From 1a466e351e6a036bdbee4f76c6827e27c64fab08 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 5 Apr 2024 03:43:26 +0000
Subject: [PATCH 01/16] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 dpdata/plugins/ase.py | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/dpdata/plugins/ase.py b/dpdata/plugins/ase.py
index c07e3ca9..cd7620ba 100644
--- a/dpdata/plugins/ase.py
+++ b/dpdata/plugins/ase.py
@@ -1,4 +1,4 @@
-from typing import TYPE_CHECKING, Optional, Type, Generator, List
+from typing import TYPE_CHECKING, Generator, List, Optional, Type
 
 import numpy as np
 
@@ -298,10 +298,7 @@ def from_labeled_system(
 
         return dict_frames
 
-    def to_system(self,
-                  data,
-                  file_name: str = "confs.traj",
-                  **kwargs) -> None:
+    def to_system(self, data, file_name: str = "confs.traj", **kwargs) -> None:
         """Convert System to ASE Atoms object.
 
         Parameters
@@ -310,23 +307,23 @@ def to_system(self,
             path to file
         """
         list_atoms = ASEStructureFormat().to_system(data, **kwargs)
-        traj = Trajectory(file_name, 'a')
+        traj = Trajectory(file_name, "a")
         _ = [traj.write(atom) for atom in list_atoms]
         traj.close()
         return
 
-    def to_labeled_system(self,
-                          data,
-                          file_name: str = "labeled_confs.traj",
-                          *args, **kwargs) -> None:
+    def to_labeled_system(
+        self, data, file_name: str = "labeled_confs.traj", *args, **kwargs
+    ) -> None:
         """Convert System to ASE Atoms object.
+
         Parameters
         ----------
         file_name : str
             path to file
         """
         list_atoms = ASEStructureFormat().to_labeled_system(data, *args, **kwargs)
-        traj = Trajectory(file_name, 'a')
+        traj = Trajectory(file_name, "a")
         _ = [traj.write(atom) for atom in list_atoms]
         traj.close()
         return

From 4c7b3efaa22c295d246c0e23c5b72188b42dfcac Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 27 May 2024 12:37:07 +0000
Subject: [PATCH 02/16] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 dpdata/plugins/ase.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/dpdata/plugins/ase.py b/dpdata/plugins/ase.py
index 683f80f2..c25b393f 100644
--- a/dpdata/plugins/ase.py
+++ b/dpdata/plugins/ase.py
@@ -10,8 +10,8 @@
 
 if TYPE_CHECKING:
     import ase
-    from ase.optimize.optimize import Optimizer
     from ase.io import Trajectory
+    from ase.optimize.optimize import Optimizer
 
 
 @Format.register("ase/structure")
@@ -111,7 +111,7 @@ def from_multi_systems(
         step: int | None = None,
         ase_fmt: str | None = None,
         **kwargs,
-    ) -> Generator["ase.Atoms", None, None]:
+    ) -> Generator[ase.Atoms, None, None]:
         """Convert a ASE supported file to ASE Atoms.
 
         It will finally be converted to MultiSystems.
@@ -141,7 +141,7 @@ def from_multi_systems(
         frames = ase.io.read(file_name, format=ase_fmt, index=slice(begin, end, step))
         yield from frames
 
-    def to_system(self, data, **kwargs) -> List["ase.Atoms"]:
+    def to_system(self, data, **kwargs) -> List[ase.Atoms]:
         """Convert System to ASE Atom obj."""
         from ase import Atoms
 
@@ -159,7 +159,7 @@ def to_system(self, data, **kwargs) -> List["ase.Atoms"]:
 
         return structures
 
-    def to_labeled_system(self, data, *args, **kwargs) -> List["ase.Atoms"]:
+    def to_labeled_system(self, data, *args, **kwargs) -> List[ase.Atoms]:
         """Convert System to ASE Atoms object."""
         from ase import Atoms
         from ase.calculators.singlepoint import SinglePointCalculator

From 7f424fcfe1c5f6fb5c9b50e3e7d0a2e8acb676a8 Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Mon, 27 May 2024 21:50:29 +0900
Subject: [PATCH 03/16] Update test_ase_traj.py

