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merge devel to master #535

Merged
merged 41 commits into from
Sep 8, 2023
Merged

merge devel to master #535

merged 41 commits into from
Sep 8, 2023

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njzjz
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@njzjz njzjz commented Sep 6, 2023

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amcadmus and others added 30 commits May 4, 2023 09:27
@amcadmus
Merge master into devel (deepmodeling#465)
af6b72b
@njzjz
fix RTD builds (deepmodeling#468)
0ccc570 
per
readthedocs/readthedocs.org#10290 (comment)
@ChiahsinChu @njzjz
fix bug in reading cp2k/output of cp2k v9.1 (compatible with old ver) (…
63904ed 
…deepmodeling#466)

Co-authored-by: Jia-Xin Zhu <xmuchiahsin@gmail.com>
Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
@pre-commit-ci @njzjz
[pre-commit.ci] pre-commit autoupdate (deepmodeling#467)
c5b96d8 
<!--pre-commit.ci start-->
updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.263 →
v0.0.265](astral-sh/ruff-pre-commit@v0.0.263...v0.0.265)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
@njzjz
deepmd/hdf5: handle empty systems and files (deepmodeling#469)
0d2b823
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#470)
939fe6f 
<!--pre-commit.ci start-->
updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.265 →
v0.0.267](astral-sh/ruff-pre-commit@v0.0.265...v0.0.267)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz
keep atom types when using DP models (deepmodeling#471)
bc72db3 
Before this PR, when using DP models to predict energies and forces, the
atom types were changed in the returned system according to the type map
in the model. This is not an expected behavior. The changed atom types
should only be used for internal inference.
@njzjz @pre-commit-ci
allow custom data types for deepmd format (deepmodeling#476)
e31b42e 
In this commit, the deepmd format reads data types from
`dpdata.system.LabeledSystem.DTYPES` and load or dump the corresponding
data. One can modify `dpdata.system.LabeledSystem.DTYPES` before using
it or in a plugin (see tests), so deepmd format can be extended in this
way.

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#474)
7b67af0 
<!--pre-commit.ci start-->
updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.267 →
v0.0.269](astral-sh/ruff-pre-commit@v0.0.267...v0.0.269)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@iProzd @pre-commit-ci
fix set_size in to_deepmd_npy_mixed func (deepmodeling#477)
1b9daf4 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@starinthesky72
fix: writing abacus stru. (deepmodeling#478)
ded4354 
When using system.to() and convert data to write ABACUS `STRU` file,
func `make_unlabeled_stru` won't use `atom_types` in data and miswriting
the atom order.
For example when using data from gaussian/log and other file using
ungrouped atom coordinations,as the `atom_types=[0,1,1,1,2,1]` the func
will write wrong coordinations and regard the atom as
`atom_types=[0,1,1,1,1,2]` which cause serious problem.
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#479)
5bb84c9 
<!--pre-commit.ci start-->
updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.269 →
v0.0.270](astral-sh/ruff-pre-commit@v0.0.269...v0.0.270)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz
fix customized data shape in deepmd/hdf5 (deepmodeling#481)
f83c5b0 
Follow up deepmodeling#476. `deepmd/npy` and `deepmd/raw` are ok, and only
`deepmd/hdf5` has this bug.
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#482)
ec232f8 
<!--pre-commit.ci start-->
updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.270 →
v0.0.272](astral-sh/ruff-pre-commit@v0.0.270...v0.0.272)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz @pre-commit-ci
Use stable sorting algorithms (deepmodeling#487)
c333c19 
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz
avoid modifying appended system (deepmodeling#483)
3931dfc 
When `sys1.append(sys2)`, we do not hope that `sys2` to be modified in
any way.

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#485)
c6d9611 
<!--pre-commit.ci start-->
updates:
- [github.com/asottile/blacken-docs: 1.13.0 →
1.14.0](adamchainz/blacken-docs@1.13.0...1.14.0)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#488)
5242c1b 
<!--pre-commit.ci start-->
updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.272 →
v0.0.275](astral-sh/ruff-pre-commit@v0.0.272...v0.0.275)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz
docs: add badges to README (deepmodeling#490)
ee6f38b
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#493)
f1b269a 
<!--pre-commit.ci start-->
updates:
- https://github.com/charliermarsh/ruff-pre-commit →
https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.275 →
v0.0.276](astral-sh/ruff-pre-commit@v0.0.275...v0.0.276)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#494)
119fb45 
<!--pre-commit.ci start-->
updates:
- [github.com/psf/black: 23.3.0 →
23.7.0](psf/black@23.3.0...23.7.0)
- [github.com/astral-sh/ruff-pre-commit: v0.0.276 →
v0.0.277](astral-sh/ruff-pre-commit@v0.0.276...v0.0.277)
- [github.com/asottile/blacken-docs: 1.14.0 →
1.15.0](adamchainz/blacken-docs@1.14.0...1.15.0)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz
pin pymatgen to 2023.7.11 (deepmodeling#501)
7bb6392 
Revert after materialsproject/pymatgen#3166 is
fixed.
@YuLiu98 @pre-commit-ci @wanghan-iapcm
Fix: bug in reading abacus md files (deepmodeling#496)
a091a59 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
@pre-commit-ci @wanghan-iapcm
[pre-commit.ci] pre-commit autoupdate (deepmodeling#497)
be669c8 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.277 →
v0.0.278](astral-sh/ruff-pre-commit@v0.0.277...v0.0.278)
<!--pre-commit.ci end-->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
@njzjz
Revert "pin pymatgen to 2023.7.11" (deepmodeling#504)
7531150 
Reverts deepmodeling#501

Let's see if the error got fixed.
@njzjz @pre-commit-ci
add a public method to register new DataType in a plugin (deepmodelin…
b61144f 
…g#505)

Move DataType to an independent module, so register it will be eaiser.
No breaking changes are made.

