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# ##### BEGIN GPL LICENSE BLOCK #####
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# This program is free software; you can redistribute it and/or
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# modify it under the terms of the GNU General Public License
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# as published by the Free Software Foundation; either version 2
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# of the License, or (at your option) any later version.
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# This program is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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# You should have received a copy of the GNU General Public License
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# along with this program; if not, write to the Free Software Foundation,
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# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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# ##### END GPL LICENSE BLOCK #####
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# Authors : Clemens Barth (Blendphys@root-1.de), ...
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# Homepage(Wiki) : http://development.root-1.de/Atomic_Blender.php
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# Start of project : 2011-12-01 by Clemens Barth
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# First publication in Blender : 2011-12-18
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# Last modified : 2012-04-18
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# Acknowledgements: Thanks to ideasman, meta_androcto, truman, kilon,
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# dairin0d, PKHG, Valter, etc
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from math import pi, cos, sin
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from mathutils import Vector, Matrix
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# These are variables, which contain the name of the XYZ file and
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# the path of the XYZ file.
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# They are used almost everywhere, which is the reason why they
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# should stay global. First, they are empty and get 'filled' directly
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# after having chosen the XYZ file (see 'class LoadXYZ' further below).
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ATOM_XYZ_FILEPATH = ""
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# Some string stuff for the console.
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ATOM_XYZ_STRING = "Atomic Blender\n==================="
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# -----------------------------------------------------------------------------
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# Atom and element data
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# This is a list that contains some data of all possible elements. The structure
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# 1, "Hydrogen", "H", [0.0,0.0,1.0], 0.32, 0.32, 0.32 , -1 , 1.54 means
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# No., name, short name, color, radius (used), radius (covalent), radius (atomic),
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# charge state 1, radius (ionic) 1, charge state 2, radius (ionic) 2, ... all
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# charge states for any atom are listed, if existing.
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# The list is fixed and cannot be changed ... (see below)
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ATOM_XYZ_ELEMENTS_DEFAULT = (
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( 1, "Hydrogen", "H", ( 1.0, 1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ),
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( 2, "Helium", "He", ( 0.85, 1.0, 1.0), 0.93, 0.93, 0.49 ),
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( 3, "Lithium", "Li", ( 0.8, 0.50, 1.0), 1.23, 1.23, 2.05 , 1 , 0.68 ),
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( 4, "Beryllium", "Be", ( 0.76, 1.0, 0.0), 0.90, 0.90, 1.40 , 1 , 0.44 , 2 , 0.35 ),
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( 5, "Boron", "B", ( 1.0, 0.70, 0.70), 0.82, 0.82, 1.17 , 1 , 0.35 , 3 , 0.23 ),
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( 6, "Carbon", "C", ( 0.56, 0.56, 0.56), 0.77, 0.77, 0.91 , -4 , 2.60 , 4 , 0.16 ),
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( 7, "Nitrogen", "N", ( 0.18, 0.31, 0.97), 0.75, 0.75, 0.75 , -3 , 1.71 , 1 , 0.25 , 3 , 0.16 , 5 , 0.13 ),
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( 8, "Oxygen", "O", ( 1.0, 0.05, 0.05), 0.73, 0.73, 0.65 , -2 , 1.32 , -1 , 1.76 , 1 , 0.22 , 6 , 0.09 ),
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( 9, "Fluorine", "F", ( 0.56, 0.87, 0.31), 0.72, 0.72, 0.57 , -1 , 1.33 , 7 , 0.08 ),
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(10, "Neon", "Ne", ( 0.70, 0.89, 0.96), 0.71, 0.71, 0.51 , 1 , 1.12 ),
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(11, "Sodium", "Na", ( 0.67, 0.36, 0.94), 1.54, 1.54, 2.23 , 1 , 0.97 ),
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(12, "Magnesium", "Mg", ( 0.54, 1.0, 0.0), 1.36, 1.36, 1.72 , 1 , 0.82 , 2 , 0.66 ),
