From 3c19cedeba8e65cc93604cdf9900dcc58fa75100 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 13 Aug 2024 08:50:07 +0800
Subject: [PATCH 01/33] [pre-commit.ci] pre-commit autoupdate (#696)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.6 →
v0.5.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.5.6...v0.5.7)
<!--pre-commit.ci end-->

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Chores**
- Updated the Ruff pre-commit hook to the latest version (v0.5.7) for
improved linting of Python code.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1bb2fcc0..4f16df29 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.5.6
+    rev: v0.5.7
     hooks:
     - id: ruff
       args: ["--fix"]

From cbcbb92ce959ff08647c5e2587599a54c9cc3663 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 20 Aug 2024 14:15:49 +0800
Subject: [PATCH 02/33] [pre-commit.ci] pre-commit autoupdate (#697)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.5.7 →
v0.6.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.5.7...v0.6.1)
<!--pre-commit.ci end-->

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Chores**
- Updated the version of the Ruff pre-commit hook from v0.5.7 to v0.6.1,
potentially enhancing linting and formatting during pre-commit checks.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4f16df29..c255e2b1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.5.7
+    rev: v0.6.1
     hooks:
     - id: ruff
       args: ["--fix"]

From 2fb0804116761aef072021e412b589be551c2f69 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Mon, 26 Aug 2024 20:53:38 -0400
Subject: [PATCH 03/33] docs: migrate from m2r2 to myst-parser (#701)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Documentation Updates**
- Updated documentation generation tools to use `myst_parser`, enhancing
Markdown compatibility and features.
	- Improved documentation processing and rendering capabilities.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---
 docs/conf.py   | 2 +-
 pyproject.toml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index e3c0b3d4..a21d19d5 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -49,7 +49,7 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
     "numpydoc",
-    "m2r2",
+    "myst_parser",
     "sphinxarg.ext",
     "jupyterlite_sphinx",
 ]
diff --git a/pyproject.toml b/pyproject.toml
index 05a6e243..4bf2e64b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -57,7 +57,7 @@ docs = [
     'recommonmark',
     'sphinx_rtd_theme>=1.0.0rc1',
     'numpydoc',
-    'm2r2',
+    'myst-parser',
     'deepmodeling-sphinx>=0.1.1',
     'sphinx-argparse<0.5.0',
     'rdkit',

From 0a50f4d5d62b070b92f708ace0c83b8281476d62 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 27 Aug 2024 01:25:03 +0000
Subject: [PATCH 04/33] [pre-commit.ci] pre-commit autoupdate (#700)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.1 →
v0.6.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.1...v0.6.2)
<!--pre-commit.ci end-->

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Chores**
- Updated the version of the Ruff pre-commit hook to enhance performance
and reliability.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

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-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c255e2b1..f4abb50c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.1
+    rev: v0.6.2
     hooks:
     - id: ruff
       args: ["--fix"]

From 676517aa64b6b2825a6551655c79cd93449a15be Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Wed, 28 Aug 2024 21:34:11 -0400
Subject: [PATCH 05/33] feat: customized dtypes for unlabeled deepmd (#702)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Enhanced flexibility in data type handling for system data processing
based on the presence of labels.
- New data type registration for "foo" with updated shape and
configuration.

- **Bug Fixes**
- Improved adaptability and performance in data processing functions by
refining dtype selection.

- **Refactor**
- Streamlined test structure for loading and dumping data types,
improving organization and maintainability of test cases.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 dpdata/deepmd/comp.py                       | 76 ++++++++++++---------
 dpdata/deepmd/hdf5.py                       | 13 +++-
 dpdata/deepmd/raw.py                        | 76 +++++++++++----------
 tests/plugin/dpdata_plugin_test/__init__.py |  4 ++
 tests/test_custom_data_type.py              | 38 ++++++++---
 5 files changed, 126 insertions(+), 81 deletions(-)

diff --git a/dpdata/deepmd/comp.py b/dpdata/deepmd/comp.py
index ab004447..d6ccf3ff 100644
--- a/dpdata/deepmd/comp.py
+++ b/dpdata/deepmd/comp.py
@@ -67,40 +67,43 @@ def to_system_data(folder, type_map=None, labels=True):
         data["virials"] = np.concatenate(all_virs, axis=0)
     # allow custom dtypes
     if labels:
-        for dtype in dpdata.system.LabeledSystem.DTYPES:
-            if dtype.name in (
-                "atom_numbs",
-                "atom_names",
-                "atom_types",
-                "orig",
-                "cells",
-                "coords",
-                "real_atom_types",
-                "real_atom_names",
-                "nopbc",
-                "energies",
-                "forces",
-                "virials",
-            ):
-                # skip as these data contains specific rules
-                continue
-            if not (len(dtype.shape) and dtype.shape[0] == dpdata.system.Axis.NFRAMES):
-                warnings.warn(
-                    f"Shape of {dtype.name} is not (nframes, ...), but {dtype.shape}. This type of data will not converted from deepmd/npy format."
-                )
-                continue
-            natoms = data["coords"].shape[1]
-            shape = [
-                natoms if xx == dpdata.system.Axis.NATOMS else xx
-                for xx in dtype.shape[1:]
-            ]
-            all_data = []
-            for ii in sets:
-                tmp = _cond_load_data(os.path.join(ii, dtype.name + ".npy"))
-                if tmp is not None:
-                    all_data.append(np.reshape(tmp, [tmp.shape[0], *shape]))
-            if len(all_data) > 0:
-                data[dtype.name] = np.concatenate(all_data, axis=0)
+        dtypes = dpdata.system.LabeledSystem.DTYPES
+    else:
+        dtypes = dpdata.system.System.DTYPES
+
+    for dtype in dtypes:
+        if dtype.name in (
+            "atom_numbs",
+            "atom_names",
+            "atom_types",
+            "orig",
+            "cells",
+            "coords",
+            "real_atom_types",
+            "real_atom_names",
+            "nopbc",
+            "energies",
+            "forces",
+            "virials",
+        ):
+            # skip as these data contains specific rules
+            continue
+        if not (len(dtype.shape) and dtype.shape[0] == dpdata.system.Axis.NFRAMES):
+            warnings.warn(
+                f"Shape of {dtype.name} is not (nframes, ...), but {dtype.shape}. This type of data will not converted from deepmd/npy format."
+            )
+            continue
+        natoms = data["coords"].shape[1]
+        shape = [
+            natoms if xx == dpdata.system.Axis.NATOMS else xx for xx in dtype.shape[1:]
+        ]
+        all_data = []
+        for ii in sets:
+            tmp = _cond_load_data(os.path.join(ii, dtype.name + ".npy"))
+            if tmp is not None:
+                all_data.append(np.reshape(tmp, [tmp.shape[0], *shape]))
+        if len(all_data) > 0:
+            data[dtype.name] = np.concatenate(all_data, axis=0)
     return data
 
 
@@ -173,6 +176,11 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
         with open(os.path.join(folder, "nopbc"), "w") as fw_nopbc:
             pass
     # allow custom dtypes
+    labels = "energies" in data
+    if labels:
+        dtypes = dpdata.system.LabeledSystem.DTYPES
+    else:
+        dtypes = dpdata.system.System.DTYPES
     for dtype in dpdata.system.LabeledSystem.DTYPES:
         if dtype.name in (
             "atom_numbs",
diff --git a/dpdata/deepmd/hdf5.py b/dpdata/deepmd/hdf5.py
index 34ae9dbe..78f4e33f 100644
--- a/dpdata/deepmd/hdf5.py
+++ b/dpdata/deepmd/hdf5.py
@@ -102,7 +102,11 @@ def to_system_data(
         },
     }
     # allow custom dtypes
-    for dtype in dpdata.system.LabeledSystem.DTYPES:
+    if labels:
+        dtypes = dpdata.system.LabeledSystem.DTYPES
+    else:
+        dtypes = dpdata.system.System.DTYPES
+    for dtype in dtypes:
         if dtype.name in (
             "atom_numbs",
             "atom_names",
@@ -210,8 +214,13 @@ def dump(
         "virials": {"fn": "virial", "shape": (nframes, 9), "dump": True},
     }
 
+    labels = "energies" in data
+    if labels:
+        dtypes = dpdata.system.LabeledSystem.DTYPES
+    else:
+        dtypes = dpdata.system.System.DTYPES
     # allow custom dtypes
-    for dtype in dpdata.system.LabeledSystem.DTYPES:
+    for dtype in dtypes:
         if dtype.name in (
             "atom_numbs",
             "atom_names",
diff --git a/dpdata/deepmd/raw.py b/dpdata/deepmd/raw.py
index e772714a..11a9ff6e 100644
--- a/dpdata/deepmd/raw.py
+++ b/dpdata/deepmd/raw.py
@@ -64,40 +64,41 @@ def to_system_data(folder, type_map=None, labels=True):
             data["nopbc"] = True
         # allow custom dtypes
         if labels:
-            for dtype in dpdata.system.LabeledSystem.DTYPES:
-                if dtype.name in (
-                    "atom_numbs",
-                    "atom_names",
-                    "atom_types",
-                    "orig",
-                    "cells",
-                    "coords",
-                    "real_atom_types",
-                    "real_atom_names",
-                    "nopbc",
-                    "energies",
-                    "forces",
-                    "virials",
-                ):
-                    # skip as these data contains specific rules
-                    continue
-                if not (
-                    len(dtype.shape) and dtype.shape[0] == dpdata.system.Axis.NFRAMES
-                ):
-                    warnings.warn(
-                        f"Shape of {dtype.name} is not (nframes, ...), but {dtype.shape}. This type of data will not converted from deepmd/raw format."
-                    )
-                    continue
-                natoms = data["coords"].shape[1]
-                shape = [
-                    natoms if xx == dpdata.system.Axis.NATOMS else xx
-                    for xx in dtype.shape[1:]
-                ]
-                if os.path.exists(os.path.join(folder, f"{dtype.name}.raw")):
-                    data[dtype.name] = np.reshape(
-                        np.loadtxt(os.path.join(folder, f"{dtype.name}.raw")),
-                        [nframes, *shape],
-                    )
+            dtypes = dpdata.system.LabeledSystem.DTYPES
+        else:
+            dtypes = dpdata.system.System.DTYPES
+        for dtype in dtypes:
+            if dtype.name in (
+                "atom_numbs",
+                "atom_names",
+                "atom_types",
+                "orig",
+                "cells",
+                "coords",
+                "real_atom_types",
+                "real_atom_names",
+                "nopbc",
+                "energies",
+                "forces",
+                "virials",
+            ):
+                # skip as these data contains specific rules
+                continue
+            if not (len(dtype.shape) and dtype.shape[0] == dpdata.system.Axis.NFRAMES):
+                warnings.warn(
+                    f"Shape of {dtype.name} is not (nframes, ...), but {dtype.shape}. This type of data will not converted from deepmd/raw format."
+                )
+                continue
+            natoms = data["coords"].shape[1]
+            shape = [
+                natoms if xx == dpdata.system.Axis.NATOMS else xx
+                for xx in dtype.shape[1:]
+            ]
+            if os.path.exists(os.path.join(folder, f"{dtype.name}.raw")):
+                data[dtype.name] = np.reshape(
+                    np.loadtxt(os.path.join(folder, f"{dtype.name}.raw")),
+                    [nframes, *shape],
+                )
         return data
     else:
         raise RuntimeError("not dir " + folder)
@@ -144,7 +145,12 @@ def dump(folder, data):
         with open(os.path.join(folder, "nopbc"), "w") as fw_nopbc:
             pass
     # allow custom dtypes
-    for dtype in dpdata.system.LabeledSystem.DTYPES:
+    labels = "energies" in data
+    if labels:
+        dtypes = dpdata.system.LabeledSystem.DTYPES
+    else:
+        dtypes = dpdata.system.System.DTYPES
+    for dtype in dtypes:
         if dtype.name in (
             "atom_numbs",
             "atom_names",
diff --git a/tests/plugin/dpdata_plugin_test/__init__.py b/tests/plugin/dpdata_plugin_test/__init__.py
index ef26e7c1..4e445eb2 100644
--- a/tests/plugin/dpdata_plugin_test/__init__.py
+++ b/tests/plugin/dpdata_plugin_test/__init__.py
@@ -10,6 +10,10 @@
     DataType("foo", np.ndarray, (Axis.NFRAMES, 2, 4), required=False), labeled=True
 )
 
+register_data_type(
+    DataType("foo", np.ndarray, (Axis.NFRAMES, 3, 3), required=False), labeled=False
+)
+
 register_data_type(
     DataType("bar", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, -1), required=False),
     labeled=True,
diff --git a/tests/test_custom_data_type.py b/tests/test_custom_data_type.py
index e94ba5e0..a319af35 100644
--- a/tests/test_custom_data_type.py
+++ b/tests/test_custom_data_type.py
@@ -9,10 +9,12 @@
 from dpdata.data_type import Axis, DataType
 
 
-class TestDeepmdLoadDumpComp(unittest.TestCase):
+class DeepmdLoadDumpCompTest:
     def setUp(self):
-        self.system = dpdata.LabeledSystem("poscars/OUTCAR.h2o.md", fmt="vasp/outcar")
-        self.foo = np.ones((len(self.system), 2, 4))
+        self.system = self.cls(
+            data=dpdata.LabeledSystem("poscars/OUTCAR.h2o.md", fmt="vasp/outcar").data
+        )
+        self.foo = np.ones((len(self.system), *self.shape))
         self.system.data["foo"] = self.foo
         self.system.check_data()
 
@@ -23,7 +25,7 @@ def test_to_deepmd_raw(self):
 
     def test_from_deepmd_raw(self):
         self.system.to_deepmd_raw("data_foo")
-        x = dpdata.LabeledSystem("data_foo", fmt="deepmd/raw")
+        x = self.cls("data_foo", fmt="deepmd/raw")
         np.testing.assert_allclose(x.data["foo"], self.foo)
 
     def test_to_deepmd_npy(self):
@@ -33,7 +35,7 @@ def test_to_deepmd_npy(self):
 
     def test_from_deepmd_npy(self):
         self.system.to_deepmd_npy("data_foo")
-        x = dpdata.LabeledSystem("data_foo", fmt="deepmd/npy")
+        x = self.cls("data_foo", fmt="deepmd/npy")
         np.testing.assert_allclose(x.data["foo"], self.foo)
 
     def test_to_deepmd_hdf5(self):
@@ -44,18 +46,34 @@ def test_to_deepmd_hdf5(self):
 
     def test_from_deepmd_hdf5(self):
         self.system.to_deepmd_hdf5("data_foo.h5")
-        x = dpdata.LabeledSystem("data_foo.h5", fmt="deepmd/hdf5")
+        x = self.cls("data_foo.h5", fmt="deepmd/hdf5")
         np.testing.assert_allclose(x.data["foo"], self.foo)
 
     def test_duplicated_data_type(self):
-        dt = DataType("foo", np.ndarray, (Axis.NFRAMES, 2, 4), required=False)
-        n_dtypes_old = len(dpdata.LabeledSystem.DTYPES)
+        dt = DataType("foo", np.ndarray, (Axis.NFRAMES, *self.shape), required=False)
+        n_dtypes_old = len(self.cls.DTYPES)
         with self.assertWarns(UserWarning):
-            dpdata.LabeledSystem.register_data_type(dt)
-        n_dtypes_new = len(dpdata.LabeledSystem.DTYPES)
+            self.cls.register_data_type(dt)
+        n_dtypes_new = len(self.cls.DTYPES)
         self.assertEqual(n_dtypes_old, n_dtypes_new)
 
 
+class TestDeepmdLoadDumpCompUnlabeled(unittest.TestCase, DeepmdLoadDumpCompTest):
+    cls = dpdata.System
+    shape = (3, 3)
+
+    def setUp(self):
+        DeepmdLoadDumpCompTest.setUp(self)
+
+
+class TestDeepmdLoadDumpCompLabeled(unittest.TestCase, DeepmdLoadDumpCompTest):
+    cls = dpdata.LabeledSystem
+    shape = (2, 4)
+
+    def setUp(self):
+        DeepmdLoadDumpCompTest.setUp(self)
+
+
 class TestDeepmdLoadDumpCompAny(unittest.TestCase):
     def setUp(self):
         self.system = dpdata.LabeledSystem("poscars/OUTCAR.h2o.md", fmt="vasp/outcar")

From f8a1b6b20eb9ac7f1aa6d20ee806a59e6fb00c11 Mon Sep 17 00:00:00 2001
From: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
Date: Sat, 31 Aug 2024 18:33:46 +0800
Subject: [PATCH 06/33] test: support comparison between two multi systems
 (#705)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit


- **New Features**
- Introduced functions and classes to enhance testing capabilities for
multi-system comparisons.
- Added validation classes for periodic boundary conditions across
multi-system objects.

- **Bug Fixes**
- Updated test classes to utilize new multi-system handling, improving
clarity and functionality.

- **Documentation**
- Enhanced clarity in variable naming for better alignment with
multi-system concepts.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
---
 tests/comp_sys.py          | 84 ++++++++++++++++++++++++++++++++++++++
 tests/test_deepmd_mixed.py | 26 +++++++-----
 2 files changed, 100 insertions(+), 10 deletions(-)

diff --git a/tests/comp_sys.py b/tests/comp_sys.py
index 99879af6..a3a916a0 100644
--- a/tests/comp_sys.py
+++ b/tests/comp_sys.py
@@ -105,6 +105,72 @@ def test_virial(self):
         )
 
 
+def _make_comp_ms_test_func(comp_sys_test_func):
+    """
+    Dynamically generates a test function for multi-system comparisons.
+
+    Args:
+        comp_sys_test_func (Callable): The original test function for single systems.
+
+    Returns
+    -------
+    Callable: A new test function that can handle comparisons between multi-systems.
+    """
+
+    def comp_ms_test_func(iobj):
+        assert hasattr(iobj, "ms_1") and hasattr(
+            iobj, "ms_2"
+        ), "Multi-system objects must be present"
+        iobj.assertEqual(len(iobj.ms_1), len(iobj.ms_2))
+        keys = [ii.formula for ii in iobj.ms_1]
+        keys_2 = [ii.formula for ii in iobj.ms_2]
+        assert sorted(keys) == sorted(
+            keys_2
+        ), f"Keys of two MS are not equal: {keys} != {keys_2}"
+        for kk in keys:
+            iobj.system_1 = iobj.ms_1[kk]
+            iobj.system_2 = iobj.ms_2[kk]
+            comp_sys_test_func(iobj)
+        del iobj.system_1
+        del iobj.system_2
+
+    return comp_ms_test_func
+
+
+def _make_comp_ms_class(comp_class):
+    """
+    Dynamically generates a test class for multi-system comparisons.
+
+    Args:
+        comp_class (type): The original test class for single systems.
+
+    Returns
+    -------
+    type: A new test class that can handle comparisons between multi-systems.
+    """
+
+    class CompMS:
+        pass
+
+    test_methods = [
+        func
+        for func in dir(comp_class)
+        if callable(getattr(comp_class, func)) and func.startswith("test_")
+    ]
+
+    for func in test_methods:
+        setattr(CompMS, func, _make_comp_ms_test_func(getattr(comp_class, func)))
+
+    return CompMS
+
+
+# MultiSystems comparison from single System comparison
+CompMultiSys = _make_comp_ms_class(CompSys)
+
+# LabeledMultiSystems comparison from single LabeledSystem comparison
+CompLabeledMultiSys = _make_comp_ms_class(CompLabeledSys)
+
+
 class MultiSystems:
     def test_systems_name(self):
         self.assertEqual(set(self.systems.systems), set(self.system_names))
@@ -127,3 +193,21 @@ class IsNoPBC:
     def test_is_nopbc(self):
         self.assertTrue(self.system_1.nopbc)
         self.assertTrue(self.system_2.nopbc)
+
+
+class MSAllIsPBC:
+    def test_is_pbc(self):
+        assert hasattr(self, "ms_1") and hasattr(
+            self, "ms_2"
+        ), "Multi-system objects must be present and iterable"
+        self.assertTrue(all([not ss.nopbc for ss in self.ms_1]))
+        self.assertTrue(all([not ss.nopbc for ss in self.ms_2]))
+
+
+class MSAllIsNoPBC:
+    def test_is_nopbc(self):
+        assert hasattr(self, "ms_1") and hasattr(
+            self, "ms_2"
+        ), "Multi-system objects must be present and iterable"
+        self.assertTrue(all([ss.nopbc for ss in self.ms_1]))
+        self.assertTrue(all([ss.nopbc for ss in self.ms_2]))
diff --git a/tests/test_deepmd_mixed.py b/tests/test_deepmd_mixed.py
index 70a09dbe..3c28d1b1 100644
--- a/tests/test_deepmd_mixed.py
+++ b/tests/test_deepmd_mixed.py
@@ -6,12 +6,18 @@
 from glob import glob
 
 import numpy as np
-from comp_sys import CompLabeledSys, IsNoPBC, MultiSystems
+from comp_sys import (
+    CompLabeledMultiSys,
+    CompLabeledSys,
+    IsNoPBC,
+    MSAllIsNoPBC,
+    MultiSystems,
+)
 from context import dpdata
 
 
 class TestMixedMultiSystemsDumpLoad(
-    unittest.TestCase, CompLabeledSys, MultiSystems, IsNoPBC
+    unittest.TestCase, CompLabeledMultiSys, MultiSystems, MSAllIsNoPBC
 ):
     def setUp(self):
         self.places = 6
@@ -62,8 +68,8 @@ def setUp(self):
         self.place_holder_ms.from_deepmd_npy("tmp.deepmd.mixed", fmt="deepmd/npy")
         self.systems = dpdata.MultiSystems()
         self.systems.from_deepmd_npy_mixed("tmp.deepmd.mixed", fmt="deepmd/npy/mixed")
-        self.system_1 = self.ms["C1H4A0B0D0"]
-        self.system_2 = self.systems["C1H4A0B0D0"]
+        self.ms_1 = self.ms
+        self.ms_2 = self.systems
         mixed_sets = glob("tmp.deepmd.mixed/*/set.*")
         self.assertEqual(len(mixed_sets), 2)
         for i in mixed_sets:
@@ -112,7 +118,7 @@ def test_str(self):
 
 
 class TestMixedMultiSystemsDumpLoadSetSize(
-    unittest.TestCase, CompLabeledSys, MultiSystems, IsNoPBC
+    unittest.TestCase, CompLabeledMultiSys, MultiSystems, MSAllIsNoPBC
 ):
     def setUp(self):
         self.places = 6
@@ -163,8 +169,8 @@ def setUp(self):
         self.place_holder_ms.from_deepmd_npy("tmp.deepmd.mixed", fmt="deepmd/npy")
         self.systems = dpdata.MultiSystems()
         self.systems.from_deepmd_npy_mixed("tmp.deepmd.mixed", fmt="deepmd/npy/mixed")
-        self.system_1 = self.ms["C1H4A0B0D0"]
-        self.system_2 = self.systems["C1H4A0B0D0"]
+        self.ms_1 = self.ms
+        self.ms_2 = self.systems
         mixed_sets = glob("tmp.deepmd.mixed/*/set.*")
         self.assertEqual(len(mixed_sets), 5)
         for i in mixed_sets:
@@ -213,7 +219,7 @@ def test_str(self):
 
 
 class TestMixedMultiSystemsTypeChange(
-    unittest.TestCase, CompLabeledSys, MultiSystems, IsNoPBC
+    unittest.TestCase, CompLabeledMultiSys, MultiSystems, MSAllIsNoPBC
 ):
     def setUp(self):
         self.places = 6
@@ -265,8 +271,8 @@ def setUp(self):
         self.place_holder_ms.from_deepmd_npy("tmp.deepmd.mixed", fmt="deepmd/npy")
         self.systems = dpdata.MultiSystems(type_map=["TOKEN"])
         self.systems.from_deepmd_npy_mixed("tmp.deepmd.mixed", fmt="deepmd/npy/mixed")
-        self.system_1 = self.ms["TOKEN0C1H4A0B0D0"]
-        self.system_2 = self.systems["TOKEN0C1H4A0B0D0"]
+        self.ms_1 = self.ms
+        self.ms_2 = self.systems
         mixed_sets = glob("tmp.deepmd.mixed/*/set.*")
         self.assertEqual(len(mixed_sets), 2)
         for i in mixed_sets:

From 6d082f162dc05c0980567a7544a8024b7c024a78 Mon Sep 17 00:00:00 2001
From: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
Date: Sat, 31 Aug 2024 18:39:10 +0800
Subject: [PATCH 07/33] test: mixed data format: test if the index_map (when
 type_map is provided) works  (#706)

consider the PR after #705

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Enhanced testing framework for multi-system comparisons, allowing for
dynamic generation of test functions and classes.
- Introduced new test classes to validate properties of multi-system
objects regarding periodic boundary conditions.
	- Added a new test class for handling type mapping in labeled systems.

- **Bug Fixes**
- Updated existing test classes to improve clarity and consistency in
naming conventions for multi-system variables.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
---
 tests/test_deepmd_mixed.py | 113 +++++++++++++++++++++++++++++++++++++
 1 file changed, 113 insertions(+)

diff --git a/tests/test_deepmd_mixed.py b/tests/test_deepmd_mixed.py
index 3c28d1b1..9f0c5ed4 100644
--- a/tests/test_deepmd_mixed.py
+++ b/tests/test_deepmd_mixed.py
@@ -117,6 +117,119 @@ def test_str(self):
         )
 
 
+class TestMixedMultiSystemsDumpLoadTypeMap(
+    unittest.TestCase, CompLabeledMultiSys, MultiSystems, MSAllIsNoPBC
+):
+    def setUp(self):
+        self.places = 6
+        self.e_places = 6
+        self.f_places = 6
+        self.v_places = 6
+
+        # C1H4
+        system_1 = dpdata.LabeledSystem(
+            "gaussian/methane.gaussianlog", fmt="gaussian/log"
+        )
+
+        # C1H3
+        system_2 = dpdata.LabeledSystem(
+            "gaussian/methane_sub.gaussianlog", fmt="gaussian/log"
+        )
+
+        tmp_data = system_1.data.copy()
+        tmp_data["atom_numbs"] = [1, 1, 1, 2]
+        tmp_data["atom_names"] = ["C", "H", "A", "B"]
+        tmp_data["atom_types"] = np.array([0, 1, 2, 3, 3])
+        # C1H1A1B2
+        system_1_modified_type_1 = dpdata.LabeledSystem(data=tmp_data)
+
+        tmp_data = system_1.data.copy()
+        tmp_data["atom_numbs"] = [1, 1, 2, 1]
+        tmp_data["atom_names"] = ["C", "H", "A", "B"]
+        tmp_data["atom_types"] = np.array([0, 1, 2, 2, 3])
+        # C1H1A2B1
+        system_1_modified_type_2 = dpdata.LabeledSystem(data=tmp_data)
+
+        tmp_data = system_1.data.copy()
+        tmp_data["atom_numbs"] = [1, 1, 1, 2]
+        tmp_data["atom_names"] = ["C", "H", "A", "D"]
+        tmp_data["atom_types"] = np.array([0, 1, 2, 3, 3])
+        # C1H1A1C2
+        system_1_modified_type_3 = dpdata.LabeledSystem(data=tmp_data)
+
+        self.ms = dpdata.MultiSystems(
+            system_1,
+            system_2,
+            system_1_modified_type_1,
+            system_1_modified_type_2,
+            system_1_modified_type_3,
+        )
+
+        self.ms.to_deepmd_npy_mixed("tmp.deepmd.mixed")
+        self.place_holder_ms = dpdata.MultiSystems()
+        self.place_holder_ms.from_deepmd_npy("tmp.deepmd.mixed", fmt="deepmd/npy")
+
+        new_type_map = ["H", "C", "D", "A", "B"]
+        self.systems = dpdata.MultiSystems()
+        self.systems.from_deepmd_npy_mixed(
+            "tmp.deepmd.mixed", fmt="deepmd/npy/mixed", type_map=new_type_map
+        )
+        for kk in [ii.formula for ii in self.ms]:
+            # apply type_map to each system
+            self.ms[kk].apply_type_map(new_type_map)
+            # revise keys in dict according because the type_map is updated.
+            tmp_ss = self.ms.systems.pop(kk)
+            self.ms.systems[tmp_ss.formula] = tmp_ss
+
+        self.ms_1 = self.ms
+        self.ms_2 = self.systems
+        mixed_sets = glob("tmp.deepmd.mixed/*/set.*")
+        self.assertEqual(len(mixed_sets), 2)
+        for i in mixed_sets:
+            self.assertEqual(
+                os.path.exists(os.path.join(i, "real_atom_types.npy")), True
+            )
+
+        self.system_names = [
+            "H4C1D0A0B0",
+            "H3C1D0A0B0",
+            "H1C1D0A1B2",
+            "H1C1D0A2B1",
+            "H1C1D2A1B0",
+        ]
+        self.system_sizes = {
+            "H4C1D0A0B0": 1,
+            "H3C1D0A0B0": 1,
+            "H1C1D0A1B2": 1,
+            "H1C1D0A2B1": 1,
+            "H1C1D2A1B0": 1,
+        }
+        self.atom_names = ["H", "C", "D", "A", "B"]
+
+    def tearDown(self):
+        if os.path.exists("tmp.deepmd.mixed"):
+            shutil.rmtree("tmp.deepmd.mixed")
+
+    def test_len(self):
+        self.assertEqual(len(self.ms), 5)
+        self.assertEqual(len(self.place_holder_ms), 2)
+        self.assertEqual(len(self.systems), 5)
+
+    def test_get_nframes(self):
+        self.assertEqual(self.ms.get_nframes(), 5)
+        self.assertEqual(self.place_holder_ms.get_nframes(), 5)
+        self.assertEqual(self.systems.get_nframes(), 5)
+
+    def test_str(self):
+        self.assertEqual(str(self.ms), "MultiSystems (5 systems containing 5 frames)")
+        self.assertEqual(
+            str(self.place_holder_ms), "MultiSystems (2 systems containing 5 frames)"
+        )
+        self.assertEqual(
+            str(self.systems), "MultiSystems (5 systems containing 5 frames)"
+        )
+
+
 class TestMixedMultiSystemsDumpLoadSetSize(
     unittest.TestCase, CompLabeledMultiSys, MultiSystems, MSAllIsNoPBC
 ):

From 35fdbb8df25e79fd50c072f17ec2ddf903bcb9d9 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Sat, 31 Aug 2024 07:59:26 -0400
Subject: [PATCH 08/33] fix: reuse regular methods for deepmd/mixed (#704)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit


- **New Features**
- Streamlined data loading process with improved handling of atom types.
- Enhanced modularization in data dumping, reducing complexity and
improving maintainability.
- Added a new test for verifying data conversion and loading processes
for mixed format systems.

- **Bug Fixes**
	- Improved clarity and efficiency in processing atom names and counts.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
---
 dpdata/deepmd/comp.py          |   2 -
 dpdata/deepmd/mixed.py         | 179 ++++-----------------------------
 dpdata/deepmd/raw.py           |  10 +-
 tests/test_custom_data_type.py |  10 ++
 4 files changed, 31 insertions(+), 170 deletions(-)

diff --git a/dpdata/deepmd/comp.py b/dpdata/deepmd/comp.py
index d6ccf3ff..66111016 100644
--- a/dpdata/deepmd/comp.py
+++ b/dpdata/deepmd/comp.py
@@ -79,7 +79,6 @@ def to_system_data(folder, type_map=None, labels=True):
             "orig",
             "cells",
             "coords",
-            "real_atom_types",
             "real_atom_names",
             "nopbc",
             "energies",
@@ -189,7 +188,6 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
             "orig",
             "cells",
             "coords",
-            "real_atom_types",
             "real_atom_names",
             "nopbc",
             "energies",
diff --git a/dpdata/deepmd/mixed.py b/dpdata/deepmd/mixed.py
index ccf9b2f5..2aff3a28 100644
--- a/dpdata/deepmd/mixed.py
+++ b/dpdata/deepmd/mixed.py
@@ -1,54 +1,16 @@
 from __future__ import annotations
 
 import copy
-import glob
-import os
-import shutil
 
 import numpy as np
 
-
-def load_type(folder):
-    data = {}
-    data["atom_names"] = []
-    # if find type_map.raw, use it
-    assert os.path.isfile(
-        os.path.join(folder, "type_map.raw")
-    ), "Mixed type system must have type_map.raw!"
-    with open(os.path.join(folder, "type_map.raw")) as fp:
-        data["atom_names"] = fp.read().split()
-
-    return data
-
-
-def formula(atom_names, atom_numbs):
-    """Return the formula of this system, like C3H5O2."""
-    return "".join([f"{symbol}{numb}" for symbol, numb in zip(atom_names, atom_numbs)])
-
-
-def _cond_load_data(fname):
-    tmp = None
-    if os.path.isfile(fname):
-        tmp = np.load(fname)
-    return tmp
-
-
-def _load_set(folder, nopbc: bool):
-    coords = np.load(os.path.join(folder, "coord.npy"))
-    if nopbc:
-        cells = np.zeros((coords.shape[0], 3, 3))
-    else:
-        cells = np.load(os.path.join(folder, "box.npy"))
-    eners = _cond_load_data(os.path.join(folder, "energy.npy"))
-    forces = _cond_load_data(os.path.join(folder, "force.npy"))
-    virs = _cond_load_data(os.path.join(folder, "virial.npy"))
-    real_atom_types = np.load(os.path.join(folder, "real_atom_types.npy"))
-    return cells, coords, eners, forces, virs, real_atom_types
+from .comp import dump as comp_dump
+from .comp import to_system_data as comp_to_system_data
 
 
 def to_system_data(folder, type_map=None, labels=True):
+    data = comp_to_system_data(folder, type_map, labels)
     # data is empty
-    data = load_type(folder)
     old_type_map = data["atom_names"].copy()
     if type_map is not None:
         assert isinstance(type_map, list)
@@ -60,50 +22,16 @@ def to_system_data(folder, type_map=None, labels=True):
         data["atom_names"] = type_map.copy()
     else:
         index_map = None
-    data["orig"] = np.zeros([3])
-    if os.path.isfile(os.path.join(folder, "nopbc")):
-        data["nopbc"] = True
-    sets = sorted(glob.glob(os.path.join(folder, "set.*")))
-    all_cells = []
-    all_coords = []
-    all_eners = []
-    all_forces = []
-    all_virs = []
-    all_real_atom_types = []
-    for ii in sets:
-        cells, coords, eners, forces, virs, real_atom_types = _load_set(
-            ii, data.get("nopbc", False)
-        )
-        nframes = np.reshape(cells, [-1, 3, 3]).shape[0]
-        all_cells.append(np.reshape(cells, [nframes, 3, 3]))
-        all_coords.append(np.reshape(coords, [nframes, -1, 3]))
-        if index_map is None:
-            all_real_atom_types.append(np.reshape(real_atom_types, [nframes, -1]))
-        else:
-            all_real_atom_types.append(
-                np.reshape(index_map[real_atom_types], [nframes, -1])
-            )
-        if eners is not None:
-            eners = np.reshape(eners, [nframes])
-        if labels:
-            if eners is not None and eners.size > 0:
-                all_eners.append(np.reshape(eners, [nframes]))
-            if forces is not None and forces.size > 0:
-                all_forces.append(np.reshape(forces, [nframes, -1, 3]))
-            if virs is not None and virs.size > 0:
-                all_virs.append(np.reshape(virs, [nframes, 3, 3]))
-    all_cells_concat = np.concatenate(all_cells, axis=0)
-    all_coords_concat = np.concatenate(all_coords, axis=0)
-    all_real_atom_types_concat = np.concatenate(all_real_atom_types, axis=0)
-    all_eners_concat = None
-    all_forces_concat = None
-    all_virs_concat = None
-    if len(all_eners) > 0:
-        all_eners_concat = np.concatenate(all_eners, axis=0)
-    if len(all_forces) > 0:
-        all_forces_concat = np.concatenate(all_forces, axis=0)
-    if len(all_virs) > 0:
-        all_virs_concat = np.concatenate(all_virs, axis=0)
+    all_real_atom_types_concat = data.pop("real_atom_types").astype(int)
+    if index_map is not None:
+        all_real_atom_types_concat = index_map[all_real_atom_types_concat]
+    all_cells_concat = data["cells"]
+    all_coords_concat = data["coords"]
+    if labels:
+        all_eners_concat = data.get("energies")
+        all_forces_concat = data.get("forces")
+        all_virs_concat = data.get("virials")
+
     data_list = []
     while True:
         if all_real_atom_types_concat.size == 0:
@@ -143,20 +71,6 @@ def to_system_data(folder, type_map=None, labels=True):
 
 
 def dump(folder, data, set_size=2000, comp_prec=np.float32, remove_sets=True):
-    os.makedirs(folder, exist_ok=True)
-    sets = sorted(glob.glob(os.path.join(folder, "set.*")))
-    if len(sets) > 0:
-        if remove_sets:
-            for ii in sets:
-                shutil.rmtree(ii)
-        else:
-            raise RuntimeError(
-                "found "
-                + str(sets)
-                + " in "
-                + folder
-                + "not a clean deepmd raw dir. please firstly clean set.* then try compress"
-            )
     # if not converted to mixed
     if "real_atom_types" not in data:
         from dpdata import LabeledSystem, System
@@ -169,69 +83,10 @@ def dump(folder, data, set_size=2000, comp_prec=np.float32, remove_sets=True):
         else:
             temp_sys = System(data=data)
         temp_sys.convert_to_mixed_type()
-    # dump raw
-    np.savetxt(os.path.join(folder, "type.raw"), data["atom_types"], fmt="%d")
-    np.savetxt(os.path.join(folder, "type_map.raw"), data["real_atom_names"], fmt="%s")
-    # BondOrder System
-    if "bonds" in data:
-        np.savetxt(
-            os.path.join(folder, "bonds.raw"),
-            data["bonds"],
-            header="begin_atom, end_atom, bond_order",
-        )
-    if "formal_charges" in data:
-        np.savetxt(os.path.join(folder, "formal_charges.raw"), data["formal_charges"])
-    # reshape frame properties and convert prec
-    nframes = data["cells"].shape[0]
-    cells = np.reshape(data["cells"], [nframes, 9]).astype(comp_prec)
-    coords = np.reshape(data["coords"], [nframes, -1]).astype(comp_prec)
-    eners = None
-    forces = None
-    virials = None
-    real_atom_types = None
-    if "energies" in data:
-        eners = np.reshape(data["energies"], [nframes]).astype(comp_prec)
-    if "forces" in data:
-        forces = np.reshape(data["forces"], [nframes, -1]).astype(comp_prec)
-    if "virials" in data:
-        virials = np.reshape(data["virials"], [nframes, 9]).astype(comp_prec)
-    if "atom_pref" in data:
-        atom_pref = np.reshape(data["atom_pref"], [nframes, -1]).astype(comp_prec)
-    if "real_atom_types" in data:
-        real_atom_types = np.reshape(data["real_atom_types"], [nframes, -1]).astype(
-            np.int64
-        )
-    # dump frame properties: cell, coord, energy, force and virial
-    nsets = nframes // set_size
-    if set_size * nsets < nframes:
-        nsets += 1
-    for ii in range(nsets):
-        set_stt = ii * set_size
-        set_end = (ii + 1) * set_size
-        set_folder = os.path.join(folder, "set.%06d" % ii)
-        os.makedirs(set_folder)
-        np.save(os.path.join(set_folder, "box"), cells[set_stt:set_end])
-        np.save(os.path.join(set_folder, "coord"), coords[set_stt:set_end])
-        if eners is not None:
-            np.save(os.path.join(set_folder, "energy"), eners[set_stt:set_end])
-        if forces is not None:
-            np.save(os.path.join(set_folder, "force"), forces[set_stt:set_end])
-        if virials is not None:
-            np.save(os.path.join(set_folder, "virial"), virials[set_stt:set_end])
-        if real_atom_types is not None:
-            np.save(
-                os.path.join(set_folder, "real_atom_types"),
-                real_atom_types[set_stt:set_end],
-            )
-        if "atom_pref" in data:
-            np.save(os.path.join(set_folder, "atom_pref"), atom_pref[set_stt:set_end])
-    try:
-        os.remove(os.path.join(folder, "nopbc"))
-    except OSError:
-        pass
-    if data.get("nopbc", False):
-        with open(os.path.join(folder, "nopbc"), "w") as fw_nopbc:
-            pass
+
+    data = data.copy()
+    data["atom_names"] = data.pop("real_atom_names")
+    comp_dump(folder, data, set_size, comp_prec, remove_sets)
 
 
 def mix_system(*system, type_map, **kwargs):
diff --git a/dpdata/deepmd/raw.py b/dpdata/deepmd/raw.py
index 11a9ff6e..717c73f9 100644
--- a/dpdata/deepmd/raw.py
+++ b/dpdata/deepmd/raw.py
@@ -14,9 +14,6 @@ def load_type(folder, type_map=None):
         int
     )
     ntypes = np.max(data["atom_types"]) + 1
-    data["atom_numbs"] = []
-    for ii in range(ntypes):
-        data["atom_numbs"].append(np.count_nonzero(data["atom_types"] == ii))
     data["atom_names"] = []
     # if find type_map.raw, use it
     if os.path.isfile(os.path.join(folder, "type_map.raw")):
@@ -30,9 +27,10 @@ def load_type(folder, type_map=None):
         my_type_map = []
         for ii in range(ntypes):
             my_type_map.append("Type_%d" % ii)
-    assert len(my_type_map) >= len(data["atom_numbs"])
-    for ii in range(len(data["atom_numbs"])):
-        data["atom_names"].append(my_type_map[ii])
+    data["atom_names"] = my_type_map
+    data["atom_numbs"] = []
+    for ii, _ in enumerate(data["atom_names"]):
+        data["atom_numbs"].append(np.count_nonzero(data["atom_types"] == ii))
 
     return data
 
diff --git a/tests/test_custom_data_type.py b/tests/test_custom_data_type.py
index a319af35..230475ab 100644
--- a/tests/test_custom_data_type.py
+++ b/tests/test_custom_data_type.py
@@ -57,6 +57,16 @@ def test_duplicated_data_type(self):
         n_dtypes_new = len(self.cls.DTYPES)
         self.assertEqual(n_dtypes_old, n_dtypes_new)
 
+    def test_to_deepmd_npy_mixed(self):
+        ms = dpdata.MultiSystems(self.system)
+        ms.to_deepmd_npy_mixed("data_foo_mixed")
+        x = dpdata.MultiSystems().load_systems_from_file(
+            "data_foo_mixed",
+            fmt="deepmd/npy/mixed",
+            labeled=issubclass(self.cls, dpdata.LabeledSystem),
+        )
+        np.testing.assert_allclose(list(x.systems.values())[0].data["foo"], self.foo)
+
 
 class TestDeepmdLoadDumpCompUnlabeled(unittest.TestCase, DeepmdLoadDumpCompTest):
     cls = dpdata.System

From f4d0adf8ca3aceab813f0bab0fdaeb9b55bf6ed6 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Sat, 31 Aug 2024 08:45:45 -0400
Subject: [PATCH 09/33] docs: reformat README and documentation (#707)

Move most of the contents from `README.md` to `docs`.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Introduced `BondOrderSystem` class for managing chemical bonds and
formal charges.
- Added `MultiSystems` class for handling multiple system data from
files or directories.
- Implemented new `deepmd/npy/mixed` format for combining systems with
different formulas.
- Launched plugin documentation to enhance extensibility for
user-created plugins.

- **Documentation**
- Updated README for clearer installation instructions and streamlined
content.
	- Created dedicated installation guide for user-friendly setup.
- Enhanced documentation structure with new entries and improved
navigation.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 README.md                         | 323 +++---------------------------
 docs/index.rst                    |   9 +-
 docs/installation.md              |  13 ++
 docs/plugin.md                    |   9 +
 docs/systems/bond_order_system.md |  51 +++++
 docs/systems/index.rst            |  11 +
 docs/systems/mixed.md             |  24 +++
 docs/systems/multi.md             |  62 ++++++
 docs/systems/system.md            | 112 +++++++++++
 9 files changed, 312 insertions(+), 302 deletions(-)
 create mode 100644 docs/installation.md
 create mode 100644 docs/plugin.md
 create mode 100644 docs/systems/bond_order_system.md
 create mode 100644 docs/systems/index.rst
 create mode 100644 docs/systems/mixed.md
 create mode 100644 docs/systems/multi.md
 create mode 100644 docs/systems/system.md

diff --git a/README.md b/README.md
index ab489a75..6f9246b1 100644
--- a/README.md
+++ b/README.md
@@ -4,320 +4,47 @@
 [![pip install](https://img.shields.io/pypi/dm/dpdata?label=pip%20install&logo=pypi)](https://pypi.org/project/dpdata)
 [![Documentation Status](https://readthedocs.org/projects/dpdata/badge/)](https://dpdata.readthedocs.io/)
 
-**dpdata** is a python package for manipulating data formats of software in computational science, including DeePMD-kit, VASP, LAMMPS, GROMACS, Gaussian.
-dpdata only works with python 3.7 or above.
-
+**dpdata** is a Python package for manipulating atomistic data of software in computational science.
 
