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updata #2

Merged
merged 62 commits into from
Nov 29, 2023
Merged

updata #2

merged 62 commits into from
Nov 29, 2023

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amcadmus and others added 30 commits May 4, 2023 09:27
@amcadmus
Merge master into devel (#465)
af6b72b
@njzjz
fix RTD builds (#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 
…#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 (#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 (#469)
0d2b823
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#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 (#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 (#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 (#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 (#477)
1b9daf4 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@starinthesky72
fix: writing abacus stru. (#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 (#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 (#481)
f83c5b0 
Follow up #476. `deepmd/npy` and `deepmd/raw` are ok, and only
`deepmd/hdf5` has this bug.
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#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 (#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 (#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 (#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 (#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 (#490)
ee6f38b
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#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 (#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 (#501)
7bb6392 
Revert after materialsproject/pymatgen#3166 is
fixed.
@YuLiu98 @pre-commit-ci @wanghan-iapcm
Fix: bug in reading abacus md files (#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 (#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" (#504)
7531150 
Reverts #501

Let's see if the error got fixed.
@njzjz @pre-commit-ci
add a public method to register new DataType in a plugin (#505)
b61144f 
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 (#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 (#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 (#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+ (#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>
ZhouXY-PKU and others added 29 commits August 15, 2023 21:06
@ZhouXY-PKU
Update system.py (#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 (#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 (#527)
5db6410 
unclear what this file is used for
@pre-commit-ci @njzjz
[pre-commit.ci] pre-commit autoupdate (#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 (#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 (#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 (#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 (#533)
ec7985b 
fix #508,
#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>
@wanghan-iapcm
merge devel to master (#535)
acdc06f
@njzjz
merge master to devel (#538)
7fcbbc5
@robinzyb
Update README.md for recommendation of using cp2kdata (#537)
63f2888
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#539)
b45911a 
<!--pre-commit.ci start-->
updates:
- [github.com/psf/black: 23.7.0 →
23.9.1](psf/black@23.7.0...23.9.1)
- [github.com/astral-sh/ruff-pre-commit: v0.0.287 →
v0.0.288](astral-sh/ruff-pre-commit@v0.0.287...v0.0.288)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@iProzd @pre-commit-ci
support assigning 'type_map' for mixed_type (#540)
037c2b8 
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz @pre-commit-ci
replace the old data type with the same name and throw warning (#541)
9b21f6f 
When a data type is unexpectedly registered twice, the behavior of some
methods will be strange (for example, `append`).

For this reason, the old one is replaced, and a warning is thrown.

---------

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 (#542)
88696bf 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.288 →
v0.0.290](astral-sh/ruff-pre-commit@v0.0.288...v0.0.290)
<!--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 (#545)
93b3add 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.290 →
v0.0.291](astral-sh/ruff-pre-commit@v0.0.290...v0.0.291)
<!--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 (#547)
8c653ba 
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.0.291 →
v0.0.292](astral-sh/ruff-pre-commit@v0.0.291...v0.0.292)
<!--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 (#548)
ee70942 
<!--pre-commit.ci start-->
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 →
v4.5.0](pre-commit/pre-commit-hooks@v4.4.0...v4.5.0)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@pxlxingliang @pre-commit-ci
fix(abacus): fix bug to read the data when relax job not set cal_stre…
57c5004 
…ss (#549)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@njzjz @pre-commit-ci
docs: try dpdata online (#552)
5e8f0ba 
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 @pre-commit-ci
limit the filename length dumped by MultiSystems (#554)
e73531b 
Fix #553.

