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

This module provides a high-level Python interface for generating input files and executing atomic structure calculations using the ‘atorb’ program (part of the Barbieri/Van Hove LEED phase shift package).

The core functionality allows users to: 1. Determine the ground-state electronic configuration of elements. 2. Construct formatted input files for the atorb Fortran solver. 3. Calculate radial charge densities \(\rho(r)\) by solving the

Dirac-Fock (relativistic) or Hartree-Fock (non-relativistic) equations for a free atom.

These charge densities serve as the starting potential for calculating scattering phase shifts in Low-Energy Electron Diffraction (LEED) and photoelectron diffraction experiments.

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)

Bases: object

Wrapper for the atorb atomic structure solver.

This class encapsulates the logic for interacting with the Barbieri/Van Hove atorb program. It calculates atomic orbitals and radial charge densities on a logarithmic grid.

The solver numerically integrates the radial Dirac equation (or Schrödinger equation if relativistic effects are disabled) to find the eigenvalues and eigenfunctions of the bound electrons.

Notes

The Breit interaction is neglected, which is a valid approximation for valence states dominating the scattering potential in LEED.

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)

Execute the atomic structure calculation to obtain radial charge densities.

This method serves as the primary driver for the ‘atorb’ Fortran routine. It either generates a new input file based on an element symbol or validates an existing input file, then invokes the solver (hartfock) via libphsh.

The solver computes the radial wavefunctions \(\phi_{n,l,j}(r)\) and constructs the total spherical charge density \(\rho(r)\).

Parameters:

**kwargsdict, optional

Keyword arguments passed to gen_input() if element is provided.

elementstr or int

Target element. If provided, an input file is generated on-the-fly.

inputstr

Path to an existing atorb input file. Ignored if element is provided.

output_dirstr

Directory where the output file (containing phase shifts or charge densities) should be placed. Defaults to current directory.

Returns:

str

Path to the output file containing the calculated atomic charge densities.

Raises:

ValueError

If neither element nor input is specified.

IOError

If the output directory cannot be created or accessed.

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)

Generate the input file for the ‘atorb’ atomic structure solver.

This method constructs a formatted input file required by the Barbieri/Van Hove ‘atorb’ program (encapsulated in libphsh). It determines the electronic configuration of the specified element, handles noble gas core expansion, and sets up the radial grid and exchange-correlation parameters for the Dirac-Fock calculation.

Parameters:

elementstr or int

The chemical symbol (e.g., ‘Cu’) or atomic number (e.g., 29) of the target element.

**kwargsdict, optional

Configuration options for the calculation:

outputstr

Filename for the resulting charge density output (default: ‘at_<symbol>.i’).

ngridint

Number of points in the logarithmic radial grid (default: 1000). Higher values provide better numerical resolution near the nucleus.

relint or bool

Relativistic flag (default: 1). 1 (or True): Solve Dirac equations (includes spin-orbit coupling). 0 (or False): Solve non-relativistic Schrödinger equations.

filenamestr

Filename for the generated input text file (default: ‘atorb_<symbol>.txt’).

headerstr

Comment line at the top of the input file (default: auto-generated).

methodstr

Exchange-correlation potential approximation (default: ‘0.d0’ for Hartree-Fock). ‘0.d0’: Hartree-Fock (HF). ‘1.d0’: Local Density Approximation (LDA). ‘-alpha’: X-alpha method (requires providing alpha value).

relicfloat

Mixing parameter for the self-consistency cycle (default: 0.0).

mixing_SCFfloat

Mixing parameter for Self-Consistent Field convergence (default: 0.5).

tolerancefloat

Convergence tolerance for orbital eigenvalues (default: 0.0005 Hartrees).

echint

Parameter for the exchange potential (default: 100).

Returns:

str

The path to the generated input file.

Notes

The resulting file allows libphsh to solve the radial Dirac equation:

\[H \Psi = E \Psi\]

where density functional theory (DFT) or Hartree-Fock approximations define the potential.

static get_quantum_info(shell)

Parse quantum numbers from a subshell string (e.g., ‘3d6’).

