Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add spin for abacus/stru #751

Merged
merged 5 commits into from
Nov 7, 2024
Merged

add spin for abacus/stru #751

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
cf29c0e
abacus: add spin information for fmt=abacus/stru
Nov 5, 2024
46592e9
add test
Nov 5, 2024
222148f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 5, 2024
d0cc5f9
Merge branch 'devel' of https://github.com/deepmodeling/dpdata into s…
Nov 6, 2024
35e0d83
fix
Nov 6, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion dpdata/abacus/md.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -167,7 +167,7 @@ def get_frame(fname):
with open_file(geometry_path_in) as fp:
geometry_inlines = fp.read().split("\n")
celldm, cell = get_cell(geometry_inlines)
atom_names, natoms, types, coords, move = get_coords(
atom_names, natoms, types, coords, move, magmom = get_coords(
celldm, cell, geometry_inlines, inlines
)
# This coords is not to be used.
Expand Down
2 changes: 1 addition & 1 deletion dpdata/abacus/relax.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -183,7 +183,7 @@ def get_frame(fname):
with open_file(geometry_path_in) as fp:
geometry_inlines = fp.read().split("\n")
celldm, cell = get_cell(geometry_inlines)
atom_names, natoms, types, coord_tmp, move = get_coords(
atom_names, natoms, types, coord_tmp, move, magmom = get_coords(
celldm, cell, geometry_inlines, inlines
)

Expand Down
71 changes: 61 additions & 10 deletions dpdata/abacus/scf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -258,6 +258,51 @@
return pos, move, velocity, magmom, angle1, angle2, constrain, lambda1


def get_atom_mag_cartesian(atommag, angle1, angle2):
"""Transform atommag, angle1, angle2 to magmom in cartesian coordinates.

Parameters
----------
atommag : float/list of float/None
Atom magnetic moment.
angle1 : float/None
value of angle1.
angle2 : float/None
value of angle2.
ABACUS support defining mag, angle1, angle2 at the same time.
angle1 is the angle between z-axis and real spin (in degrees).
angle2 is the angle between x-axis and real spin projection in xy-plane (in degrees).
If only mag is defined, then transfer it to magmom directly.
And if mag, angle1, angle2 are defined, then mag is only the norm of magmom, and the direction is defined by angle1 and angle2.
"""
if atommag is None:
return None
if not (isinstance(atommag, list) or isinstance(atommag, float)):
raise RuntimeError(f"Invalid atommag: {atommag}")

Check warning on line 281 in dpdata/abacus/scf.py

View check run for this annotation

Codecov / codecov/patch

dpdata/abacus/scf.py#L281 

Added line #L281 was not covered by tests

if angle1 is None and angle2 is None:
if isinstance(atommag, list):
return atommag
else:
return [0, 0, atommag]
else:
a1 = 0
a2 = 0
if angle1 is not None:
a1 = angle1
if angle2 is not None:
a2 = angle2
if isinstance(atommag, list):
mag_norm = np.linalg.norm(atommag)
else:
mag_norm = atommag
return [
mag_norm * np.sin(np.radians(a1)) * np.cos(np.radians(a2)),
mag_norm * np.sin(np.radians(a1)) * np.sin(np.radians(a2)),
mag_norm * np.cos(np.radians(a1)),
]


def get_coords(celldm, cell, geometry_inlines, inlines=None):
coords_lines = get_stru_block(geometry_inlines, "ATOMIC_POSITIONS")
# assuming that ATOMIC_POSITIONS is at the bottom of the STRU file
Expand All @@ -268,16 +313,15 @@
coords = [] # coordinations of atoms
move = [] # move flag of each atom
velocity = [] # velocity of each atom
mag = [] # magnetic moment of each atom
angle1 = [] # angle1 of each atom
angle2 = [] # angle2 of each atom
mags = [] # magnetic moment of each atom
sc = [] # spin constraint flag of each atom
lambda_ = [] # lambda of each atom

ntype = get_nele_from_stru(geometry_inlines)
line_idx = 1 # starting line of first element
for it in range(ntype):
atom_names.append(coords_lines[line_idx].split()[0])
atom_type_mag = float(coords_lines[line_idx + 1].split()[0])
line_idx += 2
atom_numbs.append(int(coords_lines[line_idx].split()[0]))
line_idx += 1
Expand All @@ -302,17 +346,20 @@
if imove is not None:
move.append(imove)
velocity.append(ivelocity)
mag.append(imagmom)
angle1.append(iangle1)
angle2.append(iangle2)
sc.append(iconstrain)
lambda_.append(ilambda1)

