u

Author: thangckt

dpgen/data/gen.py

@@ -167,9 +167,7 @@ def stru_ele(supercell_stru, stru_out, eles, natoms, jdata, path_work):
                 os.path.join(path_work, orb_file_names[ipp]),
             )
     if "dpks_descriptor" in jdata:
-        os.symlink(
-            absolute_dpks_descriptor_path, os.path.join(path_work, dpks_descriptor_name)
-        )
+        os.symlink(absolute_dpks_descriptor_path, os.path.join(path_work, dpks_descriptor_name))
 
 
 def poscar_natoms(lines):
@@ -255,9 +253,7 @@ def poscar_scale_abacus(poscar_in, poscar_out, scale, jdata):
         orb_file_names = [os.path.basename(a) for a in jdata["orb_files"]]
     if "dpks_descriptor" in jdata:
         dpks_descriptor_name = os.path.basename(jdata["dpks_descriptor"])
-    ret = make_abacus_scf_stru(
-        stru, pp_files, orb_file_names, dpks_descriptor_name, type_map=jdata["elements"]
-    )
+    ret = make_abacus_scf_stru(stru, pp_files, orb_file_names, dpks_descriptor_name, type_map=jdata["elements"])
     # ret = make_abacus_scf_stru(stru, pp_files)
     with open(poscar_out, "w") as fp:
         fp.write(ret)
@@ -572,9 +568,7 @@ def make_vasp_relax(jdata, mdata):
 
 def make_abacus_relax(jdata, mdata):
     relax_incar = jdata["relax_incar"]
-    standard_incar = get_abacus_input_parameters(
-        relax_incar
-    )  # a dictionary in which all of the values are strings
+    standard_incar = get_abacus_input_parameters(relax_incar)  # a dictionary in which all of the values are strings
     if "kspacing" not in standard_incar:
         if "gamma_only" in standard_incar:
             if isinstance(standard_incar["gamma_only"], str):
@@ -584,9 +578,7 @@ def make_abacus_relax(jdata, mdata):
                     raise RuntimeError("Cannot find any k-points information.")
                 else:
                     relax_kpt_path = jdata["relax_kpt"]
-                    assert os.path.isfile(
-                        relax_kpt_path
-                    ), f"file {relax_kpt_path} should exists"
+                    assert os.path.isfile(relax_kpt_path), f"file {relax_kpt_path} should exists"
             else:
                 gamma_param = {"k_points": [1, 1, 1, 0, 0, 0]}
                 ret_kpt = make_abacus_scf_kpt(gamma_param)
@@ -595,9 +587,7 @@ def make_abacus_relax(jdata, mdata):
                 raise RuntimeError("Cannot find any k-points information.")
             else:
                 relax_kpt_path = jdata["relax_kpt"]
-                assert os.path.isfile(
-                    relax_kpt_path
-                ), f"file {relax_kpt_path} should exists"
+                assert os.path.isfile(relax_kpt_path), f"file {relax_kpt_path} should exists"
 
     out_dir = jdata["out_dir"]
     cwd = os.getcwd()
@@ -675,9 +665,7 @@ def make_scale(jdata):
             else:
                 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"
-                )
+                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)
@@ -763,13 +751,8 @@ def pert_scaled(jdata):
         fp_style = "abacus"
         poscar_name = "STRU"
 
-    python_exec = os.path.join(
-        os.path.dirname(__file__), "tools", "create_random_disturb.py"
-    )
-    pert_cmd = (
-        sys.executable
-        + f" {python_exec} -etmax {pert_box} -ofmt {fp_style} {poscar_name} {pert_numb} {pert_atom} > /dev/null"
-    )
+    python_exec = os.path.join(os.path.dirname(__file__), "tools", "create_random_disturb.py")
+    pert_cmd = f"{sys.executable} {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:
@@ -917,9 +900,7 @@ def make_vasp_md(jdata, mdata):
 
