def penalty_inverse(alpha,coef3,x,y,z,l,charges,x_atom,y_atom,z_atom,natoms,nbasis,ne,max_scf,max_d,lbda,eigen,name,write):
energy = rhfenergy(alpha,coef3,x,y,z,l,charges,x_atom,y_atom,z_atom,natoms,nbasis,ne,max_scf,max_d,eigen,name,write)
## Rebuild xyz for basis
x = np.reshape(x,(1,nbasis))
y = np.reshape(y,(1,nbasis))
z = np.reshape(z,(1,nbasis))
xyz = np.concatenate((np.concatenate((x,y),axis=0),z),axis=0).T
coef = np.ones(nbasis,dtype=dtype)
coef = normalization(alpha,coef,l,nbasis)
S = overlapmatrix2(alpha,coef,l,nbasis)
penalty = lbda*1.0e-3/np.sqrt(np.linalg.det(S))
return energy + penalty
def rhfenergy(alpha_old, coef2, xyz, l, charges, xyz_atom, natoms, nbasis,
contr_list, ne, max_scf, max_d, log, eigen, printguess,
readguess, name, write, dtype):
'''
This function returns the rhf function
Parameters:
alpha_old : array
Gaussian exponents
coef2 : array
Contraction coeffients
xyz : array 3N
Gaussian centers
l : array 3N
Angular momentum each entry is a vector
eg. s orbital (0,0,0) or pz (1,0,0)
charges : array
Atom charges
nbasis : int
Number of basis
contr_list: list of integers
Specify the number of orbitals in each atom
ne : int
Number of electrons
max_scf : int
maximum number of scf cycles
log : bool
The exponents are given in log
printguess: str or None
File to print coeff matrix initial guess
readguess : str or None
File that contains coeff matrix initial guess
name : str
Output file name
write : bool
True if printing
dtype : type of output
This is the directive to know if algopy will be used or not
np.float64(1.0) if it is a single point calculation
otherwise, it specify the size of the UTMP, autodifferentiation
Returns:
energy : float
RHF energy
'''
tool_D = 1e-8
tool = 1e-8
if log:
alpha = algopy.exp(alpha_old)
else:
alpha = alpha_old
if type(xyz_atom) != np.ndarray: ## Cover the case of diff xyz atom
coef = normalization(alpha,
coef2,
l,
contr_list,
dtype=np.float64(1.0))
V = nuclearmatrix(alpha,
coef,
xyz,
l,
nbasis,
charges,
xyz_atom,
natoms,
contr_list,
dtype=dtype)
S = overlapmatrix(alpha,
coef,
xyz,
l,
nbasis,
contr_list,
dtype=np.float64(1.0))
T = kineticmatrix(alpha,
coef,
xyz,
l,
nbasis,
contr_list,
dtype=np.float64(1.0))
Eri = erivector(alpha,
coef,
xyz,
l,
nbasis,
contr_list,
dtype=np.float(1.0))
else:
coef = normalization(alpha, coef2, l, contr_list, dtype=dtype)
S = overlapmatrix(alpha, coef, xyz, l, nbasis, contr_list, dtype=dtype)
V = nuclearmatrix(alpha,
coef,
xyz,
l,
nbasis,
charges,
xyz_atom,
natoms,
contr_list,
dtype=dtype)
T = kineticmatrix(alpha, coef, xyz, l, nbasis, contr_list, dtype=dtype)
Eri = erivector(alpha, coef, xyz, l, nbasis, contr_list, dtype=dtype)
Hcore = T + V
if eigen:
eigsys = eigensolver(S)
SqrtLambda = algopy.diag(1. / algopy.sqrt(eigsys[0]))
L = eigsys[1]
LT = algopy.transpose(L)
SqrtS = algopy.dot(algopy.dot(L, SqrtLambda), LT)
SqrtST = algopy.transpose(SqrtS)
else:
Sinv = np.linalg.inv(S)
if readguess != None:
C = np.load(readguess)
D = np.zeros((nbasis, nbasis))
for i in range(nbasis):
for j in range(nbasis):
tmp = 0.0
for k in range(ne):
tmp = tmp + C[i, k] * C[j, k]
D[i, j] = tmp
F = fockmatrix(Hcore, Eri, D, nbasis, alpha, dtype)
else:
F = Hcore
OldE = 1e8
status = False
E_step = []
for scf_iter in range(max_scf):
if eigen:
Fprime = algopy.dot(algopy.dot(SqrtST, F), SqrtS)
eigsysFockOp = eigensolver(Fprime)
Cprime = eigsysFockOp[1]
C = algopy.dot(SqrtS, Cprime)
Fprime = algopy.dot(algopy.dot(SqrtST, F), SqrtS)
eigsysFockOp = eigensolver(Fprime)
Cprime = eigsysFockOp[1]
C = algopy.dot(SqrtS, Cprime)
D = algopy.zeros((nbasis, nbasis), dtype=dtype)
for i in range(nbasis):
for j in range(nbasis):
tmp = 0.0
for k in range(ne):
tmp = tmp + C[i, k] * C[j, k]
D[i, j] = tmp
else:
D = newdensity(F, Sinv, nbasis, ne)
for i in range(max_d):
D = cannonicalputication(D, S)
err = np.linalg.norm(D - np.dot(np.dot(D, S), D))
if err < tool_D:
break
F = fockmatrix(Hcore, Eri, D, nbasis, alpha, dtype)
E_elec = algopy.sum(np.multiply(D, Hcore + F))
E_step.append(E_elec)
E_nuc = nuclearrepulsion(xyz_atom, charges, natoms)
if np.absolute(E_elec - OldE) < tool:
status = True
break
OldE = E_elec
E_nuc = nuclearrepulsion(xyz_atom, charges, natoms)
if printguess != None:
np.save(printguess, C)
def update_system():
mol.energy = E_elec + E_nuc
mol.erepulsion = Eri
mol.hcore = Hcore
mol.mo_coeff = C
return
def write_molden():
import Data
from Data import select_atom
## Details of calculation
tape.write('[Energy] \n')
tape.write('E_elec: ' + str(E_elec) + '\n')
tape.write('E_nuc: ' + str(E_nuc) + '\n')
tape.write('E_tot: ' + str(E_nuc + E_elec) + '\n')
tape.write('SCF Details\n')
line = 'Eigen: '
if eigen:
tape.write(line + 'True')
else:
tape.write(line + 'False')
tape.write('\n')
for i, step in enumerate(E_step):
line = 'Step: ' + str(i) + ' ' + str(step)
tape.write(line + '\n')
### C Matrix
tape.write('[CM] \n')
tape.write('C AO times MO\n')
printmatrix(C, tape)
### D Matrix
tape.write('[DM] \n')
tape.write('D \n')
printmatrix(D, tape)
### D Matrix
tape.write('[NMO] \n')
tape.write('NMO \n')
printmatrix(mo_naturalorbital(D), tape)
### MO energies
tape.write('[MOE] \n')
tape.write('MOE \n')
for i, energ in enumerate(eigsysFockOp[0]):
tape.write(str(i) + ' ' + str(energ) + '\n')
### MO energies
tape.write('[INPUT] \n')
line = 'mol = ['
for i, coord in enumerate(xyz_atom):
line += '(' + str(charges[i]) + ','
line += '(' + str(coord[0]) + ',' + str(coord[1]) + ',' + str(
coord[2]) + ')),\n'
tape.write(line)
cont = 0
line = 'basis = ['
for i, ci in enumerate(contr_list):
line += '['
line += '(' + str(l[i][0]) + ',' + str(l[i][1]) + ',' + str(
l[i][2]) + '),'
for ii in range(ci):
line += str(alpha[cont]) + ',' + str(coef[i])
line += ',(' + str(xyz[i, 0]) + ',' + str(
xyz[i, 1]) + ',' + str(xyz[i, 2]) + ')],\n'
cont += 1
line += ']\n'
tape.write(line)
### Atom coordinates
tape.write('[Atoms]\n')
for i, coord in enumerate(xyz_atom):
line = select_atom.get(charges[i])
line += ' ' + str(i + 1) + ' ' + str(charges[i])
line += ' ' + str(coord[0]) + ' ' + str(coord[1]) + ' ' + str(
coord[2]) + '\n'
tape.write(line)
### Basis coordinates
for i, coord in enumerate(xyz):
line = 'XX'
line += ' ' + str(i + natoms + 1) + ' ' + str(0)
line += ' ' + str(coord[0]) + ' ' + str(coord[1]) + ' ' + str(
coord[2]) + '\n'
tape.write(line)
### Basis set
cont = 0
tape.write('[GTO]\n')
for i, ci in enumerate(contr_list):
tape.write(' ' + str(i + 1 + natoms) + ' 0\n')
if np.sum(l[i]) == 0:
tape.write(' s ' + str(ci) + ' 1.0 ' + str(l[i][0]) + ' ' +
str(l[i][1]) + ' ' + str(l[i][2]) + '\n')
else:
tape.write(' p ' + str(ci) + ' 1.0 ' + str(l[i][0]) + ' ' +
str(l[i][1]) + ' ' + str(l[i][2]) + '\n')
#tape.write(' p '+str(1)+' 1.0 '+ str(l[i])+'\n')
for ii in range(ci):
line = ' ' + str(alpha[cont]) + ' ' + str(coef[cont]) + '\n'
tape.write(line)
cont += 1
line = ' \n'
tape.write(line)
### MOs
tape.write('[MO]\n')
for j in range(nbasis):
tape.write(' Sym= None\n')
tape.write(' Ene= ' + str(eigsysFockOp[0][j]) + '\n')
tape.write(' Spin= Alpha\n')
if j > ne:
tape.write(' Occup= 0.0\n')
else:
tape.write(' Occup= 2.0\n')
for i in range(nbasis):
tape.write(str(i + 1 + natoms) + ' ' + str(C[i, j]) + '\n')
if status:
if write:
tape = open(name + '.molden', "w")
write_molden()
tape.close()
return E_elec + E_nuc
else:
print('E_elec: ' + str(E_elec) + '\n')
print('E_nuc: ' + str(E_nuc) + '\n')
print('E_tot: ' + str(E_nuc + E_elec) + '\n')
print('SCF DID NOT CONVERGED')
return 99999
return E_elec + E_nuc