
 246                 # Go through all elements and find the element of the current atom.
 247                 FLAG_FOUND = False
 248                 for element in ELEMENTS:
 249                     if str.upper(short_name) == str.upper(element.short_name):
 250                         # Give the atom its proper name, color and radius:
 251                         name = element.name
 252                         # int(radiustype) => type of radius:
 253                         # pre-defined (0), atomic (1) or van der Waals (2)
 254                         radius = float(element.radii[int(radiustype)])
 255                         color = element.color
 256                         FLAG_FOUND = True
 257                         break
 258
 259                 # Is it a vacancy or an 'unknown atom' ?
 260                 if FLAG_FOUND == False:
 261                     # Give this atom also a name. If it is an 'X' then it is a
 262                     # vacancy. Otherwise ...
 263                     if "X" in short_name:
 264                         short_name = "VAC"
 265                         name = "Vacancy"
 266                         radius = float(ELEMENTS[-3].radii[int(radiustype)])
 267                         color = ELEMENTS[-3].color
 268                     # ... take what is written in the xyz file. These are somewhat
 269                     # unknown atoms. This should never happen, the element list is
 270                     # almost complete. However, we do this due to security reasons.
 271                     else:
 272                         name = str.upper(short_name)
 273                         radius = float(ELEMENTS[-2].radii[int(radiustype)])
 274                         color = ELEMENTS[-2].color
 275
 276                 x = float(split_list[1])
 277                 y = float(split_list[2])
 278                 z = float(split_list[3])
 279
 280                 location = Vector((x,y,z))
 281
 282                 all_atoms.append([short_name, name, location, radius, color])
 283
 284             # We note here all elements. This needs to be done only once.
 285             if number_frames == 0:
 286
 287                 # This is a guarantee that only the total number of atoms of the
 288                 # first frame is used. Condition is, so far, that the number of
 289                 # atoms in a xyz file is constant. However, sometimes the number
 290                 # may increase (or decrease). If it decreases, the addon crashes.
 291                 # If it increases, only the tot number of atoms of the first frame
 292                 # is used.
 293                 # By time, I will allow varying atom numbers ... but this takes
 294                 # some time ...
 295                 total_number_atoms = number_atoms
 296
 297
 298                 elements = []
 299                 for atom in all_atoms:
 300                     FLAG_FOUND = False
 301                     for element in elements:
 302                         # If the atom name is already in the list,
 303                         # FLAG on 'True'.
 304                         if element == atom[1]:
 305                             FLAG_FOUND = True
 306                             break
 307                     # No name in the current list has been found? => New entry.
 308                     if FLAG_FOUND == False:
 309                         # Stored are: Atom label (e.g. 'Na'), the corresponding
 310                         # atom name (e.g. 'Sodium') and its color.
 311                         elements.append(atom[1])
 312
 313             # Sort the atoms: create lists of atoms of one type
 314             structure = []
 315             for element in elements:
 316                 atoms_one_type = []
 317                 for atom in all_atoms:
 318                     if atom[1] == element:
 319                         atoms_one_type.append(AtomProp(atom[0],
 320                                                        atom[1],
 321                                                        atom[2],
 322                                                        atom[3],
 323                                                        atom[4],[]))
 324                 structure.append(atoms_one_type)
 325
 326             ALL_FRAMES.append(structure)
 327             number_frames += 1
 328             FLAG = False
 329
 330     filepath_xyz_p.close()
 331
 332     return total_number_atoms
 333
 334
 335 # Rotate an object.
 336 def rotate_object(rot_mat, obj):
 337
 338     bpy.ops.object.select_all(action='DESELECT')
 339     obj.select_set(True)
 340
 341     # Decompose world_matrix's components, and from them assemble 4x4 matrices.
