diff options
Diffstat (limited to 'io_mesh_atomic/xyz_import.py')
| -rw-r--r-- | io_mesh_atomic/xyz_import.py | 810 |
1 files changed, 810 insertions, 0 deletions
diff --git a/io_mesh_atomic/xyz_import.py b/io_mesh_atomic/xyz_import.py new file mode 100644 index 00000000..fe903f4e --- /dev/null +++ b/io_mesh_atomic/xyz_import.py @@ -0,0 +1,810 @@ +# ##### BEGIN GPL LICENSE BLOCK ##### +# +# This program is free software; you can redistribute it and/or +# modify it under the terms of the GNU General Public License +# as published by the Free Software Foundation; either version 2 +# of the License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +# +# ##### END GPL LICENSE BLOCK ##### + +import os +import bpy +from math import pi, sqrt +from mathutils import Vector, Matrix + +# ----------------------------------------------------------------------------- +# Atom and element data + + +# This is a list that contains some data of all possible elements. The structure +# is as follows: +# +# 1, "Hydrogen", "H", [0.0,0.0,1.0], 0.32, 0.32, 0.32 , -1 , 1.54 means +# +# No., name, short name, color, radius (used), radius (covalent), radius (atomic), +# +# charge state 1, radius (ionic) 1, charge state 2, radius (ionic) 2, ... all +# charge states for any atom are listed, if existing. +# The list is fixed and cannot be changed ... (see below) + +ELEMENTS_DEFAULT = ( +( 1, "Hydrogen", "H", ( 1.0, 1.0, 1.0, 1.0), 0.32, 0.32, 0.79 , -1 , 1.54 ), +( 2, "Helium", "He", ( 0.85, 1.0, 1.0, 1.0), 0.93, 0.93, 0.49 ), +( 3, "Lithium", "Li", ( 0.8, 0.50, 1.0, 1.0), 1.23, 1.23, 2.05 , 1 , 0.68 ), +( 4, "Beryllium", "Be", ( 0.76, 1.0, 0.0, 1.0), 0.90, 0.90, 1.40 , 1 , 0.44 , 2 , 0.35 ), +( 5, "Boron", "B", ( 1.0, 0.70, 0.70, 1.0), 0.82, 0.82, 1.17 , 1 , 0.35 , 3 , 0.23 ), +( 6, "Carbon", "C", ( 0.56, 0.56, 0.56, 1.0), 0.77, 0.77, 0.91 , -4 , 2.60 , 4 , 0.16 ), +( 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 ), +( 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 ), +( 9, "Fluorine", "F", ( 0.56, 0.87, 0.31, 1.0), 0.72, 0.72, 0.57 , -1 , 1.33 , 7 , 0.08 ), +(10, "Neon", "Ne", ( 0.70, 0.89, 0.96, 1.0), 0.71, 0.71, 0.51 , 1 , 1.12 ), +(11, "Sodium", "Na", ( 0.67, 0.36, 0.94, 1.0), 1.54, 1.54, 2.23 , 1 , 0.97 ), +(12, "Magnesium", "Mg", ( 0.54, 1.0, 0.0, 1.0), 1.36, 1.36, 1.72 , 1 , 0.82 , 2 , 0.66 ), +(13, "Aluminium", "Al", ( 0.74, 0.65, 0.65, 1.0), 1.18, 1.18, 1.82 , 3 , 0.51 ), +(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 ), +(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 ), +(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 ), +(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 ), +(18, "Argon", "Ar", ( 0.50, 0.81, 0.89, 1.0), 0.98, 0.98, 0.88 , 1 , 1.54 ), +(19, "Potassium", "K", ( 0.56, 0.25, 0.83, 1.0), 2.03, 2.03, 2.77 , 1 , 0.81 ), +(20, "Calcium", "Ca", ( 0.23, 1.0, 0.0, 1.0), 1.74, 1.74, 2.23 , 1 , 1.18 , 2 , 0.99 ), +(21, "Scandium", "Sc", ( 0.90, 0.90, 0.90, 1.0), 1.44, 1.44, 2.09 , 3 , 0.73 ), +(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 ), +(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 ), +(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 ), +(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 ), +(26, "Iron", "Fe", ( 0.87, 0.4, 0.2, 1.0), 1.17, 1.17, 1.72 , 2 , 0.74 , 3 , 0.64 ), +(27, "Cobalt", "Co", ( 0.94, 0.56, 0.62, 1.0), 1.16, 1.16, 1.67 , 2 , 0.72 , 3 , 0.63 ), +(28, "Nickel", "Ni", ( 0.31, 0.81, 0.31, 1.0), 1.15, 1.15, 1.62 , 2 , 0.69 ), +(29, "Copper", "Cu", ( 0.78, 0.50, 0.2, 1.0), 1.17, 1.17, 1.57 , 1 , 0.96 , 2 , 0.72 ), +(30, "Zinc", "Zn", ( 0.49, 0.50, 0.69, 1.0), 1.25, 1.25, 1.53 , 1 , 0.88 , 2 , 0.74 ), +(31, "Gallium", "Ga", ( 0.76, 0.56, 0.56, 1.0), 1.26, 1.26, 1.81 , 1 , 0.81 , 3 , 0.62 ), +(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 ), +(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 ), +(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 ), +(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 ), +(36, "Krypton", "Kr", ( 0.36, 0.72, 0.81, 1.0), 1.31, 1.31, 1.24 ), +(37, "Rubidium", "Rb", ( 0.43, 0.18, 0.69, 1.0), 2.16, 2.16, 2.98 , 1 , 1.47 ), +(38, "Strontium", "Sr", ( 0.0, 1.0, 0.0, 1.0), 1.91, 1.91, 2.45 , 2 , 1.12 ), +(39, "Yttrium", "Y", ( 0.58, 1.0, 1.0, 1.0), 1.62, 1.62, 2.27 , 3 , 0.89 ), +(40, "Zirconium", "Zr", ( 0.58, 0.87, 0.87, 1.0), 1.45, 1.45, 2.16 , 1 , 1.09 , 4 , 0.79 ), +(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 ), +(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 ), +(43, "Technetium", "Tc", ( 0.23, 0.61, 0.61, 1.0), 1.27, 1.27, 1.95 , 7 , 0.97 ), +(44, "Ruthenium", "Ru", ( 0.14, 0.56, 0.56, 1.0), 1.25, 1.25, 1.89 , 4 , 0.67 ), +(45, "Rhodium", "Rh", ( 0.03, 0.49, 0.54, 1.0), 1.25, 1.25, 1.83 , 3 , 0.68 ), +(46, "Palladium", "Pd", ( 0.0, 0.41, 0.52, 1.0), 1.28, 1.28, 1.79 , 2 , 0.80 , 4 , 0.65 ), +(47, "Silver", "Ag", ( 0.75, 0.75, 0.75, 1.0), 1.34, 1.34, 1.75 , 1 , 1.26 , 2 , 0.89 ), +(48, "Cadmium", "Cd", ( 1.0, 0.85, 0.56, 1.0), 1.48, 1.48, 1.71 , 1 , 1.14 , 2 , 0.97 ), +(49, "Indium", "In", ( 0.65, 0.45, 0.45, 1.0), 1.44, 1.44, 2.00 , 3 , 0.81 ), +(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 ), +(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 ), +(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 ), +(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 ), +(54, "Xenon", "Xe", ( 0.25, 0.61, 0.69, 1.0), 1.31, 1.31, 1.24 ), +(55, "Caesium", "Cs", ( 0.34, 0.09, 0.56, 1.0), 2.35, 2.35, 3.35 , 1 , 1.67 ), +(56, "Barium", "Ba", ( 0.0, 0.78, 0.0, 1.0), 1.98, 1.98, 2.78 , 1 , 1.53 , 2 , 1.34 ), +(57, "Lanthanum", "La", ( 0.43, 0.83, 1.0, 1.0), 1.69, 1.69, 2.74 , 1 , 1.39 , 3 , 1.06 ), +(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 ), +(59, "Praseodymium", "Pr", ( 0.85, 1.0, 0.78, 1.0), 1.65, 1.65, 2.67 , 3 , 1.01 , 4 , 0.90 ), +(60, "Neodymium", "Nd", ( 0.78, 1.0, 0.78, 1.0), 1.64, 1.64, 2.64 , 3 , 0.99 ), +(61, "Promethium", "Pm", ( 0.63, 1.0, 0.78, 1.0), 1.63, 1.63, 2.62 , 3 , 0.97 ), +(62, "Samarium", "Sm", ( 0.56, 1.0, 0.78, 1.0), 1.62, 1.62, 2.59 , 3 , 0.96 ), +(63, "Europium", "Eu", ( 0.38, 1.0, 0.78, 1.0), 1.85, 1.85, 2.56 , 2 , 1.09 , 3 , 0.95 ), +(64, "Gadolinium", "Gd", ( 0.27, 1.0, 0.78, 1.0), 1.61, 1.61, 2.54 , 3 , 0.93 ), +(65, "Terbium", "Tb", ( 0.18, 1.0, 0.78, 1.0), 1.59, 1.59, 2.51 , 3 , 0.92 , 4 , 0.84 ), +(66, "Dysprosium", "Dy", ( 0.12, 1.0, 0.78, 1.0), 1.59, 1.59, 2.49 , 3 , 0.90 ), +(67, "Holmium", "Ho", ( 0.0, 1.0, 0.61, 1.0), 1.58, 1.58, 2.47 , 3 , 0.89 ), +(68, "Erbium", "Er", ( 0.0, 0.90, 0.45, 1.0), 1.57, 1.57, 2.45 , 3 , 0.88 ), +(69, "Thulium", "Tm", ( 0.0, 0.83, 0.32, 1.0), 1.56, 1.56, 2.42 , 3 , 0.87 ), +(70, "Ytterbium", "Yb", ( 0.0, 0.74, 0.21, 1.0), 1.74, 1.74, 2.40 , 2 , 0.93 , 3 , 0.85 ), +(71, "Lutetium", "Lu", ( 0.0, 0.67, 0.14, 1.0), 1.56, 1.56, 2.25 , 3 , 0.85 ), +(72, "Hafnium", "Hf", ( 0.30, 0.76, 1.0, 1.0), 1.44, 1.44, 2.16 , 4 , 0.78 ), +(73, "Tantalum", "Ta", ( 0.30, 0.65, 1.0, 1.0), 1.34, 1.34, 2.09 , 5 , 0.68 ), +(74, "Tungsten", "W", ( 0.12, 0.58, 0.83, 1.0), 1.30, 1.30, 2.02 , 4 , 0.70 , 6 , 0.62 ), +(75, "Rhenium", "Re", ( 0.14, 0.49, 0.67, 1.0), 1.28, 1.28, 1.97 , 4 , 0.72 , 7 , 0.56 ), +(76, "Osmium", "Os", ( 0.14, 0.4, 0.58, 1.0), 1.26, 1.26, 1.92 , 4 , 0.88 , 6 , 0.69 ), +(77, "Iridium", "Ir", ( 0.09, 0.32, 0.52, 1.0), 1.27, 1.27, 1.87 , 4 , 0.68 ), +(78, "Platinum", "Pt", ( 0.81, 0.81, 0.87, 1.0), 1.30, 1.30, 1.83 , 2 , 0.80 , 4 , 0.65 ), +(79, "Gold", "Au", ( 1.0, 0.81, 0.13, 1.0), 1.34, 1.34, 1.79 , 1 , 1.37 , 3 , 0.85 ), +(80, "Mercury", "Hg", ( 0.72, 0.72, 0.81, 1.0), 1.49, 1.49, 1.76 , 1 , 1.27 , 2 , 1.10 ), +(81, "Thallium", "Tl", ( 0.65, 0.32, 0.30, 1.0), 1.48, 1.48, 2.08 , 1 , 1.47 , 3 , 0.95 ), +(82, "Lead", "Pb", ( 0.34, 0.34, 0.38, 1.0), 1.47, 1.47, 1.81 , 2 , 1.20 , 4 , 0.84 ), +(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 ), +(84, "Polonium", "Po", ( 0.67, 0.36, 0.0, 1.0), 1.46, 1.46, 1.53 , 6 , 0.67 ), +(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 ), +(86, "Radon", "Rn", ( 0.25, 0.50, 0.58, 1.0), 1.00, 1.00, 1.34 ), +(87, "Francium", "Fr", ( 0.25, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 , 1 , 1.80 ), +(88, "Radium", "Ra", ( 0.0, 0.49, 0.0, 1.0), 1.00, 1.00, 1.00 , 2 , 1.43 ), +(89, "Actinium", "Ac", ( 0.43, 0.67, 0.98, 1.0), 1.00, 1.00, 1.00 , 3 , 1.18 ), +(90, "Thorium", "Th", ( 0.0, 0.72, 1.0, 1.0), 1.65, 1.65, 1.00 , 4 , 1.02 ), +(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 ), +(92, "Uranium", "U", ( 0.0, 0.56, 1.0, 1.0), 1.42, 1.42, 1.00 , 4 , 0.97 , 6 , 0.80 ), +(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 ), +(94, "Plutonium", "Pu", ( 0.0, 0.41, 1.0, 1.0), 1.00, 1.00, 1.00 , 3 , 1.08 , 4 , 0.93 ), +(95, "Americium", "Am", ( 0.32, 0.36, 0.94, 1.0), 1.00, 1.00, 1.00 , 3 , 1.07 , 4 , 0.92 ), +(96, "Curium", "Cm", ( 0.47, 0.36, 0.89, 1.0), 1.00, 1.00, 1.00 ), +(97, "Berkelium", "Bk", ( 0.54, 0.30, 0.89, 1.0), 1.00, 1.00, 1.00 ), +(98, "Californium", "Cf", ( 0.63, 0.21, 0.83, 1.0), 1.00, 1.00, 1.00 ), +(99, "Einsteinium", "Es", ( 0.70, 0.12, 0.83, 1.0), 1.00, 1.00, 1.00 ), +(100, "Fermium", "Fm", ( 0.70, 0.12, 0.72, 1.0), 1.00, 1.00, 1.00 ), +(101, "Mendelevium", "Md", ( 0.70, 0.05, 0.65, 1.0), 1.00, 1.00, 1.00 ), +(102, "Nobelium", "No", ( 0.74, 0.05, 0.52, 1.0), 1.00, 1.00, 1.00 ), +(103, "Lawrencium", "Lr", ( 0.78, 0.0, 0.4, 1.0), 1.00, 1.00, 1.00 ), +(104, "Vacancy", "Vac", ( 0.5, 0.5, 0.5, 1.0), 1.00, 1.00, 1.00), +(105, "Default", "Default", ( 1.0, 1.0, 1.0, 1.0), 1.00, 1.00, 1.00), +(106, "Stick", "Stick", ( 0.5, 0.5, 0.5, 1.0), 1.00, 1.00, 1.00), +) + +# This list here contains all data of the elements and will be used during +# runtime. It is a list of classes. +# During executing Atomic Blender, the list will be initialized with the fixed +# data from above via the class structure below (ElementProp). We +# have then one fixed list (above), which will never be changed, and a list of +# classes with same data. The latter can be modified via loading a separate +# custom data file for instance. +ELEMENTS = [] + +# This is the list, which contains all atoms of all frames! Each item is a +# list which contains the atoms of a single frame. It is a list of +# 'AtomProp'. +ALL_FRAMES = [] + +# A list of ALL balls which are put into the scene +STRUCTURE = [] + + +# This is the class, which stores the properties for one element. +class ElementProp(object): + __slots__ = ('number', 'name', 'short_name', 'color', 'radii', 'radii_ionic') + def __init__(self, number, name, short_name, color, radii, radii_ionic): + self.number = number + self.name = name + self.short_name = short_name + self.color = color + self.radii = radii + self.radii_ionic = radii_ionic + +# This is the class, which stores the properties of one atom. +class AtomProp(object): + __slots__ = ('element', 'name', 'location', 'radius', 'color', 'material') + def __init__(self, element, name, location, radius, color, material): + self.element = element + self.name = name + self.location = location + self.radius = radius + self.color = color + self.material = material + + +# ----------------------------------------------------------------------------- +# Some basic routines + +def read_elements(): + + del ELEMENTS[:] + + for item in ELEMENTS_DEFAULT: + + # All three radii into a list + radii = [item[4],item[5],item[6]] + # The handling of the ionic radii will be done later. So far, it is an + # empty list. + radii_ionic = [] + + li = ElementProp(item[0],item[1],item[2],item[3], + radii,radii_ionic) + ELEMENTS.append(li) + + +# filepath_pdb: path to pdb file +# radiustype : '0' default +# '1' atomic radii +# '2' van der Waals +def read_xyz_file(filepath_xyz,radiustype): + + number_frames = 0 + total_number_atoms = 0 + + # Open the file ... + filepath_xyz_p = open(filepath_xyz, "r") + + #Go through the whole file. + FLAG = False + for line in filepath_xyz_p: + + # ... the loop is broken here (EOF) ... + if line == "": + continue + + split_list = line.rsplit() + + if len(split_list) == 1: + number_atoms = int(split_list[0]) + FLAG = True + + if FLAG == True: + + line = filepath_xyz_p.readline() + line = line.rstrip() + + all_atoms= [] + for i in range(number_atoms): + + + # This is a guarantee that only the total number of atoms of the + # first frame is used. Condition is, so far, that the number of + # atoms in a xyz file is constant. However, sometimes the number + # may increase (or decrease). If it decreases, the addon crashes. + # If it increases, only the tot number of atoms of the first frame + # is used. + # By time, I will allow varying atom numbers ... but this takes + # some time ... + if number_frames != 0: + if i >= total_number_atoms: + break + + + line = filepath_xyz_p.readline() + line = line.rstrip() + split_list = line.rsplit() + short_name = str(split_list[0]) + + # Go through all elements and find the element of the current atom. + FLAG_FOUND = False + for element in ELEMENTS: + if str.upper(short_name) == str.upper(element.short_name): + # Give the atom its proper name, color and radius: + name = element.name + # int(radiustype) => type of radius: + # pre-defined (0), atomic (1) or van der Waals (2) + radius = float(element.radii[int(radiustype)]) + color = element.color + FLAG_FOUND = True + break + + # Is it a vacancy or an 'unknown atom' ? + if FLAG_FOUND == False: + # Give this atom also a name. If it is an 'X' then it is a + # vacancy. Otherwise ... + if "X" in short_name: + short_name = "VAC" + name = "Vacancy" + radius = float(ELEMENTS[-3].radii[int(radiustype)]) + color = ELEMENTS[-3].color + # ... take what is written in the xyz file. These are somewhat + # unknown atoms. This should never happen, the element list is + # almost complete. However, we do this due to security reasons. + else: + name = str.upper(short_name) + radius = float(ELEMENTS[-2].radii[int(radiustype)]) + color = ELEMENTS[-2].color + + x = float(split_list[1]) + y = float(split_list[2]) + z = float(split_list[3]) + + location = Vector((x,y,z)) + + all_atoms.append([short_name, name, location, radius, color]) + + # We note here all elements. This needs to be done only once. + if number_frames == 0: + + # This is a guarantee that only the total number of atoms of the + # first frame is used. Condition is, so far, that the number of + # atoms in a xyz file is constant. However, sometimes the number + # may increase (or decrease). If it decreases, the addon crashes. + # If it increases, only the tot number of atoms of the first frame + # is used. + # By time, I will allow varying atom numbers ... but this takes + # some time ... + total_number_atoms = number_atoms + + + elements = [] + for atom in all_atoms: + FLAG_FOUND = False + for element in elements: + # If the atom name is already in the list, + # FLAG on 'True'. + if element == atom[1]: + FLAG_FOUND = True + break + # No name in the current list has been found? => New entry. + if FLAG_FOUND == False: + # Stored are: Atom label (e.g. 'Na'), the corresponding + # atom name (e.g. 'Sodium') and its color. + elements.append(atom[1]) + + # Sort the atoms: create lists of atoms of one type + structure = [] + for element in elements: + atoms_one_type = [] + for atom in all_atoms: + if atom[1] == element: + atoms_one_type.append(AtomProp(atom[0], + atom[1], + atom[2], + atom[3], + atom[4],[])) + structure.append(atoms_one_type) + + ALL_FRAMES.append(structure) + number_frames += 1 + FLAG = False + + filepath_xyz_p.close() + + return total_number_atoms + + +# Rotate an object. +def rotate_object(rot_mat, obj): + + bpy.ops.object.select_all(action='DESELECT') + obj.select_set(True) + + # Decompose