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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
import bmesh
from mathutils import Vector
from math import sqrt
from copy import copy
# -----------------------------------------------------------------------------
# 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),
)
# The list 'ELEMENTS' contains all data of the elements and will be used during
# runtime. The list will be initialized with the fixed
# data from above via the class below (ElementProp). One fixed list (above),
# which cannot be changed, and a list of classes with same data (ELEMENTS) exist.
# The list 'ELEMENTS' can be modified by e.g. loading a separate custom
# data file.
ELEMENTS = []
# 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 function measures the distance between two selected objects.
def distance():
# In the 'EDIT' mode
if bpy.context.mode == 'EDIT_MESH':
atom = bpy.context.edit_object
bm = bmesh.from_edit_mesh(atom.data)
locations = []
for v in bm.verts:
if v.select:
locations.append(atom.matrix_world @ v.co)
if len(locations) > 1:
location1 = locations[0]
location2 = locations[1]
else:
return "N.A"
# In the 'OBJECT' mode
else:
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location1 = bpy.context.selected_objects[0].location
location2 = bpy.context.selected_objects[1].location
else:
return "N.A."
dv = location2 - location1
dist = str(dv.length)
pos = str.find(dist, ".")
dist = dist[:pos+4]
dist = dist + " A"
return dist
def choose_objects(action_type,
who,
radius_all,
radius_pm,
radius_type,
radius_type_ionic,
sticks_all):
# For selected objects of all selected layers
if who == "ALL_IN_LAYER":
# Determine all selected layers.
layers = []
for i, layer in enumerate(bpy.context.scene.layers):
if layer == True:
layers.append(i)
# Put all objects, which are in the layers, into a list.
change_objects_all = []
for atom in bpy.context.scene.objects:
for layer in layers:
if atom.layers[layer] == True:
change_objects_all.append(atom)
# For selected objects of the visible layer
elif who == "ALL_ACTIVE":
change_objects_all = []
# Note all selected objects first.
for atom in bpy.context.selected_objects:
change_objects_all.append(atom)
# This is very important now: If there are dupliverts structures, note
# only the parents and NOT the children! Otherwise the double work is
# done or the system can even crash if objects are deleted. - The
# chidlren are accessed anyways (see below).
change_objects = []
for atom in change_objects_all:
if atom.parent != None:
FLAG = False
for atom2 in change_objects:
if atom2 == atom.parent:
FLAG = True
if FLAG == False:
change_objects.append(atom)
else:
change_objects.append(atom)
# And now, consider all objects, which are in the list 'change_objects'.
for atom in change_objects:
if len(atom.children) != 0:
for atom_child in atom.children:
if atom_child.type in {'SURFACE', 'MESH', 'META'}:
modify_objects(action_type,
atom_child,
radius_all,
radius_pm,
radius_type,
radius_type_ionic,
sticks_all)
else:
if atom.type in {'SURFACE', 'MESH', 'META'}:
modify_objects(action_type,
atom,
radius_all,
radius_pm,
radius_type,
radius_type_ionic,
sticks_all)
# Modifying the radius of a selected atom or stick
def modify_objects(action_type,
atom,
radius_all,
radius_pm,
radius_type,
radius_type_ionic,
sticks_all):
# Modify atom radius (in pm)
if action_type == "ATOM_RADIUS_PM" and "STICK" not in atom.name.upper():
if radius_pm[0] in atom.name:
atom.scale = (radius_pm[1]/100,) * 3
# Modify atom radius (all selected)
if action_type == "ATOM_RADIUS_ALL" and "STICK" not in atom.name.upper():
atom.scale *= radius_all
# Modify atom radius (type, van der Waals, atomic or ionic)
if action_type == "ATOM_RADIUS_TYPE" and "STICK" not in atom.name.upper():
for element in ELEMENTS:
if element.name in atom.name:
# For ionic radii
if radius_type == '3':
charge_states = element.radii_ionic[::2]
charge_radii = element.radii_ionic[1::2]
charge_state_chosen = int(radius_type_ionic) - 4
find = (lambda searchList, elem:
[[i for i, x in enumerate(searchList) if x == e]
for e in elem])
index = find(charge_states,[charge_state_chosen])[0]
# Is there a charge state?
if index != []:
atom.scale = (charge_radii[index[0]],) * 3
# For atomic and van der Waals radii.
else:
atom.scale = (element.radii[int(radius_type)],) * 3
# Modify atom sticks
if (action_type == "STICKS_RADIUS_ALL" and 'STICK' in atom.name.upper() and
('CUP' in atom.name.upper() or
'CYLINDER' in atom.name.upper())):
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# For dupliverts structures only: Make the cylinder or cup visible
