4075885785

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Committed by Shyue Ping Ong

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Merge branch 'master' of github.com:materialsproject/pymatgen

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98.53

/pymatgen/io/cp2k/tests/test_sets.py

# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

from __future__ import annotations

import unittest
from pathlib import Path

import pytest
from pytest import approx

from pymatgen.core.structure import Molecule, Structure
from pymatgen.io.cp2k.sets import (
    SETTINGS,
    Cp2kValidationError,
    DftSet,
    GaussianTypeOrbitalBasisSet,
    GthPotential,
)
from pymatgen.util.testing import PymatgenTest

Si_structure = Structure(
    lattice=[[0, 2.734364, 2.734364], [2.734364, 0, 2.734364], [2.734364, 2.734364, 0]],
    species=["Si", "Si"],
    coords=[[0, 0, 0], [0.25, 0.25, 0.25]],
)
molecule = Molecule(species=["Si"], coords=[[0, 0, 0]])


class SetTest(PymatgenTest):
    def setUp(self) -> None:
        self.TEST_FILES_DIR = Path.joinpath(self.TEST_FILES_DIR, "cp2k")
        SETTINGS["PMG_CP2K_DATA_DIR"] = self.TEST_FILES_DIR
        self.setkwargs = {
            "print_pdos": False,
            "print_dos": False,
            "print_v_hartree": False,
            "print_e_density": False,
        }
        return super().setUp()

    def test_dft_set(self):
        # Basis sets / potentials searching
        basis_and_potential = {"basis_type": "SZV", "potential_type": "Pseudopotential", "functional": None}
        ss = DftSet(Si_structure, basis_and_potential=basis_and_potential, xc_functionals="PBE")

        # Basis sets / potentials by name
        basis_and_potential = {"Si": {"basis": "SZV-GTH-q4", "potential": "GTH-PBE-q4"}}
        ss = DftSet(Si_structure, basis_and_potential=basis_and_potential, xc_functionals="PBE")

        # Basis sets / potentials by name with ADMM
        basis_and_potential = {"Si": {"basis": "SZV-GTH-q4", "potential": "GTH-PBE-q4", "aux_basis": "cFIT3"}}
        ss = DftSet(Si_structure, basis_and_potential=basis_and_potential, xc_functionals="PBE")
        basis_sets = ss["force_eval"]["subsys"]["Si_1"].get("basis_set")
        assert any("AUX_FIT" in b.values for b in basis_sets)
        assert any("cFIT3" in b.values for b in basis_sets)

        # Basis sets / potentials by hash value
        basis_and_potential = {
            "Si": {"basis": "30767c18f6e7e46c1b56c1d34ff6007d", "potential": "21e2f468a18404ff6119fe801da81e43"}
        }
        ss = DftSet(Si_structure, basis_and_potential=basis_and_potential, xc_functionals="PBE")

        # Basis set / potential with objects
        gto = """
         Si SZV-MOLOPT-GTH SZV-MOLOPT-GTH-q4
            1
            2 0 1 6 1 1
                2.693604434572  0.015333179500 -0.005800105400
                1.359613855428 -0.283798205000 -0.059172026000
                0.513245176029 -0.228939692700  0.121487149900
                0.326563011394  0.728834000900  0.423382421100
                0.139986977410  0.446205299300  0.474592116300
                0.068212286977  0.122025292800  0.250129397700
        """
        pot = """Si GTH-BLYP-q4 GTH-BLYP
                2    2
                0.44000000    1    -6.25958674
                2
                0.44465247    2     8.31460936    -2.33277947
                                                    3.01160535
                0.50279207    1     2.33241791"""
        basis_and_potential = {
            "Si": {"basis": GaussianTypeOrbitalBasisSet.from_string(gto), "potential": GthPotential.from_string(pot)}
        }
        ss = DftSet(Si_structure, basis_and_potential=basis_and_potential, xc_functionals="PBE", **self.setkwargs)
        assert ss.cutoff == approx(150)

        # Test that printing will activate sections
        assert not ss.check("motion")
        ss.activate_motion()
        assert ss.check("motion")
        assert not ss.check("force_eval/dft/print/pdos")
        ss.print_pdos()
        assert ss.check("force_eval/dft/print/pdos")
        assert not ss.check("force_eval/dft/print/v_hartree_cube")
        ss.print_v_hartree()
        assert ss.check("force_eval/dft/print/v_hartree_cube")

