io_mesh_atomic/xyz_import.py

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  17 # ##### END GPL LICENSE BLOCK #####
  18
  19 import os
  20 import bpy
  21 from math import pi, sqrt
  22 from mathutils import Vector, Matrix
  23
  24 # -----------------------------------------------------------------------------
  25 #                                                  Atom and element data
  26
  27
  28 # This is a list that contains some data of all possible elements. The structure
  29 # is as follows:
  30 #
  31 # 1, "Hydrogen", "H", [0.0,0.0,1.0], 0.32, 0.32, 0.32 , -1 , 1.54   means
  32 #
  33 # No., name, short name, color, radius (used), radius (covalent), radius (atomic),
  34 #
  35 # charge state 1, radius (ionic) 1, charge state 2, radius (ionic) 2, ... all
  36 # charge states for any atom are listed, if existing.
  37 # The list is fixed and cannot be changed ... (see below)
  38
  39 ELEMENTS_DEFAULT = (
  40 ( 1,      "Hydrogen",        "H", (  1.0,   1.0,   1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
  41 ( 2,        "Helium",       "He", ( 0.85,   1.0,   1.0, 1.0), 0.93, 0.93, 0.49 ),
  42 ( 3,       "Lithium",       "Li", (  0.8,  0.50,   1.0, 1.0), 1.23, 1.23, 2.05 ,  1 , 0.68 ),
  43 ( 4,     "Beryllium",       "Be", ( 0.76,   1.0,   0.0, 1.0), 0.90, 0.90, 1.40 ,  1 , 0.44 ,  2 , 0.35 ),
  44 ( 5,         "Boron",        "B", (  1.0,  0.70,  0.70, 1.0), 0.82, 0.82, 1.17 ,  1 , 0.35 ,  3 , 0.23 ),
  45 ( 6,        "Carbon",        "C", ( 0.56,  0.56,  0.56, 1.0), 0.77, 0.77, 0.91 , -4 , 2.60 ,  4 , 0.16 ),
  46 ( 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 ),
  47 ( 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 ),
  48 ( 9,      "Fluorine",        "F", ( 0.56,  0.87,  0.31, 1.0), 0.72, 0.72, 0.57 , -1 , 1.33 ,  7 , 0.08 ),
  49 (10,          "Neon",       "Ne", ( 0.70,  0.89,  0.96, 1.0), 0.71, 0.71, 0.51 ,  1 , 1.12 ),
  50 (11,        "Sodium",       "Na", ( 0.67,  0.36,  0.94, 1.0), 1.54, 1.54, 2.23 ,  1 , 0.97 ),
  51 (12,     "Magnesium",       "Mg", ( 0.54,   1.0,   0.0, 1.0), 1.36, 1.36, 1.72 ,  1 , 0.82 ,  2 , 0.66 ),
  52 (13,     "Aluminium",       "Al", ( 0.74,  0.65,  0.65, 1.0), 1.18, 1.18, 1.82 ,  3 , 0.51 ),
  53 (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 ),
  54 (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 ),
  55 (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 ),
  56 (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 ),
  57 (18,         "Argon",       "Ar", ( 0.50,  0.81,  0.89, 1.0), 0.98, 0.98, 0.88 ,  1 , 1.54 ),
  58 (19,     "Potassium",        "K", ( 0.56,  0.25,  0.83, 1.0), 2.03, 2.03, 2.77 ,  1 , 0.81 ),
  59 (20,       "Calcium",       "Ca", ( 0.23,   1.0,   0.0, 1.0), 1.74, 1.74, 2.23 ,  1 , 1.18 ,  2 , 0.99 ),
  60 (21,      "Scandium",       "Sc", ( 0.90,  0.90,  0.90, 1.0), 1.44, 1.44, 2.09 ,  3 , 0.73 ),
  61 (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 ),
  62 (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 ),
  63 (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 ),
  64 (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 ),
  65 (26,          "Iron",       "Fe", ( 0.87,   0.4,   0.2, 1.0), 1.17, 1.17, 1.72 ,  2 , 0.74 ,  3 , 0.64 ),
  66 (27,        "Cobalt",       "Co", ( 0.94,  0.56,  0.62, 1.0), 1.16, 1.16, 1.67 ,  2 , 0.72 ,  3 , 0.63 ),
  67 (28,        "Nickel",       "Ni", ( 0.31,  0.81,  0.31, 1.0), 1.15, 1.15, 1.62 ,  2 , 0.69 ),
  68 (29,        "Copper",       "Cu", ( 0.78,  0.50,   0.2, 1.0), 1.17, 1.17, 1.57 ,  1 , 0.96 ,  2 , 0.72 ),
  69 (30,          "Zinc",       "Zn", ( 0.49,  0.50,  0.69, 1.0), 1.25, 1.25, 1.53 ,  1 , 0.88 ,  2 , 0.74 ),
