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 run_hse_prep_calculation(dim=2, submit=True):
"""
Submits a quick static calculation to calculate the IBZKPT
file using a smaller number of k-points (200/atom instead of
1000/atom). The other outputs from this calculation are
essentially useless.
Args:
dim (int): 2 for relaxing a 2D material, 3 for a 3D material.
submit (bool): Whether or not to submit the job.
"""
if not os.path.isdir('hse_prep'):
os.mkdir('hse_prep')
os.chdir('hse_prep')
shutil.copy('../CONTCAR', 'POSCAR')
if os.path.isfile('../POTCAR'):
shutil.copy('POTCAR', '.')
relax(dim=2, submit=False)
incar_dict = Incar.from_file('INCAR').as_dict()
incar_dict.update({
'NSW': 0,
'NELM': 1,
'LWAVE': False,
'LCHARG': False,
'LAECHG': False
})
Incar.from_dict(incar_dict).write_file('INCAR')
Kpoints.automatic_density(Structure.from_file('POSCAR'),
200).write_file('KPOINTS')
if dim == 2:
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')
if QUEUE_SYSTEM == 'pbs':
write_pbs_runjob('{}_prep'.format(os.getcwd().split('/')[-2]), 1, 16,
'800mb', '6:00:00', VASP_STD_BIN)
submission_command = 'qsub runjob'
elif QUEUE_SYSTEM == 'slurm':
write_slurm_runjob('{}_prep'.format(os.getcwd().split('/')[-2]), 16,
'800mb', '6:00:00', VASP_STD_BIN)
submission_command = 'sbatch runjob'
if submit:
_ = subprocess.check_output(submission_command.split())
os.chdir('../')
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_normal_force_calculations(basin_and_saddle_dirs,
spacings=(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)
top_layer = structure.sites[int(n_sites / 2):]
bottom_of_top_layer = min([
z_coord for z_coord in [site.coords[2] for site in top_layer]
])
remove_indices = range(int(n_sites / 2), n_sites)
structure.remove_sites(remove_indices)
max_height = 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 + max_height + float(spacing)
],
coords_are_cartesian=True)
structure.to('POSCAR', 'POSCAR')
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_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 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('../../')
