diff --git a/dpdata/abacus/md.py b/dpdata/abacus/md.py index aa4215d8..f2512cf7 100644 --- a/dpdata/abacus/md.py +++ b/dpdata/abacus/md.py @@ -220,7 +220,7 @@ def get_frame(fname): if len(magmom) > 0: data["spins"] = magmom if len(magforce) > 0: - data["mag_forces"] = magforce + data["force_mags"] = magforce if len(move) > 0: data["move"] = move diff --git a/dpdata/abacus/relax.py b/dpdata/abacus/relax.py index 63f13678..85dfd4aa 100644 --- a/dpdata/abacus/relax.py +++ b/dpdata/abacus/relax.py @@ -217,7 +217,7 @@ def get_frame(fname): if len(magmom) > 0: data["spins"] = magmom if len(magforce) > 0: - data["mag_forces"] = magforce + data["force_mags"] = magforce if len(move) > 0: data["move"] = move diff --git a/dpdata/abacus/scf.py b/dpdata/abacus/scf.py index 43e65f7e..9d56aaec 100644 --- a/dpdata/abacus/scf.py +++ b/dpdata/abacus/scf.py @@ -511,7 +511,7 @@ def get_frame(fname): if len(magmom) > 0: data["spins"] = magmom if len(magforce) > 0: - data["mag_forces"] = magforce + data["force_mags"] = magforce if len(move) > 0: data["move"] = move[np.newaxis, :, :] # print("atom_names = ", data['atom_names']) diff --git a/dpdata/plugins/abacus.py b/dpdata/plugins/abacus.py index b3e7c98a..5b9e41a8 100644 --- a/dpdata/plugins/abacus.py +++ b/dpdata/plugins/abacus.py @@ -56,9 +56,9 @@ def register_mag_data(data): deepmd_name="spin", ) dpdata.LabeledSystem.register_data_type(dt) - if "mag_forces" in data: + if "force_mags" in data: dt = DataType( - "mag_forces", + "force_mags", np.ndarray, (Axis.NFRAMES, Axis.NATOMS, 3), required=False, diff --git a/dpdata/plugins/deepmd.py b/dpdata/plugins/deepmd.py index 1ed79f72..2726e1d4 100644 --- a/dpdata/plugins/deepmd.py +++ b/dpdata/plugins/deepmd.py @@ -10,6 +10,7 @@ import dpdata.deepmd.hdf5 import dpdata.deepmd.mixed import dpdata.deepmd.raw +from dpdata.data_type import Axis, DataType from dpdata.driver import Driver from dpdata.format import Format @@ -17,10 +18,33 @@ import h5py +def register_spin(): + dt = DataType( + "spins", + np.ndarray, + (Axis.NFRAMES, Axis.NATOMS, 3), + required=False, + deepmd_name="spin", + ) + dpdata.System.register_data_type(dt) + dpdata.LabeledSystem.register_data_type(dt) + + dt = DataType( + "force_mags", + np.ndarray, + (Axis.NFRAMES, Axis.NATOMS, 3), + required=False, + deepmd_name="force_mag", + ) + dpdata.System.register_data_type(dt) + dpdata.LabeledSystem.register_data_type(dt) + + @Format.register("deepmd") @Format.register("deepmd/raw") class DeePMDRawFormat(Format): def from_system(self, file_name, type_map=None, **kwargs): + register_spin() return dpdata.deepmd.raw.to_system_data( file_name, type_map=type_map, labels=False ) @@ -30,6 +54,7 @@ def to_system(self, data, file_name, **kwargs): dpdata.deepmd.raw.dump(file_name, data) def from_labeled_system(self, file_name, type_map=None, **kwargs): + register_spin() return dpdata.deepmd.raw.to_system_data( file_name, type_map=type_map, labels=True ) @@ -41,6 +66,7 @@ def from_labeled_system(self, file_name, type_map=None, **kwargs): @Format.register("deepmd/comp") class DeePMDCompFormat(Format): def from_system(self, file_name, type_map=None, **kwargs): + register_spin() return dpdata.deepmd.comp.to_system_data( file_name, type_map=type_map, labels=False ) @@ -69,6 +95,7 @@ def to_system(self, data, file_name, set_size=5000, prec=np.float64, **kwargs): dpdata.deepmd.comp.dump(file_name, data, set_size=set_size, comp_prec=prec) def