def relax_system(lammps_command: str,
system: am.System,
potential: lmp.Potential,
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'),
lammps_date: Optional[datetime.date] = None) -> dict:
"""
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).
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 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
if lammps_date is None:
lammps_date = lmp.checkversion(lammps_command)['date']
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data', f='system.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'] = 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'
template = read_calc_file('iprPy.calculation.surface_energy_static',
'min.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)
# 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 relax_static(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,
dispmult: float = 0.0,
etol: float = 0.0,
ftol: float = 0.0,
maxiter: int = 100000,
maxeval: int = 1000000,
dmax: float = uc.set_in_units(0.01, 'angstrom'),
maxcycles: int = 100,
ctol: float = 1e-10) -> dict:
"""
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:
- **'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.
- **'lx'** (*float*) - The relaxed lx box length.
- **'ly'** (*float*) - The relaxed ly box length.
- **'lz'** (*float*) - The relaxed lz box length.
- **'xy'** (*float*) - The relaxed xy box tilt.
- **'xz'** (*float*) - The relaxed xz box tilt.
- **'yz'** (*float*) - The relaxed yz box tilt.
- **'E_pot'** (*float*) - The potential energy per atom for the final
configuration.
- **'measured_pxx'** (*float*) - The measured x tensile pressure
component for the final configuration.
- **'measured_pyy'** (*float*) - The measured y tensile pressure
component for the final configuration.
- **'measured_pzz'** (*float*) - The measured z tensile pressure
component for the final configuration.
- **'measured_pxy'** (*float*) - The measured xy shear pressure
component for the final configuration.
- **'measured_pxz'** (*float*) - The measured xz shear pressure
component for the final configuration.
- **'measured_pyz'** (*float*) - The measured yz shear pressure
component for the final configuration.
"""
# 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):
# Define lammps variables
lammps_variables = {}
system_info = system.dump('atom_data',
f='init.dat',
potential=potential)
lammps_variables['atomman_system_pair_info'] = system_info
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_keys based on atom_style
if potential.atom_style in ['charge']:
lammps_variables['dump_keys'] = 'id type q x y z c_peatom'
else:
lammps_variables['dump_keys'] = 'id type x y z c_peatom'
# 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"'
else:
lammps_variables[
'dump_modify_format'] = '"%d %d %.13e %.13e %.13e %.13e"'
else:
lammps_variables['dump_modify_format'] = 'float %.13e'
# Write lammps input script
lammps_script = 'minbox.in'
template = read_calc_file('iprPy.calculation.relax_static',
'minbox.template')
with open(lammps_script, 'w') as f:
f.write(filltemplate(template, lammps_variables, '<', '>'))
# Run LAMMPS and extract thermo data
logfile = 'log-' + str(cycle) + '.lammps'
output = lmp.run(lammps_command,
script_name=lammps_script,
mpi_command=mpi_command,
logfile=logfile)
thermo = output.simulations[0]['thermo']
# Clean up dump files
Path('0.dump').unlink()
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_pot'] = 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