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(13, "Aluminium", "Al", ( 0.74, 0.65, 0.65), 1.18, 1.18, 1.82 , 3 , 0.51 ),
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(14, "Silicon", "Si", ( 0.94, 0.78, 0.62), 1.11, 1.11, 1.46 , -4 , 2.71 , -1 , 3.84 , 1 , 0.65 , 4 , 0.42 ),
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(15, "Phosphorus", "P", ( 1.0, 0.50, 0.0), 1.06, 1.06, 1.23 , -3 , 2.12 , 3 , 0.44 , 5 , 0.35 ),
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(16, "Sulfur", "S", ( 1.0, 1.0, 0.18), 1.02, 1.02, 1.09 , -2 , 1.84 , 2 , 2.19 , 4 , 0.37 , 6 , 0.30 ),
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(17, "Chlorine", "Cl", ( 0.12, 0.94, 0.12), 0.99, 0.99, 0.97 , -1 , 1.81 , 5 , 0.34 , 7 , 0.27 ),
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(18, "Argon", "Ar", ( 0.50, 0.81, 0.89), 0.98, 0.98, 0.88 , 1 , 1.54 ),
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(19, "Potassium", "K", ( 0.56, 0.25, 0.83), 2.03, 2.03, 2.77 , 1 , 0.81 ),
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(20, "Calcium", "Ca", ( 0.23, 1.0, 0.0), 1.74, 1.74, 2.23 , 1 , 1.18 , 2 , 0.99 ),
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(21, "Scandium", "Sc", ( 0.90, 0.90, 0.90), 1.44, 1.44, 2.09 , 3 , 0.73 ),
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(22, "Titanium", "Ti", ( 0.74, 0.76, 0.78), 1.32, 1.32, 2.00 , 1 , 0.96 , 2 , 0.94 , 3 , 0.76 , 4 , 0.68 ),
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(23, "Vanadium", "V", ( 0.65, 0.65, 0.67), 1.22, 1.22, 1.92 , 2 , 0.88 , 3 , 0.74 , 4 , 0.63 , 5 , 0.59 ),
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(24, "Chromium", "Cr", ( 0.54, 0.6, 0.78), 1.18, 1.18, 1.85 , 1 , 0.81 , 2 , 0.89 , 3 , 0.63 , 6 , 0.52 ),
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(25, "Manganese", "Mn", ( 0.61, 0.47, 0.78), 1.17, 1.17, 1.79 , 2 , 0.80 , 3 , 0.66 , 4 , 0.60 , 7 , 0.46 ),
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(26, "Iron", "Fe", ( 0.87, 0.4, 0.2), 1.17, 1.17, 1.72 , 2 , 0.74 , 3 , 0.64 ),
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(27, "Cobalt", "Co", ( 0.94, 0.56, 0.62), 1.16, 1.16, 1.67 , 2 , 0.72 , 3 , 0.63 ),
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(28, "Nickel", "Ni", ( 0.31, 0.81, 0.31), 1.15, 1.15, 1.62 , 2 , 0.69 ),
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(29, "Copper", "Cu", ( 0.78, 0.50, 0.2), 1.17, 1.17, 1.57 , 1 , 0.96 , 2 , 0.72 ),
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(30, "Zinc", "Zn", ( 0.49, 0.50, 0.69), 1.25, 1.25, 1.53 , 1 , 0.88 , 2 , 0.74 ),
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(31, "Gallium", "Ga", ( 0.76, 0.56, 0.56), 1.26, 1.26, 1.81 , 1 , 0.81 , 3 , 0.62 ),
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(32, "Germanium", "Ge", ( 0.4, 0.56, 0.56), 1.22, 1.22, 1.52 , -4 , 2.72 , 2 , 0.73 , 4 , 0.53 ),
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(33, "Arsenic", "As", ( 0.74, 0.50, 0.89), 1.20, 1.20, 1.33 , -3 , 2.22 , 3 , 0.58 , 5 , 0.46 ),
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(34, "Selenium", "Se", ( 1.0, 0.63, 0.0), 1.16, 1.16, 1.22 , -2 , 1.91 , -1 , 2.32 , 1 , 0.66 , 4 , 0.50 , 6 , 0.42 ),
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(35, "Bromine", "Br", ( 0.65, 0.16, 0.16), 1.14, 1.14, 1.12 , -1 , 1.96 , 5 , 0.47 , 7 , 0.39 ),
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(36, "Krypton", "Kr", ( 0.36, 0.72, 0.81), 1.31, 1.31, 1.24 ),
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(37, "Rubidium", "Rb", ( 0.43, 0.18, 0.69), 2.16, 2.16, 2.98 , 1 , 1.47 ),
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(38, "Strontium", "Sr", ( 0.0, 1.0, 0.0), 1.91, 1.91, 2.45 , 2 , 1.12 ),
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(39, "Yttrium", "Y", ( 0.58, 1.0, 1.0), 1.62, 1.62, 2.27 , 3 , 0.89 ),
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(40, "Zirconium", "Zr", ( 0.58, 0.87, 0.87), 1.45, 1.45, 2.16 , 1 , 1.09 , 4 , 0.79 ),
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(41, "Niobium", "Nb", ( 0.45, 0.76, 0.78), 1.34, 1.34, 2.08 , 1 , 1.00 , 4 , 0.74 , 5 , 0.69 ),
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(42, "Molybdenum", "Mo", ( 0.32, 0.70, 0.70), 1.30, 1.30, 2.01 , 1 , 0.93 , 4 , 0.70 , 6 , 0.62 ),
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(43, "Technetium", "Tc", ( 0.23, 0.61, 0.61), 1.27, 1.27, 1.95 , 7 , 0.97 ),
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(44, "Ruthenium", "Ru", ( 0.14, 0.56, 0.56), 1.25, 1.25, 1.89 , 4 , 0.67 ),
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(45, "Rhodium", "Rh", ( 0.03, 0.49, 0.54), 1.25, 1.25, 1.83 , 3 , 0.68 ),
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(46, "Palladium", "Pd", ( 0.0, 0.41, 0.52), 1.28, 1.28, 1.79 , 2 , 0.80 , 4 , 0.65 ),
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(47, "Silver", "Ag", ( 0.75, 0.75, 0.75), 1.34, 1.34, 1.75 , 1 , 1.26 , 2 , 0.89 ),
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(48, "Cadmium", "Cd", ( 1.0, 0.85, 0.56), 1.48, 1.48, 1.71 , 1 , 1.14 , 2 , 0.97 ),
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(49, "Indium", "In", ( 0.65, 0.45, 0.45), 1.44, 1.44, 2.00 , 3 , 0.81 ),
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(50, "Tin", "Sn", ( 0.4, 0.50, 0.50), 1.41, 1.41, 1.72 , -4 , 2.94 , -1 , 3.70 , 2 , 0.93 , 4 , 0.71 ),
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(51, "Antimony", "Sb", ( 0.61, 0.38, 0.70), 1.40, 1.40, 1.53 , -3 , 2.45 , 3 , 0.76 , 5 , 0.62 ),
