cif2cell is not updated on conda-forge (it's only available for Python 2.7). It is up to date on pip at version 2.0.0a3. However, it's also not possible to pip install to build a conda-forge recipe.

Possible options to fix this are:

• Don't make cif2cell a strict dependency (make it optional) until it's updated on conda-forge. Good option if it's only a niche usage in Jarvis. Raise an error in jarvis where it's used and say that you need to install with pip install. Try to quarantine it's usage a bit so the import is only in the function where it's used.
• Contact the authors and ask them to update conda-forge recipe
• Remove its usage and look for alternatives.

See, conda-forge/staged-recipes#12896 (comment).

I think that it requires editing setup.py appropriately https://stackoverflow.com/questions/9977889/how-to-include-license-file-in-setup-py-script

ZrTe5 shows as rTe5, example: JVASP-86924

There is some problem with our existing code to generate wien2k k-path given a cif file, namely it gives some weird lines in the band plot. No problem in running and getting the energy eignevalues. This is due to sudden jump in the k-path that happens for certain lattice vectors. Simple cubics are fine.

Using pages.nist.gov would allow the site to use templates without requiring a backend app. Jekyll is very good for processing smalll/medium volume static data, which is currently an issue for the jarvis web site.

Make the dependencies in setup.py just the build time dependencies and not the run time dependencies. Try not to use == as this makes things difficult to install. Use requirements.txt to have the full set of dependencies.

CHGCAR gives error for JVASP-4798
UnboundLocalError: local variable 'found' referenced before assignment

• pylint
• flake8
• black

For phonon DOS , bandstructure etc.

When tests are run no files should be written to anywhere but temporary directories given by the OS. Furthermore all files in temporary directories should be removed.

setup.py lists the wrong license

https://www.ctcms.nist.gov/~knc6/static/JARVIS-DFT/JVASP-6187.xml

• Check orthorhombic cell has 90 degree angle
• https://github.com/usnistgov/jarvis/blob/497d2f76b4513b7151acb36e2ea4c162db8c2bfe/jarvis/analysis/structure/spacegroup.py

Apparently, it's not good pracitce to pin versions in setup.py, see https://packaging.python.org/discussions/install-requires-vs-requirements/.

It is not considered best practice to use install_requires to pin dependencies to specific versions, or to specify sub-dependencies (i.e. dependencies of your dependencies). This is overly-restrictive, and prevents the user from gaining the benefit of dependency upgrades.

git filter-branch --force --index-filter "git rm --cached --ignore-unmatch jarvis/examples/vasp/JVASP-1002_PBEBO/MAIN-MBJ-bulk@JVASP-1002/PROCAR"

• check that it works on linux
• check that it works on mac
• add README

Hi everyone.

I'm a newbie to using Jarvis.I have encountered some problems.I want to use this code to get the dielectric matrix.
https://github.com/usnistgov/jarvis/blob/master/jarvis/io/vasp/outputs.py
dielectric_loptics

When I use vasp.5.4.1 the code to extract the data works, but when I use vasp.5.4.4 an error occurs.

It shows :
Traceback (most recent call last):
real, imag = self.dielectric_loptics
File "/home/***/anaconda3/lib/python3.8/site-packages/jarvis/io/vasp/outputs.py", line 1130, in dielectric_loptics
tmp = self.ionic_steps[-1]["dielectricfunction"]["real"]["array"][
TypeError: list indices must be integers or slices, not str

Could anyone help me how I should solve this problem?
Thank you all!

Lin

The following files are written to the working directory when running the tests

jarvis/db/jdft_2d-4-26-2020.json
jarvis/db/jdft_3d-4-26-2020.json
jarvis/db/jff1.json
jarvis/db/jml_3d-4-26-2020.json
jarvis/examples/vasp/SiOptb88/CHGCAR

It might be better to write those to a temporary directory that's written and read from within a context manager so they are always deleted even if the test suite doesn't finish or something goes wrong. py.test and flask have things to help with that during testing.

