Computational Modeling of the Electron Momentum Density
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Free and Open Source Software for Computational Chemistry Education
Free and Open Source Software for Computational Chemistry Education Susi Lehtola∗,y and Antti J. Karttunenz yMolecular Sciences Software Institute, Blacksburg, Virginia 24061, United States zDepartment of Chemistry and Materials Science, Aalto University, Espoo, Finland E-mail: [email protected].fi Abstract Long in the making, computational chemistry for the masses [J. Chem. Educ. 1996, 73, 104] is finally here. We point out the existence of a variety of free and open source software (FOSS) packages for computational chemistry that offer a wide range of functionality all the way from approximate semiempirical calculations with tight- binding density functional theory to sophisticated ab initio wave function methods such as coupled-cluster theory, both for molecular and for solid-state systems. By their very definition, FOSS packages allow usage for whatever purpose by anyone, meaning they can also be used in industrial applications without limitation. Also, FOSS software has no limitations to redistribution in source or binary form, allowing their easy distribution and installation by third parties. Many FOSS scientific software packages are available as part of popular Linux distributions, and other package managers such as pip and conda. Combined with the remarkable increase in the power of personal devices—which rival that of the fastest supercomputers in the world of the 1990s—a decentralized model for teaching computational chemistry is now possible, enabling students to perform reasonable modeling on their own computing devices, in the bring your own device 1 (BYOD) scheme. In addition to the programs’ use for various applications, open access to the programs’ source code also enables comprehensive teaching strategies, as actual algorithms’ implementations can be used in teaching. -
Open Babel Documentation Release 2.3.1
Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options ................................................. -
Metalloboranes from First-Principles Calculations: a Candidate for High-Density Hydrogen Storage
Metalloboranes from first-principles calculations: A candidate for high-density hydrogen storage A. R. Akbarzadeh, D. Vrinceanu, and C.J. Tymczak Department of Physics, Texas Southern University, Houston, Texas 77004, USA Abstract Using first principles calculations, we show the high hydrogen storage capacity of a new class of compounds, metalloboranes. Metalloboranes are transition metal (TM) and borane compounds that obey a novel-bonding scheme. We have found that the transition metal atoms can bind up to 10 H2-molecules with an average binding energy of 30 kJ/mole of H2, which lies favorably within the reversible adsorption range. Among the first row TM atoms, Sc and Ti are found to be the optimum in maximizing the H2 storage on the metalloborane cluster. Additionally, being ionically bonded to the borane molecule, the TMs do not suffer from the aggregation problem, which has been the biggest hurdle for the success of TM- decorated graphitic materials for hydrogen storage. Furthermore, since the borane 6-atom ring has identical bonding properties as carbon rings it is possible to link the metalloboranes into metal organic frameworks (MOF’s), which are thus able to adsorb hydrogen via Kubas interaction as well as the well-known van der Waals interaction. Finally, we construct a simple Monte-Catlo algorithm for Hydrogen uptake and show that Titanium metalloboranes in a MOF5 structure can absorb up to 11.5% hydrogen per weight at 100 bar of pressure. I. Introduction Due to the geographical distribution and supply limitation of fossil fuel resources and the increasing perceived negative impact of carbon dioxide emission in the environment, it is advantageous for the societies to take action in the search and implementation of alternative energy systems. -
In Quantum Chemistry
