latticeinputs package¶

latticeinputs.batch module¶

Created on Wed Dec 3 15:09:24 2014

@author: Matti Ropo @author: Henrik Levämäki

class latticeinputs.batch.Batch(jobname_lat=None, lat=None, runtime=None, latpath=None, EMTOdir=None, runBMDL=None, runKSTR=None, runKSTR2=None, runSHAPE=None, kappaw=None, kappalen=None, slurm_options=None, account=None)[source]¶

Bases: object

Creates a batch script for running BMDL, KSTR and SHAPE calculations

This class is used to to create batch scripts for a supercomputer environment (EMTO 5.8). !!! Currently only SLURM is supported. !!!

Parameters:	jobname_lat – (Default value = None) lat – (Default value = None) runtime – (Default value = None) latpath – (Default value = None) EMTOdir – (Default value = None) runBMDL – (Default value = None) runKSTR – (Default value = None) runKSTR2 – (Default value = None) runSHAPE – (Default value = None) kappaw – (Default value = None) kappalen – (Default value = None)
Returns:	None
Return type:	None

check_input_file()[source]¶

Perform various checks on the class data to: make sure that all necessary data exists before we attempt to write the input file to disk

Returns:
Return type:

output()[source]¶

(self) -> (str)

Output first part of the kgrn input file in formated string

Returns:
Return type:

set_values(key, value)[source]¶

Parameters:	key – value –
Returns:
Return type:

write_input_file(folder=None)[source]¶

(self,str) ->(None)

Save batch input data to file named filename

Parameters:	folder – (Default value = None)
Returns:
Return type:

latticeinputs.bmdl module¶

Created on Wed Dec 3 15:09:24 2014

@author: Matti Ropo @author: Henrik Levämäki

class latticeinputs.bmdl.Bmdl(jobname_lat=None, lat=None, latparams=None, latvectors=None, basis=None, msgl=None, nprn=None, bmdl_nl=None, lamda=None, amax=None, bmax=None, nqr2=None, ca=None)[source]¶

Bases: object

Contains information about BMDL input files for EMTO 5.8 program.

Parameters:	jobname_lat – (Default value = None) lat – (Default value = None) latparams – (Default value = None) latvectors – (Default value = None) basis – (Default value = None) msgl – (Default value = None) nprn – (Default value = None) bmdl_nl – (Default value = None) lamda – (Default value = None) amax – (Default value = None) bmax – (Default value = None) nqr2 – (Default value = None) ca (float) – hcp c/a ratio (Default value = None)
Returns:	None
Return type:	None

check_input_file()[source]¶

Perform various checks on the class data.

Makes sure that all necessary data exists before we attempt to write the input file to disk.

Returns:	None
Return type:	None

output()[source]¶

Outputs BMDL input file as a formatted string

Creates a long string containing the batch job script which will later be written on disk.

Returns:	batch script input file
Return type:	str

set_values(key, value)[source]¶

Parameters:	key – value –
Returns:
Return type:

write_input_file(folder=None)[source]¶

Save BMDL input data to file named by self.jobname_lat

Parameters:	folder – (Default value = None)
Returns:
Return type:

latticeinputs.kstr module¶

Created on Wed Dec 3 15:00:14 2014

@author: Matti Ropo @author: Henrik Levämäki

class latticeinputs.kstr.Kstr(jobname_lat=None, lat=None, latparams=None, ca=None, latvectors=None, basis=None, kappaw=None, dmax=None, msgl=None, nprn=None, lamda=None, amax=None, bmax=None, nqr2=None, mode=None, store=None, high=None, kstr_nl=None, nlh=None, nlw=None, nder=None, itrans=None, rwats=None, nghbp=None, awIQ=None, numvec_target=None)[source]¶

Bases: object

Contains information about KSTR input files for EMTO 5.8 program

Parameters:	jobname_lat – (Default value = None) lat – (Default value = None) latparams – (Default value = None) ca – (Default value = None) latvectors – (Default value = None) basis – (Default value = None) kappaw – (Default value = None) dmax – (Default value = None) msgl – (Default value = None) nprn – (Default value = None) lamda – (Default value = None) amax – (Default value = None) bmax – (Default value = None) nqr2 – (Default value = None) mode – (Default value = None) store – (Default value = None) high – (Default value = None) kstr_nl – (Default value = None) nlh – (Default value = None) nlw – (Default value = None) nder – (Default value = None) itrans – (Default value = None) rwats – (Default value = None) nghbp – (Default value = None) awIQ – (Default value = None)
Returns:	None
Return type:	None

check_input_file()[source]¶

Perform various checks on the class data.

Checking function to make sure that all necessary data exists before we attempt to write the input file to disk.

