Merge remote-tracking branch 'pyscf/master'

.github/workflows/ci.yml

@@ -59,7 +59,7 @@ jobs:
         run: |
             docker run --rm -v ${{ github.workspace }}:/src/pyscf:rw --workdir=/src/pyscf ${{ env.img }} \
             bash -exc '/opt/python/${{ matrix.pyver }}/bin/pip install --upgrade pip setuptools && \
-            /opt/python/${{ matrix.pyver }}/bin/pip install "numpy!=1.16,!=1.17" "scipy!=1.5" h5py pytest pytest-cov pytest-timer pyberny geometric && \
+            /opt/python/${{ matrix.pyver }}/bin/pip install "numpy!=1.16,!=1.17" "scipy!=1.5" h5py==3.10 pytest pytest-cov pytest-timer pyberny geometric && \
             yum install -y epel-release && \
             yum-config-manager --enable epel && \
             yum install -y openblas-devel gcc cmake curl && \
@@ -72,7 +72,7 @@ jobs:
             echo 'pbc_tools_pbc_fft_engine = "NUMPY"' > .pyscf_conf.py && \
             echo "dftd3_DFTD3PATH = './pyscf/lib/deps/lib'" >> .pyscf_conf.py && \
             echo "scf_hf_SCF_mute_chkfile = True" >> .pyscf_conf.py && \
-            ulimit -s 20000 && /opt/python/${{ matrix.pyver }}/bin/pytest pyscf/ --ignore=pyscf/adc --ignore=pyscf/pbc/df --ignore=pyscf/pbc/cc -s -c setup.cfg pyscf'
+            ulimit -s 20000 && /opt/python/${{ matrix.pyver }}/bin/pytest pyscf/ --ignore=pyscf/adc --ignore=pyscf/pbc/df --ignore=pyscf/pbc/cc -s -c pytest.ini pyscf'
 
   macos-build:
     runs-on: macos-latest

.github/workflows/ci_linux/python_deps.sh

@@ -2,13 +2,12 @@
 python -m pip install --upgrade pip
 pip install "numpy!=1.16,!=1.17" "scipy!=1.5" h5py pytest pytest-cov pytest-timer
 pip install pyberny
+pip install --no-deps pyscf-dispersion
 
 version=$(python -c 'import sys; version=sys.version_info[:2]; print("{0}.{1}".format(*version))')
 if [ $version != '3.12' ]; then
     pip install geometric
     pip install spglib
-    pip install dftd3
-    pip install dftd4
 fi
 
 #cppe

.github/workflows/ci_macos/deps_apt.sh

@@ -1,2 +1 @@
 #!/usr/bin/env bash
-exit 0

.github/workflows/publish.yml

@@ -16,7 +16,9 @@ jobs:
       - uses: actions/checkout@v3
       - name: Build wheels
         run: |
-            docker run --rm -v ${{ github.workspace }}:/src/pyscf pyscf/pyscf-pypa-env:latest \
+            docker run --rm -v ${{ github.workspace }}:/src/pyscf \
+            -e CMAKE_BUILD_PARALLEL_LEVEL=4 \
+            pyscf/pyscf-pypa-env:latest \
             bash /src/pyscf/docker/pypa-env/build-wheels.sh
       - name: List available wheels
         run: |
@@ -57,6 +59,7 @@ jobs:
             export src=${GITHUB_WORKSPACE:-/src/pyscf} && \
             export dst=${GITHUB_WORKSPACE:-/src/pyscf}/linux-wheels && \
             export CMAKE_CONFIGURE_ARGS="-DWITH_F12=OFF" && \
+            export CMAKE_BUILD_PARALLEL_LEVEL=4 && \
             mkdir -p /root/wheelhouse $src/linux-wheels && \
             sed -i "/            if basename(fn) not in needed_libs:/s/basename.*libs/1/" /opt/_internal/pipx/venvs/auditwheel/lib/python*/site-packages/auditwheel/wheel_abi.py && \
             /opt/python/${{ matrix.pyver }}/bin/pip wheel -v --no-deps --no-clean -w /root/wheelhouse $src && \
@@ -82,7 +85,8 @@ jobs:
       - uses: actions/checkout@v3
       - name: Build sdist
         run: |
-          python3 setup.py sdist
+          pip install build
+          python3 -m build -s
       - name: List available sdist
         run: |
           ls ${{ github.workspace }}/dist
@@ -108,6 +112,7 @@ jobs:
           CIBW_BUILD: cp311-macosx_x86_64
           CIBW_BUILD_VERBOSITY: "1"
           CMAKE_CONFIGURE_ARGS: "-DWITH_F12=OFF"
+          CMAKE_BUILD_PARALLEL_LEVEL: "4"
         with:
           output-dir: mac-wheels
       - name: List available wheels
@@ -133,6 +138,7 @@ jobs:
           # Cross-platform build for arm64 wheels on x86 platform
           CIBW_ARCHS_MACOS: "x86_64 universal2 arm64"
           CMAKE_CONFIGURE_ARGS: "-DWITH_F12=OFF"
+          CMAKE_BUILD_PARALLEL_LEVEL: "4"
           CMAKE_OSX_ARCHITECTURES: arm64
         with:
           output-dir: mac-wheels
@@ -161,6 +167,7 @@ jobs:
       - run: which python
       - name: Publish to conda
         run: |
+          export CMAKE_BUILD_PARALLEL_LEVEL=4
           export ANACONDA_API_TOKEN=${{ secrets.ANACONDA_TOKEN }}
           conda install -y anaconda-client conda-build
           conda config --set anaconda_upload yes

