def derJ(D,d2Ints_dXa,d2Ints_dYa,d2Ints_dZa):
#modified from Ints.py -> getJ
"Form the Coulomb operator corresponding to a density matrix D"
nbf = D.shape[0]
D1d = reshape(D,(nbf*nbf,)) #1D version of Dens
dJx = zeros((nbf,nbf),'d')
dJy = zeros((nbf,nbf),'d')
dJz = zeros((nbf,nbf),'d')
for i in xrange(nbf):
for j in xrange(i+1):
xtemp = zeros(nbf*nbf,'d')
ytemp = zeros(nbf*nbf,'d')
ztemp = zeros(nbf*nbf,'d')
kl = 0
for k in xrange(nbf):
for l in xrange(nbf):
index = ijkl2intindex(i,j,k,l)
xtemp[kl] = d2Ints_dXa[index]
ytemp[kl] = d2Ints_dYa[index]
ztemp[kl] = d2Ints_dZa[index]
kl += 1
dJx[i,j] = dot(xtemp,D1d)
dJx[j,i] = dJx[i,j]
dJy[i,j] = dot(ytemp,D1d)
dJy[j,i] = dJy[i,j]
dJz[i,j] = dot(ztemp,D1d)
dJz[j,i] = dJz[i,j]
return dJx,dJy,dJz
def derK(D,d2Ints_dXa,d2Ints_dYa,d2Ints_dZa):
#modified from Ints.py -> getK
"Form the exchange operator corresponding to a density matrix D"
nbf = D.shape[0]
D1d = reshape(D,(nbf*nbf,)) #1D version of Dens
dKx = zeros((nbf,nbf),'d')
dKy = zeros((nbf,nbf),'d')
dKz = zeros((nbf,nbf),'d')
for i in xrange(nbf):
for j in xrange(i+1):
xtemp = zeros(nbf*nbf,'d')
ytemp = zeros(nbf*nbf,'d')
ztemp = zeros(nbf*nbf,'d')
kl = 0
for k in xrange(nbf):
for l in xrange(nbf):
index_k1 = ijkl2intindex(i,k,j,l)
index_k2 = ijkl2intindex(i,l,k,j)
xtemp[kl] = 0.5*(d2Ints_dXa[index_k1]+d2Ints_dXa[index_k2])
ytemp[kl] = 0.5*(d2Ints_dYa[index_k1]+d2Ints_dYa[index_k2])
ztemp[kl] = 0.5*(d2Ints_dZa[index_k1]+d2Ints_dZa[index_k2])
kl += 1
dKx[i,j] = dot(xtemp,D1d)
dKx[j,i] = dKx[i,j]
dKy[i,j] = dot(ytemp,D1d)
dKy[j,i] = dKy[i,j]
dKz[i,j] = dot(ztemp,D1d)
dKz[j,i] = dKz[i,j]
return dKx,dKy,dKz
def derJ(D, d2Ints_dXa, d2Ints_dYa, d2Ints_dZa):
#modified from Ints.py -> getJ
"Form the Coulomb operator corresponding to a density matrix D"
nbf = D.shape[0]
D1d = reshape(D, (nbf * nbf, )) #1D version of Dens
dJx = zeros((nbf, nbf), 'd')
dJy = zeros((nbf, nbf), 'd')
dJz = zeros((nbf, nbf), 'd')
for i in xrange(nbf):
for j in xrange(i + 1):
xtemp = zeros(nbf * nbf, 'd')
ytemp = zeros(nbf * nbf, 'd')
ztemp = zeros(nbf * nbf, 'd')
kl = 0
for k in xrange(nbf):
for l in xrange(nbf):
index = ijkl2intindex(i, j, k, l)
xtemp[kl] = d2Ints_dXa[index]
ytemp[kl] = d2Ints_dYa[index]
ztemp[kl] = d2Ints_dZa[index]
kl += 1
dJx[i, j] = dot(xtemp, D1d)
dJx[j, i] = dJx[i, j]
dJy[i, j] = dot(ytemp, D1d)
dJy[j, i] = dJy[i, j]
dJz[i, j] = dot(ztemp, D1d)
dJz[j, i] = dJz[i, j]
return dJx, dJy, dJz
def derK(D, d2Ints_dXa, d2Ints_dYa, d2Ints_dZa):
#modified from Ints.py -> getK
"Form the exchange operator corresponding to a density matrix D"
nbf = D.shape[0]
D1d = reshape(D, (nbf * nbf, )) #1D version of Dens
dKx = zeros((nbf, nbf), 'd')
dKy = zeros((nbf, nbf), 'd')
dKz = zeros((nbf, nbf), 'd')
for i in xrange(nbf):
for j in xrange(i + 1):
xtemp = zeros(nbf * nbf, 'd')
ytemp = zeros(nbf * nbf, 'd')
ztemp = zeros(nbf * nbf, 'd')
