Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs

Abstract

Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.

Exploration and validation of force field design protocols through QM-to-MM mapping

“…As mentioned, our first implementation of QUBEKit 34 interfaced with the ONETEP DFT code, 63 which uses the PBE exchange-correlation functional, for non-bonded parameter derivation. However, this new version of QUBEKit is interfaced, via QCEngine, 61 with both Gaussian09 53 and PSI4, 60 which gives us access to a wide range of alternative quantum chemistry methods. If using PSI4, the electron density partitioning is performed using MBIS.…”

“…28 MBIS charges, along with all AIM properties (atomic multipoles up to quadrupole order and radial moments) that we require for force field derivation have recently been implemented in the PSI4 quantum chemistry package, 60 which we can now access through our latest interface with QCengine. 61 Model 3b thus investigates the use of MBIS as the AIM partitioning method in force field derivation. For technical reasons, it was necessary to use the B3LYP exchange-correlation functional, and the IEFPCM implicit solvent model (with a chloroform solvent to mimic a dielectric of approximately 4), 76 for the underlying QM calculations.…”

“…It is gratifying that a range of AIM methods has been shown to be promising for flexible force field design, and is available through our QUBEKit interface with QCEngine. 61 Lennard-Jones parameters. As discussed in the Methods section, the default QUBE protocol for deriving the attractive part of the Lennard-Jones potential (B ij in eqn ( 4)) from QM tends to lead to dispersion coefficients that are lower than those used in common effective force fields 45 and energy well depths that are constant across atoms of the same element.…”

Conformational energy benchmark for longer n-alkane chains

“…83 Calculations with the OpenFF toolkit and RDKit were driven via QCEngine. 84 All tested DFT methods were evaluated in combination with one out of the following three London dispersion corrections, D3, 85,86 D4, 32,87 or VV10 31,88,89 (also called NL or V). The two former were applied together with the rational (Becke-Johnson) damping function, [90][91][92] except for the M06-L functional, where zero (Chai-Head-Gordon) damping 93 was employed.…”

eChem: A notebook exploration of quantum chemistry

“…Furthermore, we favor free and open-source software packages, which enable wider adoption, improved user friendliness, flexibility, and a democratization of science. 40,41 The move to more interactive software modules and improving interoperability between software packages has been realized by many groups, 28,29,40,[42][43][44][45][46] including program packages and projects with education in mind. [47][48][49][50] Projects such as Psi4NumPy also include a number of tutorials for explaining the underlying theory, 47 and thus have some additional overlap with the eChem project.…”