Dear Alex,
Thank you for developing and maintaining that code.
I am trying to calculate with CoAs3 with this code.
I keep getting NaN values while performing the IMP calculation. I do not what happened. How to solve it?
setting.yaml:
general settings
scattering_type: auto
doping: [‘1.e13’, ‘1.e14’, ‘1.e15’, ‘1.e16’, ‘1.e17’, ‘1.e18’, ‘1.e19’, ‘1.e20’, ‘1.e21’, ‘0’]
temperatures: [300]
bandgap: 0.498
free_carrier_screening: true
energy_cutoff: 1.5
fd_tol: 0.01
#scissor: 0.1
electronic_structure settings
interpolation_factor: 50
materials properties
deformation_potential: deformation.h5
pop_frequency: 7.16
elastic_constant:
- [238, 46, 46, 0, 0, 0]
- [ 46, 238, 46, 0, 0, 0]
- [ 46, 46, 238, 0, 0, 0]
- [ 0, 0, 0, 75, 0, 0]
- [ 0, 0, 0, 0, 75, 0]
- [ 0, 0, 0, 0, 0, 75]
static_dielectric: - [42.033142, 0, 0]
- [0, 42.033142, 0]
- [0, 0, 42.033142]
high_frequency_dielectric: - [34.062727 , 0, 0]
- [0, 34.062727 , 0]
- [0, 0, 34.062727]
performance settings
write_mesh: false
The output：
/$$$$$$ /$$ /$$ /$$$$$$ /$$$$$$$$ /$$$$$$$$
/$$__ $$| $$$ /$$$ /$$__ $$| $$_____/|__ $$__/
| $$ \ $$| $$$$ /$$$$| $$ \__/| $$ | $$
| $$$$$$$$| $$ $$/$$ $$| $$$$$$ | $$$$$ | $$
| $$__ $$| $$ $$$| $$ \____ $$| $$__/ | $$
| $$ | $$| $$\ $ | $$ /$$ \ $$| $$ | $$
| $$ | $$| $$ \/ | $$| $$$$$$/| $$$$$$$$ | $$
|__/ |__/|__/ |__/ \______/ |________/ |__/
v0.4.22
Ganose, A. M., Park, J., Faghaninia, A., Woods-Robinson,
R., Persson, K. A., Jain, A. Efficient calculation of
carrier scattering rates from first principles.
Nat. Commun. 12, 2222 (2021)
amset starting on 31 May 2025 at 08:26
Run parameters:
- scattering_type: auto
- doping: [1.e+13 1.e+14 1.e+15 1.e+16 1.e+17 1.e+18 1.e+19 1.e+20 1.e+21 0.e+00]
- temperatures: [300]
- bandgap: 0.498
- soc: False
- zero_weighted_kpoints: prefer
- interpolation_factor: 50
- wavefunction_coefficients: wavefunction.h5
- use_projections: False
- unity_overlap: False
- free_carrier_screening: True
- high_frequency_dielectric:
[[ 34.06 0.00 0.00]
[ 0.00 34.06 0.00]
[ 0.00 0.00 34.06]]
- static_dielectric:
[[ 42.03 0.00 0.00]
[ 0.00 42.03 0.00]
[ 0.00 0.00 42.03]]
- elastic_constant:
[[ 238.0 46.0 46.0 0.0 0.0 0.0]
[ 46.0 238.0 46.0 0.0 0.0 0.0]
[ 46.0 46.0 238.0 0.0 0.0 0.0]
[ 0.0 0.0 0.0 75.0 0.0 0.0]
[ 0.0 0.0 0.0 0.0 75.0 0.0]
[ 0.0 0.0 0.0 0.0 0.0 75.0]]
- deformation_potential: deformation.h5
- defect_charge: 1
- compensation_factor: 2
- pop_frequency: 7.16
- energy_cutoff: 1.5
- fd_tol: 0.01
- dos_estep: 0.01
- symprec: 0.01
- nworkers: -1
- cache_wavefunction: True
- calculate_mobility: True
- separate_mobility: True
- mobility_rates_only: False
- file_format: json
- write_input: False
- write_mesh: False
- print_log: True
- write_log: True
~~~~~~~~~~~~~~~~~~~~~~~~~~~~ STRUCTURE ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Structure information:
- formula: CoAs3
- # sites: 16
- space group: Im3-
Lattice:
- a, b, c [angstrom]: 7.18, 7.18, 7.18
- a, b, y [deg]: 109, 109, 109
~~~~~~~~~~~~~~~~~~~~~~~~~~ BAND STRUCTURE ~~~~~~~~~~~~~~~~~~~~~~~~~
Input band structure information:
- # bands: 96
- # k-points: 61
- Fermi level: 6.510 eV
- spin polarized: False
- metallic: False
Band gap:
- direct band gap: 0.498 eV
- direct k-point: [0.00, 0.00, 0.00]
Valence band maximum:
- energy: 6.346 eV
- k-point: [0.00, 0.00, 0.00]
- band indices: 48
Conduction band minimum:
- energy: 6.844 eV
- k-point: [0.00, 0.00, 0.00]
