Software

    1. MISTER-T (Manipulating an Interacting System of Total Electrons in Real-Time): enables quantum optimal control for multi-electron systems on nonuniform meshes with arbitrary two-dimensional cross-sectional geometries. The software is enabled by forward and backward propagator integration methods to evolve the Kohn-Sham equations with a pseudoskeleton decomposition algorithm for enhanced computational efficiency [for further details, see: Y. Chen, M. S. Okyay, and B. M. Wong*, Computer Physics Communications, 302, 109248 (2024)]. Click here for the software and some sample input files.
    2. SHORYUKEN (Streamlined High-level Operations in Real-space to Yield, Understand, and Keep Exchange in Nanowires): calculates nonlocal exchange interactions in nanowires with arbitrary geometries, sizes, doping densities, and compositions. In addition to enabling new calculations of nonlocal exchange, this software package is a significant enhancement of our previous HADOKEN code and includes new algorithmic improvements as well as an improved treatment of surface states for nanowires with intrinsic polarization [for further details, see: Y. Chen, S. N. Sandhofer, and B. M. Wong*, Computer Physics Communications, 300, 109197 (2024)]. Click here for the software and some sample input files.
    3. TRAVOLTA (Terrific Refinements to Accelerate, Validate, and Optimize Large Time-dependent Algorithms): carries out massively parallelized quantum optimal control calculations on GPUs. This software package is a significant overhaul of our previous NIC-CAGE algorithm and also includes algorithmic improvements to the gradient ascent procedure to enable faster convergence [for further details, see: J. M. Rodríguez-Borbón, X. Wang, A. P. Diéguez, K. Z. Ibrahim, and B. M. Wong*, Computer Physics Communications, 296, 109017 (2024)]. Click here for the software and some sample input files.
    4. Quantum Optimal Control of Multi-Qubit Systems: accelerates quantum optimal control calculations of large multi-qubit systems used in a variety of quantum computing applications. By leveraging the intrinsic symmetry of finite groups, this software package reduces the computational runtime of qubit optimal control calculations by orders of magnitude while maintaining the same accuracy as the conventional method [for further details, see: X. Wang, M. S. Okyay, A. Kumar, and B. M. Wong*, AVS Quantum Science, 5, 043801 (2023)]. Click here for the software and some sample input files.
    5. FLUID-GPT (Fast Learning to Understand and Investigate Dynamics with a Generative Pre-trained Transformer): utilizes a Generative Pre-Trained Transformer 2 (GPT-2) with a convolutional neural network (CNN) for accurately predicting particle trajectories and erosion on an industrial-scale steam header geometry [for further details, see: S. D. Yang, Z. A. Ali, and B. M. Wong*, Industrial & Engineering Chemistry Research, 296, 109017 (2024)]. Click here for the software and some sample input files.
    6. Semi-Supervised Machine Learning to Automatically Predict Bioactivities of PFASs: unsupervised/semi-supervised machine learning models to automatically predict bioactivities of PFASs in various human biological targets, including enzymes, genes, proteins, and cell lines [for further details, see: H. Kwon, Z. A. Ali, and B. M. Wong*, AVS Quantum Science, 5, 043801 (2023)]. Click here for the software and some sample input files.
    7. Computational Fluid Dynamics and Machine Learning: harnesses convolutional neural network (CNN) and long- and short-term memory (LSTM) machine learning approaches to predict complex surface erosion profiles in steam distribution headers [for further details, see: S. D. Yang, Z. A. Ali, H. Kwon, and B. M. Wong*, Industrial & Engineering Chemistry Research, 61, 8520-8529 (2022)]. Click here for the software and some sample input files.
    8. HADOKEN (High-level Algorithms to Design, Optimize, and Keep Electrons in Nanowires): predicts electron confinement/localization effects in nanowires with various geometries, arbitrary number of concentric shell layers, doping densities, and external boundary conditions. This software package contains several examples and outputs on a variety of different nanowire geometries, boundary conditions, and doping densities to demonstrate its capabilities [for further details, see: C. Chevalier, and B. M. Wong*, Computer Physics Communications, 274, 108299 (2022)]. Click here for the software and some sample input files.
    9. NIC-CAGE (Novel Implementation of Constrained Calculations for Automated Generation of Excitations): calculates quantum optimal control fields that can drive a system from a known initial vibrational eigenstate to a specified final quantum state. This software utilizes newly derived analytic gradients for maximizing the transition probability based on a norm-conserving Crank–Nicolson propagation scheme [for further details, see: A. Raza, C. Hong, X. Wang, A. Kumar, C. R. Shelton, and B. M. Wong*, Computer Physics Communications, 258, 107541 (2021)]. Click here for the software and some sample input files.
    10. PFAS Carbon-Fluorine Bond Descriptors: a modified Java code [based on the approach in J. Cheminformatics 5, 34 (2013)] for calculating molecular descriptors in various per- and polyfluroalkyl substances (PFAS). These molecular descriptors can be subsequently used in other machine learning algorithms to predict carbon-fluorine bond dissociation energies in other PFAS structures [for further details, see: A. Raza, S. Bardhan, L. Xu, S. S. R. K. C. Yamijala, C. Lian, H. Kwon, and B. M. Wong*, Environmental Science & Technology Letters, 2, 624-629 (2019)]. Click here for the software and some sample input files.

    11. PAMELA (Pseudospectral Analysis Method with Exchange & Local Approximations): calculates electronic energies, densities, wavefunctions, and band-bending diagrams for core-shell nanowires within a self-consistent Schrodinger-Poisson formalism [for further details, see: A. W. Long and B. M. Wong*, AIP Advances, 2, 032173 (2012)]. Click here for the software and some sample input files.

    12. Franck-Condon Overlap Integrals: calculates the vibrational overlap integral between two nuclear wavefunctions using the formalism developed by Sharp and Rosenstock [J. Chem. Phys., 41, 3453-3463 (1964)]. Click here for the software and some sample input files.
    13. Eckart Inertias: calculates effective Eckart inertias for large-amplitude torsions. The Eckart inertias are obtained by solving a system of transcendental equations using the Powell dogleg method. Since this system is highly nonlinear, analytical Jacobians have been implemented in the dogleg method to maximize computational efficiency [for further details, see: B. M. Wong, R. L. Thom, and R. W. Field, Journal of Physical Chemistry A, 110, 7406-7413 (2006)]. Click here for the software and some sample input files.
    14. Pitzer Inertias: calculates effective Pitzer inertias for large-amplitude torsions [for further details, see: B. M. Wong, R. L. Thom, and R. W. Field, Journal of Physical Chemistry A, 110, 7406-7413 (2006)]. Click here for the software and some sample input files.
    15. Mandelbrotx: plots interesting Mandelbrot-like sets. These codes make pretty nice pictures. Click here for the software and some sample pictures.