Validators and Jobs for Lobster

custodian/lobster/__init__.py

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+from __future__ import unicode_literals
+
+"""
+This package implements various VASP Jobs and Error Handlers.
+"""
+
+__author__ = "Janine George, Guido Petretto"
+__version__ = "0.1"
+__maintainer__ = "Janine George, Guido Petretto"
+__email__ = "[email protected]"
+__status__ = "Production"
+__date__ = "30/3/20"

custodian/lobster/handlers.py

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+import os
+
+from custodian.custodian import Validator
+from pymatgen.io.lobster import Lobsterout
+
+
+class EnoughBandsValidator(Validator):
+    """
+    validates if enough bands for COHP calculation are available
+    """
+
+    def __init__(self, output_filename: str = "lobsterout"):
+        """
+
+        Args:
+            output_filename: filename of output file, usually lobsterout
+        """
+        self.output_filename = output_filename
+
+    def check(self) -> bool:
+        """
+        checks if the VASP calculation had enough bands
+        Returns:
+            (bool) if True, too few bands have been applied
+        """
+        # checks if correct number of bands is available
+        try:
+            with open(self.output_filename) as f:
+                data = f.read()
+            return 'You are employing too few bands in your PAW calculation.' in data
+        except OSError:
+            return False
+
+
+class LobsterFilesValidator(Validator):
+    """
+    Check for existence of some of the files that lobster
+        normally create upon running.
+    Check if lobster terminated normally by looking for finished
+    """
+
+    def __init__(self):
+        pass
+
+    def check(self) -> bool:
+        for vfile in ["lobsterout"]:
+            if not os.path.exists(vfile):
+                return True
+        with open("lobsterout") as f:
+            data = f.read()
+        return ('finished' not in data)
+
+
+class ChargeSpillingValidator(Validator):
+    """
+    Check if spilling is below certain threshold!
+    """
+
+    def __init__(self, output_filename: str = 'lobsterout', charge_spilling_limit: float = 0.05):
+        """
+
+        Args:
+            output_filename: filename of the output file of lobter, usually lobsterout
+            charge_spilling_limit: limit of the charge spilling that will be considered okay
+        """
+
+        self.output_filename = output_filename
+        self.charge_spilling_limit = charge_spilling_limit
+
+    def check(self) -> bool:
+        # open lobsterout and find charge spilling
+
+        if os.path.exists(self.output_filename):
+            lobsterout = Lobsterout(self.output_filename)
+            if lobsterout.chargespilling[0] > self.charge_spilling_limit:
+                return True
+            if len(lobsterout.chargespilling) > 1:
+                if lobsterout.chargespilling[1] > self.charge_spilling_limit:
+                    return True
+            return False
+        else:
+            return False

custodian/lobster/jobs.py

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+import logging
+import os
+import shutil
+import subprocess
+
+from monty.io import zopen
+from monty.shutil import compress_file
+
+from custodian.custodian import Job
+
+LOBSTERINPUT_FILES = ["lobsterin"]
+LOBSTEROUTPUT_FILES = ["lobsterout", "CHARGE.lobster", "COHPCAR.lobster", "COOPCAR.lobster", "DOSCAR.lobster",
+                       "GROSSPOP.lobster", "ICOHPLIST.lobster", "ICOOPLIST.lobster", "lobster.out",
+                       "projectionData.lobster"]
+
+logger = logging.getLogger(__name__)
+
+
+class LobsterJob(Job):
+    """
+    Runs the Lobster Job
+    """
+
+    def __init__(self, lobster_cmd: str, output_file: str = "lobsterout", stderr_file: str = "std_err_lobster.txt",
+                 gzipped: bool = True, add_files_to_gzip=[], backup: bool = True):
+        """
+
+        Args:
+            lobster_cmd: command to run lobster
+            output_file: usually lobsterout
+            stderr_file: standard output
+            gzipped: if True, Lobster files and add_files_to_gzip will be gzipped
+            add_files_to_gzip: list of files that should be gzipped
+            backup: if True, lobsterin will be copied to lobsterin.orig
+        """
+        self.lobster_cmd = lobster_cmd
+        self.output_file = output_file
+        self.stderr_file = stderr_file
+        self.gzipped = gzipped
+        self.add_files_to_gzip = add_files_to_gzip
+        self.backup = backup
+
+    def setup(self):
+        """
+        will backup lobster input files
+        """
+        if self.backup:
+            for f in LOBSTERINPUT_FILES:
+                shutil.copy(f, "{}.orig".format(f))
+
+    def run(self):
+        """
+        runs the job
+        """
+        cmd = self.lobster_cmd
+
+        logger.info("Running {}".format(" ".join(cmd)))
+
+        with zopen(self.output_file, 'w') as f_std, \
+                zopen(self.stderr_file, "w", buffering=1) as f_err:
+            # use line buffering for stderr
+            p = subprocess.Popen(cmd, stdout=f_std, stderr=f_err)
+
+        return p
+
+    def postprocess(self):
+        """
+        will gzip relevant files (won't gzip custodian.json and other output files from the cluster)
+        """
+        if self.gzipped:
+            for file in LOBSTEROUTPUT_FILES:
+                if os.path.exists(file):
+                    compress_file(file, compression="gz")
+            for file in LOBSTERINPUT_FILES:
+                if os.path.exists(file):
+                    compress_file(file, compression="gz")
+            if self.backup:
+                if os.path.exists("lobsterin.orig"):
+                    compress_file("lobsterin.orig", compression="gz")
+            for file in self.add_files_to_gzip:
+                compress_file(file, compression="gz")

