def load(self, style, *args, **kwargs):
"""
Wrapper around atomman.load() for loading files that also saves the
file loading options as class attributes. Any parameters not given
will use the values already set to the object.
"""
# Load ucell
self.__ucell = am.load(style, *args, **kwargs)
self.ucell.wrap()
# Check if first variable positional argument is a file
try:
load_file = Path(args[0])
except:
self.load_file = None
else:
if load_file.is_file():
self.load_file = load_file
else:
self.load_file = None
# Set load style
if self.load_file is None:
self.load_style = style
else:
self.load_style = 'system_model'
def load_model(self, model):
"""Loads subset attributes from an existing model."""
sub = model[self.modelroot]
d = {}
d['family'] = sub['family']
if 'artifact' in sub:
if 'initial-atomic-system' in sub:
ValueError('found both load file and embedded content for the initial system')
d['load_style'] = sub['artifact']['format']
d['load_file'] = sub['artifact']['file']
load_options = sub['artifact'].get('load_options', None)
elif 'initial-atomic-system' in sub:
d['ucell'] = am.load('system_model', sub, key='initial-atomic-system')
else:
ValueError('neither load file nor embedded content found for the initial system')
d['symbols'] = sub['symbol']
d['composition'] = sub.get('composition', None)
if load_options is not None:
d['load_options'] = {}
load_options_keys = ['key', 'index', 'data_set', 'pbc', 'atom_style',
'units', 'prop_info']
d['load_options'] = termtodict(load_options, load_options_keys)
if 'index' in d['load_options']:
d['load_options']['index'] = int(d['load_options']['index'])
self.set_values(**d)
def stacking_fault_generation(structure, sizemults, a1, a2, hkl, a1vect_uvw, a2vect_uvw):
'''
Generate stacking fault struture using Atomman.
Please note the below about Atomman:
One layer means one 'ucell' in the defect.StackingFault, along the 'hkl' direction.
So 'sizemults[2]=6' means 6 ucell above the stacking fault slide plane, and 6 layers below.
i.e. totally 12 ucell/layers in the surface system
Args:
structure: pymatgen structure
sizemults: how to extend the struture when building surface
a1: fraction of the slide movement along a1vect_uvu
a2: fraction of the slide movement along a2vect_uvu
hkl: the stacking fault slide plane
a1vect_uvw: the stacking fault moving direction
a2vect_uvw: the stacking fault moving direction
Return:
pymatgen structure containing stacking fault
'''
# generate stakcing fault object using atomman, and then change to pymatgen for random occupuation
stru_atomman = atomman.load('pymatgen_Structure', structure)
stack_fault = atomman.defect.StackingFault(hkl=hkl, ucell=stru_atomman,
a1vect_uvw=a1vect_uvw, a2vect_uvw=a2vect_uvw)
# it is a bit wired that surface_sys is not used in the rest of the code,
# but that is how atomman is designed
surface_sys = stack_fault.surface(shift=stack_fault.shifts[0], even=True,
sizemults=sizemults, vacuumwidth=15)
fault_sys = stack_fault.fault(a1=a1, a2=a2)
fault_sys_pymatgen = Structure.from_str(fault_sys.dump('poscar'), fmt='poscar')
return fault_sys_pymatgen
def spg_ucell(self):
"""atomman.System: The unit cell identified following the space-group analysis"""
if self.__spg_ucell is None:
raise ValueError('No results yet!')
if not isinstance(self.__spg_ucell, am.System):
self.__spg_ucell = am.load('system_model', self.__spg_ucell)
return self.__spg_ucell
def load_system_defect(self):
if self.__system_defect is None:
fname = self.dumpfile_defect
tar = self.database.get_tar(record=self)
f = tar.extractfile(fname)
self.__system_defect = am.load('atom_dump',
f,
symbols=self.symbols_defect)
def todict(self, full=True, flat=False):
"""
Converts the structured content to a simpler dictionary.
Parameters
----------
full : bool, optional
Flag used by the calculation records. A True value will include
terms for both the calculation's input and results, while a value
of False will only include input terms (Default is True).
flat : bool, optional
Flag affecting the format of the dictionary terms. If True, the
dictionary terms are limited to having only str, int, and float
values, which is useful for comparisons. If False, the term
values can be of any data type, which is convenient for analysis.
(Default is False).
Returns
-------
dict
A dictionary representation of the record's content.
"""
# Fetch universal record params
params = super().todict(full=full, flat=flat)
crystal = self.content[self.contentroot]
params['method'] = crystal['method']
params['standing'] = crystal.get('standing', 'good')
# Extract potential info
subset('lammps_potential').todict(crystal, params, full=full, flat=flat)
params['family'] = crystal['system-info']['family']
params['parent_key'] = crystal['system-info']['parent_key']
ucell = am.load('system_model', self.content, key='atomic-system')
params['composition'] = ucell.composition
#print('potential-energy' in crystal)
if 'potential-energy' in crystal:
params['E_pot'] = uc.value_unit(crystal['potential-energy'])
params['E_coh'] = uc.value_unit(crystal['cohesive-energy'])
else:
params['E_coh'] = params['E_pot'] = uc.value_unit(crystal['cohesive-energy'])
if flat is True:
params['symbols'] = list(ucell.symbols)
params['a'] = ucell.box.a
params['b'] = ucell.box.b
params['c'] = ucell.box.c
params['alpha'] = ucell.box.alpha
params['beta'] = ucell.box.beta
params['gamma'] = ucell.box.gamma
params['natoms'] = ucell.natoms
else:
params['ucell'] = ucell
return params
def load(self, style, input, **kwargs):
"""Load a System."""
system, symbols = am.load(style, input, **kwargs)
self.__box = system.box
self.__atoms = system.atoms
self.__pbc = system.pbc
self.__prop = system.prop
return symbols
def min_cells(self):
"""list : atomman.Systems for the dimensions scanned with local energy minima."""
if self.__min_cells is None:
raise ValueError('No results yet!')
for i in range(len(self.__min_cells)):
if not isinstance(self.__min_cells[i], am.System):
self.__min_cells[i] = am.load('system_model',
self.__min_cells[i])
return self.__min_cells
def todict(self, full=True, flat=False):
"""
Converts the structured content to a simpler dictionary.
Parameters
----------
full : bool, optional
Flag used by the calculation records. A True value will include
terms for both the calculation's input and results, while a value
of False will only include input terms (Default is True).
flat : bool, optional
Flag affecting the format of the dictionary terms. If True, the
dictionary terms are limited to having only str, int, and float
values, which is useful for comparisons. If False, the term
values can be of any data type, which is convenient for analysis.
(Default is False).
Returns
-------
dict
A dictionary representation of the record's content.
"""
# Fetch universal record params
params = super().todict(full=full, flat=flat)
proto = self.content[self.contentroot]
params['name'] = proto['name']
params['prototype'] = proto['prototype']
params['Pearson_symbol'] = proto['Pearson-symbol']
params['Strukturbericht'] = proto['Strukturbericht']
params['sg_number'] = proto['space-group']['number']
params['sg_HG'] = proto['space-group']['Hermann-Maguin']
params['sg_Schoen'] = proto['space-group']['Schoenflies']
ucell = am.load('system_model', self.content, key='atomic-system')
params['crystal_family'] = am.tools.identifyfamily(ucell.box)
params['natypes'] = ucell.natypes
if flat is True:
params['a'] = ucell.box.a
params['b'] = ucell.box.b
params['c'] = ucell.box.c
params['alpha'] = ucell.box.alpha
params['beta'] = ucell.box.beta
params['gamma'] = ucell.box.gamma
params['natoms'] = ucell.natoms
else:
params['ucell'] = ucell
return params
def assign_composition(df, database, lib_directory=None):
"""
Assigns compositions to calculations.
"""
# Build counts for available prototypes
prototypes = database.get_records(style='crystal_prototype')
counts = {}
for prototype in prototypes:
counts[prototype.name] = np.unique(
prototype.content.finds('component'), return_counts=True)[1]
# Set default lib_directory (for ref structures)
if lib_directory is None:
lib_directory = Settings().library_directory
# Identify compositions
compositions = []
for i in range(len(df)):
series = df.iloc[i]
# Use ucell system if available (crystal_space_group)
if 'ucell' in series:
composition = series.ucell.composition
if composition is not None:
compositions.append(composition)
else:
compositions.append(np.nan)
# Use symbols and family info if available (E_vs_r_scan, relax_*)
elif 'symbols' in series and 'family' in series:
# If family is a prototype
if series.family in counts:
compositions.append(
am.tools.compositionstr(series.symbols,
counts[series.family]))
# If family is a ref
else:
fname = Path(lib_directory, 'reference_crystal',
series.family + '.json')
try:
ucell = am.load('system_model', fname)
except:
compositions.append(np.nan)
else:
count = np.unique(ucell.atoms.atype, return_counts=True)[1]
compositions.append(
am.tools.compositionstr(ucell.symbols, count))
else:
compositions.append(np.nan)
df['composition'] = compositions
def todict(self, full=True, flat=False):
"""
Converts the structured content to a simpler dictionary.
Parameters
----------
full : bool, optional
Flag used by the calculation records. A True value will include
terms for both the calculation's input and results, while a value
of False will only include input terms (Default is True).
flat : bool, optional
Flag affecting the format of the dictionary terms. If True, the
dictionary terms are limited to having only str, int, and float
values, which is useful for comparisons. If False, the term
values can be of any data type, which is convenient for analysis.
(Default is False).
Returns
-------
dict
A dictionary representation of the record's content.
"""
# Fetch universal record params
params = super().todict(full=full, flat=flat)
crystal = self.content[self.contentroot]
params['sourcename'] = crystal['source']['name']
params['sourcelink'] = crystal['source']['link']
ucell = am.load('system_model', self.content, key='atomic-system')
params['composition'] = ucell.composition
params['natypes'] = ucell.natypes
if flat is True:
params['symbols'] = list(ucell.symbols)
params['a'] = ucell.box.a
params['b'] = ucell.box.b
params['c'] = ucell.box.c
params['alpha'] = ucell.box.alpha
params['beta'] = ucell.box.beta
params['gamma'] = ucell.box.gamma
params['natoms'] = ucell.natoms
else:
params['ucell'] = ucell
return params
def load_dump(self, system1, atom_style=None, units=None, potential=None):
"""
Utility function that dumps, loads, and dumps, then asserts two dumps
are equivalent
"""
# dump system1 to content1
content1 = system1.dump('atom_data', atom_style=atom_style,
units=units, potential=potential,
return_info=False)
# load content1 to system2
system2 = am.load('atom_data', content1, pbc=system1.pbc,
symbols=system1.symbols, atom_style=atom_style,
units=units, potential=potential)
# dump system2 to content2
content2 = system2.dump('atom_data', atom_style=atom_style,
units=units, potential=potential,
return_info=False)
# Check that the two dumps are equivalent
assert content1 == content2
def test_badfile_no_box(self):
"""Raise FileFormatError if any *lo *hl lines are missing"""
# missing xlo xhi
content = '\n'.join(self.data_lines[:3] + self.data_lines[4:])
with pytest.raises(FileFormatError):
am.load('atom_data', content)
# missing ylo yhi
content = '\n'.join(self.data_lines[:4] + self.data_lines[5:])
with pytest.raises(FileFormatError):
am.load('atom_data', content)
# missing zlo zhi
content = '\n'.join(self.data_lines[:5] + self.data_lines[6:])
with pytest.raises(FileFormatError):
am.load('atom_data', content)
def relax_static(lammps_command,
system,
potential,
mpi_command=None,
p_xx=0.0,
p_yy=0.0,
p_zz=0.0,
p_xy=0.0,
p_xz=0.0,
p_yz=0.0,
dispmult=0.0,
etol=0.0,
ftol=0.0,
maxiter=10000,
maxeval=100000,
dmax=uc.set_in_units(0.01, 'angstrom'),
maxcycles=100,
ctol=1e-10):
"""
Repeatedly runs the ELASTIC example distributed with LAMMPS until box
dimensions converge within a tolerance.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
system : atomman.System
The system to perform the calculation on.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
mpi_command : str, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
p_xx : float, optional
The value to relax the x tensile pressure component to (default is
0.0).
p_yy : float, optional
The value to relax the y tensile pressure component to (default is
0.0).
p_zz : float, optional
The value to relax the z tensile pressure component to (default is
0.0).
p_xy : float, optional
The value to relax the xy shear pressure component to (default is
0.0).
p_xz : float, optional
The value to relax the xz shear pressure component to (default is
0.0).
p_yz : float, optional
The value to relax the yz shear pressure component to (default is
0.0).
dispmult : float, optional
Multiplier for applying a random displacement to all atomic positions
prior to relaxing. Default value is 0.0.
etol : float, optional
The energy tolerance for the structure minimization. This value is
unitless. (Default is 0.0).
ftol : float, optional
The force tolerance for the structure minimization. This value is in
units of force. (Default is 0.0).
maxiter : int, optional
The maximum number of minimization iterations to use (default is 10000).
maxeval : int, optional
The maximum number of minimization evaluations to use (default is
100000).
dmax : float, optional
The maximum distance in length units that any atom is allowed to relax
in any direction during a single minimization iteration (default is
0.01 Angstroms).
pressure_unit : str, optional
The unit of pressure to calculate the elastic constants in (default is
'GPa').
maxcycles : int, optional
The maximum number of times the minimization algorithm is called.
Default value is 100.
ctol : float, optional
The relative tolerance used to determine if the lattice constants have
converged (default is 1e-10).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'relaxed_system'** (*float*) - The relaxed system.
- **'E_coh'** (*float*) - The cohesive energy of the relaxed system.
- **'measured_pxx'** (*float*) - The measured x tensile pressure of the
relaxed system.
- **'measured_pyy'** (*float*) - The measured y tensile pressure of the
relaxed system.
- **'measured_pzz'** (*float*) - The measured z tensile pressure of the
relaxed system.
- **'measured_pxy'** (*float*) - The measured xy shear pressure of the
relaxed system.
- **'measured_pxz'** (*float*) - The measured xz shear pressure of the
relaxed system.
- **'measured_pyz'** (*float*) - The measured yz shear pressure of the
relaxed system.
