def bondlengths(Ea, dE):
"""Calculate bond lengths and write to bondlengths.csv file"""
B = []
E0 = []
csv = open('bondlengths.csv', 'w')
for formula, energies in dE:
bref = diatomic[formula][1]
b = np.linspace(0.96 * bref, 1.04 * bref, 5)
e = np.polyfit(b, energies, 3)
if not formula in Ea:
continue
ea, eavasp = Ea[formula]
dedb = np.polyder(e, 1)
b0 = np.roots(dedb)[1]
assert abs(b0 - bref) < 0.1
b = np.linspace(0.96 * bref, 1.04 * bref, 20)
e = np.polyval(e, b) - ea
if formula == 'O2':
plt.plot(b, e, '-', color='0.7', label='GPAW')
else:
plt.plot(b, e, '-', color='0.7', label='_nolegend_')
name = latex(data[formula]['name'])
plt.text(b[0], e[0] + 0.2, name)
B.append(bref)
E0.append(-eavasp)
csv.write('`%s`, %.3f, %.3f, %+.3f\n' %
(name[1:-1], b0, bref, b0 - bref))
plt.plot(B, E0, 'g.', label='reference')
plt.legend(loc='lower right')
plt.xlabel('Bond length $\mathrm{\AA}$')
plt.ylabel('Energy [eV]')
plt.savefig('bondlengths.png')
def atomization_energies(E):
"""Write given atomization energies to file atomization_energies.csv."""
Ea = {}
fd = open('atomization_energies.csv', 'w')
for formula in sorted(molecules):
ea = -E[formula]
for a in string2symbols(data[formula]['symbols']):
ea += E[a]
eavasp = atomization_vasp[formula][1] * kcal / mol
Ea[formula] = (ea, eavasp)
name = latex(data[formula]['name'])
fd.write('`%s`, %.3f, %.3f, %+.3f\n' %
(name[1:-1], ea, eavasp, ea - eavasp))
return Ea
}[v]
label += l + ' ' + str(round(value[n], 3)) + '\n'
pylab.annotate(
label,
xy=(n + 0.0, 0.0),
xytext=errorslocation(n, n1),
arrowprops=None,
horizontalalignment='left',
verticalalignment='center',
fontsize=ann_fontsize,
)
# plot compounds with largest errors
for n, l in enumerate(largest):
for n1, (c, e) in enumerate(l):
name = latex(c) + '\n'
# matplotlib.pyparsing.ParseFatalException: Expected end of math '$'
# $\rm{SiH}2_\rm{s}3\rm{B}1\rm{d}$ (at char 0), (line:1, col:1)
name = name.replace('\\rm', '')
label = name + ' ' + str(round(e, 2))
pylab.annotate(
label,
xy=(n + 0.05, e),
xytext=formulaslocation(n, n1),
arrowprops=dict(width=0.05,
headwidth=5.0,
facecolor='black',
shrink=1.00),
horizontalalignment='left',
verticalalignment='center',
fontsize=ann_fontsize,
value = {"average": average, "absaverage": absaverage, "std": std}[v]
label += l + " " + str(round(value[n], 3)) + "\n"
pylab.annotate(
label,
xy=(n + 0.0, 0.0),
xytext=errorslocation(n, n1),
arrowprops=None,
horizontalalignment="left",
verticalalignment="center",
fontsize=ann_fontsize,
)
# plot compounds with largest errors
for n, l in enumerate(largest):
for n1, (c, e) in enumerate(l):
name = latex(c) + "\n"
# matplotlib.pyparsing.ParseFatalException: Expected end of math '$'
# $\rm{SiH}2_\rm{s}3\rm{B}1\rm{d}$ (at char 0), (line:1, col:1)
name = name.replace("\\rm", "")
label = name + " " + str(round(e, 2))
pylab.annotate(
label,
xy=(n + 0.05, e),
xytext=formulaslocation(n, n1),
arrowprops=dict(width=0.05, headwidth=5.0, facecolor="black", shrink=1.00),
horizontalalignment="left",
verticalalignment="center",
fontsize=ann_fontsize,
)
# pylab.show()
plot_save(".", tag + "_ea_vs")
'absaverage': absaverage,
'std': std,
}[v]
label += l + ' ' + str(round(value[n], 3)) + '\n'
pylab.annotate(label,
xy=(n + 0.0, 0.0),
xytext=errorslocation(n, n1),
arrowprops=None,
horizontalalignment='left', verticalalignment='center',
fontsize=ann_fontsize,
)
# plot compounds with largest errors
for n, l in enumerate(largest):
for n1, (c, e) in enumerate(l):
name = latex(c) + '\n'
# matplotlib.pyparsing.ParseFatalException: Expected end of math '$'
# $\rm{SiH}2_\rm{s}3\rm{B}1\rm{d}$ (at char 0), (line:1, col:1)
name = name.replace('\\rm', '')
label = name + ' ' + str(round(e, 2))
pylab.annotate(label,
xy=(n + 0.05, e),
xytext=formulaslocation(n, n1),
arrowprops=dict(width=0.05, headwidth=5.0, facecolor='black', shrink=1.00),
horizontalalignment='left', verticalalignment='center',
fontsize=ann_fontsize,
)
#pylab.show()
plot_save(".", tag + '_ea_vs')
#pylab.close(1)