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dft_zmp/n2v.patched/inverter.py

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import
2024-02-26 10:43:50 +01:00
"""
Inverter.py
"""
from warnings import warn
from dataclasses import dataclass
import numpy as np
from opt_einsum import contract
from .methods.zmp import ZMP
from .methods.wuyang import WuYang
from .methods.pdeco import PDECO
from .methods.oucarter import OC
from .methods.mrks import MRKS
from .methods.direct import Direct
#Grider was imported by Ehsan
from .grid.grider import Grider
@dataclass
class V:
"""Stores Potentials on AO"""
T : np.ndarray
class E:
"""Stores Energies"""
# Grider was added by Ehsan
class Inverter(Direct, ZMP, WuYang, PDECO, OC, MRKS, Grider):
"""
Attributes:
----------
mol : Engine.molecule
Molecule class of engine used
basis : Engine.basis
Basis class of engine used
basis_str : str
Basis set
nbf : int
Number of basis functions for main calculation
nalpha : int
Number of alpha electrons
nbeta : int
Number of beta electrons
ref : {1,2}
Reference calculation
1 -> Restricted
2 -> Unrestricted
Dt : List
List of np.ndarray for target density matrices (on AO).
ct : List
List of np.ndarray for input occupied orbitals. This might not be correct for post-HartreeFock methods.
pbs_str: string
name of Potential basis set
pbs : Engine.basis
Basis class for Potential basis set of the engine used.
npbs : int
the length of pbs
v_pbs : np.ndarray shape (npbs, ) for ref==1 and (2*npbs, ) for ref==2.
potential vector on the Potential Baiss Set.
If the potential is not represented on the basis set, this should
remain 0. It will be initialized to a 0 array. One can set this
value for initial guesses before Wu-Yang method (WY) or PDE-Constrained
Optimization method (PDE-CO). For example, if PDE-CO is ran after
a WY calculation, the initial for PDE-CO will be the result of WY
if v_pbs is not zeroed.
S2 : np.ndarray
The ao overlap matrix (i.e. S matrix)
S3 : np.ndarray
The three ao overlap matrix (ao, ao, pbs)
S4 : np.ndarray
The four ao overlap matrix, the size should be (ao, ao, ao, ao)
jk : Engine.jk
Engine jk object.
T : np.ndarray
kinetic matrix on ao
V : np.ndarray
external potential matrix on ao
T_pbs: np.ndarray
kinetic matrix on pbs. Useful for regularization.
guide_potential_components: list of string
guide potential components name
va, vb: np.ndarray of shape (nbasis, nbasis)
guide potential Fock matrix.
"""
def __init__( self, engine='psi4' ):
engine = 'psi4'
self.eng_str = engine.lower()
if engine.lower() == 'psi4':
from .engines import Psi4Engine
self.eng = Psi4Engine()
elif engine.lower() == 'pyscf':
from .engines import PySCFEngine
self.eng = PySCFEngine()
else:
raise ValueError("Engine name is incorrect. The availiable engines are: {psi4, pyscf}")
def __repr__( self ):
return "n2v.Inverter"
def set_system( self, molecule, basis, ref=1, pbs='same' , **kwargs):
"""
Stores relevant information and intitializes Engine
Parameters
----------
molecule: Engine.molecule
Molecule object of selected engine
basis: str
Basis set of the main calculation
ref: int
reference for system. Restricted -> 1
Unrestricted -> 2
pbs: str, default='same'
Basis set for the potential
**kwargs:
Optional Parameters for different Engiens
Psi4 Engine:
wfn : psi4.core.{RHF, UHF, RKS, UKS, Wavefunction, CCWavefuncion...}
Psi4 wavefunction object
PySCF Engine:
None
"""
# Communicate TO engine
self.eng.set_system(molecule, basis, ref, pbs, **kwargs)
self.ref = ref
#added by Ehsan
self.basis = basis
#added by Ehsan
self.molecule = molecule
self.nalpha = self.eng.nalpha
self.nbeta = self.eng.nbeta
# Initialize ecompasses everything the engine builds with basis set
self.eng.initialize()
self.set_basis_matrices()
# Receive FROM engine
self.nbf = self.eng.nbf
self.npbs = self.eng.npbs
self.v_pbs = np.zeros( (self.npbs) ) if self.ref == 1 \
else np.zeros( 2 * self.npbs )
@classmethod
def from_wfn( self, wfn, pbs='same' ):
"""
Generates Inverter directly from wavefunction.
