7. phaseshifts API

7.1. Package Contents

This chapter covers the main modules of the phaseshifts and provides some API documentation for those wishing to incorporate this package into their own projects.

7.2. Subpackages

The main sub packages are listed below:

phaseshifts.gui - includes all the necessary files for the graphical user interface.
phaseshifts.lib - contains the Fortran libphsh library and the python wrappings.
phaseshifts.doc - source documentation for the phaseshifts package.
phaseshifts.test - modules for testing the phaseshift package.

7.3. Submodules

7.3.1. phaseshifts.atorb

atorb.py

Provides convenience functions for generating input and calculating atomic charge densities for use with the Barbieri/Van Hove phase shift calculation package.

See:: http://www.icts.hkbu.edu.hk/surfstructinfo/SurfStrucInfo_files/leed/
Requires:: f2py (for libphsh fortran wrapper generation)

Note

To generate libphsh fortran wrappers (libphsh.pyd) for your platform then use ‘python setup.py’ in the lib directory of this package to install into your python distribution. Alternatively, use:

f2py -c -m libphsh libphsh.f

Windows users may have to add appropriate compiler switches, e.g.

# 32-bit
f2py -c -m libphsh --fcompiler=gfortran --compiler=mingw-32 libphsh.f

# 64-bit
f2py -c -m libphsh --fcompiler=gfortran --compiler=mingw-64 libphsh.f

class phaseshifts.atorb.Atorb(**kwargs)[source]

Bases: object

Notes

Original author: Eric Shirley

There are nr grid points, and distances are in Bohr radii $a_0 \simeq 0.539 \mathrm{\AA}$

$r(i) = r_{min} \cdot (r_{max} / r_{min})^{(i/n_r)}$ , $i=1,2,3,...n_r-1,n_r$

The orbitals are stored in phe(), first index goes $1...n_r$ , the second index is the orbital index ( $i...n_{el}$ )

Look at the atomic files after printing this out to see everything… Suffice it to say, that the charge density at radius $r(i)$ in units of electrons per cubic Bohr radius is given by:

$\sum_{j-1}^{n_el}{occ(j) \cdot phe(i,j)^2 / (4.0\,\pi\,{r(i)^2)}}$

Think of the phe functions as plotting the radial wave-functions as a function of radius on a logarithmic mesh…

The Dirac equation is solved for the orbitals, whereas their density is treated by setting $phe(i,j)$ to Dirac’s $\sqrt{F(i,j)^2 + G(i,j)^2}$ times the sign of $G(i,j)$ …

So we are doing Dirac-Fock, except that we are not treating exchange exactly, in terms of working with major and minor components of the orbitals, and the phe’s give the CORRECT CHARGE DENSITY…

The above approximation ought to be very small for valence states, so you need not worry about it…

The Breit interaction has been neglected altogether…it should not have a huge effect on the charge density you are concerned with…

static calculate_Q_density(**kwargs)[source]

Parameters:

kwargs may be any of the following.
elementint or str, optional: Generate element atorb input file on the fly. Additional kwargs may be used to govern the structure of the input file - please use help(phaseshifts.Atorb.gen_input) for more information.
inputstr, optional: Specify atorb input file otherwise will use the class instance value.
output_dirstr, optional: Specify the output directory for the at_*.i file generated, otherwise the default current working directory is used.

Returns:

strfilename

Examples

>>> Atorb.calculate_Q_density(input='atorb_C.txt')
      18.008635    -33.678535
       4.451786    -36.654271
       1.569616    -37.283660
       0.424129    -37.355634
       0.116221    -37.359816
       0.047172    -37.360317
       0.021939    -37.360435
       0.010555    -37.360464
       0.005112    -37.360471
       0.002486    -37.360473
       0.001213    -37.360473
       0.000593    -37.360473
       0.000290    -37.360474
    N L M J S OCC.
    1   0 0  -1/2   1    2.0000        -11.493862
    2   0 0  -1/2   1    2.0000         -0.788618
    2   1 1  -1/2   1    0.6667         -0.133536
    2   1 1  -3/2   1    1.3333         -0.133311
 TOTAL ENERGY =      -37.360474  -1016.638262

