def lammps_ELASTIC(lammps_command, system, potential, symbols, mpi_command=None,
strainrange=1e-6, etol=0.0, ftol=0.0, maxiter=100, maxeval=1000,
dmax=0.01, pressure_unit='GPa'):
"""Sets up and runs the ELASTIC example distributed with LAMMPS"""
#Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Define lammps variables
lammps_variables = {}
lammps_variables['atomman_system_info'] = lmp.atom_data.dump(system, 'init.dat', units=potential.units, atom_style=potential.atom_style)
lammps_variables['atomman_pair_info'] = potential.pair_info(symbols)
lammps_variables['strainrange'] = strainrange
lammps_variables['pressure_unit_scaling'] = uc.get_in_units(uc.set_in_units(1.0, lammps_units['pressure']), pressure_unit)
lammps_variables['pressure_unit'] = pressure_unit
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'])
#Fill in mod.template files
with open('init.mod.template') as template_file:
template = template_file.read()
with open('init.mod', 'w') as in_file:
in_file.write(iprPy.tools.filltemplate(template, lammps_variables, '<', '>'))
with open('potential.mod.template') as template_file:
template = template_file.read()
with open('potential.mod', 'w') as in_file:
in_file.write(iprPy.tools.filltemplate(template, lammps_variables, '<', '>'))
output = lmp.run(lammps_command, 'in.elastic', mpi_command)
#Extract output values
relaxed = output['LAMMPS-log-thermo-data']['simulation'][0]
results = {}
results['E_coh'] = uc.set_in_units(relaxed['thermo']['PotEng'][-1], lammps_units['energy']) / system.natoms
results['lx'] = uc.set_in_units(relaxed['thermo']['Lx'][-1], lammps_units['length'])
results['ly'] = uc.set_in_units(relaxed['thermo']['Ly'][-1], lammps_units['length'])
results['lz'] = uc.set_in_units(relaxed['thermo']['Lz'][-1], lammps_units['length'])
with open('log.lammps') as log_file:
log = log_file.read()
start = log.find('print "Elastic Constant C11all = ${C11all} ${cunits}"')
lines = log[start+54:].split('\n')
for line in lines:
terms = line.split()
if len(terms) > 0 and terms[0] == 'Elastic':
c_term = terms[2][:3]
c_value = terms[4]
results['c_unit'] = terms[5]
results[c_term] = c_value
return results
def gb_energy(lammps_command, potential, symbols, alat, axes_1, axes_2, E_coh,
mpi_command=None, xshift=0.0, zshift=0.0):
"""Computes the grain boundary energy using the grain_boundary.in LAMMPS script"""
axes_1 = np.asarray(axes_1, dtype=int)
axes_2 = np.asarray(axes_2, dtype=int)
lx = alat * np.linalg.norm(axes_1[0])
lz = 2 * alat * np.linalg.norm(axes_1[2])
mesh_dir = 'mesh-%.8f-%.8f' %(xshift, zshift)
if not os.path.isdir(mesh_dir):
os.makedirs(mesh_dir)
#Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Define lammps variables
lammps_variables = {}
lammps_variables['units'] = potential.units
lammps_variables['atom_style'] = potential.atom_style
lammps_variables['atomman_pair_info'] = potential.pair_info(symbols)
lammps_variables['alat'] = uc.get_in_units(alat, lammps_units['length'])
lammps_variables['xsize'] = uc.get_in_units(lx, lammps_units['length'])
lammps_variables['zsize'] = uc.get_in_units(lz, lammps_units['length'])
lammps_variables['xshift'] = uc.get_in_units(xshift, lammps_units['length'])
lammps_variables['zshift'] = uc.get_in_units(zshift, lammps_units['length'])
lammps_variables['x_axis_1'] = str(axes_1[0]).strip('[] ')
lammps_variables['y_axis_1'] = str(axes_1[1]).strip('[] ')
lammps_variables['z_axis_1'] = str(axes_1[2]).strip('[] ')
lammps_variables['x_axis_2'] = str(axes_2[0]).strip('[] ')
lammps_variables['y_axis_2'] = str(axes_2[1]).strip('[] ')
lammps_variables['z_axis_2'] = str(axes_2[2]).strip('[] ')
lammps_variables['mesh_dir'] = 'mesh-%.8f-%.8f' %(xshift, zshift)
#Fill in mod.template files
with open('grain_boundary.template') as template_file:
template = template_file.read()
lammps_input = os.path.join(mesh_dir, 'grain_boundary.in')
with open(lammps_input, 'w') as in_file:
in_file.write(iprPy.tools.filltemplate(template, lammps_variables, '<', '>'))
output = lmp.run(lammps_command, lammps_input, mpi_command)
#Extract output values
try:
E_total = uc.set_in_units(output.finds('c_eatoms')[-1], lammps_units['energy'])
natoms = output.finds('v_natoms')[-1]
except:
E_total = uc.set_in_units(output.finds('eatoms')[-1], lammps_units['energy'])
natoms = output.finds('natoms')[-1]
#Compute grain boundary energy
E_gb = (E_total - E_coh*natoms) / (lx * lz)
return E_gb
def run(self):
self.update()
self.system.update()
dL = dLmps.DataLammps(self.system)
dL.genFile()
self.create_in()
import atomman.lammps as lmp
output = lmp.run(self.lammps_exe, self.in_lmp, return_style='object')
self.parse_log()
def run(self):
self.calls += 1
dL = dLmps.DataLammps(self.settings)
dL.genFile() # create data.lamp
self.scriptLammps.create_in() # create in.min
import atomman.lammps as lmp
output = lmp.run(self.lammps_exe, self.in_lmp, return_style='object')
self.parse_log()
def energy_check(lammps_command: str,
system: am.System,
potential: lmp.Potential,
mpi_command: Optional[str] = None) -> dict:
"""
Performs a quick run 0 calculation to evaluate the potential energy of a
configuration.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
system : atomman.System
The atomic configuration to evaluate.
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.
Returns
-------
dict
Dictionary of results consisting of keys:
- **'E_pot'** (*float*) - The per-atom potential energy of the system.
"""
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data', f='init.dat',
potential=potential)
lammps_variables['atomman_system_pair_info'] = system_info
# Fill in lammps input script
template = read_calc_file('iprPy.calculation.energy_check', 'run0.template')
script = filltemplate(template, lammps_variables, '<', '>')
# Run LAMMPS
output = lmp.run(lammps_command, script=script,
mpi_command=mpi_command, logfile=None)
# Extract output values
thermo = output.simulations[-1]['thermo']
results = {}
results['E_pot'] = uc.set_in_units(thermo.v_peatom.values[-1],
lammps_units['energy'])
return results
def ecoh_vs_r(lammps_exe, ucell, potential, symbols, rmin=2.0, rmax=5.0, rsteps=200):
"""Measure cohesive energy of a crystal as a function of nearest neighbor distance, r0"""
#Initial size setup
r_a = r_a_ratio(ucell)
amin = rmin / r_a
amax = rmax / r_a
alat0 = (amax + amin) / 2.
delta = (amax-amin)/alat0
#Create unit cell with a = alat0
ucell.box_set(a = alat0, b = alat0 * ucell.box.b / ucell.box.a, c = alat0 * ucell.box.c / ucell.box.a, scale=True)
#LAMMPS script setup
pair_info = potential.pair_info(symbols)
system_info = lmp.sys_gen(units = potential.units,
atom_style = potential.atom_style,
ucell = ucell,
size = np.array([[0,3], [0,3], [0,3]], dtype=np.int))
#Write the LAMMPS input file
with open('alat.in','w') as script:
script.write(alat_script(system_info, pair_info, delta=delta, steps=rsteps))
#Run LAMMPS
data = lmp.run(lammps_exe, 'alat.in')
#extract thermo data from log output
avalues = np.array(data.finds('Lx')) / 3.
rvalues = avalues * r_a
evalues = np.array(data.finds('peatom'))
#Use potential units and atom_style terms to convert values to appropriate length and energy units
lmp_units = lmp.style.unit(potential.units)
avalues = uc.set_in_units(avalues, lmp_units['length'])
rvalues = uc.set_in_units(rvalues, lmp_units['length'])
evalues = uc.set_in_units(evalues, lmp_units['energy'])
return rvalues, avalues, evalues
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 diatom_scan(lammps_command: str,
potential: am.lammps.Potential,
symbols: list,
mpi_command: Optional[str] = None,
rmin: float = uc.set_in_units(0.02, 'angstrom'),
rmax: float = uc.set_in_units(6.0, 'angstrom'),
rsteps: int = 300) -> dict:
"""
Performs a diatom energy scan over a range of interatomic spaces, r.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
potential : atomman.lammps.Potential
The LAMMPS implemented potential to use.
symbols : list
The potential symbols associated with the two atoms in the diatom.
mpi_command : str, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
rmin : float, optional
The minimum r spacing to use (default value is 0.02 angstroms).
rmax : float, optional
The maximum r spacing to use (default value is 6.0 angstroms).
rsteps : int, optional
The number of r spacing steps to evaluate (default value is 300).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'r_values'** (*numpy.array of float*) - All interatomic spacings,
r, explored.
- **'energy_values'** (*numpy.array of float*) - The computed potential
energies for each r value.
"""
# Build lists of values
r_values = np.linspace(rmin, rmax, rsteps)
energy_values = np.empty(rsteps)
# Define atype based on symbols
symbols = aslist(symbols)
if len(symbols) == 1:
atype = [1, 1]
elif len(symbols) == 2:
atype = [1, 2]
else:
raise ValueError('symbols must have one or two values')
# Initialize system (will shift second atom's position later...)
box = am.Box.cubic(a=rmax + 1)
atoms = am.Atoms(atype=atype, pos=[[0.1, 0.1, 0.1], [0.1, 0.1, 0.1]])
system = am.System(atoms=atoms,
box=box,
pbc=[False, False, False],
symbols=symbols)
# Add charges if required
if potential.atom_style == 'charge':
system.atoms.prop_atype('charge', potential.charges(system.symbols))
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
# Define lammps variables
lammps_variables = {}
# Loop over values
for i in range(rsteps):
# Shift second atom's x position
system.atoms.pos[1] = np.array([0.1 + r_values[i], 0.1, 0.1])
# Save configuration
system_info = system.dump('atom_data',
f='diatom.dat',
potential=potential)
lammps_variables['atomman_system_pair_info'] = system_info
# Write lammps input script
lammps_script = 'run0.in'
template = read_calc_file('iprPy.calculation.diatom_scan',
'run0.template')
with open(lammps_script, 'w') as f:
f.write(filltemplate(template, lammps_variables, '<', '>'))
# Run lammps and extract data
try:
output = lmp.run(lammps_command,
script_name=lammps_script,
mpi_command=mpi_command)
except:
energy_values[i] = np.nan
else:
energy = output.simulations[0]['thermo'].PotEng.values[-1]
energy_values[i] = uc.set_in_units(energy, lammps_units['energy'])
if len(energy_values[np.isfinite(energy_values)]) == 0:
raise ValueError(
'All LAMMPS runs failed. Potential likely invalid or incompatible.'
)
# Collect results
results_dict = {}
results_dict['r_values'] = r_values
results_dict['energy_values'] = energy_values
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.
"""
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']
# Handle default values
if dumpsteps is None:
dumpsteps = runsteps
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data', f='init.dat',
potential=potential,
return_pair_info=True)
lammps_variables['atomman_system_pair_info'] = system_info
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_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'] = '"%d %d %.13e %.13e %.13e %.13e %.13e %.13e %.13e %.13e %.13e %.13e %.13e %.13e"'
else:
lammps_variables['dump_modify_format'] = '"%d %d %.13e %.13e %.13e %.13e %.13e %.13e %.13e %.13e %.13e %.13e %.13e"'
else:
lammps_variables['dump_modify_format'] = 'float %.13e'
# Write lammps input script
template_file = Path(script_dir, '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
def calc_cij(lammps_command,
system,
potential,
mpi_command=None,
p_xx=0.0,
p_yy=0.0,
p_zz=0.0,
strainrange=1e-6,
cycle=0):
"""
Runs cij.in LAMMPS script to evaluate Cij, and E_coh of the current system,
and define a new system with updated box dimensions to test.
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.
strainrange : float, optional
The small strain value to apply when calculating the elastic
constants (default is 1e-6).
