MICCoM School 2017 Ex#3 : The GW self-energy¶
We are going to dive into the GW calculation done in Exercise #1.
In this excercixe we will focus on the input for wfreq.x.
[1]:
# download the pseudopotentials
!wget -N -q http://www.quantum-simulation.org/potentials/sg15_oncv/upf/Si_ONCV_PBE-1.2.upf
!wget -N -q http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.2.upf
# download the input files
!wget -N -q https://west-code.org/doc/training/silane/pw.in
!wget -N -q https://west-code.org/doc/training/silane/wstat.in
!wget -N -q https://west-code.org/doc/training/silane/wfreq.in
We need to read the output of a DFT calculation, therefore as first step we run the DFT calculation invoking the executable pw.x on 8 cores.
[ ]:
!mpirun -n 8 pw.x -i pw.in > pw.out
We also need the dielectric matrix eigenpotentials in order to build G and W, therefore as second step we run the PDEP calculation invoking the executable wstat.x on 8 cores.
[ ]:
!mpirun -n 8 wstat.x -i wstat.in > wstat.out
3.1 : Calculation of the GW self-energy¶
Let’s give a quick look at the input for wfreq.x (description of the input variables for wfreq.x can be found here: https://west-code.org/doc/West/latest/manual.html#wfreq-control).
[2]:
!cat wfreq.in
input_west:
qe_prefix: silane
west_prefix: silane
outdir: ./
wstat_control:
wstat_calculation: S
n_pdep_eigen: 50
wfreq_control:
wfreq_calculation: XWGQ
n_pdep_eigen_to_use: 50
qp_bandrange: [1,5]
n_refreq: 300
ecut_refreq: 2.0
The keywords “XWGQ” instruct the code to compute the exact exchange operator (“X”), the screened Coulomb operator (“W”), the Green’s function (“G”), and the quasiparticle energies (“Q”).
In this case we are using the 50 eigenpotentials \(\phi_i\) obtained by wstat.x.
We are going to compute the GW energy of the states 1, 2, 3, 4 (HOMO), and 5 (LUMO). Remember that in this example (spin-unpolarized) each state can host two electrons.
The frequency cutoff controls the contour deformation integration.
Details about the implementation are described in J. Chem. Theory Comput. 11, 2680 (2015) :
[ ]:
!mpirun -n 8 wfreq.x -i wfreq.in > wfreq.out
We now load the output (JSON) of the wfreq.x calculation, which can be found in the wfreq.save folder.
[3]:
import json
# read data from JSON file
with open('silane.wfreq.save/wfreq.json', 'r') as file:
data = json.load(file)
# pretty print the data
print(json.dumps(data, indent=2))
{
"runjob": {
"startdate": "17Aug2022",
"starttime": "11:49:24",
"completed": true,
"endtime": "11:49:53",
"enddate": "17Aug2022"
},
"software": {
"package": "WEST",
"program": "WFREQ",
"version": "5.0.0",
"westgit": "v5.0.0-117-ga4764c0",
"website": "https://west-code.org",
"citation": "M. Govoni et al., J. Chem. Theory Comput. 11, 2680 (2015).",
"qeversion": "7.1"
},
"config": {
"io": {
"islittleendian": true
}
},
"parallel": {
"nranks": 2,
"nimage": 1,
"npool": 1,
"nbgrp": 1,
"nrg": 2,
"nproc": 36,
"nthreads": 18
},
"input": {
"input_west": {
"qe_prefix": "silane",
"west_prefix": "silane",
"outdir": "./"
},
"wstat_control": {
"wstat_calculation": "S",
"n_pdep_eigen": 50,
"n_pdep_times": 4,
"n_pdep_maxiter": 100,
"n_dfpt_maxiter": 250,
"n_pdep_read_from_file": 0,
"n_steps_write_restart": 1,
"trev_pdep": 0.001,
"trev_pdep_rel": 0.1,
"tr2_dfpt": 1e-12,
"l_kinetic_only": false,
"l_minimize_exx_if_active": false,
"l_use_ecutrho": false,
"qlist": [
1
]
},
"wfreq_control": {
"wfreq_calculation": "XWGQ",
"n_pdep_eigen_to_use": 50,
"qp_bandrange": [
1,
5
],
"macropol_calculation": "N",
"n_lanczos": 30,
"n_imfreq": 128,
"n_refreq": 300,
"ecut_imfreq": 100.0,
"ecut_refreq": 2.0,
"wfreq_eta": 0.0036749308824745378,
"n_secant_maxiter": 21,
"trev_secant": 0.0036749308824745378,
"l_enable_lanczos": true,
"o_restart_time": 0.0,
"ecut_spectralf": [
-2.0,
1.0
],
"n_spectralf": 204
}
},
"system": {
"basis": {
"npw": {
"proc": [
0,
0
],
"min": 0,
"max": 0,
"sum": 0
},
"ngm": {
"proc": [
33761,
33761
],
"min": 33761,
"max": 33761,
"sum": 67522
},
"gamma_only": true,
"ecutwfc:ry": 25.0,
"ecutrho:ry": 100.0
},
"cell": {
"units": "a.u.",
"omega": 8000.0,
"a1": [
20.0,
0.0,
0.0
],
"a2": [
0.0,
20.0,
0.0
],
"a3": [
0.0,
0.0,
20.0
],
"b1": [
0.3141592653589793,
0.0,
0.0
],
"b2": [
0.0,
0.3141592653589793,
0.0
],
"b3": [
0.0,
0.0,
0.3141592653589793
],
"alat": 20.0,
"tpiba": 0.3141592653589793
},
"electron": {
"nbnd": 10,
"nkstot": 1,
"nspin": 1,
"nelec": 8.0,