http://www.cca-forum.org Computational Quality of Service (CQoS) in Quantum Chemistry Joseph Kenny1, Kevin Huck2, Li Li3, Lois Curfman McInnes3, Heather Netzloff4, Boyana Norris3, Meng-Shiou Wu4, Alexander Gaenko4 , and Hirotoshi Mori5 1Sandia National Laboratories, 2University of Oregon, 3Argonne National Laboratory, 4Ames Laboratory, 5Ochanomizu University, Japan This work is a collaboration among participants in the SciDAC Center for Technology for Advanced Scientific Component Software (TASCS), Performance Engineering Research Institute (PERI), Quantum Chemistry Science Application Partnership (QCSAP), and the Tuning and Analysis Utilities (TAU) group at the University of Oregon. Quantum Chemistry and the CQoS in Quantum Chemistry: Motivation and Approach Common Component Architecture (CCA) Motivation: CQoS Approach: CCA Overview: • QCSAP Challenges: How, during runtime, can we make the best choices • Overall: Develop infrastructure for dynamic component adaptivity, i.e., • The CCA Forum provides a specification and software tools for the for reliability, accuracy, and performance of interoperable quantum composing, substituting, and reconfiguring running CCA component development of high-performance components. chemistry components based on NWChem, MPQC, and GAMESS? applications in response to changing conditions – Performance, accuracy, mathematical consistency, reliability, etc. • Components = Composition – When several QC components provide the same functionality, what • Approach: Develop CQoS tools for – A component is a unit -
Application Profiling at the HPCAC High Performance Center Pak Lui 157 Applications Best Practices Published
Best Practices: Application Profiling at the HPCAC High Performance Center Pak Lui 157 Applications Best Practices Published • Abaqus • COSMO • HPCC • Nekbone • RFD tNavigator • ABySS • CP2K • HPCG • NEMO • SNAP • AcuSolve • CPMD • HYCOM • NWChem • SPECFEM3D • Amber • Dacapo • ICON • Octopus • STAR-CCM+ • AMG • Desmond • Lattice QCD • OpenAtom • STAR-CD • AMR • DL-POLY • LAMMPS • OpenFOAM • VASP • ANSYS CFX • Eclipse • LS-DYNA • OpenMX • WRF • ANSYS Fluent • FLOW-3D • miniFE • OptiStruct • ANSYS Mechanical• GADGET-2 • MILC • PAM-CRASH / VPS • BQCD • Graph500 • MSC Nastran • PARATEC • BSMBench • GROMACS • MR Bayes • Pretty Fast Analysis • CAM-SE • Himeno • MM5 • PFLOTRAN • CCSM 4.0 • HIT3D • MPQC • Quantum ESPRESSO • CESM • HOOMD-blue • NAMD • RADIOSS For more information, visit: http://www.hpcadvisorycouncil.com/best_practices.php 2 35 Applications Installation Best Practices Published • Adaptive Mesh Refinement (AMR) • ESI PAM-CRASH / VPS 2013.1 • NEMO • Amber (for GPU/CUDA) • GADGET-2 • NWChem • Amber (for CPU) • GROMACS 5.1.2 • Octopus • ANSYS Fluent 15.0.7 • GROMACS 4.5.4 • OpenFOAM • ANSYS Fluent 17.1 • GROMACS 5.0.4 (GPU/CUDA) • OpenMX • BQCD • Himeno • PyFR • CASTEP 16.1 • HOOMD Blue • Quantum ESPRESSO 4.1.2 • CESM • LAMMPS • Quantum ESPRESSO 5.1.1 • CP2K • LAMMPS-KOKKOS • Quantum ESPRESSO 5.3.0 • CPMD • LS-DYNA • WRF 3.2.1 • DL-POLY 4 • MrBayes • WRF 3.8 • ESI PAM-CRASH 2015.1 • NAMD For more information, visit: http://www.hpcadvisorycouncil.com/subgroups_hpc_works.php 3 HPC Advisory Council HPC Center HPE Apollo 6000 HPE ProLiant -
High-Performance Algorithms and Software for Large-Scale Molecular Simulation
HIGH-PERFORMANCE ALGORITHMS AND SOFTWARE FOR LARGE-SCALE MOLECULAR SIMULATION A Thesis Presented to The Academic Faculty by Xing Liu In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the School of Computational Science and Engineering Georgia Institute of Technology May 2015 Copyright ⃝c 2015 by Xing Liu HIGH-PERFORMANCE ALGORITHMS AND SOFTWARE FOR LARGE-SCALE MOLECULAR SIMULATION Approved by: Professor Edmond Chow, Professor Richard Vuduc Committee Chair School of Computational Science and School of Computational Science and Engineering Engineering Georgia Institute of Technology Georgia Institute of Technology Professor Edmond Chow, Advisor Professor C. David Sherrill School of Computational Science and School of Chemistry and Biochemistry Engineering Georgia Institute of Technology Georgia Institute of Technology Professor David A. Bader Professor Jeffrey Skolnick School of Computational Science and Center for the Study of Systems Biology Engineering Georgia Institute of Technology Georgia Institute of Technology Date Approved: 10 December 2014 To my wife, Ying Huang the woman of my life. iii ACKNOWLEDGEMENTS I would like to first extend my deepest gratitude to my advisor, Dr. Edmond Chow, for his expertise, valuable time and unwavering support throughout my PhD study. I would also like to sincerely thank Dr. David A. Bader for recruiting me into Georgia Tech and inviting me to join in this interesting research area. My appreciation is extended to my committee members, Dr. Richard Vuduc, Dr. C. David Sherrill and Dr. Jeffrey Skolnick, for their advice and helpful discussions during my research. Similarly, I want to thank all of the faculty and staff in the School of Compu- tational Science and Engineering at Georgia Tech. -
Core Software Blocks in Quantum Chemistry: Tensors and Integrals Workshop Program
