Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

psiresp calculation on molecules (using example code) gets validation errors #102

Open
wg12385 opened this issue Oct 7, 2022 · 1 comment
Open

psiresp calculation on molecules (using example code) gets validation errors #102

wg12385 opened this issue Oct 7, 2022 · 1 comment

Comments

@wg12385
Copy link

wg12385 commented Oct 7, 2022

I am testing using psiresp for our own molecules, some of which may be in slightly odd configurations as they're from transition states, so this error may be a result of our molecule just being a bit weird, but the molecule doesn't appear to present problems in psi4 in other configurations. I am using more or less the example code from the wiki.

Expected behavior
The calculation should complete and return charges, as it does in the example, OR if the molecule isn't valid for some reason return an error saying that.

Actual behavior
The calculation fails after the psi4 calculations with this error message:

pydantic.error_wrappers.ValidationError: 2 validation errors for WavefunctionProperties
orbitals_b
  Return quantity scf_orbitals_b does not exist in the values. (type=value_error)
eigenvalues_b
  Return quantity scf_eigenvalues_b does not exist in the values. (type=value_error)

To Reproduce
The following python script reproduces the error. In order to restore the correct behaviour the string can just be replaced with the example one here: https://psiresp.readthedocs.io/en/latest/molecule.html (and yes i know my molecule isn't dmso)

import psiresp
import qcelemental as qcel
from rdkit import Chem
import numpy as np

# server stuff
import qcfractal.interface as ptl
from psiresp.testing import FractalSnowflake

dmso_spec = """\
    20
    ! test molecule
    S	24.58	-19.607	31.661
    N	20.167	-19.023	27.319
    N	18.498	-20.322	26.509
    O	22.182	-19.453	28.456
    N	17.93	-20.341	23.396
    O	22.563	-16.868	30.759
    C	25.324	-21.631	32.538
    N	19.728	-18.841	23.288
    O	19.993	-16.869	29.713
    C	23.642	-20.181	30.2
    N	20.934	-18.004	25.213
    C	22.979	-18.958	29.56
    C	22.012	-18.143	30.485
    C	20.67	-18.096	29.663
    C	21.147	-18.452	28.226
    C	19.184	-19.94	27.597
    C	19.084	-19.604	25.45
    C	18.885	-19.598	24.044
    C	20.683	-18.078	23.891
    C	20.117	-18.805	25.96
    """

    qcdmso = qcel.models.Molecule.from_data(dmso_spec, dtype='xyz')
    dmso = psiresp.Molecule(qcmol=qcdmso)

    dmso.add_conformer(qcmol=qcdmso)

    server = FractalSnowflake()
    client = ptl.FractalClient(server, verify=False)

    # QMGeometryOptimizationOptions(method='b3lyp', basis='sto-3g', pcm_options=None, 
    #                               driver='gradient', query_interval=20, 
    #                               protocols={'wavefunction': 'orbitals_and_eigenvalues'}, 
    #                               g_convergence='gau_tight', max_iter=200, full_hess_every=10, jobname='optimization')
    geometry_options = psiresp.QMGeometryOptimizationOptions(
        method="b3lyp", basis="sto-3g")
    # QMEnergyOptions(method='b3lyp', basis='sto-3g', pcm_options=None, driver='energy', 
    #                   query_interval=20, protocols={'wavefunction': 'orbitals_and_eigenvalues'}, 
    #                   jobname='single_point')
    esp_options = psiresp.QMEnergyOptions(
        method="b3lyp", basis="sto-3g",
    )
    resp_options = psiresp.RespOptions()


    job = psiresp.Job(molecules=[dmso],
                    qm_optimization_options=geometry_options,
                    qm_esp_options=esp_options,
                    resp_options=resp_options,
                    update_molecules=True)

    job.run(client=client)

    print(job.charges)
    for molecule in job.molecules:
        print(molecule.stage_1_unrestrained_charges)

Computing environment:

  • Operating system: Linux, ubuntu 22.04
  • Python version: 3.8.13
  • Version of PsiRESP: 0.4.2
  • Output of running conda list:
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                  2_kmp_llvm    conda-forge
alembic                   1.8.1              pyhd8ed1ab_0    conda-forge
ambit                     0.6              py38h53dec33_2    psi4
arrow-cpp                 9.0.0           py38h6933191_6_cpu    conda-forge
attrs                     22.1.0             pyh71513ae_1    conda-forge
aws-c-cal                 0.5.11               h95a6274_0    conda-forge
aws-c-common              0.6.2                h7f98852_0    conda-forge
aws-c-event-stream        0.2.7               h3541f99_13    conda-forge
aws-c-io                  0.10.5               hfb6a706_0    conda-forge
aws-checksums             0.1.11               ha31a3da_7    conda-forge
aws-sdk-cpp               1.8.186              hb4091e7_3    conda-forge
bcrypt                    3.2.2            py38h0a891b7_0    conda-forge
blas                      1.0                         mkl  
boost                     1.74.0           py38h2b96118_5    conda-forge
boost-cpp                 1.74.0               h75c5d50_8    conda-forge
brotli                    1.0.9                h166bdaf_7    conda-forge
brotli-bin                1.0.9                h166bdaf_7    conda-forge
brotlipy                  0.7.0           py38h0a891b7_1004    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.9.24            ha878542_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.16.0               h19f5f5c_2  
certifi                   2022.9.24          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py38h74dc2b5_0  
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
chemps2                   1.8.11               hbe8a562_0    psi4
colorama                  0.4.5              pyhd8ed1ab_0    conda-forge
conda                     22.9.0           py38h578d9bd_1    conda-forge
conda-package-handling    1.9.0            py38h0a891b7_0    conda-forge
contourpy                 1.0.5            py38h43d8883_0    conda-forge
cryptography              38.0.1           py38h2b5fc30_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
dftd3                     3.2.1                h84218bc_2    psi4
dkh                       1.2                  h173d85e_2    psi4
double-conversion         3.2.0                h27087fc_1    conda-forge
expat                     2.4.9                h27087fc_0    conda-forge
fftw                      3.3.9                h27cfd23_1  
fontconfig                2.14.0               hc2a2eb6_1    conda-forge
fonttools                 4.37.4           py38h0a891b7_0    conda-forge
freetype                  2.12.1               hca18f0e_0    conda-forge
gau2grid                  2.0.7                hd18ef5c_0    psi4
gcp                       2.0.2                he991be0_2    psi4
gdma                      2.2.6                h0e1e685_6    psi4
geometric                 0.9.7.2                    py_0    conda-forge
gflags                    2.2.2             he1b5a44_1004    conda-forge
glib                      2.69.1               h4ff587b_1  
glog                      0.6.0                h6f12383_0    conda-forge
grpc-cpp                  1.47.1               h05bd8bd_6    conda-forge
h5py                      3.1.0           nompi_py38hafa665b_100    conda-forge
hdf5                      1.10.6          nompi_h6a2412b_1114    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.4           py38h578d9bd_0    conda-forge
importlib_resources       5.9.0              pyhd8ed1ab_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
intel-openmp              2021.4.0          h06a4308_3561  
jpeg                      9e                   h166bdaf_2    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4            py38h43d8883_0    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.38                 h1181459_1  
lerc                      3.0                  h9c3ff4c_0    conda-forge
libabseil                 20220623.0      cxx17_h48a1fff_4    conda-forge
libarchive                3.5.2                hb890918_3    conda-forge
libbrotlicommon           1.0.9                h166bdaf_7    conda-forge
libbrotlidec              1.0.9                h166bdaf_7    conda-forge
libbrotlienc              1.0.9                h166bdaf_7    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcurl                   7.85.0               h7bff187_0    conda-forge
libdeflate                1.10                 h7f98852_0    conda-forge
libecpint                 1.0.7                hfebba4c_0    psi4
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.3                  he6710b0_2  
libgcc-ng                 12.1.0              h8d9b700_16    conda-forge
libgfortran-ng            12.1.0              h69a702a_16    conda-forge
libgfortran5              12.1.0              hdcd56e2_16    conda-forge
libgoogle-cloud           2.2.0                h838d150_1    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libint2                   2.7.1               h2fe1556_15    psi4
libmamba                  0.27.0               h0dd8ff0_0    conda-forge
libmambapy                0.27.0           py38h923e62a_0    conda-forge
libnghttp2                1.47.0               hdcd2b5c_1    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libpng                    1.6.38               h753d276_0    conda-forge
libpq                     14.5                 hd77ab85_0    conda-forge
libprotobuf               3.21.7               h6239696_0    conda-forge
libsolv                   0.7.22               h6239696_0    conda-forge
libssh2                   1.10.0               haa6b8db_3    conda-forge
libstdcxx-ng              12.1.0              ha89aaad_16    conda-forge
libthrift                 0.16.0               h491838f_2    conda-forge
libtiff                   4.3.0                h0fcbabc_4    conda-forge
libutf8proc               2.7.0                h7f98852_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp-base              1.2.4                h166bdaf_0    conda-forge
libxc                     5.1.5                h84b9e52_1    psi4
libxcb                    1.15                 h7f8727e_0  