"npol": 1,
"lsda": false,
"noncolin": false,
"lspinorb": false
},
"3dfft": {
"s": [
64,
64,
64
],
"p": [
64,
64,
64
]
},
"bzsamp": {
"k": [
{
"id": 1,
"crystcoord": [
0.0,
0.0,
0.0
]
}
]
}
},
"exec": {
"Q": {
"secitr": 3,
"en": [
{
"ksb": [
1,
1,
1
],
"ein": [
-13.236948730745993,
-16.274079895237996,
-16.113118881544086
],
"eout": [
-16.274079895237996,
-16.113118881544086,
-16.135751705765212
],
"sc_ein": [
[
1.7648786805436507,
0.014572339286581349
],
[
3.5765028709322677,
0.07577914694131388
],
[
3.4384458185468487,
0.11603251905188436
]
]
},
{
"ksb": [
1,
1,
2
],
"ein": [
-8.231838447080957,
-12.152440223683891,
-12.045168866769844
],
"eout": [
-12.152440223683891,
-12.045168866769844,
-12.047981701915175
],
"sc_ein": [
[
0.009840666434917919,
0.003269648759422666
],
[
0.7294770853239745,
0.008919886475089428
],
[
0.7063683707165244,
0.0087855155566386
]
]
},
{
"ksb": [
1,
1,
3
],
"ein": [
-8.230714368411038,
-12.14867626806817,
-12.041327347372851
],
"eout": [
-12.14867626806817,
-12.041327347372851,
-12.044133556216615
],
"sc_ein": [
[
0.012755402617866242,
0.0032697391091808365
],
[
0.7319348278418772,
0.008920672846219913
],
[
0.7088194370441542,
0.008786259213802905
]
]
},
{
"ksb": [
1,
1,
4
],
"ein": [
-8.230556032205104,
-12.147747634498469,
-12.04036492867603
],
"eout": [
-12.147747634498469,
-12.04036492867603,
-12.0431690105994
],
"sc_ein": [
[
0.01361081347029257,
0.0032697883548870464
],
[
0.7326835382931621,
0.008921251741771392
],
[
0.7095636523063199,
0.008786812381482984
]
]
},
{
"ksb": [
1,
1,
5
],
"ein": [
-0.46558623738333965,
0.6657316496384642,
0.6646203810762062
],
"eout": [
0.6657316496384642,
0.6646203810762062,
0.6646203810762062
],
"sc_ein": [
[
-0.3489198339072822,
-1.0634900239576885e-05
],
[
-0.3727187208565701,
-0.0001168438798018746
],
[
-0.37269430531199454,
-0.0001168438798018746
]
]
}
]
}
},
"output": {
"Q": {
"bandmap": [
1,
2,
3,
4,
5
],
"K000001": {
"sigmax": [
-17.60635669245776,
-15.766143243592401,
-15.765429517122184,
-15.765268997624062,
-0.5872822308075556
],
"vxcl": [
-11.249695614342661,
-11.24302566873253,
-11.242586632689184,
-11.242488637916345,
-2.0901841930028935
],
"vxcnl": [
0.0,
0.0,
0.0,
0.0,
0.0
],
"hf": [
-6.356661078115098,
-4.523117574859871,
-4.522842884433,
-4.522780359707718,
1.502901962195338
],
"z": [
0.6614275027706701,
0.8686818593568523,
0.8687108432939544,
0.8687168584206324,
0.980359972038844
],
"eks": [
-13.236948730745993,
-8.231838447080957,
-8.230714368411038,
-8.230556032205104,
-0.46558623738333965
],
"eqpLin": [
-16.274079895237996,
-12.152440223683891,
-12.14867626806817,
-12.147747634498469,
0.6657316496384642
],
"eqpSec": [
-16.135751705765212,
-12.047981701915175,
-12.044133556216615,
-12.0431690105994,
0.6646203810762062
],
"sigmac_eks": {
"re": [
1.7648786805436507,
0.009840666434917919,
0.012755402617866242,
0.01361081347029257,
-0.3489198339072822
],
"im": [
0.014572339286581349,
0.003269648759422666,
0.0032697391091808365,
0.0032697883548870464,
-1.0634900239576885e-05
]
},
"sigmac_eqpLin": {
"re": [
3.5765028709322677,
0.7294770853239745,
0.7319348278418772,
0.7326835382931621,
-0.3727187208565701
],
"im": [
0.07577914694131388,
0.008919886475089428,
0.008920672846219913,
0.008921251741771392,
-0.0001168438798018746
]
},
"sigmac_eqpSec": {
"re": [
3.4384458185468487,
0.7063683707165244,
0.7088194370441542,
0.7095636523063199,
-0.37269430531199454
],
"im": [
0.11603251905188436,
0.0087855155566386,
0.008786259213802905,
0.008786812381482984,
-0.0001168438798018746
]
},
"sigma_diff": [
-0.022632824221126488,
-0.00281283514533227,
-0.002806208843762687,
-0.0028040819233693345,
0.0
]
}
}
},
"timing": {
"WFREQ": {
"cpu:sec": 433.02074700000003,
"cpu:hum": "07m-13.0s",
"wall:sec": 28.02621102333069,
"wall:hum": "28.0s",
"nocalls": 2
},
"wfreq_readin": {
"cpu:sec": 1.4224249999999998,
"cpu:hum": "01.4s",
"wall:sec": 0.5878539085388184,
"wall:hum": "00.5s",
"nocalls": 1
},
"fetch_input": {
"cpu:sec": 0.11673500000000003,
"cpu:hum": "00.1s",
"wall:sec": 0.013164997100830078,
"wall:hum": "< 00.1s",
"nocalls": 2
},
"fft": {
"cpu:sec": 0.7475280000000002,
"cpu:hum": "00.7s",
"wall:sec": 0.4337337017059326,
"wall:hum": "00.4s",
"nocalls": 14
},
"fft_scatter": {
"cpu:sec": 79.40591099999807,
"cpu:hum": "01m-19.4s",
"wall:sec": 5.015791416168213,
"wall:hum": "05.0s",
"nocalls": 14473
},
"init_vloc": {
