schrodinger.application.matsci.espresso.utils module¶

class schrodinger.application.matsci.espresso.utils.MagElement(mag, hubb_u, hubb_j0, zval)¶

Bases: tuple

hubb_j0¶: Alias for field number 2

hubb_u¶: Alias for field number 1

mag¶: Alias for field number 0

zval¶: Alias for field number 3

schrodinger.application.matsci.espresso.utils.get_null_mag_element()¶

class schrodinger.application.matsci.espresso.utils.PseudoData(element, ecutwfc, ecutrho, zval, nwfc, nbeta, pp_type, is_fully_rel, dft_functional, has_gipaw)¶

Bases: tuple

dft_functional¶: Alias for field number 8

ecutrho¶: Alias for field number 2

ecutwfc¶: Alias for field number 1

element¶: Alias for field number 0

has_gipaw¶: Alias for field number 9

is_fully_rel¶: Alias for field number 7

nbeta¶: Alias for field number 5

nwfc¶: Alias for field number 4

pp_type¶: Alias for field number 6

zval¶: Alias for field number 3

class schrodinger.application.matsci.espresso.utils.PPSpecies(ecutwfc, ecutrho, zval, basepath)¶

Bases: tuple

basepath¶: Alias for field number 3

ecutrho¶: Alias for field number 1

ecutwfc¶: Alias for field number 0

zval¶: Alias for field number 2

schrodinger.application.matsci.espresso.utils.get_shell_runner()¶

Get path to the shell runner script.

Return type: bool, str
Returns: Whether runner has been found. If true, path to the runner otherwise error message

class schrodinger.application.matsci.espresso.utils.ArgumentParserNoExit(prog=None, usage=None, description=None, epilog=None, parents=[], formatter_class=<class 'argparse.HelpFormatter'>, prefix_chars='-', fromfile_prefix_chars=None, argument_default=None, conflict_handler='error', add_help=True, allow_abbrev=True, exit_on_error=True)¶

Bases: argparse.ArgumentParser

Subclass that raises instead of exiting on error.

error(message)¶: From python docs: If you override this in a subclass, it should not return – it should either exit or raise an exception.

schrodinger.application.matsci.espresso.utils.add_qe_parallel_parser_arguments(parser)¶

Add QE parallel arguments to the parser.

Parameters: parser (argparse.ArgumentParser) – The parser to add arguments to

schrodinger.application.matsci.espresso.utils.get_pkeywords(options, ncpus)¶

Validate and get string of parallel keywords for QE binaries (pw.x, etc.).

Parameters

options (argparse Namespace object) – The input options
ncpus (int) – Number of total requested CPUs

Return type

bool, str or list

Returns

If converted successfully, True and a list of [keyword, value] are returned, otherwise, False and error message are returned

schrodinger.application.matsci.espresso.utils.get_mag_hubbu(atom, decimals=10)¶

Get starting magnetization and Hubbard U parameters from atom property. If not present, return the default.

Parameters

atom (schrodinger.structure._StructureAtom) – Atom from which values are taken
decimals (int) – Number of decimals to round to

Return type

MagElement namedtuple

Returns

Tuple of starting magnetization and Hubbard parameters

schrodinger.application.matsci.espresso.utils.has_hubbard(struct)¶

Check if input structure has at least one atom with Hubbard U set.

Parameters: struct (structure.Structure) – Input structure
Return bool: Whether at least one atom has Hubbard U set

schrodinger.application.matsci.espresso.utils.set_mag_hubbu(atom, mag_element)¶

Set starting magnetization and Hubbard U parameters in atom property.

Parameters

atom (schrodinger.structure._StructureAtom) – Atom for which values are set
mag_element (MagElement namedtuple) – Tuple of starting magnetization and Hubbard parameters

schrodinger.application.matsci.espresso.utils.sync_pbc(struct, lattice_params=None, chorus_params=None, prioritize_cparams=False)¶

Sync PBC properties in place (without creating a new structure) for struct. If all PBC properties are absent (both chorus and PDB) return False. It is possible to provide new lattice or chorus parameters and to prioritize one of the sets.

Type

schrodinger.structure.Structure

Param

Structure to be modified

Parameters

lattice_params (list or numpy.array or None) – contains the a, b, c, alpha, beta, and gamma lattice parameters or None. These will be used instead of ones possibly obtained from the struct
chorus_params (list or numpy.array or None) – contains the nine chorus properties, i.e. ax, ay, az, bx, …, cz or None. These will be used instead of ones possibly obtained from the struct

Param

Prioritize chorus params over lattice params if True. If False, lattice params have priority

Return type

bool

Returns

True on syncing success, False if both sets were not provided or empty

schrodinger.application.matsci.espresso.utils.get_mpircores(from_environ_only=False)¶

Get -MPICORES flag value from SCHRODINGER_COMMANDLINE environment variable. If not found, return 1.

