class PDPlotterTest(unittest.TestCase):
def setUp(self):
(elements, entries) = PDEntryIO.from_csv(
os.path.join(module_dir, "pdentries_test.csv"))
self.pd = PhaseDiagram(entries)
self.plotter = PDPlotter(self.pd, show_unstable=True)
entrieslio = [
e for e in entries
if len(e.composition) < 3 and ("Fe" not in e.composition)
]
self.pd_formation = PhaseDiagram(entrieslio)
self.plotter_formation = PDPlotter(self.pd_formation,
show_unstable=True)
entries.append(PDEntry("C", 0))
self.pd3d = PhaseDiagram(entries)
self.plotter3d = PDPlotter(self.pd3d, show_unstable=True)
def test_pd_plot_data(self):
(lines, labels, unstable_entries) = self.plotter.pd_plot_data
self.assertEqual(len(lines), 22)
self.assertEqual(len(labels), len(self.pd.stable_entries),
"Incorrect number of lines generated!")
self.assertEqual(
len(unstable_entries),
len(self.pd.all_entries) - len(self.pd.stable_entries),
"Incorrect number of lines generated!")
(lines, labels, unstable_entries) = self.plotter3d.pd_plot_data
self.assertEqual(len(lines), 33)
self.assertEqual(len(labels), len(self.pd3d.stable_entries))
self.assertEqual(
len(unstable_entries),
len(self.pd3d.all_entries) - len(self.pd3d.stable_entries))
(lines, labels, unstable_entries) = self.plotter_formation.pd_plot_data
self.assertEqual(len(lines), 3)
self.assertEqual(len(labels), len(self.pd_formation.stable_entries))
@unittest.skipIf("DISPLAY" not in os.environ, "Need display")
def test_get_plot(self):
# Some very basic non-tests. Just to make sure the methods are callable.
import matplotlib
matplotlib.use("pdf")
self.plotter.get_plot()
self.plotter3d.get_plot()
self.plotter.get_plot(energy_colormap="Reds", process_attributes=True)
plt = self.plotter3d.get_plot(energy_colormap="Reds",
process_attributes=True)
self.plotter.get_plot(energy_colormap="Reds", process_attributes=False)
plt = self.plotter3d.get_plot(energy_colormap="Reds",
process_attributes=False)
self.plotter.get_chempot_range_map_plot([Element("Li"), Element("O")])
class PDPlotterTest(unittest.TestCase):
def setUp(self):
(elements, entries) = PDEntryIO.from_csv(os.path.join(
module_dir, "pdentries_test.csv"))
self.pd = PhaseDiagram(entries)
self.plotter = PDPlotter(self.pd, show_unstable=True)
entrieslio = [e for e in entries
if len(e.composition) < 3 and ("Fe" not in e.composition)]
self.pd_formation = PhaseDiagram(entrieslio)
self.plotter_formation = PDPlotter(self.pd_formation, show_unstable=True)
entries.append(PDEntry("C", 0))
self.pd3d = PhaseDiagram(entries)
self.plotter3d = PDPlotter(self.pd3d, show_unstable=True)
def test_pd_plot_data(self):
(lines, labels, unstable_entries) = self.plotter.pd_plot_data
self.assertEqual(len(lines), 22)
self.assertEqual(len(labels), len(self.pd.stable_entries),
"Incorrect number of lines generated!")
self.assertEqual(len(unstable_entries),
len(self.pd.all_entries) - len(self.pd.stable_entries),
"Incorrect number of lines generated!")
(lines, labels, unstable_entries) = self.plotter3d.pd_plot_data
self.assertEqual(len(lines), 33)
self.assertEqual(len(labels), len(self.pd3d.stable_entries))
self.assertEqual(len(unstable_entries),
len(self.pd3d.all_entries) - len(self.pd3d.stable_entries))
(lines, labels, unstable_entries) = self.plotter_formation.pd_plot_data
self.assertEqual(len(lines), 3)
self.assertEqual(len(labels), len(self.pd_formation.stable_entries))
def test_get_plot(self):
# Some very basic non-tests. Just to make sure the methods are callable.
self.plotter.get_plot()
self.plotter3d.get_plot()
# self.plotter.get_plot(energy_colormap="Reds", process_attributes=True)
# plt = self.plotter3d.get_plot(energy_colormap="Reds", process_attributes=True)
# self.plotter.get_plot(energy_colormap="Reds", process_attributes=False)
# plt = self.plotter3d.get_plot(energy_colormap="Reds",
# process_attributes=False)
self.plotter.get_chempot_range_map_plot([Element("Li"), Element("O")])
def get_phase_diagram_plot(self):
"""
Returns a phase diagram plot, as a matplotlib plot object.