 ## Installation
-One can download the source code of dpdata by
-```bash
-git clone https://github.com/deepmodeling/dpdata.git dpdata
-```
-then use `pip` to install the module from source
-```bash
-cd dpdata
-pip install .
-```
-
-`dpdata` can also by install via pip without source
-```bash
-pip install dpdata
-```
-
 
-## Quick start
-
-This section gives some examples on how dpdata works. Firstly one needs to import the module in a python 3.x compatible code.
-```python
-import dpdata
-```
-The typicall workflow of `dpdata` is
-
-1. Load data from vasp or lammps or deepmd-kit data files.
-2. Manipulate data
-3. Dump data to in a desired format
-
-
-### Load data
-```python
-d_poscar = dpdata.System("POSCAR", fmt="vasp/poscar")
-```
-or let dpdata infer the format (`vasp/poscar`) of the file from the file name extension
-```python
-d_poscar = dpdata.System("my.POSCAR")
-```
-The number of atoms, atom types, coordinates are loaded from the `POSCAR` and stored to a data `System` called `d_poscar`.
-A data `System` (a concept used by [deepmd-kit](https://github.com/deepmodeling/deepmd-kit)) contains frames that has the same number of atoms of the same type. The order of the atoms should be consistent among the frames in one `System`.
-It is noted that `POSCAR` only contains one frame.
-If the multiple frames stored in, for example, a `OUTCAR` is wanted,
-```python
-d_outcar = dpdata.LabeledSystem("OUTCAR")
-```
-The labels provided in the `OUTCAR`, i.e. energies, forces and virials (if any), are loaded by `LabeledSystem`. It is noted that the forces of atoms are always assumed to exist. `LabeledSystem` is a derived class of `System`.
+DP-GEN only supports Python 3.7 and above. You can [setup a conda/pip environment](https://docs.deepmodeling.com/faq/conda.html), and then use one of the following methods to install DP-GEN:
 
-The `System` or `LabeledSystem` can be constructed from the following file formats with the `format key` in the table passed to argument `fmt`:
+- Install via pip: `pip install dpdata`
+- Install via conda: `conda install -c conda-forge dpdata`
+- Install from source code: `git clone https://github.com/deepmodeling/dpdata && pip install ./dpdata`
 
-| Software| format | multi frames | labeled | class	    | format key    |
-| ------- | :---   | :---:        | :---:   | :---          | :---          |
-| vasp	  | poscar | False        | False   | System	    | 'vasp/poscar' |
-| vasp    | outcar | True         | True    | LabeledSystem | 'vasp/outcar' |
-| vasp    | xml    | True         | True    | LabeledSystem | 'vasp/xml'    |
-| lammps  | lmp    | False        | False   | System        | 'lammps/lmp'  |
-| lammps  | dump   | True         | False   | System        | 'lammps/dump' |
-| deepmd  | raw    | True         | False   | System	    | 'deepmd/raw'  |
-| deepmd  | npy    | True         | False   | System        | 'deepmd/npy'  |
-| deepmd  | raw    | True         | True    | LabeledSystem | 'deepmd/raw'  |
-| deepmd  | npy    | True         | True    | LabeledSystem | 'deepmd/npy'  |
-| deepmd  | npy    | True         | True    | MultiSystems | 'deepmd/npy/mixed'  |
-| deepmd  | npy    | True         | False    | MultiSystems | 'deepmd/npy/mixed'  |
-| gaussian| log    | False        | True    | LabeledSystem | 'gaussian/log'|
-| gaussian| log    | True         | True    | LabeledSystem | 'gaussian/md' |
-| siesta  | output | False        | True    | LabeledSystem | 'siesta/output'|
-| siesta  | aimd_output  | True         | True    | LabeledSystem | 'siesta/aimd_output' |
-| cp2k(deprecated in future)    | output | False        | True    | LabeledSystem | 'cp2k/output' |
-| cp2k(deprecated in future)    | aimd_output  | True         | True    | LabeledSystem | 'cp2k/aimd_output' |
-| cp2k([plug-in](https://github.com/robinzyb/cp2kdata#plug-in-for-dpdata))    | stdout | False        | True    | LabeledSystem | 'cp2kdata/e_f' |
-| cp2k([plug-in](https://github.com/robinzyb/cp2kdata#plug-in-for-dpdata))    | stdout  | True         | True    | LabeledSystem | 'cp2kdata/md' |
-| QE      | log    | False        | True    | LabeledSystem | 'qe/pw/scf'   |
-| QE      | log    | True         | False   | System        | 'qe/cp/traj'  |
-| QE      | log    | True         | True    | LabeledSystem | 'qe/cp/traj'  |
-| Fhi-aims| output | True         | True    | LabeledSystem | 'fhi_aims/md'  |
-| Fhi-aims| output | False        | True    | LabeledSystem | 'fhi_aims/scf'  |
-|quip/gap|xyz|True|True|MultiSystems|'quip/gap/xyz'|
-| PWmat   | atom.config | False        | False   | System        | 'pwmat/atom.config'  |
-| PWmat   | movement    | True         | True    | LabeledSystem | 'pwmat/movement'     |
-| PWmat   | OUT.MLMD    | True         | True    | LabeledSystem | 'pwmat/out.mlmd'     |
-| Amber   | multi       | True         | True    | LabeledSystem | 'amber/md'           |
-| Amber/sqm | sqm.out   | False        | False   | System        | 'sqm/out'            |
-| Gromacs | gro         | True         | False   | System        | 'gromacs/gro'        |
-| ABACUS  | STRU        | False        | False   | System        | 'abacus/stru'        |
-| ABACUS  | STRU        | False        | True    | LabeledSystem | 'abacus/scf'         |
-| ABACUS  | cif         | True         | True    | LabeledSystem | 'abacus/md'          |
-| ABACUS  | STRU        | True         | True    | LabeledSystem | 'abacus/relax'       |
-| ase     | structure   | True         | True    | MultiSystems  | 'ase/structure'      |
-| DFTB+   | dftbplus    | False        | True    | LabeledSystem | 'dftbplus'           |
-| n2p2    | n2p2        | True         | True    | LabeledSystem | 'n2p2'               |
-
-
-The Class `dpdata.MultiSystems`  can read data  from a dir which may contains many files of different systems, or from single xyz file which contains different systems.
-
-Use `dpdata.MultiSystems.from_dir` to read from a  directory, `dpdata.MultiSystems` will walk in the directory
-Recursively  and  find all file with specific file_name. Supports all the file formats that `dpdata.LabeledSystem` supports.
-
-Use  `dpdata.MultiSystems.from_file` to read from single file. Single-file support is available for the `quip/gap/xyz` and `ase/structure` formats.
-
-For example, for `quip/gap xyz` files, single .xyz file may contain many different configurations with different atom numbers and atom type.
-
-The following commands relating to `Class dpdata.MultiSystems` may be useful.
-```python
-# load data
-
-xyz_multi_systems = dpdata.MultiSystems.from_file(
-    file_name="tests/xyz/xyz_unittest.xyz", fmt="quip/gap/xyz"
-)
-vasp_multi_systems = dpdata.MultiSystems.from_dir(
-    dir_name="./mgal_outcar", file_name="OUTCAR", fmt="vasp/outcar"
-)
-
-# use wildcard
-vasp_multi_systems = dpdata.MultiSystems.from_dir(
-    dir_name="./mgal_outcar", file_name="*OUTCAR", fmt="vasp/outcar"
-)
-
-# print the multi_system infomation
-print(xyz_multi_systems)
-print(xyz_multi_systems.systems)  # return a dictionaries
-
-# print the system infomation
-print(xyz_multi_systems.systems["B1C9"].data)
-
-# dump a system's data to ./my_work_dir/B1C9_raw folder
-xyz_multi_systems.systems["B1C9"].to_deepmd_raw("./my_work_dir/B1C9_raw")
-
-# dump all systems
-xyz_multi_systems.to_deepmd_raw("./my_deepmd_data/")
-```
-
-You may also use the following code to parse muti-system:
-```python
-from dpdata import LabeledSystem, MultiSystems
-from glob import glob
-
-"""
-process multi systems
-"""
-fs = glob("./*/OUTCAR")  # remeber to change here !!!
-ms = MultiSystems()
-for f in fs:
-    try:
-        ls = LabeledSystem(f)
-    except:
-        print(f)
-    if len(ls) > 0:
-        ms.append(ls)
-
-ms.to_deepmd_raw("deepmd")
-ms.to_deepmd_npy("deepmd")
-```
+To test if the installation is successful, you may execute
 
-### Access data
-These properties stored in `System` and `LabeledSystem` can be accessed by operator `[]` with the key of the property supplied, for example
-```python
-coords = d_outcar["coords"]
-```
-Available properties are (nframe: number of frames in the system, natoms: total number of atoms in the system)
-
-| key		|  type		| dimension		| are labels	| description
-| ---		| ---		| ---			| ---		| ---
-| 'atom_names'	| list of str	| ntypes		| False		| The name of each atom type
-| 'atom_numbs'	| list of int	| ntypes		| False		| The number of atoms of each atom type
-| 'atom_types'	| np.ndarray	| natoms		| False		| Array assigning type to each atom
-| 'cells'	| np.ndarray	| nframes x 3 x 3	| False		| The cell tensor of each frame
-| 'coords'	| np.ndarray	| nframes x natoms x 3	| False		| The atom coordinates
-| 'energies'	| np.ndarray	| nframes		| True		| The frame energies
-| 'forces'	| np.ndarray	| nframes x natoms x 3	| True		| The atom forces
-| 'virials'	| np.ndarray	| nframes x 3 x 3	| True		| The virial tensor of each frame
-
-
-### Dump data
-The data stored in `System` or `LabeledSystem` can be dumped in 'lammps/lmp' or 'vasp/poscar' format, for example:
-```python
-d_outcar.to("lammps/lmp", "conf.lmp", frame_idx=0)
-```
-The first frames of `d_outcar` will be dumped to 'conf.lmp'
-```python
-d_outcar.to("vasp/poscar", "POSCAR", frame_idx=-1)
-```
-The last frames of `d_outcar` will be dumped to 'POSCAR'.
-
-The data stored in `LabeledSystem` can be dumped to deepmd-kit raw format, for example
-```python
-d_outcar.to("deepmd/raw", "dpmd_raw")
-```
-Or a simpler command:
-```python
-dpdata.LabeledSystem("OUTCAR").to("deepmd/raw", "dpmd_raw")
-```
-Frame selection can be implemented by
-```python
-dpdata.LabeledSystem("OUTCAR").sub_system([0, -1]).to("deepmd/raw", "dpmd_raw")
-```
-by which only the first and last frames are dumped to `dpmd_raw`.
-
-
-### replicate
-dpdata will create a super cell of the current atom configuration.
-```python
-dpdata.System("./POSCAR").replicate(
-    (
-        1,
-        2,
-        3,
-    )
-)
-```
-tuple(1,2,3) means don't copy atom configuration in x direction, make 2 copys in y direction, make 3 copys in z direction.
-
-
-### perturb
-By the following example, each frame of the original system (`dpdata.System('./POSCAR')`) is perturbed to generate three new frames. For each frame, the cell is perturbed by 5% and the atom positions are perturbed by 0.6 Angstrom. `atom_pert_style` indicates that the perturbation to the atom positions is subject to normal distribution. Other available options to `atom_pert_style` are`uniform` (uniform in a ball), and `const` (uniform on a sphere).
-```python
-perturbed_system = dpdata.System("./POSCAR").perturb(
-    pert_num=3,
-    cell_pert_fraction=0.05,
-    atom_pert_distance=0.6,
-    atom_pert_style="normal",
-)
-print(perturbed_system.data)
-```
-
-### replace
-By the following example, Random 8 Hf atoms in the system will be replaced by Zr atoms with the atom postion unchanged.
-```python
-s = dpdata.System("tests/poscars/POSCAR.P42nmc", fmt="vasp/poscar")
-s.replace("Hf", "Zr", 8)
-s.to_vasp_poscar("POSCAR.P42nmc.replace")
-```
-
-## BondOrderSystem
-A new class `BondOrderSystem` which inherits from class `System` is introduced in dpdata. This new class contains information of chemical bonds and formal charges (stored in `BondOrderSystem.data['bonds']`, `BondOrderSystem.data['formal_charges']`). Now BondOrderSystem can only read from .mol/.sdf formats, because of its dependency on rdkit (which means rdkit must be installed if you want to use this function). Other formats, such as pdb, must be converted to .mol/.sdf format (maybe with software like open babel).
-```python
-import dpdata
-
-system_1 = dpdata.BondOrderSystem(
-    "tests/bond_order/CH3OH.mol", fmt="mol"
-)  # read from .mol file
-system_2 = dpdata.BondOrderSystem(
-    "tests/bond_order/methane.sdf", fmt="sdf"
-)  # read from .sdf file
-```
-In sdf file, all molecules must be of the same topology (i.e. conformers of the same molecular configuration).
-`BondOrderSystem` also supports initialize from a `rdkit.Chem.rdchem.Mol` object directly.
-```python
-from rdkit import Chem
-from rdkit.Chem import AllChem
-import dpdata
-
-mol = Chem.MolFromSmiles("CC")
-mol = Chem.AddHs(mol)
-AllChem.EmbedMultipleConfs(mol, 10)
-system = dpdata.BondOrderSystem(rdkit_mol=mol)
-```
-
-### Bond Order Assignment
-The `BondOrderSystem` implements a more robust sanitize procedure for rdkit Mol, as defined in `dpdata.rdkit.santizie.Sanitizer`. This class defines 3 level of sanitization process by: low, medium and high. (default is medium).
-+ low: use `rdkit.Chem.SanitizeMol()` function to sanitize molecule.
-+ medium: before using rdkit, the programm will first assign formal charge of each atom to avoid inappropriate valence exceptions. However, this mode requires the rightness of the bond order information in the given molecule.
-+ high: the program will try to fix inappropriate bond orders in aromatic hetreocycles, phosphate, sulfate, carboxyl, nitro, nitrine, guanidine groups. If this procedure fails to sanitize the given molecule, the program will then try to call `obabel` to pre-process the mol and repeat the sanitization procedure. **That is to say, if you wan't to use this level of sanitization, please ensure `obabel` is installed in the environment.**
-According to our test, our sanitization procedure can successfully read 4852 small molecules in the PDBBind-refined-set. It is necessary to point out that the in the molecule file (mol/sdf), the number of explicit hydrogens has to be correct. Thus, we recommend to use
- `obabel xxx -O xxx -h` to pre-process the file. The reason why we do not implement this hydrogen-adding procedure in dpdata is that we can not ensure its correctness.
-
-```python
-import dpdata
-
-for sdf_file in glob.glob("bond_order/refined-set-ligands/obabel/*sdf"):
-    syst = dpdata.BondOrderSystem(sdf_file, sanitize_level="high", verbose=False)
-```
-### Formal Charge Assignment
-BondOrderSystem implement a method to assign formal charge for each atom based on the 8-electron rule (see below). Note that it only supports common elements in bio-system: B,C,N,O,P,S,As
-```python
-import dpdata
-
-syst = dpdata.BondOrderSystem("tests/bond_order/CH3NH3+.mol", fmt="mol")
-print(syst.get_formal_charges())  # return the formal charge on each atom
-print(syst.get_charge())  # return the total charge of the system
+```bash
+dpdata --version
 ```
 
-If a valence of 3 is detected on carbon, the formal charge will be assigned to -1. Because for most cases (in alkynyl anion, isonitrile, cyclopentadienyl anion), the formal charge on 3-valence carbon is -1, and this is also consisent with the 8-electron rule.
+## Supported packages
 
-## Mixed Type Format
-The format `deepmd/npy/mixed` is the mixed type numpy format for DeePMD-kit, and can be loaded or dumped through class `dpdata.MultiSystems`.
+`dpdata` is aimmed to support different kinds of atomistic packages:
 
-Under this format, systems with the same number of atoms but different formula can be put together
-for a larger system, especially when the frame numbers in systems are sparse.
+- Atomistic machine learning packages, such as [DeePMD-kit](https://github.com/deepmodeling/deepmd-kit);
+- Molecular dynamics packages, such as [LAMMPS](https://github.com/lammps/lammps) and [GROMACS](https://gitlab.com/gromacs/gromacs);
+- Quantum chemistry packages, such as [VASP](https://www.vasp.at/), [Gaussian](https://gaussian.com), and [ABACUS](https://github.com/deepmodeling/abacus-develop);
+- Atomistic visualization packages, such as [3Dmol.js](https://3dmol.csb.pitt.edu/).
+- Other atomistic tools, such as [ASE](https://gitlab.com/ase/ase).
+- Common formats such as `xyz`.
 
-This also helps to mixture the type information together for model training with type embedding network.
+All supported formats are listed [here](https://docs.deepmodeling.com/projects/dpdata/en/master/formats.html).
 
-Here are examples using `deepmd/npy/mixed` format:
+## Quick start
 
-- Dump a MultiSystems into a mixed type numpy directory:
-```python
-import dpdata
+The quickest way to convert a simple file from one format to another one is to use the [command line](https://docs.deepmodeling.com/projects/dpdata/en/master/cli.html).
 
-dpdata.MultiSystems(*systems).to_deepmd_npy_mixed("mixed_dir")
+```sh
+dpdata OUTCAR -i vasp/outcar -o deepmd/npy -O deepmd_data
 ```
 
-- Load a mixed type data into a MultiSystems:
-```python
-import dpdata
-
-dpdata.MultiSystems().load_systems_from_file("mixed_dir", fmt="deepmd/npy/mixed")
-```
+For advanced usage with Python APIs, [read dpdata documentation](https://docs.deepmodeling.com/projects/dpdata/).
 
 ## Plugins
 
-One can follow [a simple example](plugin_example/) to add their own format by creating and installing plugins. It's critical to add the [Format](dpdata/format.py) class to `entry_points['dpdata.plugins']` in [`pyproject.toml`](plugin_example/pyproject.toml):
-```toml
-[project.entry-points.'dpdata.plugins']
-random = "dpdata_random:RandomFormat"
-```
+- [cp2kdata](https://github.com/robinzyb/cp2kdata) adds the latest CP2K support for dpdata.
+
+For how to create your own plugin packages, [read dpdata documentation](https://docs.deepmodeling.com/projects/dpdata/).
diff --git a/docs/index.rst b/docs/index.rst
index 07e381de..3d98bd56 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -6,22 +6,23 @@
 Welcome to dpdata's documentation!
 ==================================
 
+dpdata is a Python package for manipulating atomistic data of software in computational science.
+
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
-   Overview <self>
+   installation
+   systems/index
    try_dpdata
    cli
    formats
    drivers
    minimizers
+   plugin
    api/api
    credits
 
-.. mdinclude:: ../README.md
-
-
 Indices and tables
 ==================
 
diff --git a/docs/installation.md b/docs/installation.md
new file mode 100644
index 00000000..064f9133
--- /dev/null
+++ b/docs/installation.md
@@ -0,0 +1,13 @@
+# Installation
+
+DP-GEN only supports Python 3.7 and above. You can [setup a conda/pip environment](https://docs.deepmodeling.com/faq/conda.html), and then use one of the following methods to install DP-GEN:
+
+- Install via pip: `pip install dpdata`
+- Install via conda: `conda install -c conda-forge dpdata`
+- Install from source code: `git clone https://github.com/deepmodeling/dpdata && pip install ./dpdata`
+
+To test if the installation is successful, you may execute
+
+```bash
+dpdata --version
+```
diff --git a/docs/plugin.md b/docs/plugin.md
new file mode 100644
index 00000000..44e8eabf
--- /dev/null
+++ b/docs/plugin.md
@@ -0,0 +1,9 @@
+# Plugins
+
+One can follow a simple example under `plugin_example/` directory to add their own format by creating and installing plugins.
+It's critical to add the :class:`Format` class to `entry_points['dpdata.plugins']` in `pyproject.toml`:
+
+```toml
+[project.entry-points.'dpdata.plugins']
+random = "dpdata_random:RandomFormat"
+```
diff --git a/docs/systems/bond_order_system.md b/docs/systems/bond_order_system.md
new file mode 100644
index 00000000..443120a7
--- /dev/null
+++ b/docs/systems/bond_order_system.md
@@ -0,0 +1,51 @@
+
+## BondOrderSystem
+A new class :class:`BondOrderSystem` which inherits from class :class:`System` is introduced in dpdata. This new class contains information of chemical bonds and formal charges (stored in `BondOrderSystem.data['bonds']`, `BondOrderSystem.data['formal_charges']`). Now BondOrderSystem can only read from .mol/.sdf formats, because of its dependency on rdkit (which means rdkit must be installed if you want to use this function). Other formats, such as pdb, must be converted to .mol/.sdf format (maybe with software like open babel).
+```python
+import dpdata
+
+system_1 = dpdata.BondOrderSystem(
+    "tests/bond_order/CH3OH.mol", fmt="mol"
+)  # read from .mol file
+system_2 = dpdata.BondOrderSystem(
+    "tests/bond_order/methane.sdf", fmt="sdf"
+)  # read from .sdf file
+```
+In sdf file, all molecules must be of the same topology (i.e. conformers of the same molecular configuration).
+`BondOrderSystem` also supports initialize from a :class:`rdkit.Chem.rdchem.Mol` object directly.
+```python
+from rdkit import Chem
+from rdkit.Chem import AllChem
+import dpdata
+
+mol = Chem.MolFromSmiles("CC")
+mol = Chem.AddHs(mol)
+AllChem.EmbedMultipleConfs(mol, 10)
+system = dpdata.BondOrderSystem(rdkit_mol=mol)
+```
+
+### Bond Order Assignment
+The :class:`BondOrderSystem` implements a more robust sanitize procedure for rdkit Mol, as defined in :class:`dpdata.rdkit.santizie.Sanitizer`. This class defines 3 level of sanitization process by: low, medium and high. (default is medium).
++ low: use `rdkit.Chem.SanitizeMol()` function to sanitize molecule.
++ medium: before using rdkit, the programm will first assign formal charge of each atom to avoid inappropriate valence exceptions. However, this mode requires the rightness of the bond order information in the given molecule.
++ high: the program will try to fix inappropriate bond orders in aromatic hetreocycles, phosphate, sulfate, carboxyl, nitro, nitrine, guanidine groups. If this procedure fails to sanitize the given molecule, the program will then try to call `obabel` to pre-process the mol and repeat the sanitization procedure. **That is to say, if you wan't to use this level of sanitization, please ensure `obabel` is installed in the environment.**
+According to our test, our sanitization procedure can successfully read 4852 small molecules in the PDBBind-refined-set. It is necessary to point out that the in the molecule file (mol/sdf), the number of explicit hydrogens has to be correct. Thus, we recommend to use
+ `obabel xxx -O xxx -h` to pre-process the file. The reason why we do not implement this hydrogen-adding procedure in dpdata is that we can not ensure its correctness.
+
+```python
+import dpdata
+
+for sdf_file in glob.glob("bond_order/refined-set-ligands/obabel/*sdf"):
+    syst = dpdata.BondOrderSystem(sdf_file, sanitize_level="high", verbose=False)
+```
+### Formal Charge Assignment
+BondOrderSystem implement a method to assign formal charge for each atom based on the 8-electron rule (see below). Note that it only supports common elements in bio-system: B,C,N,O,P,S,As
+```python
+import dpdata
+
+syst = dpdata.BondOrderSystem("tests/bond_order/CH3NH3+.mol", fmt="mol")
+print(syst.get_formal_charges())  # return the formal charge on each atom
+print(syst.get_charge())  # return the total charge of the system
+```
+
+If a valence of 3 is detected on carbon, the formal charge will be assigned to -1. Because for most cases (in alkynyl anion, isonitrile, cyclopentadienyl anion), the formal charge on 3-valence carbon is -1, and this is also consisent with the 8-electron rule.
diff --git a/docs/systems/index.rst b/docs/systems/index.rst
new file mode 100644
index 00000000..dfcbe698
--- /dev/null
+++ b/docs/systems/index.rst
@@ -0,0 +1,11 @@
+Systems
+=======
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   system
+   multi
+   bond_order_system
+   mixed
diff --git a/docs/systems/mixed.md b/docs/systems/mixed.md
new file mode 100644
index 00000000..69bf80ea
--- /dev/null
+++ b/docs/systems/mixed.md
@@ -0,0 +1,24 @@
+# Mixed Type Format
+
+The format `deepmd/npy/mixed` is the mixed type numpy format for DeePMD-kit, and can be loaded or dumped through class :class:`dpdata.MultiSystems`.
+
+Under this format, systems with the same number of atoms but different formula can be put together
+for a larger system, especially when the frame numbers in systems are sparse.
+
+This also helps to mixture the type information together for model training with type embedding network.
+
+Here are examples using `deepmd/npy/mixed` format:
+
+- Dump a MultiSystems into a mixed type numpy directory:
+```python
+import dpdata
+
+dpdata.MultiSystems(*systems).to_deepmd_npy_mixed("mixed_dir")
+```
+
+- Load a mixed type data into a MultiSystems:
+```python
+import dpdata
+
+dpdata.MultiSystems().load_systems_from_file("mixed_dir", fmt="deepmd/npy/mixed")
+```
diff --git a/docs/systems/multi.md b/docs/systems/multi.md
new file mode 100644
index 00000000..8e47acf7
--- /dev/null
+++ b/docs/systems/multi.md
@@ -0,0 +1,62 @@
+# `MultiSystems`
+
+The Class :class:`dpdata.MultiSystems`  can read data  from a dir which may contains many files of different systems, or from single xyz file which contains different systems.
+
+Use :meth:`dpdata.MultiSystems.from_dir` to read from a  directory, :class:`dpdata.MultiSystems` will walk in the directory
+Recursively  and  find all file with specific file_name. Supports all the file formats that :class:`dpdata.LabeledSystem` supports.
+
+Use :meth:`dpdata.MultiSystems.from_file` to read from single file. Single-file support is available for the `quip/gap/xyz` and `ase/structure` formats.
+
+For example, for `quip/gap xyz` files, single .xyz file may contain many different configurations with different atom numbers and atom type.
+
+The following commands relating to :class:`dpdata.MultiSystems` may be useful.
+```python
+# load data
+
+xyz_multi_systems = dpdata.MultiSystems.from_file(
+    file_name="tests/xyz/xyz_unittest.xyz", fmt="quip/gap/xyz"
+)
+vasp_multi_systems = dpdata.MultiSystems.from_dir(
+    dir_name="./mgal_outcar", file_name="OUTCAR", fmt="vasp/outcar"
+)
+
+# use wildcard
+vasp_multi_systems = dpdata.MultiSystems.from_dir(
+    dir_name="./mgal_outcar", file_name="*OUTCAR", fmt="vasp/outcar"
+)
+
+# print the multi_system infomation
+print(xyz_multi_systems)
+print(xyz_multi_systems.systems)  # return a dictionaries
+
+# print the system infomation
+print(xyz_multi_systems.systems["B1C9"].data)
+
+# dump a system's data to ./my_work_dir/B1C9_raw folder
+xyz_multi_systems.systems["B1C9"].to_deepmd_raw("./my_work_dir/B1C9_raw")
+
+# dump all systems
+xyz_multi_systems.to_deepmd_raw("./my_deepmd_data/")
+```
+
+You may also use the following code to parse muti-system:
+```python
+from dpdata import LabeledSystem, MultiSystems
+from glob import glob
+
+"""
+process multi systems
+"""
+fs = glob("./*/OUTCAR")  # remeber to change here !!!
+ms = MultiSystems()
+for f in fs:
+    try:
+        ls = LabeledSystem(f)
+    except:
+        print(f)
+    if len(ls) > 0:
+        ms.append(ls)
+
+ms.to_deepmd_raw("deepmd")
+ms.to_deepmd_npy("deepmd")
+```
diff --git a/docs/systems/system.md b/docs/systems/system.md
new file mode 100644
index 00000000..0401a311
--- /dev/null
+++ b/docs/systems/system.md
@@ -0,0 +1,112 @@
+# `System` and `LabeledSystem`
+
+This section gives some examples on how dpdata works. Firstly one needs to import the module in a python 3.x compatible code.
+```python
+import dpdata
+```
+The typicall workflow of `dpdata` is
+
+1. Load data from vasp or lammps or deepmd-kit data files.
+2. Manipulate data
+3. Dump data to in a desired format
+
+
+### Load data
+```python
+d_poscar = dpdata.System("POSCAR", fmt="vasp/poscar")
+```
+or let dpdata infer the format (`vasp/poscar`) of the file from the file name extension
+```python
+d_poscar = dpdata.System("my.POSCAR")
+```
+The number of atoms, atom types, coordinates are loaded from the `POSCAR` and stored to a data :class:`System` called `d_poscar`.
+A data :class:`System` (a concept used by [deepmd-kit](https://github.com/deepmodeling/deepmd-kit)) contains frames that has the same number of atoms of the same type. The order of the atoms should be consistent among the frames in one :class:`System`.
+It is noted that `POSCAR` only contains one frame.
+If the multiple frames stored in, for example, a `OUTCAR` is wanted,
+```python
+d_outcar = dpdata.LabeledSystem("OUTCAR")
+```
+The labels provided in the `OUTCAR`, i.e. energies, forces and virials (if any), are loaded by :class:`LabeledSystem`. It is noted that the forces of atoms are always assumed to exist. :class:`LabeledSystem` is a derived class of :class:`System`.
+
+The :class:`System` or :class:`LabeledSystem` can be constructed from the following file formats with the `format key` in the table passed to argument `fmt`:
+
+
+
+### Access data
+These properties stored in :class:`System` and :class:`LabeledSystem` can be accessed by operator `[]` with the key of the property supplied, for example
+```python
+coords = d_outcar["coords"]
+```
+Available properties are (nframe: number of frames in the system, natoms: total number of atoms in the system)
+
+| key		|  type		| dimension		| are labels	| description
+| ---		| ---		| ---			| ---		| ---
+| 'atom_names'	| list of str	| ntypes		| False		| The name of each atom type
+| 'atom_numbs'	| list of int	| ntypes		| False		| The number of atoms of each atom type
+| 'atom_types'	| np.ndarray	| natoms		| False		| Array assigning type to each atom
+| 'cells'	| np.ndarray	| nframes x 3 x 3	| False		| The cell tensor of each frame
+| 'coords'	| np.ndarray	| nframes x natoms x 3	| False		| The atom coordinates
+| 'energies'	| np.ndarray	| nframes		| True		| The frame energies
+| 'forces'	| np.ndarray	| nframes x natoms x 3	| True		| The atom forces
+| 'virials'	| np.ndarray	| nframes x 3 x 3	| True		| The virial tensor of each frame
+
+
+### Dump data
+The data stored in :class:`System` or :class:`LabeledSystem` can be dumped in 'lammps/lmp' or 'vasp/poscar' format, for example:
+```python
+d_outcar.to("lammps/lmp", "conf.lmp", frame_idx=0)
+```
+The first frames of `d_outcar` will be dumped to 'conf.lmp'
+```python
+d_outcar.to("vasp/poscar", "POSCAR", frame_idx=-1)
+```
+The last frames of `d_outcar` will be dumped to 'POSCAR'.
+
+The data stored in `LabeledSystem` can be dumped to deepmd-kit raw format, for example
+```python
+d_outcar.to("deepmd/raw", "dpmd_raw")
+```
+Or a simpler command:
+```python
+dpdata.LabeledSystem("OUTCAR").to("deepmd/raw", "dpmd_raw")
+```
+Frame selection can be implemented by
+```python
+dpdata.LabeledSystem("OUTCAR").sub_system([0, -1]).to("deepmd/raw", "dpmd_raw")
+```
+by which only the first and last frames are dumped to `dpmd_raw`.
+
+
+### replicate
+dpdata will create a super cell of the current atom configuration.
+```python
+dpdata.System("./POSCAR").replicate(
+    (
+        1,
+        2,
+        3,
+    )
+)
+```
+tuple(1,2,3) means don't copy atom configuration in x direction, make 2 copys in y direction, make 3 copys in z direction.
+
+
+### perturb
+By the following example, each frame of the original system (`dpdata.System('./POSCAR')`) is perturbed to generate three new frames. For each frame, the cell is perturbed by 5% and the atom positions are perturbed by 0.6 Angstrom. `atom_pert_style` indicates that the perturbation to the atom positions is subject to normal distribution. Other available options to `atom_pert_style` are`uniform` (uniform in a ball), and `const` (uniform on a sphere).
+```python
+perturbed_system = dpdata.System("./POSCAR").perturb(
+    pert_num=3,
+    cell_pert_fraction=0.05,
+    atom_pert_distance=0.6,
+    atom_pert_style="normal",
+)
+print(perturbed_system.data)
+```
+
+### replace
+By the following example, Random 8 Hf atoms in the system will be replaced by Zr atoms with the atom postion unchanged.
+```python
+s = dpdata.System("tests/poscars/POSCAR.P42nmc", fmt="vasp/poscar")
+s.replace("Hf", "Zr", 8)
+s.to_vasp_poscar("POSCAR.P42nmc.replace")
+```

From 5df6acd266589b131c961390414337472e0880d9 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Mon, 2 Sep 2024 22:18:50 -0400
Subject: [PATCH 10/33] fix: fix a typo in #702 (#710)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Improvements**
- Enhanced the flexibility of data handling by modifying how data types
are processed, allowing for better adaptability based on context.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 dpdata/deepmd/comp.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dpdata/deepmd/comp.py b/dpdata/deepmd/comp.py
index 66111016..ad638408 100644
--- a/dpdata/deepmd/comp.py
+++ b/dpdata/deepmd/comp.py
@@ -180,7 +180,7 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
         dtypes = dpdata.system.LabeledSystem.DTYPES
     else:
         dtypes = dpdata.system.System.DTYPES
-    for dtype in dpdata.system.LabeledSystem.DTYPES:
+    for dtype in dtypes:
         if dtype.name in (
             "atom_numbs",
             "atom_names",

From 6bf41e31b4952e54e7cec6f8b6c9cc3aabdc05cb Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Mon, 2 Sep 2024 22:58:22 -0400
Subject: [PATCH 11/33] feat: file object passed to open (#709)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Introduced a new utility function `open_file` for improved file
handling across various modules.
- Enhanced type annotations for multiple functions to specify
`FileType`, improving code clarity and type safety.

- **Bug Fixes**
- Improved file handling robustness by replacing the built-in `open`
function with the custom `open_file` function in several modules.

- **Tests**
- Added unit tests for the new `open_file` utility function to ensure
reliable functionality.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

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>
---
 dpdata/abacus/md.py        | 10 +++++----
 dpdata/abacus/relax.py     |  8 ++++---
 dpdata/abacus/scf.py       | 10 +++++----
 dpdata/amber/md.py         |  7 +++---
 dpdata/amber/sqm.py        | 14 ++++++++----
 dpdata/deepmd/comp.py      |  3 ++-
 dpdata/deepmd/raw.py       |  5 +++--
 dpdata/dftbplus/output.py  | 15 ++++++++++---
 dpdata/gaussian/log.py     | 11 +++++++--
 dpdata/gromacs/gro.py      | 10 +++++++--
 dpdata/lammps/dump.py      | 10 +++++++--
 dpdata/openmx/omx.py       | 21 +++++++++++------
 dpdata/orca/output.py      | 13 +++++++++--
 dpdata/plugins/abacus.py   | 10 +++++++--
 dpdata/plugins/amber.py    |  3 ++-
 dpdata/plugins/gaussian.py | 19 ++++++++++------
 dpdata/plugins/gromacs.py  | 12 ++++++++--
 dpdata/plugins/lammps.py   | 14 ++++++++----
 dpdata/plugins/n2p2.py     | 14 ++++++++----
 dpdata/plugins/orca.py     |  9 ++++++--
 dpdata/plugins/psi4.py     | 14 ++++++++----
 dpdata/plugins/pwmat.py    | 14 ++++++++----
 dpdata/plugins/vasp.py     | 15 ++++++++-----
 dpdata/plugins/xyz.py      | 14 ++++++++----
 dpdata/psi4/output.py      | 10 +++++++--
 dpdata/qe/scf.py           |  6 +++--
 dpdata/qe/traj.py          | 20 +++++++++++------
 dpdata/utils.py            | 46 +++++++++++++++++++++++++++++++++++++-
 tests/test_read_file.py    | 22 ++++++++++++++++++
 29 files changed, 289 insertions(+), 90 deletions(-)
 create mode 100644 tests/test_read_file.py

diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py
index fa184177..9e0a416a 100644
--- a/dpdata/abacus/md.py
+++ b/dpdata/abacus/md.py
@@ -5,6 +5,8 @@
 
 import numpy as np
 
+from dpdata.utils import open_file
+
 from .scf import (
     bohr2ang,
     get_cell,
@@ -156,12 +158,12 @@ def get_frame(fname):
         path_in = os.path.join(fname, "INPUT")
     else:
         raise RuntimeError("invalid input")
-    with open(path_in) as fp:
+    with open_file(path_in) as fp:
         inlines = fp.read().split("\n")
     geometry_path_in = get_geometry_in(fname, inlines)  # base dir of STRU
     path_out = get_path_out(fname, inlines)
 
-    with open(geometry_path_in) as fp:
+    with open_file(geometry_path_in) as fp:
         geometry_inlines = fp.read().split("\n")
     celldm, cell = get_cell(geometry_inlines)
     atom_names, natoms, types, coords = get_coords(
@@ -172,11 +174,11 @@ def get_frame(fname):
     # ndump = int(os.popen("ls -l %s | grep 'md_pos_' | wc -l" %path_out).readlines()[0])
     # number of dumped geometry files
     # coords = get_coords_from_cif(ndump, dump_freq, atom_names, natoms, types, path_out, cell)
-    with open(os.path.join(path_out, "MD_dump")) as fp:
+    with open_file(os.path.join(path_out, "MD_dump")) as fp:
         dumplines = fp.read().split("\n")
     coords, cells, force, stress = get_coords_from_dump(dumplines, natoms)
     ndump = np.shape(coords)[0]
-    with open(os.path.join(path_out, "running_md.log")) as fp:
+    with open_file(os.path.join(path_out, "running_md.log")) as fp:
         outlines = fp.read().split("\n")
     energy = get_energy(outlines, ndump, dump_freq)
 
diff --git a/dpdata/abacus/relax.py b/dpdata/abacus/relax.py
index 976243b8..7a4abf35 100644
--- a/dpdata/abacus/relax.py
+++ b/dpdata/abacus/relax.py
@@ -4,6 +4,8 @@
 
 import numpy as np
 
+from dpdata.utils import open_file
+
 from .scf import (
     bohr2ang,
     collect_force,
@@ -174,10 +176,10 @@ def get_frame(fname):
         path_in = os.path.join(fname, "INPUT")
     else:
         raise RuntimeError("invalid input")
-    with open(path_in) as fp:
+    with open_file(path_in) as fp:
         inlines = fp.read().split("\n")
     geometry_path_in = get_geometry_in(fname, inlines)  # base dir of STRU
-    with open(geometry_path_in) as fp:
+    with open_file(geometry_path_in) as fp:
         geometry_inlines = fp.read().split("\n")
     celldm, cell = get_cell(geometry_inlines)
     atom_names, natoms, types, coord_tmp = get_coords(
@@ -186,7 +188,7 @@ def get_frame(fname):
 
     logf = get_log_file(fname, inlines)
     assert os.path.isfile(logf), f"Error: can not find {logf}"
-    with open(logf) as f1:
+    with open_file(logf) as f1:
         lines = f1.readlines()
 
     atomnumber = 0
diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py
index c06f8cd3..93e3d6e1 100644
--- a/dpdata/abacus/scf.py
+++ b/dpdata/abacus/scf.py
@@ -6,6 +6,8 @@
 
 import numpy as np
 
+from dpdata.utils import open_file
+
 from ..unit import EnergyConversion, LengthConversion, PressureConversion
 
 bohr2ang = LengthConversion("bohr", "angstrom").value()
@@ -253,7 +255,7 @@ def get_frame(fname):
     if not CheckFile(path_in):
         return data
 
-    with open(path_in) as fp:
+    with open_file(path_in) as fp:
         inlines = fp.read().split("\n")
 
     geometry_path_in = get_geometry_in(fname, inlines)
@@ -261,9 +263,9 @@ def get_frame(fname):
     if not (CheckFile(geometry_path_in) and CheckFile(path_out)):
         return data
 
-    with open(geometry_path_in) as fp:
+    with open_file(geometry_path_in) as fp:
         geometry_inlines = fp.read().split("\n")
-    with open(path_out) as fp:
+    with open_file(path_out) as fp:
         outlines = fp.read().split("\n")
 
     celldm, cell = get_cell(geometry_inlines)
@@ -338,7 +340,7 @@ def get_nele_from_stru(geometry_inlines):
 
 def get_frame_from_stru(fname):
     assert isinstance(fname, str)
-    with open(fname) as fp:
+    with open_file(fname) as fp:
         geometry_inlines = fp.read().split("\n")
     nele = get_nele_from_stru(geometry_inlines)
     inlines = ["ntype %d" % nele]
diff --git a/dpdata/amber/md.py b/dpdata/amber/md.py
index f3217fbd..cb4f2d25 100644
--- a/dpdata/amber/md.py
+++ b/dpdata/amber/md.py
@@ -7,6 +7,7 @@
 
 from dpdata.amber.mask import pick_by_amber_mask
 from dpdata.unit import EnergyConversion
+from dpdata.utils import open_file
 
 from ..periodic_table import ELEMENTS
 
@@ -51,7 +52,7 @@ def read_amber_traj(
     flag_atom_numb = False
     amber_types = []
     atomic_number = []
-    with open(parm7_file) as f:
+    with open_file(parm7_file) as f:
         for line in f:
             if line.startswith("%FLAG"):
                 flag_atom_type = line.startswith("%FLAG AMBER_ATOM_TYPE")
@@ -101,14 +102,14 @@ def read_amber_traj(
         # load energy from mden_file or mdout_file
         energies = []
         if mden_file is not None and os.path.isfile(mden_file):
-            with open(mden_file) as f:
+            with open_file(mden_file) as f:
                 for line in f:
                     if line.startswith("L6"):
                         s = line.split()
                         if s[2] != "E_pot":
                             energies.append(float(s[2]))
         elif mdout_file is not None and os.path.isfile(mdout_file):
-            with open(mdout_file) as f:
+            with open_file(mdout_file) as f:
                 for line in f:
                     if "EPtot" in line:
                         s = line.split()
diff --git a/dpdata/amber/sqm.py b/dpdata/amber/sqm.py
index 1be3802a..93e41f9a 100644
--- a/dpdata/amber/sqm.py
+++ b/dpdata/amber/sqm.py
@@ -1,9 +1,15 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 
 from dpdata.periodic_table import ELEMENTS
 from dpdata.unit import EnergyConversion
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
 
 kcal2ev = EnergyConversion("kcal_mol", "eV").value()
 
@@ -14,7 +20,7 @@
 READ_FORCES = 7
 
 
-def parse_sqm_out(fname):
+def parse_sqm_out(fname: FileType):
     """Read atom symbols, charges and coordinates from ambertools sqm.out file."""
     atom_symbols = []
     coords = []
@@ -22,7 +28,7 @@ def parse_sqm_out(fname):
     forces = []
     energies = []
 
-    with open(fname) as f:
+    with open_file(fname) as f:
         flag = START
         for line in f:
             if line.startswith(" Total SCF energy"):
@@ -81,7 +87,7 @@ def parse_sqm_out(fname):
     return data
 
 
-def make_sqm_in(data, fname=None, frame_idx=0, **kwargs):
+def make_sqm_in(data, fname: FileType | None = None, frame_idx=0, **kwargs):
     symbols = [data["atom_names"][ii] for ii in data["atom_types"]]
     atomic_numbers = [ELEMENTS.index(ss) + 1 for ss in symbols]
     charge = kwargs.get("charge", 0)
@@ -109,6 +115,6 @@ def make_sqm_in(data, fname=None, frame_idx=0, **kwargs):
             f"{data['coords'][frame_idx][ii, 2]:.6f}",
         )
     if fname is not None:
-        with open(fname, "w") as fp:
+        with open_file(fname, "w") as fp:
             fp.write(ret)
     return ret
diff --git a/dpdata/deepmd/comp.py b/dpdata/deepmd/comp.py
index ad638408..5ba3914e 100644
--- a/dpdata/deepmd/comp.py
+++ b/dpdata/deepmd/comp.py
@@ -8,6 +8,7 @@
 import numpy as np
 
 import dpdata
+from dpdata.utils import open_file
 
 from .raw import load_type
 
@@ -172,7 +173,7 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
     except OSError:
         pass
     if data.get("nopbc", False):
-        with open(os.path.join(folder, "nopbc"), "w") as fw_nopbc:
+        with open_file(os.path.join(folder, "nopbc"), "w") as fw_nopbc:
             pass
     # allow custom dtypes
     labels = "energies" in data
diff --git a/dpdata/deepmd/raw.py b/dpdata/deepmd/raw.py
index 717c73f9..f8ddcaf3 100644
--- a/dpdata/deepmd/raw.py
+++ b/dpdata/deepmd/raw.py
@@ -6,6 +6,7 @@
 import numpy as np
 
 import dpdata
+from dpdata.utils import open_file
 
 
 def load_type(folder, type_map=None):
@@ -17,7 +18,7 @@ def load_type(folder, type_map=None):
     data["atom_names"] = []
     # if find type_map.raw, use it
     if os.path.isfile(os.path.join(folder, "type_map.raw")):
-        with open(os.path.join(folder, "type_map.raw")) as fp:
+        with open_file(os.path.join(folder, "type_map.raw")) as fp:
             my_type_map = fp.read().split()
     # else try to use arg type_map
     elif type_map is not None:
@@ -140,7 +141,7 @@ def dump(folder, data):
     except OSError:
         pass
     if data.get("nopbc", False):
-        with open(os.path.join(folder, "nopbc"), "w") as fw_nopbc:
+        with open_file(os.path.join(folder, "nopbc"), "w") as fw_nopbc:
             pass
     # allow custom dtypes
     labels = "energies" in data
diff --git a/dpdata/dftbplus/output.py b/dpdata/dftbplus/output.py
index 0f10c3ac..49fdd2b1 100644
--- a/dpdata/dftbplus/output.py
+++ b/dpdata/dftbplus/output.py
@@ -1,9 +1,18 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
+
 
-def read_dftb_plus(fn_1: str, fn_2: str) -> tuple[str, np.ndarray, float, np.ndarray]:
+def read_dftb_plus(
+    fn_1: FileType, fn_2: FileType
+) -> tuple[str, np.ndarray, float, np.ndarray]:
     """Read from DFTB+ input and output.
 
     Parameters
@@ -29,7 +38,7 @@ def read_dftb_plus(fn_1: str, fn_2: str) -> tuple[str, np.ndarray, float, np.nda
     symbols = None
     forces = None
     energy = None
-    with open(fn_1) as f:
+    with open_file(fn_1) as f:
         flag = 0
         for line in f:
             if flag == 1:
@@ -49,7 +58,7 @@ def read_dftb_plus(fn_1: str, fn_2: str) -> tuple[str, np.ndarray, float, np.nda
                 flag += 1
                 if flag == 7:
                     flag = 0
-    with open(fn_2) as f:
+    with open_file(fn_2) as f:
         flag = 0
         for line in f:
             if line.startswith("Total Forces"):
diff --git a/dpdata/gaussian/log.py b/dpdata/gaussian/log.py
index 204cf464..08a65b9d 100644
--- a/dpdata/gaussian/log.py
+++ b/dpdata/gaussian/log.py
@@ -1,7 +1,14 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
+
 from ..periodic_table import ELEMENTS
 from ..unit import EnergyConversion, ForceConversion, LengthConversion
 
@@ -12,7 +19,7 @@
 symbols = ["X"] + ELEMENTS
 
 
-def to_system_data(file_name, md=False):
+def to_system_data(file_name: FileType, md=False):
     """Read Gaussian log file.
 
     Parameters
@@ -43,7 +50,7 @@ def to_system_data(file_name, md=False):
     nopbc = True
     coords = None
 
-    with open(file_name) as fp:
+    with open_file(file_name) as fp:
         for line in fp:
             if line.startswith(" SCF Done"):
                 # energies
diff --git a/dpdata/gromacs/gro.py b/dpdata/gromacs/gro.py
index aca2443b..fe83e0c5 100644
--- a/dpdata/gromacs/gro.py
+++ b/dpdata/gromacs/gro.py
@@ -2,9 +2,15 @@
 from __future__ import annotations
 
 import re
+from typing import TYPE_CHECKING
 
 import numpy as np
 
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
+
 from ..unit import LengthConversion
 
 nm2ang = LengthConversion("nm", "angstrom").value()
@@ -48,9 +54,9 @@ def _get_cell(line):
     return cell
 
 
-def file_to_system_data(fname, format_atom_name=True, **kwargs):
+def file_to_system_data(fname: FileType, format_atom_name=True, **kwargs):
     system = {"coords": [], "cells": []}
-    with open(fname) as fp:
+    with open_file(fname) as fp:
         frame = 0
         while True:
             flag = fp.readline()
diff --git a/dpdata/lammps/dump.py b/dpdata/lammps/dump.py
index f0ade2b0..72fee27d 100644
--- a/dpdata/lammps/dump.py
+++ b/dpdata/lammps/dump.py
@@ -3,9 +3,15 @@
 
 import os
 import sys
+from typing import TYPE_CHECKING
 
 import numpy as np
 
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
+
 lib_path = os.path.dirname(os.path.realpath(__file__))
 sys.path.append(lib_path)
 import warnings
@@ -169,11 +175,11 @@ def box2dumpbox(orig, box):
     return bounds, tilt
 
 
-def load_file(fname, begin=0, step=1):
+def load_file(fname: FileType, begin=0, step=1):
     lines = []
     buff = []
     cc = -1
-    with open(fname) as fp:
+    with open_file(fname) as fp:
         while True:
             line = fp.readline().rstrip("\n")
             if not line:
diff --git a/dpdata/openmx/omx.py b/dpdata/openmx/omx.py
index d3afff00..aae9b578 100644
--- a/dpdata/openmx/omx.py
+++ b/dpdata/openmx/omx.py
@@ -1,8 +1,15 @@
 #!/usr/bin/python3
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
+
 from ..unit import (
     EnergyConversion,
     ForceConversion,
@@ -98,12 +105,12 @@ def load_cells(lines):
 
 
 # load atom_names, atom_numbs, atom_types, cells
-def load_param_file(fname, mdname):
-    with open(fname) as dat_file:
+def load_param_file(fname: FileType, mdname: FileType):
+    with open_file(fname) as dat_file:
         lines = dat_file.readlines()
     atom_names, atom_types, atom_numbs = load_atom(lines)
 
-    with open(mdname) as md_file:
+    with open_file(mdname) as md_file:
         lines = md_file.readlines()
     cells = load_cells(lines)
     return atom_names, atom_numbs, atom_types, cells
@@ -133,15 +140,15 @@ def load_coords(lines, atom_names, natoms):
     return coords
 
 
-def load_data(mdname, atom_names, natoms):
-    with open(mdname) as md_file:
+def load_data(mdname: FileType, atom_names, natoms):
+    with open_file(mdname) as md_file:
         lines = md_file.readlines()
     coords = load_coords(lines, atom_names, natoms)
     steps = [str(i) for i in range(1, coords.shape[0] + 1)]
     return coords, steps
 
 
-def to_system_data(fname, mdname):
+def to_system_data(fname: FileType, mdname: FileType):
     data = {}
     (
         data["atom_names"],
@@ -194,7 +201,7 @@ def load_force(lines, atom_names, atom_numbs):
 # load energy, force
 def to_system_label(fname, mdname):
     atom_names, atom_numbs, atom_types, cells = load_param_file(fname, mdname)
-    with open(mdname) as md_file:
+    with open_file(mdname) as md_file:
         lines = md_file.readlines()
     energy = load_energy(lines)
     force = load_force(lines, atom_names, atom_numbs)
diff --git a/dpdata/orca/output.py b/dpdata/orca/output.py
index a23013fd..a0915162 100644
--- a/dpdata/orca/output.py
+++ b/dpdata/orca/output.py
@@ -1,9 +1,18 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
+
 
-def read_orca_sp_output(fn: str) -> tuple[np.ndarray, np.ndarray, float, np.ndarray]:
+def read_orca_sp_output(
+    fn: FileType,
+) -> tuple[np.ndarray, np.ndarray, float, np.ndarray]:
     """Read from ORCA output.
 
     Note that both the energy and the gradient should be printed.
@@ -28,7 +37,7 @@ def read_orca_sp_output(fn: str) -> tuple[np.ndarray, np.ndarray, float, np.ndar
     symbols = None
     forces = None
     energy = None
-    with open(fn) as f:
+    with open_file(fn) as f:
         flag = 0
         for line in f:
             if flag in (1, 3, 4):
diff --git a/dpdata/plugins/abacus.py b/dpdata/plugins/abacus.py
index eb2d7786..e3367b35 100644
--- a/dpdata/plugins/abacus.py
+++ b/dpdata/plugins/abacus.py
@@ -1,9 +1,15 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import dpdata.abacus.md
 import dpdata.abacus.relax
 import dpdata.abacus.scf
 from dpdata.format import Format
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
 
 
 @Format.register("abacus/stru")
@@ -12,7 +18,7 @@ class AbacusSTRUFormat(Format):
     def from_system(self, file_name, **kwargs):
         return dpdata.abacus.scf.get_frame_from_stru(file_name)
 
-    def to_system(self, data, file_name, frame_idx=0, **kwargs):
+    def to_system(self, data, file_name: FileType, frame_idx=0, **kwargs):
         """Dump the system into ABACUS STRU format file.
 
         Parameters
@@ -46,7 +52,7 @@ def to_system(self, data, file_name, frame_idx=0, **kwargs):
             numerical_descriptor=numerical_descriptor,
             mass=mass,
         )
-        with open(file_name, "w") as fp:
+        with open_file(file_name, "w") as fp:
             fp.write(stru_string)
 
 
diff --git a/dpdata/plugins/amber.py b/dpdata/plugins/amber.py
index 42fce552..361e0d8a 100644
--- a/dpdata/plugins/amber.py
+++ b/dpdata/plugins/amber.py
@@ -8,6 +8,7 @@
 import dpdata.amber.sqm
 from dpdata.driver import Driver, Minimizer
 from dpdata.format import Format
+from dpdata.utils import open_file
 
 
 @Format.register("amber/md")
@@ -143,7 +144,7 @@ def label(self, data: dict) -> dict:
                         [*self.sqm_exec.split(), "-O", "-i", inp_fn, "-o", out_fn]
                     )
                 except sp.CalledProcessError as e:
-                    with open(out_fn) as f:
+                    with open_file(out_fn) as f:
                         raise RuntimeError(
                             "Run sqm failed! Output:\n" + f.read()
                         ) from e
diff --git a/dpdata/plugins/gaussian.py b/dpdata/plugins/gaussian.py
index b55447b9..55bee5a4 100644
--- a/dpdata/plugins/gaussian.py
+++ b/dpdata/plugins/gaussian.py
@@ -3,16 +3,21 @@
 import os
 import subprocess as sp
 import tempfile
+from typing import TYPE_CHECKING
 
 import dpdata.gaussian.gjf
 import dpdata.gaussian.log
 from dpdata.driver import Driver
 from dpdata.format import Format
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
 
 
 @Format.register("gaussian/log")
 class GaussianLogFormat(Format):
-    def from_labeled_system(self, file_name, md=False, **kwargs):
+    def from_labeled_system(self, file_name: FileType, md=False, **kwargs):
         try:
             return dpdata.gaussian.log.to_system_data(file_name, md=md)
         except AssertionError:
@@ -21,7 +26,7 @@ def from_labeled_system(self, file_name, md=False, **kwargs):
 
 @Format.register("gaussian/md")
 class GaussianMDFormat(Format):
-    def from_labeled_system(self, file_name, **kwargs):
+    def from_labeled_system(self, file_name: FileType, **kwargs):
         return GaussianLogFormat().from_labeled_system(file_name, md=True)
 
 
@@ -29,7 +34,7 @@ def from_labeled_system(self, file_name, **kwargs):
 class GaussiaGJFFormat(Format):
     """Gaussian input file."""
 
-    def from_system(self, file_name: str, **kwargs):
+    def from_system(self, file_name: FileType, **kwargs):
         """Read Gaussian input file.
 
         Parameters
@@ -39,11 +44,11 @@ def from_system(self, file_name: str, **kwargs):
         **kwargs : dict
             keyword arguments
         """
-        with open(file_name) as fp:
+        with open_file(file_name) as fp:
             text = fp.read()
         return dpdata.gaussian.gjf.read_gaussian_input(text)
 
-    def to_system(self, data: dict, file_name: str, **kwargs):
+    def to_system(self, data: dict, file_name: FileType, **kwargs):
         """Generate Gaussian input file.
 
         Parameters
@@ -56,7 +61,7 @@ def to_system(self, data: dict, file_name: str, **kwargs):
             Other parameters to make input files. See :meth:`dpdata.gaussian.gjf.make_gaussian_input`
         """
         text = dpdata.gaussian.gjf.make_gaussian_input(data, **kwargs)
-        with open(file_name, "w") as fp:
+        with open_file(file_name, "w") as fp:
             fp.write(text)
 
 
@@ -110,7 +115,7 @@ def label(self, data: dict) -> dict:
                 try:
                     sp.check_output([*self.gaussian_exec.split(), inp_fn])
                 except sp.CalledProcessError as e:
-                    with open(out_fn) as f:
+                    with open_file(out_fn) as f:
                         out = f.read()
                     raise RuntimeError("Run gaussian failed! Output:\n" + out) from e
                 labeled_system.append(dpdata.LabeledSystem(out_fn, fmt="gaussian/log"))
diff --git a/dpdata/plugins/gromacs.py b/dpdata/plugins/gromacs.py
index 12dece71..a7066bbc 100644
--- a/dpdata/plugins/gromacs.py
+++ b/dpdata/plugins/gromacs.py
@@ -1,7 +1,13 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import dpdata.gromacs.gro
 from dpdata.format import Format
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
 
 
 @Format.register("gro")
@@ -23,7 +29,9 @@ def from_system(self, file_name, format_atom_name=True, **kwargs):
             file_name, format_atom_name=format_atom_name, **kwargs
         )
 
-    def to_system(self, data, file_name=None, frame_idx=-1, **kwargs):
+    def to_system(
+        self, data, file_name: FileType | None = None, frame_idx=-1, **kwargs
+    ):
         """Dump the system in gromacs .gro format.
 
         Parameters
@@ -52,5 +60,5 @@ def to_system(self, data, file_name=None, frame_idx=-1, **kwargs):
         if file_name is None:
             return gro_str
         else:
-            with open(file_name, "w+") as fp:
+            with open_file(file_name, "w+") as fp:
                 fp.write(gro_str)
diff --git a/dpdata/plugins/lammps.py b/dpdata/plugins/lammps.py
index 65e7f570..0327d444 100644
--- a/dpdata/plugins/lammps.py
+++ b/dpdata/plugins/lammps.py
@@ -1,20 +1,26 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import dpdata.lammps.dump
 import dpdata.lammps.lmp
 from dpdata.format import Format
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
 
 
 @Format.register("lmp")
 @Format.register("lammps/lmp")
 class LAMMPSLmpFormat(Format):
     @Format.post("shift_orig_zero")
-    def from_system(self, file_name, type_map=None, **kwargs):
-        with open(file_name) as fp:
+    def from_system(self, file_name: FileType, type_map=None, **kwargs):
+        with open_file(file_name) as fp:
             lines = [line.rstrip("\n") for line in fp]
         return dpdata.lammps.lmp.to_system_data(lines, type_map)
 
-    def to_system(self, data, file_name, frame_idx=0, **kwargs):
+    def to_system(self, data, file_name: FileType, frame_idx=0, **kwargs):
         """Dump the system in lammps data format.
 
         Parameters
@@ -30,7 +36,7 @@ def to_system(self, data, file_name, frame_idx=0, **kwargs):
         """
         assert frame_idx < len(data["coords"])
         w_str = dpdata.lammps.lmp.from_system_data(data, frame_idx)
-        with open(file_name, "w") as fp:
+        with open_file(file_name, "w") as fp:
             fp.write(w_str)
 
 
diff --git a/dpdata/plugins/n2p2.py b/dpdata/plugins/n2p2.py
index b70d6e6f..28942ff5 100644
--- a/dpdata/plugins/n2p2.py
+++ b/dpdata/plugins/n2p2.py
@@ -1,8 +1,14 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 
 from dpdata.format import Format
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
 
 from ..unit import EnergyConversion, ForceConversion, LengthConversion
 
@@ -44,7 +50,7 @@ class N2P2Format(Format):
     For more information about the n2p2 format, please refer to https://compphysvienna.github.io/n2p2/topics/cfg_file.html
     """
 
-    def from_labeled_system(self, file_name, **kwargs):
+    def from_labeled_system(self, file_name: FileType, **kwargs):
         """Read from n2p2 format.
 