world_matrix's components, and from them assemble 4x4 matrices. + orig_loc, orig_rot, orig_scale = obj.matrix_world.decompose() + + orig_loc_mat = Matrix.Translation(orig_loc) + orig_rot_mat = orig_rot.to_matrix().to_4x4() + orig_scale_mat = (Matrix.Scale(orig_scale[0],4,(1,0,0)) @ + Matrix.Scale(orig_scale[1],4,(0,1,0)) @ + Matrix.Scale(orig_scale[2],4,(0,0,1))) + + # Assemble the new matrix. + obj.matrix_world = orig_loc_mat @ rot_mat @ orig_rot_mat @ orig_scale_mat + + +# Function, which puts a camera and light source into the 3D scene +def camera_light_source(use_camera, + use_light, + object_center_vec, + object_size): + + camera_factor = 15.0 + + # If chosen a camera is put into the scene. + if use_camera == True: + + # Assume that the object is put into the global origin. Then, the + # camera is moved in x and z direction, not in y. The object has its + # size at distance sqrt(object_size) from the origin. So, move the + # camera by this distance times a factor of camera_factor in x and z. + # Then add x, y and z of the origin of the object. + object_camera_vec = Vector((sqrt(object_size) * camera_factor, + 0.0, + sqrt(object_size) * camera_factor)) + camera_xyz_vec = object_center_vec + object_camera_vec + + # Create the camera + camera_data = bpy.data.cameras.new("A_camera") + camera_data.lens = 45 + camera_data.clip_end = 500.0 + camera = bpy.data.objects.new("A_camera", camera_data) + camera.location = camera_xyz_vec + bpy.context.collection.objects.link(camera) + + # Here the camera is rotated such it looks towards the center of + # the object. The [0.0, 0.0, 1.0] vector along the z axis + z_axis_vec = Vector((0.0, 0.0, 1.0)) + # The angle between the last two vectors + angle = object_camera_vec.angle(z_axis_vec, 0) + # The cross-product of z_axis_vec and object_camera_vec + axis_vec = z_axis_vec.cross(object_camera_vec) + # Rotate 'axis_vec' by 'angle' and convert this to euler parameters. + # 4 is the size of the matrix. + camera.rotation_euler = Matrix.Rotation(angle, 4, axis_vec).to_euler() + + # Rotate the camera around its axis by 90° such that we have a nice + # camera position and view onto the object. + bpy.ops.object.select_all(action='DESELECT') + camera.select_set(True) + + # Rotate the camera around its axis 'object_camera_vec' by 90° such + # that we have a nice camera view onto the object. + matrix_rotation = Matrix.Rotation(90/360*2*pi, 4, object_camera_vec) + rotate_object(matrix_rotation, camera) + + # Here a lamp is put into the scene, if chosen. + if use_light == True: + + # This is the distance from the object measured in terms of % + # of the camera distance. It is set onto 50% (1/2) distance. + light_dl = sqrt(object_size) * 15 * 0.5 + # This is a factor to which extend the lamp shall go to the right + # (from the camera point of view). + light_dy_right = light_dl * (3.0/4.0) + + # Create x, y and z for the lamp. + object_light_vec = Vector((light_dl,light_dy_right,light_dl)) + light_xyz_vec = object_center_vec + object_light_vec + + # Create the lamp + light_data = bpy.data.lights.new(name="A_light", type="SUN") + light_data.distance = 500.0 + light_data.energy = 3.0 + lamp = bpy.data.objects.new("A_light", light_data) + lamp.location = light_xyz_vec + bpy.context.collection.objects.link(lamp) + + # Some settings for the World: a bit ambient occlusion + bpy.context.scene.world.light_settings.use_ambient_occlusion = True + bpy.context.scene.world.light_settings.ao_factor = 0.2 + # Some properties for cycles + lamp.data.use_nodes = True + lmp_P_BSDF = lamp.data.node_tree.nodes['Emission'] + lmp_P_BSDF.inputs['Strength'].default_value = 5 + +# ----------------------------------------------------------------------------- +# The main routine + +def import_xyz(Ball_type, + Ball_azimuth, + Ball_zenith, + Ball_radius_factor, + radiustype, + Ball_distance_factor, + put_to_center, + put_to_center_all, + use_camera, + use_light, + filepath_xyz): + + # List