Subsystem Density-Functional Theory As an Effective Tool for Modeling
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
An Ab Initio Materials Simulation Code
CP2K: An ab initio materials simulation code Lianheng Tong Physics on Boat Tutorial , Helsinki, Finland 2015-06-08 Faculty of Natural & Mathematical Sciences Department of Physics Brief Overview • Overview of CP2K - General information about the package - QUICKSTEP: DFT engine • Practical example of using CP2K to generate simulated STM images - Terminal states in AGNR segments with 1H and 2H termination groups What is CP2K? Swiss army knife of molecular simulation www.cp2k.org • Geometry and cell optimisation Energy and • Molecular dynamics (NVE, Force Engine NVT, NPT, Langevin) • STM Images • Sampling energy surfaces (metadynamics) • DFT (LDA, GGA, vdW, • Finding transition states Hybrid) (Nudged Elastic Band) • Quantum Chemistry (MP2, • Path integral molecular RPA) dynamics • Semi-Empirical (DFTB) • Monte Carlo • Classical Force Fields (FIST) • And many more… • Combinations (QM/MM) Development • Freely available, open source, GNU Public License • www.cp2k.org • FORTRAN 95, > 1,000,000 lines of code, very active development (daily commits) • Currently being developed and maintained by community of developers: • Switzerland: Paul Scherrer Institute Switzerland (PSI), Swiss Federal Institute of Technology in Zurich (ETHZ), Universität Zürich (UZH) • USA: IBM Research, Lawrence Livermore National Laboratory (LLNL), Pacific Northwest National Laboratory (PNL) • UK: Edinburgh Parallel Computing Centre (EPCC), King’s College London (KCL), University College London (UCL) • Germany: Ruhr-University Bochum • Others: We welcome contributions from -
Automated Construction of Quantum–Classical Hybrid Models Arxiv:2102.09355V1 [Physics.Chem-Ph] 18 Feb 2021
Automated construction of quantum{classical hybrid models Christoph Brunken and Markus Reiher∗ ETH Z¨urich, Laboratorium f¨urPhysikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Z¨urich, Switzerland February 18, 2021 Abstract We present a protocol for the fully automated construction of quantum mechanical-(QM){ classical hybrid models by extending our previously reported approach on self-parametri- zing system-focused atomistic models (SFAM) [J. Chem. Theory Comput. 2020, 16 (3), 1646{1665]. In this QM/SFAM approach, the size and composition of the QM region is evaluated in an automated manner based on first principles so that the hybrid model describes the atomic forces in the center of the QM region accurately. This entails the au- tomated construction and evaluation of differently sized QM regions with a bearable com- putational overhead that needs to be paid for automated validation procedures. Applying SFAM for the classical part of the model eliminates any dependence on pre-existing pa- rameters due to its system-focused quantum mechanically derived parametrization. Hence, QM/SFAM is capable of delivering a high fidelity and complete automation. Furthermore, since SFAM parameters are generated for the whole system, our ansatz allows for a con- venient re-definition of the QM region during a molecular exploration. For this purpose, a local re-parametrization scheme is introduced, which efficiently generates additional clas- sical parameters on the fly when new covalent bonds are formed (or broken) and moved to the classical region. arXiv:2102.09355v1 [physics.chem-ph] 18 Feb 2021 ∗Corresponding author; e-mail: [email protected] 1 1 Introduction In contrast to most protocols of computational quantum chemistry that consider isolated molecules, chemical processes can take place in a vast variety of complex environments. -
Kepler Gpus and NVIDIA's Life and Material Science
