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Edit and run



In [1]:

    
import matplotlib.pyplot as plt
%matplotlib inline
from pymatgen.util.plotting_utils import get_publication_quality_plot



In [2]:

    
import numpy as np
import pandas as pd



In [3]:

    
ls









    



Q9.ipynb           Si_50_9_10.22.out  Si_50_9_10.28.out  Si_50_9_10.32.out  Si_50_9_10.35.out  Si_50_9_10.38.out  Si_50_9_10.42.out  Si_50_9_10.48.out  Si_50_9_10.75.out  Si_50_9_9.5.out    run_pw.py*
Si_50_9_10.1.out   Si_50_9_10.24.out  Si_50_9_10.3.out   Si_50_9_10.33.out  Si_50_9_10.36.out  Si_50_9_10.39.out  Si_50_9_10.44.out  Si_50_9_10.5.out   Si_50_9_10.out     analyze.py*
Si_50_9_10.2.out   Si_50_9_10.26.out  Si_50_9_10.31.out  Si_50_9_10.34.out  Si_50_9_10.37.out  Si_50_9_10.4.out   Si_50_9_10.46.out  Si_50_9_10.7.out   Si_50_9_6.out      results.csv



In [4]:

    
datafile = pd.read_csv('results.csv')



In [5]:

    
datafile.head(0)









    Out[5]:






  
    
      
      filename
      ecut
      nkpts
      alat
      energy
      total_force
      cpu_time
    
  
  
    
      0 
         Si_50_9_9.5.out
       50
       35
        9.50
      -89.242348
       0
       2.4
    
    
      1 
          Si_50_9_10.out
       50
       35
       10.00
      -89.285942
       0
       3.2
    
    
      2 
        Si_50_9_10.1.out
       50
       35
       10.10
      -89.288451
       0
       5.9
    
    
      3 
        Si_50_9_10.2.out
       50
       35
       10.20
      -89.289287
       0
       9.2
    
    
      4 
       Si_50_9_10.22.out
       50
       35
       10.22
      -89.289271
       0
       9.4
    
    
      5 
       Si_50_9_10.24.out
       50
       35
       10.24
      -89.289192
       0
       9.6
    
    
      6 
       Si_50_9_10.26.out
       50
       35
       10.26
      -89.289054
       0
       9.5
    
    
      7 
       Si_50_9_10.28.out
       50
       35
       10.28
      -89.288863
       0
       9.5
    
    
      8 
        Si_50_9_10.3.out
       50
       35
       10.30
      -89.288612
       0
       9.6
    
    
      9 
       Si_50_9_10.31.out
       50
       35
       10.31
      -89.288465
       0
       8.1
    
    
      10
       Si_50_9_10.32.out
       50
       35
       10.32
      -89.288305
       0
       4.8
    
    
      11
       Si_50_9_10.33.out
       50
       35
       10.33
      -89.288132
       0
       4.8
    
    
      12
       Si_50_9_10.34.out
       50
       35
       10.34
      -89.287945
       0
       4.9
    
    
      13
       Si_50_9_10.35.out
       50
       35
       10.35
      -89.287745
       0
       4.8
    
    
      14
       Si_50_9_10.36.out
       50
       35
       10.36
      -89.287532
       0
       4.8
    
    
      15
       Si_50_9_10.37.out
       50
       35
       10.37
      -89.287305
       0
       4.8
    
    
      16
       Si_50_9_10.38.out
       50
       35
       10.38
      -89.287066
       0
       4.9
    
    
      17
       Si_50_9_10.39.out
       50
       35
       10.39
      -89.286815
       0
       4.8
    
    
      18
        Si_50_9_10.4.out
       50
       35
       10.40
      -89.286550
       0
       4.8
    
    
      19
       Si_50_9_10.42.out
       50
       35
       10.42
      -89.285987
       0
       4.8
    
    
      20
       Si_50_9_10.44.out
       50
       35
       10.44
      -89.285372
       0
       4.8
    
    
      21
       Si_50_9_10.46.out
       50
       35
       10.46
      -89.284709
       0
       4.9
    
    
      22
       Si_50_9_10.48.out
       50
       35
       10.48
      -89.284000
       0
       4.8
    
    
      23
        Si_50_9_10.5.out
       50
       35
       10.50
      -89.283244
       0
       4.9
    
    
      24
        Si_50_9_10.7.out
       50
       35
       10.70
      -89.273379
       0
       4.9
    
    
      25
       Si_50_9_10.75.out
       50
       35
       10.75
      -89.270314
       0
       4.9



In [6]:

    
datafile.ix[datafile['energy'].idxmin()]









    Out[6]:





filename       Si_50_9_10.2.out
ecut                         50
nkpts                        35
alat                       10.2
energy                -89.28929
total_force                   0
cpu_time                    9.2
Name: 3, dtype: object



In [7]:

    
datafile_mod = datafile[(datafile['alat']>9.5) & (datafile['alat']<11.5)]



In [56]:

    
datafile_mod.head()









    Out[56]:






  
    
      
      filename
      ecut
      nkpts
      alat
      energy
      total_force
      cpu_time
    
  
  
    
      1
          Si_50_9_10.out
       50
       35
       10.00
      -93.445675
       0
       3.8
    
    
      2
        Si_50_9_10.1.out
       50
       35
       10.10
      -93.450191
       0
       5.3
    
    
      3
        Si_50_9_10.2.out
       50
       35
       10.20
      -93.452963
       0
       5.2
    
    
      4
       Si_50_9_10.22.out
       50
       35
       10.22
      -93.453322
       0
       5.4
    
    
      5
       Si_50_9_10.24.out
       50
       35
       10.24
      -93.453618
       0
       5.4



In [8]:

    
x = datafile_mod['alat'].tolist()
x









    Out[8]:





[10.0,
 10.1,
 10.199999999999999,
 10.220000000000001,
 10.24,
 10.26,
 10.279999999999999,
 10.300000000000001,
 10.31,
 10.32,
 10.33,
 10.34,
 10.35,
 10.359999999999999,
 10.369999999999999,
 10.380000000000001,
 10.390000000000001,
 10.4,
 10.42,
 10.44,
 10.460000000000001,
 10.48,
 10.5,
 10.699999999999999,
 10.75]



In [9]:

    
y_energy = datafile_mod['energy'].tolist()
# y_conver = datafile['Force Difference (meV/Angstrom)'].tolist()



In [11]:

    
fig, ax0=plt.subplots(nrows=1)
fig.set_size_inches(10,10)

ax0.scatter(x, y_energy,marker='o',alpha=0.75,s=60,c='r')
ax0.plot(x,y_energy,c='black')
ax0.set_title('Energy VS Lattice Constant',fontsize=30,y=1.05)
ax0.set_xlabel('Lattice Parameter (a.u)',fontsize=24)
ax0.set_ylabel(r'Total Energy (Ry)',fontsize=20)
# ax0.set_ylim(-93.456,-93.44)
ax0.tick_params(labelsize = 18)
ax0.annotate('Lowest Energy: 10.33 a.u.', xy=(10.33, -93.45421),  xycoords='data',
                xytext=(-50, -30), textcoords='offset points',
                arrowprops=dict(arrowstyle="->",
                                connectionstyle="angle3,angleA=0,angleB=-90"),fontsize=15
                )

# ax1.scatter(x,y_conver,marker='o',alpha=0.75, s=60,c='b')
# ax1.plot(x,y_conver,c='black')
# ax1.set_title('Force Convergence Vs K-points',fontsize=24,y=1.05)
# ax1.set_xlabel('# of K-points',fontsize=24)
# ax1.set_ylabel(r'Force Converge $meV/\AA$',fontsize=18)
# # ax1.set_yscale('log')
# ax1.set_ylim(-1,40)
# ax1.annotate(r'Convergence < 5 $meV/\AA$ # Kpoints: 205', xy=(207, 5),  xycoords='data',
#                 xytext=(0.95, 0.95), textcoords='axes fraction',
#                 arrowprops=dict(facecolor='black', shrink=0.05),
#                 horizontalalignment='right', verticalalignment='top',fontsize=16
#                 )
# ax1.tick_params(labelsize = 18)

plt.subplots_adjust(hspace=0.5)
plt.show()



In [17]:









    Out[17]:





<matplotlib.text.Text at 0x10891e9d0>



In [18]:

    
plt.show()

	filename	ecut	nkpts	alat	energy	cpu_time
0	Si_50_9_9.5.out	50	35	9.50	-89.242348	2.4
1	Si_50_9_10.out	50	35	10.00	-89.285942	3.2
2	Si_50_9_10.1.out	50	35	10.10	-89.288451	5.9
3	Si_50_9_10.2.out	50	35	10.20	-89.289287	9.2
4	Si_50_9_10.22.out	50	35	10.22	-89.289271	9.4
5	Si_50_9_10.24.out	50	35	10.24	-89.289192	9.6
6	Si_50_9_10.26.out	50	35	10.26	-89.289054	9.5
7	Si_50_9_10.28.out	50	35	10.28	-89.288863	9.5
8	Si_50_9_10.3.out	50	35	10.30	-89.288612	9.6
9	Si_50_9_10.31.out	50	35	10.31	-89.288465	8.1
10	Si_50_9_10.32.out	50	35	10.32	-89.288305	4.8
11	Si_50_9_10.33.out	50	35	10.33	-89.288132	4.8
12	Si_50_9_10.34.out	50	35	10.34	-89.287945	4.9
13	Si_50_9_10.35.out	50	35	10.35	-89.287745	4.8
14	Si_50_9_10.36.out	50	35	10.36	-89.287532	4.8
15	Si_50_9_10.37.out	50	35	10.37	-89.287305	4.8
16	Si_50_9_10.38.out	50	35	10.38	-89.287066	4.9
17	Si_50_9_10.39.out	50	35	10.39	-89.286815	4.8
18	Si_50_9_10.4.out	50	35	10.40	-89.286550	4.8
19	Si_50_9_10.42.out	50	35	10.42	-89.285987	4.8
20	Si_50_9_10.44.out	50	35	10.44	-89.285372	4.8
21	Si_50_9_10.46.out	50	35	10.46	-89.284709	4.9
22	Si_50_9_10.48.out	50	35	10.48	-89.284000	4.8
23	Si_50_9_10.5.out	50	35	10.50	-89.283244	4.9
24	Si_50_9_10.7.out	50	35	10.70	-89.273379	4.9
25	Si_50_9_10.75.out	50	35	10.75	-89.270314	4.9

	filename	ecut	nkpts	alat	energy	cpu_time
1	Si_50_9_10.out	50	35	10.00	-93.445675	3.8
2	Si_50_9_10.1.out	50	35	10.10	-93.450191	5.3
3	Si_50_9_10.2.out	50	35	10.20	-93.452963	5.2
4	Si_50_9_10.22.out	50	35	10.22	-93.453322	5.4
5	Si_50_9_10.24.out	50	35	10.24	-93.453618	5.4