- band indices: 49, 50, 51
~~~~~~~~~~~~~~~~~~~~~~~~~~ INTERPOLATION ~~~~~~~~~~~~~~~~~~~~~~~~~~
Getting band interpolation coefficients
- time: 0.4336 s
Interpolation parameters:
- k-point mesh: 59x59x59
- energy cutoff: 1.5 eV
Interpolating spin-up bands 47-56
- time: 1.2378 s
bandgap set to 0.498 eV, applying scissor of 0.000 eV
Generating tetrahedron mesh vertices
- time: 1.8961 s
Initializing tetrahedron band structure
- time: 9.0177 s
Initializing momentum relaxation time factor calculator
Initializing wavefunction overlap calculator
Desymmetrizing k-point mesh
- Found initial mesh: 10.000 x 10.000 x 10.000
- Integer mesh: 10 x 10 x 10
- Using 24 symmetry operations
Desymmetrizing wavefunction coefficients
- time: 1.8353 s
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DOS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DOS parameters:
- emin: 4.02 eV
- emax: 9.12 eV
- dos weight: 2
- n points: 509
Generating tetrahedral DOS:
- time: 27.4226 s
Intrinsic DOS Fermi level: 6.5954 eV
DOS contains 3.996 electrons
Calculated Fermi levels:
conc [cm-3] temp [K] E_fermi [eV]
------------- ---------- --------------
1.00e+13 300.0 6.5360
1.00e+14 300.0 6.5333
1.00e+15 300.0 6.5107
1.00e+16 300.0 6.4549
1.00e+17 300.0 6.3945
1.00e+18 300.0 6.3268
1.00e+19 300.0 6.2072
1.00e+20 300.0 5.9013
1.00e+21 300.0 5.2954
0.00e+00 300.0 6.8079
Calculated Fermi-Dirac cut-offs:
- min: 5.017 eV
- max: 7.161 eV
~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SCATTERING ~~~~~~~~~~~~~~~~~~~~~~~~~~~
Examining material properties to determine possible scattering
mechanisms
Scattering mechanisms to be calculated: ADP, IMP, POP
Initializing deformation potential interpolator
Inverse screening length (b) and impurity concentration (N_i):
conc [cm-3] temp [K] b2 [a^-2] N_i [cm-3]
------------- ---------- ----------- ------------
1.00e+13 300.0 4.03e-08 2.00e+13
1.00e+14 300.0 4.05e-08 2.00e+14
1.00e+15 300.0 6.16e-08 2.00e+15
1.00e+16 300.0 4.66e-07 2.00e+16
1.00e+17 300.0 4.50e-06 2.00e+17
1.00e+18 300.0 3.49e-05 2.00e+18
1.00e+19 300.0 1.51e-04 2.00e+19
1.00e+20 300.0 6.00e-04 2.00e+20
1.00e+21 300.0 7.03e-03 2.00e+21
0.00e+00 300.0 7.16e-04 0.00e+00
Initializing POP scattering
- average N_po: 0.4665
- w_po: 44.99 2pi THz
- hbar.omega: 0.0296 eV
Forking 56 processes to calculate scattering
- time: 19.8486 s
Scattering information:
- # ir k-points: 9020
Calculating rates for spin-up band 1
- # k-points within Fermi-Dirac cut-offs: 0
- time: 0.4036 s
Calculating rates for spin-up band 2
- # k-points within Fermi-Dirac cut-offs: 170325
- time: 2651.1876 s
Calculating rates for spin-up band 3
- # k-points within Fermi-Dirac cut-offs: 204251
- time: 3866.0272 s
Calculating rates for spin-up band 4
- # k-points within Fermi-Dirac cut-offs: 62989
- time: 1482.9833 s
Calculating rates for spin-up band 5
- # k-points within Fermi-Dirac cut-offs: 18067
- time: 469.4807 s
Calculating rates for spin-up band 6
- # k-points within Fermi-Dirac cut-offs: 7652
- time: 214.2296 s
Calculating rates for spin-up band 7
- # k-points within Fermi-Dirac cut-offs: 2682
- time: 79.4027 s
Calculating rates for spin-up band 8
- # k-points within Fermi-Dirac cut-offs: 1872
- time: 56.4824 s
Calculating rates for spin-up band 9
- # k-points within Fermi-Dirac cut-offs: 0
- time: 0.0811 s
Calculating rates for spin-up band 10
