Merge pull request #109 from BoothGroup/formatting

Formatting experiment

.git-blame-ignore-revs

@@ -0,0 +1,6 @@
+# Run this command to always ignore formatting commits in `git blame`
+# git config blame.ignoreRevsFile .git-blame-ignore-revs
+
+# Formatted entire existing codebase with black
+3f80f568262b20fb82fbaa3d780d8a0d5cfebc3f
+

.pre-commit-config.yaml

@@ -0,0 +1,14 @@
+    # Install via pre-commit by running
+    # `pre-commit install`
+    # See https://pre-commit.com for more information
+    # See https://pre-commit.com/hooks.html for more hooks
+    # We'll need to manually update the version of black used in our pre-commits via
+    # `pre-commit autoupdate`.
+    # This is a conscious decision on the part of the pre-commit developers; for more information
+    # see https://pre-commit.com/#using-the-latest-version-for-a-repository
+    repos:
+      - repo: https://github.com/ambv/black
+        rev: 23.7.0
+        hooks:
+          - id: black
+            language_version: python3.10

docs/source/conf.py

@@ -14,31 +14,28 @@
 import sys
 import vayesta
 
-sys.path.insert(0, os.path.abspath('../vayesta/'))
+sys.path.insert(0, os.path.abspath("../vayesta/"))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'Vayesta'
-copyright = '2022'
-author = 'All contributors'
+project = "Vayesta"
+copyright = "2022"
+author = "All contributors"
 
 # The full version, including alpha/beta/rc tags
-release = '1.0.0'
+release = "1.0.0"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.todo',
-              'sphinx.ext.viewcode',
-              'sphinx.ext.autodoc',
-              'sphinx.ext.napoleon']
+extensions = ["sphinx.ext.todo", "sphinx.ext.viewcode", "sphinx.ext.autodoc", "sphinx.ext.napoleon"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -51,24 +48,24 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-#html_static_path = ['_static']
+# html_static_path = ['_static']
 html_static_path = []
 
 # Numbering for Figures, Tables, etc
 numfig = True
 numfig_format = {
-    'figure': 'Fig. %s',
-    'table': 'Table %s',
+    "figure": "Fig. %s",
+    "table": "Table %s",
 }
 
 # -- Autodoc defaults --------------------------------------------------------
 
 autodoc_default_options = {
-    'member-order': 'bysource',
-    'inherited-members': True,
+    "member-order": "bysource",
+    "inherited-members": True,
 }

docs/source/quickstart/1d_hubbard.py

@@ -5,24 +5,24 @@
 nsite = 16
 nelectron = nsite
 hubbard_u = 2.0
-mol = vayesta.lattmod.Hubbard1D(nsite, nelectron=nelectron, hubbard_u=hubbard_u, output='pyscf.out')
+mol = vayesta.lattmod.Hubbard1D(nsite, nelectron=nelectron, hubbard_u=hubbard_u, output="pyscf.out")
 
 mf = vayesta.lattmod.LatticeMF(mol)
 mf.kernel()
 
 # Single site embedding:
-ewf = vayesta.ewf.EWF(mf, bno_threshold=1e-8, fragment_type='Site')
+ewf = vayesta.ewf.EWF(mf, bno_threshold=1e-8, fragment_type="Site")
 ewf.site_fragmentation()
 ewf.add_atomic_fragment(0, sym_factor=nsite)
 ewf.kernel()
-print("E(MF)=       %+16.8f Ha" % (mf.e_tot/nelectron))
-print("E(EWF-CCSD)= %+16.8f Ha" % (ewf.e_tot/nelectron))
+print("E(MF)=       %+16.8f Ha" % (mf.e_tot / nelectron))
+print("E(EWF-CCSD)= %+16.8f Ha" % (ewf.e_tot / nelectron))
 
 # Double site embedding:
-ewf = vayesta.ewf.EWF(mf, bno_threshold=1e-8, fragment_type='Site')
+ewf = vayesta.ewf.EWF(mf, bno_threshold=1e-8, fragment_type="Site")
 ewf.site_fragmentation()
-ewf.add_atomic_fragment([0,1], sym_factor=nsite/2)
+ewf.add_atomic_fragment([0, 1], sym_factor=nsite / 2)
 
 ewf.kernel()
-print("E(MF)=       %+16.8f Ha" % (mf.e_tot/nelectron))
-print("E(EWF-CCSD)= %+16.8f Ha" % (ewf.e_tot/nelectron))
+print("E(MF)=       %+16.8f Ha" % (mf.e_tot / nelectron))
+print("E(EWF-CCSD)= %+16.8f Ha" % (ewf.e_tot / nelectron))

docs/source/quickstart/edmetfinite.py

@@ -13,36 +13,39 @@
 H  0.0000   0.7572  -0.4692
 H  0.0000  -0.7572  -0.4692
 """
-mol.basis = 'cc-pVDZ'
-mol.output = 'pyscf.out'
+mol.basis = "cc-pVDZ"
+mol.output = "pyscf.out"
 mol.build()
 
