Merge remote-tracking branch 'origin/fix-pmg' into fix-pmg

.github/workflows/test.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.12"]
+        python-version: ["3.8", "3.12"]
 
     steps:
     - uses: actions/checkout@v4

.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.8.4
+    rev: v0.9.1
     hooks:
     - id: ruff
       args: ["--fix"]

docs/installation.md

@@ -1,6 +1,6 @@
 # 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:
+dpdata only supports Python 3.8 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 dpdata:
 
 - Install via pip: `pip install dpdata`
 - Install via conda: `conda install -c conda-forge dpdata`

docs/make_format.py

@@ -2,14 +2,9 @@
 
 import csv
 import os
-import sys
 from collections import defaultdict
 from inspect import Parameter, Signature, cleandoc, signature
-
-if sys.version_info >= (3, 8):
-    from typing import Literal
-else:
-    from typing_extensions import Literal
+from typing import Literal
 
 from numpydoc.docscrape import Parameter as numpydoc_Parameter
 from numpydoc.docscrape_sphinx import SphinxDocString

dpdata/abacus/md.py

@@ -56,9 +56,9 @@ def get_coords_from_dump(dumplines, natoms):
     if "VIRIAL" in dumplines[6]:
         calc_stress = True
         check_line = 10
-    assert (
-        "POSITION" in dumplines[check_line]
-    ), "keywords 'POSITION' cannot be found in the 6th line. Please check."
+    assert "POSITION" in dumplines[check_line], (
+        "keywords 'POSITION' cannot be found in the 6th line. Please check."
+    )
     if "FORCE" in dumplines[check_line]:
         calc_force = True
 

dpdata/ase_calculator.py

@@ -62,7 +62,8 @@ def calculate(
         self.results["energy"] = data["energies"][0]
         # see https://gitlab.com/ase/ase/-/merge_requests/2485
         self.results["free_energy"] = data["energies"][0]
-        self.results["forces"] = data["forces"][0]
+        if "forces" in data:
+            self.results["forces"] = data["forces"][0]
         if "virials" in data:
             self.results["virial"] = data["virials"][0].reshape(3, 3)
 

dpdata/deepmd/mixed.py

@@ -15,9 +15,9 @@ def to_system_data(folder, type_map=None, labels=True):
     if type_map is not None:
         assert isinstance(type_map, list)
         missing_type = [i for i in old_type_map if i not in type_map]
-        assert (
-            not missing_type
-        ), f"These types are missing in selected type_map: {missing_type} !"
+        assert not missing_type, (
+            f"These types are missing in selected type_map: {missing_type} !"
+        )
         index_map = np.array([type_map.index(i) for i in old_type_map])
         data["atom_names"] = type_map.copy()
     else:

dpdata/driver.py

@@ -166,7 +166,8 @@ def label(self, data: dict) -> dict:
                 labeled_data = lb_data.copy()
             else:
                 labeled_data["energies"] += lb_data["energies"]
-                labeled_data["forces"] += lb_data["forces"]
+                if "forces" in labeled_data and "forces" in lb_data:
+                    labeled_data["forces"] += lb_data["forces"]
                 if "virials" in labeled_data and "virials" in lb_data:
                     labeled_data["virials"] += lb_data["virials"]
         return labeled_data

dpdata/plugins/ase.py

@@ -175,7 +175,9 @@ def to_labeled_system(self, data, *args, **kwargs) -> list[ase.Atoms]:
                 cell=data["cells"][ii],
             )
 
