Merge devel into master #1059
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Merge devel into master #1059
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Merge master to devel
Merge master into devel
…mplify fix post_fp_vasp and make_fp_configs for simplify
deepmodeling#804) (cherry picked from commit f5782ea2b33c3ee638ab23bc0e1e4a19b8d578e3)
* fix UT test_make_md * remove debug line
* args: add `shuffle_poscar` to run jdata * Update arginfo.py * add default to shuffle_poscar Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
* fix README * remove "load_ckpt" * remove `load_ckpt`
…#818) The arguments deepmodeling#786 added should be optional.
* add entire arguments of gaussian style Resolves deepmodeling#780. * add args for relative model deviation
check examples
…g#836) * test: update abacus input paramters * refactor: add fp_incar function for abacus users * modify make_abacus_scf_input * modify make_abacus_scf_input for on-off keys * modify make_abacus_scf_input for on-off keys 2rd * modify README.md * revise abacus_scf.py * refactor: change ways of gen KPT file in run step * revise run.py * modify dpgen/generator/arginfo.py as zjz said * modify abacus_scf.py * delete redundant lines for forward_files of abacus * delete redundant lines for forward_files of abacus 2nd
…deepmodeling#963) Fix incompatibility of Interstitial.py and Vacancy.py with pymatgen>2022.7.9 add pymatgen-analysis-defect and pybind11 in setup.py. add reminder for user to install pymatgen-analysis-defect if this package is not in their environment Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
```json "init_data_sys": [ "123/456/789.hdf5" ] ``` Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
…eepmodeling#989) In ABACUS-DEEPKS, ABACUS need the deepks descriptor file when one of 'deepks_out_labels' and 'deepks_scf' is set to 1.
# Patching CVE-2007-4559 Hi, we are security researchers from the Advanced Research Center at [Trellix](https://www.trellix.com). We have began a campaign to patch a widespread bug named CVE-2007-4559. CVE-2007-4559 is a 15 year old bug in the Python tarfile package. By using extract() or extractall() on a tarfile object without sanitizing input, a maliciously crafted .tar file could perform a directory path traversal attack. We found at least one unsantized extractall() in your codebase and are providing a patch for you via pull request. The patch essentially checks to see if all tarfile members will be extracted safely and throws an exception otherwise. We encourage you to use this patch or your own solution to secure against CVE-2007-4559. Further technical information about the vulnerability can be found in this [blog](https://www.trellix.com/en-us/about/newsroom/stories/research/tarfile-exploiting-the-world.html). If you have further questions you may contact us through this projects lead researcher [Kasimir Schulz](mailto:kasimir.schulz@trellix.com).
Follows PEP 621. This PR also removes the automatic `__date__` -- it only reflects the installation date.
Fixes deepmodeling#1000. Add tests.
…pmodeling#1020) python3.10 support: collection.Mapping -> collection.abc.Mapping repair this: deepmodeling#1019
Since "forward_files" for init_surf is supported (see deepmodeling#909), here add the relevant doc.
Note: some documentation links will be available once the devel branch is merged into the master branch.
For deepmodeling#782 , WIP. @tuoping @taipinghu @Vibsteamer please give some advice on the arguments' introduction, thanks!
Fixes deepmodeling#1029. Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
Fix deepmodeling#1029. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Codecov python package is deprecated does not work any more. This patch migrates it to another version. Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
The previous PBC implementation is to create ghost atoms and pass them to the OpenBabel. Since OpenBabel has supported PBC condition in v3.1.0, the previous implementation is migrated to the native one in this PR. Co-authored-by: AnguseZhang <529133328@qq.com>
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #1059 +/- ##
==========================================
+ Coverage 35.13% 39.48% +4.35%
==========================================
Files 96 99 +3
Lines 16804 17989 +1185
==========================================
+ Hits 5904 7103 +1199
+ Misses 10900 10886 -14 ☔ View full report in Codecov by Sentry. |
AnguseZhang
approved these changes
Dec 1, 2022
njzjz
approved these changes
Dec 1, 2022
This reminds me to update the documentation in #1060. |
|
warning: #957 has not been fixed yet. |
I agree. it will be released as 0.11.0 |
…odeling#957 (deepmodeling#961) The added unittest is to check that the process of extracting the configuration from model_devi.out to generate the first principles calculation task is correct. When issue deepmodeling#957 exists:  When issue deepmodeling#957 is solved: 
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