"""
# set the font to Times, rendered with Latex
plt.rc('font', **{'family': 'serif', 'serif': ['Times']})
plt.rc('text', usetex=True)
# parse the composition space endpoints
endpoints_line = self.lines[0].split()
endpoints = []
for word in endpoints_line[::-1]:
if word == 'endpoints:':
break
else:
endpoints.append(Composition(word))
if len(endpoints) < 2:
print('There must be at least 2 endpoint compositions to make a '
'phase diagram.')
quit()
# parse the compositions and total energies of all the structures
compositions = []
total_energies = []
for i in range(4, len(self.lines)):
line = self.lines[i].split()
compositions.append(Composition(line[1]))
total_energies.append(float(line[2]))
# make a list of PDEntries
pdentries = []
for i in range(len(compositions)):
pdentries.append(PDEntry(compositions[i], total_energies[i]))
# make a CompoundPhaseDiagram
compound_pd = CompoundPhaseDiagram(pdentries, endpoints)
# make a PhaseDiagramPlotter
pd_plotter = PDPlotter(compound_pd, show_unstable=100)
return pd_plotter.get_plot(label_unstable=False)
gy.append(x2 * math.sqrt(3.0) / 2.0)
grid_triang = tri.Triangulation(gx, gy)
fields_strings = [
"xas normalization to min and max -> normalization factor",
"xas xmcd minmax -> xmcd max",
"xas xmcd minmax -> xmcd_min",
'sum([xmcd max - xmcd min]*f*N) ~ "total magnetic moment"',
]
norms, xmcd_diffs, mag = {}, {}, 0.0
factors = {"Co": 1.7 / 3.2 / 0.6, "Fe": 2.1 / 3.9 / 0.6}
for fldidx, fields_str in enumerate(fields_strings):
fields = fields_str.split(" -> ")
for elidx, elem in enumerate(chemsys[:-1]):
print fields_str, elem
plt = plotter.get_plot()
title = elem + ": " + fields_str
if fldidx == 3 and elidx == 1:
title = fields_str
plt.suptitle(title, fontsize=24)
plt.triplot(grid_triang, "k:")
# heatmap
x, y, z = [], [], []
for idx, (comp, cid) in enumerate(comps_cids):
comp_str = comp if args.dev else doc[cid]["_id"]
composition = Composition(comp_str)
x0, x1, x2 = [
composition.get_atomic_fraction(el) for el in chemsys
]
x.append(x0 +
gx.append(x0+x2/2.) # NOTE x0 might need to be replace with x1
gy.append(x2*math.sqrt(3.)/2.)
grid_triang = tri.Triangulation(gx, gy)
fields_strings = [
'xas normalization to min and max -> normalization factor',
'xas xmcd minmax -> xmcd max', 'xas xmcd minmax -> xmcd_min',
'sum([xmcd max - xmcd min]*f*N) ~ "total magnetic moment"'
]
norms, xmcd_diffs, mag = {}, {}, 0.
factors = {'Co': 1.7/3.2/0.6, 'Fe': 2.1/3.9/0.6}
for fldidx,fields_str in enumerate(fields_strings):
fields = fields_str.split(' -> ')
for elidx,elem in enumerate(chemsys[:-1]):
print fields_str, elem
plt = plotter.get_plot()
title = elem+': '+fields_str
if fldidx == 3 and elidx == 1: title = fields_str
plt.suptitle(title, fontsize=24)
plt.triplot(grid_triang, 'k:')
# heatmap
x, y, z = [], [], []
for idx,(comp,cid) in enumerate(comps_cids):
comp_str = comp if args.dev else doc[cid]['_id']
composition = Composition(comp_str)
x0, x1, x2 = [composition.get_atomic_fraction(el) for el in chemsys]
x.append(x0+x2/2.) # NOTE x0 might need to be replace with x1
y.append(x2*math.sqrt(3.)/2.)
if fldidx < 3:
zval = mpfile.document[comp_str]['{} XMCD'.format(elem)][fields[0]][fields[1]]