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).
cycle : int, optional
Indicates the iteration cycle of quick_a_Cij(). This is used to
uniquely save the LAMMPS input and output files.
Returns
-------
dict
Dictionary of results consisting of keys:
- **'E_coh'** (*float*) - The cohesive energy of the supplied system.
- **'stress'** (*numpy.array*) - The measured stress state of the
supplied system.
- **'C_elastic'** (*atomman.ElasticConstants*) - The supplied system's
elastic constants.
- **'system_new'** (*atomman.System*) - System with updated box
dimensions.
Raises
------
RuntimeError
If any of the new box dimensions are less than zero.
"""
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)
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data',
f='init' + str(cycle) + '.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['delta'] = strainrange
lammps_variables['steps'] = 2
# Write lammps input script
template_file = Path(script_dir, 'cij.template')
lammps_script = 'cij.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=mpi_command,
return_style='model')
shutil.move('log.lammps', 'cij-' + str(cycle) + '-log.lammps')
# Extract LAMMPS thermo data. Each term ranges i=0-12 where i=0 is undeformed
# The remaining values are for -/+ strain pairs in the six unique directions
lx = uc.set_in_units(np.array(output.finds('Lx')), lammps_units['length'])
ly = uc.set_in_units(np.array(output.finds('Ly')), lammps_units['length'])
lz = uc.set_in_units(np.array(output.finds('Lz')), lammps_units['length'])
xy = uc.set_in_units(np.array(output.finds('Xy')), lammps_units['length'])
xz = uc.set_in_units(np.array(output.finds('Xz')), lammps_units['length'])
yz = uc.set_in_units(np.array(output.finds('Yz')), lammps_units['length'])
pxx = uc.set_in_units(np.array(output.finds('Pxx')),
lammps_units['pressure'])
pyy = uc.set_in_units(np.array(output.finds('Pyy')),
lammps_units['pressure'])
pzz = uc.set_in_units(np.array(output.finds('Pzz')),
lammps_units['pressure'])
pxy = uc.set_in_units(np.array(output.finds('Pxy')),
lammps_units['pressure'])
pxz = uc.set_in_units(np.array(output.finds('Pxz')),
lammps_units['pressure'])
pyz = uc.set_in_units(np.array(output.finds('Pyz')),
lammps_units['pressure'])
pe = uc.set_in_units(
np.array(output.finds('PotEng')) / system.natoms,
lammps_units['energy'])
# Set the six non-zero strain values
strains = np.array([(lx[2] - lx[1]) / lx[0], (ly[4] - ly[3]) / ly[0],
(lz[6] - lz[5]) / lz[0], (yz[8] - yz[7]) / lz[0],
(xz[10] - xz[9]) / lz[0], (xy[12] - xy[11]) / ly[0]])
# Calculate cij using stress changes associated with each non-zero strain
cij = np.empty((6, 6))
for i in range(6):
delta_stress = np.array([
pxx[2 * i + 1] - pxx[2 * i + 2], pyy[2 * i + 1] - pyy[2 * i + 2],
pzz[2 * i + 1] - pzz[2 * i + 2], pyz[2 * i + 1] - pyz[2 * i + 2],
pxz[2 * i + 1] - pxz[2 * i + 2], pxy[2 * i + 1] - pxy[2 * i + 2]
])
cij[i] = delta_stress / strains[i]
for i in range(6):
for j in range(i):
cij[i, j] = cij[j, i] = (cij[i, j] + cij[j, i]) / 2
C = am.ElasticConstants(Cij=cij)
S = C.Sij
# Extract the current stress state
stress = -1 * np.array([[pxx[0], pxy[0], pxz[0]], [pxy[0], pyy[0], pyz[0]],
[pxz[0], pyz[0], pzz[0]]])
s_xx = stress[0, 0] + p_xx
s_yy = stress[1, 1] + p_yy
s_zz = stress[2, 2] + p_zz
new_a = system.box.a / (S[0, 0] * s_xx + S[0, 1] * s_yy + S[0, 2] * s_zz +
1)
new_b = system.box.b / (S[1, 0] * s_xx + S[1, 1] * s_yy + S[1, 2] * s_zz +
1)
new_c = system.box.c / (S[2, 0] * s_xx + S[2, 1] * s_yy + S[2, 2] * s_zz +
1)
if new_a <= 0 or new_b <= 0 or new_c <= 0:
raise RuntimeError('Divergence of box dimensions to <= 0')
system_new = deepcopy(system)
system_new.box_set(a=new_a, b=new_b, c=new_c, scale=True)
results_dict = {}
results_dict['E_coh'] = pe[0]
results_dict['system_new'] = system_new
results_dict['measured_pxx'] = pxx[0]
results_dict['measured_pyy'] = pyy[0]
results_dict['measured_pzz'] = pzz[0]
results_dict['measured_pxy'] = pxy[0]
results_dict['measured_pxz'] = pxz[0]
results_dict['measured_pyz'] = pyz[0]
return results_dict
def pointdiffusion(lammps_command,
system,
potential,
point_kwargs,
mpi_command=None,
temperature=300,
runsteps=200000,
thermosteps=None,
dumpsteps=0,
equilsteps=20000,
randomseed=None):
"""
Evaluates the diffusion rate of a point defect at a given temperature. This
method will run two simulations: an NVT run at the specified temperature to
equilibrate the system, then an NVE run to measure the defect's diffusion
rate. The diffusion rate is evaluated using the mean squared displacement of
all atoms in the system, and using the assumption that diffusion is only due
to the added defect(s).
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.
temperature : float, optional
The temperature to run at (default is 300.0).
runsteps : int, optional
The number of integration steps to perform (default is 200000).
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 0,
which does not output dump files).
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:
- **'natoms'** (*int*) - The number of atoms in the system.
- **'temp'** (*float*) - The mean measured temperature.
- **'pxx'** (*float*) - The mean measured normal xx pressure.
- **'pyy'** (*float*) - The mean measured normal yy pressure.
- **'pzz'** (*float*) - The mean measured normal zz pressure.
- **'Epot'** (*numpy.array*) - The mean measured total potential
energy.
- **'temp_std'** (*float*) - The standard deviation in the measured
temperature values.
- **'pxx_std'** (*float*) - The standard deviation in the measured
normal xx pressure values.
- **'pyy_std'** (*float*) - The standard deviation in the measured
normal yy pressure values.
- **'pzz_std'** (*float*) - The standard deviation in the measured
normal zz pressure values.
- **'Epot_std'** (*float*) - The standard deviation in the measured
total potential energy values.
- **'dx'** (*float*) - The computed diffusion constant along the
x-direction.
- **'dy'** (*float*) - The computed diffusion constant along the
y-direction.
- **'dz'** (*float*) - The computed diffusion constant along the
y-direction.
- **'d'** (*float*) - The total computed diffusion constant.
"""
try:
# Get script's location if __file__ exists
script_dir = Path(__file__).parent
except:
# Use cwd otherwise
script_dir = Path.cwd()
# Add defect(s) to the initially perfect system
if not isinstance(point_kwargs, (list, tuple)):
point_kwargs = [point_kwargs]
for pkwargs in point_kwargs:
system = am.defect.point(system, **pkwargs)
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Get lammps version date
lammps_date = lmp.checkversion(lammps_command)['date']
# Check that temperature is greater than zero
if temperature <= 0.0:
raise ValueError('Temperature must be greater than zero')
# Handle default values
if thermosteps is None:
thermosteps = runsteps // 1000
if thermosteps == 0:
thermosteps = 1
if dumpsteps is None:
dumpsteps = runsteps
if randomseed is None:
randomseed = random.randint(1, 900000000)
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data',
f='initial.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['temperature'] = temperature
lammps_variables['runsteps'] = runsteps
lammps_variables['equilsteps'] = equilsteps
lammps_variables['thermosteps'] = thermosteps
lammps_variables['dumpsteps'] = dumpsteps
lammps_variables['randomseed'] = randomseed
lammps_variables['timestep'] = lmp.style.timestep(potential.units)
# Set dump_info
if dumpsteps == 0:
lammps_variables['dump_info'] = ''
else:
lammps_variables['dump_info'] = '\n'.join([
'',
'# Define dump files',
'dump dumpit all custom ${dumpsteps} *.dump id type x y z c_peatom',
'dump_modify dumpit format <dump_modify_format>',
'',
])
# 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 = Path(script_dir, 'diffusion.template')
lammps_script = 'diffusion.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, 'diffusion.in', mpi_command)
# Extract LAMMPS thermo data.
thermo = output.simulations[1]['thermo']
temps = thermo.Temp.values
pxxs = uc.set_in_units(thermo.Pxx.values, lammps_units['pressure'])
pyys = uc.set_in_units(thermo.Pyy.values, lammps_units['pressure'])
pzzs = uc.set_in_units(thermo.Pzz.values, lammps_units['pressure'])
potengs = uc.set_in_units(thermo.PotEng.values, lammps_units['energy'])
steps = thermo.Step.values
# Read user-defined thermo data
if output.lammps_date < datetime.date(2016, 8, 1):
msd_x = uc.set_in_units(thermo['msd[1]'].values,
lammps_units['length'] + '^2')
msd_y = uc.set_in_units(thermo['msd[2]'].values,
lammps_units['length'] + '^2')
msd_z = uc.set_in_units(thermo['msd[3]'].values,
lammps_units['length'] + '^2')
msd = uc.set_in_units(thermo['msd[4]'].values,
lammps_units['length'] + '^2')
else:
msd_x = uc.set_in_units(thermo['c_msd[1]'].values,
lammps_units['length'] + '^2')
msd_y = uc.set_in_units(thermo['c_msd[2]'].values,
lammps_units['length'] + '^2')
msd_z = uc.set_in_units(thermo['c_msd[3]'].values,
lammps_units['length'] + '^2')
msd = uc.set_in_units(thermo['c_msd[4]'].values,
lammps_units['length'] + '^2')
# Initialize results dict
results = {}
results['natoms'] = system.natoms
# Get mean and std for temperature, pressure, and potential energy
results['temp'] = np.mean(temps)
results['temp_std'] = np.std(temps)
results['pxx'] = np.mean(pxxs)
results['pxx_std'] = np.std(pxxs)
results['pyy'] = np.mean(pyys)
results['pyy_std'] = np.std(pyys)
results['pzz'] = np.mean(pzzs)
results['pzz_std'] = np.std(pzzs)
results['Epot'] = np.mean(potengs)
results['Epot_std'] = np.std(potengs)
# Convert steps to times
times = steps * uc.set_in_units(lammps_variables['timestep'],
lammps_units['time'])
# Estimate diffusion rates
# MSD_ptd = natoms * MSD_atoms (if one defect in system)
# MSD = 2 * ndim * D * t --> D = MSD/t / (2 * ndim)
mx = np.polyfit(times, system.natoms * msd_x, 1)[0]
my = np.polyfit(times, system.natoms * msd_y, 1)[0]
mz = np.polyfit(times, system.natoms * msd_z, 1)[0]
m = np.polyfit(times, system.natoms * msd, 1)[0]
results['dx'] = mx / 2
results['dy'] = my / 2
results['dz'] = mz / 2
results['d'] = m / 6
return results
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 calc_cij(lammps_command,
system,
potential,
symbols,
p_xx=0.0,
p_yy=0.0,
p_zz=0.0,
delta=1e-5,
cycle=0):
"""Runs cij_script and returns current Cij, stress, Ecoh, and new system guess."""
#Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Define lammps variables
lammps_variables = {}
lammps_variables['atomman_system_info'] = lmp.sys_gen(
units=potential.units,
atom_style=potential.atom_style,
ucell=system,
size=np.array([[0, 3], [0, 3], [0, 3]]))
lammps_variables['atomman_pair_info'] = potential.pair_info(symbols)
lammps_variables['delta'] = delta
lammps_variables['steps'] = 2
#Write lammps input script
template_file = 'cij.template'
lammps_script = 'cij.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)
shutil.move('log.lammps', 'cij-' + str(cycle) + '-log.lammps')
#Extract LAMMPS thermo data. Each term ranges i=0-12 where i=0 is undeformed
#The remaining values are for -/+ strain pairs in the six unique directions
lx = uc.set_in_units(np.array(output.finds('Lx')), lammps_units['length'])
ly = uc.set_in_units(np.array(output.finds('Ly')), lammps_units['length'])
lz = uc.set_in_units(np.array(output.finds('Lz')), lammps_units['length'])
xy = uc.set_in_units(np.array(output.finds('Xy')), lammps_units['length'])
xz = uc.set_in_units(np.array(output.finds('Xz')), lammps_units['length'])
yz = uc.set_in_units(np.array(output.finds('Yz')), lammps_units['length'])
pxx = uc.set_in_units(np.array(output.finds('Pxx')),
lammps_units['pressure'])
pyy = uc.set_in_units(np.array(output.finds('Pyy')),
lammps_units['pressure'])
pzz = uc.set_in_units(np.array(output.finds('Pzz')),
lammps_units['pressure'])
pxy = uc.set_in_units(np.array(output.finds('Pxy')),
lammps_units['pressure'])
pxz = uc.set_in_units(np.array(output.finds('Pxz')),
lammps_units['pressure'])
pyz = uc.set_in_units(np.array(output.finds('Pyz')),
lammps_units['pressure'])
try:
pe = uc.set_in_units(np.array(output.finds('v_peatom')),
lammps_units['energy'])
assert len(pe) > 0
except:
pe = uc.set_in_units(np.array(output.finds('peatom')),
lammps_units['energy'])
#Set the six non-zero strain values
strains = np.array([(lx[2] - lx[1]) / lx[0], (ly[4] - ly[3]) / ly[0],
(lz[6] - lz[5]) / lz[0], (yz[8] - yz[7]) / lz[0],
(xz[10] - xz[9]) / lz[0], (xy[12] - xy[11]) / ly[0]])
#calculate cij using stress changes associated with each non-zero strain
cij = np.empty((6, 6))
for i in xrange(6):
delta_stress = np.array([
pxx[2 * i + 1] - pxx[2 * i + 2], pyy[2 * i + 1] - pyy[2 * i + 2],
pzz[2 * i + 1] - pzz[2 * i + 2], pyz[2 * i + 1] - pyz[2 * i + 2],
pxz[2 * i + 1] - pxz[2 * i + 2], pxy[2 * i + 1] - pxy[2 * i + 2]
])
cij[i] = delta_stress / strains[i]
for i in xrange(6):
for j in xrange(i):
cij[i, j] = cij[j, i] = (cij[i, j] + cij[j, i]) / 2
C = am.ElasticConstants(Cij=cij)
if np.allclose(C.Cij, 0.0):
raise RuntimeError('Divergence of elastic constants to <= 0')
try:
S = C.Sij
except:
raise RuntimeError('singular C:\n' + str(C.Cij))
#extract the current stress state
stress = -1 * np.array([[pxx[0], pxy[0], pxz[0]], [pxy[0], pyy[0], pyz[0]],
[pxz[0], pyz[0], pzz[0]]])
s_xx = stress[0, 0] + p_xx
s_yy = stress[1, 1] + p_yy
s_zz = stress[2, 2] + p_zz
new_a = system.box.a / (S[0, 0] * s_xx + S[0, 1] * s_yy + S[0, 2] * s_zz +
1)
new_b = system.box.b / (S[1, 0] * s_xx + S[1, 1] * s_yy + S[1, 2] * s_zz +
1)
new_c = system.box.c / (S[2, 0] * s_xx + S[2, 1] * s_yy + S[2, 2] * s_zz +
1)
if new_a <= 0 or new_b <= 0 or new_c <= 0:
raise RuntimeError('Divergence of box dimensions to <= 0')
newbox = am.Box(a=new_a, b=new_b, c=new_c)
system_new = deepcopy(system)
system_new.box_set(vects=newbox.vects, scale=True)
return {'C': C, 'stress': stress, 'ecoh': pe[0], 'system_new': system_new}
def relax_system(lammps_command,
system,
potential,
mpi_command=None,
etol=0.0,
ftol=0.0,
maxiter=10000,
maxeval=100000,
dmax=uc.set_in_units(0.01, 'angstrom')):
"""
Sets up and runs the min.in LAMMPS script for performing an energy/force
minimization to relax a system.
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.
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:
- **'logfile'** (*str*) - The name of the LAMMPS log file.
- **'initialdatafile'** (*str*) - The name of the LAMMPS data file
used to import an inital configuration.
- **'initialdumpfile'** (*str*) - The name of the LAMMPS dump file
corresponding to the inital configuration.
- **'finaldumpfile'** (*str*) - The name of the LAMMPS dump file
corresponding to the relaxed configuration.
- **'potentialenergy'** (*float*) - The total potential energy of
the relaxed system.
"""
try:
# Get script's location if __file__ exists
script_dir = Path(__file__).parent
except:
# Use cwd otherwise
script_dir = Path.cwd()
# Ensure all atoms are within the system's box
system.wrap()
# 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 = {}
# Generate system and pair info
system_info = system.dump('atom_data',
f='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(system.symbols)
# Pass in run parameters
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 = Path(script_dir, '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
output = lmp.run(lammps_command, lammps_script, mpi_command)
# Extract output values
thermo = output.simulations[-1]['thermo']
results = {}
results['logfile'] = 'log.lammps'
results['initialdatafile'] = 'system.dat'
results['initialdumpfile'] = 'atom.0'
results['finaldumpfile'] = 'atom.%i' % thermo.Step.values[-1]
results['potentialenergy'] = uc.set_in_units(thermo.PotEng.values[-1],
lammps_units['energy'])
return results
def stackingfaultrelax(lammps_command, system, potential,
mpi_command=None, sim_directory=None,
cutboxvector='c',
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 containing a stacking fault.
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 simulation in. If not
given, will use the current working directory.
cutboxvector : str, optional
Indicates which of the three system box vectors, 'a', 'b', or 'c', has
the non-periodic boundary (default is 'c'). Fault plane normal is
defined by the cross of the other two box vectors.
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).
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.
- **'E_total'** (*float*) - The total potential energy of the relaxed
system.
Raises
------
ValueError
For invalid cutboxvectors.
"""
# Get script's location
script_dir = Path(__file__).parent
# Give correct LAMMPS fix setforce command
if cutboxvector == 'a':
fix_cut_setforce = 'fix cut all setforce NULL 0 0'
elif cutboxvector == 'b':
fix_cut_setforce = 'fix cut all setforce 0 NULL 0'
elif cutboxvector == 'c':
fix_cut_setforce = 'fix cut all setforce 0 0 NULL'
else:
raise ValueError('Invalid cutboxvector')
if sim_directory is not None:
# Create sim_directory if it doesn't exist
sim_directory = Path(sim_directory)
if not sim_directory.is_dir():
sim_directory.mkdir()
sim_directory = sim_directory.as_posix()+'/'
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 = system.dump('atom_data',
f=Path(sim_directory, 'system.dat').as_posix(),
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['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 = Path(script_dir, 'sfmin.template')
lammps_script = Path(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.as_posix(), mpi_command,
logfile=Path(sim_directory, 'log.lammps').as_posix())
# Extract output values
thermo = output.simulations[-1]['thermo']
logfile = Path(sim_directory, 'log.lammps').as_posix()
dumpfile = Path(sim_directory, '%i.dump' % thermo.Step.values[-1]).as_posix()
E_total = uc.set_in_units(thermo.PotEng.values[-1],
lammps_units['energy'])
# Load relaxed system
system = am.load('atom_dump', dumpfile, symbols=system.symbols)
# Return results
results_dict = {}
results_dict['logfile'] = logfile
results_dict['dumpfile'] = dumpfile
results_dict['system'] = system
results_dict['E_total'] = E_total
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 pointdiffusion(lammps_command, system, potential, point_kwargs,
mpi_command=None, temperature=300,
runsteps=200000, thermosteps=None, dumpsteps=0,
equilsteps=20000, randomseed=None):
"""
Evaluates the diffusion rate of a point defect at a given temperature. This
method will run two simulations: an NVT run at the specified temperature to
equilibrate the system, then an NVE run to measure the defect's diffusion
rate. The diffusion rate is evaluated using the mean squared displacement of
all atoms in the system, and using the assumption that diffusion is only due
to the added defect(s).
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.
temperature : float, optional
The temperature to run at (default is 300.0).
runsteps : int, optional
The number of integration steps to perform (default is 200000).
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 0,
which does not output dump files).
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:
- **'natoms'** (*int*) - The number of atoms in the system.
- **'temp'** (*float*) - The mean measured temperature.
- **'pxx'** (*float*) - The mean measured normal xx pressure.
- **'pyy'** (*float*) - The mean measured normal yy pressure.
- **'pzz'** (*float*) - The mean measured normal zz pressure.
- **'Epot'** (*numpy.array*) - The mean measured total potential
energy.
- **'temp_std'** (*float*) - The standard deviation in the measured
temperature values.
- **'pxx_std'** (*float*) - The standard deviation in the measured
normal xx pressure values.
- **'pyy_std'** (*float*) - The standard deviation in the measured
normal yy pressure values.
- **'pzz_std'** (*float*) - The standard deviation in the measured
normal zz pressure values.
- **'Epot_std'** (*float*) - The standard deviation in the measured
total potential energy values.
- **'dx'** (*float*) - The computed diffusion constant along the
x-direction.
- **'dy'** (*float*) - The computed diffusion constant along the
y-direction.
- **'dz'** (*float*) - The computed diffusion constant along the
y-direction.
- **'d'** (*float*) - The total computed diffusion constant.
"""
# Add defect(s) to the initially perfect system
if not isinstance(point_kwargs, (list, tuple)):
point_kwargs = [point_kwargs]
for pkwargs in point_kwargs:
system = am.defect.point(system, **pkwargs)
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Get lammps version date
lammps_date = lmp.checkversion(lammps_command)['date']
# Check that temperature is greater than zero
if temperature <= 0.0:
raise ValueError('Temperature must be greater than zero')
# Handle default values
if thermosteps is None:
thermosteps = runsteps // 1000
if thermosteps == 0:
thermosteps = 1
if dumpsteps is None:
dumpsteps = runsteps
if randomseed is None:
randomseed = random.randint(1, 900000000)
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data', f='initial.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['temperature'] = temperature
lammps_variables['runsteps'] = runsteps
lammps_variables['equilsteps'] = equilsteps
lammps_variables['thermosteps'] = thermosteps
lammps_variables['dumpsteps'] = dumpsteps
lammps_variables['randomseed'] = randomseed
lammps_variables['timestep'] = lmp.style.timestep(potential.units)
# Set dump_info
if dumpsteps == 0:
lammps_variables['dump_info'] = ''
else:
lammps_variables['dump_info'] = '\n'.join([
'',
'# Define dump files',
'dump dumpit all custom ${dumpsteps} *.dump id type x y z c_peatom',
'dump_modify dumpit format <dump_modify_format>',
'',
])
# 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 = 'diffusion.template'
lammps_script = 'diffusion.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, 'diffusion.in', mpi_command)
# Extract LAMMPS thermo data.
thermo = output.simulations[1]['thermo']
temps = thermo.Temp.values
pxxs = uc.set_in_units(thermo.Pxx.values, lammps_units['pressure'])
pyys = uc.set_in_units(thermo.Pyy.values, lammps_units['pressure'])
pzzs = uc.set_in_units(thermo.Pzz.values, lammps_units['pressure'])
potengs = uc.set_in_units(thermo.PotEng.values, lammps_units['energy'])
steps = thermo.Step.values
# Read user-defined thermo data
if output.lammps_date < datetime.date(2016, 8, 1):
msd_x = uc.set_in_units(thermo['msd[1]'].values,
lammps_units['length']+'^2')
msd_y = uc.set_in_units(thermo['msd[2]'].values,
lammps_units['length']+'^2')
msd_z = uc.set_in_units(thermo['msd[3]'].values,
lammps_units['length']+'^2')
msd = uc.set_in_units(thermo['msd[4]'].values,
lammps_units['length']+'^2')
else:
msd_x = uc.set_in_units(thermo['c_msd[1]'].values,
lammps_units['length']+'^2')
msd_y = uc.set_in_units(thermo['c_msd[2]'].values,
lammps_units['length']+'^2')
msd_z = uc.set_in_units(thermo['c_msd[3]'].values,
lammps_units['length']+'^2')
msd = uc.set_in_units(thermo['c_msd[4]'].values,
lammps_units['length']+'^2')
# Initialize results dict
results = {}
results['natoms'] = system.natoms
# Get mean and std for temperature, pressure, and potential energy
results['temp'] = np.mean(temps)
results['temp_std'] = np.std(temps)
results['pxx'] = np.mean(pxxs)
results['pxx_std'] = np.std(pxxs)
results['pyy'] = np.mean(pyys)
results['pyy_std'] = np.std(pyys)
results['pzz'] = np.mean(pzzs)
results['pzz_std'] = np.std(pzzs)
results['Epot'] = np.mean(potengs)
results['Epot_std'] = np.std(potengs)
# Convert steps to times
times = steps * uc.set_in_units(lammps_variables['timestep'], lammps_units['time'])
# Estimate diffusion rates
# MSD_ptd = natoms * MSD_atoms (if one defect in system)
# MSD = 2 * ndim * D * t --> D = MSD/t / (2 * ndim)
mx = np.polyfit(times, system.natoms * msd_x, 1)[0]
my = np.polyfit(times, system.natoms * msd_y, 1)[0]
mz = np.polyfit(times, system.natoms * msd_z, 1)[0]
m = np.polyfit(times, system.natoms * msd, 1)[0]
results['dx'] = mx / 2
results['dy'] = my / 2
results['dz'] = mz / 2
results['d'] = m / 6
return results
def disl_relax(lammps_command, system, potential,
mpi_command=None, annealtemp=0.0, randomseed=None,
etol=0.0, ftol=1e-6, maxiter=10000, maxeval=100000,
dmax=uc.set_in_units(0.01, 'angstrom')):
"""
Sets up and runs the disl_relax.in LAMMPS script for relaxing a
dislocation monopole system.
