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Tutorial 3: PXRD module in PyXtal¶

Source code: https://github.com/qzhu2017/PyXtal

Created by Qiang Zhu (2020/11/25)

Last updated: 2022/08/11

An interactive webpage can be found at the following link

In [1]:

# load the necessary libraries

from pyxtal import pyxtal
from pyxtal.XRD import Similarity
from pkg_resources import resource_filename

In [2]:

# specify the path of an experimental structure
cif_nacl = resource_filename("pyxtal", "database/cifs/NaCl.cif")
cif_aspirin = resource_filename("pyxtal", "database/cifs/aspirin.cif")

# load the structure from pyxtal

# if you load the atomic crystal
#xtal1 = pyxtal()
#xtal1.from_seed(seed = cif_nacl)    

# to load a molecular crystal, also needs to specify the molecule tag
xtal1 = pyxtal(molecular=True)
xtal1.from_seed(seed=cif_aspirin, molecules=['aspirin'])
print(xtal1)

# visualize the structure
# xtal1.show()

------Crystal from Seed------
Dimension: 3
Composition: [aspirin]4
Group: P 1 21/c 1 (14)
 11.2330,   6.5440,  11.2310,  90.0000,  95.8900,  90.0000, monoclinic
Wyckoff sites:
	H8C9O4       @ [ 0.2414  0.5782  0.0168]  WP [4e] Site [1] Euler [   0.0    0.0    0.0]

In [3]:

# compute the xrd project
xrd = xtal1.get_XRD(thetas=[0, 35])

# you can easily access the diffraction information by hkl indices
print(xrd)

  2theta     d_hkl     hkl       Intensity  Multi
   7.912    11.174   [ 1  0  0]    43.69        2
  15.693     5.647   [ 1  1  0]    11.94        4
  15.694     5.647   [ 0  1  1]    13.85        4
  15.863     5.587   [ 2  0  0]    15.35        2
  15.866     5.586   [ 0  0  2]   100.00        2
  17.002     5.215   [ 1  0 -2]     6.52        2
  17.224     5.148   [ 1  1 -1]     1.15        4
  17.965     4.938   [ 1  1  1]     2.18        4
  18.472     4.803   [ 1  0  2]     1.69        2
  20.907     4.249   [ 2  1  0]     8.59        4
  20.909     4.249   [ 0  1  2]    22.40        4
  21.308     4.170   [ 2  0 -2]     6.03        2
  21.791     4.079   [ 2  1 -1]     6.94        4
  21.792     4.078   [ 1  1 -2]     1.73        4
  22.967     3.872   [ 2  1  1]    49.23        4
  22.968     3.872   [ 1  1  2]    46.39        4
  23.651     3.762   [ 2  0  2]    17.19        2
  23.891     3.725   [ 3  0  0]     2.41        2
  25.327     3.517   [ 2  1 -2]     4.51        4
  27.255     3.272   [ 0  2  0]    13.80        2
  27.346     3.261   [ 2  1  2]    50.63        4
  27.384     3.257   [ 3  0 -2]     1.87        2
  27.556     3.237   [ 3  1  0]    50.62        4
  27.560     3.237   [ 0  1  3]     0.76        4
  28.006     3.186   [ 3  1 -1]     5.42        4
  28.009     3.186   [ 1  1 -3]     3.34        4
  28.423     3.140   [ 1  2  0]     1.21        4
  28.424     3.140   [ 0  2  1]     0.02        4
  29.322     3.046   [ 1  2 -1]     0.25        4
  29.405     3.038   [ 3  1  1]     7.16        4
  29.408     3.037   [ 1  1  3]     2.32        4
  29.776     3.001   [ 1  2  1]     2.25        4
  30.175     2.962   [ 3  0  2]     2.27        2
  30.662     2.916   [ 3  1 -2]     6.68        4
  30.664     2.916   [ 2  1 -3]     1.43        4
  31.691     2.823   [ 2  2  0]     3.22        4
  31.693     2.823   [ 0  2  2]     2.77        4
  32.040     2.793   [ 4  0  0]     3.69        2
  32.046     2.793   [ 0  0  4]     0.02        2
  32.230     2.777   [ 1  0 -4]     2.15        2
  32.298     2.772   [ 2  2 -1]     0.25        4
  32.299     2.772   [ 1  2 -2]     0.18        4
  33.127     2.704   [ 2  2  1]     1.38        4
  33.128     2.704   [ 1  2  2]     2.22        4
  33.203     2.698   [ 3  1  2]    11.60        4
  33.204     2.698   [ 2  1  3]    13.36        4
  33.872     2.646   [ 1  0  4]     0.00        2
  34.390     2.608   [ 4  0 -2]     0.70        2
  34.394     2.607   [ 2  0 -4]     2.82        2
  34.854     2.574   [ 2  2 -2]     2.34        4
  34.923     2.569   [ 4  1  0]     0.01        4
  34.929     2.569   [ 0  1  4]     2.85        4

In [4]:

# plot XRD
fig = xrd.plot_pxrd(fontsize=18, 
                    figsize=(16,6), 
                    show_hkl=False, 
                    xlim=[5,36], 
                    width=0.5, 
                    minimum_I=0.1)

In [5]:

# plot XRD
xrd.plotly_pxrd()

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