 342     orig_loc, orig_rot, orig_scale = obj.matrix_world.decompose()
 343
 344     orig_loc_mat   = Matrix.Translation(orig_loc)
 345     orig_rot_mat   = orig_rot.to_matrix().to_4x4()
 346     orig_scale_mat = (Matrix.Scale(orig_scale[0],4,(1,0,0)) @
 347                       Matrix.Scale(orig_scale[1],4,(0,1,0)) @
 348                       Matrix.Scale(orig_scale[2],4,(0,0,1)))
 349
 350     # Assemble the new matrix.
 351     obj.matrix_world = orig_loc_mat @ rot_mat @ orig_rot_mat @ orig_scale_mat
 352
 353
 354 # Function, which puts a camera and light source into the 3D scene
 355 def camera_light_source(use_camera,
 356                         use_light,
 357                         object_center_vec,
 358                         object_size):
 359
 360     camera_factor = 15.0
 361
 362     # If chosen a camera is put into the scene.
 363     if use_camera == True:
 364
 365         # Assume that the object is put into the global origin. Then, the
 366         # camera is moved in x and z direction, not in y. The object has its
 367         # size at distance sqrt(object_size) from the origin. So, move the
 368         # camera by this distance times a factor of camera_factor in x and z.
 369         # Then add x, y and z of the origin of the object.
 370         object_camera_vec = Vector((sqrt(object_size) * camera_factor,
 371                                     0.0,
 372                                     sqrt(object_size) * camera_factor))
 373         camera_xyz_vec = object_center_vec + object_camera_vec
 374
 375         # Create the camera
 376         camera_data = bpy.data.cameras.new("A_camera")
 377         camera_data.lens = 45
 378         camera_data.clip_end = 500.0
 379         camera = bpy.data.objects.new("A_camera", camera_data)
 380         camera.location = camera_xyz_vec
 381         bpy.context.collection.objects.link(camera)
 382
 383         # Here the camera is rotated such it looks towards the center of
 384         # the object. The [0.0, 0.0, 1.0] vector along the z axis
 385         z_axis_vec             = Vector((0.0, 0.0, 1.0))
 386         # The angle between the last two vectors
 387         angle                  = object_camera_vec.angle(z_axis_vec, 0)
 388         # The cross-product of z_axis_vec and object_camera_vec
 389         axis_vec               = z_axis_vec.cross(object_camera_vec)
 390         # Rotate 'axis_vec' by 'angle' and convert this to euler parameters.
 391         # 4 is the size of the matrix.
 392         camera.rotation_euler  = Matrix.Rotation(angle, 4, axis_vec).to_euler()
 393
 394         # Rotate the camera around its axis by 90° such that we have a nice
 395         # camera position and view onto the object.
 396         bpy.ops.object.select_all(action='DESELECT')
 397         camera.select_set(True)
 398
 399         # Rotate the camera around its axis 'object_camera_vec' by 90° such
 400         # that we have a nice camera view onto the object.
 401         matrix_rotation = Matrix.Rotation(90/360*2*pi, 4, object_camera_vec)
 402         rotate_object(matrix_rotation, camera)
 403
 404     # Here a lamp is put into the scene, if chosen.
 405     if use_light == True:
 406
 407         # This is the distance from the object measured in terms of %
 408         # of the camera distance. It is set onto 50% (1/2) distance.
 409         lamp_dl = sqrt(object_size) * 15 * 0.5
 410         # This is a factor to which extend the lamp shall go to the right
 411         # (from the camera  point of view).
 412         lamp_dy_right = lamp_dl * (3.0/4.0)
 413
 414         # Create x, y and z for the lamp.
 415         object_lamp_vec = Vector((lamp_dl,lamp_dy_right,lamp_dl))
 416         lamp_xyz_vec = object_center_vec + object_lamp_vec
 417         length = lamp_xyz_vec.length
 418
 419         # As a lamp we use a point source.
 420         lamp_data = bpy.data.lights.new(name="A_lamp", type="POINT")
 421         # We now determine the emission strength of the lamp. Note that the
 422         # intensity depends on 1/r^2. For this we use a value of 100000.0 at a
 423         # distance of 58. This value was determined manually inside Blender.
