Resolve conflicts

.github/workflows/ci.yml

@@ -62,7 +62,7 @@ jobs:
             yum install -y epel-release && \
             yum-config-manager --enable epel && \
             yum install -y openblas-devel gcc cmake curl && \
-            cd ./pyscf/lib && curl -o deps.tar.gz -L "https://github.com/kkyusuke/pyscf-build-deps/blob/master/pyscf-2.1a-aarch64-deps.tar.gz?raw=true"  && \
+            cd ./pyscf/lib && curl -o deps.tar.gz -L "https://github.com/pyscf/pyscf-build-deps/blob/master/pyscf-2.1-aarch64-deps.tar.gz?raw=true"  && \
             tar xzf deps.tar.gz && \
             mkdir build && cd build && \
             cmake -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF -DBUILD_LIBCINT=OFF .. && \

.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-2.1a-deps.tar.gz?raw=true" | tar xzf -
+curl -L "https://github.com/pyscf/pyscf-build-deps/blob/master/pyscf-2.1-deps.tar.gz?raw=true" | tar xzf -
 mkdir build; cd build
 cmake -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF -DBUILD_LIBCINT=OFF ..
 make -j4

.github/workflows/ci_linux/python_deps.sh

@@ -2,6 +2,7 @@
 python -m pip install --upgrade pip
 pip install "numpy!=1.16,!=1.17" "scipy!=1.5" h5py pytest pytest-cov pytest-timer codecov
 pip install pyberny geometric
+pip install spglib
 
 #cppe
 version=$(python -c 'import sys; version=sys.version_info[:2]; print("{0}.{1}".format(*version))')

examples/adc/03-closed_shell_different_setup.py

@@ -23,13 +23,13 @@
 
 #IP-RADC(2) for 3 roots
 myadc.verbose = 4
-myadcip = adc.radc.RADCIP(myadc)
+myadcip = adc.radc_ip.RADCIP(myadc)
 eip,vip,pip,xip = myadcip.kernel(nroots=3)
 
 #EA-RADC(3) for 3 roots
 myadc.method = "adc(3)"
 myadc.kernel_gs()
-myadcea = adc.radc.RADCEA(myadc)
+myadcea = adc.radc_ea.RADCEA(myadc)
 eea,vea,pea,xea = myadcea.kernel(nroots=3)
 
 #Analyze eigenvectors only

examples/dft/24-define_xc_functional.py

@@ -30,7 +30,7 @@ def eval_xc(xc_code, rho, spin=0, relativity=0, deriv=1, verbose=None):
     rho0, dx, dy, dz = rho[:4]
     gamma = (dx**2 + dy**2 + dz**2)
     exc = .01 * rho0**2 + .02 * (gamma+.001)**.5
-    vrho = .01 * 2 * rho0
+    vrho = .01 * 3 * rho0**2 + .02 * (gamma+.001)**.5
     vgamma = .02 * .5 * (gamma+.001)**(-.5)
     vlapl = None
     vtau = None

examples/gto/02-dump_input.py

@@ -8,12 +8,12 @@
 '''
 Mute input dumping
 
-Input file is dump at the beginning of the output by default.  Siwtch it off
-by setting dump_input=False.  Also the command line arguments can be ignored
+Input file is dump at the beginning of the output by default. Switch it off
+by setting dump_input=False. Also the command line arguments can be ignored
 if parse_arg=False.
 
 dump_input and parse_arg are the first two arguments of the Mole.build
-function.  They can be turned off by short notation .build(0, 0).  This trick
+function. They can be turned off by short notation .build(0, 0). This trick
 can be found many places in the package.
 '''
 
@@ -25,4 +25,3 @@
 )
 
