def __init__(self, symbol, configuration = None, xc = LDA,
maxiter = 200, mixing = 0.4, tol = 1e-6, output = None,
write = None):
"""
DFT atomic calculation.
Parameters:
symbol chemical symbol
configuration '[He] 2s2 2p2', overrides default from table
xc XC functional (LDA default)
"""
# store parameters
self.element = Element(symbol)
if configuration == None:
self.configuration = self.element.get_configuration()
else:
self.configuration = configuration
self.xc = xc
self.maxiter = maxiter
self.mixing = mixing
self.tol = tol
self.write = write
self.set_output(output)
# initialize grid, orbitals, energies
self.grid = RadialGrid(self.element.get_atomic_number())
self.setup_orbitals()
# print header
self.print_header()
def inertia(atoms, xyz):
## This function calculate principal axis
xyz = np.array([i for i in xyz]) # copy the array to avoid changing it
mass = []
for i in atoms:
m = Element(i).getMass()
mass.append(m)
mass = np.array(mass)
xyz -= np.average(xyz, weights=mass, axis=0)
xx = 0.0
yy = 0.0
zz = 0.0
xy = 0.0
xz = 0.0
yz = 0.0
for n, i in enumerate(xyz):
xx += mass[n] * (i[1]**2 + i[2]**2)
yy += mass[n] * (i[0]**2 + i[2]**2)
zz += mass[n] * (i[0]**2 + i[1]**2)
xy += -mass[n] * i[0] * i[1]
xz += -mass[n] * i[0] * i[2]
yz += -mass[n] * i[1] * i[2]
I = np.array([[xx, xy, xz], [xy, yy, yz], [xz, yz, zz]])
eigval, eigvec = np.linalg.eig(I)
return eigvec[np.argmax(eigval)]
def _read_coord(self, xyz):
xyz = np.array(xyz)
natom = len(xyz)
T = xyz[:, 0]
R = xyz[:, 1:].astype(float)
M = np.array([Element(x).getMass() * 1822.8852
for x in T]).reshape([-1, 1])
return T, R, M
def Readinitcond(trvm):
## This function read coordinates from sampled initial condition
## This function return coordinates in a numpy array
## The elements are presented by the nuclear number
## This function also return a list of atomic mass in amu
## 1 g/mol = 1822.8852 amu
natom = len(trvm)
xyz = []
velo = np.zeros((natom, 3))
mass = np.zeros((natom, 1))
for i, line in enumerate(trvm):
e, x, y, z, vx, vy, vz, m, chrg = line
xyz.append([e, x, y, z])
m = Element(e).getMass()
velo[i, 0:3] = float(vx), float(vy), float(vz)
mass[i, 0:1] = float(m) * 1822.8852
return xyz, mass, velo
def Readcoord(title):
## This function read coordinates from a xyz file
## This function return coordinates in a numpy array
## The elements are presented by the nuclear number
## This function also return a list of atomic mass in amu
## 1 g/mol = 1822.8852 amu
file = open('%s.xyz' % (title)).read().splitlines()
natom = int(file[0])
xyz = []
mass = np.zeros((natom, 1))
for i, line in enumerate(file[2:2 + natom]):
e, x, y, z = line.split()
xyz.append([e, x, y, z])
m = Element(e).getMass()
mass[i, 0:1] = m * 1822.8852
return xyz, mass