Decomposes a standard spectroscopic notation into the set of quantum numbers required for the radial equation solver. Handles the splitting of shells into spin-orbit coupled states (\(j = l \pm 1/2\)).

Parameters:

shellstr

Subshell string, e.g., ‘1s2’, ‘4f14’, ‘3d5’.

Returns:

tuple

(n, l, j_list, occ_list)

• n (int): Principal quantum number.

• l (int): Azimuthal quantum number.

• j_list (list[float]): Total angular momentum values \(j\) associated with this shell. For \(l > 0\), this will be [\(l-1/2\), \(l+1/2\)].

• occ_list (list[float]): Occupancy for each \(j\) level. Electrons are distributed according to statistical weight (\(2j+1\)).

Examples

For a full ‘3d10’ shell:

>>> Atorb.get_quantum_info('3d10')
(3, 2, [1.5, 2.5], [4.0, 6.0])

Here, \(n=3\), \(l=2\). The states are \(d_{3/2}\) (occupancy 4) and \(d_{5/2}\) (occupancy 6).

static replace_core_config(electron_config)

Expand noble gas core abbreviations into full orbital strings.

The atorb solver requires explicit definitions for all orbitals starting from 1s. This function replaces ‘[Ar]’, ‘[Xe]’, etc., with their constituent subshells.

Parameters:

electron_configstr

Electronic configuration string, potentially containing noble gas cores (e.g., ‘[Ar] 4s2’).

Returns:

str

The fully expanded configuration string.

Examples

>>> Atorb.replace_core_config('[He] 2s1')
'1s2 2s1'

static validate_input_file(input_path)

Validate a generated or user-supplied atorb input file.

Parses the input file using the phaseshifts.validation.atorb logic to ensure it meets the strict formatting and physical requirements of the solver.

Parameters:

input_pathstr

Path to the file to validate.

Returns:

AtorbInputModel

Parsed and validated representation of the input file.

phaseshifts.atorb.get_electron_config(element_obj)

Extract the electronic configuration string from an element object.

Retrieves the standard ground-state configuration (e.g., ‘[Ar] 4s2 3d10 4p5’) from the backend-specific element object.

Parameters:

element_objobject

The element object returned by get_element.

Returns:

str

The electronic configuration string.

phaseshifts.atorb.get_element(element: str, backend: Literal['mendeleev', 'elementy', 'periodictable'] | None = None) → object

Retrieve an element object from the specified chemical data backend.

This function abstracts the details of various chemistry libraries (mendeleev, elementy, periodictable) to provide a unified interface for accessing atomic properties like proton count (Z) and electronic configurations.

Parameters:

elementstr or int

The symbol (e.g., ‘Fe’) or atomic number (e.g., 26) of the element.

backendstr, optional

The preferred backend library to use (‘mendeleev’, ‘elementy’, ‘periodictable’). If None, tries available backends in order.

Returns:

object

An object containing element data (attributes vary by backend but usually include protons, symbol, name).

Raises:

LookupError

If the element cannot be found in any available 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, v0_params=None, **kwargs)

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)

static _chunked(sequence, size=10)

Yield successive chunks from a sequence.

_resolve_v0_params()

Resolve Rundgren inner potential parameters for ViPErLEED output.

Returns:

tuple(float, float, float, float)

c0-c3 parameters; defaults to ViPErLEED’s documented values if none are provided. Raises a ValueError if an invalid v0_params configuration is supplied.

_write_viper_output(file_handle, conpha, energy, n_phases)

Write phase shifts in ViPErLEED PHASESHIFTS format.

