Ivan Ufimtsev

All Publications

• Analytic first derivatives of floating occupation molecular orbital-complete active space configuration interaction on graphical processing units. journal of chemical physics Hohenstein, E. G., Bouduban, M. E., Song, C., Luehr, N., Ufimtsev, I. S., Martínez, T. J. 2015; 143 (1): 014111-?

  Abstract

  The floating occupation molecular orbital-complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the state-averaged complete active space self-consistent field (SA-CASSCF) method. We have formulated the analytic first derivative of FOMO-CASCI in a manner that is well-suited for a highly efficient implementation using graphical processing units (GPUs). Using this implementation, we demonstrate that FOMO-CASCI gradients are of similar computational expense to configuration interaction singles (CIS) or time-dependent density functional theory (TDDFT). In contrast to CIS and TDDFT, FOMO-CASCI can describe multireference character of the electronic wavefunction. We show that FOMO-CASCI compares very favorably to SA-CASSCF in its ability to describe molecular geometries and potential energy surfaces around minimum energy conical intersections. Finally, we apply FOMO-CASCI to the excited state hydrogen transfer reaction in methyl salicylate.

  View details for DOI 10.1063/1.4923259

  View details for PubMedID 26156469

• Analytic first derivatives of floating occupation molecular orbital-complete active space configuration interaction on graphical processing units. journal of chemical physics Hohenstein, E. G., Bouduban, M. E., Song, C., Luehr, N., Ufimtsev, I. S., Martínez, T. J. 2015; 143 (1): 014111-?

  Abstract

  The floating occupation molecular orbital-complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the state-averaged complete active space self-consistent field (SA-CASSCF) method. We have formulated the analytic first derivative of FOMO-CASCI in a manner that is well-suited for a highly efficient implementation using graphical processing units (GPUs). Using this implementation, we demonstrate that FOMO-CASCI gradients are of similar computational expense to configuration interaction singles (CIS) or time-dependent density functional theory (TDDFT). In contrast to CIS and TDDFT, FOMO-CASCI can describe multireference character of the electronic wavefunction. We show that FOMO-CASCI compares very favorably to SA-CASSCF in its ability to describe molecular geometries and potential energy surfaces around minimum energy conical intersections. Finally, we apply FOMO-CASCI to the excited state hydrogen transfer reaction in methyl salicylate.

  View details for DOI 10.1063/1.4923259

  View details for PubMedID 26156469

• An atomic orbital-based formulation of the complete active space self-consistent field method on graphical processing units. journal of chemical physics Hohenstein, E. G., Luehr, N., Ufimtsev, I. S., Martínez, T. J. 2015; 142 (22): 224103-?

  Abstract

  Despite its importance, state-of-the-art algorithms for performing complete active space self-consistent field (CASSCF) computations have lagged far behind those for single reference methods. We develop an algorithm for the CASSCF orbital optimization that uses sparsity in the atomic orbital (AO) basis set to increase the applicability of CASSCF. Our implementation of this algorithm uses graphical processing units (GPUs) and has allowed us to perform CASSCF computations on molecular systems containing more than one thousand atoms. Additionally, we have implemented analytic gradients of the CASSCF energy; the gradients also benefit from GPU acceleration as well as sparsity in the AO basis.

  View details for DOI 10.1063/1.4921956

  View details for PubMedID 26071697

• An atomic orbital-based formulation of the complete active space self-consistent field method on graphical processing units JOURNAL OF CHEMICAL PHYSICS Hohenstein, E. G., Luehr, N., Ufimtsev, I. S., Martinez, T. J. 2015; 142 (22)

  Abstract

  Despite its importance, state-of-the-art algorithms for performing complete active space self-consistent field (CASSCF) computations have lagged far behind those for single reference methods. We develop an algorithm for the CASSCF orbital optimization that uses sparsity in the atomic orbital (AO) basis set to increase the applicability of CASSCF. Our implementation of this algorithm uses graphical processing units (GPUs) and has allowed us to perform CASSCF computations on molecular systems containing more than one thousand atoms. Additionally, we have implemented analytic gradients of the CASSCF energy; the gradients also benefit from GPU acceleration as well as sparsity in the AO basis.

