def fun(args, consts):
log = {}
# get uuid
calc_uuid = uuid.uuid4().hex[:8]
# logging
log["uuid"] = calc_uuid
# make directories for the calculation
dirname = os.path.join(calc["element"], calc_uuid)
if not os.path.exists(dirname):
os.makedirs(dirname)
os.chdir(dirname)
# generate radii iterable
radii = list(args) + list(consts)
log["radii"] = radii
pseudo_file, log["err_pseudo"] = generate_pseudo(calc, electrons, radii)
log["err_mean"], log["err_max"] = test_pseudo(calc, configs)
volumes = np.linspace(0.98, 1.02, 3)
alats = (volumes * equil_volume * nat) ** (1./3.)
x, y = [], []
for alat in alats:
prepare_siesta_calc(fdf_file, pseudo_file, alat, siesta_calc)
run_siesta_calc(alat, siesta_calc)
e = read_energy(alat)
if e is not None:
x.append(float(e[0]))
y.append(e[1])
os.chdir(cwd)
# making x and y arrays
x = (np.array(x) ** 3) / nat
y = np.array(y)
p = np.polyfit(x, y, 2)
min_p = -p[1] / (2*p[0])
log["min_p"] = min_p
x_p = np.linspace(0.94*min_p, 1.06*min_p, 7)
y_p = np.polyval(p, x_p)
vol, bulk_mod, bulk_deriv, res = BM(np.vstack((x_p, y_p)).T)
our_data = np.core.records.fromrecords([(element, vol, bulk_mod, bulk_deriv), ], names=('element', 'V0', 'B0', 'BP'))
delta, delta_rel, delta1 = calcDelta_one(our_data, ref_data_el, useasymm=False)
log["delta"] = delta
log["delta_rel"] = delta_rel
log["delta1"] = delta1
log_entry(log, element)
return delta
log["radii"] = radii
pseudo_file, log["err_pseudo"] = generate_pseudo(calc, electrons, radii)
log["err_mean"], log["err_max"] = test_pseudo(calc, configs)
volumes = np.linspace(0.98, 1.02, 3)
# possible alats (3 points near Wien2K equilibrium)
alats = (volumes * equil_volume * nat) ** (1./3.)
x, y = [], []
for alat in alats:
prepare_siesta_calc(fdf_file, pseudo_file, alat, siesta_calc)
run_siesta_calc(alat, siesta_calc)
e = read_energy(alat)
if e is not None:
x.append(float(e[0]))
y.append(e[1])
os.chdir(cwd)
# making x and y arrays
x = (np.array(x) ** 3) / nat
y = np.array(y)
p = np.polyfit(x, y, 2)
min_p = -p[1] / (2*p[0])
log["min_p"] = min_p
x_p = np.linspace(0.94*min_p, 1.06*min_p, 7)
y_p = np.polyval(p, x_p)
vol, bulk_mod, bulk_deriv, res = BM(np.vstack((x_p, y_p)).T)
our_data = np.core.records.fromrecords([(element, vol, bulk_mod, bulk_deriv), ], names=('element', 'V0', 'B0', 'BP'))
delta, delta_rel, delta1 = calcDelta_one(our_data, ref_data_el, useasymm=False)
log["delta"] = delta
log["delta_rel"] = delta_rel
log["delta1"] = delta1
log_entry(log, element)
for root, dirs, files in os.walk(os.getcwd()):
for dir_i in dirs:
try:
alat = float(dir_i)
except:
continue
energies = read_energy(alat)
if energies is not None:
x_i, y_i = energies
x.append(x_i)
y.append(y_i)
os.chdir(wd)
x = (np.array(x) ** 3) / nat
y = np.array(y)
p = np.polyfit(x, y, 2)
x_min = -p[1] / (2*p[0])
x_p = np.linspace(0.94*x_min, 1.06*x_min, 7)
y_p = np.polyval(p, x_p)
# vol, bulk_mod, bulk_deriv, res = BM(np.vstack((x_p, y_p)).T)
vol, bulk_mod, bulk_deriv, res = BM(np.vstack((x, y)).T)
ref_data = read_ref_data("delta/WIEN2k.txt")
ref_data_el = ref_data[ref_data['element'] == element]
our_data = np.core.records.fromrecords([(element, vol, bulk_mod, bulk_deriv), ], names=('element', 'V0', 'B0', 'BP'))
print calcDelta_one(our_data, ref_data_el, useasymm=False)
plt.plot(np.array(x), np.array(y), "o")
plt.plot(x_p, y_p, "--")
plt.show()