Parameters:

file_handleIO

Open file handle for writing.

conphalist

Continuous phase shifts per atom/site.

energylist

Energies in eV as parsed from phasout.

n_phasesint

Number of energy points to write.

calculate()

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)

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)

Read in discontinuous phase shift file

Parameters:

filenamestr

The path to the discontinuous phase shift file

set_format(formatting=None)

Set appropriate format from available options

Parameters:

formatstr, optional

The format identifier for different packages; can be ‘cleed’, ‘curve’, ‘viperleed’, or None.

set_input_files(input_files=[])

set list of input filenames

set_lmax(lmax)

Set max orbital angular momentum (azimuthal quantum number)

Parameters:

lmaxint

Maximum azimuthal quantum number to be considered in calculations.

set_output_file(output_file)

set output filename

static split_phasout(filename, output_filenames=[])

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

1. http://physics.nist.gov/PhysRefData/Compositions/

2. http://physics.nist.gov/PhysRefData/IonEnergy/tblNew.html

3. http://en.wikipedia.org/wiki/%(element.name)s

4. http://www.miranda.org/~jkominek/elements/elements.db

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))

7.3.4. phaseshifts.leed

Provides CLEED validator and Converter classes.

The CLEEDInputValidator() class provides a method for checking the input files for errors, whereas the Converter.import_CLEED() method allows importing CLEED input files as a MTZ_model class

class phaseshifts.leed.CLEEDInputValidator

Bases: object

Class for validation of CLEED input files

static is_cleed_file(filename)

Determine if file is a CLEED input file

Returns:

True

if a valid filename ending in any of .bul, .inp, .bsr, .bmin

False

otherwise

validate(filename, aoi=False)

Checks CLEED input file for errors

Parameters:

filenamestr

Path to input file. Should be *.bul , *.ctr, *.inp or *.bmin

aoibool

Check for angle of incidence parameters

class phaseshifts.leed.CSearch(model_name, leed_command=None)

Bases: object

class for csearch related data exchange

_getResults()

getIteration(iteration)

getRFactor(iteration)

getTimeStamp(iteration)

setModel(name)

sets the model name

class phaseshifts.leed.Converter

Bases: object

Convert different input into phaseshift compatible input

static _apply_superstructure(a1, a2, m1, m2)

static _build_atoms(layers, minimum_radius, lmax_global)

static _build_unitcell(data, superstructure)

static _load_structured_input(filename, yaml_loader=None)

Load structured input (JSON or YAML).

static _resolve_element(tag)

Extract element symbol from cleedpy phase_file.

static _validate_structured_input(data)

Validate cleedpy-style input if jsonschema is available.

static _vector_length(vec)

static cleedpy_to_inputs(filename, tmp_dir=None, yaml_loader=None, **kwargs)

Convert cleedpy YAML to temporary bulk/slab .i files for phase-shift generation.

Returns:

tuple(str, str, dict)

Paths to generated bulk and slab input files, plus parsed metadata.

static import_CLEED(filename, **kwargs)

Imports CLEED input file and converts model to muffin-tin input.

It assumes the following:

• the basis vectors \(a_1\), \(a_2\), & \(a_3\) are \(x\),:math:y,:math:z cartezian coordinates

• if no \(a_3\) is found, the maximum \(z\) distance between atoms multiplied by four is given.

• the unitcell is converted from cartezian to fractional coordinates

• atom sites are converted from Angstrom to Bohr units

• additional info from the phase shift filename is provided by splitting the ‘_’ chars:

  1. First string segment is element or symbol, e.g. Ni

  2. Second string segment is the oxidation (valence), e.g. +2

• lines with rm: provide the radii dictionary of the individual phase shifts, whereas lines starting with lmax: provide the lmax dictionary for individual phase shifts. Additionally, the valency can be given in lines starting with ox:. Both bulk and surface input files will be searched for these.

• if no rm: found for that species, the atomic radius is used for zero valence, otherwise the covalent radius is used.

• if no lmax values are found for the specific phase shift, then the global value will be used instead.

• if no valence values are found for the specific phase shift, then the guessed oxidation value from the phase shift filename is used instead. However, if the oxidation state cannot be parsed using the filename then a default oxidation state of zero is used.

