def __init__(self, xc):
"""xc: exchange-correlation functional e.g. PBE or PW."""
self.db = gbrv_database(xc)
def __init__(self):
self._db = gbrv_database()
def compute_eos(self):
results = self.get_results()
# Read etotals and fit E(V) with a parabola to find the minimum
etotals = self.read_etotals(unit="eV")[1:]
assert len(etotals) == len(self.volumes)
results.update(dict(
etotals=list(etotals),
volumes=list(self.volumes),
num_sites=len(self.relaxed_structure),
))
try:
eos_fit = EOS.Quadratic().fit(self.volumes, etotals)
except EOS.Error as exc:
results.push_exceptions(exc)
# Function to compute cubic a0 from primitive v0 (depends on struct_type)
vol2a = {"fcc": lambda vol: (4 * vol) ** (1/3.),
"bcc": lambda vol: (2 * vol) ** (1/3.),
}[self.struct_type]
a0 = vol2a(eos_fit.v0)
results.update(dict(
v0=eos_fit.v0,
b0=eos_fit.b0,
b1=eos_fit.b1,
a0=a0,
struct_type=self.struct_type
))
db = gbrv_database()
entry = db.get_entry(self.pseudo.symbol, stype=self.struct_type)
pawabs_err = a0 - entry.gbrv_paw
pawrel_err = 100 * (a0 - entry.gbrv_paw) / entry.gbrv_paw
# AE results for P and Hg are missing.
if entry.ae is not None:
abs_err = a0 - entry.ae
rel_err = 100 * (a0 - entry.ae) / entry.ae
else:
# Use GBRV_PAW as reference.
abs_err = pawabs_err
rel_err = pawrel_err
print("for GBRV struct_type: ", self.struct_type, "a0= ", a0, "Angstrom")
print("AE - THIS: abs_err = %f, rel_err = %f %%" % (abs_err, rel_err))
print("GBRV-PAW - THIS: abs_err = %f, rel_err = %f %%" % (pawabs_err, pawrel_err))
d = {k: results[k] for k in ("a0", "etotals", "volumes")}
d["a0_abs_err"] = abs_err
d["a0_rel_err"] = rel_err
if results.exceptions:
d["_exceptions"] = str(results.exceptions)
self.write_dojo_report(d)
return results
def __init__(self, xc):
"""xc: Exchange-correlation functional."""
self.db = gbrv_database(xc)
def compute_eos(self):
"""Compute the EOS as describedin the GBRV paper."""
self.history.info("Computing EOS")
# Read etotals and fit E(V) with a parabola to find the minimum
etotals = self.read_etotals(unit="eV")[1:]
assert len(etotals) == len(self.volumes)
results = {}
results.update(dict(
etotals=list(etotals),
volumes=list(self.volumes),
num_sites=len(self.relaxed_structure),
#pseudos=self.pseudos.as_dict(),
))
try:
eos_fit = EOS.Quadratic().fit(self.volumes, etotals)
except EOS.Error as exc:
results.push_exceptions(exc)
# Function to compute cubic a0 from primitive v0 (depends on struct_type)
vol2a = {"fcc": lambda vol: (4 * vol) ** (1/3.),
"bcc": lambda vol: (2 * vol) ** (1/3.),
"rocksalt": lambda vol: (4 * vol) ** (1/3.),
"ABO3": lambda vol: vol ** (1/3.),
"hH": lambda vol: (4 * vol) ** (1/3.),
}[self.struct_type]
a0 = vol2a(eos_fit.v0)
results.update(dict(
ecut=self.ecut,
pawecutdg=self.pawecutdg,
struct_type=self.struct_type,
v0=eos_fit.v0,
b0=eos_fit.b0,
#b1=eos_fit.b1, # infinity
a0=a0,
))
db = gbrv_database(xc=self.xc)
entry = db.get_entry(self.formula, stype=self.struct_type)
try:
pawabs_err = a0 - entry.gbrv_paw
pawrel_err = 100 * (a0 - entry.gbrv_paw) / entry.gbrv_paw
except:
# Some paw_abinit entries are not available.
pawabs_err = np.inf
pawrel_err = np.inf
# If AE results are missing we use GBRV_PAW as reference.
if entry.ae is not None:
ref_a0 = entry.ae
abs_err = a0 - entry.ae
rel_err = 100 * (a0 - entry.ae) / entry.ae
else:
assert pawabs_err is not None
assert pawrel_err is not None
ref_a0 = entry.gbrv_paw
abs_err = pawabs_err
rel_err = pawrel_err
results["a0_abs_err"] = abs_err
results["a0_rel_err"] = rel_err
print(80 * "=")
print("pseudos:", list(p.basename for p in self.pseudos))
print("for %s (%s): my_a0=%.3f, ref_a0=%.3f Angstrom" % (self.formula, self.struct_type, a0, ref_a0))
print("AE - THIS: abs_err=%f, rel_err=%f %%" % (abs_err, rel_err))
print("GBRV-PAW - THIS: abs_err=%f, rel_err=%f %%" % (pawabs_err, pawrel_err))
print(80 * "=")
# Write results in outdir in JSON format.
with open(self.outdir.path_in("gbrv_results.json"), "wt") as fh:
json.dump(results, fh, indent=-1, sort_keys=True) #, cls=MontyEncoder)
# Update the database.
if self.outdb_path is not None:
GbrvOutdb.insert_results(self.outdb_path, self.struct_type, self.formula,
self.accuracy, self.pseudos, results)
return results
def __init__(self, xc):
"""xc: Exchange-correlation functional."""
