From a2f058a77d246eaccf22433a0f936b6a0d0b8713 Mon Sep 17 00:00:00 2001
From: marvinfriede <51965259+marvinfriede@users.noreply.github.com>
Date: Thu, 21 Dec 2023 23:30:17 +0100
Subject: [PATCH] Typing refactor
---
.pre-commit-config.yaml | 7 +
docs/modules/data/index.rst | 2 +
docs/modules/data/radii.rst | 1 +
docs/modules/data/zeff.rst | 2 +
docs/modules/typing/builtin.rst | 2 +
docs/modules/typing/index.rst | 8 +
docs/modules/typing/pytorch.rst | 2 +
pyproject.toml | 4 +
src/tad_dftd4/cutoff.py | 2 +-
src/tad_dftd4/damping/atm.py | 8 +-
src/tad_dftd4/damping/rational.py | 2 +-
src/tad_dftd4/data/__init__.py | 4 +-
src/tad_dftd4/data/hardness.py | 10 +-
src/tad_dftd4/data/r4r2.py | 6 +-
src/tad_dftd4/data/radii.py | 26 +
src/tad_dftd4/data/zeff.py | 26 +
src/tad_dftd4/disp.py | 7 +-
src/tad_dftd4/model.py | 11 +-
src/tad_dftd4/typing/__init__.py | 25 +
src/tad_dftd4/typing/builtin.py | 25 +
src/tad_dftd4/typing/pytorch.py | 34 +
test/conftest.py | 6 +-
test/test_cutoff/test_general.py | 2 +-
test/test_cutoff/test_types.py | 10 +-
test/test_disp/samples.py | 2205 +++++-----
test/test_disp/test_atm.py | 2 +-
test/test_disp/test_full.py | 7 +-
test/test_disp/test_twobody.py | 6 +-
test/test_grad/samples_grad.py | 2353 +++++-----
test/test_grad/samples_hessian.py | 6669 +++++++++++++++--------------
test/test_grad/test_hessian.py | 2 +-
test/test_grad/test_nan.py | 2 +-
test/test_grad/test_param.py | 2 +-
test/test_grad/test_pos.py | 2 +-
test/test_model/samples.py | 2325 +++++-----
test/test_model/test_c6.py | 2 +-
test/test_model/test_general.py | 2 +-
test/test_model/test_model.py | 2 +-
test/test_model/test_params.py | 4 +-
test/test_model/test_weights.py | 2 +-
40 files changed, 7017 insertions(+), 6802 deletions(-)
create mode 100644 docs/modules/data/radii.rst
create mode 100644 docs/modules/data/zeff.rst
create mode 100644 docs/modules/typing/builtin.rst
create mode 100644 docs/modules/typing/index.rst
create mode 100644 docs/modules/typing/pytorch.rst
create mode 100644 src/tad_dftd4/data/radii.py
create mode 100644 src/tad_dftd4/data/zeff.py
create mode 100644 src/tad_dftd4/typing/__init__.py
create mode 100644 src/tad_dftd4/typing/builtin.py
create mode 100644 src/tad_dftd4/typing/pytorch.py
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b4324da..c9e30ca 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -59,3 +59,10 @@ repos:
hooks:
- id: black
stages: [commit]
+
+ - repo: https://github.com/pre-commit/mirrors-mypy
+ rev: v1.7.1
+ hooks:
+ - id: mypy
+ additional_dependencies: [types-all]
+ exclude: 'test/conftest.py'
diff --git a/docs/modules/data/index.rst b/docs/modules/data/index.rst
index ec656e6..7cbfada 100644
--- a/docs/modules/data/index.rst
+++ b/docs/modules/data/index.rst
@@ -6,3 +6,5 @@
hardness
r4r2
+ radii
+ zeff
diff --git a/docs/modules/data/radii.rst b/docs/modules/data/radii.rst
new file mode 100644
index 0000000..cd71f70
--- /dev/null
+++ b/docs/modules/data/radii.rst
@@ -0,0 +1 @@
+.. automodule:: tad_dftd4.data.radii
diff --git a/docs/modules/data/zeff.rst b/docs/modules/data/zeff.rst
new file mode 100644
index 0000000..2342b77
--- /dev/null
+++ b/docs/modules/data/zeff.rst
@@ -0,0 +1,2 @@
+.. automodule:: tad_dftd4.data.zeff
+ :members:
diff --git a/docs/modules/typing/builtin.rst b/docs/modules/typing/builtin.rst
new file mode 100644
index 0000000..3177905
--- /dev/null
+++ b/docs/modules/typing/builtin.rst
@@ -0,0 +1,2 @@
+.. automodule:: tad_dftd4.typing.builtin
+ :members:
diff --git a/docs/modules/typing/index.rst b/docs/modules/typing/index.rst
new file mode 100644
index 0000000..ec16460
--- /dev/null
+++ b/docs/modules/typing/index.rst
@@ -0,0 +1,8 @@
+.. _typing:
+
+.. automodule:: tad_dftd4.typing
+
+.. toctree::
+
+ builtin
+ pytorch
diff --git a/docs/modules/typing/pytorch.rst b/docs/modules/typing/pytorch.rst
new file mode 100644
index 0000000..0a28eea
--- /dev/null
+++ b/docs/modules/typing/pytorch.rst
@@ -0,0 +1,2 @@
+.. automodule:: tad_dftd4.typing.pytorch
+ :members:
diff --git a/pyproject.toml b/pyproject.toml
index 7ea1187..a1dfcfc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,6 +38,10 @@ disallow_untyped_defs = true
warn_redundant_casts = true
warn_unreachable = true
warn_unused_ignores = true
+exclude = '''
+ (?x)
+ ^test?s/conftest.py$
+'''
[tool.coverage.run]
diff --git a/src/tad_dftd4/cutoff.py b/src/tad_dftd4/cutoff.py
