XYZ Example

In this tutorial we load an XYZ trajectory.



In [1]:

    
%matplotlib inline
import numpy as np
import exatomic
import bz2, os
if not hasattr(bz2, "open"):
    bz2.open = bz2.BZ2File

The extra stuff, bz2, is due to the fact that the data is compressed
Typically, the syntax is as simple as exatomic.XYZ("myfile.xyz")



In [3]:

    
xyz = exatomic.XYZ(exatomic.base.resource("H2O.traj.xyz"))

The xyz object is an Editor
Editors are representations of text files on disk
These objects facilitate parsing of output data



In [4]:

    
xyz.head()









    



     0: 192
     1: frame: 500
     2: O   10.28508956   8.14460938   13.52695208
     3: O   11.35249854   11.35175769   9.48063013
     4: O   12.13309196   8.16159606   4.40491549
     5: O   13.08212337   0.82074230   8.49852496
     6: O   11.61851733   6.25548970   6.55479391
     7: O   9.43623192   4.76428163   2.98272836
     8: O   13.09122527 -0.60466753   1.95264245
     9: O   12.99597287   5.17908995   0.11265448



In [5]:

    
xyz.tail()









    



227941: H   6.04990327   3.24458779   2.04330157
227942: H   3.57922006 -0.35624345 -2.44128726
227943: H -3.88712344   4.80109139   4.02831396
227944: H -1.25442119   5.64846732   2.59449545
227945: H   5.15913457   2.78450812   10.49242229
227946: H   3.73656644   16.44876653   12.33820213
227947: H   1.84052508   5.15303842   9.75342242
227948: H -0.71357806   4.52787046   1.57043161
227949: H   3.75299748   1.08580857   6.38535047

We expect 1175 frames (remember that frames are states - in this case denoting steps in time)



In [6]:

    
len(xyz) // (192 + 2)     # 192 atoms per frame plus 2 for the xyz file syntax









    Out[6]:





1175

Parsing is performed automatically if the attribute of interest is requested



In [7]:

    
xyz.atom.head()



In [8]:

    
xyz.frame.head()

Always check that data was correctly constructed



In [9]:

    
xyz.frame.tail()

This happens to be a periodic calculations so lets quickly add that information
This is important for periodic two-body calculations



In [10]:

    
for i, r in enumerate(("x", "y", "z")):
    for j, q in enumerate(("i", "j", "k")):
        if i == j:
            xyz.frame[r+q] = 12.4/0.529
        else:
            xyz.frame[r+q] = 0.0
    xyz.frame["o"+r] = 0.0
xyz.frame['periodic'] = True



In [11]:

    
xyz.atom.tail()



In [12]:

    
np.all(xyz.atom.groupby("frame").size() == 192)









    Out[12]:





True

The XYZ object has a convenience method for creating a Universe



In [13]:

    
uni = xyz.to_universe()
len(uni)









    Out[13]:





1175

Note that data is not duplicated!



In [14]:

    
uni.atom is xyz.atom









    Out[14]:





True



In [15]:

    
uni.frame is xyz.frame









    Out[15]:





True

We can ask exatomic to compute distances (bonds)
WARNING this operation might take a minute!



In [16]:

    
%time uni.compute_atom_two()









    



CPU times: user 11.5 s, sys: 2.56 s, total: 14.1 s
Wall time: 16.1 s



In [17]:

    
uni.atom_two.shape









    Out[17]:





(3564092, 5)



In [18]:

    
uni.atom_two[uni.atom_two['bond'] == True].shape









    Out[18]:





(150395, 5)

This means that changes to xyz.atom will appear in uni.atom
The network method helps keep track of what data objects exist



In [19]:

    
uni.network()









    Out[19]:





<networkx.classes.graph.Graph at 0x7f755061d240>

Since atom_two scales quadractically its size is large compared to the other datatables
The unit_atom table is needed for computing periodic two-body data



In [20]:

    
uni.atom_two.dtypes









    Out[20]:





atom0         category
atom1         category
dr             float64
projection       int64
bond              bool
dtype: object

Of course we can also visualize the animation of the trajectory!



In [21]:

    
exatomic.UniverseWidget(uni)



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In [ ]:

	symbol	x	y	z	frame
atom
0	O	19.4359	15.39100	25.56210	0
1	O	21.4530	21.45160	17.91570	0
2	O	22.9281	15.42310	8.32404	0
3	O	24.7215	1.55097	16.05980	0
4	O	21.9557	11.82110	12.38670	0

	symbol	x	y	z	frame
atom
225595	H	9.74930	5.26193	19.82770	1174
225596	H	7.06105	31.08350	23.31570	1174
225597	H	3.47807	9.73778	18.43120	1174
225598	H	-1.34846	8.55639	2.96767	1174
225599	H	7.09210	2.05187	12.06650	1174