Returns:	None
Return type:	None

compute_num_of_vecs(prims, basis, nghbp, dmax)[source]¶: Computes the number of vectors for a given dmax value.

finalize()[source]¶: Re-initializes input parameters.

generate_prims(angles)[source]¶: Generates the primitive lattice vectors from the angle and Bravais-lattice type information.

optimize_dmax(prims, basis)[source]¶: Calculates the best possible dmax value, which gives the closest number of vectors given some target value (which is typically 80-90).

output(index)[source]¶

Outputs KSTR input file as a formatted string.

Parameters:	index –
Returns:	KSTR input file string
Return type:	str

set_values(key, value)[source]¶

Set input parameter values.

Parameters:	key – value –
Returns:	None
Return type:	None

write_input_file(folder=None)[source]¶

Save KSTR input data to file named filename.

Parameters:	folder – (Default value = None)
Returns:	None
Return type:	None

latticeinputs.latticeinputs module¶

Created on Wed Dec 3 14:25:06 2014

@author: Matti Ropo @author: Henrik Levämäki

class latticeinputs.latticeinputs.Latticeinputs[source]¶

Bases: object

Class which is used to communicate with the Bmdl, Kstr and Shape classes.

Returns:	None
Return type:	None

basis_transform(basis, matrix)[source]¶

Calculates a basis vector transform given by the transformation matrix.

Parameters:	basis (np.array) – Basis vectors matrix (np.array) – Transformation matrix

distortion(lat=None, dist=None, ca=None, index=None, deltas=None, dmaxs=None, relax=True, relax_index=None, basis=None)[source]¶

A function which sets various class data to create distorted lattice structures.

Distorted lattices are used to calculate elastic constants. An integer index is used to specify for which delta and dmax value we want to generate the distortion input file data.

Default naming convention for the structure files:

bcc bco	=	bcco
bcc fco	=	bccm
fcc bco	=	fccm
fcc fco	=	fcco

lat	Original undistorted lattice
dist	Which distortion we want to calculate. Possible values: ‘ortho’ or ‘mono’ for lat=’bcc’, ‘fcc’ or ‘hcp’.
ca	c over a for hcp structures.
index	Index specifying an element in the delta array. Possible values: 0,1,2,3,4 or 5. 0 = No distortion.
delta	Array of displacement values. Optional, default value is good enough almost always (if not always).
dmax	Array of ‘dmax’ values for KSTR. They have to be chosen in such fashion so as to keep the number of lattice vectors constant (or as close to a constant as possible) for all of the distorted lattices. Optional, only needed when a custom delta array is used.

Parameters:	lat (str) – The original, undistorted lattice (Default value = None) dist (str) – The type of distortion (Default value = None) ca (float) – hcp c/a ratio (Default value = None) index (int) – Index for selecting a delta and dmax from the arrays (Default value = None) deltas (np.array(float)) – List of delta values (Default value = None) dmaxs (np.array(float)) – List of dmax values (Default value = None)
Returns:	None
Return type:	None

set_values(**kwargs)[source]¶

Passes various input parameters down to the Kgrn and Kfcd classes.

Parameters:	**kwargs –
Returns:
Return type:

write_structure_input_files(jobname_lat=None, lat=None, folder=None, **kwargs)[source]¶

For a given lattice type, this function writes the corresponding structure input files into a given folder

Parameters:	jobname_lat (str) – Name of the job lat (str) – Name of the lattice folder (str) – Name of the folder

latticeinputs.shape module¶

Created on Wed Dec 3 15:10:00 2014

@author: Matti Ropo @author: Henrik Levämäki

class latticeinputs.shape.Shape(jobname_lat=None, lat=None, lmax=None, nsr=None, nfi=None, ivef=None, msgl=None, nprn=None)[source]¶

Bases: object

Contains information about SHAPE input files for EMTO 5.8 program.

Parameters:	jobname_lat – (Default value = None) lat – (Default value = None) lmax – (Default value = None) nsr – (Default value = None) nfi – (Default value = None) ivef – (Default value = None) msgl – (Default value = None) nprn – (Default value = None)
Returns:
Return type:

check_input_file()[source]¶

Perform various checks on the class data to: make sure that all necessary data exists before we attempt to write the input file to disk

Returns:
Return type:

output()[source]¶

Output SHAPE input file in formatted string.

Returns:	SHAPE input file as a string.
Return type:	str

set_values(key, value)[source]¶

Parameters:	key – value –
Returns:
Return type:

write_input_file(folder=None)[source]¶

Save SHAPE input data to file named filename

Parameters:	folder – directory to write (Default value = None)
Returns:
Return type: