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
%matplotlib inline
read_database()
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="d.aksenov",host="10.30.16.168",pkey="/home/aksenov/.ssh/id_rsa")
In [2]:
#Creating new set 'dos' with parameters for DOS calculations
dos_pack = {'NSW':0, 'LORBIT':12,
'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'
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In [4]:
add_loop('Bi2Se3', 'dos', 1, input_geo_file = 'Bi2Se3_mp-541837_computed.POSCAR', run = 0) # calculting DOS
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res_loop('Bi2Se3', ['dos'], [1]) #reading results
write_database() # writing database
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plot_dos(header.db['Bi2Se3', 'dos', 1], dostype = 'total', up =1) #plotting total DOS; files saved in DOS folder
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header.calc['Bi2Se3', 'dos', 1].end.get_elements() # just showing list of elements in cell
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plot_dos(header.calc['Bi2Se3', 'dos', 1], iatom = 1, dostype = 'partial', orbitals = ['s', 'p', 'd']) #plotting for atom 1
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