         Parameters
@@ -67,7 +73,7 @@ def from_labeled_system(self, file_name, **kwargs):
         natom0 = None
         natoms0 = None
         atom_types0 = None
-        with open(file_name) as file:
+        with open_file(file_name) as file:
             for line in file:
                 line = line.strip()  # Remove leading/trailing whitespace
                 if line.lower() == "begin":
@@ -155,7 +161,7 @@ def from_labeled_system(self, file_name, **kwargs):
             "forces": forces,
         }
 
-    def to_labeled_system(self, data, file_name, **kwargs):
+    def to_labeled_system(self, data, file_name: FileType, **kwargs):
         """Write n2p2 format.
 
         By default, LabeledSystem.to will fallback to System.to.
@@ -193,5 +199,5 @@ def to_labeled_system(self, data, file_name, **kwargs):
             buff.append(f"energy {energy:15.6f}")
             buff.append(f"charge {0:15.6f}")
             buff.append("end")
-        with open(file_name, "w") as fp:
+        with open_file(file_name, "w") as fp:
             fp.write("\n".join(buff))
diff --git a/dpdata/plugins/orca.py b/dpdata/plugins/orca.py
index 9dc32c32..7a0b806c 100644
--- a/dpdata/plugins/orca.py
+++ b/dpdata/plugins/orca.py
@@ -1,11 +1,16 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 
 from dpdata.format import Format
 from dpdata.orca.output import read_orca_sp_output
 from dpdata.unit import EnergyConversion, ForceConversion
 
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
+
 energy_convert = EnergyConversion("hartree", "eV").value()
 force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value()
 
@@ -18,12 +23,12 @@ class ORCASPOutFormat(Format):
     printed into the output file.
     """
 
-    def from_labeled_system(self, file_name: str, **kwargs) -> dict:
+    def from_labeled_system(self, file_name: FileType, **kwargs) -> dict:
         """Read from ORCA single point energy output.
 
         Parameters
         ----------
-        file_name : str
+        file_name : FileType
             file name
         **kwargs
             keyword arguments
diff --git a/dpdata/plugins/psi4.py b/dpdata/plugins/psi4.py
index a0cf00e4..2bbfc232 100644
--- a/dpdata/plugins/psi4.py
+++ b/dpdata/plugins/psi4.py
@@ -1,11 +1,17 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 
 from dpdata.format import Format
 from dpdata.psi4.input import write_psi4_input
 from dpdata.psi4.output import read_psi4_output
 from dpdata.unit import EnergyConversion, ForceConversion
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
 
 energy_convert = EnergyConversion("hartree", "eV").value()
 force_convert = ForceConversion("hartree/bohr", "eV/angstrom").value()
@@ -19,12 +25,12 @@ class PSI4OutFormat(Format):
     printed into the output file.
     """
 
-    def from_labeled_system(self, file_name: str, **kwargs) -> dict:
+    def from_labeled_system(self, file_name: FileType, **kwargs) -> dict:
         """Read from Psi4 output.
 
         Parameters
         ----------
-        file_name : str
+        file_name : FileType
             file name
         **kwargs
             keyword arguments
@@ -61,7 +67,7 @@ class PSI4InputFormat(Format):
     def to_system(
         self,
         data: dict,
-        file_name: str,
+        file_name: FileType,
         method: str,
         basis: str,
         charge: int = 0,
@@ -91,7 +97,7 @@ def to_system(
             keyword arguments
         """
         types = np.array(data["atom_names"])[data["atom_types"]]
-        with open(file_name, "w") as fout:
+        with open_file(file_name, "w") as fout:
             fout.write(
                 write_psi4_input(
                     types=types,
diff --git a/dpdata/plugins/pwmat.py b/dpdata/plugins/pwmat.py
index 80f219b6..ba3dab16 100644
--- a/dpdata/plugins/pwmat.py
+++ b/dpdata/plugins/pwmat.py
@@ -1,10 +1,16 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 
 import dpdata.pwmat.atomconfig
 import dpdata.pwmat.movement
 from dpdata.format import Format
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
 
 
 @Format.register("movement")
@@ -47,12 +53,12 @@ def from_labeled_system(
 @Format.register("pwmat/final.config")
 class PwmatAtomconfigFormat(Format):
     @Format.post("rot_lower_triangular")
-    def from_system(self, file_name, **kwargs):
-        with open(file_name) as fp:
+    def from_system(self, file_name: FileType, **kwargs):
+        with open_file(file_name) as fp:
             lines = [line.rstrip("\n") for line in fp]
         return dpdata.pwmat.atomconfig.to_system_data(lines)
 
-    def to_system(self, data, file_name, frame_idx=0, *args, **kwargs):
+    def to_system(self, data, file_name: FileType, frame_idx=0, *args, **kwargs):
         """Dump the system in pwmat atom.config format.
 
         Parameters
@@ -70,5 +76,5 @@ def to_system(self, data, file_name, frame_idx=0, *args, **kwargs):
         """
         assert frame_idx < len(data["coords"])
         w_str = dpdata.pwmat.atomconfig.from_system_data(data, frame_idx)
-        with open(file_name, "w") as fp:
+        with open_file(file_name, "w") as fp:
             fp.write(w_str)
diff --git a/dpdata/plugins/vasp.py b/dpdata/plugins/vasp.py
index d0681ceb..0160bde2 100644
--- a/dpdata/plugins/vasp.py
+++ b/dpdata/plugins/vasp.py
@@ -1,12 +1,17 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 
 import dpdata.vasp.outcar
 import dpdata.vasp.poscar
 import dpdata.vasp.xml
 from dpdata.format import Format
-from dpdata.utils import uniq_atom_names
+from dpdata.utils import open_file, uniq_atom_names
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
 
 
 @Format.register("poscar")
@@ -15,14 +20,14 @@
 @Format.register("vasp/contcar")
 class VASPPoscarFormat(Format):
     @Format.post("rot_lower_triangular")
-    def from_system(self, file_name, **kwargs):
-        with open(file_name) as fp:
+    def from_system(self, file_name: FileType, **kwargs):
+        with open_file(file_name) as fp:
             lines = [line.rstrip("\n") for line in fp]
         data = dpdata.vasp.poscar.to_system_data(lines)
         data = uniq_atom_names(data)
         return data
 
-    def to_system(self, data, file_name, frame_idx=0, **kwargs):
+    def to_system(self, data, file_name: FileType, frame_idx=0, **kwargs):
         """Dump the system in vasp POSCAR format.
 
         Parameters
@@ -37,7 +42,7 @@ def to_system(self, data, file_name, frame_idx=0, **kwargs):
             other parameters
         """
         w_str = VASPStringFormat().to_system(data, frame_idx=frame_idx)
-        with open(file_name, "w") as fp:
+        with open_file(file_name, "w") as fp:
             fp.write(w_str)
 
 
diff --git a/dpdata/plugins/xyz.py b/dpdata/plugins/xyz.py
index 322bf77c..d56a8618 100644
--- a/dpdata/plugins/xyz.py
+++ b/dpdata/plugins/xyz.py
@@ -1,8 +1,14 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 
 from dpdata.format import Format
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
 from dpdata.xyz.quip_gap_xyz import QuipGapxyzSystems
 from dpdata.xyz.xyz import coord_to_xyz, xyz_to_coord
 
@@ -16,16 +22,16 @@ class XYZFormat(Format):
     >>> s.to("xyz", "a.xyz")
     """
 
-    def to_system(self, data, file_name, **kwargs):
+    def to_system(self, data, file_name: FileType, **kwargs):
         buff = []
         types = np.array(data["atom_names"])[data["atom_types"]]
         for cc in data["coords"]:
             buff.append(coord_to_xyz(cc, types))
-        with open(file_name, "w") as fp:
+        with open_file(file_name, "w") as fp:
             fp.write("\n".join(buff))
 
-    def from_system(self, file_name, **kwargs):
-        with open(file_name) as fp:
+    def from_system(self, file_name: FileType, **kwargs):
+        with open_file(file_name) as fp:
             coords, types = xyz_to_coord(fp.read())
         atom_names, atom_types, atom_numbs = np.unique(
             types, return_inverse=True, return_counts=True
diff --git a/dpdata/psi4/output.py b/dpdata/psi4/output.py
index c06eb182..c3594ffb 100644
--- a/dpdata/psi4/output.py
+++ b/dpdata/psi4/output.py
@@ -1,11 +1,17 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import numpy as np
 
 from dpdata.unit import LengthConversion
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
 
 
-def read_psi4_output(fn: str) -> tuple[str, np.ndarray, float, np.ndarray]:
+def read_psi4_output(fn: FileType) -> tuple[str, np.ndarray, float, np.ndarray]:
     """Read from Psi4 output.
 
     Note that both the energy and the gradient should be printed.
@@ -31,7 +37,7 @@ def read_psi4_output(fn: str) -> tuple[str, np.ndarray, float, np.ndarray]:
     forces = None
     energy = None
     length_unit = None
-    with open(fn) as f:
+    with open_file(fn) as f:
         flag = 0
         for line in f:
             if flag in (1, 3, 4, 5, 6):
diff --git a/dpdata/qe/scf.py b/dpdata/qe/scf.py
index 37e5fbab..f8670860 100755
--- a/dpdata/qe/scf.py
+++ b/dpdata/qe/scf.py
@@ -5,6 +5,8 @@
 
 import numpy as np
 
+from dpdata.utils import open_file
+
 ry2ev = 13.605693009
 bohr2ang = 0.52917721067
 kbar2evperang3 = 1e3 / 1.602176621e6
@@ -142,9 +144,9 @@ def get_frame(fname):
         path_out = fname[1]
     else:
         raise RuntimeError("invalid input")
-    with open(path_out) as fp:
+    with open_file(path_out) as fp:
         outlines = fp.read().split("\n")
-    with open(path_in) as fp:
+    with open_file(path_in) as fp:
         inlines = fp.read().split("\n")
     cell = get_cell(inlines)
     atom_names, natoms, types, coords = get_coords(inlines, cell)
diff --git a/dpdata/qe/traj.py b/dpdata/qe/traj.py
index 1fbf0f71..b4be303a 100644
--- a/dpdata/qe/traj.py
+++ b/dpdata/qe/traj.py
@@ -2,9 +2,15 @@
 from __future__ import annotations
 
 import warnings
+from typing import TYPE_CHECKING
 
 import numpy as np
 
+from dpdata.utils import open_file
+
+if TYPE_CHECKING:
+    from dpdata.utils import FileType
+
 from ..unit import (
     EnergyConversion,
     ForceConversion,
@@ -87,8 +93,8 @@ def load_atom_types(lines, natoms, atom_names):
     return np.array(ret, dtype=int)
 
 
-def load_param_file(fname):
-    with open(fname) as fp:
+def load_param_file(fname: FileType):
+    with open_file(fname) as fp:
         lines = fp.read().split("\n")
     natoms = int(load_key(lines, "nat"))
     ntypes = int(load_key(lines, "ntyp"))
@@ -127,11 +133,11 @@ def _load_pos_block(fp, natoms):
         return blk, ss
 
 
-def load_data(fname, natoms, begin=0, step=1, convert=1.0):
+def load_data(fname: FileType, natoms, begin=0, step=1, convert=1.0):
     coords = []
     steps = []
     cc = 0
-    with open(fname) as fp:
+    with open_file(fname) as fp:
         while True:
             blk, ss = _load_pos_block(fp, natoms)
             if blk is None:
@@ -147,7 +153,7 @@ def load_data(fname, natoms, begin=0, step=1, convert=1.0):
 
 # def load_pos(fname, natoms) :
 #     coords = []
-#     with open(fname) as fp:
+#     with open_file(fname) as fp:
 #         while True:
 #             blk = _load_pos_block(fp, natoms)
 #             # print(blk)
@@ -164,7 +170,7 @@ def load_energy(fname, begin=0, step=1):
     steps = []
     for ii in data[begin::step, 0]:
         steps.append("%d" % ii)
-    with open(fname) as fp:
+    with open_file(fname) as fp:
         while True:
             line = fp.readline()
             if not line:
@@ -178,7 +184,7 @@ def load_energy(fname, begin=0, step=1):
 
 # def load_force(fname, natoms) :
 #     coords = []
-#     with open(fname) as fp:
+#     with open_file(fname) as fp:
 #         while True:
 #             blk = _load_pos_block(fp, natoms)
 #             # print(blk)
diff --git a/dpdata/utils.py b/dpdata/utils.py
index e008120e..8942bd54 100644
--- a/dpdata/utils.py
+++ b/dpdata/utils.py
@@ -1,7 +1,10 @@
 from __future__ import annotations
 
+import io
+import os
 import sys
-from typing import overload
+from contextlib import contextmanager
+from typing import TYPE_CHECKING, Generator, overload
 
 if sys.version_info >= (3, 8):
     from typing import Literal
@@ -129,3 +132,44 @@ def uniq_atom_names(data):
 def utf8len(s: str) -> int:
     """Return the byte length of a string."""
     return len(s.encode("utf-8"))
+
+
+if TYPE_CHECKING:
+    FileType = io.IOBase | str | os.PathLike
+
+
+@contextmanager
+def open_file(file: FileType, *args, **kwargs) -> Generator[io.IOBase, None, None]:
+    """A context manager that yields a file object.
+
+    Parameters
+    ----------
+    file : file object or file path
+        A file object or a file path.
+
+    Yields
+    ------
+    file : io.IOBase
+        A file object.
+    *args
+        parameters to open
+    **kwargs
+        other parameters
+
+    Raises
+    ------
+    ValueError
+        If file is not a file object or a file
+
+    Examples
+    --------
+    >>> with open_file("file.txt") as file:
+    ...     print(file.read())
+    """
+    if isinstance(file, io.IOBase):
+        yield file
+    elif isinstance(file, (str, os.PathLike)):
+        with open(file, *args, **kwargs) as f:
+            yield f
+    else:
+        raise ValueError("file must be a file object or a file path.")
diff --git a/tests/test_read_file.py b/tests/test_read_file.py
new file mode 100644
index 00000000..e7dca54e
--- /dev/null
+++ b/tests/test_read_file.py
@@ -0,0 +1,22 @@
+from __future__ import annotations
+
+import io
+import unittest
+from pathlib import Path
+
+from dpdata.utils import open_file
+
+
+class TestReadFile(unittest.TestCase):
+    def test_open_file_from_string_io(self):
+        string_io = io.StringIO("Hello, world!")
+        with open_file(string_io) as file:
+            self.assertEqual(file.read(), "Hello, world!")
+
+    def test_open_file_from_file_str(self):
+        with open_file("/dev/null") as file:
+            self.assertEqual(file.read(), Path("/dev/null").read_text())
+
+    def test_open_file_from_file_path(self):
+        with open_file(Path("/dev/null")) as file:
+            self.assertEqual(file.read(), Path("/dev/null").read_text())

From c311d16ff9db600815acdf23b005fa4ad388607c Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Mon, 2 Sep 2024 22:59:20 -0400
Subject: [PATCH 12/33] fix: only apply comp_prec for floating dtypes (#711)

Fix #703.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Improved handling of data types during the reshaping process, ensuring
type conversion only occurs for floating-point data.

- **Bug Fixes**
- Enhanced robustness of data processing by preventing unnecessary type
casting for non-floating-point data types.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 dpdata/deepmd/comp.py | 4 +++-
 dpdata/deepmd/hdf5.py | 7 ++++---
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/dpdata/deepmd/comp.py b/dpdata/deepmd/comp.py
index 5ba3914e..3d656b70 100644
--- a/dpdata/deepmd/comp.py
+++ b/dpdata/deepmd/comp.py
@@ -204,7 +204,9 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
                 f"Shape of {dtype.name} is not (nframes, ...), but {dtype.shape}. This type of data will not converted to deepmd/npy format."
             )
             continue
-        ddata = np.reshape(data[dtype.name], [nframes, -1]).astype(comp_prec)
+        ddata = np.reshape(data[dtype.name], [nframes, -1])
+        if np.issubdtype(ddata.dtype, np.floating):
+            ddata = ddata.astype(comp_prec)
         for ii in range(nsets):
             set_stt = ii * set_size
             set_end = (ii + 1) * set_size
diff --git a/dpdata/deepmd/hdf5.py b/dpdata/deepmd/hdf5.py
index 78f4e33f..6b587893 100644
--- a/dpdata/deepmd/hdf5.py
+++ b/dpdata/deepmd/hdf5.py
@@ -252,9 +252,10 @@ def dump(
     for dt, prop in data_types.items():
         if dt in data:
             if prop["dump"]:
-                reshaped_data[dt] = np.reshape(data[dt], prop["shape"]).astype(
-                    comp_prec
-                )
+                ddata = np.reshape(data[dt], prop["shape"])
+                if np.issubdtype(ddata.dtype, np.floating):
+                    ddata = ddata.astype(comp_prec)
+                reshaped_data[dt] = ddata
 
     # dump frame properties: cell, coord, energy, force and virial
     nsets = nframes // set_size

From bad02850c7cb982f937ce89e296809948081f9c7 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 3 Sep 2024 11:00:47 +0800
Subject: [PATCH 13/33] [pre-commit.ci] pre-commit autoupdate (#712)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.2 →
v0.6.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.2...v0.6.3)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f4abb50c..3f43b697 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.2
+    rev: v0.6.3
     hooks:
     - id: ruff
       args: ["--fix"]

From e393a8c58f3cfbea48705cb017110d952e0ce991 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Tue, 3 Sep 2024 20:15:43 -0400
Subject: [PATCH 14/33] docs: fix directives (#715)

The previous syntax is for RST files.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit


- **New Features**
- Introduced the `BondOrderSystem` class for managing chemical bond
information with enhanced sanitization capabilities.

- **Documentation**
- Updated class reference formatting across multiple documentation files
for clarity and consistency, changing from colon to curly brace syntax.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---
 docs/plugin.md                    |  2 +-
 docs/systems/bond_order_system.md |  6 +++---
 docs/systems/mixed.md             |  2 +-
 docs/systems/multi.md             | 10 +++++-----
 docs/systems/system.md            | 12 ++++++------
 5 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/docs/plugin.md b/docs/plugin.md
index 44e8eabf..bf3266d5 100644
--- a/docs/plugin.md
+++ b/docs/plugin.md
@@ -1,7 +1,7 @@
 # Plugins
 
 One can follow a simple example under `plugin_example/` directory to add their own format by creating and installing plugins.
-It's critical to add the :class:`Format` class to `entry_points['dpdata.plugins']` in `pyproject.toml`:
+It's critical to add the {class}`Format <dpdata.format.Format>` class to `entry_points['dpdata.plugins']` in `pyproject.toml`:
 
 ```toml
 [project.entry-points.'dpdata.plugins']
diff --git a/docs/systems/bond_order_system.md b/docs/systems/bond_order_system.md
index 443120a7..8d92d724 100644
--- a/docs/systems/bond_order_system.md
+++ b/docs/systems/bond_order_system.md
@@ -1,6 +1,6 @@
 
 ## BondOrderSystem
-A new class :class:`BondOrderSystem` which inherits from class :class:`System` is introduced in dpdata. This new class contains information of chemical bonds and formal charges (stored in `BondOrderSystem.data['bonds']`, `BondOrderSystem.data['formal_charges']`). Now BondOrderSystem can only read from .mol/.sdf formats, because of its dependency on rdkit (which means rdkit must be installed if you want to use this function). Other formats, such as pdb, must be converted to .mol/.sdf format (maybe with software like open babel).
+A new class {class}`BondOrderSystem <dpdata.BondOrderSystem>` which inherits from class {class}`System <dpdata.System>` is introduced in dpdata. This new class contains information of chemical bonds and formal charges (stored in `BondOrderSystem.data['bonds']`, `BondOrderSystem.data['formal_charges']`). Now BondOrderSystem can only read from .mol/.sdf formats, because of its dependency on rdkit (which means rdkit must be installed if you want to use this function). Other formats, such as pdb, must be converted to .mol/.sdf format (maybe with software like open babel).
 ```python
 import dpdata
 
@@ -12,7 +12,7 @@ system_2 = dpdata.BondOrderSystem(
 )  # read from .sdf file
 ```
 In sdf file, all molecules must be of the same topology (i.e. conformers of the same molecular configuration).
-`BondOrderSystem` also supports initialize from a :class:`rdkit.Chem.rdchem.Mol` object directly.
+`BondOrderSystem <dpdata.BondOrderSystem>` also supports initialize from a {class}`rdkit.Chem.rdchem.Mol` object directly.
 ```python
 from rdkit import Chem
 from rdkit.Chem import AllChem
@@ -25,7 +25,7 @@ system = dpdata.BondOrderSystem(rdkit_mol=mol)
 ```
 
 ### Bond Order Assignment
-The :class:`BondOrderSystem` implements a more robust sanitize procedure for rdkit Mol, as defined in :class:`dpdata.rdkit.santizie.Sanitizer`. This class defines 3 level of sanitization process by: low, medium and high. (default is medium).
+The {class}`BondOrderSystem <dpdata.BondOrderSystem>` implements a more robust sanitize procedure for rdkit Mol, as defined in {class}`dpdata.rdkit.santizie.Sanitizer`. This class defines 3 level of sanitization process by: low, medium and high. (default is medium).
 + low: use `rdkit.Chem.SanitizeMol()` function to sanitize molecule.
 + medium: before using rdkit, the programm will first assign formal charge of each atom to avoid inappropriate valence exceptions. However, this mode requires the rightness of the bond order information in the given molecule.
 + high: the program will try to fix inappropriate bond orders in aromatic hetreocycles, phosphate, sulfate, carboxyl, nitro, nitrine, guanidine groups. If this procedure fails to sanitize the given molecule, the program will then try to call `obabel` to pre-process the mol and repeat the sanitization procedure. **That is to say, if you wan't to use this level of sanitization, please ensure `obabel` is installed in the environment.**
diff --git a/docs/systems/mixed.md b/docs/systems/mixed.md
index 69bf80ea..25837ea6 100644
--- a/docs/systems/mixed.md
+++ b/docs/systems/mixed.md
@@ -1,6 +1,6 @@
 # Mixed Type Format
 
-The format `deepmd/npy/mixed` is the mixed type numpy format for DeePMD-kit, and can be loaded or dumped through class :class:`dpdata.MultiSystems`.
+The format `deepmd/npy/mixed` is the mixed type numpy format for DeePMD-kit, and can be loaded or dumped through class {class}`dpdata.MultiSystems`.
 
 Under this format, systems with the same number of atoms but different formula can be put together
 for a larger system, especially when the frame numbers in systems are sparse.
diff --git a/docs/systems/multi.md b/docs/systems/multi.md
index 8e47acf7..20551c7e 100644
--- a/docs/systems/multi.md
+++ b/docs/systems/multi.md
@@ -1,15 +1,15 @@
 # `MultiSystems`
 
-The Class :class:`dpdata.MultiSystems`  can read data  from a dir which may contains many files of different systems, or from single xyz file which contains different systems.
+The Class {class}`dpdata.MultiSystems`  can read data  from a dir which may contains many files of different systems, or from single xyz file which contains different systems.
 
-Use :meth:`dpdata.MultiSystems.from_dir` to read from a  directory, :class:`dpdata.MultiSystems` will walk in the directory
-Recursively  and  find all file with specific file_name. Supports all the file formats that :class:`dpdata.LabeledSystem` supports.
+Use {meth}`dpdata.MultiSystems.from_dir` to read from a  directory, {class}`dpdata.MultiSystems` will walk in the directory
+Recursively  and  find all file with specific file_name. Supports all the file formats that {class}`dpdata.LabeledSystem` supports.
 
-Use :meth:`dpdata.MultiSystems.from_file` to read from single file. Single-file support is available for the `quip/gap/xyz` and `ase/structure` formats.
+Use {meth}`dpdata.MultiSystems.from_file` to read from single file. Single-file support is available for the `quip/gap/xyz` and `ase/structure` formats.
 
 For example, for `quip/gap xyz` files, single .xyz file may contain many different configurations with different atom numbers and atom type.
 
-The following commands relating to :class:`dpdata.MultiSystems` may be useful.
+The following commands relating to {class}`dpdata.MultiSystems` may be useful.
 ```python
 # load data
 
diff --git a/docs/systems/system.md b/docs/systems/system.md
index 0401a311..9f01fc40 100644
--- a/docs/systems/system.md
+++ b/docs/systems/system.md
@@ -19,21 +19,21 @@ or let dpdata infer the format (`vasp/poscar`) of the file from the file name ex
 ```python
 d_poscar = dpdata.System("my.POSCAR")
 ```
-The number of atoms, atom types, coordinates are loaded from the `POSCAR` and stored to a data :class:`System` called `d_poscar`.
-A data :class:`System` (a concept used by [deepmd-kit](https://github.com/deepmodeling/deepmd-kit)) contains frames that has the same number of atoms of the same type. The order of the atoms should be consistent among the frames in one :class:`System`.
+The number of atoms, atom types, coordinates are loaded from the `POSCAR` and stored to a data {class}`System <dpdata.System>` called `d_poscar`.
+A data {class}`System <dpdata.System>` (a concept used by [deepmd-kit](https://github.com/deepmodeling/deepmd-kit)) contains frames that has the same number of atoms of the same type. The order of the atoms should be consistent among the frames in one {class}`System <dpdata.System>`.
 It is noted that `POSCAR` only contains one frame.
 If the multiple frames stored in, for example, a `OUTCAR` is wanted,
 ```python
 d_outcar = dpdata.LabeledSystem("OUTCAR")
 ```
-The labels provided in the `OUTCAR`, i.e. energies, forces and virials (if any), are loaded by :class:`LabeledSystem`. It is noted that the forces of atoms are always assumed to exist. :class:`LabeledSystem` is a derived class of :class:`System`.
+The labels provided in the `OUTCAR`, i.e. energies, forces and virials (if any), are loaded by {class}`LabeledSystem <dpdata.LabeledSystem>`. It is noted that the forces of atoms are always assumed to exist. {class}`LabeledSystem <dpdata.LabeledSystem>` is a derived class of {class}`System <dpdata.System>`.
 
-The :class:`System` or :class:`LabeledSystem` can be constructed from the following file formats with the `format key` in the table passed to argument `fmt`:
+The {class}`System <dpdata.System>` or {class}`LabeledSystem <dpdata.LabeledSystem>` can be constructed from the [supported file formats](../formats.rst) with the `format key` in the table passed to argument `fmt`.
 
 
 
 ### Access data
-These properties stored in :class:`System` and :class:`LabeledSystem` can be accessed by operator `[]` with the key of the property supplied, for example
+These properties stored in {class}`System <dpdata.System>` and {class}`LabeledSystem <dpdata.LabeledSystem>` can be accessed by operator `[]` with the key of the property supplied, for example
 ```python
 coords = d_outcar["coords"]
 ```
@@ -52,7 +52,7 @@ Available properties are (nframe: number of frames in the system, natoms: total
 
 
 ### Dump data
-The data stored in :class:`System` or :class:`LabeledSystem` can be dumped in 'lammps/lmp' or 'vasp/poscar' format, for example:
+The data stored in {class}`System <dpdata.System>` or {class}`LabeledSystem <dpdata.LabeledSystem>` can be dumped in 'lammps/lmp' or 'vasp/poscar' format, for example:
 ```python
 d_outcar.to("lammps/lmp", "conf.lmp", frame_idx=0)
 ```

From 976cf16ab6ad0c975ee259c17cd7f06f8aa201a8 Mon Sep 17 00:00:00 2001
From: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
Date: Wed, 4 Sep 2024 21:49:48 +0800
Subject: [PATCH 15/33] Update ase.py: To avoid errors in writing to the
 .extxyz format from an Atom object coverted from .npy with dpdata. (#717)

---
 dpdata/plugins/ase.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/dpdata/plugins/ase.py b/dpdata/plugins/ase.py
index 2ca22926..83a6bcf9 100644
--- a/dpdata/plugins/ase.py
+++ b/dpdata/plugins/ase.py
@@ -181,7 +181,17 @@ def to_labeled_system(self, data, *args, **kwargs) -> list[ase.Atoms]:
                 # v_pref = 1 * 1e4 / 1.602176621e6
                 vol = structure.get_volume()
                 # results['stress'] = data["virials"][ii] / (v_pref * vol)
-                results["stress"] = -data["virials"][ii] / vol
+                stress33 = -data["virials"][ii] / vol
+                results["stress"] = np.array(
+                    [
+                        stress33[0][0],
+                        stress33[1][1],
+                        stress33[2][2],
+                        stress33[1][2],
+                        stress33[0][2],
+                        stress33[0][1],
+                    ]
+                )
 
             structure.calc = SinglePointCalculator(structure, **results)
             structures.append(structure)

From 1de5acea87683d9d4ac4d0055d55ab6aad931016 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 10 Sep 2024 15:22:00 +0800
Subject: [PATCH 16/33] [pre-commit.ci] pre-commit autoupdate (#720)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.3 →
v0.6.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.3...v0.6.4)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3f43b697..dfe604f3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.3
+    rev: v0.6.4
     hooks:
     - id: ruff
       args: ["--fix"]

From fb942bb94cd142d03f52d2def952df954592f42c Mon Sep 17 00:00:00 2001
From: Chenqqian Zhang <100290172+Chengqian-Zhang@users.noreply.github.com>
Date: Wed, 11 Sep 2024 11:39:55 +0800
Subject: [PATCH 17/33] Feat: Support specifying proportion of atoms to be
 perturbed in System (#716)

See title.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit


- **New Features**
- Introduced a new parameter for controlled atom perturbation in the
perturb function, enhancing flexibility.

- **Bug Fixes**
- Improved logic for selecting atoms to perturb, ensuring only a
specified proportion is affected.

- **Tests**
- Added a new test class to validate the perturbation functionality for
atomic systems, increasing test coverage and reliability.
- Introduced a structured representation of a Silicon Carbide crystal
for validation in tests.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 dpdata/system.py                  | 13 ++++++++++-
 tests/poscars/POSCAR.SiC.partpert | 16 +++++++++++++
 tests/test_perturb.py             | 39 +++++++++++++++++++++++++++++++
 3 files changed, 67 insertions(+), 1 deletion(-)
 create mode 100644 tests/poscars/POSCAR.SiC.partpert

diff --git a/dpdata/system.py b/dpdata/system.py
index 2613166a..42b3f4e7 100644
--- a/dpdata/system.py
+++ b/dpdata/system.py
@@ -849,6 +849,7 @@ def perturb(
         cell_pert_fraction: float,
         atom_pert_distance: float,
         atom_pert_style: str = "normal",
+        atom_pert_prob: float = 1.0,
     ):
         """Perturb each frame in the system randomly.
         The cell will be deformed randomly, and atoms will be displaced by a random distance in random direction.
@@ -877,6 +878,8 @@ def perturb(
                     These points are treated as vector used by atoms to move.
                     Obviously, the max length of the distance atoms move is `atom_pert_distance`.
                 - `'const'`: The distance atoms move will be a constant `atom_pert_distance`.
+        atom_pert_prob : float
+            Determine the proportion of the total number of atoms in a frame that are perturbed.
 
         Returns
         -------
@@ -900,7 +903,15 @@ def perturb(
                 tmp_system.data["coords"][0] = np.matmul(
                     tmp_system.data["coords"][0], cell_perturb_matrix
                 )
-                for kk in range(len(tmp_system.data["coords"][0])):
+                pert_natoms = int(atom_pert_prob * len(tmp_system.data["coords"][0]))
+                pert_atom_id = sorted(
+                    np.random.choice(
+                        range(len(tmp_system.data["coords"][0])),
+                        pert_natoms,
+                        replace=False,
+                    ).tolist()
+                )
+                for kk in pert_atom_id:
                     atom_perturb_vector = get_atom_perturb_vector(
                         atom_pert_distance, atom_pert_style
                     )
diff --git a/tests/poscars/POSCAR.SiC.partpert b/tests/poscars/POSCAR.SiC.partpert
new file mode 100644
index 00000000..859de7ca
--- /dev/null
+++ b/tests/poscars/POSCAR.SiC.partpert
@@ -0,0 +1,16 @@
+C4 Si4 
+1.0
+4.0354487481064565e+00 1.1027270790560616e-17 2.5642993008475204e-17 
+2.0693526054669642e-01 4.1066892997402196e+00 -8.6715682899078028e-18 
+4.2891472979598610e-01 5.5796885749827474e-01 4.1100061517204542e+00 
+C Si 
+4 4 
+Cartesian
+ 0.03122504  0.15559669  2.1913045
+ 1.93908836 -0.08678864  0.06748919
+ 0.13114716  2.15827511  0.06333341
+ 2.36161952  1.42824405  2.58837618
+-0.03895165  0.12197669  0.05496244
+ 1.79528462  2.48830207 -0.55733221
+ 2.11363589  0.09280028  2.0301803
+ 0.19221505  2.16245144  2.07930701
diff --git a/tests/test_perturb.py b/tests/test_perturb.py
index eea71116..5c2f4a7b 100644
--- a/tests/test_perturb.py
+++ b/tests/test_perturb.py
@@ -12,6 +12,7 @@ class NormalGenerator:
     def __init__(self):
         self.randn_generator = self.get_randn_generator()
         self.rand_generator = self.get_rand_generator()
+        self.choice_generator = self.get_choice_generator()
 
     def randn(self, number):
         return next(self.randn_generator)
@@ -19,6 +20,9 @@ def randn(self, number):
     def rand(self, number):
         return next(self.rand_generator)
 
+    def choice(self, total_natoms, pert_natoms, replace):
+        return next(self.choice_generator)[:pert_natoms]
+
     @staticmethod
     def get_randn_generator():
         data = np.asarray(
@@ -44,11 +48,16 @@ def get_rand_generator():
             [0.23182233, 0.87106847, 0.68728511, 0.94180274, 0.92860453, 0.69191187]
         )
 
+    @staticmethod
+    def get_choice_generator():
+        yield np.asarray([5, 3, 7, 6, 2, 1, 4, 0])
+
 
 class UniformGenerator:
     def __init__(self):
         self.randn_generator = self.get_randn_generator()
         self.rand_generator = self.get_rand_generator()
+        self.choice_generator = self.get_choice_generator()
 
     def randn(self, number):
         return next(self.randn_generator)
@@ -56,6 +65,9 @@ def randn(self, number):
     def rand(self, number):
         return next(self.rand_generator)
 
+    def choice(self, total_natoms, pert_natoms, replace):
+        return next(self.choice_generator)
+
     @staticmethod
     def get_randn_generator():
         data = [
@@ -97,11 +109,16 @@ def get_rand_generator():
             yield np.asarray(data[count])
             count += 1
 
+    @staticmethod
+    def get_choice_generator():
+        yield np.asarray([5, 3, 7, 6, 2, 1, 4, 0])
+
 
 class ConstGenerator:
     def __init__(self):
         self.randn_generator = self.get_randn_generator()
         self.rand_generator = self.get_rand_generator()
+        self.choice_generator = self.get_choice_generator()
 
     def randn(self, number):
         return next(self.randn_generator)
@@ -109,6 +126,9 @@ def randn(self, number):
     def rand(self, number):
         return next(self.rand_generator)
 
+    def choice(self, total_natoms, pert_natoms, replace):
+        return next(self.choice_generator)
+
     @staticmethod
     def get_randn_generator():
         data = np.asarray(
@@ -135,6 +155,10 @@ def get_rand_generator():
             [0.01525907, 0.68387374, 0.39768541, 0.55596047, 0.26557088, 0.60883073]
         )
 
+    @staticmethod
+    def get_choice_generator():
+        yield np.asarray([5, 3, 7, 6, 2, 1, 4, 0])
+
 
 # %%
 class TestPerturbNormal(unittest.TestCase, CompSys, IsPBC):
@@ -142,6 +166,7 @@ class TestPerturbNormal(unittest.TestCase, CompSys, IsPBC):
     def setUp(self, random_mock):
         random_mock.rand = NormalGenerator().rand
         random_mock.randn = NormalGenerator().randn
+        random_mock.choice = NormalGenerator().choice
         system_1_origin = dpdata.System("poscars/POSCAR.SiC", fmt="vasp/poscar")
         self.system_1 = system_1_origin.perturb(1, 0.05, 0.6, "normal")
         self.system_2 = dpdata.System("poscars/POSCAR.SiC.normal", fmt="vasp/poscar")
@@ -153,6 +178,7 @@ class TestPerturbUniform(unittest.TestCase, CompSys, IsPBC):
     def setUp(self, random_mock):
         random_mock.rand = UniformGenerator().rand
         random_mock.randn = UniformGenerator().randn
+        random_mock.choice = UniformGenerator().choice
         system_1_origin = dpdata.System("poscars/POSCAR.SiC", fmt="vasp/poscar")
         self.system_1 = system_1_origin.perturb(1, 0.05, 0.6, "uniform")
         self.system_2 = dpdata.System("poscars/POSCAR.SiC.uniform", fmt="vasp/poscar")
@@ -164,11 +190,24 @@ class TestPerturbConst(unittest.TestCase, CompSys, IsPBC):
     def setUp(self, random_mock):
         random_mock.rand = ConstGenerator().rand
         random_mock.randn = ConstGenerator().randn
+        random_mock.choice = ConstGenerator().choice
         system_1_origin = dpdata.System("poscars/POSCAR.SiC", fmt="vasp/poscar")
         self.system_1 = system_1_origin.perturb(1, 0.05, 0.6, "const")
         self.system_2 = dpdata.System("poscars/POSCAR.SiC.const", fmt="vasp/poscar")
         self.places = 6
 
 
+class TestPerturbPartAtoms(unittest.TestCase, CompSys, IsPBC):
+    @patch("numpy.random")
+    def setUp(self, random_mock):
+        random_mock.rand = NormalGenerator().rand
+        random_mock.randn = NormalGenerator().randn
+        random_mock.choice = NormalGenerator().choice
+        system_1_origin = dpdata.System("poscars/POSCAR.SiC", fmt="vasp/poscar")
+        self.system_1 = system_1_origin.perturb(1, 0.05, 0.6, "normal", 0.25)
+        self.system_2 = dpdata.System("poscars/POSCAR.SiC.partpert", fmt="vasp/poscar")
+        self.places = 6
+
+
 if __name__ == "__main__":
     unittest.main()

From 480242e3114f711a2d94e99f4b6ab7faaf7ba4ea Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 18 Sep 2024 08:35:41 +0800
Subject: [PATCH 18/33] [pre-commit.ci] pre-commit autoupdate (#722)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.4 →
v0.6.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.4...v0.6.5)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index dfe604f3..8da028de 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.4
+    rev: v0.6.5
     hooks:
     - id: ruff
       args: ["--fix"]

From a2fbdd8dae6417dbe3704922c9fc4d9b9ed5b9e1 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Thu, 19 Sep 2024 20:29:21 -0400
Subject: [PATCH 19/33] feat: support data type dumped to a different name
 (#727)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Introduced an optional `deepmd_name` parameter in the `DataType` class
for enhanced naming flexibility.
- Updated data type declarations in the `System` and `LabeledSystem`
classes for better integration with the DeepMD framework.

- **Bug Fixes**
- Removed handling of energy, force, and virial data to simplify data
processing and storage.

- **Documentation**
- Updated documentation for the `DataType` class to clarify the new
`deepmd_name` parameter.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 dpdata/data_type.py   |  4 +++
 dpdata/deepmd/comp.py | 62 ++++---------------------------------------
 dpdata/deepmd/hdf5.py | 61 +++++-------------------------------------
 dpdata/deepmd/raw.py  | 45 +++----------------------------
 dpdata/system.py      | 20 ++++++++++----
 5 files changed, 35 insertions(+), 157 deletions(-)

diff --git a/dpdata/data_type.py b/dpdata/data_type.py
index bbc7401d..851a65c9 100644
--- a/dpdata/data_type.py
+++ b/dpdata/data_type.py
@@ -46,6 +46,8 @@ class DataType:
         represents numbers
     required : bool, default=True
         whether this data is required
+    deepmd_name : str, optional
+        DeePMD-kit data type name. When not given, it is the same as `name`.
     """
 
     def __init__(
@@ -54,11 +56,13 @@ def __init__(
         dtype: type,
         shape: tuple[int | Axis, ...] | None = None,
         required: bool = True,
+        deepmd_name: str | None = None,
     ) -> None:
         self.name = name
         self.dtype = dtype
         self.shape = shape
         self.required = required
+        self.deepmd_name = name if deepmd_name is None else deepmd_name
 
     def real_shape(self, system: System) -> tuple[int]:
         """Returns expected real shape of a system."""
diff --git a/dpdata/deepmd/comp.py b/dpdata/deepmd/comp.py
index 3d656b70..67eddd9f 100644
--- a/dpdata/deepmd/comp.py
+++ b/dpdata/deepmd/comp.py
@@ -26,10 +26,7 @@ def _load_set(folder, nopbc: bool):
         cells = np.zeros((coords.shape[0], 3, 3))
     else:
         cells = np.load(os.path.join(folder, "box.npy"))
-    eners = _cond_load_data(os.path.join(folder, "energy.npy"))
-    forces = _cond_load_data(os.path.join(folder, "force.npy"))
-    virs = _cond_load_data(os.path.join(folder, "virial.npy"))
-    return cells, coords, eners, forces, virs
+    return cells, coords
 
 
 def to_system_data(folder, type_map=None, labels=True):
@@ -41,31 +38,13 @@ def to_system_data(folder, type_map=None, labels=True):
     sets = sorted(glob.glob(os.path.join(folder, "set.*")))
     all_cells = []
     all_coords = []
-    all_eners = []
-    all_forces = []
-    all_virs = []
     for ii in sets:
-        cells, coords, eners, forces, virs = _load_set(ii, data.get("nopbc", False))
+        cells, coords = _load_set(ii, data.get("nopbc", False))
         nframes = np.reshape(cells, [-1, 3, 3]).shape[0]
         all_cells.append(np.reshape(cells, [nframes, 3, 3]))
         all_coords.append(np.reshape(coords, [nframes, -1, 3]))
-        if eners is not None:
-            eners = np.reshape(eners, [nframes])
-        if labels:
-            if eners is not None and eners.size > 0:
-                all_eners.append(np.reshape(eners, [nframes]))
-            if forces is not None and forces.size > 0:
-                all_forces.append(np.reshape(forces, [nframes, -1, 3]))
-            if virs is not None and virs.size > 0:
-                all_virs.append(np.reshape(virs, [nframes, 3, 3]))
     data["cells"] = np.concatenate(all_cells, axis=0)
     data["coords"] = np.concatenate(all_coords, axis=0)
-    if len(all_eners) > 0:
-        data["energies"] = np.concatenate(all_eners, axis=0)
-    if len(all_forces) > 0:
-        data["forces"] = np.concatenate(all_forces, axis=0)
-    if len(all_virs) > 0:
-        data["virials"] = np.concatenate(all_virs, axis=0)
     # allow custom dtypes
     if labels:
         dtypes = dpdata.system.LabeledSystem.DTYPES
@@ -82,9 +61,6 @@ def to_system_data(folder, type_map=None, labels=True):
             "coords",
             "real_atom_names",
             "nopbc",
-            "energies",
-            "forces",
-            "virials",
         ):
             # skip as these data contains specific rules
             continue
@@ -93,13 +69,13 @@ def to_system_data(folder, type_map=None, labels=True):
                 f"Shape of {dtype.name} is not (nframes, ...), but {dtype.shape}. This type of data will not converted from deepmd/npy format."
             )
             continue
-        natoms = data["coords"].shape[1]
+        natoms = data["atom_types"].shape[0]
         shape = [
             natoms if xx == dpdata.system.Axis.NATOMS else xx for xx in dtype.shape[1:]
         ]
         all_data = []
         for ii in sets:
-            tmp = _cond_load_data(os.path.join(ii, dtype.name + ".npy"))
+            tmp = _cond_load_data(os.path.join(ii, dtype.deepmd_name + ".npy"))
             if tmp is not None:
                 all_data.append(np.reshape(tmp, [tmp.shape[0], *shape]))
         if len(all_data) > 0:
@@ -136,19 +112,6 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
         np.savetxt(os.path.join(folder, "formal_charges.raw"), data["formal_charges"])
     # reshape frame properties and convert prec
     nframes = data["cells"].shape[0]
-    cells = np.reshape(data["cells"], [nframes, 9]).astype(comp_prec)
-    coords = np.reshape(data["coords"], [nframes, -1]).astype(comp_prec)
-    eners = None
-    forces = None
-    virials = None
-    if "energies" in data:
-        eners = np.reshape(data["energies"], [nframes]).astype(comp_prec)
-    if "forces" in data:
-        forces = np.reshape(data["forces"], [nframes, -1]).astype(comp_prec)
-    if "virials" in data:
-        virials = np.reshape(data["virials"], [nframes, 9]).astype(comp_prec)
-    if "atom_pref" in data:
-        atom_pref = np.reshape(data["atom_pref"], [nframes, -1]).astype(comp_prec)
     # dump frame properties: cell, coord, energy, force and virial
     nsets = nframes // set_size
     if set_size * nsets < nframes:
@@ -158,16 +121,6 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
         set_end = (ii + 1) * set_size
         set_folder = os.path.join(folder, "set.%03d" % ii)
         os.makedirs(set_folder)
-        np.save(os.path.join(set_folder, "box"), cells[set_stt:set_end])
-        np.save(os.path.join(set_folder, "coord"), coords[set_stt:set_end])
-        if eners is not None:
-            np.save(os.path.join(set_folder, "energy"), eners[set_stt:set_end])
-        if forces is not None:
-            np.save(os.path.join(set_folder, "force"), forces[set_stt:set_end])
-        if virials is not None:
-            np.save(os.path.join(set_folder, "virial"), virials[set_stt:set_end])
-        if "atom_pref" in data:
-            np.save(os.path.join(set_folder, "atom_pref"), atom_pref[set_stt:set_end])
     try:
         os.remove(os.path.join(folder, "nopbc"))
     except OSError:
@@ -187,13 +140,8 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
             "atom_names",
             "atom_types",
             "orig",
-            "cells",
-            "coords",
             "real_atom_names",
             "nopbc",
-            "energies",
-            "forces",
-            "virials",
         ):
             # skip as these data contains specific rules
             continue
@@ -211,4 +159,4 @@ def dump(folder, data, set_size=5000, comp_prec=np.float32, remove_sets=True):
             set_stt = ii * set_size
             set_end = (ii + 1) * set_size
             set_folder = os.path.join(folder, "set.%03d" % ii)
-            np.save(os.path.join(set_folder, dtype.name), ddata[set_stt:set_end])
+            np.save(os.path.join(set_folder, dtype.deepmd_name), ddata[set_stt:set_end])
diff --git a/dpdata/deepmd/hdf5.py b/dpdata/deepmd/hdf5.py
index 6b587893..cbdaa632 100644
--- a/dpdata/deepmd/hdf5.py
+++ b/dpdata/deepmd/hdf5.py
@@ -69,38 +69,7 @@ def to_system_data(
         data["nopbc"] = True
     sets = globfilter(g.keys(), "set.*")
 
-    data_types = {
-        "cells": {
-            "fn": "box",
-            "labeled": False,
-            "shape": (3, 3),
-            "required": "nopbc" not in data,
-        },
-        "coords": {
-            "fn": "coord",
-            "labeled": False,
-            "shape": (natoms, 3),
-            "required": True,
-        },
-        "energies": {
-            "fn": "energy",
-            "labeled": True,
-            "shape": tuple(),
-            "required": False,
-        },
-        "forces": {
-            "fn": "force",
-            "labeled": True,
-            "shape": (natoms, 3),
-            "required": False,
-        },
-        "virials": {
-            "fn": "virial",
-            "labeled": True,
-            "shape": (3, 3),
-            "required": False,
-        },
-    }
+    data_types = {}
     # allow custom dtypes
     if labels:
         dtypes = dpdata.system.LabeledSystem.DTYPES
@@ -112,14 +81,9 @@ def to_system_data(
             "atom_names",
             "atom_types",
             "orig",
-            "cells",
-            "coords",
             "real_atom_types",
             "real_atom_names",
             "nopbc",
-            "energies",
-            "forces",
-            "virials",
         ):
             # skip as these data contains specific rules
             continue
@@ -133,10 +97,10 @@ def to_system_data(
         ]
 
         data_types[dtype.name] = {
-            "fn": dtype.name,
-            "labeled": True,
+            "fn": dtype.deepmd_name,
             "shape": shape,
-            "required": False,
+            "required": dtype.required
+            and not (dtype.name == "cells" and data.get("nopbc", False)),
         }
 
     for dt, prop in data_types.items():
@@ -206,13 +170,7 @@ def dump(
     nopbc = data.get("nopbc", False)
     reshaped_data = {}
 
-    data_types = {
-        "cells": {"fn": "box", "shape": (nframes, 9), "dump": not nopbc},
-        "coords": {"fn": "coord", "shape": (nframes, -1), "dump": True},
-        "energies": {"fn": "energy", "shape": (nframes,), "dump": True},
-        "forces": {"fn": "force", "shape": (nframes, -1), "dump": True},
-        "virials": {"fn": "virial", "shape": (nframes, 9), "dump": True},
-    }
+    data_types = {}
 
     labels = "energies" in data
     if labels:
@@ -226,14 +184,9 @@ def dump(
             "atom_names",
             "atom_types",
             "orig",
-            "cells",
-            "coords",
             "real_atom_types",
             "real_atom_names",
             "nopbc",
-            "energies",
-            "forces",
-            "virials",
         ):
             # skip as these data contains specific rules
             continue
@@ -244,9 +197,9 @@ def dump(
             continue
 
         data_types[dtype.name] = {
-            "fn": dtype.name,
+            "fn": dtype.deepmd_name,
             "shape": (nframes, -1),
-            "dump": True,
+            "dump": not (dtype.name == "cells" and nopbc),
         }
 
     for dt, prop in data_types.items():
diff --git a/dpdata/deepmd/raw.py b/dpdata/deepmd/raw.py
index f8ddcaf3..81b01cc0 100644
--- a/dpdata/deepmd/raw.py
+++ b/dpdata/deepmd/raw.py
@@ -49,16 +49,6 @@ def to_system_data(folder, type_map=None, labels=True):
             data["cells"] = np.loadtxt(os.path.join(folder, "box.raw"), ndmin=2)
         data["cells"] = np.reshape(data["cells"], [nframes, 3, 3])
         data["coords"] = np.reshape(data["coords"], [nframes, -1, 3])
-        if labels:
-            if os.path.exists(os.path.join(folder, "energy.raw")):
-                data["energies"] = np.loadtxt(os.path.join(folder, "energy.raw"))
-                data["energies"] = np.reshape(data["energies"], [nframes])
-            if os.path.exists(os.path.join(folder, "force.raw")):
-                data["forces"] = np.loadtxt(os.path.join(folder, "force.raw"))
-                data["forces"] = np.reshape(data["forces"], [nframes, -1, 3])
-            if os.path.exists(os.path.join(folder, "virial.raw")):
-                data["virials"] = np.loadtxt(os.path.join(folder, "virial.raw"))
-                data["virials"] = np.reshape(data["virials"], [nframes, 3, 3])
         if os.path.isfile(os.path.join(folder, "nopbc")):
             data["nopbc"] = True
         # allow custom dtypes
@@ -77,9 +67,6 @@ def to_system_data(folder, type_map=None, labels=True):
                 "real_atom_types",
                 "real_atom_names",
                 "nopbc",
-                "energies",
-                "forces",
-                "virials",
             ):
                 # skip as these data contains specific rules
                 continue
@@ -88,14 +75,14 @@ def to_system_data(folder, type_map=None, labels=True):
                     f"Shape of {dtype.name} is not (nframes, ...), but {dtype.shape}. This type of data will not converted from deepmd/raw format."
                 )
                 continue
-            natoms = data["coords"].shape[1]
+            natoms = data["atom_types"].shape[0]
             shape = [
                 natoms if xx == dpdata.system.Axis.NATOMS else xx
                 for xx in dtype.shape[1:]
             ]
-            if os.path.exists(os.path.join(folder, f"{dtype.name}.raw")):
+            if os.path.exists(os.path.join(folder, f"{dtype.deepmd_name}.raw")):
                 data[dtype.name] = np.reshape(
-                    np.loadtxt(os.path.join(folder, f"{dtype.name}.raw")),
+                    np.loadtxt(os.path.join(folder, f"{dtype.deepmd_name}.raw")),
                     [nframes, *shape],
                 )
         return data
@@ -108,10 +95,6 @@ def dump(folder, data):
     nframes = data["cells"].shape[0]
     np.savetxt(os.path.join(folder, "type.raw"), data["atom_types"], fmt="%d")
     np.savetxt(os.path.join(folder, "type_map.raw"), data["atom_names"], fmt="%s")
-    np.savetxt(os.path.join(folder, "box.raw"), np.reshape(data["cells"], [nframes, 9]))
-    np.savetxt(
-        os.path.join(folder, "coord.raw"), np.reshape(data["coords"], [nframes, -1])
-    )
     # BondOrder System
     if "bonds" in data:
         np.savetxt(
@@ -121,21 +104,6 @@ def dump(folder, data):
         )
     if "formal_charges" in data:
         np.savetxt(os.path.join(folder, "formal_charges.raw"), data["formal_charges"])
-    # Labeled System
-    if "energies" in data:
-        np.savetxt(
-            os.path.join(folder, "energy.raw"),
-            np.reshape(data["energies"], [nframes, 1]),
-        )
-    if "forces" in data:
-        np.savetxt(
-            os.path.join(folder, "force.raw"), np.reshape(data["forces"], [nframes, -1])
-        )
-    if "virials" in data:
-        np.savetxt(
-            os.path.join(folder, "virial.raw"),
-            np.reshape(data["virials"], [nframes, 9]),
-        )
     try:
         os.remove(os.path.join(folder, "nopbc"))
     except OSError:
@@ -155,14 +123,9 @@ def dump(folder, data):
             "atom_names",
             "atom_types",
             "orig",
-            "cells",
-            "coords",
             "real_atom_types",
             "real_atom_names",
             "nopbc",
-            "energies",
-            "forces",
-            "virials",
         ):
             # skip as these data contains specific rules
             continue
@@ -174,4 +137,4 @@ def dump(folder, data):
             )
             continue
         ddata = np.reshape(data[dtype.name], [nframes, -1])
-        np.savetxt(os.path.join(folder, f"{dtype.name}.raw"), ddata)
+        np.savetxt(os.path.join(folder, f"{dtype.deepmd_name}.raw"), ddata)
diff --git a/dpdata/system.py b/dpdata/system.py
index 42b3f4e7..08136cb9 100644
--- a/dpdata/system.py
+++ b/dpdata/system.py
@@ -91,8 +91,10 @@ class System:
         DataType("atom_names", list, (Axis.NTYPES,)),
         DataType("atom_types", np.ndarray, (Axis.NATOMS,)),
         DataType("orig", np.ndarray, (3,)),
-        DataType("cells", np.ndarray, (Axis.NFRAMES, 3, 3)),
-        DataType("coords", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3)),
+        DataType("cells", np.ndarray, (Axis.NFRAMES, 3, 3), deepmd_name="box"),
+        DataType(
+            "coords", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3), deepmd_name="coord"
+        ),
         DataType(
             "real_atom_types", np.ndarray, (Axis.NFRAMES, Axis.NATOMS), required=False
         ),
@@ -1204,9 +1206,17 @@ class LabeledSystem(System):
     """
 
     DTYPES: tuple[DataType, ...] = System.DTYPES + (
-        DataType("energies", np.ndarray, (Axis.NFRAMES,)),
-        DataType("forces", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3)),
-        DataType("virials", np.ndarray, (Axis.NFRAMES, 3, 3), required=False),
+        DataType("energies", np.ndarray, (Axis.NFRAMES,), deepmd_name="energy"),
+        DataType(
+            "forces", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3), deepmd_name="force"
+        ),
+        DataType(
+            "virials",
+            np.ndarray,
+            (Axis.NFRAMES, 3, 3),
+            required=False,
+            deepmd_name="virial",
+        ),
         DataType("atom_pref", np.ndarray, (Axis.NFRAMES, Axis.NATOMS), required=False),
     )
 

From 2648d50c12d9bb5b970ff21a9283c36840047d67 Mon Sep 17 00:00:00 2001
From: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
Date: Fri, 20 Sep 2024 08:29:41 +0800
Subject: [PATCH 20/33] fix: qe input blocks not seperated by empty lines
 (#724)

the qe support only parse input file, in which cell blocks are separated
by empty lines, like
```
ATOMIC_SPECIES
 Na  22.989769  Na_ONCV_PBE-1.0.upf

CELL_PARAMETERS {angstrom}
 7.171683039200000  0.000000000000000  0.000000000000000
```
however, the input file is valid when no empty line exists, like the
following
```
ATOMIC_SPECIES
 Na  22.989769  Na_ONCV_PBE-1.0.upf
CELL_PARAMETERS {angstrom}
 7.171683039200000  0.000000000000000  0.000000000000000
```
This pr fixes the issue

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

## Summary by CodeRabbit

- **New Features**
- Improved handling of Quantum Espresso output data for better parsing
and clarity.
	- Enhanced error handling for missing force and stress data.
- Added configuration parameters for self-consistent field (SCF)
calculations for sodium.