LIFE AND MATERIAL SCIENCES Mark Berger; [email protected] Founded 1993 Invented GPU 1999 – Computer Graphics Visual Computing, Supercomputing, Cloud & Mobile Computing NVIDIA - Core Technologies and Brands GPU Mobile Cloud ® ® GeForce Tegra GRID Quadro® , Tesla® Accelerated Computing Multi-core plus Many-cores GPU Accelerator CPU Optimized for Many Optimized for Parallel Tasks Serial Tasks 3-10X+ Comp Thruput 7X Memory Bandwidth 5x Energy Efficiency How GPU Acceleration Works Application Code Compute-Intensive Functions Rest of Sequential 5% of Code CPU Code GPU CPU + GPUs : Two Year Heart Beat 32 Volta Stacked DRAM 16 Maxwell Unified Virtual Memory 8 Kepler Dynamic Parallelism 4 Fermi 2 FP64 DP GFLOPS GFLOPS per DP Watt 1 Tesla 0.5 CUDA 2008 2010 2012 2014 Kepler Features Make GPU Coding Easier Hyper-Q Dynamic Parallelism Speedup Legacy MPI Apps Less Back-Forth, Simpler Code FERMI 1 Work Queue CPU Fermi GPU CPU Kepler GPU KEPLER 32 Concurrent Work Queues Developer Momentum Continues to Grow 100M 430M CUDA –Capable GPUs CUDA-Capable GPUs 150K 1.6M CUDA Downloads CUDA Downloads 1 50 Supercomputer Supercomputers 60 640 University Courses University Courses 4,000 37,000 Academic Papers Academic Papers 2008 2013 Explosive Growth of GPU Accelerated Apps # of Apps Top Scientific Apps 200 61% Increase Molecular AMBER LAMMPS CHARMM NAMD Dynamics GROMACS DL_POLY 150 Quantum QMCPACK Gaussian 40% Increase Quantum Espresso NWChem Chemistry GAMESS-US VASP CAM-SE 100 Climate & COSMO NIM GEOS-5 Weather WRF Chroma GTS 50 Physics Denovo ENZO GTC MILC ANSYS Mechanical ANSYS Fluent 0 CAE MSC Nastran OpenFOAM 2010 2011 2012 SIMULIA Abaqus LS-DYNA Accelerated, In Development NVIDIA GPU Life Science Focus Molecular Dynamics: All codes are available AMBER, CHARMM, DESMOND, DL_POLY, GROMACS, LAMMPS, NAMD Great multi-GPU performance GPU codes: ACEMD, HOOMD-Blue Focus: scaling to large numbers of GPUs Quantum Chemistry: key codes ported or optimizing Active GPU acceleration projects: VASP, NWChem, Gaussian, GAMESS, ABINIT, Quantum Espresso, BigDFT, CP2K, GPAW, etc. -
Modern Quantum Chemistry with [Open]Molcas
Modern quantum chemistry with [Open]Molcas Cite as: J. Chem. Phys. 152, 214117 (2020); https://doi.org/10.1063/5.0004835 Submitted: 17 February 2020 . Accepted: 11 May 2020 . Published Online: 05 June 2020 Francesco Aquilante , Jochen Autschbach , Alberto Baiardi , Stefano Battaglia , Veniamin A. Borin , Liviu F. Chibotaru , Irene Conti , Luca De Vico , Mickaël Delcey , Ignacio Fdez. Galván , Nicolas Ferré , Leon Freitag , Marco Garavelli , Xuejun Gong , Stefan Knecht , Ernst D. Larsson , Roland Lindh , Marcus Lundberg , Per Åke Malmqvist , Artur Nenov , Jesper Norell , Michael Odelius , Massimo Olivucci , Thomas B. Pedersen , Laura Pedraza-González , Quan M. Phung , Kristine Pierloot , Markus Reiher , Igor Schapiro , Javier Segarra-Martí , Francesco Segatta , Luis Seijo , Saumik Sen , Dumitru-Claudiu Sergentu , Christopher J. Stein , Liviu Ungur , Morgane Vacher , Alessio Valentini , and Valera Veryazov J. Chem. Phys. 152, 214117 (2020); https://doi.org/10.1063/5.0004835 152, 214117 © 2020 Author(s). The Journal ARTICLE of Chemical Physics scitation.org/journal/jcp Modern quantum chemistry with [Open]Molcas Cite as: J. Chem. Phys. 152, 214117 (2020); doi: 10.1063/5.0004835 Submitted: 17 February 2020 • Accepted: 11 May 2020 • Published Online: 5 June 2020 Francesco Aquilante,1,a) Jochen Autschbach,2,b) Alberto Baiardi,3,c) Stefano Battaglia,4,d) Veniamin A. Borin,5,e) Liviu F. Chibotaru,6,f) Irene Conti,7,g) Luca De Vico,8,h) Mickaël Delcey,9,i) Ignacio Fdez. Galván,4,j) Nicolas Ferré,10,k) Leon Freitag,3,l) Marco Garavelli,7,m) Xuejun Gong,11,n) Stefan Knecht,3,o) Ernst D. Larsson,12,p) Roland Lindh,4,q) Marcus Lundberg,9,r) Per Åke Malmqvist,12,s) Artur Nenov,7,t) Jesper Norell,13,u) Michael Odelius,13,v) Massimo Olivucci,8,14,w) Thomas B. -
Arxiv:1911.06836V1 [Physics.Chem-Ph] 8 Aug 2019 A
