Psi4 1.4: Open-Source Software for High-Throughput Quantum Chemistry

Smith, Daniel G. A.; Burns, Lori A.; Simmonett, Andrew C.; Parrish, Robert M.; Schieber, Matthew; Galvelis, Raimondas; Kraus, Peter; Kruse, Holger; Remigio, Roberto Di; Alenaizan, Asem; James, Andrew; Lehtola, Susi; Misiewicz, Jonathon; Scheurer, Maximilian; Shaw, Robert A.; Schriber, Jeffrey B.; Glick, Zachary L.; Sirianni, Dominic A.; O'Brien, Joseph; Waldrop, Jonathan M.; Kumar, Ashutosh; Hohenstein, Edward G.; Pritchard, Benjamin P.; Brooks, Bernard R.; Schaefer, Henry F.; Sokolov, Alexander Yu.; Patkowski, Konrad; DePrince, A. Eugene; Bozkaya, Uğur; King, Rollin; Evangelista, Francesco A.; Turney, Justin M.; Crawford, Thomas O.; Sherrill, C. David

doi:10.26434/chemrxiv.11930031

Cited by 47 publications

(51 citation statements)

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“…For comparison to conventional linear response results, we also carried out EOM-CCSD/cc-pVDZ excitation-energy calculations, which are included as stick spectra. These results were obtained using the Psi4 code 66 with the same frozen-core approximation. of the relevant CC equations in single precision were adequate for most applications, and a limited number of "cleanup" iterations in double-precision could recover higher accuracy.…”

Section: Computational Detailsmentioning

confidence: 99%

Accelerating Real-Time Coupled Cluster Methods with Single-Precision Arithmetic and Adaptive Numerical Integration

Wang¹,

Peyton²,

Daniel³

2022

Preprint

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We explore the framework of a real-time coupled cluster method with a focus on improving its computational efficiency. Propagation of the wave function via the time-dependent Schrödinger equation places high demands on computing resources, particularly for high level theories such as coupled cluster with polynomial scaling. Similar to earlier investigations of coupled cluster properties, we demonstrate that the use of single-precision arithmetic reduces both the storage and multiplicative costs of the real-time simulation by approximately a factor of two with no significant impact on the resulting UV/vis absorption spectrum computed via the Fourier transform of the time-dependent dipole moment. Additional speedups -of up to a factor of 14 in test simulations of water clusters -are obtained via a straightforward GPU-based implementation as compared to conventional CPU calculations. We also find that further performance optimization is accessible through sagacious selection of numerical integration algorithms, and the adaptive methods, such as the Cash-Karp integrator provide an effective balance between computing costs and numerical stability. Finally, 1

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Section: Computational Detailsmentioning

confidence: 99%

Accelerating Real-Time Coupled Cluster Methods with Single-Precision Arithmetic and Adaptive Numerical Integration

Wang¹,

Peyton²,

Daniel³

2022

Preprint

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“…19 This calculation, which we term a "serial relaxed scan", is a standard feature in several widely used quantum chemistry and geometry optimization codes. [20][21][22][23][24][25][26][27][28] The serial relaxed scanning approach has some major drawbacks. 29 For one, the resulting optimized structures are dependent on the chosen sequence of calculations, such as the direction of the one-dimensional scan.…”

Section: E(φ Abcdmentioning

confidence: 99%

“…These calculations were performed within the QCArchive infrastructure that provides TorsionDrive calculations as a service, as described in Section 4.2. Energies and gradients were calculated using the B3LYP-D3(BJ) functional and DZVP basis optimized for DFT 42 as implemented in the Psi4 software package, 23 and optimizations were carried out using the geomeTRIC software. 28 The results show that a 1D torsion scan started from a conformation where the hydroxyl groups are facing in opposite directions (4b upper) will fail to find the lowest energy con- 3.4 Generalized dihedral scanning and restricted grid improper -marked by red in above chemical structure) for characterizing PES of a molecular motor at B3LYP-D3/3-21G level of theory.…”

Section: Multiple Initial Structuresmentioning

confidence: 99%

Driving torsion scans with wavefront propagation

Qiu

Smith

Stern

et al. 2020

The Journal of Chemical Physics

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The parameterization of torsional / dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields.Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms.To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values.However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses.In this paper we propose a systematic and versatile workflow called \textit{TorsionDrive} to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development.The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described.The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes. File list (2)download file view on ChemRxiv TorsionDrive_manuscript_submitted.pdf (3.57 MiB) download file view on ChemRxiv TorsionDrive_SI.zip (5.32 MiB)

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“…By contrast, the energy profile generated by TorsionDrive is more symmetrical, as ex- in the Psi4 software package, 23 and optimizations were carried out using the geomeTRIC software. 28 The results show that a 1D torsion scan started from a conformation where the hydroxyl groups are facing in opposite directions (4b upper) will fail to find the lowest energy conformer.…”

Section: E(φ Abcdmentioning

confidence: 99%

“…These calculations were performed within the QCArchive infrastructure that provides TorsionDrive calculations as a service, as described in Section 4.2. Energies and gradients were calculated using the B3LYP-D3(BJ) functional and DZVP basis optimized for DFT 42 as implemented in the Psi4 software package, 23 and optimizations were carried out using the geomeTRIC software. 28 The results show that a 1D torsion scan started from a conformation where the hydroxyl groups are facing in opposite directions (4b upper) will fail to find the lowest energy con- 3.4 Generalized dihedral scanning and restricted grid TorsionDrive has several additional features for flexibility in setting scanning coordinates for different molecular systems.…”

Section: Torsion Grid Pointmentioning

confidence: 99%

Driving Torsion Scans with Wavefront Propagation

Qiu¹,

Smith²,

Stern³

et al. 2020

Preprint

Self Cite

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<div>The parameterization of torsional / dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields.</div><div>Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms.</div><div>To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values.</div><div>However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses.</div><div>In this paper we propose a systematic and versatile workflow called \textit{TorsionDrive} to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development.</div><div>The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described.</div><div>The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.</div>

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Psi4 1.4: Open-Source Software for High-Throughput Quantum Chemistry

Cited by 47 publications

References 0 publications

Accelerating Real-Time Coupled Cluster Methods with Single-Precision Arithmetic and Adaptive Numerical Integration

Accelerating Real-Time Coupled Cluster Methods with Single-Precision Arithmetic and Adaptive Numerical Integration

Driving torsion scans with wavefront propagation

Driving Torsion Scans with Wavefront Propagation

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