- **Bug Fixes**
- Updated functions to prevent unwanted lines in data extraction,
ensuring cleaner output.

- **Tests**
- Introduced a new test class to validate the functionality of the
`dpdata.LabeledSystem` class with Quantum Espresso output, enhancing
test coverage.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
---
 dpdata/qe/scf.py        |  23 ++-
 tests/qe.scf/na.in      |  44 ++++++
 tests/qe.scf/na.out     | 343 ++++++++++++++++++++++++++++++++++++++++
 tests/test_qe_pw_scf.py |  43 +++++
 4 files changed, 450 insertions(+), 3 deletions(-)
 create mode 100644 tests/qe.scf/na.in
 create mode 100644 tests/qe.scf/na.out

diff --git a/dpdata/qe/scf.py b/dpdata/qe/scf.py
index f8670860..7b6a70aa 100755
--- a/dpdata/qe/scf.py
+++ b/dpdata/qe/scf.py
@@ -11,15 +11,32 @@
 bohr2ang = 0.52917721067
 kbar2evperang3 = 1e3 / 1.602176621e6
 
+_QE_BLOCK_KEYWORDS = [
+    "ATOMIC_SPECIES",
+    "ATOMIC_POSITIONS",
+    "K_POINTS",
+    "ADDITIONAL_K_POINTS",
+    "CELL_PARAMETERS",
+    "CONSTRAINTS",
+    "OCCUPATIONS",
+    "ATOMIC_VELOCITIES",
+    "ATOMIC_FORCES",
+    "SOLVENTS",
+    "HUBBARD",
+]
+
 
 def get_block(lines, keyword, skip=0):
     ret = []
     for idx, ii in enumerate(lines):
         if keyword in ii:
             blk_idx = idx + 1 + skip
-            while len(lines[blk_idx]) == 0:
+            while len(lines[blk_idx].split()) == 0:
                 blk_idx += 1
-            while len(lines[blk_idx]) != 0 and blk_idx != len(lines):
+            while (
+                len(lines[blk_idx].split()) != 0
+                and (lines[blk_idx].split()[0] not in _QE_BLOCK_KEYWORDS)
+            ) and blk_idx != len(lines):
                 ret.append(lines[blk_idx])
                 blk_idx += 1
             break
@@ -123,7 +140,7 @@ def get_force(lines, natoms):
 def get_stress(lines):
     blk = get_block(lines, "total   stress")
     if len(blk) == 0:
-        return
+        return None
     ret = []
     for ii in blk:
         ret.append([float(jj) for jj in ii.split()[3:6]])
diff --git a/tests/qe.scf/na.in b/tests/qe.scf/na.in
new file mode 100644
index 00000000..56a2d2e1
--- /dev/null
+++ b/tests/qe.scf/na.in
@@ -0,0 +1,44 @@
+
+&control
+    calculation = 'scf'
+    restart_mode = 'from_scratch',
+    prefix = 'Na'
+    outdir = './tmp'
+    pseudo_dir = './'
+/
+&SYSTEM
+ ibrav=0,   
+ nosym=.true.,                     
+ nat=3,                         
+ ntyp=1,                        
+ occupations = 'smearing',       
+ smearing = 'gauss',                
+ degauss = 0.02,                   
+ ecutwfc = 100,                   
+ ecutrho = 960,                   
+ lspinorb = .false.,                
+ noncolin = .false.,                
+/
+&ELECTRONS
+ conv_thr = 1.0d-9,                  
+ mixing_beta = 0.7,               
+ electron_maxstep = 200,          
+/
+&ions
+/
+&cell
+/
+ATOMIC_SPECIES
+ Na  22.989769  Na_ONCV_PBE-1.0.upf
+CELL_PARAMETERS {angstrom}        
+ 7.171683039200000  0.000000000000000  0.000000000000000
+ -4.270578118300000  5.761527588200000  0.000000000000000
+ -0.000000045600000  0.000000023000000  12.826457854999999
+ATOMIC_POSITIONS (crystal)       
+   
+ Na  0.940587444301534  0.397635863676890  0.059472381901808
+ Na  0.059413515648061  0.602364552456546  0.559472465518034
+ Na  0.602364619812068  0.059413062489401  0.059472381901808
+K_POINTS {automatic} 
+ 8 8 4  0 0 0
+ 
\ No newline at end of file
diff --git a/tests/qe.scf/na.out b/tests/qe.scf/na.out
new file mode 100644
index 00000000..a1f0042e
--- /dev/null
+++ b/tests/qe.scf/na.out
@@ -0,0 +1,343 @@
+
+     Program PWSCF v.7.0 starts on 18Sep2024 at  9:37:38 
+
+     This program is part of the open-source Quantum ESPRESSO suite
+     for quantum simulation of materials; please cite
+         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
+         "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
+         "P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
+          URL http://www.quantum-espresso.org", 
+     in publications or presentations arising from this work. More details at
+     http://www.quantum-espresso.org/quote
+
+     Parallel version (MPI & OpenMP), running on      32 processor cores
+     Number of MPI processes:                32
+     Threads/MPI process:                     1
+
+     MPI processes distributed on     1 nodes
+     R & G space division:  proc/nbgrp/npool/nimage =      32
+     124265 MiB available memory on the printing compute node when the environment starts
+ 
+     Waiting for input...
+     Reading input from standard input
+Warning: card &CELL ignored
+Warning: card / ignored
+
+     Current dimensions of program PWSCF are:
+     Max number of different atomic species (ntypx) = 10
+     Max number of k-points (npk) =  40000
+     Max angular momentum in pseudopotentials (lmaxx) =  4
+     Message from routine setup:
+     no reason to have ecutrho>4*ecutwfc
+
+     Subspace diagonalization in iterative solution of the eigenvalue problem:
+     a serial algorithm will be used
+
+ 
+     Parallelization info
+     --------------------
+     sticks:   dense  smooth     PW     G-vecs:    dense   smooth      PW
+     Min         352     146     40                56132    15094    2202
+     Max         353     147     41                56139    15101    2213
+     Sum       11267    4699   1301              1796313   483165   70641
+ 
+     Using Slab Decomposition
+ 
+
+
+     bravais-lattice index     =            0
+     lattice parameter (alat)  =      13.5525  a.u.
+     unit-cell volume          =    3576.5316 (a.u.)^3
+     number of atoms/cell      =            3
+     number of atomic types    =            1
+     number of electrons       =       540.00
+     number of Kohn-Sham states=          324
+     kinetic-energy cutoff     =     100.0000  Ry
+     charge density cutoff     =     960.0000  Ry
+     scf convergence threshold =      1.0E-09
+     mixing beta               =       0.7000
+     number of iterations used =            8  plain     mixing
+     Exchange-correlation= PBE
+                           (   1   4   3   4   0   0   0)
+
+     celldm(1)=  13.552517  celldm(2)=   0.000000  celldm(3)=   0.000000
+     celldm(4)=   0.000000  celldm(5)=   0.000000  celldm(6)=   0.000000
+
+     crystal axes: (cart. coord. in units of alat)
+               a(1) = (   1.000000   0.000000   0.000000 )  
+               a(2) = (  -0.595478   0.803372   0.000000 )  
+               a(3) = (  -0.000000   0.000000   1.788486 )  
+
+     reciprocal axes: (cart. coord. in units 2 pi/alat)
+               b(1) = (  1.000000  0.741223  0.000000 )  
+               b(2) = (  0.000000  1.244754 -0.000000 )  
+               b(3) = (  0.000000  0.000000  0.559132 )  
+
+
+     PseudoPot. # 1 for Na read from file:
+     ./Na_ONCV_PBE-1.0.upf
+     MD5 check sum: d7d7bc8e018c79acd8ed72114b17dc6b
+     Pseudo is Norm-conserving, Zval =  9.0
+     Generated using ONCVPSP code by D. R. Hamann
+     Using radial grid of  602 points,  4 beta functions with: 
+                l(1) =   0
+                l(2) =   0
+                l(3) =   1
+                l(4) =   1
+
+     atomic species   valence    mass     pseudopotential
+        Na             9.00    22.98977     Na( 1.00)
+
+     No symmetry found
+
+
+
+   Cartesian axes
+
+     site n.     atom                  positions (alat units)
+         1           Na  tau(   1) = (   0.7038041   0.3194494   0.1063655  )
+         2           Na  tau(   2) = (  -0.2992812   0.4839227   1.0006089  )
+         3           Na  tau(   3) = (   0.5669855   0.0477308   0.1063655  )
+
+     number of k points=   132  Gaussian smearing, width (Ry)=  0.0200
+
+     Number of k-points >= 100: set verbosity='high' to print them.
+
+     Dense  grid:  1796313 G-vectors     FFT dimensions: ( 135, 135, 240)
+
+     Smooth grid:   483165 G-vectors     FFT dimensions: (  90,  90, 160)
+
+     Estimated max dynamical RAM per process >       1.32 GB
+
+     Estimated total dynamical RAM >      42.10 GB
+
+     Initial potential from superposition of free atoms
+
+     starting charge     531.7976, renormalised to     540.0000
+     Starting wfcs are random
+
+     total cpu time spent up to now is      114.9 secs
+
+     Self-consistent Calculation
+
+     iteration #  1     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  1.00E-02,  avg # of iterations =  9.1
+
+     Threshold (ethr) on eigenvalues was too large:
+     Diagonalizing with lowered threshold
+
+     Davidson diagonalization with overlap
+     ethr =  5.78E-04,  avg # of iterations =  1.8
+
+     total cpu time spent up to now is     1816.0 secs
+
+     total energy              =   -5091.43713858 Ry
+     estimated scf accuracy    <       2.93415295 Ry
+
+     iteration #  2     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  5.43E-04,  avg # of iterations =  3.1
+
+     total cpu time spent up to now is     2304.9 secs
+
+     total energy              =   -5091.87662866 Ry
+     estimated scf accuracy    <       0.18067264 Ry
+
+     iteration #  3     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  3.35E-05,  avg # of iterations =  9.2
+
+     total cpu time spent up to now is     2929.4 secs
+
+     total energy              =   -5091.86348124 Ry
+     estimated scf accuracy    <       0.24741291 Ry
+
+     iteration #  4     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  3.35E-05,  avg # of iterations =  6.2
+
+     total cpu time spent up to now is     3422.9 secs
+
+     total energy              =   -5091.91697077 Ry
+     estimated scf accuracy    <       0.03279724 Ry
+
+     iteration #  5     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  6.07E-06,  avg # of iterations =  6.5
+
+     total cpu time spent up to now is     3919.2 secs
+
+     total energy              =   -5091.92159622 Ry
+     estimated scf accuracy    <       0.01385226 Ry
+
+     iteration #  6     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  2.57E-06,  avg # of iterations =  4.9
+
+     total cpu time spent up to now is     4362.4 secs
+
+     total energy              =   -5091.92392162 Ry
+     estimated scf accuracy    <       0.00067159 Ry
+
+     iteration #  7     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     c_bands:  1 eigenvalues not converged
+     ethr =  1.24E-07,  avg # of iterations =  2.4
+
+     total cpu time spent up to now is     4735.1 secs
+
+     total energy              =   -5091.92383567 Ry
+     estimated scf accuracy    <       0.00330792 Ry
+
+     iteration #  8     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  1.24E-07,  avg # of iterations =  2.0
+
+     total cpu time spent up to now is     5089.7 secs
+
+     total energy              =   -5091.92408732 Ry
+     estimated scf accuracy    <       0.00023165 Ry
+
+     iteration #  9     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  4.29E-08,  avg # of iterations =  2.0
+
+     total cpu time spent up to now is     5447.8 secs
+
+     total energy              =   -5091.92409876 Ry
+     estimated scf accuracy    <       0.00005097 Ry
+
+     iteration # 10     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  9.44E-09,  avg # of iterations =  2.0
+
+     total cpu time spent up to now is     5804.4 secs
+
+     total energy              =   -5091.92409732 Ry
+     estimated scf accuracy    <       0.00020843 Ry
+
+     iteration # 11     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  9.44E-09,  avg # of iterations =  1.8
+
+     total cpu time spent up to now is     6150.7 secs
+
+     total energy              =   -5091.92411078 Ry
+     estimated scf accuracy    <       0.00000218 Ry
+
+     iteration # 12     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  4.03E-10,  avg # of iterations =  2.0
+
+     total cpu time spent up to now is     6512.7 secs
+
+     total energy              =   -5091.92411112 Ry
+     estimated scf accuracy    <       0.00000056 Ry
+
+     iteration # 13     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  1.04E-10,  avg # of iterations =  2.0
+
+     total cpu time spent up to now is     6874.7 secs
+
+     total energy              =   -5091.92411124 Ry
+     estimated scf accuracy    <       0.00000010 Ry
+
+     iteration # 14     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  1.90E-11,  avg # of iterations =  2.0
+
+     total cpu time spent up to now is     7236.4 secs
+
+     total energy              =   -5091.92411126 Ry
+     estimated scf accuracy    <       0.00000002 Ry
+
+     iteration # 15     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  3.88E-12,  avg # of iterations =  2.0
+
+     total cpu time spent up to now is     7598.0 secs
+
+     total energy              =   -5091.92411126 Ry
+     estimated scf accuracy    <          3.1E-09 Ry
+
+     iteration # 16     ecut=   100.00 Ry     beta= 0.70
+     Davidson diagonalization with overlap
+     ethr =  5.74E-13,  avg # of iterations =  2.0
+
+     total cpu time spent up to now is     7958.9 secs
+
+     End of self-consistent calculation
+
+     Number of k-points >= 100: set verbosity='high' to print the bands.
+
+     the Fermi energy is    17.2707 ev
+
+!    total energy              =   -5091.92411126 Ry
+     estimated scf accuracy    <          9.4E-10 Ry
+     smearing contrib. (-TS)   =      -0.02510189 Ry
+     internal energy E=F+TS    =   -5091.89900937 Ry
+
+     The total energy is F=E-TS. E is the sum of the following terms:
+     one-electron contribution =   -1954.47492763 Ry
+     hartree contribution      =    1190.28239393 Ry
+     xc contribution           =    -772.17810332 Ry
+     ewald contribution        =   -3555.52837235 Ry
+
+     convergence has been achieved in  16 iterations
+
+     Forces acting on atoms (Ry/au):
+
+     atom    1 type  1   force =    -0.0   -0.0    0.0
+     atom    2 type  1   force =    -0.0    0.0    0.0
+     atom    3 type  1   force =    -0.0    0.0   -0.0
+
+     Writing all to output data dir ./tmp/Na.save/
+ 
+     init_run     :    106.04s CPU    113.67s WALL (       1 calls)
+     electrons    :   7468.59s CPU   7844.89s WALL (       1 calls)
+
+     Called by init_run:
+     wfcinit      :    103.82s CPU    111.27s WALL (       1 calls)
+     potinit      :      0.41s CPU      0.45s WALL (       1 calls)
+     hinit0       :      0.77s CPU      0.83s WALL (       1 calls)
+
+     Called by electrons:
+     c_bands      :   7022.30s CPU   7363.43s WALL (      17 calls)
+     sum_band     :    444.25s CPU    478.23s WALL (      17 calls)
+     v_of_rho     :      1.61s CPU      1.93s WALL (      17 calls)
+     mix_rho      :      0.31s CPU      0.40s WALL (      17 calls)
+
+     Called by c_bands:
+     init_us_2    :     22.26s CPU     23.03s WALL (    4620 calls)
+     init_us_2:cp :     22.22s CPU     23.01s WALL (    4620 calls)
+     cegterg      :   6883.35s CPU   7219.17s WALL (    2244 calls)
+
+     Called by *egterg:
+     cdiaghg      :   1863.67s CPU   1931.50s WALL (   10175 calls)
+     h_psi        :   2890.75s CPU   3087.99s WALL (   10439 calls)
+     g_psi        :     14.56s CPU     14.97s WALL (    8063 calls)
+
+     Called by h_psi:
+     h_psi:calbec :    479.18s CPU    494.17s WALL (   10439 calls)
+     vloc_psi     :   1926.22s CPU   2091.42s WALL (   10439 calls)
+     add_vuspsi   :    470.49s CPU    486.00s WALL (   10439 calls)
+
+     General routines
+     calbec       :    479.12s CPU    494.13s WALL (   10439 calls)
+     fft          :      0.84s CPU      1.04s WALL (     202 calls)
+     ffts         :      0.03s CPU      0.04s WALL (      34 calls)
+     fftw         :   2059.48s CPU   2242.08s WALL ( 4338058 calls)
+     interpolate  :      0.09s CPU      0.11s WALL (      17 calls)
+ 
+     Parallel routines
+ 
+     PWSCF        :      2h 6m CPU      2h19m WALL
+
+ 
+   This run was terminated on:  11:57:29  18Sep2024            
+
+=------------------------------------------------------------------------------=
+   JOB DONE.
+=------------------------------------------------------------------------------=
diff --git a/tests/test_qe_pw_scf.py b/tests/test_qe_pw_scf.py
index 8703e7c2..a38e2d05 100644
--- a/tests/test_qe_pw_scf.py
+++ b/tests/test_qe_pw_scf.py
@@ -188,5 +188,48 @@ def setUp(self):
         )
 
 
+class TestNa(unittest.TestCase):
+    def test(self):
+        ss = dpdata.LabeledSystem("qe.scf/na.out", fmt="qe/pw/scf")
+        self.assertEqual(ss["atom_numbs"], [3])
+        self.assertEqual(ss["atom_names"], ["Na"])
+        self.assertEqual(ss.get_nframes(), 1)
+        np.testing.assert_array_equal(ss["atom_types"], [0, 0, 0])
+        np.testing.assert_allclose(
+            ss["coords"][0],
+            np.array(
+                [
+                    0.940587444301534,
+                    0.397635863676890,
+                    0.059472381901808,
+                    0.059413515648061,
+                    0.602364552456546,
+                    0.559472465518034,
+                    0.602364619812068,
+                    0.059413062489401,
+                    0.059472381901808,
+                ]
+            ).reshape(3, 3)
+            @ ss["cells"][0],
+        )
+        np.testing.assert_allclose(
+            ss["cells"][0],
+            np.array(
+                [
+                    7.171683039200000,
+                    0.000000000000000,
+                    0.000000000000000,
+                    -4.270578118300000,
+                    5.761527588200000,
+                    0.000000000000000,
+                    -0.000000045600000,
+                    0.000000023000000,
+                    12.826457854999999,
+                ]
+            ).reshape(3, 3),
+        )
+        np.testing.assert_allclose(ss["forces"][0], np.zeros([3, 3]))
+
+
 if __name__ == "__main__":
     unittest.main()

From 482775f19e11ae77e7ee9835ee23068da11c52cb Mon Sep 17 00:00:00 2001
From: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
Date: Fri, 20 Sep 2024 09:27:41 +0800
Subject: [PATCH 21/33] Fix: qe/pw/scf unit conversion is not consistent with
 dpdata (#725)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Introduced a configuration file for sodium SCF calculations, enhancing
quantum mechanical simulations.
- Added a new test class to verify properties of sodium systems,
improving test coverage.

- **Bug Fixes**
- Improved logic for block extraction and stress block handling to
enhance robustness.

- **Tests**
- Updated energy validation method to use relative comparisons for more
accurate results.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 dpdata/qe/scf.py                   | 10 +++++++---
 tests/test_qe_pw_scf.py            |  6 +++---
 tests/test_qe_pw_scf_energy_bug.py |  2 +-
 3 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/dpdata/qe/scf.py b/dpdata/qe/scf.py
index 7b6a70aa..341261d2 100755
--- a/dpdata/qe/scf.py
+++ b/dpdata/qe/scf.py
@@ -7,9 +7,13 @@
 
 from dpdata.utils import open_file
 
-ry2ev = 13.605693009
-bohr2ang = 0.52917721067
-kbar2evperang3 = 1e3 / 1.602176621e6
+from .traj import (
+    kbar2evperang3,
+    ry2ev,
+)
+from .traj import (
+    length_convert as bohr2ang,
+)
 
 _QE_BLOCK_KEYWORDS = [
     "ATOMIC_SPECIES",
diff --git a/tests/test_qe_pw_scf.py b/tests/test_qe_pw_scf.py
index a38e2d05..7fe803b9 100644
--- a/tests/test_qe_pw_scf.py
+++ b/tests/test_qe_pw_scf.py
@@ -161,11 +161,11 @@ def test_virial(self):
 
     def test_energy(self):
         ref_energy = -219.74425946528794
-        self.assertAlmostEqual(self.system_ch4.data["energies"][0], ref_energy)
+        self.assertAlmostEqual(self.system_ch4.data["energies"][0] / ref_energy, 1.0)
         ref_energy = -30007.651851226798
-        self.assertAlmostEqual(self.system_h2o.data["energies"][0], ref_energy)
+        self.assertAlmostEqual(self.system_h2o.data["energies"][0] / ref_energy, 1.0)
         ref_energy = -219.7153691367526562
-        self.assertAlmostEqual(self.system_ch4_2.data["energies"][0], ref_energy)
+        self.assertAlmostEqual(self.system_ch4_2.data["energies"][0] / ref_energy, 1.0)
 
 
 class TestPWSCFLabeledOutput(unittest.TestCase, TestPWSCFSinglePointEnergy):
diff --git a/tests/test_qe_pw_scf_energy_bug.py b/tests/test_qe_pw_scf_energy_bug.py
index b66ce924..a513dc7c 100644
--- a/tests/test_qe_pw_scf_energy_bug.py
+++ b/tests/test_qe_pw_scf_energy_bug.py
@@ -8,7 +8,7 @@
 class TestPWSCFSinglePointEnergy:
     def test_energy(self):
         ref_energy = -296.08379065679094669
-        self.assertAlmostEqual(self.system_al.data["energies"][0], ref_energy)
+        self.assertAlmostEqual(self.system_al.data["energies"][0] / ref_energy, 1.0)
 
 
 class TestPWSCFLabeledOutput(unittest.TestCase, TestPWSCFSinglePointEnergy):

From c1d6c73726b7b3ffe42ba72add54aa03102abfa5 Mon Sep 17 00:00:00 2001
From: Peng Xingliang <91927439+pxlxingliang@users.noreply.github.com>
Date: Fri, 20 Sep 2024 15:50:46 +0800
Subject: [PATCH 22/33] feat: support spin for ABACUS (#718)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Enhanced data retrieval capabilities with the inclusion of magnetic
moment and force data in the output.
- Streamlined method for handling parameters in the ABACUS plugin,
improving usability.
- New function added for registering magnetic data types, enhancing
functionality.
- Comprehensive test suite introduced for validating ABACUS spin
simulation functionalities.

- **Bug Fixes**
- Improved control flow to ensure accurate integration of new magnetic
data.

- **Tests**
- Introduced new test cases to validate the accuracy of ABACUS spin
simulation outputs, enhancing overall test coverage.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: root <pxlxingliang>
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>
---
 dpdata/abacus/md.py                           |    8 +
 dpdata/abacus/relax.py                        |    8 +
 dpdata/abacus/scf.py                          |  468 +++++++-
 dpdata/plugins/abacus.py                      |   55 +-
 tests/abacus.relax/INPUT.spin                 |   35 +
 tests/abacus.relax/STRU.spin                  |   21 +
 tests/abacus.scf/C.orb                        |    0
 tests/abacus.scf/C.upf                        |    0
 tests/abacus.scf/H.orb                        |    0
 tests/abacus.scf/H.upf                        |    0
 tests/abacus.scf/jle.orb                      |    0
 tests/abacus.scf/stru.ref                     |   29 +
 tests/abacus.spin/INPUT                       |   27 +
 tests/abacus.spin/INPUT.md                    |   34 +
 tests/abacus.spin/INPUT.relax                 |   34 +
 tests/abacus.spin/INPUT.scf                   |   27 +
 tests/abacus.spin/OUT.ABACUS/MD_dump          |   44 +
 tests/abacus.spin/OUT.ABACUS/running_md.log   |  997 ++++++++++++++++
 .../abacus.spin/OUT.ABACUS/running_relax.log  | 1002 +++++++++++++++++
 tests/abacus.spin/OUT.ABACUS/running_scf.log  |  565 ++++++++++
 tests/abacus.spin/STRU                        |   21 +
 tests/test_abacus_spin.py                     |  157 +++
 tests/test_abacus_stru_dump.py                |  161 ++-
 23 files changed, 3647 insertions(+), 46 deletions(-)
 create mode 100644 tests/abacus.relax/INPUT.spin
 create mode 100644 tests/abacus.relax/STRU.spin
 create mode 100644 tests/abacus.scf/C.orb
 create mode 100644 tests/abacus.scf/C.upf
 create mode 100644 tests/abacus.scf/H.orb
 create mode 100644 tests/abacus.scf/H.upf
 create mode 100644 tests/abacus.scf/jle.orb
 create mode 100644 tests/abacus.scf/stru.ref
 create mode 100644 tests/abacus.spin/INPUT
 create mode 100644 tests/abacus.spin/INPUT.md
 create mode 100644 tests/abacus.spin/INPUT.relax
 create mode 100644 tests/abacus.spin/INPUT.scf
 create mode 100644 tests/abacus.spin/OUT.ABACUS/MD_dump
 create mode 100644 tests/abacus.spin/OUT.ABACUS/running_md.log
 create mode 100644 tests/abacus.spin/OUT.ABACUS/running_relax.log
 create mode 100644 tests/abacus.spin/OUT.ABACUS/running_scf.log
 create mode 100644 tests/abacus.spin/STRU
 create mode 100644 tests/test_abacus_spin.py

diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py
index 9e0a416a..bbb02343 100644
--- a/dpdata/abacus/md.py
+++ b/dpdata/abacus/md.py
@@ -12,6 +12,7 @@
     get_cell,
     get_coords,
     get_geometry_in,
+    get_mag_force,
     kbar2evperang3,
 )
 
@@ -199,6 +200,9 @@ def get_frame(fname):
         stress[iframe] *= np.linalg.det(cells[iframe, :, :].reshape([3, 3]))
     if np.sum(np.abs(stress[0])) < 1e-10:
         stress = None
+
+    magmom, magforce = get_mag_force(outlines)
+
     data = {}
     data["atom_names"] = atom_names
     data["atom_numbs"] = natoms
@@ -213,5 +217,9 @@ def get_frame(fname):
     if not isinstance(data["virials"], np.ndarray):
         del data["virials"]
     data["orig"] = np.zeros(3)
+    if len(magmom) > 0:
+        data["spins"] = magmom
+    if len(magforce) > 0:
+        data["mag_forces"] = magforce
 
     return data
diff --git a/dpdata/abacus/relax.py b/dpdata/abacus/relax.py
index 7a4abf35..be80bc90 100644
--- a/dpdata/abacus/relax.py
+++ b/dpdata/abacus/relax.py
@@ -13,6 +13,7 @@
     get_cell,
     get_coords,
     get_geometry_in,
+    get_mag_force,
     kbar2evperang3,
 )
 
@@ -198,6 +199,8 @@ def get_frame(fname):
         lines, atomnumber
     )
 
+    magmom, magforce = get_mag_force(lines)
+
     data = {}
     data["atom_names"] = atom_names
     data["atom_numbs"] = natoms
@@ -211,4 +214,9 @@ def get_frame(fname):
     data["stress"] = stress
     data["orig"] = np.zeros(3)
 
+    if len(magmom) > 0:
+        data["spins"] = magmom
+    if len(magforce) > 0:
+        data["mag_forces"] = magforce
+
     return data
diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py
index 93e3d6e1..9919e912 100644
--- a/dpdata/abacus/scf.py
+++ b/dpdata/abacus/scf.py
@@ -112,6 +112,152 @@ def get_cell(geometry_inlines):
     return celldm, cell
 
 
+def parse_stru_pos(pos_line):
+    """Parses a line from the atom position block in a structure file.
+
+    The content in atom position block can include:
+    - `m` or NO key word: Three numbers (0 or 1) controlling atom movement in geometry relaxation calculations.
+    - `v`, `vel`, or `velocity`: Three components of initial velocity of atoms in geometry relaxation calculations.
+    - `mag` or `magmom`: Start magnetization for each atom. Can be one number (colinear) or three numbers (non-colinear).
+    - `angle1`: In non-colinear case, angle between c-axis and real spin (in degrees).
+    - `angle2`: In non-colinear case, angle between a-axis and real spin projection in ab-plane (in degrees).
+    - `cs` or `constrain`: Three numbers (0 or 1) controlling the spin constraint of the atom.
+    - `lambda`: Three numbers controlling the lambda of the atom.
+
+    Parameters
+    ----------
+    pos_line : A line from the atom position block.
+
+    Returns
+    -------
+    tuple: A tuple containing:
+          - pos (list of float): The position coordinates.
+          - move (list of int or None): Movement control values.
+          - velocity (list of float or None): Initial velocity components.
+          - magmom (float, list of float, or None): Magnetization values.
+          - angle1 (float or None): Angle1 value.
+          - angle2 (float or None): Angle2 value.
+          - constrain (list of bool or None): Spin constraint values.
+          - lambda1 (float, list of float, or None): Lambda values.
+
+        e.g.:
+        ```
+        Fe
+        1.0
+        2
+        0.0 0.0 0.0 m 0 0 0 mag 1.0 angle1 90 angle2 0 cs 0 0 0
+        0.5 0.5 0.5 m 1 1 1 mag 1.0 angle1 90 angle2 180
+        ```
+    """
+    pos_line = pos_line.split("#")[0]  # remove comments
+    sline = pos_line.split()
+    pos = [float(i) for i in sline[:3]]
+    move = None
+    velocity = None
+    magmom = None
+    angle1 = None
+    angle2 = None
+    constrain = None
+    lambda1 = None
+    if len(sline) > 3:
+        mag_list = None
+        velocity_list = None
+        move_list = []
+        angle1_list = None
+        angle2_list = None
+        constrain_list = None
+        lambda_list = None
+        label = "move"
+        for i in range(3, len(sline)):
+            # firstly read the label
+            if sline[i] == "m":
+                label = "move"
+            elif sline[i] in ["v", "vel", "velocity"]:
+                label = "velocity"
+                velocity_list = []
+            elif sline[i] in ["mag", "magmom"]:
+                label = "magmom"
+                mag_list = []
+            elif sline[i] == "angle1":
+                label = "angle1"
+                angle1_list = []
+            elif sline[i] == "angle2":
+                label = "angle2"
+                angle2_list = []
+            elif sline[i] in ["constrain", "sc"]:
+                label = "constrain"
+                constrain_list = []
+            elif sline[i] in ["lambda"]:
+                label = "lambda"
+                lambda_list = []
+
+            # the read the value to the list
+            elif label == "move":
+                move_list.append(int(sline[i]))
+            elif label == "velocity":
+                velocity_list.append(float(sline[i]))
+            elif label == "magmom":
+                mag_list.append(float(sline[i]))
+            elif label == "angle1":
+                angle1_list.append(float(sline[i]))
+            elif label == "angle2":
+                angle2_list.append(float(sline[i]))
+            elif label == "constrain":
+                constrain_list.append(bool(int(sline[i])))
+            elif label == "lambda":
+                lambda_list.append(float(sline[i]))
+
+        if move_list is not None and len(move_list) > 0:
+            if len(move_list) == 3:
+                move = move_list
+            else:
+                raise RuntimeError(f"Invalid setting of move: {pos_line}")
+
+        if velocity_list is not None:
+            if len(velocity_list) == 3:
+                velocity = velocity_list
+            else:
+                raise RuntimeError(f"Invalid setting of velocity: {pos_line}")
+
+        if mag_list is not None:
+            if len(mag_list) == 3:
+                magmom = mag_list
+            elif len(mag_list) == 1:
+                magmom = mag_list[0]
+            else:
+                raise RuntimeError(f"Invalid magnetic moment {pos_line}")
+
+        if angle1_list is not None:
+            if len(angle1_list) == 1:
+                angle1 = angle1_list[0]
+            else:
+                raise RuntimeError(f"Invalid angle1 {pos_line}")
+
+        if angle2_list is not None:
+            if len(angle2_list) == 1:
+                angle2 = angle2_list[0]
+            else:
+                raise RuntimeError(f"Invalid angle2 {pos_line}")
+
+        if constrain_list is not None:
+            if len(constrain_list) == 3:
+                constrain = constrain_list
+            elif len(constrain_list) == 1:
+                constrain = constrain_list[0]
+            else:
+                raise RuntimeError(f"Invalid constrain {pos_line}")
+
+        if lambda_list is not None:
+            if len(lambda_list) == 3:
+                lambda1 = lambda_list
+            elif len(lambda_list) == 1:
+                lambda1 = lambda_list[0]
+            else:
+                raise RuntimeError(f"Invalid lambda {pos_line}")
+
+    return pos, move, velocity, magmom, angle1, angle2, constrain, lambda1
+
+
 def get_coords(celldm, cell, geometry_inlines, inlines=None):
     coords_lines = get_stru_block(geometry_inlines, "ATOMIC_POSITIONS")
     # assuming that ATOMIC_POSITIONS is at the bottom of the STRU file
@@ -120,6 +266,14 @@ def get_coords(celldm, cell, geometry_inlines, inlines=None):
     atom_types = []  # index of atom_names of each atom in the geometry
     atom_numbs = []  # of atoms for each element
     coords = []  # coordinations of atoms
+    move = []  # move flag of each atom
+    velocity = []  # velocity of each atom
+    mag = []  # magnetic moment of each atom
+    angle1 = []  # angle1 of each atom
+    angle2 = []  # angle2 of each atom
+    sc = []  # spin constraint flag of each atom
+    lambda_ = []  # lambda of each atom
+
     ntype = get_nele_from_stru(geometry_inlines)
     line_idx = 1  # starting line of first element
     for it in range(ntype):
@@ -128,7 +282,10 @@ def get_coords(celldm, cell, geometry_inlines, inlines=None):
         atom_numbs.append(int(coords_lines[line_idx].split()[0]))
         line_idx += 1
         for iline in range(atom_numbs[it]):
-            xyz = np.array([float(xx) for xx in coords_lines[line_idx].split()[0:3]])
+            pos, imove, ivelocity, imagmom, iangle1, iangle2, iconstrain, ilambda1 = (
+                parse_stru_pos(coords_lines[line_idx])
+            )
+            xyz = np.array(pos)
             if coord_type == "cartesian":
                 xyz = xyz * celldm
             elif coord_type == "direct":
@@ -141,6 +298,15 @@ def get_coords(celldm, cell, geometry_inlines, inlines=None):
                 )
             coords.append(xyz)
             atom_types.append(it)
+
+            move.append(imove)
+            velocity.append(ivelocity)
+            mag.append(imagmom)
+            angle1.append(iangle1)
+            angle2.append(iangle2)
+            sc.append(iconstrain)
+            lambda_.append(ilambda1)
+
             line_idx += 1
     coords = np.array(coords)  # need transformation!!!
     atom_types = np.array(atom_types)
@@ -234,15 +400,57 @@ def get_stress(outlines):
         return np.array(stress[-1]) * kbar2evperang3  # only return the last stress
 
 
+def get_mag_force(outlines):
+    """Read atomic magmom and magnetic force from OUT.ABACUS/running_scf.log.
+
+    Returns
+    -------
+    magmom: list of list of atomic magnetic moments (three dimensions: ION_STEP * NATOMS * 1/3)
+    magforce: list of list of atomic magnetic forces (three dimensions: ION_STEP * NATOMS * 1/3)
+    e.g.:
+    -------------------------------------------------------------------------------------------
+    Total Magnetism (uB)
+    -------------------------------------------------------------------------------------------
+        Fe         0.0000000001         0.0000000000         3.0000000307
+        Fe        -0.0000000000        -0.0000000000         3.0000001151
+    -------------------------------------------------------------------------------------------
+    -------------------------------------------------------------------------------------------
+    Magnetic force (eV/uB)
+    -------------------------------------------------------------------------------------------
+        Fe         0.0000000000         0.0000000000        -1.2117698671
+        Fe         0.0000000000         0.0000000000        -1.2117928796
+    -------------------------------------------------------------------------------------------
+
+    """
+    mags = []
+    magforces = []
+    for i, line in enumerate(outlines):
+        if "Total Magnetism (uB)" in line:
+            j = i + 2
+            mag = []
+            while "-------------------------" not in outlines[j]:
+                mag.append([float(ii) for ii in outlines[j].split()[1:]])
+                j += 1
+            mags.append(mag)
+        if "Magnetic force (eV/uB)" in line:
+            j = i + 2
+            magforce = []
+            while "-------------------------" not in outlines[j]:
+                magforce.append([float(ii) for ii in outlines[j].split()[1:]])
+                j += 1
+            magforces.append(magforce)
+    return np.array(mags), np.array(magforces)
+
+
 def get_frame(fname):
     data = {
         "atom_names": [],
         "atom_numbs": [],
         "atom_types": [],
-        "cells": [],
-        "coords": [],
-        "energies": [],
-        "forces": [],
+        "cells": np.array([]),
+        "coords": np.array([]),
+        "energies": np.array([]),
+        "forces": np.array([]),
     }
 
     if isinstance(fname, str):
@@ -272,6 +480,12 @@ def get_frame(fname):
     atom_names, natoms, types, coords = get_coords(
         celldm, cell, geometry_inlines, inlines
     )
+    magmom, magforce = get_mag_force(outlines)
+    if len(magmom) > 0:
+        magmom = magmom[-1:]
+    if len(magforce) > 0:
+        magforce = magforce[-1:]
+
     data["atom_names"] = atom_names
     data["atom_numbs"] = natoms
     data["atom_types"] = types
@@ -291,6 +505,11 @@ def get_frame(fname):
     if stress is not None:
         data["virials"] = stress[np.newaxis, :, :]
     data["orig"] = np.zeros(3)
+
+    if len(magmom) > 0:
+        data["spins"] = magmom
+    if len(magforce) > 0:
+        data["mag_forces"] = magforce
     # print("atom_names = ", data['atom_names'])
     # print("natoms = ", data['atom_numbs'])
     # print("types = ", data['atom_types'])
@@ -313,12 +532,9 @@ def get_nele_from_stru(geometry_inlines):
     ]
     keyword_sequence = []
     keyword_line_index = []
-    atom_names = []
-    atom_numbs = []
     for iline, line in enumerate(geometry_inlines):
         if line.split() == []:
             continue
-        have_key_word = False
         for keyword in key_words_list:
             if keyword in line and keyword == line.split()[0]:
                 keyword_sequence.append(keyword)
@@ -343,7 +559,7 @@ def get_frame_from_stru(fname):
     with open_file(fname) as fp:
         geometry_inlines = fp.read().split("\n")
     nele = get_nele_from_stru(geometry_inlines)
-    inlines = ["ntype %d" % nele]
+    inlines = [f"ntype {nele}"]
     celldm, cell = get_cell(geometry_inlines)
     atom_names, natoms, types, coords = get_coords(
         celldm, cell, geometry_inlines, inlines
@@ -366,32 +582,180 @@ def make_unlabeled_stru(
     numerical_orbital=None,
     numerical_descriptor=None,
     mass=None,
+    move=None,
+    velocity=None,
+    mag=None,
+    angle1=None,
+    angle2=None,
+    sc=None,
+    lambda_=None,
+    link_file=False,
+    dest_dir=None,
+    **kwargs,
 ):
+    """Make an unlabeled STRU file from a dictionary.
+
+    Parameters
+    ----------
+    data : dict
+        System data
+    frame_idx : int
+        The index of the frame to dump
+    pp_file : list of string or dict, optional
+        List of pseudo potential files, or a dictionary of pseudo potential files for each atomnames
+    numerical_orbital : list of string or dict, optional
+        List of orbital files, or a dictionary of orbital files for each atomnames
+    numerical_descriptor : str, optional
+        numerical descriptor file
+    mass : list of float, optional
+        List of atomic masses
+    move : list of list of bool, optional
+        List of the move flag of each xyz direction of each atom
+    velocity : list of list of float, optional
+        List of the velocity of each xyz direction of each atom
+    mag : list of (list of float or float), optional
+        List of the magnetic moment of each atom, can be a list of three floats or one float
+        For noncollinear, three floats are the xyz component of the magnetic moment.
+        For collinear, one float is the norm of the magnetic moment.
+    angle1 : list of float, optional
+        List of the angle1 of each atom. For noncollinear calculation, it is the angle between the magnetic moment and the z-axis.
+    angle2 : list of float, optional
+        List of the angle2 of each atom. For noncollinear calculation, it is the angle between the projection of magnetic moment on xy plane and the x-axis.
+    sc : list of (bool or list of 3 bool), optional
+        List of the spin constraint flag of each atom. Each element can be a bool or a list of three bools or None.
+    lambda_ : list of (float or list of 3 float), optional
+        List of the lambda of each atom. Each element can be a float or a list of three floats.
+    link_file : bool, optional
+        Whether to link the pseudo potential files and orbital files in the STRU file.
+        If True, then only filename will be written in the STRU file, and make a soft link to the real file.
+    For velocity, mag, angle1, angle2, sc, and lambda_, if the value is None, then the corresponding information will not be written.
+    ABACUS support defining "mag" and "angle1"/"angle2" at the same time, and in this case, the "mag" only define the norm of the magnetic moment, and "angle1" and "angle2" define the direction of the magnetic moment.
+    If data has spins, then it will be written as mag to STRU file; while if mag is passed at the same time, then mag will be used.
+    """
+
+    def _link_file(dest_dir, src_file):
+        if not os.path.isfile(src_file):
+            print(f"ERROR: link_file: {src_file} is not a file.")
+            return False
+        src_file = os.path.abspath(src_file)
+        if not os.path.isdir(dest_dir):
+            os.makedirs(dest_dir)
+        dest_file = os.path.join(dest_dir, os.path.basename(src_file))
+        if os.path.isfile(dest_file):
+            if os.path.samefile(src_file, dest_file):
+                return True
+            else:
+                os.remove(dest_file)
+        os.symlink(src_file, dest_file)
+        return True
+
+    def ndarray2list(i):
+        if isinstance(i, np.ndarray):
+            return i.tolist()
+        else:
+            return i
+
+    if link_file and dest_dir is None:
+        print(
+            "WARNING: make_unlabeled_stru: link_file is True, but dest_dir is None. Will write the filename to STRU but not making soft link."
+        )
+    if dest_dir is not None and dest_dir.strip() == "":
+        dest_dir = "."
+
+    if mag is None and data.get("spins") is not None and len(data["spins"]) > 0:
+        mag = data["spins"][frame_idx]
+
+    atom_numbs = sum(data["atom_numbs"])
+    for key in [move, velocity, mag, angle1, angle2, sc, lambda_]:
+        if key is not None:
+            if (
+                not isinstance(ndarray2list(key), (list, tuple))
+                and len(key) != atom_numbs
+            ):
+                key_name = [name for name, value in locals().items() if value is key][0]
+                print(
+                    f"ERROR: make_unlabeled_stru: the length of '{key_name}' ({len(key)}) should be equal to the number of atom number ({atom_numbs})."
+                )
+                return ""
+
+    # ATOMIC_SPECIES block
     out = "ATOMIC_SPECIES\n"
+    if pp_file is not None:
+        pp_file = ndarray2list(pp_file)
     for iele in range(len(data["atom_names"])):
+        if data["atom_numbs"][iele] == 0:
+            continue
         out += data["atom_names"][iele] + " "
         if mass is not None:
             out += f"{mass[iele]:.3f} "
         else:
             out += "1 "
         if pp_file is not None:
-            out += f"{pp_file[iele]}\n"
-        else:
-            out += "\n"
+            if isinstance(pp_file, (list, tuple)):
+                ipp_file = pp_file[iele]
+            elif isinstance(pp_file, dict):
+                if data["atom_names"][iele] not in pp_file:
+                    print(
+                        f"ERROR: make_unlabeled_stru: pp_file does not contain {data['atom_names'][iele]}"
+                    )
+                    ipp_file = None
+                else:
+                    ipp_file = pp_file[data["atom_names"][iele]]
+            else:
+                ipp_file = None
+            if ipp_file is not None:
+                if not link_file:
+                    out += ipp_file
+                else:
+                    out += os.path.basename(ipp_file.rstrip("/"))
+                    if dest_dir is not None:
+                        _link_file(dest_dir, ipp_file)
+
+        out += "\n"
     out += "\n"
 
+    # NUMERICAL_ORBITAL block
     if numerical_orbital is not None:
         assert len(numerical_orbital) == len(data["atom_names"])
+        numerical_orbital = ndarray2list(numerical_orbital)
         out += "NUMERICAL_ORBITAL\n"
-        for iele in range(len(numerical_orbital)):
-            out += f"{numerical_orbital[iele]}\n"
+        for iele in range(len(data["atom_names"])):
+            if data["atom_numbs"][iele] == 0:
+                continue
+            if isinstance(numerical_orbital, (list, tuple)):
+                inum_orbital = numerical_orbital[iele]
+            elif isinstance(numerical_orbital, dict):
+                if data["atom_names"][iele] not in numerical_orbital:
+                    print(
+                        f"ERROR: make_unlabeled_stru: numerical_orbital does not contain {data['atom_names'][iele]}"
+                    )
+                    inum_orbital = None
+                else:
+                    inum_orbital = numerical_orbital[data["atom_names"][iele]]
+            else:
+                inum_orbital = None
+            if inum_orbital is not None:
+                if not link_file:
+                    out += inum_orbital
+                else:
+                    out += os.path.basename(inum_orbital.rstrip("/"))
+                    if dest_dir is not None:
+                        _link_file(dest_dir, inum_orbital)
+            out += "\n"
         out += "\n"
 
+    # deepks block
     if numerical_descriptor is not None:
         assert isinstance(numerical_descriptor, str)
-        out += f"NUMERICAL_DESCRIPTOR\n{numerical_descriptor}\n"
+        if not link_file:
+            out += f"NUMERICAL_DESCRIPTOR\n{numerical_descriptor}\n"
+        else:
+            out += f"NUMERICAL_DESCRIPTOR\n{os.path.basename(numerical_descriptor)}\n"
+            if dest_dir is not None:
+                _link_file(dest_dir, numerical_descriptor)
         out += "\n"
 
+    # LATTICE_CONSTANT and LATTICE_VECTORS block
     out += "LATTICE_CONSTANT\n"
     out += str(1 / bohr2ang) + "\n\n"
 
@@ -402,24 +766,80 @@ def make_unlabeled_stru(
         out += "\n"
     out += "\n"
 
