quantum chemistry common driver and databases
| Status |    |
|---|---|
| Communication |   |
| Foundation |    |
Example
A simple example of QCDB’s capabilities is as follows:
>>> import qcdb
>>> mol = qcdb.set_molecule("""
O
H 1 0.96
H 1 0.96 2 104.5
""")
>>> qcdb.set_keywords({
"freeze_core": True,
})
These input specifications plus a model chemistry can be executed with energy(), gradient(), or hessian() API functions along with a program specifier:
>>> ene = qcdb.energy("c4-mp2/cc-pvdz")
>>> ene
-76.22847548367803
>>> print(qcdb.print_variables())
Variable Map:
----------------------------------------------------------------------------
"CURRENT CORRELATION ENERGY" => -0.201821821791 [Eh]
"CURRENT ENERGY" => -76.228475483678 [Eh]
"CURRENT REFERENCE ENERGY" => -76.026653661887 [Eh]
"HF TOTAL ENERGY" => -76.026653661887 [Eh]
"MP2 CORRELATION ENERGY" => -0.201821821791 [Eh]
"MP2 DOUBLES ENERGY" => -0.201821821791 [Eh]
"MP2 OPPOSITE-SPIN CORRELATION ENERGY" => -0.151079672317 [Eh]
"MP2 SAME-SPIN CORRELATION ENERGY" => -0.050742149474 [Eh]
"MP2 SINGLES ENERGY" => 0.000000000000 [Eh]
"MP2 TOTAL ENERGY" => -76.228475483678 [Eh]
"N ALPHA ELECTRONS" => 5.000000000000 []
"N ATOMS" => 3.000000000000 [Eh]
"N BASIS FUNCTIONS" => 24.000000000000 []
"N BETA ELECTRONS" => 5.000000000000 []
"N MOLECULAR ORBITALS" => 24.000000000000 []
"NUCLEAR REPULSION ENERGY" => 9.168193296400 [Eh]
"SCS(N)-MP2 CORRELATION ENERGY" => -0.089306183074 [Eh]
"SCS(N)-MP2 TOTAL ENERGY" => -76.115959844961 [Eh]
"SCS-MP2 CORRELATION ENERGY" => -0.198209656605 [Eh]
"SCS-MP2 TOTAL ENERGY" => -76.224863318492 [Eh]
For a fuller record of the computation, request the AtomicResult-like return
>>> ene, ret = qcdb.energy("c4-mp2/cc-pvdz", return_wfn=True)
>>> ret["return_result"]
-76.228475483678
>>> ret["properties"]["mp2_correlation_energy"]
-0.201821821791
>>> ret["provenance"]["cpu"]
'Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz'
The accustomed output (and generated input) are also accessible
>>> >>> pprint.pprint(ret["stdout"], width=200)
(' --invoking executable--\n'
'/home/psilocaluser/gits/cfour-public/bin/xjoda\n'
'\n'
'\n'
' *************************************************************************\n'
' <<< CCCCCC CCCCCC ||| CCCCCC CCCCCC >>>\n'
' <<< CCC CCC ||| CCC CCC >>>\n'
' <<< CCC CCC ||| CCC CCC >>>\n'
' <<< CCC CCC ||| CCC CCC >>>\n'
' <<< CCC CCC ||| CCC CCC >>>\n'
' <<< CCC CCC ||| CCC CCC >>>\n'
' <<< CCCCCC CCCCCC ||| CCCCCC CCCCCC >>>\n'
' *************************************************************************\n'
'\n'
' ****************************************************************\n'
' * CFOUR Coupled-Cluster techniques for Computational Chemistry *\n'
' ****************************************************************\n'
' \n'
'\n'
' Department of Chemistry Institut fuer Physikalische Chemie\n'
' University of Florida Universitaet Mainz\n'
' Gainesville, FL 32611, USA D-55099 Mainz, Germany\n'
'\n'
' Department of Chemistry Fakultaet fuer Chemie und Biowiss.\n'
' Johns Hopkins University Karlsruher Institut fuer Technologie\n'
' Baltimore, MD 21218, USA D-76131 Karlsruhe, Germany\n'
'\n'
' Department of Chemistry Department of Physical Chemistry\n'
' Southern Methodist University Eotvos Lorand University\n'
' Dallas, TX 75275, USA H-1053 Budapest, Hungary\n'
'\n'
' \n'
' Version 2.1\n'
' \n'
' psinet \n'
