Merge branch 'master' into sr-eri-estimator-improved

.github/workflows/ci_conda.yml

@@ -0,0 +1,25 @@
+name: CI_conda
+
+on:
+  workflow_dispatch:
+
+jobs:
+  build-conda-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup conda
+        uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          conda-channels: conda-forge
+      - run: conda --version
+      - run: which python
+      - name: Build conda package
+        run: |
+          export CMAKE_BUILD_PARALLEL_LEVEL=4
+          conda install -y conda-build
+          conda config --set anaconda_upload False
+          conda build --output-folder . conda

.github/workflows/ci_linux/build_pyscf.sh

@@ -3,7 +3,7 @@
 set -e
 
 cd ./pyscf/lib
-curl -L "https://github.com/pyscf/pyscf-build-deps/blob/master/pyscf-2.4a-deps.tar.gz?raw=true" | tar xzf -
+curl -L "https://github.com/pyscf/pyscf-build-deps/blob/master/pyscf-2.8a-deps.tar.gz?raw=true" | tar xzf -
 mkdir build; cd build
 cmake -DBUILD_LIBXC=OFF -DBUILD_XCFUN=ON -DBUILD_LIBCINT=OFF -DXCFUN_MAX_ORDER=4 ..
 make -j4

.github/workflows/publish.yml

@@ -39,7 +39,7 @@ jobs:
     strategy:
       fail-fast: false
     env:
-      img: quay.io/pypa/manylinux2014_aarch64:2023-03-12-25fd859
+      img: quay.io/pypa/manylinux2014_aarch64:latest
     steps:
     - name: Checkout
       uses: actions/checkout@v4

CHANGELOG

@@ -366,6 +366,7 @@ PySCF 1.7.6 (2021-03-28)
   - Auxiliary second-order Green's function perturbation theory (AGF2)
   - Smearing for molecules
   - Visscher small component correction approximation for DHF
+  - DFT+U
 * Improved
   - Threading safety in Mole temporary context
   - Basis parser to support arithmetic expressions in basis data

README.md

@@ -14,6 +14,7 @@ Python-based Simulations of Chemistry Framework
 * [Documentation](http://www.pyscf.org)
 * [Installation](#installation)
 * [Features](../master/FEATURES)
+* [News](https://pyscf.org/news.html): **2nd PySCF Developers Meeting!**
 
 
 # Installation

examples/dft/16-dft_d3.py

@@ -6,18 +6,21 @@
 '''
 D3 and D4 Dispersion.
 
-This is a simplified dispersion interface to
-d3 (https://github.com/dftd3/simple-dftd3) and
-d4 (https://github.com/dftd4/dftd4) libraries.
-This interface can automatically configure the necessary settings including
-dispersion, xc, and nlc attributes of PySCF mean-field objects. However,
-advanced features of d3 and d4 program are not available.
+This example shows the functionality of the pyscf-dispersion extension, which
+implements a simplified interface to d3 (https://github.com/dftd3/simple-dftd3)
+and d4 (https://github.com/dftd4/dftd4) libraries. This interface can
+automatically configure the necessary settings including dispersion, xc, and nlc
+attributes of PySCF mean-field objects. However, advanced features of d3 and d4
+program are not available. To execute the code in this example, you would need
+to install the pyscf-dispersion extension:
+
+pip install pyscf-dispersion
 
 If you need to access more features d3 and d4 libraries, such as overwriting the
 dispersion parameters, you can use the wrapper provided by the simple-dftd3 and
-dftd4 libraries. When using these libraries, please disable the .disp attribute
-of the underlying mean-field object, and properly set the .xc and .nlc attributes
-following this example.
+dftd4 libraries. When accessing dispersion through the APIs of these libraries,
+please disable the .disp attribute of the mean-field object, and properly set
+the .xc and .nlc attributes as shown in this example.
 '''
 
 mol = pyscf.M(
@@ -134,7 +137,7 @@
 mf.disp = 'd4'
 mf.kernel() # Crash
 
-# Please note, not every xc functional can be used for D3/D4 corrections.
+# Please note, NOT every xc functional can be used for D3/D4 corrections.
 # For the valid xc and D3/D4 combinations, please refer to
 # https://github.com/dftd3/simple-dftd3/blob/main/assets/parameters.toml
 # https://github.com/dftd4/dftd4/blob/main/assets/parameters.toml

examples/geomopt/16-apply_soscf.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+
+'''
+Automatically apply SOSCF for unconverged SCF calculations in geometry optimization.
+'''
+
+import pyscf
+from pyscf.geomopt import geometric_solver, as_pyscf_method
+
+# Force SCF to stop early at an unconverged state
+pyscf.scf.hf.RHF.max_cycle = 5
+
+mol = pyscf.M(
+    atom='''
+    O 0 0 0
+    H 0 .7 .8
+    H 0 -.7 .8
+    ''')
+mf = mol.RHF()
+try:
+    mol_eq = geometric_solver.optimize(mf)
+except RuntimeError:
+    print('geometry optimization should stop for unconverged calculation')
+
+# Apply SOSCF when SCF is not converged
+mf_scanner = mf.as_scanner()
+def apply_soscf_as_needed(mol):
+    mf_scanner(mol)
+    if not mf_scanner.converged:
+        mf_soscf = mf_scanner.newton().run()
+        for key in ['converged', 'mo_energy', 'mo_coeff', 'mo_occ', 'e_tot', 'scf_summary']:
+            setattr(mf_scanner, key, getattr(mf_soscf, key))
+    grad = mf_scanner.Gradients().kernel()
+    return mf_scanner.e_tot, grad
+
+mol_eq = geometric_solver.optimize(as_pyscf_method(mol, apply_soscf_as_needed))

examples/gto/04-input_basis.py

@@ -65,7 +65,7 @@
 mol = gto.M(
     atom = '''O 0 0 0; H1 0 1 0; H2 0 0 1''',
     basis = {'O': gto.parse('''
-# Parse NWChem format basis string (see https://bse.pnl.gov/bse/portal).
+# Parse NWChem format basis string (see https://www.basissetexchange.org/).
 # Comment lines are ignored
 #BASIS SET: (6s,3p) -> [2s,1p]
 O    S

examples/gto/31-basis_set_exchange.py

@@ -14,6 +14,22 @@
 a local copy of the Basis Set Exchange.
 '''
 