Core Software Blocks in Quantum Chemistry: Tensors and Integrals Workshop Program Start: Sunday, May 7, 2017 afternoon. Resort check-in at 4:00 pm. Finish: Wednesday, May 10, noon Lectures are in Scripps, posters are in Heather. Sunday 6:00-7:00: Dinner 7:30-9:00 Opening session 7:30–7:45 Anna Krylov (USC): “MolSSI and some lessons from previous workshop, goals of the workshop” 7:45-8:00 Theresa Windus (Iowa): “Mission of the Molecular Science Consortium” 8:00-9:00 Introduction of participants: 2 min presentation, can have one slide (send in advance) 9:00-10:30 Reception and posters Monday Breakfast: 7:30-9:00 9:00-11:45 Session I: Overview of tensors projects and current developments (moderator Daniel Smith) 9:00-9:10 Daniel Smith (MolSSI): Overview of tensor projects 9:10-9:30 Evgeny Epifanovsky (Q-Chem): Overview of Libtensor 9:30-9:50 Ed Solomonik: "An Overview of Cyclops Tensor Framework" 9:50-10:10 Ed Valeev (VT): "TiledArray: A composable massively parallel block-sparse tensor framework" 10:10-10:30 Coffee break 10:30-10:50 Devin Matthews (UT Austin): "Aquarius and TBLIS: Orthogonal Axes in Multilinear Algebra" 10:50-11:10 Karol Kowalskii (PNNL, NWChem): "NWChem, NWChemEX , and new tensor algebra systems for many-body methods" 11:10-11:30 Peng Chong (VT): "Many-body toolkit in re-designed Massively Parallel Quantum Chemistry package" 11:30-11:55 Moderated discussion: "What problems are we *still* solving?” Lunch: 12:00-1:00 Free time for unstructured discussions 5:00 Posters (coffee/tea) Dinner: 6-7:00 7:15-9:00 Session II: Computer -
Presidential Search Committee Meets, Reviews Upcoming Work
ETHEMedford, MA 02155 TUFTSTuesday, November 26,1991 DAILYJVol XXIII, Number 58 Faculty tables vote on Presidential search committee World Civ proposal meets, reviews upcoming work courses iUC to be intcrdiscipli by SCHAEF1cR nary. intcgr;ltblg disciplines fr()n by MAUREEN LENIHAN Senior Staff Writer Daily Editorial Board and PATRICK HEALY at leiist three of the five distribu The 19-member search com- Dally Edil(~r1alhtUd tion areas. mittee fonned to begin the pro- Although the proposed World Since 1986. threeteamsoffac cess of selecting anew university CivilizationsFoundation rcquire- ult y. including one professor frorr president met for the first time inent was briefly presented at the the School ofEngineering,devel yesterday, familiariz,ing them- Liberal Arts and Jackson facully oped three two-semester course: selves with their task and the meeting yesterday. the LAM fac- which were ultiinately opened tc committee‘s initial duties includ- ulty postponed further discussion students to take on a voluntce ing formali~inga Job description and voting on the prognun until basis. These courses, titled “P for the post. Dec. 11. Sense of Place.” “Time and Cal The committee. representing Dean of College of Liberal endars,“and “Memory and Iden trustees. administrators, faculty Arts and Jackson Mary Ella tity.“wereestablishedwith fincan members. staff members. stu- Fcinleibmoved tocrcate the Dec. cia1 support from ihe Davis Foun dents. and alumni, was fonncd in 1 I meeting since other meeting dation. the National Endowmen response toai miouiiccmcnt last topics preceding the World Civ for the Humimities, and the Uni May that University president presentation took up most of the versit y. -
A Summary of ERCAP Survey of the Users of Top Chemistry Codes
A survey of codes and algorithms used in NERSC chemical science allocations Lin-Wang Wang NERSC System Architecture Team Lawrence Berkeley National Laboratory We have analyzed the codes and their usages in the NERSC allocations in chemical science category. This is done mainly based on the ERCAP NERSC allocation data. While the MPP hours are based on actually ERCAP award for each account, the time spent on each code within an account is estimated based on the user’s estimated partition (if the user provided such estimation), or based on an equal partition among the codes within an account (if the user did not provide the partition estimation). Everything is based on 2007 allocation, before the computer time of Franklin machine is allocated. Besides the ERCAP data analysis, we have also conducted a direct user survey via email for a few most heavily used codes. We have received responses from 10 users. The user survey not only provide us with the code usage for MPP hours, more importantly, it provides us with information on how the users use their codes, e.g., on which machine, on how many processors, and how long are their simulations? We have the following observations based on our analysis. (1) There are 48 accounts under chemistry category. This is only second to the material science category. The total MPP allocation for these 48 accounts is 7.7 million hours. This is about 12% of the 66.7 MPP hours annually available for the whole NERSC facility (not accounting Franklin). The allocation is very tight. The majority of the accounts are only awarded less than half of what they requested for. -
O (N) Methods in Electronic Structure Calculations
