# useful to autoreload the module without restarting the kernel
%load_ext autoreload
%autoreload 2

from mppi import Parsers as P

Tutorial of the PwParser class

This tutorial describes the usage of the class PwParser of mppi used to extract information for the XML output file data-file-schema produced by pw.

Parse of a output file of Silicon

Follow the tutorial for the QeCalculator to produce the xml file used by the PwParser.

The class is initialized by specifying the name of the xml file including its relative path

results = P.PwParser('QeCalculator_test/ecut_40.save/data-file-schema.xml')

Parse file : QeCalculator_test/ecut_40.save/data-file-schema.xml

When the object is initialized several attributes are set, for instance

results.units

'Hartree atomic units'

print(results.natoms)
print(results.atomic_species)
print(results.atomic_positions)
print(results.nbands)
print(results.nkpoints)
print(results.spin_degen)

2
{'Si': ['2.808600000000000e1', 'Si.pbe-mt_fhi.UPF']}
[['Si', [-1.2875, 1.2875, 1.2875]], ['Si', [1.2875, -1.2875, -1.2875]]]
4
32
2

We can print the ks energies and weight for each kpoint

for k,e,w in zip(results.kpoints,results.evals,results.weights):
    print(k,e,w)

[0. 0. 0.] [-0.21237932  0.22480586  0.22480586  0.22480586] [0.00925926]
[-0.16666667  0.16666667 -0.16666667] [-0.19919102  0.13751175  0.20843984  0.20843984] [0.05555556]
[-0.33333333  0.33333333 -0.33333333] [-0.16220083  0.02987301  0.18835642  0.18835642] [0.05555556]
[ 0.5 -0.5  0.5] [-0.12757113 -0.02957086  0.18109825  0.18109825] [0.02777778]
[0.         0.33333333 0.        ] [-0.19470782  0.14932662  0.18151751  0.18151751] [0.05555556]
[-0.16666667  0.5        -0.16666667] [-0.16499801  0.06224724  0.15213876  0.16134166] [0.11111111]
[ 0.66666667 -0.33333333  0.66666667] [-0.12170161 -0.01655811  0.1235651   0.16017894] [0.11111111]
[ 0.5        -0.16666667  0.5       ] [-0.13567139  0.00519533  0.11383623  0.1775689 ] [0.11111111]
[3.33333333e-01 2.77555756e-17 3.33333333e-01] [-0.17775389  0.08840259  0.137224    0.20418049] [0.05555556]
[0.         0.66666667 0.        ] [-0.1429486   0.04085118  0.13689062  0.13689062] [0.05555556]
[ 0.83333333 -0.16666667  0.83333333] [-0.10058122 -0.01575679  0.09290269  0.13189392] [0.11111111]
[ 6.66666667e-01 -5.55111512e-17  6.66666667e-01] [-0.09353762 -0.02311024  0.06458375  0.1479812 ] [0.05555556]
[ 0. -1.  0.] [-0.06133252 -0.06133252  0.1210312   0.1210312 ] [0.02777778]
[ 0.66666667 -0.33333333  1.        ] [-0.12894983  0.01788475  0.09513755  0.14145801] [0.11111111]
[ 0.5        -0.16666667  0.83333333] [-0.09319151 -0.02566662  0.07905522  0.12455972] [0.11111111]
[-0.33333333 -1.          0.        ] [-0.05705807 -0.05705807  0.0924765   0.09247651] [0.11111111]
[-0.16666667  0.16666667  0.16666667] [-0.19919102  0.13751175  0.20843984  0.20843984] [0.01851852]
[-0.33333333  0.33333333  0.33333333] [-0.16220083  0.02987301  0.18835642  0.18835642] [0.01851852]
[ 0.5 -0.5 -0.5] [-0.12757113 -0.02957086  0.18109825  0.18109825] [0.00925926]
[ 0.16666667 -0.16666667  0.5       ] [-0.16499801  0.06224724  0.15213876  0.16134165] [0.05555556]
[-0.16666667  0.16666667  0.5       ] [-0.16499801  0.06224724  0.15213877  0.16134165] [0.05555556]
[-0.66666667  0.66666667 -0.33333333] [-0.12170161 -0.01655811  0.1235651   0.16017894] [0.05555556]
[ 0.66666667 -0.66666667 -0.33333333] [-0.12170161 -0.01655811  0.1235651   0.16017894] [0.05555556]
[-0.5         0.5        -0.16666667] [-0.13567139  0.00519533  0.11383624  0.1775689 ] [0.05555556]
[ 0.5        -0.5        -0.16666667] [-0.13567139  0.00519533  0.11383624  0.1775689 ] [0.05555556]
[-0.33333333  0.33333333  0.        ] [-0.17775389  0.08840259  0.137224    0.20418049] [0.05555556]
[-0.83333333  0.83333333 -0.16666667] [-0.10058122 -0.01575679  0.09290269  0.13189392] [0.05555556]
[ 0.83333333 -0.83333333 -0.16666667] [-0.10058122 -0.01575679  0.0929027   0.13189392] [0.05555556]
[-0.66666667  0.66666667  0.        ] [-0.09353762 -0.02311024  0.06458376  0.14798119] [0.05555556]
[-0.66666667  1.         -0.33333333] [-0.12894983  0.01788475  0.09513755  0.14145801] [0.11111111]
[0.5        0.83333333 0.16666667] [-0.09319151 -0.02566662  0.07905522  0.12455972] [0.05555556]
[ 0.5        -0.83333333 -0.16666667] [-0.09319151 -0.02566662  0.07905522  0.12455972] [0.05555556]