+# PySCF has a native interface to the Basis Set Exchange, which is
+# used as a fall-through if the basis set was not found within PySCF
+# itself
+mol = gto.M(
+    atom = '''
+N          0.6683566134        0.2004327755        0.0000000000
+H          0.9668193796       -0.3441960976        0.8071193402
+H          0.9668193796       -0.3441960976       -0.8071193402
+F         -0.7347916126       -0.0467759204        0.0000000000
+''',
+    basis = 'HGBSP1-7',
+    verbose = 4
+)
+
+
+# One can also use the Basis Set Exchange in a more direct fashion
 mol = gto.M(
     atom = '''
 N          0.6683566134        0.2004327755        0.0000000000

examples/pbc/01-input_output_geometry.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+
+'''
+This example demonstrates some ways to input the Cell geometry, including
+lattice vectors, and to write the Cell geometry to file.
+
+Example solid is wurtzite BN.
+'''
+
+from pyscf.pbc import gto
+
+# Input Cartesian coordinates for the lattice vectors a and the atomic
+# positions. Coordinates are in Angstrom by default
+
+cell = gto.Cell()
+cell.a = [[  2.5539395809,  0.0000000000,  0.0000000000],
+          [ -1.2769697905,  2.2117765568,  0.0000000000],
+          [  0.0000000000,  0.0000000000,  4.2268548012]]
+cell.atom = '''
+            B     1.276969829         0.737258874         4.225688066
+            N     1.276969829         0.737258874         2.642950986
+            B     0.000000000         1.474517748         2.112260792
+            N     0.000000000         1.474517748         0.529523459
+            '''
+cell.pseudo = 'gth-pade'
+cell.basis = 'gth-szv'
+cell.build()
+
+# Write cell geometry to file
+# - Format is guessed from filename
+# - These can be read by VESTA, Avogadro, etc.
+# - XYZ is Extended XYZ file format, which includes lattice vectors in the
+#   comment line
+cell.tofile('bn.vasp')
+cell.tofile('POSCAR')
+cell.tofile('bn.xyz')
+
+# Read a and atom from file
+from pyscf.pbc.gto.cell import fromfile
+a, atom = fromfile('bn.vasp')
+a, atom = fromfile('bn.xyz')
+
+# Read a and atom from file directly into Cell
+cell = gto.Cell()
+cell.fromfile('bn.vasp')
+cell.pseudo = 'gth-pade'
+cell.basis = 'gth-szv'
+cell.build()

examples/pbc/09-band_ase.py

@@ -4,7 +4,7 @@
 
 import matplotlib.pyplot as plt
 
-from ase.lattice import bulk
+from ase.build import bulk
 from ase.dft.kpoints import sc_special_points as special_points, get_bandpath
 
 c = bulk('C', 'diamond', a=3.5668)

examples/pbc/22-dft+u.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+
+'''
+DFT+U with kpoint sampling
+'''
+
+from pyscf.pbc import gto, dft
+cell = gto.Cell()
+cell.unit = 'A'
+cell.atom = 'C 0.,  0.,  0.; C 0.8917,  0.8917,  0.8917'
+cell.a = '''0.      1.7834  1.7834
+            1.7834  0.      1.7834
+            1.7834  1.7834  0.    '''
+
+cell.basis = 'gth-dzvp'
+cell.pseudo = 'gth-pade'
+cell.verbose = 4
+cell.build()
+
+kmesh = [2, 2, 2]
+kpts = cell.make_kpts(kmesh)
+# Add U term to the 2p orbital of the second Carbon atom
+U_idx = ['1 C 2p']
+U_val = [5.0]
+mf = dft.KRKSpU(cell, kpts, U_idx=U_idx, U_val=U_val, minao_ref='gth-szv')
+print(mf.U_idx)
+print(mf.U_val)
+mf.run()
+
+# When space group symmetry in k-point samples is enabled, the symmetry adapted
+# DFT+U method will be invoked automatically.
+kpts = cell.make_kpts(
+    kmesh, wrap_around=True, space_group_symmetry=True, time_reversal_symmetry=True)
+# Add U term to 2s and 2p orbitals
+U_idx = ['2p', '2s']
+U_val = [5.0, 2.0]
+mf = dft.KUKSpU(cell, kpts, U_idx=U_idx, U_val=U_val, minao_ref='gth-szv')
+print(mf.U_idx)
+print(mf.U_val)
+mf.run()

examples/solvent/05-pcm.py

@@ -63,4 +63,13 @@
 td.kernel()
 
 mf = mol.RHF().PCM().run()
-td = mf.TDA().run()
+td = mf.TDA().run()
+
+# infinite epsilon with any PCM computations
+cm = pcm.PCM(mol)
+cm.eps = float('inf') # ideal conductor
+mf = dft.RKS(mol, xc='b3lyp')
+mf = mf.PCM(cm)
+mf.kernel()
+
+