def step2(**kwargs):
"""
post process:
get energies from the jobs in the previous step and
generate the phase diagram
"""
chkfile = kwargs['checkpoint_files'][0]
all_jobs = jobs_from_file(chkfile)
entries = []
# add endpoint data
Al = Composition("Al1O0")
energy_al = -3.36
O = Composition("Al0O1")
energy_o = -2.58
entries.append(PDEntry(Al, energy_al))
entries.append(PDEntry(O, energy_o))
# get data and create entries
for job in all_jobs:
comp = job.vis.mplmp.structure.composition
energy = job.final_energy
entries.append(PDEntry(comp, energy))
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd, show_unstable=True)
plotter.write_image('Al_O_phasediagram.jpg')
return None
def step2(**kwargs):
"""
post process:
get energies from the jobs in the previous step and
generate the phase diagram
"""
chkfile = kwargs['checkpoint_files'][0]
all_jobs = jobs_from_file(chkfile)
entries = []
# add endpoint data
Al = Composition("Al1O0")
energy_al = -3.36
O = Composition("Al0O1")
energy_o = -2.58
entries.append(PDEntry(Al, energy_al))
entries.append(PDEntry(O, energy_o))
# get data and create entries
for job in all_jobs:
comp = job.vis.mplmp.structure.composition
energy = job.final_energy
entries.append(PDEntry(comp, energy))
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd, show_unstable=True)
plotter.write_image('Al_O_phasediagram.jpg')
return None
def pd_plot(system='Ni-Nb'):
object_file = pickle.load(open('form_en_gbsave_v25h', "rb"))
output = []
l = system.split('-')
comb = []
for i in range(len(l)):
comb += itertools.combinations(l, i + 1)
comb_list = [list(t) for t in comb]
# comb_list=['Zn','O','Zn-O']
with MPRester("") as m:
for i in comb_list:
dd = '-'.join(i)
print dd
data = m.get_data(dd)
for d in data:
x = {}
x['material_id'] = str(d['material_id'])
structure = m.get_structure_by_material_id(x['material_id'])
X = get_comp_descp(struct=structure)
print "X", X
pred = object_file.predict(X)
print structure.composition.reduced_formula, pred[0], d[
'formation_energy_per_atom'], str(d['material_id'])
output.append(
PDEntry(Composition(structure.composition),
float(pred[0])))
pd = PhaseDiagram(output)
print output
plotter = PDPlotter(pd, show_unstable=True)
name = str(system) + str('_phasediagram.png')
plotter.write_image(name, image_format="png")
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 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 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)
def test_dim1(self):
#Ensure that dim 1 PDs can eb generated.
for el in ["Li", "Fe", "O2"]:
entries = [
e for e in self.entries if e.composition.reduced_formula == el
]
pd = PhaseDiagram(entries)
self.assertEqual(len(pd.stable_entries), 1)
a = PDAnalyzer(pd)
for e in entries:
decomp, ehull = a.get_decomp_and_e_above_hull(e)
self.assertGreaterEqual(ehull, 0)
plotter = PDPlotter(pd)
lines, stable_entries, unstable_entries = plotter.pd_plot_data
self.assertEqual(lines[0][1], [0, 0])
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")])
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")])
el1) and x['forcefield'] == ff:
output.append(
PDEntry(Composition(x['composition']),
float(x['totenergy'])))
return output
##Used for phase diagram
entries = get_entries_from_json(key='search',
value='Cu-H-O',
out='energy',
ff='ffield.CuOCH.comb3',
json_f='data.json',
PD=True)
#entries=get_entries_from_json(key='search',value='Fe-H-O',out='energy',ff='ffield.reax.Fe_O_C_H',json_f='data.json',PD=True)
#entries=get_entries_from_json(key='search',value='Al-Ni',out='energy',ff='Mishin-Ni-Al-2009.eam.alloy',json_f='data.json',PD=True)
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd, show_unstable=False)
#plotter = PDPlotter(pd, show_unstable=True)
#print plotter.pd_plot_data
print plotter.get_plot
name = str('Cu-H-Ocomb') + str('_LMP_phasediagram.png')
plotter.write_image(name, image_format="png")
##
##INDIVIDUAL
#output=get_entries_from_json(key='mpid',value='mp-13',out='energy',ff='ffield.reax.Fe_O_C_H',json_f='data.json')
get_entries_from_json(key='mpid', value='mp-134', out='Bv', json_f='data.json')
##
projection=projection,
collection="compositions",
contributor_only=False,
)[0]
# append spectra to output PDF
plotly_urls = doc[cid]["LBNL"][str(cid)]["plotly_urls"]
for plotly_url in plotly_urls:
image_bytes = requests.get("{}.pdf".format(plotly_url)).content
merger.append(StringIO(image_bytes))
# get phase diagram from MP and append to PDF
chemsys = ["Co", "Fe", "V"] # ["Ni", "Fe", "Pt"] # alphabetic
cmap = ["Reds", "Blues", "Greens"]
entries = mpr.get_entries_in_chemsys(chemsys)
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd)
# grid
gx, gy = [], []
n = 20
fn = float(n)
for i in range(0, n, 1):
for k in range(n - i + 1, 0, -1):
j = n + 1 - i - k
x0, x1, x2 = i / fn, k / fn, j / fn
gx.append(x0 +
x2 / 2.0) # NOTE x0 might need to be replace with x1
gy.append(x2 * math.sqrt(3.0) / 2.0)
grid_triang = tri.Triangulation(gx, gy)
fields_strings = [
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)
#for val in content:
# if val != '' and val !='\n' and val !='\r\n':
# list_el.append(val)
# for i in range(0,len(list_el)):
# if i!=0:
# element_ff.append(list_el[i])
# print ff,' ',element_ff
element_ff=['Ti','O','N']
with MPRester(MAPI_KEY) as m:
data = m.get_entries_in_chemsys(element_ff,inc_structure='final', property_data=["unit_cell_formula","material_id","icsd_id","spacegroup","energy_per_atom","formation_energy_per_atom","pretty_formula","band_gap","total_magnetization","e_above_hull"])
if (len(element_ff)>1):
try:
entries = m.get_entries_in_chemsys(element_ff)
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd, show_unstable=True)
image=str(ff)+str("_DFT")+str(".jpg")
plotter.write_image(image)
except:
pass
structures=[]
structures_cvn=[]
icsd_arr=[]
mp_arr=[]
sg_arr=[]
enp_arr=[]
fenp_arr=[]
pf_arr=[]
ucf_arr=[]
bg_arr=[]
tm_arr=[]
doc[cid] = mpr.query_contributions(
criteria=criteria, projection=projection,
collection='compositions', contributor_only=False
)[0]
# append spectra to output PDF
plotly_urls = doc[cid]['LBNL'][str(cid)]['plotly_urls']
for plotly_url in plotly_urls:
image_bytes = requests.get('{}.pdf'.format(plotly_url)).content
merger.append(StringIO(image_bytes))
# get phase diagram from MP and append to PDF
chemsys = ["Co", "Fe", "V"]#["Ni", "Fe", "Pt"] # alphabetic
cmap = ['Reds', 'Blues', 'Greens']
entries = mpr.get_entries_in_chemsys(chemsys)
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd)
# grid
gx, gy = [], []
n = 20
fn = float(n)
for i in range(0, n, 1):
for k in range(n-i+1, 0, -1):
j = n+1-i-k
x0, x1, x2 = i/fn, k/fn, j/fn
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',
Composition(formula).reduced_formula
]
relevant_entries = sorted(relevant_entries,
key=lambda e: e.energy_per_atom)
return relevant_entries[0]
def get_comp_entries(formula, all_entries):
relevant_entries = [
entry for entry in all_entries if entry.composition.reduced_formula ==
Composition(formula).reduced_formula
]
return relevant_entries
def find_entry_index(formula, all_entries):
entry_index = [
all_entries.index(entry) for entry in all_entries
if entry.composition.reduced_formula == Composition(
formula).reduced_formula
]
return entry_index
rester = MPRester(
'5TxDLF4Iwa7rGcAl') #Generate your own key from materials project..
mp_entries = rester.get_entries_in_chemsys(["Li", "Fe", "O", "S"])
pd = PhaseDiagram(mp_entries)
plotter = PDPlotter(pd)
plotter.show()
#content=(lines[3]).split("' '|\n|\r\n")
for val in content:
if val != '' and val !='\n' and val !='\r\n':
list_el.append(val)
for i in range(0,len(list_el)):
if i!=0:
element_ff.append(list_el[i])
# print ff,' ',element_ff
with MPRester(MAPI_KEY) as m:
data = m.get_entries_in_chemsys(element_ff,inc_structure='final', property_data=["unit_cell_formula","material_id","icsd_id","spacegroup","energy_per_atom","formation_energy_per_atom","pretty_formula","band_gap","total_magnetization","e_above_hull"])
if (len(element_ff)>1):
try:
entries = m.get_entries_in_chemsys(element_ff)
pd = PhaseDiagram(entries)
plotter = PDPlotter(pd, show_unstable=True)
image=str(ff)+str("_DFT")+str(".jpg")
plotter.write_image(image)
except:
pass
structures=[]
structures_cvn=[]
icsd_arr=[]
mp_arr=[]
sg_arr=[]
enp_arr=[]
fenp_arr=[]
pf_arr=[]
ucf_arr=[]
bg_arr=[]
tm_arr=[]
]
return relevant_entries
def find_entry_index(formula, all_entries):
entry_index = [
all_entries.index(entry) for entry in all_entries
if entry.composition.reduced_formula == Composition(
formula).reduced_formula
]
return entry_index
rester = MPRester(
'5TxDLF4Iwa7rGcAl') #Generate your own key from materials project..
mp_entries = rester.get_entries_in_chemsys(["Li", "Fe", "O", "S"])
pd = PhaseDiagram(mp_entries)
plotter = PDPlotter(pd)
analyzer = PDAnalyzer(pd)
li_entries = [e for e in mp_entries if e.composition.reduced_formula == "Li"]
uli0 = min(li_entries, key=lambda e: e.energy_per_atom).energy_per_atom
el_profile = analyzer.get_element_profile(Element("Li"),
Composition("Li2FeSO"))
for i, d in enumerate(el_profile):
voltage = -(d["chempot"] - uli0)
print("Voltage: %s V" % voltage)
print(d["reaction"])
print("")
try:
# Create phase diagram!
with warnings.catch_warnings():
warnings.simplefilter("ignore")
phase = PhaseDiagram(Computed_entries)
except Exception as e:
result["error"] = str(e)
json_dir = output_Path + "/" + "output.json"
with open(json_dir, "w") as outfile:
json.dump(result, outfile)
print(result)
exit()
# Plot!
plotter = PDPlotter(phase, show_unstable=True)
#plotter.show()
lines, stable, unstable = plotter.pd_plot_data
### NEED_TO_CHANGE ###
plt = plotter.get_plot()
f = plt.gcf()
f.set_size_inches((15, 12))
fig_dir = output_Path + "/" + "phase.png"
plt.savefig(fig_dir, image_format="png")
# Analyze phase diagram!
pda = PDAnalyzer(phase)
# elements : enum Element to array