  70 (31,       "Gallium",       "Ga", ( 0.76,  0.56,  0.56, 1.0), 1.26, 1.26, 1.81 ,  1 , 0.81 ,  3 , 0.62 ),
  71 (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 ),
  72 (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 ),
  73 (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 ),
  74 (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 ),
  75 (36,       "Krypton",       "Kr", ( 0.36,  0.72,  0.81, 1.0), 1.31, 1.31, 1.24 ),
  76 (37,      "Rubidium",       "Rb", ( 0.43,  0.18,  0.69, 1.0), 2.16, 2.16, 2.98 ,  1 , 1.47 ),
  77 (38,     "Strontium",       "Sr", (  0.0,   1.0,   0.0, 1.0), 1.91, 1.91, 2.45 ,  2 , 1.12 ),
  78 (39,       "Yttrium",        "Y", ( 0.58,   1.0,   1.0, 1.0), 1.62, 1.62, 2.27 ,  3 , 0.89 ),
  79 (40,     "Zirconium",       "Zr", ( 0.58,  0.87,  0.87, 1.0), 1.45, 1.45, 2.16 ,  1 , 1.09 ,  4 , 0.79 ),
  80 (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 ),
  81 (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 ),
  82 (43,    "Technetium",       "Tc", ( 0.23,  0.61,  0.61, 1.0), 1.27, 1.27, 1.95 ,  7 , 0.97 ),
  83 (44,     "Ruthenium",       "Ru", ( 0.14,  0.56,  0.56, 1.0), 1.25, 1.25, 1.89 ,  4 , 0.67 ),
  84 (45,       "Rhodium",       "Rh", ( 0.03,  0.49,  0.54, 1.0), 1.25, 1.25, 1.83 ,  3 , 0.68 ),
  85 (46,     "Palladium",       "Pd", (  0.0,  0.41,  0.52, 1.0), 1.28, 1.28, 1.79 ,  2 , 0.80 ,  4 , 0.65 ),
  86 (47,        "Silver",       "Ag", ( 0.75,  0.75,  0.75, 1.0), 1.34, 1.34, 1.75 ,  1 , 1.26 ,  2 , 0.89 ),
  87 (48,       "Cadmium",       "Cd", (  1.0,  0.85,  0.56, 1.0), 1.48, 1.48, 1.71 ,  1 , 1.14 ,  2 , 0.97 ),
  88 (49,        "Indium",       "In", ( 0.65,  0.45,  0.45, 1.0), 1.44, 1.44, 2.00 ,  3 , 0.81 ),
  89 (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 ),
  90 (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 ),
  91 (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 ),
  92 (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 ),
  93 (54,         "Xenon",       "Xe", ( 0.25,  0.61,  0.69, 1.0), 1.31, 1.31, 1.24 ),
  94 (55,       "Caesium",       "Cs", ( 0.34,  0.09,  0.56, 1.0), 2.35, 2.35, 3.35 ,  1 , 1.67 ),
  95 (56,        "Barium",       "Ba", (  0.0,  0.78,   0.0, 1.0), 1.98, 1.98, 2.78 ,  1 , 1.53 ,  2 , 1.34 ),
  96 (57,     "Lanthanum",       "La", ( 0.43,  0.83,   1.0, 1.0), 1.69, 1.69, 2.74 ,  1 , 1.39 ,  3 , 1.06 ),
  97 (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 ),
  98 (59,  "Praseodymium",       "Pr", ( 0.85,   1.0,  0.78, 1.0), 1.65, 1.65, 2.67 ,  3 , 1.01 ,  4 , 0.90 ),
  99 (60,     "Neodymium",       "Nd", ( 0.78,   1.0,  0.78, 1.0), 1.64, 1.64, 2.64 ,  3 , 0.99 ),
 100 (61,    "Promethium",       "Pm", ( 0.63,   1.0,  0.78, 1.0), 1.63, 1.63, 2.62 ,  3 , 0.97 ),
 101 (62,      "Samarium",       "Sm", ( 0.56,   1.0,  0.78, 1.0), 1.62, 1.62, 2.59 ,  3 , 0.96 ),
 102 (63,      "Europium",       "Eu", ( 0.38,   1.0,  0.78, 1.0), 1.85, 1.85, 2.56 ,  2 , 1.09 ,  3 , 0.95 ),
 103 (64,    "Gadolinium",       "Gd", ( 0.27,   1.0,  0.78, 1.0), 1.61, 1.61, 2.54 ,  3 , 0.93 ),
 104 (65,       "Terbium",       "Tb", ( 0.18,   1.0,  0.78, 1.0), 1.59, 1.59, 2.51 ,  3 , 0.92 ,  4 , 0.84 ),
 105 (66,    "Dysprosium",       "Dy", ( 0.12,   1.0,  0.78, 1.0), 1.59, 1.59, 2.49 ,  3 , 0.90 ),
 106 (67,       "Holmium",       "Ho", (  0.0,   1.0,  0.61, 1.0), 1.58, 1.58, 2.47 ,  3 , 0.89 ),
 107 (68,        "Erbium",       "Er", (  0.0,  0.90,  0.45, 1.0), 1.57, 1.57, 2.45 ,  3 , 0.88 ),
 108 (69,       "Thulium",       "Tm", (  0.0,  0.83,  0.32, 1.0), 1.56, 1.56, 2.42 ,  3 , 0.87 ),