"""
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
# Get lammps version date
lammps_date = lmp.checkversion(lammps_command)['date']
# Save initial configuration as a dump file
system.dump('atom_dump', f='initial.dump')
# Apply small random distortions to atoms
system.atoms.pos += dispmult * np.random.rand(
*system.atoms.pos.shape) - dispmult / 2
# Initialize parameters
old_vects = system.box.vects
converged = False
# Run minimizations up to maxcycles times
for cycle in range(maxcycles):
old_system = deepcopy(system)
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data',
f='init.dat',
units=potential.units,
atom_style=potential.atom_style)
lammps_variables['atomman_system_info'] = system_info
lammps_variables['atomman_pair_info'] = potential.pair_info(
system.symbols)
lammps_variables['p_xx'] = uc.get_in_units(p_xx,
lammps_units['pressure'])
lammps_variables['p_yy'] = uc.get_in_units(p_yy,
lammps_units['pressure'])
lammps_variables['p_zz'] = uc.get_in_units(p_zz,
lammps_units['pressure'])
lammps_variables['p_xy'] = uc.get_in_units(p_xy,
lammps_units['pressure'])
lammps_variables['p_xz'] = uc.get_in_units(p_xz,
lammps_units['pressure'])
lammps_variables['p_yz'] = uc.get_in_units(p_yz,
lammps_units['pressure'])
lammps_variables['etol'] = etol
lammps_variables['ftol'] = uc.get_in_units(ftol, lammps_units['force'])
lammps_variables['maxiter'] = maxiter
lammps_variables['maxeval'] = maxeval
lammps_variables['dmax'] = uc.get_in_units(dmax,
lammps_units['length'])
# Set dump_modify_format based on lammps_date
if lammps_date < datetime.date(2016, 8, 3):
lammps_variables[
'dump_modify_format'] = '"%d %d %.13e %.13e %.13e %.13e"'
else:
lammps_variables['dump_modify_format'] = 'float %.13e'
# Write lammps input script
template_file = 'minbox.template'
lammps_script = 'minbox.in'
with open(template_file) as f:
template = f.read()
with open(lammps_script, 'w') as f:
f.write(
iprPy.tools.filltemplate(template, lammps_variables, '<', '>'))
# Run LAMMPS and extract thermo data
logfile = 'log-' + str(cycle) + '.lammps'
output = lmp.run(lammps_command,
lammps_script,
mpi_command,
logfile=logfile)
thermo = output.simulations[0]['thermo']
# Clean up dump files
os.remove('0.dump')
last_dump_file = str(thermo.Step.values[-1]) + '.dump'
renamed_dump_file = 'relax_static-' + str(cycle) + '.dump'
shutil.move(last_dump_file, renamed_dump_file)
# Load relaxed system
system = am.load('atom_dump',
renamed_dump_file,
symbols=system.symbols)
# Test if box dimensions have converged
if np.allclose(old_vects, system.box.vects, rtol=ctol, atol=0):
converged = True
break
else:
old_vects = system.box.vects
# Check for convergence
if converged is False:
raise RuntimeError('Failed to converge after ' + str(maxcycles) +
' cycles')
# Zero out near-zero tilt factors
lx = system.box.lx
ly = system.box.ly
lz = system.box.lz
xy = system.box.xy
xz = system.box.xz
yz = system.box.yz
if np.isclose(xy / ly, 0.0, rtol=0.0, atol=1e-10):
xy = 0.0
if np.isclose(xz / lz, 0.0, rtol=0.0, atol=1e-10):
xz = 0.0
if np.isclose(yz / lz, 0.0, rtol=0.0, atol=1e-10):
yz = 0.0
system.box.set(lx=lx, ly=ly, lz=lz, xy=xy, xz=xz, yz=yz)
system.wrap()
# Build results_dict
results_dict = {}
results_dict['dumpfile_initial'] = 'initial.dump'
results_dict['symbols_initial'] = system.symbols
results_dict['dumpfile_final'] = renamed_dump_file
results_dict['symbols_final'] = system.symbols
results_dict['E_coh'] = uc.set_in_units(
thermo.PotEng.values[-1] / system.natoms, lammps_units['energy'])
results_dict['lx'] = uc.set_in_units(lx, lammps_units['length'])
results_dict['ly'] = uc.set_in_units(ly, lammps_units['length'])
results_dict['lz'] = uc.set_in_units(lz, lammps_units['length'])
results_dict['xy'] = uc.set_in_units(xy, lammps_units['length'])
results_dict['xz'] = uc.set_in_units(xz, lammps_units['length'])
results_dict['yz'] = uc.set_in_units(yz, lammps_units['length'])
results_dict['measured_pxx'] = uc.set_in_units(thermo.Pxx.values[-1],
lammps_units['pressure'])
results_dict['measured_pyy'] = uc.set_in_units(thermo.Pyy.values[-1],
lammps_units['pressure'])
results_dict['measured_pzz'] = uc.set_in_units(thermo.Pzz.values[-1],
lammps_units['pressure'])
results_dict['measured_pxy'] = uc.set_in_units(thermo.Pxy.values[-1],
lammps_units['pressure'])
results_dict['measured_pxz'] = uc.set_in_units(thermo.Pxz.values[-1],
lammps_units['pressure'])
results_dict['measured_pyz'] = uc.set_in_units(thermo.Pyz.values[-1],
lammps_units['pressure'])
return results_dict
def pointdefect(
lammps_command: str,
system: am.System,
potential: lmp.Potential,
point_kwargs: Union[list, dict],
mpi_command: Optional[str] = None,
etol: float = 0.0,
ftol: float = 0.0,
maxiter: int = 10000,
maxeval: int = 100000,
dmax: float = uc.set_in_units(0.01, 'angstrom')
) -> dict:
"""
Adds one or more point defects to a system and evaluates the defect
formation energy.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
system : atomman.System
The system to perform the calculation on.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
point_kwargs : dict or list of dict
One or more dictionaries containing the keyword arguments for
the atomman.defect.point() function to generate specific point
defect configuration(s).
mpi_command : str, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
sim_directory : str, optional
The path to the directory to perform the simulation in. If not
given, will use the current working directory.
etol : float, optional
The energy tolerance for the structure minimization. This value is
unitless. (Default is 0.0).
ftol : float, optional
The force tolerance for the structure minimization. This value is in
units of force. (Default is 0.0).
maxiter : int, optional
The maximum number of minimization iterations to use (default is
10000).
maxeval : int, optional
The maximum number of minimization evaluations to use (default is
100000).
dmax : float, optional
The maximum distance in length units that any atom is allowed to relax
in any direction during a single minimization iteration (default is
0.01 Angstroms).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'E_pot'** (*float*) - The per-atom potential energy of the bulk system.
- **'E_ptd_f'** (*float*) - The point defect formation energy.
- **'E_total_base'** (*float*) - The total potential energy of the
relaxed bulk system.
- **'E_total_ptd'** (*float*) - The total potential energy of the
relaxed defect system.
- **'pij_tensor'** (*numpy.ndarray of float*) - The elastic dipole
tensor associated with the defect.
- **'system_base'** (*atomman.System*) - The relaxed bulk system.
- **'system_ptd'** (*atomman.System*) - The relaxed defect system.
- **'dumpfile_base'** (*str*) - The filename of the LAMMPS dump file
for the relaxed bulk system.
- **'dumpfile_ptd'** (*str*) - The filename of the LAMMPS dump file
for the relaxed defect system.
"""
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Get lammps version date
lammps_date = lmp.checkversion(lammps_command)['date']
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data',
f='perfect.dat',
potential=potential)
lammps_variables['atomman_system_pair_info'] = system_info
lammps_variables['etol'] = etol
lammps_variables['ftol'] = uc.get_in_units(ftol, lammps_units['force'])
lammps_variables['maxiter'] = maxiter
lammps_variables['maxeval'] = maxeval
lammps_variables['dmax'] = dmax
# Set dump_modify_format based on lammps_date
if lammps_date < datetime.date(2016, 8, 3):
lammps_variables[
'dump_modify_format'] = '"%d %d %.13e %.13e %.13e %.13e %.13e %.13e %.13e"'
else:
lammps_variables['dump_modify_format'] = 'float %.13e'
# Write lammps input script
lammps_script = 'min.in'
template = read_calc_file('iprPy.calculation.point_defect_static',
'min.template')
with open(lammps_script, 'w') as f:
f.write(filltemplate(template, lammps_variables, '<', '>'))
# Run lammps to relax perfect.dat
output = lmp.run(lammps_command,
script_name=lammps_script,
mpi_command=mpi_command)
# Extract LAMMPS thermo data.
thermo = output.simulations[0]['thermo']
E_total_base = uc.set_in_units(thermo.PotEng.values[-1],
lammps_units['energy'])
E_pot = E_total_base / system.natoms
pxx = uc.set_in_units(thermo.Pxx.values[-1], lammps_units['pressure'])
pyy = uc.set_in_units(thermo.Pyy.values[-1], lammps_units['pressure'])
pzz = uc.set_in_units(thermo.Pzz.values[-1], lammps_units['pressure'])
pxy = uc.set_in_units(thermo.Pxy.values[-1], lammps_units['pressure'])
pxz = uc.set_in_units(thermo.Pxz.values[-1], lammps_units['pressure'])
pyz = uc.set_in_units(thermo.Pyz.values[-1], lammps_units['pressure'])
pressure_base = np.array([[pxx, pxy, pxz], [pxy, pyy, pyz],
[pxz, pyz, pzz]])
# Rename log file
shutil.move('log.lammps', 'min-perfect-log.lammps')
# Load relaxed system from dump file and copy old box vectors because
# dump files crop the values.
last_dump_file = 'atom.' + str(thermo.Step.values[-1])
system_base = am.load('atom_dump', last_dump_file, symbols=system.symbols)
system_base.box_set(vects=system.box.vects)
system_base.dump('atom_dump', f='perfect.dump')
# Add defect(s)
system_ptd = deepcopy(system_base)
if not isinstance(point_kwargs, (list, tuple)):
point_kwargs = [point_kwargs]
for pkwargs in point_kwargs:
system_ptd = am.defect.point(system_ptd, **pkwargs)
# Update lammps variables
system_info = system_ptd.dump('atom_data',
f='defect.dat',
potential=potential)
lammps_variables['atomman_system_pair_info'] = system_info
# Write lammps input script
with open(lammps_script, 'w') as f:
f.write(filltemplate(template, lammps_variables, '<', '>'))
# Run lammps
output = lmp.run(lammps_command,
script_name=lammps_script,
mpi_command=mpi_command)
# Extract lammps thermo data
thermo = output.simulations[0]['thermo']
E_total_ptd = uc.set_in_units(thermo.PotEng.values[-1],
lammps_units['energy'])
pxx = uc.set_in_units(thermo.Pxx.values[-1], lammps_units['pressure'])
pyy = uc.set_in_units(thermo.Pyy.values[-1], lammps_units['pressure'])
pzz = uc.set_in_units(thermo.Pzz.values[-1], lammps_units['pressure'])
pxy = uc.set_in_units(thermo.Pxy.values[-1], lammps_units['pressure'])
pxz = uc.set_in_units(thermo.Pxz.values[-1], lammps_units['pressure'])
pyz = uc.set_in_units(thermo.Pyz.values[-1], lammps_units['pressure'])
pressure_ptd = np.array([[pxx, pxy, pxz], [pxy, pyy, pyz], [pxz, pyz,
pzz]])
# Rename log file
shutil.move('log.lammps', 'min-defect-log.lammps')
# Load relaxed system from dump file and copy old vects as
# the dump files crop the values
last_dump_file = 'atom.' + str(thermo.Step.values[-1])
system_ptd = am.load('atom_dump',
last_dump_file,
symbols=system_ptd.symbols)
system_ptd.box_set(vects=system.box.vects)
system_ptd.dump('atom_dump', f='defect.dump')
# Compute defect formation energy
E_ptd_f = E_total_ptd - E_pot * system_ptd.natoms
# Compute strain tensor
pij = -(pressure_base - pressure_ptd) * system_base.box.volume
# Cleanup files
for fname in Path.cwd().glob('atom.*'):
fname.unlink()
for dumpjsonfile in Path.cwd().glob('*.dump.json'):
dumpjsonfile.unlink()
# Return results
results_dict = {}
results_dict['E_pot'] = E_pot
results_dict['E_ptd_f'] = E_ptd_f
results_dict['E_total_base'] = E_total_base
results_dict['E_total_ptd'] = E_total_ptd
results_dict['pij_tensor'] = pij
results_dict['system_base'] = system_base
results_dict['system_ptd'] = system_ptd
results_dict['dumpfile_base'] = 'perfect.dump'
results_dict['dumpfile_ptd'] = 'defect.dump'
return results_dict
def get_oqmd_structures(elements, lib_directory=None):
"""
Accesses the Materials Project and downloads all structures for a list of
elements as poscar files.
Parameters
----------
elements : list
A list of element symbols.
lib_directory : str
Path to the lib_directory to save the poscar files to. Default uses
the iprPy library/dft_structures directory.
"""
# Function-specific imports
import requests
# Get default lib_directory
if lib_directory is None:
lib_directory = os.path.join(os.path.dirname(rootdir), 'library', 'ref')
lib_directory = os.path.abspath(lib_directory)
# Set comp_directory
elements.sort()
have = []
for subelements in subsets(elements):
elements_string = '-'.join(subelements)
comp_directory = os.path.join(lib_directory, elements_string)
if not os.path.isdir(comp_directory):
os.makedirs(comp_directory)
# Build list of downloaded entries
for fname in glob.iglob(os.path.join(comp_directory, 'oqmd-*.poscar')):
have.append(os.path.splitext(os.path.basename(fname))[0])
#print('Have', len(have), 'records')
# Build list of missing OQMD entries
elements_string = '-'.join(elements)
composition_r = requests.get('http://oqmd.org/materials/composition/' + elements_string)
composition_html = composition_r.text
missing = []
count = 0
while True:
count += 1
try:
start = composition_html.index('href="/materials/entry/') + len('href="/materials/entry/')
except:
break
else:
end = start + composition_html[start:].index('">')
entry_number = composition_html[start:end]
composition_html = composition_html[end+2:]
entry_id = 'oqmd-'+entry_number
if entry_id not in have and entry_id not in missing:
missing.append(entry_id)
if count > 100:
raise ValueError('Loop likely infinite')
#print('Missing', len(missing), 'records')
# Download missing entries
for entry_id in missing:
entry_number = entry_id.replace('oqmd-', '')
entry_r = requests.get('http://oqmd.org/materials/entry/' + entry_number)
entry_html = entry_r.text
start = entry_html.index('href="/materials/structure/') + len('href="/materials/structure/')
end = start + entry_html[start:].index('">')
structure_number = entry_html[start:end]
try:
structure_url = 'http://oqmd.org/materials/export/conventional/poscar/' + structure_number
structure_r = requests.get(structure_url)
structure_r.raise_for_status()
except:
try:
structure_url = 'http://oqmd.org/materials/export/primitive/poscar/' + structure_number
structure_r = requests.get(structure_url)
structure_r.raise_for_status()
except:
continue
# Save poscar
poscar = structure_r.text
system = am.load('poscar', poscar)
system = system.normalize()
elements_string = '-'.join(system.symbols)
structure_file = os.path.join(lib_directory, elements_string, entry_id + '.poscar')
with open(structure_file, 'w') as f:
f.write(poscar)
print('Added', entry_id)
def atomman_systemload(input_dict, build=True, **kwargs):
"""
Interprets calculation parameters associated with building a ucell system.
The input_dict keys used by this function (which can be renamed using the
function's keyword arguments):
- **'load_file'** file to load system information from.
- **'load_style'** file format of load_file.
- **'load_content'** alternate file or content to load instead of
specified load_file. This is used by prepare functions.
- **'load_options'** any additional options associated with loading the
load file as an atomman.System.
- **'symbols'** the list of atomic symbols associated with ucell's atom
types. Optional if this information is in load/load_content.
- **'box_parameters'** the string of box parameters to scale the system
by. Optional if the load file already is properly scaled.
- **'family'** if input_dict or the load file contains a family term, then
it is passed on. Otherwise, a new family is created based on the
load file's name.
- **'ucell'** this is where the resulting system is saved.
Parameters
----------
input_dict : dict
Dictionary containing input parameter key-value pairs.
build : bool
If False, parameters will be interpreted, but objects won't be built
from them (Default is True).
load_file : str
Replacement parameter key name for 'load_file'.
load_style : str
Replacement parameter key name for 'load_style'.
load_options : str
Replacement parameter key name for 'load_options'.
symbols : str
Replacement parameter key name for 'symbols'.
box_parameters : str
Replacement parameter key name for 'box_parameters'.
family : str
Replacement parameter key name for 'family'.
ucell : str
Replacement parameter key name for 'ucell'.
"""
# Set default keynames
keynames = [
'load_file', 'load_style', 'load_options', 'load_content',
'box_parameters', 'family', 'ucell', 'symbols'
]
for keyname in keynames:
kwargs[keyname] = kwargs.get(keyname, keyname)
# Extract input values and assign default values
load_file = input_dict[kwargs['load_file']]
load_style = input_dict.get(kwargs['load_style'], 'system_model')
load_options = input_dict.get(kwargs['load_options'], None)
load_content = input_dict.get(kwargs['load_content'], None)
family = input_dict.get(kwargs['family'], None)
symbols = input_dict.get(kwargs['symbols'], None)
box_parameters = input_dict.get(kwargs['box_parameters'], None)
# Use load_content instead of load_file if given
if load_content is not None:
load_file = load_content
# Separate load_options terms
load_options_kwargs = {}
if load_options is not None:
load_options_keys = [
'key', 'index', 'data_set', 'pbc', 'atom_style', 'units',
'prop_info'
]
load_options_kwargs = termtodict(load_options, load_options_keys)
if 'index' in load_options_kwargs:
load_options_kwargs['index'] = int(load_options_kwargs['index'])
# Build ucell
if build is True:
# Load ucell
ucell = am.load(load_style, load_file, **load_options_kwargs)
# Replace symbols if given
if symbols is not None:
ucell.symbols = symbols.split()
symbols = list(ucell.symbols)
# Scale ucell by box_parameters
if box_parameters is not None:
box_params = box_parameters.split()
# len of 4 or 7 indicates that last term is a length unit
if len(box_params) == 4 or len(box_params) == 7:
unit = box_params[-1]
box_params = box_params[:-1]
# Use calculation's length_unit if unit not given in box_parameters
else:
unit = input_dict['length_unit']
# Convert to the specified units
box_params = np.array(box_params, dtype=float)
box_params[:3] = uc.set_in_units(box_params[:3], unit)
# Three box_parameters means a, b, c
if len(box_params) == 3:
ucell.box_set(a=box_params[0],
b=box_params[1],
c=box_params[2],
scale=True)
# Six box_parameters means a, b, c, alpha, beta, gamma
elif len(box_params) == 6:
ucell.box_set(a=box_params[0],
b=box_params[1],
c=box_params[2],
alpha=box_params[3],
beta=box_params[4],
gamma=box_params[5],
scale=True)
# Other options are invalid
else:
ValueError('Invalid box_parameters command')
# Don't build
else:
# Try to get symbols by loading file
if symbols is None:
try:
ucell = am.load(load_style, load_file, **load_options_kwargs)
except:
pass
else:
symbols = list(ucell.symbols)
ucell = None
# Extract system_family (and possibly symbols) from system_model
if load_style == 'system_model':
model = DM(load_file)
# Check if family in model
if family is None:
try:
family = model.find('system-info')['family']
except:
family = None
# Extract symbols if needed
if symbols is None or symbols[0] is None:
try:
symbols = model.find('system-info')['symbol']
except:
pass
else:
if ucell is not None:
ucell.symbols = symbols
symbols = list(ucell.symbols)
# Pull single symbols out of the list
if len(symbols) == 1:
symbols = symbols[0]
# If no family given/found, use load_file's basename
if family is None:
family = os.path.splitext(
os.path.basename(input_dict[kwargs['load_file']]))[0]
# Save processed terms
input_dict[kwargs['load_style']] = load_style
input_dict[kwargs['load_options']] = load_options
input_dict[kwargs['box_parameters']] = box_parameters
input_dict[kwargs['family']] = family
input_dict[kwargs['ucell']] = ucell
input_dict[kwargs['symbols']] = symbols
def todict(self, full=True, flat=False):
"""
Converts the structured content to a simpler dictionary.
