Python Custodian.from_spec Exemples

Exemple #1

Fichier : test_custodian.py Projet : squiton/custodian

    def test_from_spec(self):
        spec = """jobs:
- jb: custodian.vasp.jobs.VaspJob
  params:
    final: False
    suffix: .relax1
- jb: custodian.vasp.jobs.VaspJob
  params:
    final: True
    suffix: .relax2
    settings_override: {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}
jobs_common_params:
  $vasp_cmd: ["mpirun", "-machinefile", "$PBS_NODEFILE", "-np", "24", "/opt/vasp/5.4.1/bin/vasp"]
handlers:
- hdlr: custodian.vasp.handlers.VaspErrorHandler
- hdlr: custodian.vasp.handlers.AliasingErrorHandler
- hdlr: custodian.vasp.handlers.MeshSymmetryErrorHandler
validators:
- vldr: custodian.vasp.validators.VasprunXMLValidator
custodian_params:
  $scratch_dir: $TMPDIR"""

        os.environ["TMPDIR"] = "/tmp/random"
        os.environ["PBS_NODEFILE"] = "whatever"
        d = yaml.safe_load(spec)
        c = Custodian.from_spec(d)
        self.assertEqual(c.jobs[0].vasp_cmd[2], "whatever")
        self.assertEqual(c.scratch_dir, "/tmp/random")
        self.assertEqual(len(c.jobs), 2)
        self.assertEqual(len(c.handlers), 3)
        self.assertEqual(len(c.validators), 1)

Exemple #2

Fichier : cstdn.py Projet : czhengsci/custodian

def run(args):
    FORMAT = '%(asctime)s %(message)s'
    logging.basicConfig(format=FORMAT, level=logging.INFO, filename="run.log")
    logging.info("Spec file is %s" % args.spec_file)
    d = loadfn(args.spec_file[0])
    c = Custodian.from_spec(d)
    c.run()

Exemple #3

def run(args):
    FORMAT = "%(asctime)s %(message)s"
    logging.basicConfig(format=FORMAT, level=logging.INFO, filename="run.log")
    logging.info("Spec file is %s" % args.spec_file)
    d = loadfn(args.spec_file[0])
    c = Custodian.from_spec(d)
    c.run()

Exemple #4

Fichier : test_custodian.py Projet : pombredanne/custodian

    def test_from_spec(self):
        spec =  """jobs:
- jb: custodian.vasp.jobs.VaspJob
  params:
    final: False
    suffix: .relax1
- jb: custodian.vasp.jobs.VaspJob
  params:
    final: True
    suffix: .relax2
    settings_override: {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}
jobs_common_params:
  $vasp_cmd: ["mpirun", "-machinefile", "$PBS_NODEFILE", "-np", "24", "/opt/vasp/5.4.1/bin/vasp"]
handlers:
- hdlr: custodian.vasp.handlers.VaspErrorHandler
- hdlr: custodian.vasp.handlers.AliasingErrorHandler
- hdlr: custodian.vasp.handlers.MeshSymmetryErrorHandler
validators:
- vldr: custodian.vasp.validators.VasprunXMLValidator
custodian_params:
  $scratch_dir: $TMPDIR"""
        import yaml
        os.environ["TMPDIR"] = "/tmp/random"
        os.environ["PBS_NODEFILE"] = "whatever"
        d = yaml.load(spec)
        c = Custodian.from_spec(d)
        self.assertEqual(c.jobs[0].vasp_cmd[2], "whatever")
        self.assertEqual(c.scratch_dir, "/tmp/random")
        self.assertEqual(len(c.jobs), 2)
        self.assertEqual(len(c.handlers), 3)
        self.assertEqual(len(c.validators), 1)