Return type: int
Returns: MPICORES value or 1 (if not defined)

schrodinger.application.matsci.espresso.utils.get_gpu_qarg()¶

Get QE GPU QARG from the environment.

Return type: str
Returns: QE GPU QARG. Empty string if not set

schrodinger.application.matsci.espresso.utils.get_element(element)¶

Get element name with the removed digits from atom type. Those might be present to due starting magnetization.

Parameters: element (str) – Element
Return type: str
Returns: Element without digits

schrodinger.application.matsci.espresso.utils.copy_atom_constr(src_atom, dest_atom)¶

Copy Cartesian atomic constraints (if any) from source atom to destination atom.

Parameters

src_atom (structure._StructureAtom) – Source atom
dest_atom (structure._StructureAtom) – Destination atom

schrodinger.application.matsci.espresso.utils.set_atom_cart_constr(atom, constr)¶

schrodinger.application.matsci.espresso.utils.set_job_builder_opts(job_builder, cfg_fn=None, add_pps=False)¶

Set options to job builder.

Parameters

job_builder (launchapi.JobSpecificationArgsBuilder) – Job builder to update
cfg_fn (str) – Config file to set as input
add_pps (bool) – Whether to add pseudopotential files

schrodinger.application.matsci.espresso.utils.struct2spglib(struct)¶

Given a structure, return a spglib cell.

Parameters: struct (structure.Structure) – Input structure
Return type: numpy.array, numpy.array, list
Returns: Lattice vectors, fractional coordinates, atomic numbers

class schrodinger.application.matsci.espresso.utils.PPHeaderHTMLParser(*args, **kwargs)¶

Bases: html.parser.HTMLParser

Parse and store pp_header tag attributes.

PP_HEADER_TAG = 'pp_header'¶

__init__(*args, **kwargs)¶: Initialize object. See parent class for documentation.

handle_starttag(tag, attrs)¶: Save PP_HEADER attributes in dictionary.

class schrodinger.application.matsci.espresso.utils.UPFParser(path, file_fh=None, binary=False)¶

Bases: object

Class that handles UPF parsing.

PP_TYPE_NC = 'NC'¶

PP_TYPE_PAW = 'PAW'¶

PP_TYPES = ('1/r', 'US', 'NC', 'PAW')¶

FULLY_REL = 'full'¶

UPF2_TRUE = ['T']¶

__init__(path, file_fh=None, binary=False)¶

Initialize UPFParser.

Parameters: path (str) – Path to the UPF file

getPseudo()¶: Return a copy of the pseudo data.

class schrodinger.application.matsci.espresso.utils.HighSymmetryKPath(spg_symbol, pbc, is_2d=False)¶

Bases: object

Based on symmetry/bandstructure.py :: HighSymmKpath (MIT license)

This class looks for path along high symmetry lines in the Brillouin Zone. It is based on Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure calculations: Challenges and tools. Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010

TWOD = '_2D'¶

__init__(spg_symbol, pbc, is_2d=False)¶

Initialize kpath class. self.kpath will contain ‘edge’ points.

Parameters

spg_symbol (str) – Space group symbol
pbc (infrastructure.PBC) – PBC object
struct (structure.Structure) – Structure that has space group or unit cell data
is_2d (bool) – Whether to build K-point path for 2D/ESM calcs

cubic()¶

Generate ‘edge’ k-points for the cubic lattice.

Return type: dict
Returns: keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

fcc()¶

Generate ‘edge’ k-points for the FCC cubic lattice.

Return type: dict
Returns: keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

bcc()¶

Generate ‘edge’ k-points for the BCC cubic lattice.

Return type: dict
Returns: keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

tet()¶

Generate ‘edge’ k-points for the tetrahedral lattice.

Return type: dict
Returns: keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

bctet1(c, a)¶

Generate ‘edge’ k-points for the tetrahedral lattice with I setting.

Parameters

c (float) – C length
a (float) – A length

Return type

dict

Returns

keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

bctet2(c, a)¶

Generate ‘edge’ k-points for the tetrahedral lattice with I setting.

Parameters

c (float) – C length
a (float) – A length

Return type

dict

Returns

keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

orc()¶

Generate ‘edge’ k-points for the orthorhombic lattice.

Return type: dict
Returns: keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

orcf1(a, b, c)¶

Generate ‘edge’ k-points for the orthorhombic lattice with F setting.

Parameters

a (float) – A length
b (float) – B length
c (float) – C length

Return type

dict

Returns

keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

orcf2(a, b, c)¶

Generate ‘edge’ k-points for the orthorhombic lattice with F setting.

Parameters

a (float) – A length
b (float) – B length
c (float) – C length

Return type

dict

Returns

keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

orcf3(a, b, c)¶

Generate ‘edge’ k-points for the orthorhombic lattice with F setting.

Parameters

a (float) – A length
b (float) – B length
c (float) – C length

Return type

dict

Returns

keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

orci(a, b, c)¶

Generate ‘edge’ k-points for the orthorhombic lattice with I setting.

