def getCube(inp, dv=None, cube_header=None, **kwargs):
if dv is None:
dv = inp.dv
if not cube_header:
if 'resolution' not in kwargs:
res = 0.2
else:
res = float(kwargs['resolution'])
if 'margin' not in kwargs:
margin = 7.0
else:
margin = float(kwargs['resolution'])
cube_header = getCubeGrid(inp, margin, res)
def getSpace(i):
coord_min = cube_header[0, 1+i]
step = cube_header[1+i, 0]
size = cube_header[1+i, 1+i]
coord_max = coord_min + (step-1)*size
return np.linspace(coord_min, coord_max, step)
coord_axes = [getSpace(i) for i in range(3)]
X, Y, Z = np.meshgrid(*coord_axes, indexing='ij')
step = X.shape
X = X.reshape(X.size)
Y = Y.reshape(Y.size)
Z = Z.reshape(Z.size)
coords = np.array([X,Y,Z]).T
rho = gp.getRho(inp, coords, new=True, dv=dv)
rho = rho.reshape(*step)
cube = qtk.CUBE()
cube.build(inp.molecule, cube_header, rho)
return cube
def coord_rho_sigma(inp, rhoSigma):
coords = inp.grid.points
if rhoSigma is None:
rho = gp.getRho(inp, coords)
sigma = gp.getSigma(inp, coords)
else:
rho, sigma = rhoSigma
return coords, rho, sigma
def E_dv(inp, dv):
dv = inp.normalize(dv)
coords = inp.grid.points
dm = outer(dv, dv)
rho = gp.getRho(inp, coords, dv=dv, new=True)
sigma = gp.getSigma(inp, coords, dv=dv, new=True)
dft = inp.setting['dft_setting']
e_k = np.zeros(len(coords))
for fraction, kf in dft['K'].iteritems():
e_k += fraction * xcio.exc(inp, kf, [rho, sigma], False)
K = inp.grid.integrate(rho * e_k)
V = trace(dm.dot(inp.ext))
int_vee_rho = td(dm, inp.vee, axes=([0, 1], [0, 1]))
U = trace(dm.dot(int_vee_rho)) / 2.
intc = xcio.exc(inp, dft['C'], [rho, sigma], False)
intx = xcio.exc(inp, dft['X'], [rho, sigma], False)
XC = inp.grid.integrate(rho * (intc + intx))
E = K + V + U + XC
return E
def vxc(inp, xcFlag=1, rhoSigma = None, report=True):
if type(xcFlag) is int:
if xcFlag not in xc_dict.values():
qtk.exit("libxc functional id number %d is not valid" % xcFlag)
else:
xc_id = xcFlag
elif type(xcFlag) is str:
if xcFlag not in xc_dict:
qtk.exit("libxc functional id %s is not valid" % xcFlag)
else:
xc_id = xc_dict[xcFlag]
if report:
inp.libxc_report(xc_id, 'vxc')
coords = inp.grid.points
if rhoSigma is None:
rho = gp.getRho(inp, coords)
sigma = gp.getSigma(inp, coords)
else:
rho, sigma = rhoSigma
return libxc_vxc(rho, sigma, len(coords), xc_id)
def dE_ddv(inp, coords=None):
if coords is None:
coords = inp.grid.points
# derivative is buggy...
rho = gp.getRho(inp, coords)
sigma = gp.getSigma(inp, coords)
dft = inp.setting['dft_setting']
dEk_drho = np.zeros(len(coords))
dEk_dsigma = np.zeros(len(coords))
Ek = np.zeros(len(coords))
for fraction, kf in dft['K'].iteritems():
dEk_drho_f, dEk_dsigma_f = xcio.vxc(inp, kf, [rho, sigma], False)
dEk_drho += fraction * dEk_drho_f
dEk_dsigma += fraction * dEk_dsigma_f
Ek += xcio.exc(inp, kf, [rho, sigma], False)
dEc_drho, dEc_dsigma = xcio.vxc(inp, dft['C'], [rho, sigma], False)
dEx_drho, dEx_dsigma = xcio.vxc(inp, dft['X'], [rho, sigma], False)
#Ec = xcio.exc(inp, dft['C'], [rho, sigma], False)
#Ex = xcio.exc(inp, dft['X'], [rho, sigma], False)
dE_drho = dEk_drho + dEc_drho + dEx_drho
dE_dsigma = dEk_dsigma + dEc_dsigma + dEx_dsigma
#epsilon = Ek + Ec + Ex
dE_kxc = np.zeros(len(inp.dv))
for i in range(len(inp.dv)):
drho_dci, dsigma_dci = drhoSigma_dc(inp, i)
rho_dE_dc = dE_drho * drho_dci + dE_dsigma * dsigma_dci
#E_drho_dc = drho_dci * epsilon
integrand = rho_dE_dc
dE_kxc[i] = inp.grid.integrate(integrand)
vee_rho = td(inp.dm, inp.vee, axes=([0, 1], [0, 1]))
dE_ee = 2 * vee_rho.dot(inp.dv)
dE_ext = 2 * inp.ext.dot(inp.dv)
out = dE_kxc + dE_ee + dE_ext
return out
def E(inp, coords=None, **kwargs):
if coords is None:
coords = inp.grid.points
rho = gp.getRho(inp, coords)
sigma = gp.getSigma(inp, coords)
dft = inp.setting['dft_setting']
if 'term' not in kwargs:
e_k = np.zeros(len(coords))
for fraction, kf in dft['K'].iteritems():
e_k += fraction * xcio.exc(inp, kf, [rho, sigma], False)
K = inp.grid.integrate(rho * e_k)
V = trace(inp.dm.dot(inp.ext))
int_vee_rho = td(inp.dm, inp.vee, axes=([0, 1], [0, 1]))
U = trace(inp.dm.dot(int_vee_rho)) / 2.
intc = xcio.exc(inp, dft['C'], [rho, sigma], False)
intx = xcio.exc(inp, dft['X'], [rho, sigma], False)
XC = inp.grid.integrate(rho * (intc + intx))
E = K + V + U + XC
elif kwargs['term'] == 'K':
e_k = np.zeros(len(coords))
for fraction, kf in dft['K'].iteritems():
e_k += fraction * xcio.exc(inp, kf, [rho, sigma], False)
E = inp.grid.integrate(rho * e_k)
elif kwargs['term'] == 'vw':
E = trace(inp.dm.dot(inp.kin))
elif kwargs['term'] == 'U':
int_vee_rho = td(inp.dm, inp.vee, axes=([0, 1], [0, 1]))
E = trace(inp.dm.dot(int_vee_rho)) / 2.
elif kwargs['term'] == 'V':
E = trace(inp.dm.dot(inp.ext))
elif kwargs['term'] == 'X':
intx = xcio.exc(inp, dft['X'], [rho, sigma], False)
E = inp.grid.integrate(rho * intx)
elif kwargs['term'] == 'C':
intc = xcio.exc(inp, dft['C'], [rho, sigma], False)
E = inp.grid.integrate(rho * intc)
elif kwargs['term'] in xc_dict.values() \
or kwargs['term'] in xc_dict:
epsilon = xcio.exc(inp, kwargs['term'], [rho, sigma])
E = inp.grid.integrate(rho * epsilon)
return E