def dump2POSCAR(self, dumpname, poscar='POSCAR', rotate=True):
atoms = self.atoms_from_dump(dumpname)
if rotate:
rot = np.loadtxt(tl.dirname(dumpname) + '/POSCARrot')
d, p, d1, p1 = rot[:3], rot[3], rot[4:7], rot[7]
atoms.rotate(d1, -p1, rotate_cell=True)
atoms.rotate(d, -p, rotate_cell=True)
# write_vasp(poscar,atoms,sort="True",direct=True,vasp5=True)
writevasp(atoms, poscar)
return atoms
def dump2POSCAR(self, dumpname, poscar='POSCAR', rotate=True):
atoms = self.atoms_from_dump(dumpname)
if rotate:
rot = np.loadtxt(tl.dirname(dumpname) + '/POSCARrot')
d, p, d1, p1 = rot[:3], rot[3], rot[4:7], rot[7]
atoms.rotate(d1, -p1, rotate_cell=True)
atoms.rotate(d, -p, rotate_cell=True)
# write_vasp(poscar,atoms,sort="True",direct=True,vasp5=True)
writevasp(atoms, poscar)
return atoms
def optimize(self):
mkcd('optimize')
cp('../minimize/POSCAR', '.')
atoms = io.read('POSCAR')
for i in range(100):
dir = "%i" % i
mkcd(dir)
writevasp(atoms)
forces, stress, energy = self.energyForce()
pos = atoms.get_scaled_positions()
pos += forces * 0.01
def optimize(self):
mkcd('optimize')
cp('../minimize/POSCAR', '.')
atoms = io.read('POSCAR')
for i in range(100):
dir = "%i" % i
mkcd(dir)
writevasp(atoms)
forces, stress, energy = self.energyForce()
pos = atoms.get_scaled_positions()
pos += forces * 0.01
def run_next(self, dir0, dir, lz):
m = self.m
atoms = io.read("POSCAR_" + dir0)
m.forceThick = True
cell = atoms.get_cell()
cell[2][2] = lz
atoms.set_cell(cell, scale_atoms=True)
m.atoms = atoms
self.creatmini(dir)
atoms = m.atoms_from_dump('%s/range' % dir)
writevasp(atoms, "POSCAR_" + dir)
def run_next(self, dir0, dir, lz):
m = self.m
atoms = io.read("POSCAR_" + dir0)
m.forceThick = True
cell = atoms.get_cell()
cell[2][2] = lz
atoms.set_cell(cell, scale_atoms=True)
m.atoms = atoms
self.creatmini(dir)
atoms = m.atoms_from_dump('%s/range' % dir)
writevasp(atoms, "POSCAR_" + dir)
def getlead(self):
cd('center')
left = self.findlead('left')
right = self.findlead('right')
cd('..')
return
from aces.io.vasp import writevasp
mkcd('leftlead')
writevasp(left, 'POSCAR')
self.runlead()
cd('..')
mkcd('rightlead')
writevasp(right, 'POSCAR')
self.runlead()
cd('..')
def watoms(self, atoms):
# atoms.write("structure.xyz")
writevasp(atoms)
# write_vasp("POSCAR",atoms,sort="True",direct=True,vasp5=True)
self.POSCAR2data()
def watoms(self, atoms):
# atoms.write("structure.xyz")
writevasp(atoms)
# write_vasp("POSCAR",atoms,sort="True",direct=True,vasp5=True)
self.POSCAR2data()
def rearangefc_center(self, fc, satoms, left, right):
ax = self.m.negfaxis
right_idx = satoms.positions[:, ax].argsort()[-1]
x_right = satoms[right_idx].position[ax]
left_idx = satoms.positions[:, ax].argsort()[0]
x_left = satoms[left_idx].position[ax]
# don't put these after satoms=satoms[order]
lpos = satoms[left_idx].position
rpos = satoms[right_idx].position
# find the index of left part in satoms
atoms = left.copy()
# remove the offset
offset = [0, 0, 0]
offset[ax] = x_left
atoms.translate(offset)
lidx = self.match_idx(atoms, satoms)
lidx = list(lidx)
atoms.translate(left.cell[ax])
lidx1 = self.match_idx(atoms, satoms)
lidx1 = list(lidx1)
# find the index of right part in satoms
atoms = right.copy()
offset = [0, 0, 0]
offset[ax] = x_right
atoms.translate(np.array(offset) - right.cell[ax])
ridx = self.match_idx(atoms, satoms)
ridx = list(ridx)
atoms.translate(-right.cell[ax])
ridx1 = self.match_idx(atoms, satoms)
ridx1 = list(ridx1)
# find the center index
cidx = []
for i in range(len(satoms)):
if i in lidx:
continue
if i in ridx:
continue
cidx.append(i)
order = lidx + cidx + ridx
print(order)
fccenter = fc[order][:, order]
oatoms = satoms
satoms = satoms.copy()
satoms = satoms[order]
writevasp(satoms, "POSCAR_ordered")
cut = self.m.negfcut
if cut > 0:
self.elimiPeriodic(satoms, fccenter, cut, left, right, lpos, rpos)
else:
# the default assumption is that cell length is larger than interaction length,
# so for | x x | x x | x x | the interaction of cell 1 and cell 3 is only from periodic and the periodic interction only apparear in between 1 and 3
# F_13 <==> periodic interaction so if we want to eliminate
# periodic interaction we only have to set F_13=0
n1 = len(lidx)
n2 = len(ridx)
