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Adaptive Application Composition in Quantum Chemistry [chapter]

Li Li, Joseph P. Kenny, Meng-Shiou Wu, Kevin Huck, Alexander Gaenko, Mark S. Gordon, Curtis L. Janssen, Lois Curfman McInnes, Hirotoshi Mori, Heather M. Netzloff, Boyana Norris, Theresa L. Windus
2009 Lecture Notes in Computer Science  
Motivated by the need for faster runtimes and increased productivity for chemists, we present a flexible CQoS approach for quantum chemistry that uses a generic CQoS database component to create a training  ...  Several leading quantum chemistry packages have achieved interoperability by adopting CCA components.  ...  This work is a collaboration among the Quantum Chemistry Scientific Application Partnership (QCSAP) [5] , the Center for Component Technology for Terascale Simulation Software [39] , and the Performance  ... 
doi:10.1007/978-3-642-02351-4_13 fatcat:asegaa2t6rd4tgvwcmosn37pty

Computational Science and Engineering On-line: an integrated web-based environment for multi-scale modelling of complex reaction systems

Thanh N. Truong, Tom Cook, Manohar Nayak, Chaiwoot Boonyasiriwat, Le-Thuy T. Tran, Shaowen Zhang
2004 Molecular Physics  
Our initial efforts are focusing on an integrated environment for multi-scale modelling of complex reacting systems from fundamental quantum chemistry with different entry points.  ...  In addition, it provides a set of web-based graphic-user interfaces (GUIs) to different scientific applications. Current available GUIs are for quantum chemistry, thermodynamics and kinetics.  ...  an available quantum chemistry package for calculating potential energy surface information.  ... 
doi:10.1080/00268970310001649392 fatcat:hhwy2srfabhvhahmnnzjgtzjz4

Open source molecular modeling

Somayeh Pirhadi, Jocelyn Sunseri, David Ryan Koes
2016 Journal of Molecular Graphics and Modelling  
In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry.  ...  The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications.  ...  helpful feedback on a draft of this manuscript.  ... 
doi:10.1016/j.jmgm.2016.07.008 pmid:27631126 pmcid:PMC5037051 fatcat:jxdvghsiszadjevub22qbjywwm

Highlights of (bio-)chemical tools and visualization software for computational science

David Dubbeldam, Jocelyne Vreede, Thijs JH Vlugt, Sofia Calero
2019 Current Opinion in Chemical Engineering  
In this review, we describe and highlight tools and visualization packages that are commonly used in the field of (bio-)chemistry and material science.  ...  Highlights of (bio-)chemical tools and visualization software for computational science Dubbeldam, D.; Vreede, J.; Vlugt, T.J.H.; Calero, S.  ...  TJHV acknowledges NWO-CW for a VICI grant.  ... 
doi:10.1016/j.coche.2019.02.001 fatcat:lntih5hdgjcsxpizloatezhg5a

Modern Software for Computer Modeling in Quantum Chemistry and Molecular Dynamics

Marina V. Malyshkina, Alexander S. Novikov
2021 Compounds  
The most popular modern programs for quantum chemical and molecular dynamics (classical, ab initio, and QM/MM) calculations, which are relevant for the investigation of nature and various properties of  ...  ErgoSCF [16] is a quantum chemistry program. Large-scale self-consistent field calculations can be implemented by ErgoSCF.  ...  ORCA [39] is a program package that implies a general purpose tool for quantum chemistry.  ... 
doi:10.3390/compounds1030012 fatcat:v2ibexq4gfgivf5oe6kf5bzdza

SPAHM: the Spectrum of Approximated Hamiltonian Matrices Representations

Alberto Fabrizio, Ksenia R. Briling, Clemence Corminboeuf
2022 Digital Discovery  
Despite their conceptual and mathematical diversity, this class of descriptors shares a common underlying philosophy: they...  ...  Acknowledgements The authors acknowledge Ruben Laplaza and Puck van Gerwen for helpful discussion and critical propositions.  ...  Using the QM7 and the L11 databases, we tested the performance of a hierarchy of representations for a set of four representative quantum chemical properties.  ... 
doi:10.1039/d1dd00050k pmid:35769206 pmcid:PMC9189859 fatcat:iis7kwlb5jgijnkmpzou4b2moa

The Computational Chemistry Prototyping Environment

K.K. Baldridge, J.P. Greenberg, W. Sudholt, S. Mock, I. Altintas, C. Amoreira, Y. Potier, A. Birnbaum, K. Bhatia, M. Taufer
2005 Proceedings of the IEEE  
We will describe our efforts in creating a Computational Chemistry Environment that encompasses a general scientific workflow environment, a domain specific example for quantum chemistry, our ongoing design  ...  of a workflow user interface, and our efforts at database integration.  ...  Abramson and his group from Monash University, Australia, for collaboration regarding Nimrod and to P. Murray-Rust and his group from Cambridge University, U.K., for collaboration regarding CML.  ... 
doi:10.1109/jproc.2004.842747 fatcat:pe4c5gn7r5coddtvszwgmmgw2e

