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dft_zmp/n2v.patched/methods/zmp.py

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import
2024-02-26 10:43:50 +01:00
"""
zmp.py
Functions associated with zmp inversion
"""
import psi4
psi4.core.be_quiet()
import numpy as np
from functools import reduce
eps = np.finfo(float).eps
#added by Ehsan
import matplotlib.pyplot as plt
class ZMP():
"""
ZMP Class
Performs ZMP optimization according to:
1) 'From electron densities to Kohn-Sham kinetic energies, orbital energies,
exchange-correlation potentials, and exchange-correlation energies' by
Zhao + Morrison + Parr.
https://doi.org/10.1103/PhysRevA.50.2138
"""
def zmp(self,
opt_max_iter=100,
opt_tol= psi4.core.get_option("SCF", "D_CONVERGENCE"),
lambda_list=[70],
zmp_mixing = 1,
print_scf = False,
):
"""
Performs ZMP optimization according to:
1) 'From electron densities to Kohn-Sham kinetic energies, orbital energies,
exchange-correlation potentials, and exchange-correlation energies' by
Zhao + Morrison + Parr.
https://doi.org/10.1103/PhysRevA.50.2138
Additional DIIS algorithms obtained from:
2) 'Psi4NumPy: An interactive quantum chemistry programming environment
for reference implementations and rapid development.' by
Daniel G.A. Smith and others.
https://doi.org/10.1021/acs.jctc.8b00286
Functionals that drive the SCF procedure are obtained from:
https://doi.org/10.1002/qua.26400
Parameters:
-----------
lambda_list: list
List of Lamda parameters used as a coefficient for Hartree
difference in SCF cycle.
zmp_mixing: float, optional
mixing \in [0,1]. How much of the new potential is added in.
For example, zmp_mixing = 0 means the traditional ZMP, i.e. all the potentials from previous
smaller lambda are ignored.
Zmp_mixing = 1 means that all the potentials of previous lambdas are accumulated, the larger lambda
potential are meant to fix the wrong/inaccurate region of the potential of the sum of the previous
potentials instead of providing an entire new potentials.
default: 1
opt_max_iter: float
Maximum number of iterations for scf cycle
opt_tol: float
Convergence criteria set for Density Difference and DIIS error.
return:
The result will be stored in self.proto_density_a and self.proto_density_b
For zmp_mixing==1, restricted (ref==1):
self.proto_density_a = \sum_i lambda_i * (Da_i - Dt[0]) - 1/N * (Dt[0])
self.proto_density_b = \sum_i lambda_i * (Db_i - Dt[1]) - 1/N * (Dt[1]);
unrestricted (ref==1):
self.proto_density_a = \sum_i lambda_i * (Da_i - Dt[0]) - 1/N * (Dt[0] + Dt[1])
self.proto_density_b = \sum_i lambda_i * (Db_i - Dt[1]) - 1/N * (Dt[0] + Dt[1]);
For restricted (ref==1):
vxc = \int dr' \frac{self.proto_density_a + self.proto_density_b}{|r-r'|}
= 2 * \int dr' \frac{self.proto_density_a}{|r-r'|};
for unrestricted (ref==2):
vxc_up = \int dr' \frac{self.proto_density_a}{|r-r'|}
vxc_down = \int dr' \frac{self.proto_density_b}{|r-r'|}.
To get potential on grid, one needs to do
vxc = self.on_grid_esp(Da=self.proto_density_a, Db=self.proto_density_b, grid=grid) for restricted;
vxc_up = self.on_grid_esp(Da=self.proto_density_a, Db=np.zeros_like(self.proto_density_a),
grid=grid) for unrestricted;
"""
self.diis_space = 100
self.mixing = zmp_mixing
print("\nRunning ZMP:")
self.zmp_scf(lambda_list, opt_max_iter, print_scf, D_conv=opt_tol)
def zmp_scf(self,
lambda_list,
maxiter,
print_scf,
D_conv):
"""
Performs scf cycle
Parameters:
zmp_functional: options the penalty term.