libxml2                   2.10.2               h4c7fe37_1    conda-forge
libzlib                   1.2.12               h166bdaf_3    conda-forge
llvm-openmp               14.0.4               he0ac6c6_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mako                      1.2.3              pyhd8ed1ab_0    conda-forge
mamba                     0.27.0           py38h1abaa86_0    conda-forge
markupsafe                2.1.1            py38h0a891b7_1    conda-forge
matplotlib-base           3.6.0            py38hb021067_0    conda-forge
mkl                       2021.4.0           h06a4308_640  
mkl-service               2.4.0            py38h7f8727e_0  
mkl_fft                   1.3.1            py38hd3c417c_0  
mkl_random                1.2.2            py38h51133e4_0  
msgpack-python            1.0.4            py38h43d8883_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.3                  h5eee18b_3  
networkx                  2.8.7              pyhd8ed1ab_0    conda-forge
numpy                     1.23.1           py38h6c91a56_0  
numpy-base                1.23.1           py38ha15fc14_0  
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjpeg                  2.5.0                h7d73246_0    conda-forge
openssl                   1.1.1q               h7f8727e_0  
orc                       1.7.6                h09e0d61_1    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.5.0            py38h8f669ce_0    conda-forge
parquet-cpp               1.5.1                         2    conda-forge
pcmsolver                 1.2.1.1          py38h6d17ec8_2    psi4
pcre                      8.45                 h9c3ff4c_0    conda-forge
pillow                    8.4.0            py38h8e6f84c_0    conda-forge
pint                      0.19.2             pyhd8ed1ab_0    conda-forge
pip                       22.2.2           py38h06a4308_0  
pixman                    0.40.0               h36c2ea0_0    conda-forge
plotly                    5.10.0             pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0            py38h578d9bd_3    conda-forge
postgresql                14.5                 hfdbbde3_0    conda-forge
psi4                      1.6.1+5b9f6e3    py38h1bd450f_0    psi4
psiresp                   0.4.2              pyhd8ed1ab_0    conda-forge
psiresp-base              0.4.2              pyhd8ed1ab_0    conda-forge
psutil                    5.9.2            py38h0a891b7_0    conda-forge
psycopg2                  2.9.3            py38h497a2fe_0    conda-forge
py                        1.11.0             pyh6c4a22f_0    conda-forge
py-cpuinfo                8.0.0              pyhd8ed1ab_0    conda-forge
pyarrow                   9.0.0           py38h8617f3d_6_cpu    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycairo                   1.21.0           py38h9c00e7a_1    conda-forge
pycosat                   0.6.3           py38h0a891b7_1010    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.2           py38h0a891b7_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_1    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytest                    7.1.3            py38h578d9bd_0    conda-forge
python                    3.8.13               h12debd9_0  
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      2_cp38    conda-forge
pytz                      2022.4             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py38h0a891b7_4    conda-forge
qcelemental               0.25.0             pyhd8ed1ab_0    conda-forge
qcengine                  0.24.1             pyhd8ed1ab_0    conda-forge
qcfractal                 0.15.8.1         py38h578d9bd_0    conda-forge
qcfractal-core            0.15.8.1         py38h578d9bd_0    conda-forge
rdkit                     2022.03.5        py38ha829ea6_0    conda-forge
re2                       2022.06.01           h27087fc_0    conda-forge
readline                  8.1.2                h7f8727e_1  
reportlab                 3.5.68           py38hadf75a6_1    conda-forge
reproc                    14.2.3               h7f98852_0    conda-forge
reproc-cpp                14.2.3               h9c3ff4c_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
ruamel_yaml               0.15.80         py38h0a891b7_1007    conda-forge
s2n                       1.0.10               h9b69904_0    conda-forge
scipy                     1.9.1            py38h14f4228_0  
setuptools                63.4.1           py38h06a4308_0  
simint                    0.7                  h642920c_1    psi4
six                       1.16.0             pyh6c4a22f_0    conda-forge
snappy                    1.1.9                hbd366e4_1    conda-forge
sqlalchemy                1.3.24           py38h0a891b7_1    conda-forge
sqlite                    3.39.3               h5082296_0  
tenacity                  8.1.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h1ccaba5_0  
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.2              py38h0a891b7_0    conda-forge
tqdm                      4.64.1             pyhd8ed1ab_0    conda-forge
typing-extensions         4.3.0                hd8ed1ab_0    conda-forge
typing_extensions         4.3.0              pyha770c72_0    conda-forge
tzcode                    2022d                h166bdaf_0    conda-forge
tzdata                    2022d                h191b570_0    conda-forge
unicodedata2              14.0.0           py38h0a891b7_1    conda-forge
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
wheel                     0.37.1             pyhd3eb1b0_0  
xz                        5.2.6                h5eee18b_0  
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.7.0                h27087fc_2    conda-forge
zipp                      3.8.1              pyhd8ed1ab_0    conda-forge
zlib                      1.2.12               h5eee18b_3  
zstd                      1.5.2                h6239696_4    conda-forge
@lilyminium
Copy link
Owner

Hmm. Firstly, sorry for the lack of response to this -- I'm watching the repository but not getting notifications :/

Secondly, I think this might be because the Psi4 calculation failed in some way and I'm failing to propagate the error. I'll have a look at it more closely.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@lilyminium @wg12385