 def make_abacus_md(jdata, mdata):
     md_incar = jdata["md_incar"]
-    standard_incar = get_abacus_input_parameters(
-        md_incar
-    )  # a dictionary in which all of the values are strings
+    standard_incar = get_abacus_input_parameters(md_incar)  # a dictionary in which all of the values are strings
     # assert("md_kpt" in jdata or "kspacing" in standard_incar or "gamma_only" in standard_incar) \
     #        "Cannot find any k-points information."
     if "kspacing" not in standard_incar:
@@ -931,9 +912,7 @@ def make_abacus_md(jdata, mdata):
                     raise RuntimeError("Cannot find any k-points information.")
                 else:
                     md_kpt_path = jdata["md_kpt"]
-                    assert os.path.isfile(
-                        md_kpt_path
-                    ), f"file {md_kpt_path} should exists"
+                    assert os.path.isfile(md_kpt_path), f"file {md_kpt_path} should exists"
             else:
                 ret_kpt = make_abacus_scf_kpt({"k_points": [1, 1, 1, 0, 0, 0]})
         else:
@@ -981,9 +960,7 @@ def make_abacus_md(jdata, mdata):
     if "dpks_descriptor" in jdata:
         dpks_descriptor_name = os.path.basename(jdata["dpks_descriptor"])
         dpks_descriptor_abspath = os.path.abspath(jdata["dpks_descriptor"])
-        shutil.copy2(
-            dpks_descriptor_abspath, os.path.join(path_md, dpks_descriptor_name)
-        )
+        shutil.copy2(dpks_descriptor_abspath, os.path.join(path_md, dpks_descriptor_name))
     if "dpks_model" in jdata:
         dpks_model_name = os.path.basename(jdata["dpks_model"])
         dpks_model_abspath = os.path.abspath(jdata["dpks_model"])
@@ -1019,9 +996,7 @@ def make_abacus_md(jdata, mdata):
                     pass
                 try:
                     for pp_file in [os.path.basename(a) for a in jdata["potcars"]]:
-                        os.symlink(
-                            os.path.relpath(os.path.join(path_md, pp_file)), pp_file
-                        )
+                        os.symlink(os.path.relpath(os.path.join(path_md, pp_file)), pp_file)
                     if "orb_files" in jdata:
                         for orb_file in orb_file_names:
                             os.symlink(
@@ -1035,9 +1010,7 @@ def make_abacus_md(jdata, mdata):
                         )
                     if "dpks_descriptor" in jdata:
                         os.symlink(
-                            os.path.relpath(
-                                os.path.join(path_md, dpks_descriptor_name)
-                            ),
+                            os.path.relpath(os.path.join(path_md, dpks_descriptor_name)),
                             dpks_descriptor_name,
                         )
                 except FileExistsError:
@@ -1222,9 +1195,7 @@ def coll_abacus_md(jdata):
                                 )
                             )
                 else:
-                    dlog.info(
-                        f"WARNING : in directory {os.getcwd()} NO running_md.log file found."
-                    )
+                    dlog.info(f"WARNING : in directory {os.getcwd()} NO running_md.log file found.")
         arg_cvt = " "
         if len(valid_outcars) == 0:
             raise RuntimeError(
@@ -1276,9 +1247,7 @@ def run_abacus_relax(jdata, mdata):
     if "dpks_model" in jdata:
         dpks_model_name = [os.path.basename(jdata["dpks_model"])]
     relax_incar = jdata["relax_incar"]
-    standard_incar = get_abacus_input_parameters(
-        relax_incar
-    )  # a dictionary in which all of the values are strings
+    standard_incar = get_abacus_input_parameters(relax_incar)  # a dictionary in which all of the values are strings
     forward_files = ["STRU", "INPUT"]
     if "kspacing" not in standard_incar:
         forward_files = ["STRU", "INPUT", "KPT"]
@@ -1398,9 +1367,7 @@ def run_abacus_md(jdata, mdata):
     if "dpks_model" in jdata:
         dpks_model_name = [os.path.basename(jdata["dpks_model"])]
     md_incar = jdata["md_incar"]
-    standard_incar = get_abacus_input_parameters(
-        md_incar
-    )  # a dictionary in which all of the values are strings
+    standard_incar = get_abacus_input_parameters(md_incar)  # a dictionary in which all of the values are strings
     forward_files = ["STRU", "INPUT"]
     if "kspacing" not in standard_incar:
         forward_files = ["STRU", "INPUT", "KPT"]
@@ -1492,9 +1459,7 @@ def gen_init_bulk(args):
                     nsw_steps = int(standard_incar["md_nstep"])
             if nsw_flag:
                 if nsw_steps != md_nstep_jdata:
-                    dlog.info(
-                        "WARNING: your set-up for MD steps in PARAM and md_incar are not consistent!"
-                    )
+                    dlog.info("WARNING: your set-up for MD steps in PARAM and md_incar are not consistent!")
                     dlog.info("MD steps in PARAM is %d" % (md_nstep_jdata))
                     dlog.info("MD steps in md_incar is %d" % (nsw_steps))
                     dlog.info("DP-GEN will use settings in md_incar!")
@@ -1575,9 +1540,7 @@ def gen_init_bulk(args):
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        description="Generating initial data for bulk systems."
-    )
+    parser = argparse.ArgumentParser(description="Generating initial data for bulk systems.")
     parser.add_argument("PARAM", type=str, help="parameter file, json/yaml format")
     parser.add_argument(
         "MACHINE",

