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Merge pull request #358 from Liang-jianxin/develop 

support non-collinear magmom add for PWmat caculator
This commit is contained in:
Atsushi Togo 2024-05-11 15:55:08 +02:00 committed by GitHub
parent 430bb717fd bb610eeba0
commit 9b58b1c58b
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GPG Key ID: B5690EEEBB952194
3 changed files with 119 additions and 13 deletions
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25
phonopy/interface/pwmat.py
View File

@ -118,6 +118,15 @@ def read_atom_config(filename):
except ValueError:
read_magnetic = False
if line.lower().startswith("magnetic_xyz"):
read_magnetic = True
elif read_magnetic:
try:
parts = [float(part) for part in line.split()]
element_mag.append(parts[1:4])
except ValueError:
read_magnetic = False
cell_args = {
"numbers": element_index,
"cell": lattice_vectors,
@ -141,6 +150,7 @@ def get_pwmat_structure(cell):
positions = cell.scaled_positions
numbers = cell.numbers
mag_mom = cell.magnetic_moments
line = []
line.append(f" {len(positions)}")
line.append("Lattice vector (Angstrom)")
@ -153,10 +163,17 @@ def get_pwmat_structure(cell):
+ " ".join(f"{val:.16f}" for val in position)
+ " 1 1 1"
)
if isinstance(mag_mom, np.ndarray) and mag_mom.size > 0:
line.append("magnetic")
for number, mag in zip(numbers, mag_mom):
line.append(f" {number} {mag:.16f}")
if mag_mom is not None and len(mag_mom) == len(cell.numbers):
if np.size(mag_mom[0]) == 1:
line.append("magnetic")
for number, mag in zip(numbers, mag_mom):
line.append(f" {number} {mag:.16f}")
if np.size(mag_mom[0]) == 3:
line.append("magnetic_xyz")
for number, mag in zip(numbers, mag_mom):
line.append(f" {number} {mag[0]:.6f} {mag[1]:.6f} {mag[2]:.6f}")
return "\n".join(line)