Parameters
----------
full : bool, optional
Flag used by the calculation records. A True value will include
terms for both the calculation's input and results, while a value
of False will only include input terms (Default is True).
flat : bool, optional
Flag affecting the format of the dictionary terms. If True, the
dictionary terms are limited to having only str, int, and float
values, which is useful for comparisons. If False, the term
values can be of any data type, which is convenient for analysis.
(Default is False).
Returns
-------
dict
A dictionary representation of the record's content.
"""
calc = self.content[self.contentroot]
params = {}
params['key'] = calc['key']
params['script'] = calc['calculation']['script']
params['iprPy_version'] = calc['calculation']['iprPy-version']
params['symmetryprecision'] = calc['calculation']['run-parameter']['symmetryprecision']
params['primitivecell'] = calc['calculation']['run-parameter']['primitivecell']
params['idealcell'] = calc['calculation']['run-parameter']['idealcell']
params['load_file'] = calc['system-info']['artifact']['file']
params['load_style'] = calc['system-info']['artifact']['format']
params['load_options'] = calc['system-info']['artifact']['load_options']
params['family'] = calc['system-info']['family']
symbols = aslist(calc['system-info']['symbol'])
if flat is True:
try:
params['symbols'] = ' '.join(symbols)
except:
params['symbols'] = np.nan
else:
params['symbols'] = symbols
params['status'] = calc.get('status', 'finished')
params['error'] = calc.get('error', np.nan)
if full is True and params['status'] == 'finished':
ucell = am.load('system_model', self.content, key='unit-cell-atomic-system')
params['pearson_symbol'] = calc['Pearson-symbol']
params['spacegroup_number'] = calc['space-group']['number']
params['spacegroup_international'] = calc['space-group']['Hermann-Maguin']
params['spacegroup_Schoenflies'] = calc['space-group']['Schoenflies']
params['wykoff_letters'] = ' '.join(calc['space-group'].finds('letter'))
if flat is True:
params['a'] = ucell.box.a
params['b'] = ucell.box.b
params['c'] = ucell.box.c
params['alpha'] = ucell.box.alpha
params['beta'] = ucell.box.beta
params['gamma'] = ucell.box.gamma
params['natoms'] = ucell.natoms
else:
params['ucell'] = ucell
return params
def dislocation_monopole(lammps_command: str,
ucell: am.System,
potential: lmp.Potential,
C: am.ElasticConstants,
burgers: Union[list, np.ndarray],
ξ_uvw: Union[list, np.ndarray],
slip_hkl: Union[list, np.ndarray],
mpi_command: Optional[str] = None,
m: Union[list, np.ndarray] = [0, 1, 0],
n: Union[list, np.ndarray] = [0, 0, 1],
sizemults=None,
amin: float = None,
bmin: float = None,
cmin: float = None,
shift: Union[list, np.ndarray, None] = None,
shiftscale: bool = False,
shiftindex: int = None,
tol: float = 1e-8,
etol: float = 0.0,
ftol: float = 0.0,
maxiter: int = 10000,
maxeval: int = 100000,
dmax: float = uc.set_in_units(0.01, 'angstrom'),
annealtemp: float = 0.0,
annealsteps: Optional[int] = None,
randomseed: Optional[int] = None,
boundaryshape: str = 'cylinder',
boundarywidth: float = 0.0,
boundaryscale: bool = False) -> dict:
"""
Creates and relaxes a dislocation monopole system.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
ucell : atomman.System
The unit cell to use as the seed for generating the dislocation
monopole system.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
C : atomman.ElasticConstants
The elastic constants associated with the bulk crystal structure
for ucell.
burgers : array-like object
The dislocation's Burgers vector given as a Miller or
Miller-Bravais vector relative to ucell.
ξ_uvw : array-like object
The dislocation's line direction given as a Miller or
Miller-Bravais vector relative to ucell.
slip_hkl : array-like object
The dislocation's slip plane given as a Miller or Miller-Bravais
plane relative to ucell.
mpi_command : str or None, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
m : array-like object, optional
The m unit vector for the dislocation solution. m, n, and ξ
(dislocation line) should be right-hand orthogonal. Default value
is [0,1,0] (y-axis).
n : array-like object, optional
The n unit vector for the dislocation solution. m, n, and ξ
(dislocation line) should be right-hand orthogonal. Default value
is [0,0,1] (z-axis). n is normal to the dislocation slip plane.
sizemults : tuple, optional
The size multipliers to use when generating the system. Values are
limited to being positive integers. The multipliers for the two
non-periodic directions must be even. If not given, the default
multipliers will be 2 for the non-periodic directions and 1 for the
periodic direction.
amin : float, optional
A minimum thickness to use for the a box vector direction of the
final system. Default value is 0.0. For the non-periodic
directions, the resulting vector multiplier will be even. If both
amin and sizemults is given, then the larger multiplier for the two
will be used.
bmin : float, optional
A minimum thickness to use for the b box vector direction of the
final system. Default value is 0.0. For the non-periodic
directions, the resulting vector multiplier will be even. If both
bmin and sizemults is given, then the larger multiplier for the two
will be used.
cmin : float, optional
A minimum thickness to use for the c box vector direction of the
final system. Default value is 0.0. For the non-periodic
directions, the resulting vector multiplier will be even. If both
cmin and sizemults is given, then the larger multiplier for the two
will be used.
shift : float, optional
A rigid body shift to apply to the rotated cell prior to inserting
the dislocation. Should be selected such that the ideal slip plane
does not correspond to any atomic planes. Is taken as absolute if
shiftscale is False, or relative to the rotated cell's box vectors
if shiftscale is True. Cannot be given with shiftindex. If
neither shift nor shiftindex is given then shiftindex = 0 is used.
shiftindex : float, optional
The index of the identified optimum shifts based on the rotated
cell to use. Different values allow for the selection of different
atomic planes neighboring the slip plane. Note that shiftindex
values only apply shifts normal to the slip plane; best shifts for
non-planar dislocations (like bcc screw) may also need a shift in
the slip plane. Cannot be given with shiftindex. If neither shift
nor shiftindex is given then shiftindex = 0 is used.
shiftscale : bool, optional
If False (default), a given shift value will be taken as absolute
Cartesian. If True, a given shift will be taken relative to the
rotated cell's box vectors.
tol : float
A cutoff tolerance used with obtaining the dislocation solution.
Only needs to be changed if there are issues with obtaining a
solution.
etol : float, optional
The energy tolerance for the structure minimization. This value is
unitless. Default is 0.0.
ftol : float, optional
The force tolerance for the structure minimization. This value is in
units of force. Default is 0.0.
maxiter : int, optional
The maximum number of minimization iterations to use. Default is
10000.
maxeval : int, optional
The maximum number of minimization evaluations to use. Default is
100000.
dmax : float, optional
The maximum distance in length units that any atom is allowed to relax
in any direction during a single minimization iteration. Default is
0.01 Angstroms.
annealtemp : float, optional
The temperature to perform a dynamic relaxation at. Default is 0.0,
which will skip the dynamic relaxation.
annealsteps : int, optional
The number of time steps to run the dynamic relaxation for. Default
is None, which will run for 10000 steps if annealtemp is not 0.0.
randomseed : int or None, optional
Random number seed used by LAMMPS in creating velocities and with
the Langevin thermostat. Default is None which will select a
random int between 1 and 900000000.
boundaryshape : str, optional
Indicates the shape of the boundary region to use. Options are
'cylinder' (default) and 'box'. For 'cylinder', the non-boundary
region is defined by a cylinder with axis along the dislocation
line and a radius that ensures the boundary is at least
boundarywidth thick. For 'box', the boundary region will be
exactly boundarywidth thick all around.
boundarywidth : float, optional
The width of the boundary region to apply. Default value is 0.0,
i.e. no boundary region. All atoms in the boundary region will
have their atype values changed.
boundaryscale : bool, optional
If False (Default), the boundarywidth will be taken as absolute.
If True, the boundarywidth will be taken relative to the magnitude
of the unit cell's a box vector.
Returns
-------
dict
Dictionary of results consisting of keys:
- **'dumpfile_base'** (*str*) - The filename of the LAMMPS dump file
for the relaxed base system.
- **'symbols_base'** (*list of str*) - The list of element-model
symbols for the Potential that correspond to the base system's
atypes.
- **'dumpfile_disl'** (*str*) - The filename of the LAMMPS dump file
for the relaxed dislocation monopole system.
- **'symbols_disl'** (*list of str*) - The list of element-model
symbols for the Potential that correspond to the dislocation
monopole system's atypes.
- **'dislocation'** (*atomman.defect.Dislocation*) - The Dislocation
object used to generate the monopole system.
- **'E_total_disl'** (*float*) - The total potential energy of the
dislocation monopole system.
"""
# Construct dislocation configuration generator
dislocation = am.defect.Dislocation(ucell,
C,
burgers,
ξ_uvw,
slip_hkl,
m=m,
n=n,
shift=shift,
shiftindex=shiftindex,
shiftscale=shiftscale,
tol=tol)
# Generate the base and dislocation systems
base_system, disl_system = dislocation.monopole(
sizemults=sizemults,
amin=amin,
bmin=bmin,
cmin=cmin,
shift=shift,
shiftindex=shiftindex,
shiftscale=shiftscale,
boundaryshape=boundaryshape,
boundarywidth=boundarywidth,
boundaryscale=boundaryscale,
return_base_system=True)
# Initialize results dict
results_dict = {}
# Save initial perfect system
base_system.dump('atom_dump', f='base.dump')
results_dict['dumpfile_base'] = 'base.dump'
results_dict['symbols_base'] = base_system.symbols
# Save dislocation generator
results_dict['dislocation'] = dislocation
# Relax system
relaxed = disl_relax(lammps_command,
disl_system,
potential,
mpi_command=mpi_command,
annealtemp=annealtemp,
annealsteps=annealsteps,
randomseed=randomseed,
etol=etol,
ftol=ftol,
maxiter=maxiter,
maxeval=maxeval,
dmax=dmax)
# Save relaxed dislocation system with original box vects
system_disl = am.load('atom_dump',
relaxed['dumpfile'],
symbols=disl_system.symbols)
system_disl.box_set(vects=disl_system.box.vects,
origin=disl_system.box.origin)
system_disl.dump('atom_dump', f='disl.dump')
results_dict['dumpfile_disl'] = 'disl.dump'
results_dict['symbols_disl'] = system_disl.symbols
results_dict['E_total_disl'] = relaxed['E_total']
# Cleanup files
Path('0.dump').unlink()
Path(relaxed['dumpfile']).unlink()
for dumpjsonfile in Path('.').glob('*.dump.json'):
dumpjsonfile.unlink()
return results_dict
def plot_vitek(dislo, bulk, show=True, save_file=None,
alat=3.16, plot_axes=None, xyscale=10):
"""Plots vitek map from ase configurations.
Parameters
----------
dislo : ase.Atoms
Dislocation configuration.
bulk : ase.Atoms
Corresponding bulk configuration for calculation of displacements.
show : bool
Show the figure after plotting. Default is True.
save_file : str, optional
If given then the plot will be saved to a file with this name.
alat : float
Lattice parameter for calculation of neghbour list cutoff.
plot_axes : matplotlib.Axes.axes object
Existing axes to plot on, allows to pass existing matplotlib axes
have full control of the graph outside the function.
Makes possible to plot multiple differential displacement
maps using subplots.
Default is None, then new graph is created by plt.subplots()
Description of parameter `plot_axes`.
xyscale : float
xyscale of the graph
Returns
-------
None
"""
lengthB = 0.5*np.sqrt(3.)*alat
burgers = np.array([0.0, 0.0, lengthB])
base_system = am.load("ase_Atoms", bulk)
disl_system = am.load("ase_Atoms", dislo)
neighborListCutoff = 0.95 * alat
# plot window is +-10 angstroms in x,y directions, and one Burgerx vector
# thickness along z direction
plot_range = np.array([[-xyscale, xyscale],
[-xyscale, xyscale],
[-0.1, alat * 3.**(0.5) / 2.]])
# This scales arrows such that b/2 corresponds to the
# distance between atoms on the plot
plot_scale = 1.885618083
am.defect.differential_displacement(base_system, disl_system,
burgers,
cutoff=neighborListCutoff,
xlim=plot_range[0],
ylim=plot_range[1],
zlim=plot_range[2],
plot_scale=plot_scale,
show=show, save_file=save_file,
plot_axes=plot_axes)
return None
def pointdefect(lammps_command, system, potential, point_kwargs,
mpi_command=None, etol=0.0, ftol=0.0, maxiter=10000,
maxeval=100000, dmax=uc.set_in_units(0.01, 'angstrom')):
"""
Adds one or more point defects to a system and evaluates the defect
formation energy.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
system : atomman.System
The system to perform the calculation on.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
point_kwargs : dict or list of dict
One or more dictionaries containing the keyword arguments for
the atomman.defect.point() function to generate specific point
defect configuration(s).
mpi_command : str, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
sim_directory : str, optional
The path to the directory to perform the simuation in. If not
given, will use the current working directory.
etol : float, optional
The energy tolerance for the structure minimization. This value is
unitless. (Default is 0.0).
ftol : float, optional
The force tolerance for the structure minimization. This value is in
units of force. (Default is 0.0).
maxiter : int, optional
The maximum number of minimization iterations to use (default is
10000).
maxeval : int, optional
The maximum number of minimization evaluations to use (default is
100000).
dmax : float, optional
The maximum distance in length units that any atom is allowed to relax
in any direction during a single minimization iteration (default is
0.01 Angstroms).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'E_coh'** (*float*) - The cohesive energy of the bulk system.
- **'E_ptd_f'** (*float*) - The point.defect formation energy.
- **'E_total_base'** (*float*) - The total potential energy of the
relaxed bulk system.
- **'E_total_ptd'** (*float*) - The total potential energy of the
relaxed defect system.
- **'system_base'** (*atomman.System*) - The relaxed bulk system.
- **'system_ptd'** (*atomman.System*) - The relaxed defect system.
- **'dumpfile_base'** (*str*) - The filename of the LAMMPS dump file
for the relaxed bulk system.
- **'dumpfile_ptd'** (*str*) - The filename of the LAMMPS dump file
for the relaxed defect system.
