def plot_bonds(listabifile, listidtset):
pp = PdfPages("bonds.pdf")
plt.ioff()
if not listidtset:
allbonds = get_all_bonds(listabifile)
else:
allbonds = get_all_bonds(listabifile, listidtset)
plt.figure(figsize=(32, 20), dpi=100)
plt.subplots_adjust(left=0.05,
bottom=0.05,
right=0.95,
top=0.95,
wspace=None,
hspace=None)
abivar = InputVariables(listabifile[0].get_input_filename())
nbond = len(allbonds[0])
n = 0
for ibond in allbonds:
if len(ibond) != nbond:
print('ERROR: Number of bonds changed')
if not listidtset:
print(
(listabifile[n].basedir, 'contains', len(ibond), 'bonds'))
else:
print(
(listabifile[n].filename + ':' + listidtset[n], 'contains',
len(ibond), 'bonds'))
n += 1
iplot = 1
for ibond in range(nbond):
plt.subplot(5, 4, iplot)
y = [bohr_angstrom * seti[ibond][2] for seti in allbonds]
label = abivar.atom_name(seti[ibond][0]) + ' ' + abivar.atom_name(
seti[ibond][1])
plt.plot(y, label=label)
plt.plot(y, 'ro')
iplot += 1
plt.legend()
pp.savefig()
plt.clf()
for ibond in range(nbond):
y = [bohr_angstrom * seti[ibond][2] for seti in allbonds]
label = abivar.atom_name(seti[ibond][0]) + ' ' + abivar.atom_name(
seti[ibond][1])
plt.plot(y, label=label)
plt.plot(y, 'ro')
plt.text(0.09, y[0] + 0.001, label, size='small')
iplot += 1
plt.legend()
pp.savefig()
pp.close()
def plot_history(abinitfile, dataset=""):
history = get_history(abinitfile, dataset)
av = InputVariables(abinitfile.get_input_filename())
if dataset == "":
filep = abinitfile.basedir + "/" + abinitfile.files['tmpout'] + ".pdf"
else:
filep = abinitfile.basedir + "/" + abinitfile.files['tmpout'] + "_DS" + str(dataset) + ".pdf"
xcart = history.variables['xcart'][:]
fcart = history.variables['fcart'][:]
# rprimd = history.variables['rprimd'][:]
etotal = history.variables['etotal'][:]
if 'ekin' in history.variables:
ekin = history.variables['ekin'][:]
if max(history.variables['ekin'][:]) == 0.0:
ekin = None
else:
ekin = None
# Getting Labels of atoms
labels = [av.atom_name(i) for i in range(av.get_value('natom', dataset))]
znucl = av.get_value('znucl', idtset=dataset)
typat = av.get_value('typat', idtset=dataset)
bonds = compute_bonds(typat, xcart, znucl)
# natom = len(xcart[0])
# ComputeAngles(bonds,natom)
plot_history_energy(etotal, ekin, fcart, labels, bonds, filep)
def plot_history(abinitfile, dataset=""):
history = get_history(abinitfile, dataset)
av = InputVariables(abinitfile.get_input_filename())
if dataset == "":
filep = abinitfile.basedir + "/" + abinitfile.files['tmpout'] + ".pdf"
else:
filep = abinitfile.basedir + "/" + abinitfile.files[
'tmpout'] + "_DS" + str(dataset) + ".pdf"
xcart = history.variables['xcart'][:]
fcart = history.variables['fcart'][:]
# rprimd = history.variables['rprimd'][:]
etotal = history.variables['etotal'][:]
if 'ekin' in history.variables:
ekin = history.variables['ekin'][:]
if max(history.variables['ekin'][:]) == 0.0:
ekin = None
else:
ekin = None
# Getting Labels of atoms
labels = [av.atom_name(i) for i in range(av.get_value('natom', dataset))]
znucl = av.get_value('znucl', idtset=dataset)
typat = av.get_value('typat', idtset=dataset)
bonds = compute_bonds(typat, xcart, znucl)
# natom = len(xcart[0])
# ComputeAngles(bonds,natom)
plot_history_energy(etotal, ekin, fcart, labels, bonds, filep)