def sub():
box = uni.dimensions[0:3]
v1 = sel2.positions - sel1.positions
v2 = sel1.positions - sel3.positions
v1 = vft.pbc_corr(v1.T, box)
v2 = vft.pbc_corr(v2.T, box)
return v1, v2
def sub():
box = uni.dimensions[0:3]
vZ = sel1.positions - sel2.positions
vXZ = sel3.positions - sel2.positions
vZ = vft.pbc_corr(vZ.T, box)
vXZ = vft.pbc_corr(vXZ.T, box)
return vZ, vXZ
def vfun():
v = list()
for v1, v2, v3, v4, v5 in zip(sel1, sel2, sel3, sel4, sel5):
v0 = np.array([
v2.position - v1.position, v3.position - v1.position,
v4.position - v1.position, v5.position - v1.position
])
box = uni.dimensions[:3]
v.append(vft.pbc_corr(v0.T, box))
return v
def sub():
R = list()
box = uni.dimensions[:3]
for s, vr, i in zip(sel, vref, i0):
v = vft.pbc_corr(
np.diff(s.positions[i], axis=0).T,
box) #Calculate vectors, periodic boundary correction
R.append(vft.RMSalign(vr, v)) #Get alignment to reference vector
return vft.R2vec(R) #This converts R back into two vectors
def vfun():
v = list()
for CA, H, N, Cm1, Om1, CAm1 in zip(selCA, selH, selN, selCm1,
selOm1, selCAm1):
v0 = np.array([
CA.position - N.position, H.position - N.position,
N.position - Cm1.position, Cm1.position - Om1.position,
Cm1.position - CAm1.position
])
box = uni.dimensions[:3]
v.append(vft.pbc_corr(v0.T, box))
return v
def sub():
"Calculate planes for each element in grid"
X, Y = grid()
v = list()
box = uni.dimensions[:3]
for x, y in zip(X, Y):
v0 = vft.pbc_corr(np.transpose(sel.positions - [x, y, 0]), box)
d2 = v0[0]**2 + v0[1]**2
i = d2 > 3 * sigma
weight = np.exp(-d2[i] / (2 * sigma**2))
v.append(vft.RMSplane(v0[:, i], np.sqrt(weight)))
v = np.transpose(v)
return v / np.sign(v[2])
def sub():
vnorm = list()
box = uni.dimensions[:3]
for s in sel:
v0 = vft.pbc_pos(s.positions.T, box)
vnorm.append(vft.principle_axis_MOI(v0)[:, 0])
vnorm = np.array(vnorm)
#Pre-allocate output vector, to point along z
v1 = np.zeros([3, sel1.n_atoms])
v1[2] = 1
v2 = v1.copy()
v0 = vft.pbc_corr((sel1.positions - sel2.positions).T, box)
for k, vn in enumerate(vnorm):
v1[:, k == index] = vft.projXY(v0[:, k == index], vn)
v2[:, k == index] = np.array([vn]).T.repeat((k == index).sum(),
axis=1)
return v1, v2
def sub():
vnorm = MOIsub()
#Pre-allocate output vector, to point along z
vZ = np.zeros([3, sel1.n_atoms])
vZ[2] = 1 #If a bond not in index, then vZ just on Z
# vXZ=np.zeros([3,sel1.n_atoms])
# vXZ[0]=1 #If a bond not in index, then vXZ just along x
sc = np.array(vft.getFrame(vnorm)).T
v00 = vft.norm(vft.pbc_corr((sel1.positions - sel2.positions).T, box))
for k, (vn, sc0) in enumerate(zip(vnorm.T, sc)):
v0 = v00[:, k == index]
cb = v0[0] * vn[0] + v0[1] * vn[1] + v0[2] * vn[
2] #Angle between MOI and bond
cb[cb > 1] = 1.0
sb = np.sqrt(1 - cb**2)
v0 = np.concatenate(([sb], [np.zeros(sb.shape)], [cb]), axis=0)
"Here, we keep the vector fixed in the xz plane of the MOI frame"
vZ[:, k == index] = vft.R(v0, *sc0)
# vZ[:,k==index]=v0
# vXZ[:,k==index]=np.atleast_2d(vn).T.repeat(v0.shape[1],1)
return vZ
def sub():
box = molecule.mda_object.dimensions[:3]
v = selC1.positions - selC2.positions
v = vft.pbc_corr(v.T, box)
return v
def sub():
box = uni.dimensions[0:3]
v = sel2.positions - sel1.positions
v = vft.pbc_corr(v.T, box)
return v
