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Benchmark Study of the Performance of Density
DOI: 10.1002/open.201300012 Benchmark Study of the Performance of Density Functional Theory for Bond Activations with (Ni,Pd)-Based Transition-Metal Catalysts Marc Steinmetz and Stefan Grimme*[a] The performance of 23 density functionals, including one LDA, due to partial breakdown of the perturbative treatment for the four GGAs, three meta-GGAs, three hybrid GGAs, eight hybrid correlation energy in cases with difficult electronic structures meta-GGAs, and ten double-hybrid functionals, was investigat- (partial multi-reference character). Only double hybrids either ed for the computation of activation energies of various cova- with very low amounts of perturbative correlation (e.g., PBE0- lent main-group single bonds by four catalysts: Pd, PdClÀ , DH) or that use the opposite-spin correlation component only PdCl2, and Ni (all in the singlet state). A reactant complex, the (e.g., PWPB95) seem to be more robust. We also investigated barrier, and reaction energy were considered, leading to 164 the effect of the D3 dispersion correction. While the barriers energy data points for statistical analysis. Extended Gaussian are not affected by this correction, significant and mostly posi- AO basis sets were used in all calculations. The best functional tive results were observed for reaction energies. Furthermore, for the complete benchmark set relative to estimated CCSD(T)/ six very recently proposed double-hybrid functionals were ana- CBS reference data is PBE0-D3, with an MAD value of 1.1 kcal lyzed regarding the influence of the amount of Fock exchange molÀ1 followed by PW6B95-D3, the double hybrid PWPB95-D3, as well as the type of perturbative correlation treatment. -
Supporting Information
Electronic Supplementary Material (ESI) for RSC Advances. This journal is © The Royal Society of Chemistry 2020 Supporting Information How to Select Ionic Liquids as Extracting Agent Systematically? Special Case Study for Extractive Denitrification Process Shurong Gaoa,b,c,*, Jiaxin Jina,b, Masroor Abroc, Ruozhen Songc, Miao Hed, Xiaochun Chenc,* a State Key Laboratory of Alternate Electrical Power System with Renewable Energy Sources, North China Electric Power University, Beijing, 102206, China b Research Center of Engineering Thermophysics, North China Electric Power University, Beijing, 102206, China c Beijing Key Laboratory of Membrane Science and Technology & College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China d Office of Laboratory Safety Administration, Beijing University of Technology, Beijing 100124, China * Corresponding author, Tel./Fax: +86-10-6443-3570, E-mail: [email protected], [email protected] 1 COSMO-RS Computation COSMOtherm allows for simple and efficient processing of large numbers of compounds, i.e., a database of molecular COSMO files; e.g. the COSMObase database. COSMObase is a database of molecular COSMO files available from COSMOlogic GmbH & Co KG. Currently COSMObase consists of over 2000 compounds including a large number of industrial solvents plus a wide variety of common organic compounds. All compounds in COSMObase are indexed by their Chemical Abstracts / Registry Number (CAS/RN), by a trivial name and additionally by their sum formula and molecular weight, allowing a simple identification of the compounds. We obtained the anions and cations of different ILs and the molecular structure of typical N-compounds directly from the COSMObase database in this manuscript. -
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. -
Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions
J. Chem. Theory Comput. XXXX, xxx, 000 A Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions Yan Zhao and Donald G. Truhlar* Department of Chemistry and Supercomputing Institute, UniVersity of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431 Received June 25, 2008 Abstract: The hybrid meta density functionals M05-2X and M06-2X have been shown to provide broad accuracy for main group chemistry. In the present article we make the functional form more flexible and improve the self-interaction term in the correlation functional to improve its self-consistent-field convergence. We also explore the constraint of enforcing the exact forms of the exchange and correlation functionals through second order (SO) in the reduced density gradient. This yields two new functionals called M08-HX and M08-SO, with different exact constraints. The new functionals are optimized against 267 diverse main-group energetic data consisting of atomization energies, ionization potentials, electron affinities, proton affinities, dissociation energies, isomerization energies, barrier heights, noncovalent complexation energies, and atomic energies. Then the M08-HX, M08-SO, M05-2X, and M06-2X functionals and the popular B3LYP functional are tested against 250 data that were not part of the original training data for any of the functionals, in particular 164 main-group energetic data in 7 databases, 39 bond lengths, 38 vibrational frequencies, and 9 multiplicity-changing electronic transition energies. These tests include a variety of new challenges for complex systems, including large-molecule atomization energies, organic isomerization energies, interaction energies in uracil trimers, and bond distances in crowded molecules (in particular, cyclophanes). -
Performance of DFT Procedures for the Calculation of Proton-Exchange
Article pubs.acs.org/JCTC Performance of Density Functional Theory Procedures for the Calculation of Proton-Exchange Barriers: Unusual Behavior of M06- Type Functionals Bun Chan,*,†,‡ Andrew T. B. Gilbert,¶ Peter M. W. Gill,*,¶ and Leo Radom*,†,‡ † School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia ‡ ¶ ARC Centre of Excellence for Free Radical Chemistry and Biotechnology and Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia *S Supporting Information ABSTRACT: We have examined the performance of a variety of density functional theory procedures for the calculation of complexation energies and proton-exchange barriers, with a focus on the Minnesota-class of functionals that are generally highly robust and generally show good accuracy. A curious observation is that M05-type and M06-type methods show an atypical decrease in calculated barriers with increasing proportion of Hartree−Fock exchange. To obtain a clearer picture of the performance of the underlying components of M05-type and M06-type functionals, we have investigated the combination of MPW-type and PBE-type exchange and B95-type and PBE-type correlation procedures. We find that, for the extensive E3 test set, the general performance of the various hybrid-DFT procedures improves in the following order: PBE1-B95 → PBE1-PBE → MPW1-PBE → PW6-B95. As M05-type and M06-type procedures are related to PBE1-B95, it would be of interest to formulate and examine the general performance of an alternative Minnesota DFT method related to PW6-B95. 1. INTRODUCTION protocol.13,14 In a recent study,15 however, it was shown that, Density functional theory (DFT) procedures1 are undeniably for complexation energies of water, ammonia and hydrogen the workhorse for many computational chemists. -