custodian/lobster/tests/test_handlers.py

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+import os
+import unittest
+
+from custodian.lobster.handlers import ChargeSpillingValidator, EnoughBandsValidator, LobsterFilesValidator
+
+# get location of module
+TEST_DIR = os.path.dirname(os.path.abspath(__file__))
+test_files_lobster = os.path.join(TEST_DIR, '../../../test_files/lobster/lobsterouts')
+
+
+class TestChargeSpillingValidator(unittest.TestCase):
+
+    def test_check_and_correct(self):
+        v = ChargeSpillingValidator(output_filename=os.path.join(test_files_lobster, "lobsterout.normal"))
+        self.assertFalse(v.check())
+
+        v2 = ChargeSpillingValidator(output_filename=os.path.join(test_files_lobster, "lobsterout.largespilling"))
+        self.assertTrue(v2.check())
+
+        v2b = ChargeSpillingValidator(output_filename=os.path.join(test_files_lobster, "lobsterout.largespilling_2"))
+        self.assertTrue(v2b.check())
+
+        v3 = ChargeSpillingValidator(output_filename=os.path.join(test_files_lobster, "nolobsterout", "lobsterout"))
+        self.assertFalse(v3.check())
+
+        v4 = ChargeSpillingValidator(output_filename=os.path.join(test_files_lobster, "no_spin", "lobsterout"))
+        self.assertFalse(v4.check())
+
+    def test_as_dict(self):
+        v = ChargeSpillingValidator(output_filename=os.path.join(test_files_lobster, "lobsterout.normal"))
+        d = v.as_dict()
+        v2 = ChargeSpillingValidator.from_dict(d)
+        self.assertIsInstance(v2, ChargeSpillingValidator)
+
+
+class TestLobsterFilesValidator(unittest.TestCase):
+
+    def test_check_and_correct_1(self):
+        os.chdir(test_files_lobster)
+        v = LobsterFilesValidator()
+        self.assertFalse(v.check())
+
+    def test_check_and_correct_2(self):
+        os.chdir(os.path.join(test_files_lobster, "nolobsterout"))
+        v2 = LobsterFilesValidator()
+        self.assertTrue(v2.check())
+
+    def test_check_and_correct_3(self):
+        os.chdir(os.path.join(test_files_lobster, "crash"))
+        v3 = LobsterFilesValidator()
+        self.assertTrue(v3.check())
+
+    def test_as_dict(self):
+        os.chdir(test_files_lobster)
+        v = LobsterFilesValidator()
+        d = v.as_dict()
+        v2 = LobsterFilesValidator.from_dict(d)
+        self.assertIsInstance(v2, LobsterFilesValidator)
+
+
+class TestEnoughBandsValidator(unittest.TestCase):
+
+    def test_check_and_correct(self):
+        v = EnoughBandsValidator(output_filename=os.path.join(test_files_lobster, "lobsterout.normal"))
+        self.assertFalse(v.check())
+
+    def test_check_and_correct2(self):
+        v2 = EnoughBandsValidator(output_filename=os.path.join(test_files_lobster, "lobsterout.nocohp"))
+        self.assertTrue(v2.check())
+
+    def test_check_and_correct3(self):
+        v3 = EnoughBandsValidator(output_filename=os.path.join(test_files_lobster, "nolobsterout/lobsterout"))
+        self.assertFalse(v3.check())
+
+    def test_as_dict(self):
+        v = EnoughBandsValidator(output_filename=os.path.join(test_files_lobster, "lobsterout.normal"))
+        d = v.as_dict()
+        v2 = EnoughBandsValidator.from_dict(d)
+        self.assertIsInstance(v2, EnoughBandsValidator)
+
+
+if __name__ == '__main__':
+    unittest.main()

