Improve function pert_scaled

dpgen/data/gen.py

@@ -728,8 +728,7 @@ def make_scale_ABACUS(jdata):
 
 
 def pert_scaled(jdata):
- if "init_fp_style" not in jdata:
- jdata["init_fp_style"] = "VASP"
+ ### Extract data from jdata
  out_dir = jdata["out_dir"]
  scale = jdata["scale"]
  pert_box = jdata["pert_box"]
@@ -746,6 +745,7 @@ def pert_scaled(jdata):
  if "from_poscar" in jdata:
  from_poscar = jdata["from_poscar"]
 
+ ### Get the current working directory and the system path
  cwd = os.getcwd()
  path_sp = os.path.join(out_dir, global_dirname_03)
  assert os.path.isdir(path_sp)
@@ -754,35 +754,38 @@ def pert_scaled(jdata):
  sys_pe.sort()
  os.chdir(cwd)
 
- pert_cmd = os.path.dirname(__file__)
- pert_cmd = os.path.join(pert_cmd, "tools")
- pert_cmd = os.path.join(pert_cmd, "create_random_disturb.py")
- fp_style = "vasp"
- poscar_name = "POSCAR"
- if jdata["init_fp_style"] == "ABACUS":
+ ### Construct the perturbation command
+ init_fp_style = jdata.get("init_fp_style", "VASP")
+ if init_fp_style == "VASP":
+  fp_style = "vasp"
+  poscar_name = "POSCAR"
+ elif init_fp_style == "ABACUS":
  fp_style = "abacus"
  poscar_name = "STRU"
+
+ python_exec = os.path.join(
+ os.path.dirname(__file__), "tools", "create_random_disturb.py"
+ )
  pert_cmd = (
  sys.executable
- + " "
- + pert_cmd
- + " -etmax %f -ofmt %s %s %d %f > /dev/null"
- % (pert_box, fp_style, poscar_name, pert_numb, pert_atom)
+ + f" {python_exec} -etmax {pert_box} -ofmt {fp_style} {poscar_name} {pert_numb} {pert_atom} > /dev/null"
  )
+
+ ### Loop over each system and scale
  for ii in sys_pe:
  for jj in scale:
- path_work = path_sp
- path_work = os.path.join(path_work, ii)
- path_work = os.path.join(path_work, f"scale-{jj:.3f}")
+ path_work = os.path.join(path_sp, ii, f"scale-{jj:.3f}")
  assert os.path.isdir(path_work)
  os.chdir(path_work)
  sp.check_call(pert_cmd, shell=True)
+
+ ### Loop over each perturbation
  for kk in range(pert_numb):
  if fp_style == "vasp":
- pos_in = "POSCAR%d.vasp" % (kk + 1)
+ pos_in = f"POSCAR{kk+1}.vasp"
  elif fp_style == "abacus":
- pos_in = "STRU%d.abacus" % (kk + 1)
- dir_out = "%06d" % (kk + 1)
+ pos_in = f"STRU{kk+1}.abacus"
+ dir_out = f"{kk+1:06d}"
  create_path(dir_out)
  if fp_style == "vasp":
  pos_out = os.path.join(dir_out, "POSCAR")
@@ -807,12 +810,14 @@ def pert_scaled(jdata):
  else:
  shutil.copy2(pos_in, pos_out)
  os.remove(pos_in)
+
+ ### Handle special case (unperturbed ?)
  kk = -1
  if fp_style == "vasp":
  pos_in = "POSCAR"
  elif fp_style == "abacus":
  pos_in = "STRU"
- dir_out = "%06d" % (kk + 1)
+ dir_out = f"{kk+1:06d}"
  create_path(dir_out)
  if fp_style == "vasp":
  pos_out = os.path.join(dir_out, "POSCAR")
@@ -836,6 +841,7 @@ def pert_scaled(jdata):
  )
  else:
  shutil.copy2(pos_in, pos_out)
+
  os.chdir(cwd)
 
 

dpgen/data/surf.py

@@ -18,7 +18,7 @@
 import dpgen.data.tools.fcc as fcc
 import dpgen.data.tools.hcp as hcp
 import dpgen.data.tools.sc as sc
-from dpgen import ROOT_PATH, dlog
+from dpgen import dlog
 from dpgen.dispatcher.Dispatcher import make_submission_compat
 from dpgen.generator.lib.utils import symlink_user_forward_files
 from dpgen.remote.decide_machine import convert_mdata
@@ -354,15 +354,16 @@
  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:
@@ -442,15 +443,12 @@
  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)
@@ -503,46 +501,48 @@
  sys_pe.sort()
  os.chdir(cwd)
 
+ ### Construct the perturbation command
+ 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}")
+ 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)
  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+1}.vasp"
+ dir_out = f"{kk+1:06d}"
  create_path(dir_out)
  pos_out = os.path.join(dir_out, "POSCAR")
  poscar_shuffle(pos_in, pos_out)
  os.remove(pos_in)
+
+ ### Handle special case (unperturbed ?)
  kk = -1
  pos_in = "POSCAR"
- dir_out = "%06d" % (kk + 1)
+ dir_out = f"{kk+1:06d}"
  create_path(dir_out)
  pos_out = os.path.join(dir_out, "POSCAR")
  poscar_shuffle(pos_in, pos_out)
+
  os.chdir(cwd)