def relax(dim=2, submit=True, force_overwrite=False):
"""
Writes input files and (optionally) submits a self-consistent
relaxation. Should be run before pretty much anything else, in
order to get the right energy and structure of the material.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
"""
if force_overwrite or not utl.is_converged(os.getcwd()):
directory = os.getcwd().split('/')[-1]
# vdw_kernel.bindat file required for VDW calculations.
if VDW_KERNEL:
os.system('cp {} .'.format(VDW_KERNEL))
# KPOINTS
Kpoints.automatic_density(Structure.from_file('POSCAR'),
1000).write_file('KPOINTS')
# INCAR
INCAR_DICT.update(
{'MAGMOM': utl.get_magmom_string(Structure.from_file('POSCAR'))}
)
Incar.from_dict(INCAR_DICT).write_file('INCAR')
# POTCAR
utl.write_potcar()
# Special tasks only performed for 2D materials.
if dim == 2:
# Ensure 20A interlayer vacuum
utl.ensure_vacuum(Structure.from_file('POSCAR'), 20)
# Remove all z k-points.
kpts_lines = open('KPOINTS').readlines()
with open('KPOINTS', 'w') as kpts:
for line in kpts_lines[:3]:
kpts.write(line)
kpts.write(kpts_lines[3].split()[0] + ' '
+ kpts_lines[3].split()[1] + ' 1')
# Submission script
if dim == 2:
binary = VASP_TWOD_BIN
elif dim == 3:
binary = VASP_STD_BIN
if QUEUE_SYSTEM == 'pbs':
utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00', binary)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00', binary)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
def relax(dim=2, submit=True, force_overwrite=False):
"""
Writes input files and (optionally) submits a self-consistent
relaxation. Should be run before pretty much anything else, in
order to get the right energy and structure of the material.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
"""
if force_overwrite or not utl.is_converged(os.getcwd()):
directory = os.getcwd().split('/')[-1]
# vdw_kernel.bindat file required for VDW calculations.
if VDW_KERNEL:
os.system('cp {} .'.format(VDW_KERNEL))
# KPOINTS
Kpoints.automatic_density(Structure.from_file('POSCAR'),
1000).write_file('KPOINTS')
# INCAR
INCAR_DICT.update(
{'MAGMOM': utl.get_magmom_string(Structure.from_file('POSCAR'))})
Incar.from_dict(INCAR_DICT).write_file('INCAR')
# POTCAR
utl.write_potcar()
# Special tasks only performed for 2D materials.
if dim == 2:
# Ensure 20A interlayer vacuum
utl.ensure_vacuum(Structure.from_file('POSCAR'), 20)
# Remove all z k-points.
kpts_lines = open('KPOINTS').readlines()
with open('KPOINTS', 'w') as kpts:
for line in kpts_lines[:3]:
kpts.write(line)
kpts.write(kpts_lines[3].split()[0] + ' ' +
kpts_lines[3].split()[1] + ' 1')
# Submission script
if dim == 2:
binary = VASP_TWOD_BIN
elif dim == 3:
binary = VASP_STD_BIN
if QUEUE_SYSTEM == 'pbs':
utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00', binary)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00', binary)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
def GW_step1(name,
spin_polarized=True,
submit=True,
incar_dict={},
force_overwrite=False):
#name is the name of the job that will be used in submit file
incar = Incar.from_string("""ISMEAR = 1 ; SIGMA = 0.2
ALGO = Exact ; NELM = 1 # exact diagonalization one step suffices
EDIFF = 1E-8 # high precision for groundstate calculation
NBANDS = 96 # need for a lot of bands in GW
LOPTICS = .TRUE. # we need d phi/ d k for GW calculations
KPAR = 2""")
if spin_polarized:
if os.path.exists('POSCAR'):
incar.update({
'LORBIT':
11,
'ISPIN':
2,
'MAGMOM':
get_magmom_string(Structure.from_file('POSCAR'))
})
else:
raise IOError('No POSCAR found at ' + os.getcwd())
if os.path.isdir('step1'):
os.chdir('step1')
else:
os.mkdir('step1')
os.chdir('step1')
if force_overwrite:
os.system('rm -rf *')
incar.update(incar_dict)
incar.write_file('INCAR')
os.system('cp ../{KPOINTS,POSCAR,CONTCAR,POTCAR} .')
if os.path.exists('CONTCAR') and os.stat('CONTCAR').st_size > 10:
shutil.move('CONTCAR', 'POSCAR')
submit_builder(update_dict={
'--mem-per-cpu': '3gb',
'--job-name': name,
'--nodes': 2,
'--ntasks': 32
})
if submit:
os.system('sbatch submit')
os.chdir('../')
def run_major_axis_anisotropy_calculations(submit=True):
"""
Perform static calculations with the magnetic axis along
100, 010, and 001.
Args:
submit (bool): Whether or not to submit the job.
