Source code for pennylane.qchem.structure

# Copyright 2018-2020 Xanadu Quantum Technologies Inc.

# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at

#     http://www.apache.org/licenses/LICENSE-2.0

# Unless required by applicable law or agreed to in writing, software
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"""This module contains functions to read the structure of molecules, build a Hartree-Fock state,
build an active space and generate single and double excitations.
"""
# pylint: disable=too-many-locals
import os
from shutil import copyfile

from pennylane import numpy as np

# Bohr-Angstrom correlation coefficient (https://physics.nist.gov/cgi-bin/cuu/Value?bohrrada0)
bohr_angs = 0.529177210903


[docs]def read_structure(filepath, outpath="."): r"""Read the structure of the polyatomic system from a file and returns a list with the symbols of the atoms in the molecule and a 1D array with their positions :math:`[x_1, y_1, z_1, x_2, y_2, z_2, \dots]` in atomic units (Bohr radius = 1). The atomic coordinates in the file must be in Angstroms. The `xyz <https://en.wikipedia.org/wiki/XYZ_file_format>`_ format is supported. Additionally, the new file ``structure.xyz``, containing the input geometry, is created in a directory with path given by ``outpath``. Args: filepath (str): name of the molecular structure file in the working directory or the absolute path to the file if it is located in a different folder outpath (str): path to the output directory Returns: tuple[list, array]: symbols of the atoms in the molecule and a 1D array with their positions in atomic units. **Example** >>> symbols, coordinates = read_structure('h2.xyz') >>> print(symbols, coordinates) ['H', 'H'] [0. 0. -0.66140414 0. 0. 0.66140414] """ file_in = filepath.strip() file_out = os.path.join(outpath, "structure.xyz") copyfile(file_in, file_out) symbols = [] coordinates = [] with open(file_out, encoding="utf-8") as f: for line in f.readlines()[2:]: symbol, x, y, z = line.split() symbols.append(symbol) coordinates.append(float(x)) coordinates.append(float(y)) coordinates.append(float(z)) return symbols, np.array(coordinates) / bohr_angs
[docs]def active_space(electrons, orbitals, mult=1, active_electrons=None, active_orbitals=None): r"""Build the active space for a given number of active electrons and active orbitals. Post-Hartree-Fock (HF) electron correlation methods expand the many-body wave function as a linear combination of Slater determinants, commonly referred to as configurations. This configurations are generated by exciting electrons from the occupied to the unoccupied HF orbitals as sketched in the figure below. Since the number of configurations increases combinatorially with the number of electrons and orbitals this expansion can be truncated by defining an active space. The active space is created by classifying the HF orbitals as core, active and external orbitals: - Core orbitals are always occupied by two electrons - Active orbitals can be occupied by zero, one, or two electrons - The external orbitals are never occupied | .. figure:: ../../_static/qchem/sketch_active_space.png :align: center :width: 50% | .. note:: The number of active *spin*-orbitals ``2*active_orbitals`` determines the number of qubits required to perform the quantum simulations of the electronic structure of the many-electron system. Args: electrons (int): total number of electrons orbitals (int): total number of orbitals mult (int): Spin multiplicity :math:`\mathrm{mult}=N_\mathrm{unpaired} + 1` for :math:`N_\mathrm{unpaired}` unpaired electrons occupying the HF orbitals. Possible values for ``mult`` are :math:`1, 2, 3, \ldots`. If not specified, a closed-shell HF state is assumed. active_electrons (int): Number of active electrons. If not specified, all electrons are treated as active. active_orbitals (int): Number of active orbitals. If not specified, all orbitals are treated as active. Returns: tuple: lists of indices for core and active orbitals **Example** >>> electrons = 4 >>> orbitals = 4 >>> core, active = active_space(electrons, orbitals, active_electrons=2, active_orbitals=2) >>> print(core) # core orbitals [0] >>> print(active) # active orbitals [1, 2] """ # pylint: disable=too-many-branches if