def accept_pseudo(self, pseudo, **kwargs):
"""Returns True if the master can train the pseudo."""
ready = super(DeltaFactorMaster, self).accept_pseudo(pseudo, **kwargs)
# Do we have this element in the deltafactor database?
from pseudo_dojo.refdata.deltafactor import df_database
return (ready and df_database().has_symbol(self.pseudo.symbol))
def compare_delta_factor(self, accuracy="normal", exclude_na=True):
"""Returns a table (list of lists) comparing the deltafactor results."""
from pseudo_dojo.refdata.deltafactor import df_database
dfdb = df_database()
def fmt(float):
return "%.3f" % float
table = []; app = table.append
app(["pseudo", "V0", "B0", "B1", "%V0", "%B0", "%B1", "Delta"])
deltas, names = [], []
for pseudo in self:
if not pseudo.has_dojo_report or "delta_factor" not in pseudo.dojo_report:
if not exclude_na: app([pseudo.name] + 7 * ["N/A"])
continue
ref = dfdb.get_entry(pseudo.symbol)
vals = pseudo.dojo_report["delta_factor"][accuracy]
v0, b0_GPa, b1, dfact = vals["v0"], vals["b0_GPa"], vals["b1"], vals["dfact"]
rerr_v0 = 100 * (v0 - ref.v0) / ref.v0
rerr_b0 = 100 * (b0_GPa - ref.b0_GPa) / ref.b0_GPa
rerr_b1 = 100 * (b1 - ref.b1) / ref.b1
app([pseudo.name] + map(fmt, [v0, b0_GPa, b1, rerr_v0, rerr_b0, rerr_b1, dfact]))
deltas.append(dfact)
names.append(pseudo.name)
stats = compute_stats(deltas, labels=names)
print(stats)
return table
def get_results(self):
results = super(DeltaFactorWork, self).get_results()
num_sites = self._input_structure.num_sites
etotals = self.read_etotals(unit="eV")
results.update(dict(
etotals=list(etotals),
volumes=list(self.volumes),
num_sites=num_sites))
d = {}
try:
# Use same fit as the one employed for the deltafactor.
eos_fit = EOS.DeltaFactor().fit(self.volumes/num_sites, etotals/num_sites)
# Get reference results (Wien2K).
wien2k = df_database().get_entry(self.pseudo.symbol)
# Compute deltafactor estimator.
dfact = df_compute(wien2k.v0, wien2k.b0_GPa, wien2k.b1,
eos_fit.v0, eos_fit.b0_GPa, eos_fit.b1, b0_GPa=True)
dfact = dfact if not isinstance(dfact, complex) else float('NaN')
dfactprime_meV = dfact * (30 * 100) / (eos_fit.v0 * eos_fit.b0_GPa)
dfactprime_meV = dfactprime_meV if not isinstance(dfactprime_meV, complex) else float('NaN')
print("delta", eos_fit)
print("Ecut %.1f, dfact = %.3f meV, dfactprime %.3f meV" % (self.ecut, dfact, dfactprime_meV))
results.update({
"dfact_meV": dfact,
"v0": eos_fit.v0,
"b0": eos_fit.b0,
"b0_GPa": eos_fit.b0_GPa,
"b1": eos_fit.b1,
"dfactprime_meV": dfactprime_meV
})
d = {k: results[k] for k in
("dfact_meV", "v0", "b0", "b0_GPa", "b1", "etotals", "volumes", "num_sites", "dfactprime_meV")}
# Write data for the computation of the delta factor
with open(self.outdir.path_in("deltadata.txt"), "w") as fh:
fh.write("# Deltafactor = %s meV\n" % dfact)
fh.write("# Volume/natom [Ang^3] Etotal/natom [eV]\n")
for v, e in zip(self.volumes, etotals):
fh.write("%s %s\n" % (v/num_sites, e/num_sites))
except EOS.Error as exc:
results.push_exceptions(exc)
if results.exceptions:
d["_exceptions"] = str(results.exceptions)
self.write_dojo_report(d)
return results
def get_results(self):
num_sites = self._input_structure.num_sites
etotal = ArrayWithUnit(self.read_etotal(), "Ha").to("eV")
wf_results = super(DeltaFactorWorkflow, self).get_results()
wf_results.update({
"etotal" : list(etotal),
"volumes" : list(self.volumes),
"natom" : num_sites,
"dojo_level": 1,
})
try:
#eos_fit = EOS.Murnaghan().fit(self.volumes/num_sites, etotal/num_sites)
#print("murn",eos_fit)
#eos_fit.plot(show=False, savefig=self.path_in_workdir("murn_eos.pdf"))
# Use same fit as the one employed for the deltafactor.
eos_fit = EOS.DeltaFactor().fit(self.volumes/num_sites, etotal/num_sites)
eos_fit.plot(show=False, savefig=self.outdir.path_in("eos.pdf"))
# FIXME: This object should be moved to pseudo_dojo.
# Get reference results (Wien2K).
from pseudo_dojo.refdata.deltafactor import df_database, df_compute
wien2k = df_database().get_entry(self.pseudo.symbol)
# Compute deltafactor estimator.
dfact = df_compute(wien2k.v0, wien2k.b0_GPa, wien2k.b1, eos_fit.v0, eos_fit.b0_GPa, eos_fit.b1, b0_GPa=True)
print("delta",eos_fit)
print("Deltafactor = %.3f meV" % dfact)
wf_results.update({
"v0": eos_fit.v0,
"b0": eos_fit.b0,
"b0_GPa": eos_fit.b0_GPa,
"b1": eos_fit.b1,
})
except EOS.Error as exc:
wf_results.push_exceptions(exc)
#if kwargs.get("json_dump", True):
# wf_results.json_dump(self.path_in_workdir("results.json"))
# Write data for the computation of the delta factor
with open(self.outdir.path_in("deltadata.txt"), "w") as fh:
fh.write("# Deltafactor = %s meV\n" % dfact)
fh.write("# Volume/natom [Ang^3] Etotal/natom [eV]\n")
for (v, e) in zip(self.volumes, etotal):
fh.write("%s %s\n" % (v/num_sites, e/num_sites))
return wf_results
def make_report(self, results, **kwargs):
# Get reference results (Wien2K).
from pseudo_dojo.refdata.deltafactor import df_database, df_compute
wien2k = df_database().get_entry(self.pseudo.symbol)
# Get our results and compute deltafactor estimator.
v0, b0_GPa, b1 = results["v0"], results["b0_GPa"], results["b1"]
dfact = df_compute(wien2k.v0, wien2k.b0_GPa, wien2k.b1, v0, b0_GPa, b1, b0_GPa=True)
print("Deltafactor = %.3f meV" % dfact)
d = dict(v0=v0,
b0_GPa=b0_GPa,
b1=b1,
dfact=dfact
)
if results.exceptions:
d["_exceptions"] = str(results.exceptions)
d = {self.accuracy: d}
return {self.dojo_key: d}
def __init__(self):
self._dfdb = df_database()
def __init__(self, xc):
"""xc is the exchange-correlation functional e.g. PBE, PW."""
# Get reference to the deltafactor database
self._dfdb = df_database(xc)
def __init__(self, manager=None, workdir=None):
# reference to the deltafactor database
# use the elemental solid in the gs configuration
self._dfdb = df_database()
self.manager = manager
self.workdir = workdir
def __init__(self):
# Get a reference to the deltafactor database
self._dfdb = df_database()
def __init__(self, xc='PBE'):
# Get a reference to the deltafactor database
self._dfdb = df_database(xc=xc)