---
 tests/test_ase_traj.py | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py
index 8e4a6e12..e35da8e7 100644
--- a/tests/test_ase_traj.py
+++ b/tests/test_ase_traj.py
@@ -67,5 +67,29 @@ def setUp(self):
         self.v_places = 4
 
 
+@unittest.skipIf(skip_ase, "skip ase related test. install ase to fix")
+class TestASEtraj4(unittest.TestCase, CompLabeledSys, IsPBC):
+    def setUp(self):
+        self.system_1 = dpdata.System("ase_traj/MoS2", fmt="deepmd")
+        self.system_1.to_system(file_name="tmp.traj")
+        self.system_2 = dpdata.System("tmp.traj", fmt="ase/traj")
+        self.places = 6
+        self.e_places = 6
+        self.f_places = 6
+        self.v_places = 4
+
+
+@unittest.skipIf(skip_ase, "skip ase related test. install ase to fix")
+class TestASEtraj4Labeled(unittest.TestCase, CompLabeledSys, IsPBC):
+    def setUp(self):
+        self.system_1 = dpdata.LabeledSystem("ase_traj/MoS2", fmt="deepmd")
+        self.system_1.to_system(file_name="tmp.traj")
+        self.system_2 = dpdata.LabeledSystem("tmp.traj", fmt="ase/traj")
+        self.places = 6
+        self.e_places = 6
+        self.f_places = 6
+        self.v_places = 4
+
+
 if __name__ == "__main__":
     unittest.main()

From aa969333264afbcb1955f54243d48b2898903610 Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Mon, 27 May 2024 21:53:21 +0900
Subject: [PATCH 04/16] Update test_ase_traj.py

---
 tests/test_ase_traj.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py
index e35da8e7..7add0f4b 100644
--- a/tests/test_ase_traj.py
+++ b/tests/test_ase_traj.py
@@ -83,7 +83,7 @@ def setUp(self):
 class TestASEtraj4Labeled(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp(self):
         self.system_1 = dpdata.LabeledSystem("ase_traj/MoS2", fmt="deepmd")
-        self.system_1.to_system(file_name="tmp.traj")
+        self.system_1.to_labeled_system(file_name="tmp.traj")
         self.system_2 = dpdata.LabeledSystem("tmp.traj", fmt="ase/traj")
         self.places = 6
         self.e_places = 6

From d1f02a3b796a1366a42b4d8ad112ce208fd10c13 Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Mon, 27 May 2024 21:56:05 +0900
Subject: [PATCH 05/16] Update test_ase_traj.py

---
 tests/test_ase_traj.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py
index 7add0f4b..4163ddeb 100644
--- a/tests/test_ase_traj.py
+++ b/tests/test_ase_traj.py
@@ -83,8 +83,8 @@ def setUp(self):
 class TestASEtraj4Labeled(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp(self):
         self.system_1 = dpdata.LabeledSystem("ase_traj/MoS2", fmt="deepmd")
-        self.system_1.to_labeled_system(file_name="tmp.traj")
-        self.system_2 = dpdata.LabeledSystem("tmp.traj", fmt="ase/traj")
+        self.system_1.to_labeled_system(file_name="tmp1.traj")
+        self.system_2 = dpdata.LabeledSystem("tmp1.traj", fmt="ase/traj")
         self.places = 6
         self.e_places = 6
         self.f_places = 6

From bdcb8871e52fdd14e333b23e587a8f77d696882f Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Mon, 27 May 2024 22:00:52 +0900
Subject: [PATCH 06/16] Update test_ase_traj.py

---
 tests/test_ase_traj.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py
index 4163ddeb..9979072f 100644
--- a/tests/test_ase_traj.py
+++ b/tests/test_ase_traj.py
@@ -68,7 +68,7 @@ def setUp(self):
 
 
 @unittest.skipIf(skip_ase, "skip ase related test. install ase to fix")
-class TestASEtraj4(unittest.TestCase, CompLabeledSys, IsPBC):
+class TestASEtraj4(unittest.TestCase, CompSys, IsPBC):
     def setUp(self):
         self.system_1 = dpdata.System("ase_traj/MoS2", fmt="deepmd")
         self.system_1.to_system(file_name="tmp.traj")

