def get_nebout_structures():
"""
Extract structures from NEB results in the current directory.
There must be:
* neb.dat
* pw_X.in, where X=(1,...,N) and N is the number of images.
* pw.crd in which the final coordinates are written.
"""
from ase.atoms import Atoms
fnebdat = 'neb.dat'
fpwin = 'pw_1.in'
fcrd = 'pw.crd'
num_images = get_num_images(fnebdat)
natm, cell, elems, pos, cell_unit, pos_unit = read_espresso_in(fpwin)
list_pos = get_images(fcrd, natm, num_images)
list_atoms = []
for i in range(num_images):
atoms = Atoms(symbols=elems,
cell=cell,
scaled_positions=list_pos[i],
pbc=[1, 1, 1])
list_atoms.append(atoms)
return list_atoms
def get_nebout_structures():
"""
Extract structures from NEB results in the current directory.
There must be:
* neb.dat
* pw_X.in, where X=(1,...,N) and N is the number of images.
* pw.crd in which the final coordinates are written.
"""
from ase.atoms import Atoms
fnebdat = 'neb.dat'
fpwin = 'pw_1.in'
fcrd = 'pw.crd'
num_images = get_num_images(fnebdat)
natm,cell,elems,pos,cell_unit,pos_unit = read_espresso_in(fpwin)
list_pos = get_images(fcrd,natm,num_images)
list_atoms = []
for i in range(num_images):
atoms = Atoms(symbols=elems,
cell=cell,
scaled_positions=list_pos[i],
pbc=[1,1,1])
list_atoms.append(atoms)
return list_atoms
def read_espresso_out(fname,):
"""
Read cell info, atom coordinates, energy, forces from Quantum Espresso output.
"""
f= open(fname,'r')
lines = f.readlines()
f.close()
il_cell = -1
il_spcs = -1
il_forces = -1
il_pos = -1
il_stress = -1
infname = None
nspcs = None
for il in range(len(lines)):
if ' atomic species ' in lines[il]:
il_spcs = il
elif '! total energy' in lines[il]:
erg = float(lines[il].split()[4])
elif 'Forces acting on atoms' in lines[il]:
il_forces= il
elif 'CELL_PARAMETERS' in lines[il]:
il_cell = il
elif 'ATOMIC_POSITIONS' in lines[il]:
il_pos = il
elif 'number of atoms/cell' in lines[il]:
natm = int(lines[il].split()[4])
elif 'number of atomic types' in lines[il]:
nspcs = int(lines[il].split()[5])
elif 'total stress' in lines[il]:
il_stress = il
if ' Reading input from ' in lines[il]:
infname = lines[il].split()[3]
# some checks
if infname is None:
raise IOError('No input file read...')
try:
natm_in,cell_in,elems_in,pos_in,cell_unit,pos_unit = read_espresso_in(infname)
if natm_in != natm:
raise ValueError('natm_in != natm; natm_in,natm=',natm_in,natm)
except:
#print('Error: {} !!!'.format(e.message))
raise
if il_cell == -1 and cell_in is None:
raise IOError('No cell info in {} and {}.'.format(fname,infname))
if il_spcs == -1:
raise IOError('No species info in the output file.')
if nspcs == None:
raise IOError('No atoimc-type info in the output file.')
# read atom species
il= il_spcs +1
spcs = []
for isp in range(nspcs):
l = lines[il+isp].split()
spcs.append(l[0])
# read cell parameters
if il_cell == -1:
cell = cell_in
else:
il= il_cell
cell = np.zeros((3,3),dtype=float)
ixyz = 0
while True:
il += 1
l = lines[il].split()
if len(l) == 0:
break
cell[:,ixyz] = [ float(x) for x in l ]
ixyz += 1
# read atom coordinates
if il_pos == -1:
pos = pos_in
elems = elems_in
else:
elems = []
pos = np.zeros((natm,3),dtype=float)
il = il_pos + 1
for ia in range(natm):
l = lines[il+ia].split()
elems.append(l[0])
pos[ia,:] = [ float(x) for x in l[1:4] ]
# read forces
frcs = np.zeros((natm,3),dtype=float)
if il_forces != -1:
il = il_forces +2
for ia in range(natm):
l = lines[il+ia].split()
frcs[ia,:] = [ float(x) for x in l[6:9] ]
#...read stress
stnsr = np.zeros((3,3),dtype=float)
strs = np.zeros(6,dtype=float)
if il_stress != -1:
il = il_stress +1
for iil in range(3):
l = lines[il+iil].split()
stnsr[iil,:] = [ float(x) for x in l[3:6] ]
#...Reduce to 6 components in GPa and opposite sign
strs[0] = stnsr[0,0] *(-0.1)
strs[1] = stnsr[1,1] *(-0.1)
strs[2] = stnsr[2,2] *(-0.1)
strs[3] = stnsr[1,2] *(-0.1)
strs[4] = stnsr[0,2] *(-0.1)
strs[5] = stnsr[0,1] *(-0.1)
return natm,nspcs,spcs,cell,pos,elems,erg,frcs,pos_unit,strs