 mol.build(0, 0)
-

examples/pbc/20-k_points_scf_ksymm.py

@@ -0,0 +1,81 @@
+#!/usr/bin/env python
+
+'''
+Mean field with k-points sampling when Brillouin Zone symmetry is considered
+'''
+
+import numpy
+from pyscf.pbc import gto, scf, dft
+
+cell = gto.M(
+    a = numpy.asarray([[0.0, 2.6935121974, 2.6935121974], 
+                       [2.6935121974, 0.0, 2.6935121974], 
+                       [2.6935121974, 2.6935121974, 0.0]]),
+    atom = '''Si  0.0000000000 0.0000000000 0.0000000000
+              Si  1.3467560987 1.3467560987 1.3467560987''', 
+    basis = 'gth-szv',
+    pseudo = 'gth-pade',
+    mesh = [24,24,24],
+    verbose = 5,
+)
+
+nk = [2,2,2]
+#The Brillouin Zone symmetry info is contained in the kpts object
+#symmorphic: if True, only the symmorphic subgroup is considered
+kpts = cell.make_kpts(nk, 
+                      space_group_symmetry=True, 
+                      time_reversal_symmetry=True,
+                      symmorphic=True)
+print(kpts)
+
+kmf = scf.KRHF(cell, kpts)
+kmf.kernel()
+
+kmf = dft.KRKS(cell, kpts)
+kmf.xc = 'camb3lyp'
+kmf.kernel()
+
+#
+# The mean-field object with k-point symmetry can be converted back to
+# the correponding non-symmetric mean-field object
+#
+
+kmf = kmf.to_khf()
+kmf.kernel(kmf.make_rdm1())
+
+#
+# Second order SCF solver can be used in the PBC SCF code the same way in the
+# molecular calculation
+#
+kmf = scf.KRHF(cell, kpts).newton()
+kmf.kernel()
+
+#
+#KUHF
+#
+kumf = scf.KUHF(cell, kpts)
+kumf.kernel()
+
+#
+# The mean-field object with k-point symmetry can be converted back to
+# the correponding non-symmetric mean-field object
+#
+kumf = kumf.to_khf()
+kumf.kernel(kumf.make_rdm1())
+
+#
+#KUHF with smearing
+#
+cell.spin = 2 * 2**3 #assume S=1 in each cell
+kumf = scf.KUHF(cell, kpts)
+#fix_spin: 
+#   if True:
+#       the final solution will have the same spin as input
+#   if False: 
+#       alpha and beta orbitals are sorted together based on energies,
+#       and the final solution can have different spin from input
+#
+#Note: when gap is small, symmetry broken solution is usually the case,
+#      which should be computed by turning off the symmstry options
+kumf = scf.addons.smearing_(kumf, sigma=0.001, method='fermi',fix_spin=True)
+kumf.kernel()

examples/pbc/22-k_points_mp2.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 '''
-MP2 at an individual k-point
+MP2 with k-points sampling
 '''
 
 from functools import reduce

examples/pbc/22-k_points_mp2_ksymm.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+'''
+MP2 with k-points sampling when Brillouin Zone symmetry is considered
+'''
+
+import numpy
+from pyscf.pbc import gto, scf, mp
+
+cell = gto.M(
+    a = numpy.asarray([[0.0, 2.6935121974, 2.6935121974],
+                       [2.6935121974, 0.0, 2.6935121974],
+                       [2.6935121974, 2.6935121974, 0.0]]),
+    atom = '''Si  0.0000000000 0.0000000000 0.0000000000
+              Si  1.3467560987 1.3467560987 1.3467560987''',
+    basis = 'gth-szv',
+    pseudo = 'gth-pade',
+    mesh = [24,24,24],
+    verbose = 5,
+)
+
+nk = [2,2,2]
+kpts = cell.make_kpts(nk,
+                      space_group_symmetry=True,
+                      time_reversal_symmetry=True)
+
+kmf = scf.KRHF(cell, kpts)
+kmf.kernel()
+
+kmp2 = mp.KMP2(kmf)
+kmp2.kernel()
+print("KMP2 energy (per unit cell) =", kmp2.e_tot)

