def get_task(task_name):
cell = vasp.parse_poscar(Si_str.split('\n'))
# Vasp settings
incar = vasp.incar()
incar.set_structure_optimization()
incar.set_nsw(20)
incar.set_encut(300)
incar_ph_rx = vasp.incar()
incar_ph_rx.set_structure_optimization()
incar_ph_rx.set_nsw(20)
incar_ph_rx.set_encut(300)
incar_ph_rx.set_isif(4) # volume constant
incar_ph_dsp = vasp.incar()
incar_ph_dsp.set_electronic_structure()
incar_ph_dsp.set_encut(300)
# Queue
job = ge.job(script="mpirun vasp5212mpi",
shell="/bin/zsh",
jobname=task_name,
pe="mpi* 8",
stdout="std.log",
stderr="err.log")
# Task
task = vasp.quasiharmonic_phonon(max_iteration=10,
min_iteration=1,
sampling_mesh=[20, 20, 20],
supercell_matrix=np.diag([2, 2, 2]),
cell=cell,
pseudo_potential_map=ps_map,
incar=[incar,
incar_ph_rx,
incar_ph_dsp],
k_mesh=[[8, 8, 8],
[8, 8, 8],
[4, 4, 4]],
job=[job,
job.copy(task_name + "-ph_relax"),
job.copy(task_name + "-ph")],
traverse=False)
return task
def get_task(task_name):
cell = vasp.parse_poscar(Si_str.split('\n'))
# Vasp settings
incar = vasp.incar()
incar.set_structure_optimization()
incar.set_nsw(20)
incar.set_encut(300)
incar_ph_rx = vasp.incar()
incar_ph_rx.set_structure_optimization()
incar_ph_rx.set_nsw(20)
incar_ph_rx.set_encut(300)
incar_ph_rx.set_isif(4) # volume constant
incar_ph_dsp = vasp.incar()
incar_ph_dsp.set_electronic_structure()
incar_ph_dsp.set_encut(300)
# Queue
job = ge.job(script="mpirun vasp5212mpi",
shell="/bin/zsh",
jobname=task_name,
pe="mpi* 8",
stdout="std.log",
stderr="err.log")
# Task
task = vasp.quasiharmonic_phonon(max_iteration=10,
min_iteration=1,
sampling_mesh=[20, 20, 20],
supercell_matrix=np.diag([2, 2, 2]),
cell=cell,
pseudo_potential_map=ps_map,
incar=[incar, incar_ph_rx, incar_ph_dsp],
k_mesh=[[8, 8, 8], [8, 8, 8], [4, 4, 4]],
job=[
job,
job.copy(task_name + "-ph_relax"),
job.copy(task_name + "-ph")
],
traverse=False)
return task
[0, 4.75, 0],
[0, 0, 3.25]] # Orthorhombic
points=np.transpose([[0.0, 0.0, 0.0],
[0.5, 0.5, 0.5],
[0.3, 0.3, 0.0],
[0.7, 0.7, 0.0],
[0.2, 0.8, 0.5],
[0.8, 0.2, 0.5]])
cell = cogue.cell(lattice=lattice,
points=points,
symbols=symbols)
# Vasp settings
ps_map = {'Si': 'Si_PBE',
'O': 'O_PBE'}
incar = vasp.incar()
incar.set_structure_optimization()
incar.set_nsw(20)
incar_ph_rx = vasp.incar()
incar_ph_rx.set_structure_optimization()
incar_ph_rx.set_nsw(20)
incar_ph_rx.set_isif(4) # volume constant
# incar_ph_rx.set_isif(2) # lattice vectors constant
incar_ph_dsp = vasp.incar()
incar_ph_dsp.set_electronic_structure()
# Queue
job = ge.job(script="mpirun vasp5212mpi",
shell="/bin/zsh",
[0, 4.75, 0],
[0, 0, 3.25]] # Orthorhombic
points=np.transpose([[0.0, 0.0, 0.0],
[0.5, 0.5, 0.5],
[0.3, 0.3, 0.0],
[0.7, 0.7, 0.0],
[0.2, 0.8, 0.5],
[0.8, 0.2, 0.5]])
cell = cogue.cell(lattice=lattice,
points=points,
symbols=symbols)
# Vasp settings
ps_map = {'Si': 'Si_PBE',
'O': 'O_PBE'}
incar = vasp.incar()
incar.set_structure_optimization()
incar.set_encut(500)
incar.set_nsw(20)
incar.set_pstress(800)
# Queue
job = ge.job(script="mpirun vasp5212mpi",
