root / ase / md / logger.py @ 20
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| 1 | 1 | tkerber | """Logging for molecular dynamics."""
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| 2 | 1 | tkerber | |
| 3 | 1 | tkerber | import weakref |
| 4 | 1 | tkerber | import sys |
| 5 | 1 | tkerber | import ase.units as units |
| 6 | 1 | tkerber | # ase.parallel imported in __init__
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| 7 | 1 | tkerber | |
| 8 | 1 | tkerber | class MDLogger: |
| 9 | 1 | tkerber | """Class for logging molecular dynamics simulations.
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| 10 | 1 | tkerber |
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| 11 | 1 | tkerber | Parameters:
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| 12 | 1 | tkerber | dyn: The dynamics. Only a weak reference is kept.
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| 13 | 1 | tkerber |
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| 14 | 1 | tkerber | atoms: The atoms.
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| 15 | 1 | tkerber |
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| 16 | 1 | tkerber | logfile: File name or open file, "-" meaning standart output.
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| 17 | 1 | tkerber |
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| 18 | 1 | tkerber | stress=False: Include stress in log.
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| 19 | 1 | tkerber |
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| 20 | 1 | tkerber | peratom=False: Write energies per atom.
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| 21 | 1 | tkerber |
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| 22 | 1 | tkerber | mode="a": How the file is opened if logfile is a filename.
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| 23 | 1 | tkerber | """
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| 24 | 1 | tkerber | def __init__(self, dyn, atoms, logfile, header=True, stress=False, |
| 25 | 1 | tkerber | peratom=False, mode="a"): |
| 26 | 1 | tkerber | import ase.parallel |
| 27 | 1 | tkerber | if ase.parallel.rank > 0: |
| 28 | 1 | tkerber | logfile="/dev/null" # Only log on master |
| 29 | 1 | tkerber | if hasattr(dyn, "get_time"): |
| 30 | 1 | tkerber | self.dyn = weakref.proxy(dyn)
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| 31 | 1 | tkerber | else:
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| 32 | 1 | tkerber | self.dyn = None |
| 33 | 1 | tkerber | self.atoms = atoms
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| 34 | 1 | tkerber | self.natoms = atoms.get_number_of_atoms()
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| 35 | 1 | tkerber | if logfile == "-": |
| 36 | 1 | tkerber | self.logfile = sys.stdout
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| 37 | 1 | tkerber | self.ownlogfile = False |
| 38 | 1 | tkerber | elif hasattr(logfile, "write"): |
| 39 | 1 | tkerber | self.logfile = logfile
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| 40 | 1 | tkerber | self.ownlogfile = False |
| 41 | 1 | tkerber | else:
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| 42 | 1 | tkerber | self.logfile = open(logfile, mode) |
| 43 | 1 | tkerber | self.ownlogfile = True |
| 44 | 1 | tkerber | self.stress = stress
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| 45 | 1 | tkerber | self.peratom = peratom
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| 46 | 1 | tkerber | if self.dyn is not None: |
| 47 | 1 | tkerber | self.hdr = "%-8s " % ("Time[ps]",) |
| 48 | 1 | tkerber | self.fmt = "%-8.2f " |
| 49 | 1 | tkerber | else:
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| 50 | 1 | tkerber | self.hdr = "" |
| 51 | 1 | tkerber | self.fmt = "" |
| 52 | 1 | tkerber | if self.peratom: |
| 53 | 1 | tkerber | self.hdr += "%12s %12s %12s %6s" % ("Etot/N[eV]", "Epot/N[eV]", |
| 54 | 1 | tkerber | "Ekin/N[eV]", "T[K]") |
| 55 | 1 | tkerber | self.fmt += "%12.4f %12.4f %12.4f %6.1f" |
| 56 | 1 | tkerber | else:
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| 57 | 1 | tkerber | self.hdr += "%12s %12s %12s %6s" % ("Etot[eV]", "Epot[eV]", |
| 58 | 1 | tkerber | "Ekin[eV]", "T[K]") |
| 59 | 1 | tkerber | # Choose a sensible number of decimals
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| 60 | 1 | tkerber | if self.natoms <= 10: |
| 61 | 1 | tkerber | digits = 4
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| 62 | 1 | tkerber | elif self.natoms <= 100: |
| 63 | 1 | tkerber | digits = 3
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| 64 | 1 | tkerber | elif self.natoms <= 1000: |
| 65 | 1 | tkerber | digits = 2
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| 66 | 1 | tkerber | else:
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| 67 | 1 | tkerber | digits = 1
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| 68 | 1 | tkerber | self.fmt += 3*("%%12.%df " % (digits,)) + " %6.1f" |
| 69 | 1 | tkerber | if self.stress: |
| 70 | 1 | tkerber | self.hdr += "---------------- stress [GPa] -----------------" |
| 71 | 1 | tkerber | self.fmt += 6*" %10.3f" |
| 72 | 1 | tkerber | self.fmt += "\n" |
| 73 | 1 | tkerber | if header:
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| 74 | 1 | tkerber | self.logfile.write(self.hdr+"\n") |
| 75 | 1 | tkerber | |
| 76 | 1 | tkerber | def __del__(self): |
| 77 | 1 | tkerber | self.close()
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| 78 | 1 | tkerber | |
| 79 | 1 | tkerber | def close(self): |
| 80 | 1 | tkerber | if self.ownlogfile: |
| 81 | 1 | tkerber | self.logfile.close()
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| 82 | 1 | tkerber | |
| 83 | 1 | tkerber | def __call__(self): |
| 84 | 1 | tkerber | epot = self.atoms.get_potential_energy()
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| 85 | 1 | tkerber | ekin = self.atoms.get_kinetic_energy()
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| 86 | 1 | tkerber | temp = ekin / (1.5 * units.kB * self.natoms) |
| 87 | 1 | tkerber | if self.peratom: |
| 88 | 1 | tkerber | epot /= self.natoms
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| 89 | 1 | tkerber | ekin /= self.natoms
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| 90 | 1 | tkerber | if self.dyn is not None: |
| 91 | 1 | tkerber | t = self.dyn.get_time() / (1000*units.fs) |
| 92 | 1 | tkerber | dat = (t,) |
| 93 | 1 | tkerber | else:
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| 94 | 1 | tkerber | dat = () |
| 95 | 1 | tkerber | dat += (epot+ekin, epot, ekin, temp) |
| 96 | 1 | tkerber | if self.stress: |
| 97 | 1 | tkerber | dat += tuple(self.atoms.get_stress() / units.GPa) |
| 98 | 1 | tkerber | self.logfile.write(self.fmt % dat) |
| 99 | 1 | tkerber | self.logfile.flush()
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