def smart_vac(strt=None,tol=0.1):
"""
Umbrell function for vacancy formation energies with convergence
Args:
strt: Structure object
tol: defect energy convergence tolerance in eV
Returns:
def_list: list of defect energies
def_header_list: list of defect names
"""
vac_arr=[]
sg_mat = SpacegroupAnalyzer(strt)
mat_cvn = sg_mat.get_conventional_standard_structure()
mat_cvn.sort()
cellmax=1 #int(mat_cvn.composition.num_atoms)+int(mat_cvn.ntypesp)#5
ase_atoms = AseAtomsAdaptor().get_atoms(mat_cvn)
ase_atoms=ase_atoms*(cellmax,cellmax,cellmax)
#if len(ase_atoms) >200:
# cellmax=1
#else:
# cellmax=2
#cellmax=int(mat_cvn.composition.num_atoms)+int(mat_cvn.ntypesp)#5
print ("type of trt is= celmmax",type(strt),cellmax)
try:
print ("int(strt.composition.num_atoms)",int(strt.composition.num_atoms))
print (int(strt.ntypesp))
except:
pass
#cellmax=int(strt.composition.num_atoms)+int(strt.ntypesp)
vac_done=0
vac=vac_antisite_def_struct_gen(cellmax=cellmax,struct=strt)
def_list=[100000 for y in range(len(vac)-1)]
while vac_done !=1:
vac=vac_antisite_def_struct_gen(cellmax=cellmax,struct=strt)
if vac not in vac_arr:
vac_arr.append(vac)
print ("in smart_vac(strt=None), cellmax,vac,vac_done=",cellmax,vac,vac_done)
def_list2,header_list=def_energy(vac=vac)
diff=matrix(def_list)-matrix(def_list2)
diff_arr=np.array(diff).flatten()
print ("in smart_vac(strt=None diff_arr=",diff_arr)
if any(diff_arr)>tol:
# for el in diff_arr:
# if abs(el)>tol :
# print ("in smart_vac(strt=None abs_el=",abs(el))
vac_done=0
cellmax=cellmax+1
ase_atoms = AseAtomsAdaptor().get_atoms(mat_cvn)
ase_atoms=ase_atoms*(cellmax,cellmax,cellmax)
if len(ase_atoms) >100:
vac_done=1
def_list=def_list2
else:
vac_done=1
# cellmax=cellmax+1
return def_list,header_list
def smart_converge(mat=None,encut='',leng='',band_str=True,elast_prop=True,optical_prop=True,mbj_prop=True,spin_orb=False,phonon=False,surf_en=False,def_en=False):
"""
Main function to converge k-points/cut-off
optimize structure, and run subsequent property calculations
Args:
mat: Poscar object with structure information
encut: if '' then automataic convergence, else use defined fixed-cutoff
leng: if '' then automataic convergence, else use defined fixed-line density
band_str: if True then do band-structure calculations along high-symmetry points
elast_prop: if True then do elastic property calculations using finite-difference
optical_prop: if True do frequency dependent dielectric function calculations using he independent-particle (IP) approximation
mbj_prop: if True do METAGGA-TBmBJ optical property calculations with IP approximation
spin_orb: if True do spin-orbit calculations
phonon: if True do phonon calculations using DFPT
surf_en: if True do surface enrgy calculations
def_en: if True do defect enrgy calculations
Returns:
en2: final energy
mat_f: final structure
"""
if encut=="":
encut=converg_encut(encut=500,mat=mat)
if leng=="":
leng= converg_kpoints(length=0,mat=mat)
kpoints=Auto_Kpoints(mat=mat,length=leng)
isif=2
commen=str(mat.comment)
lcharg='.FALSE.'
if commen.split('@')[0] =='bulk' :
isif=3
lcharg='.TRUE.'