custodian/lobster/tests/test_jobs.py

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+import os
+import shutil
+import unittest
+
+from custodian.lobster.jobs import LobsterJob
+from monty.os import cd
+from monty.tempfile import ScratchDir
+
+MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
+test_files_lobster2 = os.path.join(MODULE_DIR, '../../../test_files/lobster/lobsterins')
+test_files_lobster3 = os.path.join(MODULE_DIR, '../../../test_files/lobster/vasp_lobster_output')
+
+VASP_OUTPUT_FILES = ["OUTCAR", "vasprun.xml", "CHG", "CHGCAR", "CONTCAR", "INCAR", "KPOINTS", "POSCAR", "POTCAR",
+                     "DOSCAR", "EIGENVAL", "IBZKPT", "OSZICAR", "PCDAT", "PROCAR", "REPORT", "WAVECAR", "XDATCAR"]
+
+
+class LobsterJobTest(unittest.TestCase):
+    """
+    similar to VaspJobTest
+    ommit test of run
+    """
+
+    def test_to_from_dict(self):
+        v = LobsterJob(lobster_cmd="hello")
+        v2 = LobsterJob.from_dict(v.as_dict())
+        self.assertEqual(type(v2), type(v))
+        self.assertEqual(v2.lobster_cmd, "hello")
+
+    def test_setup(self):
+        with cd(test_files_lobster2):
+            with ScratchDir('.', copy_from_current_on_enter=True) as d:
+                # check if backup is done correctly
+                v = LobsterJob("hello", backup=True)
+                v.setup()
+                self.assertTrue(os.path.exists("lobsterin.orig"))
+                # check if backup id done correctly
+            with ScratchDir('.', copy_from_current_on_enter=True) as d:
+                v = LobsterJob("hello", backup=False)
+                v.setup()
+                self.assertFalse(os.path.exists("lobsterin.orig"))
+
+    def test_postprocess(self):
+        # test gzipped and zipping of additional files
+        with cd(os.path.join(test_files_lobster3)):
+            with ScratchDir('.', copy_from_current_on_enter=True) as d:
+                shutil.copy('lobsterin', 'lobsterin.orig')
+                v = LobsterJob("hello", gzipped=True, add_files_to_gzip=VASP_OUTPUT_FILES)
+                v.postprocess()
+                self.assertTrue(os.path.exists("WAVECAR.gz"))
+                self.assertTrue(os.path.exists("lobsterin.gz"))
+                self.assertTrue(os.path.exists("lobsterout.gz"))
+                self.assertTrue(os.path.exists("INCAR.gz"))
+                self.assertTrue(os.path.exists("lobsterin.orig.gz"))
+
+            with ScratchDir('.', copy_from_current_on_enter=True) as d:
+                shutil.copy('lobsterin', 'lobsterin.orig')
+                v = LobsterJob("hello", gzipped=False, add_files_to_gzip=VASP_OUTPUT_FILES)
+                v.postprocess()
+                self.assertTrue(os.path.exists("WAVECAR"))
+                self.assertTrue(os.path.exists("lobsterin"))
+                self.assertTrue(os.path.exists("lobsterout"))
+                self.assertTrue(os.path.exists("INCAR"))
+                self.assertTrue(os.path.exists("lobsterin.orig"))
+
+
+if __name__ == '__main__':
+    unittest.main()

test_files/lobster/lobsterins/lobsterin

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+COHPstartEnergy -15.0
+COHPendEnergy 5.0
+basisSet pbeVaspFit2015
+cohpGenerator from 0.1 to 6.0 orbitalwise
+gaussianSmearingWidth 0.05
+saveProjectionToFile
+basisfunctions K 3p 3s 4s 
+basisfunctions Sn 4d 5p 5s 
+basisfunctions O 2p 2s 

test_files/lobster/lobsterins/lobsterin2

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+COHPstartEnergy -15.0
+COHPendEnergy 10.0
+basisSet pbeVaspFit2015
+cohpGenerator from 0.1 to 6.0 orbitalwise
+gaussianSmearingWidth 0.05
+saveProjectionToFile
+basisfunctions K 3p 3s 4s 
+basisfunctions Sn 4d 5p 5s 
+basisfunctions O 2p 2s 

test_files/lobster/lobsterouts/crash/lobsterout

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+LOBSTER v3.2.0 (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 mb-ivy205.cism.ucl.ac.be on 2019-10-08 at 20:25:15 CEST using 8 threads
+detecting used PAW program... VASP
+initializing PW system...
+initializing Augmentations...
+recommended basis functions:
+K 3p 3s 4s 
+O 2p 2s 
+Sn 4d 5p 5s 
+initializing LCAO system...
+setting up local basis functions...
+ K (pbeVaspFit2015) 3s 4s 3p_y 3p_z 3p_x 
+ O (pbeVaspFit2015) 2s 2p_y 2p_z 2p_x 
+Sn (pbeVaspFit2015) 5s 5p_y 5p_z 5p_x 4d_xy 4d_yz 4d_z^2 4d_xz 4d_x^2-y^2 
+setting up CO interactions... found 520 interactions.
+projecting...
+WARNING: Cannot use the tetrahedron method for k-space integration and must fall
+WARNING: back to Gaussian smearing which can take significantly longer. Make
+WARNING: sure to use the tetrahedron method whenever applicable.
+
+calculating overlaps...
+post-processing projection...
+saving projection to projectionData.lobster...
+spillings for spin channel 1
+abs. total  spilling:   6.31%
+abs. charge spilling:   0.80%
+
+spillings for spin channel 2
+abs. total  spilling:   6.33%
+abs. charge spilling:   0.80%
+
+calculating pDOS... using Gaussian smearing integration (sigma=0.05eV)
+writing DOSCAR.lobster...
+writing COOPCAR.lobster and ICOOPLIST.lobster...
+calculating pCOHPs... using Gaussian smearing integration (sigma=0.05eV)
+writing COHPCAR.lobster and ICOHPLIST.lobster...
+writing CHARGE.lobster and GROSSPOP.lobster...
+
+
+