"""
if not os.path.isdir('MAE'):
os.mkdir('MAE')
os.chdir('MAE')
for d in ['100', '010', '001']:
if not os.path.isdir(d):
os.mkdir(d)
os.chdir(d)
os.system('cp ../CONTCAR POSCAR')
os.system('cp ../POTCAR .')
axis = [float(char) for char in d]
# Small positive number, see vasp manual
if d in ['001', '010']:
axis[0] = 0.00000001
else:
axis[1] = 0.00000001
saxis = ' '.join(axis)
incar_dict = INCAR_DICT
incar_dict.update({'EDIFF': 1e-8,
'GGA_COMPAT': False,
'ISMEAR': -5,
'LORBIT': 11,
'LSORBIT': True,
'LWAVE': False,
'LCHARG': False,
'LAECHG': False,
'MAGMOM': get_magmom_string(
Structure.from_file('POSCAR')
),
'SAXIS': saxis})
Incar.from_dict(incar_dict).write_file('INCAR')
if QUEUE_SYSTEM == 'pbs':
utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00',
VASP_TWOD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00',
VASP_TWOD_BIN)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
def run_major_axis_anisotropy_calculations(submit=True):
"""
Perform static calculations with the magnetic axis along
100, 010, and 001.
Args:
submit (bool): Whether or not to submit the job.
"""
if not os.path.isdir('MAE'):
os.mkdir('MAE')
os.chdir('MAE')
for d in ['100', '010', '001']:
if not os.path.isdir(d):
os.mkdir(d)
os.chdir(d)
os.system('cp ../CONTCAR POSCAR')
os.system('cp ../POTCAR .')
axis = [float(char) for char in d]
# Small positive number, see vasp manual
if d in ['001', '010']:
axis[0] = 0.00000001
else:
axis[1] = 0.00000001
saxis = ' '.join(axis)
incar_dict = INCAR_DICT
incar_dict.update({
'EDIFF':
1e-8,
'GGA_COMPAT':
False,
'ISMEAR':
-5,
'LORBIT':
11,
'LSORBIT':
True,
'LWAVE':
False,
'LCHARG':
False,
'LAECHG':
False,
'MAGMOM':
get_magmom_string(Structure.from_file('POSCAR')),
'SAXIS':
saxis
})
Incar.from_dict(incar_dict).write_file('INCAR')
if QUEUE_SYSTEM == 'pbs':
utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00',
VASP_TWOD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00',
VASP_TWOD_BIN)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
def run_pbe_calculation(dim=2, submit=True, force_overwrite=False):
"""
Setup and submit a normal PBE calculation for band structure along
high symmetry k-paths.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
"""
PBE_INCAR_DICT = {
'EDIFF': 1e-6,
'IBRION': 2,
'ISIF': 3,
'ISMEAR': 1,
'NSW': 0,
'LVTOT': True,
'LVHAR': True,
'LORBIT': 1,
'LREAL': 'Auto',
'NPAR': 4,
'PREC': 'Accurate',
'LWAVE': True,
'SIGMA': 0.1,
'ENCUT': 500,
'ISPIN': 2
}
directory = os.path.basename(os.getcwd())
if not os.path.isdir('pbe_bands'):
os.mkdir('pbe_bands')
if force_overwrite or not is_converged('pbe_bands'):
shutil.copy("CONTCAR", "pbe_bands/POSCAR")
if os.path.isfile('POTCAR'):
shutil.copy("POTCAR", "pbe_bands")
PBE_INCAR_DICT.update(
{'MAGMOM': get_magmom_string(Structure.from_file('POSCAR'))})
Incar.from_dict(PBE_INCAR_DICT).write_file('pbe_bands/INCAR')
structure = Structure.from_file('POSCAR')
kpath = HighSymmKpath(structure)
Kpoints.automatic_linemode(20, kpath).write_file('pbe_bands/KPOINTS')
os.chdir('pbe_bands')
if dim == 2:
remove_z_kpoints()
if QUEUE_SYSTEM == 'pbs':
write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00',
VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
write_slurm_runjob(directory, 16, '800mb', '6:00:00', VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
_ = subprocess.check_output(submission_command.split())
os.chdir('../')
def run_hse_calculation(dim=2,
submit=True,
force_overwrite=False,
destroy_prep_directory=False):
"""
Setup/submit an HSE06 calculation to get an accurate band structure.
Requires a previous IBZKPT from a standard DFT run. See
http://cms.mpi.univie.ac.at/wiki/index.php/Si_bandstructure for more
details.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
destroy_prep_directory (bool): whether or not to remove
(rm -r) the hse_prep directory, if it exists. This
can help to automatically clean up and save space.
"""
HSE_INCAR_DICT = {
'LHFCALC': True,
'HFSCREEN': 0.2,
'AEXX': 0.25,
'ALGO': 'D',
'TIME': 0.4,
'NSW': 0,
'LVTOT': True,
'LVHAR': True,
'LORBIT': 11,
'LWAVE': True,
'NPAR': 8,
'PREC': 'Accurate',
'EDIFF': 1e-4,
'ENCUT': 450,
'ICHARG': 2,
'ISMEAR': 1,
'SIGMA': 0.1,
'IBRION': 2,
'ISIF': 3,
'ISPIN': 2
}
if not os.path.isdir('hse_bands'):
os.mkdir('hse_bands')
if force_overwrite or not is_converged('hse_bands'):
os.chdir('hse_bands')
os.system('cp ../CONTCAR ./POSCAR')
if os.path.isfile('../POTCAR'):
os.system('cp ../POTCAR .')