"cpu:sec": 0.18284699999999976,
"cpu:hum": "00.1s",
"wall:sec": 0.012270927429199219,
"wall:hum": "< 00.1s",
"nocalls": 2
},
"init_us_1": {
"cpu:sec": 0.2363050000000002,
"cpu:hum": "00.2s",
"wall:sec": 0.016676902770996094,
"wall:hum": "< 00.1s",
"nocalls": 2
},
"v_of_rho": {
"cpu:sec": 0.7574919999999999,
"cpu:hum": "00.7s",
"wall:sec": 0.04927706718444824,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"v_xc": {
"cpu:sec": 1.115234,
"cpu:hum": "01.1s",
"wall:sec": 0.07056808471679688,
"wall:hum": "< 00.1s",
"nocalls": 2
},
"v_h": {
"cpu:sec": 0.05118299999999998,
"cpu:hum": "< 00.1s",
"wall:sec": 0.0036971569061279297,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"do_setup": {
"cpu:sec": 0.420706,
"cpu:hum": "00.4s",
"wall:sec": 0.0266110897064209,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"init_pw_ar": {
"cpu:sec": 0.36714,
"cpu:hum": "00.3s",
"wall:sec": 0.02280116081237793,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"hinit0": {
"cpu:sec": 0.2794049999999999,
"cpu:hum": "00.2s",
"wall:sec": 0.017242908477783203,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"solve_hf": {
"cpu:sec": 2.3319,
"cpu:hum": "02.3s",
"wall:sec": 0.14495205879211426,
"wall:hum": "00.1s",
"nocalls": 1
},
"sigmavxc": {
"cpu:sec": 0.21133500000000005,
"cpu:hum": "00.2s",
"wall:sec": 0.013345956802368164,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"init_us_2": {
"cpu:sec": 0.13846300000000156,
"cpu:hum": "00.1s",
"wall:sec": 0.009094953536987305,
"wall:hum": "< 00.1s",
"nocalls": 3
},
"init_us_2:cp": {
"cpu:sec": 0.13784399999997277,
"cpu:hum": "00.1s",
"wall:sec": 0.009055852890014648,
"wall:hum": "< 00.1s",
"nocalls": 3
},
"fftw": {
"cpu:sec": 300.84294200000045,
"cpu:hum": "05m-00.8s",
"wall:sec": 18.790026664733887,
"wall:hum": "18.7s",
"nocalls": 14439
},
"sigmax": {
"cpu:sec": 1.681152,
"cpu:hum": "01.6s",
"wall:sec": 0.10448408126831055,
"wall:hum": "00.1s",
"nocalls": 1
},
"sqvc_init": {
"cpu:sec": 0.25548900000006824,
"cpu:hum": "00.2s",
"wall:sec": 0.03452634811401367,
"wall:hum": "< 00.1s",
"nocalls": 11
},
"ffts": {
"cpu:sec": 0.681279,
"cpu:hum": "00.6s",
"wall:sec": 0.04274606704711914,
"wall:hum": "< 00.1s",
"nocalls": 20
},
"write_hf": {
"cpu:sec": 0.011789000000000271,
"cpu:hum": "< 00.1s",
"wall:sec": 0.0008139610290527344,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"wlanczos": {
"cpu:sec": 193.496094,
"cpu:hum": "03m-13.4s",
"wall:sec": 12.330339908599854,
"wall:hum": "12.3s",
"nocalls": 1
},
"pdep_read": {
"cpu:sec": 1.6891720000000987,
"cpu:hum": "01.6s",
"wall:sec": 0.18372178077697754,
"wall:hum": "00.1s",
"nocalls": 100
},
"alphapc": {
"cpu:sec": 4.381300000000294,
"cpu:hum": "04.3s",
"wall:sec": 0.27483534812927246,
"wall:hum": "00.2s",
"nocalls": 283
},
"lan_H": {
"cpu:sec": 381.59998600000006,
"cpu:hum": "06m-21.5s",
"wall:sec": 23.84375834465027,
"wall:hum": "23.8s",
"nocalls": 9
},
"h_psi": {
"cpu:sec": 326.9270000000007,
"cpu:hum": "05m-26.9s",
"wall:sec": 20.43570113182068,
"wall:hum": "20.4s",
"nocalls": 270
},
"h_psi:pot": {
"cpu:sec": 325.50325600000025,
"cpu:hum": "05m-25.5s",
"wall:sec": 20.345640420913696,
"wall:hum": "20.3s",
"nocalls": 270
},
"vloc_psi": {
"cpu:sec": 320.40288400000026,
"cpu:hum": "05m-20.4s",
"wall:sec": 20.026703596115112,
"wall:hum": "20.0s",
"nocalls": 270
},
"h_psi:calbec": {
"cpu:sec": 2.607253000000128,
"cpu:hum": "02.6s",
"wall:sec": 0.16390728950500488,
"wall:hum": "00.1s",
"nocalls": 270
},
"calbec": {
"cpu:sec": 2.5379690000000323,
"cpu:hum": "02.5s",
"wall:sec": 0.1596684455871582,
"wall:hum": "00.1s",
"nocalls": 270
},
"add_vuspsi": {
"cpu:sec": 2.3486820000000534,
"cpu:hum": "02.3s",
"wall:sec": 0.14653515815734863,
"wall:hum": "00.1s",
"nocalls": 270
},
"brak": {
"cpu:sec": 7.758552000000066,
"cpu:hum": "07.7s",
"wall:sec": 0.49863171577453613,
"wall:hum": "00.4s",
"nocalls": 9
},
"sw_restart": {
"cpu:sec": 0.41395099999996887,
"cpu:hum": "00.4s",
"wall:sec": 0.08451104164123535,
"wall:hum": "< 00.1s",
"nocalls": 4
},
"chi_invert": {
"cpu:sec": 0.02574999999998795,
"cpu:hum": "< 00.1s",
"wall:sec": 0.03121185302734375,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"glanczos": {
"cpu:sec": 235.154872,
"cpu:hum": "03m-55.1s",
"wall:sec": 14.784619808197021,
"wall:hum": "14.7s",
"nocalls": 1
},
"write_over": {
"cpu:sec": 0.07077600000008033,
"cpu:hum": "< 00.1s",
"wall:sec": 0.004719734191894531,