But others are not currently working except for Hartree penalty (original ZMP).
----------
"""
# Target density on grid
if self.ref == 1:
# density() is a method in the class Psi4Grider() in module psi4grider.py (added by Ehsan)
D0 = self.eng.grid.density(Da=self.Dt[0])
else:
D0 = self.eng.grid.density(Da=self.Dt[0], Db=self.Dt[1])
# Initialize Stuff
vc_previous_a = np.zeros((self.nbf, self.nbf))
vc_previous_b = np.zeros((self.nbf, self.nbf))
self.Da = self.Dt[0]
self.Db = self.Dt[1]
Da = self.Dt[0]
Db = self.Dt[1]
Cocca = self.ct[0]
#print("Cocca: ", Cocca, type(Cocca))
Coccb = self.ct[1]
grid_diff_old = 1/np.finfo(float).eps
self.proto_density_a = np.zeros_like(Da)
self.proto_density_b = np.zeros_like(Db)
#-------------> Iterating over lambdas:
Ddif = []
L = []
for lam_i in lambda_list:
self.shift = 0.1 * lam_i
D_old = self.Dt[0]
# Trial & Residual Vector Lists
state_vectors_a, state_vectors_b = [], []
error_vectors_a, error_vectors_b = [], []
for SCF_ITER in range(1,maxiter):
#-------------> Generate Fock Matrix:
vc = self.generate_s_functional(lam_i,
Cocca, Coccb,
Da, Db)
#Equation 10 of Reference (1). Level shift.
Fa = self.T + self.V + self.va + vc[0] + vc_previous_a
Fa += (self.S2 - reduce(np.dot, (self.S2, Da, self.S2))) * self.shift
#added by Ehsan: a function (np.dot : dot product) applies on an iterable (self.S2, Da, self.S2) and gives one output (a new matrix)
if self.ref == 2:
Fb = self.T + self.V + self.vb + vc[1] + vc_previous_b
Fb += (self.S2 - reduce(np.dot, (self.S2, Db, self.S2))) * self.shift
#-------------> DIIS:
if SCF_ITER > 1:
#Construct the AO gradient
# r = (A(FDS - SDF)A)_mu_nu
# added by Ehsan (self.A: Inverse squared root of S matrix), grad_a is a matrix showing the gradients
grad_a = self.A.dot(Fa.dot(Da).dot(self.S2) - self.S2.dot(Da).dot(Fa)).dot(self.A)
grad_a[np.abs(grad_a) < eps] = 0.0
if SCF_ITER < self.diis_space:
state_vectors_a.append(Fa.copy())
error_vectors_a.append(grad_a.copy())
else:
state_vectors_a.append(Fa.copy())
error_vectors_a.append(grad_a.copy())
del state_vectors_a[0]
del error_vectors_a[0]
#Build inner product of error vectors
#dimension of the DIIS subspace = Bdim (by Ehsan)
Bdim = len(state_vectors_a)
# one column and one row are added to the matrix to be fiiled with -1 (this is part of the DIIS prodecure)
#np.empty: the elements of the array will initially contain whatever data was already in the memory allocated for the array
Ba = np.empty((Bdim + 1, Bdim + 1))
# sets the last row and the last column of the matrix Ba to -1
Ba[-1, :] = -1
Ba[:, -1] = -1
Ba[-1, -1] = 0
Bb = Ba.copy()
for i in range(len(state_vectors_a)):
for j in range(len(state_vectors_a)):
# Ba[i,j] will be a number made of the sum of inner products of corresponding elements in matrices
Ba[i,j] = np.einsum('ij,ij->', error_vectors_a[i], error_vectors_a[j])
#Build almost zeros matrix to generate inverse.
