250 lines
8.4 KiB
Python
250 lines
8.4 KiB
Python
#!/usr/bin/env python
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"""
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@package projects.twoatom
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Two-atom demo scattering calculation project
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this file is specific to the project and the state of the data analysis,
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as it contains particular parameter values.
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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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# adjust the system path so that the main PMSCO code is found
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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 TwoatomProject(mp.Project):
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"""
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two-atom calculation project class.
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the cluster contains a nitrogen in the top layer,
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and a nickel atom in the second layer.
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The layer distance and the angle can be adjusted by parameters.
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the model parameters are:
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@arg @c model['dNNi'] : vertical distance N - Ni in Angstrom.
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@arg @c model['pNNi'] : polar angle of axis N - Ni in degrees. 0 = on top geometry.
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@arg @c model['V0'] : inner potential
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@arg @c model['Zsurf'] : position of surface
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"""
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def __init__(self):
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super(TwoatomProject, self).__init__()
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self.scan_dict = {}
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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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the cluster contains a nitrogen in the top layer,
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and a nickel atom in the second layer.
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The layer distance and the angle can be adjusted by parameters.
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@param model: (dict) optimizable parameters
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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(10.0)
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a_N = np.array((0.0, 0.0, 0.0))
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rad_pNNi = math.radians(model['pNNi'])
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a_Ni1 = np.array((0.0,
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-model['dNNi'] * math.sin(rad_pNNi),
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-model['dNNi'] * math.cos(rad_pNNi)))
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clu.add_atom(pt.N.number, a_N, 1)
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clu.add_atom(pt.Ni.number, a_Ni1, 0)
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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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@param model: (dict) optimizable parameters
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"""
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params = mp.Params()
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params.title = "two-atom demo"
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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 = [7, 28]
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params.phase_file = ["hbn_n.pha", "ni.pha"]
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params.msq_displacement = [0.01, 0.01, 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 = 3.6
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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 = 58.69
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params.experiment_temperature = 300.0
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params.debye_temperature = 356.0
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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('dNNi', 2.109, 2.000, 2.250, 0.050)
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dom.add_param('pNNi', 15.000, 0.000, 30.000, 1.000)
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dom.add_param('V0', 21.966, 15.000, 25.000, 1.000)
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dom.add_param('Zsurf', 1.449, 0.500, 2.000, 0.250)
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elif self.mode == "swarm":
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dom.add_param('dNNi', 2.109, 2.000, 2.250, 0.050)
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dom.add_param('pNNi', 15.000, 0.000, 30.000, 1.000)
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dom.add_param('V0', 21.966, 15.000, 25.000, 1.000)
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dom.add_param('Zsurf', 1.449, 0.500, 2.000, 0.250)
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elif self.mode == "grid":
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dom.add_param('dNNi', 2.109, 2.000, 2.250, 0.050)
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dom.add_param('pNNi', 15.000, 0.000, 30.000, 1.000)
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dom.add_param('V0', 21.966, 15.000, 25.000, 1.000)
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dom.add_param('Zsurf', 1.449, 0.500, 2.000, 0.250)
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else:
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dom.add_param('dNNi', 2.109, 2.000, 2.250, 0.050)
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dom.add_param('pNNi', 15.000, 0.000, 30.000, 1.000)
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dom.add_param('V0', 21.966, 15.000, 25.000, 1.000)
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dom.add_param('Zsurf', 1.449, 0.500, 2.000, 0.250)
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return dom
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def create_project():
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"""
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create a new TwoatomProject calculation project.
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the default experimental data file is @c twoatom_hemi_scan_250e.etpi
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in the same directory as this Python module.
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it defines a classic hemispherical angle scan grid
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but does not include measured data for optimization.
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@return project instance.
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"""
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project = TwoatomProject()
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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['ea'] = {'filename': os.path.join(project_dir, "twoatom_energy_alpha.etpai"),
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'emitter': "N", 'initial_state': "1s"}
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project.scan_dict['et0p'] = {'filename': os.path.join(project_dir, "twoatom_energy_theta_0p.etpi"),
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'emitter': "N", 'initial_state': "1s"}
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project.scan_dict['et180p'] = {'filename': os.path.join(project_dir, "twoatom_energy_theta_180p.etpi"),
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'emitter': "N", 'initial_state': "1s"}
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project.scan_dict['tp215e'] = {'filename': os.path.join(project_dir, "twoatom_hemi_215e.etpi"),
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'emitter': "N", 'initial_state': "1s"}
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project.scan_dict['tp250e'] = {'filename': os.path.join(project_dir, "twoatom_hemi_250e.etpi"),
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'emitter': "N", 'initial_state': "1s"}
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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-specific arguments.
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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 = ['tp250e']
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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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project.add_symmetry({'default': 0.0})
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def parse_project_args(_args):
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"""
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parse project-specific command line arguments.
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@param _args: list of project-specific arguments from the command line.
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this is typically the unknown_args return value from argparse.ArgumentParser.parse_known_args().
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@return: namespace object containing the specified arguments as attributes.
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"""
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parser = argparse.ArgumentParser()
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# main arguments
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parser.add_argument('-s', '--scans', nargs="*", default=['tp250e'],
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help="nick names of scans to use in calculation (see create_project function)")
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parsed_args = parser.parse_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()
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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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