"""
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Get lammps version date
lammps_date = lmp.checkversion(lammps_command)['date']
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data', f='perfect.dat',
units=potential.units,
atom_style=potential.atom_style)
lammps_variables['atomman_system_info'] = system_info
lammps_variables['atomman_pair_info'] = potential.pair_info(system.symbols)
lammps_variables['etol'] = etol
lammps_variables['ftol'] = uc.get_in_units(ftol, lammps_units['force'])
lammps_variables['maxiter'] = maxiter
lammps_variables['maxeval'] = maxeval
lammps_variables['dmax'] = dmax
# Set dump_modify_format based on lammps_date
if lammps_date < datetime.date(2016, 8, 3):
lammps_variables['dump_modify_format'] = '"%d %d %.13e %.13e %.13e %.13e"'
else:
lammps_variables['dump_modify_format'] = 'float %.13e'
# Write lammps input script
template_file = 'min.template'
lammps_script = 'min.in'
with open(template_file) as f:
template = f.read()
with open(lammps_script, 'w') as f:
f.write(iprPy.tools.filltemplate(template, lammps_variables, '<', '>'))
# Run lammps to relax perfect.dat
output = lmp.run(lammps_command, lammps_script, mpi_command)
# Extract LAMMPS thermo data.
thermo = output.simulations[0]['thermo']
E_total_base = uc.set_in_units(thermo.PotEng.values[-1],
lammps_units['energy'])
E_coh = E_total_base / system.natoms
# Rename log file
shutil.move('log.lammps', 'min-perfect-log.lammps')
# Load relaxed system from dump file and copy old box vectors because
# dump files crop the values.
last_dump_file = 'atom.' + str(thermo.Step.values[-1])
system_base = am.load('atom_dump', last_dump_file, symbols=system.symbols)
system_base.box_set(vects=system.box.vects)
system_base.dump('atom_dump', f='perfect.dump')
# Add defect(s)
system_ptd = deepcopy(system_base)
if not isinstance(point_kwargs, (list, tuple)):
point_kwargs = [point_kwargs]
for pkwargs in point_kwargs:
system_ptd = am.defect.point(system_ptd, **pkwargs)
# Update lammps variables
system_info = system_ptd.dump('atom_data', f='defect.dat',
units = potential.units,
atom_style = potential.atom_style)
lammps_variables['atomman_system_info'] = system_info
# Write lammps input script
with open(lammps_script, 'w') as f:
f.write(iprPy.tools.filltemplate(template, lammps_variables,
'<', '>'))
# Run lammps
output = lmp.run(lammps_command, lammps_script, mpi_command)
# Extract lammps thermo data
thermo = output.simulations[0]['thermo']
E_total_ptd = uc.set_in_units(thermo.PotEng.values[-1],
lammps_units['energy'])
# Rename log file
shutil.move('log.lammps', 'min-defect-log.lammps')
# Load relaxed system from dump file and copy old vects as
# the dump files crop the values
last_dump_file = 'atom.'+str(thermo.Step.values[-1])
system_ptd = am.load('atom_dump', last_dump_file, symbols=system_ptd.symbols)
system_ptd.box_set(vects=system.box.vects)
system_ptd.dump('atom_dump', f='defect.dump')
# Compute defect formation energy
E_ptd_f = E_total_ptd - E_coh * system_ptd.natoms
# Cleanup files
for fname in glob.iglob('atom.*'):
os.remove(fname)
for dumpjsonfile in glob.iglob('*.dump.json'):
os.remove(dumpjsonfile)
# Return results
results_dict = {}
results_dict['E_coh'] = E_coh
results_dict['E_ptd_f'] = E_ptd_f
results_dict['E_total_base'] = E_total_base
results_dict['E_total_ptd'] = E_total_ptd
results_dict['system_base'] = system_base
results_dict['system_ptd'] = system_ptd
results_dict['dumpfile_base'] = 'perfect.dump'
results_dict['dumpfile_ptd'] = 'defect.dump'
return results_dict
def phonon(lammps_command,
ucell,
potential,
mpi_command=None,
a_mult=3,
b_mult=3,
c_mult=3,
distance=0.01,
symprec=1e-5):
try:
# Get script's location if __file__ exists
script_dir = Path(__file__).parent
except:
# Use cwd otherwise
script_dir = Path.cwd()
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
# Get lammps version date
lammps_date = lmp.checkversion(lammps_command)['date']
# Generate pair_info
pair_info = potential.pair_info(ucell.symbols)
# Use spglib to find primitive unit cell of ucell
convcell = ucell.dump('spglib_cell')
primcell = spglib.find_primitive(convcell, symprec=symprec)
primucell = am.load('spglib_cell', primcell,
symbols=ucell.symbols).normalize()
# Initialize Phonopy object
phonon = phonopy.Phonopy(primucell.dump('phonopy_Atoms'),
[[a_mult, 0, 0], [0, b_mult, 0], [0, 0, c_mult]])
phonon.generate_displacements(distance=distance)
# Loop over displaced supercells to compute forces
forcearrays = []
for supercell in phonon.supercells_with_displacements:
# Save to LAMMPS data file
system = am.load('phonopy_Atoms', supercell)
system_info = system.dump('atom_data', f='disp.dat')
# Define lammps variables
lammps_variables = {}
lammps_variables['atomman_system_info'] = system_info
lammps_variables['atomman_pair_info'] = pair_info
# Set dump_modify_format based on lammps_date
if lammps_date < datetime.date(2016, 8, 3):
lammps_variables[
'dump_modify_format'] = '"%d %d %.13e %.13e %.13e %.13e %.13e %.13e"'
else:
lammps_variables['dump_modify_format'] = 'float %.13e'
# Write lammps input script
template_file = Path(script_dir, 'phonon.template')
lammps_script = 'phonon.in'
with open(template_file) as f:
template = f.read()
with open(lammps_script, 'w') as f:
f.write(
iprPy.tools.filltemplate(template, lammps_variables, '<', '>'))
# Run LAMMPS
lmp.run(lammps_command, 'phonon.in', mpi_command=mpi_command)
# Extract forces from dump file
results = am.load('atom_dump', 'forces.dump')
forces = uc.set_in_units(results.atoms.force, lammps_units['force'])
forcearrays.append(forces)
# Set computed forces
phonon.set_forces(forcearrays)
# Save to yaml file
phonon.save('phonopy_params.yaml')
# Compute band structure
phonon.produce_force_constants()
phonon.auto_band_structure(plot=True)
plt.savefig(Path('.', 'band.png'), dpi=400)
plt.close()
# Compute total density of states
phonon.auto_total_dos(plot=True)
plt.savefig('total_dos.png', dpi=400)
plt.close()
# Compute partial density of states
phonon.auto_projected_dos(plot=True)
plt.savefig('projected_dos.png', dpi=400)
plt.close()
# Compute thermal properties
phonon.run_thermal_properties()
phonon.plot_thermal_properties()
plt.savefig('thermal.png', dpi=400)
plt.close()
return {}
def interpret(self, input_dict, build=True):
"""
Interprets calculation parameters.
Parameters
----------
input_dict : dict
Dictionary containing input parameter key-value pairs.
"""
# Set default keynames
keymap = self.keymap
# Extract input values and assign default values
load_file = input_dict[keymap['load_file']]
load_style = input_dict.get(keymap['load_style'], 'system_model')
load_options = input_dict.get(keymap['load_options'], None)
load_content = input_dict.get(keymap['load_content'], None)
family = input_dict.get(keymap['family'], None)
symbols = input_dict.get(keymap['symbols'], None)
box_parameters = input_dict.get(keymap['box_parameters'], None)
elastic_file = input_dict.get(keymap['elasticconstants_content'], None)
# Use load_content instead of load_file if given
if load_content is not None:
load_file = load_content
# Separate load_options terms
load_options_kwargs = {}
if load_options is not None:
load_options_keys = [
'key', 'index', 'data_set', 'pbc', 'atom_style', 'units',
'prop_info'
]
load_options_kwargs = termtodict(load_options, load_options_keys)
if 'index' in load_options_kwargs:
load_options_kwargs['index'] = int(
load_options_kwargs['index'])
# Build ucell
if build is True:
# Load ucell
ucell = am.load(load_style, load_file, **load_options_kwargs)
# Replace symbols if given
if symbols is not None:
ucell.symbols = symbols.split()
symbols = list(ucell.symbols)
# Scale ucell by box_parameters
if box_parameters is not None:
box_params = box_parameters.split()
# len of 4 or 7 indicates that last term is a length unit
if len(box_params) == 4 or len(box_params) == 7:
unit = box_params[-1]
box_params = box_params[:-1]
# Use calculation's length_unit if unit not given in box_parameters
else:
unit = input_dict['length_unit']
# Convert to the specified units
box_params = np.array(box_params, dtype=float)
box_params[:3] = uc.set_in_units(box_params[:3], unit)
# Three box_parameters means a, b, c
if len(box_params) == 3:
ucell.box_set(a=box_params[0],
b=box_params[1],
c=box_params[2],
scale=True)
# Six box_parameters means a, b, c, alpha, beta, gamma
elif len(box_params) == 6:
ucell.box_set(a=box_params[0],
b=box_params[1],
c=box_params[2],
alpha=box_params[3],
beta=box_params[4],
gamma=box_params[5],
scale=True)
# Other options are invalid
else:
ValueError('Invalid box_parameters command')
# Add model-specific charges if needed
if (keymap['potential'] in input_dict
and 'charge' not in ucell.atoms_prop()):
potential = input_dict[keymap['potential']]
ucell.atoms.prop_atype('charge',
potential.charges(ucell.symbols))
# Don't build
else:
# Try to get symbols by loading file
if symbols is None:
try:
ucell = am.load(load_style, load_file,
**load_options_kwargs)
except:
pass
else:
symbols = list(ucell.symbols)
ucell = None
# Extract system_family (and possibly symbols) from parent model
if elastic_file is not None:
model = DM(elastic_file)
elif load_style == 'system_model':
model = DM(load_file)
else:
model = None
if model is not None:
# Check if family in model
if family is None:
try:
family = model.find('system-info')['family']
except:
family = None
# Extract symbols if needed
if symbols is None or symbols[0] is None:
try:
symbols = model.find('system-info')['symbol']
except:
pass
else:
if ucell is not None:
ucell.symbols = symbols
symbols = list(ucell.symbols)
# Pull single symbols out of the list
if len(symbols) == 1:
symbols = symbols[0]
# If no family given/found, use load_file's stem
if family is None:
family = Path(input_dict[keymap['load_file']]).stem
# Save processed terms
input_dict[keymap['load_style']] = load_style
input_dict[keymap['load_options']] = load_options
input_dict[keymap['box_parameters']] = box_parameters
input_dict[keymap['family']] = family
input_dict[keymap['ucell']] = ucell
input_dict[keymap['symbols']] = symbols
def stackingfaultpoint(lammps_command, system, potential,
mpi_command=None, sim_directory=None,
cutboxvector='c', faultpos=0.5,
faultshift=[0.0, 0.0, 0.0], etol=0.0, ftol=0.0,
maxiter=10000, maxeval=100000,
dmax=uc.set_in_units(0.01, 'angstrom'),
lammps_date=None):
"""
Perform a stacking fault relaxation simulation for a single faultshift.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
system : atomman.System
The system to perform the calculation on.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
mpi_command : str, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
sim_directory : str, optional
The path to the directory to perform the simuation in. If not
given, will use the current working directory.
etol : float, optional
The energy tolerance for the structure minimization. This value is
unitless. (Default is 0.0).
ftol : float, optional
The force tolerance for the structure minimization. This value is in
units of force. (Default is 0.0).
maxiter : int, optional
The maximum number of minimization iterations to use (default is
10000).
maxeval : int, optional
The maximum number of minimization evaluations to use (default is
100000).
dmax : float, optional
The maximum distance in length units that any atom is allowed to relax
in any direction during a single minimization iteration (default is
0.01 Angstroms).
cutboxvector : str, optional
Indicates which of the three system box vectors, 'a', 'b', or 'c', to
cut with a non-periodic boundary (default is 'c').
faultpos : float, optional
The fractional position along the cutboxvector where the stacking
fault plane will be placed (default is 0.5).
faultshift : list of float, optional
The vector shift to apply to all atoms above the fault plane defined
by faultpos (default is [0,0,0], i.e. no shift applied).
lammps_date : datetime.date or None, optional
The date version of the LAMMPS executable. If None, will be identified from the lammps_command (default is None).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'logfile'** (*str*) - The filename of the LAMMPS log file.
- **'dumpfile'** (*str*) - The filename of the LAMMPS dump file
of the relaxed system.
- **'system'** (*atomman.System*) - The relaxed system.
- **'A_fault'** (*float*) - The area of the fault surface.
- **'E_total'** (*float*) - The total potential energy of the relaxed
system.
- **'disp'** (*float*) - The center of mass difference between atoms
above and below the fault plane in the cutboxvector direction.
Raises
------
ValueError
For invalid cutboxvectors.
"""
# Set options based on cutboxvector
if cutboxvector == 'a':
# Assert system is compatible with planeaxis value
if system.box.xy != 0.0 or system.box.xz != 0.0:
raise ValueError("box tilts xy and xz must be 0 for cutboxvector='a'")
# Specify cutindex
cutindex = 0
# Identify atoms above fault
faultpos = system.box.xlo + system.box.lx * faultpos
abovefault = system.atoms.pos[:, cutindex] > (faultpos)
# Compute fault area
faultarea = np.linalg.norm(np.cross(system.box.bvect,
system.box.cvect))
# Give correct LAMMPS fix setforce command
fix_cut_setforce = 'fix cut all setforce NULL 0 0'
elif cutboxvector == 'b':
# Assert system is compatible with planeaxis value
if system.box.yz != 0.0:
raise ValueError("box tilt yz must be 0 for cutboxvector='b'")
# Specify cutindex
cutindex = 1
# Identify atoms above fault
faultpos = system.box.ylo + system.box.ly * faultpos
abovefault = system.atoms.pos[:, cutindex] > (faultpos)
# Compute fault area
faultarea = np.linalg.norm(np.cross(system.box.avect,
system.box.cvect))
# Give correct LAMMPS fix setforce command
fix_cut_setforce = 'fix cut all setforce 0 NULL 0'
elif cutboxvector == 'c':
# Specify cutindex
cutindex = 2
# Identify atoms above fault
faultpos = system.box.zlo + system.box.lz * faultpos
abovefault = system.atoms.pos[:, cutindex] > (faultpos)
# Compute fault area
faultarea = np.linalg.norm(np.cross(system.box.avect,
system.box.bvect))
# Give correct LAMMPS fix setforce command
fix_cut_setforce = 'fix cut all setforce 0 0 NULL'
else:
raise ValueError('Invalid cutboxvector')
# Assert faultshift is in cut plane
if faultshift[cutindex] != 0.0:
raise ValueError('faultshift must be in cut plane')
# Generate stacking fault system by shifting atoms above the fault
sfsystem = deepcopy(system)
sfsystem.pbc = [True, True, True]
sfsystem.pbc[cutindex] = False
sfsystem.atoms.pos[abovefault] += faultshift
sfsystem.wrap()
if sim_directory is not None:
# Create sim_directory if it doesn't exist
if not os.path.isdir(sim_directory):
os.mkdir(sim_directory)
# Add '/' to end of sim_directory string if needed
if sim_directory[-1] != '/':
sim_directory = sim_directory + '/'
else:
# Set sim_directory if is None
sim_directory = ''
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Get lammps version date
if lammps_date is None:
lammps_date = lmp.checkversion(lammps_command)['date']
# Define lammps variables
lammps_variables = {}
system_info = sfsystem.dump('atom_data',
f=os.path.join(sim_directory, 'system.dat'),
units=potential.units,
atom_style=potential.atom_style)
lammps_variables['atomman_system_info'] = system_info
lammps_variables['atomman_pair_info'] = potential.pair_info(sfsystem.symbols)
lammps_variables['fix_cut_setforce'] = fix_cut_setforce
lammps_variables['sim_directory'] = sim_directory
lammps_variables['etol'] = etol
lammps_variables['ftol'] = uc.get_in_units(ftol, lammps_units['force'])
lammps_variables['maxiter'] = maxiter
lammps_variables['maxeval'] = maxeval
lammps_variables['dmax'] = uc.get_in_units(dmax, lammps_units['length'])
# Set dump_modify format based on dump_modify_version
if lammps_date < datetime.date(2016, 8, 3):
lammps_variables['dump_modify_format'] = '"%i %i %.13e %.13e %.13e %.13e"'
else:
lammps_variables['dump_modify_format'] = 'float %.13e'
# Write lammps input script
template_file = 'sfmin.template'
lammps_script = os.path.join(sim_directory, 'sfmin.in')
with open(template_file) as f:
template = f.read()
with open(lammps_script, 'w') as f:
f.write(iprPy.tools.filltemplate(template, lammps_variables,
'<', '>'))
# Run LAMMPS
output = lmp.run(lammps_command, lammps_script, mpi_command,
logfile=os.path.join(sim_directory, 'log.lammps'))
# Extract output values
thermo = output.simulations[-1]['thermo']
logfile = os.path.join(sim_directory, 'log.lammps')
dumpfile = os.path.join(sim_directory, '%i.dump' % thermo.Step.values[-1])
E_total = uc.set_in_units(thermo.PotEng.values[-1],
lammps_units['energy'])
#Load relaxed system
sfsystem = am.load('atom_dump', dumpfile, symbols=sfsystem.symbols)
# Find center of mass difference in top/bottom planes
disp = (sfsystem.atoms.pos[abovefault, cutindex].mean()
- sfsystem.atoms.pos[~abovefault, cutindex].mean())
# Return results
results_dict = {}
results_dict['logfile'] = logfile
results_dict['dumpfile'] = dumpfile
results_dict['system'] = sfsystem
results_dict['A_fault'] = faultarea
results_dict['E_total'] = E_total
results_dict['disp'] = disp
return results_dict
def crystal_space_group(system,
symprec=1e-5,
to_primitive=False,
no_idealize=False):
"""
Uses spglib to evaluate space group information for a given system.
