Update {Elastic,run,surf,Vasp,vasp}.py: To be compatible with Pymatgen (

#1302)

To be compatible with old and new versions of Pymatgen
(materialsproject/pymatgen#3158)

---------

Signed-off-by: Levi Zhou  <31941107+ZhouXY-PKU@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

dpgen/auto_test/Elastic.py

@@ -221,7 +221,10 @@ def post_process(self, task_list):
                 kspacing = incar.get("KSPACING")
                 kgamma = incar.get("KGAMMA", False)
                 ret = vasp.make_kspacing_kpoints(poscar_start, kspacing, kgamma)
-                kp = Kpoints.from_string(ret)
+                try:
+                    kp = Kpoints.from_string(ret)
+                except AttributeError:
+                    kp = Kpoints.from_str(ret)
                 if os.path.isfile("KPOINTS"):
                     os.remove("KPOINTS")
                 kp.write_file("KPOINTS")

dpgen/auto_test/VASP.py

@@ -194,7 +194,10 @@ def make_input_file(self, output_dir, task_type, task_param):
             os.symlink("../INCAR", "INCAR")
         os.chdir(cwd)
         ret = vasp.make_kspacing_kpoints(self.path_to_poscar, kspacing, kgamma)
-        kp = Kpoints.from_string(ret)
+        try:
+            kp = Kpoints.from_string(ret)
+        except AttributeError:
+            kp = Kpoints.from_str(ret)
         kp.write_file(os.path.join(output_dir, "KPOINTS"))
 
     def compute(self, output_dir):

dpgen/auto_test/lib/vasp.py

@@ -510,7 +510,10 @@ def make_vasp_kpoints_from_incar(work_dir, jdata):
     assert os.path.exists("INCAR")
     with open("INCAR") as fp:
         incar = fp.read()
-    standard_incar = incar_upper(Incar.from_string(incar))
+    try:
+        standard_incar = incar_upper(Incar.from_string(incar))
+    except AttributeError:
+        standard_incar = incar_upper(Incar.from_str(incar))
     if fp_aniso_kspacing is None:
         try:
             kspacing = standard_incar["KSPACING"]
@@ -533,6 +536,9 @@ def make_vasp_kpoints_from_incar(work_dir, jdata):
     assert os.path.exists("POSCAR")
     # make kpoints
     ret = make_kspacing_kpoints("POSCAR", kspacing, gamma)
-    kp = Kpoints.from_string(ret)
+    try:
+        kp = Kpoints.from_string(ret)
+    except AttributeError:
+        kp = Kpoints.from_str(ret)
     kp.write_file("KPOINTS")
     os.chdir(cwd)

dpgen/data/surf.py

@@ -410,7 +410,10 @@ def poscar_scale(poscar_in, poscar_out, scale):
     else:
         raise RuntimeError("Unknow poscar style at line 7: %s" % lines[7])
 
-    poscar = Poscar.from_string("".join(lines))
+    try:
+        poscar = Poscar.from_string("".join(lines))
+    except AttributeError:
+        poscar = Poscar.from_str("".join(lines))
     with open(poscar_out, "w") as fout:
         fout.write(poscar.get_string(direct=False))
 

dpgen/generator/run.py

@@ -2924,14 +2924,20 @@ def make_pwmat_input(jdata, filename):
 def make_vasp_incar_ele_temp(jdata, filename, ele_temp, nbands_esti=None):
     with open(filename) as fp:
         incar = fp.read()
-    incar = incar_upper(Incar.from_string(incar))
+    try:
+        incar = incar_upper(Incar.from_string(incar))
+    except AttributeError:
+        incar = incar_upper(Incar.from_str(incar))
     incar["ISMEAR"] = -1
     incar["SIGMA"] = ele_temp * pc.Boltzmann / pc.electron_volt
     incar.write_file("INCAR")
     if nbands_esti is not None:
         nbands = nbands_esti.predict(".")
         with open(filename) as fp:
-            incar = Incar.from_string(fp.read())
+            try:
+                incar = Incar.from_string(fp.read())
+            except AttributeError:
+                incar = Incar.from_str(fp.read())
         incar["NBANDS"] = nbands
         incar.write_file("INCAR")
 
@@ -3008,7 +3014,10 @@ def make_fp_vasp_kp(iter_index, jdata):
         assert os.path.exists("INCAR")
         with open("INCAR") as fp:
             incar = fp.read()
-        standard_incar = incar_upper(Incar.from_string(incar))
+        try:
+            standard_incar = incar_upper(Incar.from_string(incar))
+        except AttributeError:
+            standard_incar = incar_upper(Incar.from_str(incar))
         if fp_aniso_kspacing is None:
             try:
                 kspacing = standard_incar["KSPACING"]
@@ -3031,7 +3040,10 @@ def make_fp_vasp_kp(iter_index, jdata):
         assert os.path.exists("POSCAR")
         # make kpoints
         ret = make_kspacing_kpoints("POSCAR", kspacing, gamma)
-        kp = Kpoints.from_string(ret)
+        try:
+            kp = Kpoints.from_string(ret)
+        except AttributeError:
+            kp = Kpoints.from_str(ret)
         kp.write_file("KPOINTS")
         os.chdir(cwd)