active_electrons is None: ncore_orbs = 0 core = [] else: if active_electrons <= 0: raise ValueError( f"The number of active electrons ({active_electrons}) " f"has to be greater than 0." ) if active_electrons > electrons: raise ValueError( f"The number of active electrons ({active_electrons}) " f"can not be greater than the total " f"number of electrons ({electrons})." ) if active_electrons < mult - 1: raise ValueError( f"For a reference state with multiplicity {mult}, " f"the number of active electrons ({active_electrons}) should be " f"greater than or equal to {mult - 1}." ) if mult % 2 == 1: if active_electrons % 2 != 0: raise ValueError( f"For a reference state with multiplicity {mult}, " f"the number of active electrons ({active_electrons}) should be even." ) else: if active_electrons % 2 != 1: raise ValueError( f"For a reference state with multiplicity {mult}, " f"the number of active electrons ({active_electrons}) should be odd." ) ncore_orbs = (electrons - active_electrons) // 2 core = list(range(ncore_orbs)) if active_orbitals is None: active = list(range(ncore_orbs, orbitals)) else: if active_orbitals <= 0: raise ValueError( f"The number of active orbitals ({active_orbitals}) " f"has to be greater than 0." ) if ncore_orbs + active_orbitals > orbitals: raise ValueError( f"The number of core ({ncore_orbs}) + active orbitals ({active_orbitals}) cannot " f"be greater than the total number of orbitals ({orbitals})" ) homo = (electrons + mult - 1) / 2 if ncore_orbs + active_orbitals <= homo: raise ValueError( f"For n_active_orbitals={active_orbitals}, there are no virtual orbitals " f"in the active space." ) active = list(range(ncore_orbs, ncore_orbs + active_orbitals)) return core, active
[docs]def excitations(electrons, orbitals, delta_sz=0): r"""Generate single and double excitations from a Hartree-Fock reference state. Single and double excitations can be generated by acting with the operators :math:`\hat T_1` and :math:`\hat T_2` on the Hartree-Fock reference state: .. math:: && \hat{T}_1 = \sum_{r \in \mathrm{occ} \\ p \in \mathrm{unocc}} \hat{c}_p^\dagger \hat{c}_r \\ && \hat{T}_2 = \sum_{r>s \in \mathrm{occ} \\ p>q \in \mathrm{unocc}} \hat{c}_p^\dagger \hat{c}_q^\dagger \hat{c}_r \hat{c}_s. In the equations above the indices :math:`r, s` and :math:`p, q` run over the occupied (occ) and unoccupied (unocc) *spin* orbitals and :math:`\hat c` and :math:`\hat c^\dagger` are the electron annihilation and creation operators, respectively. | .. figure:: ../../_static/qchem/sd_excitations.png :align: center :width: 80% | Args: electrons (int): Number of electrons. If an active space is defined, this is the number of active electrons. orbitals (int): Number of *spin* orbitals. If an active space is defined, this is the number of active spin-orbitals. delta_sz (int): Specifies the selection rules ``sz[p] - sz[r] = delta_sz`` and ``sz[p] + sz[p] - sz[r] - sz[s] = delta_sz`` for the spin-projection ``sz`` of the orbitals involved in the single and double excitations, respectively. ``delta_sz`` can take the values :math:`0`, :math:`\pm 1` and :math:`\pm 2`. Returns: tuple(list, list): lists with the indices of the spin orbitals involved in the single and double excitations **Example** >>> electrons = 2 >>> orbitals = 4 >>> singles, doubles = excitations(electrons, orbitals) >>> print(singles) [[0, 2], [1, 3]] >>> print(doubles) [[0, 1, 2, 3]] """ if not electrons > 0: raise ValueError( f"The number of active electrons has to be greater than 0 \n" f"Got n_electrons = {electrons}" ) if orbitals <= electrons: raise ValueError( f"The number of active spin-orbitals ({orbitals}) " f"has to be greater than the number of active electrons ({electrons})." ) if delta_sz not in (0, 1, -1, 2, -2): raise ValueError( f"Expected values for 'delta_sz' are 0, +/- 1 and +/- 2 but got ({delta_sz})." ) # define the spin projection 'sz' of the single-particle states sz = np.array([0.5 if (i % 2 == 0) else -0.5 for i in range(orbitals)]) singles = [ [r, p] for r in range(electrons) for p in range(electrons, orbitals) if sz[p] - sz[r] == delta_sz ] doubles = [ [s, r, q, p] for s in range(electrons - 1) for r in range(s + 1, electrons) for q in range(electrons, orbitals - 1) for p in range(q + 1, orbitals) if (sz[p] + sz[q] - sz[r] - sz[s]) == delta_sz ] return singles, doubles
