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_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, incar_dict=incar_dict, submit=submit,
force_overwrite=force_overwrite)
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, incar_dict=incar_dict, submit=submit,
force_overwrite=force_overwrite)
utl.write_potcar(types=[element, oxygen_potcar])
os.chdir('../')
os.chdir('../')
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_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_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('../../')