# -*- coding: utf-8 -*-
###############################################################################
# Copyright (c), 2018 Forschungszentrum Jülich GmbH, IAS-1/PGI-1, Germany. #
# All rights reserved. #
# This file is part of the Masci-tools package. #
# (Material science tools) #
# #
# The code is hosted on GitHub at https://github.com/judftteam/masci-tools #
# For further information on the license, see the LICENSE.txt file #
# #
###############################################################################
[docs]def plot_shapefun(pos, out, mode):
"""
Creates a simple matplotlib image to show the shapefunctions given it's positions in the unit cell, the atoms's vertices in `ut` and the plotting mode
:author: Philipp Ruessmann
:param pos: positions of the centers of the cells
:param verts: array of vertices of the shapefunction (outlines of shapes)
:param mode: 'all' or 'single' determines whether or not all shapes are combined in a single figure or plotted as individual figures
:returns ax: return the axis in which the plot was done (useful to pass to 'change_zoom' and 'zoom_in' functions of this module
"""
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from numpy import array, shape
if mode=='all':
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
Natm = len(pos)
for j in range(1,Natm+1):
if mode=='single':
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
for i in out.keys():
if i[0]==j:
linecolor = 'r'
if j in [2,3,6,7]:
linecolor='b'
d = array(out[i])
if len(shape(pos))>1 and len(pos)>2 and mode=='all':
dx, dy, dz = pos[j-1,0], pos[j-1,1], pos[j-1,2]
else:
dx, dy, dz = 0, 0, 0
ax.plot(d[:,0]+dx,d[:,1]+dy,d[:,2]+dz,linecolor)
if mode=='all':
xy_scale = 1
scale = 1
ax.set_xlim(-scale*xy_scale,scale*xy_scale)
ax.set_ylim(-scale*xy_scale,scale*xy_scale)
ax.set_zlim(-scale,scale)
return ax
[docs]def change_zoom(ax, zoom_range, center=[0,0,0]):
"""
Change the zoom of a 3d plot
:author: Philipp Ruessmann
:param ax: axis which is zoomed
:param zoom_range: range to which the image is zoomed, total range from center-zoom_range to center+zoom_range
:param center: center of the zoomed region (optional, defaults to origin)
"""
ax.set_xlim(center[0]-zoom_range,center[0]+zoom_range)
ax.set_ylim(center[1]-zoom_range,center[1]+zoom_range)
ax.set_zlim(center[2]-zoom_range,center[2]+zoom_range)
[docs]def zoom_in(ax, atm, pos, zoom_range=10):
"""
Zoom into shapefun of a single atom
:author: Philipp Ruessmann
:param ax: axis in which shapefun plot is found
:param atm: atom index whose shapefunction is zoomed
:param pos: array of positions of centers of the shapes (needed to shift center of zommed region to correct atom
:param zoom_range: range of the zoomed region (optional, defaults to 10)
"""
center = pos[atm-1]
print 'zoom in to atom', atm, ':', center
change_zoom(ax, zoom_range, center)