HSE_INCAR_DICT.update(
{'MAGMOM': get_magmom_string(Structure.from_file('POSCAR'))})
Incar.from_dict(HSE_INCAR_DICT).write_file('INCAR')
# Re-use the irreducible brillouin zone KPOINTS from a
# previous standard DFT run.
if os.path.isdir('../hse_prep'):
ibz_lines = open('../hse_prep/IBZKPT').readlines()
if destroy_prep_directory:
os.system('rm -r ../hse_prep')
else:
ibz_lines = open('../IBZKPT').readlines()
n_ibz_kpts = int(ibz_lines[1].split()[0])
kpath = HighSymmKpath(Structure.from_file('POSCAR'))
Kpoints.automatic_linemode(20, kpath).write_file('KPOINTS')
if dim == 2:
remove_z_kpoints()
linemode_lines = open('KPOINTS').readlines()
abs_path = []
i = 4
while i < len(linemode_lines):
start_kpt = linemode_lines[i].split()
end_kpt = linemode_lines[i + 1].split()
increments = [(float(end_kpt[0]) - float(start_kpt[0])) / 20,
(float(end_kpt[1]) - float(start_kpt[1])) / 20,
(float(end_kpt[2]) - float(start_kpt[2])) / 20]
abs_path.append(start_kpt[:3] + ['0', start_kpt[4]])
for n in range(1, 20):
abs_path.append([
str(float(start_kpt[0]) + increments[0] * n),
str(float(start_kpt[1]) + increments[1] * n),
str(float(start_kpt[2]) + increments[2] * n), '0'
])
abs_path.append(end_kpt[:3] + ['0', end_kpt[4]])
i += 3
n_linemode_kpts = len(abs_path)
with open('KPOINTS', 'w') as kpts:
kpts.write('Automatically generated mesh\n')
kpts.write('{}\n'.format(n_ibz_kpts + n_linemode_kpts))
kpts.write('Reciprocal Lattice\n')
for line in ibz_lines[3:]:
kpts.write(line)
for point in abs_path:
kpts.write('{}\n'.format(' '.join(point)))
if QUEUE_SYSTEM == 'pbs':
write_pbs_runjob('{}_hsebands'.format(os.getcwd().split('/')[-2]),
2, 64, '1800mb', '50:00:00', VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
write_slurm_runjob(
'{}_hsebands'.format(os.getcwd().split('/')[-2]), 64, '1800mb',
'50:00:00', VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
_ = subprocess.check_output(submission_command.split())
os.chdir('../')
def run_gamma_calculations(submit=True, step_size=0.5):
"""
Setup a 2D grid of static energy calculations to plot the Gamma
surface between two layers of the 2D material. These calculations
are run and stored in subdirectories under 'friction/lateral'.
Args:
submit (bool): Whether or not to submit the jobs.
step_size (float): the distance between grid points in
Angstroms.
"""
if not os.path.isdir('friction'):
os.mkdir('friction')
os.chdir('friction')
if not os.path.isdir('lateral'):
os.mkdir('lateral')
os.chdir('lateral')
os.system('cp ../../CONTCAR POSCAR')
# Pad the bottom layer with 20 Angstroms of vacuum.
utl.ensure_vacuum(Structure.from_file('POSCAR'), 20)
structure = Structure.from_file('POSCAR')
n_sites_per_layer = structure.num_sites
n_divs_x = int(math.ceil(structure.lattice.a / step_size))
n_divs_y = int(math.ceil(structure.lattice.b / step_size))
# Get the thickness of the material.
max_height = max([site.coords[2] for site in structure.sites])
min_height = min([site.coords[2] for site in structure.sites])
thickness = max_height - min_height
# Make a new layer.
species, coords = [], []
for site in structure.sites:
# Original site
species.append(site.specie)
coords.append(site.coords)
# New layer site
species.append(site.specie)
coords.append(
[site.coords[0], site.coords[1], site.coords[2] + thickness + 3.5])
Structure(structure.lattice, species, coords,
coords_are_cartesian=True).to('POSCAR', 'POSCAR')
for x in range(n_divs_x):
for y in range(n_divs_y):
dir = '{}x{}'.format(x, y)
if not os.path.isdir(dir):
os.mkdir(dir)
# Copy input files
os.chdir(dir)
os.system('cp ../../../INCAR .')
os.system('cp ../../../KPOINTS .')
os.system('cp ../POSCAR .')