 109 (70,     "Ytterbium",       "Yb", (  0.0,  0.74,  0.21, 1.0), 1.74, 1.74, 2.40 ,  2 , 0.93 ,  3 , 0.85 ),
 110 (71,      "Lutetium",       "Lu", (  0.0,  0.67,  0.14, 1.0), 1.56, 1.56, 2.25 ,  3 , 0.85 ),
 111 (72,       "Hafnium",       "Hf", ( 0.30,  0.76,   1.0, 1.0), 1.44, 1.44, 2.16 ,  4 , 0.78 ),
 112 (73,      "Tantalum",       "Ta", ( 0.30,  0.65,   1.0, 1.0), 1.34, 1.34, 2.09 ,  5 , 0.68 ),
 113 (74,      "Tungsten",        "W", ( 0.12,  0.58,  0.83, 1.0), 1.30, 1.30, 2.02 ,  4 , 0.70 ,  6 , 0.62 ),
 114 (75,       "Rhenium",       "Re", ( 0.14,  0.49,  0.67, 1.0), 1.28, 1.28, 1.97 ,  4 , 0.72 ,  7 , 0.56 ),
 115 (76,        "Osmium",       "Os", ( 0.14,   0.4,  0.58, 1.0), 1.26, 1.26, 1.92 ,  4 , 0.88 ,  6 , 0.69 ),
 116 (77,       "Iridium",       "Ir", ( 0.09,  0.32,  0.52, 1.0), 1.27, 1.27, 1.87 ,  4 , 0.68 ),
 117 (78,      "Platinum",       "Pt", ( 0.81,  0.81,  0.87, 1.0), 1.30, 1.30, 1.83 ,  2 , 0.80 ,  4 , 0.65 ),
 118 (79,          "Gold",       "Au", (  1.0,  0.81,  0.13, 1.0), 1.34, 1.34, 1.79 ,  1 , 1.37 ,  3 , 0.85 ),
 119 (80,       "Mercury",       "Hg", ( 0.72,  0.72,  0.81, 1.0), 1.49, 1.49, 1.76 ,  1 , 1.27 ,  2 , 1.10 ),
 120 (81,      "Thallium",       "Tl", ( 0.65,  0.32,  0.30, 1.0), 1.48, 1.48, 2.08 ,  1 , 1.47 ,  3 , 0.95 ),
 121 (82,          "Lead",       "Pb", ( 0.34,  0.34,  0.38, 1.0), 1.47, 1.47, 1.81 ,  2 , 1.20 ,  4 , 0.84 ),
 122 (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 ),
 123 (84,      "Polonium",       "Po", ( 0.67,  0.36,   0.0, 1.0), 1.46, 1.46, 1.53 ,  6 , 0.67 ),
 124 (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 ),
 125 (86,         "Radon",       "Rn", ( 0.25,  0.50,  0.58, 1.0), 1.00, 1.00, 1.34 ),
 126 (87,      "Francium",       "Fr", ( 0.25,   0.0,   0.4, 1.0), 1.00, 1.00, 1.00 ,  1 , 1.80 ),
 127 (88,        "Radium",       "Ra", (  0.0,  0.49,   0.0, 1.0), 1.00, 1.00, 1.00 ,  2 , 1.43 ),
 128 (89,      "Actinium",       "Ac", ( 0.43,  0.67,  0.98, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.18 ),
 129 (90,       "Thorium",       "Th", (  0.0,  0.72,   1.0, 1.0), 1.65, 1.65, 1.00 ,  4 , 1.02 ),
 130 (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 ),
 131 (92,       "Uranium",        "U", (  0.0,  0.56,   1.0, 1.0), 1.42, 1.42, 1.00 ,  4 , 0.97 ,  6 , 0.80 ),
 132 (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 ),
 133 (94,     "Plutonium",       "Pu", (  0.0,  0.41,   1.0, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.08 ,  4 , 0.93 ),
 134 (95,     "Americium",       "Am", ( 0.32,  0.36,  0.94, 1.0), 1.00, 1.00, 1.00 ,  3 , 1.07 ,  4 , 0.92 ),
 135 (96,        "Curium",       "Cm", ( 0.47,  0.36,  0.89, 1.0), 1.00, 1.00, 1.00 ),
 136 (97,     "Berkelium",       "Bk", ( 0.54,  0.30,  0.89, 1.0), 1.00, 1.00, 1.00 ),
 137 (98,   "Californium",       "Cf", ( 0.63,  0.21,  0.83, 1.0), 1.00, 1.00, 1.00 ),
 138 (99,   "Einsteinium",       "Es", ( 0.70,  0.12,  0.83, 1.0), 1.00, 1.00, 1.00 ),
 139 (100,       "Fermium",       "Fm", ( 0.70,  0.12, 0.72, 1.0), 1.00, 1.00, 1.00 ),
 140 (101,   "Mendelevium",       "Md", ( 0.70,  0.05, 0.65, 1.0), 1.00, 1.00, 1.00 ),
 141 (102,      "Nobelium",       "No", ( 0.74,  0.05, 0.52, 1.0), 1.00, 1.00, 1.00 ),
 142 (103,    "Lawrencium",       "Lr", ( 0.78,   0.0,  0.4, 1.0), 1.00, 1.00, 1.00 ),
 143 (104,       "Vacancy",      "Vac", (  0.5,   0.5,  0.5, 1.0), 1.00, 1.00, 1.00),
 144 (105,       "Default",  "Default", (  1.0,   1.0,  1.0, 1.0), 1.00, 1.00, 1.00),
 145 (106,         "Stick",    "Stick", (  0.5,   0.5,  0.5, 1.0), 1.00, 1.00, 1.00),
 146 )
 147
 148 # This list here contains all data of the elements and will be used during
 149 # runtime. It is a list of classes.