dpgen/data/surf.py

@@ -182,9 +182,7 @@ def poscar_elong(poscar_in, poscar_out, elong, shift_center=True):
         z_mean = cart_coords[:, 2].mean()
         z_shift = st.lattice.c / 2 - z_mean
         cart_coords[:, 2] = cart_coords[:, 2] + z_shift
-        nst = Structure(
-            st.lattice, st.species, coords=cart_coords, coords_are_cartesian=True
-        )
+        nst = Structure(st.lattice, st.species, coords=cart_coords, coords_are_cartesian=True)
         nst.to(poscar_out, "poscar")
     else:
         with open(poscar_out, "w") as fout:
@@ -265,15 +263,11 @@ def make_super_cell_pymatgen(jdata):
         os.chdir(path_cur_surf)
         # slabgen = SlabGenerator(ss, miller, z_min, 1e-3)
         if user_layer_numb:
-            slab = general_surface.surface(
-                ss, indices=miller, vacuum=vacuum_min, layers=user_layer_numb
-            )
+            slab = general_surface.surface(ss, indices=miller, vacuum=vacuum_min, layers=user_layer_numb)
         else:
             # build slab according to z_min value
             for layer_numb in range(1, max_layer_numb + 1):
-                slab = general_surface.surface(
-                    ss, indices=miller, vacuum=vacuum_min, layers=layer_numb
-                )
+                slab = general_surface.surface(ss, indices=miller, vacuum=vacuum_min, layers=layer_numb)
                 if slab.cell.lengths()[-1] >= z_min:
                     break
                 if layer_numb == max_layer_numb:
@@ -446,9 +440,7 @@ def make_scale(jdata):
             else:
                 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"
-                )
+                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)
@@ -470,9 +462,7 @@ def pert_scaled(jdata):
             elongs = np.arange(vacuum_resol[0], vacuum_max, vacuum_resol[0])
         elif len(vacuum_resol) == 2:
             mid_point = jdata.get("mid_point")
-            head_elongs = np.arange(
-                vacuum_resol[0], mid_point, vacuum_resol[0]
-            ).tolist()
+            head_elongs = np.arange(vacuum_resol[0], mid_point, vacuum_resol[0]).tolist()
             tail_elongs = np.arange(mid_point, vacuum_max, vacuum_resol[1]).tolist()
             elongs = np.unique(head_elongs + tail_elongs).tolist()
         else:
@@ -502,13 +492,8 @@ def pert_scaled(jdata):
     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
-        + f" {python_exec} -etmax {pert_box} -ofmt vasp POSCAR {pert_numb} {pert_atom} > /dev/null"
-    )
+    python_exec = os.path.join(os.path.dirname(__file__), "tools", "create_random_disturb.py")
+    pert_cmd = f"{sys.executable} {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:
@@ -571,9 +556,7 @@ def run_vasp_relax(jdata, mdata):
     work_path_list = glob.glob(os.path.join(work_dir, "surf-*"))
     task_format = {"fp": "sys-*"}
     for work_path in work_path_list:
-        symlink_user_forward_files(
-            mdata=mdata, task_type="fp", work_path=work_path, task_format=task_format
-        )
+        symlink_user_forward_files(mdata=mdata, task_type="fp", work_path=work_path, task_format=task_format)
     user_forward_files = mdata.get("fp" + "_user_forward_files", [])
     forward_files += [os.path.basename(file) for file in user_forward_files]
     backward_files += mdata.get("fp" + "_user_backward_files", [])
@@ -639,9 +622,7 @@ def gen_init_surf(args):
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        description="Generating initial data for surface systems."
-    )
+    parser = argparse.ArgumentParser(description="Generating initial data for surface systems.")
     parser.add_argument("PARAM", type=str, help="parameter file, json/yaml format")
     parser.add_argument(
         "MACHINE",