 424         lamp_data.energy = 500000.0 * ( (length * length) / (58.0 * 58.0) )
 425         lamp = bpy.data.objects.new("A_lamp", lamp_data)
 426         lamp.location = lamp_xyz_vec
 427         bpy.context.collection.objects.link(lamp)
 428
 429         # Some settings for the World: a bit ambient occlusion
 430         bpy.context.scene.world.light_settings.use_ambient_occlusion = True
 431         bpy.context.scene.world.light_settings.ao_factor = 0.1
 432
 433 # -----------------------------------------------------------------------------
 434 #                                                            The main routine
 435
 436 def import_xyz(Ball_type,
 437                Ball_azimuth,
 438                Ball_zenith,
 439                Ball_radius_factor,
 440                radiustype,
 441                Ball_distance_factor,
 442                put_to_center,
 443                put_to_center_all,
 444                use_camera,
 445                use_light,
 446                filepath_xyz):
 447
 448     # List of materials
 449     atom_material_list = []
 450
 451     # ------------------------------------------------------------------------
 452     # INITIALIZE THE ELEMENT LIST
 453
 454     read_elements()
 455
 456     # ------------------------------------------------------------------------
 457     # READING DATA OF ATOMS
 458
 459     Number_of_total_atoms = read_xyz_file(filepath_xyz, radiustype)
 460
 461     # We show the atoms of the first frame.
 462     first_frame = ALL_FRAMES[0]
 463
 464     # ------------------------------------------------------------------------
 465     # MATERIAL PROPERTIES FOR ATOMS
 466
 467     # Create first a new list of materials for each type of atom
 468     # (e.g. hydrogen)
 469     for atoms_of_one_type in first_frame:
 470         # Take the first atom
 471         atom = atoms_of_one_type[0]
 472         material = bpy.data.materials.new(atom.name)
 473         material.diffuse_color = atom.color
 474         material.use_nodes = True
 475         mat_P_BSDF = next(n for n in material.node_tree.nodes
 476                           if n.type == "BSDF_PRINCIPLED")
 477         mat_P_BSDF.inputs['Base Color'].default_value = atom.color
 478         material.name = atom.name
 479         atom_material_list.append(material)
 480
 481     # Now, we go through all atoms and give them a material. For all atoms ...
 482     for atoms_of_one_type in first_frame:
 483         for atom in atoms_of_one_type:
 484             # ... and all materials ...
 485             for material in atom_material_list:
 486                 # ... select the correct material for the current atom via
 487                 # comparison of names ...
 488                 if atom.name in material.name:
 489                     # ... and give the atom its material properties.
 490                     # However, before we check if it is a vacancy
 491                     # The vacancy is represented by a transparent cube.
 492                     if atom.name == "Vacancy":
 493                         # For cycles and eevee.
 494                         material.use_nodes = True
 495                         mat_P_BSDF = next(n for n in material.node_tree.nodes
 496                                           if n.type == "BSDF_PRINCIPLED")
 497                         mat_P_BSDF.inputs['Metallic'].default_value = 0.1
 498                         mat_P_BSDF.inputs['Specular'].default_value = 0.15
 499                         mat_P_BSDF.inputs['Roughness'].default_value = 0.05
 500                         mat_P_BSDF.inputs['Clearcoat Roughness'].default_value = 0.37
 501                         mat_P_BSDF.inputs['IOR'].default_value = 0.8
 502                         mat_P_BSDF.inputs['Transmission'].default_value = 0.6
 503                         mat_P_BSDF.inputs['Transmission Roughness'].default_value = 0.0
 504                         mat_P_BSDF.inputs['Alpha'].default_value = 0.5
 505                         # Some additional stuff for eevee.
 506                         material.blend_method = 'HASHED'
 507                         material.shadow_method = 'HASHED'
 508                         material.use_backface_culling = False
 509                     # The atom gets its properties.
