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Add lattice velocities to Poscar #3428

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Oct 27, 2023
Merged

Add lattice velocities to Poscar #3428

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36a1bc2
Add lattice velocities to Poscar
gpetretto Oct 27, 2023
58b8b58
use auto-cleaned PymatgenTest.tmp_path over tmp_file.unlink()
janosh Oct 27, 2023
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37 changes: 36 additions & 1 deletion pymatgen/io/vasp/inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,6 +89,7 @@ def __init__(
velocities: ArrayLike | None = None,
predictor_corrector: ArrayLike | None = None,
predictor_corrector_preamble: str | None = None,
lattice_velocities: ArrayLike | None = None,
sort_structure: bool = False,
):
"""
Expand All @@ -108,6 +109,8 @@ def __init__(
Typically parsed in MD runs. Defaults to None.
predictor_corrector_preamble (str | None, optional): Preamble to the predictor
corrector. Defaults to None.
lattice_velocities (ArrayLike | None, optional): Lattice velocities and current
lattice for the POSCAR. Available in MD runs with variable cell. Defaults to None.
sort_structure (bool, optional): Whether to sort the structure. Useful if species
are not grouped properly together. Defaults to False.
"""
Expand Down Expand Up @@ -137,6 +140,9 @@ def __init__(
self.comment = structure.formula if comment is None else comment
if predictor_corrector_preamble:
self.structure.properties["predictor_corrector_preamble"] = predictor_corrector_preamble

if lattice_velocities is not None and np.any(lattice_velocities):
self.structure.properties["lattice_velocities"] = np.asarray(lattice_velocities)
else:
raise ValueError("Disordered structure with partial occupancies cannot be converted into POSCAR!")

Expand All @@ -162,6 +168,11 @@ def predictor_corrector_preamble(self):
"""Predictor corrector preamble in Poscar."""
return self.structure.properties.get("predictor_corrector_preamble")

@property
def lattice_velocities(self):
"""Lattice velocities in Poscar (including the current lattice vectors)."""
return self.structure.properties.get("lattice_velocities")

@velocities.setter # type: ignore
def velocities(self, velocities):
"""Setter for Poscar.velocities."""
Expand All @@ -182,6 +193,11 @@ def predictor_corrector_preamble(self, predictor_corrector_preamble):
"""Setter for Poscar.predictor_corrector."""
self.structure.properties["predictor_corrector"] = predictor_corrector_preamble

@lattice_velocities.setter # type: ignore
def lattice_velocities(self, lattice_velocities: ArrayLike) -> None:
"""Setter for Poscar.lattice_velocities."""
self.structure.properties["lattice_velocities"] = np.asarray(lattice_velocities)

@property
def site_symbols(self) -> list[str]:
"""
Expand Down Expand Up @@ -422,6 +438,15 @@ def from_str(data, default_names=None, read_velocities=True):
)

if read_velocities:
# Parse the lattice velocities and current lattice, if present.
# The header line should contain "Lattice velocities and vectors"
# There is no space between the coordinates and this section, so
# it appears in the lines of the first chunk
lattice_velocities = []
if len(lines) > ipos + n_sites + 1 and lines[ipos + n_sites + 1].lower().startswith("l"):
for line in lines[ipos + n_sites + 3 : ipos + n_sites + 9]:
lattice_velocities.append([float(tok) for tok in line.split()])

# Parse velocities if any
velocities = []
if len(chunks) > 1:
Expand Down Expand Up @@ -450,7 +475,7 @@ def from_str(data, default_names=None, read_velocities=True):
d3 = [float(tok) for tok in lines[st + 2 * n_sites].split()]
predictor_corrector.append([d1, d2, d3])
else:
velocities = predictor_corrector = predictor_corrector_preamble = None
velocities = predictor_corrector = predictor_corrector_preamble = lattice_velocities = None

return Poscar(
struct,
Expand All @@ -460,6 +485,7 @@ def from_str(data, default_names=None, read_velocities=True):
velocities=velocities,
predictor_corrector=predictor_corrector,
predictor_corrector_preamble=predictor_corrector_preamble,
lattice_velocities=lattice_velocities,
)

@np.deprecate(message="Use get_str instead")
Expand Down Expand Up @@ -514,6 +540,15 @@ def get_str(self, direct: bool = True, vasp4_compatible: bool = False, significa
line += " " + site.species_string
lines.append(line)

if self.lattice_velocities is not None:
try:
lines.append("Lattice velocities and vectors")
lines.append(" 1")
for v in self.lattice_velocities:
lines.append(" ".join(format_str.format(i) for i in v))
except Exception:
warnings.warn("Lattice velocities are missing or corrupted.")

if self.velocities:
try:
lines.append("")
Expand Down
61 changes: 61 additions & 0 deletions tests/files/CONTCAR.MD.npt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,61 @@
Si8
1.00000000000000
5.6029196758839159 -0.0603693499677626 0.1110429263825206
-0.0000000000000100 5.3747130151091689 0.0034014855406440
0.0000000000000068 -0.0000000000000120 5.4692974031883859
Si
8
Direct
0.6539918994283490 0.8969172295968553 0.0676681342693018
-0.2312437400904284 0.5904002014657854 0.3939526918410268
0.8235113603041605 0.3274668347998835 0.7376879470910200
0.0234540394811329 -0.0006436675535249 -0.1173920341194730
0.4494229071161935 0.8354718770893421 0.6950789454078377
0.5785762144444008 0.4746645739302746 0.0005135261381124
0.0419959757024323 0.1291469345761019 0.3339785656099613
0.5094723570400191 0.1350290791632852 0.4745741352855470
Lattice velocities and vectors
1
0.11376865E-02 -0.20054010E-02 0.10745440E-02
-0.80980926E-03 -0.54988058E-03 -0.11593411E-02
0.40755213E-03 -0.91838934E-03 0.10978311E-02
0.56062799E+01 -0.68862342E-01 0.11555075E+00
-0.98606785E-14 0.53730639E+01 -0.27835157E-02
0.64062547E-14 -0.12698742E-13 0.54725901E+01