+    # ATOMIC_POSITIONS block
     out += "ATOMIC_POSITIONS\n"
     out += "Cartesian    # Cartesian(Unit is LATTICE_CONSTANT)\n"
     # ret += "\n"
-    natom_tot = 0
+    natom_tot = 0  # in for loop, it is also the atom index
     for iele in range(len(data["atom_names"])):
+        if data["atom_numbs"][iele] == 0:
+            continue
         out += data["atom_names"][iele] + "\n"
         out += "0.0\n"
         out += str(data["atom_numbs"][iele]) + "\n"
         for iatom in range(data["atom_numbs"][iele]):
             iatomtype = np.nonzero(data["atom_types"] == iele)[0][iatom]
-            out += "%.12f %.12f %.12f %d %d %d\n" % (
-                data["coords"][frame_idx][iatomtype, 0],
-                data["coords"][frame_idx][iatomtype, 1],
-                data["coords"][frame_idx][iatomtype, 2],
-                1,
-                1,
-                1,
-            )
+            iout = f"{data['coords'][frame_idx][iatomtype, 0]:.12f} {data['coords'][frame_idx][iatomtype, 1]:.12f} {data['coords'][frame_idx][iatomtype, 2]:.12f}"
+            # add flags for move, velocity, mag, angle1, angle2, and sc
+            if move is not None:
+                if (
+                    isinstance(ndarray2list(move[natom_tot]), (list, tuple))
+                    and len(move[natom_tot]) == 3
+                ):
+                    iout += " " + " ".join(
+                        ["1" if ii else "0" for ii in move[natom_tot]]
+                    )
+                elif isinstance(ndarray2list(move[natom_tot]), (int, float, bool)):
+                    iout += " 1 1 1" if move[natom_tot] else " 0 0 0"
+            else:
+                iout += " 1 1 1"
+
+            if (
+                velocity is not None
+                and isinstance(ndarray2list(velocity[natom_tot]), (list, tuple))
+                and len(velocity[natom_tot]) == 3
+            ):
+                iout += " v " + " ".join([f"{ii:.12f}" for ii in velocity[natom_tot]])
+
+            if mag is not None:
+                if isinstance(ndarray2list(mag[natom_tot]), (list, tuple)) and len(
+                    mag[natom_tot]
+                ) in [1, 3]:
+                    iout += " mag " + " ".join([f"{ii:.12f}" for ii in mag[natom_tot]])
+                elif isinstance(ndarray2list(mag[natom_tot]), (int, float)):
+                    iout += " mag " + f"{mag[natom_tot]:.12f}"
+
+            if angle1 is not None and isinstance(
+                ndarray2list(angle1[natom_tot]), (int, float)
+            ):
+                iout += " angle1 " + f"{angle1[natom_tot]:.12f}"
+
+            if angle2 is not None and isinstance(
+                ndarray2list(angle2[natom_tot]), (int, float)
+            ):
+                iout += " angle2 " + f"{angle2[natom_tot]:.12f}"
+
+            if sc is not None:
+                if isinstance(ndarray2list(sc[natom_tot]), (list, tuple)) and len(
+                    sc[natom_tot]
+                ) in [1, 3]:
+                    iout += " sc " + " ".join(
+                        ["1" if ii else "0" for ii in sc[natom_tot]]
+                    )
+                elif isinstance(ndarray2list(sc[natom_tot]), (int, float, bool)):
+                    iout += " sc " + "1" if sc[natom_tot] else "0"
+
+            if lambda_ is not None:
+                if isinstance(ndarray2list(lambda_[natom_tot]), (list, tuple)) and len(
+                    lambda_[natom_tot]
+                ) in [1, 3]:
+                    iout += " lambda " + " ".join(
+                        [f"{ii:.12f}" for ii in lambda_[natom_tot]]
+                    )
+                elif isinstance(ndarray2list(lambda_[natom_tot]), (int, float)):
+                    iout += " lambda " + f"{lambda_[natom_tot]:.12f}"
+
+            out += iout + "\n"
             natom_tot += 1
     assert natom_tot == sum(data["atom_numbs"])
     return out
diff --git a/dpdata/plugins/abacus.py b/dpdata/plugins/abacus.py
index e3367b35..cbd1475f 100644
--- a/dpdata/plugins/abacus.py
+++ b/dpdata/plugins/abacus.py
@@ -1,10 +1,14 @@
 from __future__ import annotations
 
+import os
 from typing import TYPE_CHECKING
 
+import numpy as np
+
 import dpdata.abacus.md
 import dpdata.abacus.relax
 import dpdata.abacus.scf
+from dpdata.data_type import Axis, DataType
 from dpdata.format import Format
 from dpdata.utils import open_file
 
@@ -29,40 +33,49 @@ def to_system(self, data, file_name: FileType, frame_idx=0, **kwargs):
             The output file name
         frame_idx : int
             The index of the frame to dump
-        pp_file : list of string, optional
-            List of pseudo potential files
-        numerical_orbital : list of string, optional
-            List of orbital files
-        mass : list of float, optional
-            List of atomic masses
-        numerical_descriptor : str, optional
-            numerical descriptor file
         **kwargs : dict
             other parameters
         """
-        pp_file = kwargs.get("pp_file")
-        numerical_orbital = kwargs.get("numerical_orbital")
-        mass = kwargs.get("mass")
-        numerical_descriptor = kwargs.get("numerical_descriptor")
         stru_string = dpdata.abacus.scf.make_unlabeled_stru(
             data=data,
             frame_idx=frame_idx,
-            pp_file=pp_file,
-            numerical_orbital=numerical_orbital,
-            numerical_descriptor=numerical_descriptor,
-            mass=mass,
+            dest_dir=os.path.dirname(file_name),
+            **kwargs,
         )
         with open_file(file_name, "w") as fp:
             fp.write(stru_string)
 
 
+def register_mag_data(data):
+    if "spins" in data:
+        dt = DataType(
+            "spins",
+            np.ndarray,
+            (Axis.NFRAMES, Axis.NATOMS, 3),
+            required=False,
+            deepmd_name="spin",
+        )
+        dpdata.LabeledSystem.register_data_type(dt)
+    if "mag_forces" in data:
+        dt = DataType(
+            "mag_forces",
+            np.ndarray,
+            (Axis.NFRAMES, Axis.NATOMS, 3),
+            required=False,
+            deepmd_name="force_mag",
+        )
+        dpdata.LabeledSystem.register_data_type(dt)
+
+
 @Format.register("abacus/scf")
 @Format.register("abacus/pw/scf")
 @Format.register("abacus/lcao/scf")
 class AbacusSCFFormat(Format):
     # @Format.post("rot_lower_triangular")
     def from_labeled_system(self, file_name, **kwargs):
-        return dpdata.abacus.scf.get_frame(file_name)
+        data = dpdata.abacus.scf.get_frame(file_name)
+        register_mag_data(data)
+        return data
 
 
 @Format.register("abacus/md")
@@ -71,7 +84,9 @@ def from_labeled_system(self, file_name, **kwargs):
 class AbacusMDFormat(Format):
     # @Format.post("rot_lower_triangular")
     def from_labeled_system(self, file_name, **kwargs):
-        return dpdata.abacus.md.get_frame(file_name)
+        data = dpdata.abacus.md.get_frame(file_name)
+        register_mag_data(data)
+        return data
 