Parameters
----------
wfn: Psi4.Core.{RHF, RKS, ROHF, CCWavefunction, UHF, UKS, CUHF}
Wavefunction Object
Returns
-------
inv: n2v.Inverter
Inverter Object.
"""
from .engines import Psi4Engine
inv = self( engine='psi4' )
inv.eng = Psi4Engine()
ref = 1 if wfn.to_file()['boolean']['same_a_b_dens'] else 2
inv.set_system( wfn.molecule(), wfn.basisset().name(), pbs=pbs, ref=ref, wfn=wfn )
# done by Ehsan
#inv.Dt = [ np.array(wfn.Da()), np.array(wfn.Db()) ]
self.Dt = [ np.array(wfn.Da()), np.array(wfn.Db()) ]
# done by Ehsan
#inv.ct = [ np.array(wfn.Ca_subset("AO", "OCC")), np.array(wfn.Cb_subset("AO", "OCC")) ]
# ct contains matrices of occupied orbitals alpah and betta (n x m)
self.ct = [ np.array(wfn.Ca_subset("AO", "OCC")), np.array(wfn.Cb_subset("AO", "OCC")) ]
inv.et = [ np.array(wfn.epsilon_a_subset("AO", "OCC")), np.array(wfn.epsilon_b_subset("AO", "OCC")) ]
inv.eng_str = 'psi4'
inv.eng.wfn = wfn
return inv
def set_basis_matrices( self ):
"""
Generate basis dependant matrices
"""
self.T = self.eng.get_T()
self.V = self.eng.get_V()
self.A = self.eng.get_A()
self.S2 = self.eng.get_S()
self.S3 = self.eng.get_S3()
if self.eng.pbs_str != 'same':
self.T_pbs = self.eng.get_Tpbas()
self.S4 = None
def compute_hartree( self, Cocc_a, Cocc_b ):
"""
Computes Hartree Potential on AO basis set.
Parameters
----------
Cocc_a, Cocc_b: np.ndarray (nbf, nbf)
Occupied orbitals in ao basis
Returns
-------
J: List of np.ndarray
Hartree potential due to density from Cocc_a and Cocc_b
"""
return self.eng.compute_hartree(Cocc_a, Cocc_b )
def diagonalize( self, matrix, ndocc ):
"""
Diagonalizes Fock Matrix
Parameters
----------
marrix: np.ndarray
Matrix to be diagonalized
ndocc: int
Number of occupied orbitals
Returns
-------
C: np.ndarray
Orbital Matrix
Cocc: np.ndarray
Occupied Orbital Matrix
D: np.ndarray
Density Matrix
eigves: np.ndarray
Eigenvalues
"""
# np.linalg.eigh() gives eigenvalues and eigenvectors for a symmetric matrix of choice
Fp = self.A.dot(matrix).dot(self.A)
# eigvecs must be eigenvalues or energies here!
eigvecs, Cp = np.linalg.eigh(Fp)
C = self.A.dot(Cp)
Cocc = C[:, :ndocc]
# contract converts pi and qi to pq . here two matrices with n x m dimension
#are converted to one matrix with n x n shape,
#In fact it gives the product of Cocc matrix and its transpose matrix
D = contract('pi,qi->pq', Cocc, Cocc)
return C, Cocc, D, eigvecs
def diagonalize_with_potential_vFock(self, v=None):
"""
Diagonalize Fock matrix with additional external potential
Stores values in object.