Parameters
----------
system : atomman.System
The system to analyze.
symprec : float
Absolute length tolerance to use in identifying symmetry of atomic
sites and system boundaries.
to_primitive : bool
Indicates if the returned unit cell is conventional (False) or
primitive (True). Default value is False.
no_idealize : bool
Indicates if the atom positions in the returned unit cell are averaged
(True) or idealized based on the structure (False). Default value is
False.
Returns
-------
dict
Results dictionary containing space group information and an associated
unit cell system.
"""
# Identify the standardized unit cell representation
ucell = spglib.standardize_cell(system.dump('spglib_cell'),
to_primitive=to_primitive,
no_idealize=no_idealize,
symprec=symprec)
# Convert back to atomman systems and normalize
ucell = am.load('spglib_cell', ucell, symbols=system.symbols)
ucell.atoms.pos -= ucell.atoms.pos[0]
ucell = ucell.normalize()
# Get space group metadata
sym_data = spglib.get_symmetry_dataset(ucell.dump('spglib_cell'))
spg_type = spglib.get_spacegroup_type(sym_data['hall_number'])
# Generate Pearson symbol
if spg_type['number'] <= 2:
crystalclass = 'a'
elif spg_type['number'] <= 15:
crystalclass = 'm'
elif spg_type['number'] <= 74:
crystalclass = 'o'
elif spg_type['number'] <= 142:
crystalclass = 't'
elif spg_type['number'] <= 194:
crystalclass = 'h'
else:
crystalclass = 'c'
latticetype = spg_type['international'][0]
if latticetype in ['A', 'B']:
latticetype = 'C'
natoms = str(ucell.natoms)
pearson = crystalclass + latticetype + natoms
# Return results
results_dict = spg_type
results_dict['ucell'] = ucell
results_dict['hall_number'] = sym_data['hall_number']
results_dict['wyckoffs'] = sym_data['wyckoffs']
results_dict['pearson'] = pearson
return results_dict
def get_mp_structures(elements, api_key=None, lib_directory=None):
"""
Accesses the Materials Project and downloads all structures for a list of
elements as poscar files.
Parameters
----------
elements : list
A list of element symbols.
api_key : str, optional
The user's Materials Project API key. If not given, will use "MAPI_KEY"
environment variable
lib_directory : str
Path to the lib_directory to save the poscar files to. Default uses
the iprPy library/dft_structures directory.
"""
# Function-specific imports
import pymatgen as pmg
from pymatgen.ext.matproj import MPRester
# Handle lib_directory
if lib_directory is None:
lib_directory = os.path.join(os.path.dirname(rootdir), 'library', 'ref')
lib_directory = os.path.abspath(lib_directory)
elements.sort()
# Open connection to Materials Project
with MPRester(api_key) as m:
# Loop over subsets of elements
for subelements in subsets(elements):
# Set comp_directory
elements_string = '-'.join(subelements)
comp_directory = os.path.join(lib_directory, elements_string)
if not os.path.isdir(comp_directory):
os.makedirs(comp_directory)
# Build list of downloaded entries
have = []
for fname in glob.iglob(os.path.join(comp_directory, 'mp-*.poscar')):
have.append(os.path.splitext(os.path.basename(fname))[0])
#print('Have', len(have), elements_string, 'records')
# Query MP for all entries corresponding to the elements
entries = m.query({"elements": subelements}, ["material_id"])
# Add entries to the list if not there
missing = []
for entry in entries:
if entry['material_id'] not in have and entry['material_id'] not in missing:
missing.append(entry['material_id'])
#print('Missing', len(missing), elements_string, 'records')
# Download missing entries
entries = m.query({"material_id": {"$in": missing}}, ['material_id', 'cif'])
# Convert cif to poscar and save
for entry in entries:
struct = pmg.Structure.from_str(entry['cif'], fmt='cif')
struct = pmg.symmetry.analyzer.SpacegroupAnalyzer(struct).get_conventional_standard_structure()
system = am.load('pymatgen_Structure', struct)
system = system.normalize()
structure_file = os.path.join(comp_directory, entry['material_id']+'.poscar')
system.dump('poscar', f=structure_file)
print('Added', entry['material_id'])
def crystal_space_group(system,
symprec=1e-5,
to_primitive=False,
no_idealize=False):
"""
Uses spglib to evaluate space group information for a given system.
Parameters
----------
system : atomman.System
The system to analyze.
symprec : float
Absolute length tolerance to use in identifying symmetry of atomic
sites and system boundaries.
to_primitive : bool
Indicates if the returned unit cell is conventional (False) or
primitive (True). Default value is False.
no_idealize : bool
Indicates if the atom positions in the returned unit cell are averaged
(True) or idealized based on the structure (False). Default value is
False.
Returns
-------
dict
Results dictionary containing space group information and an associated
unit cell system.
"""
# Identify the standardized unit cell representation
sym_data = spglib.get_symmetry_dataset(system.dump('spglib_cell'),
symprec=symprec)
ucell = spglib.standardize_cell(system.dump('spglib_cell'),
to_primitive=to_primitive,
no_idealize=no_idealize,
symprec=symprec)
# Convert back to atomman systems and normalize
ucell = am.load('spglib_cell', ucell, symbols=system.symbols)
ucell.atoms.pos -= ucell.atoms.pos[0]
ucell = ucell.normalize()
# Average extra per-atom properties by mappings to primitive
for index in np.unique(sym_data['mapping_to_primitive']):
for key in system.atoms.prop():
if key in ['atype', 'pos']:
continue
value = system.atoms.view[key][sym_data['mapping_to_primitive'] ==
index].mean()
if key not in ucell.atoms.prop():
ucell.atoms.view[key] = np.zeros_like(value)
ucell.atoms.view[key][sym_data['std_mapping_to_primitive'] ==
index] = value
# Get space group metadata
sym_data = spglib.get_symmetry_dataset(ucell.dump('spglib_cell'))
spg_type = spglib.get_spacegroup_type(sym_data['hall_number'])
# Generate Pearson symbol
if spg_type['number'] <= 2:
crystalclass = 'a'
elif spg_type['number'] <= 15:
crystalclass = 'm'
elif spg_type['number'] <= 74:
crystalclass = 'o'
elif spg_type['number'] <= 142:
crystalclass = 't'
elif spg_type['number'] <= 194:
crystalclass = 'h'
else:
crystalclass = 'c'
latticetype = spg_type['international'][0]
if latticetype in ['A', 'B']:
latticetype = 'C'
natoms = str(ucell.natoms)
pearson = crystalclass + latticetype + natoms
# Generate Wyckoff fingerprint
fingerprint_dict = {}
usites, uindices = np.unique(sym_data['equivalent_atoms'],
return_index=True)
for usite, uindex in zip(usites, uindices):
atype = ucell.atoms.atype[uindex]
wykoff = sym_data['wyckoffs'][uindex]
if atype not in fingerprint_dict:
fingerprint_dict[atype] = [wykoff]
else:
fingerprint_dict[atype].append(wykoff)
fingerprint = []
for atype in sorted(fingerprint_dict.keys()):
fingerprint.append(''.join(sorted(fingerprint_dict[atype])))
fingerprint = ' '.join(fingerprint)
# Return results
results_dict = spg_type
results_dict['ucell'] = ucell
results_dict['hall_number'] = sym_data['hall_number']
results_dict['wyckoffs'] = sym_data['wyckoffs']
results_dict['equivalent_atoms'] = sym_data['equivalent_atoms']
results_dict['pearson'] = pearson
results_dict['wyckoff_fingerprint'] = fingerprint
return results_dict
def stackingfaultpoint(lammps_command,
system,
potential,
mpi_command=None,
sim_directory=None,
cutboxvector='c',
faultpos=0.5,
faultshift=[0.0, 0.0, 0.0],
etol=0.0,
ftol=0.0,
maxiter=10000,
maxeval=100000,
dmax=uc.set_in_units(0.01, 'angstrom'),
lammps_date=None):
"""
Perform a stacking fault relaxation simulation for a single faultshift.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
system : atomman.System
The system to perform the calculation on.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
mpi_command : str, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
sim_directory : str, optional
The path to the directory to perform the simuation in. If not
given, will use the current working directory.
etol : float, optional
The energy tolerance for the structure minimization. This value is
unitless. (Default is 0.0).
ftol : float, optional
The force tolerance for the structure minimization. This value is in
units of force. (Default is 0.0).
maxiter : int, optional
The maximum number of minimization iterations to use (default is
10000).
maxeval : int, optional
The maximum number of minimization evaluations to use (default is
100000).
dmax : float, optional
The maximum distance in length units that any atom is allowed to relax
in any direction during a single minimization iteration (default is
0.01 Angstroms).
cutboxvector : str, optional
Indicates which of the three system box vectors, 'a', 'b', or 'c', to
cut with a non-periodic boundary (default is 'c').
faultpos : float, optional
The fractional position along the cutboxvector where the stacking
fault plane will be placed (default is 0.5).
faultshift : list of float, optional
The vector shift to apply to all atoms above the fault plane defined
by faultpos (default is [0,0,0], i.e. no shift applied).
lammps_date : datetime.date or None, optional
The date version of the LAMMPS executable. If None, will be identified from the lammps_command (default is None).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'logfile'** (*str*) - The filename of the LAMMPS log file.
- **'dumpfile'** (*str*) - The filename of the LAMMPS dump file
of the relaxed system.
- **'system'** (*atomman.System*) - The relaxed system.
- **'A_fault'** (*float*) - The area of the fault surface.
- **'E_total'** (*float*) - The total potential energy of the relaxed
system.
- **'disp'** (*float*) - The center of mass difference between atoms
above and below the fault plane in the cutboxvector direction.
Raises
------
ValueError
For invalid cutboxvectors.
"""
# Set options based on cutboxvector
if cutboxvector == 'a':
# Assert system is compatible with planeaxis value
if system.box.xy != 0.0 or system.box.xz != 0.0:
raise ValueError(
"box tilts xy and xz must be 0 for cutboxvector='a'")
# Specify cutindex
cutindex = 0
# Identify atoms above fault
faultpos = system.box.xlo + system.box.lx * faultpos
abovefault = system.atoms.pos[:, cutindex] > (faultpos)
# Compute fault area
faultarea = np.linalg.norm(np.cross(system.box.bvect,
system.box.cvect))
# Give correct LAMMPS fix setforce command
fix_cut_setforce = 'fix cut all setforce NULL 0 0'
elif cutboxvector == 'b':
# Assert system is compatible with planeaxis value
if system.box.yz != 0.0:
raise ValueError("box tilt yz must be 0 for cutboxvector='b'")
# Specify cutindex
cutindex = 1
# Identify atoms above fault
faultpos = system.box.ylo + system.box.ly * faultpos
abovefault = system.atoms.pos[:, cutindex] > (faultpos)
# Compute fault area
faultarea = np.linalg.norm(np.cross(system.box.avect,
system.box.cvect))
# Give correct LAMMPS fix setforce command
fix_cut_setforce = 'fix cut all setforce 0 NULL 0'
elif cutboxvector == 'c':
# Specify cutindex
cutindex = 2
# Identify atoms above fault
faultpos = system.box.zlo + system.box.lz * faultpos
abovefault = system.atoms.pos[:, cutindex] > (faultpos)
# Compute fault area
faultarea = np.linalg.norm(np.cross(system.box.avect,
system.box.bvect))
# Give correct LAMMPS fix setforce command
fix_cut_setforce = 'fix cut all setforce 0 0 NULL'
else:
raise ValueError('Invalid cutboxvector')
# Assert faultshift is in cut plane
if faultshift[cutindex] != 0.0:
raise ValueError('faultshift must be in cut plane')
# Generate stacking fault system by shifting atoms above the fault
sfsystem = deepcopy(system)
sfsystem.pbc = [True, True, True]
sfsystem.pbc[cutindex] = False
sfsystem.atoms.pos[abovefault] += faultshift
sfsystem.wrap()
if sim_directory is not None:
# Create sim_directory if it doesn't exist
if not os.path.isdir(sim_directory):
os.mkdir(sim_directory)
# Add '/' to end of sim_directory string if needed
if sim_directory[-1] != '/':
sim_directory = sim_directory + '/'
else:
# Set sim_directory if is None
sim_directory = ''
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Get lammps version date
if lammps_date is None:
lammps_date = lmp.checkversion(lammps_command)['date']
# Define lammps variables
lammps_variables = {}
system_info = sfsystem.dump('atom_data',
f=os.path.join(sim_directory, 'system.dat'),
units=potential.units,
atom_style=potential.atom_style)
lammps_variables['atomman_system_info'] = system_info
lammps_variables['atomman_pair_info'] = potential.pair_info(
sfsystem.symbols)
lammps_variables['fix_cut_setforce'] = fix_cut_setforce
lammps_variables['sim_directory'] = sim_directory
lammps_variables['etol'] = etol
lammps_variables['ftol'] = uc.get_in_units(ftol, lammps_units['force'])
lammps_variables['maxiter'] = maxiter
lammps_variables['maxeval'] = maxeval
lammps_variables['dmax'] = uc.get_in_units(dmax, lammps_units['length'])
# Set dump_modify format based on dump_modify_version
if lammps_date < datetime.date(2016, 8, 3):
lammps_variables[
'dump_modify_format'] = '"%i %i %.13e %.13e %.13e %.13e"'
else:
lammps_variables['dump_modify_format'] = 'float %.13e'
# Write lammps input script
template_file = 'sfmin.template'
lammps_script = os.path.join(sim_directory, 'sfmin.in')
with open(template_file) as f:
template = f.read()
with open(lammps_script, 'w') as f:
f.write(iprPy.tools.filltemplate(template, lammps_variables, '<', '>'))
# Run LAMMPS
output = lmp.run(lammps_command,
lammps_script,
mpi_command,
logfile=os.path.join(sim_directory, 'log.lammps'))
# Extract output values
thermo = output.simulations[-1]['thermo']
logfile = os.path.join(sim_directory, 'log.lammps')
dumpfile = os.path.join(sim_directory, '%i.dump' % thermo.Step.values[-1])
E_total = uc.set_in_units(thermo.PotEng.values[-1], lammps_units['energy'])
# Load relaxed system
sfsystem = am.load('atom_dump', dumpfile, symbols=sfsystem.symbols)
# Find center of mass difference in top/bottom planes
disp = (sfsystem.atoms.pos[abovefault, cutindex].mean() -
sfsystem.atoms.pos[~abovefault, cutindex].mean())
# Return results
results_dict = {}
results_dict['logfile'] = logfile
results_dict['dumpfile'] = dumpfile
results_dict['system'] = sfsystem
results_dict['A_fault'] = faultarea
results_dict['E_total'] = E_total
results_dict['disp'] = disp
return results_dict
def get_mp_structures(elements, api_key=None, lib_directory=None):
"""
Accesses the Materials Project and downloads all structures for a list of
elements as poscar files.
Parameters
----------
elements : list
A list of element symbols.
api_key : str, optional
The user's Materials Project API key. If not given, will use "MAPI_KEY"
environment variable
lib_directory : str
Path to the lib_directory to save the poscar files to. Default uses
the iprPy library/reference_crystal directory.
