pyiron | integrated development environment

by pyiron Jupyter Notebook Version: 0.5.2 License: BSD-3-Clause

X-Ray Key Features Code Snippets Community Discussions(7)Vulnerabilities Install Support

kandi X-RAY | pyiron Summary

pyiron is a Jupyter Notebook library typically used in Simulation applications. pyiron has no bugs, it has no vulnerabilities, it has a Permissive License and it has high support. You can download it from GitHub.

pyiron - an integrated development environment (IDE) for computational materials science.

Support

Quality

Security

License

Reuse

Support

pyiron has a highly active ecosystem.

It has 283 star(s) with 40 fork(s). There are 15 watchers for this library.

There were 1 major release(s) in the last 12 months.

There are 0 open issues and 328 have been closed. On average issues are closed in 43 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of pyiron is 0.5.2

Quality

pyiron has 0 bugs and 0 code smells.

Security

pyiron has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

pyiron code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

pyiron is licensed under the BSD-3-Clause License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

pyiron releases are available to install and integrate.

pyiron saves you 740 person hours of effort in developing the same functionality from scratch.

It has 1712 lines of code, 53 functions and 6 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed pyiron and discovered the below as its top functions. This is intended to give you an instant insight into pyiron implemented functionality, and help decide if they suit your requirements.

Return a dict containing the command - line arguments
Extract version information from VCS
Get the project root directory
Create a ConfigParser from a root
Create the versioneer config file
Install a versioneer package
Get the list of installed versions
Scans the setup py and returns a boolean indicating if it is missing
Update the dependencies
Update dependencies

Get all kandi verified functions for this library.

pyiron Key Features

No Key Features are available at this moment for pyiron.

pyiron Examples and Code Snippets

No Code Snippets are available at this moment for pyiron.

Community Discussions

Trending Discussions on pyiron

Spin constraining in PyIron+Sphinx

How to use masking with structures to modify only selected atoms?

How to choose the mesh for phonon calculation with PyIron

TypeError--using slurm queue to submit pyiron jobs

Setting environment variables before the execution of the pyiron wrapper on remote cluster

User defined job type not available during calculation via SLURM

Is there a way to store data in hdf5 file in ScriptJob in pyiron?

QUESTION

Spin constraining in PyIron+Sphinx

Asked 2021-May-26 at 15:19

I want to constrain the spin of the bulk atoms while letting the free surface atoms of my supercell relax their magnetic moment. Is it possible in PyIron+SPhinx to constrain the spin of a subset of atoms (not all of them) in the supercell?

...

ANSWER

Answered 2021-May-26 at 15:19

Yes in principle it is possible:

Source https://stackoverflow.com/questions/67707478

QUESTION

How to use masking with structures to modify only selected atoms?

Asked 2021-May-12 at 11:48

I want to modify the position of atoms that fulfil a specific condition.

Currently, I can apply translation to all atoms or one atom but not multiple selected atoms.

...

ANSWER

Answered 2021-May-12 at 11:48

This one should work:

Source https://stackoverflow.com/questions/67501812

QUESTION

How to choose the mesh for phonon calculation with PyIron

Asked 2021-Jan-28 at 23:35

I would like to calculate phonon density of states and band structure with pyiron, using the phononpy package. I created a job, following the tutorial:

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ANSWER

Answered 2021-Jan-28 at 23:35

You can specify the input in:

Source https://stackoverflow.com/questions/65941881

QUESTION

TypeError--using slurm queue to submit pyiron jobs

Asked 2020-Nov-23 at 14:37

I'm facing some issues while running pyiron jobs on my HPC via the pysqa adapter. I had accidentally erased the main pyiron directory containing pyiron, projects and resources folders. I had copied all the three from another cluster. The only thing that I think will cause problem is sqlite.db file in the resources folder. Previously, I had no issues running interactive VASP jobs through the adapter. I'm guessing something happened after the deletion incident.

The pyiron version I'm using is: 0.2.17

Here is a minimal example using an Interactive vasp job that I have tried:

...

ANSWER

Answered 2020-Nov-23 at 14:37

We updated the queuing system interface in pyiron 0.3.X you can read more about this here: https://pyiron.org/news/releases/2020/09/06/pyiron-0-3-X-HPC-release.html

For pyiron 0.3.X we have a detailed installation guide available on readthedocs.org: https://pyiron.readthedocs.io/en/latest/source/installation.html#remote-hpc-cluster

So I highly recommend updating to pyiron 0.3.13.

Apart from this the error message basically says that the submission was not successful. If you navigate to the jobs working directory job.working_directory you should find a run_queue.sh script in the working directory. This is the script pyiron is using to submit the job to the queuing system. You can try to submit it manually using sbatch run_queue.sh this should print the queue id if successful and otherwise the error message from your queuing system.

Source https://stackoverflow.com/questions/64967185

QUESTION

Setting environment variables before the execution of the pyiron wrapper on remote cluster

Asked 2020-Oct-20 at 10:30

I use a jobfile for SLURM in ~/pyiron/resources/queues/, which looks roughly like this:

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ANSWER

Answered 2020-Oct-20 at 10:30

To explain the example in a bit more detail:

I create a notebook named: reading.ipynb with the following content:

Source https://stackoverflow.com/questions/64440651

QUESTION

User defined job type not available during calculation via SLURM

Asked 2020-Oct-12 at 19:44

I am trying to setup a pyiron calculation (version 0.3.6.). I want to execute a non-python script on a computer cluster via SLURM. I have written an own OwnProgramJob class, which inherits from the GenericJob class. Everything is running smoothly on my local computer. When running on the cluster, however, my own class is not available in pyiron:

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ANSWER

Answered 2020-Oct-12 at 19:44

For the job class to be available when submitting to the queuing system it is necessary that it is included in the python path. So I suggest splitting the class definition in a separate python module named ownprogramjob.py:

Source https://stackoverflow.com/questions/64322699

QUESTION

Is there a way to store data in hdf5 file in ScriptJob in pyiron?

Asked 2020-Sep-30 at 12:21

I have my own Monte Carlo code (which is not part of pyiron), which I launch via ScriptJob in pyiron. Currently, I store the output data in a file, but since the script job is a pyiron object and an hdf5 is created, I would love to store the data there. So, I'd love to have something like:

...

ANSWER

Answered 2020-Sep-30 at 12:21

You can summarise your output in a dictionary named output_dict and then use:

Source https://stackoverflow.com/questions/64136671

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install pyiron

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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