Merge devel into master#245
Merged
Merged
Conversation
* skip the UTs on machines that do not have rdkit. fix bug in mirror-gitee * Update test_amber_sqm.py * Update test_bond_order_system.py * Update test_amber_sqm.py * Update tests/test_amber_sqm.py Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> * Update tests/test_bond_order_system.py Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: Han Wang <wang_han@iapcm.ac.cn> Co-authored-by: Han Wang <amcadmus@gmail.com> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
* fix bug: nonconverged cp2k ouput should return None virial * fix bug for duplicated header cp2k output
…for cp2k output (deepmodeling#234) * add element replace parser for cp2k output and refactor the unittest for cp2k output * fix typo
Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com> Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
…ing#235) * enhance the cp2k aimd output parser by reading atomic kind * add log file
1. Changes keyword argument in `from_multii_systems` for file format from `fmt` to `ase_fmt` to not collide with the keyword argument name used in `MultiSystems.from_file`. 2. Adds documentation to the main README and ASE plugin class Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com> Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
This commit adds support for converting data to pure XYZ format. It's a quick way to visualize data using VMD or PyMol - these two software do support XYZ format file.
…ling#239) * Update outcar.py VASP6 writes NELMIN(minimum number of electronic steps) ahead of NELM(max num), dpdata reads the first line contains "NEIM", then will take the value of NELMIN as that of NELM, inducing "false" in scf_convergence_check this revise includes this such cases by request a stronger check that the line should not be initiated by "NELMIN" or "NELMDL" * bug_fix | read "nelm" | compatible with vasp6 adding a stricter check for whether the line is actually assigning value for "NELM". expecting the assignment follows the format : ``` "anywhere_in_the_line"+"NELM"+"any_number_of_spaces"+"="+"value(data-type-check_omitted_don't-believe-it's-needed-here)"+"whatever_else" ``` * Apply suggestions from code review Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> * Apply suggestions from code review Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com> Co-authored-by: Han Wang <wang_han@iapcm.ac.cn> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
* bump test python version to 3.7-3.10 * rm 3.10 * fix test error
Codecov Report
@@ Coverage Diff @@
## master #245 +/- ##
==========================================
- Coverage 82.04% 82.00% -0.04%
==========================================
Files 58 59 +1
Lines 5034 5124 +90
==========================================
+ Hits 4130 4202 +72
- Misses 904 922 +18
Continue to review full report at Codecov.
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.