' Thu Sep 9 15:52:23 EDT 2021 \n'
' integer*8 version is running\n'
' \n'
'********************************************************************************\n'
'* Input from ZMAT file *\n'
'********************************************************************************\n'
'auto-generated by QCElemental from molecule H2O \n'
'O 0.000000000000 0.000000000000 -0.124297814080 \n'
'H 0.000000000000 -1.434419274846 0.986348254917 \n'
'H 0.000000000000 1.434419274846 0.986348254917 \n'
' \n'
' \n'
'*CFOUR(BASIS=SPECIAL \n'
'CALC_LEVEL=MP2 \n'
'CHARGE=0 \n'
'COORDINATES=CARTESIAN \n'
'DERIV_LEVEL=ZERO \n'
'FROZEN_CORE=1 \n'
'MEMORY_SIZE=2694957760 \n'
'MEM_UNIT=INTEGERWORDS \n'
'MULTIPLICITY=1 \n'
'SCF_DAMPING=0 \n'
'SCF_MAXCYC=100 \n'
'SPHERICAL=1 \n'
'UNITS=BOHR) \n'
' \n'
'O:CD_1 \n'
'H:CD_2 \n'
'H:CD_3 \n'
' \n'
'********************************************************************************\n'
...
'********************************************************************************\n'
' The full molecular point group is C2v .\n'
' The largest Abelian subgroup of the full molecular point group is C2v .\n'
' The computational point group is C2v .\n'
'********************************************************************************\n'
'\n'
'\n'
' ----------------------------------------------------------------\n'
' Coordinates used in calculation (QCOMP) \n'
' ----------------------------------------------------------------\n'
' Z-matrix Atomic Coordinates (in bohr)\n'
' Symbol Number X Y Z\n'
' ----------------------------------------------------------------\n'
' O 8 0.00000000 0.00000000 -0.12429781\n'
' H 1 0.00000000 -1.43441927 0.98634825\n'
' H 1 0.00000000 1.43441927 0.98634825\n'
' ----------------------------------------------------------------\n'
' \n'
' Interatomic distance matrix (Angstroms) \n'
' \n'
' O H H \n'
' [ 1] [ 2] [ 3]\n'
' O [ 1] 0.00000\n'
' H [ 2] 0.96000 0.00000\n'
' H [ 3] 0.96000 1.51812 0.00000\n'
' rotcon2\n'
' Rotational constants (in cm-1): \n'
' 9.4721706374 27.2629827680 14.5153365101\n'
' Rotational constants (in MHz): \n'
' 283968.5715813829 817323.7761473177 435158.9020696688\n'
' ECPDATA file not present. Using default ECPDATA. \n'
' There is 1 frozen-core orbital.\n'
' There are 24 basis functions.\n'
...
' --invoking executable--\n'
'/home/psilocaluser/gits/cfour-public/bin/xvcc\n'
' @GETMEM-I, Allocated 20560 MB of main memory.\n'
' MBPT(2) energy will be calculated.\n'
' The total correlation energy is -0.201821821791 a.u.\n'
' -----------------------------------------------------------\n'
' Correction Increment Cumulative\n'
' -----------------------------------------------------------\n'
' D-MBPT(2) -0.201821821791 -76.228475483678\n'
' -----------------------------------------------------------\n'
' Total MBPT(2) energy: -76.228475483678 a.u.\n'
' @CHECKOUT-I, Total execution time (CPU/WALL): 0.00/ 0.00 seconds.\n'
'--executable xvcc finished with status 0 in 0.02 seconds (walltime).\n'
' The final electronic energy is -76.228475483677684 a.u. \n'
' This computation required 0.33 seconds (walltime).\n')
Some tutorial tests
Environment
A snapshot dev environment is available through conda create -n qcdbenv python=3.9 psi4 qcdb pytest-xdist -c psi4/label/qcdb -c psi4/label/dev -c defaults. QC programs besides Psi4 are bring-your-own. Testing through pytest --pyargs qcdb -n<nproc>