"""
# Function-specific imports
import pymatgen as pmg
from pymatgen.ext.matproj import MPRester
# Set source name and link
sourcename = "Materials Project"
sourcelink = "https://materialsproject.org/"
# Handle lib_directory
if lib_directory is None:
lib_directory = Path(libdir, 'reference_crystal')
if not lib_directory.is_dir():
lib_directory.mkdir()
elements.sort()
# Build list of downloaded entries
have = []
for fname in lib_directory.glob('*.json'):
have.append(fname.stem)
# Open connection to Materials Project
with MPRester(api_key) as m:
# Loop over subsets of elements
for subelements in subsets(elements):
# Query MP for all entries corresponding to the elements
entries = m.query({"elements": subelements}, ["material_id"])
# Add entries to the list if not there
missing = []
for entry in entries:
if entry['material_id'] not in have and entry[
'material_id'] not in missing:
missing.append(entry['material_id'])
# Download missing entries
try:
entries = m.query({"material_id": {
"$in": missing
}}, ['material_id', 'cif'])
except:
pass
else:
# Convert cif to model and save
for entry in entries:
name = entry['material_id']
struct = pmg.Structure.from_str(entry['cif'], fmt='cif')
struct = pmg.symmetry.analyzer.SpacegroupAnalyzer(
struct).get_conventional_standard_structure()
ucell = am.load('pymatgen_Structure', struct).normalize()
model = build_reference_crystal_model(
name, ucell, sourcename, sourcelink)
with open(Path(lib_directory, name + '.json'), 'w') as f:
model.json(fp=f, indent=4)
print('Added', entry['material_id'])
def crystal_space_group(system, symprec=1e-5, to_primitive=False,
no_idealize=False):
"""
Uses spglib to evaluate space group information for a given system.
Parameters
----------
system : atomman.System
The system to analyze.
symprec : float
Absolute length tolerance to use in identifying symmetry of atomic
sites and system boundaries.
to_primitive : bool
Indicates if the returned unit cell is conventional (False) or
primitive (True). Default value is False.
no_idealize : bool
Indicates if the atom positions in the returned unit cell are averaged
(True) or idealized based on the structure (False). Default value is
False.
Returns
-------
dict
Results dictionary containing space group information and an associated
unit cell system.
"""
# Identify the standardized unit cell representation
ucell = spglib.standardize_cell(system.dump('spglib_cell'),
to_primitive=to_primitive,
no_idealize=no_idealize, symprec=symprec)
# Convert back to atomman systems and normalize
ucell = am.load('spglib_cell', ucell, symbols=system.symbols)
ucell.atoms.pos -= ucell.atoms.pos[0]
ucell = ucell.normalize()
# Get space group metadata
sym_data = spglib.get_symmetry_dataset(ucell.dump('spglib_cell'))
spg_type = spglib.get_spacegroup_type(sym_data['hall_number'])
# Generate Pearson symbol
if spg_type['number'] <= 2:
crystalclass = 'a'
elif spg_type['number'] <= 15:
crystalclass = 'm'
elif spg_type['number'] <= 74:
crystalclass = 'o'
elif spg_type['number'] <= 142:
crystalclass = 't'
elif spg_type['number'] <= 194:
crystalclass = 'h'
else:
crystalclass = 'c'
latticetype = spg_type['international'][0]
if latticetype in ['A', 'B']:
latticetype = 'C'
natoms = str(ucell.natoms)
pearson = crystalclass + latticetype + natoms
# Return results
results_dict = spg_type
results_dict['ucell'] = ucell
results_dict['hall_number'] = sym_data['hall_number']
results_dict['wyckoffs'] = sym_data['wyckoffs']
results_dict['pearson'] = pearson
return results_dict
def phononcalc(lammps_command,
ucell,
potential,
mpi_command=None,
a_mult=3,
b_mult=3,
c_mult=3,
distance=0.01,
symprec=1e-5,
savefile='phonopy_params.yaml',
plot=True,
lammps_date=None):
"""
Uses phonopy to compute the phonons for a unit cell structure using a
LAMMPS interatomic potential.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
ucell : atomman.System
The unit cell system to perform the calculation on.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
mpi_command : str, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
a_mult : int, optional
The a size multiplier to use on ucell before running the phonon
calculation. Must be an int and not a tuple. Default value is 3.
b_mult : int, optional
The b size multiplier to use on ucell before running the phonon
calculation. Must be an int and not a tuple. Default value is 3.
c_mult : int, optional
The c size multiplier to use on ucell before running the phonon
calculation. Must be an int and not a tuple. Default value is 3.
distance : float, optional
The atomic displacement distance used for computing the phonons.
Default value is 0.01.
symprec : float, optional
Absolute length tolerance to use in identifying symmetry of atomic
sites and system boundaries. Default value is 1e-5.
savefile: str, optional
The name of the phonopy yaml backup file. Default value is
'phonopy_params.yaml'.
plot : bool, optional
Flag indicating if band structure and DOS figures are to be generated.
Default value is True.
lammps_date : datetime.date, optional
The version date associated with lammps_command. If not given, the
version will be identified.
"""
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
# Get lammps version date
if lammps_date is None:
lammps_date = lmp.checkversion(lammps_command)['date']
# Use spglib to find primitive unit cell of ucell
convcell = ucell.dump('spglib_cell')
primcell = spglib.find_primitive(convcell, symprec=symprec)
primucell = am.load('spglib_cell', primcell,
symbols=ucell.symbols).normalize()
# Initialize Phonopy object
phonon = phonopy.Phonopy(primucell.dump('phonopy_Atoms',
symbols=potential.elements(
primucell.symbols)),
[[a_mult, 0, 0], [0, b_mult, 0], [0, 0, c_mult]],
factor=phonopy.units.VaspToTHz)
phonon.generate_displacements(distance=distance)
# Loop over displaced supercells to compute forces
forcearrays = []
for supercell in phonon.supercells_with_displacements:
# Save to LAMMPS data file
system = am.load('phonopy_Atoms', supercell, symbols=primucell.symbols)
system_info = system.dump('atom_data',
f='disp.dat',
potential=potential)
# Define lammps variables
lammps_variables = {}
lammps_variables['atomman_system_pair_info'] = system_info
# Set dump_modify_format based on lammps_date
if lammps_date < datetime.date(2016, 8, 3):
lammps_variables[
'dump_modify_format'] = '"%d %d %.13e %.13e %.13e %.13e %.13e %.13e"'
else:
lammps_variables['dump_modify_format'] = 'float %.13e'
# Write lammps input script
lammps_script = 'phonon.in'
template = read_calc_file('iprPy.calculation.phonon',
'phonon.template')
with open(lammps_script, 'w') as f:
f.write(filltemplate(template, lammps_variables, '<', '>'))
# Run LAMMPS
lmp.run(lammps_command,
script_name=lammps_script,
mpi_command=mpi_command)
# Extract forces from dump file
forcestructure = am.load('atom_dump', 'forces.dump')
forces = uc.set_in_units(forcestructure.atoms.force,
lammps_units['force'])
forcearrays.append(forces)
results = {}
# Set computed forces
phonon.set_forces(forcearrays)
# Save to yaml file
phonon.save(savefile)
# Compute band structure
phonon.produce_force_constants()
phonon.auto_band_structure(plot=plot)
results['band_structure'] = phonon.get_band_structure_dict()
if plot:
plt.ylabel('Frequency (THz)')
plt.savefig(Path('.', 'band.png'), dpi=400)
plt.close()
# Compute density of states
phonon.auto_total_dos(plot=False)
phonon.auto_projected_dos(plot=False)
dos = phonon.get_total_dos_dict()
dos['frequency'] = uc.set_in_units(dos.pop('frequency_points'), 'THz')
dos['projected_dos'] = phonon.get_projected_dos_dict()['projected_dos']
results['dos'] = dos
# Compute thermal properties
phonon.run_thermal_properties()
results['thermal_properties'] = phonon.get_thermal_properties_dict()
results['phonon'] = phonon
return results
def relax_dynamic(lammps_command: str,
system: am.System,
potential: lmp.Potential,
mpi_command: Optional[str] = None,
p_xx: float = 0.0,
p_yy: float = 0.0,
p_zz: float = 0.0,
p_xy: float = 0.0,
p_xz: float = 0.0,
p_yz: float = 0.0,
temperature: float = 0.0,
integrator: Optional[str] = None,
runsteps: int = 220000,
thermosteps: int = 100,
dumpsteps: Optional[int] = None,
restartsteps: Optional[int] = None,
equilsteps: int = 20000,
randomseed: Optional[int] = None) -> dict:
"""
Performs a full dynamic relax on a given system at the given temperature
to the specified pressure state.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
system : atomman.System
The system to perform the calculation on.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
symbols : list of str
The list of element-model symbols for the Potential that correspond to
system's atypes.
mpi_command : str, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
p_xx : float, optional
The value to relax the x tensile pressure component to (default is
0.0).
p_yy : float, optional
The value to relax the y tensile pressure component to (default is
0.0).
p_zz : float, optional
The value to relax the z tensile pressure component to (default is
0.0).
temperature : float, optional
The temperature to relax at (default is 0.0).
runsteps : int, optional
The number of integration steps to perform (default is 220000).
integrator : str or None, optional
The integration method to use. Options are 'npt', 'nvt', 'nph',
'nve', 'nve+l', 'nph+l'. The +l options use Langevin thermostat.
(Default is None, which will use 'nph+l' for temperature == 0, and
'npt' otherwise.)
thermosteps : int, optional
Thermo values will be reported every this many steps (default is
100).
dumpsteps : int or None, optional
Dump files will be saved every this many steps (default is None,
which sets dumpsteps equal to runsteps).
restartsteps : int or None, optional
Restart files will be saved every this many steps (default is None,
which sets restartsteps equal to runsteps).
equilsteps : int, optional
The number of timesteps at the beginning of the simulation to
exclude when computing average values (default is 20000).
randomseed : int or None, optional
Random number seed used by LAMMPS in creating velocities and with
the Langevin thermostat. (Default is None which will select a
random int between 1 and 900000000.)
Returns
-------
dict
Dictionary of results consisting of keys:
- **'dumpfile_initial'** (*str*) - The name of the initial dump file
created.
- **'symbols_initial'** (*list*) - The symbols associated with the
initial dump file.
- **'dumpfile_final'** (*str*) - The name of the final dump file
created.
- **'symbols_final'** (*list*) - The symbols associated with the final
dump file.
- **'nsamples'** (*int*) - The number of thermodynamic samples included
in the mean and standard deviation estimates. Can also be used to
estimate standard error values assuming that the thermo step size is
large enough (typically >= 100) to assume the samples to be
independent.
- **'E_pot'** (*float*) - The mean measured potential energy.
- **'measured_pxx'** (*float*) - The measured x tensile pressure of the
relaxed system.
- **'measured_pyy'** (*float*) - The measured y tensile pressure of the
relaxed system.
- **'measured_pzz'** (*float*) - The measured z tensile pressure of the
relaxed system.
- **'measured_pxy'** (*float*) - The measured xy shear pressure of the
relaxed system.
- **'measured_pxz'** (*float*) - The measured xz shear pressure of the
relaxed system.
- **'measured_pyz'** (*float*) - The measured yz shear pressure of the
relaxed system.
- **'temp'** (*float*) - The mean measured temperature.
- **'E_pot_std'** (*float*) - The standard deviation in the measured
potential energy values.
- **'measured_pxx_std'** (*float*) - The standard deviation in the
measured x tensile pressure of the relaxed system.
- **'measured_pyy_std'** (*float*) - The standard deviation in the
measured y tensile pressure of the relaxed system.
- **'measured_pzz_std'** (*float*) - The standard deviation in the
measured z tensile pressure of the relaxed system.
- **'measured_pxy_std'** (*float*) - The standard deviation in the
measured xy shear pressure of the relaxed system.
- **'measured_pxz_std'** (*float*) - The standard deviation in the
measured xz shear pressure of the relaxed system.
- **'measured_pyz_std'** (*float*) - The standard deviation in the
measured yz shear pressure of the relaxed system.
- **'temp_std'** (*float*) - The standard deviation in the measured
temperature values.
"""
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Get lammps version date
lammps_date = lmp.checkversion(lammps_command)['date']
# Handle default values
if dumpsteps is None:
dumpsteps = runsteps
if restartsteps is None:
restartsteps = runsteps
# Define lammps variables
lammps_variables = {}
# Dump initial system as data and build LAMMPS inputs
system_info = system.dump('atom_data', f='init.dat', potential=potential)
lammps_variables['atomman_system_pair_info'] = system_info
# Generate LAMMPS inputs for restarting
system_info2 = potential.pair_restart_info('*.restart', system.symbols)
lammps_variables['atomman_pair_restart_info'] = system_info2
# Integrator lines for main run
integ_info = integrator_info(integrator=integrator,
p_xx=p_xx,
p_yy=p_yy,
p_zz=p_zz,
p_xy=p_xy,
p_xz=p_xz,
p_yz=p_yz,
temperature=temperature,
randomseed=randomseed,
units=potential.units,
lammps_date=lammps_date)
lammps_variables['integrator_info'] = integ_info
# Integrator lines for restarts
integ_info2 = integrator_info(integrator=integrator,
p_xx=p_xx,
p_yy=p_yy,
p_zz=p_zz,
p_xy=p_xy,
p_xz=p_xz,
p_yz=p_yz,
temperature=temperature,
velocity_temperature=0.0,
randomseed=randomseed,
units=potential.units,
lammps_date=lammps_date)
lammps_variables['integrator_restart_info'] = integ_info2
# Other run settings
lammps_variables['thermosteps'] = thermosteps
lammps_variables['runsteps'] = runsteps
lammps_variables['dumpsteps'] = dumpsteps
lammps_variables['restartsteps'] = restartsteps
# Set compute stress/atom based on LAMMPS version
if lammps_date < datetime.date(2014, 2, 12):
lammps_variables['stressterm'] = ''
else:
lammps_variables['stressterm'] = 'NULL'
# Set dump_keys based on atom_style
if potential.atom_style in ['charge']:
lammps_variables['dump_keys'] = 'id type q xu yu zu c_pe c_ke &\n'
lammps_variables[
'dump_keys'] += 'c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]'
else:
lammps_variables['dump_keys'] = 'id type xu yu zu c_pe c_ke &\n'
lammps_variables[
'dump_keys'] += 'c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]'
# Set dump_modify_format based on lammps_date
if lammps_date < datetime.date(2016, 8, 3):
if potential.atom_style in ['charge']:
lammps_variables['dump_modify_format'] = f'"%d %d{12 * " %.13e"}"'
else:
lammps_variables['dump_modify_format'] = f'"%d %d{11 * " %.13e"}"'
else:
lammps_variables['dump_modify_format'] = 'float %.13e'
# Write lammps input script
lammps_script = 'full_relax.in'
template = read_calc_file('iprPy.calculation.relax_dynamic',
'full_relax.template')
with open(lammps_script, 'w') as f:
f.write(filltemplate(template, lammps_variables, '<', '>'))
# Write lammps restart input script
restart_script = 'full_relax_restart.in'
template = read_calc_file('iprPy.calculation.relax_dynamic',
'full_relax_restart.template')
with open(restart_script, 'w') as f:
f.write(filltemplate(template, lammps_variables, '<', '>'))
# Run lammps
output = lmp.run(lammps_command,
script_name=lammps_script,
restart_script_name=restart_script,
mpi_command=mpi_command,
screen=False)