of materials + atom_material_list = [] + + # ------------------------------------------------------------------------ + # INITIALIZE THE ELEMENT LIST + + read_elements() + + # ------------------------------------------------------------------------ + # READING DATA OF ATOMS + + Number_of_total_atoms = read_xyz_file(filepath_xyz, radiustype) + + # We show the atoms of the first frame. + first_frame = ALL_FRAMES[0] + + # ------------------------------------------------------------------------ + # MATERIAL PROPERTIES FOR ATOMS + + # Create first a new list of materials for each type of atom + # (e.g. hydrogen) + for atoms_of_one_type in first_frame: + # Take the first atom + atom = atoms_of_one_type[0] + material = bpy.data.materials.new(atom.name) + material.name = atom.name + material.diffuse_color = atom.color + atom_material_list.append(material) + + # Now, we go through all atoms and give them a material. For all atoms ... + for atoms_of_one_type in first_frame: + for atom in atoms_of_one_type: + # ... and all materials ... + for material in atom_material_list: + # ... select the correct material for the current atom via + # comparison of names ... + if atom.name in material.name: + # ... and give the atom its material properties. + # However, before we check if it is a vacancy + # The vacancy is represented by a transparent cube. + if atom.name == "Vacancy": + material.metallic = 0.8 + material.specular_intensity = 0.5 + material.roughness = 0.3 + material.blend_method = 'ADD' + material.show_transparent_back = False + # Some properties for cycles + material.use_nodes = True + mat_P_BSDF = material.node_tree.nodes['Principled BSDF'] + mat_P_BSDF.inputs['Metallic'].default_value = 0.1 + mat_P_BSDF.inputs['Roughness'].default_value = 0.2 + mat_P_BSDF.inputs['Transmission'].default_value = 0.97 + mat_P_BSDF.inputs['IOR'].default_value = 0.8 + # The atom gets its properties. + atom.material = material + + # ------------------------------------------------------------------------ + # TRANSLATION OF THE STRUCTURE TO THE ORIGIN + + # It may happen that the structure in a XYZ file already has an offset + + + # If chosen, the structure is put into the center of the scene + # (only the first frame). + if put_to_center == True and put_to_center_all == False: + + sum_vec = Vector((0.0,0.0,0.0)) + + # Sum of all atom coordinates + for atoms_of_one_type in first_frame: + sum_vec = sum([atom.location for atom in atoms_of_one_type], sum_vec) + + # Then the average is taken + sum_vec = sum_vec / Number_of_total_atoms + + # After, for each atom the center of gravity is substracted + for atoms_of_one_type in first_frame: + for atom in atoms_of_one_type: + atom.location -= sum_vec + + # If chosen, the structure is put into the center of the scene + # (all frames). + if put_to_center_all == True: + + # For all frames + for frame in ALL_FRAMES: + + sum_vec = Vector((0.0,0.0,0.0)) + + # Sum of all atom coordinates + for (i, atoms_of_one_type) in enumerate(frame): + + # This is a guarantee that only the total number of atoms of the + # first frame is used. Condition is, so far, that the number of + # atoms in a xyz file is constant. However, sometimes the number + # may increase (or decrease). If it decreases, the addon crashes. + # If it increases, only the tot number of atoms of the first frame + # is used. + # By time, I will allow varying atom numbers ... but this takes + # some time ... + if i >= Number_of_total_atoms: + break + + sum_vec = sum([atom.location for atom in atoms_of_one_type], sum_vec) + + # Then the average is taken + sum_vec = sum_vec / Number_of_total_atoms + + # After, for each atom the center of gravity is substracted + for atoms_of_one_type in frame: + for atom in atoms_of_one_type: + atom.location -= sum_vec + + + # ------------------------------------------------------------------------ + # SCALING + + # Take all atoms and adjust their radii and scale the distances. + for atoms_of_one_type in first_frame: + for atom in atoms_of_one_type: + atom.location *= Ball_distance_factor + + # ------------------------------------------------------------------------ + # DETERMINATION OF SOME GEOMETRIC PROPERTIES + + # In the following, some geometric properties of the whole object are + # determined: center, size, etc. + sum_vec = Vector((0.0,0.0,0.0)) + + # First the center is determined. All coordinates are summed up ... + for atoms_of_one_type in first_frame: + sum_vec = sum([atom.location for atom in atoms_of_one_type], sum_vec) + + # ... and the average is taken. This gives the center of the object. + object_center_vec = sum_vec / Number_of_total_atoms + + # Now, we determine the size.The farthest atom from the object center is + # taken as a measure. The size is used to place well the camera and light + # into the scene. + + object_size_vec = [] + for atoms_of_one_type in first_frame: + object_size_vec += [atom.location - object_center_vec for atom in atoms_of_one_type] + + object_size = 0.0 + object_size = max(object_size_vec).length + + # ------------------------------------------------------------------------ + # COLLECTION + + # Before we start to draw the atoms, we first create a collection for the + # atomic structure. All atoms (balls) are put into this collection. + coll_structure_name = os.path.basename(filepath_xyz) + scene = bpy.context.scene + coll_structure = bpy.data.collections.new(coll_structure_name) + scene.collection.children.link(coll_structure) + + # ------------------------------------------------------------------------ + # DRAWING THE ATOMS + + bpy.ops.object.select_all(action='DESELECT') + + # For each list of atoms of ONE type (e.g. Hydrogen) + for atoms_of_one_type in first_frame: + + # Create first the vertices composed of the coordinates of all + # atoms of one type + atom_vertices = [] + for atom in atoms_of_one_type: + # In fact, the object is created in the World's origin. + # This is why 'object_center_vec' is substracted. At the end + # the whole object is translated back to 'object_center_vec'. + atom_vertices.append( atom.location - object_center_vec ) + + # First, we create a collection of the element, which + # contains the atoms (balls + mesh)! + coll_element_name = atom.name # the element name + # Create the new collection and ... + coll_element = bpy.data.collections.new(coll_element_name) + # ... link it to the collection, which contains all parts of the + # structure. + coll_structure.children.link(coll_element) + + # Now, create a collection for the atoms, which includes the + # representative ball and the mesh. + coll_atom_name = atom.name + "_atom" + # Create the new collection and ... + coll_atom = bpy.data.collections.new(coll_atom_name) + # ... link it to the collection, which contains all parts of the + # element (ball and mesh). + coll_element.children.link(coll_atom) + + # Build the mesh + atom_mesh = bpy.data.meshes.new("Mesh_"+atom.name) + atom_mesh.from_pydata(atom_vertices, [], []) + atom_mesh.update() + new_atom_mesh = bpy.data.objects.new(atom.name + "_mesh", atom_mesh) + + # Link active object to the new collection + coll_atom.objects.link(new_atom_mesh) + + # Now, build a representative sphere (atom) + if atom.name == "Vacancy": + bpy.ops.mesh.primitive_cube_add( + view_align=False, enter_editmode=False, + location=(0.0, 0.0, 0.0), + rotation=(0.0, 0.0, 0.0)) + else: + # NURBS balls + if Ball_type == "0": + bpy.ops.surface.primitive_nurbs_surface_sphere_add( + view_align=False, enter_editmode=False, + location=(0,0,0), rotation=(0.0, 0.0, 0.0)) + # UV balls + elif Ball_type == "1": + bpy.ops.mesh.primitive_uv_sphere_add( + segments=Ball_azimuth, ring_count=Ball_zenith, + size=1, view_align=False, enter_editmode=False, + location=(0,0,0), rotation=(0, 