 150 # During executing Atomic Blender, the list will be initialized with the fixed
 151 # data from above via the class structure below (ElementProp). We
 152 # have then one fixed list (above), which will never be changed, and a list of
 153 # classes with same data. The latter can be modified via loading a separate
 154 # custom data file for instance.
 155 ELEMENTS = []
 156
 157 # This is the list, which contains all atoms of all frames! Each item is a
 158 # list which contains the atoms of a single frame. It is a list of
 159 # 'AtomProp'.
 160 ALL_FRAMES = []
 161
 162 # A list of ALL balls which are put into the scene
 163 STRUCTURE = []
 164
 165
 166 # This is the class, which stores the properties for one element.
 167 class ElementProp(object):
 168     __slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic')
 169     def __init__(self, number, name, short_name, color, radii, radii_ionic):
 170         self.number = number
 171         self.name = name
 172         self.short_name = short_name
 173         self.color = color
 174         self.radii = radii
 175         self.radii_ionic = radii_ionic
 176
 177 # This is the class, which stores the properties of one atom.
 178 class AtomProp(object):
 179     __slots__ = ('element', 'name', 'location', 'radius', 'color', 'material')
 180     def __init__(self, element, name, location, radius, color, material):
 181         self.element = element
 182         self.name = name
 183         self.location = location
 184         self.radius = radius
 185         self.color = color
 186         self.material = material
 187
 188
 189 # -----------------------------------------------------------------------------
 190 #                                                           Some basic routines
 191
 192 def read_elements():
 193
 194     del ELEMENTS[:]
 195
 196     for item in ELEMENTS_DEFAULT:
 197
 198         # All three radii into a list
 199         radii = [item[4],item[5],item[6]]
 200         # The handling of the ionic radii will be done later. So far, it is an
 201         # empty list.
 202         radii_ionic = []
 203
 204         li = ElementProp(item[0],item[1],item[2],item[3],
 205                                      radii,radii_ionic)
 206         ELEMENTS.append(li)
 207
 208
 209 # filepath_pdb: path to pdb file
 210 # radiustype  : '0' default
 211 #               '1' atomic radii
 212 #               '2' van der Waals
 213 def read_xyz_file(filepath_xyz,radiustype):
 214
 215     number_frames = 0
 216     total_number_atoms = 0
 217
 218     # Open the file ...
 219     filepath_xyz_p = open(filepath_xyz, "r")
 220
 221     #Go through the whole file.
 222     FLAG = False
 223     for line in filepath_xyz_p:
 224
 225         # ... the loop is broken here (EOF) ...
 226         if line == "":
 227             continue
 228
 229         split_list = line.rsplit()
 230
 231         if len(split_list) == 1:
 232             number_atoms = int(split_list[0])
 233             FLAG = True
 234
 235         if FLAG == True:
 236
 237             line = filepath_xyz_p.readline()
 238             line = line.rstrip()
 239
 240             all_atoms= []
 241             for i in range(number_atoms):
 242
 243
 244                 # This is a guarantee that only the total number of atoms of the
 245                 # first frame is used. Condition is, so far, that the number of
 246                 # atoms in a xyz file is constant. However, sometimes the number
 247                 # may increase (or decrease). If it decreases, the addon crashes.
 248                 # If it increases, only the tot number of atoms of the first frame
 249                 # is used.
 250                 # By time, I will allow varying atom numbers ... but this takes
 251                 # some time ...
 252                 if number_frames != 0:
 253                     if i >= total_number_atoms:
 254                         break
 255
 256
 257                 line = filepath_xyz_p.readline()
 258                 line = line.rstrip()
 259                 split_list = line.rsplit()
 260                 short_name = str(split_list[0])
 261
 262                 # Go through all elements and find the element of the current atom.
 263                 FLAG_FOUND = False
 264                 for element in ELEMENTS:
 265                     if str.upper(short_name) == str.upper(element.short_name):
 266                         # Give the atom its proper name, color and radius:
 267                         name = element.name
 268                         # int(radiustype) => type of radius:
 269                         # pre-defined (0), atomic (1) or van der Waals (2)
 270                         radius = float(element.radii[int(radiustype)])
 271                         color = element.color
 272                         FLAG_FOUND = True
 273                         break
 274
 275                 # Is it a vacancy or an 'unknown atom' ?
 276                 if FLAG_FOUND == False:
 277                     # Give this atom also a name. If it is an 'X' then it is a
 278                     # vacancy. Otherwise ...
 279                     if "X" in short_name:
 280                         short_name = "VAC"
 281                         name = "Vacancy"
 282                         radius = float(ELEMENTS[-3].radii[int(radiustype)])
 283                         color = ELEMENTS[-3].color
 284                     # ... take what is written in the xyz file. These are somewhat
 285                     # unknown atoms. This should never happen, the element list is
 286                     # almost complete. However, we do this due to security reasons.
 287                     else:
 288                         name = str.upper(short_name)
 289                         radius = float(ELEMENTS[-2].radii[int(radiustype)])
 290                         color = ELEMENTS[-2].color
 291
 292                 x = float(split_list[1])
 293                 y = float(split_list[2])
 294                 z = float(split_list[3])
 295
 296                 location = Vector((x,y,z))
 297
 298                 all_atoms.append([short_name, name, location, radius, color])
 299
 300             # We note here all elements. This needs to be done only once.