# first, otherwise one cannot go into EDIT mode. Note that 'atom' here
# is in fact a 'stick' (cylinder or cup).
# First, identify if it is a normal cylinder object or a dupliverts
# structure. The identifier for a dupliverts structure is the parent's
# name, which includes "_sticks_mesh"
if "_sticks_mesh" in atom.parent.name:
atom.hide_set(False)
bpy.context.view_layer.objects.active = atom
bpy.ops.object.mode_set(mode='EDIT', toggle=False)
bm = bmesh.from_edit_mesh(atom.data)
locations = []
for v in bm.verts:
locations.append(v.co)
center = Vector((0.0,0.0,0.0))
center = sum([location for location in locations], center)/len(locations)
radius = sum([(loc[0]-center[0])**2+(loc[1]-center[1])**2
for loc in locations], 0)
radius_new = radius * sticks_all
for v in bm.verts:
v.co[0] = ((v.co[0] - center[0]) / radius) * radius_new + center[0]
v.co[1] = ((v.co[1] - center[1]) / radius) * radius_new + center[1]
bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
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# Hide again the representative stick (cylinder or cup) if it is a
# dupliverts structure.
if "_sticks_mesh" in atom.parent.name:
atom.hide_set(True)
bpy.context.view_layer.objects.active = None
# Change the atom objects
if action_type == "ATOM_REPLACE_OBJ" and "STICK" not in atom.name.upper():
scn = bpy.context.scene.atom_blend
material = atom.active_material
new_material = draw_obj_material(scn.replace_objs_material, material)
# Special object (like halo, etc.)
if scn.replace_objs_special != '0':
atom = draw_obj_special(scn.replace_objs_special, atom)
# Standard geometrical objects
else:
# If the atom shape shall not be changed, then:
if scn.replace_objs == '0':
atom.active_material = new_material
# If the atom shape shall change, then:
else:
atom = draw_obj(scn.replace_objs, atom, new_material)
# If the atom is the representative ball of a dupliverts structure,
# then make it invisible.
if atom.parent != None:
atom.hide_set(True)
# Default shapes and colors for atoms
if action_type == "ATOM_DEFAULT_OBJ" and "STICK" not in atom.name.upper():
scn = bpy.context.scene.atom_blend
# Create new material
new_material = bpy.data.materials.new("tmp")
# Create new object (NURBS sphere = '1b')
new_atom = draw_obj('1b', atom, new_material)
new_atom.active_material = new_material
new_material = draw_obj_material('0', new_material)
# Change size and color of the new object
for element in ELEMENTS:
if element.name in new_atom.name:
new_atom.scale = (element.radii[0],) * 3
new_atom.active_material.diffuse_color = element.color
new_atom.name = element.name + "_ball"
new_atom.active_material.name = element.name
break
# Separating atoms from a dupliverts structure.
def separate_atoms(scn):
# Get the mesh.
mesh = bpy.context.edit_object
# Do nothing if it is not a dupliverts structure.
if not mesh.instance_type == "VERTS":
return {'FINISHED'}
# This is the name of the mesh
mesh_name = mesh.name
# Get the collection
coll = mesh.users_collection[0]
# Get the coordinates of the selected vertices (atoms)
bm = bmesh.from_edit_mesh(mesh.data)
locations = []
for v in bm.verts:
if v.select:
locations.append(mesh.matrix_world @ v.co)
# Free memory
bm.free()
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# Delete already the selected vertices
bpy.ops.mesh.delete(type='VERT')
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# Find the representative ball within the collection.
for obj in coll.objects:
if obj.parent != None:
if obj.parent.name == mesh_name:
break
# Create balls and put them at the places where the vertices (atoms) have
# been before.
for location in locations:
obj_dupli = obj.copy()
obj_dupli.data = obj.data.copy()
obj_dupli.parent = None
coll.objects.link(obj_dupli)
obj_dupli.location = location
obj_dupli.name = obj.name + "_sep"
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# Do not hide the object!