From 1c1ebdc0a352e1f35a9dfdcec035cfe0c2ce3c36 Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Mon, 27 May 2024 22:04:10 +0900
Subject: [PATCH 07/16] Update test_ase_traj.py

---
 tests/test_ase_traj.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py
index 9979072f..96ed532e 100644
--- a/tests/test_ase_traj.py
+++ b/tests/test_ase_traj.py
@@ -71,7 +71,7 @@ def setUp(self):
 class TestASEtraj4(unittest.TestCase, CompSys, IsPBC):
     def setUp(self):
         self.system_1 = dpdata.System("ase_traj/MoS2", fmt="deepmd")
-        self.system_1.to_system(file_name="tmp.traj")
+        self.system_1.to(file_name="tmp.traj", fmt='ase/traj')
         self.system_2 = dpdata.System("tmp.traj", fmt="ase/traj")
         self.places = 6
         self.e_places = 6
@@ -83,7 +83,7 @@ def setUp(self):
 class TestASEtraj4Labeled(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp(self):
         self.system_1 = dpdata.LabeledSystem("ase_traj/MoS2", fmt="deepmd")
-        self.system_1.to_labeled_system(file_name="tmp1.traj")
+        self.system_1.to(file_name="tmp1.traj", fmt='ase/traj')
         self.system_2 = dpdata.LabeledSystem("tmp1.traj", fmt="ase/traj")
         self.places = 6
         self.e_places = 6

From ca474a97c0f4e48210dffff7367ded24f1ca8759 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 27 May 2024 13:04:29 +0000
Subject: [PATCH 08/16] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/test_ase_traj.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py
index 96ed532e..7ecb685a 100644
--- a/tests/test_ase_traj.py
+++ b/tests/test_ase_traj.py
@@ -71,7 +71,7 @@ def setUp(self):
 class TestASEtraj4(unittest.TestCase, CompSys, IsPBC):
     def setUp(self):
         self.system_1 = dpdata.System("ase_traj/MoS2", fmt="deepmd")
-        self.system_1.to(file_name="tmp.traj", fmt='ase/traj')
+        self.system_1.to(file_name="tmp.traj", fmt="ase/traj")
         self.system_2 = dpdata.System("tmp.traj", fmt="ase/traj")
         self.places = 6
         self.e_places = 6
@@ -83,7 +83,7 @@ def setUp(self):
 class TestASEtraj4Labeled(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp(self):
         self.system_1 = dpdata.LabeledSystem("ase_traj/MoS2", fmt="deepmd")
-        self.system_1.to(file_name="tmp1.traj", fmt='ase/traj')
+        self.system_1.to(file_name="tmp1.traj", fmt="ase/traj")
         self.system_2 = dpdata.LabeledSystem("tmp1.traj", fmt="ase/traj")
         self.places = 6
         self.e_places = 6

From b304fc902e391f506041675564ecdf47087cd43a Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Mon, 27 May 2024 22:08:01 +0900
Subject: [PATCH 09/16] Update ase.py

---
 dpdata/plugins/ase.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/dpdata/plugins/ase.py b/dpdata/plugins/ase.py
index c25b393f..5c129b6b 100644
--- a/dpdata/plugins/ase.py
+++ b/dpdata/plugins/ase.py
@@ -10,9 +10,13 @@
 
 if TYPE_CHECKING:
     import ase
-    from ase.io import Trajectory
     from ase.optimize.optimize import Optimizer
 
+try:
+    from ase.io import Trajectory
+except ImportError:
+    pass
+
 
 @Format.register("ase/structure")
 class ASEStructureFormat(Format):

From 7a0530b177e566b2c41668589ccaa0a1e044d568 Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Mon, 27 May 2024 23:14:16 +0900
Subject: [PATCH 10/16] u

