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deepmodeling · May 30, 2024 · ee921da · ee921da
1 parent 7208872
commit ee921da
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Showing 3 changed files with 14 additions and 20 deletions.
diff --git a/dpgen/data/surf.py b/dpgen/data/surf.py
@@ -501,26 +501,25 @@ def pert_scaled(jdata):
  sys_pe.sort()
  os.chdir(cwd)
 
+ python_exec = os.path.join(
+ os.path.dirname(__file__), "tools", "create_random_disturb.py"
+ )
  pert_cmd = (
  sys.executable
- + " "
- + os.path.join(ROOT_PATH, "data/tools/create_random_disturb.py")
- )
- pert_cmd += " -etmax %f -ofmt vasp POSCAR %d %f > /dev/null" % (
- pert_box,
- pert_numb,
- pert_atom,
+ + f" {python_exec} -etmax {pert_box} -ofmt vasp POSCAR {pert_numb} {pert_atom} > /dev/null"
  )
+
+ ### Loop over each system and scale
  for ii in sys_pe:
  for jj in scale:
- path_scale = path_sp
- path_scale = os.path.join(path_scale, ii)
- path_scale = os.path.join(path_scale, f"scale-{jj:.3f}")
+ path_scale = os.path.join(path_sp, ii, f"scale-{jj:.3f}")
  assert os.path.isdir(path_scale)
  os.chdir(path_scale)
  dlog.info(os.getcwd())
  poscar_in = os.path.join(path_scale, "POSCAR")
  assert os.path.isfile(poscar_in)
+
+ ### Loop over each perturbation
  for ll in elongs:
  path_elong = path_scale
  path_elong = os.path.join(path_elong, f"elong-{ll:3.3f}")
@@ -529,18 +528,13 @@ def pert_scaled(jdata):
  poscar_elong(poscar_in, "POSCAR", ll)
  sp.check_call(pert_cmd, shell=True)
  for kk in range(pert_numb):
- pos_in = "POSCAR%d.vasp" % (kk + 1)
- dir_out = "%06d" % (kk + 1)
+ pos_in = f"POSCAR{kk}.vasp"
+ dir_out = f"{kk:06d}"
  create_path(dir_out)
  pos_out = os.path.join(dir_out, "POSCAR")
  poscar_shuffle(pos_in, pos_out)
  os.remove(pos_in)
- kk = -1
- pos_in = "POSCAR"
- dir_out = "%06d" % (kk + 1)
- create_path(dir_out)
- pos_out = os.path.join(dir_out, "POSCAR")
- poscar_shuffle(pos_in, pos_out)
+
  os.chdir(cwd)
 
 

diff --git a/tests/data/test_gen_bulk.py b/tests/data/test_gen_bulk.py
@@ -69,7 +69,7 @@ def test(self):
  self.assertEqual(len(scales), self.scale_numb)
  for scale in scales:
  perts = glob.glob(os.path.join(scale, "[0-9]*"))
- self.assertEqual(len(perts), self.pert_numb + 1)
+ self.assertEqual(len(perts), self.pert_numb)
 
 
 if __name__ == "__main__":

diff --git a/tests/data/test_gen_bulk_abacus.py b/tests/data/test_gen_bulk_abacus.py
@@ -103,7 +103,7 @@ def testSTRU(self):
  self.assertEqual(len(scales), self.scale_numb)
  for scale in scales:
  perts = glob.glob(os.path.join(scale, "[0-9]*"))
- self.assertEqual(len(perts), self.pert_numb + 1)
+ self.assertEqual(len(perts), self.pert_numb)
 
 
 if __name__ == "__main__":