Python Poscar.as_dict方法代码示例

# 需要导入模块: from pymatgen.io.vasp.inputs import Poscar [as 别名]
# 或者: from pymatgen.io.vasp.inputs.Poscar import as_dict [as 别名]
class Calibrate(PMGSONable):    
    """
    The base class for creating vasp work flows for
    calibrating the input parameters for different systems

    A wrapper around Custodian
    """
    LOG_FILE = "calibrate.json"

    def __init__(self, incar, poscar, potcar, kpoints, system=None,
                 is_matrix = False, Grid_type = 'A',
                 parent_job_dir='.',job_dir='Job',
                 qadapter=None, job_cmd='qsub', wait=True,
                 mappings_override = None, functional="PBE",
                 turn_knobs=OrderedDict( [ ('ENCUT',[]),
                                           ('KPOINTS',[])] ),
                 checkpoint_file=None, cal_logger=None):
        """
        Calibrate constructor

        Args:
            incar (Incar object): input INCAR
            poscar (Poscar object): input POSCAR
            potcar (Potcar object): input POTCAR
            kpoints: input KPOINTS
            system: system info as a dictionary,
                slab or interface example:
                system={'hkl':[1,1,1], 'ligand':None}, 
            is_matrix (bool): whether the jobs are dependent on each
                other
            Grid_type: kpoints grid_type
            parent_job_dir: the directory from which all the jobs are
                launched
            job_dir: job directory
            qadapter: adapter for the batch system
            job_cmd: command to be used for submitting the job. If 
                qadapter is specified then job_cmd is ignored
            wait: whther to wait for the job to finish. If the job is
                being submitted to the queue then there is no need for
                waiting
            turn_knobs: an ordered dictionary of parmaters and the 
                corresponding values
            mappings_override: override symbol mapping in potcar
                               eg:- {'S':'S_sv'}
            functional: exchange-correlation functional

        Note: input structure if needed will be obtained from the
            provided poscar object
        """
        self.name = datetime.datetime.now().isoformat()
        self.system = system
        self.parent_job_dir = os.path.abspath(parent_job_dir)
        self.job_dir = job_dir
        self.incar = incar               
        self.poscar = poscar
        self.potcar = potcar
        if poscar:
            self.potcar = Potcar(symbols=poscar.site_symbols,
                                 functional=functional)
        self.kpoints = kpoints
        if incar:
            self.incar_orig = incar.as_dict()
        if poscar:
            self.poscar_orig = poscar.as_dict()
        if self.potcar:
            self.potcar_orig = self.potcar.as_dict()
        if kpoints:
            self.kpoints_orig = kpoints.as_dict()
        self.qadapter = qadapter
        self.job_dir_list = []
        self.jobs = []
        self.job_ids = []        
        self.handlers = []
        self.job_cmd = job_cmd
        self.n_atoms = 0
        self.turn_knobs = turn_knobs
        self.response_to_knobs = {}
        self.sorted_response_to_knobs = {}        
        for k, v in turn_knobs.items():
            self.response_to_knobs[k] = {}
            self.sorted_response_to_knobs[k] = {}            
        self.is_matrix = is_matrix
        self.Grid_type = Grid_type
        self.wait = wait
        self.cal_log = []
        self.mappings_override = mappings_override
        self.functional = functional
        self.checkpoint_file = checkpoint_file
        if cal_logger:
            self.logger = cal_logger
        else:
            self.logger = logger
    
    def setup(self):
        """
        set up the jobs for the given turn_knobs dict
        is_matrix = True implies that the params in the dict are 
        interrelated. Otherwise calcs corresponding to each dict key
        is independent
        """
#.........这里部分代码省略.........

# 需要导入模块: from pymatgen.io.vasp.inputs import Poscar [as 别名]
# 或者: from pymatgen.io.vasp.inputs.Poscar import as_dict [as 别名]

#.........这里部分代码省略.........
        where the fuel (input file sources) and driving method (kind of calculation)
        are decided . The Engine itself is instrument.py which creates the input set
        configured in Calibrate.

        Current fueling methods:
          1. simplest test case involving a single job:
               - specify the incar, kpoints, poscar, potcar (aka the VASP 4)
                 explicitly as pymatgen objects
               - turn_knobs = {} , is_matrix = False
          2. test case for calibration of parameters:
               - specify an initial configuration for the VASP 4
               - specify parameters to calibrate via turn_knobs,
                 set is_matrix = True only if number of parameters > 1
          3. Database production case: (possibly most used)
               - specify initial configuration for the VASP 4 based on
                 a database.yaml
               - specify an input.yaml that details the workflow

        Note: input structure if needed will be obtained from the
            provided poscar object
        """
        self.name = datetime.datetime.now().isoformat()
        self.system = system
        self.parent_job_dir = os.path.abspath(parent_job_dir)
        self.job_dir = job_dir
        self.incar = incar
        self.poscar = poscar
        self.potcar = potcar
        if poscar:
            self.potcar = Potcar(symbols=poscar.site_symbols,
                                 functional=functional)
        self.kpoints = kpoints
        if incar:
            self.incar_orig = incar.as_dict()
        if poscar:
            self.poscar_orig = poscar.as_dict()
        if self.potcar:
            self.potcar_orig = self.potcar.as_dict()
        if kpoints:
            self.kpoints_orig = kpoints.as_dict()
        self.qadapter = qadapter
        self.job_dir_list = []
        self.jobs = []
        self.job_ids = []
        self.handlers = []
        self.job_cmd = job_cmd
        self.n_atoms = 0
        self.turn_knobs = turn_knobs
        self.response_to_knobs = {}
        self.sorted_response_to_knobs = {}
        for k, v in turn_knobs.items():
            self.response_to_knobs[k] = {}
            self.sorted_response_to_knobs[k] = {}
        self.is_matrix = is_matrix
        self.Grid_type = Grid_type
        self.wait = wait
        self.cal_log = []
        self.mappings_override = mappings_override
        self.database = database
        self.magnetism = magnetism
        self.mag_init = mag_init
        self.solvation = solvation
        self.reuse = reuse
        self.reuse_incar = reuse_incar
        self.reuse_override = reuse_override
        self.reuse_paths = None  # list object communicated to instrument