index 946c949..c2669e1 100644
--- a/src/tad_dftd4/cutoff.py
+++ b/src/tad_dftd4/cutoff.py
@@ -25,9 +25,9 @@
from __future__ import annotations
import torch
-from tad_mctc.typing import Tensor, TensorLike
from . import defaults
+from .typing import Tensor, TensorLike
class Cutoff(TensorLike):
diff --git a/src/tad_dftd4/damping/atm.py b/src/tad_dftd4/damping/atm.py
index a57594f..0f3bfd9 100644
--- a/src/tad_dftd4/damping/atm.py
+++ b/src/tad_dftd4/damping/atm.py
@@ -38,10 +38,9 @@
import torch
from tad_mctc import storch
from tad_mctc.batch import real_pairs, real_triples
-from tad_mctc.typing import DD, Tensor
-from .. import defaults
-from ..data import r4r2
+from .. import data, defaults
+from ..typing import DD, Tensor
def get_atm_dispersion(
@@ -103,7 +102,8 @@ def get_atm_dispersion(
torch.abs(c6.unsqueeze(-1) * c6.unsqueeze(-2) * c6.unsqueeze(-3)),
)
- radii = r4r2[numbers].unsqueeze(-1) * r4r2[numbers].unsqueeze(-2)
+ rad = data.R4R2[numbers]
+ radii = rad.unsqueeze(-1) * rad.unsqueeze(-2)
temp = a1 * storch.sqrt(3.0 * radii) + a2
r0ij = temp.unsqueeze(-1)
diff --git a/src/tad_dftd4/damping/rational.py b/src/tad_dftd4/damping/rational.py
index bcdf8db..81fe84d 100644
--- a/src/tad_dftd4/damping/rational.py
+++ b/src/tad_dftd4/damping/rational.py
@@ -31,9 +31,9 @@
from __future__ import annotations
import torch
-from tad_mctc.typing import Tensor
from .. import defaults
+from ..typing import Tensor
def rational_damping(
diff --git a/src/tad_dftd4/data/__init__.py b/src/tad_dftd4/data/__init__.py
index 5167620..605e54e 100644
--- a/src/tad_dftd4/data/__init__.py
+++ b/src/tad_dftd4/data/__init__.py
@@ -26,7 +26,9 @@
- covalent radii
- effective nuclear charge
-Some atomic data is imported from the `tad_mctc` library.
+Some atomic data is imported from the `tad_mctc` library or indirectly used within the `tad_mctc` library.
"""
from .hardness import *
from .r4r2 import *
+from .radii import *
+from .zeff import *
diff --git a/src/tad_dftd4/data/hardness.py b/src/tad_dftd4/data/hardness.py
index ce07394..04a6d3f 100644
--- a/src/tad_dftd4/data/hardness.py
+++ b/src/tad_dftd4/data/hardness.py
@@ -16,18 +16,18 @@
# You should have received a copy of the GNU Lesser General Public License
# along with tad-dftd4. If not, see .
"""
-Atomic data: Chemical hardnesses
-================================
+Data: Chemical hardnesses
+=========================
Element-specific chemical hardnesses for the charge scaling function used
to extrapolate the C6 coefficients in DFT-D4.
"""
-
import torch
-__all__ = ["gam"]
+__all__ = ["GAM"]
+
-gam = torch.tensor(
+GAM = torch.tensor(
[
0.00000000, # None
0.47259288, # H
diff --git a/src/tad_dftd4/data/r4r2.py b/src/tad_dftd4/data/r4r2.py
index ad310f7..d30b0ad 100644
--- a/src/tad_dftd4/data/r4r2.py
+++ b/src/tad_dftd4/data/r4r2.py
@@ -24,10 +24,10 @@
Also new super heavies Cn, Nh, Fl, Lv, Og and Am-Rg calculated at
4c-PBE/Dyall-AE4Z level (Dirac 2022).
"""
-
import torch
-__all__ = ["r4r2"]
+__all__ = ["R4R2"]
+
# fmt: off
r4_over_r2 = torch.tensor([
@@ -60,5 +60,5 @@
# fmt: on
-r4r2 = torch.sqrt(0.5 * (r4_over_r2 * torch.sqrt(torch.arange(r4_over_r2.shape[0]))))
+R4R2 = torch.sqrt(0.5 * (r4_over_r2 * torch.sqrt(torch.arange(r4_over_r2.shape[0]))))
"""r⁴ over r² expectation values."""
diff --git a/src/tad_dftd4/data/radii.py b/src/tad_dftd4/data/radii.py
new file mode 100644
index 0000000..dbd36b3
--- /dev/null
+++ b/src/tad_dftd4/data/radii.py
@@ -0,0 +1,26 @@
+# This file is part of tad-dftd4.
+#
+# SPDX-Identifier: LGPL-3.0
+# Copyright (C) 2022 Marvin Friede
+#
+# tad-dftd4 is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# tad-dftd4 is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with tad-dftd4. If not, see .
+"""
+Data: Radii
+===========
+
+Covalent radii (imported from *tad-mctc*).
+"""
+from tad_mctc.data import COV_D3
+
+__all__ = ["COV_D3"]
diff --git a/src/tad_dftd4/data/zeff.py b/src/tad_dftd4/data/zeff.py
new file mode 100644
index 0000000..b7aa41b
--- /dev/null
+++ b/src/tad_dftd4/data/zeff.py
@@ -0,0 +1,26 @@
+# This file is part of tad-dftd4.
+#
+# SPDX-Identifier: LGPL-3.0
+# Copyright (C) 2022 Marvin Friede
+#
+# tad-dftd4 is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# tad-dftd4 is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with tad-dftd4. If not, see .
+"""
+Data: Charges
+=============
+
+Effective charges (imported from *tad-mctc*).
