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 != '/path/to/vdw_kernel.bindat':
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()})
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.add_vacuum(20 - utl.get_spacing(), 0.9)
# 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 QUEUE == 'pbs':
utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00',
VASP_2D)
submission_command = 'qsub runjob'
elif QUEUE == 'slurm':
utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00',
VASP_2D)
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 != '/path/to/vdw_kernel.bindat':
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()})
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.add_vacuum(20 - utl.get_spacing(), 0.9)
# 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 QUEUE == 'pbs':
utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00', VASP_2D)
submission_command = 'qsub runjob'
elif QUEUE == 'slurm':
utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00', VASP_2D)
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.add_vacuum(20 - utl.get_spacing(), 0.8)
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.
new_sites = []
for site in structure.sites:
new_sites.append((site.specie,
[site.coords[0], site.coords[1],
site.coords[2] + thickness + 3.5]))
for site in new_sites:
structure.append(site[0], site[1], coords_are_cartesian=True)
#structure.get_sorted_structure().to('POSCAR', 'POSCAR')
structure.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 != '/path/to/vdw_kernel.bindat':
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,
'MAGMOM': utl.get_magmom_string()})
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')
if QUEUE == 'pbs':
utl.write_pbs_runjob(dir, 1, 4, '800mb', '1:00:00', VASP)
submission_command = 'qsub runjob'
elif QUEUE == 'slurm':
utl.write_slurm_runjob(dir, 4, '800mb', '1:00:00', VASP)
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 (list): 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 == 'pbs':
utl.write_pbs_runjob('{}_{}'.format(subdirectory, spacing), 1,
4, '400mb', '1:00:00', VASP)
submission_command = 'qsub runjob'
elif QUEUE == 'slurm':
utl.write_slurm_runjob('{}_{}'.format(subdirectory, spacing), 4,
'400mb', '1:00:00', VASP)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
os.chdir('../../')
os.chdir('../../')
def prepare(self, submit=False):
"""
Set up calculation directories to calibrate
the ion corrections to match a specified framework of INCAR
parameters, k-points, and potcar hashes.
Args:
submit (bool): whether or not to submit each job
after preparing it.
"""
for elt in self._potcar_dict:
# Set up reference directory for the pure element.
if not os.path.isdir(elt):
os.mkdir(elt)
os.chdir(elt)
# Poscar
s = MPR.get_structure_by_material_id(
self._config['Mpids'][elt]['self'])
s.to('POSCAR', 'POSCAR')
plines = open('POSCAR').readlines()
elements = plines[5].split()
# Kpoints
kp = Kpoints.automatic_density(s, self._n_kpts_per_atom)
kp.write_file('KPOINTS')
# Incar
incar = Incar.from_dict(self._incar_dict)
incar.write_file('INCAR')
# Potcar
utl.write_potcar(types=[self._potcar_dict[el] for el in elements])
# Runjob
if QUEUE == 'pbs':
utl.write_pbs_runjob('{}_cal'.format(elt), self._ncores,
self._nprocs, self._pmem, self._walltime,
self._binary)
submission_command = 'qsub runjob'
elif QUEUE == 'slurm':
utl.write_slurm_runjob('{}_cal'.format(elt), self._nprocs,
self._pmem, self._walltime,
self._binary)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
# Set up reference oxide compound subdirectory.
if elt not in ['O', 'S', 'F', 'Cl', 'Br', 'I']:
if not os.path.isdir('ref'):
os.mkdir('ref')
os.chdir('ref')
# Poscar
s = MPR.get_structure_by_material_id(
self._config['Mpids'][elt]['ref'])
s.to('POSCAR', 'POSCAR')
plines = open('POSCAR').readlines()
elements = plines[5].split()
# Kpoints
kp = Kpoints.automatic_density(s, self._n_kpts_per_atom)
kp.write_file('KPOINTS')
# Incar
incar = Incar.from_dict(self._incar_dict)
incar.write_file('INCAR')
# Potcar
utl.write_potcar(
types=[self._potcar_dict[el] for el in elements])
# Runjob
if QUEUE == 'slurm':
utl.write_pbs_runjob('{}_cal'.format(elt), self._ncores,
self._nprocs, self._pmem,
self._walltime, self._binary)
submission_command = 'qsub runjob'
elif QUEUE == 'pbs':
utl.write_slurm_runjob('{}_cal'.format(elt), self._nprocs,
self._pmem, self._walltime,
self._binary)
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')
os.system('cp ../../CONTCAR POSCAR')
# Pad the bottom layer with 20 Angstroms of vacuum.
utl.add_vacuum(20 - utl.get_spacing(), 0.8)
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.
new_sites = []
for site in structure.sites:
new_sites.append((site.specie,
[site.coords[0], site.coords[1],
site.coords[2] + thickness + 3.5]))
for site in new_sites:
structure.append(site[0], site[1], coords_are_cartesian=True)
#structure.get_sorted_structure().to('POSCAR', 'POSCAR')
structure.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 != '/path/to/vdw_kernel.bindat':
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()})
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')
if QUEUE == 'pbs':
utl.write_pbs_runjob(dir, 1, 8, '1000mb', '2:00:00', VASP)
submission_command = 'qsub runjob'
elif QUEUE == 'slurm':
utl.write_slurm_runjob(dir, 8, '1000mb', '2:00:00', VASP)
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 (list): 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 == 'pbs':
utl.write_pbs_runjob('{}_{}'.format(subdirectory, spacing), 1,
8, '1000mb', '2:00:00', VASP)
submission_command = 'qsub runjob'
elif QUEUE == 'slurm':
utl.write_slurm_runjob('{}_{}'.format(subdirectory, spacing), 8,
'1000mb', '2:00:00', VASP)
submission_command = 'sbatch runjob'
if submit:
os.system(submission_command)
os.chdir('../../')
os.chdir('../../')