- # k-points within Fermi-Dirac cut-offs: 0
- time: 0.0793 s
Interpolating missing scattering rates
- time: 1.7703 s
Filling scattering rates [s⁻¹] outside FD cutoffs with:
conc [cm-3] temp [K] ADP IMP POP
------------- ---------- -------- -------- --------
1.00e+13 300.0 1.39e+12 nan 8.20e+12
1.00e+14 300.0 1.39e+12 nan 8.20e+12
1.00e+15 300.0 1.39e+12 nan 8.20e+12
1.00e+16 300.0 1.39e+12 nan 8.19e+12
1.00e+17 300.0 1.39e+12 nan 8.10e+12
1.00e+18 300.0 1.39e+12 nan 7.63e+12
1.00e+19 300.0 1.39e+12 nan 6.71e+12
1.00e+20 300.0 1.39e+12 nan 5.29e+12
1.00e+21 300.0 1.39e+12 nan 2.33e+12
0.00e+00 300.0 1.39e+12 1.00e-32 5.08e+12
~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TRANSPORT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Calculating conductivity, Seebeck, and electronic thermal
conductivity
ERROR: amset exiting on 31 May 2025 at 10:55
Traceback (most recent call last):
File "/home/hyj/.local/bin/amset", line 8, in <module>
sys.exit(cli())
File "/home/hyj/.local/lib/python3.10/site-
packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/home/hyj/.local/lib/python3.10/site-
packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/hyj/.local/lib/python3.10/site-
packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/hyj/.local/lib/python3.10/site-
packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/hyj/.local/lib/python3.10/site-
packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/hyj/.local/lib/python3.10/site-
packages/amset/tools/run.py", line 139, in run
runner.run()
File "/home/hyj/.local/lib/python3.10/site-
packages/amset/core/run.py", line 65, in run
mem_usage, (amset_data, usage_stats) = memory_usage(
File "/home/hyj/.local/lib/python3.10/site-
packages/memory_profiler.py", line 379, in memory_usage
returned = f(*args, **kw)
File "/home/hyj/.local/lib/python3.10/site-
packages/amset/core/run.py", line 124, in _run_wrapper
amset_data, timing = self._do_fd_tol(amset_data, directory,
prefix, timing)
File "/home/hyj/.local/lib/python3.10/site-
packages/amset/core/run.py", line 135, in _do_fd_tol
amset_data, transport_time = self._do_transport(amset_data)
File "/home/hyj/.local/lib/python3.10/site-
packages/amset/core/run.py", line 282, in _do_transport
transport_properties = solve_boltzman_transport_equation(
File "/home/hyj/.local/lib/python3.10/site-
packages/amset/core/transport.py", line 39, in
solve_boltzman_transport_equation
sigma, seebeck, kappa = _calculate_transport_properties(
File "/home/hyj/.local/lib/python3.10/site-
packages/amset/core/transport.py", line 186, in
_calculate_transport_properties
sigma[n, t], seebeck[n, t], kappa[n, t], _ =
calc_Onsager_coefficients(
File "/home/hyj/.local/lib/python3.10/site-
packages/BoltzTraP2/bandlib.py", line 538, in
calc_Onsager_coefficients
pL11 = np.linalg.pinv(L11[iT, imu])
File "/home/hyj/.local/lib/python3.10/site-
packages/numpy/linalg/linalg.py", line 2022, in pinv
u, s, vt = svd(a, full_matrices=False, hermitian=hermitian)
File "/home/hyj/.local/lib/python3.10/site-
packages/numpy/linalg/linalg.py", line 1681, in svd
u, s, vh = gufunc(a, signature=signature, extobj=extobj)
File "/home/hyj/.local/lib/python3.10/site-
packages/numpy/linalg/linalg.py", line 121, in
_raise_linalgerror_svd_nonconvergence
raise LinAlgError("SVD did not converge")
numpy.linalg.LinAlgError: SVD did not converge
Thank you very much!
Best wishes,
Y. J.Hao