+"""
+from tad_mctc.data.zeff import ZEFF
+
+__all__ = ["ZEFF"]
diff --git a/src/tad_dftd4/disp.py b/src/tad_dftd4/disp.py
index 2a14a60..77d420a 100644
--- a/src/tad_dftd4/disp.py
+++ b/src/tad_dftd4/disp.py
@@ -29,15 +29,14 @@
import torch
from tad_mctc import storch
from tad_mctc.batch import real_pairs
-from tad_mctc.data import radii
from tad_mctc.ncoord import cn_d4, erf_count
-from tad_mctc.typing import DD, Any, CountingFunction, DampingFunction, Tensor
from tad_multicharge.eeq import get_charges
from . import data, defaults
from .cutoff import Cutoff
from .damping import get_atm_dispersion, rational_damping
from .model import D4Model
+from .typing import DD, Any, CountingFunction, DampingFunction, Tensor
def dftd4(
@@ -108,9 +107,9 @@ def dftd4(
cutoff = Cutoff(**dd)
if rcov is None:
- rcov = radii.COV_D3.to(**dd)[numbers]
+ rcov = data.COV_D3.to(**dd)[numbers]
if r4r2 is None:
- r4r2 = data.r4r2.to(**dd)[numbers]
+ r4r2 = data.R4R2.to(**dd)[numbers]
if q is None:
q = get_charges(numbers, positions, charge, cutoff=cutoff.cn_eeq)
diff --git a/src/tad_dftd4/model.py b/src/tad_dftd4/model.py
index 7b2e222..9d07909 100644
--- a/src/tad_dftd4/model.py
+++ b/src/tad_dftd4/model.py
@@ -41,10 +41,9 @@
from __future__ import annotations
import torch
-from tad_mctc.data.zeff import ZEFF
-from tad_mctc.typing import Tensor, TensorLike
from . import data, params
+from .typing import Tensor, TensorLike
ga_default = 3.0
gc_default = 2.0
@@ -230,8 +229,8 @@ def refc_pow(n: int) -> Tensor:
)
# unsqueeze for reference dimension
- zeff = ZEFF.to(self.device)[self.numbers].unsqueeze(-1)
- gam = data.gam.to(**self.dd)[self.numbers].unsqueeze(-1) * self.gc
+ zeff = data.ZEFF.to(self.device)[self.numbers].unsqueeze(-1)
+ gam = data.GAM.to(**self.dd)[self.numbers].unsqueeze(-1) * self.gc
q = q.unsqueeze(-1)
# charge scaling
@@ -322,8 +321,8 @@ def _set_refalpha_eeq(self) -> Tensor:
mask = refsys > 0
- zeff = ZEFF.to(self.device)[refsys]
- gam = data.gam.to(**self.dd)[refsys] * self.gc
+ zeff = data.ZEFF.to(self.device)[refsys]
+ gam = data.GAM.to(**self.dd)[refsys] * self.gc
# charge scaling
zeta = torch.where(
diff --git a/src/tad_dftd4/typing/__init__.py b/src/tad_dftd4/typing/__init__.py
new file mode 100644
index 0000000..6a169f0
--- /dev/null
+++ b/src/tad_dftd4/typing/__init__.py
@@ -0,0 +1,25 @@
+# This file is part of tad-dftd4.
+#
+# SPDX-Identifier: LGPL-3.0
+# Copyright (C) 2022 Marvin Friede
+#
+# tad-dftd4 is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# tad-dftd4 is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with tad-dftd4. If not, see .
+"""
+Type annotations
+================
+
+All type annotations for this project.
+"""
+from .builtin import *
+from .pytorch import *
diff --git a/src/tad_dftd4/typing/builtin.py b/src/tad_dftd4/typing/builtin.py
new file mode 100644
index 0000000..ae0e6fb
--- /dev/null
+++ b/src/tad_dftd4/typing/builtin.py
@@ -0,0 +1,25 @@
+# This file is part of tad-dftd4.
+#
+# SPDX-Identifier: LGPL-3.0
+# Copyright (C) 2022 Marvin Friede
+#
+# tad-dftd4 is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# tad-dftd4 is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with tad-dftd4. If not, see .
+"""
+Type annotations: Built-ins
+===========================
+
+Built-in type annotations are imported from the *tad-mctc* library, which
+handles some version checking.
+"""
+from tad_mctc.typing import Any, Callable, NoReturn, TypedDict
diff --git a/src/tad_dftd4/typing/pytorch.py b/src/tad_dftd4/typing/pytorch.py
new file mode 100644
index 0000000..4128e6c
--- /dev/null
+++ b/src/tad_dftd4/typing/pytorch.py
@@ -0,0 +1,34 @@
+# This file is part of tad-dftd4.
+#
+# SPDX-Identifier: LGPL-3.0
+# Copyright (C) 2022 Marvin Friede
+#
+# tad-dftd4 is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# tad-dftd4 is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with tad-dftd4. If not, see .
+"""
+Type annotations: PyTorch
+=========================
+
+PyTorch-related type annotations for this project.
