NWChem

[1]:

%matplotlib inline
import os, bz2
import exatomic
from exatomic import nwchem

[4]:

out = nwchem.Output(exatomic.base.resource("nw-ch3nh2-augccpvdz.out"))
out.head()

   0:  argument  1 = ch3nh2.nw
   1:
   2:
   3:
   4: ============================== echo of input deck ==============================
   5: echo
   6: start ch3nh2
   7: title ch3nh2
   8:
   9: geometry  units angstrom  noautoz nocenter

[5]:

out.tail()

2954:         K. Hirao, R. A. Kendall, J. A. Nichols, K. Tsemekhman, K. Wolinski,
2955:      J. Anchell, D. E. Bernholdt, P. Borowski, T. Clark, D. Clerc, H. Dachsel,
2956:    M. J. O. Deegan, K. Dyall, D. Elwood, E. Glendening, M. Gutowski, A. C. Hess,
2957:          J. Jaffe, B. G. Johnson, J. Ju, R. Kobayashi, R. Kutteh, Z. Lin,
2958:    R. Littlefield, X. Long, B. Meng, T. Nakajima, S. Niu, L. Pollack, M. Rosing,
2959:    K. Glaesemann, G. Sandrone, M. Stave, H. Taylor, G. Thomas, J. H. van Lenthe,
2960:                                A. T. Wong, Z. Zhang.
2961:
2962:  Total times  cpu:        3.9s     wall:        4.1s


[6]:

out.parse_atom()
out.atom

[6]:
tag Z x y z symbol Zeff frame
atom
0 C 6 1.409566 0.020987 0.000000 C 6 0
1 N 7 -1.363889 -0.135772 0.000000 N 7 0
2 H 1 1.969196 2.003298 0.000000 H 1 0
3 H 1 2.134053 -0.913404 1.686645 H 1 0
4 H 1 2.134053 -0.913404 -1.686645 H 1 0
5 H 1 -2.035202 0.730039 -1.562856 H 1 0
6 H 1 -2.035202 0.730039 1.562856 H 1 0 
[7]:

out.parse_basis_set()
out.basis_set.tail()

[7]:
shell L alpha d set frame
function
52 0 0 0.44460 0.478148 2 0
53 1 0 0.12200 1.000000 2 0
54 2 0 0.02974 1.000000 2 0
55 3 1 0.72700 1.000000 2 0
56 4 1 0.14100 1.000000 2 0 
[8]:

out.parse_basis_set_order()
out.basis_set_order.tail()

[8]:
center shell L ml frame
chi
86 6 3 1 -1 0
87 6 3 1 0 0
88 6 4 1 1 0
89 6 4 1 -1 0
90 6 4 1 0 0 
[9]:

out.parse_frame()
out.frame

[9]:
atom_count total_energy
frame
0 7 -95.229252 
[10]:

out.parse_momatrix()
out.momatrix.shape

[10]:

(8281, 4)

[11]:

out.parse_orbital()
out.orbital.tail()

[11]:
energy frame occupation vector x y z spin group
orbital
86 3.034495 0 0.0 86 0.079 -3.900000e-14 -3.900000e-14 0 0
87 3.059546 0 0.0 87 -0.370 3.000000e-13 3.000000e-13 0 0
88 3.074835 0 0.0 88 0.095 -6.900000e-13 -6.900000e-13 0 0
89 3.380757 0 0.0 89 -0.800 1.800000e-13 1.800000e-13 0 0
90 3.634046 0 0.0 90 -0.670 -2.200000e-13 -2.200000e-13 0 0 
[12]:

uni = out.to_universe()

[13]:

uni.network()

[13]:

<networkx.classes.graph.Graph at 0x7f82eb582630>
../_images/notebooks_nwchem_11_1.png 
[14]:

uni.compute_atom_two()
uni.atom_two.bonded

[14]:
atom0 atom1 dr bond
two
0 0 1 2.777882 True
1 0 2 2.059791 True
2 0 3 2.059791 True
3 0 4 2.059791 True
9 1 5 1.908614 True
10 1 6 1.908614 True 
[15]:

uni.orbital[uni.orbital['occupation'] != 0.0]

[15]:
energy frame occupation vector x y z spin group
orbital
0 -15.544670 0 2.0 0 -0.72 -3.700000e-15 -3.700000e-15 0 0
1 -11.248320 0 2.0 1 0.75 1.300000e-15 1.300000e-15 0 0
2 -1.170266 0 2.0 2 -0.45 1.200000e-13 1.200000e-13 0 0
3 -0.893624 0 2.0 3 0.46 1.200000e-13 1.200000e-13 0 0
4 -0.668444 0 2.0 4 -0.43 -3.800000e-13 -3.800000e-13 0 0
5 -0.597788 0 2.0 5 0.40 1.100000e-13 1.100000e-13 0 0
6 -0.555492 0 2.0 6 0.18 9.200000e-13 9.200000e-13 0 0
7 -0.522872 0 2.0 7 0.51 -1.800000e-12 -1.800000e-12 0 0
8 -0.385592 0 2.0 8 -0.45 -1.600000e-13 -1.600000e-13 0 0 
[16]:

uni.add_molecular_orbitals(field_params={'rmin': -20, 'rmax': 20, 'nr': 51})

Warning: Check spherical shell parameter for nwchem molecular orbital generation
Evaluating 91 basis functions once.
Timing: compute orbitals -     3.56s.

[17]:

exatomic.UniverseWidget(uni)

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