---
 tests/ase_traj/#MoS2/box.raw      |   3 +
 tests/ase_traj/#MoS2/coord.raw    |   3 +
 tests/ase_traj/#MoS2/energy.raw   |   3 +
 tests/ase_traj/#MoS2/force.raw    |   3 +
 tests/ase_traj/#MoS2/type.raw     | 104 ++++++++++++++++++++++++++++++
 tests/ase_traj/#MoS2/type_map.raw |   2 +
 tests/ase_traj/#MoS2/virial.raw   |   3 +
 7 files changed, 121 insertions(+)
 create mode 100644 tests/ase_traj/#MoS2/box.raw
 create mode 100644 tests/ase_traj/#MoS2/coord.raw
 create mode 100644 tests/ase_traj/#MoS2/energy.raw
 create mode 100644 tests/ase_traj/#MoS2/force.raw
 create mode 100644 tests/ase_traj/#MoS2/type.raw
 create mode 100644 tests/ase_traj/#MoS2/type_map.raw
 create mode 100644 tests/ase_traj/#MoS2/virial.raw

diff --git a/tests/ase_traj/#MoS2/box.raw b/tests/ase_traj/#MoS2/box.raw
new file mode 100644
index 00000000..c104fa1a
--- /dev/null
+++ b/tests/ase_traj/#MoS2/box.raw
@@ -0,0 +1,3 @@
+1.571723287959847148e+01 1.382976769974756167e-14 -4.335347714314398588e-27 -2.135776446678914908e+01 3.745820611488967700e+01 -5.045434369425391968e-16 2.142284677455918376e-24 8.545634906358754423e-15 2.312999999999935952e+01
+1.571734059897834079e+01 1.382976314475292595e-14 -4.334590580314998760e-27 -2.135791084402753981e+01 3.745820611488959173e+01 -5.045434369425390982e-16 2.155934654129174673e-24 8.545634906358737068e-15 2.312999999999930978e+01
+1.571733836538147244e+01 1.382976369106826543e-14 1.070818208280100644e-26 -2.135790780884721940e+01 3.745820611488941410e+01 -2.741620021286372525e-14 -1.227011684011214072e-23 -4.602381967266446384e-15 2.312999999999919609e+01
diff --git a/tests/ase_traj/#MoS2/coord.raw b/tests/ase_traj/#MoS2/coord.raw
new file mode 100644
index 00000000..3fdeab79
--- /dev/null
+++ b/tests/ase_traj/#MoS2/coord.raw
@@ -0,0 +1,3 @@
+-5.698917181841744117e+00 1.006790679306580394e+01 1.159245053571848239e+01 -4.124148015489565999e+00 1.088802337022864286e+01 1.315383735185872993e+01 -4.133118968716363639e+00 1.086190741420796613e+01 1.000733134883523334e+01 -7.267890536356554243e+00 1.273698271989690234e+01 1.158891517840854313e+01 -5.683596759923723596e+00 1.368706277403957472e+01 1.313437400602857785e+01 -5.709284394070140323e+00 1.366162503042886378e+01 1.000793735424933928e+01 -8.841702832703273174e+00 1.550089578223382780e+01 1.158717571654348610e+01 -7.251303482056198568e+00 1.643579562597492583e+01 1.313984541628219560e+01 -7.281059165397710586e+00 1.642087870241086378e+01 1.000323716977040078e+01 -1.041692876545396551e+01 1.825873596754246009e+01 1.158119272673626909e+01 -8.821943846043978965e+00 1.918508074987153122e+01 