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")
# 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=[]
ehull_arr=[]
for d in data:
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')
##
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=[]
ehull_arr=[]
for d in data:
