Pull upstream PySCF updates

.github/workflows/ci_linux/deps_apt.sh

@@ -1,6 +1,9 @@
 #!/usr/bin/env bash
 sudo apt-get -qq install \
     gcc \
+    g++ \
+    gfortran \
+    liblapack-dev \
     libblas-dev \
     cmake \
     curl

.github/workflows/ci_linux/python_deps.sh

@@ -1,17 +1,16 @@
 #!/usr/bin/env bash
 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 git+https://github.com/jhrmnn/pyberny.git@36a4be9
 pip install --no-deps pyscf-dispersion==1.3.0
+pip install geometric
 
 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
-fi
 
-if [ $version != '3.8' ]; then
+if [ $version == '3.12' ]; then
+    pip install spglib
     pip install pytblis
+    pip install git+https://github.com/sunqm/zquatev
 fi
 
 #cppe

.github/workflows/run_tests.sh

@@ -13,6 +13,7 @@ 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 pytest.ini \
+    --durations=20 \
     --cov-report xml --cov-report term --cov-config .coveragerc --cov pyscf
 else
   pytest pyscf/ -s -c pytest.ini pyscf

CHANGELOG

@@ -1,3 +1,12 @@
+PySCF 2.13.1 (2026-06-01)
+-------------------------
+* Fixes
+  - Missing CP2K basis set data in wheel distributions
+  - Small-rotor error.
+  - Corrected SG1 grid radii handling for ghost atoms.
+  - Fixed ECP loading to correctly fall back to Basis Set Exchange when local data is unavailable.
+
+
 PySCF 2.13.0 (2026-04-20)
 -------------------------
 * Added

MANIFEST.in

@@ -11,12 +11,16 @@ include pyscf/lib/deps/lib*/libcint.[4-9].dylib
 include pyscf/lib/deps/lib*/libxc.*.dylib
 include pyscf/lib/deps/lib*/libxcfun.[2-9].dylib
 
+# windows dynamic libraries
+include pyscf/lib/*.dll
+include pyscf/lib/deps/bin/*.dll
+
 include pyscf/geomopt/log.ini
 include pyscf/gto/basis/bse_meta.json
 
 # CP2K basis set
-include pyscf/lib/pbc/gto/basis/*BASIS*
-include pyscf/lib/pbc/gto/pseudo/*POTENTIAL*
+include pyscf/pbc/gto/basis/*BASIS*
+include pyscf/pbc/gto/pseudo/*POTENTIAL*
 
 # source code
 recursive-include pyscf/lib *.c *.h CMakeLists.txt

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)
 
-2026-04-20
+2026-06-01
 
-* [Stable release 2.13.0](https://github.com/pyscf/pyscf/releases/tag/v2.13.0)
+* [Stable release 2.13.1](https://github.com/pyscf/pyscf/releases/tag/v2.13.1)
 * [Changelog](../master/CHANGELOG)
 * [Documentation](http://www.pyscf.org)
 * [Installation](#installation)

examples/2-benchmark/benchmarking_utils.py

@@ -4,13 +4,24 @@
 
 def setup_logger():
     log = pyscf.lib.logger.Logger(verbose=5)
-    with open('/proc/cpuinfo') as f:
-        for line in f:
-            if 'model name' in line:
-                log.note(line[:-1])
-                break
-    with open('/proc/meminfo') as f:
-        log.note(f.readline()[:-1])
+    try:
+        with open('/proc/cpuinfo') as f:
+            for line in f:
+                if 'model name' in line:
+                    log.note(line[:-1])
+                    break
+    except FileNotFoundError:
+        pass
+    try:
+        with open('/proc/meminfo') as f:
+            log.note(f.readline()[:-1])
+    except FileNotFoundError:
+        try:
+            import psutil
+            mem = psutil.virtual_memory()
+            log.note(f'MemTotal: {mem.total // 1024} kB')
+        except ImportError:
+            pass
     log.note('OMP_NUM_THREADS=%s\n', os.environ.get('OMP_NUM_THREADS', None))
     return log
 

examples/ao2mo/01-outcore.py

@@ -3,9 +3,9 @@
 # Author: Qiming Sun <osirpt.sun@gmail.com>
 #
 
-import tempfile
 import h5py
 from pyscf import gto, scf, ao2mo
+from pyscf import lib
 