-0.26486997E-01 0.15289665E-01 -0.24183306E-01
-0.21835373E-01 -0.48466524E-02 0.34963571E-02
-0.36389021E-02 -0.28571877E-02 -0.18926241E-02
0.49389009E-02 0.28594559E-02 -0.48140896E-02
0.20044174E-01 -0.32290274E-03 0.67317795E-02
0.51447245E-02 0.75356806E-02 -0.13128815E-01
-0.12148614E-01 -0.19846176E-01 0.16721524E-01
-0.73911890E-02 0.29807035E-02 -0.42831313E-02

1
3.00000000000000
0.10000000E+01 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.63981833E+00 0.90527242E+00 0.54714689E-01
0.75707184E+00 0.58754437E+00 0.39611461E+00
0.82156413E+00 0.32584659E+00 0.73669073E+00
0.26096915E-01 0.98675463E-03 0.87991397E+00
0.46014883E+00 0.83542905E+00 0.69854272E+00
0.58132923E+00 0.47890733E+00 0.99326052E+00
0.35495080E-01 0.11798269E+00 0.34327666E+00
0.50551723E+00 0.13664264E+00 0.47231051E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
40 changes: 30 additions & 10 deletions tests/io/vasp/test_inputs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
import os
import pickle
import unittest
from pathlib import Path
from typing import TYPE_CHECKING

import numpy as np
import pytest
Expand Down Expand Up @@ -32,6 +32,9 @@
)
from pymatgen.util.testing import TEST_FILES_DIR, PymatgenTest

if TYPE_CHECKING:
from pathlib import Path


class TestPoscar(PymatgenTest):
def test_init(self):
Expand Down Expand Up @@ -265,24 +268,42 @@ def test_str(self):
def test_from_md_run(self):
# Parsing from an MD type run with velocities and predictor corrector data
poscar = Poscar.from_file(f"{TEST_FILES_DIR}/CONTCAR.MD", check_for_potcar=False)
assert np.sum(np.array(poscar.velocities)) == approx(0.0065417961324)
assert np.sum(poscar.velocities) == approx(0.0065417961324)
assert poscar.predictor_corrector[0][0][0] == 0.33387820e00
assert poscar.predictor_corrector[0][1][1] == -0.10583589e-02
assert poscar.lattice_velocities is None

# Parsing from an MD type run with velocities, predictor corrector data and lattice velocities
poscar = Poscar.from_file(f"{TEST_FILES_DIR}/CONTCAR.MD.npt", check_for_potcar=False)
assert np.sum(poscar.velocities) == approx(-0.06193299494)
assert poscar.predictor_corrector[0][0][0] == 0.63981833
assert poscar.lattice_velocities.sum() == approx(16.49411358474)

def test_write_md_poscar(self):
# Parsing from an MD type run with velocities and predictor corrector data
# And writing a new POSCAR from the new structure
poscar = Poscar.from_file(f"{TEST_FILES_DIR}/CONTCAR.MD", check_for_potcar=False)

path = Path("POSCAR.testing.md")
path = f"{self.tmp_path}/POSCAR.testing.md"
poscar.write_file(path)
p3 = Poscar.from_file(path)

assert_allclose(poscar.structure.lattice.abc, p3.structure.lattice.abc, 5)
assert_allclose(poscar.velocities, p3.velocities, 5)
assert_allclose(poscar.predictor_corrector, p3.predictor_corrector, 5)
assert poscar.predictor_corrector_preamble == p3.predictor_corrector_preamble

# Same as above except also has lattice velocities
poscar = Poscar.from_file(f"{TEST_FILES_DIR}/CONTCAR.MD.npt", check_for_potcar=False)

poscar.write_file(path)
p3 = Poscar.from_file(path)

assert_allclose(poscar.structure.lattice.abc, p3.structure.lattice.abc, 5)
assert_allclose(poscar.velocities, p3.velocities, 5)
assert_allclose(poscar.predictor_corrector, p3.predictor_corrector, 5)
assert poscar.predictor_corrector_preamble == p3.predictor_corrector_preamble
path.unlink()
assert_allclose(poscar.lattice_velocities, p3.lattice_velocities, 5)

def test_setattr(self):
filepath = f"{TEST_FILES_DIR}/POSCAR"
Expand Down Expand Up @@ -395,7 +416,7 @@ def test_selective_dynamics(self):
]


class TestIncar(unittest.TestCase):
class TestIncar(PymatgenTest):
def setUp(self):
file_name = f"{TEST_FILES_DIR}/INCAR"
self.incar = Incar.from_file(file_name)
Expand Down Expand Up @@ -564,11 +585,10 @@ def test_as_dict_and_from_dict(self):
assert incar3["MAGMOM"] == [Magmom([1, 2, 3])]

def test_write(self):
tempfname = Path("INCAR.testing")
self.incar.write_file(tempfname)
i = Incar.from_file(tempfname)
assert i == self.incar
tempfname.unlink()
tmp_file = f"{self.tmp_path}/INCAR.testing"
self.incar.write_file(tmp_file)
incar = Incar.from_file(tmp_file)
assert incar == self.incar

def test_get_str(self):
s = self.incar.get_str(pretty=True, sort_keys=True)
Expand Down