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")
/home/aksenov/simanrc.py was read
#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'
Attention! You have chosen to override set dos Warning! You did not change NSW in dos set
{'aks': <siman.set_functions.InputSet at 0x7f7dd12d26a0>, 'dos': <siman.set_functions.InputSet at 0x7f7e00434358>, 'ion_relax': <siman.set_functions.InputSet at 0x7f7dd12d80b8>, 'opt': <siman.set_functions.InputSet at 0x7f7dd12d2518>, 'static': <siman.set_functions.InputSet at 0x7f7dd12d2630>}
add_loop('Bi2Se3', 'dos', 1, input_geo_file = 'Bi2Se3_mp-541837_computed.POSCAR', run = 0) # calculting DOS
-- 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 and kspacing = 0.15 Calculation ('Bi2Se3', 'dos', 1) successfully created
'Bi2Se3'
res_loop('Bi2Se3', ['dos'], [1]) #reading results
write_database() # writing database
-- name | energy(eV)| Vector lenghts (A) | Stresses (MPa) | N MD, N SCF -- Bi2Se3.dos.1 | -20.1559 | 10.27;10.27;10.27 | -687,-688,-649 | 1,13, 13 Database has been successfully updated
plot_dos(header.db['Bi2Se3', 'dos', 1], dostype = 'total', up =1) #plotting total DOS; files saved in DOS folder
-- ------Start plot_dos()----- -- Bi2Se3.dos.1 e_fermi 4.2271
{'name': 'Bi2Se3.dos.1'}
header.calc['Bi2Se3', 'dos', 1].end.get_elements() # just showing list of elements in cell
['Bi', 'Bi', 'Se', 'Se', 'Se']
plot_dos(header.calc['Bi2Se3', 'dos', 1], iatom = 1, dostype = 'partial', orbitals = ['s', 'p', 'd']) #plotting for atom 1
-- ------Start plot_dos()----- -- Bi2Se3.dos.1 e_fermi 4.2271
{'name': 'Bi2Se3.dos.1'}