 
 @Format.register("abacus/relax")
@@ -80,4 +95,6 @@ def from_labeled_system(self, file_name, **kwargs):
 class AbacusRelaxFormat(Format):
     # @Format.post("rot_lower_triangular")
     def from_labeled_system(self, file_name, **kwargs):
-        return dpdata.abacus.relax.get_frame(file_name)
+        data = dpdata.abacus.relax.get_frame(file_name)
+        register_mag_data(data)
+        return data
diff --git a/tests/abacus.relax/INPUT.spin b/tests/abacus.relax/INPUT.spin
new file mode 100644
index 00000000..cbdc3fdd
--- /dev/null
+++ b/tests/abacus.relax/INPUT.spin
@@ -0,0 +1,35 @@
+INPUT_PARAMETERS
+suffix                          spin
+calculation                     relax
+ecutwfc                         100
+scf_thr                         1.0e-3
+scf_nmax                        200
+smearing_method                 gauss
+smearing_sigma                  0.01
+#ks_solver                       genelpa
+basis_type                      pw
+symmetry                        0
+noncolin			1
+nspin                           4
+
+onsite_radius 3
+
+relax_nmax 3
+
+force_thr 0.00001
+
+sc_mag_switch                   1
+decay_grad_switch               1
+sc_thr                          1e-4
+nsc                             100
+nsc_min                         2
+alpha_trial                     0.01
+sccut                           3
+
+
+
+#md_nstep 3
+#md_type                nve
+#md_dt                  1
+#md_tfirst              300
+
diff --git a/tests/abacus.relax/STRU.spin b/tests/abacus.relax/STRU.spin
new file mode 100644
index 00000000..441b30d1
--- /dev/null
+++ b/tests/abacus.relax/STRU.spin
@@ -0,0 +1,21 @@
+ATOMIC_SPECIES
+Fe 55.845 Fe.upf
+
+NUMERICAL_ORBITAL
+Fe_gga_8au_100Ry_4s2p2d1f.orb
+
+LATTICE_CONSTANT
+1.880277359
+LATTICE_VECTORS
+    2.8274254848     0.0000000000     0.0000000000 #latvec1
+    0.0000000000     2.8274254848     0.0000000000 #latvec2
+    0.0000000000     0.0000000000     2.8274254848 #latvec3
+
+ATOMIC_POSITIONS
+Direct
+
+Fe #label
+1 #magnetism
+2 #number of atoms
+    0.0000000000     0.0000000000     0.0000000000 mag 1.25 1.25 1.25 sc 1 1 1
+    0.500000000     0.500000000     0.500000000 mag 1.25 1.25 1.25 sc 1 1 1
diff --git a/tests/abacus.scf/C.orb b/tests/abacus.scf/C.orb
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/abacus.scf/C.upf b/tests/abacus.scf/C.upf
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/abacus.scf/H.orb b/tests/abacus.scf/H.orb
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/abacus.scf/H.upf b/tests/abacus.scf/H.upf
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/abacus.scf/jle.orb b/tests/abacus.scf/jle.orb
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/abacus.scf/stru.ref b/tests/abacus.scf/stru.ref
new file mode 100644
index 00000000..8485de36
--- /dev/null
+++ b/tests/abacus.scf/stru.ref
@@ -0,0 +1,29 @@
+ATOMIC_SPECIES
+C 12.000 C.upf
+H 1.000 H.upf
+
+NUMERICAL_ORBITAL
+C.orb
+H.orb
+
+LATTICE_CONSTANT
+1.8897261246257702
+
+LATTICE_VECTORS
+5.291772109029999 0.0 0.0 
+0.0 5.291772109029999 0.0 
+0.0 0.0 5.291772109029999 
+
+ATOMIC_POSITIONS
+Cartesian    # Cartesian(Unit is LATTICE_CONSTANT)
+C
+0.0
+1
+5.192682633809 4.557725978258 4.436846615358 1 1 1 mag 4.000000000000 angle2 100.000000000000 sc 1 lambda 0.100000000000 0.200000000000 0.300000000000
+H
+0.0
+4
+5.416431453540 4.011298860305 3.511161492417 1 1 1 mag 1.000000000000 1.000000000000 1.000000000000 angle2 90.000000000000 sc 1 lambda 0.400000000000 0.500000000000 0.600000000000
+4.131588222365 4.706745191323 4.431136645083 1 1 1 mag 1.000000000000 angle1 100.000000000000 angle2 80.000000000000 sc 1 0 1 lambda 0.700000000000 0.800000000000 0.900000000000
+5.630930319126 5.521640894956 4.450356541303 0 0 0 mag 1.000000000000 angle1 90.000000000000 angle2 70.0000000000000
+5.499851012568 4.003388899277 5.342621842622 0 0 0 mag 1.000000000000 angle1 80.000000000000 sc 1
diff --git a/tests/abacus.spin/INPUT b/tests/abacus.spin/INPUT
new file mode 100644
index 00000000..bc0b1df0
--- /dev/null
+++ b/tests/abacus.spin/INPUT
@@ -0,0 +1,27 @@
+INPUT_PARAMETERS
+suffix	ABACUS
+calculation	scf
+ecutwfc	100
+scf_thr	1e-07
+scf_nmax	100
+out_chg	0
+smearing_method	gauss
+smearing_sigma	0.01
+mixing_type	broyden
+mixing_ndim	10
+ks_solver	genelpa
+basis_type	lcao
+symmetry	0
+noncolin	1
+lspinorb	0
+nspin	4
+out_mul	true
+sc_mag_switch	1
+decay_grad_switch	1
+sc_thr	1e-07
+sc_scf_thr	1e-09
+nsc	100
+nsc_min	2
+alpha_trial	0.01
+sccut	3
+cal_force	1
diff --git a/tests/abacus.spin/INPUT.md b/tests/abacus.spin/INPUT.md
new file mode 100644
index 00000000..2be67861
--- /dev/null
+++ b/tests/abacus.spin/INPUT.md
@@ -0,0 +1,34 @@
+INPUT_PARAMETERS
+calculation                     md
+ecutwfc                         100
+scf_thr                         1.0e-3
+scf_nmax                        200
+smearing_method                 gauss
+smearing_sigma                  0.01
+#ks_solver                       genelpa
+basis_type                      pw
+symmetry                        0
+noncolin			1
+nspin                           4
+
+onsite_radius 3
+
+relax_nmax 3
+
+force_thr 0.00001
+
+sc_mag_switch                   1
+decay_grad_switch               1
+sc_thr                          1e-4
+nsc                             100
+nsc_min                         2
+alpha_trial                     0.01
+sccut                           3
+
+
+md_type                nvt
+md_nstep               3
+md_dt                  1
+md_tfirst              300
+md_tfreq               1
+
diff --git a/tests/abacus.spin/INPUT.relax b/tests/abacus.spin/INPUT.relax
new file mode 100644
index 00000000..9a9466d3
--- /dev/null
+++ b/tests/abacus.spin/INPUT.relax
@@ -0,0 +1,34 @@
+INPUT_PARAMETERS
+calculation                     relax
+ecutwfc                         100
+scf_thr                         1.0e-3
+scf_nmax                        200
+smearing_method                 gauss
+smearing_sigma                  0.01
+#ks_solver                       genelpa
+basis_type                      pw
+symmetry                        0
+noncolin			1
+nspin                           4
+
+onsite_radius 3
+
+relax_nmax 3
+
+force_thr 0.00001
+
+sc_mag_switch                   1
+decay_grad_switch               1
+sc_thr                          1e-4
+nsc                             100
+nsc_min                         2
+alpha_trial                     0.01
+sccut                           3
+
+
+
+#md_nstep 3
+#md_type                nve
+#md_dt                  1
+#md_tfirst              300
+
diff --git a/tests/abacus.spin/INPUT.scf b/tests/abacus.spin/INPUT.scf
new file mode 100644
index 00000000..bc0b1df0
--- /dev/null
+++ b/tests/abacus.spin/INPUT.scf
@@ -0,0 +1,27 @@
+INPUT_PARAMETERS
+suffix	ABACUS
+calculation	scf
+ecutwfc	100
+scf_thr	1e-07
+scf_nmax	100
+out_chg	0
+smearing_method	gauss
+smearing_sigma	0.01
+mixing_type	broyden
+mixing_ndim	10
+ks_solver	genelpa
+basis_type	lcao
+symmetry	0
+noncolin	1
+lspinorb	0
+nspin	4
+out_mul	true
+sc_mag_switch	1
+decay_grad_switch	1
+sc_thr	1e-07
+sc_scf_thr	1e-09
+nsc	100
+nsc_min	2
+alpha_trial	0.01
+sccut	3
+cal_force	1
diff --git a/tests/abacus.spin/OUT.ABACUS/MD_dump b/tests/abacus.spin/OUT.ABACUS/MD_dump
new file mode 100644
index 00000000..a4d41a9b
--- /dev/null
+++ b/tests/abacus.spin/OUT.ABACUS/MD_dump
@@ -0,0 +1,44 @@
+MDSTEP:  0
+LATTICE_CONSTANT: 0.994999532004 Angstrom
+LATTICE_VECTORS
+  2.827425484800  0.000000000000  0.000000000000
+  0.000000000000  2.827425484800  0.000000000000
+  0.000000000000  0.000000000000  2.827425484800
+INDEX    LABEL    POSITION (Angstrom)    FORCE (eV/Angstrom)    VELOCITY (Angstrom/fs)
+  0  Fe  0.000000000000  0.000000000000  0.000000000000  -0.000023448027  0.000084873040  0.000395963967  0.001501148908  0.001168257569  -0.001755430621
+  1  Fe  1.406643426095  1.406643426095  1.406643426095  0.000023448027  -0.000084873040  -0.000395963967  -0.001501148908  -0.001168257569  0.001755430621
+
+
+MDSTEP:  1
+LATTICE_CONSTANT: 0.994999532004 Angstrom
+LATTICE_VECTORS
+  2.827425484800  0.000000000000  0.000000000000
+  0.000000000000  2.827425484800  0.000000000000
+  0.000000000000  0.000000000000  2.827425484800
+INDEX    LABEL    POSITION (Angstrom)    FORCE (eV/Angstrom)    VELOCITY (Angstrom/fs)
+  0  Fe  0.001501146882  0.001168264901  2.811531455776  -0.082174998068  -0.064183237637  0.094555758230  0.001495732780  0.001164031434  -0.001749198271
+  1  Fe  1.405142279213  1.405475161194  1.408398822510  0.082174998068  0.064183237637  -0.094555758230  -0.001495732780  -0.001164031434  0.001749198271
+
+
+MDSTEP:  2
+LATTICE_CONSTANT: 0.994999532004 Angstrom
+LATTICE_VECTORS
+  2.827425484800  0.000000000000  0.000000000000
+  0.000000000000  2.827425484800  0.000000000000
+  0.000000000000  0.000000000000  2.827425484800
+INDEX    LABEL    POSITION (Angstrom)    FORCE (eV/Angstrom)    VELOCITY (Angstrom/fs)
+  0  Fe  0.002994040541  0.002330066808  2.809785444314  -0.026325867140  -0.019829200318  0.032814119442  0.001497639352  0.001165552232  -0.001751386047
+  1  Fe  1.403649385554  1.404313359287  1.410144833972  0.026325867140  0.019829200318  -0.032814119442  -0.001497639352  -0.001165552232  0.001751386047
+
+
+MDSTEP:  3
+LATTICE_CONSTANT: 0.994999532004 Angstrom
+LATTICE_VECTORS
+  2.827425484800  0.000000000000  0.000000000000
+  0.000000000000  2.827425484800  0.000000000000
+  0.000000000000  0.000000000000  2.827425484800
+INDEX    LABEL    POSITION (Angstrom)    FORCE (eV/Angstrom)    VELOCITY (Angstrom/fs)
+  0  Fe  0.004498128094  0.003500694358  2.808026692717  -0.044129139592  -0.028138926921  0.059726500602  0.001507997443  0.001174209539  -0.001762617927
+  1  Fe  1.402145298001  1.403142731738  1.411903585568  0.044129139592  0.028138926921  -0.059726500602  -0.001507997443  -0.001174209539  0.001762617927
+
+
diff --git a/tests/abacus.spin/OUT.ABACUS/running_md.log b/tests/abacus.spin/OUT.ABACUS/running_md.log
new file mode 100644
index 00000000..272a44ce
--- /dev/null
+++ b/tests/abacus.spin/OUT.ABACUS/running_md.log
@@ -0,0 +1,997 @@
+                                                                                     
+                              ABACUS v3.7.1
+
+               Atomic-orbital Based Ab-initio Computation at UStc                    
+
+                     Website: http://abacus.ustc.edu.cn/                             
+               Documentation: https://abacus.deepmodeling.com/                       
+                  Repository: https://github.com/abacusmodeling/abacus-develop       
+                              https://github.com/deepmodeling/abacus-develop         
+                      Commit: 8443c42b5 (Thu Sep 5 14:19:05 2024 +0800)
+
+    Start Time is Fri Sep  6 10:04:51 2024
+                                                                                     
+ ------------------------------------------------------------------------------------
+
+ READING GENERAL INFORMATION
+                           global_out_dir = OUT.ABACUS/
+                           global_in_card = INPUT
+                               pseudo_dir = ./
+                              orbital_dir = ./
+                                    DRANK = 1
+                                    DSIZE = 1
+                                   DCOLOR = 1
+                                    GRANK = 1
+                                    GSIZE = 1
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Reading atom information in unitcell:                              |
+ | From the input file and the structure file we know the number of   |
+ | different elments in this unitcell, then we list the detail        |
+ | information for each element, especially the zeta and polar atomic |
+ | orbital number for each element. The total atom number is counted. |
+ | We calculate the nearest atom distance for each atom and show the  |
+ | Cartesian and Direct coordinates for each atom. We list the file   |
+ | address for atomic orbitals. The volume and the lattice vectors    |
+ | in real and reciprocal space is also shown.                        |
+ |                                                                    |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+ READING UNITCELL INFORMATION
+                                    ntype = 1
+                  lattice constant (Bohr) = 1.88028
+              lattice constant (Angstrom) = 0.995
+
+ READING ATOM TYPE 1
+                               atom label = Fe
+                      L=0, number of zeta = 4
+                      L=1, number of zeta = 2
+                      L=2, number of zeta = 2
+                      L=3, number of zeta = 1
+             number of atom for this type = 2
+               magnetization of element 1 = [ 1.25, 1.25, 1.25 ]
+
+                        TOTAL ATOM NUMBER = 2
+DIRECT COORDINATES
+    atom                   x                   y                   z     mag                  vx                  vy                  vz
+taud_Fe1            0.0000000000        0.0000000000        0.0000000000  2.1651        0.0000000000        0.0000000000        0.0000000000
+taud_Fe2            0.5000000000        0.5000000000        0.5000000000  2.1651        0.0000000000        0.0000000000        0.0000000000
+
+
+
+                          Volume (Bohr^3) = 150.259
+                             Volume (A^3) = 22.266
+
+ Lattice vectors: (Cartesian coordinate: in unit of a_0)
+             +2.82743                  +0                  +0
+                   +0            +2.82743                  +0
+                   +0                  +0            +2.82743
+ Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0)
+            +0.353679                  -0                  +0
+                   -0           +0.353679                  -0
+                   +0                  -0           +0.353679
+ The esolver type has been set to : ksdft_pw
+
+ RUNNING WITH DEVICE  : CPU / Intel(R) Xeon(R) Platinum
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Reading pseudopotentials files:                                    |
+ | The pseudopotential file is in UPF format. The 'NC' indicates that |
+ | the type of pseudopotential is 'norm conserving'. Functional of    |
+ | exchange and correlation is decided by 4 given parameters in UPF   |
+ | file.  We also read in the 'core correction' if there exists.      |
+ | Also we can read the valence electrons number and the maximal      |
+ | angular momentum used in this pseudopotential. We also read in the |
+ | trail wave function, trail atomic density and local-pseudopotential|
+ | on logrithmic grid. The non-local pseudopotential projector is also|
+ | read in if there is any.                                           |
+ |                                                                    |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+                PAO radial cut off (Bohr) = 15
+
+ Read in pseudopotential file is Fe.upf
+                     pseudopotential type = NC
+          exchange-correlation functional = PBE
+                 nonlocal core correction = 1
+                        valence electrons = 16
+                                     lmax = 2
+                           number of zeta = 4
+                     number of projectors = 6
+                           L of projector = 0
+                           L of projector = 0
+                           L of projector = 1
+                           L of projector = 1
+                           L of projector = 2
+                           L of projector = 2
+     initial pseudo atomic orbital number = 40
+                                   NLOCAL = 108
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ Warning: the number of valence electrons in pseudopotential > 8 for Fe: [Ar] 3d6 4s2
+ Pseudopotentials with additional electrons can yield (more) accurate outcomes, but may be less efficient.
+ If you're confident that your chosen pseudopotential is appropriate, you can safely ignore this warning.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+                  
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Setup plane waves of charge/potential:                             |
+ | Use the energy cutoff and the lattice vectors to generate the      |
+ | dimensions of FFT grid. The number of FFT grid on each processor   |
+ | is 'nrxx'. The number of plane wave basis in reciprocal space is   |
+ | different for charege/potential and wave functions. We also set    |
+ | the 'sticks' for the parallel of FFT. The number of plane waves    |
+ | is 'npw' in each processor.                                        |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+
+ SETUP THE PLANE WAVE BASIS
+ energy cutoff for charge/potential (unit:Ry) = 400
+            fft grid for charge/potential = [ 36, 36, 36 ]
+                        fft grid division = [ 1, 1, 1 ]
+        big fft grid for charge/potential = [ 36, 36, 36 ]
+                                     nbxx = 46656
+                                     nrxx = 46656
+
+ SETUP PLANE WAVES FOR CHARGE/POTENTIAL
+                    number of plane waves = 20341
+                         number of sticks = 885
+
+ PARALLEL PW FOR CHARGE/POTENTIAL
+     PROC   COLUMNS(POT)             PW
+        1            885          20341
+ --------------- sum -------------------
+        1            885          20341
+                            number of |g| = 241
+                                  max |g| = 35.7753
+                                  min |g| = 0
+
+----------- Double Check Mixing Parameters Begin ------------
+mixing_type: broyden
+mixing_beta: 0.4
+mixing_gg0: 1
+mixing_gg0_min: 0.1
+mixing_beta_mag: 1.6
+mixing_gg0_mag: 0
+mixing_ndim: 8
+----------- Double Check Mixing Parameters End ------------
+
+ SETUP THE ELECTRONS NUMBER
+            electron number of element Fe = 16
+      total electron number of element Fe = 32
+            AUTOSET number of electrons:  = 32
+ DONE : SETUP UNITCELL Time : 0.102785 (SEC)
+
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Setup K-points                                                     |
+ | We setup the k-points according to input parameters.               |
+ | The reduced k-points are set according to symmetry operations.     |
+ | We treat the spin as another set of k-points.                      |
+ |                                                                    |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+
+ SETUP K-POINTS
+                                    nspin = 4
+                   Input type of k points = Monkhorst-Pack(Gamma)
+                                   nkstot = 1
+                               nkstot_ibz = 1
+K-POINTS REDUCTION ACCORDING TO SYMMETRY
+     IBZ    DIRECT_X    DIRECT_Y    DIRECT_Z  WEIGHT  ibz2bz
+       1  0.00000000  0.00000000  0.00000000  1.0000       0
+
+                               nkstot now = 1
+K-POINTS DIRECT COORDINATES
+ KPOINTS    DIRECT_X    DIRECT_Y    DIRECT_Z  WEIGHT
+       1  0.00000000  0.00000000  0.00000000  1.0000
+
+
+           k-point number in this process = 1
+       minimum distributed K point number = 1
+
+K-POINTS CARTESIAN COORDINATES
+ KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z  WEIGHT
+       1  0.00000000  0.00000000  0.00000000  1.0000
+
+
+K-POINTS DIRECT COORDINATES
+ KPOINTS    DIRECT_X    DIRECT_Y    DIRECT_Z  WEIGHT
+       1  0.00000000  0.00000000  0.00000000  1.0000
+
+ DONE : INIT K-POINTS Time : 0.112353 (SEC)
+
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Setup plane waves of wave functions:                               |
+ | Use the energy cutoff and the lattice vectors to generate the      |
+ | dimensions of FFT grid. The number of FFT grid on each processor   |
+ | is 'nrxx'. The number of plane wave basis in reciprocal space is   |
+ | different for charege/potential and wave functions. We also set    |
+ | the 'sticks' for the parallel of FFT. The number of plane wave of  |
+ | each k-point is 'npwk[ik]' in each processor                       |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+
+ SETUP PLANE WAVES FOR WAVE FUNCTIONS
+     energy cutoff for wavefunc (unit:Ry) = 100
+              fft grid for wave functions = [ 36, 36, 36 ]
+                    number of plane waves = 2517
+                         number of sticks = 221
+
+ PARALLEL PW FOR WAVE FUNCTIONS
+     PROC   COLUMNS(POT)             PW
+        1            221           2517
+ --------------- sum -------------------
+        1            221           2517
+ DONE : INIT PLANEWAVE Time : 0.113487 (SEC)
+
+                           occupied bands = 16
+                                   NBANDS = 52
+
+ SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS
+ Fe non-local projectors:
+ projector 1 L=0
+ projector 2 L=0
+ projector 3 L=1
+ projector 4 L=1
+ projector 5 L=2
+ projector 6 L=2
+      TOTAL NUMBER OF NONLOCAL PROJECTORS = 36
+ DONE : LOCAL POTENTIAL Time : 0.128854 (SEC)
+
+
+ Init Non-Local PseudoPotential table : 
+ Init Non-Local-Pseudopotential done.
+ DONE : NON-LOCAL POTENTIAL Time : 0.15862 (SEC)
+
+                                     npwx = 2517
+
+ Make real space PAO into reciprocal space.
+       max mesh points in Pseudopotential = 1425
+     dq(describe PAO in reciprocal space) = 0.01
+                                    max q = 1204
+
+ number of pseudo atomic orbitals for Fe is 4
+WARNING: norm of atomic wavefunction # 2 of atomic type Fe is 0.999981, renormalized
+WARNING: norm of atomic wavefunction # 3 of atomic type Fe is 0.999997, renormalized
+ DONE : INIT BASIS Time : 0.330341 (SEC)
+
+
+ -------------------------------------------
+ STEP OF MOLECULAR DYNAMICS : 0
+ -------------------------------------------
+                                 init_chg = atomic
+ DONE : INIT SCF Time : 0.528545 (SEC)
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   1--------------------------------
+total magnetism (Bohr mag/cell)	2.30943	2.30938	2.30941
+       absolute magnetism (Bohr mag/cell) = 4.01976
+ Notice: Threshold on eigenvalues was too large.
+ hsover_error=0.32 > DRHO=0.0686869
+ Origin diag_ethr = 0.01
+ New    diag_ethr = 0.000214646
+total magnetism (Bohr mag/cell)	2.30943	2.30937	2.3094
+       absolute magnetism (Bohr mag/cell) = 4.01964
+
+ Density error is 0.0548949686243
+                          Error Threshold = 0.000214646406708
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6632803550      -6825.4790901992     
+ E_Harris       -501.6647758269      -6825.4994371390     
+ E_Fermi        1.4575316668         19.8307356840        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   2--------------------------------
+total magnetism (Bohr mag/cell)	2.3094424965	2.30934448798	2.30941621651
+       absolute magnetism (Bohr mag/cell) = 4.13707180938
+
+ Density error is 0.00986449919003
+                          Error Threshold = 0.000171546776951
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6774595966      -6825.6720086784     
+ E_Harris       -499.7039503033      -6798.8210372331     
+ E_Fermi        1.4964230898         20.3598806394        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   3--------------------------------
+total magnetism (Bohr mag/cell)	2.30944490813	2.30935345105	2.30940487564
+       absolute magnetism (Bohr mag/cell) = 4.08853707061
+
+ Density error is 0.00240445773415
+                          Error Threshold = 3.08265599688e-05
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6784060189      -6825.6848854146     
+ E_Harris       -501.4802459250      -6822.9887790210     
+ E_Fermi        1.4994551309         20.4011336751        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   4--------------------------------
+total magnetism (Bohr mag/cell)	2.30944724752	2.30935862214	2.30939736766
+       absolute magnetism (Bohr mag/cell) = 4.08848804651
+
+ Density error is 0.00057214611471
+                          Error Threshold = 7.51393041921e-06
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6784787714      -6825.6858752634     
+ E_KS(sigma->0) -501.6746222162      -6825.6334041381     
+ E_Harris       -501.6738375513      -6825.6227282240     
+ E_band         -27.9117558414       -379.7589206280      
+ E_one_elec     -203.4207485774      -2767.6812720784     
+ E_Hartree      123.6718684724       1682.6420935310      
+ E_xc           -71.4390193374       -971.9777225215      
+ E_Ewald        -350.4828662186      -4768.5640319440     
+ E_entropy(-TS) -0.0077131104        -0.1049422506        
+ E_descf        0.0000000000         0.0000000000         
+ E_exx          0.0000000000         0.0000000000         
+ E_Fermi        1.5017611709         20.4325089589        
+----------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Magnetic force (eV/uB)                                                                    
+-------------------------------------------------------------------------------------------
+                         Fe         0.0000000000         0.0000000000         0.0000000000 
+                         Fe         0.0000000000         0.0000000000         0.0000000000 
+-------------------------------------------------------------------------------------------
+
+
+-------------------------------------------------------------------------------------------
+Orbital Charge Analysis      Charge         Mag(x)         Mag(y)         Mag(z)
+-------------------------------------------------------------------------------------------
+Fe1                 
+                   s         1.1149         0.0010         0.0010         0.0010
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5931         1.1679         1.1678         1.1678
+                 Sum        13.7051         1.1691         1.1690         1.1690
+Fe2                 
+                   s         1.1150         0.0010         0.0010         0.0010
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5959         1.1671         1.1671         1.1672
+                 Sum        13.7079         1.1683         1.1683         1.1684
+-------------------------------------------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Total Magnetism (uB)                                                                      
+-------------------------------------------------------------------------------------------
+                         Fe         1.1690981855         1.1689596529         1.1689548475 
+                         Fe         1.1682782547         1.1683271615         1.1683689897 
+-------------------------------------------------------------------------------------------
+
+
+ charge density convergence is achieved
+ final etot is -6825.6858753 eV
+
+
+------------------------------------------------------------------------------------------
+ TOTAL-FORCE (eV/Angstrom)                                                                
+------------------------------------------------------------------------------------------
+                       Fe1        -0.0000234480         0.0000848730         0.0003959639 
+                       Fe2         0.0000234480        -0.0000848730        -0.0003959639 
+------------------------------------------------------------------------------------------
+
+
+
+ ------------------------------------------------------------------------------------------------
+ Energy (Ry)         Potential (Ry)      Kinetic (Ry)        Temperature (K)     
+ -501.67563          -501.67848          0.0028501339        300                 
+ ------------------------------------------------------------------------------------------------
+
+
+
+ -------------------------------------------
+ STEP OF MOLECULAR DYNAMICS : 1
+ -------------------------------------------
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ NEW-OLD atomic charge density approx. for the potential !
+ DONE : INIT SCF Time : 4.69025 (SEC)
+
+
+ PW ALGORITHM --------------- ION=2     ELEC=1   --------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0 ; where current threshold is: 7.51393e-06 . 
+total magnetism (Bohr mag/cell)	2.46069	2.4606	2.46063
+ absolute magnetism (Bohr mag/cell)       = 4.35476
+ Notice: Threshold on eigenvalues was too large.
+ hsover_error=0.32 > DRHO=0.00192412
+ Origin diag_ethr = 0.01
+ New    diag_ethr = 6.01286e-06
+total magnetism (Bohr mag/cell)	2.46066	2.46058	2.46061
+ absolute magnetism (Bohr mag/cell)       = 4.36174
+
+ Density error is 0.00201217065486
+                          Error Threshold = 6.01286073232e-06
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6717206991      -6825.5939269727     
+ E_Harris       -501.6715817664      -6825.5920366956     
+ E_Fermi        1.4766917900         20.0914225341        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   2  ELEC=   2--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0 ; where current threshold is: 6.01286073232e-06 . 
+total magnetism (Bohr mag/cell)	2.45367664792	2.45369451898	2.45369632661
+       absolute magnetism (Bohr mag/cell) = 4.36076913778
+
+ Density error is 0.00924150911613
+                          Error Threshold = 6.28803329643e-06
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6713570140      -6825.5889787830     
+ E_Harris       -501.5122751175      -6823.4245585418     
+ E_Fermi        1.4801602125         20.1386128426        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   2  ELEC=   3--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0 ; where current threshold is: 6.28803329643e-06 . 
+total magnetism (Bohr mag/cell)	2.45535480016	2.45535779838	2.45535744914
+       absolute magnetism (Bohr mag/cell) = 4.36222821556
+
+ Density error is 0.00222730537898
+                          Error Threshold = 6.28803329643e-06
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6723462878      -6825.6024385430     
+ E_Harris       -501.6357961303      -6825.1051481383     
+ E_Fermi        1.4800078639         20.1365400332        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   2  ELEC=   4--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0 ; where current threshold is: 6.28803329643e-06 . 
+total magnetism (Bohr mag/cell)	2.4557794855	2.45578128279	2.45578053957
+       absolute magnetism (Bohr mag/cell) = 4.36171007414
+
+ Density error is 6.47878398594e-06
+                          Error Threshold = 6.28803329643e-06
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6724876966      -6825.6043625085     
+ E_KS(sigma->0) -501.6678952474      -6825.5418790320     
+ E_Harris       -501.6633376598      -6825.4798698707     
+ E_band         -27.8834155884       -379.3733317038      
+ E_one_elec     -203.5744480246      -2769.7724603392     
+ E_Hartree      123.7840339882       1684.1681836654      
+ E_xc           -71.4833250872       -972.5805331721      
+ E_Ewald        -350.4821832426      -4768.5547395789     
+ E_entropy(-TS) -0.0091848983        -0.1249669530        
+ E_descf        0.0000000000         0.0000000000         
+ E_exx          0.0000000000         0.0000000000         
+ E_Fermi        1.4799614353         20.1359083399        
+----------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Magnetic force (eV/uB)                                                                    
+-------------------------------------------------------------------------------------------
+                         Fe        -0.1674727502        -0.1674714507        -0.1674677599 
+                         Fe        -0.1685388103        -0.1685393463        -0.1685411873 
+-------------------------------------------------------------------------------------------
+
+
+-------------------------------------------------------------------------------------------
+Orbital Charge Analysis      Charge         Mag(x)         Mag(y)         Mag(z)
+-------------------------------------------------------------------------------------------
+Fe1                 
+                   s         1.1147         0.0019         0.0019         0.0019
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5877         1.2479         1.2479         1.2479
+                 Sum        13.6994         1.2500         1.2501         1.2501
+Fe2                 
+                   s         1.1148         0.0019         0.0019         0.0019
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5911         1.2480         1.2480         1.2480
+                 Sum        13.7030         1.2502         1.2502         1.2502
+-------------------------------------------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Total Magnetism (uB)                                                                      
+-------------------------------------------------------------------------------------------
+                         Fe         1.2500362016         1.2500750113         1.2500654974 
+                         Fe         1.2501907811         1.2501525281         1.2501618807 
+-------------------------------------------------------------------------------------------
+
+
+ charge density convergence is achieved
+ final etot is -6825.6043625 eV
+
+
+------------------------------------------------------------------------------------------
+ TOTAL-FORCE (eV/Angstrom)                                                                
+------------------------------------------------------------------------------------------
+                       Fe1        -0.0821749928        -0.0641832335         0.0945557521 
+                       Fe2         0.0821749928         0.0641832335        -0.0945557521 
+------------------------------------------------------------------------------------------
+
+
+
+ ------------------------------------------------------------------------------------------------
+ Energy (Ry)         Potential (Ry)      Kinetic (Ry)        Temperature (K)     
+ -501.66966          -501.67249          0.0028297442        297.85381           
+ ------------------------------------------------------------------------------------------------
+
+
+
+ -------------------------------------------
+ STEP OF MOLECULAR DYNAMICS : 2
+ -------------------------------------------
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ first order charge density extrapolation !
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ DONE : INIT SCF Time : 20.3341 (SEC)
+
+
+ PW ALGORITHM --------------- ION=3     ELEC=1   --------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0 ; where current threshold is: 6.28803e-06 . 
+total magnetism (Bohr mag/cell)	2.45486	2.45489	2.45489
+ absolute magnetism (Bohr mag/cell)       = 4.36543
+ Notice: Threshold on eigenvalues was too large.
+ hsover_error=0.32 > DRHO=0.00210159
+ Origin diag_ethr = 0.01
+ New    diag_ethr = 6.56747e-06
+total magnetism (Bohr mag/cell)	2.45485	2.45488	2.45488
+ absolute magnetism (Bohr mag/cell)       = 4.36511
+
+ Density error is 0.00210610440114
+                          Error Threshold = 6.56747174472e-06
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6717145278      -6825.5938430078     
+ E_Harris       -501.6715861090      -6825.5920957801     
+ E_Fermi        1.4832199190         20.1802422850        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   3  ELEC=   2--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0 ; where current threshold is: 6.56747174472e-06 . 
+total magnetism (Bohr mag/cell)	2.45728332606	2.45728465763	2.45728362282
+       absolute magnetism (Bohr mag/cell) = 4.36144612893
+
+ Density error is 0.0100994423697
+                          Error Threshold = 6.58157625357e-06
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6712030534      -6825.5868840416     
+ E_Harris       -501.8309806843      -6827.7607702341     
+ E_Fermi        1.4801826654         20.1389183308        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   3  ELEC=   3--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0 ; where current threshold is: 6.58157625357e-06 . 
+total magnetism (Bohr mag/cell)	2.45602003892	2.45602235568	2.45602305001
+       absolute magnetism (Bohr mag/cell) = 4.36008011062
+
+ Density error is 0.0022259696948
+                          Error Threshold = 6.58157625357e-06
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6723719367      -6825.6027875138     
+ E_Harris       -501.7036416542      -6826.0282338473     
+ E_Fermi        1.4800402952         20.1369812842        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   3  ELEC=   4--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0 ; where current threshold is: 6.58157625357e-06 . 
+total magnetism (Bohr mag/cell)	2.45568827013	2.45568820365	2.45568816609
+       absolute magnetism (Bohr mag/cell) = 4.36059357058
+
+ Density error is 0.000113741995613
+                          Error Threshold = 6.58157625357e-06
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6725298576      -6825.6049361390     
+ E_KS(sigma->0) -501.6679841586      -6825.5430887303     
+ E_Harris       -501.6890083521      -6825.8291375583     
+ E_band         -27.8841363403       -379.3831380370      
+ E_one_elec     -203.5689978550      -2769.6983069772     
+ E_Hartree      123.7762138387       1684.0617850727      
+ E_xc           -71.4816492900       -972.5577327814      
+ E_Ewald        -350.4801490952      -4768.5270635846     
+ E_entropy(-TS) -0.0090913981        -0.1236948175        
+ E_descf        0.0000000000         0.0000000000         
+ E_exx          0.0000000000         0.0000000000         
+ E_Fermi        1.4800346303         20.1369042091        
+----------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Magnetic force (eV/uB)                                                                    
+-------------------------------------------------------------------------------------------
+                         Fe        -0.1652181739        -0.1652325578        -0.1652321249 
+                         Fe        -0.1654941827        -0.1654786653        -0.1654791319 
+-------------------------------------------------------------------------------------------
+
+
+-------------------------------------------------------------------------------------------
+Orbital Charge Analysis      Charge         Mag(x)         Mag(y)         Mag(z)
+-------------------------------------------------------------------------------------------
+Fe1                 
+                   s         1.1147         0.0019         0.0019         0.0019
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5895         1.2477         1.2476         1.2476
+                 Sum        13.7013         1.2499         1.2498         1.2498
+Fe2                 
+                   s         1.1147         0.0019         0.0019         0.0019
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5893         1.2478         1.2479         1.2479
+                 Sum        13.7011         1.2500         1.2500         1.2500
+-------------------------------------------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Total Magnetism (uB)                                                                      
+-------------------------------------------------------------------------------------------
+                         Fe         1.2498513779         1.2497690096         1.2497695030 
+                         Fe         1.2499638767         1.2500461778         1.2500456124 
+-------------------------------------------------------------------------------------------
+
+
+ charge density convergence is achieved
+ final etot is -6825.6049361 eV
+
+
+------------------------------------------------------------------------------------------
+ TOTAL-FORCE (eV/Angstrom)                                                                
+------------------------------------------------------------------------------------------
+                       Fe1        -0.0263258654        -0.0198291990         0.0328141173 
+                       Fe2         0.0263258654         0.0198291990        -0.0328141173 
+------------------------------------------------------------------------------------------
+
+
+
+ ------------------------------------------------------------------------------------------------
+ Energy (Ry)         Potential (Ry)      Kinetic (Ry)        Temperature (K)     
+ -501.66969          -501.67253          0.0028369371        298.61093           
+ ------------------------------------------------------------------------------------------------
+
+
+
+ -------------------------------------------
+ STEP OF MOLECULAR DYNAMICS : 3
+ -------------------------------------------
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ second order charge density extrapolation !
+ alpha = -0.46539717
+ beta = 1.4648176
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ Find the file, try to read charge from file.
+ read in fermi energy = 0
+ DONE : INIT SCF Time : 41.017 (SEC)
+
+
+ PW ALGORITHM --------------- ION=4     ELEC=1   --------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0 ; where current threshold is: 6.58158e-06 . 
+total magnetism (Bohr mag/cell)	2.45395	2.45395	2.45395
+ absolute magnetism (Bohr mag/cell)       = 4.36621
+ Notice: Threshold on eigenvalues was too large.
+ hsover_error=0.32 > DRHO=0.00327757
+ Origin diag_ethr = 0.01
+ New    diag_ethr = 1.02424e-05
+total magnetism (Bohr mag/cell)	2.45393	2.45393	2.45393
+ absolute magnetism (Bohr mag/cell)       = 4.36585
+
+ Density error is 0.00328180767194
+                          Error Threshold = 1.02424082459e-05
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6714819577      -6825.5906787296     
+ E_Harris       -501.6704871756      -6825.5771440242     
+ E_Fermi        1.4848945022         20.2030261586        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   4  ELEC=   2--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0 ; where current threshold is: 1.02424082459e-05 . 
+total magnetism (Bohr mag/cell)	2.45834495411	2.45824446616	2.45825644792
+       absolute magnetism (Bohr mag/cell) = 4.36143824469
+
+ Density error is 0.00407139541475
+                          Error Threshold = 1.02556489748e-05
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6718059210      -6825.5950864757     
+ E_Harris       -501.8968017467      -6828.6563117308     
+ E_Fermi        1.4803720649         20.1414952427        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   4  ELEC=   3--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0 ; where current threshold is: 1.02556489748e-05 . 
+total magnetism (Bohr mag/cell)	2.4561430127	2.4561402075	2.45614046704
+       absolute magnetism (Bohr mag/cell) = 4.36006713268
+
+ Density error is 0.00621121698173
+                          Error Threshold = 1.02556489748e-05
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6723961915      -6825.6031175180     
+ E_Harris       -501.7084280186      -6826.0933556758     
+ E_Fermi        1.4808558000         20.1480767961        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   4  ELEC=   4--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0 ; where current threshold is: 1.02556489748e-05 . 
+total magnetism (Bohr mag/cell)	2.45642597595	2.45642438896	2.45642568116
+       absolute magnetism (Bohr mag/cell) = 4.36090201409
+
+ Density error is 0.000907798588431
+                          Error Threshold = 1.02556489748e-05
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6725094449      -6825.6046584088     
+ E_KS(sigma->0) -501.6682437690      -6825.5466209109     
+ E_Harris       -501.6882798535      -6825.8192258261     
+ E_band         -27.8806642947       -379.3358984328      
+ E_one_elec     -203.5720364691      -2769.7396494442     
+ E_Hartree      123.7795681857       1684.1074233046      
+ E_xc           -71.4830945963       -972.5773971831      
+ E_Ewald        -350.4767334207      -4768.4805909482     
+ E_entropy(-TS) -0.0085313518        -0.1160749959        
+ E_descf        0.0000000000         0.0000000000         
+ E_exx          0.0000000000         0.0000000000         
+ E_Fermi        1.4811684035         20.1523299848        
+----------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Magnetic force (eV/uB)                                                                    
+-------------------------------------------------------------------------------------------
+                         Fe        -0.1614117188        -0.1614064417        -0.1614126965 
+                         Fe        -0.1590151938        -0.1590593187        -0.1590482375 
+-------------------------------------------------------------------------------------------
+
+
+-------------------------------------------------------------------------------------------
+Orbital Charge Analysis      Charge         Mag(x)         Mag(y)         Mag(z)
+-------------------------------------------------------------------------------------------
+Fe1                 
+                   s         1.1148         0.0020         0.0020         0.0020
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5942         1.2476         1.2477         1.2477
+                 Sum        13.7061         1.2498         1.2499         1.2499
+Fe2                 
+                   s         1.1146         0.0018         0.0018         0.0018
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5847         1.2480         1.2480         1.2480
+                 Sum        13.6964         1.2501         1.2500         1.2500
+-------------------------------------------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Total Magnetism (uB)                                                                      
+-------------------------------------------------------------------------------------------
+                         Fe         1.2498251342         1.2498544518         1.2498533551 
+                         Fe         1.2500507306         1.2500181434         1.2500206507 
+-------------------------------------------------------------------------------------------
+
+
+ charge density convergence is achieved
+ final etot is -6825.6046584 eV
+
+
+------------------------------------------------------------------------------------------
+ TOTAL-FORCE (eV/Angstrom)                                                                
+------------------------------------------------------------------------------------------
+                       Fe1        -0.0441291367        -0.0281389251         0.0597264967 
+                       Fe2         0.0441291367         0.0281389251        -0.0597264967 
+------------------------------------------------------------------------------------------
+
+
+
+ ------------------------------------------------------------------------------------------------
+ Energy (Ry)         Potential (Ry)      Kinetic (Ry)        Temperature (K)     
+ -501.66963          -501.67251          0.0028755884        302.67929           
+ ------------------------------------------------------------------------------------------------
+
+
+
+
+ --------------------------------------------
+ !FINAL_ETOT_IS -6825.60465840883 eV
+ --------------------------------------------
+
+
+TIME STATISTICS
+-----------------------------------------------------------------------------
+    CLASS_NAME                NAME             TIME/s  CALLS   AVG/s  PER/%  
+-----------------------------------------------------------------------------
+                   total                       59.14  21       2.82   100.00 
+ Driver            reading                     0.03   1        0.03   0.05   
+ Input_Conv        Convert                     0.00   1        0.00   0.00   
+ Driver            driver_line                 59.11  1        59.11  99.95  
+ UnitCell          check_tau                   0.00   1        0.00   0.00   
+ PW_Basis_Sup      setuptransform              0.00   1        0.00   0.01   
+ PW_Basis_Sup      distributeg                 0.00   1        0.00   0.00   
+ mymath            heapsort                    0.00   7        0.00   0.00   
+ PW_Basis_K        setuptransform              0.00   1        0.00   0.00   
+ PW_Basis_K        distributeg                 0.00   1        0.00   0.00   
+ PW_Basis          setup_struc_factor          0.01   4        0.00   0.01   
+ ppcell_vnl        init                        0.00   1        0.00   0.00   
+ ppcell_vl         init_vloc                   0.01   1        0.01   0.01   
+ ppcell_vnl        init_vnl                    0.03   1        0.03   0.05   
+ WF_atomic         init_at_1                   0.17   1        0.17   0.29   
+ wavefunc          wfcinit                     0.00   1        0.00   0.00   
+ Run_MD            md_line                     58.80  1        58.80  99.43  
+ Nose_Hoover       setup                       4.18   1        4.18   7.06   
+ MD_func           force_virial                58.73  4        14.68  99.31  
+ ESolver_KS_PW     runner                      58.35  4        14.59  98.66  
+ H_Ewald_pw        compute_ewald               0.00   4        0.00   0.01   
+ Charge            set_rho_core                0.03   4        0.01   0.05   
+ PW_Basis_Sup      recip2real                  0.35   492      0.00   0.60   
+ PW_Basis_Sup      gathers_scatterp            0.06   492      0.00   0.10   
+ Charge            atomic_rho                  0.09   8        0.01   0.15   
+ Potential         init_pot                    0.28   4        0.07   0.47   
+ Potential         update_from_charge          1.36   20       0.07   2.29   
+ Potential         cal_fixed_v                 0.00   4        0.00   0.01   
+ PotLocal          cal_fixed_v                 0.00   4        0.00   0.00   
+ Potential         cal_v_eff                   1.34   20       0.07   2.27   
+ H_Hartree_pw      v_hartree                   0.04   20       0.00   0.06   
+ PW_Basis_Sup      real2recip                  0.33   648      0.00   0.56   
+ PW_Basis_Sup      gatherp_scatters            0.03   648      0.00   0.05   
+ PotXC             cal_v_eff                   1.30   20       0.06   2.20   
+ XC_Functional     v_xc                        1.55   24       0.06   2.63   
+ Potential         interpolate_vrs             0.01   20       0.00   0.01   
+ OnsiteProj        cubspl_tabulate             0.09   1        0.09   0.16   
+ Charge_Mixing     init_mixing                 0.00   4        0.00   0.01   
+ ESolver_KS_PW     hamilt2density              10.19  20       0.51   17.24  
+ HSolverPW         solve                       16.62  32       0.52   28.10  
+ pp_cell_vnl       getvnl                      0.86   330      0.00   1.46   
+ Structure_Factor  get_sk                      0.10   340      0.00   0.16   
+ OnsiteProj        getvnl                      0.00   330      0.00   0.00   
+ OnsiteProj        tabulate_atomic             0.00   366      0.00   0.00   
+ WF_atomic         atomic_wfc                  0.01   1        0.01   0.01   
+ DiagoIterAssist   diagH_subspace_init         0.13   1        0.13   0.23   
+ Operator          hPsi                        48.88  4254     0.01   82.65  
+ Operator          EkineticPW                  0.25   4254     0.00   0.41   
+ Operator          VeffPW                      43.72  4254     0.01   73.93  
+ PW_Basis_K        recip2real                  12.72  43840    0.00   21.51  
+ PW_Basis_K        gathers_scatterp            1.93   43840    0.00   3.26   
+ PW_Basis_K        real2recip                  11.60  41760    0.00   19.62  
+ PW_Basis_K        gatherp_scatters            0.85   41760    0.00   1.44   
+ Operator          NonlocalPW                  3.23   4254     0.00   5.46   
+ Nonlocal          add_nonlocal_pp             1.98   4254     0.00   3.35   
+ Operator          OnsiteProjPW                1.67   4254     0.00   2.82   
+ OnsiteProj        overlap                     0.82   4290     0.00   1.39   
+ FS_Nonlocal_tools cal_becp                    0.83   4298     0.00   1.40   
+ OnsiteProj        add_onsite_proj             0.70   4254     0.00   1.19   
+ DiagoIterAssist   diagH_LAPACK                0.36   326      0.00   0.61   
+ DiagoCG           diag_once                   12.02  32       0.38   20.33  
+ DiagoCG_New       spsi_func                   0.11   7856     0.00   0.19   
+ DiagoCG_New       hpsi_func                   10.47  3928     0.00   17.70  
+ ElecStatePW       psiToRho                    0.90   20       0.05   1.52   
+ Charge_Mixing     get_drho                    0.10   20       0.00   0.17   
+ Charge_Mixing     inner_product_recip_rho     0.00   20       0.00   0.01   
+ Charge            mix_rho                     0.14   12       0.01   0.24   
+ Charge            Broyden_mixing              0.02   12       0.00   0.03   
+ DiagoIterAssist   diagH_subspace              3.39   27       0.13   5.73   
+ Charge_Mixing     inner_product_recip_hartree 0.01   24       0.00   0.01   
+ OnsiteProj        cal_occupation              0.01   4        0.00   0.01   
+ Forces            cal_force_loc               0.01   4        0.00   0.01   
+ Forces            cal_force_ew                0.01   4        0.00   0.01   
+ Forces            cal_force_nl                0.03   4        0.01   0.06   
+ FS_Nonlocal_tools cal_dbecp_f                 0.04   24       0.00   0.06   
+ Forces            cal_force_onsite            0.02   4        0.00   0.03   
+ Forces            cal_force_cc                0.29   4        0.07   0.49   
+ Forces            cal_force_scc               0.03   4        0.01   0.05   
+ Nose_Hoover       first_half                  0.00   3        0.00   0.00   
+ SpinConstrain     cal_mw_from_lambda          44.69  310      0.14   75.57  
+ DiagoIterAssist   diag_responce               37.41  298      0.13   63.25  
+ Nose_Hoover       second_half                 0.00   3        0.00   0.00   
+ ModuleIO          write_istate_info           0.01   1        0.01   0.01   
+-----------------------------------------------------------------------------
+
+
+ NAME-------------------------|MEMORY(MB)--------
+total                         24.43          
+Psi_PW                        3.994          
+DiagSub::temp                 3.994          
+FFT::grid                     1.424          
+Chg::rho                      1.424          
+Chg::rho_save                 1.424          
+Pot::veff                     1.424          
+Pot::veff_smooth              1.424          
+VNL::vkb                      1.383          
+ -------------   < 1.0 MB has been ignored ----------------
+ ----------------------------------------------------------
+
+ Start  Time  : Fri Sep  6 10:04:51 2024
+ Finish Time  : Fri Sep  6 10:05:51 2024
+ Total  Time  : 0 h 1 mins 0 secs 
diff --git a/tests/abacus.spin/OUT.ABACUS/running_relax.log b/tests/abacus.spin/OUT.ABACUS/running_relax.log
new file mode 100644
index 00000000..d94c8f89
--- /dev/null
+++ b/tests/abacus.spin/OUT.ABACUS/running_relax.log
@@ -0,0 +1,1002 @@
+                                                                                     
+                              ABACUS v3.7.1
+
+               Atomic-orbital Based Ab-initio Computation at UStc                    
+
+                     Website: http://abacus.ustc.edu.cn/                             
+               Documentation: https://abacus.deepmodeling.com/                       
+                  Repository: https://github.com/abacusmodeling/abacus-develop       
+                              https://github.com/deepmodeling/abacus-develop         
+                      Commit: 8443c42b5 (Thu Sep 5 14:19:05 2024 +0800)
+
+    Start Time is Fri Sep  6 09:29:43 2024
+                                                                                     
+ ------------------------------------------------------------------------------------
+
+ READING GENERAL INFORMATION
+                           global_out_dir = OUT.spin/
+                           global_in_card = INPUT
+                               pseudo_dir = ./
+                              orbital_dir = ./
+                                    DRANK = 1
+                                    DSIZE = 1
+                                   DCOLOR = 1
+                                    GRANK = 1
+                                    GSIZE = 1
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Reading atom information in unitcell:                              |
+ | From the input file and the structure file we know the number of   |
+ | different elments in this unitcell, then we list the detail        |
+ | information for each element, especially the zeta and polar atomic |
+ | orbital number for each element. The total atom number is counted. |
+ | We calculate the nearest atom distance for each atom and show the  |
+ | Cartesian and Direct coordinates for each atom. We list the file   |
+ | address for atomic orbitals. The volume and the lattice vectors    |
+ | in real and reciprocal space is also shown.                        |
+ |                                                                    |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+ READING UNITCELL INFORMATION
+                                    ntype = 1
+                  lattice constant (Bohr) = 1.88028
+              lattice constant (Angstrom) = 0.995
+
+ READING ATOM TYPE 1
+                               atom label = Fe
+                      L=0, number of zeta = 4
+                      L=1, number of zeta = 2
+                      L=2, number of zeta = 2
+                      L=3, number of zeta = 1
+             number of atom for this type = 2
+               magnetization of element 1 = [ 1.25, 1.25, 1.25 ]
+
+                        TOTAL ATOM NUMBER = 2
+DIRECT COORDINATES
+    atom                   x                   y                   z     mag                  vx                  vy                  vz
+taud_Fe1            0.0000000000        0.0000000000        0.0000000000  2.1651        0.0000000000        0.0000000000        0.0000000000
+taud_Fe2            0.5000000000        0.5000000000        0.5000000000  2.1651        0.0000000000        0.0000000000        0.0000000000
+
+
+
+                          Volume (Bohr^3) = 150.259
+                             Volume (A^3) = 22.266
+
+ Lattice vectors: (Cartesian coordinate: in unit of a_0)
+             +2.82743                  +0                  +0
+                   +0            +2.82743                  +0
+                   +0                  +0            +2.82743
+ Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0)
+            +0.353679                  -0                  +0
+                   -0           +0.353679                  -0
+                   +0                  -0           +0.353679
+ The esolver type has been set to : ksdft_pw
+
+ RUNNING WITH DEVICE  : CPU / Intel(R) Xeon(R) Platinum
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Reading pseudopotentials files:                                    |
+ | The pseudopotential file is in UPF format. The 'NC' indicates that |
+ | the type of pseudopotential is 'norm conserving'. Functional of    |
+ | exchange and correlation is decided by 4 given parameters in UPF   |
+ | file.  We also read in the 'core correction' if there exists.      |
+ | Also we can read the valence electrons number and the maximal      |
+ | angular momentum used in this pseudopotential. We also read in the |
+ | trail wave function, trail atomic density and local-pseudopotential|
+ | on logrithmic grid. The non-local pseudopotential projector is also|
+ | read in if there is any.                                           |
+ |                                                                    |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+                PAO radial cut off (Bohr) = 15
+
+ Read in pseudopotential file is Fe.upf
+                     pseudopotential type = NC
+          exchange-correlation functional = PBE
+                 nonlocal core correction = 1
+                        valence electrons = 16
+                                     lmax = 2
+                           number of zeta = 4
+                     number of projectors = 6
+                           L of projector = 0
+                           L of projector = 0
+                           L of projector = 1
+                           L of projector = 1
+                           L of projector = 2
+                           L of projector = 2
+     initial pseudo atomic orbital number = 40
+                                   NLOCAL = 108
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ Warning: the number of valence electrons in pseudopotential > 8 for Fe: [Ar] 3d6 4s2
+ Pseudopotentials with additional electrons can yield (more) accurate outcomes, but may be less efficient.
+ If you're confident that your chosen pseudopotential is appropriate, you can safely ignore this warning.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+                  
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Setup plane waves of charge/potential:                             |
+ | Use the energy cutoff and the lattice vectors to generate the      |
+ | dimensions of FFT grid. The number of FFT grid on each processor   |
+ | is 'nrxx'. The number of plane wave basis in reciprocal space is   |
+ | different for charege/potential and wave functions. We also set    |
+ | the 'sticks' for the parallel of FFT. The number of plane waves    |
+ | is 'npw' in each processor.                                        |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+
+ SETUP THE PLANE WAVE BASIS
+ energy cutoff for charge/potential (unit:Ry) = 400
+            fft grid for charge/potential = [ 36, 36, 36 ]
+                        fft grid division = [ 1, 1, 1 ]
+        big fft grid for charge/potential = [ 36, 36, 36 ]
+                                     nbxx = 46656
+                                     nrxx = 46656
+
+ SETUP PLANE WAVES FOR CHARGE/POTENTIAL
+                    number of plane waves = 20341
+                         number of sticks = 885
+
+ PARALLEL PW FOR CHARGE/POTENTIAL
+     PROC   COLUMNS(POT)             PW
+        1            885          20341
+ --------------- sum -------------------
+        1            885          20341
+                            number of |g| = 241
+                                  max |g| = 35.7753
+                                  min |g| = 0
+
+----------- Double Check Mixing Parameters Begin ------------
+mixing_type: broyden
+mixing_beta: 0.4
+mixing_gg0: 1
+mixing_gg0_min: 0.1
+mixing_beta_mag: 1.6
+mixing_gg0_mag: 0
+mixing_ndim: 8
+----------- Double Check Mixing Parameters End ------------
+
+ SETUP THE ELECTRONS NUMBER
+            electron number of element Fe = 16
+      total electron number of element Fe = 32
+            AUTOSET number of electrons:  = 32
+ DONE : SETUP UNITCELL Time : 0.0957571 (SEC)
+
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Setup K-points                                                     |
+ | We setup the k-points according to input parameters.               |
+ | The reduced k-points are set according to symmetry operations.     |
+ | We treat the spin as another set of k-points.                      |
+ |                                                                    |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+
+ SETUP K-POINTS
+                                    nspin = 4
+                   Input type of k points = Monkhorst-Pack(Gamma)
+                                   nkstot = 1
+                               nkstot_ibz = 1
+K-POINTS REDUCTION ACCORDING TO SYMMETRY
+     IBZ    DIRECT_X    DIRECT_Y    DIRECT_Z  WEIGHT  ibz2bz
+       1  0.00000000  0.00000000  0.00000000  1.0000       0
+
+                               nkstot now = 1
+K-POINTS DIRECT COORDINATES
+ KPOINTS    DIRECT_X    DIRECT_Y    DIRECT_Z  WEIGHT
+       1  0.00000000  0.00000000  0.00000000  1.0000
+
+
+           k-point number in this process = 1
+       minimum distributed K point number = 1
+
+K-POINTS CARTESIAN COORDINATES
+ KPOINTS CARTESIAN_X CARTESIAN_Y CARTESIAN_Z  WEIGHT
+       1  0.00000000  0.00000000  0.00000000  1.0000
+
+
+K-POINTS DIRECT COORDINATES
+ KPOINTS    DIRECT_X    DIRECT_Y    DIRECT_Z  WEIGHT
+       1  0.00000000  0.00000000  0.00000000  1.0000
+
+ DONE : INIT K-POINTS Time : 0.105664 (SEC)
+
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Setup plane waves of wave functions:                               |
+ | Use the energy cutoff and the lattice vectors to generate the      |
+ | dimensions of FFT grid. The number of FFT grid on each processor   |
+ | is 'nrxx'. The number of plane wave basis in reciprocal space is   |
+ | different for charege/potential and wave functions. We also set    |
+ | the 'sticks' for the parallel of FFT. The number of plane wave of  |
+ | each k-point is 'npwk[ik]' in each processor                       |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+
+ SETUP PLANE WAVES FOR WAVE FUNCTIONS
+     energy cutoff for wavefunc (unit:Ry) = 100
+              fft grid for wave functions = [ 36, 36, 36 ]
+                    number of plane waves = 2517
+                         number of sticks = 221
+
+ PARALLEL PW FOR WAVE FUNCTIONS
+     PROC   COLUMNS(POT)             PW
+        1            221           2517
+ --------------- sum -------------------
+        1            221           2517
+ DONE : INIT PLANEWAVE Time : 0.106715 (SEC)
+
+                           occupied bands = 16
+                                   NBANDS = 52
+
+ SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS
+ Fe non-local projectors:
+ projector 1 L=0
+ projector 2 L=0
+ projector 3 L=1
+ projector 4 L=1
+ projector 5 L=2
+ projector 6 L=2
+      TOTAL NUMBER OF NONLOCAL PROJECTORS = 36
+ DONE : LOCAL POTENTIAL Time : 0.122677 (SEC)
+
+
+ Init Non-Local PseudoPotential table : 
+ Init Non-Local-Pseudopotential done.
+ DONE : NON-LOCAL POTENTIAL Time : 0.153353 (SEC)
+
+                                     npwx = 2517
+
+ Make real space PAO into reciprocal space.
+       max mesh points in Pseudopotential = 1425
+     dq(describe PAO in reciprocal space) = 0.01
+                                    max q = 1204
+
+ number of pseudo atomic orbitals for Fe is 4
+WARNING: norm of atomic wavefunction # 2 of atomic type Fe is 0.999981, renormalized
+WARNING: norm of atomic wavefunction # 3 of atomic type Fe is 0.999997, renormalized
+ DONE : INIT BASIS Time : 0.325415 (SEC)
+
+
+ -------------------------------------------
+ STEP OF RELAXATION : 1
+ -------------------------------------------
+                                 init_chg = atomic
+ DONE : INIT SCF Time : 0.524608 (SEC)
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   1--------------------------------
+total magnetism (Bohr mag/cell)	2.30943	2.30938	2.30941
+       absolute magnetism (Bohr mag/cell) = 4.01976
+ Notice: Threshold on eigenvalues was too large.
+ hsover_error=0.32 > DRHO=0.0686869
+ Origin diag_ethr = 0.01
+ New    diag_ethr = 0.000214646
+total magnetism (Bohr mag/cell)	2.30943	2.30937	2.3094
+       absolute magnetism (Bohr mag/cell) = 4.01964
+
+ Density error is 0.0548949686243
+                          Error Threshold = 0.000214646406708
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6632803550      -6825.4790901992     
+ E_Harris       -501.6647758269      -6825.4994371390     
+ E_Fermi        1.4575316668         19.8307356840        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   2--------------------------------
+total magnetism (Bohr mag/cell)	2.3094424965	2.30934448798	2.30941621651
+       absolute magnetism (Bohr mag/cell) = 4.13707180938
+
+ Density error is 0.00986449919003
+                          Error Threshold = 0.000171546776951
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6774595966      -6825.6720086784     
+ E_Harris       -499.7039503033      -6798.8210372331     
+ E_Fermi        1.4964230898         20.3598806394        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   3--------------------------------
+total magnetism (Bohr mag/cell)	2.30944490813	2.30935345105	2.30940487564
+       absolute magnetism (Bohr mag/cell) = 4.08853707061
+
+ Density error is 0.00240445773415
+                          Error Threshold = 3.08265599688e-05
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6784060189      -6825.6848854146     
+ E_Harris       -501.4802459250      -6822.9887790210     
+ E_Fermi        1.4994551309         20.4011336751        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   4--------------------------------
+total magnetism (Bohr mag/cell)	2.30944724752	2.30935862214	2.30939736766
+       absolute magnetism (Bohr mag/cell) = 4.08848804651
+
+ Density error is 0.00057214611471
+                          Error Threshold = 7.51393041921e-06
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6784787714      -6825.6858752634     
+ E_KS(sigma->0) -501.6746222162      -6825.6334041381     
+ E_Harris       -501.6738375513      -6825.6227282240     
+ E_band         -27.9117558414       -379.7589206280      
+ E_one_elec     -203.4207485774      -2767.6812720784     
+ E_Hartree      123.6718684724       1682.6420935310      
+ E_xc           -71.4390193374       -971.9777225215      
+ E_Ewald        -350.4828662186      -4768.5640319440     
+ E_entropy(-TS) -0.0077131104        -0.1049422506        
+ E_descf        0.0000000000         0.0000000000         
+ E_exx          0.0000000000         0.0000000000         
+ E_Fermi        1.5017611709         20.4325089589        
+----------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Magnetic force (eV/uB)                                                                    
+-------------------------------------------------------------------------------------------
+                         Fe         0.0000000000         0.0000000000         0.0000000000 
+                         Fe         0.0000000000         0.0000000000         0.0000000000 
+-------------------------------------------------------------------------------------------
+
+
+-------------------------------------------------------------------------------------------
+Orbital Charge Analysis      Charge         Mag(x)         Mag(y)         Mag(z)
+-------------------------------------------------------------------------------------------
+Fe1                 
+                   s         1.1149         0.0010         0.0010         0.0010
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5931         1.1679         1.1678         1.1678
+                 Sum        13.7051         1.1691         1.1690         1.1690
+Fe2                 
+                   s         1.1150         0.0010         0.0010         0.0010
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5959         1.1671         1.1671         1.1672
+                 Sum        13.7079         1.1683         1.1683         1.1684
+-------------------------------------------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Total Magnetism (uB)                                                                      
+-------------------------------------------------------------------------------------------
+                         Fe         1.1690981855         1.1689596529         1.1689548475 
+                         Fe         1.1682782547         1.1683271615         1.1683689897 
+-------------------------------------------------------------------------------------------
+
+
+ charge density convergence is achieved
+ final etot is -6825.6858753 eV
+ EFERMI = 20.432508959 eV
+
+ STATE ENERGY(eV) AND OCCUPATIONS    NSPIN == 4
+ 1/1 kpoint (Cartesian) = 0.0000 0.0000 0.0000 (2517 pws)
+       1       -67.4569        1.00000
+       2       -67.2982        1.00000
+       3       -65.2976        1.00000
+       4       -65.1287        1.00000
+       5       -33.6978        1.00000
+       6       -33.6978        1.00000
+       7       -33.6978        1.00000
+       8       -33.3602        1.00000
+       9       -33.3602        1.00000
+      10       -33.3602        1.00000
+      11       -31.4558        1.00000
+      12       -31.4557        1.00000
+      13       -31.4553        1.00000
+      14       -31.0894        1.00000
+      15       -31.0892        1.00000
+      16       -31.0888        1.00000
+      17        10.4705        1.00000
+      18        10.6689        1.00000
+      19        14.7652        1.00000
+      20        14.7654        1.00000
+      21        16.3838        1.00000
+      22        16.3838        1.00000
+      23        17.7210        1.00000
+      24        17.7211        1.00000
+      25        17.7213        1.00000
+      26        19.1329        1.00000
+      27        19.1332        1.00000
+      28        19.5268        1.00000
+      29        19.5272        1.00000
+      30        19.5274        1.00000
+      31        20.3909       0.667123
+      32        20.3910       0.666801
+      33        20.3912       0.666076
+      34        21.6006        0.00000
+      35        21.6007        0.00000
+      36        22.5186        0.00000
+      37        22.5192        0.00000
+      38        22.5194        0.00000
+      39        29.2339        0.00000
+      40        29.2339        0.00000
+      41        29.2339        0.00000
+      42        29.4154        0.00000
+      43        29.4154        0.00000
+      44        29.4155        0.00000
+      45        35.3354        0.00000
+      46        35.3355        0.00000
+      47        36.5789        0.00000
+      48        36.5789        0.00000
+      49        40.4434        0.00000
+      50        41.3886        0.00000
+      51        43.5577        0.00000
+      52        43.5578        0.00000
+
+
+
+------------------------------------------------------------------------------------------
+ TOTAL-FORCE (eV/Angstrom)                                                                
+------------------------------------------------------------------------------------------
+                       Fe1        -0.0000234480         0.0000848730         0.0003959639 
+                       Fe2         0.0000234480        -0.0000848730        -0.0003959639 
+------------------------------------------------------------------------------------------
+
+
+ Relaxation is not converged yet!
+DIRECT COORDINATES
+    atom                   x                   y                   z     mag                  vx                  vy                  vz
+taud_Fe1            0.9999995833        0.0000015084        0.0000070374  2.1651        0.0000000000        0.0000000000        0.0000000000
+taud_Fe2            0.5000004167        0.4999984916        0.4999929626  2.1651        0.0000000000        0.0000000000        0.0000000000
+
+
+
+ -------------------------------------------
+ STEP OF RELAXATION : 2
+ -------------------------------------------
+ Find the file, try to read charge from file.
+ read in fermi energy = 0.000000
+ Find the file, try to read charge from file.
+ read in fermi energy = 0.000000
+ Find the file, try to read charge from file.
+ read in fermi energy = 0.000000
+ Find the file, try to read charge from file.
+ read in fermi energy = 0.000000
+ NEW-OLD atomic charge density approx. for the potential !
+ DONE : INIT SCF Time : 4.144735 (SEC)
+
+
+ PW ALGORITHM --------------- ION=   2  ELEC=   1--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0.000000 ; where current threshold is: 0.000008 . 
+total magnetism (Bohr mag/cell)	2.460713	2.460629	2.460667
+       absolute magnetism (Bohr mag/cell) = 4.354773
+ Notice: Threshold on eigenvalues was too large.
+ hsover_error=0.320000 > DRHO=0.001904
+ Origin diag_ethr = 0.010000
+ New    diag_ethr = 0.000006
+total magnetism (Bohr mag/cell)	2.460685	2.460607	2.460642
+       absolute magnetism (Bohr mag/cell) = 4.361930
+
+ Density error is 0.001992966717
+                          Error Threshold = 0.000005950543
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6717345462      -6825.5941153720     
+ E_Harris       -501.6715923037      -6825.5921800627     
+ E_Fermi        1.4766962002         20.0914825374        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   2  ELEC=   2--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0.000000000000 ; where current threshold is: 0.000005950543 . 
+total magnetism (Bohr mag/cell)	2.454388903679	2.454380662451	2.454379655944
+       absolute magnetism (Bohr mag/cell) = 4.361912797650
+
+ Density error is 0.009228272161
+                          Error Threshold = 0.000006228021
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6713440630      -6825.5888025749     
+ E_Harris       -501.5133874565      -6823.4396926906     
+ E_Fermi        1.4801385565         20.1383181977        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   2  ELEC=   3--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0.000000000000 ; where current threshold is: 0.000006228021 . 
+total magnetism (Bohr mag/cell)	2.455337730187	2.455339212147	2.455339333866
+       absolute magnetism (Bohr mag/cell) = 4.362219771057
+
+ Density error is 0.002195963526
+                          Error Threshold = 0.000006228021
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6723554230      -6825.6025628342     
+ E_Harris       -501.6387445550      -6825.1452635146     
+ E_Fermi        1.4799798703         20.1361591613        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   2  ELEC=   4--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0.000000000000 ; where current threshold is: 0.000006228021 . 
+total magnetism (Bohr mag/cell)	2.455780448000	2.455781001768	2.455780765168
+       absolute magnetism (Bohr mag/cell) = 4.361708226902
+
+ Density error is 0.000005361548
+                          Error Threshold = 0.000006228021
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6724951355      -6825.6044637205     
+ E_KS(sigma->0) -501.6679025517      -6825.5419784114     
+ E_Harris       -501.6617290453      -6825.4579835487     
+ E_band         -27.8843141296       -379.3855569848      
+ E_one_elec     -203.5744655302      -2769.7726985160     
+ E_Hartree      123.7850811379       1684.1824308678      
+ E_xc           -71.4835967872       -972.5842298408      
+ E_Ewald        -350.4828661766      -4768.5640313736     
+ E_entropy(-TS) -0.0091851677        -0.1249706181        
+ E_descf        0.0000000000         0.0000000000         
+ E_exx          0.0000000000         0.0000000000         
+ E_Fermi        1.4799376237         20.1355843666        
+----------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Magnetic force (eV/uB)                                                                    
+-------------------------------------------------------------------------------------------
+                         Fe        -0.1673462642        -0.1673537756        -0.1673561712 
+                         Fe        -0.1683646747        -0.1683589722        -0.1683562492 
+-------------------------------------------------------------------------------------------
+
+
+-------------------------------------------------------------------------------------------
+Orbital Charge Analysis      Charge         Mag(x)         Mag(y)         Mag(z)
+-------------------------------------------------------------------------------------------
+Fe1                 
+                   s         1.1147         0.0019         0.0019         0.0019
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5877         1.2479         1.2479         1.2479
+                 Sum        13.6995         1.2501         1.2501         1.2500
+Fe2                 
+                   s         1.1148         0.0019         0.0019         0.0019
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5911         1.2480         1.2480         1.2480
+                 Sum        13.7029         1.2502         1.2502         1.2502
+-------------------------------------------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Total Magnetism (uB)                                                                      
+-------------------------------------------------------------------------------------------
+                         Fe         1.2500714313         1.2500616663         1.2500458747 
+                         Fe         1.2501576398         1.2501678047         1.2501834374 
+-------------------------------------------------------------------------------------------
+
+
+ charge density convergence is achieved
+ final etot is -6825.60446372048 eV
+ EFERMI = 20.13558436665 eV
+
+ STATE ENERGY(eV) AND OCCUPATIONS    NSPIN == 4
+ 1/1 kpoint (Cartesian) = 0.00000 0.00000 0.00000 (2517 pws)
+       1     -67.494313       1.000000
+       2     -67.340218       1.000000
+       3     -65.146260       1.000000
+       4     -64.972269       1.000000
+       5     -34.011284       1.000000
+       6     -34.011263       1.000000
+       7     -34.011242       1.000000
+       8     -33.673639       1.000000
+       9     -33.673617       1.000000
+      10     -33.673596       1.000000
+      11     -31.014754       1.000000
+      12     -31.014713       1.000000
+      13     -31.014689       1.000000
+      14     -30.647472       1.000000
+      15     -30.647431       1.000000
+      16     -30.647407       1.000000
+      17      10.202179       1.000000
+      18      10.967145       1.000000
+      19      14.534082       1.000000
+      20      14.534103       1.000000
+      21      16.670113       1.000000
+      22      16.670140       1.000000
+      23      17.413528       1.000000
+      24      17.413556       1.000000
+      25      17.413589       1.000000
+      26      18.850839       1.000000
+      27      18.850854       1.000000
+      28      19.969576       0.957785
+      29      19.969617       0.957746
+      30      19.969666       0.957700
+      31      20.082615       0.709038
+      32      20.082645       0.708930
+      33      20.082682       0.708801
+      34      21.999005       0.000000
+      35      21.999021       0.000000
+      36      22.978862       0.000000
+      37      22.978908       0.000000
+      38      22.978962       0.000000
+      39      29.262993       0.000000
+      40      29.263007       0.000000
+      41      29.263018       0.000000
+      42      29.450239       0.000000
+      43      29.450247       0.000000
+      44      29.450271       0.000000
+      45      35.322294       0.000000
+      46      35.322339       0.000000
+      47      36.677233       0.000000
+      48      36.677283       0.000000
+      49      40.233768       0.000000
+      50      41.594113       0.000000
+      51      43.613799       0.000000
+      52      43.613882       0.000000
+
+
+
+------------------------------------------------------------------------------------------
+ TOTAL-FORCE (eV/Angstrom)                                                                
+------------------------------------------------------------------------------------------
+                       Fe1         0.0000423260         0.0001601470         0.0005255426 
+                       Fe2        -0.0000423260        -0.0001601470        -0.0005255426 
+------------------------------------------------------------------------------------------
+
+
+ Relaxation is not converged yet!
+DIRECT COORDINATES
+    atom                   x                   y                   z     mag                  vx                  vy                  vz
+taud_Fe1            0.9999983331        0.0000060337        0.0000281496  2.1651        0.0000000000        0.0000000000        0.0000000000
+taud_Fe2            0.5000016669        0.4999939663        0.4999718504  2.1651        0.0000000000        0.0000000000        0.0000000000
+
+
+
+ -------------------------------------------
+ STEP OF RELAXATION : 3
+ -------------------------------------------
+ Find the file, try to read charge from file.
+ read in fermi energy = 0.000000
+ Find the file, try to read charge from file.
+ read in fermi energy = 0.000000
+ Find the file, try to read charge from file.
+ read in fermi energy = 0.000000
+ Find the file, try to read charge from file.
+ read in fermi energy = 0.000000
+ first order charge density extrapolation !
+ Find the file, try to read charge from file.
+ read in fermi energy = 0.000000
+ Find the file, try to read charge from file.
+ read in fermi energy = 0.000000
+ Find the file, try to read charge from file.
+ read in fermi energy = 0.000000
+ Find the file, try to read charge from file.
+ read in fermi energy = 0.000000
+ DONE : INIT SCF Time : 19.338131 (SEC)
+
+
+ PW ALGORITHM --------------- ION=   3  ELEC=   1--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0.000000 ; where current threshold is: 0.000006 . 
+total magnetism (Bohr mag/cell)	2.455075	2.455068	2.455069
+       absolute magnetism (Bohr mag/cell) = 4.365921
+ Notice: Threshold on eigenvalues was too large.
+ hsover_error=0.320000 > DRHO=0.002000
+ Origin diag_ethr = 0.010000
+ New    diag_ethr = 0.000006
+total magnetism (Bohr mag/cell)	2.455050	2.455043	2.455045
+       absolute magnetism (Bohr mag/cell) = 4.365458
+
+ Density error is 0.002011456982
+                          Error Threshold = 0.000006249033
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6717775158      -6825.5947000038     
+ E_Harris       -501.6716068292      -6825.5923776932     
+ E_Fermi        1.4833035949         20.1813807543        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   3  ELEC=   2--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0.000000000000 ; where current threshold is: 0.000006249033 . 
+total magnetism (Bohr mag/cell)	2.457174616872	2.457187849929	2.457184529753
+       absolute magnetism (Bohr mag/cell) = 4.361364469883
+
+ Density error is 0.008790489237
+                          Error Threshold = 0.000006285803
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6713261044      -6825.5885582359     
+ E_Harris       -501.8313917187      -6827.7663626437     
+ E_Fermi        1.4802224904         20.1394601766        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   3  ELEC=   3--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0.000000000000 ; where current threshold is: 0.000006285803 . 
+total magnetism (Bohr mag/cell)	2.455913724950	2.455916535345	2.455916133793
+       absolute magnetism (Bohr mag/cell) = 4.360083340583
+
+ Density error is 0.002354066573
+                          Error Threshold = 0.000006285803
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6723623430      -6825.6026569852     
+ E_Harris       -501.7081536771      -6826.0896230689     
+ E_Fermi        1.4800610576         20.1372637709        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   3  ELEC=   4--------------------------------
+Average iterative diagonalization steps for k-points 0 is: 0.000000000000 ; where current threshold is: 0.000006285803 . 
+total magnetism (Bohr mag/cell)	2.455552549274	2.455552935684	2.455553065202
+       absolute magnetism (Bohr mag/cell) = 4.360588456959
+
+ Density error is 0.000003562109
+                          Error Threshold = 0.000006285803
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.6725119610      -6825.6046926422     
+ E_KS(sigma->0) -501.6679202282      -6825.5422189132     
+ E_Harris       -501.6917485490      -6825.8664198503     
+ E_band         -27.8833131578       -379.3719380647      
+ E_one_elec     -203.5627195010      -2769.6128855894     
+ E_Hartree      123.7718909794       1684.0029695549      
+ E_xc           -71.4811134180       -972.5504418684      
+ E_Ewald        -350.4828655476      -4768.5640228156     
+ E_entropy(-TS) -0.0091834655        -0.1249474581        
+ E_descf        0.0000000000         0.0000000000         
+ E_exx          0.0000000000         0.0000000000         
+ E_Fermi        1.4799197855         20.1353416661        
+----------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Magnetic force (eV/uB)                                                                    
+-------------------------------------------------------------------------------------------
+                         Fe        -0.1657340600        -0.1657462694        -0.1657444988 
+                         Fe        -0.1661948902        -0.1661794752        -0.1661827215 
+-------------------------------------------------------------------------------------------
+
+
+-------------------------------------------------------------------------------------------
+Orbital Charge Analysis      Charge         Mag(x)         Mag(y)         Mag(z)
+-------------------------------------------------------------------------------------------
+Fe1                 
+                   s         1.1147         0.0019         0.0019         0.0019
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5891         1.2477         1.2476         1.2476
+                 Sum        13.7008         1.2498         1.2498         1.2498
+Fe2                 
+                   s         1.1147         0.0019         0.0019         0.0019
+                   p         5.9971         0.0002         0.0002         0.0002
+                   d         6.5897         1.2478         1.2479         1.2479
+                 Sum        13.7015         1.2500         1.2500         1.2500
+-------------------------------------------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Total Magnetism (uB)                                                                      
+-------------------------------------------------------------------------------------------
+                         Fe         1.2498499353         1.2497710829         1.2497831345 
+                         Fe         1.2499653291         1.2500441039         1.2500320770 
+-------------------------------------------------------------------------------------------
+
+
+ charge density convergence is achieved
+ final etot is -6825.60469264220 eV
+ EFERMI = 20.13534166609 eV
+
+ STATE ENERGY(eV) AND OCCUPATIONS    NSPIN == 4
+ 1/1 kpoint (Cartesian) = 0.00000 0.00000 0.00000 (2517 pws)
+       1     -67.494346       1.000000
+       2     -67.340195       1.000000
+       3     -65.142147       1.000000
+       4     -64.968232       1.000000
+       5     -34.009462       1.000000
+       6     -34.009434       1.000000
+       7     -34.009266       1.000000
+       8     -33.671810       1.000000
+       9     -33.671781       1.000000
+      10     -33.671615       1.000000
+      11     -31.015112       1.000000
+      12     -31.014434       1.000000
+      13     -31.014342       1.000000
+      14     -30.647876       1.000000
+      15     -30.647195       1.000000
+      16     -30.647103       1.000000
+      17      10.203611       1.000000
+      18      10.967020       1.000000
+      19      14.532886       1.000000
+      20      14.532987       1.000000
+      21      16.668995       1.000000
+      22      16.669002       1.000000
+      23      17.413224       1.000000
+      24      17.413591       1.000000
+      25      17.413900       1.000000
+      26      18.850000       1.000000
+      27      18.850124       1.000000
+      28      19.968700       0.958374
+      29      19.969266       0.957847
+      30      19.969947       0.957208
+      31      20.082043       0.710209
+      32      20.082447       0.708773
+      33      20.082779       0.707589
+      34      21.997966       0.000000
+      35      21.997988       0.000000
+      36      22.976716       0.000000
+      37      22.977326       0.000000
+      38      22.978087       0.000000
+      39      29.262086       0.000000
+      40      29.262096       0.000000
+      41      29.262190       0.000000
+      42      29.456009       0.000000
+      43      29.456271       0.000000
+      44      29.456319       0.000000
+      45      35.320363       0.000000
+      46      35.320446       0.000000
+      47      36.677678       0.000000
+      48      36.677685       0.000000
+      49      40.231928       0.000000
+      50      41.593535       0.000000
+      51      43.611156       0.000000
+      52      43.611230       0.000000
+
+
+
+------------------------------------------------------------------------------------------
+ TOTAL-FORCE (eV/Angstrom)                                                                
+------------------------------------------------------------------------------------------
+                       Fe1         0.0000917195        -0.0005088150        -0.0021920644 
+                       Fe2        -0.0000917195         0.0005088150         0.0021920644 
+------------------------------------------------------------------------------------------
+
+
+ Relaxation is not converged yet!
+DIRECT COORDINATES
+    atom                   x                   y                   z     mag                  vx                  vy                  vz
+taud_Fe1            0.9999984177        0.0000055644        0.0000261275  2.1651        0.0000000000        0.0000000000        0.0000000000
+taud_Fe2            0.5000015823        0.4999944356        0.4999738725  2.1651        0.0000000000        0.0000000000        0.0000000000
+
+
+
+
+ --------------------------------------------
+ !FINAL_ETOT_IS -6825.6046926421959142 eV
+ --------------------------------------------
+
+
+TIME STATISTICS
+-----------------------------------------------------------------------------
+    CLASS_NAME                NAME             TIME/s  CALLS   AVG/s  PER/%  
+-----------------------------------------------------------------------------
+                   total                       38.86  19       2.05   100.00 
+ Driver            reading                     0.02   1        0.02   0.05   
+ Input_Conv        Convert                     0.00   1        0.00   0.00   
+ Driver            driver_line                 38.84  1        38.84  99.95  
+ UnitCell          check_tau                   0.00   1        0.00   0.00   
+ PW_Basis_Sup      setuptransform              0.00   1        0.00   0.01   
+ PW_Basis_Sup      distributeg                 0.00   1        0.00   0.00   
+ mymath            heapsort                    0.00   6        0.00   0.01   
+ PW_Basis_K        setuptransform              0.00   1        0.00   0.00   
+ PW_Basis_K        distributeg                 0.00   1        0.00   0.00   
+ PW_Basis          setup_struc_factor          0.00   3        0.00   0.01   
+ ppcell_vnl        init                        0.00   1        0.00   0.01   
+ ppcell_vl         init_vloc                   0.01   1        0.01   0.01   
+ ppcell_vnl        init_vnl                    0.03   1        0.03   0.08   
+ WF_atomic         init_at_1                   0.17   1        0.17   0.44   
+ wavefunc          wfcinit                     0.00   1        0.00   0.00   
+ Ions              opt_ions                    38.53  1        38.53  99.14  
+ ESolver_KS_PW     runner                      38.20  3        12.73  98.28  
+ H_Ewald_pw        compute_ewald               0.00   3        0.00   0.01   
+ Charge            set_rho_core                0.02   3        0.01   0.06   
+ PW_Basis_Sup      recip2real                  0.22   369      0.00   0.57   
+ PW_Basis_Sup      gathers_scatterp            0.03   369      0.00   0.08   
+ Charge            atomic_rho                  0.07   6        0.01   0.18   
+ Potential         init_pot                    0.21   3        0.07   0.54   
+ Potential         update_from_charge          1.03   15       0.07   2.64   
+ Potential         cal_fixed_v                 0.00   3        0.00   0.01   
+ PotLocal          cal_fixed_v                 0.00   3        0.00   0.01   
+ Potential         cal_v_eff                   1.02   15       0.07   2.62   
+ H_Hartree_pw      v_hartree                   0.02   15       0.00   0.06   
+ PW_Basis_Sup      real2recip                  0.25   486      0.00   0.64   
+ PW_Basis_Sup      gatherp_scatters            0.02   486      0.00   0.06   
+ PotXC             cal_v_eff                   0.99   15       0.07   2.54   
+ XC_Functional     v_xc                        1.18   18       0.07   3.04   
+ Potential         interpolate_vrs             0.01   15       0.00   0.01   
+ OnsiteProj        cubspl_tabulate             0.09   1        0.09   0.24   
+ Charge_Mixing     init_mixing                 0.00   3        0.00   0.01   
+ ESolver_KS_PW     hamilt2density              7.41   15       0.49   19.07  
+ HSolverPW         solve                       11.45  23       0.50   29.46  
+ pp_cell_vnl       getvnl                      0.57   213      0.00   1.46   
+ Structure_Factor  get_sk                      0.06   221      0.00   0.16   
+ OnsiteProj        getvnl                      0.00   213      0.00   0.00   
+ OnsiteProj        tabulate_atomic             0.00   239      0.00   0.00   
+ WF_atomic         atomic_wfc                  0.01   1        0.01   0.01   
+ DiagoIterAssist   diagH_subspace_init         0.14   1        0.14   0.35   
+ Operator          hPsi                        31.99  2952     0.01   82.32  
+ Operator          EkineticPW                  0.15   2952     0.00   0.39   
+ Operator          VeffPW                      28.61  2952     0.01   73.61  
+ PW_Basis_K        recip2real                  8.33   28782    0.00   21.42  
+ PW_Basis_K        gathers_scatterp            1.23   28782    0.00   3.16   
+ PW_Basis_K        real2recip                  7.66   27222    0.00   19.72  
+ PW_Basis_K        gatherp_scatters            0.58   27222    0.00   1.49   
+ Operator          NonlocalPW                  2.14   2952     0.00   5.51   
+ Nonlocal          add_nonlocal_pp             1.30   2952     0.00   3.35   
+ Operator          OnsiteProjPW                1.09   2952     0.00   2.79   
+ OnsiteProj        overlap                     0.55   2978     0.00   1.42   
+ FS_Nonlocal_tools cal_becp                    0.56   2984     0.00   1.43   
+ OnsiteProj        add_onsite_proj             0.47   2952     0.00   1.20   
+ DiagoIterAssist   diagH_LAPACK                0.23   209      0.00   0.59   
+ DiagoCG           diag_once                   8.26   23       0.36   21.24  
+ DiagoCG_New       spsi_func                   0.07   5486     0.00   0.17   
+ DiagoCG_New       hpsi_func                   7.20   2743     0.00   18.52  
+ ElecStatePW       psiToRho                    0.63   15       0.04   1.62   
+ Charge_Mixing     get_drho                    0.07   15       0.00   0.19   
+ Charge_Mixing     inner_product_recip_rho     0.00   15       0.00   0.01   
+ Charge            mix_rho                     0.05   9        0.01   0.14   
+ Charge            Broyden_mixing              0.01   9        0.00   0.03   
+ DiagoIterAssist   diagH_subspace              2.30   18       0.13   5.92   
+ Charge_Mixing     inner_product_recip_hartree 0.00   18       0.00   0.01   
+ OnsiteProj        cal_occupation              0.00   3        0.00   0.01   
+ Forces            cal_force_loc               0.01   3        0.00   0.02   
+ Forces            cal_force_ew                0.00   3        0.00   0.01   
+ Forces            cal_force_nl                0.03   3        0.01   0.07   
+ FS_Nonlocal_tools cal_dbecp_f                 0.03   18       0.00   0.07   
+ Forces            cal_force_onsite            0.01   3        0.00   0.04   
+ Forces            cal_force_cc                0.22   3        0.07   0.57   
+ Forces            cal_force_scc               0.02   3        0.01   0.06   
+ SpinConstrain     cal_mw_from_lambda          28.58  198      0.14   73.53  
+ DiagoIterAssist   diag_responce               23.97  190      0.13   61.69  
+ ModuleIO          write_istate_info           0.01   1        0.01   0.02   
+-----------------------------------------------------------------------------
+
+
+ NAME-------------------------|MEMORY(MB)--------
+                         total        24.4333
+                        Psi_PW         3.9943
+                 DiagSub::temp         3.9943
+                     FFT::grid         1.4238
+                      Chg::rho         1.4238
+                 Chg::rho_save         1.4238
+                     Pot::veff         1.4238
+              Pot::veff_smooth         1.4238
+                      VNL::vkb         1.3826
+ -------------   < 1.0 MB has been ignored ----------------
+ ----------------------------------------------------------
+
+ Start  Time  : Fri Sep  6 09:29:43 2024
+ Finish Time  : Fri Sep  6 09:30:22 2024
+ Total  Time  : 0 h 0 mins 39 secs 
diff --git a/tests/abacus.spin/OUT.ABACUS/running_scf.log b/tests/abacus.spin/OUT.ABACUS/running_scf.log
new file mode 100644
index 00000000..2e6e98cc
--- /dev/null
+++ b/tests/abacus.spin/OUT.ABACUS/running_scf.log
@@ -0,0 +1,565 @@
+                                                                                     
+                              ABACUS v3.7.1
+
+               Atomic-orbital Based Ab-initio Computation at UStc                    
+
+                     Website: http://abacus.ustc.edu.cn/                             
+               Documentation: https://abacus.deepmodeling.com/                       
+                  Repository: https://github.com/abacusmodeling/abacus-develop       
+                              https://github.com/deepmodeling/abacus-develop         
+                      Commit: 1a7a3158b (Fri Aug 23 00:52:25 2024 +0800)
+
+    Start Time is Fri Aug 23 16:06:02 2024
+                                                                                     
+ ------------------------------------------------------------------------------------
+
+ READING GENERAL INFORMATION
+                           global_out_dir = OUT.ABACUS/
+                           global_in_card = INPUT
+                               pseudo_dir = ./
+                              orbital_dir = ./
+                                    DRANK = 1
+                                    DSIZE = 16
+                                   DCOLOR = 1
+                                    GRANK = 1
+                                    GSIZE = 1
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Reading atom information in unitcell:                              |
+ | From the input file and the structure file we know the number of   |
+ | different elments in this unitcell, then we list the detail        |
+ | information for each element, especially the zeta and polar atomic |
+ | orbital number for each element. The total atom number is counted. |
+ | We calculate the nearest atom distance for each atom and show the  |
+ | Cartesian and Direct coordinates for each atom. We list the file   |
+ | address for atomic orbitals. The volume and the lattice vectors    |
+ | in real and reciprocal space is also shown.                        |
+ |                                                                    |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+ READING UNITCELL INFORMATION
+                                    ntype = 1
+                  lattice constant (Bohr) = 1.88028
+              lattice constant (Angstrom) = 0.995
+
+ READING ATOM TYPE 1
+                               atom label = Fe
+                      L=0, number of zeta = 4
+                      L=1, number of zeta = 2
+                      L=2, number of zeta = 2
+                      L=3, number of zeta = 1
+             number of atom for this type = 2
+               magnetization of element 1 = [ 0, 0, 2.4 ]
+
+                        TOTAL ATOM NUMBER = 2
+DIRECT COORDINATES
+    atom                   x                   y                   z     mag                  vx                  vy                  vz
+taud_Fe1            0.0500000000        0.1000000000        0.1500000000  2.4000        0.0000000000        0.0000000000        0.0000000000
+taud_Fe2            0.5000000000        0.5000000000        0.5000000000  2.4000        0.0000000000        0.0000000000        0.0000000000
+
+
+
+                          Volume (Bohr^3) = 150.259
+                             Volume (A^3) = 22.266
+
+ Lattice vectors: (Cartesian coordinate: in unit of a_0)
+             +2.82743                  +0                  +0
+                   +0            +2.82743                  +0
+                   +0                  +0            +2.82743
+ Reciprocal vectors: (Cartesian coordinate: in unit of 2 pi/a_0)
+            +0.353679                  -0                  +0
+                   -0           +0.353679                  -0
+                   +0                  -0           +0.353679
+ The esolver type has been set to : ksdft_pw
+
+ RUNNING WITH DEVICE  : CPU / Intel(R) Xeon(R) Platinum 8255C CPU @ 2.50GHz
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Reading pseudopotentials files:                                    |
+ | The pseudopotential file is in UPF format. The 'NC' indicates that |
+ | the type of pseudopotential is 'norm conserving'. Functional of    |
+ | exchange and correlation is decided by 4 given parameters in UPF   |
+ | file.  We also read in the 'core correction' if there exists.      |
+ | Also we can read the valence electrons number and the maximal      |
+ | angular momentum used in this pseudopotential. We also read in the |
+ | trail wave function, trail atomic density and local-pseudopotential|
+ | on logrithmic grid. The non-local pseudopotential projector is also|
+ | read in if there is any.                                           |
+ |                                                                    |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+                PAO radial cut off (Bohr) = 15
+
+ Read in pseudopotential file is Fe.upf
+                     pseudopotential type = NC
+          exchange-correlation functional = PBE
+                 nonlocal core correction = 1
+                        valence electrons = 16
+                                     lmax = 2
+                           number of zeta = 6
+                     number of projectors = 10
+                           L of projector = 0
+                           L of projector = 0
+                           L of projector = 1
+                           L of projector = 1
+                           L of projector = 1
+                           L of projector = 1
+                           L of projector = 2
+                           L of projector = 2
+                           L of projector = 2
+                           L of projector = 2
+     initial pseudo atomic orbital number = 40
+                                   NLOCAL = 108
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ Warning: the number of valence electrons in pseudopotential > 8 for Fe: [Ar] 3d6 4s2
+ Pseudopotentials with additional electrons can yield (more) accurate outcomes, but may be less efficient.
+ If you're confident that your chosen pseudopotential is appropriate, you can safely ignore this warning.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+                  
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Setup plane waves of charge/potential:                             |
+ | Use the energy cutoff and the lattice vectors to generate the      |
+ | dimensions of FFT grid. The number of FFT grid on each processor   |
+ | is 'nrxx'. The number of plane wave basis in reciprocal space is   |
+ | different for charege/potential and wave functions. We also set    |
+ | the 'sticks' for the parallel of FFT. The number of plane waves    |
+ | is 'npw' in each processor.                                        |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+
+ SETUP THE PLANE WAVE BASIS
+ energy cutoff for charge/potential (unit:Ry) = 320
+            fft grid for charge/potential = [ 32, 32, 32 ]
+                        fft grid division = [ 1, 1, 1 ]
+        big fft grid for charge/potential = [ 32, 32, 32 ]
+                                     nbxx = 2048
+                                     nrxx = 2048
+
+ SETUP PLANE WAVES FOR CHARGE/POTENTIAL
+                    number of plane waves = 14531
+                         number of sticks = 725
+
+ PARALLEL PW FOR CHARGE/POTENTIAL
+     PROC   COLUMNS(POT)             PW
+        1             45            909
+        2             45            909
+        3             46            908
+        4             46            908
+        5             45            909
+        6             45            909
+        7             45            909
+        8             45            909
+        9             45            909
+       10             46            908
+       11             46            908
+       12             46            908
+       13             45            907
+       14             45            907
+       15             45            907
+       16             45            907
+ --------------- sum -------------------
+       16            725          14531
+                            number of |g| = 165
+                                  max |g| = 28.6453
+                                  min |g| = 0.500354
+
+----------- Double Check Mixing Parameters Begin ------------
+mixing_type: broyden
+mixing_beta: 0.4
+mixing_gg0: 1
+mixing_gg0_min: 0.1
+mixing_beta_mag: 1.6
+mixing_gg0_mag: 0
+mixing_ndim: 10
+----------- Double Check Mixing Parameters End ------------
+
+ SETUP THE ELECTRONS NUMBER
+            electron number of element Fe = 16
+      total electron number of element Fe = 32
+            AUTOSET number of electrons:  = 32
+ DONE : SETUP UNITCELL Time : 0.316237 (SEC)
+
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Setup K-points                                                     |
+ | We setup the k-points according to input parameters.               |
+ | The reduced k-points are set according to symmetry operations.     |
+ | We treat the spin as another set of k-points.                      |
+ |                                                                    |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+
+ SETUP K-POINTS
+                                    nspin = 4
+                   Input type of k points = Monkhorst-Pack(Gamma)
+                                   nkstot = 216
+K-POINTS DIRECT COORDINATES
+ KPOINTS    DIRECT_X    DIRECT_Y    DIRECT_Z  WEIGHT
+
+ DONE : INIT K-POINTS Time : 0.376998 (SEC)
+
+
+
+
+
+ >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+ |                                                                    |
+ | Setup plane waves of wave functions:                               |
+ | Use the energy cutoff and the lattice vectors to generate the      |
+ | dimensions of FFT grid. The number of FFT grid on each processor   |
+ | is 'nrxx'. The number of plane wave basis in reciprocal space is   |
+ | different for charege/potential and wave functions. We also set    |
+ | the 'sticks' for the parallel of FFT. The number of plane wave of  |
+ | each k-point is 'npwk[ik]' in each processor                       |
+ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+
+
+
+ SETUP PLANE WAVES FOR WAVE FUNCTIONS
+     energy cutoff for wavefunc (unit:Ry) = 80
+              fft grid for wave functions = [ 32, 32, 32 ]
+                    number of plane waves = 3071
+                         number of sticks = 253
+
+ PARALLEL PW FOR WAVE FUNCTIONS
+     PROC   COLUMNS(POT)             PW
+        1             16            192
+        2             16            192
+        3             16            192
+        4             16            192
+        5             15            191
+        6             15            191
+        7             16            194
+        8             16            192
+        9             16            192
+       10             16            192
+       11             16            192
+       12             16            192
+       13             16            192
+       14             16            192
+       15             16            192
+       16             15            191
+ --------------- sum -------------------
+       16            253           3071
+ DONE : INIT PLANEWAVE Time : 0.380345 (SEC)
+
+                           occupied bands = 32
+                                   NBANDS = 52
+
+ SETUP NONLOCAL PSEUDOPOTENTIALS IN PLANE WAVE BASIS
+ Fe non-local projectors:
+ projector 1 L=0
+ projector 2 L=0
+ projector 3 L=1
+ projector 4 L=1
+ projector 5 L=1
+ projector 6 L=1
+ projector 7 L=2
+ projector 8 L=2
+ projector 9 L=2
+ projector 10 L=2
+      TOTAL NUMBER OF NONLOCAL PROJECTORS = 68
+ DONE : LOCAL POTENTIAL Time : 0.40963 (SEC)
+
+
+ Init Non-Local PseudoPotential table : 
+ Init Non-Local-Pseudopotential done.
+ DONE : NON-LOCAL POTENTIAL Time : 0.443773 (SEC)
+
+                                     npwx = 128
+
+ Warning_Memory_Consuming allocated:  Psi_PW 43.875 MB
+
+ Make real space PAO into reciprocal space.
+       max mesh points in Pseudopotential = 1425
+     dq(describe PAO in reciprocal space) = 0.01
+                                    max q = 1078
+
+ number of pseudo atomic orbitals for Fe is 6
+ DONE : INIT BASIS Time : 0.620862 (SEC)
+
+
+ -------------------------------------------
+ SELF-CONSISTENT
+ -------------------------------------------
+                                 init_chg = atomic
+ DONE : INIT SCF Time : 0.761759 (SEC)
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   1--------------------------------
+total magnetism (Bohr mag/cell)	-8.56154e-05	-3.16838e-05	3.87672
+       absolute magnetism (Bohr mag/cell) = 3.90219
+ Notice: Threshold on eigenvalues was too large.
+ hsover_error=0.32 > DRHO=0.0810864
+ Origin diag_ethr = 0.01
+ New    diag_ethr = 0.000253395
+total magnetism (Bohr mag/cell)	-9.09654e-05	-3.00029e-05	3.87658
+       absolute magnetism (Bohr mag/cell) = 3.90286
+
+ Density error is 0.0818013187196
+                          Error Threshold = 0.000253394954616
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.1638820263      -6818.6844273569     
+ E_Harris       -501.1650591987      -6818.7004436094     
+ E_Fermi        1.4203911993         19.3254136999        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   2--------------------------------
+total magnetism (Bohr mag/cell)	-2.92622585913e-05	-0.000266812474323	3.65800660509
+       absolute magnetism (Bohr mag/cell) = 3.88387266047
+
+ Density error is 0.0165562104235
+                          Error Threshold = 0.000255629120999
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.1785311471      -6818.8837388713     
+ E_Harris       -501.4729927600      -6822.8900946492     
+ E_Fermi        1.4123735299         19.2163277107        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   3--------------------------------
+total magnetism (Bohr mag/cell)	-1.41288005953e-05	-0.000388528787066	3.72548472333
+       absolute magnetism (Bohr mag/cell) = 3.91023806289
+
+ Density error is 0.00318633115585
+                          Error Threshold = 5.17381575736e-05
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.1785047719      -6818.8833800180     
+ E_Harris       -501.0742053019      -6817.4643129270     
+ E_Fermi        1.4117399370         19.2077072372        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   4--------------------------------
+total magnetism (Bohr mag/cell)	2.26526732328e-05	-0.000450436470697	3.73775099313
+       absolute magnetism (Bohr mag/cell) = 3.92308219614
+
+ Density error is 0.000165938860835
+                          Error Threshold = 9.95728486202e-06
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.1804562269      -6818.9099309251     
+ E_Harris       -501.0912756169      -6817.6965664782     
+ E_Fermi        1.4131895976         19.2274308815        
+----------------------------------------------------------
+
+
+ PW ALGORITHM --------------- ION=   1  ELEC=   5--------------------------------
+
+total magnetism (Bohr mag/cell)	-0.000682480084963	-0.000407948602903	4.47635324671
+       absolute magnetism (Bohr mag/cell) = 4.82248432181
+
+ Density error is 6.61858307885e-09
+                          Error Threshold = 5.40730613116e-10
+----------------------------------------------------------
+     Energy           Rydberg                 eV          
+----------------------------------------------------------
+ E_KohnSham     -501.1664531630      -6818.7194094666     
+ E_KS(sigma->0) -501.1658847659      -6818.7116760274     
+ E_Harris       -501.1680065331      -6818.7405441510     
+ E_band         -30.1701507306       -410.4859594555      
+ E_one_elec     -214.9321986489      -2924.3025852934     
+ E_Hartree      128.2299640744       1744.6581657467      
+ E_xc           -71.3503189041       -970.7708912124      
+ E_Ewald        -343.2422281761      -4670.0500974110     
+ E_entropy(-TS) -0.0011367942        -0.0154668785        
+ E_descf        0.0000000000         0.0000000000         
+ E_exx          0.0000000000         0.0000000000         
+ E_Fermi        1.4108073605         19.1950188828        
+----------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Total Magnetism (uB)                                                                      
+-------------------------------------------------------------------------------------------
+                         Fe        -0.0000002724        -0.0000001728         2.4000001004 
+                         Fe        -0.0000003180        -0.0000002299         2.3999994597 
+-------------------------------------------------------------------------------------------
+
+-------------------------------------------------------------------------------------------
+ Magnetic force (eV/uB)                                                                    
+-------------------------------------------------------------------------------------------
+                         Fe        -0.0000175013        -0.0000418680        -0.3669618965 
+                         Fe        -0.0000161517        -0.0000195198        -0.3669821632 
+-------------------------------------------------------------------------------------------
+
+Charge and Mag of Atom 0
+ Orbital 1 Charge: 1.99985926204 Mag: -8.50835272933e-09 -8.84955876115e-09 2.84869655853e-06
+ Orbital 2 Charge: 5.99701367096 Mag: -2.18088393737e-07 -2.40618119919e-07 0.000105269162551
+ Orbital 3 Charge: 6.37379729477 Mag: -4.581340875e-08 7.66548679323e-08 2.39989198254
+Sum of atom 0 is: 14.3706702278 -2.72410155216e-07 -1.72812810748e-07 2.4000001004
+Charge and Mag of Atom 1
+ Orbital 1 Charge: 1.99985925962 Mag: -6.91586723071e-09 -8.93979594505e-09 2.85090960195e-06
+ Orbital 2 Charge: 5.99701367924 Mag: -2.16539560943e-07 -2.55979271358e-07 0.000105265428294
+ Orbital 3 Charge: 6.37381969542 Mag: -9.45758719447e-08 3.50118887944e-08 2.3998913434
+Sum of atom 1 is: 14.3706926343 -3.18031300118e-07 -2.29907178509e-07 2.39999945974
+
+ charge density convergence is achieved
+ final etot is -6818.7194095 eV
+ EFERMI = 19.195018883 eV
+
+------------------------------------------------------------------------------------------
+ TOTAL-FORCE (eV/Angstrom)                                                                
+------------------------------------------------------------------------------------------
+                       Fe1        -0.0000234480         0.0000848730         0.0003959639 
+                       Fe2         0.0000234480        -0.0000848730        -0.0003959639 
+------------------------------------------------------------------------------------------
+
+ --------------------------------------------
+ !FINAL_ETOT_IS -6818.719409466637 eV
+ --------------------------------------------
+
+
+TIME STATISTICS
+----------------------------------------------------------------------------
+    CLASS_NAME               NAME             TIME/s  CALLS   AVG/s  PER/%  
+----------------------------------------------------------------------------
+                  total                       563.56 15       37.57  100.00 
+ Driver           reading                     0.11   1        0.11   0.02   
+ Input_Conv       Convert                     0.00   1        0.00   0.00   
+ Driver           driver_line                 563.45 1        563.45 99.98  
+ UnitCell         check_tau                   0.00   1        0.00   0.00   
+ PW_Basis_Sup     setuptransform              0.06   1        0.06   0.01   
+ PW_Basis_Sup     distributeg                 0.00   1        0.00   0.00   
+ mymath           heapsort                    0.00   3        0.00   0.00   
+ PW_Basis_K       setuptransform              0.00   1        0.00   0.00   
+ PW_Basis_K       distributeg                 0.00   1        0.00   0.00   
+ PW_Basis         setup_struc_factor          0.00   1        0.00   0.00   
+ ppcell_vnl       init                        0.00   1        0.00   0.00   
+ ppcell_vl        init_vloc                   0.02   1        0.02   0.00   
+ ppcell_vnl       init_vnl                    0.03   1        0.03   0.01   
+ WF_atomic        init_at_1                   0.18   1        0.18   0.03   
+ wavefunc         wfcinit                     0.00   1        0.00   0.00   
+ Ions             opt_ions                    562.87 1        562.87 99.88  
+ ESolver_KS_PW    runner                      562.87 1        562.87 99.88  
+ H_Ewald_pw       compute_ewald               0.00   1        0.00   0.00   
+ Charge           set_rho_core                0.01   1        0.01   0.00   
+ PW_Basis_Sup     recip2real                  0.03   202      0.00   0.00   
+ PW_Basis_Sup     gathers_scatterp            0.01   202      0.00   0.00   
+ Charge           atomic_rho                  0.00   1        0.00   0.00   
+ Potential        init_pot                    0.01   1        0.01   0.00   
+ Potential        update_from_charge          0.07   13       0.01   0.01   
+ Potential        cal_fixed_v                 0.00   1        0.00   0.00   
+ PotLocal         cal_fixed_v                 0.00   1        0.00   0.00   
+ Potential        cal_v_eff                   0.06   13       0.00   0.01   
+ H_Hartree_pw     v_hartree                   0.00   13       0.00   0.00   
+ PW_Basis_Sup     real2recip                  0.02   247      0.00   0.00   
+ PW_Basis_Sup     gatherp_scatters            0.02   247      0.00   0.00   
+ PotXC            cal_v_eff                   0.06   13       0.00   0.01   
+ XC_Functional    v_xc                        0.06   13       0.00   0.01   
+ Potential        interpolate_vrs             0.00   13       0.00   0.00   
+ OnsiteProj       init_k_stage0               0.08   1        0.08   0.01   
+ Charge_Mixing    init_mixing                 0.00   2        0.00   0.00   
+ ESolver_KS_PW    hamilt2density              184.77 13       14.21  32.79  
+ HSolverPW        solve                       287.77 21       13.70  51.06  
+ pp_cell_vnl      getvnl                      4.21   21384    0.00   0.75   
+ Structure_Factor get_sk                      2.26   492264   0.00   0.40   
+ OnsiteProj       getvnl                      3.45   21384    0.00   0.61   
+ OnsiteProj       init_k                      4.11   26136    0.00   0.73   
+ OnsiteProj       init_k_stage1               1.73   26136    0.00   0.31   
+ OnsiteProj       init_k_stage2               2.37   26136    0.00   0.42   
+ WF_atomic        atomic_wfc                  0.10   216      0.00   0.02   
+ DiagoDavid       diag_mock                   259.79 4536     0.06   46.10  
+ DiagoDavid       first                       83.93  4536     0.02   14.89  
+ David            spsi_func                   1.10   1075598  0.00   0.20   
+ DiagoDavid       SchmidtOrth                 14.54  537799   0.00   2.58   
+ David            hpsi_func                   149.60 14979    0.01   26.55  
+ Operator         hPsi                        396.41 31827    0.01   70.34  
+ Operator         EkineticPW                  2.03   31827    0.00   0.36   
+ Operator         VeffPW                      344.42 31827    0.01   61.12  
+ PW_Basis_K       recip2real                  183.20 3119822  0.00   32.51  
+ PW_Basis_K       gathers_scatterp            160.47 3119822  0.00   28.47  
+ PW_Basis_K       real2recip                  155.75 2827790  0.00   27.64  
+ PW_Basis_K       gatherp_scatters            136.28 2827790  0.00   24.18  
+ Operator         NonlocalPW                  42.43  31827    0.00   7.53   
+ Nonlocal         add_nonlocal_pp             34.57  31827    0.00   6.13   
+ Operator         OnsiteProjPW                7.38   31827    0.00   1.31   
+ OnsiteProj       add_onsite_proj             7.35   31827    0.00   1.30   
+ OnsiteProj       overlap                     5.91   36579    0.00   1.05   
+ DiagoDavid       cal_elem                    35.38  14979    0.00   6.28   
+ DiagoDavid       diag_zhegvx                 51.18  14979    0.00   9.08   
+ DiagoDavid       cal_grad                    101.08 10443    0.01   17.94  
+ DiagoDavid       check_update                0.01   10443    0.00   0.00   
+ DiagoDavid       last                        1.75   4536     0.00   0.31   
+ ElecStatePW      psiToRho                    18.60  13       1.43   3.30   
+ Charge_Mixing    get_drho                    0.01   13       0.00   0.00   
+ Charge_Mixing    inner_product_recip_rho     0.00   13       0.00   0.00   
+ Charge           mix_rho                     0.01   10       0.00   0.00   
+ Charge           Broyden_mixing              0.01   10       0.00   0.00   
+ Charge_Mixing    inner_product_recip_hartree 0.00   48       0.00   0.00   
+ SpinConstrain    cal_mw_from_lambda          377.05 86       4.38   66.90  
+ DiagoIterAssist  diag_responce               266.63 16848    0.02   47.31  
+ DiagoIterAssist  diagH_LAPACK                12.16  16848    0.00   2.16   
+ OnsiteProj       cal_occupation              0.06   1        0.06   0.01   
+ ModuleIO         write_istate_info           0.07   1        0.07   0.01   
+----------------------------------------------------------------------------
+
+
+ NAME-------------------------|MEMORY(MB)--------
+                         total          786.3
+                        Psi_PW          668.8
+                    DAV::basis          12.38
+                     DAV::hpsi          12.38
+                     DAV::spsi          12.38
+                      DAV::hcc          10.56
+                      DAV::scc          10.56
+                      DAV::vcc          10.56
+                      MTransOp          10.56
+                  PW_B_K::gcar          9.645
+                   PW_B_K::gk2          3.215
+                 DiagSub::temp          3.096
+                      VNL::tab          2.632
+                      VNL::vkb          2.024
+            Nonlocal<PW>::becp          1.727
+              Nonlocal<PW>::ps          1.727
+                   VNL::tab_at          1.579
+                     FFT::grid          1.000
+                      Chg::rho          1.000
+                 Chg::rho_save          1.000
+                     Pot::veff          1.000
+              Pot::veff_smooth          1.000
+ -------------   < 1.0 MB has been ignored ----------------
+ ----------------------------------------------------------
+
+ Start  Time  : Fri Aug 23 16:06:02 2024
+ Finish Time  : Fri Aug 23 16:15:04 2024
+ Total  Time  : 0 h 9 mins 2 secs 
diff --git a/tests/abacus.spin/STRU b/tests/abacus.spin/STRU
new file mode 100644
index 00000000..6ec77f1a
--- /dev/null
+++ b/tests/abacus.spin/STRU
@@ -0,0 +1,21 @@
+ATOMIC_SPECIES
+Fe 55.845 Fe.upf
+
+NUMERICAL_ORBITAL
+Fe_gga_10au_200.0Ry_4s2p2d1f.orb
+
+LATTICE_CONSTANT
+1.880277359
+LATTICE_VECTORS
+    2.8274254848     0.0000000000     0.0000000000 #latvec1
+    0.0000000000     2.8274254848     0.0000000000 #latvec2
+    0.0000000000     0.0000000000     2.8274254848 #latvec3
+
+ATOMIC_POSITIONS
+Direct
+
+Fe #label
+1 #magnetism
+2 #number of atoms
+    0.0500000000     0.100000000     0.1500000000 mag 0 0 2.4 sc 1 1 1
+    0.5000000000     0.5000000000     0.5000000000 mag 0 0 2.4 sc 1 1 1
diff --git a/tests/test_abacus_spin.py b/tests/test_abacus_spin.py
new file mode 100644
index 00000000..df8ef7d0
--- /dev/null
+++ b/tests/test_abacus_spin.py
@@ -0,0 +1,157 @@
+from __future__ import annotations
+
+import os
+import shutil
+import unittest
+
+import numpy as np
+from context import dpdata
+
+
+class TestABACUSSpin(unittest.TestCase):
+    def setUp(self):
+        self.dump_path = "abacus.spin/dump"
+        os.makedirs(self.dump_path, exist_ok=True)
+
+    def tearDown(self):
+        if os.path.isdir(self.dump_path):
+            shutil.rmtree(self.dump_path)
+
+    def test_scf(self):
+        os.system("cp abacus.spin/INPUT.scf abacus.spin/INPUT")
+        mysys = dpdata.LabeledSystem("abacus.spin", fmt="abacus/scf")
+        data = mysys.data
+        self.assertAlmostEqual(data["energies"][0], -6818.719409466637)
+        np.testing.assert_almost_equal(
+            data["spins"][0],
+            [
+                [-0.0000002724, -0.0000001728, 2.4000001004],
+                [-0.0000003180, -0.0000002299, 2.3999994597],
+            ],
+            decimal=8,
+        )
+        np.testing.assert_almost_equal(
+            data["mag_forces"][0],
+            [
+                [-0.0000175013, -0.0000418680, -0.3669618965],
+                [-0.0000161517, -0.0000195198, -0.3669821632],
+            ],
+            decimal=8,
+        )
+
+        # dump to deepmd-npy
+        mysys.to(file_name=self.dump_path, fmt="deepmd/npy")
+        self.assertTrue(os.path.isfile(f"{self.dump_path}/set.000/spin.npy"))
+        self.assertTrue(os.path.isfile(f"{self.dump_path}/set.000/force_mag.npy"))
+
+        sys2 = dpdata.LabeledSystem(self.dump_path, fmt="deepmd/npy")
+        np.testing.assert_almost_equal(data["spins"], sys2.data["spins"], decimal=8)
+        np.testing.assert_almost_equal(
+            data["mag_forces"], sys2.data["mag_forces"], decimal=8
+        )
+
+    def test_relax(self):
+        os.system("cp abacus.spin/INPUT.relax abacus.spin/INPUT")
+        mysys = dpdata.LabeledSystem("abacus.spin", fmt="abacus/relax")
+        data = mysys.data
+        spins_ref = np.array(
+            [
+                [
+                    [1.16909819, 1.16895965, 1.16895485],
+                    [1.16827825, 1.16832716, 1.16836899],
+                ],
+                [
+                    [1.25007143, 1.25006167, 1.25004587],
+                    [1.25015764, 1.2501678, 1.25018344],
+                ],
+                [
+                    [1.24984994, 1.24977108, 1.24978313],
+                    [1.24996533, 1.2500441, 1.25003208],
+                ],
+            ]
+        )
+        magforces_ref = np.array(
+            [
+                [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]],
+                [
+                    [-0.16734626, -0.16735378, -0.16735617],
+                    [-0.16836467, -0.16835897, -0.16835625],
+                ],
+                [
+                    [-0.16573406, -0.16574627, -0.1657445],
+                    [-0.16619489, -0.16617948, -0.16618272],
+                ],
+            ]
+        )
+        self.assertEqual(len(data["spins"]), 3)
+        self.assertEqual(len(data["mag_forces"]), 3)
+        np.testing.assert_almost_equal(data["spins"], spins_ref, decimal=8)
+        np.testing.assert_almost_equal(data["mag_forces"], magforces_ref, decimal=8)
+
+        # dump to deepmd-npy
+        mysys.to(file_name=self.dump_path, fmt="deepmd/npy")
+        self.assertTrue(os.path.isfile(f"{self.dump_path}/set.000/spin.npy"))
+        self.assertTrue(os.path.isfile(f"{self.dump_path}/set.000/force_mag.npy"))
+
+        sys2 = dpdata.LabeledSystem(self.dump_path, fmt="deepmd/npy")
+        np.testing.assert_almost_equal(data["spins"], sys2.data["spins"], decimal=8)
+        np.testing.assert_almost_equal(
+            data["mag_forces"], sys2.data["mag_forces"], decimal=8
+        )
+
+    def test_md(self):
+        os.system("cp abacus.spin/INPUT.md abacus.spin/INPUT")
+        mysys = dpdata.LabeledSystem("abacus.spin", fmt="abacus/md")
+        data = mysys.data
+        spins_ref = np.array(
+            [
+                [
+                    [1.16909819, 1.16895965, 1.16895485],
+                    [1.16827825, 1.16832716, 1.16836899],
+                ],
+                [
+                    [1.2500362, 1.25007501, 1.2500655],
+                    [1.25019078, 1.25015253, 1.25016188],
+                ],
+                [
+                    [1.24985138, 1.24976901, 1.2497695],
+                    [1.24996388, 1.25004618, 1.25004561],
+                ],
+                [
+                    [1.24982513, 1.24985445, 1.24985336],
+                    [1.25005073, 1.25001814, 1.25002065],
+                ],
+            ]
+        )
+        magforces_ref = np.array(
+            [
+                [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]],
+                [
+                    [-0.16747275, -0.16747145, -0.16746776],
+                    [-0.16853881, -0.16853935, -0.16854119],
+                ],
+                [
+                    [-0.16521817, -0.16523256, -0.16523212],
+                    [-0.16549418, -0.16547867, -0.16547913],
+                ],
+                [
+                    [-0.16141172, -0.16140644, -0.1614127],
+                    [-0.15901519, -0.15905932, -0.15904824],
+                ],
+            ]
+        )
+        self.assertEqual(len(data["spins"]), 4)
+        self.assertEqual(len(data["mag_forces"]), 4)
+        np.testing.assert_almost_equal(data["spins"], spins_ref, decimal=8)
+        np.testing.assert_almost_equal(data["mag_forces"], magforces_ref, decimal=8)
+
+        # dump to deepmd-npy
+        mysys.to(file_name=self.dump_path, fmt="deepmd/npy")
+        self.assertTrue(os.path.isfile(f"{self.dump_path}/set.000/spin.npy"))
+        self.assertTrue(os.path.isfile(f"{self.dump_path}/set.000/force_mag.npy"))
+
+        sys2 = dpdata.LabeledSystem(self.dump_path, fmt="deepmd/npy")
+        np.testing.assert_almost_equal(data["spins"], sys2.data["spins"], decimal=8)
+        np.testing.assert_almost_equal(
+            data["mag_forces"], sys2.data["mag_forces"], decimal=8
+        )
diff --git a/tests/test_abacus_stru_dump.py b/tests/test_abacus_stru_dump.py
index 356aa57f..084a5473 100644
--- a/tests/test_abacus_stru_dump.py
+++ b/tests/test_abacus_stru_dump.py
@@ -1,16 +1,23 @@
 from __future__ import annotations
 
