jjgoings
commented
5 months ago Sorry to hear that. I just ran a fresh compilation and had no issues.
$ python sample-input.py
E(SCF) = -74.942079897820 in 9 iterations
Convergence:
FPS-SPF = 8.703089748378866e-11
RMS(P) = 5.29e-10
dE(SCF) = 1.57e-07
Dipole X = 0.00000000
Dipole Y = 1.53400920
Dipole Z = 0.00000000
E(MP2) = -74.9912295425809Here's my environment if it helps:
# packages in environment
#
# Name Version Build Channel
archspec 0.2.2 pyhd8ed1ab_0 conda-forge
beartype 0.17.0 pypi_0 pypi
bitarray 2.9.2 pypi_0 pypi
bitstring 4.1.4 pypi_0 pypi
black 24.1.1 pypi_0 pypi
boltons 23.1.1 pyhd8ed1ab_0 conda-forge
brotli-python 1.1.0 py310h1253130_1 conda-forge
bzip2 1.0.8 h620ffc9_4
c-ares 1.24.0 h93a5062_0 conda-forge
ca-certificates 2023.12.12 hca03da5_0
certifi 2023.11.17 py310hca03da5_0
cffi 1.16.0 py310h80987f9_0
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 pypi_0 pypi
colorama 0.4.6 py310hca03da5_0
conda 23.11.0 py310hca03da5_0
conda-libmamba-solver 23.12.0 pyhd3eb1b0_1
conda-package-handling 2.2.0 py310hca03da5_0
conda-package-streaming 0.9.0 py310hca03da5_0
cryptography 41.0.7 py310hd4332d6_0
cython 3.0.8 pypi_0 pypi
distro 1.8.0 py310hca03da5_0
exceptiongroup 1.2.0 pypi_0 pypi
flake8 7.0.0 pypi_0 pypi
fmt 10.1.1 h6aa02a4_1 conda-forge
h5py 3.10.0 pypi_0 pypi
icu 73.2 hc8870d7_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
iniconfig 2.0.0 pypi_0 pypi
ipie 0.7.1.dev0 pypi_0 pypi
isort 5.13.2 pypi_0 pypi
jsonpatch 1.33 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py310hbe9552e_3 conda-forge
krb5 1.21.2 h92f50d5_0 conda-forge
libarchive 3.7.2 hcacb583_1 conda-forge
libcurl 8.5.0 h2d989ff_0 conda-forge
libcxx 16.0.6 h4653b0c_0 conda-forge
libedit 3.1.20230828 h80987f9_0
libev 4.33 h1a28f6b_1
libffi 3.4.4 hca03da5_0
libgfortran 5.0.0 11_3_0_hca03da5_28
libgfortran5 11.3.0 h009349e_28
libiconv 1.17 h0d3ecfb_2 conda-forge
libmamba 1.5.5 h0a6dc31_0 conda-forge
libmambapy 1.5.5 py310h3812fd7_0 conda-forge
libnghttp2 1.58.0 ha4dd798_1 conda-forge
libsolv 0.7.27 h9e231a4_0 conda-forge
libsqlite 3.44.2 h091b4b1_0 conda-forge
libssh2 1.11.0 h7a5bd25_0 conda-forge
libxml2 2.12.3 h0d0cfa8_0 conda-forge
libzlib 1.2.13 h53f4e23_5 conda-forge
llvm-openmp 14.0.6 hc6e5704_0
llvmlite 0.42.0 pypi_0 pypi
lz4-c 1.9.4 h313beb8_0
lzo 2.10 h1a28f6b_2
mamba 1.5.5 py310ha5d4528_0 conda-forge
markdown-it-py 3.0.0 pypi_0 pypi
mccabe 0.7.0 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
menuinst 2.0.1 py310hca03da5_1
mmd 0.0.1 dev_0 <develop>
mpi 1.0 mpich
mpi4py 3.1.4 py310h5a14b7f_0
mpich 3.3.2 he2630cc_1
mypy-extensions 1.0.0 pypi_0 pypi
ncurses 6.4 h313beb8_0
numba 0.59.0 pypi_0 pypi
numpy 1.25.2 pypi_0 pypi
openssl 3.2.0 h0d3ecfb_1 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pandas 1.5.1 pypi_0 pypi
pathspec 0.12.1 pypi_0 pypi
pip 23.3.2 pyhd8ed1ab_0 conda-forge
platformdirs 4.1.0 pyhd8ed1ab_0 conda-forge
pluggy 1.3.0 pyhd8ed1ab_0 conda-forge
plum-dispatch 2.3.2 pypi_0 pypi
pybind11-abi 4 hd3eb1b0_1
pycodestyle 2.11.1 pypi_0 pypi
pycosat 0.6.6 py310h80987f9_0
pycparser 2.21 pyhd3eb1b0_0
pyflakes 3.2.0 pypi_0 pypi
pygments 2.17.2 pypi_0 pypi
pyopenssl 23.2.0 py310hca03da5_0
pyscf 2.4.0 pypi_0 pypi