1.313819814976830891e+01 -8.845941842383382436e+00 1.917560395927925398e+01 1.000270590166260654e+01 -1.199618073825843112e+01 2.101155575753879390e+01 1.156390533994406589e+01 -1.041693743111767567e+01 2.193435873625131549e+01 1.313427014536195436e+01 -1.041693744539048261e+01 2.194353310684435954e+01 1.000090664546197416e+01 -1.356913420004361903e+01 2.376992782718692609e+01 1.156670372486669329e+01 -1.199579262729072227e+01 2.469462411737959329e+01 1.314429695808350473e+01 -1.198967025290584587e+01 2.470860008111487360e+01 1.000699283988100241e+01 -1.513623430404684633e+01 2.653175673146733260e+01 1.161275669332301064e+01 -1.356869490284493729e+01 2.753404029092070360e+01 1.308770381909617164e+01 -1.356108596304206593e+01 2.756170398235698826e+01 1.012504570146521665e+01 -2.558304034934836046e+00 1.006980273310816010e+01 1.158430616815146053e+01 -9.924592946396952886e-01 1.088802307619554277e+01 1.315383703252938297e+01 -9.834886043095262265e-01 1.086190701459755026e+01 1.000733101965925265e+01 -4.128804268604826078e+00 1.274232493671640576e+01 1.156519404322548894e+01 -2.558306242684514231e+00 1.370676133878904324e+01 1.310524266874485555e+01 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diff --git a/tests/ase_traj/#MoS2/energy.raw b/tests/ase_traj/#MoS2/energy.raw
new file mode 100644
index 00000000..b55ff4a4
--- /dev/null
+++ b/tests/ase_traj/#MoS2/energy.raw
@@ -0,0 +1,3 @@
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diff --git a/tests/ase_traj/#MoS2/force.raw b/tests/ase_traj/#MoS2/force.raw
new file mode 100644
index 00000000..c769e8ca
--- /dev/null
+++ b/tests/ase_traj/#MoS2/force.raw
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diff --git a/tests/ase_traj/#MoS2/type.raw b/tests/ase_traj/#MoS2/type.raw
new file mode 100644
index 00000000..fa536987
--- /dev/null
+++ b/tests/ase_traj/#MoS2/type.raw
@@ -0,0 +1,104 @@
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diff --git a/tests/ase_traj/#MoS2/type_map.raw b/tests/ase_traj/#MoS2/type_map.raw
new file mode 100644
index 00000000..53a348b3
--- /dev/null
+++ b/tests/ase_traj/#MoS2/type_map.raw
@@ -0,0 +1,2 @@
+Mo
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diff --git a/tests/ase_traj/#MoS2/virial.raw b/tests/ase_traj/#MoS2/virial.raw
new file mode 100644
index 00000000..6dbfae8b
--- /dev/null
+++ b/tests/ase_traj/#MoS2/virial.raw
@@ -0,0 +1,3 @@
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From 1f8113e185567fd1ba69c06be2c77b43a356a189 Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Mon, 27 May 2024 23:14:40 +0900
Subject: [PATCH 11/16] u