# Extract LAMMPS thermo data.
results = {}
thermo = output.flatten()['thermo']
results['dumpfile_initial'] = '0.dump'
results['symbols_initial'] = system.symbols
# Load relaxed system from dump file
last_dump_file = f'{thermo.Step.values[-1]}.dump'
results['dumpfile_final'] = last_dump_file
system = am.load('atom_dump', last_dump_file, symbols=system.symbols)
results['symbols_final'] = system.symbols
# Only consider values where Step >= equilsteps
thermo = thermo[thermo.Step >= equilsteps]
results['nsamples'] = len(thermo)
# Get cohesive energy estimates
natoms = system.natoms
results['E_pot'] = uc.set_in_units(thermo.PotEng.mean() / natoms,
lammps_units['energy'])
results['E_pot_std'] = uc.set_in_units(thermo.PotEng.std() / natoms,
lammps_units['energy'])
results['E_total'] = uc.set_in_units(thermo.TotEng.mean() / natoms,
lammps_units['energy'])
results['E_total_std'] = uc.set_in_units(thermo.TotEng.std() / natoms,
lammps_units['energy'])
results['lx'] = uc.set_in_units(thermo.Lx.mean(), lammps_units['length'])
results['lx_std'] = uc.set_in_units(thermo.Lx.std(),
lammps_units['length'])
results['ly'] = uc.set_in_units(thermo.Ly.mean(), lammps_units['length'])
results['ly_std'] = uc.set_in_units(thermo.Ly.std(),
lammps_units['length'])
results['lz'] = uc.set_in_units(thermo.Lz.mean(), lammps_units['length'])
results['lz_std'] = uc.set_in_units(thermo.Lz.std(),
lammps_units['length'])
results['xy'] = uc.set_in_units(thermo.Xy.mean(), lammps_units['length'])
results['xy_std'] = uc.set_in_units(thermo.Xy.std(),
lammps_units['length'])
results['xz'] = uc.set_in_units(thermo.Xz.mean(), lammps_units['length'])
results['xz_std'] = uc.set_in_units(thermo.Xz.std(),
lammps_units['length'])
results['yz'] = uc.set_in_units(thermo.Yz.mean(), lammps_units['length'])
results['yz_std'] = uc.set_in_units(thermo.Yz.std(),
lammps_units['length'])
results['measured_pxx'] = uc.set_in_units(thermo.Pxx.mean(),
lammps_units['pressure'])
results['measured_pxx_std'] = uc.set_in_units(thermo.Pxx.std(),
lammps_units['pressure'])
results['measured_pyy'] = uc.set_in_units(thermo.Pyy.mean(),
lammps_units['pressure'])
results['measured_pyy_std'] = uc.set_in_units(thermo.Pyy.std(),
lammps_units['pressure'])
results['measured_pzz'] = uc.set_in_units(thermo.Pzz.mean(),
lammps_units['pressure'])
results['measured_pzz_std'] = uc.set_in_units(thermo.Pzz.std(),
lammps_units['pressure'])
results['measured_pxy'] = uc.set_in_units(thermo.Pxy.mean(),
lammps_units['pressure'])
results['measured_pxy_std'] = uc.set_in_units(thermo.Pxy.std(),
lammps_units['pressure'])
results['measured_pxz'] = uc.set_in_units(thermo.Pxz.mean(),
lammps_units['pressure'])
results['measured_pxz_std'] = uc.set_in_units(thermo.Pxz.std(),
lammps_units['pressure'])
results['measured_pyz'] = uc.set_in_units(thermo.Pyz.mean(),
lammps_units['pressure'])
results['measured_pyz_std'] = uc.set_in_units(thermo.Pyz.std(),
lammps_units['pressure'])
results['temp'] = thermo.Temp.mean()
results['temp_std'] = thermo.Temp.std()
return results
def dislocationmonopole(lammps_command, system, potential, burgers,
C, mpi_command=None, axes=None, m=[0,1,0], n=[0,0,1],
lineboxvector='a', randomseed=None,
etol=0.0, ftol=0.0, maxiter=10000, maxeval=100000,
dmax=uc.set_in_units(0.01, 'angstrom'),
annealtemp=0.0, bshape='circle',
bwidth=uc.set_in_units(10, 'angstrom')):
"""
Creates and relaxes a dislocation monopole system.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
system : atomman.System
The bulk system to add the defect to.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
burgers : list or numpy.array of float
The burgers vector for the dislocation being added.
C : atomman.ElasticConstants
The system's elastic constants.
mpi_command : str or None, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
axes : numpy.array of float or None, optional
The 3x3 axes used to rotate the system by during creation. If given,
will be used to transform burgers and C from the standard
crystallographic orientations to the system's Cartesian units.
randomseed : int or None, optional
Random number seed used by LAMMPS in creating velocities and with
the Langevin thermostat. (Default is None which will select a
random int between 1 and 900000000.)
etol : float, optional
The energy tolerance for the structure minimization. This value is
unitless. (Default is 0.0).
ftol : float, optional
The force tolerance for the structure minimization. This value is in
units of force. (Default is 0.0).
maxiter : int, optional
The maximum number of minimization iterations to use (default is
10000).
maxeval : int, optional
The maximum number of minimization evaluations to use (default is
100000).
dmax : float, optional
The maximum distance in length units that any atom is allowed to relax
in any direction during a single minimization iteration (default is
0.01 Angstroms).
annealtemp : float, optional
The temperature to perform a dynamic relaxation at. (Default is 0.0,
which will skip the dynamic relaxation.)
bshape : str, optional
The shape to make the boundary region. Options are 'circle' and
'rect' (default is 'circle').
bwidth : float, optional
The minimum thickness of the boundary region (default is 10
Angstroms).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'dumpfile_base'** (*str*) - The filename of the LAMMPS dump file
for the relaxed base system.
- **'symbols_base'** (*list of str*) - The list of element-model
symbols for the Potential that correspond to the base system's
atypes.
- **'Stroh_preln'** (*float*) - The pre-logarithmic factor in the
dislocation's self-energy expression.
- **'Stroh_K_tensor'** (*numpy.array of float*) - The energy
coefficient tensor based on the dislocation's Stroh solution.
- **'dumpfile_disl'** (*str*) - The filename of the LAMMPS dump file
for the relaxed dislocation monopole system.
- **'symbols_disl'** (*list of str*) - The list of element-model
symbols for the Potential that correspond to the dislocation
monopole system's atypes.
- **'E_total_disl'** (*float*) - The total potential energy of the
dislocation monopole system.
"""
# Initialize results dict
results_dict = {}
# Save initial perfect system
system.dump('atom_dump', f='base.dump')
results_dict['dumpfile_base'] = 'base.dump'
results_dict['symbols_base'] = system.symbols
# Solve Stroh method for dislocation
stroh = am.defect.Stroh(C, burgers, axes=axes, m=m, n=n)
results_dict['Stroh_preln'] = stroh.preln
results_dict['Stroh_K_tensor'] = stroh.K_tensor
# Generate dislocation system by displacing atoms
disp = stroh.displacement(system.atoms.pos)
system.atoms.pos += disp
# Apply fixed boundary conditions
system = disl_boundary_fix(system, bwidth, bshape=bshape, lineboxvector=lineboxvector, m=m, n=n)
# Relax system
relaxed = disl_relax(lammps_command, system, potential,
mpi_command = mpi_command,
annealtemp = annealtemp,
etol = etol,
ftol = ftol,
maxiter = maxiter,
maxeval = maxeval)
# Save relaxed dislocation system with original box vects
system_disl = am.load('atom_dump', relaxed['dumpfile'], symbols=system.symbols)
system_disl.box_set(vects=system.box.vects, origin=system.box.origin)
system_disl.dump('atom_dump', f='disl.dump')
results_dict['dumpfile_disl'] = 'disl.dump'
results_dict['symbols_disl'] = system_disl.symbols
results_dict['E_total_disl'] = relaxed['E_total']
# Cleanup files
os.remove('0.dump')
os.remove(relaxed['dumpfile'])
for dumpjsonfile in glob.iglob('*.dump.json'):
os.remove(dumpjsonfile)
return results_dict
def relax_static(lammps_command, system, potential, mpi_command=None,
p_xx=0.0, p_yy=0.0, p_zz=0.0, p_xy=0.0, p_xz=0.0, p_yz=0.0,
dispmult=0.0, etol=0.0, ftol=0.0, maxiter=10000,
maxeval=100000, dmax=uc.set_in_units(0.01, 'angstrom'),
maxcycles=100, ctol=1e-10):
"""
Repeatedly runs the ELASTIC example distributed with LAMMPS until box
dimensions converge within a tolerance.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
system : atomman.System
The system to perform the calculation on.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
mpi_command : str, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
p_xx : float, optional
The value to relax the x tensile pressure component to (default is
0.0).
p_yy : float, optional
The value to relax the y tensile pressure component to (default is
0.0).
p_zz : float, optional
The value to relax the z tensile pressure component to (default is
0.0).
p_xy : float, optional
The value to relax the xy shear pressure component to (default is
0.0).
p_xz : float, optional
The value to relax the xz shear pressure component to (default is
0.0).
p_yz : float, optional
The value to relax the yz shear pressure component to (default is
0.0).
dispmult : float, optional
Multiplier for applying a random displacement to all atomic positions
prior to relaxing. Default value is 0.0.
etol : float, optional
The energy tolerance for the structure minimization. This value is
unitless. (Default is 0.0).
ftol : float, optional
The force tolerance for the structure minimization. This value is in
units of force. (Default is 0.0).
maxiter : int, optional
The maximum number of minimization iterations to use (default is 10000).
maxeval : int, optional
The maximum number of minimization evaluations to use (default is
100000).
dmax : float, optional
The maximum distance in length units that any atom is allowed to relax
in any direction during a single minimization iteration (default is
0.01 Angstroms).
pressure_unit : str, optional
The unit of pressure to calculate the elastic constants in (default is
'GPa').
maxcycles : int, optional
The maximum number of times the minimization algorithm is called.
Default value is 100.
ctol : float, optional
The relative tolerance used to determine if the lattice constants have
converged (default is 1e-10).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'relaxed_system'** (*float*) - The relaxed system.
- **'E_coh'** (*float*) - The cohesive energy of the relaxed system.
- **'measured_pxx'** (*float*) - The measured x tensile pressure of the
relaxed system.
- **'measured_pyy'** (*float*) - The measured y tensile pressure of the
relaxed system.
- **'measured_pzz'** (*float*) - The measured z tensile pressure of the
relaxed system.
- **'measured_pxy'** (*float*) - The measured xy shear pressure of the
relaxed system.
- **'measured_pxz'** (*float*) - The measured xz shear pressure of the
relaxed system.
- **'measured_pyz'** (*float*) - The measured yz shear pressure of the
relaxed system.
"""
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
# Get lammps version date
lammps_date = lmp.checkversion(lammps_command)['date']
# Save initial configuration as a dump file
system.dump('atom_dump', f='initial.dump')
# Apply small random distortions to atoms
system.atoms.pos += dispmult * np.random.rand(*system.atoms.pos.shape) - dispmult / 2
# Initialize parameters
old_vects = system.box.vects
converged = False
# Run minimizations up to maxcycles times
for cycle in range(maxcycles):
old_system = deepcopy(system)
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data', f='init.dat',
units=potential.units,
atom_style=potential.atom_style)
lammps_variables['atomman_system_info'] = system_info
lammps_variables['atomman_pair_info'] = potential.pair_info(system.symbols)
lammps_variables['p_xx'] = uc.get_in_units(p_xx, lammps_units['pressure'])
lammps_variables['p_yy'] = uc.get_in_units(p_yy, lammps_units['pressure'])
lammps_variables['p_zz'] = uc.get_in_units(p_zz, lammps_units['pressure'])
lammps_variables['p_xy'] = uc.get_in_units(p_xy, lammps_units['pressure'])
lammps_variables['p_xz'] = uc.get_in_units(p_xz, lammps_units['pressure'])
lammps_variables['p_yz'] = uc.get_in_units(p_yz, lammps_units['pressure'])
lammps_variables['etol'] = etol
lammps_variables['ftol'] = uc.get_in_units(ftol, lammps_units['force'])
lammps_variables['maxiter'] = maxiter
lammps_variables['maxeval'] = maxeval
lammps_variables['dmax'] = uc.get_in_units(dmax, lammps_units['length'])
# Set dump_modify_format based on lammps_date
if lammps_date < datetime.date(2016, 8, 3):
lammps_variables['dump_modify_format'] = '"%d %d %.13e %.13e %.13e %.13e"'
else:
lammps_variables['dump_modify_format'] = 'float %.13e'
# Write lammps input script
template_file = 'minbox.template'
lammps_script = 'minbox.in'
with open(template_file) as f:
template = f.read()
with open(lammps_script, 'w') as f:
f.write(iprPy.tools.filltemplate(template, lammps_variables, '<', '>'))
# Run LAMMPS and extract thermo data
logfile = 'log-' + str(cycle) + '.lammps'
output = lmp.run(lammps_command, lammps_script, mpi_command, logfile=logfile)
thermo = output.simulations[0]['thermo']
# Clean up dump files
os.remove('0.dump')
last_dump_file = str(thermo.Step.values[-1]) + '.dump'
renamed_dump_file = 'relax_static-' + str(cycle) + '.dump'
shutil.move(last_dump_file, renamed_dump_file)
# Load relaxed system
system = am.load('atom_dump', renamed_dump_file, symbols=system.symbols)
# Test if box dimensions have converged
if np.allclose(old_vects, system.box.vects, rtol=ctol, atol=0):
converged = True
break
else:
old_vects = system.box.vects
# Check for convergence
if converged is False:
raise RuntimeError('Failed to converge after ' + str(maxcycles) + ' cycles')
# Zero out near-zero tilt factors
lx = system.box.lx
ly = system.box.ly
lz = system.box.lz
xy = system.box.xy
xz = system.box.xz
yz = system.box.yz
if np.isclose(xy/ly, 0.0, rtol=0.0, atol=1e-10):
xy = 0.0
if np.isclose(xz/lz, 0.0, rtol=0.0, atol=1e-10):
xz = 0.0
if np.isclose(yz/lz, 0.0, rtol=0.0, atol=1e-10):
yz = 0.0
system.box.set(lx=lx, ly=ly, lz=lz, xy=xy, xz=xz, yz=yz)
system.wrap()
# Build results_dict
results_dict = {}
results_dict['dumpfile_initial'] = 'initial.dump'
results_dict['symbols_initial'] = system.symbols
results_dict['dumpfile_final'] = renamed_dump_file
results_dict['symbols_final'] = system.symbols
results_dict['E_coh'] = uc.set_in_units(thermo.PotEng.values[-1] / system.natoms,
lammps_units['energy'])
results_dict['lx'] = uc.set_in_units(lx, lammps_units['length'])
results_dict['ly'] = uc.set_in_units(ly, lammps_units['length'])
results_dict['lz'] = uc.set_in_units(lz, lammps_units['length'])
results_dict['xy'] = uc.set_in_units(xy, lammps_units['length'])
results_dict['xz'] = uc.set_in_units(xz, lammps_units['length'])
results_dict['yz'] = uc.set_in_units(yz, lammps_units['length'])
results_dict['measured_pxx'] = uc.set_in_units(thermo.Pxx.values[-1],
lammps_units['pressure'])
results_dict['measured_pyy'] = uc.set_in_units(thermo.Pyy.values[-1],
lammps_units['pressure'])
results_dict['measured_pzz'] = uc.set_in_units(thermo.Pzz.values[-1],
lammps_units['pressure'])
results_dict['measured_pxy'] = uc.set_in_units(thermo.Pxy.values[-1],
lammps_units['pressure'])
results_dict['measured_pxz'] = uc.set_in_units(thermo.Pxz.values[-1],
lammps_units['pressure'])
results_dict['measured_pyz'] = uc.set_in_units(thermo.Pyz.values[-1],
lammps_units['pressure'])
return results_dict
def todict(self, full=True, flat=False):
"""
Converts the structured content to a simpler dictionary.
Parameters
----------
full : bool, optional
Flag used by the calculation records. A True value will include
terms for both the calculation's input and results, while a value
of False will only include input terms (Default is True).
flat : bool, optional
Flag affecting the format of the dictionary terms. If True, the
dictionary terms are limited to having only str, int, and float
values, which is useful for comparisons. If False, the term
values can be of any data type, which is convenient for analysis.
(Default is False).
Returns
-------
dict
A dictionary representation of the record's content.
"""
calc = self.content[self.contentroot]
params = {}
params['key'] = calc['key']
params['script'] = calc['calculation']['script']
params['iprPy_version'] = calc['calculation']['iprPy-version']
params['symmetryprecision'] = calc['calculation']['run-parameter'][
'symmetryprecision']
params['primitivecell'] = calc['calculation']['run-parameter'][
'primitivecell']
params['idealcell'] = calc['calculation']['run-parameter']['idealcell']
params['load_file'] = calc['system-info']['artifact']['file']
params['load_style'] = calc['system-info']['artifact']['format']
params['load_options'] = calc['system-info']['artifact'][
'load_options']
params['family'] = calc['system-info']['family']
symbols = aslist(calc['system-info']['symbol'])
if flat is True:
try:
params['symbols'] = ' '.join(symbols)
except:
params['symbols'] = np.nan
else:
params['symbols'] = symbols
params['status'] = calc.get('status', 'finished')
params['error'] = calc.get('error', np.nan)
if full is True and params['status'] == 'finished':
ucell = am.load('system_model',
self.content,
key='unit-cell-atomic-system')
params['pearson_symbol'] = calc['Pearson-symbol']
params['spacegroup_number'] = calc['space-group']['number']
params['spacegroup_international'] = calc['space-group'][
'Hermann-Maguin']
params['spacegroup_Schoenflies'] = calc['space-group'][
'Schoenflies']
params['wykoff_letters'] = ' '.join(
calc['space-group'].finds('letter'))
if flat is True:
params['a'] = ucell.box.a
params['b'] = ucell.box.b
params['c'] = ucell.box.c
params['alpha'] = ucell.box.alpha
params['beta'] = ucell.box.beta
params['gamma'] = ucell.box.gamma
params['natoms'] = ucell.natoms
else:
params['ucell'] = ucell
return params
def todict(self, full=True, flat=False):
"""
Converts the structured content to a simpler dictionary.