pysocks 1.7.1 py310hca03da5_0
pytest 8.0.0 pypi_0 pypi
python 3.10.13 h2469fbe_0_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
python_abi 3.10 4_cp310 conda-forge
pytz 2023.3.post1 py310hca03da5_0
readline 8.2 h1a28f6b_0
reproc 14.2.4.post0 h93a5062_1 conda-forge
reproc-cpp 14.2.4.post0 h965bd2d_1 conda-forge
requests 2.31.0 py310hca03da5_0
rich 13.7.0 pypi_0 pypi
ruamel.yaml 0.18.5 py310hd125d64_0 conda-forge
ruamel.yaml.clib 0.2.7 py310h2aa6e3c_2 conda-forge
scipy 1.10.1 pypi_0 pypi
setuptools 68.2.2 py310hca03da5_0
six 1.16.0 pypi_0 pypi
tk 8.6.13 h5083fa2_1 conda-forge
tomli 2.0.1 pypi_0 pypi
tqdm 4.66.1 pyhd8ed1ab_0 conda-forge
truststore 0.8.0 py310hca03da5_0
typing-extensions 4.9.0 pypi_0 pypi
tzdata 2023d h04d1e81_0
urllib3 1.26.18 py310hca03da5_0
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
xz 5.4.5 h80987f9_0
yaml-cpp 0.8.0 h313beb8_0
zstandard 0.22.0 py310h6289e41_0 conda-forge
zstd 1.5.5 h4f39d0f_0 conda-forge
Hi,
Please let me know if the current code setup is working.
I tried to install mmd and tried to run a simple script from the examples, but it throws me an error,
python sample-input.py /home/varadarajan/softwares/mmd_overlap/McMurchie-Davidson/mmd/molecule.py:71: RuntimeWarning: divide by zero encountered in scalar divide self.bfs.append(Basis(np.asarray(atom.origin), /home/varadarajan/softwares/mmd_overlap/McMurchie-Davidson/mmd/molecule.py:71: RuntimeWarning: invalid value encountered in scalar multiply self.bfs.append(Basis(np.asarray(atom.origin), /home/varadarajan/softwares/mmd_overlap/McMurchie-Davidson/mmd/molecule.py:71: RuntimeWarning: invalid value encountered in scalar add self.bfs.append(Basis(np.asarray(atom.origin), Traceback (most recent call last): File "/home/varadarajan/softwares/mmd_overlap/McMurchie-Davidson/sample-input.py", line 15, in
mol.RHF()
File "/home/varadarajan/softwares/mmd_overlap/McMurchie-Davidson/mmd/scf.py", line 21, in RHF
self.build(self.direct) # build integrals
File "/home/varadarajan/softwares/mmd_overlap/McMurchie-Davidson/mmd/molecule.py", line 92, in build
self.one_electron_integrals()
File "/home/varadarajan/softwares/mmd_overlap/McMurchie-Davidson/mmd/molecule.py", line 285, in one_electron_integrals
self.X = mat_pow(self.S,-0.5)
File "/home/varadarajan/softwares/my-jupyter-env/lib/python3.10/site-packages/scipy/linalg/_matfuncs.py", line 143, in fractional_matrix_power
return scipy.linalg._matfuncs_inv_ssq._fractional_matrix_power(A, t)
File "/home/varadarajan/softwares/my-jupyter-env/lib/python3.10/site-packages/scipy/linalg/_matfuncs_inv_ssq.py", line 684, in _fractional_matrix_power
s = svdvals(A)
File "/home/varadarajan/softwares/my-jupyter-env/lib/python3.10/site-packages/scipy/linalg/_decomp_svd.py", line 225, in svdvals
a = _asarray_validated(a, check_finite=check_finite)
File "/home/varadarajan/softwares/my-jupyter-env/lib/python3.10/site-packages/scipy/_lib/_util.py", line 306, in _asarray_validated
a = toarray(a)
File "/home/varadarajan/softwares/my-jupyter-env/lib/python3.10/site-packages/numpy/lib/function_base.py", line 630, in asarray_chkfinite
raise ValueError(
ValueError: array must not contain infs or NaNs