---
 tests/ase_traj/#MoS2/box.raw      |   3 -
 tests/ase_traj/#MoS2/coord.raw    |   3 -
 tests/ase_traj/#MoS2/energy.raw   |   3 -
 tests/ase_traj/#MoS2/force.raw    |   3 -
 tests/ase_traj/#MoS2/type.raw     | 104 ------------------------------
 tests/ase_traj/#MoS2/type_map.raw |   2 -
 tests/ase_traj/#MoS2/virial.raw   |   3 -
 7 files changed, 121 deletions(-)
 delete mode 100644 tests/ase_traj/#MoS2/box.raw
 delete mode 100644 tests/ase_traj/#MoS2/coord.raw
 delete mode 100644 tests/ase_traj/#MoS2/energy.raw
 delete mode 100644 tests/ase_traj/#MoS2/force.raw
 delete mode 100644 tests/ase_traj/#MoS2/type.raw
 delete mode 100644 tests/ase_traj/#MoS2/type_map.raw
 delete mode 100644 tests/ase_traj/#MoS2/virial.raw

diff --git a/tests/ase_traj/#MoS2/box.raw b/tests/ase_traj/#MoS2/box.raw
deleted file mode 100644
index c104fa1a..00000000
--- a/tests/ase_traj/#MoS2/box.raw
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/tests/ase_traj/#MoS2/coord.raw b/tests/ase_traj/#MoS2/coord.raw
deleted file mode 100644
index 3fdeab79..00000000
--- a/tests/ase_traj/#MoS2/coord.raw
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/tests/ase_traj/#MoS2/energy.raw b/tests/ase_traj/#MoS2/energy.raw
deleted file mode 100644
index b55ff4a4..00000000
--- a/tests/ase_traj/#MoS2/energy.raw
+++ /dev/null
@@ -1,3 +0,0 @@
--7.451970583582814243e+02
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diff --git a/tests/ase_traj/#MoS2/force.raw b/tests/ase_traj/#MoS2/force.raw
deleted file mode 100644
index c769e8ca..00000000
--- a/tests/ase_traj/#MoS2/force.raw
+++ /dev/null
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-7.991651437010733759e-05 3.726008990531943198e-03 -4.661232841657057813e-03 -7.609111209138166854e-05 6.002857647846961305e-03 4.102565053782534707e-03 5.439580889607082510e-04 -1.622957683003777192e-03 1.294027283940801538e-03 9.672805152702609703e-04 -1.381957183899657502e-03 1.468111142346308160e-03 -4.659108985609984924e-04 2.857204930134563461e-03 4.793408132377589663e-03 4.324999948198305516e-04 7.662306809585755010e-03 3.385553808151033853e-03 2.057455962621575034e-04 -5.389364680675267673e-03 1.652615979077672959e-03 -3.952008266686659319e-04 -8.793251098309298394e-03 3.139768539807752563e-03 -1.394751509039696768e-06 5.367999684254079647e-03 2.133135813818606450e-04 3.801797794869484919e-05 4.615229522193060700e-03 -5.850199445623168078e-03 -5.622820816131666926e-06 2.137251840482385680e-03 5.029211825491573980e-03 -1.812230037379841479e-04 -1.296733479294044991e-03 -1.793845150226069073e-03 -8.262818757468039986e-07 6.292729721526228899e-04 -5.436309700060317288e-03 -6.507631364559736965e-07 -1.047431576755923193e-04 1.627232589538455320e-03 1.932103478703853315e-04 2.264177944674948268e-04 -2.189992521505392236e-03 3.694830178152825467e-04 1.096542943215925115e-03 -5.092143011681361971e-03 3.458138654730113907e-04 1.849136275799825608e-03 1.021150092311664138e-03 2.118057125893754418e-04 1.625285090485794931e-04 -1.497612377117401488e-03 -6.148494757537663466e-04 6.256233790714309934e-04 -4.550102267440053055e-03 4.578039624987601170e-04 2.479749391109076391e-03 2.074947171936770973e-03 1.117993900525013432e-04 2.586225328904903252e-04 -9.937748374144353240e-04 -6.233368499273384119e-04 2.483649659265782256e-03 -3.763572530815650300e-03 -8.432107167055673160e-05 5.225091612794106541e-03 4.136000969617695949e-03 -9.907221763608920688e-05 -2.012628893861698881e-03 1.651106466310555331e-03 -1.041249400223460226e-03 -1.407552853175796570e-03 1.567428057187941282e-03 3.554279377602902754e-04 2.836893197835590411e-03 4.687391406828008734e-03
diff --git a/tests/ase_traj/#MoS2/type.raw b/tests/ase_traj/#MoS2/type.raw
deleted file mode 100644
index fa536987..00000000
--- a/tests/ase_traj/#MoS2/type.raw
+++ /dev/null
@@ -1,104 +0,0 @@
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
-0
-1
-1
diff --git a/tests/ase_traj/#MoS2/type_map.raw b/tests/ase_traj/#MoS2/type_map.raw
deleted file mode 100644
index 53a348b3..00000000
--- a/tests/ase_traj/#MoS2/type_map.raw
+++ /dev/null
@@ -1,2 +0,0 @@
-Mo
-S
diff --git a/tests/ase_traj/#MoS2/virial.raw b/tests/ase_traj/#MoS2/virial.raw
deleted file mode 100644
index 6dbfae8b..00000000
--- a/tests/ase_traj/#MoS2/virial.raw
+++ /dev/null
@@ -1,3 +0,0 @@
-1.447283625952611175e+00 5.772204562819483473e-04 3.310964541556151493e-05 5.772204562819483473e-04 -7.917604909755773246e-01 -1.345296796660241240e-02 3.310964541556151493e-05 -1.345296796660241240e-02 -6.358300447090128316e-01
-5.586853587538181953e-01 6.337326882196165191e-04 -5.993546670530403622e-05 6.337326882196165191e-04 -1.582677058443358931e+00 -1.015100351640258261e-02 -5.993546670530403622e-05 -1.015100351640258261e-02 -2.287293445704379202e+00
-9.427951250569688302e-01 6.312596267151768335e-04 -3.467606461001253595e-07 6.312596267151768335e-04 -1.277208215082217491e+00 -1.391758294054182797e-02 -3.467606461001253595e-07 -1.391758294054182797e-02 -1.703385461193421380e+00