 import os
+import shutil
 import unittest
 
 from context import dpdata
 from test_vasp_poscar_dump import myfilecmp
 
+from dpdata.abacus.scf import parse_stru_pos
+
 
 class TestStruDump(unittest.TestCase):
     def setUp(self):
         self.system_ch4 = dpdata.System("abacus.scf/STRU.ch4", fmt="stru")
 
+    def tearDown(self):
+        if os.path.isfile("STRU_tmp"):
+            os.remove("STRU_tmp")
+
     def test_dump_stru(self):
         self.system_ch4.to(
             "stru",
@@ -22,9 +29,157 @@ def test_dump_stru(self):
         )
         myfilecmp(self, "abacus.scf/stru_test", "STRU_tmp")
 
-    def tearDown(self):
-        if os.path.isfile("STRU_tmp"):
-            os.remove("STRU_tmp")
+    def test_dumpStruLinkFile(self):
+        os.makedirs("abacus.scf/tmp", exist_ok=True)
+        self.system_ch4.to(
+            "stru",
+            "abacus.scf/tmp/STRU_tmp",
+            mass=[12, 1],
+            pp_file=["abacus.scf/C.upf", "abacus.scf/H.upf"],
+            numerical_orbital=["abacus.scf/C.orb", "abacus.scf/H.orb"],
+            numerical_descriptor="abacus.scf/jle.orb",
+            link_file=True,
+        )
+        myfilecmp(self, "abacus.scf/stru_test", "abacus.scf/tmp/STRU_tmp")
+
+        self.assertTrue(os.path.islink("abacus.scf/tmp/C.upf"))
+        self.assertTrue(os.path.islink("abacus.scf/tmp/H.upf"))
+        self.assertTrue(os.path.islink("abacus.scf/tmp/C.orb"))
+        self.assertTrue(os.path.islink("abacus.scf/tmp/H.orb"))
+        self.assertTrue(os.path.islink("abacus.scf/tmp/jle.orb"))
+
+        if os.path.isdir("abacus.scf/tmp"):
+            shutil.rmtree("abacus.scf/tmp")
+
+    def test_dump_spinconstrain(self):
+        self.system_ch4.to(
+            "stru",
+            "STRU_tmp",
+            mass=[12, 1],
+            pp_file={"C": "C.upf", "H": "H.upf"},
+            numerical_orbital={"C": "C.orb", "H": "H.orb"},
+            mag=[4, [1, 1, 1], 1, 1, 1],
+            sc=[True, True, [True, False, True], False, True],
+            move=[1, 1, 1, 0, 0],
+            angle1=[None, None, 100, 90, 80],
+            angle2=[100, 90, 80, 70, None],
+            lambda_=[[0.1, 0.2, 0.3], [0.4, 0.5, 0.6], [0.7, 0.8, 0.9], None, None],
+        )
+
+        assert os.path.isfile("STRU_tmp")
+        with open("STRU_tmp") as f:
+            c = f.read()
+
+        with open("abacus.scf/stru.ref") as f:
+            stru_ref = f.read()
+        assert c == stru_ref
+
+    def test_dump_spin(self):
+        sys_tmp = dpdata.System("abacus.scf/stru.ref", fmt="stru")
+        sys_tmp.data["spins"] = [
+            [[1, 2, 3], [4, 5, 6], [1, 1, 1], [2, 2, 2], [3, 3, 3]]
+        ]
+        sys_tmp.to(
+            "stru",
+            "STRU_tmp",
+            mass=[12, 1],
+            pp_file=["C.upf", "H.upf"],
+            numerical_orbital=["C.orb", "H.orb"],
+        )
+        assert os.path.isfile("STRU_tmp")
+        with open("STRU_tmp") as f:
+            c = f.read()
+        stru_ref = """C
+0.0
+1
+5.192682633809 4.557725978258 4.436846615358 1 1 1 mag 1.000000000000 2.000000000000 3.000000000000
+H
+0.0
+4
+5.416431453540 4.011298860305 3.511161492417 1 1 1 mag 4.000000000000 5.000000000000 6.000000000000
+4.131588222365 4.706745191323 4.431136645083 1 1 1 mag 1.000000000000 1.000000000000 1.000000000000
+5.630930319126 5.521640894956 4.450356541303 1 1 1 mag 2.000000000000 2.000000000000 2.000000000000
+5.499851012568 4.003388899277 5.342621842622 1 1 1 mag 3.000000000000 3.000000000000 3.000000000000
+"""
+        self.assertTrue(stru_ref in c)
+
+
+class TestABACUSParseStru(unittest.TestCase):
+    def test_parse_stru_post(self):
+        pos, move, velocity, magmom, angle1, angle2, constrain, lambda1 = (
+            parse_stru_pos(
+                "1.0 2.0 3.0 1 1 1 mag 1.0 2.0 3.0 v 1 1 1 angle1 100 angle2 90 sc 1 0 1 lambda 0.1 0.2 0.3"
+            )
+        )
+        self.assertEqual(pos, [1.0, 2.0, 3.0])
+        self.assertEqual(move, [1, 1, 1])
+        self.assertEqual(velocity, [1.0, 1.0, 1.0])
+        self.assertEqual(magmom, [1.0, 2.0, 3.0])
+        self.assertEqual(angle1, 100)
+        self.assertEqual(angle2, 90)
+        self.assertEqual(constrain, [1, 0, 1])
+        self.assertEqual(lambda1, [0.1, 0.2, 0.3])
+
+        pos, move, velocity, magmom, angle1, angle2, constrain, lambda1 = (
+            parse_stru_pos("1 2 3 mag 1 sc 1 lambda 0.1")
+        )
+        self.assertEqual(pos, [1, 2, 3])
+        self.assertEqual(move, None)
+        self.assertEqual(velocity, None)
+        self.assertEqual(magmom, 1.0)
+        self.assertEqual(angle1, None)
+        self.assertEqual(angle2, None)
+        self.assertEqual(constrain, 1)
+        self.assertEqual(lambda1, 0.1)
+
+    def test_parse_stru_error(self):
+        line = "1.0 2.0 3.0 1 1"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 1 1 1 mag 1.0 3.0 v 1 1 1"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 1 1 1 mag 1 2 3 4"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 1 1 1 v 1"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 1 1 1 v 1 1"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 1 1 1 v 1 1 1 1"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 1 1 1 1"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 1 1 1 angle1 "
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 1 1 1 angle1 1 2"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 1 1 1 angle2"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 angle2 1 2"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 sc"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 sc 1 2"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 lambda"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 lambda 1 2"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
+
+        line = "1.0 2.0 3.0 lambda 1 2 3 4"
+        self.assertRaises(RuntimeError, parse_stru_pos, line), line
 
 
 if __name__ == "__main__":

From b797acb23214f771e4eb66ff6ae1954e027eed0e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 24 Sep 2024 08:51:26 +0800
Subject: [PATCH 23/33] [pre-commit.ci] pre-commit autoupdate (#731)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.5 →
v0.6.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.5...v0.6.7)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8da028de..d921a886 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.5
+    rev: v0.6.7
     hooks:
     - id: ruff
       args: ["--fix"]

From a6ced9fb3f7ec8ba8648363b9a90d4abacd504a3 Mon Sep 17 00:00:00 2001
From: Peng Xingliang <91927439+pxlxingliang@users.noreply.github.com>
Date: Tue, 15 Oct 2024 08:08:24 +0800
Subject: [PATCH 24/33] abacus: add checks on pp and orb in construction of
 STRU (#737)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Introduced a mandatory parameter for pseudopotential files and an
optional parameter to specify the destination directory for symbolic
links.

- **Improvements**
- Enhanced clarity and functionality in handling input parameters for
pseudopotential and orbital files.
- Streamlined output construction for `pp_file` and `numerical_orbital`.

- **Bug Fixes**
- Added tests to validate error handling for mismatches between provided
pseudopotential files and numerical orbitals, ensuring appropriate
exceptions are raised.

- **Documentation**
	- Added comments for better understanding of code functionality.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: root <pxlxingliang>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 dpdata/abacus/scf.py           | 90 +++++++++++++++++-----------------
 tests/test_abacus_stru_dump.py | 43 ++++++++++++++++
 2 files changed, 87 insertions(+), 46 deletions(-)

diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py
index 9919e912..b1b2cfed 100644
--- a/dpdata/abacus/scf.py
+++ b/dpdata/abacus/scf.py
@@ -578,7 +578,7 @@ def get_frame_from_stru(fname):
 def make_unlabeled_stru(
     data,
     frame_idx,
-    pp_file=None,
+    pp_file,
     numerical_orbital=None,
     numerical_descriptor=None,
     mass=None,
@@ -601,7 +601,7 @@ def make_unlabeled_stru(
         System data
     frame_idx : int
         The index of the frame to dump
-    pp_file : list of string or dict, optional
+    pp_file : list of string or dict
         List of pseudo potential files, or a dictionary of pseudo potential files for each atomnames
     numerical_orbital : list of string or dict, optional
         List of orbital files, or a dictionary of orbital files for each atomnames
@@ -628,6 +628,8 @@ def make_unlabeled_stru(
     link_file : bool, optional
         Whether to link the pseudo potential files and orbital files in the STRU file.
         If True, then only filename will be written in the STRU file, and make a soft link to the real file.
+    dest_dir : str, optional
+        The destination directory to make the soft link of the pseudo potential files and orbital files.
     For velocity, mag, angle1, angle2, sc, and lambda_, if the value is None, then the corresponding information will not be written.
     ABACUS support defining "mag" and "angle1"/"angle2" at the same time, and in this case, the "mag" only define the norm of the magnetic moment, and "angle1" and "angle2" define the direction of the magnetic moment.
     If data has spins, then it will be written as mag to STRU file; while if mag is passed at the same time, then mag will be used.
@@ -655,6 +657,23 @@ def ndarray2list(i):
         else:
             return i
 
+    def process_file_input(file_input, atom_names, input_name):
+        # For pp_file and numerical_orbital, process the file input, and return a list of file names
+        # file_input can be a list of file names, or a dictionary of file names for each atom names
+        if isinstance(file_input, (list, tuple)):
+            if len(file_input) != len(atom_names):
+                raise ValueError(
+                    f"{input_name} length is not equal to the number of atom types"
+                )
+            return file_input
+        elif isinstance(file_input, dict):
+            for element in atom_names:
+                if element not in file_input:
+                    raise KeyError(f"{input_name} does not contain {element}")
+            return [file_input[element] for element in atom_names]
+        else:
+            raise ValueError(f"Invalid {input_name}: {file_input}")
+
     if link_file and dest_dir is None:
         print(
             "WARNING: make_unlabeled_stru: link_file is True, but dest_dir is None. Will write the filename to STRU but not making soft link."
@@ -680,8 +699,8 @@ def ndarray2list(i):
 
     # ATOMIC_SPECIES block
     out = "ATOMIC_SPECIES\n"
-    if pp_file is not None:
-        pp_file = ndarray2list(pp_file)
+    ppfiles = process_file_input(ndarray2list(pp_file), data["atom_names"], "pp_file")
+
     for iele in range(len(data["atom_names"])):
         if data["atom_numbs"][iele] == 0:
             continue
@@ -690,57 +709,36 @@ def ndarray2list(i):
             out += f"{mass[iele]:.3f} "
         else:
             out += "1 "
-        if pp_file is not None:
-            if isinstance(pp_file, (list, tuple)):
-                ipp_file = pp_file[iele]
-            elif isinstance(pp_file, dict):
-                if data["atom_names"][iele] not in pp_file:
-                    print(
-                        f"ERROR: make_unlabeled_stru: pp_file does not contain {data['atom_names'][iele]}"
-                    )
-                    ipp_file = None
-                else:
-                    ipp_file = pp_file[data["atom_names"][iele]]
-            else:
-                ipp_file = None
-            if ipp_file is not None:
-                if not link_file:
-                    out += ipp_file
-                else:
-                    out += os.path.basename(ipp_file.rstrip("/"))
-                    if dest_dir is not None:
-                        _link_file(dest_dir, ipp_file)
 
+        ipp_file = ppfiles[iele]
+        if not link_file:
+            out += ipp_file
+        else:
+            out += os.path.basename(ipp_file.rstrip("/"))
+            if dest_dir is not None:
+                _link_file(dest_dir, ipp_file)
         out += "\n"
     out += "\n"
 
     # NUMERICAL_ORBITAL block
     if numerical_orbital is not None:
-        assert len(numerical_orbital) == len(data["atom_names"])
         numerical_orbital = ndarray2list(numerical_orbital)
+        orbfiles = process_file_input(
+            numerical_orbital, data["atom_names"], "numerical_orbital"
+        )
+        orbfiles = [
+            orbfiles[i]
+            for i in range(len(data["atom_names"]))
+            if data["atom_numbs"][i] != 0
+        ]
         out += "NUMERICAL_ORBITAL\n"
-        for iele in range(len(data["atom_names"])):
-            if data["atom_numbs"][iele] == 0:
-                continue
-            if isinstance(numerical_orbital, (list, tuple)):
-                inum_orbital = numerical_orbital[iele]
-            elif isinstance(numerical_orbital, dict):
-                if data["atom_names"][iele] not in numerical_orbital:
-                    print(
-                        f"ERROR: make_unlabeled_stru: numerical_orbital does not contain {data['atom_names'][iele]}"
-                    )
-                    inum_orbital = None
-                else:
-                    inum_orbital = numerical_orbital[data["atom_names"][iele]]
+        for iorb in orbfiles:
+            if not link_file:
+                out += iorb
             else:
-                inum_orbital = None
-            if inum_orbital is not None:
-                if not link_file:
-                    out += inum_orbital
-                else:
-                    out += os.path.basename(inum_orbital.rstrip("/"))
-                    if dest_dir is not None:
-                        _link_file(dest_dir, inum_orbital)
+                out += os.path.basename(iorb.rstrip("/"))
+                if dest_dir is not None:
+                    _link_file(dest_dir, iorb)
             out += "\n"
         out += "\n"
 
diff --git a/tests/test_abacus_stru_dump.py b/tests/test_abacus_stru_dump.py
index 084a5473..4549b6d1 100644
--- a/tests/test_abacus_stru_dump.py
+++ b/tests/test_abacus_stru_dump.py
@@ -51,6 +51,49 @@ def test_dumpStruLinkFile(self):
         if os.path.isdir("abacus.scf/tmp"):
             shutil.rmtree("abacus.scf/tmp")
 
+    def test_dump_stru_pporb_mismatch(self):
+        with self.assertRaises(KeyError, msg="pp_file is a dict and lack of pp for H"):
+            self.system_ch4.to(
+                "stru",
+                "STRU_tmp",
+                mass=[12, 1],
+                pp_file={"C": "C.upf", "O": "O.upf"},
+                numerical_orbital={"C": "C.orb", "H": "H.orb"},
+            )
+
+        with self.assertRaises(
+            ValueError, msg="pp_file is a list and lack of pp for H"
+        ):
+            self.system_ch4.to(
+                "stru",
+                "STRU_tmp",
+                mass=[12, 1],
+                pp_file=["C.upf"],
+                numerical_orbital={"C": "C.orb", "H": "H.orb"},
+            )
+
+        with self.assertRaises(
+            KeyError, msg="numerical_orbital is a dict and lack of orbital for H"
+        ):
+            self.system_ch4.to(
+                "stru",
+                "STRU_tmp",
+                mass=[12, 1],
+                pp_file={"C": "C.upf", "H": "H.upf"},
+                numerical_orbital={"C": "C.orb", "O": "O.orb"},
+            )
+
+        with self.assertRaises(
+            ValueError, msg="numerical_orbital is a list and lack of orbital for H"
+        ):
+            self.system_ch4.to(
+                "stru",
+                "STRU_tmp",
+                mass=[12, 1],
+                pp_file=["C.upf", "H.upf"],
+                numerical_orbital=["C.orb"],
+            )
+
     def test_dump_spinconstrain(self):
         self.system_ch4.to(
             "stru",

From 373e0d7ec5d080bb97e83152c8173ad82f50d0aa Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Mon, 14 Oct 2024 20:32:05 -0400
Subject: [PATCH 25/33] fix(rtd): pin python to `<3.13` and mamba to `<2`
 (#735)

Fix the RTD build error. Pinning mamba to `<2` is a workaround for
https://github.com/jupyterlite/xeus/issues/122.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **Chores**
- Added a constraint specifying that the `python` dependency must be
less than version 3.13.
- Updated the Python version in the Read the Docs configuration to
`mambaforge-23.11`.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---
 .readthedocs.yaml        | 2 +-
 docs/rtd_environment.yml | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 83a36032..79c271f4 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "mambaforge-22.9"
+    python: "mambaforge-23.11"
 conda:
   environment: docs/rtd_environment.yml
 sphinx:
diff --git a/docs/rtd_environment.yml b/docs/rtd_environment.yml
index 7eae4aad..50572dca 100644
--- a/docs/rtd_environment.yml
+++ b/docs/rtd_environment.yml
@@ -2,6 +2,7 @@ name: dpdata
 channels:
   - conda-forge
 dependencies:
-  - mamba
+  - python <3.13
+  - mamba <2
   - pip:
     - ..[docs]

From dccab685734138639ee589ec6c726d865a864bb9 Mon Sep 17 00:00:00 2001
From: "A bot of @njzjz" <48687836+njzjz-bot@users.noreply.github.com>
Date: Tue, 15 Oct 2024 17:59:14 -0400
Subject: [PATCH 26/33] chore(ci): use astral-sh/setup-uv action (#734)

Generated by the task: https://github.com/njzjz-bot/njzjz-bot/issues/9.


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **Chores**
- Updated workflow configurations for benchmarking and testing to
improve the setup process for the `uv` tool.
- Replaced the previous installation method with a new action that
enables caching and specifies cache dependencies.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 .github/workflows/benchmark.yml | 7 ++++++-
 .github/workflows/test.yml      | 8 +++++++-
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
index 1dd68277..20f8dc6d 100644
--- a/.github/workflows/benchmark.yml
+++ b/.github/workflows/benchmark.yml
@@ -13,7 +13,12 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: 3.12
-    - run: curl -LsSf https://astral.sh/uv/install.sh | sh
+    - uses: astral-sh/setup-uv@v3
+      with:
+        enable-cache: true
+        cache-dependency-glob: |
+          **/requirements*.txt
+          **/pyproject.toml
     - name: Install dependencies
       run: uv pip install --system .[test,amber,ase,pymatgen,benchmark] rdkit openbabel-wheel
     - name: Run benchmarks
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a6d23270..0d855f4a 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -18,7 +18,13 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - run: curl -LsSf https://astral.sh/uv/install.sh | sh
+    - uses: astral-sh/setup-uv@v3
+      with:
+        enable-cache: true
+        cache-dependency-glob: |
+          **/requirements*.txt
+          **/pyproject.toml
+        cache-suffix: "py${{ matrix.python-version }}"
     - name: Install dependencies
       run: uv pip install --system .[test,amber,ase,pymatgen] coverage ./tests/plugin rdkit openbabel-wheel
     - name: Test

From 74bfcccdb1b92565de64c49de6baf438d741bafc Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 17 Oct 2024 14:59:32 -0400
Subject: [PATCH 27/33] [pre-commit.ci] pre-commit autoupdate (#733)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.6.0 →
v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.6.0...v5.0.0)
- [github.com/astral-sh/ruff-pre-commit: v0.6.7 →
v0.6.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.7...v0.6.9)
- [github.com/asottile/blacken-docs: 1.18.0 →
1.19.0](https://github.com/asottile/blacken-docs/compare/1.18.0...1.19.0)
<!--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-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d921a886..898923be 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     # there are many log files in tests
     # TODO: seperate py files and log files
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.7
+    rev: v0.6.9
     hooks:
     - id: ruff
       args: ["--fix"]
@@ -36,7 +36,7 @@ repos:
       args: ["--write"]
 # Python inside docs
 -   repo: https://github.com/asottile/blacken-docs
-    rev: 1.18.0
+    rev: 1.19.0
     hooks:
     -   id: blacken-docs
 ci:

From d1f1b98238607a479be1b6f2d438b5c24c8b743e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 22 Oct 2024 14:24:48 +0800
Subject: [PATCH 28/33] [pre-commit.ci] pre-commit autoupdate (#741)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.6.9 →
v0.7.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.9...v0.7.0)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 898923be..0bb47d32 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.6.9
+    rev: v0.7.0
     hooks:
     - id: ruff
       args: ["--fix"]

From cdbbe1b5c378ed0d418877c610d370617ae3eef6 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Tue, 22 Oct 2024 23:40:59 -0400
Subject: [PATCH 29/33] fix: change `project.entry-points.console_scripts` to
 `project.scripts` in `pyproject.toml` (#743)

`project.entry-points.console_scripts` is not allowed per [PEP
621](https://peps.python.org/pep-0621/).

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Updated the command entry point for the `dpdata` tool for improved
accessibility.

- **Chores**
	- Organized optional dependencies for better clarity and management.
- Maintained existing configurations for tools and package data without
functional changes.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4bf2e64b..481e6864 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,7 +37,7 @@ Homepage = "https://github.com/deepmodeling/dpdata"
 documentation = "https://docs.deepmodeling.com/projects/dpdata"
 repository = "https://github.com/deepmodeling/dpdata"
 
-[project.entry-points.console_scripts]
+[project.scripts]
 dpdata = "dpdata.cli:dpdata_cli"
 
 [project.optional-dependencies]

From 7853b7b526a5ffbd2b8a08d3a1f3ffa06c228d52 Mon Sep 17 00:00:00 2001
From: Peng Xingliang <91927439+pxlxingliang@users.noreply.github.com>
Date: Thu, 24 Oct 2024 03:47:04 +0800
Subject: [PATCH 30/33] add spin for lammps (#738)

Reference #728 to add the spin information for lammps.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Introduced functions to extract and normalize spin data from LAMMPS
dump files.
	- Added support for registering spin data types in the system.
	- Created new simulation input and output files for LAMMPS.
- Added new compute and dump commands for calculating and outputting
spin properties in LAMMPS.

- **Tests**
- Implemented unit tests for verifying the handling of spin
configurations in LAMMPS files, including scenarios with zero spin
values and incomplete data.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: root <pxlxingliang>
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>
---
 dpdata/lammps/dump.py               | 104 ++++++++++++++++++-
 dpdata/lammps/lmp.py                |  73 +++++++++++--
 dpdata/plugins/lammps.py            |  56 +++++++++-
 tests/lammps/in.lmp                 |   2 +
 tests/lammps/spin.lmp               |  12 +++
 tests/lammps/traj.dump              |  52 ++++++++++
 tests/lammps/traj_partial_spin.dump |  52 ++++++++++
 tests/test_lammps_spin.py           | 153 ++++++++++++++++++++++++++++
 8 files changed, 493 insertions(+), 11 deletions(-)
 create mode 100644 tests/lammps/in.lmp
 create mode 100644 tests/lammps/spin.lmp
 create mode 100644 tests/lammps/traj.dump
 create mode 100644 tests/lammps/traj_partial_spin.dump
 create mode 100644 tests/test_lammps_spin.py

diff --git a/dpdata/lammps/dump.py b/dpdata/lammps/dump.py
index 72fee27d..91f0c48d 100644
--- a/dpdata/lammps/dump.py
+++ b/dpdata/lammps/dump.py
@@ -197,7 +197,91 @@ def load_file(fname: FileType, begin=0, step=1):
                 buff.append(line)
 
 
-def system_data(lines, type_map=None, type_idx_zero=True, unwrap=False):
+def get_spin_keys(inputfile):
+    """
+    Read input file and get the keys for spin info in dump.
+
+    Parameters
+    ----------
+    inputfile : str
+        Path to the input file.
+
+    Returns
+    -------
+    list or None
+        List of spin info keys if found, None otherwise.
+    """
+    if inputfile is None:
+        return None
+
+    if not os.path.isfile(inputfile):
+        warnings.warn(f"Input file {inputfile} not found.")
+        return None
+
+    with open(inputfile) as f:
+        for line in f.readlines():
+            ls = line.split()
+            if (
+                len(ls) > 7
+                and ls[0] == "compute"
+                and all(key in ls for key in ["sp", "spx", "spy", "spz"])
+            ):
+                compute_name = ls[1]
+                return [
+                    f"c_{compute_name}[{ls.index(key) - 3}]"
+                    for key in ["sp", "spx", "spy", "spz"]
+                ]
+
+    return None
+
+
+def get_spin(lines, spin_keys):
+    """
+    Get the spin info from the dump file.
+
+    Parameters
+    ----------
+    lines : list
+        The content of the dump file.
+    spin_keys : list
+        The keys for spin info in dump file.
+    the spin info is stored in sp, spx, spy, spz or spin_keys, which is the spin norm and the spin vector
+    1 1 0.00141160 5.64868599 0.01005602 1.54706291 0.00000000 0.00000000 1.00000000 -1.40772100 -2.03739417 -1522.64797384 -0.00397809 -0.00190426 -0.00743976
+    """
+    blk, head = _get_block(lines, "ATOMS")
+    heads = head.split()
+
+    if spin_keys is not None and all(i in heads for i in spin_keys):
+        key = spin_keys
+    else:
+        return None
+
+    try:
+        idx_id = heads.index("id") - 2
+        idx_sp, idx_spx, idx_spy, idx_spz = (heads.index(k) - 2 for k in key)
+
+        norm = []
+        vec = []
+        atom_ids = []
+        for line in blk:
+            words = line.split()
+            norm.append([float(words[idx_sp])])
+            vec.append(
+                [float(words[idx_spx]), float(words[idx_spy]), float(words[idx_spz])]
+            )
+            atom_ids.append(int(words[idx_id]))
+
+        spin = np.array(norm) * np.array(vec)
+        atom_ids, spin = zip(*sorted(zip(atom_ids, spin)))
+        return np.array(spin)
+    except (ValueError, IndexError) as e:
+        warnings.warn(f"Error processing spin data: {str(e)}")
+        return None
+
+
+def system_data(
+    lines, type_map=None, type_idx_zero=True, unwrap=False, input_file=None
+):
     array_lines = split_traj(lines)
     lines = array_lines[0]
     system = {}
@@ -216,6 +300,12 @@ def system_data(lines, type_map=None, type_idx_zero=True, unwrap=False):
     system["cells"] = [np.array(cell)]
     system["atom_types"] = get_atype(lines, type_idx_zero=type_idx_zero)
     system["coords"] = [safe_get_posi(lines, cell, np.array(orig), unwrap)]
+    spin_keys = get_spin_keys(input_file)
+    spin = get_spin(lines, spin_keys)
+    has_spin = False
+    if spin is not None:
+        system["spins"] = [spin]
+        has_spin = True
     for ii in range(1, len(array_lines)):
         bounds, tilt = get_dumpbox(array_lines[ii])
         orig, cell = dumpbox2box(bounds, tilt)
@@ -228,6 +318,18 @@ def system_data(lines, type_map=None, type_idx_zero=True, unwrap=False):
         system["coords"].append(
             safe_get_posi(array_lines[ii], cell, np.array(orig), unwrap)[idx]
         )
+        if has_spin:
+            spin = get_spin(array_lines[ii], spin_keys)
+            if spin is not None:
+                system["spins"].append(spin[idx])
+            else:
+                warnings.warn(
+                    f"Warning: spin info is not found in frame {ii}, remove spin info."
+                )
+                system.pop("spins")
+                has_spin = False
+    if has_spin:
+        system["spins"] = np.array(system["spins"])
     system["cells"] = np.array(system["cells"])
     system["coords"] = np.array(system["coords"])
     return system
diff --git a/dpdata/lammps/lmp.py b/dpdata/lammps/lmp.py
index 604b18d1..04620166 100644
--- a/dpdata/lammps/lmp.py
+++ b/dpdata/lammps/lmp.py
@@ -127,6 +127,19 @@ def get_posi(lines):
     return np.array(posis)
 
 
+def get_spins(lines):
+    atom_lines = get_atoms(lines)
+    if len(atom_lines[0].split()) < 8:
+        return None
+    spins_ori = []
+    spins_norm = []
+    for ii in atom_lines:
+        iis = ii.split()
+        spins_ori.append([float(jj) for jj in iis[5:8]])
+        spins_norm.append([float(iis[-1])])
+    return np.array(spins_ori) * np.array(spins_norm)
+
+
 def get_lmpbox(lines):
     box_info = []
     tilt = np.zeros(3)
@@ -168,6 +181,11 @@ def system_data(lines, type_map=None, type_idx_zero=True):
     system["coords"] = [get_posi(lines)]
     system["cells"] = np.array(system["cells"])
     system["coords"] = np.array(system["coords"])
+
+    spins = get_spins(lines)
+    if spins is not None:
+        system["spins"] = np.array([spins])
+
     return system
 
 
@@ -216,14 +234,55 @@ def from_system_data(system, f_idx=0):
         + ptr_float_fmt
         + "\n"
     )
-    for ii in range(natoms):
-        ret += coord_fmt % (
-            ii + 1,
-            system["atom_types"][ii] + 1,
-            system["coords"][f_idx][ii][0] - system["orig"][0],
-            system["coords"][f_idx][ii][1] - system["orig"][1],
-            system["coords"][f_idx][ii][2] - system["orig"][2],
+
+    if "spins" in system:
+        coord_fmt = (
+            coord_fmt.strip("\n")
+            + " "
+            + ptr_float_fmt
+            + " "
+            + ptr_float_fmt
+            + " "
+            + ptr_float_fmt
+            + " "
+            + ptr_float_fmt
+            + "\n"
         )
+        spins_norm = np.linalg.norm(system["spins"][f_idx], axis=1)
+    for ii in range(natoms):
+        if "spins" in system:
+            if spins_norm[ii] != 0:
+                ret += coord_fmt % (
+                    ii + 1,
+                    system["atom_types"][ii] + 1,
+                    system["coords"][f_idx][ii][0] - system["orig"][0],
+                    system["coords"][f_idx][ii][1] - system["orig"][1],
+                    system["coords"][f_idx][ii][2] - system["orig"][2],
+                    system["spins"][f_idx][ii][0] / spins_norm[ii],
+                    system["spins"][f_idx][ii][1] / spins_norm[ii],
+                    system["spins"][f_idx][ii][2] / spins_norm[ii],
+                    spins_norm[ii],
+                )
+            else:
+                ret += coord_fmt % (
+                    ii + 1,
+                    system["atom_types"][ii] + 1,
+                    system["coords"][f_idx][ii][0] - system["orig"][0],
+                    system["coords"][f_idx][ii][1] - system["orig"][1],
+                    system["coords"][f_idx][ii][2] - system["orig"][2],
+                    system["spins"][f_idx][ii][0],
+                    system["spins"][f_idx][ii][1],
+                    system["spins"][f_idx][ii][2] + 1,
+                    spins_norm[ii],
+                )
+        else:
+            ret += coord_fmt % (
+                ii + 1,
+                system["atom_types"][ii] + 1,
+                system["coords"][f_idx][ii][0] - system["orig"][0],
+                system["coords"][f_idx][ii][1] - system["orig"][1],
+                system["coords"][f_idx][ii][2] - system["orig"][2],
+            )
     return ret
 
 
diff --git a/dpdata/plugins/lammps.py b/dpdata/plugins/lammps.py
index 0327d444..c7e5c765 100644
--- a/dpdata/plugins/lammps.py
+++ b/dpdata/plugins/lammps.py
@@ -2,8 +2,11 @@
 
 from typing import TYPE_CHECKING
 
+import numpy as np
+
 import dpdata.lammps.dump
 import dpdata.lammps.lmp
+from dpdata.data_type import Axis, DataType
 from dpdata.format import Format
 from dpdata.utils import open_file
 
