hackingmaterials / amset Goto Github PK

The new version of numpy no longer supports the float and complex data types. When I use it, I get an error message and the following prompt: The program can run normally after changing np.float and np.complex to np.float64 and np.complex128 in the code.

`np.complex` was a deprecated alias for the builtin `complex`. To avoid this error in existing code, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

np.float was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
    https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

Dear Sir/Madam, Thanks for the AMSET...
I have following queries. Can you please answer my doubts...

1. Regrading the deformation potential of VBM and CBM, can we take the average of deformation potential of +1 and -1 % strain (compressive and tensile).
2. Which way of taking high frequency dielectric constant is more reliable. One with the VASP DFPT or from the LO and TO phonon frequencies and estimate the value of the high-frequency dielectric constant using the Lyddane-Sachs-Teller
   relation.
3. For the elastic constant, whether only spherically averaged longitudinal elastic constants is enough or do we take the average of both transverse and longitudinal spherically averaged elastic constants
4. Will skipping the piezoelectric constants will effects the transport properties with AMSET...

Thanks in Advance...

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InstallationError("Invalid requirement: 'interpolation=2.1.2' (from line 2 of /home/dependabot/dependabot-updater/dependabot_tmp_dir/requirements-optional.txt)\nHint: = is not a valid operator. Did you mean == ?")

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Currently, the Amset class is very monolithic, with the core.py file running to almost 4,000 lines of code. To improve maintainability, I think it would be good to refactor out bits of the class into separate subclasses.

Initially, I think the plotting and io functions are ideal candidates for refactoring. We could do what pymatgen and other packages do, and just have an AmsetPlotter class that takes the Amset class as an initialization parameter.

I tried GaAs example. I found that the experiment's intrinsic carrier concentration is just 1.7e6. But if I reduce the doping concentration to 1.7e6, the following error appears. Is the method not suitable for low doping content or semiconductors?

  Traceback (most recent call last):
    File "~/miniconda3/lib/python3.9/site-packages/amset/core/data.py", line 219, in 
  set_doping_and_temperatures
   ) = self.dos.get_fermi(
    File "~/miniconda3/lib/python3.9/site-packages/amset/electronic_structure/dos.py", line 224, in get_fermi raise ValueError(

  ValueError: Could not find fermi within 100.0% of 
  concentration=2.652506335351714e-19

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Dear Sir,
1)Using the command amset phonon-frequency, two frequencies were obtained max. freq and eff. freq. Shall we use the use max. frequency instead of eff.frequency for AMSET calculations which matches with examples cases like GaAs and Si.
2) I understand that we can take the average of longitudinal elastic constants (C11 + C22 + C33) to determine the elastic constants. Please let us know whether full elastic tensor have been implemented in current version.
3) Is it fine to calculate properties with AMSET without wave-functions dump option. I have included LORBIT=11 in my calculation and use only the vasprun.xml.

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InstallationError("Invalid requirement: 'interpolation=2.1.2' (from line 2 of /home/dependabot/dependabot-updater/dependabot_tmp_dir/requirements-optional.txt)\nHint: = is not a valid operator. Did you mean == ?")

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Hi @utf , can you please replace the email address in README. That email of mine is no longer active (I am pretty sure the lab removed it after I left)

Great code, congrats!

This is a license question. amset is licensed under BSD (?) as per: https://github.com/hackingmaterials/amset/blob/master/LICENSE

However it uses GPLv3 licensed BoltzTrap (https://gitlab.com/sousaw/BoltzTraP2/blob/public/LICENSE.txt), for example in amset/amset/transport.py:

from BoltzTraP2.bandlib import fermiintegrals, calc_Onsager_coefficients, DOS, \
lambda_to_tau, BTPDOS

This makes the amset code also GPLv3. Can you please clarify and/or (hopefully) correct me if I'm wrong.

Currently, Amset requires a pymatgen Vasprun object as an input parameter. As we only need the structural and eigenvalue properties from this object, we should transition to requiring a pymatgen BandStructure object instead.

This will make Amset compatible with codes other than VASP.

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Dear developers!
I get the following error ValueError(f"Expected {n_expected} points but found {n_mapped}” in amset deform read module after running amset deform read command. I've tried different k-point sets as well as generation of deformations without using symmetry but nothing of this helped. It is interesting that the issue does not occur for another system for which I tried AMSET. I saw this thread regarding the issue but no solution was posted. Please fix this bug or let me know if I can try some different settings to overcome it. I can provide any additional information regarding my calculations, if necessary.