 301             if number_frames == 0:
 302
 303                 # This is a guarantee that only the total number of atoms of the
 304                 # first frame is used. Condition is, so far, that the number of
 305                 # atoms in a xyz file is constant. However, sometimes the number
 306                 # may increase (or decrease). If it decreases, the addon crashes.
 307                 # If it increases, only the tot number of atoms of the first frame
 308                 # is used.
 309                 # By time, I will allow varying atom numbers ... but this takes
 310                 # some time ...
 311                 total_number_atoms = number_atoms
 312
 313
 314                 elements = []
 315                 for atom in all_atoms:
 316                     FLAG_FOUND = False
 317                     for element in elements:
 318                         # If the atom name is already in the list,
 319                         # FLAG on 'True'.
 320                         if element == atom[1]:
 321                             FLAG_FOUND = True
 322                             break
 323                     # No name in the current list has been found? => New entry.
 324                     if FLAG_FOUND == False:
 325                         # Stored are: Atom label (e.g. 'Na'), the corresponding
 326                         # atom name (e.g. 'Sodium') and its color.
 327                         elements.append(atom[1])
 328
 329             # Sort the atoms: create lists of atoms of one type
 330             structure = []
 331             for element in elements:
 332                 atoms_one_type = []
 333                 for atom in all_atoms:
 334                     if atom[1] == element:
 335                         atoms_one_type.append(AtomProp(atom[0],
 336                                                        atom[1],
 337                                                        atom[2],
 338                                                        atom[3],
 339                                                        atom[4],[]))
 340                 structure.append(atoms_one_type)
 341
 342             ALL_FRAMES.append(structure)
 343             number_frames += 1
 344             FLAG = False
 345
 346     filepath_xyz_p.close()
 347
 348     return total_number_atoms
 349
 350
 351 # Rotate an object.
 352 def rotate_object(rot_mat, obj):
 353
 354     bpy.ops.object.select_all(action='DESELECT')
 355     obj.select_set(True)
 356
 357     # Decompose world_matrix's components, and from them assemble 4x4 matrices.
 358     orig_loc, orig_rot, orig_scale = obj.matrix_world.decompose()
 359
 360     orig_loc_mat   = Matrix.Translation(orig_loc)
 361     orig_rot_mat   = orig_rot.to_matrix().to_4x4()
 362     orig_scale_mat = (Matrix.Scale(orig_scale[0],4,(1,0,0)) @
 363                       Matrix.Scale(orig_scale[1],4,(0,1,0)) @
 364                       Matrix.Scale(orig_scale[2],4,(0,0,1)))
 365
 366     # Assemble the new matrix.
 367     obj.matrix_world = orig_loc_mat @ rot_mat @ orig_rot_mat @ orig_scale_mat
 368
 369
 370 # Function, which puts a camera and light source into the 3D scene
 371 def camera_light_source(use_camera,
 372                         use_light,
 373                         object_center_vec,
 374                         object_size):
 375
 376     camera_factor = 15.0
 377
 378     # If chosen a camera is put into the scene.
 379     if use_camera == True:
 380
 381         # Assume that the object is put into the global origin. Then, the
 382         # camera is moved in x and z direction, not in y. The object has its
 383         # size at distance sqrt(object_size) from the origin. So, move the
 384         # camera by this distance times a factor of camera_factor in x and z.
 385         # Then add x, y and z of the origin of the object.
 386         object_camera_vec = Vector((sqrt(object_size) * camera_factor,
 387                                     0.0,
 388                                     sqrt(object_size) * camera_factor))
 389         camera_xyz_vec = object_center_vec + object_camera_vec
 390
 391         # Create the camera
 392         camera_data = bpy.data.cameras.new("A_camera")
 393         camera_data.lens = 45
 394         camera_data.clip_end = 500.0
 395         camera = bpy.data.objects.new("A_camera", camera_data)
 396         camera.location = camera_xyz_vec
 397         bpy.context.collection.objects.link(camera)
 398
 399         # Here the camera is rotated such it looks towards the center of
 400         # the object. The [0.0, 0.0, 1.0] vector along the z axis
 401         z_axis_vec             = Vector((0.0, 0.0, 1.0))
 402         # The angle between the last two vectors
 403         angle                  = object_camera_vec.angle(z_axis_vec, 0)
 404         # The cross-product of z_axis_vec and object_camera_vec
 405         axis_vec               = z_axis_vec.cross(object_camera_vec)
 406         # Rotate 'axis_vec' by 'angle' and convert this to euler parameters.
 407         # 4 is the size of the matrix.
 408         camera.rotation_euler  = Matrix.Rotation(angle, 4, axis_vec).to_euler()
 409
 410         # Rotate the camera around its axis by 90° such that we have a nice
 411         # camera position and view onto the object.
 412         bpy.ops.object.select_all(action='DESELECT')
 413         camera.select_set(True)
 414
 415         # Rotate the camera around its axis 'object_camera_vec' by 90° such
 416         # that we have a nice camera view onto the object.
 417         matrix_rotation = Matrix.Rotation(90/360*2*pi, 4, object_camera_vec)
 418         rotate_object(matrix_rotation, camera)
 419
 420     # Here a lamp is put into the scene, if chosen.