kl = 0
for k in xrange(nbf):
for l in xrange(nbf):
index_k1 = ijkl2intindex(i, k, j, l)
index_k2 = ijkl2intindex(i, l, k, j)
xtemp[kl] = 0.5 * (d2Ints_dXa[index_k1] +
d2Ints_dXa[index_k2])
ytemp[kl] = 0.5 * (d2Ints_dYa[index_k1] +
d2Ints_dYa[index_k2])
ztemp[kl] = 0.5 * (d2Ints_dZa[index_k1] +
d2Ints_dZa[index_k2])
kl += 1
dKx[i, j] = dot(xtemp, D1d)
dKx[j, i] = dKx[i, j]
dKy[i, j] = dot(ytemp, D1d)
dKy[j, i] = dKy[i, j]
dKz[i, j] = dot(ztemp, D1d)
dKz[j, i] = dKz[i, j]
return dKx, dKy, dKz
def allbfs(self):
"Construct a matrix with bfs in columns over the entire grid, "
" so that R[0] is the first basis function, R[1] is the second..."
bfs = []
for agr in self.atomgrids:
bfs.extend(agr.allbfs())
bfs = array(bfs)
npts = self.npts()
nbf,nrem = divmod(len(bfs),npts)
if nrem != 0: raise Exception("Remainder in divmod allbfs")
nbf2 = self.nbf()
if nbf != nbf2: raise Exception("Wrong # bfns %d %d" % (nbf,nbf2))
bfs = reshape(bfs,(npts,nbf))
return bfs
def getK(Ints,D):
"Form the exchange operator corresponding to a density matrix D"
nbf = D.shape[0]
D1d = reshape(D,(nbf*nbf,)) #1D version of Dens
K = zeros((nbf,nbf),'d')
for i in xrange(nbf):
for j in xrange(i+1):
if sorted:
temp = kints[i,j]
else:
temp = fetch_kints(Ints,i,j,nbf)
K[i,j] = dot(temp,D1d)
K[j,i] = K[i,j]
return K
def get2JmK(Ints,D):
"Form the 2J-K integrals corresponding to a density matrix D"
nbf = D.shape[0]
D1d = reshape(D,(nbf*nbf,)) #1D version of Dens
G = zeros((nbf,nbf),'d')
for i in xrange(nbf):
for j in xrange(i+1):
if sorted:
temp = 2*jints[i,j]-kints[i,j]
else:
temp = 2*fetch_jints(Ints,i,j,nbf)-fetch_kints(Ints,i,j,nbf)
G[i,j] = dot(temp,D1d)
G[j,i] = G[i,j]
return G
def getK(Ints, D):
"Form the exchange operator corresponding to a density matrix D"
nbf = D.shape[0]
D1d = reshape(D, (nbf * nbf, )) #1D version of Dens
K = zeros((nbf, nbf), 'd')
for i in xrange(nbf):
for j in xrange(i + 1):
if sorted:
temp = kints[i, j]
else:
temp = fetch_kints(Ints, i, j, nbf)
K[i, j] = dot(temp, D1d)
K[j, i] = K[i, j]
return K
def getJ(Ints,D):
"Form the Coulomb operator corresponding to a density matrix D"
nbf = D.shape[0]
D1d = reshape(D,(nbf*nbf,)) #1D version of Dens
J = zeros((nbf,nbf),'d')
for i in xrange(nbf):
for j in xrange(i+1):
if sorted:
temp = jints[i,j]
else:
temp = fetch_jints(Ints,i,j,nbf)
J[i,j] = dot(temp,D1d)
J[j,i] = J[i,j]
return J
def getJ(Ints, D):
"Form the Coulomb operator corresponding to a density matrix D"
nbf = D.shape[0]
D1d = reshape(D, (nbf * nbf, )) #1D version of Dens
J = zeros((nbf, nbf), 'd')
for i in xrange(nbf):
for j in xrange(i + 1):
if sorted:
temp = jints[i, j]
else:
temp = fetch_jints(Ints, i, j, nbf)
J[i, j] = dot(temp, D1d)
J[j, i] = J[i, j]
return J
def make_bfgrid(self):
"Construct a matrix with bfs in columns over the entire grid, "
" so that R[0] is the first basis function, R[1] is the second..."