.github/workflows/run_tests.sh

@@ -10,8 +10,8 @@ echo "scf_hf_SCF_mute_chkfile = True" >> .pyscf_conf.py
 version=$(python -c 'import sys; print("{0}.{1}".format(*sys.version_info[:2]))')
 # pytest-cov on Python 3.12 consumes huge memory
 if [ "$RUNNER_OS" == "Linux" ] && [ $version != "3.12" ]; then
-  pytest pyscf/ -s -c setup.cfg \
+  pytest pyscf/ -s -c pytest.ini \
     --cov-report xml --cov-report term --cov-config .coveragerc --cov pyscf
 else
-  pytest pyscf/ -s -c setup.cfg pyscf
+  pytest pyscf/ -s -c pytest.ini pyscf
 fi

CHANGELOG

@@ -1,3 +1,31 @@
+PySCF 2.5.0 (2024-02-03)
+------------------------
+* Added
+  - SA-CASSCF Nonadiabatic Coupling Vectors 
+  - The to_gpu function to convert pyscf objects to gpu4pyscf objects.
+  - 4th, and 5th order XC derivatives.
+* Improved
+  - DIIS with damping for gapless systems.
+  - CPHF solver with level shift for gapless systems.
+  - The memory footprint for rsdf_builder and rsjk_builder.
+  - Use UHF natural orbital for RHF chkfile initial guess.
+  - Pipek Mezey + Stability check using Jacobi sweep.
+  - The conversion between FCI strings and addresses for more than 64 orbitals.
+  - The interface to the dftd3 and dftd4 dispersion correction modules.
+  - Switch off the sparsity treatment in DFT numerical integration for small system.
+  - Lattice-sum cutoff for non-orthogonal cell.
+  - Allow turning off AO symmetry for PBC DFT.
+* Fixes
+  - cp2k basis parsers
+  - k2gamma for dft classes.
+  - Mole.magmom attribute serialization error.
+  - post-hf Gradients with Cartesian GTOs.
+  - Basis order problem in molden.load .
+  - PBC DFT Becke grids rounding error.
+  - PBC rsdf for un-sorted basis.
+  - The get_bands function with k-point symmetry.
+
+
 PySCF 2.4.0 (2023-10-16)
 ------------------------
 * Added
@@ -37,6 +65,7 @@ PySCF 2.4.0 (2023-10-16)
   - Assume 46 and 78 core configurations to be f-in-valence.
   - Coding styles and deprecated warnings from numpy.
 
+
 PySCF 2.3.0 (2023-07-04)
 ------------------------
 * Added

NOTICE

@@ -102,7 +102,11 @@ Xiaojie Wu
 Pavel Pokhilko
 Frédéric Chapoton
 Daniel King
-
+Jiachen Li
+Felipe S. S. Schneider
+Aniruddha Seal
+Peter Reinholdt
+Christopher Hillenbrand
 
 
 ---

README.md

@@ -7,9 +7,9 @@ Python-based Simulations of Chemistry Framework
 [![Build Status](https://github.com/pyscf/pyscf/workflows/CI/badge.svg)](https://github.com/pyscf/pyscf/actions?query=workflow%3ACI)
 [![codecov](https://codecov.io/gh/pyscf/pyscf/branch/master/graph/badge.svg)](https://codecov.io/gh/pyscf/pyscf)
 
-2023-10-15
+2024-02-03
 
-* [Stable release 2.4.0](https://github.com/pyscf/pyscf/releases/tag/v2.4.0)
+* [Stable release 2.5.0](https://github.com/pyscf/pyscf/releases/tag/v2.5.0)
 * [Changelog](../master/CHANGELOG)
 * [Documentation](http://www.pyscf.org)
 * [Installation](#installation)

conda/build.sh

@@ -17,4 +17,4 @@ export CMAKE_CONFIGURE_ARGS="-DWITH_F12=OFF -DBLA_VENDOR=Intel10_64lp_seq"
 
 # env PYTHON not defined in certain conda-build version
 # $PYTHON -m pip install . -vv
-pip install -v --prefix=$PREFIX .
+MAKEFLAGS="-j4" pip install -v --prefix=$PREFIX .

examples/dft/00-simple_dft.py

@@ -34,3 +34,13 @@
 
 # Orbital energies, Mulliken population etc.
 mf.analyze()
+
+# shorten dft names
+mf = mol.KS(xc='b3lyp-d3bj')
+#mf = mol.KS(xc='b3lyp-d3zero')
+#mf = mol.KS(xc='b3lyp-d3bj2b')
+#mf = mol.KS(xc='b3lyp-d3bjatm')
+#mf = mol.KS(xc='b3lyp-d4')
+#mf = mol.KS(xc='wb97x-v')
+#mf = mol.KS(xc='wb97m-d3bj)
+#mf = mol.KS(xc='wb97x-d3)

examples/gw/03-drpa.py

@@ -0,0 +1,32 @@
+'''
+Direct RPA correlation energy
+'''
+
+from pyscf import gto, dft, gw
+
+mol = gto.M(
+    atom = """
+O          0.48387       -0.41799       -0.63869
+H          0.58103        0.36034       -0.05009
+H          1.01598       -1.09574       -0.18434
+H          0.68517       -2.88004        0.87771
+O          1.59649       -2.63873        0.61189
+H          1.72242       -3.22647       -0.15071
+H         -2.47665        1.59686       -0.33246
+O         -1.55912        1.35297       -0.13891
+H         -1.25777        0.82058       -0.89427
+H         -1.87830       -2.91357       -0.21825
+O         -1.14269       -2.57648        0.31845
+H         -0.81003       -1.77219       -0.15155
+""",
+    basis = 'ccpvqz', verbose = 5,
+    )
+
+mf = dft.RKS(mol).density_fit()
+mf.xc = 'pbe'
+mf.kernel()
+
+import pyscf.gw.rpa
+rpa = gw.rpa.dRPA(mf)
+rpa.max_memory = 50
+rpa.kernel()