RHS = np.zeros(Bdim + 1)
RHS[-1] = -1
#Find coefficient matrix:
# x = np.linalg.solve(A, b) Solve the linear system A*x = b
Ca = np.linalg.solve(Ba, RHS.copy())
Ca[np.abs(Ca) < eps] = 0.0
#Generate new fock Matrix:
Fa = np.zeros_like(Fa)
# .shape[0] gives the number of rows in a 2D array
for i in range(Ca.shape[0] - 1):
Fa += Ca[i] * state_vectors_a[i]
#diis_error_a is the maximum error element in the last error vectors matrix
diis_error_a = np.max(np.abs(error_vectors_a[-1]))
if self.ref == 1:
Fb = Fa.copy()
diis_error = 2 * diis_error_a
else:
grad_b = self.A.dot(Fb.dot(Db).dot(self.S2) - self.S2.dot(Db).dot(Fb)).dot(self.A)
grad_b[np.abs(grad_b) < eps] = 0.0
if SCF_ITER < self.diis_space:
state_vectors_b.append(Fb.copy())
error_vectors_b.append(grad_b.copy())
else:
state_vectors_b.append(Fb.copy())
error_vectors_b.append(grad_b.copy())
del state_vectors_b[0]
del error_vectors_b[0]
for i in range(len(state_vectors_b)):
for j in range(len(state_vectors_b)):
Bb[i,j] = np.einsum('ij,ij->', error_vectors_b[i], error_vectors_b[j])
diis_error_b = np.max(np.abs(error_vectors_b[-1]))
diis_error = diis_error_a + diis_error_b
Cb = np.linalg.solve(Bb, RHS.copy())
Cb[np.abs(Cb) < eps] = 0.0
Fb = np.zeros_like(Fb)
for i in range(Cb.shape[0] - 1):
Fb += Cb[i] * state_vectors_b[i]
# for the first iteration the error is set to 1.0
else:
diis_error = 1.0
#-------------> Diagonalization | Check convergence:
# diagonalize() method has been defined in inventer.py . the inputs are fock matrix and number of occupied orbitals
# this is to find the new density matrix. Here the eigenfunction is solved to get eigenvalues and coefficients
Ca, Cocca, Da, eigs_a = self.diagonalize(Fa, self.nalpha)
# eigs_a is a one dimensioanl matrix (size = nbf) of eigenvalues or enrgies
if self.ref == 2:
Cb, Coccb, Db, eigs_b = self.diagonalize(Fb, self.nbeta)
else:
Cb, Coccb, Db, eigs_b = Ca.copy(), Cocca.copy(), Da.copy(), eigs_a.copy()
#difference of the new and old density matrices
ddm = D_old - Da
D_old = Da
# the maximum element in the differnce denstiy matrix is taken as the density error value
derror = np.max(np.abs(ddm))
if print_scf:
if np.mod(SCF_ITER,5) == 0.0:
print(f"Iteration: {SCF_ITER:3d} | Self Convergence Error: {derror:10.5e} | DIIS Error: {diis_error:10.5e}")
#DIIS error may improve as fast as the D_conv. Relax the criteria an order of magnitude.
if abs(derror) < D_conv and abs(diis_error) < D_conv*10:
# here SCF convergence is reached
break
if SCF_ITER == maxiter - 1:
raise ValueError("ZMP Error: Maximum Number of SCF cycles reached. Try different settings.")
if self.ref == 1:
# map the current density on grid with n points depending on the size of basis set
density_current = self.eng.grid.density(Da=Da)
else:
density_current_a = self.eng.grid.density(Da=Da, Db=Db)
#the difference between the current and exact density is evaluated on grid
grid_diff = np.max(np.abs(D0 - density_current))
if np.abs(grid_diff_old) < np.abs(grid_diff):
# This is a greedy algorithm: if the density error stopped improving for this lambda, we will stop here.
print(f"\nZMP halted at lambda={lam_i}. Density Error Stops Updating: old: {grid_diff_old}, current: {grid_diff}.")