Example on Travis CI: https://travis-ci.org/materialsinnovation/pymks/jobs/408609998#L1395

Example configuration: https://github.com/materialsinnovation/pymks/blob/develop/setup.cfg#L6

Enable testing of an installed version of jarvis.

>>> import jarvis
>>> jarvis.test()

That way you have some idea that javis is working beyond simply importing it without having to clone and run the tests.

PyMKS does this, see this. It basically invoked pytest inside the function.

Don't generate cruft when running the tests. Use /tmp for all files created during the tests and ensure that these files are removed. For example, the following are generated when running the tests:

jarvis/tests/POSCAR-Surf-1_0_0.vasp
jarvis/tests/POSCAR-Surf-1_1_0.vasp
jarvis/tests/POSCAR-Surf-1_1_1.vasp
jarvis/tests/POSCAR-bulk.vasp
jarvis/tests/POSCAR-cvn.vasp
jarvis/tests/POSCAR-vacancy_1_mult-1_sitespecie-Al.vasp

Use "with" statements to make sure these get deleted even in the event of failures.

from jarvis.core.atoms import Atoms
a=Atoms.from_poscar('POSCAR')
from jarvis.ai.descriptors.cfid import CFID
desc=CFID(a).get_comp_descp()

####################################Example POSCAR#########################################
P4O24C2N4H40
1.0
13.18 0.0 0.0
0.0 9.275 0.0
0.0 0.0 6.245
P H C N O
4 40 12 4 24
Cartesian
12.9448688 0.053887750000000005 1.4161162
6.825131199999995 9.221112250000001 4.5386162
6.354868800000005 4.583612250000001 4.828883800000001
0.235131200000001 4.69138775 1.7063838000000002
5.113839999999999 8.162 0.18110500000000015
4.085800000000006 8.10635 3.38479
2.6755399999999923 7.948675 2.4105700000000003
1.489339999999994 7.0861 4.47142
2.662359999999999 7.151025000000001 5.277025
1.9770000000000045 5.69485 5.139635
3.874920000000006 5.741225 3.80945
9.305079999999993 1.103725 5.558050000000001
13.166820000000001 2.6248250000000004 1.3239400000000001
0.3426799999999974 4.0068 3.615855
1.4761600000000012 1.113000000000001 3.303605
2.504199999999999 1.168649999999999 0.2622899999999999
3.914460000000002 1.3263250000000002 5.53307
5.10066 2.1889 1.3489200000000001
3.9276400000000007 2.123975000000001 2.154525
4.613000000000001 3.580150000000001 2.017135
2.7150799999999995 3.5337750000000003 0.68695
3.993539999999999 3.570875 6.05765
6.576820000000007 2.0126750000000007 4.921060000000001
6.932679999999997 0.6307000000000006 2.629145
8.066160000000002 3.5244999999999993 2.941395
9.094199999999994 3.468850000000001 5.98271
10.504460000000007 3.311175 0.71193
11.690660000000006 2.4486000000000003 4.89608
10.51764 2.513524999999999 4.0904750000000005
11.202999999999996 1.057349999999999 4.227865
6.247320000000003 5.268200000000001 0.493355
6.603179999999993 6.650175 4.44644
2.596459999999989 5.704125 2.9351499999999997
10.6758 5.806150000000001 2.8602100000000004
13.193179999999998 -2.012675 1.79856
12.83732 -0.6307 -0.493355
11.70384 5.750500000000001 6.063895
9.26554 5.963825000000001 3.83443
8.07934 6.8264000000000005 1.77358
9.25236 6.761475 0.967975
8.567 8.21765 1.105365
10.464920000000001 8.171275 2.43555
10.58354000000001 1.066625 0.18735000000000018
9.186459999999999 8.208375 3.3098500000000004
8.827964 7.3476550000000005 1.571242
10.994756 6.739215000000001 4.6194265
10.107742 6.434995 3.4559830000000002
10.942035999999995 1.9273449999999999 4.693742
9.662258000000003 2.8400050000000006 0.33348300000000003
8.775244000000011 2.535785000000001 1.4969265000000003
3.5177419999999957 7.477505000000001 2.789017
4.404755999999989 7.173285 1.6255734999999998
2.237964000000005 6.564845 4.673757999999999
3.072257999999998 1.7974949999999998 5.911517
4.352036000000001 2.7101550000000003 1.551258
2.185243999999999 2.101714999999999 4.7480735
3.490064000000002 3.023650000000001 0.3834430000000001
10.08006399999999 1.6138499999999993 5.861557
3.09993600000001 6.25135 3.5059430000000003
9.689936 7.66115 2.739057
1.7194628000000032 4.7515825 1.6299450000000002
12.664662000000002 5.8775675000000005 1.1690639999999999
11.537771999999999 7.811405 4.753694
6.918182000000008 5.826555 4.077985
11.092288 5.7310225 5.4262805
13.38429 -0.07234499999999999 -0.0843075
11.4605372 0.1140825 1.4925549999999999
13.695337999999998 1.2400675 1.9534360000000002
13.508181999999998 -1.1890550000000002 2.1670149999999997
12.97571 4.565155000000001 3.2068074999999996
2.0877119999999985 1.093522500000001 3.9412195
8.677712000000003 3.543977499999999 2.3037805000000002
8.232228000000012 1.4635949999999995 1.631194
6.3857100000000075 0.07234500000000027 3.0381925
8.309462799999991 9.1609175 4.615055
6.074662000000007 8.0349325 5.075936
6.261817999999992 1.1890550000000009 5.289515
4.947771999999987 6.101095000000001 1.491306
4.502287999999996 8.1814775 0.8187194999999999
6.794289999999992 4.7098450000000005 0.0843075
4.870537200000008 4.523417500000001 4.752445
7.105337999999993 3.3974325 4.291564
1.6422280000000005 3.173905000000001 4.613806
12.851818000000002 3.4484450000000004 0.9554850000000001
#####################################################

