def record_cmd_print(fdir, readme, dir=None):
dir = fdir
#readme['finished at'] = '{}'.format(datetime.now())
if not os.path.isdir(dir):
dir = '/'.join(fdir.split('/')[0:-1])
if dir == "": dir = "./"
with open (dir+"/readme", "w") as fp:
myjsonout(readme, fp, indent="", comma="")
if "ERROR" in readme.keys():
error ="**********FATAL ERROR encountered, you may check readme and E-V plot in the folder "+dir+"/figures"
volumes = readme['E-V']['volumes']
energies = readme['E-V']['energies']
folder = os.path.join(dir,'figures')
if not os.path.exists(folder): os.mkdir(folder)
thermoplot(folder,"0 K total energies (eV/atom)",volumes, energies, plottitle=dir, lp=True)
with open (os.path.join(dir,"ERROR"), "w") as fp:
fp.write('{}\n'.format(readme['ERROR']))
if dir!=None:
fp.write('{}\n'.format(error))
print ("\n", error, "\n")
else:
if os.path.exists(os.path.join(dir,"ERROR")): os.remove(os.path.join(dir,"ERROR"))
with open ("runs.log", "a") as fp:
try:
#fp.write('phonon quality={}, LTC zigzag={}'.format(readme['phonon quality'], readme['LTC quality']))
fp.write('phonon quality={}'.format(readme['phonon quality']))
if os.path.exists(dir+'/fitF'): fp.write(', for fitF is on: {}\n'.format(dir))
else: fp.write(', for fitF is off: {}\n'.format(dir))
except:
fp.write('FATAL ERROR in {}\n'.format(dir))
pass
def EV_find(self):
evdirhome = 'E-V'
if not os.path.exists(evdirhome): os.mkdir(evdirhome)
hit = []
count = []
phases = []
volumes = []
ITEMS = []
potname = []
fp_ev = open(os.path.join(evdirhome, "E-V.dat"), "w")
for i in self.items:
mm = i['metadata']['tag']
els = i['elements']
if self.skipby("", mm, els=els): continue
if self.hit_condition is not None:
if mm not in self.hit_condition: continue
if mm in hit:
volume = i['output']['structure']['lattice']['volume']
if volume not in volumes[hit.index(mm)]:
volumes[hit.index(mm)].append(volume)
count[hit.index(mm)] += 1
else:
ITEMS.append(i)
hit.append(mm)
count.append(1)
volumes.append([i['output']['structure']['lattice']['volume']])
potsoc = get_used_pot(i)
structure = Structure.from_dict(i['output']['structure'])
formula_pretty = structure.composition.reduced_formula
try:
formula2composition(formula_pretty)
except:
formula_pretty = reduced_formula(
structure.composition.alphabetical_formula)
sa = SpacegroupAnalyzer(structure)
phasename = formula_pretty+'_'\
+ sa.get_space_group_symbol().replace('/','.')+'_'+str(sa.get_space_group_number())
potname.append(potsoc)
if phasename in phases:
for jj in range(10000):
nphasename = phasename + "#" + str(jj)
if nphasename in phases: continue
phasename = nphasename
break
phases.append(phasename)
blank_lines = False
for i, mm in enumerate(hit):
if self.hit_condition is not None:
if mm not in self.hit_condition: continue
if self.qhamode == 'phonon':
if self.hit_count[mm] < self.nV: continue
if count[i] < self.nV: continue
if self.skipby(phases[i], mm): continue
EV, POSCAR, INCAR = get_rec_from_metatag(self.vasp_db, mm)
metadata = {'tag': mm}
pname = phases[i].split('#')
if len(pname) > 1:
phases[i] = pname[0] + potname[i] + EV[
'MagState'] + '#' + pname[1]
else:
phases[i] = pname[0] + potname[i] + EV['MagState']
if EV['natoms'] < self.natoms: continue
sys.stdout.write('{}, static: {:>2}, natoms: {:>3}, {}\n'.format(
metadata, count[i], EV['natoms'], phases[i]))
folder = os.path.join(evdirhome, phases[i])
if not os.path.exists(folder): os.mkdir(folder)
with open(os.path.join(folder, 'POSCAR'), 'w') as fp:
fp.write(POSCAR)
readme = {}
readme['E-V'] = EV
readme['INCAR'] = INCAR
readme['POSCAR'] = POSCAR
natoms = readme['E-V']['natoms']
with open(os.path.join(folder, 'readme'), 'w') as fp:
myjsonout(readme, fp, indent="", comma="")