Additional information can, however, be provided using ‘phs:’ at the start of a line within the input file and may have the following formats:

1. “phs: c <float> nh <int> nform <int> exchange <float>”

2. “phs: <phase_shift> valence <float> radius <float>”

The identifiers exchange, nform, valence and radius may be abbreviated to exc, nf, val and rad, respectively.

Information given in this manner overrides any other input.

Parameters:

filenamestr

Path to input file.

Returns:

phaseshifts.model.MTZ_model

Raises:

IOErrorfilename invalid

ValueErrorbad formatting of input

static import_cleedpy_input(filename, superstructure=True, yaml_loader=None, **kwargs)

Parse a cleedpy-style structured input file (JSON or YAML) into bulk and slab MTZ models.

Parameters:

filenamestr

Path to cleedpy YAML input.

superstructurebool, optional

If True, apply the superstructure_matrix (m1/m2) to the in-plane basis vectors to construct the surface cell. Defaults to True.

Returns:

tuple(model.MTZ_model, model.MTZ_model, dict)

(bulk_model, slab_model, metadata)

Notes

This provides a bridge from cleedpy’s YAML geometry to the Barbieri/Van Hove phase-shift workflow by constructing equivalent muffin-tin models.

7.3.5. phaseshifts.model

model.py

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

class phaseshifts.model.Atom(element, coordinates=[0.0, 0.0, 0.0], **kwargs)

Bases: object

Atom class for input into cluster model for muffin-tin potential calculations.

set_coordinates(coordinates)

set_mufftin_radius(radius)

Sets the muffin-tin radius of the atom in Angstroms.

set_valence(valency)

Sets the valency of the atom

exception phaseshifts.model.CoordinatesError(msg)

Bases: Exception

Coordinate exception to raise and log duplicate coordinates.

class phaseshifts.model.MTZ_model(unitcell, atoms, **kwargs)

Bases: Model

Muffin-tin potential Model subclass for producing input file for muffin-tin calculations in the Barbieri/Van Hove phase shift calculation package.

calculate_MTZ(mtz_string='', **kwargs)

Parameters:

atomic_filestr

The path to the atomic input file. If this is omitted the default is generate one using the MTZ_model.gen_atomic() method.

cluster_filestr

The path to the cluster input file which may be a bulk or slab model.

slabint or bool

Determines whether the MTZ calculation is for a slab model (True). The default is a bulk calculation.

outputdict

Dictionary output of ‘mtz’ - muffin-tin potential & ‘output_file’ - the path to the MTZ output file.

Returns:

output_fileslist(str)

Paths to the MTZ output file.

create_atorbs(**kwargs)

Returns:

output_filesdict

Dictionary list of atorb*.i input files for the Atorb class to calculate the charge density from.

gen_atomic(**kwargs)

Parameters:

input_dirstr

Input directory where at*.i files are kept.

input_filestuple

List of input files to generate atomic input file from.

output_filestr

The filename of the resulting atomic*.i output file, which is simply a superimposed set of the radial charge densities from the individual input files.

Returns:

output_filestr

Returns the output file path string.

Raises:

IOErrorexception

If either input directory or files do not exist.

Notes

If ‘input_files’ is not given then the default list of input files are inferred from the list of atoms in the model.

gen_input(**kwargs)

Returns:

filename on success

Raises:

CoordinatesErrorexception

if the model atoms have duplicate coordinates and the ‘pos_check’ kwarg is set to True.

get_MTZ(filename)

Retrieves muffin-tin potential from file

get_elements()

Return the unique elements in model

load_from_file(filename)

Parameters:

filenamestr

The path of the input file (e.g. cluster*.i or slab.i)

Raises:

IOErrorexception

If the file cannot be read.

TypeErrorexception

If a input line cannot be parsed correctly.

set_exchange(alpha)

Sets the alpha exchange term for muffin-tin calculation

set_nform(nform)

Sets form of muffin-tin calculation

Parameters:

nformint or str

This governs the type of calculation, where nform can be:

1. “cav” or 0 - use Cavendish method

2. “wil” or 1 - use William’s method

3. “rel” or 2 - Relativistic calculations

set_nh(nh)

Sets the nh muffin-tin zero estimation parameter

set_slab_c(c)

Examples

For Re the bulk c distance is 2.76Å, whereas a possible slab c distance could be ~10Å.

class phaseshifts.model.Model(unitcell, atoms, **kwargs)

Bases: object

Generic model class.

_nineq_atoms()

Returns:

nineq_atoms, element_dicttuple

nineq_atomsThe estimated number of inequivalent atoms based on

the valence and radius of each atom.

element_dicta dictionary of each element in the atom list where

each element contains an atom dictionary of ‘nineq_atoms’, ‘n_atoms’ and a complete ‘atom_list’

add_atom(element, position, **kwargs)

Append an Atom instance to the model

Parameters:

elementstr or int

Either an element name, symbol or atomic number.

positionlist(float) or ndarray

(1x3) array of the fractional coordinates of the atom within the unit cell in terms of the lattice vector a.

check_coordinates()

Check for duplicate coordinates of different atoms in model.

Raises:

CoordinateErrorexception

If duplicate positions found.

set_atoms(atoms)

Set the atoms for the model.

Parameters:

atomslist(Atoms)

Array of Atom instances. Entries in the list which are not of type Atom will be ignored.

Raises:

TypeErrorexception

If atoms parameter is not a list.

set_unitcell(unitcell)

Set the unitcell for the model

Parameters:

unitcellUnitcell

Instance of Unitcell class to set to model.

Raises:

TypeErrorexception

If unitcell parameter is not a Unitcell.

class phaseshifts.model.Unitcell(a, c, matrix_3x3, **kwargs)

Bases: object

Unitcell class

set_a(a)

Parameters:

a: float

The magnitude of the in-plane lattice vector in Angstroms

Notes

To retrieve a in terms of Angstroms use ‘unitcell.a’, whereas the internal parameter ‘unitcell._a’ converts a into Bohr radii (1 Bohr = 0.529Å), which is used for the muffin-tin potential calculations in libphsh (CAVPOT subroutine).

set_alpha(alpha)

set_beta(beta)

set_c(c)

Parameters:

cfloat

The magnitude of the in-plane lattice vector in Angstroms

Notes

To retrieve c in terms of Angstroms use ‘unitcell.c’, whereas the internal parameter ‘unitcell._c’ converts c into Bohr radii (1 Bohr = 0.529Å), which is used for the muffin-tin potential calculations in libphsh (CAVPOT subroutine).

set_gamma(gamma)

set_vectors(m3x3)

7.3.6. phaseshifts.phsh

phsh.py - quickly generate phase shifts

Orchestrates the full phase shift calculation workflow for LEED (Low-Energy Electron Diffraction) and related surface science applications, following the Barbieri/Van Hove methodology.

This module provides a command-line interface and Python API for generating phase shift files suitable for input into LEED-IV programs such as SATLEED and CLEED. It automates the process of: - Atomic charge density calculation (Dirac-Fock/Hartree-Fock) - Muffin-tin potential generation - Phase shift calculation (relativistic/non-relativistic) - Removal of phase discontinuities (pi-jumps) - Output formatting for LEED analysis

7.3.6.1. Scientific Context

Phase shifts are central to electron scattering theory and LEED surface structure analysis. The workflow implemented here follows the Barbieri/Van Hove package, ensuring that all physical and computational steps are performed in the correct sequence, with appropriate file formats and conventions.

7.3.6.2. References

• `Barbieri, G., & Van Hove, M. A. (1979). “Phase shift calculation package for LEED.” Surf. Sci. 90, 1-25.

