Failed to run Command line interface tutorial.
#319
Comments
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Hi @hongyi-zhao , Thanks for raising this issue. I have fixed the tutorial snippet now in the docs. Somehow I overlooked to update the commands in the CLI tutorials. Sorry for the inconvenience. The correct command to get description is Command to get calculation quality description would be There are shorthand notations for acceptable arguments as well, which should be accessible from --help for each of this commands
And regarding the failing It worked fine for me in here. |
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Still failed, as shown below: |
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Ops I see, just pushing a fix in few minutes. |
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Hi @hongyi-zhao , the issue with exception should also be fixed via PR #321 . I am not able to reproduce the error you encounter for "lobsterpy description --file-json description.json", even with latest pymatgen version. Can you try to run the same command on any of the example lobster calculation files provided on the repo? |
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Hi @hongyi-zhao , I suspect you are now using LOBSTER 5.1 ? In this case, pymatgen needs to be updated to deal with ICOHP/ ICOBI / ICOOP files as I see in the changelog of 5.1.0, these file outputs have been updated.
I would suggest try using LOBSTER 5.0 or lower. As adding support to 5.1 might take time if output file format is changed, parsers need to be updated and I do not know, how much of a change it is at this point. Will try to have a look at them soon. Also, currently not all features of LOBSTER 5.0 is supported via pymatgen/lobsterpy. See #170, this is on our todo. We will then add 5.1.0 support when working on it. |
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@hongyi-zhao If you need it now, you are surely also invited to fix the input/output methods in pymatgen. We will try to get it done after the summer, likely. |
Yes. werner@x13dai-t:~$ lobster
LOBSTER v5.1.0 (g++ 9.3.0)
Copyright (C) 2024 by Chair of Solid-State and Quantum Chemistry, RWTH Aachen.
All rights reserved. Contributions by S. Maintz, V. L. Deringer, M. Esser, R. Nelson, C. Ertural, P. C. Mueller, M. Pauls, L. Sann, D. Schnieders, A. L. Tchougreeff, and R. Dronskowski
starting on host x13dai-t on 2024-07-31 at 15:12:19 CST using 96 threads
detecting used PAW program...
ERROR: could not determine which program was used for the quantum-chemical calculation.
ERROR: Make sure all required files are in the working directory and are not empty.
I wonder if there is a more elegant way to implement the interface to minimize the heavy workload caused by changes in the original program version. |
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So far, I've successfully run most of the commands shown in the tutorial. However, there are still some issues as follows:
(datasci) werner@x13dai-t:~/Public/repo/github.com/JaGeo/Create_inputs_example/Basis_0$ lobsterpy description --file-json description.json
/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/spglib/spglib.py:115: DeprecationWarning: dict interface (SpglibDataset['equivalent_atoms']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead
warnings.warn(
/home/werner/.pyenv/versions/3.11.1/envs/datasci/lib/python3.11/site-packages/spglib/spglib.py:115: DeprecationWarning: dict interface (SpglibDataset['international']) is deprecated.Use attribute interface ({self.__class__.__name__}.{key}) instead
warnings.warn(
/home/werner/Public/repo/github.com/JaGeo/LobsterPy.git/src/lobsterpy/cohp/analyze.py:870: UserWarning: The bonding, antibonding integral/percent values are numerical estimate. These values are sensitive to COHPstartEnergy parameter. If COHPstartEnergy value does not cover entire range of VASP calculations then absolute value of ICOHP_sum might not be equivalent to (bonding- antibonding) integral values.
) = self._integrate_antbdstates_below_efermi(cohp, start=self.start)
The compound CdF2 has 1 symmetry-independent cation(s) with relevant cation-anion interactions: Cd1.
Cd1 has a cubic (CN=8) coordination environment. It has 8 Cd-F (mean ICOHP: -0.62 eV, 27.743 percent antibonding interaction below EFermi) bonds.
