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Tehrani A, Richer M, Heidar-Zadeh F. CuGBasis: High-performance CUDA/Python library for efficient computation of quantum chemistry density-based descriptors for larger systems. J Chem Phys 2024; 161:072501. [PMID: 39158048 DOI: 10.1063/5.0216781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/17/2024] [Indexed: 08/20/2024] Open
Abstract
CuGBasis is a free and open-source CUDA®/Python library for efficient computation of scalar, vector, and matrix quantities crucial for the post-processing of electronic structure calculations. CuGBasis integrates high-performance Graphical Processing Unit (GPU) computing with the ease and flexibility of Python programming, making it compatible with a vast ecosystem of libraries. We showcase its utility as a Python library and demonstrate its seamless interoperability with existing Python software to gain chemical insight from quantum chemistry calculations. Leveraging GPU-accelerated code, cuGBasis exhibits remarkable performance, making it highly applicable to larger systems or large databases. Our benchmarks reveal a 100-fold performance gain compared to alternative software packages, including serial/multi-threaded Central Processing Unit and GPU implementations. This paper outlines various features and computational strategies that lead to cuGBasis's enhanced performance, guiding developers of GPU-accelerated code.
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Affiliation(s)
- Alireza Tehrani
- Department of Chemistry, Queen's University, Kingston, Ontario K7L-3N6, Canada
| | - Michelle Richer
- Department of Chemistry, Queen's University, Kingston, Ontario K7L-3N6, Canada
| | - Farnaz Heidar-Zadeh
- Department of Chemistry, Queen's University, Kingston, Ontario K7L-3N6, Canada
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2
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Affiliation(s)
- Xinying Li
- Institute for Computational Materials Science, School of Physics and Electronics; Henan University; Kaifeng 475004 People's Republic of China
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3
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Hermann G, Pohl V, Tremblay JC, Paulus B, Hege HC, Schild A. ORBKIT: A modular python toolbox for cross-platform postprocessing of quantum chemical wavefunction data. J Comput Chem 2016; 37:1511-20. [DOI: 10.1002/jcc.24358] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/16/2016] [Accepted: 02/22/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Gunter Hermann
- Institut für Chemie und Biochemie, Freie Universität Berlin; Takustraße 3 Berlin 14195 Germany
| | - Vincent Pohl
- Institut für Chemie und Biochemie, Freie Universität Berlin; Takustraße 3 Berlin 14195 Germany
| | | | - Beate Paulus
- Institut für Chemie und Biochemie, Freie Universität Berlin; Takustraße 3 Berlin 14195 Germany
| | - Hans-Christian Hege
- Department of Visual Data Analysis; Zuse Institute Berlin; Takustraße 7 Berlin 14195 Germany
| | - Axel Schild
- Max-Planck-Institut für Mikrostrukturphysik; Weinberg 2 Halle 06120 Germany
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4
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Distortion from planarity in arenes produced by internal rotation of one single hydroxyl hydrogen: The case of alternariol. J Mol Graph Model 2014; 53:140-147. [DOI: 10.1016/j.jmgm.2014.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 11/23/2022]
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5
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Xinying L, Xue C. Electron Density Properties and Interaction: Quantum Chemical Topology Investigation on AuRn n 2+ (n = 1–6). J CLUST SCI 2014. [DOI: 10.1007/s10876-014-0694-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Li J, Yang Y, Zhang P, Sounik JR, Kenney ME. Synthesis, properties and drug potential of the photosensitive alkyl- and alkylsiloxy-ligated silicon phthalocyanine Pc 227. Photochem Photobiol Sci 2014; 13:1690-8. [DOI: 10.1039/c4pp00321g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photolysis of Pc 227 yields the extensively studied photodynamic therapy drug Pc 4. The photolytic pathway is a homolysis involving a phthalocyanine π radical and low bond dissociation energy.