obj_dupli.hide_set(False)
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bpy.ops.object.mode_set(mode='OBJECT', toggle=False)
bpy.context.view_layer.objects.active = mesh
# Prepare a new material
def draw_obj_material(material_type, material):
mat_P_BSDF_default = material.node_tree.nodes['Principled BSDF']
default_color = mat_P_BSDF_default.inputs['Base Color'].default_value
if material_type == '0': # Unchanged
material_new = material
if material_type == '1': # Normal
# We create again the 'normal' material. Why? It's because the old
# one could have been deleted by the user during the course of the
# user's work in Blender ... .
material_new = bpy.data.materials.new(material.name + "_normal")
material_new.use_nodes = True
mat_P_BSDF = material_new.node_tree.nodes['Principled BSDF']
mat_P_BSDF.inputs['Base Color'].default_value = default_color
mat_P_BSDF.inputs['Metallic'].default_value = 0.0
mat_P_BSDF.inputs['Specular'].default_value = 0.5
mat_P_BSDF.inputs['Roughness'].default_value = 0.5
mat_P_BSDF.inputs['Clearcoat Roughness'].default_value = 0.03
mat_P_BSDF.inputs['IOR'].default_value = 1.45
mat_P_BSDF.inputs['Transmission'].default_value = 0.0
mat_P_BSDF.inputs['Transmission Roughness'].default_value = 0.0
mat_P_BSDF.inputs['Alpha'].default_value = 1.0
# Some additional stuff for eevee.
material_new.blend_method = 'OPAQUE'
material_new.shadow_method = 'OPAQUE'
if material_type == '2': # Transparent
material_new = bpy.data.materials.new(material.name + "_transparent")
material_new.use_nodes = True
mat_P_BSDF = material_new.node_tree.nodes['Principled BSDF']
mat_P_BSDF.inputs['Base Color'].default_value = default_color
mat_P_BSDF.inputs['Metallic'].default_value = 0.0
mat_P_BSDF.inputs['Specular'].default_value = 0.15
mat_P_BSDF.inputs['Roughness'].default_value = 0.2
mat_P_BSDF.inputs['Clearcoat Roughness'].default_value = 0.37
mat_P_BSDF.inputs['IOR'].default_value = 1.45
mat_P_BSDF.inputs['Transmission'].default_value = 0.8
mat_P_BSDF.inputs['Transmission Roughness'].default_value = 0.0
mat_P_BSDF.inputs['Alpha'].default_value = 0.4
# Some additional stuff for eevee.
material_new.blend_method = 'HASHED'
material_new.shadow_method = 'HASHED'
material_new.use_backface_culling = False
if material_type == '3': # Reflecting
material_new = bpy.data.materials.new(material.name + "_reflecting")
material_new.use_nodes = True
mat_P_BSDF = material_new.node_tree.nodes['Principled BSDF']