break
grid_diff_old = grid_diff
print(f"SCF Converged for lambda:{int(lam_i):5d}. Max density difference: {grid_diff}")
#added by Ehsan
Ddif.append(grid_diff)
L.append(lam_i)
# D0 is on grid. density_current is also on grid.
# Dt[Dta,Dtb] and Da or Db are just arrays or matrices
self.proto_density_a += lam_i * (Da - self.Dt[0]) * self.mixing
if self.ref == 2:
self.proto_density_b += lam_i * (Db - self.Dt[1]) * self.mixing
else:
self.proto_density_b = self.proto_density_a.copy()
vc_previous_a += vc[0] * self.mixing
if self.ref == 2:
#add a portion of previous vc to the new one
vc_previous_b += vc[1] * self.mixing
# this is the lambda that is already proven to be improving the density, i.e. the corresponding
# potential has updated to proto_density
successful_lam = lam_i
# The proto_density corresponds to successful_lam
successful_proto_density = [(Da - self.Dt[0]), (Db - self.Dt[1])]
# -------------> END Iterating over lambdas:
#added by Ehsan
plt.plot(L, Ddif)
plt.xlabel('Lambda')
plt.ylabel('Delta-Density')
plt.title(f"basis set: {self.basis}")
plt.savefig('Lam_D_' + self.basis+ '.pdf')
plt.close()
self.proto_density_a += successful_lam * successful_proto_density[0] * (1 - self.mixing)
if self.guide_components.lower() == "fermi_amaldi":
# for ref==1, vxc = \int dr (proto_density_a + proto_density_b)/|r-r'| - 1/N*vH
if self.ref == 1:
self.proto_density_a -= (1 / (self.nalpha + self.nbeta)) * (self.Dt[0])
# for ref==1, vxc = \int dr (proto_density_a)/|r-r'| - 1/N*vH
else:
self.proto_density_a -= (1 / (self.nalpha + self.nbeta)) * (self.Dt[0] + self.Dt[1])
self.Da = Da
self.Ca = Ca
self.Coca = Cocca
self.eigvecs_a = eigs_a
if self.ref == 2:
self.proto_density_b += successful_lam * successful_proto_density[1] * (1 - self.mixing)
if self.guide_components.lower() == "fermi_amaldi":
# for ref==1, vxc = \int dr (proto_density_a + proto_density_b)/|r-r'| - 1/N*vH
# an inner if caluse with an opposite condition!!!
if self.ref == 1:
self.proto_density_b -= (1 / (self.nalpha + self.nbeta)) * (self.Dt[1])
# for ref==1, vxc = \int dr (proto_density_a)/|r-r'| - 1/N*vH
else:
self.proto_density_b -= (1 / (self.nalpha + self.nbeta)) * (self.Dt[0] + self.Dt[1])
self.Db = Db
self.Cb = Cb
self.Cocb = Coccb
self.eigvecs_b = eigs_b
else:
self.proto_density_b = self.proto_density_a.copy()
self.Db = self.Da.copy()
self.Cb = self.Ca.copy()
self.Cocb = self.Coca.copy()
self.eigvecs_b = self.eigvecs_a.copy()
def generate_s_functional(self, lam, Cocca, Coccb, Da, Db):
"""
Generates S_n Functional as described in:
https://doi.org/10.1002/qua.26400
"""
# J is the Coulomb Matrix (note added by Ehsan)
J = self.eng.compute_hartree(Cocca, Coccb)
# J is computed from the occupied orbitals with the compoute_hartree() method in engine/psi4.py
# the matrix Cocc is typically an n×m matrix, where n is the total number of basis functions and m is the number of occupied orbitals.
# J[0] corresponds to the Coulomb Matrix based on alpha occupied orbitals (note added by Ehsan)
# Here density (D0) is not directly used!
#D0 = Cocc x Cocc*+, Cocc*+ is the conjugate transpose of the coefficient matrix of occupied orbitals
#Equation 7 of Reference (1), which gives Vc(r) for each lambda (original ZMP paper)
if self.ref == 1:
vc_a = 2 * lam * ( J[0] - self.J0[0] )
self.vca = J[0] - self.J0[0]
vc = [vc_a]
else:
vc_a = lam * ( J[0] - self.J0[0] )
vc_b = lam * ( J[1] - self.J0[1] )
vc = [vc_a, vc_b]
# in practice Vc(r) will be a matrix (nbf x nbf) obtained from the difference between two Coulomb matrices
return vc
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