bfs = []
for agr in self.atomgrids:
bfs.extend(agr.make_bfgrid())
self.bfgrid = array(bfs)
npts = self.npts()
nbf, nrem = divmod(len(self.bfgrid), npts)
if nrem != 0: raise Exception("Remainder in divmod make_bfgrid")
nbf2 = self.get_nbf()
if nbf != nbf2: raise Exception("Wrong # bfns %d %d" % (nbf, nbf2))
self.bfgrid = reshape(bfs, (npts, nbf))
return
def get2JmK(Ints, D):
"Form the 2J-K integrals corresponding to a density matrix D"
nbf = D.shape[0]
D1d = reshape(D, (nbf * nbf, )) #1D version of Dens
G = zeros((nbf, nbf), 'd')
for i in xrange(nbf):
for j in xrange(i + 1):
if sorted:
temp = 2 * jints[i, j] - kints[i, j]
else:
temp = 2 * fetch_jints(Ints, i, j, nbf) - fetch_kints(
Ints, i, j, nbf)
G[i, j] = dot(temp, D1d)
G[j, i] = G[i, j]
return G
def getK_BTF(Ints, D, nbf1, nbf2, frag_number):
if frag_number == 1:
D1d = reshape(D, (nbf2 * nbf2, )) #1D version of Dens
K = zeros((nbf1, nbf1), 'd')
for i in xrange(nbf1):
for j in xrange(i + 1):
if sorted:
temp = kintsBTF_12[i, j]
else:
temp = fetch_kintsBTF_12(Ints, i, j, nbf1, nbf2)
K[i, j] = dot(temp, D1d)
K[j, i] = K[i, j]
elif frag_number == 2:
D1d = reshape(D, (nbf1 * nbf1, )) #1D version of Dens
K = zeros((nbf2, nbf2), 'd')
for i in xrange(nbf2):
for j in xrange(i + 1):
if sorted:
temp = kintsBTF_21[i, j]
else:
temp = fetch_kintsBTF_21(Ints, i, j, nbf1, nbf2)
K[i, j] = dot(temp, D1d)
K[j, i] = K[i, j]
return K
def getK_BTF(Ints,D,nbf1,nbf2,frag_number):
if frag_number == 1:
D1d = reshape(D,(nbf2*nbf2,)) #1D version of Dens
K = zeros((nbf1,nbf1),'d')
for i in xrange(nbf1):
for j in xrange(i+1):
if sorted:
temp = kintsBTF_12[i,j]
else:
temp = fetch_kintsBTF_12(Ints,i,j,nbf1,nbf2)
K[i,j] = dot(temp,D1d)
K[j,i] = K[i,j]
elif frag_number == 2:
D1d = reshape(D,(nbf1*nbf1,)) #1D version of Dens
K = zeros((nbf2,nbf2),'d')
for i in xrange(nbf2):
for j in xrange(i+1):
if sorted:
temp = kintsBTF_21[i,j]
else:
temp = fetch_kintsBTF_21(Ints,i,j,nbf1,nbf2)
K[i,j] = dot(temp,D1d)
K[j,i] = K[i,j]
return K
