Merge branch 'devel' into pre-commit-ci-update-config

doc/conf.py

@@ -19,7 +19,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "DP-GEN"
-copyright = "2020-%d, DeepModeling" % date.today().year
+copyright = "2020-%d, DeepModeling" % date.today().year  # noqa: UP031
 author = "DeepModeling"
 
 

dpgen/__init__.py

@@ -48,11 +48,11 @@ def info():
     ]:
         try:
             mm = __import__(modui)
-            print("%10s %10s   %s" % (modui, mm.__version__, mm.__path__[0]))
+            print("%10s %10s   %s" % (modui, mm.__version__, mm.__path__[0]))  # noqa: UP031
         except ImportError:
-            print("%10s %10s Not Found" % (modui, ""))
+            print("%10s %10s Not Found" % (modui, ""))  # noqa: UP031
         except AttributeError:
-            print("%10s %10s unknown version or path" % (modui, ""))
+            print("%10s %10s unknown version or path" % (modui, ""))  # noqa: UP031
     print()
 
     # reference

dpgen/auto_test/EOS.py

@@ -198,7 +198,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     # vol = vol / 100.0
                     vol = self.vol_start + task_num * self.vol_step
                     # task_num = int((vol - self.vol_start) / self.vol_step)
-                    output_task = os.path.join(path_to_work, "task.%06d" % task_num)
+                    output_task = os.path.join(path_to_work, "task.%06d" % task_num)  # noqa: UP031
                     os.makedirs(output_task, exist_ok=True)
                     os.chdir(output_task)
                     if self.inter_param["type"] == "abacus":

dpgen/auto_test/Elastic.py

@@ -162,7 +162,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
             print("gen with norm " + str(norm_strains))
             print("gen with shear " + str(shear_strains))
             for ii in range(n_dfm):
-                output_task = os.path.join(path_to_work, "task.%06d" % ii)
+                output_task = os.path.join(path_to_work, "task.%06d" % ii)  # noqa: UP031
                 os.makedirs(output_task, exist_ok=True)
                 os.chdir(output_task)
                 for jj in [

dpgen/auto_test/Gamma.py

@@ -223,7 +223,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                 os.symlink(os.path.relpath(equi_contcar), POSCAR)
                 #           task_poscar = os.path.join(output, 'POSCAR')
                 for ii in range(len(all_slabs)):
-                    output_task = os.path.join(path_to_work, "task.%06d" % ii)
+                    output_task = os.path.join(path_to_work, "task.%06d" % ii)  # noqa: UP031
                     os.makedirs(output_task, exist_ok=True)
                     os.chdir(output_task)
                     for jj in ["INCAR", "POTCAR", POSCAR, "conf.lmp", "in.lammps"]:
@@ -232,9 +232,9 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     task_list.append(output_task)
                     # print("# %03d generate " % ii, output_task)
                     print(
-                        "# %03d generate " % ii,
+                        "# %03d generate " % ii,  # noqa: UP031
                         output_task,
-                        " \t %d atoms" % self.atom_num,
+                        " \t %d atoms" % self.atom_num,  # noqa: UP031
                     )
                     # make confs
                     all_slabs[ii].to("POSCAR.tmp", "POSCAR")
@@ -472,12 +472,15 @@ def _compute_lower(self, output_file, all_tasks, all_res):
                 )
 
                 miller_index = loadfn(os.path.join(ii, "miller.json"))
-                ptr_data += "%-25s     %7.2f   %7.3f    %8.3f %8.3f\n" % (
-                    str(miller_index) + "-" + structure_dir + ":",
-                    int(ii[-4:]) / self.n_steps,
-                    sfe,
-                    epa,
-                    equi_epa_slab,
+                ptr_data += (
+                    "%-25s     %7.2f   %7.3f    %8.3f %8.3f\n"  # noqa: UP031
+                    % (
+                        str(miller_index) + "-" + structure_dir + ":",
+                        int(ii[-4:]) / self.n_steps,
+                        sfe,
+                        epa,
+                        equi_epa_slab,
+                    )
                 )
                 res_data[int(ii[-4:]) / self.n_steps] = [sfe, epa, equi_epa]
 

dpgen/auto_test/Interstitial.py

@@ -222,7 +222,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                 #           task_poscar = os.path.join(output, 'POSCAR')
 
                 for ii in range(len(dss)):
-                    output_task = os.path.join(path_to_work, "task.%06d" % ii)
+                    output_task = os.path.join(path_to_work, "task.%06d" % ii)  # noqa: UP031
                     os.makedirs(output_task, exist_ok=True)
                     os.chdir(output_task)
                     for jj in [
@@ -262,7 +262,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
                     super_latt_param = float(pos_line[2].split()[0])
 