 '''
 Save the transformed integrals in the given file in HDF5 format
@@ -22,7 +22,7 @@
 myhf.kernel()
 
 orb = myhf.mo_coeff
-ftmp = tempfile.NamedTemporaryFile()
+ftmp = lib.NamedTemporaryFile()
 print('MO integrals are saved in file  %s  under dataset "eri_mo"' % ftmp.name)
 ao2mo.kernel(mol, orb, ftmp.name)
 

examples/ao2mo/10-diff_orbs_for_ijkl.py

@@ -3,10 +3,10 @@
 # Author: Qiming Sun <osirpt.sun@gmail.com>
 #
 
-import tempfile
 import numpy
 import h5py
 from pyscf import gto, scf, ao2mo
+from pyscf import lib
 
 '''
 Integral transformation for four different orbitals
@@ -39,7 +39,7 @@
 #
 # Given four MOs, compute the MO-integrals and saved in dataset "mp2_bz"
 #
-eritmp = tempfile.NamedTemporaryFile()
+eritmp = lib.NamedTemporaryFile()
 nocc = mol.nelectron // 2
 nvir = len(mf.mo_energy) - nocc
 co = mf.mo_coeff[:,:nocc]

examples/ao2mo/11-ump2.py

@@ -3,7 +3,6 @@
 # Author: Qiming Sun <osirpt.sun@gmail.com>
 #
 
-import tempfile
 import numpy
 import h5py
 from pyscf import gto, scf, ao2mo

examples/ao2mo/20-eri_grad_hess.py

@@ -3,10 +3,10 @@
 # Author: Qiming Sun <osirpt.sun@gmail.com>
 #
 
-import tempfile
 import numpy
 import h5py
 from pyscf import gto, scf, ao2mo
+from pyscf import lib
 
 '''
 Integral transformation for irregular operators
@@ -28,7 +28,7 @@
 #
 # Given four MOs, compute the MO-integral gradients
 #
-gradtmp = tempfile.NamedTemporaryFile()
+gradtmp = lib.NamedTemporaryFile()
 nocc = mol.nelectron // 2
 nvir = len(mf.mo_energy) - nocc
 co = mf.mo_coeff[:,:nocc]
@@ -56,7 +56,7 @@
 #       9       d/dZ  d/dZ
 #
 orb = mf.mo_coeff
-hesstmp = tempfile.NamedTemporaryFile()
+hesstmp = lib.NamedTemporaryFile()
 ao2mo.kernel(mol, orb, hesstmp.name, intor='cint2e_ipvip1_sph',
              dataname='hessints1', aosym='s4')
 with ao2mo.load(hesstmp, 'hessints1') as eri:

examples/ao2mo/22-rkb_no_pair_ints.py

@@ -10,7 +10,6 @@
 from pyscf import scf
 from pyscf import lib
 from pyscf.ao2mo import r_outcore
-import tempfile
 import os
 
 mol = gto.M(
@@ -53,7 +52,7 @@ def no_pair_ovov(mol, mo_coeff, erifile):
 
         def run_and_add(mol, mos, erifile, dataname_main, intor):
             # Use a temporary file for the intermediate integrals
-            with tempfile.NamedTemporaryFile(suffix=".h5", delete=False) as tmpfile:
+            with lib.NamedTemporaryFile(suffix=".h5", delete=False) as tmpfile:
                 tmp_erifile = tmpfile.name
 
             try:

examples/cc/03-gccsd.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+'''
+GCCSD: CCSD based on the GHF reference.
+
+The cluster amplitudes of GCCSD are represented in the spin-orbital basis and
+are solved without assuming spin symmetry. GCCSD can be applied to spin-orbit
+coupled systems.
+
+For non-relativistic calculations, GCCSD is typically equivalent to the
+corresponding UHF-CCSD calculation. When spin-orbit coupling (SOC) is included,
+for example, the X2C Hamiltonian (see examples/x2c/03-x2c_ghf.py) or SOC-ECP
+(see examples/scf/44-soc_ecp.py), the GHF orbitals become complex-valued, and
+the resulting GCCSD amplitude are also complex-valued.
+'''
+
+import pyscf
+
+mol = pyscf.M(atom='''
+O    0.   0.       0.
+H    0.   -0.757   0.587
+H    0.   0.757    0.587''',
+basis='cc-pvdz')
+#
+# Non-relativistic calculation. The CCSD object returned by mf.CCSD() is an
+# instance of the GCCSD class. The cluster amplitudes are represented in the
+# spin-orbital basis.
+#
+mf = mol.GHF().run()
+mycc = mf.CCSD().run()
+
+#
+# Enable SOC via the X2C Hamiltonian. GCCSD amplitudes are complex-valued.
+#
+mf = mol.GHF().x2c().run()
+mycc = mf.CCSD().run()
+
+#
+# For calculations using ECPs, SOC can be enabled with the setting
+#     mf.with_soc = True
+#
+# Running mf.CCSD() on such a reference will performs a GCCSD calculation
+# with complex-valued amplitudes.
+#

examples/cc/61-rccsdtq.py

@@ -52,7 +52,7 @@
 mycc2.verbose = 5
 mycc2.incore_complete = True
 mycc2.kernel()
-print('Full-T4 RCCSDQ e_corr       % .12f    Ref % .12f    Diff % .12e' % (
+print('Full-T4 RCCSDTQ e_corr       % .12f    Ref % .12f    Diff % .12e' % (
         mycc2.e_corr, ref_e_corr, mycc2.e_corr - ref_e_corr))
 
 #

examples/cc/63-check_rccsdt_uccsdt_consistency.py

@@ -63,7 +63,7 @@
 
 # Restart UCCSDT using amplitudes converted from RCCSDT
 tamps_init_uhf = [t1_rhf2uhf, t2_rhf2uhf, t3_rhf2uhf]
-myucc2 = cc.UCCSDT(mf, compact_tamps=False).set(conv_tol=1e-10, conv_tol_normt=1e-8, verbose=5)
+myucc2 = cc.UCCSDT(mf_uhf, compact_tamps=False).set(conv_tol=1e-10, conv_tol_normt=1e-8, verbose=5)
 myucc2.kernel(tamps=tamps_init_uhf)
 print('UCCSDT correlation energy % .12f    Ref % .12f    Diff % .12e' % (
         myucc2.e_corr, -0.2188784727114157, myucc2.e_corr - -0.2188784727114157))

examples/cc/64-chained_rccsd_rccsdt_rccsdtq.py

@@ -11,7 +11,6 @@
     - Examine the influence of DIIS acceleration on convergence.
 '''
 
-import numpy as np
 from pyscf import gto, scf, cc
 
 def run_rccsd_rccsdt_rccsdtq(do_diis=False, do_diis_max_t=False, verbose=0):

examples/cc/65-chained_uccsd_uccsdt.py

@@ -11,7 +11,6 @@
     - Understand and handle the difference in T2 amplitude conventions between UCCSD and UCCSDT implementations.
 '''
 
-import numpy as np
 from pyscf import gto, scf, cc
 
 def run_uccsd_uccsdt(do_diis=False, do_diis_max_t=False, verbose=0):
@@ -32,7 +31,7 @@ def run_uccsd_uccsdt(do_diis=False, do_diis_max_t=False, verbose=0):
     myccsd.verbose = verbose
     myccsd.diis = do_diis
     myccsd.kernel()
-    print('RCCSD   e_corr % .12f    Ref % .12f    Diff % .12e' % (
+    print('UCCSD   e_corr % .12f    Ref % .12f    Diff % .12e' % (
             myccsd.e_corr, ref_ccsd_e_corr, myccsd.e_corr - ref_ccsd_e_corr))
 
     # UCCSDT
@@ -99,7 +98,7 @@ def run_uccsd_uccsdt(do_diis=False, do_diis_max_t=False, verbose=0):
     do_diis_max_t = False
     run_uccsd_uccsdt(do_diis=do_diis, do_diis_max_t=do_diis_max_t)
 