• Ehull available for a lot less data than before
• Max IR mode available on much smaller range than before
• Add an automatic dataset sanity checker (Max-Min val shouldn't change, average shouldn't change much (tol = 10%), number of datapoints (shouldn't decrease)

For integrating with DMFT

Enable Conda-forge installation. I'm working on this now.

• instructions: https://conda-forge.org/docs/maintainer/adding_pkgs.html
• recipe is added: conda-forge/staged-recipes#12896
• need to check that recipe passes tests
• if this doesn't get merged in the next few weeks then ping them again in the PR, see https://conda-forge.org/docs/maintainer/adding_pkgs.html#feedback-and-revision

edit: conda-forge/staged-recipes#12896 has passed the tests so we need to wait now

how to make Ni111/Ni3Nb0001 interface usng jarvis-tools?

Since the developers are employees of NIST, their contributions to this repository are automatically dedicated to the public domain, so the assignment of copyright to "The National Institute of Standards and Technology" in LICENSE is preempted.

Please replace the contents of LICENSE with the following text, or similar, adapted from https://www.nist.gov/director/licensing:

Public Domain

This software was developed by employees of the
[National Institute of Standards and Technology](http://www.nist.gov),
an agency of the Federal Government. Pursuant to
[title 17 section 105](https://www.copyright.gov/title17/92chap1.html#105)
of the United States Code, works of NIST employees are not subject to
copyright protection in the United States and are considered to be in
the public domain. NIST assumes no responsibility whatsoever for the
use of this software by other parties, and makes no guarantees, expressed or
implied, about its quality, reliability, or any other characteristic.
We would appreciate acknowledgement if the software is used.

To the extent that NIST may hold copyright in countries other than the
United States, you are hereby granted the non-exclusive irrevocable
and unconditional right to print, publish, prepare derivative works and
distribute this software, in any medium, or authorize others to do so
on your behalf, on a royalty-free basis throughout the world.