O(N) Methods in electronic structure calculations D R Bowler1;2;3 and T Miyazaki4 1London Centre for Nanotechnology, UCL, 17-19 Gordon St, London WC1H 0AH, UK 2Department of Physics & Astronomy, UCL, Gower St, London WC1E 6BT, UK 3Thomas Young Centre, UCL, Gower St, London WC1E 6BT, UK 4National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, JAPAN E-mail: [email protected] E-mail: [email protected] Abstract. Linear scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high performance computers. The linear scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas is then discussed. The applications of linear scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear scaling methods are discussed. Submitted to: Rep. Prog. Phys. arXiv:1108.5976v5 [cond-mat.mtrl-sci] 3 Nov 2011 O(N) Methods 2 1. -
Curriculum Vitae
CURRICULUM VITAE Christopher J. Tymczak Tenured Associate Professor Director Department of Physics Texas Southern University High Texas Southern University Performance Computing Center Houston, Texas 77004 Texas Southern University Office: (713) 313-1849 Houston, Texas 77004 Email: [email protected] (http://hpcc.tsu.edu/) (http://physics.tsu.edu/) Co-Director Visiting Research Scientist NSF CREST Center for Research on Group T-1 Complex Networks Los Alamos National Laboratory Texas Southern University Los Alamos, New Mexico, 87507 Houston, Texas 77004 I specialize in the identification, development, and implementation of new scientific codes for exploiting advanced computing resources impacting large scale computation in diverse areas in Many-body physics, Quantum Chemistry and ab initio Molecular Dynamics. I am a tenured associate professor of physics at Texas Southern University, where I am spearheading the integration of supercomputing resources into various STEM programs. I am also the founder and director of the Texas Southern High Performance Computing Center (TSU-HPCC). At Los Alamos National Laboratory, I am a permanent scientific associate within the FreeON initiative, involving the development of massively parallel linear scaling quantum chemistry methods, currently under development in collaboration with Dr. Matt Challacombe (T-12) and Dr. Anders Niklasson (T-1). I was one of the first to exploit wavelet-based methods in large scale computing for understanding the electronic structure of materials. For the last six years, I have advanced the FreeON development through the exploitation of advanced data structures and advanced machine architectures. FreeON is now recognized as one of the first quantum chemical codes with demonstrable scalable parallelism within large- scale parallel clusters. -
Massive-Parallel Implementation of the Resolution-Of-Identity Coupled
Article Cite This: J. Chem. Theory Comput. 2019, 15, 4721−4734 pubs.acs.org/JCTC Massive-Parallel Implementation of the Resolution-of-Identity Coupled-Cluster Approaches in the Numeric Atom-Centered Orbital Framework for Molecular Systems † § † † ‡ § § Tonghao Shen, , Zhenyu Zhu, Igor Ying Zhang,*, , , and Matthias Scheffler † Department of Chemistry, Fudan University, Shanghai 200433, China ‡ Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Key Laboratory of Computational Physical Science, Fudan University, Shanghai 200433, China § Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany *S Supporting Information ABSTRACT: We present a massive-parallel implementation of the resolution of identity (RI) coupled-cluster approach that includes single, double, and perturbatively triple excitations, namely, RI-CCSD(T), in the FHI-aims package for molecular systems. A domain-based distributed-memory algorithm in the MPI/OpenMP hybrid framework has been designed to effectively utilize the memory bandwidth and significantly minimize the interconnect communication, particularly for the tensor contraction in the evaluation of the particle−particle ladder term. Our implementation features a rigorous avoidance of the on- the-fly disk storage and excellent strong scaling of up to 10 000 and more cores. Taking a set of molecules with different sizes, we demonstrate that the parallel performance of our CCSD(T) code is competitive with the CC implementations in state-of- the-art high-performance-computing computational chemistry packages. We also demonstrate that the numerical error due to the use of RI approximation in our RI-CCSD(T) method is negligibly small. Together with the correlation-consistent numeric atom-centered orbital (NAO) basis sets, NAO-VCC-nZ, the method is applied to produce accurate theoretical reference data for 22 bio-oriented weak interactions (S22), 11 conformational energies of gaseous cysteine conformers (CYCONF), and 32 Downloaded via FRITZ HABER INST DER MPI on January 8, 2021 at 22:13:06 (UTC).