def sheet_from_params(xyz,params):
N = len(xyz.atoms)
H = {}
S = {}
H[0,0] = matrix(zeros((N,N)))
S[0,0] = matrix(zeros((N,N)))
h00,s00 = params(0.0)
assert s00 == 1.0
for i in range(N):
H[0,0][i,i] = h00
for j in range(i+1,N):
h,s = params(norm(xyz.atoms[i].pos - xyz.atoms[j].pos))
H[0,0][i,j] = h
H[0,0][j,i] = h
S[0,0][i,j] = s
S[0,0][j,i] = s
if any(S[0,0] != 0.0):
for i in range(N):
S[0,0][i,i] = 1.0
else:
S = None
for i0,i1 in [(0,1),(1,1),(1,0),(1,-1)]:
shift = i0 * xyz.period[0] + i1 * xyz.period[1]
H_hop = matrix(zeros((N,N)))
S_hop = matrix(zeros((N,N)))
for i in range(N):
for j in range(N):
h,s = params(norm(xyz.atoms[i].pos - (xyz.atoms[j].pos + shift)))
H_hop[i,j] = h
S_hop[i,j] = h
if any(H_hop != 0.0):
H[i0,i1] = H_hop
if S is None:
assert all(S_hop == 0.0)
else:
S[i0,i1] = S_hop
else:
assert all(S_hop == 0.0)
return sheet.sheet(H,xyz,S=S)
opt = parse_opts()
opt.class_counts = (125, 352)
opt.snippet_length = 1 # Numbertemporal_transform of frames composing the snippet, 1 for RGB, 5 for optical flow
opt.snippet_channels = 3 # Number of channels in a frame, 3 for RGB, 2 for optical flow
#memory logdata
logdata = [
opt.video_root, opt.batch_size, opt.epoch_num, opt.category_num,
opt.class_type, opt.train_val, opt.crop_position, opt.cropSsize,
str(opt.cropCsize), opt.cropRsize, opt.framesize, opt.temporal_p,
opt.horizon, opt.normalization
]
#Function to pass parameter information to google spread sheet
sheet(logdata)
#image proccesing parameter
image_transforms = [
Scale(opt.cropSsize),
]
video_transforms = [RandomCornerCrop(opt.cropCsize), RandHorFlipVideo()]
vtransforms = ComposeVideo(image_transforms, video_transforms)
# dataset = EpicDataset_4_Tmodel(transforms, class_type=opt.class_type, frame_size=opt.framesize, path=opt.video_root)
dataset = EpicDataset_4_Vmodel(vtransforms,
class_type=opt.class_type,
frame_size=opt.framesize,
path=opt.video_root)
print(opt.cropCsize)
def setup_sheet(self,xyz_sheet,do_cache=True):
at = xyz_sheet.atoms
for a in at:
a.rot4 = matrix(eye(4))
a.rot4[1:4,1:4] = a.rot
period = xyz_sheet.period
Natoms = len(at)
H = {}
S = {}
rho = zeros((Natoms,))
H[0,0] = matrix(zeros((4*Natoms,4*Natoms)))
S[0,0] = matrix(zeros((4*Natoms,4*Natoms)))
for i in range(Natoms):
for j in range(i+1,Natoms):
Rvec = at[i].pos - at[j].pos
drho, h_xyz, s_xyz = self.calc_pair_HS(Rvec)
if drho is None:
continue
rho[i] += drho
rho[j] += drho
H[0,0][4*i:4*i+4,4*j:4*j+4] = at[i].rot4.T * h_xyz * at[j].rot4
S[0,0][4*i:4*i+4,4*j:4*j+4] = at[i].rot4.T * s_xyz * at[j].rot4
def calc_H_S_i0_i1(i0,i1):
shift = i0 * period[0] + i1 * period[1]
h_hop = matrix(zeros((4*Natoms,4*Natoms)))
s_hop = matrix(zeros((4*Natoms,4*Natoms)))
nonzero = False
for i in range(Natoms):
for j in range(Natoms):
Rvec = at[i].pos - (at[j].pos + shift)
drho, h_xyz, s_xyz = self.calc_pair_HS(Rvec)
if drho is None:
continue
nonzero = True
h_hop[4*i:4*i+4,4*j:4*j+4] = at[i].rot4.T * h_xyz * at[j].rot4
s_hop[4*i:4*i+4,4*j:4*j+4] = at[i].rot4.T * s_xyz * at[j].rot4
if nonzero:
H[i0,i1] = h_hop
S[i0,i1] = s_hop
else:
pass
return nonzero
i0 = 0
for i1 in count(1):
nonzero = calc_H_S_i0_i1(i0,i1)
if not nonzero:
break
for i0 in count(1):
i1 = 0
nonzero = calc_H_S_i0_i1(i0,i1)
if not nonzero:
break
for i1 in count(1):
nonzero = calc_H_S_i0_i1(i0,i1)
if not nonzero:
break
for neg_i1 in count(1):
nonzero = calc_H_S_i0_i1(i0,-neg_i1)
if not nonzero:
break
for i in range(Natoms):
rho3 = rho[i]**(1/3.)
