285 lines
10 KiB
Python
285 lines
10 KiB
Python
#!/usr/bin/env python
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"""
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@package pmsco.projects.fcc
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scattering calculation project for the (111) surface of an arbitrary face-centered cubic crystal
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@author Matthias Muntwiler, matthias.muntwiler@psi.ch
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@copyright (c) 2015 by Paul Scherrer Institut @n
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Licensed under the Apache License, Version 2.0 (the "License"); @n
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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"""
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from __future__ import division
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import sys
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import os
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import math
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import numpy as np
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import periodictable as pt
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import argparse
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import logging
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base_dir = os.path.dirname(__file__) or '.'
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package_dir = os.path.join(base_dir, '../..')
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package_dir = os.path.abspath(package_dir)
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sys.path.append(package_dir)
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import pmsco.pmsco
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import pmsco.cluster as mc
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import pmsco.project as mp
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import pmsco.data as md
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from pmsco.helpers import BraceMessage as BMsg
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logger = logging.getLogger(__name__)
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class FCC111Project(mp.Project):
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def __init__(self):
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"""
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initialize a project instance
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"""
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super(FCC111Project, self).__init__()
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self.scan_dict = {}
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self.element = "Ni"
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def create_cluster(self, model, index):
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"""
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calculate a specific set of atom positions given the optimizable parameters.
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@param model (dict) optimizable parameters
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@arg model['dlat'] bulk lattice constant in Angstrom
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@arg model['dl1l2'] distance between top and second layer (may deviate from bulk)
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@arg model['rmax'] cluster radius
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@arg model['phi'] azimuthal rotation angle in degrees
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"""
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clu = mc.Cluster()
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clu.comment = "{0} {1}".format(self.__class__, index)
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clu.set_rmax(model['rmax'])
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# fcc lattice constant
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a_lat = model['dlat']
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# surface lattice constant of the (111) surface
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a_surf = a_lat / math.sqrt(2.0)
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# lattice vectors
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# a1 and a2 span the (111) surface
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a1 = np.array((a_surf, 0.0, 0.0))
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a2 = np.array((a_surf / 2.0, a_surf * math.sqrt(3.0) / 2.0, 0.0))
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a3 = np.array((0.0, a_surf * math.sqrt(3.0) / 3.0, a_lat * math.sqrt(3.0) / 3))
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a_l1 = np.array((0.0, 0.0, 0.0))
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a_l2 = np.array(((a1[0] + a2[0]) * 2.0 / 3.0,
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(a1[1] + a2[1]) * 2.0 / 3.0,
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-(model['dl1l2'])))
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a_l3 = np.array(((a1[0] + a2[0]) / 3.0,
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(a1[1] + a2[1]) / 3.0,
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-(a3[2] + model['dl1l2'])))
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a_bulk = np.array((0.0, 0.0,
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-(2.0 * a3[2] + model['dl1l2'])))
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clu.add_layer(self.element, a_l1, a1, a2)
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clu.add_layer(self.element, a_l2, a1, a2)
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clu.add_layer(self.element, a_l3, a1, a2)
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clu.add_bulk(self.element, a_bulk, a1, a2, a3)
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clu.set_emitter(a_l1)
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clu.rotate_z(model['phi'])
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return clu
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def create_params(self, model, index):
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"""
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set a specific set of parameters given the optimizable parameters.
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par = optimizable parameters
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par['V0'] = inner potential
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par['Zsurf'] = position of surface
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"""
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params = mp.Params()
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params.title = "fcc(111)"
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params.comment = "{0} {1}".format(self.__class__, index)
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params.cluster_file = ""
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params.output_file = ""
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params.initial_state = self.scans[index.scan].initial_state
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params.spherical_order = 2
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params.polarization = "H"
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params.scattering_level = 5
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params.fcut = 15.0
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params.cut = 15.0
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params.angular_broadening = 0.0
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params.lattice_constant = 1.0
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params.z_surface = model['Zsurf']
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params.atom_types = 3
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params.atomic_number = [pt.elements.symbol(self.element).number]
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params.phase_file = []
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params.msq_displacement = [0.00]
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params.planewave_attenuation = 1.0
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params.inner_potential = model['V0']
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params.work_function = 4.5
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params.symmetry_range = 360.0
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params.polar_incidence_angle = 60.0
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params.azimuthal_incidence_angle = 0.0
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params.vibration_model = "P"
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params.substrate_atomic_mass = pt.elements.symbol(self.element).mass
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params.experiment_temperature = 300.0
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params.debye_temperature = 400.0
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params.debye_wavevector = 1.7558
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params.rme_minus_value = 0.0
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params.rme_minus_shift = 0.0
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params.rme_plus_value = 1.0
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params.rme_plus_shift = 0.0
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# used by EDAC only
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params.emitters = []
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params.lmax = 15
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params.dmax = 5.0
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params.orders = [25]
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return params
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def create_domain(self):
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"""
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define the domain of the optimization parameters.
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"""
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dom = mp.Domain()
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if self.mode == "single":
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dom.add_param('rmax', 5.00, 5.00, 15.00, 2.50)
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dom.add_param('phi', 0.00, 0.00, 0.00, 0.00)
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dom.add_param('dlat', 3.52, 2.00, 5.00, 0.10)
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dom.add_param('dl1l2', 2.03, 1.80, 2.20, 0.05)
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dom.add_param('V0', 10.00, 0.00, 20.00, 1.00)
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dom.add_param('Zsurf', 1.00, 0.00, 2.00, 0.50)
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elif self.mode == "swarm":
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dom.add_param('rmax', 7.50, 5.00, 15.00, 2.50)
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dom.add_param('phi', 0.00, 0.00, 0.00, 0.00)
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dom.add_param('dlat', 3.52, 2.00, 5.00, 0.10)
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dom.add_param('dl1l2', 2.03, 1.80, 2.20, 0.05)
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dom.add_param('V0', 10.00, 0.00, 20.00, 1.00)
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dom.add_param('Zsurf', 1.00, 0.00, 2.00, 0.50)
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elif self.mode == "grid":
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dom.add_param('rmax', 7.50, 5.00, 15.00, 2.50)
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dom.add_param('phi', 0.00, 0.00, 0.00, 0.00)
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dom.add_param('dlat', 3.52, 2.00, 5.00, 0.10)
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dom.add_param('dl1l2', 2.03, 1.80, 2.20, 0.05)
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dom.add_param('V0', 10.00, 0.00, 20.00, 1.00)
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dom.add_param('Zsurf', 1.00, 0.00, 2.00, 0.50)
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else:
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dom.add_param('rmax', 7.50, 5.00, 15.00, 2.50)
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dom.add_param('phi', 0.00, 0.00, 0.00, 0.00)
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dom.add_param('dlat', 3.52, 2.00, 5.00, 0.10)
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dom.add_param('dl1l2', 2.03, 1.80, 2.20, 0.05)
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dom.add_param('V0', 10.00, 0.00, 20.00, 1.00)
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dom.add_param('Zsurf', 1.00, 0.00, 2.00, 0.50)
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return dom
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def create_project(element):
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"""
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create an FCC111Project calculation project.
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@param element: symbol of the chemical element of the atoms contained in the cluster.
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"""
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project = FCC111Project()
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project.element = element
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project_dir = os.path.dirname(os.path.abspath(__file__))
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project.data_dir = project_dir
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# scan dictionary
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# to select any number of scans, add their dictionary keys as scans option on the command line
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project.scan_dict['default'] = {'filename': os.path.join(project_dir, "demo_holo_scan.etp"),
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'emitter': "Ni", 'initial_state': "3s"}
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project.scan_dict['holo'] = {'filename': os.path.join(project_dir, "demo_holo_scan.etp"),
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'emitter': "Ni", 'initial_state': "3s"}
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project.scan_dict['alpha'] = {'filename': os.path.join(project_dir, "demo_alpha_scan.etp"),
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'emitter': "Ni", 'initial_state': "3s"}
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project.add_symmetry({'default': 0.0})
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return project
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def set_project_args(project, project_args):
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"""
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set the project arguments of a MnGeTeProject calculation project.
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@param project: project instance
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@param project_args: (Namespace object) project arguments.
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"""
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scans = ['default']
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try:
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if project_args.scans:
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scans = project_args.scans
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else:
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logger.warning(BMsg("missing scan argument, using {0}", scans[0]))
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except AttributeError:
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logger.warning(BMsg("missing scan argument, using {0}", scans[0]))
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for scan_key in scans:
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scan_spec = project.scan_dict[scan_key]
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project.add_scan(**scan_spec)
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logger.info(BMsg("add scan {filename} ({emitter} {initial_state})", **scan_spec))
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try:
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if project_args.element:
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for scan in project.scans:
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scan.emitter = project_args.element
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logger.warning(BMsg("override emitters to {0}", project.emitter))
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except AttributeError:
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pass
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try:
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if project_args.initial_state:
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project.initial_state = project_args.initial_state
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logger.warning(BMsg("override initial states to {0}", project.initial_state))
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except AttributeError:
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pass
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try:
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if project_args.energy:
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for scan in project.scans:
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scan.energies = np.asarray((project_args.energy, ))
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logger.warning(BMsg("override scan energy, set to {0}", project_args.energy))
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except AttributeError:
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pass
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def parse_project_args(_args):
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parser = argparse.ArgumentParser()
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# main arguments
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parser.add_argument('-e', '--element', help="chemical element symbol")
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parser.add_argument('-s', '--scans', nargs="*", default=['default'],
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help="nick names of scans to use in calculation (see create_project function)")
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parser.add_argument('-i', '--initial-state',
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help="inital state of photoelectron")
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parser.add_argument('--energy', type=float,
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help="kinetic energy of photoelectron (override scan file)")
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parsed_args = parser.parse_known_args(_args)
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return parsed_args
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def main():
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args, unknown_args = pmsco.pmsco.parse_cli()
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if unknown_args:
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project_args = parse_project_args(unknown_args)
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else:
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project_args = None
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project = create_project(project_args.element)
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pmsco.pmsco.set_common_args(project, args)
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set_project_args(project, project_args)
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pmsco.pmsco.run_project(project)
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if __name__ == '__main__':
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main()
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sys.exit(0)
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