+"""
+from tad_mctc.typing import (
+ DD,
+ CountingFunction,
+ DampingFunction,
+ Molecule,
+ Tensor,
+ TensorLike,
+ TensorOrTensors,
+ get_default_device,
+ get_default_dtype,
+)
diff --git a/test/conftest.py b/test/conftest.py
index e78650e..f611b77 100644
--- a/test/conftest.py
+++ b/test/conftest.py
@@ -114,9 +114,9 @@ def pytest_configure(config: pytest.Config) -> None:
torch.autograd.anomaly_mode.set_detect_anomaly(True)
if config.getoption("--jit"):
- torch.jit._state.enable() # type: ignore # pylint: disable=protected-access
+ torch.jit._state.enable() # type:ignore # pylint: disable=protected-access
else:
- torch.jit._state.disable() # type: ignore # pylint: disable=protected-access
+ torch.jit._state.disable() # type:ignore # pylint: disable=protected-access
if config.getoption("--fast"):
FAST_MODE = True
@@ -147,7 +147,7 @@ def pytest_configure(config: pytest.Config) -> None:
if torch.__version__ < (2, 0, 0): # type: ignore
torch.set_default_tensor_type("torch.cuda.FloatTensor") # type: ignore
else:
- torch.set_default_device(DEVICE) # type: ignore
+ torch.set_default_device(DEVICE) # type: ignore[attr-defined]
else:
torch.use_deterministic_algorithms(True)
DEVICE = None
diff --git a/test/test_cutoff/test_general.py b/test/test_cutoff/test_general.py
index 0c986a8..ff61362 100644
--- a/test/test_cutoff/test_general.py
+++ b/test/test_cutoff/test_general.py
@@ -66,4 +66,4 @@ def test_change_device_fail() -> None:
# trying to use setter
with pytest.raises(AttributeError):
- cutoff.device = "cpu"
+ cutoff.device = torch.device("cpu")
diff --git a/test/test_cutoff/test_types.py b/test/test_cutoff/test_types.py
index 5fd0b7d..4d14cbe 100644
--- a/test/test_cutoff/test_types.py
+++ b/test/test_cutoff/test_types.py
@@ -22,13 +22,13 @@
import pytest
import torch
-from tad_mctc.typing import Tensor
from tad_dftd4 import defaults
from tad_dftd4.cutoff import Cutoff
+from tad_dftd4.typing import Tensor
-def test_defaults():
+def test_defaults() -> None:
cutoff = Cutoff()
assert pytest.approx(defaults.D4_DISP2_CUTOFF) == cutoff.disp2.cpu()
assert pytest.approx(defaults.D4_DISP3_CUTOFF) == cutoff.disp3.cpu()
@@ -36,8 +36,8 @@ def test_defaults():
assert pytest.approx(defaults.D4_CN_EEQ_CUTOFF) == cutoff.cn_eeq.cpu()
-def test_tensor():
- tmp = torch.randn(1)
+def test_tensor() -> None:
+ tmp = torch.tensor([1.0])
cutoff = Cutoff(disp2=tmp)
assert isinstance(cutoff.disp2, Tensor)
@@ -49,7 +49,7 @@ def test_tensor():
@pytest.mark.parametrize("vals", [(1, 2, -3, 4), (1.0, 2.0, 3.0, -4.0)])
-def test_int_float(vals: tuple[int | float, ...]):
+def test_int_float(vals: tuple[int | float, ...]) -> None:
disp2, disp3, cn, cn_eeq = vals
cutoff = Cutoff(disp2, disp3, cn, cn_eeq)
diff --git a/test/test_disp/samples.py b/test/test_disp/samples.py
index adbc843..1164f3d 100644
--- a/test/test_disp/samples.py
+++ b/test/test_disp/samples.py
@@ -22,7 +22,8 @@
import torch
from tad_mctc.data.molecules import merge_nested_dicts, mols
-from tad_mctc.typing import Molecule, Tensor, TypedDict
+
+from tad_dftd4.typing import Molecule, Tensor, TypedDict
class Refs(TypedDict):
@@ -46,1100 +47,1114 @@ class Record(Molecule, Refs):
refs: dict[str, Refs] = {
- "LiH": {
- "q": torch.tensor(
- [3.708714958301688e-01, -3.708714958301688e-01], dtype=torch.float64
- ),
- "disp": torch.tensor(
- [
- -2.5509356117699210e-04,
- -2.5509356117699210e-04,
- ],
- dtype=torch.double,
- ),
- "disp2": torch.tensor(
- [
- -2.5509356117699210e-04,
- -2.5509356117699210e-04,
- ],
- dtype=torch.double,
- ),
- "disp3": torch.tensor(
- [
- +0.0000000000000000e00,
- +0.0000000000000000e00,
- ],
- dtype=torch.double,
- ),
- },
- "SiH4": {
- "q": torch.tensor(
- [
- -8.412842390895063e-02,
- 2.103210597723753e-02,
- 2.103210597723774e-02,
- 2.103210597723764e-02,
- 2.103210597723773e-02,
- ],
- dtype=torch.float64,
- ),
- "disp": torch.tensor(
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+ -1.0712106674960588e-02,
+ -1.7865709637713410e-02,
+ ],
+ dtype=torch.double,
+ ),
+ "disp3": torch.tensor(
+ [
+ +7.2159520370904534e-06,
+ +7.5341492076903970e-06,
+ +2.4256781194729662e-05,
+ +1.4728506552354082e-05,
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+ +8.1928572872919559e-06,
+ +3.0157411385263311e-05,
+ +7.2804432801869369e-06,
+ ],
+ dtype=torch.double,
+ ),
+ }
+ ),
}
diff --git a/test/test_disp/test_atm.py b/test/test_disp/test_atm.py
index c69f971..eefa742 100644
--- a/test/test_disp/test_atm.py
+++ b/test/test_disp/test_atm.py
@@ -22,10 +22,10 @@
import torch
from tad_mctc.batch import pack
from tad_mctc.ncoord import cn_d4
-from tad_mctc.typing import DD
from tad_dftd4.disp import dispersion3