Parameters
----------
v: np.ndarray
Additional external potential to be added to hamiltonian along with:
Kinetic_nm
External_nm
Guide_Potential_nm
"""
if v is None:
fock_a = self.V + self.T + self.va
else:
if self.ref == 1:
fock_a = self.V + self.T + self.va + v
else:
valpha, vbeta = v
fock_a = self.V + self.T + self.va + valpha
fock_b = self.V + self.T + self.vb + vbeta
self.Ca, self.Coca, self.Da, self.eigvecs_a = self.diagonalize( fock_a, self.nalpha )
if self.ref == 1:
self.Cb, self.Cocb, self.Db, self.eigvecs_b = self.Ca.copy(), self.Coca.copy(), self.Da.copy(), self.eigvecs_a.copy()
else:
self.Cb, self.Cocb, self.Db, self.eigvecs_b = self.diagonalize( fock_b, self.nbeta )
# Actual Methods
def generate_components(self, guide_components, **keywords):
"""
Generates exact potential components to be added to
the Hamiltonian to aide in the inversion procedure.
Parameters:
-----------
guide_potential_components: list
Components added as to guide inversion.
Can be chosen from ["hartree", "fermi_amandi", "svwn"]
"""
self.guide_components = guide_components
self.va = np.zeros( (self.nbf, self.nbf) )
self.vb = np.zeros( (self.nbf, self.nbf) )
self.J0 = self.compute_hartree(self.ct[0], self.ct[1])
N = self.nalpha + self.nbeta
if self.eng_str == 'psi4':
J0_NO = self.eng.hartree_NO(self.Dt[0])
self.J0 = J0_NO if J0_NO is not None else self.J0
if guide_components == 'none':
warn("No guide potential was provided. Convergence may not be achieved")
elif guide_components == 'hartree':
self.va += self.J0[0] + self.J0[1]
self.vb += self.J0[0] + self.J0[1]
elif guide_components == 'fermi_amaldi':
v_fa = (1-1/N) * (self.J0[0] + self.J0[1])
self.va += v_fa
self.vb += v_fa
else:
raise ValueError("Guide component not recognized")
def invert(self, method,
guide_components = 'hartree',
opt_max_iter = 50,
**keywords):
"""
Handler to all available inversion methods
Parameters
----------
method: str
Method used to invert density.
Can be chosen from {wuyang, zmp, mrks, oc}.
See documentation below for each method.
guide_components: list, opt
Components added as to guide inversion.
Can be chosen from {"fermi_amandi", "svwn"}
Default: ["fermi_amaldi"]
opt_max_iter: int, opt
Maximum number of iterations inside the chosen inversion.
Default: 50
direct
------
Direct inversion of a set of Kohn-Sham equations.
$$v_{xc}(r) = \frac{1}{n(r)} \sum_i^N [\phi_i^{*} (r) \nabla^2 \phi_i(r) + \varepsilon_i | \phi_i(r)|^2] $$
Parameters:
-----------
grid: np.ndarray, opt
Grid where result will be expressed in.
If not provided, dft grid will be used instead.
wuyang
------
the Wu-Yang method:
The Journal of chemical physics 118.6 (2003): 2498-2509.
Parameters:
----------
opt_max_iter: int
maximum iteration
opt_method: string, opt
Method for scipy optimizer
Currently only used by wuyang and pdeco method.
Defaul: 'trust-krylov'
https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.minimize.html
reg : float, opt
Regularization constant for Wuyant Inversion.
Default: None -> No regularization is added.
Becomes attribute of inverter -> inverter.lambda_reg
tol: float
tol for scipy.optimize.minimize
gtol: float
gtol for scipy.optimize.minimize: the gradient norm for
convergence
opt: dict
options for scipy.optimize.minimize
Notice that opt has lower priorities than opt_max_iter and gtol.
return:
the result are stored in self.v_pbs
zmp
---
The Zhao-Morrison-Parr Method:
Phys. Rev. A 50, 2138
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;
mRKS
----
the modified Ryabinkin-Kohut-Staroverov method:
Phys. Rev. Lett. 115, 083001
J. Chem. Phys. 146, 084103p
Parameters:
-----------
maxiter: int
same as opt_max_iter
vxc_grid: np.ndarray of shape (3, num_grid_points), opt
When this is given, the final result will be represented
v_tol: float, opt
convergence criteria for vxc Fock matrices.
default: 1e-4
D_tol: float, opt
convergence criteria for density matrices.
default: 1e-7
eig_tol: float, opt
convergence criteria for occupied eigenvalue spectrum.
default: 1e-4
frac_old: float, opt
Linear mixing parameter for current vxc and old vxc.
