fix pre-commit errors (#1540)

Follow up #1533

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Refactor**
- Updated string formatting across various modules to use f-strings for
improved readability and consistency in error messages, log entries, and
data output.
- **Style**
- Enhanced string interpolation methods from older formatting styles to
modern f-string syntax across the application, ensuring uniformity and
clearer code presentation.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

dpgen/auto_test/ABACUS.py

@@ -26,7 +26,7 @@ def __init__(self, inter_parameter, path_to_poscar):
  def make_potential_files(self, output_dir):
  stru = os.path.abspath(os.path.join(output_dir, "STRU"))
  if not os.path.isfile(stru):
- raise FileNotFoundError("No file %s" % stru)
+ raise FileNotFoundError(f"No file {stru}")
  stru_data = abacus_scf.get_abacus_STRU(stru)
  atom_names = stru_data["atom_names"]
  orb_files = stru_data["orb_files"]
@@ -58,7 +58,7 @@ def make_potential_files(self, output_dir):
  )
  if atomname not in self.potcars:
  raise RuntimeError(
- "please specify the pseudopotential file of '%s'" % atomname
+ f"please specify the pseudopotential file of '{atomname}'"
  )
  pp_orb_file.append([pp_files[iatom], self.potcars[atomname]])
 
@@ -70,7 +70,7 @@ def make_potential_files(self, output_dir):
  )
  if atomname not in self.orbfile:
  raise RuntimeError(
- "please specify the orbital file of '%s'" % atomname
+ f"please specify the orbital file of '{atomname}'"
  )
  pp_orb_file.append([orb_files[iatom], self.orbfile[atomname]])
  elif self.orbfile:
@@ -105,7 +105,7 @@ def make_potential_files(self, output_dir):
 
  src_file = os.path.join(pp_dir, file_param)
  if not os.path.isfile(src_file):
- raise RuntimeError("Can not find file %s" % src_file)
+ raise RuntimeError(f"Can not find file {src_file}")
  tar_file = os.path.join("pp_orb", filename_in_stru)
  if os.path.isfile(tar_file):
  os.remove(tar_file)
@@ -138,8 +138,7 @@ def make_input_file(self, output_dir, task_type, task_param):
  incar_prop = os.path.abspath(cal_setting["input_prop"])
  incar = abacus_scf.get_abacus_input_parameters(incar_prop)
  dlog.info(
- "Detected 'input_prop' in 'relaxation', use %s as INPUT, and ignore 'cal_setting'"
- % incar_prop
+ f"Detected 'input_prop' in 'relaxation', use {incar_prop} as INPUT, and ignore 'cal_setting'"
  )
 
  # revise INCAR based on the INCAR provided in the "interaction"
@@ -195,9 +194,8 @@ def make_input_file(self, output_dir, task_type, task_param):
  dlog.info("'basis_type' is not defined, set to be 'pw'!")
  self.modify_input(incar, "basis_type", "pw")
  if "lcao" in incar["basis_type"].lower() and not self.if_define_orb_file:
- mess = (
- "The basis_type is %s, but not define orbital file!!!"
- % incar["basis_type"]
+ mess = "The basis_type is {}, but not define orbital file!!!".format(
+ incar["basis_type"]
  )
  raise RuntimeError(mess)
  if "deepks_model" in incar:

dpgen/auto_test/EOS.py

@@ -81,7 +81,7 @@ def __init__(self, parameter, inter_param=None):
  def make_confs(self, path_to_work, path_to_equi, refine=False):
  path_to_work = os.path.abspath(path_to_work)
  if os.path.exists(path_to_work):
- dlog.warning("%s already exists" % path_to_work)
+ dlog.warning(f"{path_to_work} already exists")
  else:
  os.makedirs(path_to_work)
  path_to_equi = os.path.abspath(path_to_equi)
@@ -177,7 +177,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
  if not os.path.isfile(equi_contcar):
  raise RuntimeError(
- "Can not find %s, please do relaxation first" % equi_contcar
+ f"Can not find {equi_contcar}, please do relaxation first"
  )
 
  if self.inter_param["type"] == "abacus":