"wall:hum": "< 00.1s",
"nocalls": 5
},
"write_gfreq": {
"cpu:sec": 0.17641399999996565,
"cpu:hum": "00.1s",
"wall:sec": 0.014179229736328125,
"wall:hum": "< 00.1s",
"nocalls": 5
},
"sg_restart": {
"cpu:sec": 0.057460999999989326,
"cpu:hum": "< 00.1s",
"wall:sec": 0.004120349884033203,
"wall:hum": "< 00.1s",
"nocalls": 5
},
"solve_qp": {
"cpu:sec": 0.07704000000001088,
"cpu:hum": "< 00.1s",
"wall:sec": 0.10379791259765625,
"wall:hum": "00.1s",
"nocalls": 1
},
"coll_gw": {
"cpu:sec": 0.029298999999980424,
"cpu:hum": "< 00.1s",
"wall:sec": 0.03835892677307129,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"read_over": {
"cpu:sec": 0.0005629999999428037,
"cpu:hum": "< 00.1s",
"wall:sec": 0.002696990966796875,
"wall:hum": "< 00.1s",
"nocalls": 5
},
"read_gfreq": {
"cpu:sec": 0.0013369999999781612,
"cpu:hum": "< 00.1s",
"wall:sec": 0.006660938262939453,
"wall:hum": "< 00.1s",
"nocalls": 5
},
"read_hf": {
"cpu:sec": 0.0,
"cpu:hum": "< 00.1s",
"wall:sec": 0.0009639263153076172,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"sigmac_i": {
"cpu:sec": 0.021983999999974912,
"cpu:hum": "< 00.1s",
"wall:sec": 0.022049903869628906,
"wall:hum": "< 00.1s",
"nocalls": 4
},
"sigmac_r": {
"cpu:sec": 0.00026799999994864265,
"cpu:hum": "< 00.1s",
"wall:sec": 0.0002789497375488281,
"wall:hum": "< 00.1s",
"nocalls": 4
},
"wfreq_db": {
"cpu:sec": 0.0027069999999866923,
"cpu:hum": "< 00.1s",
"wall:sec": 0.004580020904541016,
"wall:hum": "< 00.1s",
"nocalls": 1
}
}
}
We plot the energy levels of DFT and GW.
[4]:
import numpy as np
import matplotlib.pyplot as plt
# extracting energy levels from the data
y = {}
y['dft'] = data['output']['Q']['K000001']['eks']
y['gw'] = data['output']['Q']['K000001']['eqpSec']
# colors
c = {}
c['dft'] = 'red'
c['gw'] = 'green'
# plot
x = list(range(1, len(y)+1))
labels = y.keys()
fig, ax = plt.subplots(1, 1)
counter = 0
for i in labels :
for a in y[i] :
ax.hlines(a, x[counter]-0.25, x[counter]+0.25, color=c[i])
counter += 1
plt.xticks(x, labels)
plt.ylabel('Energy (eV)')
plt.title('Electronic structure')
plt.show()
Let’s plot the density of states (DOS) of DFT and GW, obtained as a sum of Gaussian functions
\begin{equation} \text{DOS}(E) = \sum_{i=1}^{N_{\text{states}}} \frac{1}{\sqrt{2\pi\sigma^2}} e^{-\frac{(E-E_i)^2}{2\sigma^2}} \end{equation}
We are going to set \(\sigma=0.2eV\).
[5]:
from westpy import *
es = ElectronicStructure()
for key in ['dft','gw'] :
es.addKey(key,key)
b = 0
for energy in y[key] :
es.addDataPoint([1,1,b+1],key,y[key][b])
b += 1
es.plotDOS(kk=[1],ss=[1],energyKeys=['dft','gw'],energyRange=[-18.,2.,0.01],fname='dos.png')
_ _ _____ _____ _____
| | | | ___/ ___|_ _|
| | | | |__ \ `--. | |_ __ _ _
| |/\| | __| `--. \ | | '_ \| | | |
\ /\ / |___/\__/ / | | |_) | |_| |
\/ \/\____/\____/ \_/ .__/ \__, |
| | __/ |
|_| |___/
WEST version : 5.2.0
Today : 2022-10-07 12:29:53.167016
Requested (emin,emax) : -18.0 2.0
Detected (emin,emax) : -16.135751705765212 0.6646203810762062
output written in : dos.png
waiting for user to close image preview...
5.2 : GW-full and GW-linear¶
The algorithms implemented in WEST make affordable the calculation of the quasiparticle equation self-consistently, which we can call GW-full
\begin{equation} E^{\text{GW-full}}_n = \varepsilon^{\text{DFT}}_n + \left\langle \psi_n \right | \Sigma(E^{\text{GW-full}}_n) - V_{\text{xc}}\left| \psi_n \right\rangle \end{equation}
However, in literature one often introduces a Taylor expansion of the self-energy \(\Sigma\) around the DFT energy
\begin{equation} \Sigma(E^{\text{QP}}_n) = \Sigma(\varepsilon^{\text{DFT}}_n) + \left.\frac{d\Sigma}{dE}\right|_{E=\varepsilon^{\text{DFT}}_n} (E^{\text{QP}}_n-\varepsilon^{\text{DFT}}_n)+\cdots \end{equation}
In this way, called here GW-linear, operators can be evaluated one time at DFT energies only (no iteration is needed)
\begin{equation} E^{\text{GW-linear}}_n = \varepsilon^{\text{DFT}}_n + Z_n \left\langle \psi_n \right | \Sigma(\varepsilon^{\text{DFT}}_n) - V_{\text{xc}}\left| \psi_n \right\rangle \end{equation}
where \(Z_n=\left(1-\left.\frac{d\Sigma}{dE}\right|_{E=\varepsilon^{\text{DFT}}_n}\right)^{-1}\).
WEST will always aim at computing GW-full, using a secant iteration scheme, however GW-linear is saved in output as it corresponds to the first iteration of the secant method.
We plot the energy levels of DFT and GW-full and GW-linear.
