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

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# ## The HIST.nc file
# 
# The `HIST.nc` file contains the history of structural relaxations or molecular dynamics calculations.
# One can use the `abiopen` function provide by `abilab` to open the file and generate an instance of `HistFile`.
# Alteratively, one can use the `abiopen.py` script to open the file inside the shell with the syntax:
# 
#     abiopen.py out_HIST.nc 
#     
# This command will start the ipython interpreter so that one can interact directly 
# with the `HistFile` object (named `abifile` inside ipython).
# To generate a jupyter notebook use:
# 
#     abiopen.py out_HIST.nc -nb
#       
# For a quick visualization of the data, usei the `--expose` option:
# 
#     abiopen.py out_HIST.nc -e

# In[1]:


# Use this at the beginning of your script so that your code will be compatible with python3
from __future__ import print_function, division, unicode_literals

import warnings 
warnings.filterwarnings("ignore")  # Ignore warnings

from abipy import abilab
abilab.enable_notebook() # This line tells AbiPy we are running inside a notebook
import abipy.data as abidata

# This line configures matplotlib to show figures embedded in the notebook.
# Replace `inline` with `notebook` in classic notebook
get_ipython().run_line_magic('matplotlib', 'inline')

# Option available in jupyterlab. See https://github.com/matplotlib/jupyter-matplotlib
#%matplotlib widget  


# In[2]:


hist = abilab.abiopen(abidata.ref_file("sic_relax_HIST.nc"))
print("Number of iterations performed:", hist.num_steps)


# `hist.structures` is the list of structure objects at the different iteration steps.
# `hist.etotals` is a numpy array with the total energies in eV associated to the different steps.

# In[3]:


for struct, etot in zip(hist.structures, hist.etotals):
    print("Volume:", struct.volume,", Etotal:", etot)


# To get the last structure stored in the `HIST.nc` file:

# In[4]:


print(hist.final_structure)


# To plot the evolution of the structural parameters with `matplotlib`:

# In[5]:


hist.plot(tight_layout=True);


# To plot the total energies at the different iterations steps:

# In[6]:


hist.plot_energies();


# ## Converting to other formats
# [[back to top](#top)]
# 
# Use `to_xdatcar` to get a XDATCAR pymatgen object (useful to interface AbiPy with other pymatgen tools) 

# In[7]:


# hist.write_xdatcar writes a XDATCAR file
xdatcar = hist.to_xdatcar()
print(xdatcar)


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