#!/usr/bin/env python
# coding: utf-8

# # 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](https://vxrd.physics.unlv.edu)
# 

# 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()


# 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)


# 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()


# In[6]:


# Now we randomly perturb the crystal
xtal2 = xtal1.copy()
xtal2.apply_perturbation(d_lat=0.02)
xrd2 = xtal2.get_XRD(thetas=[0, 35])


# In[7]:


# Compare the the PXRDs of two structures
p1 = xrd.get_profile()
p2 = xrd2.get_profile()
s = Similarity(p1, p2, x_range=[0,35])
print(s)
s.show()