Best regards,
Anton

It would be nice to have a way to run AMSET from the command line.

This should be in the form of a script that takes a vasprun as input and optional arguments should as dielectric constants etc.

The script should write the model_params to a dict so that users can just reload them for future runs.

If an amsetrun.json is provided as input then amset should be loaded without being run.

Also is proprietary since 4/21/2022. It could be an optional dependency? See.

Dear Developer,

Thank you for this wonderful code.

After upgrading the amset to recent release (0.3.1) I get the following error in deformation potential extraction step (amset deform read). The older version worked fine for the same system.

Traceback (most recent call last):
File "/home/alex/.local/bin/amset", line 8, in
sys.exit(cli())
File "/home/alex/.local/lib/python3.6/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/home/alex/.local/lib/python3.6/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/alex/.local/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/alex/.local/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/alex/.local/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/alex/.local/lib/python3.6/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/home/alex/.local/lib/python3.6/site-packages/amset/tools/deformation.py", line 188, in read
if "bands" in kwargs and kwargs["ibands"] is not None:
KeyError: 'ibands'

Any insights will be helpful.

One more on related noted: (This is not tested on recent version- as for me deform read step does not work)

When I try to extract deformation for a 2D materials- if I use say n x n x 1 k-grid, the "amset deform read" throws out an error. It only works if I use finite kpoints along z direction such as n x n x 2 k-grid. Not sure why there need to be finite k-mesh in all three directions.

Any thoughts on these will be helpful.

Best,
Alex kent

Any plans to add a fireworks workflow for running AMSET through atomate?

Simon Mellaerts on MatSci.org asks:

Is there an easy way to obtain .dat/.txt files when using “amset plot xxx.json”, in addition to obtain the pdf/png file? In a similar way, as one can use the ‘–gnuplot’ tag in phonopy?

As a suggestion, from someone who was briefly confused: the documentation at https://github.com/hackingmaterials/amset/blob/main/docs/src/using.md has a call-out box containing this:

Obtaining best performance

To obtain the best performance, it is recommended to run export OMP_NUM_THREADS=1 before running AMSET.

It wasn't clear to me whether this meant I would simply be running AMSET in serial by doing so until I searched the Discourse and found the nworkers setting. I think it might be worth clarifying that there, possibly with something like:

Obtaining best performance

To obtain the best performance, it is recommended to run export OMP_NUM_THREADS=1 before running AMSET.
Use the nworkers setting in the settings file if you want to run AMSET using multiple cores.

Installing AMSET through Conda downgrades lots of packages, is there any plan to update the AMSET hosted in conda?

Currently the dislocation directions defaults to the c lattice direction.

This should be controllable via an option.

I had an additional question for which I opened a new issue such that other new users can easily find the information needed.

I played a bit with the performance settings (energy_cutoff, fd_tol, dos_estep, symprec) and found quite some changes in the resulting mobility. Is it in general correct to minimize/maximize these values to increase the accuracy of the calculations or are there some inconsistencies for minimizing/maximizing these settings?

• energy_cutoff: maximize
• fd_tol: minimize
• dos_estep: minimize
• symprec: minimize

In addition is there some preference in minimizing/maximizing one of these settings?

Getting an odd error from pip install amset on M1 MacBook Pro. Anyone seen this before?

ERROR: Could not build wheels for numpy, which is required to install pyproject.toml-based projects
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

mpy_e28db8833d8c4d28b325d122e2851bbe/numpy/_build_utils/src/apple_sgemv_fix.c
            clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
            clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
            clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
            clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
            clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
            clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
            clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
            clang: error: the clang compiler does not support 'faltivec', please use -maltivec and include altivec.h explicitly
            error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -DNPY_INTERNAL_BUILD=1 -DHAVE_NPY_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-12-arm64-3.10/numpy/core/src/umath -Ibuild/src.macosx-12-arm64-3.10/numpy/core/src/npymath -Ibuild/src.macosx-12-arm64-3.10/numpy/core/src/common -Inumpy/core/include -Ibuild/src.macosx-12-arm64-3.10/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/Users/janosh/.venv/py310/include -I/opt/homebrew/Cellar/[email protected]/3.10.2/Frameworks/Python.framework/Versions/3.10/include/python3.10 -Ibuild/src.macosx-12-arm64-3.10/numpy/core/src/common -Ibuild/src.macosx-12-arm64-3.10/numpy/core/src/npymath -c numpy/core/src/multiarray/alloc.c -o build/temp.macosx-12-arm64-3.10/numpy/core/src/multiarray/alloc.o -MMD -MF build/temp.macosx-12-arm64-3.10/numpy/core/src/multiarray/alloc.o.d -faltivec -I/System/Library/Frameworks/vecLib.framework/Headers" failed with exit status 1
            [end of output]
      
