Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update all guides to calculate integrals using pyscf #109

Merged
merged 2 commits into from
Nov 8, 2024
Merged

Update all guides to calculate integrals using pyscf #109

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
fc4011b
Update all guides
caleb-johnson Nov 8, 2024
d1f9923
style
caleb-johnson Nov 8, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
48 changes: 36 additions & 12 deletions docs/how_tos/choose_subspace_dimension.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

42 changes: 33 additions & 9 deletions docs/how_tos/integrate_dice_solver.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,10 +21,11 @@
"source": [
"%%capture\n",
"\n",
"import os\n",
"\n",
"import numpy as np\n",
"from pyscf import ao2mo, tools\n",
"import pyscf\n",
"import pyscf.cc\n",
"import pyscf.mcscf\n",
"from qiskit_addon_dice_solver import solve_fermion\n",
"from qiskit_addon_sqd.configuration_recovery import recover_configurations\n",
"from qiskit_addon_sqd.counts import counts_to_arrays, generate_counts_uniform\n",
Expand All @@ -39,12 +40,35 @@
"open_shell = False\n",
"spin_sq = 0\n",
"\n",
"# Read in molecule from disk\n",
"active_space_path = os.path.abspath(os.path.join(\"..\", \"molecules\", \"n2_fci.txt\"))\n",
"mf_as = tools.fcidump.to_scf(active_space_path)\n",
"hcore = mf_as.get_hcore()\n",
"eri = ao2mo.restore(1, mf_as._eri, num_orbitals)\n",
"nuclear_repulsion_energy = mf_as.mol.energy_nuc()\n",
"# Specify molecule properties\n",
"open_shell = False\n",
"spin_sq = 0\n",
"\n",
"# Build N2 molecule\n",
"mol = pyscf.gto.Mole()\n",
"mol.build(\n",
" atom=[[\"N\", (0, 0, 0)], [\"N\", (1.0, 0, 0)]],\n",
" basis=\"6-31g\",\n",
" symmetry=\"Dooh\",\n",
")\n",
"\n",
"# Define active space\n",
"n_frozen = 2\n",
"active_space = range(n_frozen, mol.nao_nr())\n",
"\n",
"# Get molecular integrals\n",
"scf = pyscf.scf.RHF(mol).run()\n",
"num_orbitals = len(active_space)\n",
"n_electrons = int(sum(scf.mo_occ[active_space]))\n",
"num_elec_a = (n_electrons + mol.spin) // 2\n",
"num_elec_b = (n_electrons - mol.spin) // 2\n",
"cas = pyscf.mcscf.CASCI(scf, num_orbitals, (num_elec_a, num_elec_b))\n",
"mo = cas.sort_mo(active_space, base=0)\n",
"hcore, nuclear_repulsion_energy = cas.get_h1cas(mo)\n",
"eri = pyscf.ao2mo.restore(1, cas.get_h2cas(mo), num_orbitals)\n",
"\n",
"# Compute exact energy\n",
"exact_energy = cas.run().e_tot\n",
"\n",
"# Create a seed to control randomness throughout this workflow\n",
"rng = np.random.default_rng(24)\n",
Expand Down Expand Up @@ -133,7 +157,7 @@
}
],
"source": [
"print(\"Exact energy: -109.10288938\")\n",
"print(\"Exact energy: {exact_energy}\")\n",
"print(f\"Estimated energy: {np.min(e_hist[-1])}\")"
]
}
Expand Down
79 changes: 57 additions & 22 deletions docs/how_tos/use_oo_to_optimize_hamiltonian_basis.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

4 changes: 2 additions & 2 deletions docs/tutorials/01_chemistry_hamiltonian.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
"\\hat{a}_{r\\sigma}\n",
"$$\n",
"\n",
"$\\hat{a}^\\dagger_{p\\sigma}$/$\\hat{a}_{p\\sigma}$ are the fermionic creation/annihalation operators associated to the $p$-th basis set element and the spin $\\sigma$. $h_{pr}$ and $(pr|qs)$ are the one- and two-body electronic integrals. These are loaded from an ``fcidump`` file with standard chemistry software.\n",
"$\\hat{a}^\\dagger_{p\\sigma}$/$\\hat{a}_{p\\sigma}$ are the fermionic creation/annihalation operators associated to the $p$-th basis set element and the spin $\\sigma$. $h_{pr}$ and $(pr|qs)$ are the one- and two-body electronic integrals.\n",
"\n",
"The SQD workflow with self-consistent configuration recovery is depicted in the following diagram.\n",
"\n",
Expand All @@ -60,7 +60,7 @@
"\n",
"In this tutorial, we will approximate the ground state energy of an $N_2$ molecule. First, we will specify the molecule and its properties. Next, we will create a [local unitary cluster Jastrow (LUCJ)](https://pubs.rsc.org/en/content/articlelanding/2023/sc/d3sc02516k) ansatz (quantum circuit) to generate samples from a quantum computer for ground state energy estimation.\n",
"\n",
"First, we will specify the molecule and its properties"
"First, we will specify the molecule and its properties."
]
},
{
Expand Down