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.
annealtemp : float, optional
The temperature to perform a dynamic relaxation at. (Default is 0.0,
which will skip the dynamic relaxation.)
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).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'logfile'** (*str*) - The name of the LAMMPS log file.
- **'dumpfile'** (*str*) - The name of the LAMMPS dump file
for the relaxed system.
- **'E_total'** (*float*) - The total potential energy for the
relaxed 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='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(system.symbols)
lammps_variables['anneal_info'] = anneal_info(annealtemp, randomseed,
potential.units)
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
lammps_variables['group_move'] = ' '.join(np.array(range(1, system.natypes // 2 + 1), dtype=str))
# Set dump_modify format based on dump_modify_version
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 = 'disl_relax.template'
lammps_script = 'disl_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)
thermo = output.simulations[-1]['thermo']
# Extract output values
results = {}
results['logfile'] = 'log.lammps'
results['dumpfile'] = '%i.dump' % thermo.Step.values[-1]
results['E_total'] = uc.set_in_units(thermo.PotEng.values[-1],
lammps_units['energy'])
return results
def e_vs_r(lammps_command,
system,
potential,
symbols,
mpi_command=None,
ucell=None,
rmin=2.0,
rmax=6.0,
rsteps=200):
"""
Performs a cohesive energy scan over a range of interatomic spaces, r.
Arguments:
lammps_command -- command for running LAMMPS.
system -- atomman.System to perform the scan on.
potential -- atomman.lammps.Potential representation of a LAMMPS
implemented potential.
symbols -- list of element-model symbols for the Potential that
correspond to system's atypes.
Keyword Arguments:
mpi_command -- MPI command for running LAMMPS in parallel. Default value
is None (serial run).
ucell -- an atomman.System representing a fundamental unit cell of the
system. If not given, ucell will be taken as system.
rmin -- the minimum r spacing to use. Default value is 2.0.
rmax -- the minimum r spacing to use. Default value is 6.0.
rsteps -- the number of r spacing steps to evaluate. Default value is 200.
"""
#Make system a deepcopy of itself (protect original from changes)
system = deepcopy(system)
#Set ucell = system if ucell not given
if ucell is None:
ucell = system
#Calculate the r/a ratio for the unit cell
r_a = r_a_ratio(ucell)
#Get ratios of lx, ly, and lz of system relative to a of ucell
lx_a = system.box.a / ucell.box.a
ly_a = system.box.b / ucell.box.a
lz_a = system.box.c / ucell.box.a
alpha = system.box.alpha
beta = system.box.beta
gamma = system.box.gamma
#build lists of values
r_values = np.linspace(rmin, rmax, rsteps)
a_values = r_values / r_a
Ecoh_values = np.empty(rsteps)
#Loop over values
for i in xrange(rsteps):
#Rescale system's box
a = a_values[i]
system.box_set(a=a * lx_a,
b=a * ly_a,
c=a * lz_a,
alpha=alpha,
beta=beta,
gamma=gamma,
scale=True)
#Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Define lammps variables
lammps_variables = {}
lammps_variables['atomman_system_info'] = lmp.atom_data.dump(
system,
'atom.dat',
units=potential.units,
atom_style=potential.atom_style)
lammps_variables['atomman_pair_info'] = potential.pair_info(symbols)
#Write lammps input script
template_file = 'run0.template'
lammps_script = 'run0.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 data
output = lmp.run(lammps_command, lammps_script, mpi_command)
try:
Ecoh_values[i] = uc.set_in_units(
output.finds('v_peatom')[-1], lammps_units['energy'])
except:
Ecoh_values[i] = uc.set_in_units(
output.finds('peatom')[-1], lammps_units['energy'])
shutil.move('log.lammps', 'run0-' + str(i) + '-log.lammps')
#Find unit cell systems at the energy minimums
min_cells = []
for i in xrange(1, rsteps - 1):
if Ecoh_values[i] < Ecoh_values[
i - 1] and Ecoh_values[i] < Ecoh_values[i + 1]:
a = a_values[i]
cell = deepcopy(ucell)
cell.box_set(a=a,
b=a * ucell.box.b / ucell.box.a,
c=a * ucell.box.c / ucell.box.a,
alpha=alpha,
beta=beta,
gamma=gamma,
scale=True)
min_cells.append(cell)
return {
'r_values': r_values,
'a_values': a_values,
'Ecoh_values': Ecoh_values,
'min_cell': min_cells
}
def e_vs_r(lammps_command, system, potential,
mpi_command=None, ucell=None,
rmin=uc.set_in_units(2.0, 'angstrom'),
rmax=uc.set_in_units(6.0, 'angstrom'), rsteps=200):
"""
Performs a cohesive energy scan over a range of interatomic spaces, r.
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.
ucell : atomman.System, optional
The fundamental unit cell correspodning to system. This is used to
convert system dimensions to cell dimensions. If not given, ucell will
be taken as system.
rmin : float, optional
The minimum r spacing to use (default value is 2.0 angstroms).
rmax : float, optional
The maximum r spacing to use (default value is 6.0 angstroms).
rsteps : int, optional
The number of r spacing steps to evaluate (default value is 200).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'r_values'** (*numpy.array of float*) - All interatomic spacings,
r, explored.
- **'a_values'** (*numpy.array of float*) - All unit cell a lattice
constants corresponding to the values explored.
- **'Ecoh_values'** (*numpy.array of float*) - The computed cohesive
energies for each r value.
- **'min_cell'** (*list of atomman.System*) - Systems corresponding to
the minima identified in the Ecoh_values.
"""
# Make system a deepcopy of itself (protect original from changes)
system = deepcopy(system)
# Set ucell = system if ucell not given
if ucell is None:
ucell = system
# Calculate the r/a ratio for the unit cell
r_a = r_a_ratio(ucell)
# Get ratios of lx, ly, and lz of system relative to a of ucell
lx_a = system.box.a / ucell.box.a
ly_a = system.box.b / ucell.box.a
lz_a = system.box.c / ucell.box.a
alpha = system.box.alpha
beta = system.box.beta
gamma = system.box.gamma
# Build lists of values
r_values = np.linspace(rmin, rmax, rsteps)
a_values = r_values / r_a
Ecoh_values = np.empty(rsteps)
# Loop over values
for i in range(rsteps):
# Rescale system's box
a = a_values[i]
system.box_set(a = a * lx_a,
b = a * ly_a,
c = a * lz_a,
alpha=alpha, beta=beta, gamma=gamma, scale=True)
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data', f='atom.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)
# Write lammps input script
template_file = 'run0.template'
lammps_script = 'run0.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 data
output = lmp.run(lammps_command, lammps_script, mpi_command)
thermo = output.simulations[0]['thermo']
if output.lammps_date < datetime.date(2016, 8, 1):
Ecoh_values[i] = uc.set_in_units(thermo.peatom.values[-1],
lammps_units['energy'])
else:
Ecoh_values[i] = uc.set_in_units(thermo.v_peatom.values[-1],
lammps_units['energy'])
# Rename log.lammps
shutil.move('log.lammps', 'run0-'+str(i)+'-log.lammps')
# Find unit cell systems at the energy minimums
min_cells = []
for i in range(1, rsteps - 1):
if (Ecoh_values[i] < Ecoh_values[i-1]
and Ecoh_values[i] < Ecoh_values[i+1]):
a = a_values[i]
cell = deepcopy(ucell)
cell.box_set(a = a,
b = a * ucell.box.b / ucell.box.a,
c = a * ucell.box.c / ucell.box.a,
alpha=alpha, beta=beta, gamma=gamma, scale=True)
min_cells.append(cell)
# Collect results
results_dict = {}
results_dict['r_values'] = r_values
results_dict['a_values'] = a_values
results_dict['Ecoh_values'] = Ecoh_values
results_dict['min_cell'] = min_cells
return results_dict
def full_relax(lammps_command, system, potential, symbols,
mpi_command=None, p_xx=0.0, p_yy=0.0, p_zz=0.0, temperature=0.0,
runsteps=100000, integrator=None, thermosteps=None, dumpsteps=None,
randomseed=None):
"""
Performs a full dynamic relax on a given system at the given temperature
to the specified pressure state.
Arguments:
lammps_command -- directory location for lammps executable
system -- atomman.System to dynamically relax
potential -- atomman.lammps.Potential representation of a LAMMPS implemented potential
symbols -- list of element-model symbols for the Potential that correspond to the System's atypes
Keyword Arguments:
p_xx, p_yy, p_zz -- tensile pressures to equilibriate to. Default value is 0.0 for all.
temperature -- temperature to relax at. Default value is 0.
runsteps -- number of integration steps to perform. Default value is 100000.
integrator -- string giving the integration method to use. Options are 'npt', 'nvt',
'nph', 'nve', 'nve+l', 'nph+l'. The +l options use Langevin thermostat.
Default value is 'nph+l' for temperature = 0, and 'npt' otherwise.
thermosteps -- output thermo values every this many steps. Default value is
runsteps/1000.
dumpsteps -- output dump files every this many steps. Default value is runsteps
(only first and last steps are outputted as dump files).
randomseed -- random number seed used by LAMMPS for velocity creation and Langevin
thermostat. Default value generates a new random integer every time.
"""
#Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Handle default values
if thermosteps is None:
if thermosteps >= 1000: thermosteps = runsteps/1000
else: thermosteps = 1
if dumpsteps is None: dumpsteps = runsteps
#Define lammps variables
lammps_variables = {}
lammps_variables['atomman_system_info'] = lmp.atom_data.dump(system, 'init.dat',
units=potential.units,
atom_style=potential.atom_style)
lammps_variables['atomman_pair_info'] = potential.pair_info(symbols)
lammps_variables['integrator_info'] = integrator_info(integrator=integrator,
p_xx=p_xx, p_yy=p_yy, p_zz=p_zz,
temperature=temperature,
randomseed=randomseed,
units=potential.units)
lammps_variables['thermosteps'] = thermosteps
lammps_variables['runsteps'] = runsteps
lammps_variables['dumpsteps'] = dumpsteps
#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.
thermo = output.find('thermo')
lx = uc.set_in_units(np.array(thermo['Lx']), lammps_units['length'])
ly = uc.set_in_units(np.array(thermo['Ly']), lammps_units['length'])
lz = uc.set_in_units(np.array(thermo['Lz']), lammps_units['length'])
#xy = uc.set_in_units(np.array(thermo['Xy']), lammps_units['length'])
#xz = uc.set_in_units(np.array(thermo['Xz']), lammps_units['length'])
#yz = uc.set_in_units(np.array(thermo['Yz']), lammps_units['length'])
pxx = uc.set_in_units(np.array(thermo['Pxx']), lammps_units['pressure'])
pyy = uc.set_in_units(np.array(thermo['Pyy']), lammps_units['pressure'])
pzz = uc.set_in_units(np.array(thermo['Pzz']), lammps_units['pressure'])
pxy = uc.set_in_units(np.array(thermo['Pxy']), lammps_units['pressure'])
pxz = uc.set_in_units(np.array(thermo['Pxz']), lammps_units['pressure'])
pyz = uc.set_in_units(np.array(thermo['Pyz']), lammps_units['pressure'])
pe = uc.set_in_units(np.array(thermo['PotEng']), lammps_units['energy'])
#ke = uc.set_in_units(np.array(thermo['KinEng']), lammps_units['energy'])
temp = np.array(thermo['Temp'])
step = np.array(thermo['Step'], dtype=int)
return {'step':step, 'lx':lx, 'ly':ly, 'lz':lz, 'pe':pe, 'temp':temp,
'pxx':pxx, 'pyy':pyy, 'pzz':pzz, 'pxy':pxy, 'pxz':pxz, 'pyz':pyz}
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 elastic_constants_static(lammps_command, system, potential, mpi_command=None,
strainrange=1e-6, etol=0.0, ftol=0.0, maxiter=10000,
maxeval=100000, dmax=uc.set_in_units(0.01, 'angstrom')):
"""
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.
strainrange : float, optional
The small strain value to apply when calculating the elastic
constants (default is 1e-6).