        # Test property activators
        assert not ss.check("force_eval/properties")
        ss.activate_nmr()
        ss.activate_epr()
        ss.activate_hyperfine()
        ss.activate_polar()
        ss.activate_tddfpt()
        assert ss.check("force_eval/properties/linres/localize")
        assert ss.check("force_eval/properties/linres/nmr/print/chi_tensor")
        assert ss.check("force_eval/properties/linres/epr/print/g_tensor")
        assert ss.check("force_eval/properties/tddfpt")
        assert ss.check("force_eval/dft/print/hyperfine_coupling_tensor")

        # For at least up to v2022.1, DOS doesn't work without kpoints
        assert not ss.check("force_eval/dft/print/dos")
        ss.print_dos()
        assert not ss.check("force_eval/dft/print/dos")

        assert not ss.check("force_eval/dft/xc/hf")
        ss.activate_hybrid()
        assert ss.check("force_eval/dft/xc/hf")
        assert ss.check("force_eval/dft/auxiliary_density_matrix_method")

        # Validator will trip for kpoints + hfx
        ss.update({"force_eval": {"dft": {"kpoints": {}}}})
        with pytest.raises(Cp2kValidationError):
            ss.validate()

        ss = DftSet(molecule, basis_and_potential=basis_and_potential, xc_functionals="PBE")
        assert ss.check("force_eval/dft/poisson")
        assert ss["force_eval"]["dft"]["poisson"].get("periodic").values[0].upper() == "NONE"


if __name__ == "__main__":
    unittest.main()

