"""Logging for molecular dynamics."""
import weakref
from typing import IO, Any, Union
from ase import Atoms, units
from ase.parallel import world
from ase.utils import IOContext
[docs]
class MDLogger(IOContext):
"""Class for logging molecular dynamics simulations.
Parameters:
dyn: The dynamics. Only a weak reference is kept.
atoms: The atoms.
logfile: File name or open file, "-" meaning standard output.
stress=False: Include stress in log.
peratom=False: Write energies per atom.
mode="a": How the file is opened if logfile is a filename.
"""
def __init__(
self,
dyn: Any, # not fully annotated so far to avoid a circular import
atoms: Atoms,
logfile: Union[IO, str],
header: bool = True,
stress: bool = False,
peratom: bool = False,
mode: str = "a",
comm=world,
):
self.dyn = weakref.proxy(dyn) if hasattr(dyn, "get_time") else None
self.atoms = atoms
global_natoms = atoms.get_global_number_of_atoms()
self.logfile = self.openfile(file=logfile, mode=mode, comm=comm)
self.stress = stress
self.peratom = peratom
if self.dyn is not None:
self.hdr = "%-9s " % ("Time[ps]",)
self.fmt = "%-10.4f "
else:
self.hdr = ""
self.fmt = ""
if self.peratom:
self.hdr += "%12s %12s %12s %6s" % ("Etot/N[eV]", "Epot/N[eV]",
"Ekin/N[eV]", "T[K]")
self.fmt += "%12.4f %12.4f %12.4f %6.1f"
else:
self.hdr += "%12s %12s %12s %6s" % ("Etot[eV]", "Epot[eV]",
"Ekin[eV]", "T[K]")
# Choose a sensible number of decimals
if global_natoms <= 100:
digits = 4
elif global_natoms <= 1000:
digits = 3
elif global_natoms <= 10000:
digits = 2
else:
digits = 1
self.fmt += 3 * ("%%12.%df " % (digits,)) + " %6.1f"
if self.stress:
self.hdr += (' ---------------------- stress [GPa] '
'-----------------------')
self.fmt += 6 * " %10.3f"
self.fmt += "\n"
if header:
self.logfile.write(self.hdr + "\n")
def __del__(self):
self.close()
def __call__(self):
epot = self.atoms.get_potential_energy()
ekin = self.atoms.get_kinetic_energy()
temp = self.atoms.get_temperature()
global_natoms = self.atoms.get_global_number_of_atoms()
if self.peratom:
epot /= global_natoms
ekin /= global_natoms
if self.dyn is not None:
t = self.dyn.get_time() / (1000 * units.fs)
dat = (t,)
else:
dat = ()
dat += (epot + ekin, epot, ekin, temp)
if self.stress:
dat += tuple(self.atoms.get_stress(
include_ideal_gas=True) / units.GPa)
self.logfile.write(self.fmt % dat)
self.logfile.flush()