516 research outputs found
GAMESS-UJ, Carter group GAMESS-UJ documentation
No full textWe have developed two methods for calculating U and J from unrestricted Hartree-Fock calculations. Our initial effort is described in Phys. Rev. B 76, 155123 (2007), followed by a rotationally-invariant formalism described in J. Chem. Phys. 129, 014103 (2008). “GAMESS-UJ “ refers to the second method implemented in the GAMESS packag
The Component-Based Application for GAMESS
No full textGAMESS, a quantum chetnistry program for electronic structure calculations, has been freely shared by high-performance application scientists for over twenty years. It provides a rich set of functionalities and can be run on a variety of parallel platforms through a distributed data interface. While a chemistry computation is sophisticated and hard to develop, the resource sharing among different chemistry packages will accelerate the development of new computations and encourage the cooperation of scientists from universities and laboratories. Common Component Architecture (CCA) offers an enviromnent that allows scientific packages to dynamically interact with each other through components, which enable dynamic coupling of GAMESS with other chetnistry packages, such as MPQC and NWChem. Conceptually, a cotnputation can be constructed with "plug-and-play" components from scientific packages and require more than componentizing functions/subroutines of interest, especially for large-scale scientific packages with a long development history. In this research, we present our efforts to construct cotnponents for GAMESS that conform to the CCA specification. The goal is to enable the fine-grained interoperability between three quantum chemistry programs, GAMESS, MPQC and NWChem, via components. We focus on one of the three packages, GAMESS; delineate the structure of GAMESS computations, followed by our approaches to its component development. Then we use GAMESS as the driver to interoperate integral components from the other tw"o packages, arid show the solutions for interoperability problems along with preliminary results. To justify the versatility of the design, the Tuning and Analysis Utility (TAU) components have been coupled with GAMESS and its components, so that the performance of GAMESS and its components may be analyzed for a wide range of systetn parameters
Introducing LibXC into GAMESS (US)
No full textThe interface between LibXC and GAMESS (US), which enables the latter to perform calculations with >200 popular density functional approximations, including recently proposed r2SCAN, M06-SX and CAM-QTP00, is presented. The LibXC-GAMESS interface allows users to specify custom functionals as linear combinations of the present ones, exact exchange (producing hybrids) and MP2-correlation (producing double-hybrids).This is a manuscript of an article published as Gerasimov, Igor S., Federico Zahariev, Sarom S. Leang, Anton Tesliuk, Mark S. Gordon, and Michael G. Medvedev. "Introducing LibXC into GAMESS (US)." Mendeleev Communications 31, no. 3 (2021): 302-305.
DOI: 10.1016/j.mencom.2021.04.008.
Copyright 2021 Elsevier.
DOE Contract Number(s): AC02-07CH11358
USING GAMESS TO DETERMINE TRANSITION MOMENTS**
No full textThe installation and use of GAMESS (General Atomic and Molecular Electronic Structure System) a general ab initio quantum computational program is discussed. GAMESS is a free computational package that is used to evaluate the transition dipole moments of several conjugated organic compounds, including 1,4-diphenyl-1,3-butadiene and 1,6-diphenyl-1,3,5-hexatriene . The computational results are compared to results from linear dichroism analysis and to literature values where available
AutoGAMESS: A Python package for automation of GAMESS(US) Raman calculations
No full text<p>This is a python module for automating the generation of input files and parsing of log files with end goal of generating Raman data using the <a href="https://www.msg.chem.iastate.edu/gamess/">GAMESS(us)</a> Quantum Chemistry software.</p>
Applications of Parallel GAMESS
No full textIn this paper we discuss several recent applications that would have been difficult or impossible without the availability of the parallel implementation of the electronic structure code GAMESS. These applications include the study of highly strained rings, such as inorganic prismanes and bicyclobutanes, cage compounds such as cyclophanes and atranes, the neutral zwitterion isomerization of glycine, transition metal-main group binding, and the implementation of parallel graphics.Reprinted (adapted) with permission from ACS Symposium Series, vol. 592, Parallel Computing in Computational Chemistry, chapter 3 (1995): 29, doi:10.1021/bk-1995-0592.ch003. Copyright 1995 American Chemical Society.</p
Parallel Implementation of the Electronic Structure Code GAMESS
