Update surf.py

dpgen/data/surf.py

@@ -354,15 +354,16 @@ def make_vasp_relax(jdata):
  out_dir = jdata["out_dir"]
  potcars = jdata["potcars"]
  cwd = os.getcwd()
-
  work_dir = os.path.join(out_dir, global_dirname_02)
  assert os.path.isdir(work_dir)
  work_dir = os.path.abspath(work_dir)
+
  if os.path.isfile(os.path.join(work_dir, "INCAR")):
  os.remove(os.path.join(work_dir, "INCAR"))
  if os.path.isfile(os.path.join(work_dir, "POTCAR")):
  os.remove(os.path.join(work_dir, "POTCAR"))
  shutil.copy2(jdata["relax_incar"], os.path.join(work_dir, "INCAR"))
+
  out_potcar = os.path.join(work_dir, "POTCAR")
  with open(out_potcar, "w") as outfile:
  for fname in potcars:
@@ -440,15 +441,12 @@ def make_scale(jdata):
  for jj in scale:
  if skip_relax:
  pos_src = os.path.join(os.path.join(init_path, ii), "POSCAR")
- assert os.path.isfile(pos_src)
  else:
- try:
- pos_src = os.path.join(os.path.join(init_path, ii), "CONTCAR")
- assert os.path.isfile(pos_src)
- except Exception:
- raise RuntimeError(
- "not file %s, vasp relaxation should be run before scale poscar"
- )
+ pos_src = os.path.join(os.path.join(init_path, ii), "CONTCAR")
+ if not os.path.isfile(pos_src):
+ raise RuntimeError(
+ f"file {pos_src} not found, vasp relaxation should be run before scale poscar"
+ )
  scale_path = os.path.join(work_path, ii)
  scale_path = os.path.join(scale_path, f"scale-{jj:.3f}")
  create_path(scale_path)
@@ -501,6 +499,7 @@ def pert_scaled(jdata):
  sys_pe.sort()
  os.chdir(cwd)
 
+ ### Construct the perturbation command
  python_exec = os.path.join(
  os.path.dirname(__file__), "tools", "create_random_disturb.py"
  )
@@ -521,8 +520,7 @@ def pert_scaled(jdata):
 
  ### Loop over each perturbation
  for ll in elongs:
- path_elong = path_scale
- path_elong = os.path.join(path_elong, f"elong-{ll:3.3f}")
+ path_elong = os.path.join(path_scale, f"elong-{ll:3.3f}")
  create_path(path_elong)
  os.chdir(path_elong)
  poscar_elong(poscar_in, "POSCAR", ll)