emtoinputs package¶

emtoinputs.batch module¶

Created on Wed Dec 3 15:09:24 2014

@author: Matti Ropo @author: Henrik Levämäki

class emtoinputs.batch.Batch(jobname=None, runtime=None, EMTOdir=None, emtopath=None, runKGRN=None, runKFCD=None, account=None, KGRN_file_type=None, KFCD_file_type=None, slurm_options=None, parallel=None)[source]¶

Bases: object

Creates a batch script for running KGRN and KFCD calculations on a supercomputer environment (EMTO 5.8).

!!! Currently only SLURM is supported. !!!

Parameters:	jobname (str) – Name for the KGRN and KFCD jobs. This will become the first part of the input and output file names. runtime (str) – Maximum running time for the individual batch jobs. The format of this entry should be ‘xx:yy:zz’, where xx is hours, yy is minutes and zz is seconds. EMTOdir (str) – Path to the EMTO installation (Default value = ‘$HOME/EMTO5.8’) emtopath (str) – Path to the folder where the KGRN and KFCD input files are located runKGRN (boolean) – True if KGRN should be run, False if KGRN should not be run runKFCD (boolean) – True if KFCD should be run, False if KFCD should not be run
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

output()[source]¶

Output first part of the kgrn input file in formated string

Returns:	Batch job script file in the form of a long string
Return type:	str

set_values(key, value)[source]¶

Parameters:	key – value –
Returns:
Return type:

write_input_file(folder=None)[source]¶

(self,str) ->(None)

Save BMDL input data to file named filename

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

emtoinputs.emtoinputs module¶

Created on Wed Dec 3 14:25:06 2014

@author: Matti Ropo @author: Henrik Levämäki

class emtoinputs.emtoinputs.Emtoinputs[source]¶

Bases: object

Class which is used to communicate with the Kgrn and Kfcd classes.

Returns:	None
Return type:	None

set_values(**kwargs)[source]¶

Passes various input parameters down to the Kgrn and Kfcd classes

Parameters:	**kwargs – Keyword arguments
Returns:	None
Return type:	None

emtoinputs.kfcd module¶

Created on Wed Dec 3 15:05:43 2014

@author: Matti Ropo @author: Henrik Levämäki

class emtoinputs.kfcd.Kfcd(jobname=None, latname=None, latpath=None, msgl=None, nprn=None, lmaxs=None, nth=None, kfcd_nfi=None, fpot=None, ovcor=None, ubg=None, DIR001=None, DIR002=None, DIR003=None, DIR004=None, DIR006=None, sws=None, CQNA=None, KFCD_file_type=None)[source]¶

Bases: object

Handles the information and writing of kfcd file.

Parameters:	jobname – (Default value = None) latname – (Default value = None) latpath – (Default value = None) msgl – (Default value = None) nprn – (Default value = None) lmaxs – (Default value = None) nth – (Default value = None) kfcd_nfi – (Default value = None) fpot – (Default value = None) ovcor – (Default value = None) ubg – (Default value = None) DIR001 – (Default value = None) DIR002 – (Default value = None) DIR003 – (Default value = None) DIR004 – (Default value = None) DIR006 – (Default value = None) sws – (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 KFCD input file as a formatted string.

Outputs EMTO5.8 KFCD input file

Returns:	Formatted string
Return type:	str

set_values(key, value)[source]¶

Changes values of the class variables.

Parameters:	key (str) – name of the variable value (str, int or float) – value of the variable
Returns:	None
Return type:	None

write_input_file(folder=None)[source]¶

Writes input file to disk.

Save KFCD input data to file named filename.

Parameters:	folder (str) – Folder where the data will be written (Default value = None)
Returns:	None
Return type:	None

emtoinputs.kgrn module¶

Created on Wed Dec 3 14:48:25 2014

@author: Matti Ropo @author: Henrik Levämäki

class emtoinputs.kgrn.Kgrn(jobname=None, latname=None, latpath=None, ibz=None, atoms=None, concs=None, iqs=None, its=None, itas=None, qtrs=None, splts=None, fixs=None, sm_ss=None, s_wss=None, ws_wsts=None, atconf=None, sws=None, strt=None, msgl=None, expan=None, fcd=None, func=None, niter=None, nlin=None, nprn=None, ncpa=None, mode=None, frc=None, dos=None, ops=None, afm=None, crt=None, lmaxh=None, lmaxt=None, kgrn_nfi=None, fixg=None, shf=None, sofc=None, kmsh=None, nkx=None, nky=None, nkz=None, fbz=None, kmsh2=None, ibz2=None, nkx2=None, nky2=None, nkz2=None, zmsh=None, nz1=None, nz2=None, nz3=None, nres=None, nzd=None, depth=None, imagz=None, eps=None, elim=None, amix=None, efmix=None, vmtz=None, mmom=None, tole=None, tolef=None, tolcpa=None, tfermi=None, nsws=None, dsws=None, alpcpa=None, efgs=None, hx=None, nx=None, nz0=None, stmp=None, iex=None, dirac_np=None, nes=None, dirac_niter=None, iwat=None, nprna=None, vmix=None, rwat=None, rmax=None, dx=None, dr1=None, test=None, teste=None, testy=None, testv=None, FOR001=None, DIR002=None, DIR003=None, FOR004=None, DIR006=None, DIR009=None, DIR010=None, DIR011=None, ncpu=None, CQNA=None, KGRN_file_type=None, setups=None)[source]¶

Bases: object

A class which contains all the KGRN input file related information.