  <https://doi.org/10.1016/0039-6028(79)90470-7>`_

• Moritz, W. (SATLEED code): http://www.icts.hkbu.edu.hk/surfstructinfo/SurfStrucInfo_files/leed/leedpack.html

• See also: https://phaseshifts.readthedocs.io/en/latest/phshift2007.html

7.3.6.3. Examples

phsh.py -i *.inp -b *.bul -f CLEED -S phase_dir

exception phaseshifts.phsh.CLIError(msg)

Bases: Exception

Generic exception to raise and log different fatal errors.

class phaseshifts.phsh.Wrapper(**kwargs)

Bases: object

Class for automating the Barbieri/Van Hove phase shift calculation workflow.

This class provides methods to generate phase shift files from atomic and cluster input data, handling all intermediate steps: atomic charge density, muffin-tin potential, phase shift calculation, phase-jump removal, and output formatting. It supports both Python and Fortran backends, and is compatible with SATLEED and CLEED file formats.

7. Scientific Rationale

Automating the workflow ensures reproducibility and correct sequencing of physical and computational steps, as required for LEED surface structure analysis.

References

• `Barbieri, G., & Van Hove, M. A. (1979). “Phase shift calculation package for LEED.” Surf. Sci. 90, 1-25.

<https://doi.org/10.1016/0039-6028(79)90470-7>`_

• Moritz, W. (SATLEED code): http://www.icts.hkbu.edu.hk/surfstructinfo/SurfStrucInfo_files/leed/leedpack.html

• See also: https://phaseshifts.readthedocs.io/en/latest/phshift2007.html

static _copy_files(files, dst, verbose=False)

copy list of files into destination directory

static autogen_from_input(bulk_file, slab_file, tmp_dir=None, model_name=None, **kwargs)

Generate phase shifts from slab/cluster and bulk input files, following the Barbieri/Van Hove workflow.

This method automates the full sequence described in: - `Barbieri, G., & Van Hove, M. A. (1979). “Phase shift calculation package for LEED.” Surf. Sci. 90, 1-25.

<https://doi.org/10.1016/0039-6028(79)90470-7>`_

• Moritz, W. (SATLEED code): http://www.icts.hkbu.edu.hk/surfstructinfo/SurfStrucInfo_files/leed/leedpack.html

• See also: https://phaseshifts.readthedocs.io/en/latest/phshift2007.html

Steps: 1. Atomic charge density calculation (Dirac-Fock/Hartree-Fock) 2. Muffin-tin potential generation 3. Phase shift calculation (relativistic/non-relativistic) 4. Removal of phase discontinuities (pi-jumps) 5. Output formatting for LEED analysis

Parameters:

bulk_filestr

Path to the bulk MTZ or CLEED input file.

slab_filestr

Path to the slab/cluster MTZ or CLEED input file.

tmp_dirstr, optional

Temporary directory for intermediate files.

model_namestr, optional

Name of the model.

storebool or str, optional

Whether to keep generated files and where to store them.

formatstr, optional

Output format for phase shift files (‘cleed’, ‘curve’, etc.).

rangetuple(float, float, float), optional

Energy range for phase shift calculation (start, stop, step in eV).

Returns:

output_fileslist of str

List of generated phase shift output filenames.

phaseshifts.phsh.main(argv=None)

Main command-line interface for phase shift generation.

Parses user arguments, sets up the workflow, and executes the full Barbieri/Van Hove phase shift calculation sequence. Supports options for input files, output formatting, energy range, and intermediate file management.

Parameters:

argvlist of str, optional

Command-line arguments (default: sys.argv).

Returns:

int

Exit code (0 for success).

References

• `Barbieri, G., & Van Hove, M. A. (1979). “Phase shift calculation package for LEED.” Surf. Sci. 90, 1-25.

<https://doi.org/10.1016/0039-6028(79)90470-7>`_

• Moritz, W. (SATLEED code): http://www.icts.hkbu.edu.hk/surfstructinfo/SurfStrucInfo_files/leed/leedpack.html

• See also: https://phaseshifts.readthedocs.io/en/latest/phshift2007.html

phaseshifts.phsh.required_length(nmin, nmax)

custom action to check range