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:
- **'a_lat'** (*float*) - The relaxed a lattice constant.
- **'b_lat'** (*float*) - The relaxed b lattice constant.
- **'c_lat'** (*float*) - The relaxed c lattice constant.
- **'alpha_lat'** (*float*) - The alpha lattice angle.
- **'beta_lat'** (*float*) - The beta lattice angle.
- **'gamma_lat'** (*float*) - The gamma lattice angle.
- **'E_coh'** (*float*) - The cohesive energy of the relaxed system.
- **'stress'** (*numpy.array*) - The measured stress state of the
relaxed system.
- **'C_elastic'** (*atomman.ElasticConstants*) - The relaxed system's
elastic constants.
- **'system_relaxed'** (*atomman.System*) - The relaxed system.
"""
# Convert hexagonal cells to orthorhombic to avoid LAMMPS tilt issues
if am.tools.ishexagonal(system.box):
system = system.rotate([[2,-1,-1,0], [0, 1, -1, 0], [0,0,0,1]])
# 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='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['strainrange'] = strainrange
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'])
# Fill in template files
template_file = 'cij.template'
lammps_script = 'cij.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, '<', '>'))
template_file2 = 'potential.template'
lammps_script2 = 'potential.in'
with open(template_file2) as f:
template = f.read()
with open(lammps_script2, 'w') as f:
f.write(iprPy.tools.filltemplate(template, lammps_variables, '<', '>'))
# Run LAMMPS
output = lmp.run(lammps_command, lammps_script, mpi_command)
# Pull out initial state
thermo = output.simulations[0]['thermo']
pxx0 = uc.set_in_units(thermo.Pxx.values[-1], lammps_units['pressure'])
pyy0 = uc.set_in_units(thermo.Pyy.values[-1], lammps_units['pressure'])
pzz0 = uc.set_in_units(thermo.Pzz.values[-1], lammps_units['pressure'])
pyz0 = uc.set_in_units(thermo.Pyz.values[-1], lammps_units['pressure'])
pxz0 = uc.set_in_units(thermo.Pxz.values[-1], lammps_units['pressure'])
pxy0 = uc.set_in_units(thermo.Pxy.values[-1], lammps_units['pressure'])
# Negative strains
cij_n = np.empty((6,6))
for i in range(6):
j = 1 + i * 2
# Pull out strained state
thermo = output.simulations[j]['thermo']
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'])
pyz = uc.set_in_units(thermo.Pyz.values[-1], lammps_units['pressure'])
pxz = uc.set_in_units(thermo.Pxz.values[-1], lammps_units['pressure'])
pxy = uc.set_in_units(thermo.Pxy.values[-1], lammps_units['pressure'])
# Calculate cij_n using stress changes
cij_n[i] = np.array([pxx - pxx0, pyy - pyy0, pzz - pzz0,
pyz - pyz0, pxz - pxz0, pxy - pxy0])/ strainrange
# Positive strains
cij_p = np.empty((6,6))
for i in range(6):
j = 2 + i * 2
# Pull out strained state
thermo = output.simulations[j]['thermo']
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'])
pyz = uc.set_in_units(thermo.Pyz.values[-1], lammps_units['pressure'])
pxz = uc.set_in_units(thermo.Pxz.values[-1], lammps_units['pressure'])
pxy = uc.set_in_units(thermo.Pxy.values[-1], lammps_units['pressure'])
# Calculate cij_p using stress changes
cij_p[i] = -np.array([pxx - pxx0, pyy - pyy0, pzz - pzz0,
pyz - pyz0, pxz - pxz0, pxy - pxy0])/ strainrange
# Average symmetric values
cij = (cij_n + cij_p) / 2
for i in range(6):
for j in range(i):
cij[i,j] = cij[j,i] = (cij[i,j] + cij[j,i]) / 2
# Define results_dict
results_dict = {}
results_dict['raw_cij_negative'] = cij_n
results_dict['raw_cij_positive'] = cij_p
results_dict['C'] = am.ElasticConstants(Cij=cij)
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 dynamic_stress(lammps_command, system, potential, symbols,
mpi_command=None, temperature=0.0, runsteps=100000,
integrator=None, thermosteps=None, dumpsteps=None,
restartsteps=None, randomseed=None):
"""
Performs a dynamic run on a given system at the given temperature to
measure stress state.
Arguments:
lammps_command -- directory location for lammps executable
system -- atomman.System to dynamically relax
potential -- atomman.lammps.Potential representation of a LAMMPS
implemented potential
symbols -- list of element-model symbols for the Potential that correspond
to the System's atypes
Keyword Arguments:
mpi_command -- MPI command to use when running LAMMPS.
temperature -- temperature to relax at. Default value is 0.
runsteps -- number of integration steps to perform. Default value is 100000.
integrator -- string giving the integration method to use. Options are limited to
'nvt', 'nve' and 'nve+l'. The +l options use Langevin thermostat.
Default value is 'nve+l' for temperature = 0, and 'nvt' otherwise.
thermosteps -- output thermo values every this many steps. Default value is
runsteps/1000.
dumpsteps -- output dump files every this many steps. Default value is runsteps
(only first and last steps are outputted as dump files).
randomseed -- random number seed used by LAMMPS for velocity creation and Langevin
thermostat. Default value generates a new random integer every time.
"""
assert integrator in ['nvt', 'nve', 'nve+l'], 'Only nvt, nve, and nve+l integrators allowed'
#Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Handle default values
if thermosteps is None:
if thermosteps >= 1000: thermosteps = runsteps/1000
else: thermosteps = 1
if dumpsteps is None: dumpsteps = runsteps
if restartsteps is None: restartsteps = dumpsteps
#Define lammps variables
lammps_variables = {}
lammps_variables['atomman_system_info'] = lmp.atom_data.dump(system, 'init.dat',
units=potential.units,
atom_style=potential.atom_style)
lammps_variables['atomman_pair_info'] = potential.pair_info(symbols)
lammps_variables['integrator_info'] = integrator_info(integrator=integrator,
temperature=temperature,
randomseed=randomseed,
units=potential.units)
lammps_variables['thermosteps'] = thermosteps
lammps_variables['runsteps'] = runsteps
lammps_variables['restartsteps'] = restartsteps
lammps_variables['dumpsteps'] = dumpsteps
#Check LAMMPS compute stress version
compute_stress_version = iprPy.tools.lammps_version.compute_stress(lammps_command)
if compute_stress_version == 0:
lammps_variables['stressterm'] = 'NULL'
elif compute_stress_version == 1:
lammps_variables['stressterm'] = ''
#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, '<', '>'))
#Write restart input script
lammps_restart = 'full_relax_restart.in'
lammps_variables['atomman_system_info'] = 'read_restart *.restart'
with open(lammps_restart, 'w') as f:
f.write(iprPy.tools.filltemplate(template, lammps_variables, '<', '>'))
#Run lammps
output = lmp.run(lammps_command, lammps_script, mpi_command, restart_script_name=lammps_restart, flatten_thermo='last')
#Extract LAMMPS thermo data.
thermo = output.find('thermo')
#lx = uc.set_in_units(np.array(thermo['Lx']), lammps_units['length'])
#ly = uc.set_in_units(np.array(thermo['Ly']), lammps_units['length'])
#lz = uc.set_in_units(np.array(thermo['Lz']), lammps_units['length'])
#xy = uc.set_in_units(np.array(thermo['Xy']), lammps_units['length'])
#xz = uc.set_in_units(np.array(thermo['Xz']), lammps_units['length'])
#yz = uc.set_in_units(np.array(thermo['Yz']), lammps_units['length'])
pxx = uc.set_in_units(np.array(thermo['Pxx']), lammps_units['pressure'])
pyy = uc.set_in_units(np.array(thermo['Pyy']), lammps_units['pressure'])
pzz = uc.set_in_units(np.array(thermo['Pzz']), lammps_units['pressure'])
pxy = uc.set_in_units(np.array(thermo['Pxy']), lammps_units['pressure'])
pxz = uc.set_in_units(np.array(thermo['Pxz']), lammps_units['pressure'])
pyz = uc.set_in_units(np.array(thermo['Pyz']), lammps_units['pressure'])
pe = uc.set_in_units(np.array(thermo['PotEng']), lammps_units['energy'])
#ke = uc.set_in_units(np.array(thermo['KinEng']), lammps_units['energy'])
temp = np.array(thermo['Temp'])
step = np.array(thermo['Step'], dtype=int)
return {'step':step, 'pe':pe, 'temp':temp,
'pxx':pxx, 'pyy':pyy, 'pzz':pzz, 'pxy':pxy, 'pxz':pxz, 'pyz':pyz}
def isolated_atom(lammps_command: str,
potential: am.lammps.Potential,
mpi_command: Optional[str] = None) -> dict:
"""
Evaluates the isolated atom energy for each elemental model of a potential.
Parameters
----------
lammps_command :str
Command for running LAMMPS.
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.
Returns
-------
dict
Dictionary of results consisting of keys:
- **'energy'** (*dict*) - The computed potential energies for each
symbol.
"""
# Initialize dictionary
energydict = {}
# Initialize single atom system
box = am.Box.cubic(a=1)
atoms = am.Atoms(atype=1, pos=[[0.5, 0.5, 0.5]])
system = am.System(atoms=atoms, box=box, pbc=[False, False, False])
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
# Define lammps variables
lammps_variables = {}
# Loop over symbols
for symbol in potential.symbols:
system.symbols = symbol
# Add charges if required
if potential.atom_style == 'charge':
system.atoms.prop_atype('charge',
potential.charges(system.symbols))
# Save configuration
system_info = system.dump('atom_data',
f='isolated.dat',
potential=potential)
lammps_variables['atomman_system_pair_info'] = system_info
# Write lammps input script
lammps_script = 'run0.in'
template = read_calc_file('iprPy.calculation.isolated_atom',
'run0.template')
with open(lammps_script, 'w') as f:
f.write(filltemplate(template, lammps_variables, '<', '>'))
# Run lammps and extract data
output = lmp.run(lammps_command,
script_name=lammps_script,
mpi_command=mpi_command)
energy = output.simulations[0]['thermo'].PotEng.values[-1]
energydict[symbol] = uc.set_in_units(energy, lammps_units['energy'])
# Collect results
results_dict = {}
results_dict['energy'] = energydict
return results_dict
def elastic_constants_static(lammps_command,
system,
potential,
mpi_command=None,
strainrange=1e-6,
etol=0.0,
ftol=0.0,
maxiter=10000,
maxeval=100000,
dmax=uc.set_in_units(0.01, 'angstrom')):
"""
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.
strainrange : float, optional
The small strain value to apply when calculating the elastic
constants (default is 1e-6).
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:
- **'a_lat'** (*float*) - The relaxed a lattice constant.
- **'b_lat'** (*float*) - The relaxed b lattice constant.
- **'c_lat'** (*float*) - The relaxed c lattice constant.
- **'alpha_lat'** (*float*) - The alpha lattice angle.
- **'beta_lat'** (*float*) - The beta lattice angle.
- **'gamma_lat'** (*float*) - The gamma lattice angle.