from tad_dftd4.model import D4Model
+from tad_dftd4.typing import DD
from ..conftest import DEVICE
from .samples import samples
diff --git a/test/test_disp/test_full.py b/test/test_disp/test_full.py
index 37173e3..09af8f7 100644
--- a/test/test_disp/test_full.py
+++ b/test/test_disp/test_full.py
@@ -21,13 +21,12 @@
import pytest
import torch
from tad_mctc.batch import pack
-from tad_mctc.data import radii
-from tad_mctc.typing import DD
from tad_dftd4 import data
from tad_dftd4.cutoff import Cutoff
from tad_dftd4.disp import dftd4
from tad_dftd4.model import D4Model
+from tad_dftd4.typing import DD
from ..conftest import DEVICE
from .samples import samples
@@ -71,8 +70,8 @@ def single(name: str, dtype: torch.dtype) -> None:
}
model = D4Model(numbers, **dd)
- rcov = radii.COV_D3.to(**dd)[numbers]
- r4r2 = data.r4r2.to(**dd)[numbers]
+ rcov = data.COV_D3.to(**dd)[numbers]
+ r4r2 = data.R4R2.to(**dd)[numbers]
cutoff = Cutoff(**dd)
energy = dftd4(
diff --git a/test/test_disp/test_twobody.py b/test/test_disp/test_twobody.py
index 6b4ea8e..6f1a3a0 100644
--- a/test/test_disp/test_twobody.py
+++ b/test/test_disp/test_twobody.py
@@ -22,11 +22,11 @@
import torch
from tad_mctc.batch import pack
from tad_mctc.ncoord import cn_d4
-from tad_mctc.typing import DD
from tad_dftd4 import data
from tad_dftd4.disp import dftd4, dispersion2
from tad_dftd4.model import D4Model
+from tad_dftd4.typing import DD
from ..conftest import DEVICE
from .samples import samples
@@ -69,7 +69,7 @@ def single(name: str, dtype: torch.dtype) -> None:
"a2": torch.tensor(4.60230534, **dd),
}
- r4r2 = data.r4r2.to(**dd)[numbers]
+ r4r2 = data.R4R2.to(**dd)[numbers]
model = D4Model(numbers, **dd)
cn = cn_d4(numbers, positions)
weights = model.weight_references(cn, q)
@@ -201,7 +201,7 @@ def batch(name1: str, name2: str, dtype: torch.dtype) -> None:
"a2": torch.tensor(4.60230534, **dd),
}
- r4r2 = data.r4r2.to(**dd)[numbers]
+ r4r2 = data.R4R2.to(**dd)[numbers]
model = D4Model(numbers, **dd)
cn = cn_d4(numbers, positions)
weights = model.weight_references(cn, q)
diff --git a/test/test_grad/samples_grad.py b/test/test_grad/samples_grad.py
index 3df2436..5416795 100644
--- a/test/test_grad/samples_grad.py
+++ b/test/test_grad/samples_grad.py
@@ -22,7 +22,8 @@
import torch
from tad_mctc.data.molecules import merge_nested_dicts, mols
-from tad_mctc.typing import Molecule, Tensor, TypedDict
+
+from tad_dftd4.typing import Molecule, Tensor, TypedDict
class Refs(TypedDict):
@@ -37,1174 +38,1188 @@ class Record(Molecule, Refs):
refs: dict[str, Refs] = {
- "LiH": {
- "grad": torch.tensor(
- [
- [
- +0.0000000000000000e00,
- +0.0000000000000000e00,
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- ],
- [
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- +6.8677584018156501e-05,
- ],
- ],
- dtype=torch.double,
- ),
- },
- "SiH4": {
- "grad": torch.tensor(
- [
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- ],
- ],
- dtype=torch.double,
- ),
- },
- "PbH4-BiH3": {
- "grad": torch.tensor(
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- ],
- ],
- dtype=torch.double,
- ),
- },
- "MB16_43_01": {
- "grad": torch.tensor(
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- ],
- ],
- dtype=torch.double,
- ),
- },
- "MB16_43_02": {
- "grad": torch.tensor(
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- dtype=torch.double,
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- },
- "vancoh2": {
- "grad": torch.tensor(
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+ ],
+ ],
+ dtype=torch.double,
+ ),
+ }
+ ),
+ "AmF3": Refs(
+ {
+ "grad": torch.tensor(
+ [],
+ dtype=torch.double,
+ ),
+ }
+ ),
}
diff --git a/test/test_grad/samples_hessian.py b/test/test_grad/samples_hessian.py
index 1d45855..7362b3c 100644
--- a/test/test_grad/samples_hessian.py
+++ b/test/test_grad/samples_hessian.py
@@ -32,7 +32,8 @@
import torch
from tad_mctc.data.molecules import merge_nested_dicts, mols
-from tad_mctc.typing import Molecule, Tensor, TypedDict
+
+from tad_dftd4.typing import Molecule, Tensor, TypedDict
class Refs(TypedDict):
@@ -47,3334 +48,3344 @@ class Record(Molecule, Refs):
refs: dict[str, Refs] = {
- "LiH": {
- "hessian": torch.tensor(
- [
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- -3.8477807179274732e-04,
- ],
- dtype=torch.double,
- ),
- },
- "SiH4": {
- "hessian": torch.tensor(
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+ +1.9272624151417915e-06,
+ -1.1250644038832548e-05,
+ -6.0133179893725467e-07,
+ +1.0794772168563850e-05,
+ -3.0933478342839646e-06,
+ -1.6753447665756671e-05,
+ -2.5239908180521055e-06,
+ +3.7376214992061252e-05,
+ -1.0472071890199608e-05,
+ -1.1325108989029787e-05,
+ +2.1937254846736897e-06,
+ -1.3309650289785647e-05,
+ +6.2007996095648013e-06,
+ -2.1463995661667908e-05,
+ +1.1497123807936087e-07,
+ +2.0919995443125167e-06,
+ -2.3684249345534616e-05,
+ +4.0774677502681059e-05,
+ -1.6595900376875378e-06,
+ +2.2909047490556294e-04,
+ -5.0135748851098949e-05,
+ +2.4111223646176936e-05,
+ -8.6502377445252590e-06,
+ -1.6904784178685189e-04,
+ -5.3014492199399826e-06,
+ -5.2378569293946896e-06,
+ +2.1825269492207902e-06,
+ -2.9170879245672167e-06,
+ -3.3811895544831128e-06,
+ -1.2875810064417320e-05,
+ -1.9310768012859719e-05,
+ -7.0457808519302188e-06,
+ +4.4464854818959676e-05,
+ -4.0058835709287297e-05,
+ +3.0771840797450293e-05,
+ +1.1353290988881507e-05,
+ -2.6163010230777651e-06,
+ +2.2763103098147938e-06,
+ +7.7716682199933940e-06,
+ -4.1112651284942476e-05,
+ +3.5735789267251229e-05,
+ +1.9680792492124226e-05,
+ +1.7740427170042777e-06,
+ +3.9411397276668640e-06,
+ +7.1450255088157224e-06,
+ +8.5742676612330379e-06,
+ -1.4593467473274528e-05,
+ -2.0262884708078122e-05,
+ -4.4790114415641088e-05,
+ +1.2401981561670477e-06,
+ +1.8919921710984835e-05,
+ +2.4545551285880501e-06,
+ -2.1788555524160542e-05,
+ +1.5393571126852889e-05,
+ -7.6552674445275366e-06,
+ +1.2204621781377939e-05,
+ +1.7762153557059155e-05,
+ -1.6221579243839166e-05,
+ -1.3501491573312944e-05,
+ -2.0185055466647318e-05,
+ -1.7544938846891919e-05,
+ -5.0140313408652496e-06,
+ -1.3828025972774242e-05,
+ +5.6555699575291159e-06,
+ +4.4536069476394657e-05,
+ -1.3133608344753286e-05,
+ -1.9628749841641357e-05,
+ +3.7543341151842144e-06,
+ -4.4917341895630084e-05,
+ -1.1745600767226836e-05,
+ -1.8483512385578105e-05,
+ -5.3014490551412524e-06,
+ +1.4555941119112300e-04,
+ ],
+ dtype=torch.double,
+ ),
+ }
+ ),
+ "AmF3": Refs(
+ {
+ "hessian": torch.tensor(
+ [],
+ dtype=torch.double,
+ ),
+ }
+ ),
}
diff --git a/test/test_grad/test_hessian.py b/test/test_grad/test_hessian.py
index a3fe237..9c96fd0 100644
--- a/test/test_grad/test_hessian.py
+++ b/test/test_grad/test_hessian.py
@@ -35,9 +35,9 @@
from tad_mctc.autograd import hessian
from tad_mctc.batch import pack
from tad_mctc.convert import reshape_fortran
-from tad_mctc.typing import DD, Tensor
from tad_dftd4 import dftd4
+from tad_dftd4.typing import DD, Tensor
from .samples_hessian import samples
diff --git a/test/test_grad/test_nan.py b/test/test_grad/test_nan.py
index db95b4c..14e6dff 100644
--- a/test/test_grad/test_nan.py
+++ b/test/test_grad/test_nan.py
@@ -24,9 +24,9 @@
import torch
from tad_mctc.batch import pack
from tad_mctc.data.molecules import mols as samples
-from tad_mctc.typing import DD
from tad_dftd4 import dftd4
+from tad_dftd4.typing import DD
tol = 1e-8
diff --git a/test/test_grad/test_param.py b/test/test_grad/test_param.py
index d738e9f..b3c9c57 100644
--- a/test/test_grad/test_param.py
+++ b/test/test_grad/test_param.py
@@ -25,9 +25,9 @@
from tad_mctc.autograd import dgradcheck, dgradgradcheck
from tad_mctc.batch import pack
from tad_mctc.data.molecules import mols as samples
-from tad_mctc.typing import DD, Callable, Tensor
from tad_dftd4 import dftd4
+from tad_dftd4.typing import DD, Callable, Tensor
sample_list = ["LiH", "AmF3", "SiH4"]
diff --git a/test/test_grad/test_pos.py b/test/test_grad/test_pos.py
index 847d880..96f9938 100644
--- a/test/test_grad/test_pos.py
+++ b/test/test_grad/test_pos.py
@@ -24,9 +24,9 @@
import torch
from tad_mctc.autograd import dgradcheck, dgradgradcheck
from tad_mctc.batch import pack
-from tad_mctc.typing import DD, Callable, Tensor
from tad_dftd4 import dftd4
+from tad_dftd4.typing import DD, Callable, Tensor
from ..conftest import DEVICE
from .samples_grad import samples
diff --git a/test/test_model/samples.py b/test/test_model/samples.py
index 66ac3e0..44d7437 100644
--- a/test/test_model/samples.py
+++ b/test/test_model/samples.py
@@ -23,7 +23,8 @@
import torch
from tad_mctc.convert import reshape_fortran
from tad_mctc.data.molecules import merge_nested_dicts, mols
-from tad_mctc.typing import Molecule, Tensor, TypedDict
+
+from tad_dftd4.typing import Molecule, Tensor, TypedDict
class Refs(TypedDict):
@@ -46,1181 +47,1191 @@ class Record(Molecule, Refs):
refs: dict[str, Refs] = {
- "LiH": { # CN, q
- "gw": reshape_fortran(
- torch.tensor(
+ "LiH": Refs(
+ { # CN, q
+ "gw": reshape_fortran(
+ torch.tensor(
+ [
+ +1.8699287753787968e-02,
+ +9.7889292523075033e-01,
+ +1.8718044551687104e-37,
+ +7.9608926855620182e-02,
+ +3.5225968112617356e00,
+ +0.0000000000000000e00,
+ ],
+ dtype=torch.double,
+ ),
+ (3, 2),
+ ),
+ "c6": torch.tensor(
[
- +1.8699287753787968e-02,
- +9.7889292523075033e-01,
- +1.8718044551687104e-37,
- +7.9608926855620182e-02,