>>> Atorb.calculate_Q_density(element='H')
       0.500007     -0.343752
       0.152392     -0.354939
       0.065889     -0.357254
       0.028751     -0.357644
       0.012732     -0.357703
       0.005743     -0.357711
       0.002641     -0.357712
       0.001236     -0.357713
       0.000587     -0.357713
       0.000282     -0.357713
 N L M J S OCC.
    1   0 0  -1/2   1    1.0000         -0.229756
 TOTAL ENERGY =       -0.357713     -9.733932

static gen_input(element, **kwargs)[source]

Parameters:

elementint or str: Either the atomic number, symbol or name for a given element
outputstr, optional: File string for atomic orbital output (default: ‘at_<symbol>.i’)
ngridint, optional: Number of points in radial grid (default: 1000)
relbool, optional: Specify whether to consider relativistic effects
filenamestr, optional: Name for generated input file (default: ‘atorb’)
headerstr, optional: Comment at beginning of input file
methodstr, optional: Exchange correlation method using either 0.0=Hartree-Fock, 1.0=LDA, -alpha = xalpha (default: 0.0)
relicfloat, optional: Relic value for calculation (default: 0)
mixing_SCFfloat, optional: Self consisting field value (default: 0.5)
tolerancefloat, optional: Eigenvalue tolerance (default: 0.0005)
echfloat, optional: (default: 100)

static get_quantum_info(shell)[source]

Returns:

tuple(int, int, list[float, float], list[float, float]): (n, l, j=[l-s, l+s], occ=[ $n^-_r$ , $n^+_r$ ])

Notes

n is the principle quantum number ( $n > 0$ ).
l is the azimuthal quantum number ( $0 \leq l \leq n-1$ ).
s is the spin quantum number ( $s \pm \frac{1}{2}$ ).
j is the total angular momentum quantum numbers for both $l-s$ or $l+s$ , respectively.
$n_r$ is the occupancy of the spin-split $l-s$ and $l+s$ levels, respectively.

static replace_core_config(electron_config)[source]

Parameters:

electron_configstr: String containing the electronic configuration of the given element.

Returns:

str: A substituted string where the nobel gas core has been replaced.

Examples

>>> Atorb.replace_core_config('[Ar] 4s2')
 '1s2 2s2 2p6 3s2 3p6 4s2'

>>> Atorb.replace_core_config('[Xe] 6s2 5d1')
 '1s2 2s2 2p6 3s2 3p6 3d10 4s2 4p6 5s2 4d10 5p6 6s2 5d1'

phaseshifts.atorb.get_electron_config(element_obj)[source]: Obtain the electronic orbital configuration for the given element_obj.

phaseshifts.atorb.get_element(element: str, backend: Literal['mendeleev', 'elementy', 'periodictable'] | None = None) → object[source]: Obtain an element object for querying information using backend.

7.3.2. phaseshifts.conphas

conphas.py

Provides a native python version of the conphas (phsh3) FORTRAN program by W. Moritz, which is distributed as part of the SATLEED code (see “Barbieri/Van Hove phase shift calculation package” section) and can be found at: http://www.icts.hkbu.edu.hk/surfstructinfo/SurfStrucInfo_files/ leed/leedpack.html

The Conphas() class also provides a number of convenience functions (see docstrings below).