[6]:
import numpy as np
import matplotlib.pyplot as plt
# extracting energy levels from the data
y = {}
y['dft'] = data['output']['Q']['K000001']['eks']
y['gw-lin'] = data['output']['Q']['K000001']['eqpLin']
y['gw-full'] = data['output']['Q']['K000001']['eqpSec']
print('gw-lin :' , y['gw-lin'])
print('gw-full :', y['gw-full'])
# colors
c = {}
c['dft'] = 'red'
c['gw-lin'] = 'green'
c['gw-full'] = 'blue'
# plot
x = list(range(1, len(y)+1))
labels = y.keys()
fig, ax = plt.subplots(1, 1)
counter = 0
for i in labels :
for a in y[i] :
ax.hlines(a, x[counter]-0.25, x[counter]+0.25, color=c[i])
counter += 1
plt.xticks(x, labels)
plt.ylabel('Energy (eV)')
plt.title('Electronic structure')
plt.show()
gw-lin : [-16.274079895237996, -12.152440223683891, -12.14867626806817, -12.147747634498469, 0.6657316496384642]
gw-full : [-16.135751705765212, -12.047981701915175, -12.044133556216615, -12.0431690105994, 0.6646203810762062]
GW-linear and GW-full give similar results. In order to understand why Taylor exapanding the self-energy \(\Sigma\) around DFT energies, we redo the calculation turning on the runlevel P, which will compute \(\Sigma(E)\) on a regular mesh of energies.
Let’s add the part related to the plot of the self-energy in wfreq.in.
[7]:
import yaml
# read data wfreq.in
with open('wfreq.in', 'r') as file:
input_data = yaml.load(file, Loader=yaml.FullLoader)
# pretty print
print('input_data')
print(yaml.dump(input_data, sort_keys=False))
# modify the input_data
input_data['wfreq_control']['wfreq_calculation'] = 'XWGQP'
input_data['wfreq_control']['qp_bandrange'] = [4,5]
input_data['wfreq_control']['ecut_spectralf'] = [-1.5,0.5]
input_data['wfreq_control']['n_spectralf'] = 300
# write data to YAML file
with open('wfreq_P.in', 'w') as file:
yaml.dump(input_data, file, sort_keys=False)
# show content of the file
print('wfreq_P.in')
!cat wfreq_P.in
input_data
input_west:
qe_prefix: silane
west_prefix: silane
outdir: ./
wstat_control:
wstat_calculation: S
n_pdep_eigen: 50
wfreq_control:
wfreq_calculation: XWGQ
n_pdep_eigen_to_use: 50
qp_bandrange:
- 1
- 5
n_refreq: 300
ecut_refreq: 2.0
wfreq_P.in
input_west:
qe_prefix: silane
west_prefix: silane
outdir: ./
wstat_control:
wstat_calculation: S
n_pdep_eigen: 50
wfreq_control:
wfreq_calculation: XWGQP
n_pdep_eigen_to_use: 50
qp_bandrange:
- 4
- 5
n_refreq: 300
ecut_refreq: 2.0
ecut_spectralf:
- -1.5
- 0.5
n_spectralf: 300
[ ]:
!mpirun -n 8 wfreq.x -i wfreq_P.in > wfreq_P.out
We plot the self-energy.
[8]:
import json
import numpy as np
# Load the output data
with open('silane.wfreq.save/wfreq_P.json', 'r') as json_file:
data = json.load(json_file)
# Extract converged quasiparticle (QP) corrections
k = 1
kindex = f'K{k:06d}'
bandmap = data['output']['Q']['bandmap']
eqp = data['output']['Q'][kindex]
freqlist = np.array(data['output']['P']['freqlist'], dtype='f8')
spf = data['output']['P'][kindex]
# Plot
import matplotlib.pyplot as plt
for i, b in enumerate(bandmap) :
eks, eqpLin, eqpSec = eqp['eks'][i], eqp['eqpLin'][i], eqp['eqpSec'][i]
# Print QP corrections
print(f"{'k':^10} | {'band':^10} | {'eks [eV]':^15} | {'eqpLin [eV]':^15} | {'eqpSec [eV]':^15}")
print(77*'-')
print(f'{k:^10} | {b:^10} | {eks:^15.3f} | {eqpLin:^15.3f} | {eqpSec:^15.3f}')
sigmax, vxcl, vxcnl = eqp['sigmax'][i], eqp['vxcl'][i], eqp['vxcnl'][i]
sigmac_eks = eqp['sigmac_eks']['re'][i]
sigmac_eqpLin = eqp['sigmac_eqpLin']['re'][i]
sigmac_eqpSec = eqp['sigmac_eqpSec']['re'][i]
z = eqp['z'][i]
bindex = f'B{b:06d}'
sigmac = np.array(spf[bindex]['sigmac']['re'], dtype='f8')
# Left-hand side of QP equation
plt.plot(freqlist,freqlist-eks,'r-',label=r'$E-\varepsilon_{KS}$')
# Right-hand side of QP equation without linearization
plt.plot(freqlist,sigmac+sigmax-vxcl-vxcnl,'b-',label=r'$\Sigma(E)-V_{xc}$')
# Right-hand side of QP equation with linearization
plt.plot(freqlist,sigmac_eks+sigmax-vxcl-vxcnl+(1-1/z)*(freqlist-eks),'g-',label=r'$\Sigma^{lin}(E)-V_{xc}$')
plt.legend()
plt.title(kindex+' '+bindex)
plt.xlabel('frequency (eV)')
plt.ylabel('function (eV)')
xmin, xmax = min(eks, eqpLin, eqpSec), max(eks, eqpLin, eqpSec)
ymin, ymax = min(sigmac_eks, sigmac_eqpLin, sigmac_eqpSec), max(sigmac_eks, sigmac_eqpLin, sigmac_eqpSec)
ymin += sigmax - vxcl -vxcnl
ymax += sigmax - vxcl -vxcnl
plt.vlines(x=eks,ymin=ymin-0.2*(ymax-ymin),ymax=ymax+0.2*(ymax-ymin),ls='--')
plt.vlines(x=eqpLin,ymin=ymin-0.2*(ymax-ymin),ymax=ymax+0.2*(ymax-ymin),ls=':',color='g')
plt.vlines(x=eqpSec,ymin=ymin-0.2*(ymax-ymin),ymax=ymax+0.2*(ymax-ymin),ls=':',color='b')
plt.xlim([xmin-0.2*(xmax-xmin),xmax+0.2*(xmax-xmin)])
plt.ylim([ymin-0.2*(ymax-ymin),ymax+0.2*(ymax-ymin)])
plt.show()
k | band | eks [eV] | eqpLin [eV] | eqpSec [eV]
-----------------------------------------------------------------------------
1 | 1 | -13.238 | -16.275 | -16.138
k | band | eks [eV] | eqpLin [eV] | eqpSec [eV]
-----------------------------------------------------------------------------
1 | 2 | -8.232 | -12.153 | -12.048
k | band | eks [eV] | eqpLin [eV] | eqpSec [eV]
-----------------------------------------------------------------------------
1 | 3 | -8.232 | -12.150 | -12.045
k | band | eks [eV] | eqpLin [eV] | eqpSec [eV]
-----------------------------------------------------------------------------
1 | 4 | -8.231 | -12.149 | -12.044
k | band | eks [eV] | eqpLin [eV] | eqpSec [eV]
-----------------------------------------------------------------------------
1 | 5 | -0.466 | 0.665 | 0.664
Question: Why for SiH4 GW-linear energies are lower than GW-full ones?