h_s = self.alpha_s + self.beta_s * rho3**2 + self.gamma_s * rho3**4 + self.chi_s * rho3**6
h_p = self.alpha_p + self.beta_p * rho3**2 + self.gamma_p * rho3**4 + self.chi_p * rho3**6
H[0,0][4*i,4*i] = h_s
H[0,0][4*i+1,4*i+1] = h_p
H[0,0][4*i+2,4*i+2] = h_p
H[0,0][4*i+3,4*i+3] = h_p
S[0,0][4*i,4*i] = 1.0
S[0,0][4*i+1,4*i+1] = 1.0
S[0,0][4*i+2,4*i+2] = 1.0
S[0,0][4*i+3,4*i+3] = 1.0
for j in range(i):
H[0,0][4*i:4*(i+1),4*j:4*(j+1)] = H[0,0][4*j:4*(j+1),4*i:4*(i+1)].H
S[0,0][4*i:4*(i+1),4*j:4*(j+1)] = S[0,0][4*j:4*(j+1),4*i:4*(i+1)].H
return sheet.sheet(H,S=S,xyz_sheet=xyz_sheet,do_cache=do_cache)
def tight_binding_triozon(xyz_coords,do_cache=True,graphite=False):
# based on the parametrization described in
# doi:10.1103/PhysRevB.64.121401
CC_DIST = param.GRAPHENE_CC_DISTANCE
NN_HOP = param.GRAPHENE_1STNN_HOPPING
TRIO_CUTOFF = param.TRIOZON_CUTOFF
Z_CUTOFF = param.TRIOZON_Z_CUTOFF
BETA = param.TRIOZON_BETA
A = param.TRIOZON_A
DELTA = param.TRIOZON_DELTA
at = xyz_coords.atoms
period = xyz_coords.period
Natoms = len(at)
if isinstance(xyz_coords,xyz.chain):
if graphite:
def hopping(pos_a,pos_b):
if abs(pos_a[2] - pos_b[2]) > Z_CUTOFF:
return 0.0
elif abs(pos_a[1]-pos_b[1]) < CC_DIST*0.1:
if norm(pos_a - pos_b) < CC_DIST*1.1:
return -NN_HOP
else:
d = norm(pos_b-pos_a);
if d < TRIO_CUTOFF:
return -BETA * exp((A - d)/DELTA);
return 0.0
else: # MWCNT
def vdot(a,b):
sum = 0.0
for i in range(len(a)):
sum += a[i]*b[i]
return sum
def hopping(pos_a,pos_b):
if abs(pos_a[2] - pos_b[2]) > Z_CUTOFF:
return 0.0
elif abs(norm(pos_a[:2])-norm(pos_b[:2])) < CC_DIST*0.1:
if norm(pos_a - pos_b) < CC_DIST*1.1:
return -NN_HOP
else:
d = norm(pos_b-pos_a);
if d < TRIO_CUTOFF:
cos_theta = vdot(pos_a[:2],pos_b[:2])/(norm(pos_a[:2])*norm(pos_b[:2]));
return -BETA * cos_theta * exp((A - d)/DELTA);
return 0.0
elif isinstance(xyz_coords,xyz.sheet):
def hopping(pos_a,pos_b):
if abs(pos_a[2] - pos_b[2]) < CC_DIST*0.1:
if norm(pos_a - pos_b) < CC_DIST*1.1:
return -NN_HOP
else:
d = norm(pos_b-pos_a);
if d < TRIO_CUTOFF:
return -BETA * exp((A - d)/DELTA)
return 0.0
if isinstance(xyz_coords,xyz.chain):
H = [ matrix(zeros((Natoms,Natoms))) ]
for i in range(Natoms):
for j in range(i+1,Natoms):
hop = hopping(at[i].pos,at[j].pos)
if hop != 0.0:
H[0][i,j] = hop
H[0][j,i] = conj(hop)
for n in range(1,100):
h = matrix(zeros((Natoms,Natoms)))
nonzero = False
for i in range(Natoms):
for j in range(Natoms):
hop = hopping(at[i].pos,at[j].pos + period*n)
if hop != 0.0:
nonzero = True
h[i,j] = hop
if not nonzero:
break
H.append(h)
assert n < 99
return chain.chain(H,xyz_coords,do_cache=do_cache)
elif isinstance(xyz_coords,xyz.sheet):
H = {}
H[0,0] = matrix(zeros((Natoms,Natoms)))
for i in range(Natoms):
for j in range(i+1,Natoms):
hop = hopping(at[i].pos,at[j].pos)
if hop != 0.0:
H[0,0][i,j] = hop
H[0,0][j,i] = conj(hop)
for i0 in range(6):
for i1 in range(-6,6):
if i0 == 0 and i1 <= 0:
continue
shift = i0 * period[0] + i1 * period[1]
H_hop = matrix(zeros((Natoms,Natoms)))
nonzero = False
for i in range(Natoms):
for j in range(Natoms):
hop = hopping(at[i].pos,at[j].pos + shift)
if hop != 0.0:
H_hop[i,j] = hop
nonzero = True
if nonzero:
assert norm(shift) <= Z_CUTOFF + norm(period[0]) + norm(period[1])
H[i0,i1] = H_hop
return sheet.sheet(H,xyz_coords,do_cache=do_cache)
