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# ##### 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
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# 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
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# 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":
# Some properties for eevee.
material.metallic = 0.8
material.specular_intensity = 0.5
material.roughness = 0.3
material.blend_method = 'OPAQUE'
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
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# 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(
align='WORLD', 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(
align='WORLD', 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,
align='WORLD', enter_editmode=False,
location=(0,0,0), rotation=(0, 0, 0))
# Meta balls
elif Ball_type == "2":
bpy.ops.object.metaball_add(type='BALL', align='WORLD',
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!
Clemens Barth
committed
# However, hiding does not work with meta balls!
if Ball_type == "0" or Ball_type == "1":
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
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# 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")