Multireference electron correlation methods: Journeys along potential energy surfaces Jae Woo Park,1, ∗ Rachael Al-Saadon,2 Matthew K. MacLeod,3 Toru Shiozaki,2, 4 and Bess Vlaisavljevich5, y 1Department of Chemistry, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Korea. 2Department of Chemistry, Northwestern University, 2145 Sheridan Rd., Evanston, IL 60208, USA. 3Workday, 4900 Pearl Circle East, Suite 100, Boulder, CO 80301, USA. 4Quantum Simulation Technologies, Inc., 625 Massachusetts Ave., Cambridge, MA 02139, USA. 5Department of Chemistry, University of South Dakota, 414 E. Clark Street, Vermillion, SD 57069, USA. (Dated: November 19, 2019) Multireference electron correlation methods describe static and dynamical electron correlation in a balanced way, and therefore, can yield accurate and predictive results even when single-reference methods or multicon- figurational self-consistent field (MCSCF) theory fails. One of their most prominent applications in quantum chemistry is the exploration of potential energy surfaces (PES). This includes the optimization of molecular ge- ometries, such as equilibrium geometries and conical intersections, and on-the-fly photodynamics simulations; both depend heavily on the ability of the method to properly explore the PES. Since such applications require the nuclear gradients and derivative couplings, the availability of analytical nuclear gradients greatly improves the utility of quantum chemical methods. This review focuses on the developments and advances made in the past two decades. To motivate the readers, we first summarize the notable applications of multireference elec- tron correlation methods to mainstream chemistry, including geometry optimizations and on-the-fly dynamics. Subsequently, we review the analytical nuclear gradient and derivative coupling theories for these methods, and the software infrastructure that allows one to make use of these quantities in applications. -
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. -
Trends in Atomistic Simulation Software Usage [1.3]
A LiveCoMS Perpetual Review Trends in atomistic simulation software usage [1.3] Leopold Talirz1,2,3*, Luca M. Ghiringhelli4, Berend Smit1,3 1Laboratory of Molecular Simulation (LSMO), Institut des Sciences et Ingenierie Chimiques, Valais, École Polytechnique Fédérale de Lausanne, CH-1951 Sion, Switzerland; 2Theory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l’Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; 3National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; 4The NOMAD Laboratory at the Fritz Haber Institute of the Max Planck Society and Humboldt University, Berlin, Germany This LiveCoMS document is Abstract Driven by the unprecedented computational power available to scientific research, the maintained online on GitHub at https: use of computers in solid-state physics, chemistry and materials science has been on a continuous //github.com/ltalirz/ rise. This review focuses on the software used for the simulation of matter at the atomic scale. We livecoms-atomistic-software; provide a comprehensive overview of major codes in the field, and analyze how citations to these to provide feedback, suggestions, or help codes in the academic literature have evolved since 2010. An interactive version of the underlying improve it, please visit the data set is available at https://atomistic.software. GitHub repository and participate via the issue tracker. This version dated August *For correspondence: 30, 2021 [email protected] (LT) 1 Introduction Gaussian [2], were already released in the 1970s, followed Scientists today have unprecedented access to computa- by force-field codes, such as GROMOS [3], and periodic tional power. -
Porting the DFT Code CASTEP to Gpgpus
Porting the DFT code CASTEP to GPGPUs Toni Collis [email protected] EPCC, University of Edinburgh CASTEP and GPGPUs Outline • Why are we interested in CASTEP and Density Functional Theory codes. • Brief introduction to CASTEP underlying computational problems. • The OpenACC implementation http://www.nu-fuse.com CASTEP: a DFT code • CASTEP is a commercial and academic software package • Capable of Density Functional Theory (DFT) and plane wave basis set calculations. • Calculates the structure and motions of materials by the use of electronic structure (atom positions are dictated by their electrons). • Modern CASTEP is a re-write of the original serial code, developed by Universities of York, Durham, St. Andrews, Cambridge and Rutherford Labs http://www.nu-fuse.com CASTEP: a DFT code • DFT/ab