if VDW_KERNEL:
os.system('cp {} .'.format(VDW_KERNEL))
# Shift the top layer
structure = Structure.from_file("POSCAR")
all_z_coords = [s.coords[2] for s in structure.sites]
top_layer = [
s for s in structure.sites
if s.coords[2] > np.mean(all_z_coords)
]
structure.remove_sites(
[i for i, s in enumerate(structure.sites) if s in top_layer])
for site in top_layer:
structure.append(site.specie, [
site.coords[0] + float(x) / float(n_divs_x),
site.coords[1] + float(y) / float(n_divs_y), site.coords[2]
],
coords_are_cartesian=True)
structure = structure.get_sorted_structure()
structure.to("POSCAR", "POSCAR")
utl.write_potcar()
incar_dict = Incar.from_file('INCAR').as_dict()
incar_dict.update({
'NSW': 0,
'LAECHG': False,
'LCHARG': False,
'LWAVE': False,
'LVTOT': False,
'MAGMOM': utl.get_magmom_string(structure)
})
incar_dict.pop('NPAR', None)
Incar.from_dict(incar_dict).write_file('INCAR')
if QUEUE_SYSTEM == 'pbs':
utl.write_pbs_runjob(dir, 1, 8, '1000mb', '2:00:00',
VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
utl.write_slurm_runjob(dir, 8, '1000mb', '2:00:00',
VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
os.chdir('../')
os.chdir('../../')
def run_normal_force_calculations(basin_and_saddle_dirs,
spacings=np.arange(1.5, 4.25, 0.25),
submit=True):
"""
Set up and run static calculations of the basin directory and
saddle directory at specified interlayer spacings to get f_N and
f_F.
Args:
basin_and_saddle_dirs (tuple): Can be obtained by the
get_basin_and_peak_locations() function under
friction.analysis. For example,
run_normal_force_calculations(('0x0', '3x6'))
or
run_normal_force_calculations(get_basin_and_peak_locations())
will both work.
spacings (tuple): list of interlayer spacings (in Angstroms, as floats)
at which to run the calculations.
submit (bool): Whether or not to submit the jobs.
"""
spacings = [str(spc) for spc in spacings]
os.chdir('friction')
if not os.path.isdir('normal'):
os.mkdir('normal')
os.chdir('normal')
for spacing in spacings:
if not os.path.isdir(spacing):
os.mkdir(spacing)
for subdirectory in basin_and_saddle_dirs:
os.system('cp -r ../lateral/{} {}/'.format(subdirectory, spacing))
os.chdir('{}/{}'.format(spacing, subdirectory))
structure = Structure.from_file('POSCAR')
n_sites = len(structure.sites)
all_z_coords = [s.coords[2] for s in structure.sites]
top_layer = [
s for s in structure.sites
if s.coords[2] > np.mean(all_z_coords)
]
bottom_of_top_layer = min([site.coords[2] for site in top_layer])
remove_indices = [
i for i, s in enumerate(structure.sites) if s in top_layer
]
structure.remove_sites(remove_indices)
top_of_bottom_layer = max(
[site.coords[2] for site in structure.sites])
for site in top_layer:
structure.append(site.specie, [
site.coords[0], site.coords[1], site.coords[2] -
bottom_of_top_layer + top_of_bottom_layer + float(spacing)
],
coords_are_cartesian=True)
structure = structure.get_sorted_structure()
structure.to('POSCAR', 'POSCAR')
utl.write_potcar()
incar_dict = Incar.from_file('INCAR').as_dict()
incar_dict.update({"MAGMOM": utl.get_magmom_string(structure)})
Incar.from_dict(incar_dict).write_file("INCAR")
if QUEUE_SYSTEM == 'pbs':
utl.write_pbs_runjob('{}_{}'.format(subdirectory, spacing), 1,
8, '1000mb', '2:00:00', VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
utl.write_slurm_runjob('{}_{}'.format(subdirectory, spacing),
8, '1000mb', '2:00:00', VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
os.chdir('../../')
os.chdir('../../')
def run_gamma_calculations(submit=True, step_size=0.5):
"""
Setup a 2D grid of static energy calculations to plot the Gamma
surface between two layers of the 2D material. These calculations
are run and stored in subdirectories under 'friction/lateral'.
Args:
submit (bool): Whether or not to submit the jobs.
step_size (float): the distance between grid points in
Angstroms.
"""
if not os.path.isdir('friction'):
os.mkdir('friction')
os.chdir('friction')
if not os.path.isdir('lateral'):
os.mkdir('lateral')
os.chdir('lateral')
try:
os.system('cp ../../CONTCAR POSCAR')
except:
try:
os.system('cp ../../POSCAR .')
except:
raise IOError('No POSCAR or CONTCAR found in ' +
os.path.dirname(os.path.dirname(os.getcwd())))
# Pad the bottom layer with 20 Angstroms of vacuum.
utl.ensure_vacuum(Structure.from_file('POSCAR'), 20)
structure = Structure.from_file('POSCAR')
n_sites_per_layer = structure.num_sites
n_divs_x = int(math.ceil(structure.lattice.a / step_size))
n_divs_y = int(math.ceil(structure.lattice.b / step_size))
# Get the thickness of the material.
max_height = max([site.coords[2] for site in structure.sites])
min_height = min([site.coords[2] for site in structure.sites])
thickness = max_height - min_height
# Make a new layer.
species, coords = [], []
for site in structure.sites:
# Original site
species.append(site.specie)
coords.append(site.coords)
# New layer site
species.append(site.specie)
coords.append(
[site.coords[0], site.coords[1], site.coords[2] + thickness + 3.5])
Structure(structure.lattice, species, coords).to('POSCAR', 'POSCAR')
for x in range(n_divs_x):
for y in range(n_divs_y):
dir = '{}x{}'.format(x, y)
if not os.path.isdir(dir):
os.mkdir(dir)
# Copy input files
os.chdir(dir)
if not os.path.exists('../../INCAR'):
raise IOError('No INCAR found in ' +
os.path.dirname(os.path.dirname(os.getcwd())))
if not os.path.exists('../../KPOINTS'):
raise IOError('No KPOINTS found in ' +
os.path.dirname(os.path.dirname(os.getcwd())))
os.system('cp ../../../INCAR .')