 421     if use_light == True:
 422
 423         # This is the distance from the object measured in terms of %
 424         # of the camera distance. It is set onto 50% (1/2) distance.
 425         light_dl = sqrt(object_size) * 15 * 0.5
 426         # This is a factor to which extend the lamp shall go to the right
 427         # (from the camera  point of view).
 428         light_dy_right = light_dl * (3.0/4.0)
 429
 430         # Create x, y and z for the lamp.
 431         object_light_vec = Vector((light_dl,light_dy_right,light_dl))
 432         light_xyz_vec = object_center_vec + object_light_vec
 433
 434         # Create the lamp
 435         light_data = bpy.data.lights.new(name="A_light", type="SUN")
 436         light_data.distance = 500.0
 437         light_data.energy = 3.0
 438         lamp = bpy.data.objects.new("A_light", light_data)
 439         lamp.location = light_xyz_vec
 440         bpy.context.collection.objects.link(lamp)
 441
 442         # Some settings for the World: a bit ambient occlusion
 443         bpy.context.scene.world.light_settings.use_ambient_occlusion = True
 444         bpy.context.scene.world.light_settings.ao_factor = 0.2
 445         # Some properties for cycles
 446         lamp.data.use_nodes = True
 447         lmp_P_BSDF = lamp.data.node_tree.nodes['Emission']
 448         lmp_P_BSDF.inputs['Strength'].default_value = 5
 449
 450 # -----------------------------------------------------------------------------
 451 #                                                            The main routine
 452
 453 def import_xyz(Ball_type,
 454                Ball_azimuth,
 455                Ball_zenith,
 456                Ball_radius_factor,
 457                radiustype,
 458                Ball_distance_factor,
 459                put_to_center,
 460                put_to_center_all,
 461                use_camera,
 462                use_light,
 463                filepath_xyz):
 464
 465     # List of materials
 466     atom_material_list = []
 467
 468     # ------------------------------------------------------------------------
 469     # INITIALIZE THE ELEMENT LIST
 470
 471     read_elements()
 472
 473     # ------------------------------------------------------------------------
 474     # READING DATA OF ATOMS
 475
 476     Number_of_total_atoms = read_xyz_file(filepath_xyz, radiustype)
 477
 478     # We show the atoms of the first frame.
 479     first_frame = ALL_FRAMES[0]
 480
 481     # ------------------------------------------------------------------------
 482     # MATERIAL PROPERTIES FOR ATOMS
 483
 484     # Create first a new list of materials for each type of atom
 485     # (e.g. hydrogen)
 486     for atoms_of_one_type in first_frame:
 487         # Take the first atom
 488         atom = atoms_of_one_type[0]
 489         material = bpy.data.materials.new(atom.name)
 490         material.name = atom.name
 491         material.diffuse_color = atom.color
 492         atom_material_list.append(material)
 493
 494     # Now, we go through all atoms and give them a material. For all atoms ...
 495     for atoms_of_one_type in first_frame:
 496         for atom in atoms_of_one_type:
 497             # ... and all materials ...
 498             for material in atom_material_list:
 499                 # ... select the correct material for the current atom via
 500                 # comparison of names ...
 501                 if atom.name in material.name:
 502                     # ... and give the atom its material properties.
 503                     # However, before we check if it is a vacancy
 504                     # The vacancy is represented by a transparent cube.
 505                     if atom.name == "Vacancy":
 506                         # Some properties for eevee.
 507                         material.metallic = 0.8
 508                         material.specular_intensity = 0.5
 509                         material.roughness = 0.3
 510                         material.blend_method = 'OPAQUE'
 511                         material.show_transparent_back = False
 512                         # Some properties for cycles
 513                         material.use_nodes = True
 514                         mat_P_BSDF = material.node_tree.nodes['Principled BSDF']
 515                         mat_P_BSDF.inputs['Metallic'].default_value = 0.1
 516                         mat_P_BSDF.inputs['Roughness'].default_value = 0.2
 517                         mat_P_BSDF.inputs['Transmission'].default_value = 0.97
 518                         mat_P_BSDF.inputs['IOR'].default_value = 0.8
 519                     # The atom gets its properties.
 520                     atom.material = material
 521
 522     # ------------------------------------------------------------------------
 523     # TRANSLATION OF THE STRUCTURE TO THE ORIGIN
 524
 525     # It may happen that the structure in a XYZ file already has an offset
 526
 527
 528     # If chosen, the structure is put into the center of the scene
 529     # (only the first frame).
 530     if put_to_center == True and put_to_center_all == False:
 531
 532         sum_vec = Vector((0.0,0.0,0.0))
 533
 534         # Sum of all atom coordinates
 535         for atoms_of_one_type in first_frame:
 536             sum_vec = sum([atom.location for atom in atoms_of_one_type], sum_vec)
 537
 538         # Then the average is taken
 539         sum_vec = sum_vec / Number_of_total_atoms
 540
 541         # After, for each atom the center of gravity is substracted
 542         for atoms_of_one_type in first_frame:
 543             for atom in atoms_of_one_type:
 544                 atom.location -= sum_vec
 545
 546     # If chosen, the structure is put into the center of the scene
 547     # (all frames).