-            results = {"energy": data["energies"][ii], "forces": data["forces"][ii]}
+            results = {"energy": data["energies"][ii]}
+            if "forces" in data:
+                results["forces"] = data["forces"][ii]
             if "virials" in data:
                 # convert to GPa as this is ase convention
                 # v_pref = 1 * 1e4 / 1.602176621e6
@@ -296,7 +298,10 @@ def from_labeled_system(
             dict_frames["energies"] = np.append(
                 dict_frames["energies"], tmp["energies"][0]
             )
-            dict_frames["forces"] = np.append(dict_frames["forces"], tmp["forces"][0])
+            if "forces" in tmp.keys() and "forces" in dict_frames.keys():
+                dict_frames["forces"] = np.append(
+                    dict_frames["forces"], tmp["forces"][0]
+                )
             if "virials" in tmp.keys() and "virials" in dict_frames.keys():
                 dict_frames["virials"] = np.append(
                     dict_frames["virials"], tmp["virials"][0]
@@ -305,7 +310,8 @@ def from_labeled_system(
         ## Correct the shape of numpy arrays
         dict_frames["cells"] = dict_frames["cells"].reshape(-1, 3, 3)
         dict_frames["coords"] = dict_frames["coords"].reshape(len(sub_traj), -1, 3)
-        dict_frames["forces"] = dict_frames["forces"].reshape(len(sub_traj), -1, 3)
+        if "forces" in dict_frames.keys():
+            dict_frames["forces"] = dict_frames["forces"].reshape(len(sub_traj), -1, 3)
         if "virials" in dict_frames.keys():
             dict_frames["virials"] = dict_frames["virials"].reshape(-1, 3, 3)
 

dpdata/plugins/n2p2.py

@@ -85,18 +85,18 @@ def from_labeled_system(self, file_name: FileType, **kwargs):
                     energy = None
                 elif line.lower() == "end":
                     # If we are at the end of a section, process the section
-                    assert (
-                        len(coord) == len(atype) == len(force)
-                    ), "Number of atoms, atom types, and forces must match."
+                    assert len(coord) == len(atype) == len(force), (
+                        "Number of atoms, atom types, and forces must match."
+                    )
 
                     # Check if the number of atoms is consistent across all frames
                     natom = len(coord)
                     if natom0 is None:
                         natom0 = natom
                     else:
-                        assert (
-                            natom == natom0
-                        ), "The number of atoms in all frames must be the same."
+                        assert natom == natom0, (
+                            "The number of atoms in all frames must be the same."
+                        )
 
                     # Check if the number of atoms of each type is consistent across all frames
                     atype = np.array(atype)
@@ -108,9 +108,9 @@ def from_labeled_system(self, file_name: FileType, **kwargs):
                     if natoms0 is None:
                         natoms0 = natoms
                     else:
-                        assert (
-                            natoms == natoms0
-                        ), "The number of atoms of each type in all frames must be the same."
+                        assert natoms == natoms0, (
+                            "The number of atoms of each type in all frames must be the same."
+                        )
                     if atom_types0 is None:
                         atom_types0 = atype
                     atom_order = match_indices(atom_types0, atype)

dpdata/plugins/pwmat.py

@@ -31,11 +31,13 @@ def from_labeled_system(
             data["cells"],
             data["coords"],
             data["energies"],
-            data["forces"],
+            tmp_force,
             tmp_virial,
         ) = dpdata.pwmat.movement.get_frames(
             file_name, begin=begin, step=step, convergence_check=convergence_check
         )
+        if tmp_force is not None:
+            data["forces"] = tmp_force
         if tmp_virial is not None:
             data["virials"] = tmp_virial
         # scale virial to the unit of eV

dpdata/plugins/vasp.py

@@ -95,7 +95,7 @@ def from_labeled_system(
             data["cells"],
             data["coords"],
             data["energies"],
-            data["forces"],
+            tmp_force,
             tmp_virial,
         ) = dpdata.vasp.outcar.get_frames(
             file_name,
@@ -104,6 +104,8 @@ def from_labeled_system(
             ml=ml,
             convergence_check=convergence_check,
         )
+        if tmp_force is not None:
+            data["forces"] = tmp_force
         if tmp_virial is not None:
             data["virials"] = tmp_virial
         # scale virial to the unit of eV

dpdata/stat.py

@@ -55,12 +55,12 @@ class ErrorsBase(metaclass=ABCMeta):
     SYSTEM_TYPE = object
 