fccenter[:n1, -n2:] = 0
fccenter[-n2:, :n1] = 0
# with this method there is no need to calculate fc for left or right
# again, it's very important for abinitial calculation.
order = lidx + lidx1
fcleft = fc[order][:, order]
# this is for the situation of 2x1x1 supercell when the cell size if
# pretty large
if len(cidx) == 0 and cut > 0:
satoms = oatoms[order]
self.elimiPeriodic(satoms, fcleft, cut, left, left, lpos, rpos)
order = ridx1 + ridx
fcright = fc[order][:, order]
if len(cidx) == 0 and cut > 0:
satoms = oatoms[order]
self.elimiPeriodic(satoms, fcright, cut, right, right, lpos, rpos)
return fccenter, fcleft, fcright
def findlead(self, end="left", err=0.3):
"""[from center POSCAR find periodic lead POSCAR]
[the center POSCAR is expected to consist of scatter region and left lead region of 2 layers and
right lead region of 2 layers. So we can find the lead POSCAR from the two ends with this algorithm.]
Keyword Arguments:
end {str} -- [which lead do you want ,can be 'left' and 'right'] (default: {"left"})
err {number} -- [the tolerence to find an atom ] (default: {0.4})
Raises:
Exception -- [end is not set correctly]
"""
atoms = io.read('SPOSCAR')
# find the most right atom index
if end == "right":
last = -1
next_last = -2
next_last1 = -3
elif end == "left":
last = 0
next_last = 1
next_last1 = 2
else:
raise Exception("Unkown value of `end`")
ax = self.m.negfaxis
right_idx = atoms.positions[:, ax].argsort()[last]
ratom = atoms[right_idx]
print("%s end atom position:" % end, ratom.position)
# the atoms that has similar y,z to ratom , in our situatoin there is
# at least two such atoms.
cross = ~(np.arange(3, dtype='int') == ax)
fil = norm(atoms.positions[:, cross] - ratom.position[cross],
axis=1) < err / 10
# Don't forget the symbol must be the same.
# must convert to array
fil1 = np.array(atoms.get_chemical_symbols()) == ratom.symbol
fil = fil * fil1
atoms_inline = atoms[fil]
assert len(atoms_inline) >= 2
right_idx1 = atoms_inline.positions[:, ax].argsort()[next_last]
# waring this index is of atoms_inline but not of atoms
# catom is what we search
catom = atoms_inline[right_idx1]
print("next %s end similar atom position:" % end, catom.position)
# the possible lattice constant of x direction
la = np.abs(ratom.position[ax] - catom.position[ax])
refpos = ratom.position
unit, isunit = self.findunit(atoms, refpos, la, end, err)
if (isunit == False).sum() > 1:
next_last = next_last1
right_idx1 = atoms_inline.positions[:, ax].argsort()[next_last]
# waring this index is of atoms_inline but not of atoms
# catom is what we search
catom = atoms_inline[right_idx1]
print("next next %s end similar atom position:" % end,
catom.position)
la = np.abs(ratom.position[ax] - catom.position[ax])
refpos = ratom.position
unit, isunit = self.findunit(atoms, refpos, la, end, err)
assert isunit.all()
# the possible lattice constant of x direction
rightx = refpos[ax]
if end == "right":
offset = [0, 0, 0]
offset[ax] = -(rightx - la)
unit.translate(offset)
else:
offset = [0, 0, 0]
offset[ax] = -(rightx)
unit.translate(offset)
unit.cell = atoms.cell
unit.cell[ax, ax] = la
ys = unit.positions[:, (ax + 1) % 3]
order = ys.argsort()
unit = unit[order]
from aces.io.vasp import writevasp
writevasp(unit, 'POSCAR_%s' % end)
return unit