Merge pull request #1702 from JaGeo/master

Fix bug in lobsterout

pymatgen/io/lobster.py

@@ -7,25 +7,26 @@
 on LOBSTER see www.cohp.de.
 """
 
-import re
-import numpy as np
 import collections
-import os
-from monty.io import zopen
-from monty.serialization import loadfn
-from monty.json import MSONable
 import fnmatch
 import itertools
+import os
+import re
 import warnings
-import spglib
-from typing import Dict, Any, Optional, List
 from collections import defaultdict
+from typing import Dict, Any, Optional, List
+
+import numpy as np
+import spglib
+from monty.io import zopen
+from monty.json import MSONable
+from monty.serialization import loadfn
+from pymatgen.core.structure import Structure
+from pymatgen.electronic_structure.bandstructure import LobsterBandStructureSymmLine
 from pymatgen.electronic_structure.core import Spin, Orbital
-from pymatgen.io.vasp.outputs import Vasprun
 from pymatgen.electronic_structure.dos import Dos, LobsterCompleteDos
-from pymatgen.electronic_structure.bandstructure import LobsterBandStructureSymmLine
-from pymatgen.core.structure import Structure
 from pymatgen.io.vasp.inputs import Incar, Kpoints, Potcar
+from pymatgen.io.vasp.outputs import Vasprun
 from pymatgen.symmetry.bandstructure import HighSymmKpath
 
 __author__ = "Janine George, Marco Esters"
@@ -848,7 +849,7 @@ def _get_threads(self, data):
         for row in data:
             splitrow = row.split()
             if len(splitrow) > 11:
-                if (splitrow[11]) == "threads":
+                if (splitrow[11]) == "threads" or (splitrow[11] == "thread"):
                     return splitrow[10]
 
     def _get_spillings(self, data, number_of_spins):

pymatgen/io/tests/test_lobster.py

@@ -2,19 +2,20 @@
 # Copyright (c) Pymatgen Development Team.
 # Distributed under the terms of the MIT License.
 
-import unittest
-import os
 import json
+import os
+import tempfile
+import unittest
 import warnings
+
 import numpy as np
-import tempfile
 from pymatgen import Structure
+from pymatgen.electronic_structure.core import Spin, Orbital
 from pymatgen.io.lobster import Cohpcar, Icohplist, Doscar, Charge, Lobsterout, Fatband, Lobsterin, Bandoverlaps, \
     Grosspop
 from pymatgen.io.vasp import Vasprun
-from pymatgen.electronic_structure.core import Spin, Orbital
-from pymatgen.util.testing import PymatgenTest
 from pymatgen.io.vasp.inputs import Incar, Kpoints, Potcar
+from pymatgen.util.testing import PymatgenTest
 
 __author__ = "Janine George, Marco Esters"
 __copyright__ = "Copyright 2017, The Materials Project"
@@ -548,6 +549,7 @@ def setUp(self):
         self.lobsterout_twospins = Lobsterout(filename=os.path.join(test_dir, "lobsterout.twospins"))
         self.lobsterout_GaAs = Lobsterout(filename=os.path.join(test_dir, "lobsterout.GaAs"))
         self.lobsterout_from_projection = Lobsterout(filename=os.path.join(test_dir, "lobsterout_from_projection"))
+        self.lobsterout_onethread = Lobsterout(filename=os.path.join(test_dir, "lobsterout.onethread"))
 
     def tearDown(self):
         warnings.simplefilter("default")
@@ -803,6 +805,8 @@ def testattributes(self):
                                                            'sys_time': {'h': '0', 'min': '0', 's': '0', 'ms': '180'}})
         self.assertAlmostEqual(self.lobsterout_GaAs.totalspilling[0], [0.0859][0])
 
+        self.assertEqual(self.lobsterout_onethread.number_of_threads, 1)
+
     def test_get_doc(self):
         comparedict = {'restart_from_projection': False, 'lobster_version': 'v3.1.0', 'threads': 8,
                        'Dftprogram': 'VASP', 'chargespilling': [0.0268], 'totalspilling': [0.044000000000000004],

test_files/cohp/lobsterout.onethread

@@ -0,0 +1,45 @@
+LOBSTER v (g++ 5.4.0)
+Copyright (C) 2019 by Chair of Solid-State and Quantum Chemistry, RWTH Aachen.
+All rights reserved. Contributions by S. Maintz, V. L. Deringer, M. Esser, R. Nelson, C. Ertural, A. L. Tchougreeff and R. Dronskowski
+starting on host node0817 on 2019-12-07 at 11:17:50 CET using 1 thread
+detecting used PAW program... VASP
+initializing PW system...
+initializing Augmentations...
+recommended basis functions:
+O 2p 2s 
+U 5f 6d 6p 6s 7s 
+initializing LCAO system...
+setting up local basis functions...
+ O (pbeVaspFit2015) 2s 2p_y 2p_z 2p_x 
+ U (pbeVaspFit2015) 6s 7s 6p_y 6p_z 6p_x 6d_xy 6d_yz 6d_z^2 6d_xz 6d_x^2-y^2 5f_y(3x^2-y^2) 5f_xyz 5f_yz^2 5f_z^3 5f_xz^2 5f_z(x^2-y^2) 5f_x(x^2-3y^2) 
+INFO: There are more PAW bands than local basis functions available.
+INFO: To prevent trouble in orthonormalization and Hamiltonian reconstruction
+INFO: the PAW bands from 30 and upwards will be ignored.
+setting up CO interactions... found 276 interactions.
+projecting...
+calculating overlaps...
+post-processing projection...
+WARNING: 118 of 1332 k-points could not be orthonormalized with an accuracy of 1.0E-5.
+WARNING: Generally, this is not a critical error. But to help you analyze it,
+WARNING: I dumped the band overlap matrices to the file bandOverlaps.lobster.
+WARNING: Please check how much they deviate from the identity matrix and decide to
+WARNING: use your results only, if you are sure that this is ok.
+
+saving projection to projectionData.lobster...
+spillings for spin channel 1
+abs. total  spilling:   7.64%
+abs. charge spilling:   1.55%
+
+spillings for spin channel 2
+abs. total  spilling:   7.64%
+abs. charge spilling:   1.55%
+
+calculating pDOS...
+writing DOSCAR.lobster...
+writing COOPCAR.lobster and ICOOPLIST.lobster...
+calculating pCOHPs...
+writing COHPCAR.lobster and ICOHPLIST.lobster...
+writing CHARGE.lobster and GROSSPOP.lobster...
+finished in 1 h 17 min 44 s 923 ms of wall time
+            1 h 16 min 34 s 120 ms of user time
+            0 h  0 min  5 s 270 ms of sys  time