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fix: preserve surface POSCAR input paths #1952

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fix: preserve surface POSCAR input paths #1952

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3 changes: 1 addition & 2 deletions dpgen/data/surf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -229,8 +229,7 @@ def make_super_cell_pymatgen(jdata):

if from_poscar:
from_poscar_path = jdata["from_poscar_path"]
poscar_name = os.path.basename(from_poscar_path)
ss = Structure.from_file(poscar_name)
ss = Structure.from_file(from_poscar_path)
else:
from_path = path_uc
from_file = os.path.join(from_path, "POSCAR.unit")
Expand Down
21 changes: 18 additions & 3 deletions tests/data/test_gen_surf_poscar.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import os
import shutil
import sys
import tempfile
import unittest

from pymatgen.core import Element, Structure
Expand Down Expand Up @@ -34,6 +35,10 @@ def setUp(self):
]
with open(param_file) as fp:
jdata = json.load(fp)
self.input_dir = tempfile.mkdtemp()
from_poscar_path = os.path.join(self.input_dir, "nested.POSCAR")
shutil.copy2("POSCAR", from_poscar_path)
jdata["from_poscar_path"] = from_poscar_path
out_dir = out_dir_name(jdata)
jdata["out_dir"] = out_dir
self.root_dir = out_dir
Expand All @@ -47,13 +52,16 @@ def setUp(self):

def tearDown(self):
shutil.rmtree(self.root_dir)
shutil.rmtree(self.input_dir)

def test(self):
surfs = glob.glob("POSCAR.01x01x01/01.scale_pert/surf*")
surfs = glob.glob(os.path.join(self.root_dir, "01.scale_pert", "surf*"))
surfs = [ii.split("/")[-1] for ii in surfs]
surfs.sort()
self.assertEqual(surfs, self.surfs)
poscars = glob.glob("POSCAR.01x01x01/00.place_ele/surf*/sys*/POSCAR")
poscars = glob.glob(
os.path.join(self.root_dir, "00.place_ele", "surf*", "sys*", "POSCAR")
)
for poscar in poscars:
surf = poscar.split("/")[-3]
st1 = Structure.from_file(surf + ".POSCAR")
Expand All @@ -63,7 +71,14 @@ def test(self):

for surf in self.surfs:
elongs = glob.glob(
"POSCAR.01x01x01/01.scale_pert/" + surf + "/sys-*/scale-1.000/el*"
os.path.join(
self.root_dir,
"01.scale_pert",
surf,
"sys-*",
"scale-1.000",
"el*",
)
)
elongs = [ii.split("/")[-1] for ii in elongs]
elongs.sort()
Expand Down