os.system('cp ../../../KPOINTS .')
os.system('cp ../POSCAR .')
if VDW_KERNEL:
os.system('cp {} .'.format(VDW_KERNEL))
utl.write_potcar()
incar_dict = Incar.from_file('INCAR').as_dict()
incar_dict.update({
'NSW':
0,
'LAECHG':
False,
'LCHARG':
False,
'LWAVE':
False,
'LVTOT':
False,
'MAGMOM':
utl.get_magmom_string(Structure.from_file('POSCAR'))
})
incar_dict.pop('NPAR', None)
Incar.from_dict(incar_dict).write_file('INCAR')
# Shift the top layer
poscar_lines = open('POSCAR').readlines()
with open('POSCAR', 'w') as poscar:
for line in poscar_lines[:8 + n_sites_per_layer]:
poscar.write(line)
for line in poscar_lines[8 + n_sites_per_layer:]:
split_line = line.split()
new_coords = [
float(split_line[0]) + float(x) / float(n_divs_x),
float(split_line[1]) + float(y) / float(n_divs_y),
float(split_line[2])
]
poscar.write(' '.join([str(i) for i in new_coords]) + '\n')
sub_exe = True
if VASP_STD_BIN == 'None':
print 'Executable is missing in ' + os.getcwd() + '/runjob'
print 'Configure mpint_config.yaml file with your executable!'
sub_exe = False
if QUEUE_SYSTEM == 'pbs':
utl.write_pbs_runjob(dir, 1, 8, '1000mb', '2:00:00',
VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
utl.write_slurm_runjob(dir, 8, '1000mb', '2:00:00',
VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit and sub_exe:
os.system(submission_command)
os.chdir('../')
os.chdir('../../')
def run_hse_calculation(dim=2, submit=True, force_overwrite=False):
"""
Setup/submit an HSE06 calculation to get an accurate band structure.
See http://cms.mpi.univie.ac.at/wiki/index.php/Si_bandstructure for
more details.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
"""
HSE_INCAR_DICT = {
'LHFCALC': True,
'HFSCREEN': 0.2,
'AEXX': 0.25,
'ALGO': 'D',
'TIME': 0.4,
'NSW': 0,
'LVTOT': True,
'LVHAR': True,
'LORBIT': 11,
'LWAVE': True,
'NPAR': 8,
'PREC': 'Accurate',
'EDIFF': 1e-4,
'ENCUT': 450,
'ICHARG': 2,
'ISMEAR': 1,
'SIGMA': 0.1,
'IBRION': 2,
'ISIF': 3,
'ISPIN': 2
}
if not os.path.isdir('hse_bands'):
os.mkdir('hse_bands')
if force_overwrite or not is_converged('hse_bands'):
os.chdir('hse_bands')
os.system('cp ../CONTCAR ./POSCAR')
structure = Structure.from_file("POSCAR")
if os.path.isfile('../POTCAR'):
os.system('cp ../POTCAR .')
HSE_INCAR_DICT.update({'MAGMOM': get_magmom_string(structure)})
Incar.from_dict(HSE_INCAR_DICT).write_file('INCAR')
# Re-use the irreducible brillouin zone KPOINTS from a
# previous standard DFT run.
write_band_structure_kpoints(structure, dim=dim)
if QUEUE_SYSTEM == 'pbs':
write_pbs_runjob('{}_hsebands'.format(os.getcwd().split('/')[-2]),
2, 64, '1800mb', '50:00:00', VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
write_slurm_runjob(
'{}_hsebands'.format(os.getcwd().split('/')[-2]), 64, '1800mb',
'50:00:00', VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
_ = subprocess.check_output(submission_command.split())
os.chdir('../')
def setup_poscar_jobs(self, scale_list=None, poscar_list=None):
"""
for scaling the latice vectors of the original structure,
scale_list is volume scaling factor list
"""
if scale_list:
for scale in scale_list:
self.set_poscar(scale=scale)
self.set_potcar()
if not self.is_matrix:
job_dir = self.job_dir + os.sep + 'POS' + \
os.sep + 'VOLUME_' + str(scale)
self.add_job(name=job_dir, job_dir=job_dir)
elif poscar_list:
for pos in poscar_list:
# if it is a twod_database run or any general standard database run,
# the incar, kpoints and potcar follow a standard input set
# which will be activated by the twod_database tag set to true
# NOTE: this implementation means that the first turn_knobs tag
# needs to be the poscar objects list
# the database tag will be set to the name of the yaml file with the
# standard input deck definition for that database
# this incar dict provided as the init can be general format
# based on the chosen functional, cutoff
# so self.incar is a vdW incar for re-relaxation in vdW, gga for every
# other calculation or LDA+U for LSDA+U calculations
incar_dict = self.incar.as_dict()
if self.reuse:
# if this is a true list minimally, ['CONTCAR']
# it is to be ensured that the poscar list is a
# list of paths as opposed to list of poscar objects by the turn knobs
# values
# Here pos is the path and r in each self.reuse is the name of the file(s)
# to be reused
# in a reuse calculation the following are possible:
# update incar (Solvation calculations) or reset incar (HSE calculations)
# reset kpoints file with IBZKPT
# copy a CHGCAR or WAVECAR or both perhaps
try:
# first setup of POSCAR initial, INCAR, KPOINTS
poscar = Poscar.from_file(pos + os.sep + 'CONTCAR')
self.logger.info('Read previous relaxed CONTCAR file from {}'.