(datasci) werner@x13dai-t:~/Public/repo/github.com/JaGeo/Create_inputs_example/Basis_0$ jq < description.json
{
"formula": "CdF2",
"max_considered_bond_length": 5.98538,
"limit_icohp": [
-1.7976931348623157e+308,
-0.062174
],
"number_of_considered_ions": 1,
"sites": {
"0": {
"env": "C:8",
"bonds": {
"F": {
"ICOHP_mean": "-0.62",
"ICOHP_sum": "-4.97",
"has_antibdg_states_below_Efermi": true,
"number_of_bonds": 8,
"bonding": {
"integral": 8.1,
"perc": 0.72257
},
"antibonding": {
"integral": 3.11,
"perc": 0.27743
}
}
},
"ion": "Cd",
"charge": 1.57,
"relevant_bonds": [
"29",
"30",
"33",
"40",
"53",
"60",
"63",
"64"
]
}
},
"type_charges": "Mulliken"
}
(datasci) werner@x13dai-t:~/Public/repo/github.com/JaGeo/Create_inputs_example/Basis_0$ lobsterpy description-quality --potcar-symbols "Na_pv Cl" --bvacomp --doscomp --file-calc-quality-json calc_quality_description.json
/home/werner/Public/repo/github.com/materialsproject/pymatgen.git/src/pymatgen/io/vasp/outputs.py:160: UserWarning: Float overflow (*******) encountered in vasprun
warnings.warn("Float overflow (*******) encountered in vasprun")
/home/werner/Public/repo/github.com/JaGeo/LobsterPy.git/src/lobsterpy/cli.py:1085: UserWarning: Consider using DOSCAR.LSO.lobster, as non LSO DOS from LOBSTER can have negative DOS values
quality_dict = Analysis.get_lobster_calc_quality_summary(
/home/werner/Public/repo/github.com/JaGeo/LobsterPy.git/src/lobsterpy/cli.py:1085: UserWarning: Input DOS files have very few points in the energy interval and thus comparisons will not be reliable. Please rerun the calculations with higher number of DOS points. Set NEDOS and COHPSteps tags to >= 2000 in VASP and LOBSTER calculations, respectively.
quality_dict = Analysis.get_lobster_calc_quality_summary(
The LOBSTER calculation used minimal basis. The absolute and total charge spilling for the calculation is 0.65 and 0.0 %, respectively. The projected wave function is completely orthonormalized as no bandOverlaps.lobster file is generated during the LOBSTER run. The atomic charge signs from Mulliken population analysis agree with the bond valence analysis. The atomic charge signs from Loewdin population analysis agree with the bond valence analysis. The Tanimoto index from DOS comparisons in the energy range between -5, 0 eV for s, d, p, summed orbitals are: 0.7137, 0.6449, 0.3208, 0.4766.
(datasci) werner@x13dai-t:~/Public/repo/github.com/JaGeo/Create_inputs_example/Basis_0$ jq < calc_quality_description.json
{
"minimal_basis": true,
"charge_spilling": {
"abs_charge_spilling": 0.65,
"abs_total_spilling": 0
},
"band_overlaps_analysis": {
"file_exists": false,
"limit_maxDeviation": null,
"has_good_quality_maxDeviation": true,
"max_deviation": null,
"percent_kpoints_abv_limit": null
},
"charge_comparisons": {
"bva_mulliken_agree": true,
"bva_loewdin_agree": true
},
"dos_comparisons": {
"tanimoto_orb_s": 0.7137,
"tanimoto_orb_d": 0.6449,
"tanimoto_orb_p": 0.3208,
"tanimoto_summed": 0.4766,
"e_range": [
-5,
0
],
"n_bins": 56
}
}
The lobster version to do the above test is shown below: $ module list
Currently Loaded Modules:
1) lmod 2) lobster/5.0.0 |
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@hongyi-zhao thank you for reporting this to us. I hope we can check it out soon. |
I try to run the Command line interface tutorial step-by-step according to the document. But failed at the following steps:
Do you have any tips and hints for fixing these problems?
Regards,
Zhao
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