def der2JmK(D,d2Ints_dXa,d2Ints_dYa,d2Ints_dZa):
#modified from Ints.py -> get2Jmk
"Form the 2J-K integrals corresponding to a density matrix D"
nbf = D.shape[0]
D1d = reshape(D,(nbf*nbf,)) #1D version of Dens
Gx = zeros((nbf,nbf),'d')
Gy = zeros((nbf,nbf),'d')
Gz = zeros((nbf,nbf),'d')
for i in xrange(nbf):
for j in xrange(i+1):
xtemp = zeros(nbf*nbf,'d')
ytemp = zeros(nbf*nbf,'d')
ztemp = zeros(nbf*nbf,'d')
kl = 0
for k in xrange(nbf):
for l in xrange(nbf):
index_j = ijkl2intindex(i,j,k,l)
index_k1 = ijkl2intindex(i,k,j,l)
index_k2 = ijkl2intindex(i,l,k,j)
xtemp[kl] = 2.*d2Ints_dXa[index_j]-0.5*d2Ints_dXa[index_k1]\
-0.5*d2Ints_dXa[index_k2]
ytemp[kl] = 2.*d2Ints_dYa[index_j]-0.5*d2Ints_dYa[index_k1]\
-0.5*d2Ints_dYa[index_k2]
ztemp[kl] = 2.*d2Ints_dZa[index_j]-0.5*d2Ints_dZa[index_k1]\
-0.5*d2Ints_dZa[index_k2]
kl += 1
Gx[i,j] = dot(xtemp,D1d)
Gx[j,i] = Gx[i,j]
Gy[i,j] = dot(ytemp,D1d)
Gy[j,i] = Gy[i,j]
Gz[i,j] = dot(ztemp,D1d)
Gz[j,i] = Gz[i,j]
return Gx,Gy,Gz
def der2JmK(D, d2Ints_dXa, d2Ints_dYa, d2Ints_dZa):
#modified from Ints.py -> get2Jmk
"Form the 2J-K integrals corresponding to a density matrix D"
nbf = D.shape[0]
D1d = reshape(D, (nbf * nbf, )) #1D version of Dens
Gx = zeros((nbf, nbf), 'd')
Gy = zeros((nbf, nbf), 'd')
Gz = zeros((nbf, nbf), 'd')
for i in xrange(nbf):
for j in xrange(i + 1):
xtemp = zeros(nbf * nbf, 'd')
ytemp = zeros(nbf * nbf, 'd')
ztemp = zeros(nbf * nbf, 'd')
kl = 0
for k in xrange(nbf):
for l in xrange(nbf):
index_j = ijkl2intindex(i, j, k, l)
index_k1 = ijkl2intindex(i, k, j, l)
index_k2 = ijkl2intindex(i, l, k, j)
xtemp[kl] = 2.*d2Ints_dXa[index_j]-0.5*d2Ints_dXa[index_k1]\
-0.5*d2Ints_dXa[index_k2]
ytemp[kl] = 2.*d2Ints_dYa[index_j]-0.5*d2Ints_dYa[index_k1]\
-0.5*d2Ints_dYa[index_k2]
ztemp[kl] = 2.*d2Ints_dZa[index_j]-0.5*d2Ints_dZa[index_k1]\
-0.5*d2Ints_dZa[index_k2]
kl += 1
Gx[i, j] = dot(xtemp, D1d)
Gx[j, i] = Gx[i, j]
Gy[i, j] = dot(ytemp, D1d)
Gy[j, i] = Gy[i, j]
Gz[i, j] = dot(ztemp, D1d)
Gz[j, i] = Gz[i, j]
return Gx, Gy, Gz