initio software packages are one of the largest users of HECToR (UK national supercomputing service, based at University of Edinburgh). • Codes such as CASTEP, VASP and CP2K. All involve solving a Hamiltonian to explain the electronic structure. • DFT codes are becoming more complex and with more functionality. http://www.nu-fuse.com HECToR • UK National HPC Service • Currently 30- cabinet Cray XE6 system – 90,112 cores • Each node has – 2×16-core AMD Opterons (2.3GHz Interlagos) – 32 GB memory • Peak of over 800 TF and 90 TB of memory http://www.nu-fuse.com HECToR usage statistics Phase 3 statistics (Nov 2011 - Apr 2013) Ab initio codes (VASP, CP2K, CASTEP, ONETEP, NWChem, Quantum Espresso, GAMESS-US, SIESTA, GAMESS-UK, MOLPRO) GS2NEMO ChemShell 2%2% SENGA2% 3% UM Others 4% 34% MITgcm 4% CASTEP 4% GROMACS 6% DL_POLY CP2K VASP 5% 8% 19% http://www.nu-fuse.com HECToR usage statistics Phase 3 statistics (Nov 2011 - Apr 2013) 35% of the Chemistry software on HECToR is using DFT methods. -
A Tutorial for Theodore 2.0.2
A Tutorial for TheoDORE 2.0.2 Felix Plasser, Patrick Kimber Loughborough, 2019 Department of Chemistry – Loughborough University Contents 1 Before Starting3 1.1 Introduction . .3 1.2 Notation . .3 1.3 Installation . .3 2 Natural transition orbitals (Turbomole)4 2.1 Input generation . .4 2.2 Transition density matrix (1TDM) analysis . .5 2.3 Plotting of the orbitals . .6 3 Charge transfer number and exciton analysis (Turbomole)9 3.1 Input generation . .9 3.2 Transition density matrix (1TDM) analysis . 10 3.3 Electron-hole correlation plots . 11 4 Interface to the external cclib library (Gaussian 09) 12 4.1 Check the log file . 12 4.2 Input generation . 13 4.3 Transition density matrix (1TDM) analysis . 15 5 Advanced fragment input and double excitations (Columbus) 16 5.1 Fragment preparation using Avogadro . 17 5.2 Input generation . 18 5.3 Transition density matrix (1TDM) analysis . 19 6 Fragment decomposition for a transition metal complex 21 6.1 Input generation . 21 6.2 Transition density matrix analysis and decomposition . 23 7 Domain NTO and conditional density analysis 26 7.1 Input generation . 26 1 7.2 Transition density matrix analysis . 28 7.3 Plotting of the orbitals . 29 8 Attachment/detachment analysis (Molcas - natural orbitals) 31 8.1 Input generation . 31 8.2 State density matrix analysis . 32 8.3 Plotting of the orbitals . 33 9 Contact 34 TheoDORE tutorial 2 1 Before Starting 1.1 Introduction This tutorial is intended to provide an overview over the functionalities of the TheoDORE program package. Various tasks of different complexity are discussed using interfaces to dif- ferent quantum chemistry packages. -
Density Functional Theory for Transition Metals and Transition Metal Chemistry
REVIEW ARTICLE www.rsc.org/pccp | Physical Chemistry Chemical Physics Density functional theory for transition metals and transition metal chemistry Christopher J. Cramer* and Donald G. Truhlar* Received 8th April 2009, Accepted 20th August 2009 First published as an Advance Article on the web 21st October 2009 DOI: 10.1039/b907148b We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids. 1. Introduction chemical systems, in part because its cost scales more favorably with system size than does the cost of correlated WFT, and yet Density functional theory (DFT) describes the electronic states it competes well in accuracy except for very small systems. This of atoms, molecules, and materials in terms of the three- is true even in organic chemistry, but the advantages of DFT dimensional electronic density of the system, which is a great are still greater for metals, especially transition metals. The simplification over wave function theory (WFT), which involves reason for this added advantage is static electron correlation. a3N-dimensional antisymmetric wave function for a system It is now well appreciated that quantitatively accurate 1 with N electrons. Although DFT is sometimes considered the electronic structure calculations must include electron correlation. B ‘‘new kid on the block’’, it is now 45 years old in its modern It is convenient to recognize two types of electron correlation, 2 formulation (more than half as old as quantum mechanics the first called dynamical electron correlation and the second 3,4 itself), and it has roots that are almost as ancient as the called static correlation, near-degeneracy correlation, or non- Schro¨ dinger equation. -