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(52, "Tellurium", "Te", ( 0.83, 0.47, 0.0), 1.36, 1.36, 1.42 , -2 , 2.11 , -1 , 2.50 , 1 , 0.82 , 4 , 0.70 , 6 , 0.56 ),
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(53, "Iodine", "I", ( 0.58, 0.0, 0.58), 1.33, 1.33, 1.32 , -1 , 2.20 , 5 , 0.62 , 7 , 0.50 ),
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(54, "Xenon", "Xe", ( 0.25, 0.61, 0.69), 1.31, 1.31, 1.24 ),
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(55, "Caesium", "Cs", ( 0.34, 0.09, 0.56), 2.35, 2.35, 3.35 , 1 , 1.67 ),
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(56, "Barium", "Ba", ( 0.0, 0.78, 0.0), 1.98, 1.98, 2.78 , 1 , 1.53 , 2 , 1.34 ),
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(57, "Lanthanum", "La", ( 0.43, 0.83, 1.0), 1.69, 1.69, 2.74 , 1 , 1.39 , 3 , 1.06 ),
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(58, "Cerium", "Ce", ( 1.0, 1.0, 0.78), 1.65, 1.65, 2.70 , 1 , 1.27 , 3 , 1.03 , 4 , 0.92 ),
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(59, "Praseodymium", "Pr", ( 0.85, 1.0, 0.78), 1.65, 1.65, 2.67 , 3 , 1.01 , 4 , 0.90 ),
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(60, "Neodymium", "Nd", ( 0.78, 1.0, 0.78), 1.64, 1.64, 2.64 , 3 , 0.99 ),
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(61, "Promethium", "Pm", ( 0.63, 1.0, 0.78), 1.63, 1.63, 2.62 , 3 , 0.97 ),
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(62, "Samarium", "Sm", ( 0.56, 1.0, 0.78), 1.62, 1.62, 2.59 , 3 , 0.96 ),
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(63, "Europium", "Eu", ( 0.38, 1.0, 0.78), 1.85, 1.85, 2.56 , 2 , 1.09 , 3 , 0.95 ),
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(64, "Gadolinium", "Gd", ( 0.27, 1.0, 0.78), 1.61, 1.61, 2.54 , 3 , 0.93 ),
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(65, "Terbium", "Tb", ( 0.18, 1.0, 0.78), 1.59, 1.59, 2.51 , 3 , 0.92 , 4 , 0.84 ),
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(66, "Dysprosium", "Dy", ( 0.12, 1.0, 0.78), 1.59, 1.59, 2.49 , 3 , 0.90 ),
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(67, "Holmium", "Ho", ( 0.0, 1.0, 0.61), 1.58, 1.58, 2.47 , 3 , 0.89 ),
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(68, "Erbium", "Er", ( 0.0, 0.90, 0.45), 1.57, 1.57, 2.45 , 3 , 0.88 ),
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(69, "Thulium", "Tm", ( 0.0, 0.83, 0.32), 1.56, 1.56, 2.42 , 3 , 0.87 ),
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(70, "Ytterbium", "Yb", ( 0.0, 0.74, 0.21), 1.74, 1.74, 2.40 , 2 , 0.93 , 3 , 0.85 ),
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(71, "Lutetium", "Lu", ( 0.0, 0.67, 0.14), 1.56, 1.56, 2.25 , 3 , 0.85 ),
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(72, "Hafnium", "Hf", ( 0.30, 0.76, 1.0), 1.44, 1.44, 2.16 , 4 , 0.78 ),
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(73, "Tantalum", "Ta", ( 0.30, 0.65, 1.0), 1.34, 1.34, 2.09 , 5 , 0.68 ),
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(74, "Tungsten", "W", ( 0.12, 0.58, 0.83), 1.30, 1.30, 2.02 , 4 , 0.70 , 6 , 0.62 ),
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(75, "Rhenium", "Re", ( 0.14, 0.49, 0.67), 1.28, 1.28, 1.97 , 4 , 0.72 , 7 , 0.56 ),
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(76, "Osmium", "Os", ( 0.14, 0.4, 0.58), 1.26, 1.26, 1.92 , 4 , 0.88 , 6 , 0.69 ),
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(77, "Iridium", "Ir", ( 0.09, 0.32, 0.52), 1.27, 1.27, 1.87 , 4 , 0.68 ),
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(78, "Platinium", "Pt", ( 0.81, 0.81, 0.87), 1.30, 1.30, 1.83 , 2 , 0.80 , 4 , 0.65 ),
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(79, "Gold", "Au", ( 1.0, 0.81, 0.13), 1.34, 1.34, 1.79 , 1 , 1.37 , 3 , 0.85 ),
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(80, "Mercury", "Hg", ( 0.72, 0.72, 0.81), 1.49, 1.49, 1.76 , 1 , 1.27 , 2 , 1.10 ),
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(81, "Thallium", "Tl", ( 0.65, 0.32, 0.30), 1.48, 1.48, 2.08 , 1 , 1.47 , 3 , 0.95 ),
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(82, "Lead", "Pb", ( 0.34, 0.34, 0.38), 1.47, 1.47, 1.81 , 2 , 1.20 , 4 , 0.84 ),
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(83, "Bismuth", "Bi", ( 0.61, 0.30, 0.70), 1.46, 1.46, 1.63 , 1 , 0.98 , 3 , 0.96 , 5 , 0.74 ),
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(84, "Polonium", "Po", ( 0.67, 0.36, 0.0), 1.46, 1.46, 1.53 , 6 , 0.67 ),
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(85, "Astatine", "At", ( 0.45, 0.30, 0.27), 1.45, 1.45, 1.43 , -3 , 2.22 , 3 , 0.85 , 5 , 0.46 ),
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(86, "Radon", "Rn", ( 0.25, 0.50, 0.58), 1.00, 1.00, 1.34 ),
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(87, "Francium", "Fr", ( 0.25, 0.0, 0.4), 1.00, 1.00, 1.00 , 1 , 1.80 ),
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(88, "Radium", "Ra", ( 0.0, 0.49, 0.0), 1.00, 1.00, 1.00 , 2 , 1.43 ),
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(89, "Actinium", "Ac", ( 0.43, 0.67, 0.98), 1.00, 1.00, 1.00 , 3 , 1.18 ),
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(90, "Thorium", "Th", ( 0.0, 0.72, 1.0), 1.65, 1.65, 1.00 , 4 , 1.02 ),
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(91, "Protactinium", "Pa", ( 0.0, 0.63, 1.0), 1.00, 1.00, 1.00 , 3 , 1.13 , 4 , 0.98 , 5 , 0.89 ),
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(92, "Uranium", "U", ( 0.0, 0.56, 1.0), 1.42, 1.42, 1.00 , 4 , 0.97 , 6 , 0.80 ),