dpgen/auto_test/Elastic.py

@@ -55,7 +55,7 @@ def __init__(self, parameter, inter_param=None):
  def make_confs(self, path_to_work, path_to_equi, refine=False):
  path_to_work = os.path.abspath(path_to_work)
  if os.path.exists(path_to_work):
- dlog.warning("%s already exists" % path_to_work)
+ dlog.warning(f"{path_to_work} already exists")
  else:
  os.makedirs(path_to_work)
  path_to_equi = os.path.abspath(path_to_equi)
@@ -288,10 +288,10 @@ def _compute_lower(self, output_file, all_tasks, all_res):
  res_data["GV"] = GV
  res_data["EV"] = EV
  res_data["uV"] = uV
- ptr_data += "# Bulk Modulus BV = %.2f GPa\n" % BV
- ptr_data += "# Shear Modulus GV = %.2f GPa\n" % GV
- ptr_data += "# Youngs Modulus EV = %.2f GPa\n" % EV
- ptr_data += "# Poission Ratio uV = %.2f\n " % uV
+ ptr_data += f"# Bulk Modulus BV = {BV:.2f} GPa\n"
+ ptr_data += f"# Shear Modulus GV = {GV:.2f} GPa\n"
+ ptr_data += f"# Youngs Modulus EV = {EV:.2f} GPa\n"
+ ptr_data += f"# Poission Ratio uV = {uV:.2f}\n "
 
  dumpfn(res_data, output_file, indent=4)
 

dpgen/auto_test/Gamma.py

@@ -96,7 +96,7 @@ def __init__(self, parameter, inter_param=None):
  def make_confs(self, path_to_work, path_to_equi, refine=False):
  path_to_work = os.path.abspath(path_to_work)
  if os.path.exists(path_to_work):
- dlog.warning("%s already exists" % path_to_work)
+ dlog.warning(f"{path_to_work} already exists")
  else:
  os.makedirs(path_to_work)
  path_to_equi = os.path.abspath(path_to_equi)