 548     if put_to_center_all == True:
 549
 550         # For all frames
 551         for frame in ALL_FRAMES:
 552
 553             sum_vec = Vector((0.0,0.0,0.0))
 554
 555             # Sum of all atom coordinates
 556             for (i, atoms_of_one_type) in enumerate(frame):
 557
 558                 # This is a guarantee that only the total number of atoms of the
 559                 # first frame is used. Condition is, so far, that the number of
 560                 # atoms in a xyz file is constant. However, sometimes the number
 561                 # may increase (or decrease). If it decreases, the addon crashes.
 562                 # If it increases, only the tot number of atoms of the first frame
 563                 # is used.
 564                 # By time, I will allow varying atom numbers ... but this takes
 565                 # some time ...
 566                 if i >= Number_of_total_atoms:
 567                     break
 568
 569                 sum_vec = sum([atom.location for atom in atoms_of_one_type], sum_vec)
 570
 571             # Then the average is taken
 572             sum_vec = sum_vec / Number_of_total_atoms
 573
 574             # After, for each atom the center of gravity is substracted
 575             for atoms_of_one_type in frame:
 576                 for atom in atoms_of_one_type:
 577                     atom.location -= sum_vec
 578
 579
 580     # ------------------------------------------------------------------------
 581     # SCALING
 582
 583     # Take all atoms and adjust their radii and scale the distances.
 584     for atoms_of_one_type in first_frame:
 585         for atom in atoms_of_one_type:
 586             atom.location *= Ball_distance_factor
 587
 588     # ------------------------------------------------------------------------
 589     # DETERMINATION OF SOME GEOMETRIC PROPERTIES
 590
 591     # In the following, some geometric properties of the whole object are
 592     # determined: center, size, etc.
 593     sum_vec = Vector((0.0,0.0,0.0))
 594
 595     # First the center is determined. All coordinates are summed up ...
 596     for atoms_of_one_type in first_frame:
 597         sum_vec = sum([atom.location for atom in atoms_of_one_type], sum_vec)
 598
 599     # ... and the average is taken. This gives the center of the object.
 600     object_center_vec = sum_vec / Number_of_total_atoms
 601
 602     # Now, we determine the size.The farthest atom from the object center is
 603     # taken as a measure. The size is used to place well the camera and light
 604     # into the scene.
 605
 606     object_size_vec = []
 607     for atoms_of_one_type in first_frame:
 608         object_size_vec += [atom.location - object_center_vec for atom in atoms_of_one_type]
 609
 610     object_size = 0.0
 611     object_size = max(object_size_vec).length
 612
 613     # ------------------------------------------------------------------------
 614     # COLLECTION
 615
 616     # Before we start to draw the atoms, we first create a collection for the
 617     # atomic structure. All atoms (balls) are put into this collection.
 618     coll_structure_name = os.path.basename(filepath_xyz)
 619     scene = bpy.context.scene
 620     coll_structure = bpy.data.collections.new(coll_structure_name)
 621     scene.collection.children.link(coll_structure)
 622
 623     # ------------------------------------------------------------------------
 624     # DRAWING THE ATOMS
 625
 626     bpy.ops.object.select_all(action='DESELECT')
 627
 628     # For each list of atoms of ONE type (e.g. Hydrogen)
 629     for atoms_of_one_type in first_frame:
 630
 631         # Create first the vertices composed of the coordinates of all
 632         # atoms of one type
 633         atom_vertices = []
 634         for atom in atoms_of_one_type:
 635             # In fact, the object is created in the World's origin.
 636             # This is why 'object_center_vec' is substracted. At the end
 637             # the whole object is translated back to 'object_center_vec'.
 638             atom_vertices.append( atom.location - object_center_vec )
 639
 640         # First, we create a collection of the element, which
 641         # contains the atoms (balls + mesh)!
 642         coll_element_name = atom.name # the element name
 643         # Create the new collection and ...
 644         coll_element = bpy.data.collections.new(coll_element_name)
 645         # ... link it to the collection, which contains all parts of the
 646         # structure.
 647         coll_structure.children.link(coll_element)
 648
 649         # Now, create a collection for the atoms, which includes the
 650         # representative ball and the mesh.
 651         coll_atom_name = atom.name + "_atom"
 652         # Create the new collection and ...
 653         coll_atom = bpy.data.collections.new(coll_atom_name)
 654         # ... link it to the collection, which contains all parts of the
 655         # element (ball and mesh).