examples/nac/01-sacasscf_nac.py

@@ -0,0 +1,90 @@
+from pyscf import gto, scf, mcscf, lib
+
+# NAC signs are really, really hard to nail down.
+# There are arbitrary signs associated with
+# 1. The MO coefficients
+# 2. The CI vectors
+# 3. Almost any kind of post-processing (natural-orbital analysis, etc.)
+# 4. Developer convention on whether the bra index or ket index is 1st
+# It MIGHT help comparison to OpenMolcas if you load a rasscf.h5 file
+# I TRIED to choose the same convention for #4 as OpenMolcas.
+mol = gto.M (atom='Li 0 0 0;H 1.5 0 0', basis='sto-3g',
+             output='LiH_sa2casscf22_sto3g.log', verbose=lib.logger.INFO)
+
+mf = scf.RHF (mol).run ()
+mc = mcscf.CASSCF (mf, 2, 2)
+mc.fix_spin_(ss=0, shift=1)
+mc = mc.state_average ([0.5,0.5]).run (conv_tol=1e-10)
+
+mc_nacs = mc.nac_method()
+
+# 1. <1|d0/dR>
+#    Equivalent OpenMolcas input:
+#    ```
+#    &ALASKA
+#    NAC=1 2
+#    ```
+nac = mc_nacs.kernel (state=(0,1))
+print ("\nNAC <1|d0/dR>:\n", nac)
+print ("Notice that according to the NACs printed above, rigidly moving the")
+print ("molecule along the bond axis changes the electronic wave function, which")
+print ("is obviously unphysical. This broken translational symmetry is due to the")
+print ("'CSF contribution'. Omitting the CSF contribution corresponds to using the")
+print ("'electron-translation factors' of Fatehi and Subotnik and is requested by")
+print ("passing 'use_etfs=True'.")
+
+# 2. <1|d0/dR> w/ ETFs (i.e., w/out CSF contribution)
+#    Equivalent OpenMolcas input:
+#    ```
+#    &ALASKA
+#    NAC=1 2
+#    NOCSF
+#    ```
+nac = mc_nacs.kernel (state=(0,1), use_etfs=True)
+print ("\nNAC <1|d0/dR> w/ ETFs:\n", nac)
+print ("These NACs are much more well-behaved: moving the molecule rigidly around")
+print ("in space doesn't induce any change to the electronic wave function.")
+
+# 3. <0|d1/dR>
+#    Equivalent OpenMolcas input:
+#    ```
+#    &ALASKA
+#    NAC=2 1
+#    ```
+nac = mc_nacs.kernel (state=(1,0))
+print ("\nThe NACs are antisymmetric with respect to state transposition.")
+print ("NAC <0|d1/dR>:\n", nac)
+
+# 4. <0|d1/dR> w/ ETFs
+#    Equivalent OpenMolcas input:
+#    ```
+#    &ALASKA
+#    NAC=2 1
+#    NOCSF
+#    ```
+nac = mc_nacs.kernel (state=(1,0), use_etfs=True)
+print ("NAC <0|d1/dR> w/ ETFs:\n", nac)
+
+# 5. <1|d0/dR>*(E1-E0) = <0|d1/dR>*(E0-E1)
+#    I'm not aware of any OpenMolcas equivalent for this, but all the information
+#    should obviously be in the output file, as long as you aren't right at a CI.
+nac_01 = mc_nacs.kernel (state=(0,1), mult_ediff=True)
+nac_10 = mc_nacs.kernel (state=(1,0), mult_ediff=True)
+print ("\nNACs diverge at conical intersections (CI). The important question")
+print ("is how quickly it diverges. You can get at this by calculating NACs")
+print ("multiplied by the energy difference using the keyword 'mult_ediff=True'.")
+print ("This yields a quantity which is symmetric wrt state interchange and is")
+print ("finite at a CI.")
+print ("NAC <1|d0/dR>*(E1-E0):\n", nac_01)
+print ("NAC <0|d1/dR>*(E0-E1):\n", nac_10)
+
+# 6. <1|d0/dR>*(E1-E0) w/ETFs = <0|d1/dR>*(E0-E1) w/ETFs = <0|dH/dR|1>
+#    This is the quantity one uses to optimize MECIs
+v01 = mc_nacs.kernel (state=(0,1), use_etfs=True, mult_ediff=True)
+v10 = mc_nacs.kernel (state=(1,0), use_etfs=True, mult_ediff=True)
+print ("\nUsing both 'use_etfs=True' and 'mult_ediff=True' corresponds to the")
+print ("derivative of the off-diagonal element of the potential matrix. This")
+print ("tells you one of the two components of the branching plane at the CI.")
+print ("<1|d0/dR>*(E1-E0) w/ ETFs = <1|dH/dR|0>:\n", v01)
+print ("<0|d1/dR>*(E0-E1) w/ ETFs = <0|dH/dR|1>:\n", v10)
+

examples/pbc/27-multigrid.py

@@ -31,9 +31,9 @@
 #
 # There are two ways to enable multigrid numerical integration
 #
-# Method 1: use multigrid.multigrid function to update SCF object
+# Method 1: use multigrid.multigrid_fftdf function to update SCF object
 #
-mf = multigrid.multigrid(mf)
+mf = multigrid.multigrid_fftdf(mf)
 mf.kernel()
 
 #