- **'E_coh'** (*float*) - The cohesive energy of the relaxed system.
- **'stress'** (*numpy.array*) - The measured stress state of the
relaxed system.
- **'C_elastic'** (*atomman.ElasticConstants*) - The relaxed system's
elastic constants.
- **'system_relaxed'** (*atomman.System*) - The relaxed system.
"""
# Convert hexagonal cells to orthorhombic to avoid LAMMPS tilt issues
if am.tools.ishexagonal(system.box):
system = system.rotate([[2, -1, -1, 0], [0, 1, -1, 0], [0, 0, 0, 1]])
# 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='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['strainrange'] = strainrange
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'])
# Fill in template files
template_file = 'cij.template'
lammps_script = 'cij.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, '<', '>'))
template_file2 = 'potential.template'
lammps_script2 = 'potential.in'
with open(template_file2) as f:
template = f.read()
with open(lammps_script2, 'w') as f:
f.write(iprPy.tools.filltemplate(template, lammps_variables, '<', '>'))
# Run LAMMPS
output = lmp.run(lammps_command, lammps_script, mpi_command)
# Pull out initial state
thermo = output.simulations[0]['thermo']
pxx0 = uc.set_in_units(thermo.Pxx.values[-1], lammps_units['pressure'])
pyy0 = uc.set_in_units(thermo.Pyy.values[-1], lammps_units['pressure'])
pzz0 = uc.set_in_units(thermo.Pzz.values[-1], lammps_units['pressure'])
pyz0 = uc.set_in_units(thermo.Pyz.values[-1], lammps_units['pressure'])
pxz0 = uc.set_in_units(thermo.Pxz.values[-1], lammps_units['pressure'])
pxy0 = uc.set_in_units(thermo.Pxy.values[-1], lammps_units['pressure'])
# Negative strains
cij_n = np.empty((6, 6))
for i in range(6):
j = 1 + i * 2
# Pull out strained state
thermo = output.simulations[j]['thermo']
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'])
pyz = uc.set_in_units(thermo.Pyz.values[-1], lammps_units['pressure'])
pxz = uc.set_in_units(thermo.Pxz.values[-1], lammps_units['pressure'])
pxy = uc.set_in_units(thermo.Pxy.values[-1], lammps_units['pressure'])
# Calculate cij_n using stress changes
cij_n[i] = np.array([
pxx - pxx0, pyy - pyy0, pzz - pzz0, pyz - pyz0, pxz - pxz0,
pxy - pxy0
]) / strainrange
# Positive strains
cij_p = np.empty((6, 6))
for i in range(6):
j = 2 + i * 2
# Pull out strained state
thermo = output.simulations[j]['thermo']
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'])
pyz = uc.set_in_units(thermo.Pyz.values[-1], lammps_units['pressure'])
pxz = uc.set_in_units(thermo.Pxz.values[-1], lammps_units['pressure'])
pxy = uc.set_in_units(thermo.Pxy.values[-1], lammps_units['pressure'])
# Calculate cij_p using stress changes
cij_p[i] = -np.array([
pxx - pxx0, pyy - pyy0, pzz - pzz0, pyz - pyz0, pxz - pxz0,
pxy - pxy0
]) / strainrange
# Average symmetric values
cij = (cij_n + cij_p) / 2
for i in range(6):
for j in range(i):
cij[i, j] = cij[j, i] = (cij[i, j] + cij[j, i]) / 2
# Define results_dict
results_dict = {}
results_dict['raw_cij_negative'] = cij_n
results_dict['raw_cij_positive'] = cij_p
results_dict['C'] = am.ElasticConstants(Cij=cij)
return results_dict
def bain_run_calcs(input_dict, __calc_type__, step):
#-------------------SETS UP THE SYSTEM--------------------
#Read in potential
potential = lmp.Potential(
input_dict['potential'],
input_dict['potential_dir']) #reads the potential filename
system = input_dict['initial_system']
#if initial step, set up system to find difference in cohesive energy. this step is skipped when a and c values change.
if step == 'initial':
a_scale = 1
c_scale = 1
elif step == 'bain':
a_scale = input_dict['bain_a_scale']
c_scale = input_dict['bain_c_scale']
#scale box and atoms simultaneously
system.box_set(a=a_scale * system.box.a,
b=a_scale * system.box.b,
c=c_scale * system.box.c,
scale=True)
#ensure all atoms are within the box
system.wrap()
#-------------------RUN LAMMPS AND SAVE RESULTS------------------
#use above information to generate system_info and pair_info for LAMMPS
system_info = am.lammps.atom_data.dump('bain.dat',
system,
units=potential.units,
atom_style=potential.atom_style)
pair_info = potential.pair_info(
input_dict['symbols']
) #pulls the potential info when given which element the calculation is running on
#write the LAMMPS input script
with open('bain.in', 'w') as f:
f.write(
bain_relax_script('min.template',
system_info,
pair_info,
etol=input_dict['energy_tolerance'],
ftol=input_dict['force_tolerance'],
maxiter=input_dict['maximum_iterations'],
maxeval=input_dict['maximum_evaluations']))
#run LAMMPS
output = lmp.run(input_dict['lammps_command'], 'bain.in',
input_dict['mpi_command'])
atom_last = 'atom.%i' % output.finds('Step')[
-1] #prints number of iterations (?)
#save results into results_dict
if step == 'initial':
try:
os.rename(atom_last, 'initial.dump')
except:
os.remove('initial.dump')
os.rename(atom_last, 'initial.dump')
os.remove('atom.0')
d_system = lmp.atom_dump.load('initial.dump')
elif step == 'bain':
try:
os.rename(atom_last, 'bain.dump')
except:
os.remove('bain.dump')
os.rename(atom_last, 'bain.dump')
os.remove('atom.0')
d_system = lmp.atom_dump.load('bain.dump')
results_dict = {}
results_dict['potential_energy'] = float(output.finds('PotEng')[-1])
#return values
return results_dict['potential_energy']
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 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 cij_run0(lammps_command: str,
system: am.System,
potential: lmp.Potential,
mpi_command: Optional[str] = None,
strainrange: float = 1e-6,
cycle: int = 0) -> dict:
"""
Runs cij_run0.in LAMMPS script to evaluate the elastic constants,
pressure and potential energy of the current system.
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.
strainrange : float, optional
The small strain value to apply when calculating the elastic
constants (default is 1e-6).
cycle : int, optional
Indicates the iteration cycle of quick_a_Cij(). This is used to
uniquely save the LAMMPS input and output files.
Returns
-------
dict
Dictionary of results consisting of keys:
- **'E_pot'** (*float*) - The potential energy per atom for the
supplied system.
- **'pressure'** (*numpy.array*) - The measured pressure state of the
supplied system.
- **'C_elastic'** (*atomman.ElasticConstants*) - The supplied system's
elastic constants.
"""
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data', f='init.dat', potential=potential)
restart_info = potential.pair_restart_info('initial.restart',
system.symbols)
lammps_variables['pair_data_info'] = system_info
lammps_variables['pair_restart_info'] = restart_info
lammps_variables['strainrange'] = strainrange
# Write lammps input script
lammps_script = 'cij_run0.in'
template = read_calc_file('iprPy.calculation.relax_box',
'cij_run0.template')
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,
logfile=f'cij-{cycle}-log.lammps')
thermo = output.flatten('all').thermo
# Extract LAMMPS thermo data. Each term ranges i=0-12 where i=0 is undeformed
# The remaining values are for -/+ strain pairs in the six unique directions
lx = uc.set_in_units(thermo.Lx, lammps_units['length'])
ly = uc.set_in_units(thermo.Ly, lammps_units['length'])
lz = uc.set_in_units(thermo.Lz, lammps_units['length'])
xy = uc.set_in_units(thermo.Xy, lammps_units['length'])
xz = uc.set_in_units(thermo.Xz, lammps_units['length'])
yz = uc.set_in_units(thermo.Yz, lammps_units['length'])
pxx = uc.set_in_units(thermo.Pxx, lammps_units['pressure'])
pyy = uc.set_in_units(thermo.Pyy, lammps_units['pressure'])
pzz = uc.set_in_units(thermo.Pzz, lammps_units['pressure'])
pxy = uc.set_in_units(thermo.Pxy, lammps_units['pressure'])
pxz = uc.set_in_units(thermo.Pxz, lammps_units['pressure'])
pyz = uc.set_in_units(thermo.Pyz, lammps_units['pressure'])
pe = uc.set_in_units(thermo.PotEng / system.natoms, lammps_units['energy'])
# Extract the pressure tensor
pij = np.array([[pxx[0], pxy[0], pxz[0]], [pxy[0], pyy[0], pyz[0]],
[pxz[0], pyz[0], pzz[0]]])
# Set the six non-zero strain values
strains = np.array([(lx[2] - lx[1]) / lx[0], (ly[4] - ly[3]) / ly[0],
(lz[6] - lz[5]) / lz[0], (yz[8] - yz[7]) / lz[0],
(xz[10] - xz[9]) / lz[0], (xy[12] - xy[11]) / ly[0]])
# Calculate cij using stress changes associated with each non-zero strain
cij = np.empty((6, 6))
for i in range(6):
delta_stress = np.array([
pxx[2 * i + 1] - pxx[2 * i + 2], pyy[2 * i + 1] - pyy[2 * i + 2],
pzz[2 * i + 1] - pzz[2 * i + 2], pyz[2 * i + 1] - pyz[2 * i + 2],
pxz[2 * i + 1] - pxz[2 * i + 2], pxy[2 * i + 1] - pxy[2 * i + 2]
])
cij[i] = delta_stress / strains[i]
for i in range(6):
for j in range(i):
cij[i, j] = cij[j, i] = (cij[i, j] + cij[j, i]) / 2
C = am.ElasticConstants(Cij=cij)
results = {}
results['E_pot'] = pe[0]
results['pij'] = pij
results['C'] = C
return results
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 strain_system(lammps_command, system, potential, symbols, mpi_command=None,
delta_strain=np.zeros(6), initial_strain=np.zeros(6),
hold_atypes=[], number_of_steps=0,
etol=0.0, ftol=1e-5, maxiter=10000, maxeval=100000):
"""
Applies strains to an atomic system in LAMMPS and relaxes the energy.
Arguments:
lammps_command -- command for running LAMMPS.
system -- atomman.System to add the point defect to.
potential -- atomman.lammps.Potential representation of a LAMMPS implemented potential.
symbols -- list of element-model symbols for the Potential that correspond to system's atypes.
Keyword Arguments:
mpi_command -- MPI command for running LAMMPS in parallel. Default value is None (serial run).
delta_strain -- strain state in 6 term Voigt to apply incrementally. Default value is all zeros.
initial_strain -- strain state in 6 term Voigt to apply to the system prior to the incremental delta_strain.
Default value is all zeros.
number_of_steps -- number of times to apply the incremental delta_strain to the system. Default value is 0.
hold_atypes -- list of atom types that should be held fixed (not allowed to relax). Default value is [].
etol -- energy tolerance to use for the LAMMPS minimization. Default value is 0.0 (i.e. only uses ftol).
ftol -- force tolerance to use for the LAMMPS minimization. Default value is 1e-6.
maxiter -- the maximum number of iterations for the LAMMPS minimization. Default value is 100000.
maxeval -- the maximum number of evaluations for the LAMMPS minimization. Default value is 100000.