dpgen/auto_test/Interstitial.py

@@ -269,9 +269,9 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
  print(self.insert_ele[0], file=fout)
  dumpfn(self.supercell, "supercell.json")
  pos_line[chl] = (
- "%.6f" % float(latt_param / 4 / super_latt_param)
+ f"{float(latt_param / 4 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float(latt_param / 2 / super_latt_param)
+ + f"{float(latt_param / 2 / super_latt_param):.6f}"
  + " 0.000000 "
  + self.insert_ele[0]
  )
@@ -291,9 +291,9 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
  print(self.insert_ele[0], file=fout)
  dumpfn(self.supercell, "supercell.json")
  pos_line[chl] = (
- "%.6f" % float(latt_param / 2 / super_latt_param)
+ f"{float(latt_param / 2 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float(latt_param / 2 / super_latt_param)
+ + f"{float(latt_param / 2 / super_latt_param):.6f}"
  + " 0.000000 "
  + self.insert_ele[0]
  )
@@ -313,11 +313,11 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
  print(self.insert_ele[0], file=fout)
  dumpfn(self.supercell, "supercell.json")
  pos_line[chl] = (
- "%.6f" % float(latt_param / 4 / super_latt_param)
+ f"{float(latt_param / 4 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float(latt_param / 4 / super_latt_param)
+ + f"{float(latt_param / 4 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float(latt_param / 4 / super_latt_param)
+ + f"{float(latt_param / 4 / super_latt_param):.6f}"
  + " "
  + self.insert_ele[0]
  )
@@ -354,20 +354,20 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
  print(self.insert_ele[0], file=fout)
  dumpfn(self.supercell, "supercell.json")
  pos_line[chl] = (
- "%.6f" % float(latt_param / 3 / super_latt_param)
+ f"{float(latt_param / 3 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float(latt_param / 3 / super_latt_param)
+ + f"{float(latt_param / 3 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float(latt_param / 3 / super_latt_param)
+ + f"{float(latt_param / 3 / super_latt_param):.6f}"
  + " "
  + self.insert_ele[0]
  )
  pos_line[replace_label] = (
- "%.6f" % float(latt_param / 3 * 2 / super_latt_param)
+ f"{float(latt_param / 3 * 2 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float(latt_param / 3 * 2 / super_latt_param)
+ + f"{float(latt_param / 3 * 2 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float(latt_param / 3 * 2 / super_latt_param)
+ + f"{float(latt_param / 3 * 2 / super_latt_param):.6f}"
  + " "
  + self.insert_ele[0]
  )
@@ -388,24 +388,20 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
  print(self.insert_ele[0], file=fout)
  dumpfn(self.supercell, "supercell.json")
  pos_line[chl] = (
- "%.6f"
- % float((latt_param + 2.1 / 2**0.5) / 2 / super_latt_param)
+ f"{float((latt_param + 2.1 / 2**0.5) / 2 / super_latt_param):.6f}"
  + " "
- + "%.6f"
- % float((latt_param - 2.1 / 2**0.5) / 2 / super_latt_param)
+ + f"{float((latt_param - 2.1 / 2**0.5) / 2 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float(latt_param / 2 / super_latt_param)
+ + f"{float(latt_param / 2 / super_latt_param):.6f}"
  + " "
  + self.insert_ele[0]
  )
  pos_line[replace_label] = (
- "%.6f"
- % float((latt_param - 2.1 / 2**0.5) / 2 / super_latt_param)
+ f"{float((latt_param - 2.1 / 2**0.5) / 2 / super_latt_param):.6f}"
  + " "
- + "%.6f"
- % float((latt_param + 2.1 / 2**0.5) / 2 / super_latt_param)
+ + f"{float((latt_param + 2.1 / 2**0.5) / 2 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float(latt_param / 2 / super_latt_param)
+ + f"{float(latt_param / 2 / super_latt_param):.6f}"
  + " "
  + self.insert_ele[0]
  )
@@ -426,20 +422,20 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
  print(self.insert_ele[0], file=fout)
  dumpfn(self.supercell, "supercell.json")
  pos_line[chl] = (
- "%.6f" % float(latt_param / 2 / super_latt_param)
+ f"{float(latt_param / 2 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float(latt_param / 2 / super_latt_param)
+ + f"{float(latt_param / 2 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float((latt_param - 2.1) / 2 / super_latt_param)
+ + f"{float((latt_param - 2.1) / 2 / super_latt_param):.6f}"
  + " "
  + self.insert_ele[0]
  )
  pos_line[replace_label] = (
- "%.6f" % float(latt_param / 2 / super_latt_param)
+ f"{float(latt_param / 2 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float(latt_param / 2 / super_latt_param)
+ + f"{float(latt_param / 2 / super_latt_param):.6f}"
  + " "
- + "%.6f" % float((latt_param + 2.1) / 2 / super_latt_param)
+ + f"{float((latt_param + 2.1) / 2 / super_latt_param):.6f}"
  + " "
  + self.insert_ele[0]
  )
@@ -483,9 +479,9 @@ def post_process(self, task_list):
  conf_line[-2] = (
  "%6.d" % int(insert_line.split()[0])
  + "%7.d" % type_num
- + "%16.10f" % float(insert_line.split()[2])
- + "%16.10f" % float(insert_line.split()[3])
- + "%16.10f" % float(insert_line.split()[4])
+ + f"{float(insert_line.split()[2]):16.10f}"
+ + f"{float(insert_line.split()[3]):16.10f}"
+ + f"{float(insert_line.split()[4]):16.10f}"
  )
  with open(conf, "w+") as fout:
  for jj in conf_line:

dpgen/auto_test/Surface.py

@@ -87,7 +87,7 @@ def __init__(self, parameter, inter_param=None):
  def make_confs(self, path_to_work, path_to_equi, refine=False):
  path_to_work = os.path.abspath(path_to_work)
  if os.path.exists(path_to_work):
- dlog.warning("%s already exists" % path_to_work)
+ dlog.warning(f"{path_to_work} already exists")
  else:
  os.makedirs(path_to_work)
  path_to_equi = os.path.abspath(path_to_equi)

dpgen/auto_test/Vacancy.py

@@ -79,7 +79,7 @@ def __init__(self, parameter, inter_param=None):
  def make_confs(self, path_to_work, path_to_equi, refine=False):
  path_to_work = os.path.abspath(path_to_work)
  if os.path.exists(path_to_work):
- dlog.warning("%s already exists" % path_to_work)
+ dlog.warning(f"{path_to_work} already exists")
  else:
  os.makedirs(path_to_work)
  path_to_equi = os.path.abspath(path_to_equi)