from_labeled_system(self, file_name, type_map=None, **kwargs): + register_spin() return dpdata.deepmd.comp.to_system_data( file_name, type_map=type_map, labels=True ) @@ -149,6 +176,7 @@ def mix_system(self, *system, type_map, **kwargs): return dpdata.deepmd.mixed.mix_system(*system, type_map=type_map, **kwargs) def from_multi_systems(self, directory, **kwargs): + register_spin() sys_dir = [] for root, dirs, files in os.walk(directory): if ( @@ -204,6 +232,8 @@ def _from_system( """ import h5py + register_spin() + if isinstance(file_name, (h5py.Group, h5py.File)): return dpdata.deepmd.hdf5.to_system_data( file_name, "", type_map=type_map, labels=labels diff --git a/tests/test_abacus_spin.py b/tests/test_abacus_spin.py index df8ef7d0..5d8ca343 100644 --- a/tests/test_abacus_spin.py +++ b/tests/test_abacus_spin.py @@ -31,7 +31,7 @@ def test_scf(self): decimal=8, ) np.testing.assert_almost_equal( - data["mag_forces"][0], + data["force_mags"][0], [ [-0.0000175013, -0.0000418680, -0.3669618965], [-0.0000161517, -0.0000195198, -0.3669821632], @@ -47,7 +47,7 @@ def test_scf(self): 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 + data["force_mags"], sys2.data["force_mags"], decimal=8 ) def test_relax(self): @@ -84,9 +84,9 @@ def test_relax(self): ] ) self.assertEqual(len(data["spins"]), 3) - self.assertEqual(len(data["mag_forces"]), 3) + self.assertEqual(len(data["force_mags"]), 3) np.testing.assert_almost_equal(data["spins"], spins_ref, decimal=8) - np.testing.assert_almost_equal(data["mag_forces"], magforces_ref, decimal=8) + np.testing.assert_almost_equal(data["force_mags"], magforces_ref, decimal=8) # dump to deepmd-npy mysys.to(file_name=self.dump_path, fmt="deepmd/npy") @@ -96,7 +96,7 @@ def test_relax(self): 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 + data["force_mags"], sys2.data["force_mags"], decimal=8 ) def test_md(self): @@ -141,9 +141,9 @@ def test_md(self): ] ) self.assertEqual(len(data["spins"]), 4) - self.assertEqual(len(data["mag_forces"]), 4) + self.assertEqual(len(data["force_mags"]), 4) np.testing.assert_almost_equal(data["spins"], spins_ref, decimal=8) - np.testing.assert_almost_equal(data["mag_forces"], magforces_ref, decimal=8) + np.testing.assert_almost_equal(data["force_mags"], magforces_ref, decimal=8) # dump to deepmd-npy mysys.to(file_name=self.dump_path, fmt="deepmd/npy") @@ -153,5 +153,5 @@ def test_md(self): 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 + data["force_mags"], sys2.data["force_mags"], decimal=8 ) diff --git a/tests/test_deepmd_spin.py b/tests/test_deepmd_spin.py new file mode 100644 index 00000000..3b5c99a3 --- /dev/null +++ b/tests/test_deepmd_spin.py @@ -0,0 +1,48 @@ +from __future__ import annotations + +import os +import shutil +import unittest + +from context import dpdata + + +class TestDeepmdReadSpinNPY(unittest.TestCase): + def setUp(self): + self.tmp_save_path = "tmp.deepmd.spin/dump-tmp" + + def tearDown(self): + if os.path.exists(self.tmp_save_path): + shutil.rmtree(self.tmp_save_path) + + def check_Fe16(self, system): + self.assertTrue("spins" in system.data) + self.assertTrue("force_mags" in system.data) + self.assertEqual(system.data["spins"].shape, (2, 16, 3)) + self.assertEqual(system.data["force_mags"].shape, (2, 16, 3)) + + def test_read_spin_npy(self): + system = dpdata.LabeledSystem("tmp.deepmd.spin/Fe16-npy", fmt="deepmd/npy") + self.check_Fe16(system) + + system.to("deepmd/npy", self.tmp_save_path) + self.assertTrue( + os.path.isfile(os.path.join(self.tmp_save_path, "set.000/spin.npy")) + ) + self.assertTrue( + os.path.isfile(os.path.join(self.tmp_save_path, "set.000/force_mag.npy")) + ) + + def