 # LDA
 lda = pyscf.dft.RKS(mol)
-lda.xc = 'svwn'
+lda.xc = "svwn"
 lda = lda.density_fit()
 lda.kernel()
 
 # The KS object needs to be converted to a HF object:
 lda = lda.to_rhf()
 
-emb_lda = vayesta.edmet.EDMET(lda, bath_options=dict(dmet_threshold=1e-12), solver="CCSD-S-1-1",
-                              oneshot=True, make_dd_moments=False)
+emb_lda = vayesta.edmet.EDMET(
+    lda, bath_options=dict(dmet_threshold=1e-12), solver="CCSD-S-1-1", oneshot=True, make_dd_moments=False
+)
 
 with emb_lda.iao_fragmentation() as f:
     f.add_all_atomic_fragments()
 emb_lda.kernel()
 
 # b3lyp
 b3lyp = pyscf.dft.RKS(mol)
-b3lyp.xc = 'b3lyp'
+b3lyp.xc = "b3lyp"
 b3lyp = b3lyp.density_fit()
 b3lyp.kernel()
 
 # The KS opbject needs to be converted to a HF object:
 b3lyp = b3lyp.to_rhf()
 
-emb_b3lyp = vayesta.edmet.EDMET(b3lyp, bath_options=dict(dmet_threshold=1e-12), solver="CCSD-S-1-1", oneshot=True, make_dd_moments=False)
+emb_b3lyp = vayesta.edmet.EDMET(
+    b3lyp, bath_options=dict(dmet_threshold=1e-12), solver="CCSD-S-1-1", oneshot=True, make_dd_moments=False
+)
 with emb_b3lyp.iao_fragmentation() as f:
     f.add_all_atomic_fragments()
 emb_b3lyp.kernel()
@@ -51,8 +54,9 @@
 hf = pyscf.scf.RHF(mol).density_fit()
 hf.kernel()
 
-emb_hf = vayesta.edmet.EDMET(hf, bath_options=dict(dmet_threshold=1e-12), solver="CCSD-S-1-1",
-                             oneshot=True, make_dd_moments=False)
+emb_hf = vayesta.edmet.EDMET(
+    hf, bath_options=dict(dmet_threshold=1e-12), solver="CCSD-S-1-1", oneshot=True, make_dd_moments=False
+)
 
 with emb_hf.iao_fragmentation() as f:
     f.add_all_atomic_fragments()
@@ -71,4 +75,3 @@
 print("E(HF @B3LYP)=        %+16.8f Ha" % emb_b3lyp.e_mf)
 print("E(Emb. CCSD @B3LYP)= %+16.8f Ha" % emb_b3lyp.e_tot)
 print("E(Emb. CCSD @HF)=    %+16.8f Ha" % emb_hf.e_tot)
-

examples/dmet/01-simple-dmet.py

@@ -8,9 +8,9 @@
 
 # H6 ring
 mol = pyscf.gto.Mole()
-mol.atom = ring(atom='H', natom=6, bond_length=2.0)
-mol.basis = 'sto-6g'
-mol.output = 'pyscf.out'
+mol.atom = ring(atom="H", natom=6, bond_length=2.0)
+mol.basis = "sto-6g"
+mol.output = "pyscf.out"
 mol.build()
 
 # Hartree-Fock
@@ -22,24 +22,24 @@
 fci.kernel()
 
 # One-shot DMET
-dmet = vayesta.dmet.DMET(mf, solver='FCI', maxiter=1)
+dmet = vayesta.dmet.DMET(mf, solver="FCI", maxiter=1)
 with dmet.sao_fragmentation() as f:
-    f.add_atomic_fragment([0,1])
-    f.add_atomic_fragment([2,3])
-    f.add_atomic_fragment([4,5])
+    f.add_atomic_fragment([0, 1])
+    f.add_atomic_fragment([2, 3])
+    f.add_atomic_fragment([4, 5])
 dmet.kernel()
 