format(pos))
# check if it is KPOINTS altering job like HSE
if self.Grid_type == 'hse_bands_2D_prep':
# HSE prep calcualtions
# reset the INCAR file with a magmom only if exists
try:
incar_dict = {
'MAGMOM': get_magmom_string(poscar)}
except:
incar_dict = {}
incar_dict = get_2D_incar_hse_prep(incar_dict)
self.set_kpoints(poscar=poscar)
self.logger.info(
'updated input set for HSE 2D prep calcaultion')
elif self.Grid_type == 'hse_bands_2D':
# HSE calculation
# reset the incar and kpoints file builds
# on the preceding calculations (prep calculation)
# IBZKPT
try:
incar_dict = {
'MAGMOM': get_magmom_string(poscar)}
except:
incar_dict = {}
incar_dict = get_2D_incar_hse(incar_dict)
self.set_kpoints(poscar=poscar,
ibzkpth=pos + os.sep + 'IBZKPT')
self.logger.info('updated input set for HSE calcaultion\
using IBZKPT from {0}'.format(pos + os.sep + 'IBZKPT'))
elif self.Grid_type == 'hse_bands':
# general HSE bands
pass
elif self.Grid_type == 'Finer_G_Mesh':
self.logger.info('updating to Finer G Mesh')
kpoint = Kpoints.from_file(pos+os.sep+'KPOINTS')
self.set_kpoints(kpoint=kpoint.kpts[0])
else:
# use the same kpoints file and build from the old
# incar
self.kpoints = Kpoints.from_file(
pos + os.sep + 'KPOINTS')
# decide on how to use incar, use same one or
# update or afresh
if self.reuse_incar == 'old':
incar_dict = Incar.from_file(
pos + os.sep + 'INCAR').as_dict()
elif self.reuse_incar == 'update':
# way to go for cutoff updates, convergence, etc.
# but retain the old functional
incar_dict.update(Incar.from_file(pos + os.sep + 'INCAR').
as_dict())
else:
# use a fresh incar as specified by the init
# way to go for example for LDAU or other
# major removals done to INCAR
# but always retain the MAGMOM if present
old_incar_dict = Incar.from_file(
pos + os.sep + 'INCAR').as_dict()
if 'MAGMOM' in old_incar_dict.keys():
incar_dict['MAGMOM'] = old_incar_dict[
'MAGMOM']
else:
incar_dict = incar_dict
if isinstance(self.reuse, list):
reuse_paths = [
pos + os.sep + r for r in self.reuse]
self.reuse_paths = reuse_paths
# Magnetism use cases, updates to be made to the INCAR (MAE)
# and poscar (AFM)
# MAE and AFM
if self.magnetism == 'MAE':
# remove vdW tags for MAE calculations
vdW_tags = ('GGA', 'AGGAC', 'LUSE_VDW',
'PARAM1', 'PARAM2')
for key in vdW_tags:
if key in incar_dict:
del incar_dict[key]
self.logger.info(
'updating input set for MAE calculation')
self.mag_init = Outcar(
pos + os.sep + 'OUTCAR').total_mag
nbands = 2 * \
Vasprun(pos + os.sep +
'vasprun.xml').parameters['NBANDS']
# u_value = Vasprun(pos+os.sep+'vasprun.xml').incar['LDAUU']
# u_value = 4.0
self.logger.info(
"updating mag mom with value {0}".format(self.mag_init))
self.logger.info(
"updating NBANDS with {0}".format(nbands))
incar_dict.update({'NBANDS': nbands,
'LSORBIT': True,
'EDIFF': 1e-08,
'ICHARG': 11,
'LMAXMIX': 4,
'LCHARG': False,
'ISYM': 0,
'NSW': 0,
'ISPIN': 2,
'IBRION': -1,
'LORBIT': 11,
'MAGMOM': get_magmom_mae(poscar, self.mag_init)
})
# incar_dict.update({'LDAUU': u_value})
elif self.magnetism == 'AFM':
self.logger.info(
'updating INCAR and POSCAR for AFM calculation')
afm, poscar = get_magmom_afm(poscar, self.database)
incar_dict.update({'MAGMOM': afm})
except:
# check what to do if the previous calculation being reused is not
# actuall done .. system exit or adopt a user override
# with POSCAR
self.logger.warn(
'Empty relaxed CONTCAR file .. Probably job not done')
if not self.reuse_override:
self.logger.warn(
'You can set reuse_override to continue with POSCAR file, exiting now ..')
sys.exit(0)
else:
self.logger.info('Using old Poscar for rerun')
poscar = Poscar.from_file(pos + os.sep + 'POSCAR')
# case for non - reuse
else:
poscar = pos
# temporary: magnetism only set if twod flag is activated
if self.database == 'twod':
incar_dict.update(
{'MAGMOM': get_magmom_string(poscar)})
self.set_kpoints(poscar=poscar)
self.incar = Incar.from_dict(incar_dict)
self.set_poscar(poscar=poscar)
self.set_potcar()
if not self.is_matrix:
job_dir = self.job_dir + os.sep + 'POS' + \
os.sep + self.val_to_name(poscar)
self.add_job(name=job_dir, job_dir=job_dir)
def run_gamma_calculations(submit=True, step_size=0.5):
"""
Setup a 2D grid of static energy calculations to plot the Gamma
surface between two layers of the 2D material. These calculations
are run and stored in subdirectories under 'friction/lateral'.