dpgen/auto_test/common_equi.py

@@ -27,7 +27,7 @@ def make_equi(confs, inter_param, relax_param):
  else:
  ele_list = [key for key in inter_param["potcars"].keys()]
  # ele_list = inter_param['type_map']
- dlog.debug("ele_list %s" % ":".join(ele_list))
+ dlog.debug("ele_list {}".format(":".join(ele_list)))
  conf_dirs = []
  for conf in confs:
  conf_dirs.extend(glob.glob(conf))
@@ -45,8 +45,8 @@ def make_equi(confs, inter_param, relax_param):
  for ii in conf_dirs:
  os.chdir(ii)
  crys_type = ii.split("/")[-1]
- dlog.debug("crys_type: %s" % crys_type)
- dlog.debug("pwd: %s" % os.getcwd())
+ dlog.debug(f"crys_type: {crys_type}")
+ dlog.debug(f"pwd: {os.getcwd()}")
  if crys_type == "std-fcc":
  if not os.path.exists("POSCAR"):
  crys.fcc1(ele_list[element_label]).to("POSCAR", "POSCAR")
@@ -77,7 +77,7 @@ def make_equi(confs, inter_param, relax_param):
  # ...
  for ii in conf_dirs:
  crys_type = ii.split("/")[-1]
- dlog.debug("crys_type: %s" % crys_type)
+ dlog.debug(f"crys_type: {crys_type}")
 
  if "mp-" in crys_type and not os.path.exists(os.path.join(ii, "POSCAR")):
  get_structure(crys_type).to("POSCAR", os.path.join(ii, "POSCAR"))
@@ -130,7 +130,7 @@ def make_equi(confs, inter_param, relax_param):
 
  for ii in task_dirs:
  poscar = os.path.join(ii, "POSCAR")
- dlog.debug("task_dir %s" % ii)
+ dlog.debug(f"task_dir {ii}")
  inter = make_calculator(inter_param, poscar)
  inter.make_potential_files(ii)
  inter.make_input_file(ii, "relaxation", relax_param)
@@ -162,7 +162,7 @@ def run_equi(confs, inter_param, mdata):
  elif inter_type in lammps_task_type:
  mdata = convert_mdata(mdata, ["model_devi"])
  else:
- raise RuntimeError("unknown task %s, something wrong" % inter_type)
+ raise RuntimeError(f"unknown task {inter_type}, something wrong")
 
  # dispatch the tasks
  # POSCAR here is useless
@@ -173,12 +173,12 @@ def run_equi(confs, inter_param, mdata):
  # backward_files += logs
  machine, resources, command, group_size = util.get_machine_info(mdata, inter_type)
  work_path = os.getcwd()
- print("%s --> Runing... " % (work_path))
+ print(f"{work_path} --> Runing... ")
 
  api_version = mdata.get("api_version", "1.0")
  if Version(api_version) < Version("1.0"):
  raise RuntimeError(
- "API version %s has been removed. Please upgrade to 1.0." % api_version
+ f"API version {api_version} has been removed. Please upgrade to 1.0."
  )
  elif Version(api_version) >= Version("1.0"):
  submission = make_submission(

dpgen/auto_test/common_prop.py

@@ -155,7 +155,7 @@ def run_property(confs, inter_param, property_list, mdata):
  elif inter_type in lammps_task_type:
  mdata = convert_mdata(mdata, ["model_devi"])
  else:
- raise RuntimeError("unknown task %s, something wrong" % inter_type)
+ raise RuntimeError(f"unknown task {inter_type}, something wrong")
 
  work_path = path_to_work
  all_task = tmp_task_list
@@ -199,7 +199,7 @@ def worker(
  api_version = mdata.get("api_version", "1.0")
  if Version(api_version) < Version("1.0"):
  raise RuntimeError(
- "API version %s has been removed. Please upgrade to 1.0." % api_version
+ f"API version {api_version} has been removed. Please upgrade to 1.0."
  )
  elif Version(api_version) >= Version("1.0"):
  submission = make_submission(

dpgen/auto_test/gen_confs.py

@@ -134,7 +134,7 @@ def _main():
  )
  args = parser.parse_args()
 
- print("generate %s" % (args.elements))
+ print(f"generate {args.elements}")
  if len(args.elements) == 1:
  gen_element(args.elements[0], args.key)
  # gen_element_std(args.elements[0])