        note: This error originates from a subprocess, and is likely not a problem with pip.
        ERROR: Failed building wheel for numpy
      Failed to build numpy
      ERROR: Could not build wheels for numpy, which is required to install pyproject.toml-based projects
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install backend dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Output AMSET.txt
HSE_DOS.txt

Dear,

To become familiar with AMSET, I tried to re-do the example of Si that is provided with the code, with the only difference that I did the band structure calculation myself. In the attached file you can find my VASP input file that I used, I performed a hybrid functional calculation with spin-orbit coupling taken into account. However, I obtain an error which I tried to trace back in the code but I was not able to find the issue. You can find my output of the amset run in the attached file. For the settings file I simply used the same file as of the Si example with only minor changes for the input values. I hope you can help me out. Thank you in advance for your help.

Kind regards,
Simon

Dear Developers,

In the PRB 2015 paper, the anisotropic dependence is averaged. I just wonder whether the new version of amset can be used to calculate anisotropic mobilities?Thank you!

Hao Zhang

The __main__ method of core.py should be removed and possibly refactored into a script or integration test.

Use of the BoltztrapRunner without the SOC option means SOC won't work currently.

Get a basic version of the documentation up and running.

We can use sphinx-apidoc to automatically generate documentation for the api based on docstrings.

This should probably wait until after we have done some of the refactoring mentioned in #38.

Dear amset users,

How to fix the TypeError like below. Thank you!

[root@admin GaAs]# python GaAs.py
/public/software/anaconda3/lib/python3.6/site-packages/pymatgen/io/vasp/outputs.py:886: UserWarning: No POTCAR file with matching TITEL fields was found in /public/src/phys/amset/test_files/GaAs_mp-2534
" was found in {}".format(os.path.abspath(p)))
2019-06-05 19:23:24 INFO bs_is_isotropic: True
2019-06-05 19:23:24 DEBUG n-Ecut: 0.258519909 eV

2019-06-05 19:23:24 DEBUG p-Ecut: 0.17234660599999999 eV

Traceback (most recent call last):
File "GaAs.py", line 41, in
temperatures=[300, 600],
File "/public/software/anaconda3/lib/python3.6/site-packages/amset-0.1.0-py3.6.egg/amset/core.py", line 326, in from_vasprun
return Amset(band_structure, num_electrons, material_params, **kwargs)
File "/public/software/anaconda3/lib/python3.6/site-packages/amset-0.1.0-py3.6.egg/amset/core.py", line 263, in init
interpolation_type=interpolation)
File "/public/software/anaconda3/lib/python3.6/site-packages/amset-0.1.0-py3.6.egg/amset/interpolate/init.py", line 52, in get_interpolater
return BoltzTraP2Interpolater(band_structure, num_electrons)
File "/public/software/anaconda3/lib/python3.6/site-packages/amset-0.1.0-py3.6.egg/amset/interpolate/boltztrap2.py", line 40, in init
band_structure, num_electrons, **kwargs)
File "/public/software/anaconda3/lib/python3.6/site-packages/amset-0.1.0-py3.6.egg/amset/interpolate/base.py", line 47, in init
self.initialize()
File "/public/software/anaconda3/lib/python3.6/site-packages/amset-0.1.0-py3.6.egg/amset/interpolate/boltztrap2.py", line 53, in initialize
magmom=None)
TypeError: get_equivalences() got an unexpected keyword argument 'magmom'

Dear Developers,

According to the manual, the value of elastic_constant is obtained by averaging the direction-dependent elastic constant. Do you calculate this parameter by averaging the TOTAL_ELASTIC_MODULI generating by VASP when setting "IBRION=6"? If this value is calculated by averaging, how to obtain the anisotropic mobility?Thank you!

Hao Zhang

Please submit help issues to: https://matsci.org/c/amset

GitHub issues is no longer used except for development purposes.
Dear Developers,
Is amset suitable for 2D materials, in which vaccum is considered along the c-direction?