Parameters:	jobname – (Default value = None) latname – (Default value = None) latpath – (Default value = None) ibz – (Default value = None) atoms – (Default value = None) concs – (Default value = None) iqs – (Default value = None) its – (Default value = None) itas – (Default value = None) qtrs – (Default value = None) splts – (Default value = None) fixs – (Default value = None) sm_ss – (Default value = None) s_wss – (Default value = None) ws_wsts – (Default value = None) atconf – (Default value = None) sws – (Default value = None) strt – (Default value = None) msgl – (Default value = None) expan – (Default value = None) fcd – (Default value = None) func – (Default value = None) niter – (Default value = None) nlin – (Default value = None) nprn – (Default value = None) ncpa – (Default value = None) mode – (Default value = None) frc – (Default value = None) dos – (Default value = None) ops – (Default value = None) afm – (Default value = None) crt – (Default value = None) lmaxh – (Default value = None) lmaxt – (Default value = None) kgrn_nfi – (Default value = None) fixg – (Default value = None) shf – (Default value = None) sofc – (Default value = None) kmsh – (Default value = None) nkx – (Default value = None) nky – (Default value = None) nkz – (Default value = None) fbz – (Default value = None) kmsh2 – (Default value = None) ibz2 – (Default value = None) nkx2 – (Default value = None) nky2 – (Default value = None) nkz2 – (Default value = None) zmsh – (Default value = None) nz1 – (Default value = None) nz2 – (Default value = None) nz3 – (Default value = None) nres – (Default value = None) nzd – (Default value = None) depth – (Default value = None) imagz – (Default value = None) eps – (Default value = None) elim – (Default value = None) amix – (Default value = None) efmix – (Default value = None) vmtz – (Default value = None) mmom – (Default value = None) tole – (Default value = None) tolef – (Default value = None) tolcpa – (Default value = None) tfermi – (Default value = None) nsws – (Default value = None) dsws – (Default value = None) alpcpa – (Default value = None) efgs – (Default value = None) hx – (Default value = None) nx – (Default value = None) nz0 – (Default value = None) stmp – (Default value = None) iex – (Default value = None) dirac_np – (Default value = None) nes – (Default value = None) dirac_niter – (Default value = None) iwat – (Default value = None) nprna – (Default value = None) vmix – (Default value = None) rwat – (Default value = None) rmax – (Default value = None) dx – (Default value = None) dr1 – (Default value = None) test – (Default value = None) teste – (Default value = None) testy – (Default value = None) testv – (Default value = None) FOR001 – (Default value = None) DIR002 – (Default value = None) DIR003 – (Default value = None) FOR004 – (Default value = None) DIR006 – (Default value = None) DIR009 – (Default value = None) DIR010 – (Default value = None) DIR011 – (Default value = None)
Returns:	None
Return type:	None

AtomOutput()[source]¶

(self) -> str

Output of atomic lines in kgrn format

Returns:	A atomic lines for kgrn input
Return type:	str

Atomline(atom, iq, it, ita, conc, Sm_s, S_ws, WS_wst, qtr, splt, fix)[source]¶

Prints atomic line in kgrn format

Parameters:	atom – iq – it – ita – conc – Sm_s – S_ws – WS_wst – qtr – splt – fix –
Returns:
Return type:

aconflines(atype)[source]¶

Returns string containing electronic configuration lines

Contains the database of atomic orbital configuration information which is present in atomic block of the KGRN input file.

Parameters:	atype (str) – Name of the element in the periodic table
Returns:	A formatted string corresponding to the parameter atype
Return type:	str

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

create_atconf()[source]¶

Constructs the self.atconf list out of the atomic information.

Returns:	None
Return type:	None

create_atomblock()[source]¶

Constructs the KGRN input file atomblock if all the necessary parameters are present.

Returns:	None
Return type:	None

output()[source]¶

(self) -> (str)

Output first part of the kgrn input file in formated string

Returns:	A first part of the kgrn input file
Return type:	str

set_values(key, value)[source]¶

:param value:, so we have to use .any() :type value: :returns: :rtype:

write_input_file(folder=None)[source]¶

(self,str) ->(None)

Save KGRN input data to file named filename

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