- +3.5225968112617356e00,
- +0.0000000000000000e00,
+ +4.1059628873073926e01,
+ +2.9129176877403175e01,
+ +2.9129176877403175e01,
+ +4.0408036338319796e01,
],
dtype=torch.double,
+ ).reshape(2, 2),
+ }
+ ),
+ "SiH4": Refs(
+ { # CN, q
+ "gw": reshape_fortran(
+ torch.tensor(
+ [
+ +1.9334597142903089e-35,
+ +1.4946886024790536e-20,
+ +2.0260041599668397e-09,
+ +1.3096099611387583e-02,
+ +9.8937148831611499e-01,
+ +6.3922186078456374e-03,
+ +9.3633202240072710e-01,
+ +0.0000000000000000e00,
+ +0.0000000000000000e00,
+ +0.0000000000000000e00,
+ +6.3922186078456374e-03,
+ +9.3633202240072710e-01,
+ +0.0000000000000000e00,
+ +0.0000000000000000e00,
+ +0.0000000000000000e00,
+ +6.3922186078456374e-03,
+ +9.3633202240072710e-01,
+ +0.0000000000000000e00,
+ +0.0000000000000000e00,
+ +0.0000000000000000e00,
+ +6.3922186078456374e-03,
+ +9.3633202240072710e-01,
+ +0.0000000000000000e00,
+ +0.0000000000000000e00,
+ +0.0000000000000000e00,
+ ],
+ dtype=torch.double,
+ ),
+ (5, 5),
),
- (3, 2),
- ),
- "c6": torch.tensor(
- [
- +4.1059628873073926e01,
- +2.9129176877403175e01,
- +2.9129176877403175e01,
- +4.0408036338319796e01,
- ],
- dtype=torch.double,
- ).reshape(2, 2),
- },
- "SiH4": { # CN, q
- "gw": reshape_fortran(
- torch.tensor(
+ "c6": torch.tensor(
[
- +1.9334597142903089e-35,
- +1.4946886024790536e-20,
- +2.0260041599668397e-09,
- +1.3096099611387583e-02,
- +9.8937148831611499e-01,
- +6.3922186078456374e-03,
- +9.3633202240072710e-01,
- +0.0000000000000000e00,
- +0.0000000000000000e00,
- +0.0000000000000000e00,
- +6.3922186078456374e-03,
- +9.3633202240072710e-01,
- +0.0000000000000000e00,
- +0.0000000000000000e00,
- +0.0000000000000000e00,
- +6.3922186078456374e-03,
- +9.3633202240072710e-01,
- +0.0000000000000000e00,
- +0.0000000000000000e00,
- +0.0000000000000000e00,
- +6.3922186078456374e-03,
- +9.3633202240072710e-01,
- +0.0000000000000000e00,
- +0.0000000000000000e00,
- +0.0000000000000000e00,
+ +1.5985885538475173e02,
+ +2.0584140554801550e01,
+ +2.0584140554801550e01,
+ +2.0584140554801550e01,
+ +2.0584140554801550e01,
+ +2.0584140554801550e01,
+ +2.7202385043230000e00,
+ +2.7202385043230000e00,
+ +2.7202385043230000e00,
+ +2.7202385043230000e00,
+ +2.0584140554801550e01,
+ +2.7202385043230000e00,
+ +2.7202385043230000e00,
+ +2.7202385043230000e00,
+ +2.7202385043230000e00,
+ +2.0584140554801550e01,
+ +2.7202385043230000e00,
+ +2.7202385043230000e00,
+ +2.7202385043230000e00,
+ +2.7202385043230000e00,
+ +2.0584140554801550e01,
+ +2.7202385043230000e00,
+ +2.7202385043230000e00,
+ +2.7202385043230000e00,
+ +2.7202385043230000e00,
],
dtype=torch.double,
+ ).reshape(5, 5),
+ }
+ ),
+ "MB16_43_01": Refs(
+ { # CN
+ "gw": reshape_fortran(
+ torch.tensor(
+ [
+ 1.2088234202205e-11,
+ 1.0375924114812e00,
+ 2.4445602531076e-09,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 5.5306460372092e-03,
+ 9.9446935396279e-01,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 3.1404764970412e-06,
+ 6.3956931077352e-02,
+ 4.7846317290481e-01,
+ 2.9468368515225e-01,
+ 0.0000000000000e00,
+ 7.4310920077799e-05,
+ 9.9992568907992e-01,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 4.4395780891660e-02,
+ 8.5383545436310e-01,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 1.1950286131613e-02,
+ 9.8804971386839e-01,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 5.6992908407601e-05,
+ 9.9994300709159e-01,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 5.6167960886507e-07,
+ 2.9078967459651e-02,
+ 6.1859560324107e-01,
+ 1.5104287585421e-01,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 4.9771287942905e-14,
+ 1.3962072360858e-04,
+ 6.8484995485525e-01,
+ 1.6516463249478e-12,
+ 1.9880162618842e-02,
+ 9.8011983738116e-01,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 1.1966389405645e-02,
+ 9.8803361059436e-01,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 1.2874045548253e-05,
+ 9.7726740456727e-01,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 4.1491138092838e-06,
+ 8.6768202830170e-01,
+ 0.0000000000000e00,
+ 4.3169267440676e-12,
+ 3.6465051654232e-04,
+ 8.8903503100593e-01,
+ 1.2720379452861e-05,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 1.4066048552144e-05,
+ 6.8494819902320e-01,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 0.0000000000000e00,
+ 1.9574616732692e-10,
+ 1.0064486114128e00,
+ 0.0000000000000e00,
+ ],
+ dtype=torch.double,
+ ),
+ (5, 16),
),
- (5, 5),
- ),
- "c6": torch.tensor(
- [
- +1.5985885538475173e02,
- +2.0584140554801550e01,
- +2.0584140554801550e01,
- +2.0584140554801550e01,
- +2.0584140554801550e01,
- +2.0584140554801550e01,
- +2.7202385043230000e00,
- +2.7202385043230000e00,
