Merge devel into master#245
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* 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%
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Files 58 59 +1
Lines 5034 5124 +90
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+ Hits 4130 4202 +72
- Misses 904 922 +18
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