examples/pbc/22-k_points_mp2_stagger.py

@@ -0,0 +1,149 @@
+#!/usr/bin/env python
+
+'''
+Example code for
+k-point spin-restricted periodic MP2 calculation using staggered mesh method
+
+Author: Xin Xing ([email protected])
+
+Reference: Staggered Mesh Method for Correlation Energy Calculations of Solids:
+           Second-Order Møller-Plesset Perturbation Theory, J. Chem. Theory
+           Comput. 2021, 17, 8, 4733-4745
+'''
+
+
+from pyscf.pbc.mp.kmp2_stagger import KMP2_stagger
+from pyscf.pbc import df, gto, scf, mp
+
+
+'''
+Hydrogen dimer
+'''
+cell = gto.Cell()
+cell.pseudo = 'gth-pade'
+cell.basis = 'gth-szv'
+cell.ke_cutoff = 100
+cell.atom = '''
+    H 3.00   3.00   2.10
+    H 3.00   3.00   3.90
+    '''
+cell.a = '''
+    6.0   0.0   0.0
+    0.0   6.0   0.0
+    0.0   0.0   6.0
+    '''
+cell.unit = 'B'
+cell.verbose = 4
+cell.build()
+
+
+#   HF calculation using FFTDF
+nks_mf = [2, 2, 2]
+kpts = cell.make_kpts(nks_mf, with_gamma_point=True)
+kmf = scf.KRHF(cell, kpts, exxdiv='ewald')
+ehf = kmf.kernel()
+
+#   staggered mesh KMP2 using two 1*1*1 submeshes in kmf.kpts
+kmp = KMP2_stagger(kmf, flag_submesh=True)
+emp2 = kmp.kernel()
+assert((abs(emp2 - -0.0160902544091997)) < 1e-5)
+
+#   staggered mesh KMP2 using two 2*2*2 submeshes based on non-SCF
+kmp = KMP2_stagger(kmf, flag_submesh=False)
+emp2 = kmp.kernel()
+assert((abs(emp2 - -0.0140289970302513)) < 1e-5)
+
+#   standard KMP2 calculation
+kmp = mp.KMP2(kmf)
+emp2, _ = kmp.kernel()
+assert((abs(emp2 - -0.0143904878990777)) < 1e-5)
+
+
+#   HF calculation using GDF
+nks_mf = [2, 2, 2]
+kpts = cell.make_kpts(nks_mf, with_gamma_point=True)
+kmf = scf.KRHF(cell, kpts, exxdiv='ewald')
+kmf.with_df = df.GDF(cell, kpts).build()
+ehf = kmf.kernel()
+
+#   staggered mesh KMP2 using two 1*1*1 submeshes in kmf.kpts
+kmp = KMP2_stagger(kmf, flag_submesh=True)
+emp2 = kmp.kernel()
+assert((abs(emp2 - -0.0158364523431071)) < 1e-5)
+
+#   staggered mesh KMP2 using two 2*2*2 submeshes based on non-SCF
+kmp = KMP2_stagger(kmf, flag_submesh=False)
+emp2 = kmp.kernel()
+assert((abs(emp2 - -0.0140280303691396)) < 1e-5)
+
+#   standard KMP2 calculation
+kmp = mp.KMP2(kmf)
+emp2, _ = kmp.kernel()
+assert((abs(emp2 - -0.0141829343769316)) < 1e-5)
+
+
+'''
+Diamond system
+'''
+
+cell = gto.Cell()
+cell.pseudo = 'gth-pade'
+cell.basis = 'gth-szv'
+cell.ke_cutoff = 100
+cell.atom = '''
+    C     0.      0.      0.
+    C     1.26349729, 0.7294805 , 0.51582061
+    '''
+cell.a = '''
+    2.52699457, 0.        , 0.
+    1.26349729, 2.18844149, 0.
+    1.26349729, 0.7294805 , 2.06328243
+    '''
+cell.unit = 'angstrom'
+cell.verbose = 4
+cell.build()
+
+
+#   HF calculation using FFTDF
+nks_mf = [2, 2, 2]
+kpts = cell.make_kpts(nks_mf, with_gamma_point=True)
+kmf = scf.KRHF(cell, kpts, exxdiv='ewald')
+ehf = kmf.kernel()
+
+#   staggered mesh KMP2 using two 1*1*1 submeshes in kmf.kpts
+kmp = KMP2_stagger(kmf, flag_submesh=True)
+emp2 = kmp.kernel()
+assert((abs(emp2 - -0.156289981810986)) < 1e-5)
+
+#   staggered mesh KMP2 using two 2*2*2 submeshes based on non-SCF
+kmp = KMP2_stagger(kmf, flag_submesh=False)
+emp2 = kmp.kernel()
+assert((abs(emp2 - -0.105454107635884)) < 1e-5)
+
+#   standard KMP2 calculation
+kmp = mp.KMP2(kmf)
+emp2, _ = kmp.kernel()
+assert((abs(emp2 - -0.095517731535516)) < 1e-5)
+
+
+#   HF calculation using GDF
+nks_mf = [2, 2, 2]
+kpts = cell.make_kpts(nks_mf, with_gamma_point=True)
+kmf = scf.KRHF(cell, kpts, exxdiv='ewald')
+kmf.with_df = df.GDF(cell, kpts).build()
+ehf = kmf.kernel()
+
+#   staggered mesh KMP2 using two 1*1*1 submeshes in kmf.kpts
+kmp = KMP2_stagger(kmf, flag_submesh=True)
+emp2 = kmp.kernel()
+assert((abs(emp2 - -0.154923152683604)) < 1e-5)
+
+#   staggered mesh KMP2 using two 2*2*2 submeshes based on non-SCF
+kmp = KMP2_stagger(kmf, flag_submesh=False)
+emp2 = kmp.kernel()
+assert((abs(emp2 - -0.105421948003715)) < 1e-5)
+
+#   standard KMP2 calculation
+kmp = mp.KMP2(kmf)
+emp2, _ = kmp.kernel()
+assert((abs(emp2 - -0.0952009565805345)) < 1e-5)

examples/pbc/24-k_points_vs_gamma.py

@@ -5,7 +5,6 @@
 '''
 
 import numpy as np
-from pyscf import cc
 from pyscf.pbc import cc as pbccc
 from pyscf.pbc import scf as pbchf
 from pyscf.pbc import gto
@@ -34,7 +33,8 @@
 mf.kernel()
 supcell_energy = mf.energy_tot() / np.prod(nmp)
 
-mycc = cc.RCCSD(mf)
+# A wrapper calling molecular CC method for gamma point calculation.
+mycc = pbccc.RCCSD(mf)
 gccsd_energy = mycc.ccsd()[0] / np.prod(nmp)
 eip, wip = mycc.ipccsd(nroots=2)
 eea, wea = mycc.eaccsd(nroots=2)