def plot_all_pdos_s(element_types=None,
filename='DOSCAR',
ispin=2,
ymin=-2.0,
ymax=2.0,
xmin=-15.0,
xmax=5.0):
"""
plot the local dos of all atoms.
"""
symdict = get_symdict()
if element_types is not None:
atom_nums = [
x for x in list(symdict.keys())
if symnum_to_sym(x) in element_types
]
if ispin == 2:
sites = ['s+', 's-']
else:
sites = ['s']
if not os.path.exists('PDOS'):
os.mkdir('PDOS')
for atom_num in atom_nums:
copyfile(filename, 'PDOS/DOSCAR')
plotldos_group([atom_num],
sites,
ymin=ymin,
ymax=ymax,
xmin=xmin,
xmax=xmax,
special_location=None,
output='PDOS/%s_s_dos.png' % atom_num)
def write_all_octahedra_info(atoms,center_symbol_list,vertex_symbol,max_distance,output='octa_info.csv',axis_type=None,x=(1,0,0),y=(0,1,0),z=(0,0,1), var_distance=False):
"""
write all octahedra info into a file.
"""
symdict=symbol_number(atoms)
myfile=open(output,'w')
for symnum in symdict:
sym=symnum_to_sym(symnum)
print(sym)
if sym in center_symbol_list:
print(sym)
this_oct=get_octahedron(atoms,symnum,vertex_symbol,max_distance,axis_type=axis_type,x=x,y=y,z=z,var_distance=var_distance)
avg_rotations=this_oct.get_avg_rotations()
bond_lengths=this_oct.get_bond_lengths()
avg_bond_length=np.average(bond_lengths)
distortion_factor=this_oct.get_distortion()
vertex_angles=this_oct.get_vertex_angles(target_symbol_list=center_symbol_list)
myfile.write('Info of %s :\n'%symnum)
myfile.write("avg_rot: %s\n"%('\t'.join([str(a) for a in avg_rotations])))
myfile.write("avg_bond: %s\n"%avg_bond_length)
myfile.write("distrotion factor: %s\n"%distortion_factor)
myfile.write("vertex lengths: %s\n"%('\t'.join([str(a) for a in bond_lengths])))
myfile.write("vertex angles: %s\n\n"%('\t'.join([str(a) for a in list(vertex_angles.values())])))
myfile.close()
def plot_pdos(sites,
lsites=None,
element_types=None,
filename='DOSCAR',
ispin=2,
ymin=-2.0,
ymax=2.0,
xmin=-15.0,
xmax=5.0,
output_dir='PDOS'):
"""
plot the local dos of all atoms.
"""
symdict = get_symdict()
if element_types is not None:
atom_nums = [
x for x in list(symdict.keys())
if symnum_to_sym(x) in element_types
]
else:
atom_nums = list(symdict.keys())
if sites == 'eg':
if ispin == 2:
lsites = ['dx2+', 'dz2+', 'dx2-', 'dz2-']
else:
lsites = ['dx2', 'dz2']
elif sites == 't2g':
if ispin == 2:
lsites = ['dxy+', 'dyz+', 'dxz+', 'dxy-', 'dyz-', 'dxz-']
else:
lsites = ['dxy', 'dyz', 'dxz']
elif sites == 'p':
if ispin == 2:
lsites = ['px+', 'py+', 'pz+', 'px-', 'py-', 'pz-']
else:
lsites = ['px', 'py', 'pz']
elif sites == 's':
if ispin == 2:
lsites = ['s+', 's-']
else:
lsites = ['s']
else:
lsites = lsites
if not os.path.exists(output_dir):
os.mkdir(output_dir)
for atom_num in atom_nums:
copyfile(filename, join(output_dir, 'DOSCAR'))
plotldos_group([atom_num],
lsites,
ymin=ymin,
ymax=ymax,
xmin=xmin,
xmax=xmax,
special_location=None,
output=join(output_dir,
'%s_%s_dos.png' % (atom_num, sites)))
def even_or_odd_path(atoms,from_symnum,node_sym_list,to_symnum_list=None,first_neighbor_min=2.5,first_neighbor_max=4.5):
"""
Find whether the distance of the atoms with symnum in to_list to the atom(from_symnum) is even or odd.
The distance to the first neighbor is 1. The 1st neighbor's 1st neighbor is 2. etc....
Args:
atoms:
from_symnum
to_sym_list: The symbol of the atoms, eg:['Fe','Ni' ], Note the from_symnum should be start with the symbol in this list
to_symnum_list: The symbol_number of the atoms, eg:['Fe1','Fe2','Ni1'].Only one of the to_sym_list and to_symnum_list should should be specified.
first_neighbor_min/max: The min/max distance to the first neighbor
Returns:
a dict. The values are 1/-1. 1 is odd, -1: even eg {'Fe1':1,'Ni1':-1}
"""
#1. Get the first neighbor list
symdict=symbol_number(atoms)
symnums=list(symdict.keys())
node_list=[]
for s in symnums:
#print s
if symnum_to_sym(s) in node_sym_list:
node_list.append(s)
if not from_symnum in node_list:
raise Exception('from_symnum should be of one of the nodes')
positions=atoms.get_positions()
node_positions=[positions[symdict[i]] for i in node_list]
from scipy.sparse import csr_matrix
N=len(node_list)
#dmat=csr_matrix((N,N))
row=[]
col=[]
val=[]
dist=lambda pos1,pos2 :np.linalg.norm(np.asarray(pos1)-np.asarray(pos2))
for i,pi in enumerate(node_positions):
for j,pj in enumerate(node_positions):
if i==j:
row.append(i)
col.append(j)
val.append(0)
else:
#print pi,pj
#print dist(pi,pj)
if first_neighbor_min <dist(pi,pj)<first_neighbor_max:
row.append(i)
col.append(j)
val.append(1)
dmat=csr_matrix((val,(row,col)),shape=(N,N))
#print dmat
from scipy.sparse.csgraph import dijkstra
path_mat=dijkstra(dmat,directed=False,unweighted=True)
i_node=node_list.index(from_symnum)
def even_odd(x):
if int(x)%2==0:
return 1
else:
return -1
return node_list,[even_odd(x) for x in path_mat[i_node]]
start = True
text = ''
if start:
text += line
if line.startswith('tot'):
start = False
return text
def check_converge(filename='log'):
"""
check the log file to see if the calculation is converged.
If converged, return the number of steps of iteration, else return False.
"""
nstep = 0
with open(filename) as myfile:
for line in myfile:
l = line
try:
nstep = int(line.strip().split()[0])
except Exception:
pass
if l.strip().startswith('writing'):
return nstep
else:
return False
if __name__ == '__main__':
print(symnum_to_sym('1'))
