Issues with input generation

[David Guzman]

Hello,

I am not new to pyCDT, but I just installed the newer version running with pymatgen_2020.4.2. The variables in pmgrc.yaml are set, PMG_VASP_PSP_DIR and PMG_MAPI_KEY. But I still can's generate inputs.

Usually, I would run: pycdt generate_input -s POSCAR

In  this case I get:

(pymatgen_2020) davgumo@davgumo-XPS-13-9380:~/Desktop/Erato/VASP/pyCDT/Si/test$ pycdt generate_input -s POSCAR

/home/davgumo/miniconda3/envs/pymatgen_2020/lib/python3.8/site-packages/pycdt-2.0.3-py3.8.egg/pycdt/core/defects_analyzer.py:88: DeprecationWarning: Replaced PyCDT usage of ComputedDefect objects with DefectEntry objects from pymatgen.analysis.defects.core

Will remove ComputedDefect with Version 2.5 of PyCDT.

  warnings.warn("Replaced PyCDT usage of ComputedDefect objects with "

/home/davgumo/miniconda3/envs/pymatgen_2020/lib/python3.8/site-packages/pycdt-2.0.3-py3.8.egg/pycdt/core/defects_analyzer.py:162: DeprecationWarning: Replaced PyCDT usage of DefectsAnalyzer objects with DefectPhaseDiagram objects from pymatgen.analysis.defects.thermodynamics

Will remove DefectsAnalyzer with Version 2.5 of PyCDT.

  warnings.warn("Replaced PyCDT usage of DefectsAnalyzer objects with "

/home/davgumo/miniconda3/envs/pymatgen_2020/lib/python3.8/site-packages/pymatgen/io/vasp/sets.py:419: DeprecationWarning: 'potcar_functional' argument is deprecated. Use 'user_potcar_functional' instead.

  warnings.warn(

PyCDT is a script that generates vasp input files, parses vasp output files, and computes the formation energy of charged defects.

This script works based on several sub-commands with their own options. To see the options for sub-commands, type: pycdt -h

Is there anything different I should do?

Thanks for your help,

David Guzman

Brookhaven National Laboratory

[Shivani Srivastava]

Hi David,

I tried the same command with a new installation (pymatgen and pycdt) and it worked for an example POSCAR. Can you share the POSCAR you are using?

Best,

Shivani Srivastava

UC Berkeley

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[Naoki Sato]

Dear PyCDT developers,

I have the same problem regarding a generation of inputs.

I am using PyCDT-2.0.4 and  pymatgen-2020.6.8, and when I ran "pycdt generate_input -s POSCAR", I got no output file and following messages:

/home/nsato/downloads/anaconda3/envs/pycdt/lib/python3.8/site-packages/pycdt-2.0.4-py3.8.egg/pycdt/core/defects_analyzer.py:88: DeprecationWarning: Replaced PyCDT usage of ComputedDefect objects with DefectEntry objects from pymatgen.analysis.defects.core

Will remove ComputedDefect with Version 2.5 of PyCDT.

  warnings.warn("Replaced PyCDT usage of ComputedDefect objects with "

/home/nsato/downloads/anaconda3/envs/pycdt/lib/python3.8/site-packages/pycdt-2.0.4-py3.8.egg/pycdt/core/defects_analyzer.py:162: DeprecationWarning: Replaced PyCDT usage of DefectsAnalyzer objects with DefectPhaseDiagram objects from pymatgen.analysis.defects.thermodynamics

Will remove DefectsAnalyzer with Version 2.5 of PyCDT.

  warnings.warn("Replaced PyCDT usage of DefectsAnalyzer objects with "

/home/nsato/downloads/anaconda3/envs/pycdt/lib/python3.8/site-packages/pymatgen/io/vasp/sets.py:419: DeprecationWarning: 'potcar_functional' argument is deprecated. Use 'user_potcar_functional' instead.

  warnings.warn(

PyCDT is a script that generates vasp input files, parses vasp output files, and computes the formation energy of charged defects.

I guess my setting of ~/.pmgrc.yaml is correct because I can obtain a proper POTCAR file when I run "pmg potcar --symbols hoge hoge --functional PBE".

Could you please suggest anything I overlook?

Best regards,

Naoki Sato

NIMS

2020年4月19日日曜日 9時25分50秒 UTC+9 David Guzman:

[Naoki Sato]

Sorry, my POSCAR is below:

Generated by cif2cell 1.2.10 from ICSD r

   1.00000000000000

     4.5982377240540950    0.0000000000000000    0.0000000000000000

    -2.2991188620270426    3.9821906816707817    0.0000000000000000

     0.0000000000000000    0.0000000000000000    7.2730209110748580

   Sb   Mg

     2     3

Direct

  0.3333333333333286  0.6666666666666572  0.7746354705186861

  0.6666666666666572  0.3333333333333286  0.2253645294812997

 -0.0000000000000000 -0.0000000000000000 -0.0000000000000000

  0.3333333333333286  0.6666666666666572  0.3679578413824706

  0.6666666666666572  0.3333333333333286  0.6320421586175152

But, I get the same messages even when I use --mpid option.

Best regards,

Naoki Sato

NIMS

2020年6月26日金曜日 17時23分40秒 UTC+9 Naoki Sato:

[Shivani Srivastava]

Hi Naoki,

I just tested this POSCAR with the latest versions of PyCDT and pymatgen and was able to generate the input files. Can you try with these and see if it works.

Best,

Shivani Srivastava

Graduate Student Researcher

MSE, UC Berkeley

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[Naoki Sato]

Hi  Shivani,

Thank you for your prompt reply.

I re-installed the latest versions and tried again, but the result was completely the same.

Do you have any other suggestions regarding other prerequisites for pycdt?

Anyway, I will try to use it as a python module.

Best regards,

Naoki Sato

NIMS

2020年6月26日金曜日 21:04:10 UTC+9 shiv...@berkeley.edu:

[Naoki Sato]

Hi  Shivani, 

I have noticed my PATH to the older version was remained.

After correcting PATH, the generate_input works properly.

Thank you!

Best regards,

Naoki Sato

NIMS

2020年6月30日火曜日 10:00:44 UTC+9 Naoki Sato:

[David Guzman]

Hi,

I keep getting the same issues with any of the of newer versions I’ve tried. It’s not enough for the developers to just try to reproduce the problem with their installation because there is clearly a gap between their installation instructions on the website and what really needs to be done to get the code to work. There’s something missing there. 

Regards,

David Guzman

Brookhaven National Laboratory

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[David Guzman]

Hello,

New instructions work like a charm,

Thank you!

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[Bharat Medasani]

Glad it worked for you. 

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Bharat Medasani

Engineer

Princeton Plasma Physics Lab (PPPL)