Parameters
----------
full : bool, optional
Flag used by the calculation records. A True value will include
terms for both the calculation's input and results, while a value
of False will only include input terms (Default is True).
flat : bool, optional
Flag affecting the format of the dictionary terms. If True, the
dictionary terms are limited to having only str, int, and float
values, which is useful for comparisons. If False, the term
values can be of any data type, which is convenient for analysis.
(Default is False).
Returns
-------
dict
A dictionary representation of the record's content.
"""
# Extract universal content
params = super().todict(full=full, flat=flat)
calc = self.content[self.contentroot]
params['symmetryprecision'] = calc['calculation']['run-parameter'][
'symmetryprecision']
params['primitivecell'] = calc['calculation']['run-parameter'][
'primitivecell']
params['idealcell'] = calc['calculation']['run-parameter']['idealcell']
# Extract system info
subset('atomman_systemload').todict(calc, params, full=full, flat=flat)
params['status'] = calc.get('status', 'finished')
params['error'] = calc.get('error', np.nan)
if full is True and params['status'] == 'finished':
ucell = am.load('system_model',
self.content,
key='unit-cell-atomic-system')
params['pearson_symbol'] = calc['Pearson-symbol']
params['spacegroup_number'] = calc['space-group']['number']
params['spacegroup_international'] = calc['space-group'][
'Hermann-Maguin']
params['spacegroup_Schoenflies'] = calc['space-group'][
'Schoenflies']
params['wykoff_fingerprint'] = calc['space-group'][
'Wyckoff-fingerprint']
params['composition'] = ucell.composition
if flat is True:
params['a'] = ucell.box.a
params['b'] = ucell.box.b
params['c'] = ucell.box.c
params['alpha'] = ucell.box.alpha
params['beta'] = ucell.box.beta
params['gamma'] = ucell.box.gamma
params['natoms'] = ucell.natoms
else:
params['ucell'] = ucell
return params
def load_ucell(self, **kwargs):
"""
Wrapper around atomman.load() for loading files that also saves the
file loading options as class attributes. Any parameters not given
will use the values already set to the object.
Parameters
----------
load_style : str, optional
The style for atomman.load() to use.
load_file : str, optional
The path to the file to load.
symbols : list or None, optional
The list of interaction model symbols to associate with the atom
types in the load file. A value of None will default to the
symbols listed in the load file if the style contains that
information.
load_options : dict, optional
Any other atomman.load() keyword options to use when loading.
box_parameters : list or None, optional
A list of 3 orthorhombic box parameters or 6 trigonal box length
and angle parameters to scale the loaded system by. Setting a
value of None will perform no scaling.
family : str or None, optional
The system's family identifier. If None, then the family will be
set according to the family value in the load file if it has one,
or as the load file's name otherwise.
"""
self.set_values(**kwargs)
# Check for file and contents
if self.load_content is not None:
load_file = self.load_content
elif self.load_file is not None:
load_file = self.load_file
else:
raise ValueError('load_file not set')
# Change load symbols kwarg to None if symbols attribute is empty
if self.symbols is None or len(self.symbols) == 0:
symbols = None
else:
symbols = self.symbols
# Load ucell
self.__ucell = am.load(self.load_style, load_file,
symbols=symbols, **self.load_options)
self.ucell.wrap()
# Update object's symbols and composition
self.symbols = self.ucell.symbols
self.composition
self.scale_ucell()
# Add model-specific charges if needed
try:
potential = self.parent.potential.potential
if 'charge' not in self.ucell.atoms_prop():
self.ucell.atoms.prop_atype('charge', potential.charges(self.ucell.symbols))
except:
pass
def dislocationmonopole(lammps_command,
system,
potential,
burgers,
C,
mpi_command=None,
axes=None,
m=[0, 1, 0],
n=[0, 0, 1],
lineboxvector='a',
randomseed=None,
etol=0.0,
ftol=0.0,
maxiter=10000,
maxeval=100000,
dmax=uc.set_in_units(0.01, 'angstrom'),
annealtemp=0.0,
bshape='circle',
bwidth=uc.set_in_units(10, 'angstrom')):
"""
Creates and relaxes a dislocation monopole system.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
system : atomman.System
The bulk system to add the defect to.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
burgers : list or numpy.array of float
The burgers vector for the dislocation being added.
C : atomman.ElasticConstants
The system's elastic constants.
mpi_command : str or None, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
axes : numpy.array of float or None, optional
The 3x3 axes used to rotate the system by during creation. If given,
will be used to transform burgers and C from the standard
crystallographic orientations to the system's Cartesian units.
randomseed : int or None, optional
Random number seed used by LAMMPS in creating velocities and with
the Langevin thermostat. (Default is None which will select a
random int between 1 and 900000000.)
etol : float, optional
The energy tolerance for the structure minimization. This value is
unitless. (Default is 0.0).
ftol : float, optional
The force tolerance for the structure minimization. This value is in
units of force. (Default is 0.0).
maxiter : int, optional
The maximum number of minimization iterations to use (default is
10000).
maxeval : int, optional
The maximum number of minimization evaluations to use (default is
100000).
dmax : float, optional
The maximum distance in length units that any atom is allowed to relax
in any direction during a single minimization iteration (default is
0.01 Angstroms).
annealtemp : float, optional
The temperature to perform a dynamic relaxation at. (Default is 0.0,
which will skip the dynamic relaxation.)
bshape : str, optional
The shape to make the boundary region. Options are 'circle' and
'rect' (default is 'circle').
bwidth : float, optional
The minimum thickness of the boundary region (default is 10
Angstroms).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'dumpfile_base'** (*str*) - The filename of the LAMMPS dump file
for the relaxed base system.
- **'symbols_base'** (*list of str*) - The list of element-model
symbols for the Potential that correspond to the base system's
atypes.
- **'Stroh_preln'** (*float*) - The pre-logarithmic factor in the
dislocation's self-energy expression.
- **'Stroh_K_tensor'** (*numpy.array of float*) - The energy
coefficient tensor based on the dislocation's Stroh solution.
- **'dumpfile_disl'** (*str*) - The filename of the LAMMPS dump file
for the relaxed dislocation monopole system.
- **'symbols_disl'** (*list of str*) - The list of element-model
symbols for the Potential that correspond to the dislocation
monopole system's atypes.
- **'E_total_disl'** (*float*) - The total potential energy of the
dislocation monopole system.
"""
# Initialize results dict
results_dict = {}
# Save initial perfect system
system.dump('atom_dump', f='base.dump')
results_dict['dumpfile_base'] = 'base.dump'
results_dict['symbols_base'] = system.symbols
# Solve Stroh method for dislocation
stroh = am.defect.Stroh(C, burgers, axes=axes, m=m, n=n)
results_dict['Stroh_preln'] = stroh.preln
results_dict['Stroh_K_tensor'] = stroh.K_tensor
# Generate dislocation system by displacing atoms
disp = stroh.displacement(system.atoms.pos)
system.atoms.pos += disp
# Apply fixed boundary conditions
system = disl_boundary_fix(system,
bwidth,
bshape=bshape,
lineboxvector=lineboxvector,
m=m,
n=n)
# Relax system
relaxed = disl_relax(lammps_command,
system,
potential,
mpi_command=mpi_command,
annealtemp=annealtemp,
etol=etol,
ftol=ftol,
maxiter=maxiter,
maxeval=maxeval)
# Save relaxed dislocation system with original box vects
system_disl = am.load('atom_dump',
relaxed['dumpfile'],
symbols=system.symbols)
system_disl.box_set(vects=system.box.vects, origin=system.box.origin)
system_disl.dump('atom_dump', f='disl.dump')
results_dict['dumpfile_disl'] = 'disl.dump'
results_dict['symbols_disl'] = system_disl.symbols
results_dict['E_total_disl'] = relaxed['E_total']
# Cleanup files
os.remove('0.dump')
os.remove(relaxed['dumpfile'])
for dumpjsonfile in glob.iglob('*.dump.json'):
os.remove(dumpjsonfile)
return results_dict
def relax_dynamic(lammps_command, system, potential, mpi_command=None,
p_xx=0.0, p_yy=0.0, p_zz=0.0, p_xy=0.0, p_xz=0.0, p_yz=0.0,
temperature=0.0, integrator=None, runsteps=220000,
thermosteps=100, dumpsteps=None, equilsteps=20000,
randomseed=None):
"""
Performs a full dynamic relax on a given system at the given temperature
to the specified pressure state.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
system : atomman.System
The system to perform the calculation on.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
symbols : list of str
The list of element-model symbols for the Potential that correspond to
system's atypes.
mpi_command : str, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
p_xx : float, optional
The value to relax the x tensile pressure component to (default is
0.0).
p_yy : float, optional
The value to relax the y tensile pressure component to (default is
0.0).
p_zz : float, optional
The value to relax the z tensile pressure component to (default is
0.0).
temperature : float, optional
The temperature to relax at (default is 0.0).
runsteps : int, optional
The number of integration steps to perform (default is 220000).
integrator : str or None, optional
The integration method to use. Options are 'npt', 'nvt', 'nph',
'nve', 'nve+l', 'nph+l'. The +l options use Langevin thermostat.
(Default is None, which will use 'nph+l' for temperature == 0, and
'npt' otherwise.)
thermosteps : int, optional
Thermo values will be reported every this many steps (default is
100).
dumpsteps : int or None, optional
Dump files will be saved every this many steps (default is None,
which sets dumpsteps equal to runsteps).
equilsteps : int, optional
The number of timesteps at the beginning of the simulation to
exclude when computing average values (default is 20000).
randomseed : int or None, optional
Random number seed used by LAMMPS in creating velocities and with
the Langevin thermostat. (Default is None which will select a
random int between 1 and 900000000.)
Returns
-------
dict
Dictionary of results consisting of keys:
- **'relaxed_system'** (*float*) - The relaxed system.
- **'E_coh'** (*float*) - The mean measured cohesive energy.
- **'measured_pxx'** (*float*) - The measured x tensile pressure of the
relaxed system.
- **'measured_pyy'** (*float*) - The measured y tensile pressure of the
relaxed system.
- **'measured_pzz'** (*float*) - The measured z tensile pressure of the
relaxed system.
- **'measured_pxy'** (*float*) - The measured xy shear pressure of the
relaxed system.
- **'measured_pxz'** (*float*) - The measured xz shear pressure of the
relaxed system.
- **'measured_pyz'** (*float*) - The measured yz shear pressure of the
relaxed system.
- **'temp'** (*float*) - The mean measured temperature.
- **'E_coh_std'** (*float*) - The standard deviation in the measured
cohesive energy values.
- **'measured_pxx_std'** (*float*) - The standard deviation in the
measured x tensile pressure of the relaxed system.
- **'measured_pyy_std'** (*float*) - The standard deviation in the
measured y tensile pressure of the relaxed system.
- **'measured_pzz_std'** (*float*) - The standard deviation in the
measured z tensile pressure of the relaxed system.
- **'measured_pxy_std'** (*float*) - The standard deviation in the
measured xy shear pressure of the relaxed system.
- **'measured_pxz_std'** (*float*) - The standard deviation in the
measured xz shear pressure of the relaxed system.
- **'measured_pyz_std'** (*float*) - The standard deviation in the
measured yz shear pressure of the relaxed system.
- **'temp_std'** (*float*) - The standard deviation in the measured
temperature values.
"""
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Get lammps version date
lammps_date = lmp.checkversion(lammps_command)['date']
# Handle default values
if dumpsteps is None:
dumpsteps = runsteps
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data', f='init.dat',
units=potential.units,
atom_style=potential.atom_style)
lammps_variables['atomman_system_info'] = system_info
lammps_variables['atomman_pair_info'] = potential.pair_info(system.symbols)
integ_info = integrator_info(integrator=integrator,
p_xx=p_xx, p_yy=p_yy, p_zz=p_zz,
p_xy=p_xy, p_xz=p_xz, p_yz=p_yz,
temperature=temperature,
randomseed=randomseed,
units=potential.units)
lammps_variables['integrator_info'] = integ_info
lammps_variables['thermosteps'] = thermosteps
lammps_variables['runsteps'] = runsteps
lammps_variables['dumpsteps'] = dumpsteps
# Set compute stress/atom based on LAMMPS version
if lammps_date < datetime.date(2014, 2, 12):
lammps_variables['stressterm'] = ''
else:
lammps_variables['stressterm'] = 'NULL'
# Set dump_modify_format based on lammps_date
if lammps_date < datetime.date(2016, 8, 3):
lammps_variables['dump_modify_format'] = '"%d %d %.13e %.13e %.13e %.13e"'
else:
lammps_variables['dump_modify_format'] = 'float %.13e'
# Write lammps input script
template_file = 'full_relax.template'
lammps_script = 'full_relax.in'
with open(template_file) as f:
template = f.read()
with open(lammps_script, 'w') as f:
f.write(iprPy.tools.filltemplate(template, lammps_variables, '<', '>'))
# Run lammps
output = lmp.run(lammps_command, lammps_script, mpi_command)
# Extract LAMMPS thermo data.
results = {}
thermo = output.simulations[0]['thermo']
results['dumpfile_initial'] = '0.dump'
results['symbols_initial'] = system.symbols
# Load relaxed system from dump file
last_dump_file = str(thermo.Step.values[-1])+'.dump'
results['dumpfile_final'] = last_dump_file
system = am.load('atom_dump', last_dump_file, symbols=system.symbols)
results['symbols_final'] = system.symbols
# Only consider values where Step >= equilsteps
thermo = thermo[thermo.Step >= equilsteps]
results['nsamples'] = len(thermo)
# Get cohesive energy estimates
natoms = system.natoms
results['E_coh'] = uc.set_in_units(thermo.PotEng.mean() / natoms, lammps_units['energy'])
results['E_coh_std'] = uc.set_in_units(thermo.PotEng.std() / natoms, lammps_units['energy'])
results['lx'] = uc.set_in_units(thermo.Lx.mean(), lammps_units['length'])
results['lx_std'] = uc.set_in_units(thermo.Lx.std(), lammps_units['length'])
results['ly'] = uc.set_in_units(thermo.Ly.mean(), lammps_units['length'])
results['ly_std'] = uc.set_in_units(thermo.Ly.std(), lammps_units['length'])
results['lz'] = uc.set_in_units(thermo.Lz.mean(), lammps_units['length'])
results['lz_std'] = uc.set_in_units(thermo.Lz.std(), lammps_units['length'])
results['xy'] = uc.set_in_units(thermo.Xy.mean(), lammps_units['length'])
results['xy_std'] = uc.set_in_units(thermo.Xy.std(), lammps_units['length'])
results['xz'] = uc.set_in_units(thermo.Xz.mean(), lammps_units['length'])
results['xz_std'] = uc.set_in_units(thermo.Xz.std(), lammps_units['length'])
results['yz'] = uc.set_in_units(thermo.Yz.mean(), lammps_units['length'])
results['yz_std'] = uc.set_in_units(thermo.Yz.std(), lammps_units['length'])
results['measured_pxx'] = uc.set_in_units(thermo.Pxx.mean(), lammps_units['pressure'])
results['measured_pxx_std'] = uc.set_in_units(thermo.Pxx.std(), lammps_units['pressure'])
results['measured_pyy'] = uc.set_in_units(thermo.Pyy.mean(), lammps_units['pressure'])
results['measured_pyy_std'] = uc.set_in_units(thermo.Pyy.std(), lammps_units['pressure'])
results['measured_pzz'] = uc.set_in_units(thermo.Pzz.mean(), lammps_units['pressure'])
results['measured_pzz_std'] = uc.set_in_units(thermo.Pzz.std(), lammps_units['pressure'])
results['measured_pxy'] = uc.set_in_units(thermo.Pxy.mean(), lammps_units['pressure'])
results['measured_pxy_std'] = uc.set_in_units(thermo.Pxy.std(), lammps_units['pressure'])
results['measured_pxz'] = uc.set_in_units(thermo.Pxz.mean(), lammps_units['pressure'])
results['measured_pxz_std'] = uc.set_in_units(thermo.Pxz.std(), lammps_units['pressure'])
results['measured_pyz'] = uc.set_in_units(thermo.Pyz.mean(), lammps_units['pressure'])
results['measured_pyz_std'] = uc.set_in_units(thermo.Pyz.std(), lammps_units['pressure'])
results['temp'] = thermo.Temp.mean()
results['temp_std'] = thermo.Temp.std()
return results