No full textThis paper outlines various tools and techniques for the parallelization of quantum chemistry codes; in particular, for the electronic structure code GAMESS. A general overview of the parallel capabilities of GAMESS are also presented. The parallelization of quantum chemistry codes has become a very active area of research over the last decade(1,2,3,4). Until recently, most of this research has dealt with self-consistent field (SCF) theory(1). However, in the last few years parallel implementations of post-SCF methods have been presented (2). Most of the post-SCF methods and analytic Hessians for SCF wavefunctions face the substantial problem of parallelizing the atomic orbital (AO) integral to molecular orbital (MO) integral transformation (3). The objective of this paper is to provide general information about the parallel implementation of GAMESS. The following sections are presented in this paper: (A) a brief overview of the functionality of the ab initio code GAMESS (General Atomic and Molecular Electronic Structure System); (B) a short discussion of the model, software, and general ideas used to parallelize GAMESS; (C) spécifics concerning the parallelization of the SCF; (D) discussion concerning the AO to MO integral transformation; (E) the transformation as applied to multi-configuration SCF (MCSCF); (F) the transformation as applied to analytic Hessians; (G) a brief overview of the parallel MP2 code; and (H) conclusions and future areas of research will be discussed.Reprinted (adapted) with permission from ACS Symposium Series, vol. 592, Prallel Computing in Computational Chemistry, chapter 2 (1994): 16, doi:10.1021/bk-1995-0592.ch002. Copyright 1995 American Chemical Society.</p
Bulky Ligand Systems Containing Pi-Acidic Aryl and Carboranyl Groups
No full textThis thesis describes studies into the synthesis and coordination chemistry of ligands containing bulky π-acidic groups. Both π-acidic aryl and carboranyl groups have been investigated. Chapter One highlights electronic and structural aspects of ligands investigated and computational techniques employed. Chapter Two describes the synthesis of aromatic systems bearing nitrogen substituents and trifluoromethyl groups, with a view to their use in the synthesis of new ligands. The π -interaction between the nitrogen substituent and aromatic ring has been investigated and is found to vary considerably with the nature of the substituent and position of the CF(_3) groups on the ring. Chapter Three describes the synthesis of molybdenum compounds containing CF3 substituted aryl-imido ligands. The presence of the π-acidic group is found to decrease π-bonding from the ligand to the metal which results in changes in the reactivity of such complexes. Chapter Four describes the synthesis of nitrogen-substituted carboranes 1- NHX-2-R-l,2-C(_2)B (_10)H(_10) (R = Me, Ph; X = 2-R-l,2-C(_2)B(_10)H(_10), NHAr, OH, H) and 1- NX-2-R-C(_2)B(_10)H(_10) (R = Me, Ph; X = 0, NAr). The structures of many of these compounds are described and the π-interaction between the cage and substituent investigated. This 7t-interaction determines the orientation of the substituent relative to the cage and causes changes in the geometry of the cage. The "B NMR shift of the atom directly opposite the nitrogen substituent is found to give an accurate indication of the exo π-bond order. In light of these observations data from other systems have been re-examined. Chapter Five describes the incorporation of carborane containing ligands into metal systems. The π-acidic carboranyl group reduces 7i-bonding from the ligand to the metal. The consequences of this on the structure and reactivity of these complexes are discussed. Chapter Six gives experimental details for Chapters Two to Five. Richard John Peace (August 1996
All-cis 1,2,3,4,5,6-hexafluorocyclohexane is a facially polarized cyclohexane
No full textThis work was generously supported by the Engineering and Physical Sciences Research Council (EPSRC) and the European Research Council (ERC).The highest-energy stereoisomer of 1,2,3,4,5,6-hexafluorocyclohexane, in which all of the fluorines are ‘up’, is prepared in a 12-step protocol. The molecule adopts a classic chair conformation with alternate C–F bonds aligned triaxially, clustering three highly electronegative fluorine atoms in close proximity. This generates a cyclohexane with a high molecular dipole (μ = 6.2 D), unusual in an otherwise aliphatic compound. X-ray analysis indicates that the intramolecular Fax···Fax distances (∼2.77 Å) are longer than the vicinal Fax···Feq distances (∼2.73 Å) suggesting a tension stabilizing the chair conformation. In the solid state the molecules pack in an orientation consistent with electrostatic ordering. Our synthesis of this highest-energy isomer demonstrates the properties that accompany the placement of axial fluorines on a cyclohexane and the unusual property of a facially polarized ring in organic chemistry. Derivatives have potential as new motifs for the design of functional organic molecules or for applications in supramolecular chemistry design.Peer reviewe
Runtime Power Allocation Based on Multi-GPU utilization in GAMESS
No full textTo improve the power consumption of parallel applications at the runtime, modern processors provide frequency scaling and power limiting capabilities. In this work, a runtime strategy is proposed to maximize performance under a given power budget by distributing the available power according to the relative GPU utilization. Time series forecasting methods were used to develop workload prediction models that provide accurate prediction of GPU utilization during application execution. Experiments were performed on a multi-GPU computing platform DGX-1 equipped with eight NVIDIA V100 GPUs used for quantum chemistry calculations in the GAMESS package. For a limited power budget, the proposed strategy may deliver as much as hundred times better GAMESS performance than that obtained when the power is distributed equally among all the GPUs
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