def convergence_check(target,be1,be2,ENCONV,PRCONV,FOCONV):
path_list = [target,be1,be2]
nion = int(pygrep('NION',target+'/OUTCAR',0,0).splitlines()[-1].split()[11])
# nion = int(subprocess.check_output(['grep','NION',target+'/OUTCAR']).splitlines()[-1].split()[11])
# Read energy, pressure and force
ENERGY = []
PRESS = []
FORCE = []
for path in path_list:
if ENCONV > 0:
ENERGY.append(float(pygrep('free ',path+'/OUTCAR',0,0).splitlines()[-1].split()[4]))
# ENERGY.append(float(subprocess.check_output(['grep','free ',path+'/OUTCAR']).splitlines()[-1].split()[4]))
if PRCONV > 0:
line = pygrep('in kB',path+'/OUTCAR',0,0).splitlines()[-1].split()
# line = subprocess.check_output(['grep','in kB',path+'/OUTCAR']).splitlines()[-1].split()
if len(line) == 8:
PRESS.append([float(x) for x in line[2:]])
else:
PRESS.append([99999.,99999.,99999.,99999.,99999.,99999.])
if FOCONV > 0:
force_lines = pygrep('TOTAL-F',path+'/OUTCAR',0,nion+1).splitlines()[2:nion+2]
# force_lines = subprocess.check_output(['grep','TOTAL-F',path+'/OUTCAR','-A',str(nion+1)]).splitlines()[2:nion+2]
FORCE_one_sample = []
for line in force_lines:
if len(line.split()) == 6:
FORCE_one_sample.append([float(x) for x in line.split()[3:6]])
else:
FORCE_one_sample.append([999.,999.,999.])
FORCE.append(FORCE_one_sample)
converge = 0
# Convergence check for energy/atom
if ENCONV > 0 and (abs(ENERGY[0]-ENERGY[1])/nion > ENCONV or abs(ENERGY[0]-ENERGY[2])/nion > ENCONV) :
make_amp2_log(target,'Energy is not yet converged')
return 1
sys.exit()
# Convergence check for pressure
if PRCONV > 0 :
for i in range(6) :
if abs(PRESS[0][i]-PRESS[1][i]) > PRCONV or abs(PRESS[0][i]-PRESS[2][i]) > PRCONV :
# if abs(PRESS[0][i]-PRESS[1][i])/abs(PRESS[0][i]) > 0.1 or abs(PRESS[0][i]-PRESS[2][i])/abs(PRESS[0][i]) > 0.1:
# make_amp2_log(target,'Pressure is not yet converged')
# return 1
# sys.exit()
make_amp2_log(target,'Pressure is not yet converged')
return 1
sys.exit()
# Convergence check for force
if FOCONV > 0 :
for i in range(nion):
for j in range(3) :
if abs(FORCE[0][i][j]-FORCE[1][i][j]) > FOCONV or abs(FORCE[0][i][j]-FORCE[2][i][j]) > FOCONV :
make_amp2_log(target,'Force is not yet converged')
return 1
sys.exit()
return 0
def max_force(outcar_path):
nion = int(pygrep('NION',outcar_path,0,0).split()[-1])
force_list = pygrep('TOTAL-FORCE',outcar_path,0,nion+1).splitlines()
max_f = [0,[0,0,0]]
for line in force_list[2:]:
if len(line.split()) == 6:
force = [float(x) for x in line.split()[3:6]]
else:
force = [999.,999.,999.]
if dist_point(force,[0,0,0]) > max_f[0]:
max_f = [dist_point(force,[0,0,0]),force]
return max_f
def max_force(outcar_path):
nion = int(pygrep('NION',outcar_path,0,0).split()[-1])
# nion = int(subprocess.check_output(['grep','NION',outcar_path]).split()[-1])
force_list = pygrep('TOTAL-FORCE',outcar_path,0,nion+1).splitlines()
# force_list = subprocess.check_output(['grep','-A'+str(nion+1),'TOTAL-FORCE',outcar_path]).splitlines()
max_f = [0,[0,0,0]]
for line in force_list[2:]:
if len(line.split()) == 6:
force = [float(x) for x in line.split()[3:6]]
else:
force = [999.,999.,999.]