5.3 : Convergence of GW with respect to npdep¶
The basis set used to represent the dielectric matrix needs to be converged. We have computed \(50\) eigenpotentials. We can now use fewer eigenpotentials in GW and test the convergece.
Let’s prepare the input for 5 calculations done with 10, 20, 30, 40, 50 eigenpotentials. We will also stash the output file for later comparison.
[9]:
import yaml
# we need to create 5 files, each with a different value of the variable n_pdep_eigen_to_use
for npdep in [10, 20, 30, 40, 50] :
# read data wfreq.in
with open('wfreq.in', 'r') as file:
input_data = yaml.load(file, Loader=yaml.FullLoader)
# modify the input_data
input_data['wfreq_control']['n_pdep_eigen_to_use'] = npdep
# write data to YAML file
with open('wfreq_'+str(npdep)+'.in', 'w') as file:
yaml.dump(input_data, file, sort_keys=False)
[10]:
# give a quick look
!cat wfreq_10.in
!cat wfreq_20.in
!cat wfreq_30.in
!cat wfreq_40.in
!cat wfreq_50.in
input_west:
qe_prefix: silane
west_prefix: silane
outdir: ./
wstat_control:
wstat_calculation: S
n_pdep_eigen: 50
wfreq_control:
wfreq_calculation: XWGQ
n_pdep_eigen_to_use: 10
qp_bandrange:
- 1
- 5
n_refreq: 300
ecut_refreq: 2.0
input_west:
qe_prefix: silane
west_prefix: silane
outdir: ./
wstat_control:
wstat_calculation: S
n_pdep_eigen: 50
wfreq_control:
wfreq_calculation: XWGQ
n_pdep_eigen_to_use: 20
qp_bandrange:
- 1
- 5
n_refreq: 300
ecut_refreq: 2.0
input_west:
qe_prefix: silane
west_prefix: silane
outdir: ./
wstat_control:
wstat_calculation: S
n_pdep_eigen: 50
wfreq_control:
wfreq_calculation: XWGQ
n_pdep_eigen_to_use: 30
qp_bandrange:
- 1
- 5
n_refreq: 300
ecut_refreq: 2.0
input_west:
qe_prefix: silane
west_prefix: silane
outdir: ./
wstat_control:
wstat_calculation: S
n_pdep_eigen: 50
wfreq_control:
wfreq_calculation: XWGQ
n_pdep_eigen_to_use: 40
qp_bandrange:
- 1
- 5
n_refreq: 300
ecut_refreq: 2.0
input_west:
qe_prefix: silane
west_prefix: silane
outdir: ./
wstat_control:
wstat_calculation: S
n_pdep_eigen: 50
wfreq_control:
wfreq_calculation: XWGQ
n_pdep_eigen_to_use: 50
qp_bandrange:
- 1
- 5
n_refreq: 300
ecut_refreq: 2.0
[ ]:
# run them all and stash the output
!mpirun -n 8 wfreq.x -i wfreq_10.in > wfreq_10.out
!mv silane.wfreq.save/wfreq.json wfreq_10.json
!mpirun -n 8 wfreq.x -i wfreq_20.in > wfreq_20.out
!mv silane.wfreq.save/wfreq.json wfreq_20.json
!mpirun -n 8 wfreq.x -i wfreq_30.in > wfreq_30.out
!mv silane.wfreq.save/wfreq.json wfreq_30.json
!mpirun -n 8 wfreq.x -i wfreq_40.in > wfreq_40.out
!mv silane.wfreq.save/wfreq.json wfreq_40.json
!mpirun -n 8 wfreq.x -i wfreq_50.in > wfreq_50.out
!mv silane.wfreq.save/wfreq.json wfreq_50.json
[11]:
!ls -lrt wfreq_*json
-rw-r--r-- 1 vwzyu staff 19408 Oct 7 12:41 wfreq_10.json
-rw-r--r-- 1 vwzyu staff 19406 Oct 7 12:41 wfreq_20.json
-rw-r--r-- 1 vwzyu staff 19423 Oct 7 12:41 wfreq_30.json
-rw-r--r-- 1 vwzyu staff 19417 Oct 7 12:41 wfreq_40.json
-rw-r--r-- 1 vwzyu staff 19408 Oct 7 12:41 wfreq_50.json
Load the files.
