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

# # Tutorial 1: Atomic crystal module in PyXtal
# 
# Source code: https://github.com/qzhu2017/PyXtal
# 
# Created by Qiang Zhu (2020/11/23)
# 
# Last updated: 2022/08/11
# 
# More details can be found at the following [link](https://pyxtal.readthedocs.io/en/latest/)
# 
# # 1.1 Generate a random atomic crystal

# In[1]:


from pyxtal import pyxtal


# In[2]:


C1 = pyxtal()
C1.from_random(3, 227, ['C'], [8])
# Alternative, you can also generate the structure with pre-assigned sites
# C1.from_random(3, 225, ["C"], [12], sites=[["4a", "8c"]])

print(C1)


# In[3]:


C1.atom_sites[0].wp


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#display the structure can be easily accessed with the show() function
C1.show(supercell=(2,2,1))


# # 1.2 Manipulating the crystal via symmetry relation

# In[5]:


# lower the symmetry from cubic to tetragonal
C2 = C1.subgroup_once(H=141, eps=1e-2)
print(C2)


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# Compute the XRD
xrd1 = C1.get_XRD()
xrd2 = C2.get_XRD()


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# Compare two structures by XRD
from pyxtal.XRD import Similarity
p1 = xrd1.get_profile()
p2 = xrd2.get_profile()
s = Similarity(p1, p2, x_range=[15, 90])
print(s)
s.show()


# # 1.3 Chemical substitution via symmetry relation

# In[8]:


#play substitution
permutation = {"C":"Si"}
SiC = C1.subgroup_once(eps=0.01, H=None, perms=permutation)
print(C1)
print(SiC)
SiC.show(supercell=(2,2,2))


# # 1.4 Supergroup symmetry

# In[9]:


# load the experimental alpha-quartz structure from the cif file

lt_sio2 = pyxtal()
lt_sio2.from_seed('lt_quartz.cif')
print(lt_sio2)
lt_sio2.show()


# In[10]:


# Here we search for the high temperature phase

ht_sio2, _ = lt_sio2.supergroup(G=180)
print(len(ht_sio2), 'structures have been generated')
print(ht_sio2[-1])
ht_sio2[-1].show()


# # 1.5 Exporting the structure

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#In general, you can export the structure in several ways

# CIF/POSCAR file
C1.to_file('1.cif')
C1.to_ase().write('1.vasp', format='vasp', vasp5=True)

# ASE's atoms object
ase_struc = C1.to_ase()
print(ase_struc)

# Pymatgen object
pmg_struc = C1.to_pymatgen()
print(pmg_struc)


# # 1.6 Low dimensional systems

# In[12]:


# An example to generate 2D atomic crystal
C3 = pyxtal()
C3.from_random(2, 75, ['C'], [6], thickness=0.0)
C3.show(scale=0.2)


# In[13]:


# An example to generate 0D atomic cluster
C4 = pyxtal()
C4.from_random(0, 'Ih', ['C'], [60])
C4.show(scale=0.2)


# In[14]:


# to improve the quality, you can increase the minimum distance
C4.from_random(0, 'Ih', ['C'], [60], t_factor=1.2)
C4.show(scale=0.1, radius=0.01)