 510                     atom.material = material
 511
 512     # ------------------------------------------------------------------------
 513     # TRANSLATION OF THE STRUCTURE TO THE ORIGIN
 514
 515     # It may happen that the structure in a XYZ file already has an offset
 516
 517
 518     # If chosen, the structure is put into the center of the scene
 519     # (only the first frame).
 520     if put_to_center == True and put_to_center_all == False:
 521
 522         sum_vec = Vector((0.0,0.0,0.0))
 523
 524         # Sum of all atom coordinates
 525         for atoms_of_one_type in first_frame:
 526             sum_vec = sum([atom.location for atom in atoms_of_one_type], sum_vec)
 527
 528         # Then the average is taken
 529         sum_vec = sum_vec / Number_of_total_atoms
 530
 531         # After, for each atom the center of gravity is substracted
 532         for atoms_of_one_type in first_frame:
 533             for atom in atoms_of_one_type:
 534                 atom.location -= sum_vec
 535
 536     # If chosen, the structure is put into the center of the scene
 537     # (all frames).
 538     if put_to_center_all == True:
 539
 540         # For all frames
 541         for frame in ALL_FRAMES:
 542
 543             sum_vec = Vector((0.0,0.0,0.0))
 544
 545             # Sum of all atom coordinates
 546             for (i, atoms_of_one_type) in enumerate(frame):
 547
 548                 # This is a guarantee that only the total number of atoms of the
 549                 # first frame is used. Condition is, so far, that the number of
 550                 # atoms in a xyz file is constant. However, sometimes the number
 551                 # may increase (or decrease). If it decreases, the addon crashes.
 552                 # If it increases, only the tot number of atoms of the first frame
 553                 # is used.
 554                 # By time, I will allow varying atom numbers ... but this takes
 555                 # some time ...
 556                 if i >= Number_of_total_atoms:
 557                     break
 558
 559                 sum_vec = sum([atom.location for atom in atoms_of_one_type], sum_vec)
 560
 561             # Then the average is taken
 562             sum_vec = sum_vec / Number_of_total_atoms
 563
 564             # After, for each atom the center of gravity is substracted
 565             for atoms_of_one_type in frame:
 566                 for atom in atoms_of_one_type:
 567                     atom.location -= sum_vec
 568
 569
 570     # ------------------------------------------------------------------------
 571     # SCALING
 572
 573     # Take all atoms and adjust their radii and scale the distances.
 574     for atoms_of_one_type in first_frame:
 575         for atom in atoms_of_one_type:
 576             atom.location *= Ball_distance_factor
 577
 578     # ------------------------------------------------------------------------
 579     # DETERMINATION OF SOME GEOMETRIC PROPERTIES
 580
 581     # In the following, some geometric properties of the whole object are
 582     # determined: center, size, etc.
 583     sum_vec = Vector((0.0,0.0,0.0))
 584
 585     # First the center is determined. All coordinates are summed up ...
 586     for atoms_of_one_type in first_frame:
 587         sum_vec = sum([atom.location for atom in atoms_of_one_type], sum_vec)
 588
 589     # ... and the average is taken. This gives the center of the object.
 590     object_center_vec = sum_vec / Number_of_total_atoms
 591
 592     # Now, we determine the size.The farthest atom from the object center is
 593     # taken as a measure. The size is used to place well the camera and light
 594     # into the scene.
 595
 596     object_size_vec = []
 597     for atoms_of_one_type in first_frame:
 598         object_size_vec += [atom.location - object_center_vec for atom in atoms_of_one_type]
 599
 600     object_size = 0.0
 601     object_size = max(object_size_vec).length
 602
 603     # ------------------------------------------------------------------------
 604     # COLLECTION
 605
 606     # Before we start to draw the atoms, we first create a collection for the
 607     # atomic structure. All atoms (balls) are put into this collection.
