Merge branch 'format_PEP8' into enable_whole_testsuite

example/molbe_dmrg_block2.py

@@ -56,11 +56,11 @@
 
     # Next, run BE-DMRG with default parameters and maxM=100.
     mybe.oneshot(
-        solver='block2',                                # or 'DMRG', 'DMRGSCF', 'DMRGCI'
-        scratch_dir=scratch,                            # Scratch dir for fragment DMRG
-        maxM=100,                                       # Max fragment bond dimension
-        force_cleanup=True,                             # Remove all fragment DMRG tmpfiles
-        )
+        solver="block2",  # or 'DMRG', 'DMRGSCF', 'DMRGCI'
+        scratch_dir=scratch,  # Scratch dir for fragment DMRG
+        maxM=100,  # Max fragment bond dimension
+        force_cleanup=True,  # Remove all fragment DMRG tmpfiles
+    )
 
     bedmrg_ecorr.append(mybe.ebe_tot - mf.e_tot)
     # Setting `force_cleanup=True` will clean the scratch directory after each
@@ -136,5 +136,5 @@
 # and `[scratch]/dmrg.out`, which are the fragment DMRG inputs and outputs, respectively, used
 # by `block2`.
 
-#NOTE: Parameters in `schedule_kwargs` will overwrite any other DMRG kwargs.
-#NOTE: The DMRG schedule kwargs and related syntax follows the standard notation used in block2.
+# NOTE: Parameters in `schedule_kwargs` will overwrite any other DMRG kwargs.
+# NOTE: The DMRG schedule kwargs and related syntax follows the standard notation used in block2.

example/molbe_io_fcidump.py

@@ -2,7 +2,7 @@
 # can be generated using be2fcidump
 
 from molbe import BE, be_var, fragpart
-from molbe.misc import *
+from molbe.misc import be2fcidump, libint2pyscf
 
 be_var.PRINT_LEVEL = 3
 

setup.py

@@ -18,10 +18,10 @@
     package_dir={"": "src"},
     python_requires=">=3.7",
     install_requires=[
-        'numpy>=1.22.0',
-        'scipy>=1.7.0',
-        'pyscf>=2.0.0',
-        'matplotlib',
-        'libdmet @ git+https://github.com/gkclab/libdmet_preview.git',
+        "numpy>=1.22.0",
+        "scipy>=1.7.0",
+        "pyscf>=2.0.0",
+        "matplotlib",
+        "libdmet @ git+https://github.com/mcocdawc/libdmet_preview.git@add_fixes_for_BE",
     ],
 )

src/kbe/helper.py

@@ -5,6 +5,7 @@
 import numpy
 
 
+
 def get_veff(eri_, dm, S, TA, hf_veff, return_veff0=False):
     from pyscf import scf
 

src/kbe/pbe.py

@@ -13,6 +13,7 @@
 from .pfrag import Frags
 
 
+
 class BE:
     """
     Class for handling periodic bootstrap embedding (BE) calculations.

src/kbe/pfrag.py

@@ -13,6 +13,7 @@
 from .solver import schmidt_decomp_svd
 
 
+
 class Frags:
     """
     Class for handling fragments in periodic bootstrap embedding.

src/molbe/_opt.py

@@ -177,7 +177,6 @@ def optimize(self, method, J0=None, trust_region=False):
         import sys
 
         from molbe.external.optqn import FrankQN
-
         print("-----------------------------------------------------", flush=True)
         print("             Starting BE optimization ", flush=True)
         print("             Solver : ", self.solver, flush=True)

src/molbe/external/unrestricted_utils.py

@@ -6,6 +6,7 @@
 import numpy
 
 
+
 def make_uhf_obj(fobj_a, fobj_b, frozen=False):
     from pyscf import scf
 

src/molbe/fragment.py

@@ -6,6 +6,7 @@
 from .helper import get_core
 
 
+
 class fragpart:
     """Fragment/partitioning definition
 

src/molbe/misc.py

@@ -1,6 +1,7 @@
 # Author(s): Minsik Cho, Leah Weisburn
 
 import os
+import sys
 import time
 
 import numpy

src/molbe/ube.py

@@ -22,6 +22,7 @@
 from .pfrag import Frags
 
 
+
 class UBE(BE):  # 🍠
     def __init__(
         self,

tests/chem_dm_kBE_test.py

@@ -13,6 +13,7 @@
 from kbe import BE, fragpart
 
 
+
 class Test_kBE_Full(unittest.TestCase):
     try:
         import libdmet

tests/chempot_molBE_test.py

@@ -12,6 +12,7 @@
 from molbe import BE, fragpart
 
 
+
 class TestBE_restricted(unittest.TestCase):
     def test_h8_sto3g_ben(self):
         # Linear Equidistant (r=1Å) H8 Chain, STO-3G

tests/dm_molBE_test.py

@@ -11,6 +11,7 @@
 from molbe import BE, fragpart
 
 
+
 class TestBE_restricted(unittest.TestCase):
     # TODO: Add test against known values (molecular_restrict_test)
     def test_h8_sto3g_ben_trustRegion(self):

tests/dmrg_molBE_test.py

@@ -12,6 +12,7 @@
 from molbe import BE, fragpart
 
 
+
 class TestBE_DMRG(unittest.TestCase):
     try:
         from pyscf import dmrgscf

tests/eri_onthefly_test.py

@@ -12,6 +12,7 @@
 from molbe import BE, fragpart
 
 
+
 class TestDF_ontheflyERI(unittest.TestCase):
     @unittest.skipIf(
         os.getenv("QUEMB_SKIP_EXPENSIVE_TESTS") == "true",

tests/hf-in-hf_BE_test.py

@@ -12,6 +12,7 @@
 from molbe import BE, fragpart
 
 
+
 class TestHFinHF_restricted(unittest.TestCase):
     def test_h8_sto3g_ben(self):
         # Linear Equidistant (r=1Å) H8 Chain, STO-3G

tests/ube-oneshot_test.py

@@ -14,6 +14,7 @@
 from molbe import UBE, fragpart
 
 
+
 class TestOneShot_Unrestricted(unittest.TestCase):
     @unittest.skipIf(
         not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",