if dist_point(force,[0,0,0]) > max_f[0]:
max_f = [dist_point(force,[0,0,0]),force]
return max_f
def write_conv_result(target,logfile):
head = target.split('/')[-1]
energy = float(pygrep('free ',target+'/OUTCAR',0,0).splitlines()[-1].split()[4])
line = pygrep('in kB',target+'/OUTCAR',0,0).splitlines()[-1].split()
if len(line) == 8:
press = [float(x) for x in line[2:]]
else:
press = [99999.,99999.,99999.,99999.,99999.,99999.]
with open(logfile,'a') as log:
log.write(head+': '+str(energy)+' eV')
log.write('\t/ ')
for ll in press:
log.write(str(ll)+' ')
log.write('kB\n')
def make_incar(poscar, target, src_path, max_nelm):
from module_vasprun import wincar
pos = open(poscar, 'r').readlines()
atom_z = pos[5].split()
atom_cnt = pos[6].split()
nelect = 0
for j in range(len(atom_z)):
pot_line = pygrep('ZVAL', target + '/INPUT0/POTCAR_GGA', 0,
0).splitlines()[j].split()[5]
# pot_line = subprocess.check_output(['grep','ZVAL',target+'/INPUT0/POTCAR_GGA']).splitlines()[j].split()[5]
nelect = nelect + int(atom_cnt[j]) * int(float(pot_line))
# Set maximum number of electronic steps
nelm = max_nelm
# if nelect > int(max_nelm/3) :
# nelm = max_nelm
# else :
# nelm = nelect*3
# if nelm < 30:
# nelm = 30
wincar(src_path + '/INCAR0', target + '/INPUT0/INCAR0',
[['SYSTEM', target.split('/')[-1]], ['NELM', str(nelm)]], [])
with open(target + '/INPUT0/INCAR', 'w') as out_inc:
with open(target + '/INPUT0/INCAR0', 'r') as f:
out_inc.write(f.read())
with open(target + '/INPUT0/U_note', 'r') as f:
out_inc.write(f.read())
with open(target + '/INPUT0/spin_note', 'r') as f:
out_inc.write(f.read())
def check_half_metal(target):
spin = pygrep('ISPIN', target + '/OUTCAR', 0, 0).split()[2]
ncl = pygrep('NONCOL', target + '/OUTCAR', 0, 0).split()[2]
if not (spin == '2' and ncl == 'F'):
half_metal = 0
else:
[KPT, Band, nelect] = EIGEN_to_array(target + '/EIGENVAL', spin)
fermi = get_fermi_level(Band, nelect, ncl)
half_metal = 0
for i in range(int(spin)):
metal = 0
for n in range(len(Band)):
single_band = [Band[n][x][i] for x in range(len(KPT))]
band_max = max(single_band)
band_min = min(single_band)
if band_max > fermi and band_min < fermi:
metal = 1
if metal == 0:
half_metal = 1
return half_metal
def plot_band_structure(spin, Band, fermi, xtic_file, xlabel_file, plot_range,
target):
# make band.dat
make_band_dat(xtic_file, Band, spin, target)
# make band.in
nband = len(Band)
if pyhead(target + '/Band_gap.log', 1).split()[2] == 'is':
gap = 0
fermi = str(fermi)
else:
gap = round(float(pyhead(target + '/Band_gap.log', 1).split()[2]))
fermi = pygrep('VBM', target + '/Band_gap.log', 0,
0).splitlines()[0].split()[-2]
title = target.split('/')[-2]
make_band_in(title, xlabel_file, fermi, gap, nband, spin, plot_range,