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Affiliation(s)
- Jun Li
- Department of Chemistry
- Case Western Reserve University
- Cleveland, USA
| | - Yang Yang
- Department of Chemistry
- Case Western Reserve University
- Cleveland, USA
| | - Ping Zhang
- Department of Chemistry
- Case Western Reserve University
- Cleveland, USA
| | - James R. Sounik
- Department of Chemistry
- Case Western Reserve University
- Cleveland, USA
| | - Malcolm E. Kenney
- Department of Chemistry
- Case Western Reserve University
- Cleveland, USA
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Gómez-Casado C, Roth-Walter F, Jensen-Jarolim E, Díaz-Perales A, Pacios LF. Modeling iron-catecholates binding to NGAL protein. J Mol Graph Model 2013; 45:111-21. [DOI: 10.1016/j.jmgm.2013.08.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 10/26/2022]
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8
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Chemical bond between Cu(II) and Rn: ab initio study of CuRn n 2+ (n = 1–6) by coupled cluster method. Struct Chem 2013. [DOI: 10.1007/s11224-013-0285-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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9
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Adamczyk-Woźniak A, Jakubczyk M, Jankowski P, Sporzyński A, Urbański PM. Influence of the diol structure on the Lewis acidity of phenylboronates. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3102] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Michał Jakubczyk
- Faculty of Chemistry; Warsaw University of Technology; Warsaw Poland
| | - Piotr Jankowski
- Faculty of Chemistry; Warsaw University of Technology; Warsaw Poland
| | | | - Piotr M. Urbański
- Faculty of Chemistry; Warsaw University of Technology; Warsaw Poland
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Gálvez O, Gómez Martín JC, Gómez PC, Saiz-Lopez A, Pacios LF. A theoretical study on the formation of iodine oxide aggregates and monohydrates. Phys Chem Chem Phys 2013; 15:15572-83. [DOI: 10.1039/c3cp51219c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Yang Y. Two-Center Two-Electron Covalent Bonds with Deficient Bonding Densities. J Phys Chem A 2012; 116:10150-9. [DOI: 10.1021/jp304420c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yang Yang
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
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12
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Xinying L. Interaction between coinage metal cations M(II) and Xe: CCSD(T) study of MXen2+(M = Cu, Ag, and Au, n = 1–6). J Chem Phys 2012; 137:124301. [DOI: 10.1063/1.4750475] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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13
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Yang Y. Pyrrolic macrocycles with stabilized triplet states: Metal-centered and ligand-centered separation of unpaired electrons. Polyhedron 2012. [DOI: 10.1016/j.poly.2012.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Mo Y. Can QTAIM Topological Parameters Be a Measure of Hydrogen Bonding Strength? J Phys Chem A 2012; 116:5240-6. [DOI: 10.1021/jp3029769] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
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Metal–ligand coordination in subphthalocyanines and phthalocyanines: DFT, AIM and ELF analyses. Polyhedron 2012. [DOI: 10.1016/j.poly.2011.11.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Lu T, Chen F. Multiwfn: A multifunctional wavefunction analyzer. J Comput Chem 2011; 33:580-92. [PMID: 22162017 DOI: 10.1002/jcc.22885] [Citation(s) in RCA: 15400] [Impact Index Per Article: 1184.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/28/2011] [Accepted: 10/21/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Tian Lu
- Department of chemistry and chemical engineer, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, People's Republic of China.
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Pacios LF, Gómez PC, Gálvez O. Ab initio study of hydroxyl torsional barriers and molecular properties of mono- and di-iodotyrosine. J Phys Chem A 2011; 115:12616-23. [PMID: 21671639 DOI: 10.1021/jp2031225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Phenol rings with one or two iodine atoms bonded to ortho carbons are the essential organic source of iodine for living organisms. The salvage of this halogen fundamental for a variety of biological functions is accomplished through enzymatic processes that rely on recognition of mono- and di-iodotyrosine (MIT and DIT, respectively). Ab initio quantum calculations are used to investigate molecular properties of MIT and DIT associated with their recognition by cognate proteins. Energies, electron density properties, atomic charges, and electrostatic potentials are analyzed in relation with the presence of one or two iodine atoms and internal rotation of hydroxyl hydrogen. The formation of an intramolecular hydrogen bond at some conformations has little effect on the properties that might affect the recognition and further deiodination of MIT and DIT. Polarizability of iodine and the reactive nature of iodinated tyrosines as nucleophilic targets are the essential features revealed in this work.