If 0, no old vxc is mixed in.
Should be in [0,1)
default: 0.5.
init: string or psi4.core.Wavefunction, opt
Initial guess method.
default: "SCAN"
1) If None, input wfn info will be used as initial guess.
2) If "continue" is given, then it will not initialize
but use the densities and orbitals stored. Meaningly,
one can run a quick WY calculation as the initial
guess. This can also be used to user speficified
initial guess by setting Da, Coca, eigvec_a.
3) If it's not continue, it would be expecting a
method name string that works for psi4. A separate psi4 calculation
would be performed.
sing: tuple of float of length 4, opt.
Singularity parameter for _vxc_hole_quadrature()
default: (1e-5, 1e-4, 1e-5, 1e-4)
[0]: atol, [1]: atol1 for dft_spherical grid calculation.
[2]: atol, [3]: atol1 for vxc_grid calculation.
return:
The result will be stored in self.grid.vxc
oc
--
Ou-Carter method
J. Chem. Theory Comput. 2018, 14, 5680−5689
Parameters:
-----------
maxiter: int
same as opt_max_iter
vxc_grid: np.ndarray of shape (3, num_grid_points)
The final result will be represented on this grid
default: 1e-4
D_tol: float, opt
convergence criteria for density matrices.
default: 1e-7
eig_tol: float, opt
convergence criteria for occupied eigenvalue spectrum.
default: 1e-4
frac_old: float, opt
Linear mixing parameter for current vxc and old vxc.
If 0, no old vxc is mixed in.
Should be in [0,1)
default: 0.5.
init: string, opt
Initial guess method.
default: "SCAN"
1) If None, input wfn info will be used as initial guess.
2) If "continue" is given, then it will not initialize
but use the densities and orbitals stored. Meaningly,
one can run a quick WY calculation as the initial
guess. This can also be used to user speficified
initial guess by setting Da, Coca, eigvec_a.
3) If it's not continue, it would be expecting a
method name string that works for psi4. A separate psi4 calculation
would be performed.
wuyang
pdeco
-----
the PDE-Constrained Optimization method:
Int J Quantum Chem. 2018;118:e25425;
Nat Commun 10, 4497 (2019).
Parameters:
----------
opt_max_iter: int
maximum iteration
opt_method: string, opt
Method for scipy optimizer
Currently only used by wuyang and pdeco method.
Defaul: 'L-BFGS-B'
Options: ['L-BFGS-B', 'BFGS']
https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.minimize.html
reg : float, opt
Regularization constant for Wuyant Inversion.
Default: None -> No regularization is added.
Becomes attribute of inverter -> inverter.lambda_reg
gtol: float
gtol for scipy.optimize.minimize: the gradient norm for
convergence
opt: dict
options for scipy.optimize.minimize
Notice that opt has lower priorities than opt_max_iter and gtol.
return:
the result are stored in self.v_pbs
"""
self.generate_components(guide_components)
if method.lower() == "direct":
return self.direct_inversion(**keywords)
elif method.lower() == "wuyang":
self.wuyang(opt_max_iter, **keywords)
elif method.lower() == "zmp":
self.zmp(opt_max_iter, **keywords)
elif method.lower() == "mrks":
if self.eng_str == 'pyscf':
raise ValueError("mRKS method not yet available with the PySCF engine. Try another method or another engine.")
return self.mRKS(opt_max_iter, **keywords)
elif method.lower() == 'oc':
if self.eng_str == 'pyscf':
raise ValueError("OuCarter method not yet available with the PySCF engine. Try another method or another engine.")
return self.oucarter(opt_max_iter, **keywords)
elif method.lower() == 'pdeco':
return self.pdeco(opt_max_iter, **keywords)
else:
raise ValueError(f"Inversion method not available. Methods available: {['wuyang', 'zmp', 'mrks', 'oc', 'pdeco']}")
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