 # Self-consistent DMET
-dmet_sc = vayesta.dmet.DMET(mf, solver='FCI')
+dmet_sc = vayesta.dmet.DMET(mf, solver="FCI")
 with dmet_sc.sao_fragmentation() as f:
-    f.add_atomic_fragment([0,1])
-    f.add_atomic_fragment([2,3])
-    f.add_atomic_fragment([4,5])
+    f.add_atomic_fragment([0, 1])
+    f.add_atomic_fragment([2, 3])
+    f.add_atomic_fragment([4, 5])
 dmet_sc.kernel()
 
 print("Energies")
 print("========")
 print("  HF:                    %+16.8f Ha" % mf.e_tot)
 print("  FCI:                   %+16.8f Ha" % fci.e_tot)
-print("  DMET(1 iteration):     %+16.8f Ha  (error= %.1f mHa)" % (dmet.e_tot, 1000*(dmet.e_tot-fci.e_tot)))
-print("  DMET(self-consistent): %+16.8f Ha  (error= %.1f mHa)" % (dmet_sc.e_tot, 1000*(dmet_sc.e_tot-fci.e_tot)))
+print("  DMET(1 iteration):     %+16.8f Ha  (error= %.1f mHa)" % (dmet.e_tot, 1000 * (dmet.e_tot - fci.e_tot)))
+print("  DMET(self-consistent): %+16.8f Ha  (error= %.1f mHa)" % (dmet_sc.e_tot, 1000 * (dmet_sc.e_tot - fci.e_tot)))

examples/dmet/02-rotational-symmetry.py

@@ -11,9 +11,9 @@
 
 # H6 ring
 mol = pyscf.gto.Mole()
-mol.atom = ring(atom='H', natom=6, bond_length=2.0)
-mol.basis = 'sto-6g'
-mol.output = 'pyscf.out'
+mol.atom = ring(atom="H", natom=6, bond_length=2.0)
+mol.basis = "sto-6g"
+mol.output = "pyscf.out"
 mol.build()
 
 # Hartree-Fock
@@ -25,22 +25,22 @@
 fci.kernel()
 
 # One-shot DMET
-dmet = vayesta.dmet.DMET(mf, solver='FCI', maxiter=1)
+dmet = vayesta.dmet.DMET(mf, solver="FCI", maxiter=1)
 with dmet.sao_fragmentation() as f:
-    with f.rotational_symmetry(3, axis=[0,0,1]):
-        f.add_atomic_fragment([0,1])
+    with f.rotational_symmetry(3, axis=[0, 0, 1]):
+        f.add_atomic_fragment([0, 1])
 dmet.kernel()
 
 # Self-consistent DMET
-dmet_sc = vayesta.dmet.DMET(mf, solver='FCI')
+dmet_sc = vayesta.dmet.DMET(mf, solver="FCI")
 with dmet_sc.sao_fragmentation() as f:
-    with f.rotational_symmetry(3, axis=(0,0,1), center=(0,0,0)):
-        f.add_atomic_fragment([0,1])
+    with f.rotational_symmetry(3, axis=(0, 0, 1), center=(0, 0, 0)):
+        f.add_atomic_fragment([0, 1])
 dmet_sc.kernel()
 
 print("Energies")
 print("========")
 print("  HF:                    %+16.8f Ha" % mf.e_tot)
 print("  FCI:                   %+16.8f Ha" % fci.e_tot)
-print("  DMET(1 iteration):     %+16.8f Ha  (error= %.1f mHa)" % (dmet.e_tot, 1000*(dmet.e_tot-fci.e_tot)))
-print("  DMET(self-consistent): %+16.8f Ha  (error= %.1f mHa)" % (dmet_sc.e_tot, 1000*(dmet_sc.e_tot-fci.e_tot)))
+print("  DMET(1 iteration):     %+16.8f Ha  (error= %.1f mHa)" % (dmet.e_tot, 1000 * (dmet.e_tot - fci.e_tot)))
+print("  DMET(self-consistent): %+16.8f Ha  (error= %.1f mHa)" % (dmet_sc.e_tot, 1000 * (dmet_sc.e_tot - fci.e_tot)))

examples/dmet/03-density-matrices.py

@@ -7,21 +7,21 @@
 
 # H6 ring
 mol = pyscf.gto.Mole()
-mol.atom = ring(atom='H', natom=6, bond_length=2.0)
-mol.basis = 'sto-6g'
-mol.output = 'pyscf.out'
+mol.atom = ring(atom="H", natom=6, bond_length=2.0)
+mol.basis = "sto-6g"
+mol.output = "pyscf.out"
 mol.build()
 
 # Hartree-Fock
 mf = pyscf.scf.RHF(mol)
 mf.kernel()
 
 # One-shot DMET
-dmet = vayesta.dmet.DMET(mf, solver='FCI', maxiter=1)
+dmet = vayesta.dmet.DMET(mf, solver="FCI", maxiter=1)
 with dmet.sao_fragmentation() as f:
-    f.add_atomic_fragment([0,1])
-    f.add_atomic_fragment([2,3])
-    f.add_atomic_fragment([4,5])
+    f.add_atomic_fragment([0, 1])
+    f.add_atomic_fragment([2, 3])
+    f.add_atomic_fragment([4, 5])
 dmet.kernel()
 