-    print('=== UCCSD / UCCSDT with DIIS (including T3 amplitudes) ===')
+    print('=== UCCSD -> UCCSDT with DIIS (including T3 amplitudes) ===')
     do_diis = True
     do_diis_max_t = True
     run_uccsd_uccsdt(do_diis=do_diis, do_diis_max_t=do_diis_max_t)

examples/cc/66-rccsdt_q.py

@@ -0,0 +1,59 @@
+#!/usr/bin/env python
+#
+# Author: Yu Jin <yjin@flatironinstitute.org>
+#
+
+'''
+Examples of RCCSDT(Q) calculations.
+
+This script demonstrates:
+    - Consistency of the [Q] and (Q) energy corrections on top of RCCSDT between calculations
+        using full and compact T3 storage.
+'''
+
+from pyscf import gto, scf, cc
+
+mol = gto.M(atom='H 0 0 0; F 0 0 1.1', basis='ccpvdz')
+mf = scf.RHF(mol)
+mf.conv_tol = 1e-14
+mf.kernel()
+
+# Reference CCSDT correlation energy, and [Q] and (Q) energy correction
+ref_e_corr = -0.2188784733230733
+ref_e_q_bracket = -0.0005026220700017348
+ref_e_q_paren = -0.0005490746450078632
+
+mycc1 = cc.RCCSDT(mf, compact_tamps=True)
+mycc1.conv_tol = 1e-10
+mycc1.conv_tol_normt = 1e-8
+mycc1.verbose = 5
+# einsum_backend: numpy (default) | pyscf | pytblis (recommended)
+# pytblis can be installed via `pip install pytblis==0.05` (See https://github.com/chillenb/pytblis)
+mycc1.set_einsum_backend('pyscf')
+mycc1.incore_complete = True
+mycc1.kernel()
+e_q_bracket, e_q_paren = mycc1.ccsdt_q()
+print('Triangular RCCSDT e_corr % .12f    Ref % .12f    Diff % .12e' % (
+        mycc1.e_corr, ref_e_corr, mycc1.e_corr - ref_e_corr))
+print('Triangular RCCSDT [Q]    % .12f    Ref % .12f    Diff % .12e' % (
+        e_q_bracket, ref_e_q_bracket, e_q_bracket - ref_e_q_bracket))
+print('Triangular RCCSDT (Q)    % .12f    Ref % .12f    Diff % .12e' % (
+        e_q_paren, ref_e_q_paren, e_q_paren - ref_e_q_paren))
+
+#
+# RCCSDT with full T3 storage
+# Same as cc.rccsdt_highm.RCCSDT
+#
+mycc2 = cc.RCCSDT(mf, compact_tamps=False)
+mycc2.conv_tol = 1e-10
+mycc2.conv_tol_normt = 1e-8
+mycc2.verbose = 5
+mycc2.incore_complete = True
+mycc2.kernel()
+q_bracket2, q_paren2 = mycc2.ccsdt_q()
+print('Full-T3 RCCSDT e_corr    % .12f    Ref % .12f    Diff % .12e' % (
+        mycc2.e_corr, ref_e_corr, mycc2.e_corr - ref_e_corr))
+print('Full-T3 RCCSDT [Q]       % .12f    Ref % .12f    Diff % .12e' % (
+        q_bracket2, ref_e_q_bracket, q_bracket2 - ref_e_q_bracket))
+print('Full-T3 RCCSDT (Q)       % .12f    Ref % .12f    Diff % .12e' % (
+        q_paren2, ref_e_q_paren, q_paren2 - ref_e_q_paren))

examples/df/01-auxbasis.py

@@ -10,7 +10,6 @@
 See also examples/gto/04-input_basis.py
 '''
 
-import tempfile
 from pyscf import gto, scf, df
 
 #

examples/df/40-precompute_df_integrals.py

@@ -10,12 +10,12 @@
 reused many times.
 '''
 
-import tempfile
 from pyscf import gto, scf, df
+from pyscf import lib
 from pyscf.pbc import gto as pgto
 from pyscf.pbc import dft as pdft
 
-tmpf = tempfile.NamedTemporaryFile()
+tmpf = lib.NamedTemporaryFile()
 file_to_save_df_ints = tmpf.name
 print('DF integral is saved in %s' % file_to_save_df_ints)