import sys
import numpy as np
from siman import header
from siman.header import db # database dictionary
from siman.calc_manage import smart_structure_read, add, res
from siman.geo import supercell
from siman.database import read_database, write_database
from siman.SSHTools import SSHTools
from siman.set_functions import read_vasp_sets
read_database() # read saved results
({}, {'static': <siman.set_functions.InputSet at 0x7f75d6d811d0>, 'opt': <siman.set_functions.InputSet at 0x7f75d6ddf2b0>}, 56)
header.PATH2POTENTIALS = 'potcars/' # path to POTCAR files
header.ssh_object = SSHTools()
header.ssh_object.setup(user="Dmitry.Aksenov",host="10.30.17.12",pkey="/home/test_user/.ssh/id_rsa")
st = smart_structure_read(input_geo_file = 'POSCAR_LiFePO4_ifn_1m_1_end')
add('LiFePO4_t', 'static', 1, input_st = st, it_folder = 'LiFePO4', cluster = 'pardus', run = 0 )
-- check_kpoints(): Kpoint mesh is: [3, 5, 6] -- check_kpoints(): The actual k-spacings are [0.2 0.21 0.22] -- POSCAR was written to /home/test_user/rec_bands/LiFePO4//LiFePO4_t.static/1.POSCAR -- Attention! ngkpt = [3, 5, 6] is adopted from struct_des which you provided for it LiFePO4_t and kspacing = 0.235 Calculation ('LiFePO4_t', 'static', 1) successfully created 2075425.mgmt.skoltech.ru /home/Dmitry.Aksenov Job ID Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 2075420.mgmt.skoltech.ru ...c2_m.su.4uiAg Dmitry.Aksenov 0 C batch 2075425.mgmt.skoltech.ru LiFePO4_t.static Dmitry.Aksenov 0 Q batch -- To read results use res_loop('LiFePO4_t', ['static'], [1], show = 'fo' ) # , on 2018-12-05 ; possible options for show: fit, fo, fop, en, mag, magp, smag, maga, occ, occ1, mep, mepp
'LiFePO4_t'
res('LiFePO4_t', 'static', 1, check_job = 0)
Max. F. tot (meV/A) = [1107]; -- name | energy(eV)| Vector lenghts (A) | Stresses (MPa) | N MD, N SCF -- db['LiFePO4_t.static.1'] | -188.8995 |10.45;6.09;4.75|-12648,-10175,-7871 | 1,22, 22
(["db['LiFePO4_t.static.1'] | -188.8995 |10.45;6.09;4.75|-12648,-10175,-7871 | 1,22, 22 "], [])
band_pack = {'ICHARG':11, 'LORBIT':11, 'ISMEAR':0, 'SIGMA':0.1, 'NSW':0,
'k_band_structure':[40, ('G', 0, 0, 0), ('X', 1, 0, 0),
('S', 1, 1, 0), ('Y', 0, 1, 0), ('G', 0, 0, 0)]}
read_vasp_sets([('band', 'static',band_pack, 'over')])
Attention! You have chosen to override set band Warning! You did not change NSW in band set
{'static': <siman.set_functions.InputSet at 0x7f75d6d811d0>, 'opt': <siman.set_functions.InputSet at 0x7f75d6ddf2b0>, 'band': <siman.set_functions.InputSet at 0x7f75d64fd550>}
add('LiFePO4_t', 'static', 1, up = 'up2', run = 1, override = 1,
ise_new = 'band', inherit_option = 'full', savefile = 'ocx', cluster = 'pardus')
-- Warning! File ./LiFePO4/LiFePO4_t.if/LiFePO4_t.if.inherit.full.1.geo was replaced -- File xyz/LiFePO4_t.static.1.end.xyz was written -- inherit_ngkpt(): the k-grid from LiFePO4_t was inherited to LiFePO4_t.if -- check_kpoints(): Kpoint mesh is: [3, 5, 6] -- check_kpoints(): The actual k-spacings are [0.2 0.21 0.22] -- POSCAR was written to /home/test_user/rec_bands/LiFePO4//LiFePO4_t.if.band/1.POSCAR -- Writing k-points file for band structure calculation. Calculation ('LiFePO4_t.if', 'band', 1) successfully created -- Copying CHGCAR for band structure -- File 1.CHGCAR was succesfully copied to /home/Dmitry.Aksenov/./LiFePO4//LiFePO4_t.if.band// with new name CHGCAR 2075479.mgmt.skoltech.ru /home/Dmitry.Aksenov Job ID Name User Time Use S Queue ------------------------- ---------------- --------------- -------- - ----- 2075420.mgmt.skoltech.ru ...c2_m.su.4uiAg Dmitry.Aksenov 0 C batch 2075425.mgmt.skoltech.ru LiFePO4_t.static Dmitry.Aksenov 00:12:09 C batch 2075479.mgmt.skoltech.ru ...PO4_t.if.band Dmitry.Aksenov 0 Q batch -- To read results use res_loop('LiFePO4_t.if', ['band'], [1], show = 'fo' ) # , on 2018-12-05 ; possible options for show: fit, fo, fop, en, mag, magp, smag, maga, occ, occ1, mep, mepp
'LiFePO4_t.if'
res('LiFePO4_t.if', 'band', 1, up = 'x', show = 'fo')
p = 'LiFePO4_t.if.band'
plot_bands(vasprun_dos = p+'/1.vasprun.xml',
vasprun_bands = p+'/1.vasprun.xml',
kpoints = p+'/KPOINTS',
element = 'Fe',
ylim = (-3,10))