@@ -11,6 +14,18 @@
     from dpdata.utils import FileType
 
 
+def register_spin(data):
+    if "spins" in data:
+        dt = DataType(
+            "spins",
+            np.ndarray,
+            (Axis.NFRAMES, Axis.NATOMS, 3),
+            required=False,
+            deepmd_name="spin",
+        )
+        dpdata.System.register_data_type(dt)
+
+
 @Format.register("lmp")
 @Format.register("lammps/lmp")
 class LAMMPSLmpFormat(Format):
@@ -18,7 +33,9 @@ class LAMMPSLmpFormat(Format):
     def from_system(self, file_name: FileType, type_map=None, **kwargs):
         with open_file(file_name) as fp:
             lines = [line.rstrip("\n") for line in fp]
-        return dpdata.lammps.lmp.to_system_data(lines, type_map)
+        data = dpdata.lammps.lmp.to_system_data(lines, type_map)
+        register_spin(data)
+        return data
 
     def to_system(self, data, file_name: FileType, frame_idx=0, **kwargs):
         """Dump the system in lammps data format.
@@ -45,7 +62,40 @@ def to_system(self, data, file_name: FileType, frame_idx=0, **kwargs):
 class LAMMPSDumpFormat(Format):
     @Format.post("shift_orig_zero")
     def from_system(
-        self, file_name, type_map=None, begin=0, step=1, unwrap=False, **kwargs
+        self,
+        file_name: str,
+        type_map: list[str] = None,
+        begin: int = 0,
+        step: int = 1,
+        unwrap: bool = False,
+        input_file: str = None,
+        **kwargs,
     ):
+        """Read the data from a lammps dump file.
+
+        Parameters
+        ----------
+        file_name : str
+            The dump file name
+        type_map : List[str], optional
+            The atom type list
+        begin : int, optional
+            The begin step
+        step : int, optional
+            The step
+        unwrap : bool, optional
+            Whether to unwrap the coordinates
+        input_file : str, optional
+            The input file name
+
+        Returns
+        -------
+        dict
+            The system data
+        """
         lines = dpdata.lammps.dump.load_file(file_name, begin=begin, step=step)
-        return dpdata.lammps.dump.system_data(lines, type_map, unwrap=unwrap)
+        data = dpdata.lammps.dump.system_data(
+            lines, type_map, unwrap=unwrap, input_file=input_file
+        )
+        register_spin(data)
+        return data
diff --git a/tests/lammps/in.lmp b/tests/lammps/in.lmp
new file mode 100644
index 00000000..02f655fa
--- /dev/null
+++ b/tests/lammps/in.lmp
@@ -0,0 +1,2 @@
+compute 	spin all property/atom sp spx spy spz fmx fmy fmz fx fy fz
+dump            dpgen_dump all custom 10 traj.dump id type x y z c_spin[1] c_spin[2] c_spin[3] c_spin[4] c_spin[5] c_spin[6] c_spin[7] c_spin[8] c_spin[9] c_spin[10]
\ No newline at end of file
diff --git a/tests/lammps/spin.lmp b/tests/lammps/spin.lmp
new file mode 100644
index 00000000..d662cc2c
--- /dev/null
+++ b/tests/lammps/spin.lmp
@@ -0,0 +1,12 @@
+
+2 atoms
+2 atom types
+   0.0000000000    2.5243712000 xlo xhi
+   0.0000000000    2.0430257000 ylo yhi
+   0.0000000000    2.2254033000 zlo zhi
+   1.2621856000    1.2874292000    0.7485898000 xy xz yz
+
+Atoms # atomic
+
+     1      1    0.0000000000    0.0000000000    0.0000000000    0.6000000000    0.8000000000    0.0000000000    5.0000000000
+     2      2    1.2621856000    0.7018028000    0.5513885000    0.0000000000    0.8000000000    0.6000000000    5.0000000000
diff --git a/tests/lammps/traj.dump b/tests/lammps/traj.dump
new file mode 100644
index 00000000..e1682983
--- /dev/null
+++ b/tests/lammps/traj.dump
@@ -0,0 +1,52 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+17
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+-4.0080511965879438e-02 5.7039029418994556e+00 -5.9179115295410201e-03
+1.4436085788922526e-02 5.6674744441011660e+00 -1.1487414836883500e-02
+7.8239288740356017e-03 5.6734038274259646e+00 6.8277359008788905e-04
+ITEM: ATOMS id type x y z c_spin[1] c_spin[2] c_spin[3] c_spin[4] c_spin[5] c_spin[6] c_spin[7] c_spin[8] c_spin[9] c_spin[10]
+1 1 0.00141160 5.64868599 0.01005602 1.54706291 0.00000000 0.00000000 1.00000000 -1.40772100 -2.03739417 -1522.64797384 -0.00397809 -0.00190426 -0.00743976
+2 1 5.65283939 5.57449025 2.84281508 1.54412869 0.00000000 0.00000000 1.00000000 7.75304092 6.48949619 -1512.84926162 -0.00637234 -0.00733168 0.00661107
+3 1 0.00066480 2.78022036 0.01010716 1.54612979 0.00000000 0.00000000 1.00000000 -0.93618575 1.92206111 -1520.80305011 -0.00316673 0.00177893 -0.00744575
+4 1 5.65233666 2.85374747 2.84289453 1.54439093 0.00000000 0.00000000 1.00000000 8.11012818 -6.49922039 -1514.31557088 -0.00569217 0.00741000 0.00640353
+5 1 2.82063515 5.64869321 0.01007552 1.54714250 0.00000000 0.00000000 1.00000000 2.49070852 -2.14456666 -1523.53038650 0.00478410 -0.00213962 -0.00751154
+6 1 2.89579803 5.57439179 2.84287630 1.54415032 0.00000000 0.00000000 1.00000000 -8.03062338 6.63950296 -1513.41291897 0.00440396 -0.00717185 0.00633657
+7 1 2.82151287 2.78010538 0.01016303 1.54619615 0.00000000 0.00000000 1.00000000 2.71859584 1.98482729 -1521.34149633 0.00533453 0.00194532 -0.00745901
+8 1 2.89637049 2.85377083 2.84297332 1.54440023 0.00000000 0.00000000 1.00000000 -7.76758760 -6.67134514 -1514.43304618 0.00505040 0.00743195 0.00630302
+9 1 1.41106492 1.38817482 1.72302072 1.18134529 0.00000000 0.00000000 1.00000000 0.27170165 -0.00426695 -444.22843899 0.00100237 -0.00002725 -0.03385965
+10 1 1.41105247 1.38807861 3.96314606 1.18153407 0.00000000 0.00000000 1.00000000 -0.07722674 0.01368756 -337.08703133 -0.00066982 0.00007487 0.07887183
+11 1 1.41105864 4.21395432 1.43987180 1.71989299 0.00000000 0.00000000 1.00000000 -0.01511106 0.00320081 -1653.34500916 0.00010421 0.00007248 0.00634401
+12 1 1.41104843 4.21387554 4.24576823 1.71989825 0.00000000 0.00000000 1.00000000 -0.71645898 0.05923960 -1640.68070568 -0.00117959 0.00006676 -0.01467806
+13 1 4.27433865 1.38779084 1.43977211 1.72010048 0.00000000 0.00000000 1.00000000 0.45899480 0.03956420 -1653.36356942 0.00051885 0.00002313 0.00911600
+14 1 4.27436799 1.38772964 4.24586490 1.72010133 0.00000000 0.00000000 1.00000000 0.38385331 0.07301994 -1642.06086017 -0.00002034 0.00010335 -0.01688908
+15 1 4.27435427 4.21452597 1.39359689 1.65590121 0.00000000 0.00000000 1.00000000 -0.01658773 -0.06159007 -1659.12744163 0.00006470 -0.00006420 -0.01342935
+16 1 4.27434583 4.21455469 4.29208004 1.65592002 0.00000000 0.00000000 1.00000000 -0.15590720 -0.03252166 -1654.84697132 -0.00066755 -0.00003915 -0.00482188
+17 2 1.41096761 1.38958048 0.01029027 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00048351 -0.00022876 -0.00645195
+ITEM: TIMESTEP
+10
+ITEM: NUMBER OF ATOMS
+17
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+-4.0080511965879438e-02 5.7039029418994556e+00 -5.9179115295410201e-03
+1.4436085788922526e-02 5.6674744441011660e+00 -1.1487414836883500e-02
+7.8239288740356017e-03 5.6734038274259646e+00 6.8277359008788905e-04
+ITEM: ATOMS id type x y z c_spin[1] c_spin[2] c_spin[3] c_spin[4] c_spin[5] c_spin[6] c_spin[7] c_spin[8] c_spin[9] c_spin[10]
+1 1 0.00037565 5.64900783 0.00994919 1.20356102 0.17466098 0.84115562 -0.51181127 -77.61471611 -389.41594243 234.29512368 0.00514290 -0.02481576 0.01063015
+2 1 5.65299480 5.57370279 2.84182058 1.17910451 0.85296110 0.48195380 -0.20044424 -311.75775120 -175.76677913 79.45225558 -0.01239308 -0.00914070 0.01933082
+3 1 0.00076668 2.78053566 0.01181481 1.20779106 0.33415542 0.49831517 -0.80001384 -163.88630094 -248.58823709 387.72415159 -0.01738465 -0.02878227 0.01503087
+4 1 5.65188602 2.85285383 2.84413423 1.20124335 -0.83536303 -0.20314716 0.51078356 399.86863784 90.34522869 -236.39221701 0.02327635 -0.00046572 -0.00138388
+5 1 2.82101290 5.64942265 0.01091135 1.34670883 -0.98528016 0.07078135 -0.15560530 902.73741755 -62.52279896 140.44423419 0.01500524 0.00581151 0.00468238
+6 1 2.89400594 5.57477971 2.84333235 1.25424131 -0.94587492 0.11487066 0.30352161 528.43507318 -60.32699018 -171.89948334 -0.00478280 0.00069273 -0.00496159
+7 1 2.82260306 2.78052696 0.00917962 1.17249564 -0.99589145 0.06282562 -0.06521619 374.56568243 -26.39431071 20.98877908 0.01464486 -0.01010131 -0.00993410
+8 1 2.89632273 2.85545549 2.84070353 1.24297017 -0.44008251 -0.42493729 0.79104721 240.05525392 236.02796206 -448.18443804 0.00137705 0.01258804 -0.01817420
+9 1 1.41117683 1.38867159 1.72266429 1.19059484 0.71251804 -0.69714805 -0.07938914 -309.93474514 293.96860716 19.98886311 -0.03871152 0.00854863 -0.02757569
+10 1 1.41176544 1.38873530 3.96470435 1.17564502 -0.51932602 -0.74875017 0.41191463 181.72443401 263.91689829 -132.94216896 0.00122847 0.01674701 0.02707109
+11 1 1.41085716 4.21342650 1.43850987 1.19874662 -0.51890828 0.82913822 0.20800000 237.52969259 -379.65100512 -93.16140268 0.01185986 -0.01872789 0.00032128
+12 1 1.41088045 4.21340876 4.24487134 1.20157661 -0.86390154 -0.04516556 -0.50163154 388.97171693 21.75492170 227.68580658 0.02074490 0.00756366 0.01937948
+13 1 4.27525485 1.38812593 1.43912039 1.23209806 0.55809649 0.81404794 0.16079259 -335.92026314 -484.87463129 -91.14464759 -0.03675759 -0.03549076 0.00310277
+14 1 4.27483864 1.38696457 4.24782541 1.18431742 0.00519166 -0.92210080 0.38691492 -4.73957478 407.09534135 -171.59043210 -0.00911750 0.04394272 -0.01683249
+15 1 4.27528588 4.21463764 1.39334117 1.17456490 -0.93713453 -0.09927163 0.33455046 397.32993706 40.92599847 -141.68618750 0.01918926 -0.00534149 -0.01906574
+16 1 4.27407834 4.21327842 4.29226033 1.31499905 -0.21350543 -0.97682201 -0.01530327 180.98908307 848.25344747 12.36402507 0.00492895 0.04383813 0.00955221
+17 2 1.40675897 1.38612182 0.01000617 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00174929 -0.00686653 -0.01117336
diff --git a/tests/lammps/traj_partial_spin.dump b/tests/lammps/traj_partial_spin.dump
new file mode 100644
index 00000000..5ee20855
--- /dev/null
+++ b/tests/lammps/traj_partial_spin.dump
@@ -0,0 +1,52 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+17
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+-4.0080511965879438e-02 5.7039029418994556e+00 -5.9179115295410201e-03
+1.4436085788922526e-02 5.6674744441011660e+00 -1.1487414836883500e-02
+7.8239288740356017e-03 5.6734038274259646e+00 6.8277359008788905e-04
+ITEM: ATOMS id type x y z c_spin[1] c_spin[2] c_spin[3] c_spin[4] c_spin[5] c_spin[6] c_spin[7] c_spin[8] c_spin[9] c_spin[10]
+1 1 0.00141160 5.64868599 0.01005602 1.54706291 0.00000000 0.00000000 1.00000000 -1.40772100 -2.03739417 -1522.64797384 -0.00397809 -0.00190426 -0.00743976
+2 1 5.65283939 5.57449025 2.84281508 1.54412869 0.00000000 0.00000000 1.00000000 7.75304092 6.48949619 -1512.84926162 -0.00637234 -0.00733168 0.00661107
+3 1 0.00066480 2.78022036 0.01010716 1.54612979 0.00000000 0.00000000 1.00000000 -0.93618575 1.92206111 -1520.80305011 -0.00316673 0.00177893 -0.00744575
+4 1 5.65233666 2.85374747 2.84289453 1.54439093 0.00000000 0.00000000 1.00000000 8.11012818 -6.49922039 -1514.31557088 -0.00569217 0.00741000 0.00640353
+5 1 2.82063515 5.64869321 0.01007552 1.54714250 0.00000000 0.00000000 1.00000000 2.49070852 -2.14456666 -1523.53038650 0.00478410 -0.00213962 -0.00751154
+6 1 2.89579803 5.57439179 2.84287630 1.54415032 0.00000000 0.00000000 1.00000000 -8.03062338 6.63950296 -1513.41291897 0.00440396 -0.00717185 0.00633657
+7 1 2.82151287 2.78010538 0.01016303 1.54619615 0.00000000 0.00000000 1.00000000 2.71859584 1.98482729 -1521.34149633 0.00533453 0.00194532 -0.00745901
+8 1 2.89637049 2.85377083 2.84297332 1.54440023 0.00000000 0.00000000 1.00000000 -7.76758760 -6.67134514 -1514.43304618 0.00505040 0.00743195 0.00630302
+9 1 1.41106492 1.38817482 1.72302072 1.18134529 0.00000000 0.00000000 1.00000000 0.27170165 -0.00426695 -444.22843899 0.00100237 -0.00002725 -0.03385965
+10 1 1.41105247 1.38807861 3.96314606 1.18153407 0.00000000 0.00000000 1.00000000 -0.07722674 0.01368756 -337.08703133 -0.00066982 0.00007487 0.07887183
+11 1 1.41105864 4.21395432 1.43987180 1.71989299 0.00000000 0.00000000 1.00000000 -0.01511106 0.00320081 -1653.34500916 0.00010421 0.00007248 0.00634401
+12 1 1.41104843 4.21387554 4.24576823 1.71989825 0.00000000 0.00000000 1.00000000 -0.71645898 0.05923960 -1640.68070568 -0.00117959 0.00006676 -0.01467806
+13 1 4.27433865 1.38779084 1.43977211 1.72010048 0.00000000 0.00000000 1.00000000 0.45899480 0.03956420 -1653.36356942 0.00051885 0.00002313 0.00911600
+14 1 4.27436799 1.38772964 4.24586490 1.72010133 0.00000000 0.00000000 1.00000000 0.38385331 0.07301994 -1642.06086017 -0.00002034 0.00010335 -0.01688908
+15 1 4.27435427 4.21452597 1.39359689 1.65590121 0.00000000 0.00000000 1.00000000 -0.01658773 -0.06159007 -1659.12744163 0.00006470 -0.00006420 -0.01342935
+16 1 4.27434583 4.21455469 4.29208004 1.65592002 0.00000000 0.00000000 1.00000000 -0.15590720 -0.03252166 -1654.84697132 -0.00066755 -0.00003915 -0.00482188
+17 2 1.41096761 1.38958048 0.01029027 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00048351 -0.00022876 -0.00645195
+ITEM: TIMESTEP
+10
+ITEM: NUMBER OF ATOMS
+17
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+-4.0080511965879438e-02 5.7039029418994556e+00 -5.9179115295410201e-03
+1.4436085788922526e-02 5.6674744441011660e+00 -1.1487414836883500e-02
+7.8239288740356017e-03 5.6734038274259646e+00 6.8277359008788905e-04
+ITEM: ATOMS id type x y z 
+1 1 0.00037565 5.64900783 0.00994919 
+2 1 5.65299480 5.57370279 2.84182058 
+3 1 0.00076668 2.78053566 0.01181481 
+4 1 5.65188602 2.85285383 2.84413423 
+5 1 2.82101290 5.64942265 0.01091135 
+6 1 2.89400594 5.57477971 2.84333235 
+7 1 2.82260306 2.78052696 0.00917962 
+8 1 2.89632273 2.85545549 2.84070353 
+9 1 1.41117683 1.38867159 1.72266429 
+10 1 1.41176544 1.38873530 3.96470435
+11 1 1.41085716 4.21342650 1.43850987
+12 1 1.41088045 4.21340876 4.24487134
+13 1 4.27525485 1.38812593 1.43912039
+14 1 4.27483864 1.38696457 4.24782541
+15 1 4.27528588 4.21463764 1.39334117
+16 1 4.27407834 4.21327842 4.29226033
+17 2 1.40675897 1.38612182 0.01000617
diff --git a/tests/test_lammps_spin.py b/tests/test_lammps_spin.py
new file mode 100644
index 00000000..d3d58920
--- /dev/null
+++ b/tests/test_lammps_spin.py
@@ -0,0 +1,153 @@
+from __future__ import annotations
+
+import os
+import shutil
+import unittest
+
+import numpy as np
+from context import dpdata
+
+from dpdata.lammps.dump import get_spin
+
+TRAJ_NO_ID = """ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+17
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+-4.0080511965879438e-02 5.7039029418994556e+00 -5.9179115295410201e-03
+1.4436085788922526e-02 5.6674744441011660e+00 -1.1487414836883500e-02
+7.8239288740356017e-03 5.6734038274259646e+00 6.8277359008788905e-04
+ITEM: ATOMS type x y z c_spin[1] c_spin[2] c_spin[3] c_spin[4] c_spin[5] c_spin[6] c_spin[7] c_spin[8] c_spin[9] c_spin[10]
+1 0.00141160 5.64868599 0.01005602 1.54706291 0.00000000 0.00000000 1.00000000 -1.40772100 -2.03739417 -1522.64797384 -0.00397809 -0.00190426 -0.00743976
+1 5.65283939 5.57449025 2.84281508 1.54412869 0.00000000 0.00000000 1.00000000 7.75304092 6.48949619 -1512.84926162 -0.00637234 -0.00733168 0.00661107
+1 0.00066480 2.78022036 0.01010716 1.54612979 0.00000000 0.00000000 1.00000000 -0.93618575 1.92206111 -1520.80305011 -0.00316673 0.00177893 -0.00744575
+1 5.65233666 2.85374747 2.84289453 1.54439093 0.00000000 0.00000000 1.00000000 8.11012818 -6.49922039 -1514.31557088 -0.00569217 0.00741000 0.00640353
+1 2.82063515 5.64869321 0.01007552 1.54714250 0.00000000 0.00000000 1.00000000 2.49070852 -2.14456666 -1523.53038650 0.00478410 -0.00213962 -0.00751154
+1 2.89579803 5.57439179 2.84287630 1.54415032 0.00000000 0.00000000 1.00000000 -8.03062338 6.63950296 -1513.41291897 0.00440396 -0.00717185 0.00633657
+1 2.82151287 2.78010538 0.01016303 1.54619615 0.00000000 0.00000000 1.00000000 2.71859584 1.98482729 -1521.34149633 0.00533453 0.00194532 -0.00745901
+1 2.89637049 2.85377083 2.84297332 1.54440023 0.00000000 0.00000000 1.00000000 -7.76758760 -6.67134514 -1514.43304618 0.00505040 0.00743195 0.00630302
+1 1.41106492 1.38817482 1.72302072 1.18134529 0.00000000 0.00000000 1.00000000 0.27170165 -0.00426695 -444.22843899 0.00100237 -0.00002725 -0.03385965
+ 1 1.41105247 1.38807861 3.96314606 1.18153407 0.00000000 0.00000000 1.00000000 -0.07722674 0.01368756 -337.08703133 -0.00066982 0.00007487 0.07887183
+ 1 1.41105864 4.21395432 1.43987180 1.71989299 0.00000000 0.00000000 1.00000000 -0.01511106 0.00320081 -1653.34500916 0.00010421 0.00007248 0.00634401
+ 1 1.41104843 4.21387554 4.24576823 1.71989825 0.00000000 0.00000000 1.00000000 -0.71645898 0.05923960 -1640.68070568 -0.00117959 0.00006676 -0.01467806
+ 1 4.27433865 1.38779084 1.43977211 1.72010048 0.00000000 0.00000000 1.00000000 0.45899480 0.03956420 -1653.36356942 0.00051885 0.00002313 0.00911600
+ 1 4.27436799 1.38772964 4.24586490 1.72010133 0.00000000 0.00000000 1.00000000 0.38385331 0.07301994 -1642.06086017 -0.00002034 0.00010335 -0.01688908
+ 1 4.27435427 4.21452597 1.39359689 1.65590121 0.00000000 0.00000000 1.00000000 -0.01658773 -0.06159007 -1659.12744163 0.00006470 -0.00006420 -0.01342935
+ 1 4.27434583 4.21455469 4.29208004 1.65592002 0.00000000 0.00000000 1.00000000 -0.15590720 -0.03252166 -1654.84697132 -0.00066755 -0.00003915 -0.00482188
+ 2 1.41096761 1.38958048 0.01029027 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00048351 -0.00022876 -0.00645195"""
+
+
+class TestLmp(unittest.TestCase):
+    def setUp(self):
+        self.tmp_system = dpdata.System(
+            os.path.join("poscars", "conf.lmp"), type_map=["O", "H"]
+        )
+        self.tmp_system.data["spins"] = [[[3, 4, 0], [0, 4, 3]]]
+        self.lmp_coord_name = "tmp.lmp"
+
+    def tearDown(self):
+        pass  # if os.path.isfile(self.lmp_coord_name):os.remove(self.lmp_coord_name)
+
+    def test_dump_input(self):
+        self.tmp_system.to("lammps/lmp", self.lmp_coord_name)
+        self.assertTrue(os.path.isfile(self.lmp_coord_name))
+        with open(self.lmp_coord_name) as f:
+            c = f.read()
+
+        coord_ref = """     1      1    0.0000000000    0.0000000000    0.0000000000    0.6000000000    0.8000000000    0.0000000000    5.0000000000
+     2      2    1.2621856000    0.7018028000    0.5513885000    0.0000000000    0.8000000000    0.6000000000    5.0000000000"""
+        self.assertTrue(coord_ref in c)
+
+    def test_dump_input_zero_spin(self):
+        self.tmp_system.data["spins"] = [[[0, 0, 0], [0, 0, 0]]]
+        self.tmp_system.to("lammps/lmp", self.lmp_coord_name)
+        self.assertTrue(os.path.isfile(self.lmp_coord_name))
+        with open(self.lmp_coord_name) as f:
+            c = f.read()
+        coord_ref = """     1      1    0.0000000000    0.0000000000    0.0000000000    0.0000000000    0.0000000000    1.0000000000    0.0000000000
+     2      2    1.2621856000    0.7018028000    0.5513885000    0.0000000000    0.0000000000    1.0000000000    0.0000000000"""
+        self.assertTrue(coord_ref in c)
+
+    def test_read_input(self):
+        # check if dpdata can read the spins
+        tmp_system = dpdata.System(
+            "lammps/spin.lmp", fmt="lammps/lmp", type_map=["O", "H"]
+        )
+        self.assertTrue((tmp_system.data["spins"][0] == [[3, 4, 0], [0, 4, 3]]).all())
+
+        tmp_system.to(file_name="lammps/dump", fmt="deepmd/npy")
+        self.assertTrue(os.path.isfile("lammps/dump/set.000/spin.npy"))
+
+        if os.path.isdir("lammps/dump"):
+            shutil.rmtree("lammps/dump")
+
+
+class TestDump(unittest.TestCase):
+    def test_read_dump_spin(self):
+        tmp_system = dpdata.System(
+            "lammps/traj.dump",
+            fmt="lammps/dump",
+            type_map=["O", "H"],
+            input_file="lammps/in.lmp",
+        )
+        self.assertTrue(len(tmp_system.data["spins"]) == 2)
+        np.testing.assert_almost_equal(
+            tmp_system.data["spins"][0][0], [0, 0, 1.54706291], decimal=8
+        )
+        np.testing.assert_almost_equal(
+            tmp_system.data["spins"][0][1], [0, 0, 1.54412869], decimal=8
+        )
+        np.testing.assert_almost_equal(
+            tmp_system.data["spins"][0][-2], [0, 0, 1.65592002], decimal=8
+        )
+        np.testing.assert_almost_equal(
+            tmp_system.data["spins"][0][-1], [0, 0, 0], decimal=8
+        )
+
+        np.testing.assert_almost_equal(
+            tmp_system.data["spins"][1][0],
+            [0.21021514724299958, 1.0123821159859323, -0.6159960941686954],
+            decimal=8,
+        )
+        np.testing.assert_almost_equal(
+            tmp_system.data["spins"][1][1],
+            [1.0057302798645609, 0.568273899191638, -0.2363447073875224],
+            decimal=8,
+        )
+        np.testing.assert_almost_equal(
+            tmp_system.data["spins"][1][-2],
+            [-0.28075943761984146, -1.2845200151690905, -0.0201237855118935],
+            decimal=8,
+        )
+        np.testing.assert_almost_equal(
+            tmp_system.data["spins"][1][-1], [0, 0, 0], decimal=8
+        )
+
+        tmp_system.to(file_name="lammps/dump", fmt="deepmd/npy")
+        self.assertTrue(os.path.isfile("lammps/dump/set.000/spin.npy"))
+
+        if os.path.isdir("lammps/dump"):
+            shutil.rmtree("lammps/dump")
+
+    def test_read_dump_partial_spin(self):
+        # test if dpdata can read the spins when the spin data is not complete
+        with self.assertWarns(UserWarning) as cm:
+            tmp_system = dpdata.System(
+                "lammps/traj_partial_spin.dump",
+                fmt="lammps/dump",
+                type_map=["O", "H"],
+                input_file="lammps/in.lmp",
+            )
+            self.assertTrue("spins" not in tmp_system.data)
+
+        self.assertIn("Warning: spin info is not found in frame", str(cm.warning))
+
+    def test_get_spin_failed(self):
+        with self.assertWarns(UserWarning) as cm:
+            spin = get_spin(
+                TRAJ_NO_ID.split("\n"),
+                ["c_spin[1]", "c_spin[2]", "c_spin[3]", "c_spin[4]"],
+            )
+            self.assertTrue(spin is None)
+
+        self.assertIn("Error processing spin data:", str(cm.warning))

From b908c2b7be49ff6073f3215c0ac982c46715dfc8 Mon Sep 17 00:00:00 2001
From: "A bot of @njzjz" <48687836+njzjz-bot@users.noreply.github.com>
Date: Mon, 28 Oct 2024 23:39:05 -0400
Subject: [PATCH 31/33] docs: replace sphinx-rtd-theme with sphinx-book-theme
 (#745)

Compared to `sphinx-rtd-theme`, `sphinx-book-theme` is a clean and
modern Sphinx theme.

Generated by the task: https://github.com/njzjz-bot/njzjz-bot/issues/11.
---
 docs/conf.py   | 4 ++--
 pyproject.toml | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index a21d19d5..a40422d3 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -44,7 +44,7 @@
 # ones.
 extensions = [
     "deepmodeling_sphinx",
-    "sphinx_rtd_theme",
+    "sphinx_book_theme",
     "sphinx.ext.mathjax",
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
@@ -87,7 +87,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "sphinx_rtd_theme"
+html_theme = "sphinx_book_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
diff --git a/pyproject.toml b/pyproject.toml
index 481e6864..87fa8647 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -55,10 +55,10 @@ pymatgen = ['pymatgen']
 docs = [
     'sphinx',
     'recommonmark',
-    'sphinx_rtd_theme>=1.0.0rc1',
+    'sphinx-book-theme',
     'numpydoc',
     'myst-parser',
-    'deepmodeling-sphinx>=0.1.1',
+    'deepmodeling-sphinx>=0.3.0',
     'sphinx-argparse<0.5.0',
     'rdkit',
     'jupyterlite-sphinx',

From fba50f1be45389e067257247212610602d08836c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 29 Oct 2024 11:55:23 +0800
Subject: [PATCH 32/33] [pre-commit.ci] pre-commit autoupdate (#746)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.7.0 →
v0.7.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.0...v0.7.1)
- [github.com/asottile/blacken-docs: 1.19.0 →
1.19.1](https://github.com/asottile/blacken-docs/compare/1.19.0...1.19.1)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 0bb47d32..245b376b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.7.0
+    rev: v0.7.1
     hooks:
     - id: ruff
       args: ["--fix"]
@@ -36,7 +36,7 @@ repos:
       args: ["--write"]
 # Python inside docs
 -   repo: https://github.com/asottile/blacken-docs
-    rev: 1.19.0
+    rev: 1.19.1
     hooks:
     -   id: blacken-docs
 ci:

From d0a786835a00b5b35cbf6ba72cd2c8373f69443c Mon Sep 17 00:00:00 2001
From: AngelJia <yaosk@dp.tech>
Date: Tue, 29 Oct 2024 00:53:34 -0500
Subject: [PATCH 33/33] Add support for converting move flags between Abacus
 and VASP (#744)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

## Release Notes

- **New Features**
- Enhanced atomic movement handling with the addition of a `move`
parameter across multiple functions, enabling more detailed tracking of
atom movements.
- Introduced selective dynamics support in VASP POSCAR data handling,
allowing for better control over atomic movement flags.
- Added structured representation for cubic boron nitride crystal in new
test files.

- **Bug Fixes**
- Updated atomic positions and magnetic properties in test structures to
reflect accurate simulation data.

- **Tests**
- Added new test methods to validate the handling of movement flags and
ensure the integrity of output structures across various scenarios.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 dpdata/abacus/md.py                 |  4 ++-
 dpdata/abacus/relax.py              |  4 ++-
 dpdata/abacus/scf.py                | 21 +++++++----
 dpdata/plugins/abacus.py            | 15 ++++++++
 dpdata/plugins/vasp.py              | 16 +++++++++
 dpdata/vasp/poscar.py               | 55 ++++++++++++++++++++++++++---
 tests/abacus.scf/STRU.ch4           |  8 ++---
 tests/abacus.scf/stru_test          |  8 ++---
 tests/poscars/POSCAR.oh.err1        | 11 ++++++
 tests/poscars/POSCAR.oh.err2        | 11 ++++++
 tests/test_abacus_stru_dump.py      | 48 +++++++++++++++++++++++--
 tests/test_vasp_poscar_dump.py      | 15 ++++++++
 tests/test_vasp_poscar_to_system.py | 31 ++++++++++++++++
 13 files changed, 224 insertions(+), 23 deletions(-)
 create mode 100644 tests/poscars/POSCAR.oh.err1
 create mode 100644 tests/poscars/POSCAR.oh.err2

diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py
index bbb02343..aa4215d8 100644
--- a/dpdata/abacus/md.py
+++ b/dpdata/abacus/md.py
@@ -167,7 +167,7 @@ def get_frame(fname):
     with open_file(geometry_path_in) as fp:
         geometry_inlines = fp.read().split("\n")
     celldm, cell = get_cell(geometry_inlines)
-    atom_names, natoms, types, coords = get_coords(
+    atom_names, natoms, types, coords, move = get_coords(
         celldm, cell, geometry_inlines, inlines
     )
     # This coords is not to be used.
@@ -221,5 +221,7 @@ def get_frame(fname):
         data["spins"] = magmom
     if len(magforce) > 0:
         data["mag_forces"] = magforce
+    if len(move) > 0:
+        data["move"] = move
 
     return data
diff --git a/dpdata/abacus/relax.py b/dpdata/abacus/relax.py
index be80bc90..63f13678 100644
--- a/dpdata/abacus/relax.py
+++ b/dpdata/abacus/relax.py
@@ -183,7 +183,7 @@ def get_frame(fname):
     with open_file(geometry_path_in) as fp:
         geometry_inlines = fp.read().split("\n")
     celldm, cell = get_cell(geometry_inlines)
-    atom_names, natoms, types, coord_tmp = get_coords(
+    atom_names, natoms, types, coord_tmp, move = get_coords(
         celldm, cell, geometry_inlines, inlines
     )
 
@@ -218,5 +218,7 @@ def get_frame(fname):
         data["spins"] = magmom
     if len(magforce) > 0:
         data["mag_forces"] = magforce
+    if len(move) > 0:
+        data["move"] = move
 
     return data
diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py
index b1b2cfed..43e65f7e 100644
--- a/dpdata/abacus/scf.py
+++ b/dpdata/abacus/scf.py
@@ -299,7 +299,8 @@ def get_coords(celldm, cell, geometry_inlines, inlines=None):
             coords.append(xyz)
             atom_types.append(it)
 
-            move.append(imove)
+            if imove is not None:
+                move.append(imove)
             velocity.append(ivelocity)
             mag.append(imagmom)
             angle1.append(iangle1)
@@ -310,7 +311,8 @@ def get_coords(celldm, cell, geometry_inlines, inlines=None):
             line_idx += 1
     coords = np.array(coords)  # need transformation!!!
     atom_types = np.array(atom_types)
-    return atom_names, atom_numbs, atom_types, coords
+    move = np.array(move, dtype=bool)
+    return atom_names, atom_numbs, atom_types, coords, move
 
 
 def get_energy(outlines):
@@ -477,7 +479,7 @@ def get_frame(fname):
         outlines = fp.read().split("\n")
 
     celldm, cell = get_cell(geometry_inlines)
-    atom_names, natoms, types, coords = get_coords(
+    atom_names, natoms, types, coords, move = get_coords(
         celldm, cell, geometry_inlines, inlines
     )
     magmom, magforce = get_mag_force(outlines)
@@ -510,6 +512,8 @@ def get_frame(fname):
         data["spins"] = magmom
     if len(magforce) > 0:
         data["mag_forces"] = magforce
+    if len(move) > 0:
+        data["move"] = move[np.newaxis, :, :]
     # print("atom_names = ", data['atom_names'])
     # print("natoms = ", data['atom_numbs'])
     # print("types = ", data['atom_types'])
@@ -561,7 +565,7 @@ def get_frame_from_stru(fname):
     nele = get_nele_from_stru(geometry_inlines)
     inlines = [f"ntype {nele}"]
     celldm, cell = get_cell(geometry_inlines)
-    atom_names, natoms, types, coords = get_coords(
+    atom_names, natoms, types, coords, move = get_coords(
         celldm, cell, geometry_inlines, inlines
     )
     data = {}
@@ -571,6 +575,8 @@ def get_frame_from_stru(fname):
     data["cells"] = cell[np.newaxis, :, :]
     data["coords"] = coords[np.newaxis, :, :]
     data["orig"] = np.zeros(3)
+    if len(move) > 0:
+        data["move"] = move[np.newaxis, :, :]
 
     return data
 
@@ -609,8 +615,8 @@ def make_unlabeled_stru(
         numerical descriptor file
     mass : list of float, optional
         List of atomic masses
-    move : list of list of bool, optional
-        List of the move flag of each xyz direction of each atom
+    move : list of (list of list of bool), optional
+        List of the move flag of each xyz direction of each atom for each frame
     velocity : list of list of float, optional
         List of the velocity of each xyz direction of each atom
     mag : list of (list of float or float), optional
@@ -684,6 +690,9 @@ def process_file_input(file_input, atom_names, input_name):
     if mag is None and data.get("spins") is not None and len(data["spins"]) > 0:
         mag = data["spins"][frame_idx]
 
+    if move is None and data.get("move", None) is not None and len(data["move"]) > 0:
+        move = data["move"][frame_idx]
+
     atom_numbs = sum(data["atom_numbs"])
     for key in [move, velocity, mag, angle1, angle2, sc, lambda_]:
         if key is not None:
diff --git a/dpdata/plugins/abacus.py b/dpdata/plugins/abacus.py
index cbd1475f..b3e7c98a 100644
--- a/dpdata/plugins/abacus.py
+++ b/dpdata/plugins/abacus.py
@@ -67,6 +67,18 @@ def register_mag_data(data):
         dpdata.LabeledSystem.register_data_type(dt)
 
 
+def register_move_data(data):
+    if "move" in data:
+        dt = DataType(
+            "move",
+            np.ndarray,
+            (Axis.NFRAMES, Axis.NATOMS, 3),
+            required=False,
+            deepmd_name="move",
+        )
+        dpdata.System.register_data_type(dt)
+
+
 @Format.register("abacus/scf")
 @Format.register("abacus/pw/scf")
 @Format.register("abacus/lcao/scf")
@@ -75,6 +87,7 @@ class AbacusSCFFormat(Format):
     def from_labeled_system(self, file_name, **kwargs):
         data = dpdata.abacus.scf.get_frame(file_name)
         register_mag_data(data)
+        register_move_data(data)
         return data
 
 
@@ -86,6 +99,7 @@ class AbacusMDFormat(Format):
     def from_labeled_system(self, file_name, **kwargs):
         data = dpdata.abacus.md.get_frame(file_name)
         register_mag_data(data)
+        register_move_data(data)
         return data
 
 
@@ -97,4 +111,5 @@ class AbacusRelaxFormat(Format):
     def from_labeled_system(self, file_name, **kwargs):
         data = dpdata.abacus.relax.get_frame(file_name)
         register_mag_data(data)
+        register_move_data(data)
         return data
diff --git a/dpdata/plugins/vasp.py b/dpdata/plugins/vasp.py
index 0160bde2..d25d0c25 100644
--- a/dpdata/plugins/vasp.py
+++ b/dpdata/plugins/vasp.py
@@ -7,6 +7,7 @@
 import dpdata.vasp.outcar
 import dpdata.vasp.poscar
 import dpdata.vasp.xml
+from dpdata.data_type import Axis, DataType
 from dpdata.format import Format
 from dpdata.utils import open_file, uniq_atom_names
 
@@ -14,6 +15,18 @@
     from dpdata.utils import FileType
 
 
+def register_move_data(data):
+    if "move" in data:
+        dt = DataType(
+            "move",
+            np.ndarray,
+            (Axis.NFRAMES, Axis.NATOMS, 3),
+            required=False,
+            deepmd_name="move",
+        )
+        dpdata.System.register_data_type(dt)
+
+
 @Format.register("poscar")
 @Format.register("contcar")
 @Format.register("vasp/poscar")
@@ -25,6 +38,7 @@ def from_system(self, file_name: FileType, **kwargs):
             lines = [line.rstrip("\n") for line in fp]
         data = dpdata.vasp.poscar.to_system_data(lines)
         data = uniq_atom_names(data)
+        register_move_data(data)
         return data
 
     def to_system(self, data, file_name: FileType, frame_idx=0, **kwargs):
@@ -99,6 +113,7 @@ def from_labeled_system(
                 vol = np.linalg.det(np.reshape(data["cells"][ii], [3, 3]))
                 data["virials"][ii] *= v_pref * vol
         data = uniq_atom_names(data)
+        register_move_data(data)
         return data
 
 
@@ -135,4 +150,5 @@ def from_labeled_system(self, file_name, begin=0, step=1, **kwargs):
                 vol = np.linalg.det(np.reshape(data["cells"][ii], [3, 3]))
                 data["virials"][ii] *= v_pref * vol
         data = uniq_atom_names(data)
+        register_move_data(data)
         return data
diff --git a/dpdata/vasp/poscar.py b/dpdata/vasp/poscar.py
index 102e7904..30073e2b 100644
--- a/dpdata/vasp/poscar.py
+++ b/dpdata/vasp/poscar.py
@@ -4,13 +4,22 @@
 import numpy as np
 
 
-def _to_system_data_lower(lines, cartesian=True):
+def _to_system_data_lower(lines, cartesian=True, selective_dynamics=False):
+    def move_flag_mapper(flag):
+        if flag == "T":
+            return True
+        elif flag == "F":
+            return False
+        else:
+            raise RuntimeError(f"Invalid move flag: {flag}")
+
     """Treat as cartesian poscar."""
     system = {}
     system["atom_names"] = [str(ii) for ii in lines[5].split()]
     system["atom_numbs"] = [int(ii) for ii in lines[6].split()]
     scale = float(lines[1])
     cell = []
+    move_flags = []
     for ii in range(2, 5):
         boxv = [float(jj) for jj in lines[ii].split()]
         boxv = np.array(boxv) * scale
@@ -19,12 +28,21 @@ def _to_system_data_lower(lines, cartesian=True):
     natoms = sum(system["atom_numbs"])
     coord = []
     for ii in range(8, 8 + natoms):
-        tmpv = [float(jj) for jj in lines[ii].split()[:3]]
+        tmp = lines[ii].split()
+        tmpv = [float(jj) for jj in tmp[:3]]
         if cartesian:
             tmpv = np.array(tmpv) * scale
         else:
             tmpv = np.matmul(np.array(tmpv), system["cells"][0])
         coord.append(tmpv)
+        if selective_dynamics:
+            if len(tmp) == 6:
+                move_flags.append(list(map(move_flag_mapper, tmp[3:])))
+            else:
+                raise RuntimeError(
+                    f"Invalid move flags, should be 6 columns, got {tmp}"
+                )
+
     system["coords"] = [np.array(coord)]
     system["orig"] = np.zeros(3)
     atom_types = []
@@ -34,12 +52,18 @@ def _to_system_data_lower(lines, cartesian=True):
     system["atom_types"] = np.array(atom_types, dtype=int)
     system["cells"] = np.array(system["cells"])
     system["coords"] = np.array(system["coords"])
+    if move_flags:
+        move_flags = np.array(move_flags, dtype=bool)
+        move_flags = move_flags.reshape((1, natoms, 3))
+        system["move"] = np.array(move_flags, dtype=bool)
     return system
 
 
 def to_system_data(lines):
     # remove the line that has 'selective dynamics'
+    selective_dynamics = False
     if lines[7][0] == "S" or lines[7][0] == "s":
+        selective_dynamics = True
         lines.pop(7)
     is_cartesian = lines[7][0] in ["C", "c", "K", "k"]
     if not is_cartesian:
@@ -47,7 +71,7 @@ def to_system_data(lines):
             raise RuntimeError(
                 "seem not to be a valid POSCAR of vasp 5.x, may be a POSCAR of vasp 4.x?"
             )
-    return _to_system_data_lower(lines, is_cartesian)
+    return _to_system_data_lower(lines, is_cartesian, selective_dynamics)
 
 
 def from_system_data(system, f_idx=0, skip_zeros=True):
@@ -72,6 +96,10 @@ def from_system_data(system, f_idx=0, skip_zeros=True):
             continue
         ret += "%d " % ii
     ret += "\n"
+    move = system.get("move", None)
+    if move is not None and len(move) > 0:
+        ret += "Selective Dynamics\n"
+
     # should use Cartesian for VESTA software
     ret += "Cartesian\n"
     atype = system["atom_types"]
@@ -81,9 +109,26 @@ def from_system_data(system, f_idx=0, skip_zeros=True):
     sort_idx = np.lexsort((np.arange(len(atype)), atype))
     atype = atype[sort_idx]
     posis = posis[sort_idx]
+    if move is not None and len(move) > 0:
+        move = move[f_idx][sort_idx]
+
+    if isinstance(move, np.ndarray):
+        move = move.tolist()
+
     posi_list = []
-    for ii in posis:
-        posi_list.append(f"{ii[0]:15.10f} {ii[1]:15.10f} {ii[2]:15.10f}")
+    for idx in range(len(posis)):
+        ii_posi = posis[idx]
+        line = f"{ii_posi[0]:15.10f} {ii_posi[1]:15.10f} {ii_posi[2]:15.10f}"
+        if move is not None and len(move) > 0:
+            move_flags = move[idx]
+            if not isinstance(move_flags, list) or len(move_flags) != 3:
+                raise RuntimeError(
+                    f"Invalid move flags: {move_flags}, should be a list of 3 bools"
+                )
+            line += " " + " ".join("T" if flag else "F" for flag in move_flags)
+
+        posi_list.append(line)
+
     posi_list.append("")
     ret += "\n".join(posi_list)
     return ret
diff --git a/tests/abacus.scf/STRU.ch4 b/tests/abacus.scf/STRU.ch4
index cf97747a..bc33cbe9 100644
--- a/tests/abacus.scf/STRU.ch4
+++ b/tests/abacus.scf/STRU.ch4
@@ -18,11 +18,11 @@ Cartesian 				#Cartesian(Unit is LATTICE_CONSTANT)
 C 						#Name of element	
 0.0						#Magnetic for this element.
 1				#Number of atoms
-0.981274803    0.861285385    0.838442496 0 0 0
+0.981274803    0.861285385    0.838442496 1 1 1
 H
 0.0
 4
 1.023557202    0.758025625    0.66351336 0 0 0
-0.78075702    0.889445935    0.837363468 0 0 0
-1.064091613    1.043438905    0.840995502 0 0 0
-1.039321214    0.756530859    1.009609207 0 0 0
+0.78075702    0.889445935    0.837363468 1 0 1
+1.064091613    1.043438905    0.840995502 1 0 1
+1.039321214    0.756530859    1.009609207 0 1 1
diff --git a/tests/abacus.scf/stru_test b/tests/abacus.scf/stru_test
index 22d619c9..e4036409 100644
--- a/tests/abacus.scf/stru_test
+++ b/tests/abacus.scf/stru_test
@@ -26,7 +26,7 @@ C
 H
 0.0
 4
-5.416431453540 4.011298860305 3.511161492417 1 1 1
-4.131588222365 4.706745191323 4.431136645083 1 1 1
-5.630930319126 5.521640894956 4.450356541303 1 1 1
-5.499851012568 4.003388899277 5.342621842622 1 1 1
+5.416431453540 4.011298860305 3.511161492417 0 0 0
+4.131588222365 4.706745191323 4.431136645083 1 0 1
+5.630930319126 5.521640894956 4.450356541303 1 0 1
+5.499851012568 4.003388899277 5.342621842622 0 1 1
diff --git a/tests/poscars/POSCAR.oh.err1 b/tests/poscars/POSCAR.oh.err1
new file mode 100644
index 00000000..1b7521e6
--- /dev/null
+++ b/tests/poscars/POSCAR.oh.err1
@@ -0,0 +1,11 @@
+Cubic BN
+   3.57
+ 0.00 0.50 0.50
+ 0.45 0.00 0.50
+ 0.55 0.51 0.00
+ O H
+   1 1
+Selective dynamics
+Cartesian
+ 0.00 0.00 0.00 T T F
+ 0.25 0.25 0.25 F F
diff --git a/tests/poscars/POSCAR.oh.err2 b/tests/poscars/POSCAR.oh.err2
new file mode 100644
index 00000000..ed52d4d0
--- /dev/null
+++ b/tests/poscars/POSCAR.oh.err2
@@ -0,0 +1,11 @@
+Cubic BN
+   3.57
+ 0.00 0.50 0.50
+ 0.45 0.00 0.50
+ 0.55 0.51 0.00
+ O H
+   1 1
+Selective dynamics
+Cartesian
+ 0.00 0.00 0.00 T T F
+ 0.25 0.25 0.25 a T F
diff --git a/tests/test_abacus_stru_dump.py b/tests/test_abacus_stru_dump.py
index 4549b6d1..8891dee3 100644
--- a/tests/test_abacus_stru_dump.py
+++ b/tests/test_abacus_stru_dump.py
@@ -141,8 +141,52 @@ def test_dump_spin(self):
 4
 5.416431453540 4.011298860305 3.511161492417 1 1 1 mag 4.000000000000 5.000000000000 6.000000000000
 4.131588222365 4.706745191323 4.431136645083 1 1 1 mag 1.000000000000 1.000000000000 1.000000000000
-5.630930319126 5.521640894956 4.450356541303 1 1 1 mag 2.000000000000 2.000000000000 2.000000000000
-5.499851012568 4.003388899277 5.342621842622 1 1 1 mag 3.000000000000 3.000000000000 3.000000000000
+5.630930319126 5.521640894956 4.450356541303 0 0 0 mag 2.000000000000 2.000000000000 2.000000000000
+5.499851012568 4.003388899277 5.342621842622 0 0 0 mag 3.000000000000 3.000000000000 3.000000000000
+"""
+        self.assertTrue(stru_ref in c)
+
+    def test_dump_move_from_vasp(self):
+        self.system = dpdata.System()
+        self.system.from_vasp_poscar(os.path.join("poscars", "POSCAR.oh.c"))
+        self.system.to(
+            "abacus/stru",
+            "STRU_tmp",
+            pp_file={"O": "O.upf", "H": "H.upf"},
+        )
+        assert os.path.isfile("STRU_tmp")
+        with open("STRU_tmp") as f:
+            c = f.read()
+
+        stru_ref = """O
+0.0
+1
+0.000000000000 0.000000000000 0.000000000000 1 1 0
+H
+0.0
+1
+1.262185604418 0.701802783513 0.551388341420 0 0 0
+"""
+        self.assertTrue(stru_ref in c)
+
+        self.system.to(
+            "abacus/stru",
+            "STRU_tmp",
+            pp_file={"O": "O.upf", "H": "H.upf"},
+            move=[[True, False, True], [False, True, False]],
+        )
+        assert os.path.isfile("STRU_tmp")
+        with open("STRU_tmp") as f:
+            c = f.read()
+
+        stru_ref = """O
+0.0
+1
+0.000000000000 0.000000000000 0.000000000000 1 0 1
+H
+0.0
+1
+1.262185604418 0.701802783513 0.551388341420 0 1 0
 """
         self.assertTrue(stru_ref in c)
 
diff --git a/tests/test_vasp_poscar_dump.py b/tests/test_vasp_poscar_dump.py
index 62f21598..d5522811 100644
--- a/tests/test_vasp_poscar_dump.py
+++ b/tests/test_vasp_poscar_dump.py
@@ -34,6 +34,21 @@ def setUp(self):
         self.system = dpdata.System()
         self.system.from_vasp_poscar("tmp.POSCAR")
 
+    def test_dump_move_flags(self):
+        tmp_system = dpdata.System()
+        tmp_system.from_vasp_poscar(os.path.join("poscars", "POSCAR.oh.c"))
+        tmp_system.to_vasp_poscar("tmp.POSCAR")
+        self.system = dpdata.System()
+        self.system.from_vasp_poscar("tmp.POSCAR")
+        with open("tmp.POSCAR") as f:
+            content = f.read()
+
+        stru_ref = """Cartesian
+   0.0000000000    0.0000000000    0.0000000000 T T F
+   1.2621856044    0.7018027835    0.5513883414 F F F
+"""
+        self.assertTrue(stru_ref in content)
+
 
 class TestPOSCARSkipZeroAtomNumb(unittest.TestCase):
     def tearDown(self):
diff --git a/tests/test_vasp_poscar_to_system.py b/tests/test_vasp_poscar_to_system.py
index 7457d33d..9e5d7f37 100644
--- a/tests/test_vasp_poscar_to_system.py
+++ b/tests/test_vasp_poscar_to_system.py
@@ -14,6 +14,37 @@ def setUp(self):
         self.system = dpdata.System()
         self.system.from_vasp_poscar(os.path.join("poscars", "POSCAR.oh.c"))
 
+    def test_move_flags(self):
+        expected = np.array([[[True, True, False], [False, False, False]]])
+        self.assertTrue(np.array_equal(self.system["move"], expected))
+
+
+class TestPOSCARMoveFlags(unittest.TestCase):
+    def setUp(self):
+        self.tmp_file = "POSCAR.tmp.1"
+
+    def tearDown(self):
+        if os.path.exists(self.tmp_file):
+            os.remove(self.tmp_file)
+
+    def test_move_flags_error1(self):
+        with self.assertRaisesRegex(RuntimeError, "Invalid move flags.*?"):
+            dpdata.System().from_vasp_poscar(os.path.join("poscars", "POSCAR.oh.err1"))
+
+    def test_move_flags_error2(self):
+        with self.assertRaisesRegex(RuntimeError, "Invalid move flag: a"):
+            dpdata.System().from_vasp_poscar(os.path.join("poscars", "POSCAR.oh.err2"))
+
+    def test_move_flags_error3(self):
+        system = dpdata.System().from_vasp_poscar(
+            os.path.join("poscars", "POSCAR.oh.c")
+        )
+        system.data["move"] = np.array([[[True, True], [False, False]]])
+        with self.assertRaisesRegex(
+            RuntimeError, "Invalid move flags:.*?should be a list of 3 bools"
+        ):
+            system.to_vasp_poscar(self.tmp_file)
+
 
 class TestPOSCARDirect(unittest.TestCase, TestPOSCARoh):
     def setUp(self):