mat_P_BSDF.inputs['Base Color'].default_value = default_color
mat_P_BSDF.inputs['Metallic'].default_value = 0.7
mat_P_BSDF.inputs['Specular'].default_value = 0.15
mat_P_BSDF.inputs['Roughness'].default_value = 0.1
mat_P_BSDF.inputs['Clearcoat Roughness'].default_value = 0.5
mat_P_BSDF.inputs['IOR'].default_value = 0.8
mat_P_BSDF.inputs['Transmission'].default_value = 0.0
mat_P_BSDF.inputs['Transmission Roughness'].default_value = 0.0
mat_P_BSDF.inputs['Alpha'].default_value = 1.0
# Some additional stuff for eevee.
material_new.blend_method = 'OPAQUE'
material_new.shadow_method = 'OPAQUE'
if material_type == '4': # Transparent + reflecting
material_new = bpy.data.materials.new(material.name + "_trans+refl")
material_new.use_nodes = True
mat_P_BSDF = material_new.node_tree.nodes['Principled BSDF']
mat_P_BSDF.inputs['Base Color'].default_value = default_color
mat_P_BSDF.inputs['Metallic'].default_value = 0.5
mat_P_BSDF.inputs['Specular'].default_value = 0.15
mat_P_BSDF.inputs['Roughness'].default_value = 0.05
mat_P_BSDF.inputs['Clearcoat Roughness'].default_value = 0.37
mat_P_BSDF.inputs['IOR'].default_value = 1.45
mat_P_BSDF.inputs['Transmission'].default_value = 0.6
mat_P_BSDF.inputs['Transmission Roughness'].default_value = 0.0
mat_P_BSDF.inputs['Alpha'].default_value = 0.6
# Some additional stuff for eevee.
material_new.blend_method = 'HASHED'
material_new.shadow_method = 'HASHED'
material_new.use_backface_culling = False
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# Always, when the material is changed, a new name is created. Note that
# this makes sense: Imagine, an other object uses the same material as the
# selected one. After changing the material of the selected object the old
# material should certainly not change and remain the same.
if material_type in {'1','2','3','4'}:
if "_repl" in material.name:
pos = material.name.rfind("_repl")
if material.name[pos+5:].isdigit():
counter = int(material.name[pos+5:])
material_new.name = material.name[:pos]+"_repl"+str(counter+1)
else:
material_new.name = material.name+"_repl1"
else:
material_new.name = material.name+"_repl1"
material_new.diffuse_color = material.diffuse_color
return material_new
# Get the collection of an object.
def get_collection_object(obj):
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coll_all = obj.users_collection
if len(coll_all) > 0:
coll = coll_all[0]
else:
coll = bpy.context.scene.collection
return coll
# Draw an object (e.g. cube, sphere, cylinder, ...)
def draw_obj(atom_shape, atom, new_material):
# No change
if atom_shape == '0':
return None
if atom_shape == '1a': #Sphere mesh
bpy.ops.mesh.primitive_uv_sphere_add(
segments=32,
ring_count=32,
radius=1,
enter_editmode=False,
location=atom.location,
rotation=(0, 0, 0))
if atom_shape == '1b': #Sphere NURBS
bpy.ops.surface.primitive_nurbs_surface_sphere_add(
enter_editmode=False,
location=atom.location,
rotation=(0.0, 0.0, 0.0))
if atom_shape == '2': #Cube
bpy.ops.mesh.primitive_cube_add(
enter_editmode=False,
location=atom.location,
rotation=(0.0, 0.0, 0.0))
if atom_shape == '3': #Plane
bpy.ops.mesh.primitive_plane_add(
enter_editmode=False,
location=atom.location,
rotation=(0.0, 0.0, 0.0))
if atom_shape == '4a': #Circle
bpy.ops.mesh.primitive_circle_add(
vertices=32,
radius=1,
fill_type='NOTHING',
enter_editmode=False,
location=atom.location,
rotation=(0, 0, 0))
if atom_shape == '4b': #Circle NURBS
bpy.ops.surface.primitive_nurbs_surface_circle_add(
enter_editmode=False,
location=atom.location,
rotation=(0, 0, 0))
if atom_shape in {'5a','5b','5c','5d','5e'}: #Icosphere
index = {'5a':1,'5b':2,'5c':3,'5d':4,'5e':5}
bpy.ops.mesh.primitive_ico_sphere_add(
subdivisions=int(index[atom_shape]),
radius=1,
enter_editmode=False,
location=atom.location,
rotation=(0, 0, 0))
if atom_shape == '6a': #Cylinder
bpy.ops.mesh.primitive_cylinder_add(
vertices=32,
radius=1,
depth=2,
end_fill_type='NGON',
enter_editmode=False,
location=atom.location,
rotation=(0, 0, 0))
if atom_shape == '6b': #Cylinder NURBS
bpy.ops.surface.primitive_nurbs_surface_cylinder_add(
enter_editmode=False,
location=atom.location,
rotation=(0, 0, 0))
if atom_shape == '7': #Cone
bpy.ops.mesh.primitive_cone_add(
vertices=32,
radius1=1,
radius2=0,
depth=2,
end_fill_type='NGON',
enter_editmode=False,
location=atom.location,
rotation=(0, 0, 0))
if atom_shape == '8a': #Torus
bpy.ops.mesh.primitive_torus_add(
rotation=(0, 0, 0),
location=atom.location,
major_radius=1,
minor_radius=0.25,
major_segments=48,
minor_segments=12,
abso_major_rad=1,
abso_minor_rad=0.5)
if atom_shape == '8b': #Torus NURBS
bpy.ops.surface.primitive_nurbs_surface_torus_add(
enter_editmode=False,
location=atom.location,
rotation=(0, 0, 0))
new_atom = bpy.context.view_layer.objects.active
new_atom.scale = atom.scale + Vector((0.0,0.0,0.0))
new_atom.name = atom.name
new_atom.select_set(True)
new_atom.active_material = new_material
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# If it is the representative object of a duplivert structure then