1	# Copyright (c) Pymatgen Development Team.
2	# Distributed under the terms of the MIT License.
3
4	from __future__ import annotations	1✔
5
6	import unittest	1✔
7	from pathlib import Path	1✔
8
9	import pytest	1✔
10	from pytest import approx	1✔
11
12	from pymatgen.core.structure import Molecule, Structure	1✔
13	from pymatgen.io.cp2k.sets import (	1✔
14	SETTINGS,
15	Cp2kValidationError,
16	DftSet,
17	GaussianTypeOrbitalBasisSet,
18	GthPotential,
19	)
20	from pymatgen.util.testing import PymatgenTest	1✔
21
22	Si_structure = Structure(	1✔
23	lattice=[[0, 2.734364, 2.734364], [2.734364, 0, 2.734364], [2.734364, 2.734364, 0]],
24	species=["Si", "Si"],
25	coords=[[0, 0, 0], [0.25, 0.25, 0.25]],
26	)
27	molecule = Molecule(species=["Si"], coords=[[0, 0, 0]])	1✔
28
29
30	class SetTest(PymatgenTest):	1✔
31	def setUp(self) -> None:	1✔
32	self.TEST_FILES_DIR = Path.joinpath(self.TEST_FILES_DIR, "cp2k")	1✔
33	SETTINGS["PMG_CP2K_DATA_DIR"] = self.TEST_FILES_DIR	1✔
34	self.setkwargs = {	1✔
35	"print_pdos": False,
36	"print_dos": False,
37	"print_v_hartree": False,
38	"print_e_density": False,
39	}
40	return super().setUp()	1✔
41
42	def test_dft_set(self):	1✔
43	# Basis sets / potentials searching
44	basis_and_potential = {"basis_type": "SZV", "potential_type": "Pseudopotential", "functional": None}	1✔
45	ss = DftSet(Si_structure, basis_and_potential=basis_and_potential, xc_functionals="PBE")	1✔
46
47	# Basis sets / potentials by name
48	basis_and_potential = {"Si": {"basis": "SZV-GTH-q4", "potential": "GTH-PBE-q4"}}	1✔
49	ss = DftSet(Si_structure, basis_and_potential=basis_and_potential, xc_functionals="PBE")	1✔
50
51	# Basis sets / potentials by name with ADMM
52	basis_and_potential = {"Si": {"basis": "SZV-GTH-q4", "potential": "GTH-PBE-q4", "aux_basis": "cFIT3"}}	1✔
53	ss = DftSet(Si_structure, basis_and_potential=basis_and_potential, xc_functionals="PBE")	1✔
54	basis_sets = ss["force_eval"]["subsys"]["Si_1"].get("basis_set")	1✔
55	assert any("AUX_FIT" in b.values for b in basis_sets)	1✔
56	assert any("cFIT3" in b.values for b in basis_sets)	1✔
57
58	# Basis sets / potentials by hash value
59	basis_and_potential = {	1✔
60	"Si": {"basis": "30767c18f6e7e46c1b56c1d34ff6007d", "potential": "21e2f468a18404ff6119fe801da81e43"}
61	}
62	ss = DftSet(Si_structure, basis_and_potential=basis_and_potential, xc_functionals="PBE")	1✔
63
64	# Basis set / potential with objects
65	gto = """	1✔
66	Si SZV-MOLOPT-GTH SZV-MOLOPT-GTH-q4
67	1
68	2 0 1 6 1 1
69	2.693604434572 0.015333179500 -0.005800105400
70	1.359613855428 -0.283798205000 -0.059172026000
71	0.513245176029 -0.228939692700 0.121487149900
72	0.326563011394 0.728834000900 0.423382421100
73	0.139986977410 0.446205299300 0.474592116300
74	0.068212286977 0.122025292800 0.250129397700
75	"""
76	pot = """Si GTH-BLYP-q4 GTH-BLYP	1✔
77	2 2
78	0.44000000 1 -6.25958674
79	2
80	0.44465247 2 8.31460936 -2.33277947
81	3.01160535
82	0.50279207 1 2.33241791"""
83	basis_and_potential = {	1✔
84	"Si": {"basis": GaussianTypeOrbitalBasisSet.from_string(gto), "potential": GthPotential.from_string(pot)}
85	}
86	ss = DftSet(Si_structure, basis_and_potential=basis_and_potential, xc_functionals="PBE", **self.setkwargs)	1✔
87	assert ss.cutoff == approx(150)	1✔
88
89	# Test that printing will activate sections
90	assert not ss.check("motion")	1✔
91	ss.activate_motion()	1✔
92	assert ss.check("motion")	1✔
93	assert not ss.check("force_eval/dft/print/pdos")	1✔
94	ss.print_pdos()	1✔
95	assert ss.check("force_eval/dft/print/pdos")	1✔
96	assert not ss.check("force_eval/dft/print/v_hartree_cube")	1✔
97	ss.print_v_hartree()	1✔
98	assert ss.check("force_eval/dft/print/v_hartree_cube")	1✔
99
100	# Test property activators
101	assert not ss.check("force_eval/properties")	1✔
102	ss.activate_nmr()	1✔
103	ss.activate_epr()	1✔
104	ss.activate_hyperfine()	1✔
105	ss.activate_polar()	1✔
106	ss.activate_tddfpt()	1✔
107	assert ss.check("force_eval/properties/linres/localize")	1✔
108	assert ss.check("force_eval/properties/linres/nmr/print/chi_tensor")	1✔
109	assert ss.check("force_eval/properties/linres/epr/print/g_tensor")	1✔
110	assert ss.check("force_eval/properties/tddfpt")	1✔
111	assert ss.check("force_eval/dft/print/hyperfine_coupling_tensor")	1✔
112
113	# For at least up to v2022.1, DOS doesn't work without kpoints
114	assert not ss.check("force_eval/dft/print/dos")	1✔
115	ss.print_dos()	1✔
116	assert not ss.check("force_eval/dft/print/dos")	1✔
117
118	assert not ss.check("force_eval/dft/xc/hf")	1✔
119	ss.activate_hybrid()	1✔
120	assert ss.check("force_eval/dft/xc/hf")	1✔
121	assert ss.check("force_eval/dft/auxiliary_density_matrix_method")	1✔
122
123	# Validator will trip for kpoints + hfx
124	ss.update({"force_eval": {"dft": {"kpoints": {}}}})	1✔
125	with pytest.raises(Cp2kValidationError):	1✔
126	ss.validate()	1✔
127
128	ss = DftSet(molecule, basis_and_potential=basis_and_potential, xc_functionals="PBE")	1✔
129	assert ss.check("force_eval/dft/poisson")	1✔
130	assert ss["force_eval"]["dft"]["poisson"].get("periodic").values[0].upper() == "NONE"	1✔
131
132
133	if __name__ == "__main__":	1✔
134	unittest.main()	×

materialsproject / pymatgen / 4075885785

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