97
test/interface/Si-pwmat.yaml
View File

@ -1,23 +1,23 @@
phonopy:
version: "2.21.2"
version: "2.23.1"
calculator: pwmat
frequency_unit_conversion_factor: 15.633302
symmetry_tolerance: 1.00000e-05
configuration:
cell_filename: "atom.config"
create_displacements: ".true."
magmom: "1 1 1 1 1 1 1 1"
primitive_axes: "F"
dim: "2 2 2"
atom_name: "Si"
mp: "31 31 31"
tprop: ".true."
calculator: "pwmat"
physical_unit:
atomic_mass: "AMU"
length: "angstrom"
force_constants: "eV/angstrom^2"
space_group:
type: "Fd-3m"
number: 227
Hall_symbol: "F 4d 2 3 -1d"
magnetic_space_group:
uni_number: 1630
msg_type: 1
primitive_matrix:
- [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
@ -38,9 +38,11 @@ primitive_cell:
- symbol: Si # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 28.085500
magnetic_moment: 1.00000000
- symbol: Si # 2
coordinates: [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 28.085500
magnetic_moment: 1.00000000
reciprocal_lattice: # without 2pi
- [ -0.182807991366520, 0.182807991366520, 0.182807991366520 ] # a*
- [ 0.182807991366520, -0.182807991366520, 0.182807991366520 ] # b*
@ -56,34 +58,42 @@ unit_cell:
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 2
coordinates: [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 28.085500
reduced_to: 2
magnetic_moment: 1.00000000
- symbol: Si # 3
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 4
coordinates: [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 28.085500
reduced_to: 2
magnetic_moment: 1.00000000
- symbol: Si # 5
coordinates: [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 28.085500
reduced_to: 2
magnetic_moment: 1.00000000
- symbol: Si # 6
coordinates: [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 28.085500
reduced_to: 2
magnetic_moment: 1.00000000
- symbol: Si # 7
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 8
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
supercell:
lattice:
@ -95,255 +105,324 @@ supercell:
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 2
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 3
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 5
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 6
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 7
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 8
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 9
coordinates: [ 0.125000000000000, 0.125000000000000, 0.125000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 10
coordinates: [ 0.625000000000000, 0.125000000000000, 0.125000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 11
coordinates: [ 0.125000000000000, 0.625000000000000, 0.125000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 12
coordinates: [ 0.625000000000000, 0.625000000000000, 0.125000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 13
coordinates: [ 0.125000000000000, 0.125000000000000, 0.625000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 14
coordinates: [ 0.625000000000000, 0.125000000000000, 0.625000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 15
coordinates: [ 0.125000000000000, 0.625000000000000, 0.625000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 16
coordinates: [ 0.625000000000000, 0.625000000000000, 0.625000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 17
coordinates: [ 0.000000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 18
coordinates: [ 0.500000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 19
coordinates: [ 0.000000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 20
coordinates: [ 0.500000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 21
coordinates: [ 0.000000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 22
coordinates: [ 0.500000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 23
coordinates: [ 0.000000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 24
coordinates: [ 0.500000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 25
coordinates: [ 0.375000000000000, 0.125000000000000, 0.375000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 26
coordinates: [ 0.875000000000000, 0.125000000000000, 0.375000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 27
coordinates: [ 0.375000000000000, 0.625000000000000, 0.375000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 28
coordinates: [ 0.875000000000000, 0.625000000000000, 0.375000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 29
coordinates: [ 0.375000000000000, 0.125000000000000, 0.875000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 30
coordinates: [ 0.875000000000000, 0.125000000000000, 0.875000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 31
coordinates: [ 0.375000000000000, 0.625000000000000, 0.875000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 32
coordinates: [ 0.875000000000000, 0.625000000000000, 0.875000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 33
coordinates: [ 0.125000000000000, 0.375000000000000, 0.375000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 34
coordinates: [ 0.625000000000000, 0.375000000000000, 0.375000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 35
coordinates: [ 0.125000000000000, 0.875000000000000, 0.375000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 36
coordinates: [ 0.625000000000000, 0.875000000000000, 0.375000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 37
coordinates: [ 0.125000000000000, 0.375000000000000, 0.875000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 38
coordinates: [ 0.625000000000000, 0.375000000000000, 0.875000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 39
coordinates: [ 0.125000000000000, 0.875000000000000, 0.875000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 40
coordinates: [ 0.625000000000000, 0.875000000000000, 0.875000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 41
coordinates: [ 0.375000000000000, 0.375000000000000, 0.125000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 42
coordinates: [ 0.875000000000000, 0.375000000000000, 0.125000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 43
coordinates: [ 0.375000000000000, 0.875000000000000, 0.125000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 44
coordinates: [ 0.875000000000000, 0.875000000000000, 0.125000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 45
coordinates: [ 0.375000000000000, 0.375000000000000, 0.625000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 46
coordinates: [ 0.875000000000000, 0.375000000000000, 0.625000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 47
coordinates: [ 0.375000000000000, 0.875000000000000, 0.625000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 48
coordinates: [ 0.875000000000000, 0.875000000000000, 0.625000000000000 ]
mass: 28.085500
reduced_to: 9
magnetic_moment: 1.00000000
- symbol: Si # 49
coordinates: [ 0.250000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 50
coordinates: [ 0.750000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 51
coordinates: [ 0.250000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 52
coordinates: [ 0.750000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 53
coordinates: [ 0.250000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 54
coordinates: [ 0.750000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 55
coordinates: [ 0.250000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 56
coordinates: [ 0.750000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 57
coordinates: [ 0.250000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 58
coordinates: [ 0.750000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 59
coordinates: [ 0.250000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 60
coordinates: [ 0.750000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 61
coordinates: [ 0.250000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 62
coordinates: [ 0.750000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 63
coordinates: [ 0.250000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
- symbol: Si # 64
coordinates: [ 0.750000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 28.085500
reduced_to: 1
magnetic_moment: 1.00000000
displacements:
- atom: 1
displacement:
[ 0.0100000000000000, 0.0000000000000000, 0.0000000000000000 ]

10
test/interface/test_pwmat.py
View File

@ -22,3 +22,13 @@ def test_read_pwmat():
assert (np.abs(diff_pos) < 1e-5).all()
for s, s_r in zip(cell.symbols, cell_ref.symbols):
assert s == s_r
def test_magmom():
"""Test of read_PWmat_magmom."""
cell = read_atom_config(os.path.join(data_dir, "Si-pwmat.config"))
filename = os.path.join(data_dir, "Si-pwmat.yaml")
cell_ref = read_cell_yaml(filename)
assert cells.isclose(cell, cell_ref)
diff_mag = cell_ref.magnetic_moments - np.array([1] * 8)
assert (np.abs(diff_mag) < 1e-5).all()