# calculate the magnetic moment in cartesian coordinates
mag = get_atom_mag_cartesian(imagmom, iangle1, iangle2)
if mag is None:
mag = [0, 0, atom_type_mag]
mags.append(mag)

line_idx += 1
coords = np.array(coords) # need transformation!!!
atom_types = np.array(atom_types)
move = np.array(move, dtype=bool)
return atom_names, atom_numbs, atom_types, coords, move
return atom_names, atom_numbs, atom_types, coords, move, mags


def get_energy(outlines):
Expand Down Expand Up @@ -479,9 +526,12 @@
outlines = fp.read().split("\n")

celldm, cell = get_cell(geometry_inlines)
atom_names, natoms, types, coords, move = get_coords(
celldm, cell, geometry_inlines, inlines
atom_names, natoms, types, coords, move, magmom = (
get_coords( # here the magmom is the initial magnetic moment in STRU
celldm, cell, geometry_inlines, inlines
)
)

magmom, magforce = get_mag_force(outlines)
if len(magmom) > 0:
magmom = magmom[-1:]
Expand Down Expand Up @@ -565,7 +615,7 @@
nele = get_nele_from_stru(geometry_inlines)
inlines = [f"ntype {nele}"]
celldm, cell = get_cell(geometry_inlines)
atom_names, natoms, types, coords, move = get_coords(
atom_names, natoms, types, coords, move, magmom = get_coords(
celldm, cell, geometry_inlines, inlines
)
data = {}
Expand All @@ -575,6 +625,7 @@
data["cells"] = cell[np.newaxis, :, :]
data["coords"] = coords[np.newaxis, :, :]
data["orig"] = np.zeros(3)
data["spins"] = np.array([magmom])
if len(move) > 0:
data["move"] = move[np.newaxis, :, :]

Expand Down
6 changes: 5 additions & 1 deletion dpdata/plugins/abacus.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,9 @@
@Format.register("stru")
class AbacusSTRUFormat(Format):
def from_system(self, file_name, **kwargs):
return dpdata.abacus.scf.get_frame_from_stru(file_name)
data = dpdata.abacus.scf.get_frame_from_stru(file_name)
register_mag_data(data)
return data

def to_system(self, data, file_name: FileType, frame_idx=0, **kwargs):
"""Dump the system into ABACUS STRU format file.
Expand Down Expand Up @@ -55,6 +57,7 @@ def register_mag_data(data):
required=False,
deepmd_name="spin",
)
dpdata.System.register_data_type(dt)
dpdata.LabeledSystem.register_data_type(dt)
if "force_mags" in data:
dt = DataType(
Expand All @@ -64,6 +67,7 @@ def register_mag_data(data):
required=False,
deepmd_name="force_mag",
)
dpdata.System.register_data_type(dt)
dpdata.LabeledSystem.register_data_type(dt)