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(93, "Neptunium", "Np", ( 0.0, 0.50, 1.0), 1.00, 1.00, 1.00 , 3 , 1.10 , 4 , 0.95 , 7 , 0.71 ),
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(94, "Plutonium", "Pu", ( 0.0, 0.41, 1.0), 1.00, 1.00, 1.00 , 3 , 1.08 , 4 , 0.93 ),
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(95, "Americium", "Am", ( 0.32, 0.36, 0.94), 1.00, 1.00, 1.00 , 3 , 1.07 , 4 , 0.92 ),
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(96, "Curium", "Cm", ( 0.47, 0.36, 0.89), 1.00, 1.00, 1.00 ),
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(97, "Berkelium", "Bk", ( 0.54, 0.30, 0.89), 1.00, 1.00, 1.00 ),
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(98, "Californium", "Cf", ( 0.63, 0.21, 0.83), 1.00, 1.00, 1.00 ),
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(99, "Einsteinium", "Es", ( 0.70, 0.12, 0.83), 1.00, 1.00, 1.00 ),
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(100, "Fermium", "Fm", ( 0.70, 0.12, 0.72), 1.00, 1.00, 1.00 ),
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(101, "Mendelevium", "Md", ( 0.70, 0.05, 0.65), 1.00, 1.00, 1.00 ),
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(102, "Nobelium", "No", ( 0.74, 0.05, 0.52), 1.00, 1.00, 1.00 ),
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(103, "Lawrencium", "Lr", ( 0.78, 0.0, 0.4), 1.00, 1.00, 1.00 ),
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(104, "Vacancy", "Vac", ( 0.5, 0.5, 0.5), 1.00, 1.00, 1.00),
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(105, "Default", "Default", ( 1.0, 1.0, 1.0), 1.00, 1.00, 1.00),
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(106, "Stick", "Stick", ( 0.5, 0.5, 0.5), 1.00, 1.00, 1.00),
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# This list here contains all data of the elements and will be used during
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# runtime. It is a list of classes.
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# During executing Atomic Blender, the list will be initialized with the fixed
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# data from above via the class structure below (CLASS_atom_xyz_Elements). We
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# have then one fixed list (above), which will never be changed, and a list of
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# classes with same data. The latter can be modified via loading a separate
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# custom data file for instance.
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ATOM_XYZ_ELEMENTS = []
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# This is the list, which contains all atoms of all frames! Each item is a
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# list which contains the atoms of a single frame. It is a list of
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# 'CLASS_atom_xyz_atom'.
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# A list of ALL balls which are put into the scene
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# This is the class, which stores the properties for one element.
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class CLASS_atom_xyz_Elements(object):
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__slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic')
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def __init__(self, number, name, short_name, color, radii, radii_ionic):
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self.short_name = short_name
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self.radii_ionic = radii_ionic
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# This is the class, which stores the properties of one atom.
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class CLASS_atom_xyz_atom(object):
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__slots__ = ('element', 'name', 'location', 'radius', 'color', 'material')
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def __init__(self, element, name, location, radius, color, material):
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self.element = element
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self.location = location
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self.material = material
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# -----------------------------------------------------------------------------
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# Some small routines
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# This function measures the distance between two objects (atoms),
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def DEF_atom_xyz_distance():
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if len(bpy.context.selected_bases) > 1:
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object_1 = bpy.context.selected_objects[0]
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object_2 = bpy.context.selected_objects[1]
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dv = object_2.location - object_1.location
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return str(dv.length)
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# Routine to modify the radii via the type:
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# pre-defined, atomic or van der Waals
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# Explanations here are also valid for the next 3 DEFs.