From 14e48f8693da6c841bf478e02af34741c2960d3f Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Mon, 27 May 2024 23:17:37 +0900
Subject: [PATCH 12/16] Update test.yml

---
 .github/workflows/test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4a17fcde..0fbb51b2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -9,7 +9,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.12"]
+        python-version: ["3.9", "3.12"]
+        # python-version: ["3.7", "3.8", "3.12"]
 
     steps:
     - uses: actions/checkout@v4

From 7315d777899e4538a848cccf41aa6fd29e1c0f2c Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Mon, 27 May 2024 23:23:55 +0900
Subject: [PATCH 13/16] u

---
 .github/workflows/test.yml |  2 +-
 dpdata/plugins/ase.py      |  6 +++---
 tests/test_ase_traj.py     | 10 ++++++----
 3 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 0fbb51b2..a9293370 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.11"]
         # python-version: ["3.7", "3.8", "3.12"]
 
     steps:
diff --git a/dpdata/plugins/ase.py b/dpdata/plugins/ase.py
index 5c129b6b..c6a595ab 100644
--- a/dpdata/plugins/ase.py
+++ b/dpdata/plugins/ase.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Generator, List
+from typing import TYPE_CHECKING, Generator
 
 import numpy as np
 
@@ -145,7 +145,7 @@ def from_multi_systems(
         frames = ase.io.read(file_name, format=ase_fmt, index=slice(begin, end, step))
         yield from frames
 
-    def to_system(self, data, **kwargs) -> List[ase.Atoms]:
+    def to_system(self, data, **kwargs) -> list[ase.Atoms]:
         """Convert System to ASE Atom obj."""
         from ase import Atoms
 
@@ -163,7 +163,7 @@ def to_system(self, data, **kwargs) -> List[ase.Atoms]:
 
         return structures
 
-    def to_labeled_system(self, data, *args, **kwargs) -> List[ase.Atoms]:
+    def to_labeled_system(self, data, *args, **kwargs) -> list[ase.Atoms]:
         """Convert System to ASE Atoms object."""
         from ase import Atoms
         from ase.calculators.singlepoint import SinglePointCalculator
diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py
index 7ecb685a..efe3126d 100644
--- a/tests/test_ase_traj.py
+++ b/tests/test_ase_traj.py
@@ -70,9 +70,10 @@ def setUp(self):
 @unittest.skipIf(skip_ase, "skip ase related test. install ase to fix")
 class TestASEtraj4(unittest.TestCase, CompSys, IsPBC):
     def setUp(self):
-        self.system_1 = dpdata.System("ase_traj/MoS2", fmt="deepmd")
-        self.system_1.to(file_name="tmp.traj", fmt="ase/traj")
+        system_1 = dpdata.System("ase_traj/MoS2", fmt="deepmd")
+        system_1.to(file_name="tmp.traj", fmt="ase/traj")
         self.system_2 = dpdata.System("tmp.traj", fmt="ase/traj")
+        self.system_1 = system_1
         self.places = 6
         self.e_places = 6
         self.f_places = 6
@@ -82,9 +83,10 @@ def setUp(self):
 @unittest.skipIf(skip_ase, "skip ase related test. install ase to fix")
 class TestASEtraj4Labeled(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp(self):
-        self.system_1 = dpdata.LabeledSystem("ase_traj/MoS2", fmt="deepmd")
-        self.system_1.to(file_name="tmp1.traj", fmt="ase/traj")
+        system_1 = dpdata.LabeledSystem("ase_traj/MoS2", fmt="deepmd")
+        system_1.to(file_name="tmp1.traj", fmt="ase/traj")
         self.system_2 = dpdata.LabeledSystem("tmp1.traj", fmt="ase/traj")
+        self.system_1 = system_1
         self.places = 6
         self.e_places = 6
         self.f_places = 6

From be33545a39afefb804f8ce4681da0027bd6ab6eb Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Mon, 27 May 2024 23:31:55 +0900
Subject: [PATCH 14/16] u

