Merge pull request #105 from UCL-CCS/dependency-update

Dependency update, pyscf to 2.3, poetry in dev deps, trigger ci on dispatch

.github/workflows/pull_request.yaml

@@ -6,6 +6,11 @@ on:
     types:
       - opened
       - edited
+  workflow_dispatch:
+    inputs:
+      branch:
+        description: 'Branch to test'
+        required: true
 jobs:
   build:
     runs-on: ubuntu-latest

nbed/driver.py

@@ -326,7 +326,8 @@ def _subsystem_dft(self) -> None:
         logger.debug("Calculating active and environment subsystem terms.")
 
         def _rks_components(
-            rks_system: Localizer, subsystem_dm: np.ndarray,
+            rks_system: Localizer,
+            subsystem_dm: np.ndarray,
         ) -> Tuple[float, float, np.ndarray, np.ndarray, np.ndarray]:
             """Calculate the components of subsystem energy from a RKS DFT calculation.
 
@@ -767,7 +768,9 @@ def embed_dft_in_dft(self, xc_func: str, embedding_method: Callable):
         y_emb = result["scf_dft"].make_rdm1()
         # calculate correction
         result["correction"] = np.einsum(
-            "ij,ij", result["v_emb_dft"], (y_emb - self.localized_system.dm_active),
+            "ij,ij",
+            result["v_emb_dft"],
+            (y_emb - self.localized_system.dm_active),
         )
         veff = result["scf_dft"].get_veff(dm=y_emb)
         rks_e_elec = veff.exc + veff.ecoul + np.einsum("ij,ij", hcore_std, y_emb)

nbed/embed.py

@@ -99,7 +99,9 @@ def nbed(
         hamiltonians = ()
         for scf, e_classical in zip(driver.embedded_scf, driver.e_classical):
             qham = HamiltonianBuilder(
-                scf_method=scf, constant_e_shift=e_classical, transform=transform,
+                scf_method=scf,
+                constant_e_shift=e_classical,
+                transform=transform,
             ).build(n_qubits=qubits)
             converter = HamiltonianConverter(qham)
             qham = getattr(converter, output.lower())

nbed/ham_converter.py

@@ -22,7 +22,10 @@
 class HamiltonianConverter:
     """Class to create and output qubit hamiltonians."""
 
-    def __init__(self, input_hamiltonian: Union[QubitOperator, str, Path],) -> None:
+    def __init__(
+        self,
+        input_hamiltonian: Union[QubitOperator, str, Path],
+    ) -> None:
         """Initialise class and return output.
 
         Args:

nbed/localizers/base.py

@@ -172,7 +172,7 @@ def _localize_virtual_orbs(self) -> None:
         # active AOs coeffs for a given MO j
         numerator_all = np.einsum("ij->j", (c_virtual_loc[ao_active_inds, :]) ** 2)
         # all AOs coeffs for a given MO j
-        denominator_all = np.einsum("ij->j", c_virtual_loc ** 2)
+        denominator_all = np.einsum("ij->j", c_virtual_loc**2)
 
         active_percentage_MO = numerator_all / denominator_all
 

nbed/localizers/pyscf.py

@@ -104,7 +104,7 @@ def _localize(
         numerator_all = np.einsum("ij->j", (c_loc_occ[ao_active_inds, :]) ** 2)
 
         # all AOs coeffs for a given MO j
-        denominator_all = np.einsum("ij->j", c_loc_occ ** 2)
+        denominator_all = np.einsum("ij->j", c_loc_occ**2)
 
         mo_active_share = numerator_all / denominator_all
 

nbed/utils.py

@@ -75,7 +75,9 @@ def parse():
     logger.debug("Adding CLI arguments.")
     parser = argparse.ArgumentParser(description="Output embedded Qubit Hamiltonian.")
     parser.add_argument(
-        "--config", type=str, help="Path to a config file. Overwrites other arguments.",
+        "--config",
+        type=str,
+        help="Path to a config file. Overwrites other arguments.",
     )
     parser.add_argument(
         "--geometry",
@@ -90,7 +92,10 @@ def parse():
         help="Number of atoms to include in active region.",
     )
     parser.add_argument(
-        "--basis", "-b", type=str, help="Basis set to use.",
+        "--basis",
+        "-b",
+        type=str,
+        help="Basis set to use.",
     )
     parser.add_argument(
         "--xc_functional",
@@ -136,10 +141,15 @@ def parse():
         help="Convergence tolerance for calculations.",
     )
     parser.add_argument(
-        "--charge", type=int, help="Charge of molecular system.",
+        "--charge",
+        type=int,
+        help="Charge of molecular system.",
     )
     parser.add_argument(
-        "--savefile", "-s", type=str, help="Path to save file.",
+        "--savefile",
+        "-s",
+        type=str,
+        help="Path to save file.",
     )
     parser.add_argument(
         "--run_ccsd_emb",
@@ -152,10 +162,14 @@ def parse():
         help="Include if you want to run a fci calculation of the active embedded system.",
     )
     parser.add_argument(
-        "--ram", type=str, help="amount of ram in MB that PySCF can use",
+        "--ram",
+        type=str,
+        help="amount of ram in MB that PySCF can use",
     )
     parser.add_argument(
-        "--mu_shift", type=int, help="mu energy shift value",
+        "--mu_shift",
+        type=int,
+        help="mu energy shift value",
     )
     parser.add_argument(
         "--virtual_localization",