 # Calculate energy from democratically-partitioned density matrices:
@@ -30,7 +30,7 @@
 # One and two-electron integrals in AO basis:
 h1e = dmet.get_hcore()
 eris = dmet.get_eris_array(np.eye(mol.nao))
-e_dmet = dmet.e_nuc + np.einsum('ij,ij->', h1e, dm1) + np.einsum('ijkl,ijkl->', eris, dm2)/2
+e_dmet = dmet.e_nuc + np.einsum("ij,ij->", h1e, dm1) + np.einsum("ijkl,ijkl->", eris, dm2) / 2
 
 print("Energies")
 print("========")

examples/dmet/04-h-ring-diis.py

@@ -1,17 +1,17 @@
 import numpy as np
 
 import pyscf
-import pyscf.scf 
+import pyscf.scf
 
 import vayesta
 import vayesta.dmet
 from vayesta.misc.molecules import ring
 
 
 mol = pyscf.gto.Mole()
-mol.atom = ring('H', 6, 2.0)
-mol.basis = 'sto-3g'
-mol.output = 'pyscf.out'
+mol.atom = ring("H", 6, 2.0)
+mol.basis = "sto-3g"
+mol.output = "pyscf.out"
 mol.verbose = 4
 mol.build()
 
@@ -20,24 +20,22 @@
 mf.kernel()
 
 # DMET calculation with DIIS extrapolation of the high-level correlation potential.
-dmet_diis = vayesta.dmet.DMET(mf, solver='FCI', charge_consistent=False, diis=True,
-                              max_elec_err=1e-6)
+dmet_diis = vayesta.dmet.DMET(mf, solver="FCI", charge_consistent=False, diis=True, max_elec_err=1e-6)
 with dmet_diis.iao_fragmentation() as f:
     f.add_atomic_fragment([0, 1])
     f.add_atomic_fragment([2, 3])
     f.add_atomic_fragment([4, 5])
 dmet_diis.kernel()
 
 # DMET calculation without DIIS, using
-dmet_mix = vayesta.dmet.DMET(mf, solver='FCI', charge_consistent=False, diis=False,
-                             max_elec_err=1e-6)
+dmet_mix = vayesta.dmet.DMET(mf, solver="FCI", charge_consistent=False, diis=False, max_elec_err=1e-6)
 with dmet_mix.iao_fragmentation() as f:
     f.add_atomic_fragment([0, 1])
     f.add_atomic_fragment([2, 3])
     f.add_atomic_fragment([4, 5])
 dmet_mix.kernel()
 
-ediff = (dmet_diis.e_dmet - dmet_mix.e_dmet)
+ediff = dmet_diis.e_dmet - dmet_mix.e_dmet
 vdiff = np.linalg.norm(dmet_diis.vcorr - dmet_mix.vcorr)
 
 print("Difference between DIIS and mixing solution:")

examples/dmet/63-hubbard-1d.py

@@ -7,25 +7,25 @@
 nsite = 10
 nimp = 2
 hubbard_u = 6.0
-boundary = 'PBC'
+boundary = "PBC"
 nelectron = nsite
 mol = vayesta.lattmod.Hubbard1D(nsite, nelectron=nelectron, hubbard_u=hubbard_u, boundary=boundary)
 mf = vayesta.lattmod.LatticeMF(mol)
 mf.kernel()
 
 # Calculate each 2-sites fragment:
-dmet = vayesta.dmet.DMET(mf, solver='FCI')
+dmet = vayesta.dmet.DMET(mf, solver="FCI")
 with dmet.site_fragmentation() as f:
     for site in range(0, nsite, nimp):
-        f.add_atomic_fragment(list(range(site, site+nimp)))
+        f.add_atomic_fragment(list(range(site, site + nimp)))
 dmet.kernel()
 
 print(dmet.fragments)
 # Calculate a single fragment and use translational symmetry:
-dmet_sym = vayesta.dmet.DMET(mf, solver='FCI')
+dmet_sym = vayesta.dmet.DMET(mf, solver="FCI")
 # Specify the number of translational copies in direction of the three lattice vectors by passing a list with three
 # integers, [n0, n1, n2]. 1D or 2D systems have their periodic dimension along the first one or two axes.
-nimages = [nsite//nimp, 1, 1]
+nimages = [nsite // nimp, 1, 1]
 dmet_sym.symmetry.set_translations(nimages)
 # Add only a single 2-sites fragment:
 with dmet_sym.site_fragmentation() as f: