update public distribution
based on internal repository c9a2ac8 2019-01-03 16:04:57 +0100 tagged rev-master-2.0.0
This commit is contained in:
@ -1,5 +1,3 @@
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#!/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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@ -8,30 +6,129 @@ 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 absolute_import
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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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from __future__ import print_function
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import argparse
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import logging
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import math
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import numpy as np
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import os.path
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import periodictable as pt
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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 TwoatomCluster(mc.ClusterGenerator):
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"""
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cluster of two atoms.
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atom A (top) is set at position (0, 0, 0), atom B (bottom) at (-dx, -dy, -dz)
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where dx, dy and dz are calculated from model parameters.
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the type of the atoms is set upon construction.
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the model parameters are:
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@arg @c model['dAB'] : distance between the two atoms in Angstrom.
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@arg @c model['th'] : polar angle of the connection line, 0 = on top geometry.
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@arg @c model['ph'] : azimuthal angle of the connection line, 0 = polar angle affects X coordinate.
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the class is designed to be reusable in various projects.
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object attributes refine the atom types and the mapping of project-specific model parameters.
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"""
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## @var atom_types (dict)
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# chemical element numbers of the cluster atoms.
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#
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# atom 'A' is the top atom, 'B' the bottom one.
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# upon construction both atoms are set to oxygen.
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# to customize, call @ref set_atom_type.
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## @var model_dict (dict)
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# mapping of model parameters to cluster parameters
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#
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# the default model parameters used by the cluster are 'dAB', 'th' and 'ph'.
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# if the project uses other parameter names, e.g. 'dCO' instead of 'dAB',
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# the project-specific names can be declared here.
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# in the example, set model_dict['dAB'] = 'dCO'.
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def __init__(self, project):
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"""
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initialize the cluster generator.
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the atoms and model dictionary are given default values.
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see @ref set_atom_type and @ref model_dict for customization.
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@param project: project instance.
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"""
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super(TwoatomCluster, self).__init__(project)
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self.atom_types = {'A': pt.O.number, 'B': pt.O.number}
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self.model_dict = {'dAB': 'dAB', 'th': 'th', 'ph': 'ph'}
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def set_atom_type(self, atom, element):
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"""
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set the type (chemical element) of an atom.
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@param atom: atom key, 'A' (top) or 'B' (bottom).
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@param element: chemical element number or symbol.
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"""
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try:
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self.atom_types[atom] = int(element)
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except ValueError:
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self.atom_types[atom] = pt.elements.symbol(element.strip()).number
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def count_emitters(self, model, index):
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"""
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return the number of emitter configurations.
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this cluster supports only one configuration.
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@param model:
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@param index:
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@return 1
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"""
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return 1
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def create_cluster(self, model, index):
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"""
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create a cluster given the model parameters and index.
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@param model:
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@param index:
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@return a pmsco.cluster.Cluster object containing the atomic coordinates.
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"""
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r = model[self.model_dict['dAB']]
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try:
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th = math.radians(model[self.model_dict['th']])
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except KeyError:
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th = 0.
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try:
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ph = math.radians(model[self.model_dict['ph']])
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except KeyError:
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ph = 0.
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dx = r * math.sin(th) * math.cos(ph)
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dy = r * math.sin(th) * math.sin(ph)
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dz = r * math.cos(th)
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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(r * 2.0)
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a_top = np.array((0.0, 0.0, 0.0))
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a_bot = np.array((-dx, -dy, -dz))
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clu.add_atom(self.atom_types['A'], a_top, 1)
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clu.add_atom(self.atom_types['B'], a_bot, 0)
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return clu
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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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@ -49,31 +146,12 @@ class TwoatomProject(mp.Project):
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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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self.cluster_generator = TwoatomCluster(self)
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self.cluster_generator.set_atom_type('A', 'N')
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self.cluster_generator.set_atom_type('B', 'Ni')
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self.cluster_generator.model_dict['dAB'] = 'dNNi'
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self.cluster_generator.model_dict['th'] = 'pNNi'
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self.cluster_generator.model_dict['ph'] = 'aNNi'
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def create_params(self, model, index):
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"""
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@ -93,13 +171,13 @@ class TwoatomProject(mp.Project):
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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.angular_resolution = 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.phase_files = {self.cluster_generator.atom_types['A']: "",
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self.cluster_generator.atom_types['B']: ""}
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params.msq_displacement = {self.cluster_generator.atom_types['A']: 0.01,
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self.cluster_generator.atom_types['B']: 0.0}
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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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@ -153,6 +231,27 @@ class TwoatomProject(mp.Project):
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return dom
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def example_intensity(e, t, p, a):
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"""
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arbitrary intensity pattern for example data
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this function can be used to calculate the intensity in example scan files.
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the function implements an arbitrary modulation function
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@param e: energy
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@param t: theta
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@param p: phi
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@param a: alpha
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@return intensity
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"""
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i = np.random.random() * 1e6 * \
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np.cos(np.radians(t)) ** 2 * \
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np.cos(np.radians(a)) ** 2 * \
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np.cos(np.radians(p)) ** 2 * \
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np.sin(e / 1000. * np.pi * 0.1 / np.sqrt(e)) ** 2
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return i
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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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@ -230,20 +329,3 @@ def parse_project_args(_args):
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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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