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PyCDT (python charged defects toolkit) is a open-source Python library for expediting density functional calculations for point defects in semiconductors and insulators. These are some of the main features:

Sets up calculations of vacancies, interstitials, substitutional, and .antisite defects.
Supports VASP (http://cms.mpi.univie.ac.at/vasp/) input generation and output parsing
Corrections tools to finite size electrostatic errors in isotropic and anisotropic crystals.

The purpose of this group is to provide a forum to discuss usage, bugs, and features.

0 selected

Ziqi Cui, Bharat Medasani11

2/21/24

Installation issue

Hi Bharat, Here's my CONTCAR file. And the command I use is: pycdt generate_input --

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Installation issue

Hi Bharat, Here's my CONTCAR file. And the command I use is: pycdt generate_input --

2/21/24

2/16/24

Index error and work flow questions

Dear all, I've just started to use PyCDT to calculate the correction term for my charged defect

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Index error and work flow questions

Dear all, I've just started to use PyCDT to calculate the correction term for my charged defect

2/16/24

3/28/23

calculate corrections from locpot files' paths

Hi, I have a question, is it possible to calculate the fnv corrections quickly using pycdt by

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calculate corrections from locpot files' paths

Hi, I have a question, is it possible to calculate the fnv corrections quickly using pycdt by

3/28/23

elham....@gmail.com

10/28/22

How to use PyCDT for a slab

Hello every body! Is it possible to make surface defects in a slab by using PyCDT code? I just tested

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How to use PyCDT for a slab

Hello every body! Is it possible to make surface defects in a slab by using PyCDT code? I just tested

10/28/22

5/25/22

Issue computing chemical potentials

Hello, I am following the steps in Supplementary Information 1 and the example notebook to calculate

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Issue computing chemical potentials

Hello, I am following the steps in Supplementary Information 1 and the example notebook to calculate

5/25/22

Sonu Singh, … Nigel Hew9

5/7/22

Details about PyCDT original paper

Thanks for the clarification. On Friday, May 6, 2022 at 8:15:09 PM UTC+8 PyCDT forum wrote: On

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Details about PyCDT original paper

Thanks for the clarification. On Friday, May 6, 2022 at 8:15:09 PM UTC+8 PyCDT forum wrote: On

5/7/22

Swarnadip Mukherjee, PyCDT forum2

3/2/22

parsing output error

It's very hard to specify the issue with such little data On Wednesday, February 23, 2022 at 10:

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parsing output error

It's very hard to specify the issue with such little data On Wednesday, February 23, 2022 at 10:

3/2/22

张瑞, PyCDT forum5

2/24/22

Where could I change the plot code?

I have just figured that the plotter.py was not used in pycdt script. May I know how could I use it

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Where could I change the plot code?

I have just figured that the plotter.py was not used in pycdt script. May I know how could I use it

2/24/22

Jayden김창훈, PyCDT forum2

2/23/22

I don't know what this error meaning

It is a warning message. No need to worry about it. On Saturday, February 19, 2022 at 7:14:15 AM UTC-

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I don't know what this error meaning

It is a warning message. No need to worry about it. On Saturday, February 19, 2022 at 7:14:15 AM UTC-

2/23/22

Daniel Wu, Steven Hartman4

1/10/22

Problem in PyCDT incar file

Hello， Another problem, when I run the example CdTe with my own POTCAR through two methods, the value

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Problem in PyCDT incar file

Hello， Another problem, when I run the example CdTe with my own POTCAR through two methods, the value

1/10/22

张瑞, PyCDT forum2

12/16/21

Could you please check the pymatgen installation? On Friday, November 12, 2021 at 7:43:35 AM UTC-5

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Could you please check the pymatgen installation? On Friday, November 12, 2021 at 7:43:35 AM UTC-5

12/16/21

ru li, … Bharat Medasani3

7/14/21

PyCDT generate_input vasp setting

You can override or supplement the default yaml file, by supplying the settings file as input to the

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PyCDT generate_input vasp setting

You can override or supplement the default yaml file, by supplying the settings file as input to the

7/14/21

Naveen Kumar, shiv...@berkeley.edu2

7/3/21

Problem in installing

PyCDT requires pymatgen to generate VASP inputs. You need to install pymatgen and update the path to

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Problem in installing

PyCDT requires pymatgen to generate VASP inputs. You need to install pymatgen and update the path to

7/3/21

Viridi Bang, Bharat Medasani2

7/2/21

Missing phase in the phase diagram

Yes, you can. However, this can not be done from the command line. You need to write your python

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Missing phase in the phase diagram

Yes, you can. However, this can not be done from the command line. You need to write your python

7/2/21

Viridi Bang, Bharat Medasani2

7/2/21

oxi_state and oxi_range

If I remember correctly, the --oxi_state flag has to be repeated for each case. So your command will

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oxi_state and oxi_range

If I remember correctly, the --oxi_state flag has to be repeated for each case. So your command will