i_energies = np.array(EV['energies']) / natoms
i_volumes = np.array(EV['volumes']) / natoms
val, idx = min((val, idx) for (idx, val) in enumerate(i_energies))
if blank_lines: print("\n", file=fp_ev)
blank_lines = True
print("#phase:", phases[i], file=fp_ev)
print("#metadata:", mm, file=fp_ev)
print("#natoms:", natoms, file=fp_ev)
elist = ['Fe', 'Cu', 'Se', 'Al', 'Ni', 'Co', 'Pt', 'Ta', 'O']
el = []
nel = []
if len(EV['magmoms']) > 0:
fp_ev.write("#magmoms:")
magmoms = EV['magmoms'][idx]
m0 = magmoms[0]
n0 = 1
for j in range(1, len(magmoms)):
if magmoms[j] == m0:
n0 += 1
else:
if n0 == 1: fp_ev.write('{},'.format(m0))
else: fp_ev.write('{}*{},'.format(n0, m0))
idx = len(el) % len(elist)
el.append(elist[idx])
nel.append(n0)
n0 = 1
m0 = magmoms[j]
if n0 == 1: fp_ev.write('{}\n'.format(m0))
else: fp_ev.write('{}*{}\n'.format(n0, m0))
idx = len(el) % len(elist)
el.append(elist[idx])
nel.append(n0)
lines = [l for l in POSCAR.split('\n') if l != ""]
with open(os.path.join(folder, phases[i] + '.VASP'),
'w') as fp:
for j in range(0, 5):
print(lines[j], file=fp)
for j in range(len(el)):
fp.write(' {}'.format(el[j]))
fp.write('\n')
for j in range(len(nel)):
fp.write(' {}'.format(nel[j]))
fp.write('\n')
print(lines[7], file=fp)
for j in range(8, len(lines)):
print(lines[j],
float(list(magmoms[j - 8].values())[0]),
file=fp)
for j in range(len(i_volumes)):
print(i_volumes[j], i_energies[j], file=fp_ev)
thermoplot(folder, "0 K total energies (eV/atom)", i_volumes,
i_energies)
def EV_find(self):
hit = []
count = []
phases = []
volumes = []
ITEMS = []
for i in self.items:
try:
mm = i['metadata']['tag']
except:
continue
if mm in hit:
volume = i['output']['structure']['lattice']['volume']
if volume not in volumes[hit.index(mm)]:
volumes[hit.index(mm)].append(volume)
count[hit.index(mm)] += 1
#if mm=='5252ccc3-e8da-499f-bb9e-9cf7eb1c5370': print("eeeeeeeee",mm, pot)
else:
ITEMS.append(i)
hit.append(mm)
count.append(1)
volumes.append([i['output']['structure']['lattice']['volume']])
pot = i['input']['pseudo_potential']['functional'].upper()
#if mm=='5252ccc3-e8da-499f-bb9e-9cf7eb1c5370': print("eeeeeeeee",mm, pot)
if pot == "":
pot = i['orig_inputs']['potcar']['functional'].upper()
if pot == 'Perdew-Zunger81'.upper(): pot = "LDA"
try:
pot += "+" + i['input']['GGA']
except:
pass
if i['input']['is_hubbard']: pot += '+U'
try:
if i['input']['incar']['LSORBIT']: potsoc = pot + "SOC"
except:
potsoc = pot
structure = Structure.from_dict(i['output']['structure'])
natoms = len(structure.sites)
formula_pretty = structure.composition.reduced_formula
try:
formula2composition(formula_pretty)
except:
formula_pretty = reduced_formula(
structure.composition.alphabetical_formula)
sa = SpacegroupAnalyzer(structure)
phasename = formula_pretty+'_'\
+ sa.get_space_group_symbol().replace('/','.')+'_'+str(sa.get_space_group_number())+potsoc
if phasename in phases:
for jj in range(10000):
nphasename = phasename + "#" + str(jj)
if nphasename in phases: continue
phasename = nphasename
break
phases.append(phasename)
for i, m in enumerate(hit):
if count[i] < self.nV: continue
if self.skipby(phases[i]): continue
sys.stdout.write('{}, static: {:>2}, {}\n'.format(
m, count[i], phases[i]))
EV, POSCAR, INCAR = get_rec_from_metatag(self.vasp_db, m)
evdir = './E-V/'
if not os.path.exists(evdir): os.mkdir(evdir)
folder = evdir + phases[i]
if not os.path.exists(folder): os.mkdir(folder)
with open(folder + '/POSCAR', 'w') as fp:
fp.write(POSCAR)
readme = {}
readme['E-V'] = EV
readme['INCAR'] = INCAR
readme['POSCAR'] = POSCAR
with open(folder + '/readme', 'w') as fp:
myjsonout(readme, fp, indent="", comma="")
thermoplot(folder, "0 K total energies (eV/atom)", EV['volumes'],
EV['energies'])