[12]:
import json
data = {}
for npdep in [10, 20, 30, 40, 50] :
# read data wfreq_XX.json
with open('wfreq_'+str(npdep)+'.json', 'r') as file:
data[npdep] = json.load(file)
print(json.dumps(data, indent=2))
{
"10": {
"runjob": {
"startdate": " 7Oct2022",
"starttime": "12:35:58",
"completed": true,
"endtime": "12:36: 2",
"enddate": " 7Oct2022"
},
"software": {
"package": "WEST",
"program": "WFREQ",
"version": "5.2.0",
"westgit": "v5.2.0-4-ga2c3fe0",
"website": "https://west-code.org",
"citation": "M. Govoni et al., J. Chem. Theory Comput. 11, 2680 (2015).",
"qeversion": "7.1"
},
"config": {
"io": {
"islittleendian": true
}
},
"parallel": {
"nranks": 4,
"nimage": 1,
"npool": 1,
"nbgrp": 1,
"nrg": 4,
"nproc": 4,
"nthreads": 1
},
"input": {
"input_west": {
"qe_prefix": "silane",
"west_prefix": "silane",
"outdir": "./"
},
"wstat_control": {
"wstat_calculation": "S",
"n_pdep_eigen": 50,
"n_pdep_times": 4,
"n_pdep_maxiter": 100,
"n_dfpt_maxiter": 250,
"n_pdep_read_from_file": 0,
"n_steps_write_restart": 1,
"trev_pdep": 0.001,
"trev_pdep_rel": 0.1,
"tr2_dfpt": 1e-12,
"l_kinetic_only": false,
"l_minimize_exx_if_active": false,
"l_use_ecutrho": false,
"qlist": [
1
]
},
"wfreq_control": {
"wfreq_calculation": "XWGQ",
"n_pdep_eigen_to_use": 10,
"qp_bandrange": [
1,
5
],
"qp_bands": [
0
],
"macropol_calculation": "N",
"n_lanczos": 30,
"n_imfreq": 128,
"n_refreq": 300,
"ecut_imfreq": 100.0,
"ecut_refreq": 2.0,
"wfreq_eta": 0.0036749308824745378,
"n_secant_maxiter": 21,
"trev_secant": 0.0036749308824745378,
"l_enable_lanczos": true,
"l_enable_off_diagonal": false,
"o_restart_time": 0.0,
"ecut_spectralf": [
-2.0,
1.0
],
"n_spectralf": 204
}
},
"system": {
"basis": {
"npw": {
"proc": [
0,
0,
0,
0
],
"min": 0,
"max": 0,
"sum": 0
},
"ngm": {
"proc": [
16881,
16880,
16881,
16880
],
"min": 16880,
"max": 16881,
"sum": 67522
},
"gamma_only": true,
"ecutwfc:ry": 25.0,
"ecutrho:ry": 100.0
},
"cell": {
"units": "a.u.",
"omega": 8000.0,
"a1": [
20.0,
0.0,
0.0
],
"a2": [
0.0,
20.0,
0.0
],
"a3": [
0.0,
0.0,
20.0
],
"b1": [
0.3141592653589793,
0.0,
0.0
],
"b2": [
0.0,
0.3141592653589793,
0.0
],
"b3": [
0.0,
0.0,
0.3141592653589793
],
"alat": 20.0,
"tpiba": 0.3141592653589793
},
"electron": {
"nbnd": 10,
"nkstot": 1,
"nspin": 1,
"nelec": 8.0,
"npol": 1,
"lsda": false,
"noncolin": false,
"lspinorb": false
},
"3dfft": {
"s": [
64,
64,
64
],
"p": [
64,
64,
64
]
},
"bzsamp": {
"k": [
{
"id": 1,
"crystcoord": [
0.0,
0.0,
0.0
]
}
]
}
},
"exec": {
"Q": {
"secitr": 3,
"en": [
{
"ksb": [
1,
1,
1
],
"ein": [
-13.237801251667781,
-16.10114908186098,
-15.996926773724638
],
"eout": [
-16.10114908186098,
-15.996926773724638,
-15.996069868657381
],
"sc_ein": [
[
2.174215265684058,
0.013088932776563526
],
[
3.651350702151748,
0.10369252948604364
],
[
3.5988731749975758,
0.0639837647821608
]
]
},
{
"ksb": [
1,
1,
2
],
"ein": [
-8.232337181481201,
-11.826655980420275,
-11.751061056952013
],
"eout": [
-11.826655980420275,
-11.751061056952013,
-11.749570833702585
],
"sc_ein": [
[
0.47604267728628913,
0.002742712462116818
],
[
1.015679912286032,
0.007130766748654207
],
[
1.006011205583271,
0.007104461297743382
]
]
},
{
"ksb": [
1,
1,
3
],
"ein": [
-8.231818167024082,
-11.826053048682086,
-11.75211364777671
],
"eout": [
-11.826053048682086,
-11.75211364777671,
-11.748938391716393
],
"sc_ein": [
[
0.4760265625681688,
0.002743013817220383
],
[
1.0137552857611338,
0.00710465490842237
],
[
1.0061933077526124,
0.00710465490842237
]
]
},
{
"ksb": [
1,
1,
4
],
"ein": [
-8.2314429871655,
-11.82554675775416,
-11.751600925661647
],
"eout": [
-11.82554675775416,
-11.751600925661647,
-11.748425188469648
],
"sc_ein": [
[
0.4760250328657089,
0.0027431582198368266
],
[
1.013750814496553,
0.007105103333653587
],
[
1.0061880664384744,
0.007105103333653587
]
]
},
{
"ksb": [
1,
1,
5
],
"ein": [
-0.4659075354101419,
0.7956422598915397,
0.7948357168266033
],
"eout": [
0.7956422598915397,
0.7948357168266033,
0.7948357168266033
],
"sc_ein": [
[
-0.22478052433353662,
-8.605070554690743e-06
],
[
-0.24219403328296762,
-3.7369340874557545e-05
],
[
-0.24218240496305504,
-3.7369340874557545e-05
]
]
}
]
}
},
"output": {
"Q": {
"bandmap": [
1,
2,
3,
4,
5
],
"indexmap": [
[
1,
1
],
[
2,
2
],
[
3,
3
],
[
4,
4
],
[
5,