shell="/bin/zsh",
jobname=task_name,
pe="mpi* 4",
stdout="std.log",
stderr="err.log")
# Task
task = vasp.structure_optimization(max_iteration=10,
[0, 4.75, 0],
[0, 0, 3.25]]
points=np.transpose([[0.0, 0.0, 0.0],
[0.5, 0.5, 0.5],
[0.3, 0.3, 0.0],
[0.7, 0.7, 0.0],
[0.2, 0.8, 0.5],
[0.8, 0.2, 0.5]])
cell = cogue.cell(lattice=lattice,
points=points,
symbols=symbols)
# Vasp settings
ps_map = {'Sn': 'Sn_PBE',
'O': 'O_PBE'}
incar = vasp.incar()
incar.set_structure_optimization()
incar.set_encut(400)
incar.set_prec("Normal")
# Queue
job = ge.job(script="vasp5212serial",
shell="/bin/zsh",
jobname=task_name,
stdout="std.log",
stderr="err.log")
# Task
task = vasp.bulk_modulus(max_iteration=2,
cell=cell,
pseudo_potential_map=ps_map,
import cogue
import cogue.calculator.vasp as vasp
import cogue.qsystem.gridengine as ge
task_name = "SiO2-80GPa"
# Crystal structure
symbols = ['Si'] * 2 + ['O'] * 4
lattice = [[4.65, 0, 0], [0, 4.75, 0], [0, 0, 3.25]] # Orthorhombic
points = np.transpose([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.3, 0.3, 0.0],
[0.7, 0.7, 0.0], [0.2, 0.8, 0.5], [0.8, 0.2, 0.5]])
cell = cogue.cell(lattice=lattice, points=points, symbols=symbols)
# Vasp settings
ps_map = {'Si': 'Si_PBE', 'O': 'O_PBE'}
incar = vasp.incar()
incar.set_structure_optimization()
incar.set_nsw(20)
incar.set_pstress(800)
incar_phonon = vasp.incar()
incar_phonon.set_electronic_structure()
# Queue
job = ge.job(script="mpirun vasp5212mpi",
shell="/bin/zsh",
jobname=task_name,
pe="mpi* 4",
stdout="std.log",
stderr="err.log")
import cogue
import cogue.calculator.vasp as vasp
import cogue.qsystem.gridengine as ge
task_name = "SiO2-gruneisen"
# Crystal structure
symbols = ['Si'] * 2 + ['O'] * 4
lattice = [[4.65, 0, 0], [0, 4.75, 0], [0, 0, 3.25]] # Orthorhombic
points = np.transpose([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5], [0.3, 0.3, 0.0],
[0.7, 0.7, 0.0], [0.2, 0.8, 0.5], [0.8, 0.2, 0.5]])
cell = cogue.cell(lattice=lattice, points=points, symbols=symbols)
# Vasp settings
ps_map = {'Si': 'Si_PBE', 'O': 'O_PBE'}
incar = vasp.incar()
incar.set_structure_optimization()
incar.set_nsw(20)
incar_ph_rx = vasp.incar()
incar_ph_rx.set_structure_optimization()
incar_ph_rx.set_nsw(20)
incar_ph_rx.set_isif(4) # volume constant
# incar_ph_rx.set_isif(2) # lattice vectors constant
incar_ph_dsp = vasp.incar()
incar_ph_dsp.set_electronic_structure()
# Queue
job = ge.job(script="mpirun vasp5212mpi",
shell="/bin/zsh",
[0, 4.75, 0],
[0, 0, 3.25]] # Orthorhombic
points=np.transpose([[0.0, 0.0, 0.0],
[0.5, 0.5, 0.5],
[0.3, 0.3, 0.0],
[0.7, 0.7, 0.0],
[0.2, 0.8, 0.5],
[0.8, 0.2, 0.5]])
cell = cogue.cell(lattice=lattice,
points=points,
symbols=symbols)
# Vasp settings
ps_map = {'Si': 'Si_PBE',
'O': 'O_PBE'}
incar = vasp.incar()
incar.set_structure_optimization()
incar.set_nsw(20)
incar.set_pstress(800)
incar_phonon = vasp.incar()
incar_phonon.set_electronic_structure()
# Queue
job = ge.job(script="mpirun vasp5212mpi",
shell="/bin/zsh",
jobname=task_name,
pe="mpi* 4",
stdout="std.log",
stderr="err.log")
