Improve function pert_scaled

dpgen/data/gen.py

@@ -726,8 +726,7 @@
 
 
 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"]
@@ -744,6 +743,7 @@
     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)
@@ -752,35 +752,38 @@
     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}.vasp"
                 elif fp_style == "abacus":
-                    pos_in = "STRU%d.abacus" % (kk + 1)
-                dir_out = "%06d" % (kk + 1)
+                    pos_in = f"STRU{kk}.abacus"
+                dir_out = f"{kk:06d}"
                 create_path(dir_out)
                 if fp_style == "vasp":
                     pos_out = os.path.join(dir_out, "POSCAR")
@@ -805,35 +808,7 @@
                 else:
                     shutil.copy2(pos_in, pos_out)
                 os.remove(pos_in)
-            kk = -1
-            if fp_style == "vasp":
-                pos_in = "POSCAR"
-            elif fp_style == "abacus":
-                pos_in = "STRU"
-            dir_out = "%06d" % (kk + 1)
-            create_path(dir_out)
-            if fp_style == "vasp":
-                pos_out = os.path.join(dir_out, "POSCAR")
-            elif fp_style == "abacus":
-                pos_out = os.path.join(dir_out, "STRU")
-            if not from_poscar:
-                if fp_style == "vasp":
-                    poscar_shuffle(pos_in, pos_out)
-                elif fp_style == "abacus":
-                    stru_in = get_abacus_STRU(pos_in)
-                    stru_out = shuffle_stru_data(stru_in)
-                    with open(pos_out, "w") as fp:
-                        fp.write(
-                            make_abacus_scf_stru(
-                                stru_out,
-                                pp_file,
-                                orb_file_names,
-                                dpks_descriptor_name,
-                                type_map=jdata["elements"],
-                            )
-                        )
-            else:
-                shutil.copy2(pos_in, pos_out)
+
             os.chdir(cwd)
 
 
@@ -866,7 +841,7 @@
 
     for ii in sys_ps:
         for jj in scale:
-            for kk in range(pert_numb + 1):
+            for kk in range(pert_numb):
                 path_work = path_md
                 path_work = os.path.join(path_work, ii)
                 path_work = os.path.join(path_work, f"scale-{jj:.3f}")
@@ -987,7 +962,7 @@
 
     for ii in sys_ps:
         for jj in scale:
-            for kk in range(pert_numb + 1):
+            for kk in range(pert_numb):
                 path_work = path_md
                 path_work = os.path.join(path_work, ii)
                 path_work = os.path.join(path_work, f"scale-{jj:.3f}")

dpgen/data/surf.py

@@ -23,7 +23,7 @@
 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:
@@ -440,15 +441,12 @@
         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)
@@ -501,46 +499,40 @@
     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}.vasp"
+                    dir_out = f"{kk:06d}"
                     create_path(dir_out)
                     pos_out = os.path.join(dir_out, "POSCAR")
                     poscar_shuffle(pos_in, pos_out)
                     os.remove(pos_in)
-                kk = -1
-                pos_in = "POSCAR"
-                dir_out = "%06d" % (kk + 1)
-                create_path(dir_out)
-                pos_out = os.path.join(dir_out, "POSCAR")
-                poscar_shuffle(pos_in, pos_out)
+
                 os.chdir(cwd)
 
 

dpgen/data/tools/create_random_disturb.py

@@ -123,7 +123,8 @@
     cell0 = atoms.get_cell()
 
     # creat nfile ofmt files.
-    for fid in range(1, nfile + 1):
+    # for fid in range(1, nfile + 1):     # C.Thang Nguyen: Why not start from 0?
+    for fid in range(nfile):
         # Use copy(), otherwise it will modify the input atoms every time.
         atoms_d = atoms.copy()
 
@@ -194,7 +195,7 @@
     cell0 = stru["cells"]
 
     # creat nfile ofmt files.
-    for fid in range(1, nfile + 1):
+    for fid in range(nfile):
         # Use copy(), otherwise it will modify the input atoms every time.
         stru_d = stru.copy()
 

tests/data/test_disturb_abacus.py

@@ -17,7 +17,7 @@
 
 class TestPertAbacus(unittest.TestCase):
     def setUp(self):
-        create_disturbs_abacus_dev(abacus_stru_file, 1)
+        create_disturbs_abacus_dev(abacus_stru_file, 2)
 
     def tearDown(self):
         if os.path.isfile("STRU.hcp1.abacus"):

tests/data/test_gen_bulk.py

@@ -69,7 +69,7 @@ def test(self):
             self.assertEqual(len(scales), self.scale_numb)
             for scale in scales:
                 perts = glob.glob(os.path.join(scale, "[0-9]*"))
-                self.assertEqual(len(perts), self.pert_numb + 1)
+                self.assertEqual(len(perts), self.pert_numb)
 
 
 if __name__ == "__main__":

tests/data/test_gen_bulk_abacus.py

@@ -71,7 +71,7 @@ def test(self):
             self.assertEqual(len(scales), self.scale_numb)
             for scale in scales:
                 perts = glob.glob(os.path.join(scale, "[0-9]*"))
-                self.assertEqual(len(perts), self.pert_numb + 1)
+                self.assertEqual(len(perts), self.pert_numb)
 
     def testSTRU(self):
         jdata = self.jdata
@@ -103,7 +103,7 @@ def testSTRU(self):
             self.assertEqual(len(scales), self.scale_numb)
             for scale in scales:
                 perts = glob.glob(os.path.join(scale, "[0-9]*"))
-                self.assertEqual(len(perts), self.pert_numb + 1)
+                self.assertEqual(len(perts), self.pert_numb)
 
 
 if __name__ == "__main__":