7.3.2.1. Examples

>>> from os.path import join
>>> from phaseshifts.conphas import Conphas
>>> con = Conphas(output_file=join('testing', 'leedph_py.d'), lmax=10)
>>> con.set_input_files([join('testing', 'ph1')])
>>> con.set_format('cleed')
>>> con.calculate()

class phaseshifts.conphas.Conphas(input_files=[], output_file=[], formatting=None, lmax=10, **kwargs)[source]

Bases: object

Class Conphas

Notes

This work is based on the original conphas (phsh3) FORTRAN program by W. Moritz, which is distributed as part of the SATLEED code (see “Barbieri/Van Hove phase shift calculation package” section) and can be found at: http://www.icts.hkbu.edu.hk/surfstructinfo/SurfStrucInfo_files/ leed/leedpack.html

__fix_path(file_path): Fix escaped characters in filepath

__set_data(data=None)

calculate()[source]

Calculates continuous phase shifts from input file(s).

Examples

>>> con = Conphas(output_file=r'testing\leedph_py.d', lmax=10)
>>> con.set_input_files([r'testing\ph1'])
>>> con.set_format('cleed')
>>> con.calculate()
 L = 0
 jump between 25.0 eV and 30.0 eV; IFAK = -1
 L = 1
 jump between 65.0 eV and 70.0 eV; IFAK = -1
 L = 2
 jump between 20.0 eV and 25.0 eV; IFAK = 1
 jump between 80.0 eV and 85.0 eV; IFAK = 0
 L = 3
 L = 4
 jump between 275.0 eV and 280.0 eV; IFAK = 1
 L = 5
 L = 6
 L = 7
 L = 8
 L = 9
 L = 10

load_data(filename)[source]

Load (discontinuous) phase shift data from file

Parameters:

filestr: Path to phase shift file.

Returns:

tuple: (double, double, int, int, ndarray): (initial_energy, energy_step, n_phases, lmf, data)

Notes

initial_energy is the starting energy of the phase shifts.
energy_step is the change in energy between consecutive values.
n_phases is the number of phase shifts contained in the file.
lmf is the maximum azimuthal quantum number considered.
data is a (2 x n_phases) array containing the phase shift data.

read_datafile(filename)[source]

Read in discontinuous phase shift file

Parameters:

filenamestr: The path to the discontinuous phase shift file

set_format(formatting=None)[source]

Set appropriate format from available options

Parameters:

formatstr, optional: The format identifier for different packages; can be ‘cleed’ or None.

set_input_files(input_files=[])[source]: set list of input filenames

set_lmax(lmax)[source]

Set max orbital angular momentum (azimuthal quantum number)

Parameters:

lmaxint: Maximum azimuthal quantum number to be considered in calculations.

set_output_file(output_file)[source]: set output filename

static split_phasout(filename, output_filenames=[])[source]: split phasout input file into separate files

7.3.3. phaseshifts.elements

Properties of the chemical elements.

Each chemical element is represented as an object instance. Physicochemical and descriptive properties of the elements are stored as instance attributes.

Author:: Christoph Gohlke
Version:: 2013.03.18

7.3.3.1. Requirements

CPython 2.7, 3.2 or 3.3

7.3.3.2. References

7.3.3.3. Examples

>>> from elements import ELEMENTS
>>> len(ELEMENTS)
109
>>> str(ELEMENTS[109])
'Meitnerium'
>>> ele = ELEMENTS['C']
>>> ele.number, ele.symbol, ele.name, ele.eleconfig
(6, 'C', 'Carbon', '[He] 2s2 2p2')
>>> ele.eleconfig_dict
{(1, 's'): 2, (2, 'p'): 2, (2, 's'): 2}
>>> sum(ele.mass for ele in ELEMENTS)
14659.1115599
>>> for ele in ELEMENTS:
...     ele.validate()
...     ele = eval(repr(ele))

7. phaseshifts API

7.1. Package Contents

7.2. Subpackages

7.3. Submodules

7.3.1. phaseshifts.atorb

7.3.2. phaseshifts.conphas

7.3.2.1. Examples

7.3.3. phaseshifts.elements

7.3.3.1. Requirements

7.3.3.2. References

7.3.3.3. Examples

7.3.4. phaseshifts.leed

7.3.5. phaseshifts.model

7.3.6. phaseshifts.phsh