There are also several get methods, for instance

results.get_fermi()

6.117279040435398

The method get_evals return an array with the ks energies for each kpoint. The energies are expressed in eV and the energy of VBM is used as reference. A gap, both direct or indirect, can be set. In this case the energies of the empty ks states is shifted. This procedure does not update the occupation levels of the empty states

results.get_evals(set_gap=1.2)[0]

There are no empty bands. `Set gap` has not been applied

array([-1.18964146e+01, -3.99369533e-08, -1.83300486e-09,  0.00000000e+00])

results.get_gap()

There are no empty states. Gap cannot be computed.

We test the PwParser using a nscf output file, in this case empty bands are present and the gap can be computed

result_nscf = P.PwParser('QeCalculator_test/bands_12.save/data-file-schema.xml')

Parse file : QeCalculator_test/bands_12.save/data-file-schema.xml

result_nscf.occupations[0]

array([1., 1., 1., 1., 0., 0., 0., 0., 0., 0., 0., 0.])

result_nscf.get_gap()

Indirect gap system
===================
Gap : 0.7363567574170764 eV
Direct gap : 2.5651333558109854 eV

{'gap': 0.7363567574170764,
 'direct_gap': 2.5651333558109854,
 'position_cbm': 12,
 'positon_vbm': 0}

result_nscf.get_evals(set_direct_gap=3.0)[0]

Apply a scissor of 0.43486664418901455 eV

array([-1.18964110e+01, -9.74240383e-07, -9.74234497e-07,  0.00000000e+00,
        3.00000000e+00,  3.00000056e+00,  3.00000056e+00,  3.58353139e+00,
        8.17161688e+00,  8.17161688e+00,  8.29564293e+00,  1.16527216e+01])

we see that in this case the energy of the 5-th states has been shift to 3 eV to implement the set_direct_gap requirement.

It is also possible to add an explicit scissor to shift the empty bands

result_nscf.get_evals(set_scissor=1.)[0]

Apply a scissor of 1.0 eV

array([-1.18964110e+01, -9.74240383e-07, -9.74234497e-07,  0.00000000e+00,
        3.56513336e+00,  3.56513391e+00,  3.56513391e+00,  4.14866474e+00,
        8.73675023e+00,  8.73675023e+00,  8.86077629e+00,  1.22178550e+01])

We compute the transition energies from the full to empty bands. Here we show the transition for the first k point

result_nscf.get_transitions(set_direct_gap=3.0)[0]

Apply a scissor of 0.43486664418901455 eV

array([14.89641099, 14.89641154, 14.89641154, 15.47994237, 20.06802786,
       20.06802786, 20.19205392, 23.54913261,  3.00000097,  3.00000153,
        3.00000153,  3.58353236,  8.17161785,  8.17161785,  8.29564391,
       11.6527226 ,  3.00000097,  3.00000153,  3.00000153,  3.58353236,
        8.17161785,  8.17161785,  8.29564391, 11.6527226 ,  3.        ,
        3.00000056,  3.00000056,  3.58353139,  8.17161688,  8.17161688,
        8.29564293, 11.65272162])

Parse of a Graphene output file

Run the Analysis_BandStructure notebook to produce the xml file used by the PwParser.

We parse a graphene output file to test if systems without a gap are correctly parsed.

results_gra = P.PwParser('Pw_bands/graphene_nscf.save/data-file-schema.xml')

Parse file : Pw_bands/graphene_nscf.save/data-file-schema.xml

results_gra.occupations_kind

'smearing'

results_gra.occupations[0]

array([1.00000000e+00, 1.00000000e+00, 1.00000000e+00, 1.00000000e+00,
       4.22181265e-29, 6.89778699e-37, 1.76721673e-41, 1.28104982e-57])

results_gra.occupations[18] #the position of K

array([1. , 1. , 1. , 0.5, 0.5, 0. , 0. , 0. ])

results_gra.get_gap()

Direct gap system
=================
Gap : 2.715685454290906e-10 eV

{'gap': 2.715685454290906e-10,
 'direct_gap': 2.715685454290906e-10,
 'position_cbm': 18,
 'positon_vbm': 18}