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#506)
9ef8daf 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.278 →
v0.0.280](astral-sh/ruff-pre-commit@v0.0.278...v0.0.280)
<!--pre-commit.ci end-->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz @pre-commit-ci
support -1 shape in DataType (deepmodeling#510)
47619b7 
Sometimes, the shape is unknown and can be any integer. This PR supports
this situation. The shape of a dimension can be `-1`.
Note: Only one `-1` can be used.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz @pre-commit-ci
docs: add format docs (deepmodeling#516)
5b57ac4 
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@ruio248 @pre-commit-ci
new feature DFTB+ (deepmodeling#511)
452a0e5 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: liaoruihao <liaoruihao@liaoruihaodeMacBook-Pro.local>
wanghan-iapcm and others added 11 commits August 7, 2023 21:46
@wanghan-iapcm
Fix issue deepmodeling#517 (deepmodeling#520)
2d8e7f2 
Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#521)
3815b4e 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.280 →
v0.0.282](astral-sh/ruff-pre-commit@v0.0.280...v0.0.282)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz
add extra lines for code blocks in docstring (deepmodeling#523)
3da4651 
See deepmodeling#519
@ZhouXY-PKU
Update system.py (deepmodeling#524)
40d593b 
The example is wrong? "driver" should be "Driver"?

Signed-off-by: Levi Zhou  <31941107+ZhouXY-PKU@users.noreply.github.com>
@pre-commit-ci @njzjz
[pre-commit.ci] pre-commit autoupdate (deepmodeling#525)
666d199 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.282 →
v0.0.284](astral-sh/ruff-pre-commit@v0.0.282...v0.0.284)
<!--pre-commit.ci end-->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
@njzjz
Delete requirements.txt (deepmodeling#527)
5db6410 
unclear what this file is used for
@pre-commit-ci @njzjz
[pre-commit.ci] pre-commit autoupdate (deepmodeling#528)
72d5626 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.284 →
v0.0.285](astral-sh/ruff-pre-commit@v0.0.284...v0.0.285)
- [github.com/asottile/blacken-docs: 1.15.0 →
1.16.0](adamchainz/blacken-docs@1.15.0...1.16.0)
<!--pre-commit.ci end-->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#531)
e239d0b 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.285 →
v0.0.286](astral-sh/ruff-pre-commit@v0.0.285...v0.0.286)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz @pre-commit-ci
add a public API to register data types dynamically (deepmodeling#532)
6ed3c44 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (deepmodeling#534)
002e073 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.286 →
v0.0.287](astral-sh/ruff-pre-commit@v0.0.286...v0.0.287)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@link89 @pre-commit-ci
fix cp2k 2023 output (deepmodeling#533)
ec7985b 
fix deepmodeling#508,
deepmodeling#507

---------

Signed-off-by: link89 <xuweihong.cn@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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codecov bot commented Sep 6, 2023 •
edited
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Codecov Report

Patch coverage: 88.84% and project coverage change: +0.20% 🎉

Comparison is base (85a3b5e) 82.76% compared to head (ec7985b) 82.97%.

Additional details and impacted files 
@@            Coverage Diff             @@
##           master     #535      +/-   ##
==========================================
+ Coverage   82.76%   82.97%   +0.20%     
==========================================
  Files          70       73       +3     
  Lines        6313     6490     +177     
==========================================
+ Hits         5225     5385     +160     
- Misses       1088     1105      +17
Files Changed Coverage Δ
dpdata/cp2k/cell.py 80.76% <ø> (ø)
dpdata/driver.py 84.37% <ø> (ø)
dpdata/md/rdf.py 0.00% <0.00%> (ø)
dpdata/xyz/quip_gap_xyz.py 93.16% <ø> (ø)
dpdata/plugins/deepmd.py 66.40% <50.00%> (-1.08%) ⬇️
dpdata/deepmd/hdf5.py 83.00% <71.42%> (-3.08%) ⬇️
dpdata/system.py 85.65% <82.35%> (-0.05%) ⬇️
dpdata/deepmd/raw.py 91.57% <82.60%> (-2.87%) ⬇️
dpdata/deepmd/comp.py 94.92% <87.50%> (-2.25%) ⬇️
dpdata/data_type.py 89.23% <89.23%> (ø)
... and 10 more

... and 1 file with indirect coverage changes

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@wanghan-iapcm wanghan-iapcm merged commit acdc06f into deepmodeling:master Sep 8, 2023
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10 participants
@njzjz @wanghan-iapcm @amcadmus @ChiahsinChu @iProzd @starinthesky72 @YuLiu98 @ruio248 @ZhouXY-PKU @link89