if commen.split('@')[0] == 'sbulk':
isif=3
incar_dict = use_incar_dict
incar_dict.update({"ENCUT":encut,"EDIFFG":-1E-3,"ISIF":3,"NEDOS":5000,"NSW":500,"NELM":500,"LORBIT":11,"LVTOT":'.TRUE.',"LVHAR":'.TRUE.',"ISPIN":2,"LCHARG":'.TRUE.'})
incar = Incar.from_dict(incar_dict)
try:
if mat.comment.startswith('Mol'):
incar.update({"ISIF": '2'})
except:
print ("Mol error")
pass
#if commen.startswith('Surf-') :
# pol=check_polar(mat_f.structure)
# if pol==True:
# ase_atoms = AseAtomsAdaptor().get_atoms(mat_f.structure)
# COM=ase_atoms.get_center_of_mass(scaled=True)
# incar.update({"LDIPOL": '.TRUE.',"IDIPOL":4,"ISYM": 0,"DIPOL":COM})
print ("running smart_converge for",str(mat.comment)+str('-')+str('MAIN-RELAX'))
cwd=str(os.getcwd())
en2,contc=run_job(mat=mat,incar=incar,kpoints=kpoints,jobname=str('MAIN-RELAX')+str('-')+str(mat.comment))
os.chdir(cwd)
path=str(contc.split('/CONTCAR')[0])+str('/vasprun.xml')
v=open(path,"r").readlines()
for line in v:
if "NBANDS" in line:
nbands=int(line.split(">")[1].split("<")[0])
print ("nbands=",nbands)
break
strt=Structure.from_file(contc)
mat_f=Poscar(strt)
mat_f.comment=str(mat.comment)
if band_str==True:
incar_dict = use_incar_dict
incar_dict.update({"ISPIN":2,"NEDOS":5000,"LORBIT":11,"IBRION":1,"ENCUT":encut,"NBANDS":int(nbands)+10})
incar = Incar.from_dict(incar_dict)
kpath = HighSymmKpath(mat_f.structure)
frac_k_points, k_points_labels = kpath.get_kpoints(line_density=20,coords_are_cartesian=False)
kpoints = Kpoints(comment="Non SCF run along symmetry lines",style=Kpoints.supported_modes.Reciprocal,num_kpts=len(frac_k_points),kpts=frac_k_points, labels=k_points_labels,kpts_weights=[1] * len(frac_k_points))
try:
print ("running MAIN-BAND")
kpoints=mpvis.get_kpoints(mat_f.structure)
en2B,contcB=run_job(mat=mat_f,incar=incar,kpoints=kpoints,jobname=str('MAIN-BAND')+str('-')+str(mat_f.comment))
# kpoints=mpvis.get_kpoints(mat_f.structure)
# en2B,contcB=run_job(mat=mat_f,incar=incar,kpoints=kpoints,jobname=str('MAIN-BAND')+str('-')+str(mat_f.comment))
except:
print ("No band str calc.")
if str(os.getcwd)!=cwd:
print ("Changing directory")
line=str("cd ")+str(cwd)
os.chdir(cwd)
print (os.getcwd())
pass
os.chdir(cwd)
if surf_en==True:
incar_dict = use_incar_dict
incar_dict.update({"ENCUT":encut,"NEDOS":5000,"IBRION":1,"NSW":500,"LORBIT":11})
incar = Incar.from_dict(incar_dict)
surf=surfer(mat=mat_f.structure,layers=3)
for i in surf:
try:
print ("running MAIN-BAND")
#NSCF
#chg_file=str(contc).replace('CONTCAR','CHGCAR')
#print ('chrfile',chg_file)
#shutil.copy2(chg_file,'./')
kpoints=Auto_Kpoints(mat=i,length=leng)
en2s,contcs=run_job(mat=i,incar=incar,kpoints=kpoints,jobname=str('Surf_en-')+str(i.comment)+str('-')+str(mat_f.comment))
#kpoints=mpvis.get_kpoints(mat_f.structure)
#en2B,contcB=run_job(mat=mat_f,incar=incar,kpoints=kpoints,jobname=str('MAIN-BAND')+str('-')+str(mat_f.comment))
except:
pass
os.chdir(cwd)
if def_en==True:
incar_dict = use_incar_dict
incar_dict.update({"ENCUT":encut,"NEDOS":5000,"IBRION":1,"NSW":500,"LORBIT":11})
incar = Incar.from_dict(incar_dict)
#surf=surfer(mat=mat_f.structure,layers=3)
