Dear all developers or users:

Nonrad is a very powerful code. However, as I am a beginner with nonrad, I had some problems repeating the developer's tutorial.

As a rookie I have tried to repeat this literature "Nonrad: Computing nonradiative capture coefficients from first principles".

I calculated the Configuration Coordinate Diagram , the calculation results look consistent with the example.

When i calculate the Electron-Phonon Coupling Matrix Element，I found that a large error is produced. The graph I calculated is shown below.

The graph in the example is shown below.

The process of my calculations is
a. Copy the INCAR CONTCAR POTCAR KPOINTS WAVECAR calculated in the "C0" folder to the "WSWQ" folder created in all the folders under the "groud" folder;
b. Copy the calculated WAVECAR from all the "groud" folders into their respective "WSWQ" folders and rename them as WAVECAR.qqq;
c. Add ALGO=None and LWSWQ=.TRUE to INCAR and do a VASP calculation to get the WSWQ file.

The structure and calculation parameters used for the calculations were taken from https://nomad-lab.eu/. The version of VASP used is 5.4.4. I'm not quite sure if my calculation steps or parameters are correct.

I am wondering if someone could kindly share me the input files and the necessary information about it. I promise they will be used only for research purposed. If it's too much trouble, could anyone send me some relevant information?

Thank you very much for your kind consideration and I am looking forward to your early reply.

Best regards!

Changqing lin

nonrad.zip

Hello, I tried to reproduce the results being shown in the notebook. In short, I took a hexagonal GaN, then used PBESol to optimize the structure. Afterward, I made a supercell out of it and introduced C_N, I used PBEsol to optimize the geometries using PBESol considering neutral and negatively charged states. Then, on top of the PBESol optimized geometries, I did single shot HSE06 calculations. Then I computed the CC diagram, but it did not match what was shown in the notebook. Also, my el-ph coupling matrix is weird. I am adding my code and some snapshots for reference. Also, I am adding my INCAR, CONTCAR and KPOINTS file for reference for neutral state calculations.

#SYSTEM = Halide Perovskites

Global Settings

LHFCALC = .TRUE. # Use hybrid functionals
HFSCREEN = 0.2 # Use HSE06
AEXX = 0.25
ISMEAR = 1 # first order Methfessel-Paxton
SIGMA = 0.2 # broadening (default)
LREAL = A # evaluate projection operators in real space
NCORE = 32
NPAR = 8

Discretization

PREC = Normal # Normal defaults
PRECFOCK = Normal # Normal defaults for HF

NKRED = 2 # Use every k-point in HF

#for 64 MPIs
#NBANDS = 216 # For consistency; default = 210
#NSIM = 18 # Do them all at once...
#NBANDS = 256 # For consistency; default = 210
#NSIM = 8 # Do them all at once...
#NSIM = 105 # Do them all at once... (total number of atoms)

Electronic Relaxation

ALGO = All # Use Congugate Gradient to allow HF-calcs
NELM = 100 # maximum number of electronic SC steps
NELMDL = 5
EDIFF = 1E-02 # stopping-criterion for ELM

Ionic Relaxation

NSW = 0 # maximum number of ionic steps
ISIF = 0 # calculate/relax/change everything
IBRION = -1 # ion update algorithm (2 = CG)
POTIM = 0.5 # force scaling constant (think relaxation)

Input/Output

LWAVE = T # Don't store the WAVECAR
LCHARG = F # Don't store the CHGCAR
LVTOT = .TRUE.
LORBIT = 11
EMIN = -20
EMAX = 10
NEDOS = 2000