7/2/21

ru li, PyCDT forum2

6/22/21

Original data and plot

defect_data.json and transistional_level.yaml do not contain the data used for plotting. You need to

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Original data and plot

defect_data.json and transistional_level.yaml do not contain the data used for plotting. You need to

6/22/21

ru li, Bharat Medasani2

6/7/21

pycdt start error

You need to supply additional arguments. Read the Comp Phys Comm paper on pycdt. It has instructions

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pycdt start error

You need to supply additional arguments. Read the Comp Phys Comm paper on pycdt. It has instructions

6/7/21

Hexige Wuliji, Bharat Medasani3

6/5/21

IndexError: list index out of range

First of all, hope this is not too late for you On Thursday, April 22, 2021 at 11:35:20 PM UTC-4 wlj.

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IndexError: list index out of range

First of all, hope this is not too late for you On Thursday, April 22, 2021 at 11:35:20 PM UTC-4 wlj.

6/5/21

김현우, PyCDT forum2

3/9/21

parse_output error

From the error message, looks like you did a full relaxation (ISIF=3) instead of constant volume

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parse_output error

From the error message, looks like you did a full relaxation (ISIF=3) instead of constant volume

3/9/21

mimo fad, PyCDT forum2

3/4/21

pycdt generate_input

Unfortunately you need VASP pseudopotentials to generate the charge dependent parameters in the input

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pycdt generate_input

Unfortunately you need VASP pseudopotentials to generate the charge dependent parameters in the input

3/4/21

Kang Lijing, PyCDT forum2

12/7/20

PyCDT compatibility with CASTEP

Dear Lijing, The core classes of pycdt are DFT code agnostic. The corrections code uses VASP LOCPOT

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PyCDT compatibility with CASTEP

Dear Lijing, The core classes of pycdt are DFT code agnostic. The corrections code uses VASP LOCPOT

12/7/20

Brian Leininger, Bharat Medasani2

12/7/20

Pseudo Directory and Generating Charged Defects Input Files

You may have to write your own script to generate the inputs for OCTOPUS. We can guide you to write

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Pseudo Directory and Generating Charged Defects Input Files

You may have to write your own script to generate the inputs for OCTOPUS. We can guide you to write

12/7/20

Shuaishuai Yuan, PyCDT forum3

11/13/20

the sign of the potential alignment term in the Freysoldt correction scheme.

Hi Danny, Thanks very much for the quick reply! It helps a lot! I just run a calculation of the GaAs

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the sign of the potential alignment term in the Freysoldt correction scheme.

Hi Danny, Thanks very much for the quick reply! It helps a lot! I just run a calculation of the GaAs

11/13/20

huya...@gmail.com, Bharat Medasani3

9/15/20

self prepared POSCAR

Hello, Here is the link of my calculation. https://drive.google.com/file/d/

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self prepared POSCAR

Hello, Here is the link of my calculation. https://drive.google.com/file/d/

9/15/20

conrad...@gmail.com, Bharat Medasani6

9/5/20

Defect complexes

Is there a plan to integrate machine learning into the pycdt workflow,? eg, high throughput screening

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Defect complexes

Is there a plan to integrate machine learning into the pycdt workflow,? eg, high throughput screening

9/5/20

NIU BO, … Bharat Medasani8

8/18/20

No creation of interstitials for h-BN

Greatly appreciate your help and suggestions! On Tuesday, 18 August 2020 at 00:55:28 UTC+8 mbk...@

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No creation of interstitials for h-BN

Greatly appreciate your help and suggestions! On Tuesday, 18 August 2020 at 00:55:28 UTC+8 mbk...@

8/18/20

Steven Hartman, Bharat Medasani2

8/3/20

DOS quality for finding the Fermi level

My suggestion is to go for high quality DOS obtained with either the primitive or the unit cell.

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DOS quality for finding the Fermi level

My suggestion is to go for high quality DOS obtained with either the primitive or the unit cell.

8/3/20

Brian Leininger, Bharat Medasani2

8/3/20

Generating Defect Input files via Python Script

Using command line script is better for your case. Please read the pycdt paper which details out to

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Generating Defect Input files via Python Script

Using command line script is better for your case. Please read the pycdt paper which details out to

8/3/20

Md. Anower Hossain, Bharat Medasani2

7/17/20

Availability of instruction manual

Please read the article on how to use pycdt. https://doi.org/10.1016/j.cpc.2018.01.004 On Fri, Jul 17

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Availability of instruction manual

Please read the article on how to use pycdt. https://doi.org/10.1016/j.cpc.2018.01.004 On Fri, Jul 17

7/17/20

David Guzman, … Bharat Medasani10

7/15/20

Issues with input generation

Glad it worked for you. On Wed, Jul 15, 2020 at 3:22 PM David Guzman <dav...@gmail.com> wrote:

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Issues with input generation

Glad it worked for you. On Wed, Jul 15, 2020 at 3:22 PM David Guzman <dav...@gmail.com> wrote:

7/15/20

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