---
 dpdata/plugins/ase.py  |  7 +++++++
 tests/test_ase_traj.py | 14 ++++++--------
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/dpdata/plugins/ase.py b/dpdata/plugins/ase.py
index c6a595ab..6b80ebdf 100644
--- a/dpdata/plugins/ase.py
+++ b/dpdata/plugins/ase.py
@@ -1,3 +1,4 @@
+import os
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Generator
@@ -313,6 +314,9 @@ def to_system(self, data, file_name: str = "confs.traj", **kwargs) -> None:
         file_name : str
             path to file
         """
+        if os.path.isfile(file_name):
+            os.remove(file_name)
+
         list_atoms = ASEStructureFormat().to_system(data, **kwargs)
         traj = Trajectory(file_name, "a")
         _ = [traj.write(atom) for atom in list_atoms]
@@ -329,6 +333,9 @@ def to_labeled_system(
         file_name : str
             path to file
         """
+        if os.path.isfile(file_name):
+            os.remove(file_name)
+
         list_atoms = ASEStructureFormat().to_labeled_system(data, *args, **kwargs)
         traj = Trajectory(file_name, "a")
         _ = [traj.write(atom) for atom in list_atoms]
diff --git a/tests/test_ase_traj.py b/tests/test_ase_traj.py
index efe3126d..98bc8bc0 100644
--- a/tests/test_ase_traj.py
+++ b/tests/test_ase_traj.py
@@ -70,10 +70,9 @@ def setUp(self):
 @unittest.skipIf(skip_ase, "skip ase related test. install ase to fix")
 class TestASEtraj4(unittest.TestCase, CompSys, IsPBC):
     def setUp(self):
-        system_1 = dpdata.System("ase_traj/MoS2", fmt="deepmd")
-        system_1.to(file_name="tmp.traj", fmt="ase/traj")
-        self.system_2 = dpdata.System("tmp.traj", fmt="ase/traj")
-        self.system_1 = system_1
+        self.system_1 = dpdata.System("ase_traj/MoS2", fmt="deepmd")
+        self.system_1.to(file_name="ase_traj/tmp.traj", fmt="ase/traj")
+        self.system_2 = dpdata.System("ase_traj/tmp.traj", fmt="ase/traj")
         self.places = 6
         self.e_places = 6
         self.f_places = 6
@@ -83,10 +82,9 @@ def setUp(self):
 @unittest.skipIf(skip_ase, "skip ase related test. install ase to fix")
 class TestASEtraj4Labeled(unittest.TestCase, CompLabeledSys, IsPBC):
     def setUp(self):
-        system_1 = dpdata.LabeledSystem("ase_traj/MoS2", fmt="deepmd")
-        system_1.to(file_name="tmp1.traj", fmt="ase/traj")
-        self.system_2 = dpdata.LabeledSystem("tmp1.traj", fmt="ase/traj")
-        self.system_1 = system_1
+        self.system_1 = dpdata.LabeledSystem("ase_traj/MoS2", fmt="deepmd")
+        self.system_1.to(file_name="ase_traj/tmp1.traj", fmt="ase/traj")
+        self.system_2 = dpdata.LabeledSystem("ase_traj/tmp1.traj", fmt="ase/traj")
         self.places = 6
         self.e_places = 6
         self.f_places = 6

From af1c94b22c9623f960e2cb6dff9239f4164f3cc6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 27 May 2024 14:32:05 +0000
Subject: [PATCH 15/16] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 dpdata/plugins/ase.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dpdata/plugins/ase.py b/dpdata/plugins/ase.py
index 6b80ebdf..0562b3dd 100644
--- a/dpdata/plugins/ase.py
+++ b/dpdata/plugins/ase.py
@@ -1,6 +1,6 @@
-import os
 from __future__ import annotations
 
+import os
 from typing import TYPE_CHECKING, Generator
 
 import numpy as np

From a222e8ef40c42d1b5b196316a80b121952b0f474 Mon Sep 17 00:00:00 2001
From: Thang Nguyen <46436648+thangckt@users.noreply.github.com>
Date: Mon, 27 May 2024 23:35:02 +0900
Subject: [PATCH 16/16] Update test.yml

---
 .github/workflows/test.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a9293370..4a17fcde 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -9,8 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.11"]
-        # python-version: ["3.7", "3.8", "3.12"]
+        python-version: ["3.7", "3.8", "3.12"]
 
     steps:
     - uses: actions/checkout@v4