def __init__(self, name, incar, poscar, potcar, kpoints, qadapter=None, script_name='submit_script', vis_logger=None, **kwargs): """ default INCAR from config_dict """ self.name = name self.incar = Incar.from_dict(incar.as_dict()) self.poscar = Poscar.from_dict(poscar.as_dict()) self.potcar = Potcar.from_dict(potcar.as_dict()) self.kpoints = Kpoints.from_dict(kpoints.as_dict()) self.extra = kwargs if qadapter is not None: self.qadapter = qadapter.from_dict(qadapter.to_dict()) else: self.qadapter = None self.script_name = script_name config_dict = {} config_dict['INCAR'] = self.incar.as_dict() config_dict['POSCAR'] = self.poscar.as_dict() # caution the key and the value are not always the same config_dict['POTCAR'] = self.potcar.as_dict() # dict(zip(self.potcar.as_dict()['symbols'], # self.potcar.as_dict()['symbols'])) config_dict['KPOINTS'] = self.kpoints.as_dict() # self.user_incar_settings = self.incar.as_dict() DictVaspInputSet.__init__(self, name, config_dict, ediff_per_atom=False, **kwargs) if vis_logger: self.logger = vis_logger else: self.logger = logger
def __init__(self, name, incar, poscar, potcar, kpoints, qadapter=None, **kwargs ): """ default INCAR from config_dict """ self.name = name self.incar = Incar.from_dict(incar.as_dict()) self.poscar = Poscar.from_dict(poscar.as_dict()) self.potcar = Potcar.from_dict(potcar.as_dict()) self.kpoints = Kpoints.from_dict(kpoints.as_dict()) self.extra = kwargs if qadapter is not None: self.qadapter = qadapter.from_dict(qadapter.to_dict()) else: self.qadapter = None config_dict = {} config_dict['INCAR'] = self.incar.as_dict() config_dict['POSCAR'] = self.poscar.as_dict() #caution the key and the value are not always the same config_dict['POTCAR'] = self.potcar.as_dict() #dict(zip(self.potcar.as_dict()['symbols'], #self.potcar.as_dict()['symbols'])) config_dict['KPOINTS'] = self.kpoints.as_dict() #self.user_incar_settings = self.incar.as_dict() DictVaspInputSet.__init__(self, name, config_dict, ediff_per_atom=False, **kwargs)
def get_poscar(self): """ Create and return a :class:`pymatgen.io.vasp.inputs.Poscar` instance initialized from the node's stored structure data contents. :return: a pymatgen Poscar instance :rtype: :class:`pymatgen.io.vasp.inputs.Poscar` """ return Poscar.from_dict(self.get_dict())
def __init__(self, name, incar, poscar, kpoints, potcar=None, qadapter=None, script_name='submit_script', vis_logger=None, reuse_path=None, test=False, **kwargs): """ default INCAR from config_dict """ self.name = name self.test = test #print (test) self.incar_init = Incar.from_dict(incar.as_dict()) self.poscar_init = Poscar.from_dict(poscar.as_dict()) if not self.test: self.potcar_init = Potcar.from_dict(potcar.as_dict()) if not isinstance(kpoints, str): self.kpoints_init = Kpoints.from_dict(kpoints.as_dict()) #print (kpoints) else: self.kpoints_init = kpoints self.reuse_path = reuse_path # complete reuse paths self.extra = kwargs if qadapter is not None: self.qadapter = qadapter.from_dict(qadapter.to_dict()) else: self.qadapter = None self.script_name = script_name config_dict = {} config_dict['INCAR'] = self.incar_init.as_dict() config_dict['POSCAR'] = self.poscar_init.as_dict() # caution the key and the value are not always the same if not self.test: config_dict['POTCAR'] = self.potcar_init.as_dict() # dict(zip(self.potcar.as_dict()['symbols'], # self.potcar.as_dict()['symbols'])) if not isinstance(kpoints, str): #print (self.kpoints_init) config_dict['KPOINTS'] = self.kpoints_init.as_dict() else: # need to find a way to dictify this kpoints string more # appropriately config_dict['KPOINTS'] = {'kpts_hse': self.kpoints_init} # self.user_incar_settings = self.incar.as_dict() DictSet.__init__(self, poscar.structure, config_dict) #**kwargs) if vis_logger: self.logger = vis_logger else: self.logger = logger
def from_dict(cls, d): incar = Incar.from_dict(d["incar"]) poscar = Poscar.from_dict(d["poscar"]) potcar = Potcar.from_dict(d["potcar"]) kpoints = Kpoints.from_dict(d["kpoints"]) qadapter = None if d["qadapter"] is not None: qadapter = CommonAdapter.from_dict(d["qadapter"]) return MPINTVaspInputSet(d["name"], incar, poscar, potcar, kpoints, qadapter, **d["kwargs"])
def update_spec_force_convergence(spec, user_vasp_settings=None): fw_spec = spec update_set = {"ENCUT": 700, "EDIFF": 0.000001, "ALGO":"N", "NPAR":2} if user_vasp_settings and user_vasp_settings.get("incar"): update_set.update(user_vasp_settings["incar"]) fw_spec['vasp']['incar'].update(update_set) old_struct=Poscar.from_dict(fw_spec["vasp"]["poscar"]).structure if user_vasp_settings and user_vasp_settings.get("kpoints"): kpoints_density = user_vasp_settings["kpoints"]["kpoints_density"] else: kpoints_density = 7000 k=Kpoints.automatic_density(old_struct, kpoints_density) fw_spec['vasp']['kpoints'] = k.as_dict() return fw_spec