Args:
submit (bool): Whether or not to submit the jobs.
step_size (float): the distance between grid points in
Angstroms.
"""
if not os.path.isdir('friction'):
os.mkdir('friction')
os.chdir('friction')
if not os.path.isdir('lateral'):
os.mkdir('lateral')
os.chdir('lateral')
os.system('cp ../../CONTCAR POSCAR')
# Pad the bottom layer with 20 Angstroms of vacuum.
utl.ensure_vacuum(Structure.from_file('POSCAR'), 20)
structure = Structure.from_file('POSCAR')
n_sites_per_layer = structure.num_sites
n_divs_x = int(math.ceil(structure.lattice.a / step_size))
n_divs_y = int(math.ceil(structure.lattice.b / step_size))
# Get the thickness of the material.
max_height = max([site.coords[2] for site in structure.sites])
min_height = min([site.coords[2] for site in structure.sites])
thickness = max_height - min_height
# Make a new layer.
species, coords = [], []
for site in structure.sites:
# Original site
species.append(site.specie)
coords.append(site.coords)
# New layer site
species.append(site.specie)
coords.append([site.coords[0], site.coords[1],
site.coords[2] + thickness + 3.5])
Structure(structure.lattice, species, coords,
coords_are_cartesian=True).to('POSCAR', 'POSCAR')
for x in range(n_divs_x):
for y in range(n_divs_y):
dir = '{}x{}'.format(x, y)
if not os.path.isdir(dir):
os.mkdir(dir)
# Copy input files
os.chdir(dir)
os.system('cp ../../../INCAR .')
os.system('cp ../../../KPOINTS .')
os.system('cp ../POSCAR .')
if VDW_KERNEL:
os.system('cp {} .'.format(VDW_KERNEL))
# Shift the top layer
structure = Structure.from_file("POSCAR")
all_z_coords = [s.coords[2] for s in structure.sites]
top_layer = [s for s in structure.sites if s.coords[2] > np.mean(all_z_coords)]
structure.remove_sites([i for i, s in enumerate(structure.sites) if s in top_layer])
for site in top_layer:
structure.append(
site.specie,
[site.coords[0]+float(x)/float(n_divs_x),
site.coords[1]+float(y)/float(n_divs_y),
site.coords[2]], coords_are_cartesian=True
)
structure = structure.get_sorted_structure()
structure.to("POSCAR", "POSCAR")
utl.write_potcar()
incar_dict = Incar.from_file('INCAR').as_dict()
incar_dict.update({'NSW': 0, 'LAECHG': False, 'LCHARG': False,
'LWAVE': False, 'LVTOT': False,
'MAGMOM': utl.get_magmom_string(structure)})
incar_dict.pop('NPAR', None)
Incar.from_dict(incar_dict).write_file('INCAR')
if QUEUE_SYSTEM == 'pbs':
utl.write_pbs_runjob(dir, 1, 8, '1000mb', '2:00:00', VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
utl.write_slurm_runjob(dir, 8, '1000mb', '2:00:00', VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
os.chdir('../')
os.chdir('../../')
def run_normal_force_calculations(basin_and_saddle_dirs,
spacings=np.arange(1.5, 4.25, 0.25),
submit=True):
"""
Set up and run static calculations of the basin directory and
saddle directory at specified interlayer spacings to get f_N and
f_F.
Args:
basin_and_saddle_dirs (tuple): Can be obtained by the
get_basin_and_peak_locations() function under
friction.analysis. For example,
run_normal_force_calculations(('0x0', '3x6'))
or
run_normal_force_calculations(get_basin_and_peak_locations())
will both work.
spacings (tuple): list of interlayer spacings (in Angstroms, as floats)
at which to run the calculations.
submit (bool): Whether or not to submit the jobs.
