Projected Atomic Orbitals (#177)

Adds a virtual localizer class for calculating Projected Atomic Orbitals.

THE WORK TO INTEGRATE THIS INTO THE DRIVER IS NOT COMPLETE.

For this class to work, a simplified interface for the `OccupiedLocalizer` has been introduced, with a new `LocalizedSystem` being the output of the `localize` function.

Author: MIWdlB

CHANGELOG.md

@@ -5,22 +5,27 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.0.9]
+## [Unreleased]
 Major refactor, with several breaking changes!
 
 ### Added
 - `NbedConfig` pydantic model to validate user input.
+- `OccupiedLocalizerTypes`, `VirtualLocalizerTypes` and `ProjectorTypes` enums added to config.
 - `savefile` config option used to save driver output to json file.
+- `PAOLocalizer` Virtual orbital localizaion with Projected Atomic Orbitals. (Implementation in driver not complete.)
+- `LocalizedSystem` dataclass added in `localizers/system.py`.
 
 ### Removed
 - `HamiltonianConverter` removed.
 - All functions relating to generating qubit hamiltonians have been removed from `HamiltonianBuilder`, this now only handles creating a second quantised hamiltonian.
 
 ### Changed
+- `OccupiedLocalizer` classes now output `LocalizedSystem` dataclass.
 - CLI tool now expects a path to a config `.json` file which matches the `NbedConfig` model.
 - `NbedDriver` automatically calls `HamiltonianBuilder.build()`, adding output to results as `second_quantised`.
 - Removed underscore from `driver._huzinaga` and `driver._mu`.
 - Driver defaults to *unrestricted* for both whole molecule and environment, passing charge and spin to environment based on spin-aware localization.
+- Config `run_virtual_localization` removed, with new flag `virtual_localizer` allowing for "cl" or "pao", defaulting to "cl".
 
 ## [0.0.9]
 ### Fixed

docs/jupyter_execute/notebooks/1. Orbital Plotting and Localization Functions.ipynb

@@ -102,7 +102,7 @@
     "\n",
     "    plotted_orbitals = []\n",
     "    for index in index_list:\n",
-    "        File_name = f\"temp_MO_orbital_index{index}.cube\"\n",
+    "        File_name = f\"temp_mo_orbital_index{index}.cube\"\n",
     "        cubegen.orbital(PySCF_mol_obj, File_name, C_matrix[:, index])\n",
     "\n",
     "        view = py3Dmol.view(width=width, height=height)\n",

docs/jupyter_execute/notebooks/6. Long form Notes.ipynb

@@ -515,8 +515,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(f\"active inds: {localized_system.active_MO_inds}\")\n",
-    "print(f\"enviro inds: {localized_system.enviro_MO_inds}\")"
+    "print(f\"active inds: {localized_system.active_mo_inds}\")\n",
+    "print(f\"enviro inds: {localized_system.enviro_mo_inds}\")"
    ]
   },
   {
@@ -763,7 +763,7 @@
     "    charge=charge,\n",
     "    spin=spin,\n",
     ")\n",
-    "rks_emb_mol.nelectron = 2 * len(localized_system.active_MO_inds)  # <--change no e-\n",
+    "rks_emb_mol.nelectron = 2 * len(localized_system.active_mo_inds)  # <--change no e-\n",
     "rks_emb_mol.build()\n",
     "\n",
     "rks_emb = scf.RKS(rks_emb_mol)\n",
@@ -855,7 +855,7 @@
     "    spin=spin,\n",
     ")\n",
     "full_system_mol.nelectron = 2 * len(\n",
-    "    localized_system.active_MO_inds\n",
+    "    localized_system.active_mo_inds\n",
     ")  # <- change number of e-\n",
     "full_system_mol.build()\n",
     "\n",
@@ -1038,7 +1038,7 @@
     "    spin=spin,\n",
     ")\n",
     "full_system_mol_HUZ.nelectron = 2 * len(\n",
-    "    localized_system.active_MO_inds\n",
+    "    localized_system.active_mo_inds\n",
     ")  # <- change number of e-\n",
     "full_system_mol_HUZ.build()\n",
     "\n",
@@ -1139,7 +1139,7 @@
     "\n",
     "overlap_by_size = overlap.argsort()[::-1]\n",
     "\n",
-    "n_env_mo = len(localized_system.enviro_MO_inds)\n",
+    "n_env_mo = len(localized_system.enviro_mo_inds)\n",
     "frozen_enviro_orb_inds = overlap_by_size[:n_env_mo]\n",
     "active_MOs_occ_and_virt_embedded = [\n",
     "    mo_i\n",
@@ -1367,8 +1367,8 @@
     "#    note we only take MO environment indices!\n",
     "ortho_proj = np.einsum(\n",
     "    \"ik,jk->ij\",\n",
-    "    c_loc_ortho[:, localized_system.enviro_MO_inds],\n",
-    "    c_loc_ortho[:, localized_system.enviro_MO_inds],\n",
+    "    c_loc_ortho[:, localized_system.enviro_mo_inds],\n",
+    "    c_loc_ortho[:, localized_system.enviro_mo_inds],\n",
     ")"
    ]
   },