nb = 2
ncl = int(np.floor(nc / 2))
ncu = int(np.ceil(nc / 2))
if nc % 2 == 0: #even
lstzn1 = rep(zn1, lvecs, na, nb, ncu)
lstzn2 = rep(zn2, lvecs, na, nb, ncl - 1)
lsto1 = rep(o1 + lvecs[2], lvecs, na, nb, ncl - 1)
lsto2 = rep(o2, lvecs, na, nb, ncl)
else: # odd
lstzn1 = rep(zn1, lvecs, na, nb, ncl)
lstzn2 = rep(zn2, lvecs, na, nb, ncl)
lsto1 = rep(o1 + lvecs[2], lvecs, na, nb, ncl)
lsto2 = rep(o2, lvecs, na, nb, ncl)
lsave(lstzn1, 'Zn1')
lsave(lstzn2, 'Zn2')
lsave(lsto1, 'O1')
lsave(lsto2, 'O2')
sublats = ['Zn1', 'Zn2', 'O1', 'O2']
a = np.array([lvecs[0], np.zeros(3), np.zeros(3)])
b = np.array([np.zeros(3), lvecs[1], np.zeros(3)])
c = np.array([np.zeros(3), np.zeros(3), lvecs[2]])
scvecs = na * a + nb * b + nc * c
genPOSCAR(sublats,
scvecs,
sys_name='Zinc Oxide',
POS_name=str(nc) + 'pPOSCAR.vasp')
ncyl+=1
for i in comb:
dist=np.dot(np.array(i),lvecs) + np.array([2*R,2*R,0])
lstmg1.append(mg1+dist)
lstmg2.append(mg2+dist)
lstmg3.append(mg3+dist)
lstmg4.append(mg4+dist)
lsto1.append(o1+dist)
lsto2.append(o2+dist)
lsto3.append(o3+dist)
lsto4.append(o4+dist)
lsave(lstmg1,'Mg1') #array method possible?
lsave(lstmg2,'Mg2')
lsave(lstmg3,'Mg3')
lsave(lstmg4,'Mg4')
lsave(lsto1,'O1')
lsave(lsto2,'O2')
lsave(lsto3,'O3')
lsave(lsto4,'O4')
sublats=['Mg1','Mg2','Mg3','Mg4','O1','O2','O3','O4']
scvecs=[[4*R,0,0],[0,4*R,0],[0,0,(2*crange+4)*np.linalg.norm(c)]]
genPOSCAR(sublats,scvecs,sys_name='Magnesium Oxide Rod System',POS_name='MgORodPOSCAR.vasp')
rel=np.pi*crange*np.linalg.norm(c)/R
metr=100*(ncyl/nrect-rel)/rel
print(metr)
O_lst.append(dist)
elif name == 'N':
N_lst.append(dist)
else:
C_lst.append(dist)
H_rot = []
O_rot = []
N_rot = []
C_rot = []
#rotation is not about the center of the molecule but about the origin, need to translate it after the rotation
#the molecule will be incorrectly rotated if it is not reported in terms of coordinates relative to its. This may be found
alt = 90 * np.pi / 180
azi = 90 * np.pi / 180
disp = np.array([5, 5, 5])
H_lst = orient(H_lst, alt, azi) + disp
O_lst = orient(O_lst, alt, azi) + disp
N_lst = orient(N_lst, alt, azi) + disp
C_lst = orient(C_lst, alt, azi) + disp
lsave(H_lst, 'H1')
lsave(O_lst, 'O1')
lsave(N_lst, 'N1')
lsave(C_lst, 'C1')
sublats = ['H1', 'O1', 'N1', 'C1']
scvecs = [[10, 0, 0], [0, 10, 0], [0, 0, 10]]
genPOSCAR(sublats, scvecs, sys_name='molecule', POS_name='mculPOSCAR.vasp')
zn1, zn2, o1, o2 = bases
na = 1
nb = 1
nc = 1
lstzn1 = rep(zn1, lvecs, na, nb, nc)
lstzn2 = rep(zn2, lvecs, na, nb, nc)
lsto1 = rep(o1 + lvecs[0], lvecs, na, nb, nc)
lsto2 = rep(o2, lvecs, na, nb, nc)
lsave(lstzn1, 'Zn1')
lsave(lstzn2, 'Zn2')
lsave(lsto1, 'O1')
lsave(lsto2, 'O2')
sublats = ['Zn1', 'Zn2', 'O1', 'O2']
a = np.array([lvecs[0], np.zeros(3), np.zeros(3)])
b = np.array([np.zeros(3), lvecs[1], np.zeros(3)])
c = np.array([np.zeros(3), np.zeros(3), lvecs[2]])
rng = np.arange(0.85, 1.15, 0.0125)
c = 0
for i in rng:
for j in rng:
c += 1
scvecs = [lvecs[0] * i, lvecs[1], lvecs[2] * j]
genPOSCAR(sublats,
scvecs,
sys_name='nonpolar zinc oxide',
POS_name=str(c) + 'acPOSCAR.vasp')
#note that Zn_Ot is O_Ot alternatingly
Zn_Ot = o1 + (nc / 2 - 0.3) * lvecs[2] + shift
O_Ot = zn2 + (nc / 2 - 1.1) * lvecs[2] + shift
hole_Ot = lvecs[0] + lvecs[1] + (nc / 2 - 0.3) * lvecs[2] + shift
bridge_Ot = lvecs[0] / 2 + lvecs[1] / 2 + (nc / 2 - 0.3) * lvecs[2] + shift
Zn_Znt = zn2 - 0.3 * lvecs[2] + shift