Dear Developers,

I have installed the new version of amset, but I met errors when running Si and GaAs examples. I have listed the error messages here. Could you please tell me how to fix this problem? Thank you!

Hao

------------------GaAs: It ran to the end, but error messages appeared.---------------

 Timing and memory usage:
   ├── interpolation time: 98.3702 s
   ├── dos time: 14.5644 s
   ├── scattering time: 7.0594 s
   ├── transport time: 173.0009 s
   ├── writing time: 0.0019 s
   ├── total time: 293.1251 s
   └── max memory: 6108.3 MB

 amset exiting on 29 May 2020 at 07:57


   ERROR: amset exiting on 29 May 2020 at 07:57
 Traceback (most recent call last):
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/matplotlib/style/core.py", line 114, in use
     rc = rc_params_from_file(style, use_default_template=False)
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/matplotlib/__init__.py", line 984, in rc_params_from_file
     config_from_file = _rc_params_in_file(fname, fail_on_error)
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/matplotlib/__init__.py", line 914, in _rc_params_in_file
     with _open_file_or_url(fname) as fd:
   File "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/cont
 extlib.py", line 113, in __enter__
     return next(self.gen)
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/matplotlib/__init__.py", line 900, in _open_file_or_url
     with open(fname, encoding=encoding) as f:
 FileNotFoundError: [Errno 2] No such file or directory:
 '/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/amset/plot/amset_base.mplstyle'

 During handling of the above exception, another exception occurred:

 Traceback (most recent call last):
   File "GaAs.py", line 32, in <module>
     plt = plotter.get_plot()
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/sumo/plotting/__init__.py", line 60, in wrapper
     matplotlib.pyplot.style.use(list_style)
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/matplotlib/style/core.py", line 117, in use
     raise IOError(
 OSError:
 '/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/amset/plot/amset_base.mplstyle' not found in the style
 library and input is not a valid URL or path; see `style.available`
  for list of available styles




------------------------------Si: It failed at the step of calculating transport.----------------------
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TRANSPORT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 Calculating conductivity, Seebeck, and electronic thermal
 conductivity


   ERROR: amset exiting on 29 May 2020 at 07:47
 Traceback (most recent call last):
   File "Si.py", line 28, in <module>
     amset_data = runner.run()
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/amset/core/run.py", line 68, in run
     mem_usage, (amset_data, usage_stats) = memory_usage(
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/memory_profiler.py", line 343, in memory_usage
     returned = f(*args, **kw)
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/amset/core/run.py", line 123, in _run_wrapper
     amset_data, transport_time = self._do_transport(amset_data)
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/amset/core/run.py", line 206, in _do_transport
     transport_properties = solve_boltzman_transport_equation(
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/amset/core/transport.py", line 38, in
 solve_boltzman_transport_equation
     sigma, seebeck, kappa = _calculate_transport_properties(
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/amset/core/transport.py", line 189, in
 _calculate_transport_properties
     sigma[n, t], seebeck[n, t], kappa[n, t], _ =
 calc_Onsager_coefficients(
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/BoltzTraP2/bandlib.py", line 492, in
 calc_Onsager_coefficients
     pL11 = np.linalg.pinv(L11[iT, imu])
   File "<__array_function__ internals>", line 5, in pinv
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/numpy/linalg/linalg.py", line 1961, in pinv
     u, s, vt = svd(a, full_matrices=False, hermitian=hermitian)
   File "<__array_function__ internals>", line 5, in svd
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/numpy/linalg/linalg.py", line 1626, in svd
     u, s, vh = gufunc(a, signature=signature, extobj=extobj)
   File
 "/public/home/hao/.conda/envs/my_pymatgen/lib/python3.8/site-
 packages/numpy/linalg/linalg.py", line 106, in
 _raise_linalgerror_svd_nonconvergence
     raise LinAlgError("SVD did not converge")
 numpy.linalg.LinAlgError: SVD did not converge

Dear developer,

I recently met an error when trying to calculate the relaxation time of SnS compound. I have attached my amset.log and my setting.yaml. It seems that error happens when the code is trying to calculate the band overlap. But I didn't use any tags related to SOC or spin polarization in my INCAR. Hope you can tell me where it goes wrong. Thank you very much!

Best,
Zhi

settings.yaml.txt
amset.log

When we try to repeat the example of PbTe, the calculated low-frequency dielectric constant (epsilon_s) using vasp is 26 rather than the 44 value in the example. Besides, we want to know how to get the epsilon_inf and W_POP value. Thank you.