In this lesson we calculate and plot both band structure and dos for Bi2Se3

In [1]:

    

from siman import header
from siman.SSHTools import SSHTools
from siman.calc_manage import add_loop, res_loop
from siman.database import write_database, read_database
from siman.set_functions import read_vasp_sets
from siman.dos_functions import plot_dos
from siman.bands import plot_bands
%matplotlib inline
read_database() # read database if exist
header.PATH2PROJECT    = 'topologic' # path to project relative to your home folder on cluster
header.PATH2POTENTIALS = '/home/aksenov/scientific_projects/PAW_PBE_VASP' #path to VASP POTENTIALS
header.varset['static'].potdir = {83:'Bi_pv', 34:'Se'} #subfolders with required potentials
header.ssh_object = SSHTools()
header.ssh_object.setup(user="aksenov",host="10.30.16.62",pkey="/home/aksenov/.ssh/id_rsa")


    

    




/home/aksenov/simanrc.py was read

In [2]:

    

#Creating new sets for DOS and Bands
dos_pack = {'NSW':0, 'LORBIT':11, 
            'ISMEAR':-5, 'LAECHG':'.TRUE.', 
            'EMIN':-10, 'EMAX':14, 
            'NEDOS':2000, 'KSPACING':0.15, 
            'savefile':'d'}
read_vasp_sets([('dos', 'static',dos_pack, 'override')]) #new set 'dos' from 'static'

band_pack = {'ICHARG':11, 'LORBIT':11, 
             'k_band_structure':[40, ('G', 0, 0, 0), ('Z', 0.5, 0.5, 0.5), 
                                 ('F', 0.5, 0.5, 0), ('G', 0, 0, 0), ('L', 0, 0.5, 0)]
}
read_vasp_sets([('band', 'static', band_pack, 'override')]) #new set 'band' from static


    

    




Attention! You have chosen to override set dos
 

Warning! You did not change  NSW  in dos set
 


Attention! You have chosen to override set band
 







    
Out[2]:





{'static': <set_functions.InputSet at 0x7ffba5803828>,
 'band': <set_functions.InputSet at 0x7ffba5814470>,
 'dos': <set_functions.InputSet at 0x7ffba2ed4f28>}

In [4]:

    

#calculate charge density
add_loop('Bi2Se3.rho', 'static', 1, input_geo_file = 'in/Bi2Se3_mp-541837_computed.POSCAR', it_folder = 'Bi2Se3', run = 0)


    

    




command: pwd
-- You provided the following geo file explicitly  in/Bi2Se3_mp-541837_computed.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- check_kpoints(): Kpoint   mesh is:  [8, 8, 8] 

-- check_kpoints(): The actual k-spacings are  [ 0.22  0.22  0.22] 

-- Attention! ngkpt =  [8, 8, 8]  is adopted from struct_des which you provided for it  Bi2Se3.rho  and kspacing =  0.235 

command:  mkdir -p /home/aksenov/topologic/Bi2Se3//Bi2Se3.rho.static/
command: chmod +x /home/aksenov/topologic/Bi2Se3//Bi2Se3.rho.static/Bi2Se3.rho.static.run

Calculation ('Bi2Se3.rho', 'static', 1) successfully created

 







    
Out[4]:





'Bi2Se3.rho'

In [5]:

    

res_loop('Bi2Se3.rho', 'static', 1)


    

    




-- name                          |  energy(eV)|    Vector lenghts (A)   | Stresses (MPa)     | N MD, N SCF    
-- Bi2Se3.rho.static.1           |  -20.1543  |    10.27;10.27;10.27    |  -680,-680,-657    |   1,13, 13    






    
Out[5]:





(['Bi2Se3.rho.static.1           |  -20.1543  |    10.27;10.27;10.27    |  -680,-680,-657    |   1,13, 13   '],
 [])

In [3]:

    

#inherit charge density and make non-selfconsistent calculation of band structure
add_loop('Bi2Se3.rho', 'static', 1, ise_new = 'band', inherit_option = 'full', savefile = 'ocx', override = 1, run = 1)


    

    




-- Warning! File ./Bi2Se3/Bi2Se3.rho.if/Bi2Se3.rho.if.inherit.full.1.geo was replaced 

-- File xyz/Bi2Se3.rho.static.1.end.xyz was written 

-- inherit_ngkpt(): the k-grid from Bi2Se3.rho was inherited to Bi2Se3.rho.if 

-- check_kpoints(): Kpoint   mesh is:  [8, 8, 8] 

-- check_kpoints(): The actual k-spacings are  [ 0.22  0.22  0.22] 

-- Writing k-points file for band structure calculation. 


Calculation ('Bi2Se3.rho.if', 'band', 1) successfully created

 

-- Coping CHGCAR for band structure 

-- cp /home/aksenov/topologic/Bi2Se3//Bi2Se3.rho.static/1.CHGCAR.gz /home/aksenov/topologic/Bi2Se3//Bi2Se3.rho.if.band///CHGCAR.gz; gunzip -f /home/aksenov/topologic/Bi2Se3//Bi2Se3.rho.if.band///CHGCAR.gz 

Submitted batch job 78109
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
             78109       AMG Bi2Se3.r  aksenov PD       0:00      1 (None) 

-- To read results use  res_loop('Bi2Se3.rho.if', ['band'], [1], show = 'fo'  )     # , on 2016-12-13   ; possible options for show: fit, fo, fop, en, mag, magp, smag, maga, occ, occ1, mep, mepp 







    
Out[3]:





'Bi2Se3.rho.if'

In [4]:

    

#calculate dos
add_loop('Bi2Se3.rho', 'dos', 1, savefile = 'ocx', input_geo_file = 'Bi2Se3_mp-541837_computed.POSCAR', it_folder = 'Bi2Se3', run = 1)


    

    




-- You provided the following geo file explicitly  Bi2Se3_mp-541837_computed.POSCAR ; Version of file does not matter, I use *curver*= 1 as a new version 

-- check_kpoints(): Kpoint   mesh is:  [12, 12, 12] 

-- check_kpoints(): The actual k-spacings are  [ 0.15  0.15  0.15] 

-- Attention! ngkpt =  [12, 12, 12]  is adopted from struct_des which you provided for it  Bi2Se3.rho  and kspacing =  0.15 


Calculation ('Bi2Se3.rho', 'dos', 1) successfully created

 

Submitted batch job 78110
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
             78110       AMG Bi2Se3.r  aksenov PD       0:00      1 (None)
             78109       AMG Bi2Se3.r  aksenov  R       0:09      1 node-amg01 

-- To read results use  res_loop('Bi2Se3.rho', ['dos'], [1], show = 'fo'  )     # , on 2016-12-13   ; possible options for show: fit, fo, fop, en, mag, magp, smag, maga, occ, occ1, mep, mepp 







    
Out[4]:





'Bi2Se3.rho'

In [13]:

    

#read results, download xml files
res_loop('Bi2Se3.rho.if', 'band', 1,  up = 'x')
res_loop('Bi2Se3.rho',    'dos',  1,  up = 'x')


    

    




-- name                          |  energy(eV)|    Vector lenghts (A)   | Stresses (MPa)     | N MD, N SCF    
-- Bi2Se3.rho.if.band.1          |  -12.1562  |    10.27;10.27;10.27    | 21327,21908,1574   |   1,11, 11    
-- name                          |  energy(eV)|    Vector lenghts (A)   | Stresses (MPa)     | N MD, N SCF    
-- Bi2Se3.rho.dos.1              |  -20.1559  |    10.27;10.27;10.27    |  -687,-688,-649    |   1,13, 13    






    
Out[13]:





(['Bi2Se3.rho.dos.1              |  -20.1559  |    10.27;10.27;10.27    |  -687,-688,-649    |   1,13, 13   '],
 [])

In [12]:

    

#plot bands and dos using xml files
plot_bands(vasprun_dos   = 'Bi2Se3/Bi2Se3.rho.dos/1.vasprun.xml', 
           vasprun_bands = 'Bi2Se3/Bi2Se3.rho.if.band/1.vasprun.xml',
           kpoints       = 'Bi2Se3/Bi2Se3.rho.if.band/KPOINTS',
           element = 'Bi',
           ylim = (-2,2))