O_Znt = zn1 - 0.3 * lvecs[2] + shift
hole_Znt = lvecs[0] + lvecs[1] + 0.3 * lvecs[2] + shift
bridge_Znt = lvecs[0] / 2 + lvecs[1] / 2 + 0.3 * lvecs[2] + shift
lstO = rep(O_Znt - 0.1 * lvecs[2], lvecs, na, nb, 1)
lstH_Znt = rep(O_Znt - 0.325 * lvecs[2], lvecs, na, nb, 1)
lstH_Ot = rep(O_Ot - 0.0625 * lvecs[2], lvecs, na, nb, 1)
lsave(lstO, 'O3')
lsave(lstH_Znt, 'H1')
lsave(lstH_Ot, 'H2')
lstS = rep(hole_Ot + lvecs[2] * 0.1, lvecs * size, 1, 1, 1)
lsave(lstS, 'S1')
sublats = ['Zn1', 'Zn2', 'O1', 'O2', 'O3', 'H1', 'H2', 'S1']
scvecs = [na * lvecs[0], nb * lvecs[1], nc * lvecs[2]]
genPOSCAR(sublats,
scvecs,
sys_name='Zinc Oxide',
POS_name='sulf' + str(size) + 'pPOSCAR.vasp')
lsave(lstzn1,'Zn1')
lsave(lstzn2,'Zn2')
lsave(lsto1,'O1')
lsave(lsto2,'O2')
Zn_Ot=o1+(nc/2-0.3)*lvecs[2] + shift
O_Ot=zn2+(nc/2-1.1)*lvecs[2] + shift
hole_Ot=lvecs[0]+lvecs[1]+(nc/2-0.3)*lvecs[2] + shift
bridge_Ot=lvecs[0]/2+lvecs[1]/2+(nc/2-0.3)*lvecs[2] + shift
Zn_Znt=zn2-0.3*lvecs[2] + shift
O_Znt=zn1-0.3*lvecs[2] + shift
hole_Znt=lvecs[0]+lvecs[1]+0.3*lvecs[2] + shift
bridge_Znt=lvecs[0]/2+lvecs[1]/2+0.3*lvecs[2] + shift
lstO=rep(O_Znt-0.1*lvecs[2],lvecs,na,nb,1)
lstH_Znt=rep(O_Znt-0.325*lvecs[2],lvecs,na,nb,1)
if nc % 2 == 0:
lstH_Ot=rep(O_Ot-0.0625*lvecs[2],lvecs,na,nb,1)
else:
lstH_Ot=rep(Zn_Ot,lvecs,na,nb,1)
lsave(lstH_Znt,'H1')
lsave(lstO,'O3')
lsave(lstH_Ot,'H2')
sublats=['Zn1','Zn2','O1','O2','O3','H1','H2']
scvecs=[na*lvecs[0],nb*lvecs[1],nc*lvecs[2]]
genPOSCAR(sublats,scvecs,sys_name='Zinc Oxide H-terminated',POS_name=str(nc)+'HpPOSCAR.vasp')
lsto3.append(o3 + dist)
lsto4.append(o4 + dist)
lsave(lstmg1, 'Mg1') #array method possible?
lsave(lstmg2, 'Mg2')
lsave(lstmg3, 'Mg3')
lsave(lstmg4, 'Mg4')
lsave(lsto1, 'O1')
lsave(lsto2, 'O2')
lsave(lsto3, 'O3')
lsave(lsto4, 'O4')
sublats = ['Mg1', 'Mg2', 'Mg3', 'Mg4', 'O1', 'O2', 'O3', 'O4']
scvecs = [[4 * R, 0, 0], [0, 4 * R, 0], [0, 0, 4 * R]]
genPOSCAR(sublats,
scvecs,
sys_name='Magnesium Oxide Ball System',
POS_name='MgOBallPOSCAR.vasp')
metr = 100 * (nsph / ncube - np.pi / 6) / (np.pi / 6)
print(
metr
) #0.523598=pi/6 is the ratio of the volume of a sphere to the volume of a cube in which it is circumbscribed. As the size of the unit cell increases, this should approach 0.
#this structure has only dangling bonds, which might be passivated by layering heterostructures.
#MD simulations beginning at high temperatures could give the initial positions if one is fairly sloppy about distributing surface ligands or other passivation atoms.
#molecular adsorbates can be rotated with the rot function
for na in range(-arange, arange):
for nb in range(-brange, brange):
for nc in range(-crange, crange):
dist = np.linalg.norm(na * a + nb * b + nc * c)
i1 += 1
if dist < R:
i2 += 1
comb.append([na, nb, nc])
for i in comb:
dist = np.dot(np.array(i), lvecs) + np.array([2 * R, 2 * R, 2 * R])
lstzn1.append(zn1 + dist)
lstzn2.append(zn2 + dist)
lsto1.append(o1 + a + dist)
lsto2.append(
o2 + dist
) #since don't account for non-centro symmetry, get non-physical terminations. Would need logical similar to that of the slab replication
lsave(lstzn1, 'Zn1')
lsave(lstzn2, 'Zn2')
lsave(lsto1, 'O1')
lsave(lsto2, 'O2')
sublats = ['Zn1', 'Zn2', 'O1', 'O2']
scvecs = [[4 * R, 0, 0], [0, 4 * R, 0], [0, 0, 4 * R]]
genPOSCAR(sublats,
scvecs,
sys_name='zinc oxide ball',
POS_name='ZnOballPOSCAR.vasp')