5
]
],
"K000001": {
"eks": [
-13.237801251667781,
-8.232337181481201,
-8.231818167024082,
-8.2314429871655,
-0.4659075354101419
],
"z": [
0.6846028000268984,
0.888141466625856,
0.8881315611869276,
0.8881302802413489,
0.9870156947783238
],
"eqpLin": [
-16.10114908186098,
-11.826655980420275,
-11.826053048682086,
-11.82554675775416,
0.7956422598915397
],
"eqpSec": [
-15.996069868657381,
-11.749570833702585,
-11.748938391716393,
-11.748425188469648,
0.7948357168266033
],
"sigma_diff": [
0.0008569050672560701,
0.0014902232494293398,
0.003175256060317917,
0.003175737191998,
0.0
],
"occupation": [
2.0,
2.0,
2.0,
2.0,
0.0
],
"sigmax": [
-17.606465467514493,
-15.766052671933085,
-15.765818857651459,
-15.765460140908123,
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"wall:hum": "08.7s",
"nocalls": 270
},
"h_psi:calbec": {
"cpu:sec": 0.06849300000000547,
"cpu:hum": "< 00.1s",
"wall:sec": 0.06946015357971191,
"wall:hum": "< 00.1s",
"nocalls": 270
},
"calbec": {
"cpu:sec": 0.06771800000000638,
"cpu:hum": "< 00.1s",
"wall:sec": 0.06876993179321289,
"wall:hum": "< 00.1s",
"nocalls": 270
},
"add_vuspsi": {
"cpu:sec": 0.07071800000000117,
"cpu:hum": "< 00.1s",
"wall:sec": 0.07206106185913086,
"wall:hum": "< 00.1s",
"nocalls": 270
},
"brak": {
"cpu:sec": 0.20410399999999917,
"cpu:hum": "00.2s",
"wall:sec": 0.20876431465148926,
"wall:hum": "00.2s",
"nocalls": 9
},
"sw_restart": {
"cpu:sec": 0.04145599999999927,
"cpu:hum": "< 00.1s",
"wall:sec": 0.09229683876037598,
"wall:hum": "< 00.1s",
"nocalls": 4
},
"chi_invert": {
"cpu:sec": 0.012472999999999956,
"cpu:hum": "< 00.1s",
"wall:sec": 0.015166997909545898,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"glanczos": {
"cpu:sec": 6.3028640000000005,
"cpu:hum": "06.3s",
"wall:sec": 6.399578094482422,
"wall:hum": "06.3s",
"nocalls": 1
},
"write_over": {
"cpu:sec": 0.00039300000000075386,
"cpu:hum": "< 00.1s",
"wall:sec": 0.0003981590270996094,
"wall:hum": "< 00.1s",
"nocalls": 5
},
"write_gfreq": {
"cpu:sec": 0.0017250000000004206,
"cpu:hum": "< 00.1s",
"wall:sec": 0.03147578239440918,
"wall:hum": "< 00.1s",
"nocalls": 5
},
"sg_restart": {
"cpu:sec": 0.0005959999999998189,
"cpu:hum": "< 00.1s",
"wall:sec": 0.0024161338806152344,
"wall:hum": "< 00.1s",
"nocalls": 5
},
"solve_qp": {
"cpu:sec": 0.04543999999999926,
"cpu:hum": "< 00.1s",
"wall:sec": 0.06262898445129395,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"coll_gw": {
"cpu:sec": 0.011383999999999617,
"cpu:hum": "< 00.1s",
"wall:sec": 0.015905141830444336,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"read_over": {
"cpu:sec": 0.0004229999999996181,
"cpu:hum": "< 00.1s",
"wall:sec": 0.0004470348358154297,
"wall:hum": "< 00.1s",
"nocalls": 5
},
"read_gfreq": {
"cpu:sec": 0.0003879999999991668,
"cpu:hum": "< 00.1s",
"wall:sec": 0.002985715866088867,
"wall:hum": "< 00.1s",
"nocalls": 5
},
"read_hf": {
"cpu:sec": 6.4000000000064e-05,
"cpu:hum": "< 00.1s",
"wall:sec": 6.389617919921875e-05,
"wall:hum": "< 00.1s",
"nocalls": 1
},
"sigmac_i": {
"cpu:sec": 0.013606000000001117,
"cpu:hum": "< 00.1s",
"wall:sec": 0.013605117797851562,
"wall:hum": "< 00.1s",
"nocalls": 4
},
"sigmac_r": {
"cpu:sec": 0.0002770000000005268,
"cpu:hum": "< 00.1s",
"wall:sec": 0.0002760887145996094,
"wall:hum": "< 00.1s",
"nocalls": 4
},
"wfreq_db": {
"cpu:sec": 0.0005980000000000985,
"cpu:hum": "< 00.1s",
"wall:sec": 0.004639863967895508,
"wall:hum": "< 00.1s",
"nocalls": 1
}
}
}
}
We plot the energy levels of DFT and GW.
[13]:
import numpy as np
import matplotlib.pyplot as plt
# energy levels
y = {}
y[10] = data[10]['output']['Q']['K000001']['eqpSec']
y[20] = data[20]['output']['Q']['K000001']['eqpSec']
y[30] = data[30]['output']['Q']['K000001']['eqpSec']
y[40] = data[40]['output']['Q']['K000001']['eqpSec']
y[50] = data[50]['output']['Q']['K000001']['eqpSec']
# colors
c = {}
c[10] = 'red'
c[20] = 'blue'
c[30] = 'green'
c[40] = 'purple'
c[50] = 'black'
# plot
x = list(range(1, len(y)+1))
labels = y.keys()
fig, ax = plt.subplots(1, 1)
counter = 0
for i in labels :
for a in y[i] :
ax.hlines(a, x[counter]-0.25, x[counter]+0.25, color=c[i])
counter += 1
#plt.ylim([-13,-11])
plt.xticks(x, labels)
plt.ylabel('Energy (eV)')
plt.title('Energy structure')
plt.show()