# transfer the parent and hide the new object.
if atom.parent != None:
new_atom.parent = atom.parent
new_atom.hide_set(True)
# Note the collection where the old object was placed into.
coll_old_atom = get_collection_object(atom)
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# Note the collection where the new object was placed into.
coll_new_atom_past = get_collection_object(new_atom)
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# If it is not the same collection then ...
if coll_new_atom_past != coll_old_atom:
# Put the new object into the collection of the old object and ...
coll_old_atom.objects.link(new_atom)
# ... unlink the new atom from its original collection.
coll_new_atom_past.objects.unlink(new_atom)
# If necessary, remove the childrens of the old object.
for child in atom.children:
bpy.ops.object.select_all(action='DESELECT')
child.hide_set(True)
child.select_set(True)
child.parent = None
coll_child = get_collection_object(child)
coll_child.objects.unlink(child)
bpy.ops.object.delete()
# Deselect everything
bpy.ops.object.select_all(action='DESELECT')
# Make the old atom visible.
atom.hide_set(True)
# Select the old atom.
atom.select_set(True)
# Remove the parent if necessary.
atom.parent = None
# Unlink the old object from the collection.
coll_old_atom.objects.unlink(atom)
# Delete the old atom
bpy.ops.object.delete()
#if "_F2+_center" or "_F+_center" or "_F0_center" in coll_old_atom:
# print("Delete the collection")
return new_atom
# Draw a special object (e.g. halo, etc. ...)
def draw_obj_special(atom_shape, atom):
# Note the collection where 'atom' is placed into.
coll_atom = get_collection_object(atom)
# Now, create a collection for the new objects
coll_new = atom.name
# Create the new collection and ...
coll_new = bpy.data.collections.new(coll_new)
# ... link it to the collection, which contains 'atom'.
coll_atom.children.link(coll_new)
# F2+ center
if atom_shape == '1':
# Create first a cube
bpy.ops.mesh.primitive_cube_add(align='WORLD',
enter_editmode=False,
location=atom.location,
rotation=(0.0, 0.0, 0.0))
cube = bpy.context.view_layer.objects.active
cube.scale = atom.scale + Vector((0.0,0.0,0.0))
cube.name = atom.name + "_F2+_vac"
cube.select_set(True)
# New material for this cube
material_cube = bpy.data.materials.new(atom.name + "_F2+_vac")
material_cube.diffuse_color = [0.8, 0.0, 0.0, 1.0]
material_cube.metallic = 0.8
material_cube.specular_intensity = 0.5
material_cube.roughness = 0.3
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material_cube.blend_method = 'OPAQUE'
material_cube.show_transparent_back = True
# Some properties for cycles
material_cube.use_nodes = True
mat_P_BSDF = material_cube.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 = 0.9
mat_P_BSDF.inputs['IOR'].default_value = 0.8
cube.active_material = material_cube
# Put a nice point lamp inside the defect
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lamp_data = bpy.data.lights.new(name=atom.name + "_F2+_lamp",
type="POINT")
lamp_data.distance = atom.scale[0] * 2.0
lamp_data.energy = 1.0
lamp_data.color = (0.8, 0.8, 0.8)
lamp = bpy.data.objects.new(atom.name + "_F2+_lamp", lamp_data)
lamp.location = Vector((0.0, 0.0, 0.0))
bpy.context.collection.objects.link(lamp)
lamp.parent = cube
# 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 = 2000
# The new 'atom' is the F2+ defect
new_atom = cube
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# Note the collection where all the new objects were placed into.