You may improve, modify, and create derivative works of the software or any
portion of the software, and you may copy and distribute such modifications
or works. Modified works should carry a notice stating that you changed
the software and should note the date and nature of any such change. Please
explicitly acknowledge the National Institute of Standards and Technology
as the original source, by linking back to
[this repository](https://github.com/usnistgov/jarvis) or
[the website](https://www.ctcms.nist.gov/~knc6/JARVIS.html).

This software can be redistributed and/or modified freely provided that any
derivative works bear some notice that they are derived from it, and any
modified versions bear some notice that they have been modified.

https://jarvis.nist.gov/

Make docs

I'm currently implementing an automatic build of JARVIS for our HPC, using the Easybuild tool. I'm having some difficulty with Jarvis due to the variable version formatting and also the inconsistency between the GitHub versioning/tagging and the version specified inside setup.py. Can I request that this is standardised going forwards, e.g. using vYYYY.MM.DD (v2018.11.06 in the case of the most recent release)?

Running the tests modifies a bunch of json files and leaves the repository in a modified state. Tests should never modify the contents of the repository. Tests should write all data to /tmp and then delete any files that are written.

After running

$ py.tests

the repo is left with

$ git status
On branch master
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    modified:   jarvis/vasp/examples/SiOptb88/ENCUTbulk@mp_149-500.json
    modified:   jarvis/vasp/examples/SiOptb88/ENCUTbulk@mp_149-600.json
    modified:   jarvis/vasp/examples/SiOptb88/ENCUTbulk@mp_149-650.json
    modified:   jarvis/vasp/examples/SiOptb88/ENCUTbulk@mp_149-700.json
...

Do these json files need to be stored if they can be generated quickly?

Edit: also a weird directory is created jarvis/tests/tmp/. Tests should not create any directories in the repository either. Use /tmp or whatever the system directory is for the OS. Python has OS independent ways to write to temporary storage which work across multiple platforms.

or just required to run the tests. Should probably be removed from setup if so

Make code for https://arxiv.org/abs/1912.09027 available.

• Graphene STM image seems 7 degree off

This is messed up:

https://github.com/usnistgov/jarvis/blob/master/LICENSE

Let's change it to

https://github.com/usnistgov/fipy/blob/master/LICENSE.rst

but with no .rst. This is exactly the same as the official license

https://www.nist.gov/open/copyright-fair-use-and-licensing-statements-srd-data-software-and-technical-series-publications

Hello, I just wanted to let you know there seems to be a typo here (NABNDS should read NBANDS).

Convert pytests to colab notebooks.

Currently there are hardwired paths that depend on where the tests are executed. Replace these with paths that use the __file__ to determine the path. For example,

 def test_get_aea():
-   strt=Structure.from_file('../vasp/examples/SiOptb88/MAIN-ELASTIC-bulk@mp_149/POSCAR')
-   ar=get_area(strt)
-   assert ar==30.180025513225004
-
+    file_path = os.path.dirname(os.path.abspath(__file__))
+    poscar_path = '../vasp/examples/SiOptb88/MAIN-ELASTIC-bulk@mp_149/POSCAR'
+    full_path = os.path.join(file_path, poscar_path)
+    print('full_path:', full_path)
+    strt=Structure.from_file(full_path)
+    ar=get_area(strt)
+    assert ar==30.180025513225004

Fix https://github.com/usnistgov/jarvis/blob/master/jarvis/db/vasp_to_xml.py

• Make sure vasprun.xml is converged, especially for TBmBJ
• Make sure negative bandgaps are reduced to zero especially for TBmBJ, e.g. https://www.ctcms.nist.gov/~knc6/static/JARVIS-DFT/JVASP-42538.xml
• Make sure the label is spin-down in SOC spillage, not trace (https://www.ctcms.nist.gov/~knc6/static/JARVIS-DFT/JVASP-8122.xml)
• Fix order of elements in formula, e.g. https://www.ctcms.nist.gov/~knc6/static/JARVIS-DFT/JVASP-2817.xml
• Make sure See also links exist e.g. https://www.ctcms.nist.gov/~knc6/static/JARVIS-DFT/JVASP-101901.xml
• Epsilon in ir spectra
• Check bandgap