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def DEF_atom_xyz_radius_type(rtype,how):
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if how == "ALL_IN_LAYER":
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# Note all layers that are active.
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if bpy.context.scene.layers[i] == True:
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# Put all objects, which are in the layers, into a list.
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for obj in bpy.context.scene.objects:
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if obj.layers[layer] == True:
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change_objects.append(obj)
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# Consider all objects, which are in the list 'change_objects'.
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for obj in change_objects:
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if len(obj.children) != 0:
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if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
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for element in ATOM_XYZ_ELEMENTS:
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if element.name in obj.name:
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obj.children[0].scale = (element.radii[int(rtype)],) * 3
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if obj.type == "SURFACE" or obj.type == "MESH":
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for element in ATOM_XYZ_ELEMENTS:
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if element.name in obj.name:
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obj.scale = (element.radii[int(rtype)],) * 3
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if how == "ALL_ACTIVE":
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for obj in bpy.context.selected_objects:
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if len(obj.children) != 0:
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if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
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for element in ATOM_XYZ_ELEMENTS:
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if element.name in obj.name:
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obj.children[0].scale = (element.radii[int(rtype)],) * 3
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if obj.type == "SURFACE" or obj.type == "MESH":
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for element in ATOM_XYZ_ELEMENTS:
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if element.name in obj.name:
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obj.scale = (element.radii[int(rtype)],) * 3
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# Routine to modify the radii in picometer of a specific type of atom
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def DEF_atom_xyz_radius_pm(atomname, radius_pm, how):
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if how == "ALL_IN_LAYER":
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if bpy.context.scene.layers[i] == True:
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for obj in bpy.context.scene.objects:
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if obj.layers[layer] == True:
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change_objects.append(obj)
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for obj in change_objects:
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if len(obj.children) != 0:
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if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
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if atomname in obj.name:
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obj.children[0].scale = (radius_pm/100,) * 3
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if obj.type == "SURFACE" or obj.type == "MESH":
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if atomname in obj.name:
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obj.scale = (radius_pm/100,) * 3
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if how == "ALL_ACTIVE":
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for obj in bpy.context.selected_objects:
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if len(obj.children) != 0:
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if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
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if atomname in obj.name:
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obj.children[0].scale = (radius_pm/100,) * 3
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if obj.type == "SURFACE" or obj.type == "MESH":
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if atomname in obj.name:
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obj.scale = (radius_pm/100,) * 3
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# Routine to scale the radii of all atoms
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def DEF_atom_xyz_radius_all(scale, how):
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if how == "ALL_IN_LAYER":
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if bpy.context.scene.layers[i] == True:
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for obj in bpy.context.scene.objects:
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if obj.layers[layer] == True:
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change_objects.append(obj)
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for obj in change_objects:
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if len(obj.children) != 0:
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if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
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obj.children[0].scale *= scale
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if obj.type == "SURFACE" or obj.type == "MESH":
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if how == "ALL_ACTIVE":
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for obj in bpy.context.selected_objects:
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if len(obj.children) != 0:
345
if obj.children[0].type == "SURFACE" or obj.children[0].type == "MESH":
346
obj.children[0].scale *= scale
348
if obj.type == "SURFACE" or obj.type == "MESH":
352
def DEF_atom_xyz_read_elements():
354
ATOM_XYZ_ELEMENTS[:] = []
356
for item in ATOM_XYZ_ELEMENTS_DEFAULT:
358
# All three radii into a list
359
radii = [item[4],item[5],item[6]]
360
# The handling of the ionic radii will be done later. So far, it is an
364
li = CLASS_atom_xyz_Elements(item[0],item[1],item[2],item[3],
366
ATOM_XYZ_ELEMENTS.append(li)
369
def DEF_atom_xyz_read_xyz_file(filepath,radiustype):
374
ATOM_XYZ_FILEPATH_p = io.open(ATOM_XYZ_FILEPATH, "r")
376
#Go through the whole file.
378
for line in ATOM_XYZ_FILEPATH_p:
380
# ... the loop is broken here (EOF) ...
384
split_list = line.rsplit()
386
if len(split_list) == 1:
387
number_atoms = int(split_list[0])
392
line = ATOM_XYZ_FILEPATH_p.readline()
397
for i in range(number_atoms):
399
line = ATOM_XYZ_FILEPATH_p.readline()
401
split_list = line.rsplit()
402
short_name = str(split_list[0])
404
# Go through all elements and find the element of the current atom.
406
for element in ATOM_XYZ_ELEMENTS:
407
if str.upper(short_name) == str.upper(element.short_name):
408
# Give the atom its proper names, color and radius:
410
# int(radiustype) => type of radius:
411
# pre-defined (0), atomic (1) or van der Waals (2)
412
radius = float(element.radii[int(radiustype)])
413
color = element.color
417
# Is it a vacancy or an 'unknown atom' ?
418
if FLAG_FOUND == False:
419
# Give this atom also a name. If it is an 'X' then it is a
420
# vacancy. Otherwise ...
421
if "X" in short_name:
424
radius = float(ATOM_XYZ_ELEMENTS[-3].radii[int(radiustype)])
425
color = ATOM_XYZ_ELEMENTS[-3].color
426
# ... take what is written in the xyz file. These are somewhat
427
# unknown atoms. This should never happen, the element list is
428
# almost complete. However, we do this due to security reasons.
430
name = str.upper(short_name)
431
radius = float(ATOM_XYZ_ELEMENTS[-2].radii[int(radiustype)])
432
color = ATOM_XYZ_ELEMENTS[-2].color
434
x = float(split_list[1])
435
y = float(split_list[2])
436
z = float(split_list[3])
438
location = Vector((x,y,z))
440
all_atoms.append([short_name, name, location, radius, color])
442
# We note here all elements. This needs to be done only once.
443
if NUMBER_FRAMES == 0:
445
for atom in all_atoms:
447
for element in elements:
448
# If the atom name is already in the list,
450
if element == atom[1]:
453
# No name in the current list has been found? => New entry.
454
if FLAG_FOUND == False:
455
# Stored are: Atom label (e.g. 'Na'), the corresponding
456
# atom name (e.g. 'Sodium') and its color.
457
elements.append(atom[1])
460
for element in elements:
462
for atom in all_atoms:
463
if atom[1] == element:
464
atoms_one_type.append(CLASS_atom_xyz_atom(
470
structure.append(atoms_one_type)
472
ALL_FRAMES.append(structure)
476
ATOM_XYZ_FILEPATH_p.close()
479
for frame in ALL_FRAMES:
480
for element in frame:
482
print(atom.element + " " + str(atom.location))
488
# This reads a custom data file.
489
def DEF_atom_xyz_custom_datafile(path_datafile):
491
if path_datafile == "":
494
path_datafile = bpy.path.abspath(path_datafile)
496
if os.path.isfile(path_datafile) == False:
499
# The whole list gets deleted! We build it new.
500
ATOM_XYZ_ELEMENTS[:] = []
502
# Read the data file, which contains all data
503
# (atom name, radii, colors, etc.)
504
data_file_p = io.open(path_datafile, "r")
506
for line in data_file_p:
510
line = data_file_p.readline()
512
line = data_file_p.readline()
515
line = data_file_p.readline()
518
line = data_file_p.readline()
519
short_name = line[19:-1]
521
line = data_file_p.readline()
522
color_value = line[19:-1].split(',')
523
color = [float(color_value[0]),
524
float(color_value[1]),
525
float(color_value[2])]
527
line = data_file_p.readline()
528
radius_used = float(line[19:-1])
530
line = data_file_p.readline()
531
radius_atomic = float(line[19:-1])
532
# Van der Waals radius
533
line = data_file_p.readline()
534
radius_vdW = float(line[19:-1])
535
radii = [radius_used,radius_atomic,radius_vdW]
538
element = CLASS_atom_xyz_Elements(number,name,short_name,color,
541
ATOM_XYZ_ELEMENTS.append(element)
547
# -----------------------------------------------------------------------------
550
def DEF_atom_xyz_main(use_mesh,
555
Ball_distance_factor,
562
atom_material_list = []
564
# ------------------------------------------------------------------------
565
# INITIALIZE THE ELEMENT LIST
567
DEF_atom_xyz_read_elements()
569
# ------------------------------------------------------------------------
570
# READING DATA OF ATOMS
572
Number_of_total_atoms = DEF_atom_xyz_read_xyz_file(ATOM_XYZ_FILEPATH,
575
# We show the atoms of the first frame.
576
first_frame = ALL_FRAMES[0]
578
# ------------------------------------------------------------------------
579
# MATERIAL PROPERTIES FOR ATOMS
581
# Create first a new list of materials for each type of atom
583
for atoms_of_one_type in first_frame:
584
# Take the first atom
585
atom = atoms_of_one_type[0]
586
material = bpy.data.materials.new(atom.name)
587
material.name = atom.name
588
material.diffuse_color = atom.color
589
atom_material_list.append(material)
591
# Now, we go through all atoms and give them a material. For all atoms ...
592
for atoms_of_one_type in first_frame:
593
for atom in atoms_of_one_type:
594
# ... and all materials ...
595
for material in atom_material_list:
596
# ... select the correct material for the current atom via
597
# comparison of names ...
598
if atom.name in material.name:
599
# ... and give the atom its material properties.
600
# However, before we check, if it is a vacancy
601
# The vacancy is represented by a transparent cube.
602
if atom.name == "Vacancy":
603
material.transparency_method = 'Z_TRANSPARENCY'
605
material.raytrace_transparency.fresnel = 1.6
606
material.raytrace_transparency.fresnel_factor = 1.6
607
material.use_transparency = True
608
# The atom gets its properties.
609
atom.material = material
611
# ------------------------------------------------------------------------
612
# TRANSLATION OF THE STRUCTURE TO THE ORIGIN
614
# It may happen that the structure in a XYZ file already has an offset
615
# If chosen, the structure is first put into the center of the scene
616
# (the offset is substracted).
618
if put_to_center == True:
620
sum_vec = Vector((0.0,0.0,0.0))
622
# Sum of all atom coordinates
623
for atoms_of_one_type in first_frame:
624
sum_vec = sum([atom.location for atom in atoms_of_one_type], sum_vec)
626
# Then the average is taken
627
sum_vec = sum_vec / Number_of_total_atoms
629
# After, for each atom the center of gravity is substracted
630
for atoms_of_one_type in first_frame:
631
for atom in atoms_of_one_type:
632
atom.location -= sum_vec
634
# ------------------------------------------------------------------------
637
# Take all atoms and adjust their radii and scale the distances.
638
for atoms_of_one_type in first_frame:
639
for atom in atoms_of_one_type:
640
atom.location *= Ball_distance_factor
642
# ------------------------------------------------------------------------
643
# DETERMINATION OF SOME GEOMETRIC PROPERTIES
645
# In the following, some geometric properties of the whole object are
646
# determined: center, size, etc.
647
sum_vec = Vector((0.0,0.0,0.0))
649
# First the center is determined. All coordinates are summed up ...
650
for atoms_of_one_type in first_frame:
651
sum_vec = sum([atom.location for atom in atoms_of_one_type], sum_vec)
653
# ... and the average is taken. This gives the center of the object.
654
object_center_vec = sum_vec / Number_of_total_atoms
656
# Now, we determine the size.The farest atom from the object center is
657
# taken as a measure. The size is used to place well the camera and light
661
for atoms_of_one_type in first_frame:
662
object_size_vec += [atom.location - object_center_vec for atom in atoms_of_one_type]
665
object_size = max(object_size_vec).length
667
# ------------------------------------------------------------------------
671
# If chosen a camera is put into the scene.
672
if use_camera == True:
674
# Assume that the object is put into the global origin. Then, the
675
# camera is moved in x and z direction, not in y. The object has its
676
# size at distance math.sqrt(object_size) from the origin. So, move the
677
# camera by this distance times a factor of camera_factor in x and z.
678
# Then add x, y and z of the origin of the object.
679
object_camera_vec = Vector((math.sqrt(object_size) * camera_factor,
681
math.sqrt(object_size) * camera_factor))
682
camera_xyz_vec = object_center_vec + object_camera_vec
685
current_layers=bpy.context.scene.layers
686
bpy.ops.object.camera_add(view_align=False, enter_editmode=False,
687
location=camera_xyz_vec,
688
rotation=(0.0, 0.0, 0.0), layers=current_layers)
689
# Some properties of the camera are changed.
690
camera = bpy.context.scene.objects.active
691
camera.name = "A_camera"
692
camera.data.name = "A_camera"
693
camera.data.lens = 45
694
camera.data.clip_end = 500.0
696
# Here the camera is rotated such it looks towards the center of
697
# the object. The [0.0, 0.0, 1.0] vector along the z axis
698
z_axis_vec = Vector((0.0, 0.0, 1.0))
699
# The angle between the last two vectors
700
angle = object_camera_vec.angle(z_axis_vec, 0)
701
# The cross-product of z_axis_vec and object_camera_vec
702
axis_vec = z_axis_vec.cross(object_camera_vec)
703
# Rotate 'axis_vec' by 'angle' and convert this to euler parameters.
704
# 4 is the size of the matrix.
705
euler = Matrix.Rotation(angle, 4, axis_vec).to_euler()
706
camera.rotation_euler = euler
708
# Rotate the camera around its axis by 90° such that we have a nice
709
# camera position and view onto the object.
710
bpy.ops.transform.rotate(value=(90.0*2*math.pi/360.0,),
711
axis=object_camera_vec,
712
constraint_axis=(False, False, False),
713
constraint_orientation='GLOBAL',
714
mirror=False, proportional='DISABLED',
715
proportional_edit_falloff='SMOOTH',
716
proportional_size=1, snap=False,
717
snap_target='CLOSEST', snap_point=(0, 0, 0),
718
snap_align=False, snap_normal=(0, 0, 0),
719
release_confirm=False)
721
# This does not work, I don't know why.
723
#for area in bpy.context.screen.areas:
724
# if area.type == 'VIEW_3D':
725
# area.spaces[0].region_3d.view_perspective = 'CAMERA'
727
# Here a lamp is put into the scene, if chosen.
730
# This is the distance from the object measured in terms of %
731
# of the camera distance. It is set onto 50% (1/2) distance.
732
lamp_dl = math.sqrt(object_size) * 15 * 0.5
733
# This is a factor to which extend the lamp shall go to the right
734
# (from the camera point of view).
735
lamp_dy_right = lamp_dl * (3.0/4.0)
737
# Create x, y and z for the lamp.
738
object_lamp_vec = Vector((lamp_dl,lamp_dy_right,lamp_dl))
739
lamp_xyz_vec = object_center_vec + object_lamp_vec
742
current_layers=bpy.context.scene.layers
743
bpy.ops.object.lamp_add (type = 'POINT', view_align=False,
744
location=lamp_xyz_vec,
745
rotation=(0.0, 0.0, 0.0),
746
layers=current_layers)