Expand Down
10 changes: 5 additions & 5 deletions tests/abacus.scf/stru_test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,11 @@ Cartesian # Cartesian(Unit is LATTICE_CONSTANT)
C
0.0
1
5.192682633809 4.557725978258 4.436846615358 1 1 1
5.192682633809 4.557725978258 4.436846615358 1 1 1 mag 0.000000000000 0.000000000000 0.000000000000
H
0.0
4
5.416431453540 4.011298860305 3.511161492417 0 0 0
4.131588222365 4.706745191323 4.431136645083 1 0 1
5.630930319126 5.521640894956 4.450356541303 1 0 1
5.499851012568 4.003388899277 5.342621842622 0 1 1
5.416431453540 4.011298860305 3.511161492417 0 0 0 mag 0.000000000000 0.000000000000 0.000000000000
4.131588222365 4.706745191323 4.431136645083 1 0 1 mag 0.000000000000 0.000000000000 0.000000000000
5.630930319126 5.521640894956 4.450356541303 1 0 1 mag 0.000000000000 0.000000000000 0.000000000000
5.499851012568 4.003388899277 5.342621842622 0 1 1 mag 0.000000000000 0.000000000000 0.000000000000
24 changes: 24 additions & 0 deletions tests/abacus.spin/STRU.spin
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
ATOMIC_SPECIES
Fe 55.845 Fe.upf

NUMERICAL_ORBITAL
Fe_gga_10au_200.0Ry_4s2p2d1f.orb

LATTICE_CONSTANT
1.880277359
LATTICE_VECTORS
2.8274254848 0.0000000000 0.0000000000 #latvec1
0.0000000000 2.8274254848 0.0000000000 #latvec2
0.0000000000 0.0000000000 2.8274254848 #latvec3

ATOMIC_POSITIONS
Direct

Fe #label
1 #magnetism
4 #number of atoms
0.0000000000 0.000000000 0.000000000 mag 0 0 2
0.1000000000 0.1000000000 0.1000000000 mag 3
0.2000000000 0.2000000000 0.2000000000 mag 3 angle1 90
0.3000000000 0.3000000000 0.3000000000 mag 3 4 0 angle1 90 angle2 90

16 changes: 16 additions & 0 deletions tests/test_abacus_spin.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -155,3 +155,19 @@ def test_md(self):
np.testing.assert_almost_equal(
data["force_mags"], sys2.data["force_mags"], decimal=8
)

def test_read_stru_spin(self):
mysys = dpdata.System("abacus.spin/STRU.spin", fmt="abacus/stru")
self.assertTrue("spins" in mysys.data)
Comment on lines +160 to +161
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 Codebase verification

Path should be relative to test directory

The test file exists at tests/abacus.spin/STRU.spin, but the test is using abacus.spin/STRU.spin. This could cause issues when running tests from different directories. The test file path should be relative to the test directory.

  • Update the path in tests/test_abacus_spin.py:160 to use "./abacus.spin/STRU.spin" or use proper test fixtures/helpers to handle test file paths.
🔗 Analysis chain

Verify test file existence and handling.

Let's verify the test file setup and error handling.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Verify test file existence and contents
if [ -f "abacus.spin/STRU.spin" ]; then
    echo "Test file exists"
    head -n 10 "abacus.spin/STRU.spin"
else
    echo "Warning: Test file not found"
fi

# Check for similar test files in the repository
fd -e spin "STRU"

Length of output: 176

Script:

#!/bin/bash
# Check the test file content in the correct test directory
cat tests/abacus.spin/STRU.spin

# Check if the test is using relative path correctly
rg -A 5 "abacus.spin/STRU.spin" tests/test_abacus_spin.py

# Check if there are other similar test file usages
rg "STRU.spin" tests/

Length of output: 1084

print(mysys.data["spins"])

"""
0.0000000000 0.000000000 0.000000000 mag 0 0 2
0.1000000000 0.1000000000 0.1000000000 mag 3
0.2000000000 0.2000000000 0.2000000000 mag 3 angle1 90
0.3000000000 0.3000000000 0.3000000000 mag 3 4 0 angle1 90 angle2 90
"""
np.testing.assert_almost_equal(mysys.data["spins"][0][0], [0, 0, 2], decimal=8)
np.testing.assert_almost_equal(mysys.data["spins"][0][1], [0, 0, 3], decimal=8)
np.testing.assert_almost_equal(mysys.data["spins"][0][2], [3, 0, 0], decimal=8)
np.testing.assert_almost_equal(mysys.data["spins"][0][3], [0, 5, 0], decimal=8)