KPAR=4 ; NCSHMEM = -1 ; FFTWMAKEPLAN = E ; PREC=Normal

Generated by VASPKIT code
1.0000000000000000
9.5448821759636306 -0.0000001223507782 0.0000003271666213
-4.7724411930677260 8.2661103114839474 0.0000000517088665
0.0000003555989914 0.0000002699779637 10.3657172070195980
C Ga N
1 36 35
Direct
0.4444445427754928 0.2222221679046825 0.6866849657141003
0.1114942875487870 0.2219546576285509 0.4994739096721048
0.1110275570975929 0.2223441628518188 0.9999700790541439
0.1111112929480811 0.5555554014778252 0.4995887251168654
0.1111112923120245 0.5555553908996913 0.9996003583748134
0.1114941296417982 0.8895389464125145 0.4994738776249363
0.1110275782080024 0.8886828046835689 0.9999700797443936
0.4444445968724509 0.2222218994454366 0.5001595322570154
0.4444447064680404 0.2222221404005893 0.9987438271723050
0.4447120434421734 0.5551724012610109 0.4994739273027022
0.4443225092700658 0.5556391442453474 0.9999700779125860
0.4447118903757996 0.8895389826578111 0.4994739452198615
0.4443224812150035 0.8886828245814939 0.9999700771185189
0.7771276528430349 0.2219547739125787 0.4994738098969052
0.7779838020470748 0.2223441281061156 0.9999700977320884
0.7771277152993932 0.5551725363111828 0.4994737566032583
0.7779837942157570 0.5556390620991820 0.9999701239229069
0.7777779520762707 0.8888887129054623 0.4993687542584766
0.7777779332282009 0.8888887460276962 0.9997792950593336
0.2220763586843759 0.1110384369559725 0.2489290363667607
0.2225028640800062 0.1112517286793775 0.7507362769216996
0.2222326992723467 0.4444339985909096 0.2496653518297762
0.2223364158958461 0.4443303095043305 0.7495655499388008
0.2222326840937114 0.7777992595067857 0.2496653265781603
0.2223364269729373 0.7780066264593941 0.7495655657945974
0.5556282428354962 0.1110383969292670 0.2489290197942537
0.5554149349416093 0.1112517155471551 0.7507362334109047
0.5556281500400644 0.4445902641214019 0.2489291202382091
0.5554148982262888 0.4441638007290720 0.7507361800989045
0.5554596436506003 0.7777301289194440 0.2496825306638684
0.5560251909727043 0.7780128177359487 0.7500401351611785
0.8889365267546410 0.1112069606282944 0.2496825253054951
0.8886538676492819 0.1106415265563143 0.7500400605056186
0.8888674391842102 0.4444339945697280 0.2496653113294656
0.8886600554780557 0.4443302917994032 0.7495655396311207
0.8889365352463443 0.7777300919216898 0.2496824609728066
0.8886537350148700 0.7780129218039278 0.7500401747104561
0.1108988077522284 0.2225054076354738 0.1878501211656953
0.1097435801495479 0.2221124101974752 0.6878324757605299
0.1111111886867704 0.5555554933444995 0.1879271467396890
0.1111111881720959 0.5555555073636853 0.6879963275178724
0.1108987794618912 0.8883931963394147 0.1878501134667090
0.1097436014584758 0.8876309083897809 0.6878324391733841
0.4444444944823047 0.2222221734191763 0.1873606843397582
0.4441612974017275 0.5557678983395533 0.1878501352596373
0.4445542814894878 0.5569231517123043 0.6878324674298923
0.4441612624621527 0.8883931737340092 0.1878500999986841
0.4445542008575885 0.8876309076650415 0.6878324885487004
0.7782735117342199 0.2225054421545281 0.1878501326605075
0.7790358100458832 0.2221125217502689 0.6878324603326433
0.7782734413082579 0.5557678619634103 0.1878501485436601
0.7790358208642942 0.5569231546117734 0.6878324047262012
0.7777778494840462 0.8888888235468855 0.1878881046615390
0.7777779217825440 0.8888888460578954 0.6878668768998111
0.2208238680144916 0.1104119814382116 0.4357487435004899
0.2204440237881400 0.1102220698154923 0.9394223730643674
0.2222298665079094 0.4444368463392792 0.4380168502742094
0.2222081479121485 0.4444585538791515 0.9378213314868518
0.2222298151099835 0.7777932465318003 0.4380167973367861
0.2222081097779309 0.7777497994226295 0.9378213267220303
0.5562546485221276 0.1104120215708662 0.4357486995485118
0.5564445528735220 0.1102221410320752 0.9394224501348276
0.5562547033461982 0.4458428079342340 0.4357488270380756
0.5564446336985895 0.4462227262323211 0.9394223452736412
0.5555687937542828 0.7777845160900441 0.4379284033445003
0.5557088028827692 0.7778545186128270 0.9378689305273227
0.8888822074439418 0.1110979051659697 0.4379283629979653
0.8888122190206786 0.1109579126659455 0.9378689327208818
0.8888734879187297 0.4444368930539824 0.4380167925735492
0.8889168902494049 0.4444586035070017 0.9378213170379510
0.8888822001813139 0.7777845421207488 0.4379283344308718
0.8888122005257841 0.7778545175911376 0.9378689357528387

Automatic mesh

0
Gamma
2 2 2
0.000 0.000 0.000

import os
from pathlib import Path
from shutil import copyfile
from pymatgen.core import Structure
from nonrad.ccd import get_cc_structures
import numpy as np

equilibrium structures from your first-principles calculation

ground_files = Path('/scratch/negishi/rahma103/Projects_29_March_2024/NonRad/C0')
ground_struct = Structure.from_file(str(ground_files / 'CONTCAR'))
excited_files = Path('/scratch/negishi/rahma103/Projects_29_March_2024/NonRad/C-')
excited_struct = Structure.from_file(str(excited_files / 'CONTCAR'))

output directory that will contain the input files for the CC diagram

cc_dir = Path('/scratch/negishi/rahma103/Projects_29_March_2024/NonRad/cc_dir')
os.mkdir(str(cc_dir))
os.mkdir(str(cc_dir / 'ground'))
os.mkdir(str(cc_dir / 'excited'))

displacements as a percentage, this will generate the displacements

-50%, -37.5%, -25%, -12.5%, 0%, 12.5%, 25%, 37.5%, 50%

displacements = np.linspace(-0.5, 0.5, 9)

note: the returned structures won't include the 0% displacement, this is intended

it can be included by specifying remove_zero=False

ground, excited = get_cc_structures(ground_struct, excited_struct, displacements)

for i, struct in enumerate(ground):
working_dir = cc_dir / 'ground' / str(i)
os.mkdir(str(working_dir))