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Affiliation(s)
- Luis F Pacios
- Unidad de Química y Bioquímica, Departamento de Biotecnología, ETS Ingenieros de Montes, Universidad Politécnica de Madrid, Madrid, Spain.
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18
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Yang Y. Electron localization in nonplanar conjugated macrocycles: Failure of electron buffers to delocalize electrons. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Bohórquez HJ, Boyd RJ, Matta CF. Molecular Model with Quantum Mechanical Bonding Information. J Phys Chem A 2011; 115:12991-7. [DOI: 10.1021/jp204100z] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hugo J. Bohórquez
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Russell J. Boyd
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Chérif F. Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada B3M 2J6
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Kayser K, Görtler J, Borkenfeld S, Kayser G. Grid computing in image analysis. Diagn Pathol 2011; 6 Suppl 1:S12. [PMID: 21516880 PMCID: PMC3073205 DOI: 10.1186/1746-1596-6-s1-s12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Diagnostic surgical pathology or tissue–based diagnosis still remains the most reliable and specific diagnostic medical procedure. The development of whole slide scanners permits the creation of virtual slides and to work on so-called virtual microscopes. In addition to interactive work on virtual slides approaches have been reported that introduce automated virtual microscopy, which is composed of several tools focusing on quite different tasks. These include evaluation of image quality and image standardization, analysis of potential useful thresholds for object detection and identification (segmentation), dynamic segmentation procedures, adjustable magnification to optimize feature extraction, and texture analysis including image transformation and evaluation of elementary primitives. Grid technology seems to possess all features to efficiently target and control the specific tasks of image information and detection in order to obtain a detailed and accurate diagnosis. Grid technology is based upon so-called nodes that are linked together and share certain communication rules in using open standards. Their number and functionality can vary according to the needs of a specific user at a given point in time. When implementing automated virtual microscopy with Grid technology, all of the five different Grid functions have to be taken into account, namely 1) computation services, 2) data services, 3) application services, 4) information services, and 5) knowledge services. Although all mandatory tools of automated virtual microscopy can be implemented in a closed or standardized open system, Grid technology offers a new dimension to acquire, detect, classify, and distribute medical image information, and to assure quality in tissue–based diagnosis.
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Li X. Ab initio study of MKr n 2+ (M = Cu, Ag, and Au, n = 1-6) clusters. J Mol Model 2011; 18:1003-8. [DOI: 10.1007/s00894-011-1138-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 05/24/2011] [Indexed: 10/18/2022]
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22
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Xinying L, Xue C. Interaction and Electron Density Properties of MKr42+ (M=Cu, Ag and Au): ab initio Calculation. Aust J Chem 2011. [DOI: 10.1071/ch10373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Quantum chemical calculations of the structures and stabilities of the MKr42+ series at the CCSD(T) theoretical level have been performed. The role of the interaction was investigated using the natural bond orbital (NBO), Laplacian, electron density deformation, electron localization function and reduced density gradient analysis. The results show that a covalent contribution occurs in the Kr-M2+ bonding.
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23
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Yang Y. Hexacoordinate Bonding and Aromaticity in Silicon Phthalocyanine. J Phys Chem A 2010; 114:13257-67. [DOI: 10.1021/jp109278v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Yang Yang
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
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24
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Xinying L, Xue C. Theoretical treatment of (M=Cu, Ag and Au). Mol Phys 2010. [DOI: 10.1080/00268976.2010.506890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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