Parameters

a (float) – A length
b (float) – B length
c (float) – C length

Return type

dict

Returns

keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

orcc(a, b, c)¶

Generate ‘edge’ k-points for the orthorhombic lattice with C setting.

Parameters

a (float) – A length
b (float) – B length
c (float) – C length

Return type

dict

Returns

keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

hex(is_2d=False)¶

Generate ‘edge’ k-points for the hexagonal lattice.

Parameters: is_2d (bool) – Whether to return 2D path
Return type: dict
Returns: keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ - a list of labels from the ‘kpoints’.

rhl1(alpha)¶

Generate ‘edge’ k-points for the rhombohedral lattice with alpha < 90.

Parameters: alpha (float) – Alpha cell angle in radians
Return type: dict
Returns: keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

rhl2(alpha)¶

Generate ‘edge’ k-points for the rhombohedral lattice with alpha > 90.

Parameters: alpha (float) – Alpha cell angle in radians
Return type: dict
Returns: keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

mcl(b, c, beta)¶

Generate ‘edge’ k-points for the monoclinic lattice.

Parameters

b (float) – B length
c (float) – C length
beta (float) – Beta cell angle in radians

Return type

dict

Returns

keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

mclc1(a, b, c, alpha)¶

Generate ‘edge’ k-points for the monoclinic lattice with C setting.

Parameters

a (float) – A length
b (float) – B length
c (float) – C length
alpha (float) – Alpha cell angle in radians

Return type

dict

Returns

keys: ‘kpoints’ is a dict with labels as keys and coordinates as values, ‘path’ is a list of labels from the ‘kpoints’ dict.

tria(is_2d)¶

class schrodinger.application.matsci.espresso.utils.MemoryEstimator(vecs, ecutwfc, ecutrho, nproc, nks, nspin, nbnd, ntyp, nmix, lscf)¶

Bases: object

Class to estimate RAM memory for a PW (QE) job.

COMPLEX_SIZE = 16.0¶

REAL_SIZE = 8.0¶

INT_SIZE = 4.0¶

MBYTE = 1048576.0¶

NFFTX = 2049¶

__init__(vecs, ecutwfc, ecutrho, nproc, nks, nspin, nbnd, ntyp, nmix, lscf)¶

Initialize MemoryEstimator object and set several attributes.

Parameters

vecs (3 list of 3 floats) – Lattice vectors
ecutwfc (float) – Wavefunction cutoff (Ry)
ecutrho (float) – Density cutoff (Ry)
nproc (int) – Number of processors
nks (int) – Number of k-points
nspin (int) – 1 for closed-shell, 2 for spin-polarized
nbnd (int) – Number of bands
ntyp (int) – Number of atom types
nmix (int) – Beta mixing
lscf (bool) – True if the calculation is scf/relax, False if it is nscf

realSpaceGridInit(at_vecs, bg_vecs, gcutm)¶

Gets minimal 3D real-space FFT grid.

Parameters

at_vecs (3 x 3 table of floats) – Lattice vectors in the units of alat
bg_vecs (3 x 3 table of floats) – Reciprocal lattice vectors in the units of 1/alat
gctum – Radius of the sphere to fit the FFT grid

Return type

list of 3 floats

Returns

FFT grid sizes

getGoodFFTDim(fft_dim)¶

Get a good FFT dimension.

Parameters: fft_dim (int) – FFT dimension
Return type: int
Returns: Good FFT dimension, if exists

isGoodDim(fft_dim)¶

Check if FFT dimension is good.

Parameters: fft_dim (int) – FFT dimension

:rtype bool :return: True, if FFT dimension is good, False otherwise

class schrodinger.application.matsci.espresso.utils.MagSpecies(struct=None)¶

Bases: object

Class that defines species with starting magnetization.

__init__(struct=None)¶: Initialize MagSpecies class.

createUniqueElement(element, mag_element)¶

Fill self.data dict. Keys of the self.data are elements. Values are dicts with magnetization as key and unique element as value. Unique element is just the atomic symbol plus (if element has more than one magnetization value) a unique integer. Example: {‘C’: {0.0: ‘C’}, ‘H’: {0.0: ‘H’, 0.1: ‘H1’}}

self.species is a dict where unique elements are keys and elements are values. Example (based on the example above): {‘C’: ‘C’, ‘H’: ‘H’, ‘H1’: ‘H’}

Parameters

element (str) – Element
mag (float) – Starting magnetization
hubb_u (float) – Hubbard U parameter

Return type

str

Returns

Unique element

getMag(element, unique_element)¶

Get magnetization given element and unique element values.

Parameters

element (str) – Element
unique_element (str) – Unique element

Return type

tuple

Returns

Starting magnetization and Hubbard U

Raises

ValueError – If element, unique_element combination is not found

fromStructure(struct)¶

Set data from the structure.

Parameters: struct (structure.Structure) – Input structure