     def __init__(self, system_1: SYSTEM_TYPE, system_2: SYSTEM_TYPE) -> None:
-        assert isinstance(
-            system_1, self.SYSTEM_TYPE
-        ), f"system_1 should be {self.SYSTEM_TYPE.__name__}"
-        assert isinstance(
-            system_2, self.SYSTEM_TYPE
-        ), f"system_2 should be {self.SYSTEM_TYPE.__name__}"
+        assert isinstance(system_1, self.SYSTEM_TYPE), (
+            f"system_1 should be {self.SYSTEM_TYPE.__name__}"
+        )
+        assert isinstance(system_2, self.SYSTEM_TYPE), (
+            f"system_2 should be {self.SYSTEM_TYPE.__name__}"
+        )
         self.system_1 = system_1
         self.system_2 = system_2
 
@@ -116,15 +116,15 @@ class Errors(ErrorsBase):
     SYSTEM_TYPE = LabeledSystem
 
     @property
-    @lru_cache()
+    @lru_cache
     def e_errors(self) -> np.ndarray:
         """Energy errors."""
         assert isinstance(self.system_1, self.SYSTEM_TYPE)
         assert isinstance(self.system_2, self.SYSTEM_TYPE)
         return self.system_1["energies"] - self.system_2["energies"]
 
     @property
-    @lru_cache()
+    @lru_cache
     def f_errors(self) -> np.ndarray:
         """Force errors."""
         assert isinstance(self.system_1, self.SYSTEM_TYPE)
@@ -153,7 +153,7 @@ class MultiErrors(ErrorsBase):
     SYSTEM_TYPE = MultiSystems
 
     @property
-    @lru_cache()
+    @lru_cache
     def e_errors(self) -> np.ndarray:
         """Energy errors."""
         assert isinstance(self.system_1, self.SYSTEM_TYPE)
@@ -166,7 +166,7 @@ def e_errors(self) -> np.ndarray:
         return np.concatenate(errors)
 
     @property
-    @lru_cache()
+    @lru_cache
     def f_errors(self) -> np.ndarray:
         """Force errors."""
         assert isinstance(self.system_1, self.SYSTEM_TYPE)

dpdata/system.py

@@ -5,21 +5,16 @@
 import hashlib
 import numbers
 import os
-import sys
 import warnings
 from copy import deepcopy
 from typing import (
     TYPE_CHECKING,
     Any,
     Iterable,
+    Literal,
     overload,
 )
 
-if sys.version_info >= (3, 8):
-    from typing import Literal
-else:
-    from typing_extensions import Literal
-
 import numpy as np
 
 import dpdata
@@ -1209,7 +1204,11 @@ class LabeledSystem(System):
     DTYPES: tuple[DataType, ...] = System.DTYPES + (
         DataType("energies", np.ndarray, (Axis.NFRAMES,), deepmd_name="energy"),
         DataType(
-            "forces", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3), deepmd_name="force"
+            "forces",
+            np.ndarray,
+            (Axis.NFRAMES, Axis.NATOMS, 3),
+            required=False,
+            deepmd_name="force",
         ),
         DataType(
             "virials",
@@ -1269,13 +1268,17 @@ def __add__(self, others):
             raise RuntimeError("Unspported data structure")
         return self.__class__.from_dict({"data": self_copy.data})
 
+    def has_forces(self) -> bool:
+        return "forces" in self.data
+
     def has_virial(self) -> bool:
         # return ('virials' in self.data) and (len(self.data['virials']) > 0)
         return "virials" in self.data
 