0, 0)) + # Meta balls + elif Ball_type == "2": + bpy.ops.object.metaball_add(type='BALL', view_align=False, + enter_editmode=False, location=(0, 0, 0), + rotation=(0, 0, 0)) + + ball = bpy.context.view_layer.objects.active + # Hide this ball because its appearance has no meaning. It is just the + # representative ball. The ball is visible at the vertices of the mesh. + # Rememmber, this is a dupliverts construct! + ball.hide_set(True) + # Scale up/down the ball radius. + ball.scale = (atom.radius*Ball_radius_factor,) * 3 + + if atom.name == "Vacancy": + ball.name = atom.name + "_cube" + else: + ball.name = atom.name + "_ball" + ball.active_material = atom.material + ball.parent = new_atom_mesh + new_atom_mesh.instance_type = 'VERTS' + # The object is back translated to 'object_center_vec'. + new_atom_mesh.location = object_center_vec + STRUCTURE.append(new_atom_mesh) + + # Note the collection where the ball was placed into. + coll_all = ball.users_collection + if len(coll_all) > 0: + coll_past = coll_all[0] + else: + coll_past = bpy.context.scene.collection + + # Put the atom into the new collection 'atom' and ... + coll_atom.objects.link(ball) + # ... unlink the atom from the other collection. + coll_past.objects.unlink(ball) + + # ------------------------------------------------------------------------ + # CAMERA and LIGHT SOURCES + + camera_light_source(use_camera, + use_light, + object_center_vec, + object_size) + + # ------------------------------------------------------------------------ + # SELECT ALL LOADED OBJECTS + + bpy.ops.object.select_all(action='DESELECT') + obj = None + for obj in STRUCTURE: + obj.select_set(True) + # activate the last selected object (perhaps another should be active?) + if obj: + bpy.context.view_layer.objects.active = obj + + + +def build_frames(frame_delta, frame_skip): + + scn = bpy.context.scene + + # Introduce the basis for all elements that appear in the structure. + for element in STRUCTURE: + + bpy.ops.object.select_all(action='DESELECT') + bpy.context.view_layer.objects.active = element + element.select_set(True) + bpy.ops.object.shape_key_add(True) + + frame_skip += 1 + + # Introduce the keys and reference the atom positions for each key. + i = 0 + for j, frame in enumerate(ALL_FRAMES): + + if j % frame_skip == 0: + + for elements_frame, elements_structure in zip(frame,STRUCTURE): + + key = elements_structure.shape_key_add() + + for atom_frame, atom_structure in zip(elements_frame, key.data): + + atom_structure.co = (atom_frame.location + - elements_structure.location) + + key.name = atom_frame.name + "_frame_" + str(i) + + i += 1 + + num_frames = i + + scn.frame_start = 0 + scn.frame_end = frame_delta * num_frames + + # Manage the values of the keys + for element in STRUCTURE: + + scn.frame_current = 0 + + element.data.shape_keys.key_blocks[1].value = 1.0 + element.data.shape_keys.key_blocks[2].value = 0.0 + element.data.shape_keys.key_blocks[1].keyframe_insert("value") + element.data.shape_keys.key_blocks[2].keyframe_insert("value") + + scn.frame_current += frame_delta + + number = 0 + + for number in range(num_frames)[2:]:#-1]: + + element.data.shape_keys.key_blocks[number-1].value = 0.0 + element.data.shape_keys.key_blocks[number].value = 1.0 + element.data.shape_keys.key_blocks[number+1].value = 0.0 + element.data.shape_keys.key_blocks[number-1].keyframe_insert("value") + element.data.shape_keys.key_blocks[number].keyframe_insert("value") + element.data.shape_keys.key_blocks[number+1].keyframe_insert("value") + + scn.frame_current += frame_delta + + number += 1 + + element.data.shape_keys.key_blocks[number].value = 1.0 + element.data.shape_keys.key_blocks[number-1].value = 0.0 + element.data.shape_keys.key_blocks[number].keyframe_insert("value") + element.data.shape_keys.key_blocks[number-1].keyframe_insert("value") |