Tackling component interoperability in quantum chemistry software

Fang Peng, Meng-Shiou Wu, Masha Sosonkina, Theresa Windus, Jonathan Bentz, Mark Gordon, Joseph Kenny, Curtis Janssen
2007 Proceedings of the 2007 symposium on Component and framework technology in high-performance and scientific computing - CompFrame '07  
more than componentizing functions/subroutines of interest, especially for large-scale scientific packages with a long development history.  ...  In this paper, we present our efforts to construct components for the integral evaluation -a fundamental sub-problem of quantum chemistry computations -that conform to the CCA specification.  ...  Acknowledgments We thank Mike Schmidt from the department of Chemistry and Ames Laboratory, Iowa State University for the information on GAMESS and DDI.  ... 
doi:10.1145/1297385.1297403 fatcat:noimz65iwbhkppltgyztbwyokm

The PubChemQC Project: a large chemical database from the first principle calculations [article]

Maho Nakata
2015 arXiv   pre-print
In this research, we have been constructing a large database of molecules by ab initio calculations.  ...  To calculate molecules, we only refer the InChI (International Chemical Identifier) representation of chemical formula by the International Union of Pure and Applied Chemistry (IUPAC), thus, no reference  ...  We need a huge dataset for compounds to learn chemistry from data, however, we don't have a large database having many molecules and their properties.  ... 
arXiv:1512.08572v1 fatcat:ys3fmvly55crfdlbvvwrqcwyka

Computational needs of quantum mechanical calculations of materials for high-energy physics [article]

Sinéad M. Griffin
2022 arXiv   pre-print
A burgeoning direction is the accurate calculation and design of materials for HEP applications.  ...  In this Snowmass contribution, I briefly motivate the science need for quantum mechanical calculations of materials for HEP and outline the range of questions that such calculations can address.  ...  Using materials informatics approaches, novel chemistries and materials can be identified from these large databases (e.g. the Materials Project [20] ) by combining targeted high-throughput calculations  ... 
arXiv:2205.10699v1 fatcat:mp27vgu2tff2pkjuaemopysoqm

Uniform Access to the Distributed Resources for the Computational Chemistry Using UNICORE [chapter]

Jarosław Pytliński, Lukasz Skorwider, Krzysztof Benedyczak, Michał Wroński, Piotr Bała, Valentina Huber
2003 Lecture Notes in Computer Science  
We have used UNICORE infrastructure as framework for development dedicated user interface to the number of existing computational chemistry codes as well as molecular bilogy databases.  ...  Currently various computational techniques become standard tools for a large number of users.  ...  Computational grids enable sharing a wide variety of geographically distributed resources and allow selection and aggregation of distributed resources across multiple organizations for solving large scale  ... 
doi:10.1007/3-540-44862-4_33 fatcat:dktmnshqezdtrgxkw4jm7cw2bq

The quantum chemical search for novel materials and the issue of data processing: The InfoMol project

Hans P. Lüthi, Stefan Heinen, Gisbert Schneider, Andreas Glöss, Martin P. Brändle, Rollin A. King, Edward Pyzer-Knapp, Fahhad H. Alharbi, Sabre Kais
2016 Journal of Computational Science  
One key bottleneck in this regard is the lack of availability of machine-readable output for virtually all quantum chemistry codes.  ...  One key bottleneck in this regard is the lack of availability of machine-readable output for virtually all quantum chemistry codes.  ...  InfoMol Tools: TURBOMOLE / PSI4-XML-eXist TURBOMOLE is a commercially available quantum chemistry application package to solve the Schrödinger equation for molecules in gas phase or in a polarizable continuum  ... 
doi:10.1016/j.jocs.2015.10.003 fatcat:pnu3b3ubgvbcrdbjesgl5mrac4

Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives

Siddhant Sharma, Aayush Arya, Romulo Cruz, Henderson Cleaves
2021 Life  
Prebiotic chemistry often involves the study of complex systems of chemical reactions that form large networks with a large number of diverse species.  ...  Computational chemistry offers efficient ways to study such chemical systems and identify the ones most likely to display complex properties associated with life.  ...  EON was supported by a grant from the John Templeton Foundation.  ... 
doi:10.3390/life11111140 pmid:34833016 pmcid:PMC8624352 fatcat:34mvenv2kncxlpkwr4egjxwsnu

Integrating Performance Tools with Large-Scale Scientific Software

Meng-Shiou Wu, Jonathan L. Bentz, Fang Peng, Masha Sosonkina, Mark S. Gordon, Ricky A. Kendall
2007 2007 IEEE International Parallel and Distributed Processing Symposium  
For a large-scale scientific software package that has been under development for decades and with developers around the world, several obstacles must be overcome in order to utilize modern performance  ...  With performance tools integrated, we show one of the initial performance evaluation results, and discuss what other challenges we are facing to conduct performance evaluation for large-scale scientific  ...  For a large-scale software package, a developer usually knows only part of the overall software.  ... 
doi:10.1109/ipdps.2007.370567 dblp:conf/ipps/WuBPSGK07 fatcat:qpmhglx6nrchrbsgdznat5tgey

Minimum energy pathways via quantum Monte Carlo

S. Saccani, C. Filippi, S. Moroni
2013 Journal of Chemical Physics  
DFT and system sizes too large for high level quantum chemistry methods.  ...  functional theory (DFT) and quantum chemistry methods.  ...  Valsson for assistance in the usage of CHAMP and GAMESS packages, and Professor S. Baroni for helpful discussions.  ... 
doi:10.1063/1.4792717 pmid:23464142 fatcat:o6mxkojarbga7pvnrwwwsq4nou
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