Lawrence Berkeley National Laboratory Recent Work
Lawrence Berkeley National Laboratory Recent Work Title From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape. Permalink https://escholarship.org/uc/item/4sm897jh Journal Chemical reviews, 121(8) ISSN 0009-2665 Authors Kowalski, Karol Bair, Raymond Bauman, Nicholas P et al. Publication Date 2021-04-01 DOI 10.1021/acs.chemrev.0c00998 Peer reviewed eScholarship.org Powered by the California Digital Library University of California From NWChem to NWChemEx: Evolving with the computational chemistry landscape Karol Kowalski,y Raymond Bair,z Nicholas P. Bauman,y Jeffery S. Boschen,{ Eric J. Bylaska,y Jeff Daily,y Wibe A. de Jong,x Thom Dunning, Jr,y Niranjan Govind,y Robert J. Harrison,k Murat Keçeli,z Kristopher Keipert,? Sriram Krishnamoorthy,y Suraj Kumar,y Erdal Mutlu,y Bruce Palmer,y Ajay Panyala,y Bo Peng,y Ryan M. Richard,{ T. P. Straatsma,# Peter Sushko,y Edward F. Valeev,@ Marat Valiev,y Hubertus J. J. van Dam,4 Jonathan M. Waldrop,{ David B. Williams-Young,x Chao Yang,x Marcin Zalewski,y and Theresa L. Windus*,r yPacific Northwest National Laboratory, Richland, WA 99352 zArgonne National Laboratory, Lemont, IL 60439 {Ames Laboratory, Ames, IA 50011 xLawrence Berkeley National Laboratory, Berkeley, 94720 kInstitute for Advanced Computational Science, Stony Brook University, Stony Brook, NY 11794 ?NVIDIA Inc, previously Argonne National Laboratory, Lemont, IL 60439 #National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6373 @Department of Chemistry, Virginia Tech, Blacksburg, VA 24061 4Brookhaven National Laboratory, Upton, NY 11973 rDepartment of Chemistry, Iowa State University and Ames Laboratory, Ames, IA 50011 E-mail: [email protected] 1 Abstract Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. -
Statistics of Software Package Usage in Supercomputer Complexes
Statistics of Software Package Usage in Supercomputer Complexes Pavel Shvets, Vadim Voevodin, and Sergey Zhumatiy Research Computing Center of Lomonosov Moscow State University, Moscow, Russia [email protected] Abstract. Any modern high-performance computing system is a very sophisticated complex that contains a variety of hardware and software components. Performance of such systems can be high, but it reaches its maximum only if all components work consistently and parallel applica- tions efficiently use provided computational resources. The steady trend of all recent years concerning large supercomputing centers { constant growth of the share of supercomputer applications that use off-the-shelf application packages. From this point of view, supercomputer software infrastructure starts to play a significant role in the efficient supercom- puter management as a whole. In this paper we will show why the analysis of software package efficiency should be taken seriously, what is worth paying attention to, and how this type of analysis can be conducted within the supercomputer complex. Keywords: parallel computing · high-performance computing · super- computer · efficiency · efficiency analysis · software package · job flow · monitoring data 1 Introduction Low efficiency of supercomputer system functioning has been an actual problem in high-performance computing field for many years. Over the years, many pos- sible approaches and methods have been developed for analysis and optimization of both individual supercomputer applications and entire supercomputer func- tioning as a whole. Due to increasing large-scale use of this area, i.e. growing number of users of supercomputer systems, as well as the progress in the develop- ment of HPC packages, off-the-shelf software packages are more and more often used for solving different scientific problems.