target)
def make_incar_note(poscar, target, soc_target, u_value, magmom_def, src_path):
# U-J values for LDA+U method
TMU = yaml.safe_load(open(src_path + '/U_table.yaml', 'r'))
if not u_value is None:
if 'All' in u_value.keys():
for u_key in TMU.keys():
TMU[u_key] = u_value['All']
elif 'all' in u_value.keys():
for u_key in TMU.keys():
TMU[u_key] = u_value['all']
for u_key in u_value.keys():
TMU[u_key] = u_value[u_key]
for u_key in TMU.keys():
if TMU[u_key] == 0:
TMU.pop(u_key)
if soc_target is None:
SOC = []
else:
SOC = soc_target
TMd = [
'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Y', 'Zr',
'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'Hf', 'Ta', 'W', 'Re',
'Os', 'Ir', 'Pt', 'Au', 'Hg'
]
TMf = [
'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er',
'Tm', 'Yb', 'Lu'
]
NVAL = {
'H': 1,
'He': 0,
'Li': 1,
'Be': 2,
'B': 3,
'C': 4,
'N': 5,
'O': 6,
'F': 7,
'Ne': 0,
'Na': 1,
'Mg': 2,
'Al': 3,
'Si': 4,
'P': 5,
'S': 6,
'Cl': 7,
'Ar': 0,
'K': 1,
'Ca': 2,
'Sc': 3,
'Ti': 4,
'V': 5,
'Cr': 6,
'Mn': 7,
'Fe': 8,
'Co': 9,
'Ni': 10,
'Cu': 11,
'Zn': 2,
'Ga': 3,
'Ge': 4,
'As': 5,
'Se': 6,
'Br': 7,
'Kr': 0,
'Rb': 1,
'Sr': 2,
'Y': 3,
'Zr': 4,
'Nb': 5,
'Mo': 6,
'Tc': 7,
'Ru': 8,
'Rh': 9,
'Pd': 10,
'Ag': 11,
'Cd': 2,
'In': 3,
'Sn': 4,
'Sb': 5,
'Te': 6,
'I': 7,
'Xe': 0,
'Cs': 1,
'Ba': 2,
'La': 3,
'Ce': 4,
'Pr': 5,
'Nd': 6,
'Pm': 7,
'Sm': 8,
'Eu': 9,
'Gd': 10,
'Tb': 11,
'Dy': 12,
'Ho': 13,
'Er': 14,
'Tm': 15,
'Yb': 16,
'Lu': 17,
'Hf': 4,
'Ta': 5,
'W': 6,
'Re': 7,
'Os': 8,
'Ir': 9,
'Pt': 10,
'Au': 11,
'Hg': 12,
'Tl': 3,
'Pb': 4,
'Bi': 5,
'Po': 6,
'At': 7,
'Rn': 0,
'Ac': 3,
'Th': 4,
'Pa': 5,
'U': 6,
'Pu': 8,
'No': 16
}
pos = open(poscar, 'r').readlines()
atom_z = pos[5].split()
atom_cnt = pos[6].split()
# Check U_note for 3d transition metals
u_note = ""
u_val1 = ""
u_val2 = ""
u_on = 0
mag_on = 0
soc_on = 0
nelect = 0
for j in range(len(atom_z)):
pot_line = pygrep('ZVAL', target + '/INPUT0/POTCAR_GGA', 0,
0).splitlines()[j].split()[5]
# pot_line = subprocess.check_output(['grep','ZVAL',target+'/INPUT0/POTCAR_GGA']).splitlines()[j].split()[5]
nelect = nelect + int(atom_cnt[j]) * int(float(pot_line))
if atom_z[j] in TMd:
if atom_z[j] in TMU:
if u_on == 0:
u_on = 1
u_note = u_note + ' 2'
u_val1 = u_val1 + ' ' + str(TMU[atom_z[j]] + 1.0)
u_val2 = u_val2 + ' 1.0'
else:
u_note = u_note + ' -1'
u_val1 = u_val1 + ' 0.0'
u_val2 = u_val2 + ' 0.0'
mag_on = 1
elif atom_z[j] in TMf:
if atom_z[j] in TMU:
u_on = 2
u_note = u_note + ' 3'
u_val1 = u_val1 + ' ' + str(TMU[atom_z[j]] + 1.0)
u_val2 = u_val2 + ' 1.0'
else:
u_note = u_note + ' -1'
u_val1 = u_val1 + ' 0.0'
u_val2 = u_val2 + ' 0.0'
mag_on = 1
else:
u_note = u_note + ' -1'
u_val1 = u_val1 + ' 0.0'
u_val2 = u_val2 + ' 0.0'
if atom_z[j] in SOC:
soc_on = 1
# Checking metallic compounds (If all components are metallic elements, we do not impose +U.)
non_metal = [
'H', 'He', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Si', 'P', 'S', 'Cl', 'Ar',
'Ge', 'As', 'Se', 'Br', 'Kr', 'Sb', 'Te', 'I', 'Xe', 'At', 'Rn'
]
if not any([x in non_metal for x in atom_z]):
u_on = 0
maxmix = str(2 + 2 * u_on)
with open(target + '/INPUT0/U_note', 'w') as out:
if not u_on == 0:
out.write(
'\n LDA+U calculation:\n LDAU = .TRUE. !Treat L(S)DA+U\n LDAUTYPE = 2\n'
)
out.write(' LDAUL =' + u_note + '\n')
out.write(' LDAUU =' + u_val1 + '\n')
out.write(' LDAUJ =' + u_val2 + '\n')
out.write(' LDAUPRINT = 0\n LMAXMIX = ' + maxmix + '\n\n')
oxi_check = 0 # 0: no spin-polarizaton, 1: use MAGMOM, 2: no MAGMOM
tot_atom = sum([int(x) for x in atom_cnt])
if mag_on == 1 and os.path.isfile(target + '/INPUT0/final.dat'):
make_amp2_log(target + '/INPUT0', 'MAGMOM is set by cif file\n')
with open(target + '/INPUT0/final.dat', 'r') as fin_file:
final = []
for line in fin_file.readlines():
final.append(line.split())
if len(final[0]) == 3:
mag = [] # [atom_oxi, atom, mag, n_mag]
fin_idx = 0
for pos_idx in range(9, tot_atom + 9):
if pos_idx != 9 and pos[pos_idx].split()[-1] == mag[-1][0]:
mag[-1][3] = mag[-1][3] + 1
else:
# if len(final[fin_idx][2]) < 2 :
if len(final[fin_idx][2]) < 2 or float(
final[fin_idx][2][:-1]) == 0.0:
oxi_check = 2 # No oxi information
break
mag.append([
final[fin_idx][1], final[fin_idx][0],
float(final[fin_idx][2][-1] + final[fin_idx][2][:-1]),
1
]) # float part: number sign --> sign number
fin_idx = fin_idx + 1
if oxi_check != 2:
for j in range(len(mag)):
if mag[j][2] > 0:
mag[j][2] = NVAL[mag[j][1]] - mag[j][2]
if mag[j][1] in TMd and mag[j][2] > 5 and mag[j][
2] <= 10:
mag[j][2] = 10 - mag[j][2]
elif mag[j][1] in TMf and mag[j][2] > 7 and mag[j][
2] <= 14:
mag[j][2] = 14 - mag[j][2]
elif (not mag[j][1] in TMd) and (not mag[j][1] in TMf):
if mag[j][2] == 2:
mag[j][2] = 0.0
if mag[j][2] > 0:
mag[j][2] = mag[j][2] + 0.5
oxi_check = 1
else:
mag[j][2] = 0.0
# write spin note for unpaired spin electrons
if mag_on == 1:
if not os.path.isfile(target + '/INPUT0/final.dat') or not len(
final[0]) == 3 or oxi_check == 2:
make_amp2_log(target + '/INPUT0',
'MAGMOM is set by magmom default value\n')
oxi_check = 1
mag = []
for j in range(len(atom_z)):
mag.append([atom_z[j], '', 0, atom_cnt[j]])
if atom_z[j] in TMd:
mag[-1][2] = magmom_def
elif atom_z[j] in TMf:
mag[-1][2] = magmom_def
with open(target + '/INPUT0/spin_note', 'w') as out2:
if oxi_check == 1:
out2.write(
" Spin polarized caculation w/ initial magnetic moment:\n")
out2.write(" ISPIN = 2\n MAGMOM = ")
for j in range(len(mag)):
out2.write(
str(mag[j][3]) + "*" + str(round(mag[j][2], 2)) + " ")
out2.write('\n')
elif oxi_check == 2: # Manual setting part
out2.write(" ISPIN = 2\n ")
with open(target + '/valence_notice!', 'w') as out3:
out3.write(
"Unpaired spin atoms can not be clearly identified!\n")
elif nelect % 2 != 0:
out2.write(" Spin polarized caculation:\n")
out2.write(" ISPIN = 2\n ")
if soc_on == 1:
out2.write("# LSORBIT = .True.\n")
if u_on == 1:
out2.write("# LMAXMIX = " + maxmix + "\n")