"""
spacings = [str(spc) for spc in spacings]
os.chdir('friction')
if not os.path.isdir('normal'):
os.mkdir('normal')
os.chdir('normal')
for spacing in spacings:
if not os.path.isdir(spacing):
os.mkdir(spacing)
for subdirectory in basin_and_saddle_dirs:
os.system('cp -r ../lateral/{} {}/'.format(subdirectory, spacing))
os.chdir('{}/{}'.format(spacing, subdirectory))
structure = Structure.from_file('POSCAR')
n_sites = len(structure.sites)
all_z_coords = [s.coords[2] for s in structure.sites]
top_layer = [s for s in structure.sites if s.coords[2] >
np.mean(all_z_coords)]
bottom_of_top_layer = min([site.coords[2] for site in top_layer])
remove_indices = [i for i, s in enumerate(structure.sites) if s in
top_layer]
structure.remove_sites(remove_indices)
top_of_bottom_layer = max(
[site.coords[2] for site in structure.sites]
)
for site in top_layer:
structure.append(
site.specie,
[site.coords[0],
site.coords[1],
site.coords[2] - bottom_of_top_layer
+ top_of_bottom_layer + float(spacing)],
coords_are_cartesian=True)
structure = structure.get_sorted_structure()
structure.to('POSCAR', 'POSCAR')
utl.write_potcar()
incar_dict = Incar.from_file('INCAR').as_dict()
incar_dict.update({"MAGMOM": utl.get_magmom_string(structure)})
Incar.from_dict(incar_dict).write_file("INCAR")
if QUEUE_SYSTEM == 'pbs':
utl.write_pbs_runjob('{}_{}'.format(
subdirectory, spacing), 1, 8, '1000mb', '2:00:00',
VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
utl.write_slurm_runjob('{}_{}'.format(
subdirectory, spacing), 8, '1000mb', '2:00:00',
VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
os.chdir('../../')
os.chdir('../../')
def GW_step2(name,
submit=True,
spin_polarized=True,
incar_dict={},
force_overwrite=False):
#Calculation is supposed to be run in parent directory (step1 should be there as well)
#incar_dict should not have NBANDS tag, since it will be extracted from step1/INCAR
incar = Incar.from_string("""
ISMEAR = -5
NBANDS = 96 # need for a lot of bands in GW
ALGO = GW0 #
NELM = 1
PRECFOCK = Fast
ENCUTGW = 100
NOMEGA = 200
KPAR = 2""")
if not os.path.isdir('step1'):
raise ValueError(
'It is not possible to run step2 before step1. Check if you are in right directory.'
)
os.chdir('step1')
if os.path.exists('WAVECAR') and os.path.exists('WAVEDER') and os.stat(
'WAVECAR').st_size > 100 and os.stat('WAVEDER').st_size > 100:
os.chdir('../')
try:
os.mkdir('step2')
os.chdir('step2')
except:
os.chdir('step2')
else:
raise ValueError(
'step1 calculation did not finish properly. WAVECAR and/or WAVEDER files are not written properly.'
)
if force_overwrite:
os.system('rm -rf *')
os.system('cp ../step1/{WAVE*,KPOINTS,POSCAR,POTCAR} .')
NBANDS = Incar.from_file('../step1/INCAR')['NBANDS']
incar.update({'NBANDS': NBANDS})
if spin_polarized:
if os.path.exists('POSCAR'):
incar.update({
'LORBIT':
11,
'ISPIN':
2,
'MAGMOM':
get_magmom_string(Structure.from_file('POSCAR'))
})
else:
raise IOError('No POSCAR found at ' + os.getcwd())
incar.write_file('INCAR')
submit_builder(update_dict={
'--mem-per-cpu': '3gb',
'--job-name': name,
'--nodes': 2,
'--ntasks': 32
})
if submit:
os.system('sbatch submit')
os.chdir('../')
def relax_references(potcar_types,
incar_dict,
submit=True,
force_overwrite=False):
"""
Set up calculation directories to calibrate
the ion corrections to match a specified framework of INCAR
parameters and potcar hashes.
Args:
potcar_types (list): list of all elements to calibrate,
containing specifications for the kind of potential
desired for each element, e.g. ['Na_pv', 'O']. If
oxygen is not explicitly included in the list, 'O'
is used.
incar_dict (dict): a dictionary of input parameters
and their values, e.g. {'ISMEAR': -5, 'NSW': 10}
submit (bool): whether or not to submit each job
after preparing it.
force_overwrite (bool): Whether or not to overwrite files
if an already converged vasprun.xml exists in the
directory.
"""
for element in potcar_types:
if element.split('_')[0] == 'O':
oxygen_potcar = element
break
else:
oxygen_potcar = 'O'
potcar_types.append('O')
for element in potcar_types:
elt = element.split('_')[0]
# First, set up a relaxation for the pure element.
if not os.path.isdir(elt):
os.mkdir(elt)
os.chdir(elt)
s = MPR.get_structure_by_material_id(REFERENCE_MPIDS[elt]['element'])
s.to('POSCAR', 'POSCAR')
relax(dim=3, submit=submit, force_overwrite=force_overwrite)
incar_dict.update({"MAGMOM": utl.get_magmom_string(s)})
Incar.from_dict(incar_dict).write_file("INCAR")
utl.write_potcar(types=[element])
# Then set up a relaxation for its reference oxide.
if elt not in ['O', 'S', 'F', 'Cl', 'Br', 'I', 'H']:
if not os.path.isdir('oxide'):
os.mkdir('oxide')
os.chdir('oxide')
s = MPR.get_structure_by_material_id(REFERENCE_MPIDS[elt]['oxide'])
s.get_sorted_structure().to('POSCAR', 'POSCAR')
relax(dim=3, submit=submit, force_overwrite=force_overwrite)
incar_dict.update({"MAGMOM": utl.get_magmom_string(s)})
Incar.from_dict(incar_dict).write_file("INCAR")
utl.write_potcar(types=[element, oxygen_potcar])
os.chdir('../')
os.chdir('../')
