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Merge devel to master #1161

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Mar 21, 2023
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c1d582b
merge master into devel (#1064)
amcadmus Dec 4, 2022
c1937ae
Add parameter 'srtab_file_path' so that one can use DP-ZBL potential …
Chengqian-Zhang Dec 4, 2022
e3f98e0
Refactor: remove association between ABACUS/STRU and the element numb…
pxlxingliang Dec 18, 2022
2089358
Fix: remove the reading of `ntype` when treating ABACUS related info …
pxlxingliang Dec 18, 2022
6ea1812
add placeholders for variants (#1068)
njzjz Dec 19, 2022
b5da4f4
fix pass action (#1082)
njzjz Dec 21, 2022
02d7d7d
fix compatibility with NumPy and pymatgen (#1085)
njzjz Dec 22, 2022
afebf11
Doc(abacus): modify the description of parameters (#1080)
pxlxingliang Dec 22, 2022
1bb85a6
Fix(abacus): parse orbital information after parsing of INPUT (#1079)
pxlxingliang Dec 22, 2022
a9d324b
choose numb_steps/stop_batch automatically (#1086)
njzjz Dec 23, 2022
673266a
replace distutils.version.LooseVersion by packaging.version.Version (…
njzjz Dec 30, 2022
ed26994
fix doc: "structures" should be a list (#1091)
HuangJiameng Dec 30, 2022
06bd270
Support forward files for simplify (#1092)
HuangJiameng Dec 30, 2022
749e28a
breaking: remove old dispatcher (#1097)
njzjz Dec 31, 2022
ad69c27
Replace "python3" in command by sys.executable (#1105)
HuangJiameng Jan 6, 2023
b14063e
fix_bug simplify.py (#1113)
Vibsteamer Jan 14, 2023
3e1891d
fix_bug simplify.py (#1114)
Vibsteamer Jan 15, 2023
fb8668b
add an option to merge data to one H5 file (#1119)
njzjz Jan 19, 2023
57a8c16
add and run pre-commit to format codes (#1124)
njzjz Jan 27, 2023
418e0ce
fix compatibility with the latest pymatgen (#1126)
njzjz Jan 28, 2023
98f4541
refactor(abacus): link the pp/orb files defined in STRU not jdata (#1…
pxlxingliang Jan 28, 2023
1aafd33
docs: add logo to docs and README (#1128)
njzjz Jan 29, 2023
18613d6
fix restart trajectory for `merge_traj` (#1111)
wankiwi Jan 29, 2023
23a362d
Raise warnings if there is no system in the path listed in sys_config…
HuangJiameng Jan 29, 2023
b5423bf
docs: add links to DP-GUI (#1131)
njzjz Jan 31, 2023
7a1ceb4
fix numpydoc styles (#1134)
njzjz Feb 6, 2023
a4eca19
Updated the `revise_lmp_input_dump` function. (#1137)
panxiang126 Feb 13, 2023
c73ae2e
add isort to sort imports (#1133)
njzjz Mar 17, 2023
4471d17
fix a bug in make_abacus_relax (#1150)
maki49 Mar 17, 2023
29a1bf8
fix(abacus): do not write to deepmd raw/npy, if no abacus data in pos…
pxlxingliang Mar 19, 2023
5503215
bug_fix reproduce.py (#1156)
Vibsteamer Mar 19, 2023
8453131
always pass codecov status (#1157)
njzjz Mar 19, 2023
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breaking: remove old dispatcher (#1097)
Remove the old dispatcher and all related tests and examples.
Fix #1002. Close #522.

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
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njzjz authored Dec 31, 2022
commit 749e28a37026295f89fa780a4d6ab264a09049d4
2 changes: 1 addition & 1 deletion dpgen/arginfo.py
Original file line number Diff line number Diff line change
@@ -24,7 +24,7 @@ def general_mdata_arginfo(name: str, tasks: Tuple[str]) -> Argument:
doc_api_version = "Please set to 1.0"
doc_deepmd_version = "DeePMD-kit version, e.g. 2.1.3"
doc_run_mdata = "machine.json file"
arg_api_version = Argument("api_version", str, optional=False, doc=doc_api_version)
arg_api_version = Argument("api_version", str, default="1.0", optional=True, doc=doc_api_version)
arg_deepmd_version = Argument(
"deepmd_version", str, optional=True, default="2", doc=doc_deepmd_version)

17 changes: 2 additions & 15 deletions dpgen/auto_test/common_equi.py
Original file line number Diff line number Diff line change
@@ -11,7 +11,6 @@
from dpgen import dlog
from dpgen.auto_test.calculator import make_calculator
from dpgen.auto_test.mpdb import get_structure
from dpgen.dispatcher.Dispatcher import make_dispatcher
from packaging.version import Version
from dpgen.dispatcher.Dispatcher import make_submission
from dpgen.remote.decide_machine import convert_mdata
@@ -176,21 +175,9 @@ def run_equi(confs,
work_path = os.getcwd()
print("%s --> Runing... " % (work_path))

api_version = mdata.get('api_version', '0.9')
api_version = mdata.get('api_version', '1.0')
if Version(api_version) < Version('1.0'):
warnings.warn(f"the dpdispatcher will be updated to new version."
f"And the interface may be changed. Please check the documents for more details")
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
forward_common_files,
forward_files,
backward_files,
outlog='outlog',
errlog='errlog')
raise RuntimeError("API version %s has been removed. Please upgrade to 1.0." % api_version)
elif Version(api_version) >= Version('1.0'):

submission = make_submission(
17 changes: 2 additions & 15 deletions dpgen/auto_test/common_prop.py
Original file line number Diff line number Diff line change
@@ -13,7 +13,6 @@
from dpgen.auto_test.Vacancy import Vacancy
from dpgen.auto_test.Gamma import Gamma
from dpgen.auto_test.calculator import make_calculator
from dpgen.dispatcher.Dispatcher import make_dispatcher
from dpgen.dispatcher.Dispatcher import make_submission
from dpgen.remote.decide_machine import convert_mdata
from dpgen.auto_test.lib.utils import create_path
@@ -190,21 +189,9 @@ def worker(work_path,
inter_type):
run_tasks = [os.path.basename(ii) for ii in all_task]
machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
api_version = mdata.get('api_version', '0.9')
api_version = mdata.get('api_version', '1.0')
if Version(api_version) < Version('1.0'):
warnings.warn(f"the dpdispatcher will be updated to new version."
f"And the interface may be changed. Please check the documents for more details")
disp = make_dispatcher(machine, resources, work_path, run_tasks, group_size)
disp.run_jobs(resources,
command,
work_path,
run_tasks,
group_size,
forward_common_files,
forward_files,
backward_files,
outlog='outlog',
errlog='errlog')
raise RuntimeError("API version %s has been removed. Please upgrade to 1.0." % api_version)
elif Version(api_version) >= Version('1.0'):
submission = make_submission(
mdata_machine=machine,
81 changes: 0 additions & 81 deletions dpgen/auto_test/lib/BatchJob.py

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