-                    output_task1 = os.path.join(path_to_work, "task.%06d" % (len(dss)))
+                    output_task1 = os.path.join(path_to_work, "task.%06d" % (len(dss)))  # noqa: UP031
                     os.makedirs(output_task1, exist_ok=True)
                     os.chdir(output_task1)
                     task_list.append(output_task1)
@@ -283,7 +283,8 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     os.chdir(cwd)
 
                     output_task2 = os.path.join(
-                        path_to_work, "task.%06d" % (len(dss) + 1)
+                        path_to_work,
+                        "task.%06d" % (len(dss) + 1),  # noqa: UP031
                     )
                     os.makedirs(output_task2, exist_ok=True)
                     os.chdir(output_task2)
@@ -305,7 +306,8 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     os.chdir(cwd)
 
                     output_task3 = os.path.join(
-                        path_to_work, "task.%06d" % (len(dss) + 2)
+                        path_to_work,
+                        "task.%06d" % (len(dss) + 2),  # noqa: UP031
                     )
                     os.makedirs(output_task3, exist_ok=True)
                     os.chdir(output_task3)
@@ -346,7 +348,8 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                                 replace_label = idx
 
                     output_task4 = os.path.join(
-                        path_to_work, "task.%06d" % (len(dss) + 3)
+                        path_to_work,
+                        "task.%06d" % (len(dss) + 3),  # noqa: UP031
                     )
                     os.makedirs(output_task4, exist_ok=True)
                     os.chdir(output_task4)
@@ -380,7 +383,8 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     os.chdir(cwd)
 
                     output_task5 = os.path.join(
-                        path_to_work, "task.%06d" % (len(dss) + 4)
+                        path_to_work,
+                        "task.%06d" % (len(dss) + 4),  # noqa: UP031
                     )
                     os.makedirs(output_task5, exist_ok=True)
                     os.chdir(output_task5)
@@ -414,7 +418,8 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                     os.chdir(cwd)
 
                     output_task6 = os.path.join(
-                        path_to_work, "task.%06d" % (len(dss) + 5)
+                        path_to_work,
+                        "task.%06d" % (len(dss) + 5),  # noqa: UP031
                     )
                     os.makedirs(output_task6, exist_ok=True)
                     os.chdir(output_task6)
@@ -453,7 +458,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
 
                 if self.inter_param["type"] == "abacus":
                     for ii in range(total_task):
-                        output_task = os.path.join(path_to_work, "task.%06d" % ii)
+                        output_task = os.path.join(path_to_work, "task.%06d" % ii)  # noqa: UP031
                         os.chdir(output_task)
                         abacus.poscar2stru("POSCAR", self.inter_param, "STRU")
                         os.remove("POSCAR")
@@ -478,8 +483,8 @@ def post_process(self, task_list):
                         type_num = type_map[insert_ele] + 1
                         conf_line[2] = str(len(type_map_list)) + " atom types"
                         conf_line[-2] = (
-                            "%6.d" % int(insert_line.split()[0])
-                            + "%7.d" % type_num
+                            "%6.d" % int(insert_line.split()[0])  # noqa: UP031
+                            + "%7.d" % type_num  # noqa: UP031
                             + f"{float(insert_line.split()[2]):16.10f}"
                             + f"{float(insert_line.split()[3]):16.10f}"
                             + f"{float(insert_line.split()[4]):16.10f}"

dpgen/auto_test/Surface.py

@@ -198,7 +198,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                 os.symlink(os.path.relpath(equi_contcar), POSCAR)
                 #           task_poscar = os.path.join(output, 'POSCAR')
                 for ii in range(len(all_slabs)):
-                    output_task = os.path.join(path_to_work, "task.%06d" % ii)
+                    output_task = os.path.join(path_to_work, "task.%06d" % ii)  # noqa: UP031
                     os.makedirs(output_task, exist_ok=True)
                     os.chdir(output_task)
                     for jj in [
@@ -213,9 +213,9 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                             os.remove(jj)
                     task_list.append(output_task)
                     print(
-                        "# %03d generate " % ii,
+                        "# %03d generate " % ii,  # noqa: UP031
                         output_task,
-                        " \t %d atoms" % len(all_slabs[ii].sites),
+                        " \t %d atoms" % len(all_slabs[ii].sites),  # noqa: UP031
                     )
                     # make confs
                     all_slabs[ii].to("POSCAR.tmp", "POSCAR")
@@ -270,7 +270,7 @@ def _compute_lower(self, output_file, all_tasks, all_res):
                 evac = (task_result["energies"][-1] - equi_epa * natoms) / AA * Cf
 
                 miller_index = loadfn(os.path.join(ii, "miller.json"))
-                ptr_data += "%-25s     %7.3f    %8.3f %8.3f\n" % (
+                ptr_data += "%-25s     %7.3f    %8.3f %8.3f\n" % (  # noqa: UP031
                     str(miller_index) + "-" + structure_dir + ":",
                     evac,
                     epa,