 656         coll_element.children.link(coll_atom)
 657
 658         # Build the mesh
 659         atom_mesh = bpy.data.meshes.new("Mesh_"+atom.name)
 660         atom_mesh.from_pydata(atom_vertices, [], [])
 661         atom_mesh.update()
 662         new_atom_mesh = bpy.data.objects.new(atom.name + "_mesh", atom_mesh)
 663
 664         # Link active object to the new collection
 665         coll_atom.objects.link(new_atom_mesh)
 666
 667         # Now, build a representative sphere (atom)
 668         if atom.name == "Vacancy":
 669             bpy.ops.mesh.primitive_cube_add(
 670                             align='WORLD', enter_editmode=False,
 671                             location=(0.0, 0.0, 0.0),
 672                             rotation=(0.0, 0.0, 0.0))
 673         else:
 674             # NURBS balls
 675             if Ball_type == "0":
 676                 bpy.ops.surface.primitive_nurbs_surface_sphere_add(
 677                             align='WORLD', enter_editmode=False,
 678                             location=(0,0,0), rotation=(0.0, 0.0, 0.0))
 679             # UV balls
 680             elif Ball_type == "1":
 681                 bpy.ops.mesh.primitive_uv_sphere_add(
 682                             segments=Ball_azimuth, ring_count=Ball_zenith,
 683                             align='WORLD', enter_editmode=False,
 684                             location=(0,0,0), rotation=(0, 0, 0))
 685             # Meta balls
 686             elif Ball_type == "2":
 687                 bpy.ops.object.metaball_add(type='BALL', align='WORLD',
 688                             enter_editmode=False, location=(0, 0, 0),
 689                             rotation=(0, 0, 0))
 690
 691         ball = bpy.context.view_layer.objects.active
 692         # Hide this ball because its appearance has no meaning. It is just the
 693         # representative ball. The ball is visible at the vertices of the mesh.
 694         # Rememmber, this is a dupliverts construct!
 695         # However, hiding does not work with meta balls!
 696         if Ball_type == "0" or Ball_type == "1":
 697             ball.hide_set(True)
 698         # Scale up/down the ball radius.
 699         ball.scale  = (atom.radius*Ball_radius_factor,) * 3
 700
 701         if atom.name == "Vacancy":
 702             ball.name = atom.name + "_cube"
 703         else:
 704             ball.name = atom.name + "_ball"
 705         ball.active_material = atom.material
 706         ball.parent = new_atom_mesh
 707         new_atom_mesh.instance_type = 'VERTS'
 708         # The object is back translated to 'object_center_vec'.
 709         new_atom_mesh.location = object_center_vec
 710         STRUCTURE.append(new_atom_mesh)
 711
 712         # Note the collection where the ball was placed into.
 713         coll_all = ball.users_collection
 714         if len(coll_all) > 0:
 715             coll_past = coll_all[0]
 716         else:
 717             coll_past = bpy.context.scene.collection
 718
 719         # Put the atom into the new collection 'atom' and ...
 720         coll_atom.objects.link(ball)
 721         # ... unlink the atom from the other collection.
 722         coll_past.objects.unlink(ball)
 723
 724     # ------------------------------------------------------------------------
 725     # CAMERA and LIGHT SOURCES
 726
 727     camera_light_source(use_camera,
 728                         use_light,
 729                         object_center_vec,
 730                         object_size)
 731
 732     # ------------------------------------------------------------------------
 733     # SELECT ALL LOADED OBJECTS
 734
 735     bpy.ops.object.select_all(action='DESELECT')
 736     obj = None
 737     for obj in STRUCTURE:
 738         obj.select_set(True)
 739     # activate the last selected object (perhaps another should be active?)
 740     if obj:
 741         bpy.context.view_layer.objects.active = obj
 742
 743
 744
 745 def build_frames(frame_delta, frame_skip):
 746
 747     scn = bpy.context.scene
 748
 749     # Introduce the basis for all elements that appear in the structure.
 750     for element in STRUCTURE:
 751
 752         bpy.ops.object.select_all(action='DESELECT')
 753         bpy.context.view_layer.objects.active = element
 754         element.select_set(True)
 755         bpy.ops.object.shape_key_add(True)
 756
 757     frame_skip += 1
 758
 759     # Introduce the keys and reference the atom positions for each key.
 760     i = 0
 761     for j, frame in enumerate(ALL_FRAMES):
 762
 763         if j % frame_skip == 0:
 764
 765             for elements_frame, elements_structure in zip(frame,STRUCTURE):
 766
 767                 key = elements_structure.shape_key_add()
 768
 769                 for atom_frame, atom_structure in zip(elements_frame, key.data):
 770
 771                     atom_structure.co = (atom_frame.location
 772                                        - elements_structure.location)
 773
 774                 key.name = atom_frame.name + "_frame_" + str(i)
 775
 776             i += 1
 777
 778     num_frames = i
 779
 780     scn.frame_start = 0
 781     scn.frame_end = frame_delta * num_frames
 782
 783     # Manage the values of the keys
 784     for element in STRUCTURE:
 785
 786         scn.frame_current = 0
 787
 788         element.data.shape_keys.key_blocks[1].value = 1.0
 789         element.data.shape_keys.key_blocks[2].value = 0.0
 790         element.data.shape_keys.key_blocks[1].keyframe_insert("value")
 791         element.data.shape_keys.key_blocks[2].keyframe_insert("value")
 792
 793         scn.frame_current += frame_delta
 794
 795         number = 0
 796
 797         for number in range(num_frames)[2:]:#-1]:
 798
 799             element.data.shape_keys.key_blocks[number-1].value = 0.0
 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-1].keyframe_insert("value")
 803             element.data.shape_keys.key_blocks[number].keyframe_insert("value")
 804             element.data.shape_keys.key_blocks[number+1].keyframe_insert("value")
 805
 806             scn.frame_current += frame_delta
 807
 808         number += 1
 809
 810         element.data.shape_keys.key_blocks[number].value = 1.0
 811         element.data.shape_keys.key_blocks[number-1].value = 0.0
 812         element.data.shape_keys.key_blocks[number].keyframe_insert("value")
 813         element.data.shape_keys.key_blocks[number-1].keyframe_insert("value")