vac=vac_antisite_def_struct_gen(cellmax=3,struct=mat_f.structure)
for i in vac:
try:
print ("running MAIN-vac")
kpoints=Auto_Kpoints(mat=i,length=leng)
en2d,contcd=run_job(mat=i,incar=incar,kpoints=kpoints,jobname=str('Def_en-')+str(i.comment)+str('-')+str(mat_f.comment))
# kpoints=mpvis.get_kpoints(mat_f.structure)
# en2B,contcB=run_job(mat=mat_f,incar=incar,kpoints=kpoints,jobname=str('MAIN-BAND')+str('-')+str(mat_f.comment))
except:
pass
os.chdir(cwd)
#surf=surfer(mat=strt,layers=layers)
#surf=surfer(mat=strt,layers=layers)
if spin_orb==True:
#chg_file=str(contc).replace('CONTCAR','CHGCAR')
#print ('chrfile',chg_file)
#shutil.copy2(chg_file,'./')
incar_dict = use_incar_dict
incar_dict.update({"ENCUT":encut,"NPAR":ncores,"GGA_COMPAT":'.FALSE.',"LSORBIT":'.TRUE.',"IBRION":1,"ISYM":0,"NEDOS":5000,"IBRION":1,"NSW":500,"LORBIT":11})
incar = Incar.from_dict(incar_dict)
sg_mat = SpacegroupAnalyzer(mat_f.structure)
mat_cvn = sg_mat.get_conventional_standard_structure()
mat_cvn.sort()
kpoints=Auto_Kpoints(mat=Poscar(mat_cvn),length=leng/2)
try:
en2S,contcS=run_job(mat=Poscar(mat_cvn),incar=incar,kpoints=kpoints,jobname=str('MAIN-SOC')+str('-')+str(mat_f.comment))
except:
pass
os.chdir(cwd)
if optical_prop==True:
incar_dict = use_incar_dict
incar_dict.update({"NEDOS":5000,"LORBIT":11,"IBRION":1,"ENCUT":encut,"NBANDS":3*int(nbands),"LOPTICS":'.TRUE.'})
incar = Incar.from_dict(incar_dict)
kpoints=Auto_Kpoints(mat=mat_f,length=leng)
try:
en2OP,contcOP=run_job(mat=mat_f,incar=incar,kpoints=kpoints,jobname=str('MAIN-OPTICS')+str('-')+str(mat_f.comment))
except:
pass
os.chdir(cwd)
if mbj_prop==True:
incar_dict = use_incar_dict
incar_dict.update({"NEDOS":5000,"LORBIT":11,"IBRION":1,"ENCUT":encut,"NBANDS":3*int(nbands),"LOPTICS":'.TRUE.','METAGGA':'MBJ','ISYM':0,"SIGMA":0.1})
incar = Incar.from_dict(incar_dict)
kpoints=Auto_Kpoints(mat=mat_f,length=leng)
try:
en2OP,contcOP=run_job(mat=mat_f,incar=incar,kpoints=kpoints,jobname=str('MAIN-MBJ')+str('-')+str(mat_f.comment))
except:
pass
os.chdir(cwd)
if elast_prop==True:
incar_dict = use_incar_dict
incar_dict.update({"NEDOS":5000,"IBRION":6,"ENCUT":1.3*float(encut),"ISIF":3,"POTIM":0.015,"NPAR":ncores,"ISPIN":2})
incar = Incar.from_dict(incar_dict)
sg_mat = SpacegroupAnalyzer(mat_f.structure)
mat_cvn = sg_mat.get_conventional_standard_structure()
mat_cvn.sort()
kpoints=Auto_Kpoints(mat=Poscar(mat_cvn),length=leng)
try:
en2E,contcE=run_job(mat=Poscar(mat_cvn),incar=incar,kpoints=kpoints,jobname=str('MAIN-ELASTIC')+str('-')+str(mat_f.comment))
except:
pass
os.chdir(cwd)
if phonon==True:
incar_dict = use_incar_dict
incar_dict.update({"IBRION":8,"ENCUT":float(encut),"ISYM":0,"ADDGRID":'.TRUE.','EDIFF': 1e-09,'LORBIT': 11})
incar = Incar.from_dict(incar_dict)
kpoints=Auto_Kpoints(mat=mat_f,length=leng)
mat_pho=make_big(poscar=mat_f,size=11.0)
try:
en2P,contcP=run_job(mat=mat_pho,incar=incar,kpoints=kpoints,jobname=str('MAIN-PHO8')+str('-')+str(mat_f.comment))
except:
pass
os.chdir(cwd)
#if Raman_calc==True:
# Raman(strt=mat_f,encut=encut,length=leng)
os.chdir(cwd)
return en2,mat_f