 608     coll_structure_name = os.path.basename(filepath_xyz)
 609     scene = bpy.context.scene
 610     coll_structure = bpy.data.collections.new(coll_structure_name)
 611     scene.collection.children.link(coll_structure)
 612
 613     # ------------------------------------------------------------------------
 614     # DRAWING THE ATOMS
 615
 616     bpy.ops.object.select_all(action='DESELECT')
 617
 618     # For each list of atoms of ONE type (e.g. Hydrogen)
 619     for atoms_of_one_type in first_frame:
 620
 621         # Create first the vertices composed of the coordinates of all
 622         # atoms of one type
 623         atom_vertices = []
 624         for atom in atoms_of_one_type:
 625             # In fact, the object is created in the World's origin.
 626             # This is why 'object_center_vec' is substracted. At the end
 627             # the whole object is translated back to 'object_center_vec'.
 628             atom_vertices.append( atom.location - object_center_vec )
 629
 630         # First, we create a collection of the element, which
 631         # contains the atoms (balls + mesh)!
 632         coll_element_name = atom.name # the element name
 633         # Create the new collection and ...
 634         coll_element = bpy.data.collections.new(coll_element_name)
 635         # ... link it to the collection, which contains all parts of the
 636         # structure.
 637         coll_structure.children.link(coll_element)
 638
 639         # Now, create a collection for the atoms, which includes the
 640         # representative ball and the mesh.
 641         coll_atom_name = atom.name + "_atom"
 642         # Create the new collection and ...
 643         coll_atom = bpy.data.collections.new(coll_atom_name)
 644         # ... link it to the collection, which contains all parts of the
 645         # element (ball and mesh).
 646         coll_element.children.link(coll_atom)
 647
 648         # Build the mesh
 649         atom_mesh = bpy.data.meshes.new("Mesh_"+atom.name)
 650         atom_mesh.from_pydata(atom_vertices, [], [])
 651         atom_mesh.update()
 652         new_atom_mesh = bpy.data.objects.new(atom.name + "_mesh", atom_mesh)
 653
 654         # Link active object to the new collection
 655         coll_atom.objects.link(new_atom_mesh)
 656
 657         # Now, build a representative sphere (atom)
 658         if atom.name == "Vacancy":
 659             bpy.ops.mesh.primitive_cube_add(
 660                             align='WORLD', enter_editmode=False,
 661                             location=(0.0, 0.0, 0.0),
 662                             rotation=(0.0, 0.0, 0.0))
 663         else:
 664             # NURBS balls
 665             if Ball_type == "0":
 666                 bpy.ops.surface.primitive_nurbs_surface_sphere_add(
 667                             align='WORLD', enter_editmode=False,
 668                             location=(0,0,0), rotation=(0.0, 0.0, 0.0))
 669             # UV balls
 670             elif Ball_type == "1":
 671                 bpy.ops.mesh.primitive_uv_sphere_add(
 672                             segments=Ball_azimuth, ring_count=Ball_zenith,
 673                             align='WORLD', enter_editmode=False,
 674                             location=(0,0,0), rotation=(0, 0, 0))
 675             # Meta balls
 676             elif Ball_type == "2":
 677                 bpy.ops.object.metaball_add(type='BALL', align='WORLD',
 678                             enter_editmode=False, location=(0, 0, 0),
 679                             rotation=(0, 0, 0))
 680
 681         ball = bpy.context.view_layer.objects.active
 682         # Hide this ball because its appearance has no meaning. It is just the
 683         # representative ball. The ball is visible at the vertices of the mesh.
 684         # Rememmber, this is a dupliverts construct!
 685         # However, hiding does not work with meta balls!
 686         if Ball_type == "0" or Ball_type == "1":
 687             ball.hide_set(True)
 688         # Scale up/down the ball radius.
 689         ball.scale  = (atom.radius*Ball_radius_factor,) * 3
 690
 691         if atom.name == "Vacancy":
 692             ball.name = atom.name + "_cube"
 693         else:
 694             ball.name = atom.name + "_ball"
 695         ball.active_material = atom.material
 696         ball.parent = new_atom_mesh
 697         new_atom_mesh.instance_type = 'VERTS'
 698         # The object is back translated to 'object_center_vec'.
 699         new_atom_mesh.location = object_center_vec
 700         STRUCTURE.append(new_atom_mesh)
 701
 702         # Note the collection where the ball was placed into.
 703         coll_all = ball.users_collection
 704         if len(coll_all) > 0:
 705             coll_past = coll_all[0]
 706         else:
 707             coll_past = bpy.context.scene.collection
 708
 709         # Put the atom into the new collection 'atom' and ...
 710         coll_atom.objects.link(ball)
 711         # ... unlink the atom from the other collection.
 712         coll_past.objects.unlink(ball)
 713
 714     # ------------------------------------------------------------------------
 715     # CAMERA and LIGHT SOURCES
 716
 717     camera_light_source(use_camera,
 718                         use_light,
 719                         object_center_vec,
 720                         object_size)
 721
 722     # ------------------------------------------------------------------------
 723     # SELECT ALL LOADED OBJECTS
 724
 725     bpy.ops.object.select_all(action='DESELECT')
 726     obj = None
 727     for obj in STRUCTURE:
 728         obj.select_set(True)
 729     # activate the last selected object (perhaps another should be active?)
 730     if obj:
 731         bpy.context.view_layer.objects.active = obj
 732
 733
 734
 735 def build_frames(frame_delta, frame_skip):
 736
 737     scn = bpy.context.scene
 738
 739     # Introduce the basis for all elements that appear in the structure.
 740     for element in STRUCTURE:
 741
 742         bpy.ops.object.select_all(action='DESELECT')
 743         bpy.context.view_layer.objects.active = element
 744         element.select_set(True)
 745         bpy.ops.object.shape_key_add(True)
 746
 747     frame_skip += 1
 748
 749     # Introduce the keys and reference the atom positions for each key.
 750     i = 0
 751     for j, frame in enumerate(ALL_FRAMES):
 752
 753         if j % frame_skip == 0:
 754
 755             for elements_frame, elements_structure in zip(frame,STRUCTURE):
 756
 757                 key = elements_structure.shape_key_add()
 758
 759                 for atom_frame, atom_structure in zip(elements_frame, key.data):
 760
 761                     atom_structure.co = (atom_frame.location
 762                                        - elements_structure.location)
 763
 764                 key.name = atom_frame.name + "_frame_" + str(i)
 765
 766             i += 1
 767
 768     num_frames = i
 769
 770     scn.frame_start = 0
 771     scn.frame_end = frame_delta * num_frames
 772
 773     # Manage the values of the keys
 774     for element in STRUCTURE:
 775
 776         scn.frame_current = 0
 777
 778         element.data.shape_keys.key_blocks[1].value = 1.0
 779         element.data.shape_keys.key_blocks[2].value = 0.0
 780         element.data.shape_keys.key_blocks[1].keyframe_insert("value")
 781         element.data.shape_keys.key_blocks[2].keyframe_insert("value")
 782
 783         scn.frame_current += frame_delta
 784
 785         number = 0
 786
 787         for number in range(num_frames)[2:]:#-1]:
 788
 789             element.data.shape_keys.key_blocks[number-1].value = 0.0
 790             element.data.shape_keys.key_blocks[number].value = 1.0
 791             element.data.shape_keys.key_blocks[number+1].value = 0.0
 792             element.data.shape_keys.key_blocks[number-1].keyframe_insert("value")
 793             element.data.shape_keys.key_blocks[number].keyframe_insert("value")
 794             element.data.shape_keys.key_blocks[number+1].keyframe_insert("value")
 795
 796             scn.frame_current += frame_delta
 797
 798         number += 1
 799
 800         element.data.shape_keys.key_blocks[number].value = 1.0
 801         element.data.shape_keys.key_blocks[number-1].value = 0.0
 802         element.data.shape_keys.key_blocks[number].keyframe_insert("value")
 803         element.data.shape_keys.key_blocks[number-1].keyframe_insert("value")