     def affine_map_fv(self, trans, f_idx: int | numbers.Integral):
         assert np.linalg.det(trans) != 0
-        self.data["forces"][f_idx] = np.matmul(self.data["forces"][f_idx], trans)
+        if self.has_forces():
+            self.data["forces"][f_idx] = np.matmul(self.data["forces"][f_idx], trans)
         if self.has_virial():
             self.data["virials"][f_idx] = np.matmul(
                 trans.T, np.matmul(self.data["virials"][f_idx], trans)
@@ -1308,7 +1311,8 @@ def correction(self, hl_sys: LabeledSystem) -> LabeledSystem:
             raise RuntimeError("high_sys should be LabeledSystem")
         corrected_sys = self.copy()
         corrected_sys.data["energies"] = hl_sys.data["energies"] - self.data["energies"]
-        corrected_sys.data["forces"] = hl_sys.data["forces"] - self.data["forces"]
+        if "forces" in self.data and "forces" in hl_sys.data:
+            corrected_sys.data["forces"] = hl_sys.data["forces"] - self.data["forces"]
         if "virials" in self.data and "virials" in hl_sys.data:
             corrected_sys.data["virials"] = (
                 hl_sys.data["virials"] - self.data["virials"]

dpdata/utils.py

@@ -2,14 +2,9 @@
 
 import io
 import os
-import sys
 from contextlib import contextmanager
-from typing import TYPE_CHECKING, Generator, overload
+from typing import TYPE_CHECKING, Generator, Literal, overload
 
-if sys.version_info >= (3, 8):
-    from typing import Literal
-else:
-    from typing_extensions import Literal
 import numpy as np
 
 from dpdata.periodic_table import Element

dpdata/vasp/outcar.py

@@ -161,9 +161,9 @@ def analyze_block(lines, ntot, nelm, ml=False):
                 not lines[idx + in_kB_index].split()[0:2] == ["in", "kB"]
             ):
                 in_kB_index += 1
-            assert idx + in_kB_index < len(
-                lines
-            ), 'ERROR: "in kB" is not found in OUTCAR. Unable to extract virial.'
+            assert idx + in_kB_index < len(lines), (
+                'ERROR: "in kB" is not found in OUTCAR. Unable to extract virial.'
+            )
             tmp_v = [float(ss) for ss in lines[idx + in_kB_index].split()[2:8]]
             virial = np.zeros([3, 3])
             virial[0][0] = tmp_v[0]

dpdata/vasp/xml.py

@@ -7,9 +7,9 @@
 
 
 def check_name(item, name):
-    assert (
-        item.attrib["name"] == name
-    ), "item attrib '{}' dose not math required '{}'".format(item.attrib["name"], name)
+    assert item.attrib["name"] == name, (
+        "item attrib '{}' dose not math required '{}'".format(item.attrib["name"], name)
+    )
 
 
 def get_varray(varray):

dpdata/xyz/quip_gap_xyz.py

@@ -161,7 +161,7 @@ def handle_single_xyz_frame(lines):
                         list(filter(bool, field_dict["virial"].split(" ")))
                     ).reshape(3, 3)
                 ]
-            ).astype("float32")
+            ).astype(np.float64)
         else:
             virials = None
 
@@ -175,10 +175,10 @@ def handle_single_xyz_frame(lines):
                     3, 3
                 )
             ]
-        ).astype("float32")
-        info_dict["coords"] = np.array([coords_array]).astype("float32")
-        info_dict["energies"] = np.array([field_dict["energy"]]).astype("float32")
-        info_dict["forces"] = np.array([force_array]).astype("float32")
+        ).astype(np.float64)
+        info_dict["coords"] = np.array([coords_array]).astype(np.float64)
+        info_dict["energies"] = np.array([field_dict["energy"]]).astype(np.float64)
+        info_dict["forces"] = np.array([force_array]).astype(np.float64)
         if virials is not None:
             info_dict["virials"] = virials
         info_dict["orig"] = np.zeros(3)

pyproject.toml

@@ -12,7 +12,6 @@ authors = [
 ]
 license = {file = "LICENSE"}
 classifiers = [
-    "Programming Language :: Python :: 3.7",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
@@ -28,7 +27,7 @@ dependencies = [
     'importlib_metadata>=1.4; python_version < "3.8"',
     'typing_extensions; python_version < "3.8"',
 ]
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 readme = "README.md"
 keywords = ["lammps", "vasp", "deepmd-kit"]