---------

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
fix SciPy DeprecationWarning (#551)
3f35ac6
@njzjz
update issue templates (#557)
dbe2bc9 
Copied from DeePMD-kit with minor changes, which I think is good enough.
@pre-commit-ci
[pre-commit.ci] pre-commit autoupdate (#559)
36d1e2e 
<!--pre-commit.ci start-->
updates:
- [github.com/psf/black: 23.9.1 →
23.10.0](psf/black@23.9.1...23.10.0)
- [github.com/astral-sh/ruff-pre-commit: v0.0.292 →
v0.1.1](astral-sh/ruff-pre-commit@v0.0.292...v0.1.1)
<!--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 (#559)
1b55e6c 
<!--pre-commit.ci start-->
updates:
- [github.com/psf/black: 23.9.1 →
23.10.0](psf/black@23.9.1...23.10.0)
- [github.com/astral-sh/ruff-pre-commit: v0.0.292 →
v0.1.1](astral-sh/ruff-pre-commit@v0.0.292...v0.1.1)
<!--pre-commit.ci end-->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@robinzyb @njzjz
add decrecaption warning when dpdata throws errors while parsing cp2k (…
7fb45d8 
…#558)

Squashed commit of the following:

commit dfb6191
Merge: 1b55e6c 5028af6
Author: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com>
Date:   Mon Oct 30 22:02:15 2023 +0100

    add decrecaption warning when dpdata throws errors while parsing cp2k (#558)

commit 5028af6
Author: robinzyb <38876805+robinzyb@users.noreply.github.com>
Date:   Mon Oct 30 21:28:21 2023 +0100

    raise PendingDeprecationWarning

commit 3ee373d
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Mon Oct 30 19:51:57 2023 +0000

    [pre-commit.ci] auto fixes from pre-commit.com hooks

    for more information, see https://pre-commit.ci

commit cec3fc2
Author: robinzyb <38876805+robinzyb@users.noreply.github.com>
Date:   Mon Oct 30 20:51:26 2023 +0100

    add exact except for the cp2k plugin.

commit 7a09854
Author: robinzyb <38876805+robinzyb@users.noreply.github.com>
Date:   Mon Oct 30 20:38:23 2023 +0100

    fixed typo in checking cp2k pattern match.

commit 1a4b985
Author: robinzyb <38876805+robinzyb@users.noreply.github.com>
Date:   Mon Oct 30 14:34:50 2023 +0100

    update error for cp2k aimdoutput if none pattern is matched

commit a1a171a
Merge: 621d686 1b55e6c
Author: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com>
Date:   Mon Oct 30 13:59:10 2023 +0100

    Merge branch 'deepmodeling:devel' into devel

commit 621d686
Author: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date:   Fri Oct 20 22:53:54 2023 +0000

    [pre-commit.ci] auto fixes from pre-commit.com hooks

    for more information, see https://pre-commit.ci

commit 03cc010
Author: robinzyb <38876805+robinzyb@users.noreply.github.com>
Date:   Sat Oct 21 00:50:51 2023 +0200

    add decrecaption warning when dpdata throws errors while parsing cp2k

commit 0576449
Merge: 4840bbc dbe2bc9
Author: Yongbin Zhuang <38876805+robinzyb@users.noreply.github.com>
Date:   Sat Oct 21 00:30:18 2023 +0200

    Merge branch 'deepmodeling:devel' into devel

commit 4840bbc
Author: robinzyb <38876805+robinzyb@users.noreply.github.com>
Date:   Thu Sep 7 14:12:19 2023 +0200

    Update README.md for recommendation of using cp2kdata
@pxlxingliang @pre-commit-ci
abacus: update the read of stress and force for ABACUS v3.4.1 (#560)
a937461 
Signed-off-by: Peng Xingliang <91927439+pxlxingliang@users.noreply.github.com>
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 (#561)
0a3bbab 
<!--pre-commit.ci start-->
updates:
- [github.com/psf/black: 23.10.0 →
23.10.1](psf/black@23.10.0...23.10.1)
- [github.com/astral-sh/ruff-pre-commit: v0.1.1 →
v0.1.3](astral-sh/ruff-pre-commit@v0.1.1...v0.1.3)
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@wanghan-iapcm
merge devel to master (#562)
18a0ed5
@chouyoudou chouyoudou merged commit 2bb045d into chouyoudou:master Nov 29, 2023
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