"""
if am.tools.is_int(hold_atypes):
hold_atypes = np.array([hold_atypes])
else:
hold_atypes = np.asarray(hold_atypes)
if len(hold_atypes) == 0:
hold_info = ''
else:
move_atypes = np.setdiff1d(np.arange(1, system.natypes+1), hold_atypes)
hold_info = '\n'.join(['', '#Fix boundary region atoms',
'group move type ' + ' '.join(np.char.mod('%d', move_atypes)),
'group hold subtract all move',
'fix nomove hold setforce 0.0 0.0 0.0', ''])
#Get lammps units
lammps_units = lmp.style.unit(potential.units)
#Read LAMMPS input template
with open('strain_system.template') as f:
template = f.read()
#Define lammps variables
lammps_variables = {}
lammps_variables['atomman_system_info'] = lmp.atom_data.dump(system, 'initial.dat',
units=potential.units,
atom_style=potential.atom_style)
lammps_variables['atomman_pair_info'] = potential.pair_info(symbols)
lammps_variables['hold_info'] = hold_info
lammps_variables['energy_tolerance'] = etol
lammps_variables['force_tolerance'] = uc.get_in_units(ftol, lammps_units['force'])
lammps_variables['maximum_iterations'] = maxiter
lammps_variables['maximum_evaluations'] = maxeval
lammps_variables['number_of_steps'] = number_of_steps + 1
lammps_variables['delta_strain_xx'] = delta_strain[0]
lammps_variables['delta_strain_yy'] = delta_strain[1]
lammps_variables['delta_strain_zz'] = delta_strain[2]
lammps_variables['delta_strain_xy'] = delta_strain[5]
lammps_variables['delta_strain_xz'] = delta_strain[4]
lammps_variables['delta_strain_yz'] = delta_strain[3]
lammps_variables['initial_strain_xx'] = initial_strain[0]
lammps_variables['initial_strain_yy'] = initial_strain[1]
lammps_variables['initial_strain_zz'] = initial_strain[2]
lammps_variables['initial_strain_xy'] = initial_strain[5]
lammps_variables['initial_strain_xz'] = initial_strain[4]
lammps_variables['initial_strain_yz'] = initial_strain[3]
#Write lammps input script
with open('strain_system.in', 'w') as f:
f.write('\n'.join(iprPy.tools.fill_template(template, lammps_variables, '<', '>')))
#run lammps to relax perfect.dat
output = lmp.run(lammps_command, 'strain_system.in', mpi_command)
#Extract LAMMPS thermo data.
lammps_step = np.asarray(output.finds('Step'), dtype=int)[1::2]
E_total = uc.set_in_units(output.finds('PotEng'), lammps_units['energy'] )[1::2]
p_xx = uc.set_in_units(output.finds('Pxx'), lammps_units['pressure'])[1::2]
p_yy = uc.set_in_units(output.finds('Pyy'), lammps_units['pressure'])[1::2]
p_zz = uc.set_in_units(output.finds('Pzz'), lammps_units['pressure'])[1::2]
p_xy = uc.set_in_units(output.finds('Pxy'), lammps_units['pressure'])[1::2]
p_xz = uc.set_in_units(output.finds('Pxz'), lammps_units['pressure'])[1::2]
p_yz = uc.set_in_units(output.finds('Pyz'), lammps_units['pressure'])[1::2]
strain_step = np.asarray(output.finds('s_step'), dtype=int)[1::2]
return {'lammps_step':lammps_step, 'E_total':E_total, 'p_xx':p_xx, 'p_yy':p_yy, 'p_zz':p_zz,
'p_xy':p_xy, 'p_xz':p_xz, 'p_yz':p_yz, 'strain_step':strain_step}
def e_vs_r_scan(lammps_command: str,
system: am.System,
potential: am.lammps.Potential,
mpi_command: Optional[str] = None,
ucell: Optional[am.System] = None,
rmin: float = uc.set_in_units(2.0, 'angstrom'),
rmax: float = uc.set_in_units(6.0, 'angstrom'),
rsteps: int = 200) -> dict:
"""
Performs a cohesive energy scan over a range of interatomic spaces, r.
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.
ucell : atomman.System, optional
The fundamental unit cell correspodning to system. This is used to
convert system dimensions to cell dimensions. If not given, ucell will
be taken as system.
rmin : float, optional
The minimum r spacing to use (default value is 2.0 angstroms).
rmax : float, optional
The maximum r spacing to use (default value is 6.0 angstroms).
rsteps : int, optional
The number of r spacing steps to evaluate (default value is 200).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'r_values'** (*numpy.array of float*) - All interatomic spacings,
r, explored.
- **'a_values'** (*numpy.array of float*) - All unit cell a lattice
constants corresponding to the values explored.
- **'Ecoh_values'** (*numpy.array of float*) - The computed cohesive
energies for each r value.
- **'min_cell'** (*list of atomman.System*) - Systems corresponding to
the minima identified in the Ecoh_values.
"""
# Make system a deepcopy of itself (protect original from changes)
system = deepcopy(system)
# Set ucell = system if ucell not given
if ucell is None:
ucell = system
# Calculate the r/a ratio for the unit cell
r_a = ucell.r0() / ucell.box.a
# Get ratios of lx, ly, and lz of system relative to a of ucell
lx_a = system.box.a / ucell.box.a
ly_a = system.box.b / ucell.box.a
lz_a = system.box.c / ucell.box.a
alpha = system.box.alpha
beta = system.box.beta
gamma = system.box.gamma
# Build lists of values
r_values = np.linspace(rmin, rmax, rsteps)
a_values = r_values / r_a
Ecoh_values = np.empty(rsteps)
# Loop over values
for i in range(rsteps):
# Rescale system's box
a = a_values[i]
system.box_set(a=a * lx_a,
b=a * ly_a,
c=a * lz_a,
alpha=alpha,
beta=beta,
gamma=gamma,
scale=True)
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data',
f='atom.dat',
potential=potential)
lammps_variables['atomman_system_pair_info'] = system_info
# Write lammps input script
lammps_script = 'run0.in'
template = read_calc_file('iprPy.calculation.E_vs_r_scan',
'run0.template')
with open(lammps_script, 'w') as f:
f.write(filltemplate(template, lammps_variables, '<', '>'))
# Run lammps and extract data
try:
output = lmp.run(lammps_command,
script_name=lammps_script,
mpi_command=mpi_command)
except:
Ecoh_values[i] = np.nan
else:
thermo = output.simulations[0]['thermo']
if output.lammps_date < datetime.date(2016, 8, 1):
Ecoh_values[i] = uc.set_in_units(thermo.peatom.values[-1],
lammps_units['energy'])
else:
Ecoh_values[i] = uc.set_in_units(thermo.v_peatom.values[-1],
lammps_units['energy'])
# Rename log.lammps
try:
shutil.move('log.lammps', 'run0-' + str(i) + '-log.lammps')
except:
pass
if len(Ecoh_values[np.isfinite(Ecoh_values)]) == 0:
raise ValueError(
'All LAMMPS runs failed. Potential likely invalid or incompatible.'
)
# Find unit cell systems at the energy minimums
min_cells = []
for i in range(1, rsteps - 1):
if (Ecoh_values[i] < Ecoh_values[i - 1]
and Ecoh_values[i] < Ecoh_values[i + 1]):
a = a_values[i]
cell = deepcopy(ucell)
cell.box_set(a=a,
b=a * ucell.box.b / ucell.box.a,
c=a * ucell.box.c / ucell.box.a,
alpha=alpha,
beta=beta,
gamma=gamma,
scale=True)
min_cells.append(cell)
# Collect results
results_dict = {}
results_dict['r_values'] = r_values
results_dict['a_values'] = a_values
results_dict['Ecoh_values'] = Ecoh_values
results_dict['min_cell'] = min_cells
return results_dict
def dislocationarraystress(lammps_command,
system,
potential,
temperature,
mpi_command=None,
sigma_xz=0.0,
sigma_yz=0.0,
runsteps=100000,
thermosteps=100,
dumpsteps=None,
randomseed=None,
bwidth=None,
rigidbounds=False):
"""
Applies a constant external shearing stress to a periodic array of
dislocations atomic 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.
temperature : float
The temperature to run the simulation at.
mpi_command : str or None, optional
The MPI command for running LAMMPS in parallel. If not given, LAMMPS
will run serially.
sigma_xz : float, optional
The xz shear stress to apply to the system through the boundary atoms.
Default value is 0.0.
sigma_yz : float, optional
The yz shear stress to apply to the system through the boundary atoms.
Default value is 0.0.
runsteps : int, optional
The total number of steps to run the simulation for. Default value
is 100000.
thermosteps : int, optional
The system-wide thermo data will be outputted every this many steps.
Default value is 100.
dumpsteps : int, optional
The atomic configurations will be saved to LAMMPS dump files every
this many steps. Default value is equal to runsteps, which will only
save the initial and final configurations.
randomseed : int or None, optional
Random number seed used by LAMMPS in creating velocities. Default is
None which will select a random int between 1 and 900000000.
bwidth : float, optional
The thickness of the boundary region. Default value is 10 Angstroms.
rigidbounds : bool, optional
If True, the atoms in the boundary regions will be treated as a rigid
block such that they move as one and do not allow internal atomic
relaxations. Default value is False, in which case the boundaries will
be free surfaces.
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.
"""
try:
# Get script's location if __file__ exists
script_dir = Path(__file__).parent
except:
# Use cwd otherwise
script_dir = Path.cwd()
# Set default values
if bwidth is None:
bwidth = uc.set_in_units(10, 'angstrom')
if randomseed is None:
randomseed = random.randint(1, 900000000)
# 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='initial.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['temperature'] = temperature
stress_unit = lammps_units['force'] + '/' + lammps_units['length'] + '^2'
lammps_variables['sigma_xz'] = uc.get_in_units(sigma_xz, stress_unit)
lammps_variables['sigma_yz'] = uc.get_in_units(sigma_yz, stress_unit)
lammps_variables['dumpsteps'] = dumpsteps
lammps_variables['runsteps'] = runsteps
lammps_variables['thermosteps'] = thermosteps
lammps_variables['randomseed'] = randomseed
lammps_variables['bwidth'] = uc.get_in_units(bwidth,
lammps_units['length'])
lammps_variables['tdamp'] = 100 * lmp.style.timestep(potential.units)
lammps_variables['timestep'] = lmp.style.timestep(potential.units)
# Set dump_modify format based on dump_modify_version
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
if rigidbounds is True:
template_file = os.path.join(script_dir,
'dislarray_rigid_stress.template')
else:
template_file = os.path.join(script_dir,
'dislarray_free_stress.template')
lammps_script = 'dislarray_stress.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)
thermo = output.simulations[-1]['thermo']
steps = thermo.Step.values
times = uc.set_in_units(steps * lmp.style.timestep(potential.units),
lammps_units['time'])
# Read user-defined thermo data
if output.lammps_date < datetime.date(2016, 8, 1):
strains_xz = thermo['strain_xz'].values
strains_yz = thermo['strain_yz'].values
else:
strains_xz = thermo['v_strain_xz'].values
strains_yz = thermo['v_strain_yz'].values
# Compute average strain rates
strainrate_xz, b = np.polyfit(times, strains_xz, 1)
strainrate_yz, b = np.polyfit(times, strains_yz, 1)
# Extract output values
results_dict = {}
results_dict['times'] = times
results_dict['strains_xz'] = strains_xz
results_dict['strains_yz'] = strains_yz
results_dict['strainrate_xz'] = strainrate_xz
results_dict['strainrate_yz'] = strainrate_yz
return results_dict
def calc_cij(lammps_exe, ucell, potential, symbols, p_xx=0.0, p_yy=0.0, p_zz=0.0):
"""Runs cij_script and returns current Cij, stress, Ecoh, and new ucell guess."""
