From c99ff74e77d3e2a178d13ed07031494627d403c7 Mon Sep 17 00:00:00 2001
From: Cloudac7 <812556867@qq.com>
Date: Mon, 8 Mar 2021 16:13:14 +0800
Subject: [PATCH] solve pymatgen incompatible issue

---
 dpgen/auto_test/mpdb.py            | 4 ++--
 dpgen/data/gen.py                  | 2 +-
 dpgen/data/surf.py                 | 2 +-
 dpgen/dispatcher/LSF.py            | 2 +-
 tests/auto_test/test_elastic.py    | 2 +-
 tests/auto_test/test_mpdb.py       | 2 +-
 tests/auto_test/test_surface.py    | 2 +-
 tests/auto_test/test_vacancy.py    | 2 +-
 tests/data/test_gen_bulk.py        | 2 +-
 tests/data/test_gen_surf.py        | 2 +-
 tests/data/test_gen_surf_poscar.py | 2 +-
 11 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/dpgen/auto_test/mpdb.py b/dpgen/auto_test/mpdb.py
index 4a76c9c8d..fa91d72fb 100644
--- a/dpgen/auto_test/mpdb.py
+++ b/dpgen/auto_test/mpdb.py
@@ -1,7 +1,7 @@
 import os
 from dpgen import dlog
-from pymatgen import MPRester,Structure
-from pymatgen.ext.matproj import MPRestError 
+from pymatgen.ext.matproj import MPRester, MPRestError
+from pymatgen.core import Structure
 
 web="materials.org"
 
diff --git a/dpgen/data/gen.py b/dpgen/data/gen.py
index ce1573a61..91b649a2a 100644
--- a/dpgen/data/gen.py
+++ b/dpgen/data/gen.py
@@ -21,7 +21,7 @@
 import dpgen.data.tools.diamond as diamond
 import dpgen.data.tools.sc as sc
 from dpgen.generator.lib.vasp import incar_upper
-from pymatgen import Structure
+from pymatgen.core import Structure
 from pymatgen.io.vasp import Incar
 from dpgen.remote.decide_machine import  decide_fp_machine
 from dpgen import ROOT_PATH
diff --git a/dpgen/data/surf.py b/dpgen/data/surf.py
index 8cf29d39d..322d26ad4 100644
--- a/dpgen/data/surf.py
+++ b/dpgen/data/surf.py
@@ -15,7 +15,7 @@
 from dpgen.dispatcher.Dispatcher import Dispatcher, make_dispatcher
 #-----PMG---------
 from pymatgen.io.vasp import Poscar
-from pymatgen import Structure,Element
+from pymatgen.core import Structure, Element
 from pymatgen.io.ase import AseAtomsAdaptor
 #-----ASE-------
 from ase.io import read
diff --git a/dpgen/dispatcher/LSF.py b/dpgen/dispatcher/LSF.py
index b28b4eec3..0fa407f18 100644
--- a/dpgen/dispatcher/LSF.py
+++ b/dpgen/dispatcher/LSF.py
@@ -14,7 +14,7 @@ def check_status(self):
         except:
             return JobStatus.terminated
         if job_id == "" :
-            raise RuntimeError("job %s is has not been submitted" % self.remote_root)
+            raise RuntimeError("job %s has not been submitted" % self.context.remote_root)
         ret, stdin, stdout, stderr\
             = self.context.block_call ("bjobs " + job_id)
         err_str = stderr.read().decode('utf-8')
diff --git a/tests/auto_test/test_elastic.py b/tests/auto_test/test_elastic.py
index b8f464571..5750e5d48 100644
--- a/tests/auto_test/test_elastic.py
+++ b/tests/auto_test/test_elastic.py
@@ -5,7 +5,7 @@
 import dpdata
 from monty.serialization import loadfn, dumpfn
 from pymatgen.analysis.elasticity.strain import Strain, Deformation
-from pymatgen import Structure
+from pymatgen.core import Structure
 from pymatgen.io.vasp import Incar
 
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
diff --git a/tests/auto_test/test_mpdb.py b/tests/auto_test/test_mpdb.py
index 8323d77b0..1c3eca745 100644
--- a/tests/auto_test/test_mpdb.py
+++ b/tests/auto_test/test_mpdb.py
@@ -1,7 +1,7 @@
 import os
 import sys
 import unittest
-from pymatgen import Structure
+from pymatgen.core import Structure
 from pymatgen.analysis.structure_matcher import StructureMatcher
 from monty.serialization import loadfn,dumpfn
 
diff --git a/tests/auto_test/test_surface.py b/tests/auto_test/test_surface.py
index 7e02bc880..12f72f608 100644
--- a/tests/auto_test/test_surface.py
+++ b/tests/auto_test/test_surface.py
@@ -4,7 +4,7 @@
 import unittest
 import dpdata
 from monty.serialization import loadfn, dumpfn
-from pymatgen import Structure
+from pymatgen.core import Structure
 from pymatgen.io.vasp import Incar
 from pymatgen.core.surface import SlabGenerator
 
diff --git a/tests/auto_test/test_vacancy.py b/tests/auto_test/test_vacancy.py
index cb27bccd0..fa8894ed6 100644
--- a/tests/auto_test/test_vacancy.py
+++ b/tests/auto_test/test_vacancy.py
@@ -4,7 +4,7 @@
 import unittest
 import dpdata
 from monty.serialization import loadfn, dumpfn
-from pymatgen import Structure
+from pymatgen.core import Structure
 from pymatgen.io.vasp import Incar
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 from pymatgen.analysis.defects.core import Vacancy as pmg_Vacancy
diff --git a/tests/data/test_gen_bulk.py b/tests/data/test_gen_bulk.py
index 92eb29084..73572d4e8 100644
--- a/tests/data/test_gen_bulk.py
+++ b/tests/data/test_gen_bulk.py
@@ -1,6 +1,6 @@
 import os,sys,json,glob,shutil
 import unittest
-from pymatgen import Structure,Composition
+from pymatgen.core import Structure, Composition
 
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 __package__ = 'data'
diff --git a/tests/data/test_gen_surf.py b/tests/data/test_gen_surf.py
index 63e9ed7a4..d40f6e1ab 100644
--- a/tests/data/test_gen_surf.py
+++ b/tests/data/test_gen_surf.py
@@ -1,6 +1,6 @@
 import os,sys,json,glob,shutil
 import unittest
-from pymatgen import Structure,Element
+from pymatgen.core import Structure, Element
 
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 __package__ = 'data'
diff --git a/tests/data/test_gen_surf_poscar.py b/tests/data/test_gen_surf_poscar.py
index 1ed44eac3..b47cb308b 100644
--- a/tests/data/test_gen_surf_poscar.py
+++ b/tests/data/test_gen_surf_poscar.py
@@ -1,6 +1,6 @@
 import os,sys,json,glob,shutil
 import unittest
-from pymatgen import Structure,Element
+from pymatgen.core import Structure, Element
 
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 __package__ = 'data'