747
# Some properties of the lamp are changed.
748
lamp = bpy.context.scene.objects.active
749
lamp.data.name = "A_lamp"
751
lamp.data.distance = 500.0
752
lamp.data.energy = 3.0
753
lamp.data.shadow_method = 'RAY_SHADOW'
755
bpy.context.scene.world.light_settings.use_ambient_occlusion = True
756
bpy.context.scene.world.light_settings.ao_factor = 0.2
758
# ------------------------------------------------------------------------
759
# SOME OUTPUT ON THE CONSOLE
764
print(ATOM_XYZ_STRING)
766
print("Total number of atoms : " + str(Number_of_total_atoms))
767
print("Center of object (Angstrom) : ", object_center_vec)
768
print("Size of object (Angstrom) : ", object_size)
771
# ------------------------------------------------------------------------
774
bpy.ops.object.select_all(action='DESELECT')
776
# For each list of atoms of ONE type (e.g. Hydrogen)
777
for atoms_of_one_type in first_frame:
779
# Create first the vertices composed of the coordinates of all
782
for atom in atoms_of_one_type:
783
# In fact, the object is created in the World's origin.
784
# This is why 'object_center_vec' is substracted. At the end
785
# the whole object is translated back to 'object_center_vec'.
786
atom_vertices.append( atom.location - object_center_vec )
789
atom_mesh = bpy.data.meshes.new("Mesh_"+atom.name)
790
atom_mesh.from_pydata(atom_vertices, [], [])
792
new_atom_mesh = bpy.data.objects.new(atom.name, atom_mesh)
793
bpy.context.scene.objects.link(new_atom_mesh)
795
# Now, build a representative sphere (atom)
796
current_layers=bpy.context.scene.layers
798
if atom.name == "Vacancy":
799
bpy.ops.mesh.primitive_cube_add(
800
view_align=False, enter_editmode=False,
801
location=(0.0, 0.0, 0.0),
802
rotation=(0.0, 0.0, 0.0),
803
layers=current_layers)
806
if use_mesh == False:
807
bpy.ops.surface.primitive_nurbs_surface_sphere_add(
808
view_align=False, enter_editmode=False,
809
location=(0,0,0), rotation=(0.0, 0.0, 0.0),
810
layers=current_layers)
813
bpy.ops.mesh.primitive_uv_sphere_add(
814
segments=Ball_azimuth, ring_count=Ball_zenith,
815
size=1, view_align=False, enter_editmode=False,
816
location=(0,0,0), rotation=(0, 0, 0),
817
layers=current_layers)
819
ball = bpy.context.scene.objects.active
820
ball.scale = (atom.radius*Ball_radius_factor,) * 3
822
if atom.name == "Vacancy":
823
ball.name = "Cube_"+atom.name
825
ball.name = "Ball (NURBS)_"+atom.name
826
ball.active_material = atom.material
827
ball.parent = new_atom_mesh
828
new_atom_mesh.dupli_type = 'VERTS'
829
# The object is back translated to 'object_center_vec'.
830
new_atom_mesh.location = object_center_vec
831
STRUCTURE.append(new_atom_mesh)
835
# ------------------------------------------------------------------------
836
# SELECT ALL LOADED OBJECTS
838
bpy.ops.object.select_all(action='DESELECT')
840
for obj in STRUCTURE:
842
# activate the last selected object (perhaps another should be active?)
844
bpy.context.scene.objects.active = obj
845
print("\n\nAll atoms (%d) have been drawn - finished.\n\n"
846
% (Number_of_total_atoms))
848
return Number_of_total_atoms
851
def DEF_atom_xyz_build_frames(frame_delta, frame_skip):
853
scn = bpy.context.scene
854
current_layers = scn.layers
856
# Introduce the basis for all elements that appear in the structure.
857
for element in STRUCTURE:
859
bpy.ops.object.select_all(action='DESELECT')
860
bpy.context.scene.objects.active = element
861
element.select = True
862
bpy.ops.object.shape_key_add(None)
866
# Introduce the keys and reference the atom positions for each key.
868
for j, frame in enumerate(ALL_FRAMES):
870
if j % frame_skip == 0:
872
for elements_frame, elements_structure in zip(frame,STRUCTURE):
874
key = elements_structure.shape_key_add()
876
for atom_frame, atom_structure in zip(elements_frame, key.data):
878
atom_structure.co = (atom_frame.location
879
- elements_structure.location)
881
key.name = atom_frame.name + "_frame_" + str(i)
888
scn.frame_end = frame_delta * num_frames
890
# Manage the values of the keys
891
for element in STRUCTURE:
893
scn.frame_current = 0
895
element.data.shape_keys.key_blocks[1].value = 1.0
896
element.data.shape_keys.key_blocks[2].value = 0.0
897
element.data.shape_keys.key_blocks[1].keyframe_insert("value")
898
element.data.shape_keys.key_blocks[2].keyframe_insert("value")
900
scn.frame_current += frame_delta
902
for number in range(num_frames)[2:]:#-1]:
904
element.data.shape_keys.key_blocks[number-1].value = 0.0
905
element.data.shape_keys.key_blocks[number].value = 1.0
906
element.data.shape_keys.key_blocks[number+1].value = 0.0
907
element.data.shape_keys.key_blocks[number-1].keyframe_insert("value")
908
element.data.shape_keys.key_blocks[number].keyframe_insert("value")
909
element.data.shape_keys.key_blocks[number+1].keyframe_insert("value")
911
scn.frame_current += frame_delta
915
element.data.shape_keys.key_blocks[number].value = 1.0
916
element.data.shape_keys.key_blocks[number-1].value = 0.0
917
element.data.shape_keys.key_blocks[number].keyframe_insert("value")
918
element.data.shape_keys.key_blocks[number-1].keyframe_insert("value")
added
removed
release/scripts/addons_contrib/io_mesh_xyz/import_xyz.py