self.db = gbrv_database(xc)
def compute_eos(self):
"""Compute the EOS as described in the GBRV paper."""
self.history.info("Computing EOS")
# Read etotals and fit E(V) with a parabola to find the minimum
etotals = self.read_etotals(unit="eV")[1:]
assert len(etotals) == len(self.volumes)
results = {}
results.update(dict(
etotals=list(etotals),
volumes=list(self.volumes),
num_sites=len(self.relaxed_structure),
#pseudos=self.pseudos.as_dict(),
))
try:
eos_fit = EOS.Quadratic().fit(self.volumes, etotals)
except EOS.Error as exc:
results.push_exceptions(exc)
# Function to compute cubic a0 from primitive v0 (depends on struct_type)
vol2a = {"fcc": lambda vol: (4 * vol) ** (1/3.),
"bcc": lambda vol: (2 * vol) ** (1/3.),
"rocksalt": lambda vol: (4 * vol) ** (1/3.),
"ABO3": lambda vol: vol ** (1/3.),
"hH": lambda vol: (4 * vol) ** (1/3.),
}[self.struct_type]
a0 = vol2a(eos_fit.v0)
results.update(dict(
ecut=self.ecut,
pawecutdg=self.pawecutdg,
struct_type=self.struct_type,
v0=eos_fit.v0,
b0=eos_fit.b0,
#b1=eos_fit.b1, # infinity
a0=a0,
))
db = gbrv_database(xc=self.xc)
entry = db.get_entry(self.formula, stype=self.struct_type)
try:
pawabs_err = a0 - entry.gbrv_paw
pawrel_err = 100 * (a0 - entry.gbrv_paw) / entry.gbrv_paw
except Exception:
# Some paw_abinit entries are not available.
pawabs_err = np.inf
pawrel_err = np.inf
# If AE results are missing we use GBRV_PAW as reference.
if entry.ae is not None:
ref_a0 = entry.ae
abs_err = a0 - entry.ae
rel_err = 100 * (a0 - entry.ae) / entry.ae
else:
assert pawabs_err is not None
assert pawrel_err is not None
ref_a0 = entry.gbrv_paw
abs_err = pawabs_err
rel_err = pawrel_err
results["a0_rel_err"] = rel_err
results["a0_abs_err"] = abs_err
results["pseudos"] = {p.basename: p.md5 for p in self.pseudos}
print(80 * "=")
print("pseudos:", list(p.basename for p in self.pseudos))
print("for %s (%s): my_a0=%.3f, ref_a0=%.3f Angstrom" % (self.formula, self.struct_type, a0, ref_a0))
print("AE - THIS: abs_err=%f, rel_err=%f %%" % (abs_err, rel_err))
print("GBRV-PAW - THIS: abs_err=%f, rel_err=%f %%" % (pawabs_err, pawrel_err))
print(80 * "=")
# Write results in outdir in JSON format.
with open(self.outdir.path_in("gbrv_results.json"), "wt") as fh:
json.dump(results, fh, indent=-1, sort_keys=True)
# Update the database.
if self.outdb_path is not None:
GbrvOutdb.insert_results(self.outdb_path, self.struct_type, self.formula,
self.accuracy, self.pseudos, results)
return results
def compute_eos(self):
self.history.info("Computing EOS")
#results = self.get_results()
# Read etotals and fit E(V) with a parabola to find the minimum
etotals = self.read_etotals(unit="eV")[1:]
assert len(etotals) == len(self.volumes)
results = {}
results.update(dict(
etotals=list(etotals),
volumes=list(self.volumes),
num_sites=len(self.relaxed_structure),
))
try:
eos_fit = EOS.Quadratic().fit(self.volumes, etotals)
except EOS.Error as exc:
results.push_exceptions(exc)
#return results
# Function to compute cubic a0 from primitive v0 (depends on struct_type)
vol2a = {"fcc": lambda vol: (4 * vol) ** (1/3.),
"rocksalt": lambda vol: (4 * vol) ** (1/3.),
"bcc": lambda vol: (2 * vol) ** (1/3.),
"ABO3": lambda vol: vol ** (1/3.),
}[self.struct_type]
a0 = vol2a(eos_fit.v0)
results.update(dict(
v0=eos_fit.v0,
b0=eos_fit.b0,
b1=eos_fit.b1,
a0=a0,
ecut=self.ecut,
#struct_type=self.struct_type
))
# Update the database.
# TODO, handle error!
if self.outdb_path is not None:
GbrvOutdb.update_record(self.outdb_path, self.formula, self.accuracy, self.pseudos, results)
db = gbrv_database()
entry = db.get_entry(self.formula, stype=self.struct_type)
pawabs_err = a0 - entry.gbrv_paw
pawrel_err = 100 * (a0 - entry.gbrv_paw) / entry.gbrv_paw
# If AE results are missing we use GBRV_PAW as reference.
if entry.ae is not None:
abs_err = a0 - entry.ae
rel_err = 100 * (a0 - entry.ae) / entry.ae
else:
abs_err = pawabs_err
rel_err = pawrel_err
print("for %s (%s) a0=%.2f Angstrom" % (self.formula, self.struct_type, a0))
print("AE - THIS: abs_err = %f, rel_err = %f %%" % (abs_err, rel_err))
print("GBRV-PAW - THIS: abs_err = %f, rel_err = %f %%" % (pawabs_err, pawrel_err))
#d = {k: results[k] for k in ("a0", "etotals", "volumes")}
#d["a0_abs_err"] = abs_err
#d["a0_rel_err"] = rel_err
#if results.exceptions:
# d["_exceptions"] = str(results.exceptions)
return results