# We use only one object, the cube
coll_ori = get_collection_object(cube)
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# If it is not the same collection then ...
if coll_ori != coll_new:
# Put all new objects into the new collection and ...
coll_new.objects.link(cube)
coll_new.objects.link(lamp)
# ... unlink them from their original collection.
coll_ori.objects.unlink(cube)
coll_ori.objects.unlink(lamp)
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coll_new.name = atom.name + "_F2+_center"
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if atom.parent != None:
cube.parent = atom.parent
cube.hide_set(True)
lamp.hide_set(True)
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# F+ center
if atom_shape == '2':
# Create first a cube
bpy.ops.mesh.primitive_cube_add(align='WORLD',
enter_editmode=False,
location=atom.location,
rotation=(0.0, 0.0, 0.0))
cube = bpy.context.view_layer.objects.active
cube.scale = atom.scale + Vector((0.0,0.0,0.0))
cube.name = atom.name + "_F+_vac"
cube.select_set(True)
# New material for this cube
material_cube = bpy.data.materials.new(atom.name + "_F+_vac")
material_cube.diffuse_color = [0.0, 0.0, 0.8, 1.0]
material_cube.metallic = 0.8
material_cube.specular_intensity = 0.5
material_cube.roughness = 0.3
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material_cube.blend_method = 'OPAQUE'
material_cube.show_transparent_back = True
# Some properties for cycles
material_cube.use_nodes = True
mat_P_BSDF = material_cube.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 = 0.9
mat_P_BSDF.inputs['IOR'].default_value = 0.8
cube.active_material = material_cube
# Create now an electron
scale = atom.scale / 10.0
bpy.ops.surface.primitive_nurbs_surface_sphere_add(
enter_editmode=False,
location=(0.0, 0.0, 0.0),
rotation=(0.0, 0.0, 0.0))
electron = bpy.context.view_layer.objects.active
electron.scale = scale
electron.name = atom.name + "_F+_electron"
electron.parent = cube
# New material for the electron
material_electron = bpy.data.materials.new(atom.name + "_F+-center")
material_electron.diffuse_color = [0.0, 0.0, 0.8, 1.0]
material_electron.metallic = 0.8
material_electron.specular_intensity = 0.5
material_electron.roughness = 0.3
material_electron.blend_method = 'OPAQUE'
material_electron.show_transparent_back = False
electron.active_material = material_electron
# Put a nice point lamp inside the electron
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lamp_data = bpy.data.lights.new(name=atom.name + "_F+_lamp",
type="POINT")
lamp_data.distance = atom.scale[0] * 2.0
lamp_data.energy = 1.0
lamp_data.color = (0.8, 0.8, 0.8)
lamp = bpy.data.objects.new(atom.name + "_F+_lamp", lamp_data)
lamp.location = Vector((scale[0]*1.5, 0.0, 0.0))
bpy.context.collection.objects.link(lamp)
lamp.parent = cube
# 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 = 2000
# The new 'atom' is the F+ defect complex + lamp
new_atom = cube
# Note the collection where all the new objects were placed into.
# We use only one object, the cube
coll_ori = get_collection_object(cube)
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# If it is not the same collection then ...
if coll_ori != coll_new:
# Put all new objects into the new collection and ...
coll_new.objects.link(cube)
coll_new.objects.link(electron)
coll_new.objects.link(lamp)