# write structure and copy necessary input files
struct.to(filename=str(working_dir / 'POSCAR'), fmt='poscar')
for f in ['KPOINTS', 'POTCAR', 'INCAR', 'job.sh']:
    copyfile(str(ground_files / f), str(working_dir / f))

for i, struct in enumerate(excited):
working_dir = cc_dir / 'excited' / str(i)
os.mkdir(str(working_dir))

# write structure and copy necessary input files
struct.to(filename=str(working_dir / 'POSCAR'), fmt='poscar')
for f in ['KPOINTS', 'POTCAR', 'INCAR', 'job.sh']:
    copyfile(str(excited_files / f), str(working_dir / f))

from glob import glob
from nonrad.ccd import get_dQ, get_PES_from_vaspruns, get_omega_from_PES
%matplotlib inline
import matplotlib.pyplot as plt
import numpy as np

calculate dQ

dQ = get_dQ(ground_struct, excited_struct) # amu^{1/2} Angstrom

this prepares a list of all vasprun.xml's from the CCD calculations

ground_vaspruns = glob(str(cc_dir / 'ground' / '' / 'vasprun.xml'))
excited_vaspruns = glob(str(cc_dir / 'excited' / '' / 'vasprun.xml'))

remember that the 0% displacement was removed before? we need to add that back in here

ground_vaspruns = ground_vaspruns + [str(ground_files / 'vasprun.xml')]
excited_vaspruns = excited_vaspruns + [str(excited_files / 'vasprun.xml')]

extract the potential energy surface

Q_ground, E_ground = get_PES_from_vaspruns(ground_struct, excited_struct, ground_vaspruns)
Q_excited, E_excited = get_PES_from_vaspruns(ground_struct, excited_struct, excited_vaspruns)

the energy surfaces are referenced to the minimums, so we need to add dE (defined before) to E_excited

E_excited = 1.07 + E_excited

fig, ax = plt.subplots(figsize=(5, 5))
ax.scatter(Q_ground, E_ground, s=10)
ax.scatter(Q_excited, E_excited, s=10)

by passing in the axis object, it also plots the fitted curve

q = np.linspace(-1.0, 3.5, 100)
ground_omega = get_omega_from_PES(Q_ground, E_ground, ax=ax, q=q)
excited_omega = get_omega_from_PES(Q_excited, E_excited, ax=ax, q=q)

ax.set_xlabel('$Q$ [amu$^{1/2}$ $\AA$]')
ax.set_ylabel('$E$ [eV]')
plt.show()

from nonrad.elphon import get_Wif_from_wavecars
from nonrad.ccd import get_Q_from_struct
from nonrad.elphon import get_Wif_from_WSWQ

this generates a list of tuples where the first value of the tuple is a Q value

and the second is the path to the WAVECAR file that corresponds to that tuple

wavecars = []
for d in glob(str(cc_dir / 'ground' / '*')):
pd = Path(d)
Q = get_Q_from_struct(ground_struct, excited_struct, str(pd / 'CONTCAR'))
path_wavecar = str(pd / 'WAVECAR')
wavecars.append((Q, path_wavecar))

by passing a figure object, we can inspect the resulting plots

fig = plt.figure(figsize=(12, 5))
Wifs = get_Wif_from_wavecars(wavecars, str(ground_files / 'WAVECAR'), 324, [321, 322, 323], spin=1, fig=fig)
plt.tight_layout()
plt.show()

Dear Altruists

Thank you very much for developing such a nice tool to calculate the SRH recombination coefficient. I found that the notebook of the 'nonrad' code shows how to calculate the hole capture coefficient for 'C' substitution at 'N' sites of 'GaN'. To calculate the SRH recombination coefficient (A), we would also need the electron capture coefficient as well.

In the case of the electron capture coefficient, the 'nonrad' paper suggests using 'dE=Eg-ε(0/-)'. I would like to know, to calculate the electron capture coefficient, is it sufficient to use only the 'dE=Eg-ε(0/-)' in the code of capture coefficient, or do I also need to calculate the electron-phonon coupling matrix element (WSWQ files) as well. If I need to calculate the WSWQ files, then should I calculate them in the excited states?

Thank you very much for your time and kind consideration.

Sincerely
Arindam Sannyal

Hi, I am trying to compute Wif with get_Wif_from_WSWQ. However, I find that for some defect transitions the WSWQ element is not linear with Q, making it unlikely to use finite difference. I tested and find that this is not because of convergence (like cut off energy) or unreasonable displacements.

Could you please advice how to solve this issue? I wonder this may not be solved, rather it is due to the material itself.