def from_dict(cls, d): incar = Incar.from_dict(d["incar"]) poscar = Poscar.from_dict(d["poscar"]) potcar = Potcar.from_dict(d["potcar"]) kpoints = Kpoints.from_dict(d["kpoints"]) qadapter = None if d["qadapter"] is not None: qadapter = CommonAdapter.from_dict(d["qadapter"]) script_name = d["script_name"] return MPINTVaspInputSet(d["name"], incar, poscar, potcar, kpoints, qadapter, script_name=script_name, vis_logger=logging.getLogger(d["logger"]), **d["kwargs"])
def from_dict(cls, d): incar = Incar.from_dict(d["incar"]) poscar = Poscar.from_dict(d["poscar"]) potcar = Potcar.from_dict(d["potcar"]) kpoints = Kpoints.from_dict(d["kpoints"]) cal = Calibrate(incar, poscar, potcar, kpoints, system=d["system"], is_matrix = d["is_matrix"], Grid_type = d["Grid_type"], parent_job_dir=d["parent_job_dir"], job_dir=d["job_dir"], qadapter=d.get("qadapter"), job_cmd=d["job_cmd"], wait=d["wait"], turn_knobs=d["turn_knobs"]) cal.job_dir_list = d["job_dir_list"] cal.job_ids = d["job_ids"] return cal
def from_dict(cls, d): incar = Incar.from_dict(d["incar"]) poscar = Poscar.from_dict(d["poscar"]) potcar = Potcar.from_dict(d["potcar"]) kpoints = Kpoints.from_dict(d["kpoints"]) cal = Calibrate(incar, poscar, potcar, kpoints, system=d["system"], is_matrix=d["is_matrix"], Grid_type=d["Grid_type"], parent_job_dir=d["parent_job_dir"], job_dir=d["job_dir"], qadapter=d.get("qadapter"), job_cmd=d["job_cmd"], wait=d["wait"], turn_knobs=d["turn_knobs"]) cal.job_dir_list = d["job_dir_list"] cal.job_ids = d["job_ids"] return cal
def __init__(self, name, incar, poscar, kpoints, potcar=None, qadapter=None, script_name='submit_script', vis_logger=None, reuse_path=None, test=False, **kwargs): """ default INCAR from config_dict """ self.name = name self.test = test self.incar_init = Incar.from_dict(incar.as_dict()) self.poscar_init = Poscar.from_dict(poscar.as_dict()) if not self.test: self.potcar_init = Potcar.from_dict(potcar.as_dict()) if not isinstance(kpoints, str): self.kpoints_init = Kpoints.from_dict(kpoints.as_dict()) else: self.kpoints_init = kpoints self.reuse_path = reuse_path # complete reuse paths self.extra = kwargs if qadapter is not None: self.qadapter = qadapter.from_dict(qadapter.to_dict()) else: self.qadapter = None self.script_name = script_name config_dict = {} config_dict['INCAR'] = self.incar_init.as_dict() config_dict['POSCAR'] = self.poscar_init.as_dict() # caution the key and the value are not always the same if not self.test: config_dict['POTCAR'] = self.potcar_init.as_dict() # dict(zip(self.potcar.as_dict()['symbols'], # self.potcar.as_dict()['symbols'])) if not isinstance(kpoints, str): config_dict['KPOINTS'] = self.kpoints_init.as_dict() else: # need to find a way to dictify this kpoints string more # appropriately config_dict['KPOINTS'] = {'kpts_hse':self.kpoints_init} # self.user_incar_settings = self.incar.as_dict() DictSet.__init__(self, poscar.structure, config_dict) #**kwargs) if vis_logger: self.logger = vis_logger else: self.logger = logger
def test_to_from_dict(self): poscar_string = """Test3 1.0 3.840198 0.000000 0.000000 1.920099 3.325710 0.000000 0.000000 -2.217138 3.135509 1 1 Selective dynamics direct 0.000000 0.000000 0.000000 T T T Si 0.750000 0.500000 0.750000 F F F O """ poscar = Poscar.from_string(poscar_string) d = poscar.as_dict() poscar2 = Poscar.from_dict(d) self.assertEqual(poscar2.comment, "Test3") self.assertTrue(all(poscar2.selective_dynamics[0])) self.assertFalse(all(poscar2.selective_dynamics[1]))
def set_poscar(self, scale=None, poscar=None): """ perturbs given structure by volume scaling factor or takes user defined variants of Poscar Args: scale : Volume Scaling parameter poscar : Poscar object of user defined structure set the poscar: volume scaled by the scale factor """ if scale is not None: structure = Poscar.from_dict(self.poscar_orig).structure volume = structure.volume structure.scale_lattice(scale *volume) self.poscar = Poscar(structure) elif poscar is not None: self.poscar = poscar
def set_poscar(self, scale=None, poscar=None): """ perturbs given structure by volume scaling factor or takes user defined variants of Poscar Args: scale : Volume Scaling parameter poscar : Poscar object of user defined structure set the poscar: volume scaled by the scale factor """ if scale is not None: structure = Poscar.from_dict(self.poscar_orig).structure volume = structure.volume structure.scale_lattice(scale * volume) self.poscar = Poscar(structure) elif poscar is not None: self.poscar = poscar