- +2.7202385043230000e00,
- +2.7202385043230000e00,
- +2.0584140554801550e01,
- +2.7202385043230000e00,
- +2.7202385043230000e00,
- +2.7202385043230000e00,
- +2.7202385043230000e00,
- +2.0584140554801550e01,
- +2.7202385043230000e00,
- +2.7202385043230000e00,
- +2.7202385043230000e00,
- +2.7202385043230000e00,
- +2.0584140554801550e01,
- +2.7202385043230000e00,
- +2.7202385043230000e00,
- +2.7202385043230000e00,
- +2.7202385043230000e00,
- ],
- dtype=torch.double,
- ).reshape(5, 5),
- },
- "MB16_43_01": { # CN
- "gw": reshape_fortran(
- torch.tensor(
+ "c6": torch.tensor(
[
- 1.2088234202205e-11,
- 1.0375924114812e00,
- 2.4445602531076e-09,
- 0.0000000000000e00,
- 0.0000000000000e00,
- 5.5306460372092e-03,
- 9.9446935396279e-01,
- 0.0000000000000e00,
- 0.0000000000000e00,
- 0.0000000000000e00,
- 3.1404764970412e-06,
- 6.3956931077352e-02,
- 4.7846317290481e-01,
- 2.9468368515225e-01,
- 0.0000000000000e00,
- 7.4310920077799e-05,
- 9.9992568907992e-01,
- 0.0000000000000e00,
- 0.0000000000000e00,
- 0.0000000000000e00,
- 4.4395780891660e-02,
- 8.5383545436310e-01,
- 0.0000000000000e00,
- 0.0000000000000e00,
- 0.0000000000000e00,
- 1.1950286131613e-02,
- 9.8804971386839e-01,
- 0.0000000000000e00,
- 0.0000000000000e00,
- 0.0000000000000e00,
- 5.6992908407601e-05,
- 9.9994300709159e-01,
- 0.0000000000000e00,
- 0.0000000000000e00,
- 0.0000000000000e00,
- 5.6167960886507e-07,
- 2.9078967459651e-02,
- 6.1859560324107e-01,
- 1.5104287585421e-01,
- 0.0000000000000e00,
- 0.0000000000000e00,
- 4.9771287942905e-14,
- 1.3962072360858e-04,
- 6.8484995485525e-01,
- 1.6516463249478e-12,
- 1.9880162618842e-02,
- 9.8011983738116e-01,
- 0.0000000000000e00,
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- 0.0000000000000e00,
- 1.1966389405645e-02,
- 9.8803361059436e-01,
- 0.0000000000000e00,
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- 4.1491138092838e-06,
- 8.6768202830170e-01,
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- 4.3169267440676e-12,
- 3.6465051654232e-04,
- 8.8903503100593e-01,
- 1.2720379452861e-05,
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- 6.8494819902320e-01,
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- 1.9574616732692e-10,
- 1.0064486114128e00,
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+ +9.2195970681311991e01,
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- ],
- dtype=torch.double,
- ).reshape(16, 16),
- },
+ ).reshape(16, 16),
+ }
+ ),
}
diff --git a/test/test_model/test_c6.py b/test/test_model/test_c6.py
index f595467..d7e19f5 100644
--- a/test/test_model/test_c6.py
+++ b/test/test_model/test_c6.py
@@ -23,9 +23,9 @@
import torch
import torch.nn.functional as F
from tad_mctc.batch import pack
-from tad_mctc.typing import DD
from tad_dftd4.model import D4Model
+from tad_dftd4.typing import DD
from ..conftest import DEVICE
from .samples import samples
diff --git a/test/test_model/test_general.py b/test/test_model/test_general.py
index 5adee42..ee4cf3a 100644
--- a/test/test_model/test_general.py
+++ b/test/test_model/test_general.py
@@ -62,4 +62,4 @@ def test_change_device_fail() -> None:
# trying to use setter
with pytest.raises(AttributeError):
- model.device = "cpu"
+ model.device = torch.device("cpu")
diff --git a/test/test_model/test_model.py b/test/test_model/test_model.py
index 032238c..948798e 100644
--- a/test/test_model/test_model.py
+++ b/test/test_model/test_model.py
@@ -23,10 +23,10 @@
import torch
from tad_mctc.batch import pack
from tad_mctc.ncoord import cn_d4
-from tad_mctc.typing import DD
from tad_multicharge.eeq import get_charges # get rid!
from tad_dftd4.model import D4Model
+from tad_dftd4.typing import DD
from ..conftest import DEVICE
from .samples import samples
diff --git a/test/test_model/test_params.py b/test/test_model/test_params.py
index ff814bf..9100f48 100644
--- a/test/test_model/test_params.py
+++ b/test/test_model/test_params.py
@@ -37,5 +37,5 @@ def test_params_shape() -> None:
def test_data_shape() -> None:
- assert data.gam.shape == torch.Size((119,))
- assert data.r4r2.shape == torch.Size((119,))
+ assert data.GAM.shape == torch.Size((119,))
+ assert data.R4R2.shape == torch.Size((119,))
diff --git a/test/test_model/test_weights.py b/test/test_model/test_weights.py
index 1b01e4a..8861c00 100644
--- a/test/test_model/test_weights.py
+++ b/test/test_model/test_weights.py
@@ -25,10 +25,10 @@
import torch.nn.functional as F
from tad_mctc.batch import pack
from tad_mctc.ncoord import cn_d4
-from tad_mctc.typing import DD
from tad_multicharge.eeq import get_charges
from tad_dftd4.model import D4Model
+from tad_dftd4.typing import DD
from ..conftest import DEVICE
from .samples import samples