root / ase / md / logger.py
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"""Logging for molecular dynamics."""
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import weakref |
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import sys |
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import ase.units as units |
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# ase.parallel imported in __init__
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class MDLogger: |
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"""Class for logging molecular dynamics simulations.
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Parameters:
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dyn: The dynamics. Only a weak reference is kept.
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atoms: The atoms.
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logfile: File name or open file, "-" meaning standart output.
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stress=False: Include stress in log.
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peratom=False: Write energies per atom.
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mode="a": How the file is opened if logfile is a filename.
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"""
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def __init__(self, dyn, atoms, logfile, header=True, stress=False, |
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peratom=False, mode="a"): |
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import ase.parallel |
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if ase.parallel.rank > 0: |
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logfile="/dev/null" # Only log on master |
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if hasattr(dyn, "get_time"): |
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self.dyn = weakref.proxy(dyn)
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else:
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self.dyn = None |
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self.atoms = atoms
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self.natoms = atoms.get_number_of_atoms()
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if logfile == "-": |
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self.logfile = sys.stdout
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self.ownlogfile = False |
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elif hasattr(logfile, "write"): |
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self.logfile = logfile
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self.ownlogfile = False |
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else:
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self.logfile = open(logfile, mode) |
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self.ownlogfile = True |
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self.stress = stress
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self.peratom = peratom
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if self.dyn is not None: |
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self.hdr = "%-8s " % ("Time[ps]",) |
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self.fmt = "%-8.2f " |
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else:
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self.hdr = "" |
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self.fmt = "" |
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if self.peratom: |
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self.hdr += "%12s %12s %12s %6s" % ("Etot/N[eV]", "Epot/N[eV]", |
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"Ekin/N[eV]", "T[K]") |
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self.fmt += "%12.4f %12.4f %12.4f %6.1f" |
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else:
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self.hdr += "%12s %12s %12s %6s" % ("Etot[eV]", "Epot[eV]", |
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"Ekin[eV]", "T[K]") |
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# Choose a sensible number of decimals
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if self.natoms <= 10: |
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digits = 4
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elif self.natoms <= 100: |
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digits = 3
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elif self.natoms <= 1000: |
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digits = 2
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else:
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digits = 1
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self.fmt += 3*("%%12.%df " % (digits,)) + " %6.1f" |
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if self.stress: |
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self.hdr += "---------------- stress [GPa] -----------------" |
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self.fmt += 6*" %10.3f" |
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self.fmt += "\n" |
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if header:
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self.logfile.write(self.hdr+"\n") |
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def __del__(self): |
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self.close()
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def close(self): |
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if self.ownlogfile: |
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self.logfile.close()
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def __call__(self): |
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epot = self.atoms.get_potential_energy()
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ekin = self.atoms.get_kinetic_energy()
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temp = ekin / (1.5 * units.kB * self.natoms) |
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if self.peratom: |
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epot /= self.natoms
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ekin /= self.natoms
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if self.dyn is not None: |
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t = self.dyn.get_time() / (1000*units.fs) |
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dat = (t,) |
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else:
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dat = () |
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dat += (epot+ekin, epot, ekin, temp) |
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if self.stress: |
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dat += tuple(self.atoms.get_stress() / units.GPa) |
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self.logfile.write(self.fmt % dat) |
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self.logfile.flush()
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