  View details for DOI 10.1063/1.4921956

  View details for Web of Science ID 000356176600005

  View details for PubMedID 26071697

• Generating Efficient Quantum Chemistry Codes for Novel Architectures JOURNAL OF CHEMICAL THEORY AND COMPUTATION Titov, A. V., Ufimtsev, I. S., Luehr, N., Martinez, T. J. 2013; 9 (1): 213-221

  Abstract

  We describe an extension of our graphics processing unit (GPU) electronic structure program TeraChem to include atom-centered Gaussian basis sets with d angular momentum functions. This was made possible by a "meta-programming" strategy that leverages computer algebra systems for the derivation of equations and their transformation to correct code. We generate a multitude of code fragments that are formally mathematically equivalent, but differ in their memory and floating-point operation footprints. We then select between different code fragments using empirical testing to find the highest performing code variant. This leads to an optimal balance of floating-point operations and memory bandwidth for a given target architecture without laborious manual tuning. We show that this approach is capable of similar performance compared to our hand-tuned GPU kernels for basis sets with s and p angular momenta. We also demonstrate that mixed precision schemes (using both single and double precision) remain stable and accurate for molecules with d functions. We provide benchmarks of the execution time of entire self-consistent field (SCF) calculations using our GPU code and compare to mature CPU based codes, showing the benefits of the GPU architecture for electronic structure theory with appropriately redesigned algorithms. We suggest that the meta-programming and empirical performance optimization approach may be important in future computational chemistry applications, especially in the face of quickly evolving computer architectures.

  View details for DOI 10.1021/ct300321a

  View details for Web of Science ID 000313378700025

• Ab Initio Quantum Chemistry for Protein Structures JOURNAL OF PHYSICAL CHEMISTRY B Kulik, H. J., Luehr, N., Ufimtsev, I. S., Martinez, T. J. 2012; 116 (41): 12501-12509

  Abstract

  Structural properties of over 55 small proteins have been determined using both density-based and wave-function-based electronic structure methods in order to assess the ability of ab initio "force fields" to retain the properties described by experimental structures measured with crystallography or nuclear magnetic resonance. The efficiency of the GPU-based quantum chemistry algorithms implemented in our TeraChem program enables us to carry out systematic optimization of ab initio protein structures, which we compare against experimental and molecular mechanics force field references. We show that the quality of the ab initio optimized structures, as judged by conventional protein health metrics, increases with increasing basis set size. On the other hand, there is little evidence for a significant improvement of predicted structures using density functional theory as compared to Hartree-Fock methods. Although occasional pathologies of minimal basis sets are observed, these are easily alleviated with even the smallest double-ζ basis sets.

  View details for DOI 10.1021/jp307741u

  View details for Web of Science ID 000309902400013

  View details for PubMedID 22974088

• Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics JOURNAL OF PHYSICAL CHEMISTRY LETTERS Ufimtsev, I. S., Luehr, N., Martinez, T. J. 2011; 2 (14): 1789-1793

  View details for DOI 10.1021/jz200697c

  View details for Web of Science ID 000293191800027

• Excited-State Electronic Structure with Configuration Interaction Singles and Tamm-Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units JOURNAL OF CHEMICAL THEORY AND COMPUTATION Isborn, C. M., Luehr, N., Ufimtsev, I. S., Martinez, T. J. 2011; 7 (6): 1814-1823

  View details for DOI 10.1021/ct200030k

  View details for Web of Science ID 000291500400022

• Dynamic Precision for Electron Repulsion Integral Evaluation on Graphical Processing Units (GPUs) JOURNAL OF CHEMICAL THEORY AND COMPUTATION Luehr, N., Ufimtsev, I. S., Martinez, T. J. 2011; 7 (4): 949-954

  Abstract

  It has recently been demonstrated that novel streaming architectures found in consumer video gaming hardware such as graphical processing units (GPUs) are well-suited to a broad range of computations including electronic structure theory (quantum chemistry). Although recent GPUs have developed robust support for double precision arithmetic, they continue to provide 2-8× more hardware units for single precision. In order to maximize performance on GPU architectures, we present a technique of dynamically selecting double or single precision evaluation for electron repulsion integrals (ERIs) in Hartree-Fock and density functional self-consistent field (SCF) calculations. We show that precision error can be effectively controlled by evaluating only the largest integrals in double precision. By dynamically scaling the precision cutoff over the course of the SCF procedure, we arrive at a scheme that minimizes the number of double precision integral evaluations for any desired accuracy. This dynamic precision scheme is shown to be effective for an array of molecules ranging in size from 20 to nearly 2000 atoms.

