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public release 2.2.0 - see README.md and CHANGES.md for details

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muntwiler_m
2020-09-04 16:22:42 +02:00
parent fbd2d4fa8c
commit 7c61eb1b41
67 changed files with 2934 additions and 682 deletions
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projects/twoatom/twoatom.py
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@ -17,6 +17,9 @@ import numpy as np
import os.path
import periodictable as pt
from pmsco.calculators.calculator import InternalAtomicCalculator
from pmsco.calculators.edac import EdacCalculator
from pmsco.calculators.phagen.runner import PhagenCalculator
import pmsco.cluster as mc
import pmsco.project as mp
from pmsco.helpers import BraceMessage as BMsg
@ -152,6 +155,17 @@ class TwoatomProject(mp.Project):
self.cluster_generator.model_dict['dAB'] = 'dNNi'
self.cluster_generator.model_dict['th'] = 'pNNi'
self.cluster_generator.model_dict['ph'] = 'aNNi'
self.atomic_scattering_factory = PhagenCalculator
self.multiple_scattering_factory = EdacCalculator
self.phase_files = {}
self.rme_files = {}
self.bindings = {}
self.bindings['N'] = {'1s': 409.9}
self.bindings['B'] = {'1s': 188.0}
self.bindings['Ni'] = {'2s': 1008.6,
'2p': (870.0 + 852.7) / 2, '2p1/2': 870.0, '2p3/2': 852.7,
'3s': 110.8,
'3p': (68.0 + 66.2) / 2, '3p1/2': 68.0, '3p3/2': 66.2}
def create_params(self, model, index):
"""
@ -159,40 +173,40 @@ class TwoatomProject(mp.Project):
@param model: (dict) optimizable parameters
"""
params = mp.Params()
params = mp.CalculatorParams()
params.title = "two-atom demo"
params.comment = "{0} {1}".format(self.__class__, index)
params.cluster_file = ""
params.output_file = ""
params.initial_state = self.scans[index.scan].initial_state
params.spherical_order = 2
initial_state = self.scans[index.scan].initial_state
params.initial_state = initial_state
emitter = self.scans[index.scan].emitter
params.binding_energy = self.bindings[emitter][initial_state]
params.polarization = "H"
params.scattering_level = 5
params.fcut = 15.0
params.cut = 15.0
params.angular_resolution = 0.0
params.lattice_constant = 1.0
params.z_surface = model['Zsurf']
params.phase_files = {self.cluster_generator.atom_types['A']: "",
self.cluster_generator.atom_types['B']: ""}
params.msq_displacement = {self.cluster_generator.atom_types['A']: 0.01,
self.cluster_generator.atom_types['B']: 0.0}
params.planewave_attenuation = 1.0
params.inner_potential = model['V0']
params.work_function = 3.6
params.symmetry_range = 360.0
params.polar_incidence_angle = 60.0
params.azimuthal_incidence_angle = 0.0
params.vibration_model = "P"
params.substrate_atomic_mass = 58.69
params.experiment_temperature = 300.0
params.debye_temperature = 356.0
params.debye_wavevector = 1.7558
params.rme_minus_value = 0.0
if self.phase_files:
state = emitter + initial_state
try:
params.phase_files = self.phase_files[state]
except KeyError:
params.phase_files = {}
logger.warning("no phase files found for {} - using default calculator".format(state))
params.rme_files = {}
params.rme_minus_value = 0.1
params.rme_minus_shift = 0.0
params.rme_plus_value = 1.0
params.rme_plus_shift = 0.0
# used by EDAC only
params.emitters = []
params.lmax = 15
@ -201,11 +215,11 @@ class TwoatomProject(mp.Project):
return params
def create_domain(self):
def create_model_space(self):
"""
define the domain of the optimization parameters.
"""
dom = mp.Domain()
dom = mp.ModelSpace()
if self.mode == "single":
dom.add_param('dNNi', 2.109, 2.000, 2.250, 0.050)
@ -308,7 +322,7 @@ def set_project_args(project, project_args):
project.add_scan(**scan_spec)
logger.info(BMsg("add scan {filename} ({emitter} {initial_state})", **scan_spec))
project.add_symmetry({'default': 0.0})
project.add_domain({'default': 0.0})
def parse_project_args(_args):