dpgen/auto_test/VASP.py

@@ -112,7 +112,7 @@ def make_input_file(self, output_dir, task_type, task_param):
                     isif = 2
                     if not ("NSW" in incar and incar.get("NSW") == nsw):
                         dlog.info(
-                            "%s setting NSW to %d"
+                            "%s setting NSW to %d"  # noqa: UP031
                             % (self.make_input_file.__name__, nsw)
                         )
                         incar["NSW"] = nsw
@@ -121,15 +121,15 @@ def make_input_file(self, output_dir, task_type, task_param):
 
                 if not ("ISIF" in incar and incar.get("ISIF") == isif):
                     dlog.info(
-                        "%s setting ISIF to %d" % (self.make_input_file.__name__, isif)
+                        "%s setting ISIF to %d" % (self.make_input_file.__name__, isif)  # noqa: UP031
                     )
                     incar["ISIF"] = isif
 
             elif cal_type == "static":
                 nsw = 0
                 if not ("NSW" in incar and incar.get("NSW") == nsw):
                     dlog.info(
-                        "%s setting NSW to %d" % (self.make_input_file.__name__, nsw)
+                        "%s setting NSW to %d" % (self.make_input_file.__name__, nsw)  # noqa: UP031
                     )
                     incar["NSW"] = nsw
 

dpgen/auto_test/Vacancy.py

@@ -187,7 +187,7 @@ def make_confs(self, path_to_work, path_to_equi, refine=False):
                 #           task_poscar = os.path.join(output, 'POSCAR')
 
                 for ii in range(len(dss)):
-                    output_task = os.path.join(path_to_work, "task.%06d" % ii)
+                    output_task = os.path.join(path_to_work, "task.%06d" % ii)  # noqa: UP031
                     os.makedirs(output_task, exist_ok=True)
                     os.chdir(output_task)
                     for jj in [

dpgen/auto_test/common_prop.py

@@ -102,7 +102,7 @@ def run_property(confs, inter_param, property_list, mdata):
     # conf_dirs.sort()
     processes = len(property_list)
     pool = Pool(processes=processes)
-    print("Submit job via %d processes" % processes)
+    print("Submit job via %d processes" % processes)  # noqa: UP031
     conf_dirs = []
     for conf in confs:
         conf_dirs.extend(glob.glob(conf))
@@ -181,8 +181,8 @@ def run_property(confs, inter_param, property_list, mdata):
     for ii in range(len(multiple_ret)):
         if not multiple_ret[ii].successful():
             print("ERROR:", multiple_ret[ii].get())
-            raise RuntimeError("Job %d is not successful!" % ii)
-    print("%d jobs are finished" % len(multiple_ret))
+            raise RuntimeError("Job %d is not successful!" % ii)  # noqa: UP031
+    print("%d jobs are finished" % len(multiple_ret))  # noqa: UP031
 
 
 def worker(

dpgen/auto_test/lib/abacus.py

@@ -333,7 +333,7 @@ def final_stru(abacus_path):
             if lines[-i][1:27] == "STEP OF MOLECULAR DYNAMICS":
                 max_step = int(lines[-i].split()[-1])
                 break
-        return "OUT.%s/STRU_MD_%d" % (suffix, max_step)
+        return "OUT.%s/STRU_MD_%d" % (suffix, max_step)  # noqa: UP031
     elif calculation == "scf":
         return "STRU"
     else:

dpgen/auto_test/lib/lammps.py

@@ -181,7 +181,7 @@ def make_lammps_eval(conf, type_map, interaction, param):
     ret += "box         tilt large\n"
     ret += f"read_data   {conf}\n"
     for ii in range(len(type_map)):
-        ret += "mass            %d %.3f\n" % (ii + 1, Element(type_map_list[ii]).mass)
+        ret += "mass            %d %.3f\n" % (ii + 1, Element(type_map_list[ii]).mass)  # noqa: UP031
     ret += "neigh_modify    every 1 delay 0 check no\n"
     ret += interaction(param)
     ret += "compute         mype all pe\n"
@@ -239,7 +239,7 @@ def make_lammps_equi(
     ret += "box         tilt large\n"
     ret += f"read_data   {conf}\n"
     for ii in range(len(type_map)):
-        ret += "mass            %d %.3f\n" % (ii + 1, Element(type_map_list[ii]).mass)
+        ret += "mass            %d %.3f\n" % (ii + 1, Element(type_map_list[ii]).mass)  # noqa: UP031
     ret += "neigh_modify    every 1 delay 0 check no\n"
     ret += interaction(param)
     ret += "compute         mype all pe\n"
@@ -251,11 +251,11 @@ def make_lammps_equi(
     ret += "min_style       cg\n"
     if change_box:
         ret += "fix             1 all box/relax iso 0.0 \n"
-        ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)
+        ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)  # noqa: UP031
         ret += "fix             1 all box/relax aniso 0.0 \n"
-        ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)
+        ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)  # noqa: UP031
         ret += "fix             1 all box/relax tri 0.0 \n"
-    ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)
+    ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)  # noqa: UP031
     ret += "variable        N equal count(all)\n"
     ret += "variable        V equal vol\n"
     ret += 'variable        E equal "c_mype"\n'
@@ -296,7 +296,7 @@ def make_lammps_elastic(
     ret += "box         tilt large\n"
     ret += f"read_data   {conf}\n"
     for ii in range(len(type_map)):
-        ret += "mass            %d %.3f\n" % (ii + 1, Element(type_map_list[ii]).mass)
+        ret += "mass            %d %.3f\n" % (ii + 1, Element(type_map_list[ii]).mass)  # noqa: UP031
     ret += "neigh_modify    every 1 delay 0 check no\n"
     ret += interaction(param)
     ret += "compute         mype all pe\n"
@@ -306,7 +306,7 @@ def make_lammps_elastic(
     )
     ret += "dump            1 all custom 100 dump.relax id type xs ys zs fx fy fz\n"
     ret += "min_style       cg\n"
-    ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)
+    ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)  # noqa: UP031
     ret += "variable        N equal count(all)\n"
     ret += "variable        V equal vol\n"
     ret += 'variable        E equal "c_mype"\n'
@@ -361,7 +361,7 @@ def make_lammps_press_relax(
     ret += "box         tilt large\n"
     ret += f"read_data   {conf}\n"
     for ii in range(len(type_map)):
-        ret += "mass            %d %.3f\n" % (ii + 1, Element(type_map_list[ii]).mass)
+        ret += "mass            %d %.3f\n" % (ii + 1, Element(type_map_list[ii]).mass)  # noqa: UP031
     ret += "neigh_modify    every 1 delay 0 check no\n"
     ret += interaction(param)
     ret += "compute         mype all pe\n"
@@ -372,9 +372,9 @@ def make_lammps_press_relax(
     ret += "dump            1 all custom 100 dump.relax id type xs ys zs fx fy fz\n"
     ret += "min_style       cg\n"
     ret += "fix             1 all box/relax iso ${Px} \n"
-    ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)
+    ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)  # noqa: UP031
     ret += "fix             1 all box/relax aniso ${Px} \n"
-    ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)
+    ret += "minimize        %e %e %d %d\n" % (etol, ftol, maxiter, maxeval)  # noqa: UP031
     ret += "variable        N equal count(all)\n"
     ret += "variable        V equal vol\n"
     ret += 'variable        E equal "c_mype"\n'
@@ -409,7 +409,7 @@ def make_lammps_phonon(
     ret += f"read_data   {conf}\n"
     ntypes = len(masses)
     for ii in range(ntypes):
-        ret += "mass            %d %f\n" % (ii + 1, masses[ii])
+        ret += "mass            %d %f\n" % (ii + 1, masses[ii])  # noqa: UP031
     ret += "neigh_modify    every 1 delay 0 check no\n"
     ret += interaction(param)
     return ret

dpgen/auto_test/lib/lmp.py

@@ -145,7 +145,7 @@ def system_data(lines):
     system["atom_numbs"] = get_natoms_vec(lines)
     system["atom_names"] = []
     for ii in range(len(system["atom_numbs"])):
-        system["atom_names"].append("Type_%d" % ii)
+        system["atom_names"].append("Type_%d" % ii)  # noqa: UP031
     lohi, tilt = get_lmpbox(lines)
     orig, cell = lmpbox2box(lohi, tilt)
     system["orig"] = np.array(orig)
@@ -165,8 +165,8 @@ def from_system_data(system):
     ret += "\n"
     natoms = sum(system["atom_numbs"])
     ntypes = len(system["atom_numbs"])
-    ret += "%d atoms\n" % natoms
-    ret += "%d atom types\n" % ntypes
+    ret += "%d atoms\n" % natoms  # noqa: UP031
+    ret += "%d atom types\n" % ntypes  # noqa: UP031
     ret += "0 {:f} xlo xhi\n".format(system["cell"][0][0])
     ret += "0 {:f} ylo yhi\n".format(system["cell"][1][1])
     ret += "0 {:f} zlo zhi\n".format(system["cell"][2][2])
@@ -179,7 +179,7 @@ def from_system_data(system):
     ret += "Atoms # atomic\n"
     ret += "\n"
     for ii in range(natoms):
-        ret += "%d %d %f %f %f\n" % (
+        ret += "%d %d %f %f %f\n" % (  # noqa: UP031
             ii + 1,
             system["atom_types"][ii],
             system["coordinates"][ii][0] - system["orig"][0],