  View details for DOI 10.1021/ct100701w

  View details for Web of Science ID 000289315700018

• GPU-accelerated molecular modeling coming of age JOURNAL OF MOLECULAR GRAPHICS & MODELLING Stone, J. E., Hardy, D. J., Ufimtsev, I. S., Schulten, K. 2010; 29 (2): 116-125

  Abstract

  Graphics processing units (GPUs) have traditionally been used in molecular modeling solely for visualization of molecular structures and animation of trajectories resulting from molecular dynamics simulations. Modern GPUs have evolved into fully programmable, massively parallel co-processors that can now be exploited to accelerate many scientific computations, typically providing about one order of magnitude speedup over CPU code and in special cases providing speedups of two orders of magnitude. This paper surveys the development of molecular modeling algorithms that leverage GPU computing, the advances already made and remaining issues to be resolved, and the continuing evolution of GPU technology that promises to become even more useful to molecular modeling. Hardware acceleration with commodity GPUs is expected to benefit the overall computational biology community by bringing teraflops performance to desktop workstations and in some cases potentially changing what were formerly batch-mode computational jobs into interactive tasks.

  View details for DOI 10.1016/j.jmgm.2010.06.010

  View details for Web of Science ID 000282623300002

  View details for PubMedID 20675161

  View details for PubMedCentralID PMC2934899

• Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics JOURNAL OF CHEMICAL THEORY AND COMPUTATION Ufimtsev, I. S., Martinez, T. J. 2009; 5 (10): 2619-2628

  Abstract

  We demonstrate that a video gaming machine containing two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree-Fock energy + gradient calculations. Such performance makes it possible to run large scale Hartree-Fock and Density Functional Theory calculations, which typically require hundreds of traditional processor cores, on a single workstation. Benchmark Born-Oppenheimer molecular dynamics simulations are performed on two molecular systems using the 3-21G basis set - a hydronium ion solvated by 30 waters (94 atoms, 405 basis functions) and an aspartic acid molecule solvated by 147 waters (457 atoms, 2014 basis functions). Our GPU implementation can perform 27 ps/day and 0.7 ps/day of ab initio molecular dynamics simulation on a single desktop computer for these systems.

  View details for DOI 10.1021/ct9003004

  View details for Web of Science ID 000270595800005

• Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation JOURNAL OF CHEMICAL THEORY AND COMPUTATION Ufimtsev, I. S., Martinez, T. J. 2009; 5 (4): 1004-1015

  Abstract

  We demonstrate the use of graphical processing units (GPUs) to carry out complete self-consistent-field calculations for molecules with as many as 453 atoms (2131 basis functions). Speedups ranging from 28× to 650× are achieved as compared to a mature third-party quantum chemistry program (GAMESS) running on a traditional CPU. The computational organization used to construct the Coulomb and exchange operators is discussed. We also present results using three GPUs in parallel, combining coarse and fine-grained parallelism.

  View details for DOI 10.1021/ct800526s

  View details for Web of Science ID 000265268800039

• A multistate empirical valence bond model for solvation and transport simulations of OH- in aqueous solutions PHYSICAL CHEMISTRY CHEMICAL PHYSICS Ufimtsev, I. S., Kalinichev, A. G., Martinez, T. J., Kirkpatrick, R. J. 2009; 11 (41): 9420-9430

  Abstract

  We describe a new multistate empirical valence bond (MS-EVB) model of OH(-) in aqueous solutions. This model is based on the recently proposed "charged ring" parameterization for the intermolecular interaction of hydroxyl ion with water [Ufimtsev, et al., Chem. Phys. Lett., 2007, 442, 128] and is suitable for classical molecular simulations of OH(-) solvation and transport. The model reproduces the hydration structure of OH(-)(aq) in good agreement with experimental data and the results of ab initio molecular dynamics simulations. It also accurately captures the major structural, energetic, and dynamic aspects of the proton transfer processes involving OH(-) (aq). The model predicts an approximately two-fold increase of the OH(-) mobility due to proton exchange reactions.

  View details for DOI 10.1039/b907859b

  View details for Web of Science ID 000270795500014

  View details for PubMedID 19830325