test_read_spin_raw(self): + system = dpdata.LabeledSystem("tmp.deepmd.spin/Fe16-raw", fmt="deepmd/raw") + self.check_Fe16(system) + + system.to("deepmd/raw", self.tmp_save_path) + self.assertTrue(os.path.isfile(os.path.join(self.tmp_save_path, "spin.raw"))) + self.assertTrue( + os.path.isfile(os.path.join(self.tmp_save_path, "force_mag.raw")) + ) + + +if __name__ == "__main__": + unittest.main() diff --git a/tests/tmp.deepmd.spin/Fe16-npy/set.000/box.npy b/tests/tmp.deepmd.spin/Fe16-npy/set.000/box.npy new file mode 100644 index 00000000..882bf1ff Binary files /dev/null and b/tests/tmp.deepmd.spin/Fe16-npy/set.000/box.npy differ diff --git a/tests/tmp.deepmd.spin/Fe16-npy/set.000/coord.npy b/tests/tmp.deepmd.spin/Fe16-npy/set.000/coord.npy new file mode 100644 index 00000000..329503e2 Binary files /dev/null and b/tests/tmp.deepmd.spin/Fe16-npy/set.000/coord.npy differ diff --git a/tests/tmp.deepmd.spin/Fe16-npy/set.000/energy.npy b/tests/tmp.deepmd.spin/Fe16-npy/set.000/energy.npy new file mode 100644 index 00000000..4bcbcf23 Binary files /dev/null and b/tests/tmp.deepmd.spin/Fe16-npy/set.000/energy.npy differ diff --git a/tests/tmp.deepmd.spin/Fe16-npy/set.000/force.npy b/tests/tmp.deepmd.spin/Fe16-npy/set.000/force.npy new file mode 100644 index 00000000..292fc680 Binary files /dev/null and b/tests/tmp.deepmd.spin/Fe16-npy/set.000/force.npy differ diff --git a/tests/tmp.deepmd.spin/Fe16-npy/set.000/force_mag.npy b/tests/tmp.deepmd.spin/Fe16-npy/set.000/force_mag.npy new file mode 100644 index 00000000..ff0a009e Binary files /dev/null and b/tests/tmp.deepmd.spin/Fe16-npy/set.000/force_mag.npy differ diff --git a/tests/tmp.deepmd.spin/Fe16-npy/set.000/spin.npy b/tests/tmp.deepmd.spin/Fe16-npy/set.000/spin.npy new file mode 100644 index 00000000..ae00e0e5 Binary files /dev/null and b/tests/tmp.deepmd.spin/Fe16-npy/set.000/spin.npy differ diff --git a/tests/tmp.deepmd.spin/Fe16-npy/set.000/virial.npy b/tests/tmp.deepmd.spin/Fe16-npy/set.000/virial.npy new file mode 100644 index 00000000..6c298046 Binary files /dev/null and b/tests/tmp.deepmd.spin/Fe16-npy/set.000/virial.npy differ diff --git a/tests/tmp.deepmd.spin/Fe16-npy/type.raw b/tests/tmp.deepmd.spin/Fe16-npy/type.raw new file mode 100644 index 00000000..74bc717c --- /dev/null +++ b/tests/tmp.deepmd.spin/Fe16-npy/type.raw @@ -0,0 +1,16 @@ +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 diff --git a/tests/tmp.deepmd.spin/Fe16-npy/type_map.raw b/tests/tmp.deepmd.spin/Fe16-npy/type_map.raw new file mode 100644 index 00000000..08d5832e --- /dev/null +++ b/tests/tmp.deepmd.spin/Fe16-npy/type_map.raw @@ -0,0 +1 @@ +Fe diff --git a/tests/tmp.deepmd.spin/Fe16-raw/box.raw b/tests/tmp.deepmd.spin/Fe16-raw/box.raw new file mode 100644 index 00000000..1a0f0c2b --- /dev/null +++ b/tests/tmp.deepmd.spin/Fe16-raw/box.raw @@ -0,0 +1,2 @@ +4.852406756199998838e+00 0.000000000000000000e+00 0.000000000000000000e+00 2.308035870000000114e-02 4.868205980599999982e+00 0.000000000000000000e+00 2.678336190000000019e-02 -1.273453610000000076e-02 7.575130651200000287e+00 +4.852406756199998838e+00 0.000000000000000000e+00 0.000000000000000000e+00 2.308035870000000114e-02 4.868205980599999982e+00 0.000000000000000000e+00 2.678336190000000019e-02 -1.273453610000000076e-02 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