# ... unlink them from their original collection.
coll_ori.objects.unlink(cube)
coll_ori.objects.unlink(electron)
coll_ori.objects.unlink(lamp)
coll_new.name = atom.name + "_F+_center"
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if atom.parent != None:
cube.parent = atom.parent
cube.hide_set(True)
electron.hide_set(True)
lamp.hide_set(True)
# F0 center
if atom_shape == '3':
# Create first a cube
bpy.ops.mesh.primitive_cube_add(align='WORLD',
enter_editmode=False,
location=atom.location,
rotation=(0.0, 0.0, 0.0))
cube = bpy.context.view_layer.objects.active
cube.scale = atom.scale + Vector((0.0,0.0,0.0))
cube.name = atom.name + "_F0_vac"
cube.select_set(True)
# New material for this cube
material_cube = bpy.data.materials.new(atom.name + "_F0_vac")
material_cube.diffuse_color = [0.8, 0.8, 0.8, 1.0]
material_cube.metallic = 0.8
material_cube.specular_intensity = 0.5
material_cube.roughness = 0.83
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material_cube.blend_method = 'OPAQUE'
material_cube.show_transparent_back = True
# Some properties for cycles
material_cube.use_nodes = True
mat_P_BSDF = material_cube.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 = 0.9
mat_P_BSDF.inputs['IOR'].default_value = 0.8
cube.active_material = material_cube
# Create now two electrons
scale = atom.scale / 10.0
bpy.ops.surface.primitive_nurbs_surface_sphere_add(
enter_editmode=False,
location=(scale[0]*1.5,0.0,0.0),
rotation=(0.0, 0.0, 0.0))
electron1 = bpy.context.view_layer.objects.active
electron1.scale = scale
electron1.name = atom.name + "_F0_electron1"
electron1.parent = cube
bpy.ops.surface.primitive_nurbs_surface_sphere_add(
enter_editmode=False,
location=(-scale[0]*1.5,0.0,0.0),
rotation=(0.0, 0.0, 0.0))
electron2 = bpy.context.view_layer.objects.active
electron2.scale = scale
electron2.name = atom.name + "_F0_electron2"
electron2.parent = cube
# New material for the electrons
material_electron = bpy.data.materials.new(atom.name + "_F0-center")
material_electron.diffuse_color = [0.0, 0.0, 0.8, 1.0]
material_electron.metallic = 0.8
material_electron.specular_intensity = 0.5
material_electron.roughness = 0.3
material_electron.blend_method = 'OPAQUE'
material_electron.show_transparent_back = False
electron1.active_material = material_electron
electron2.active_material = material_electron
# Put two nice point lamps inside the electrons
Clemens Barth
committed
lamp1_data = bpy.data.lights.new(name=atom.name + "_F0_lamp1",
type="POINT")
lamp1_data.distance = atom.scale[0] * 2.0
lamp1_data.energy = 1.0
lamp1_data.color = (0.8, 0.8, 0.8)
lamp1 = bpy.data.objects.new(atom.name + "_F0_lamp", lamp1_data)
lamp1.location = Vector((scale[0]*1.5, 0.0, 0.0))
bpy.context.collection.objects.link(lamp1)
lamp1.parent = cube
Clemens Barth
committed
lamp2_data = bpy.data.lights.new(name=atom.name + "_F0_lamp2",
type="POINT")
lamp2_data.distance = atom.scale[0] * 2.0
lamp2_data.energy = 1.0
lamp2_data.color = (0.8, 0.8, 0.8)
lamp2 = bpy.data.objects.new(atom.name + "_F0_lamp", lamp2_data)
lamp2.location = Vector((-scale[0]*1.5, 0.0, 0.0))
bpy.context.collection.objects.link(lamp2)
lamp2.parent = cube
# Some properties for cycles
lamp1.data.use_nodes = True
lamp2.data.use_nodes = True
lmp1_P_BSDF = lamp1.data.node_tree.nodes['Emission']
lmp2_P_BSDF = lamp1.data.node_tree.nodes['Emission']
lmp1_P_BSDF.inputs['Strength'].default_value = 200
lmp2_P_BSDF.inputs['Strength'].default_value = 200
# The new 'atom' is the F0 defect complex + lamps
new_atom = cube
# Note the collection where all the new objects were placed into.
# We use only one object, the cube
coll_ori = get_collection_object(cube)
Clemens Barth
committed
# If it is not the same collection then ...
if coll_ori != coll_new:
# Put all new objects into the collection of 'atom' and ...
coll_new.objects.link(cube)
coll_new.objects.link(electron1)
coll_new.objects.link(electron2)
coll_new.objects.link(lamp1)
coll_new.objects.link(lamp2)
# ... unlink them from their original collection.
coll_ori.objects.unlink(cube)
coll_ori.objects.unlink(electron1)
coll_ori.objects.unlink(electron2)
coll_ori.objects.unlink(lamp1)
coll_ori.objects.unlink(lamp2)
coll_new.name = atom.name + "_F0_center"
if atom.parent != None:
cube.parent = atom.parent
cube.hide_set(True)
electron1.hide_set(True)
electron2.hide_set(True)
lamp1.hide_set(True)
lamp2.hide_set(True)