#setup system and pair info
system_info = lmp.sys_gen(units = potential.units,
atom_style = potential.atom_style,
ucell = ucell,
size = np.array([[0,3], [0,3], [0,3]]))
pair_info = potential.pair_info(symbols)
#create script and run
with open('cij.in','w') as f:
f.write(cij_script(system_info, pair_info))
data = lmp.run(lammps_exe, 'cij.in')
#get units for pressure and energy used by LAMMPS simulation
lmp_units = lmp.style.unit(potential.units)
p_unit = lmp_units['pressure']
e_unit = lmp_units['energy']
#Extract thermo values. Each term ranges i=0-12 where i=0 is undeformed
#The remaining values are for -/+ strain pairs in the six unique directions
lx = np.array(data.finds('Lx'))
ly = np.array(data.finds('Ly'))
lz = np.array(data.finds('Lz'))
xy = np.array(data.finds('Xy'))
xz = np.array(data.finds('Xz'))
yz = np.array(data.finds('Yz'))
pxx = uc.set_in_units(np.array(data.finds('Pxx')), p_unit)
pyy = uc.set_in_units(np.array(data.finds('Pyy')), p_unit)
pzz = uc.set_in_units(np.array(data.finds('Pzz')), p_unit)
pxy = uc.set_in_units(np.array(data.finds('Pxy')), p_unit)
pxz = uc.set_in_units(np.array(data.finds('Pxz')), p_unit)
pyz = uc.set_in_units(np.array(data.finds('Pyz')), p_unit)
pe = uc.set_in_units(np.array(data.finds('peatom')), e_unit)
#Set the six non-zero strain values
strains = np.array([ (lx[2] - lx[1]) / lx[0],
(ly[4] - ly[3]) / ly[0],
(lz[6] - lz[5]) / lz[0],
(yz[8] - yz[7]) / lz[0],
(xz[10] - xz[9]) / lz[0],
(xy[12] - xy[11]) / ly[0] ])
#calculate cij using stress changes associated with each non-zero strain
cij = np.empty((6,6))
for i in xrange(6):
delta_stress = np.array([ pxx[2*i+1]-pxx[2*i+2],
pyy[2*i+1]-pyy[2*i+2],
pzz[2*i+1]-pzz[2*i+2],
pyz[2*i+1]-pyz[2*i+2],
pxz[2*i+1]-pxz[2*i+2],
pxy[2*i+1]-pxy[2*i+2] ])
cij[i] = delta_stress / strains[i]
for i in xrange(6):
for j in xrange(i):
cij[i,j] = cij[j,i] = (cij[i,j] + cij[j,i]) / 2
C = am.tools.ElasticConstants(Cij=cij)
if np.allclose(C.Cij, 0.0):
raise RuntimeError('Divergence of elastic constants to <= 0')
try:
S = C.Sij
except:
raise RuntimeError('singular C:\n'+str(C.Cij))
#extract the current stress state
stress = -1 * np.array([[pxx[0], pxy[0], pxz[0]],
[pxy[0], pyy[0], pyz[0]],
[pxz[0], pyz[0], pzz[0]]])
s_xx = stress[0,0] + p_xx
s_yy = stress[1,1] + p_yy
s_zz = stress[2,2] + p_zz
new_a = ucell.box.a / (S[0,0]*s_xx + S[0,1]*s_yy + S[0,2]*s_zz + 1)
new_b = ucell.box.b / (S[1,0]*s_xx + S[1,1]*s_yy + S[1,2]*s_zz + 1)
new_c = ucell.box.c / (S[2,0]*s_xx + S[2,1]*s_yy + S[2,2]*s_zz + 1)
if new_a <= 0 or new_b <= 0 or new_c <=0:
raise RuntimeError('Divergence of box dimensions to <= 0')
newbox = am.Box(a=new_a, b=new_b, c=new_c)
ucell_new = deepcopy(ucell)
ucell_new.box_set(vects=newbox.vects, scale=True)
return {'C':C, 'stress':stress, 'ecoh':pe[0], 'ucell_new':ucell_new}
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_system(lammps_command, system, potential,
mpi_command=None, etol=0.0, ftol=0.0, maxiter=10000,
maxeval=100000, dmax=uc.set_in_units(0.01, 'angstrom')):
"""
Sets up and runs the min.in LAMMPS script for performing an energy/force
minimization to relax a system.
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.
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:
- **'logfile'** (*str*) - The name of the LAMMPS log file.
- **'initialdatafile'** (*str*) - The name of the LAMMPS data file
used to import an inital configuration.
- **'initialdumpfile'** (*str*) - The name of the LAMMPS dump file
corresponding to the inital configuration.
- **'finaldumpfile'** (*str*) - The name of the LAMMPS dump file
corresponding to the relaxed configuration.
- **'potentialenergy'** (*float*) - The total potential energy of
the relaxed system.
"""
# Ensure all atoms are within the system's box
system.wrap()
# 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 = {}
# Generate system and pair info
system_info = system.dump('atom_data', f='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(system.symbols)
# Pass in run parameters
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 = '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
output = lmp.run(lammps_command, lammps_script, mpi_command)
# Extract output values
thermo = output.simulations[-1]['thermo']
results = {}
results['logfile'] = 'log.lammps'
results['initialdatafile'] = 'system.dat'
results['initialdumpfile'] = 'atom.0'
results['finaldumpfile'] = 'atom.%i' % thermo.Step.values[-1]
results['potentialenergy'] = uc.set_in_units(thermo.PotEng.values[-1],
lammps_units['energy'])
return results
def phonon_quasiharmonic(lammps_command: str,
ucell: am.System,
potential: lmp.Potential,
mpi_command: Optional[str] = None,
a_mult: int = 3,
b_mult: int = 3,
c_mult: int = 3,
distance: float = 0.01,
symprec: float = 1e-5,
strainrange: float = 0.01,
numstrains: int = 5) -> dict:
"""
Function that performs phonon and quasiharmonic approximation calculations
using phonopy and LAMMPS.
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.
strainrange : float, optional
The range of strains to apply to the unit cell to use with the
quasiharmonic calculations. Default value is 0.01.
numstrains : int, optional
The number of strains to use for the quasiharmonic calculations.
Must be an odd integer. If 1, then the quasiharmonic calculations
will not be performed. Default value is 5.
"""
# Get lammps units
lammps_units = lmp.style.unit(potential.units)
# Get lammps version date
lammps_date = lmp.checkversion(lammps_command)['date']
# Get original box vectors
vects = ucell.box.vects
# Generate the range of strains
if numstrains == 1:
zerostrain = phononcalc(lammps_command,
ucell,
potential,
mpi_command=mpi_command,
a_mult=a_mult,
b_mult=b_mult,
c_mult=c_mult,
distance=distance,
symprec=symprec,
lammps_date=lammps_date)
phonons = [zerostrain['phonon']]
qha = None
elif numstrains % 2 == 0 or numstrains < 5:
raise ValueError(
'Invalid number of strains: must be odd and 1 or >= 5')
else:
strains = np.linspace(-strainrange, strainrange, numstrains)
istrains = np.linspace(-(numstrains - 1) / 2, (numstrains - 1) / 2,
numstrains,
dtype=int)
volumes = []
energies = []
phonons = []
temperatures = None
free_energy = None
heat_capacity = None
entropy = None
# Loop over all strains
for istrain, strain in zip(istrains, strains):
# Identify the zero strain run
if istrain == 0:
zerostrainrun = True
savefile = 'phonopy_params.yaml'
else:
zerostrainrun = False
savefile = f'phonopy_params_{istrain}.yaml'
# Generate system at the strain
newvects = vects * (1 + strain)
ucell.box_set(vects=newvects, scale=True)
volumes.append(ucell.box.volume)
system = ucell.supersize(a_mult, b_mult, c_mult)
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data',
f='disp.dat',
potential=potential)
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
output = lmp.run(lammps_command,
script_name='phonon.in',
mpi_command=mpi_command)
# Extract system energy
thermo = output.simulations[0]['thermo']
energy = uc.set_in_units(thermo.PotEng.values[-1],
lammps_units['energy'])
# Scale energy by sizemults and append to list
energies.append(energy / (a_mult * b_mult * c_mult))
# Compute phonon info for ucell
phononinfo = phononcalc(lammps_command,
ucell,
potential,
mpi_command=mpi_command,
a_mult=a_mult,
b_mult=b_mult,
c_mult=c_mult,
distance=distance,
symprec=symprec,
savefile=savefile,
plot=zerostrainrun,
lammps_date=lammps_date)
phonons.append(phononinfo['phonon'])
# Extract temperature values from the first run
if temperatures is None:
temperatures = phononinfo['thermal_properties']['temperatures']
# Initialize QHA input arrays
free_energy = np.empty((len(temperatures), len(strains)))
heat_capacity = np.empty((len(temperatures), len(strains)))
entropy = np.empty((len(temperatures), len(strains)))
# Get values for zerostrainrun
if zerostrainrun is True:
zerostrain = phononinfo
# Copy values to qha input arrays
free_energy[:, istrain] = phononinfo['thermal_properties'][
'free_energy']
entropy[:, istrain] = phononinfo['thermal_properties']['entropy']
heat_capacity[:, istrain] = phononinfo['thermal_properties'][
'heat_capacity']
# Compute qha
try:
qha = phonopy.PhonopyQHA(volumes=volumes,
electronic_energies=energies,
temperatures=temperatures,
free_energy=free_energy,
cv=heat_capacity,
entropy=entropy)
except:
qha = None
results = {}
# Add phonopy objects
results['phonon_objects'] = phonons
results['qha_object'] = qha
# Extract zerostrain properties
results['band_structure'] = zerostrain['band_structure']
results['density_of_states'] = zerostrain['dos']
# Convert units on thermal properties
results['thermal_properties'] = zerostrain['thermal_properties']
results['thermal_properties']['temperature'] = results[
'thermal_properties'].pop('temperatures')
results['thermal_properties']['Helmholtz'] = uc.set_in_units(
results['thermal_properties'].pop('free_energy'), 'kJ/mol')
results['thermal_properties']['entropy'] = uc.set_in_units(
results['thermal_properties'].pop('entropy'), 'J/K/mol')
results['thermal_properties']['heat_capacity_v'] = uc.set_in_units(
results['thermal_properties'].pop('heat_capacity'), 'J/K/mol')
if qha is not None:
# Create QHA plots
qha.plot_bulk_modulus()
plt.xlabel('Volume ($Å^3$)', size='large')
plt.ylabel('Energy ($eV$)', size='large')
plt.savefig('bulk_modulus.png', dpi=400, bbox_inches='tight')
plt.close()
qha.plot_helmholtz_volume()
plt.savefig('helmholtz_volume.png', dpi=400)
plt.close()
# Package volume vs energy scans
results['volume_scan'] = {}
results['volume_scan']['volume'] = np.array(volumes)
results['volume_scan']['strain'] = strains
results['volume_scan']['energy'] = np.array(energies)
# Compute and add QHA properties
properties = qha.get_bulk_modulus_parameters()
results['E0'] = uc.set_in_units(properties[0], 'eV')
results['B0'] = uc.set_in_units(properties[1], 'eV/angstrom^3')
results['B0prime'] = uc.set_in_units(properties[2], 'eV/angstrom^3')
results['V0'] = uc.set_in_units(properties[3], 'angstrom^3')
results['thermal_properties']['volume'] = uc.set_in_units(
np.hstack([qha.volume_temperature, np.nan]), 'angstrom^3')
results['thermal_properties']['thermal_expansion'] = np.hstack(
[qha.thermal_expansion, np.nan])
results['thermal_properties']['Gibbs'] = uc.set_in_units(
np.hstack([qha.gibbs_temperature, np.nan]), 'eV')
results['thermal_properties']['bulk_modulus'] = uc.set_in_units(
np.hstack([qha.bulk_modulus_temperature, np.nan]), 'GPa')
results['thermal_properties'][
'heat_capacity_p_numerical'] = uc.set_in_units(
np.hstack([qha.heat_capacity_P_numerical, np.nan]), 'J/K/mol')
results['thermal_properties'][
'heat_capacity_p_polyfit'] = uc.set_in_units(
np.hstack([qha.heat_capacity_P_polyfit, np.nan]), 'J/K/mol')
results['thermal_properties']['gruneisen'] = np.hstack(
[qha.gruneisen_temperature, np.nan])
return results
def disl_relax(lammps_command,
system,
potential,
mpi_command=None,
annealtemp=0.0,
randomseed=None,
etol=0.0,
ftol=1e-6,
maxiter=10000,
maxeval=100000,
dmax=uc.set_in_units(0.01, 'angstrom')):
"""
Sets up and runs the disl_relax.in LAMMPS script for relaxing a
dislocation monopole system.
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.
annealtemp : float, optional
The temperature to perform a dynamic relaxation at. (Default is 0.0,
which will skip the dynamic relaxation.)
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).
Returns
-------
dict
Dictionary of results consisting of keys:
- **'logfile'** (*str*) - The name of the LAMMPS log file.
- **'dumpfile'** (*str*) - The name of the LAMMPS dump file
for the relaxed system.
- **'E_total'** (*float*) - The total potential energy for the
relaxed 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='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(system.symbols)
lammps_variables['anneal_info'] = anneal_info(annealtemp, randomseed,
potential.units)
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
lammps_variables['group_move'] = ' '.join(
np.array(range(1, system.natypes // 2 + 1), dtype=str))
# Set dump_modify format based on dump_modify_version
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 = 'disl_relax.template'
lammps_script = 'disl_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)
thermo = output.simulations[-1]['thermo']
# Extract output values
results = {}
results['logfile'] = 'log.lammps'
results['dumpfile'] = '%i.dump' % thermo.Step.values[-1]
results['E_total'] = uc.set_in_units(thermo.PotEng.values[-1],
lammps_units['energy'])
return results
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