[docs]def hf_state(electrons, orbitals): r"""Generate the occupation-number vector representing the Hartree-Fock state. The many-particle wave function in the Hartree-Fock (HF) approximation is a `Slater determinant <https://en.wikipedia.org/wiki/Slater_determinant>`_. In Fock space, a Slater determinant for :math:`N` electrons is represented by the occupation-number vector: .. math:: \vert {\bf n} \rangle = \vert n_1, n_2, \dots, n_\mathrm{orbs} \rangle, n_i = \left\lbrace \begin{array}{ll} 1 & i \leq N \\ 0 & i > N \end{array} \right., where :math:`n_i` indicates the occupation of the :math:`i`-th orbital. Args: electrons (int): Number of electrons. If an active space is defined, this is the number of active electrons. orbitals (int): Number of *spin* orbitals. If an active space is defined, this is the number of active spin-orbitals. Returns: array: NumPy array containing the vector :math:`\vert {\bf n} \rangle` **Example** >>> state = hf_state(2, 6) >>> print(state) [1 1 0 0 0 0] """ if electrons <= 0: raise ValueError( f"The number of active electrons has to be larger than zero; " f"got 'electrons' = {electrons}" ) if electrons > orbitals: raise ValueError( f"The number of active orbitals cannot be smaller than the number of active electrons;" f" got 'orbitals'={orbitals} < 'electrons'={electrons}" ) state = np.where(np.arange(orbitals) < electrons, 1, 0) return np.array(state)
[docs]def excitations_to_wires(singles, doubles, wires=None): r"""Map the indices representing the single and double excitations generated with the function :func:`~.excitations` to the wires that the Unitary Coupled-Cluster (UCCSD) template will act on. Args: singles (list[list[int]]): list with the indices ``r``, ``p`` of the two qubits representing the single excitation :math:`\vert r, p \rangle = \hat{c}_p^\dagger \hat{c}_r \vert \mathrm{HF}\rangle` doubles (list[list[int]]): list with the indices ``s``, ``r``, ``q``, ``p`` of the four qubits representing the double excitation :math:`\vert s, r, q, p \rangle = \hat{c}_p^\dagger \hat{c}_q^\dagger \hat{c}_r \hat{c}_s \vert \mathrm{HF}\rangle` wires (Iterable[Any]): Wires of the quantum device. If None, will use consecutive wires. The indices :math:`r, s` and :math:`p, q` in these lists correspond, respectively, to the occupied and virtual orbitals involved in the generated single and double excitations. Returns: tuple[list[list[Any]], list[list[list[Any]]]]: lists with the sequence of wires, resulting from the single and double excitations, that the Unitary Coupled-Cluster (UCCSD) template will act on. **Example** >>> singles = [[0, 2], [1, 3]] >>> doubles = [[0, 1, 2, 3]] >>> singles_wires, doubles_wires = excitations_to_wires(singles, doubles) >>> print(singles_wires) [[0, 1, 2], [1, 2, 3]] >>> print(doubles_wires) [[[0, 1], [2, 3]]] >>> wires=['a0', 'b1', 'c2', 'd3'] >>> singles_wires, doubles_wires = excitations_to_wires(singles, doubles, wires=wires) >>> print(singles_wires) [['a0', 'b1', 'c2'], ['b1', 'c2', 'd3']] >>> print(doubles_wires) [[['a0', 'b1'], ['c2', 'd3']]] """ if (not singles) and (not doubles): raise ValueError( f"'singles' and 'doubles' lists can not be both empty; " f"got singles = {singles}, doubles = {doubles}" ) expected_shape = (2,) for single_ in singles: if np.array(single_).shape != expected_shape: raise ValueError( f"Expected entries of 'singles' to be of shape (2,); got {np.array(single_).shape}" ) expected_shape = (4,) for double_ in doubles: if np.array(double_).shape != expected_shape: raise ValueError( f"Expected entries of 'doubles' to be of shape (4,); got {np.array(double_).shape}" ) max_idx = 0 if singles: max_idx = np.max(singles) if doubles: max_idx = max(np.max(doubles), max_idx) if wires is None: wires = range(max_idx + 1) elif len(wires) != max_idx + 1: raise ValueError(f"Expected number of wires is {max_idx + 1}; got {len(wires)}") singles_wires = [] for r, p in singles: s_wires = [wires[i] for i in range(r, p + 1)] singles_wires.append(s_wires) doubles_wires = [] for s, r, q, p in doubles: d1_wires = [wires[i] for i in range(s, r + 1)] d2_wires = [wires[i] for i in range(q, p + 1)] doubles_wires.append([d1_wires, d2_wires]) return singles_wires, doubles_wires