Computer-Assisted Catalyst Development Via Automated Modelling of Conformationally Complex Molecules
www.nature.com/scientificreports OPEN Computer‑assisted catalyst development via automated modelling of conformationally complex molecules: application to diphosphinoamine ligands Sibo Lin1*, Jenna C. Fromer2, Yagnaseni Ghosh1, Brian Hanna1, Mohamed Elanany3 & Wei Xu4 Simulation of conformationally complicated molecules requires multiple levels of theory to obtain accurate thermodynamics, requiring signifcant researcher time to implement. We automate this workfow using all open‑source code (XTBDFT) and apply it toward a practical challenge: diphosphinoamine (PNP) ligands used for ethylene tetramerization catalysis may isomerize (with deleterious efects) to iminobisphosphines (PPNs), and a computational method to evaluate PNP ligand candidates would save signifcant experimental efort. We use XTBDFT to calculate the thermodynamic stability of a wide range of conformationally complex PNP ligands against isomeriation to PPN (ΔGPPN), and establish a strong correlation between ΔGPPN and catalyst performance. Finally, we apply our method to screen novel PNP candidates, saving signifcant time by ruling out candidates with non‑trivial synthetic routes and poor expected catalytic performance. Quantum mechanical methods with high energy accuracy, such as density functional theory (DFT), can opti- mize molecular input structures to a nearby local minimum, but calculating accurate reaction thermodynamics requires fnding global minimum energy structures1,2. For simple molecules, expert intuition can identify a few minima to focus study on, but an alternative approach must be considered for more complex molecules or to eventually fulfl the dream of autonomous catalyst design 3,4: the potential energy surface must be frst surveyed with a computationally efcient method; then minima from this survey must be refned using slower, more accurate methods; fnally, for molecules possessing low-frequency vibrational modes, those modes need to be treated appropriately to obtain accurate thermodynamic energies 5–7. -
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. -
An Ion Mobility-Aided, Quantum Chemical Benchmark Analysis of H+GPGG Conformers Daniel Beckett, Tarick J
Article Cite This: J. Chem. Theory Comput. 2018, 14, 5406−5418 pubs.acs.org/JCTC Electronic Energies Are Not Enough: An Ion Mobility-Aided, Quantum Chemical Benchmark Analysis of H+GPGG Conformers Daniel Beckett, Tarick J. El-Baba, David E. Clemmer, and Krishnan Raghavachari* Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States *S Supporting Information ABSTRACT: Peptides and proteins exist not as single, lowest energy structures but as ensembles of states separated by small barriers. In order to study these species we must be able to correctly identify their gas phase conformational distributions, and ion mobility spectrometry (IMS) has arisen as an experimental method for assessing the gas phase energetics of flexible peptides. Here, we present a thorough exploration and benchmarking of the low energy conformers of the small, hairpin peptide H+GPGG with the aid of ion mobility ). spectrometry against a wide swath of density functionals (35 dispersion-corrected and uncorrected functionals represented by 21 unique exchange−correlation functionals) and wave function theory methods (15 total levels of theory). The three experimentally resolved IMS peaks were found to correspond to three distinct pairs of conformers, each pair composed of species differing only by the chair or boat configuration of the proline. Two of the H+GPGG conformer pairs possess a cis configuration about the Pro−Gly1 peptide bond while the other adopts a trans configuration. While the experimental spectrum reports a higher intensity for the o legitimately share published articles. cis-1 conformer than the trans conformer, 13 WFT levels of theory, including a complete basis set CCSD(T) extrapolation, obtain trans to be favored in terms of the electronic energy. -
Car-Parrinello Molecular Dynamics
CPMD Car-Parrinello Molecular Dynamics An ab initio Electronic Structure and Molecular Dynamics Program The CPMD consortium WWW: http://www.cpmd.org/ Mailing list: [email protected] E-mail: [email protected] January 29, 2019 Send comments and bug reports to [email protected] This manual is for CPMD version 4.3.0 CPMD 4.3.0 January 29, 2019 Contents I Overview3 1 About this manual3 2 Citation 3 3 Important constants and conversion factors3 4 Recommendations for further reading4 5 History 5 5.1 CPMD Version 1.....................................5 5.2 CPMD Version 2.....................................5 5.2.1 Version 2.0....................................5 5.2.2 Version 2.5....................................5 5.3 CPMD Version 3.....................................5 5.3.1 Version 3.0....................................5 5.3.2 Version 3.1....................................5 5.3.3 Version 3.2....................................5 5.3.4 Version 3.3....................................6 5.3.5 Version 3.4....................................6 5.3.6 Version 3.5....................................6 5.3.7 Version 3.6....................................6 5.3.8 Version 3.7....................................6 5.3.9 Version 3.8....................................6 5.3.10 Version 3.9....................................6 5.3.11 Version 3.10....................................7 5.3.12 Version 3.11....................................7 5.3.13 Version 3.12....................................7 5.3.14 Version 3.13....................................7 5.3.15 Version 3.14....................................7 5.3.16 Version 3.15....................................8 5.3.17 Version 3.17....................................8 5.4 CPMD Version 4.....................................8 5.4.1 Version 4.0....................................8 5.4.2 Version 4.1....................................8 5.4.3 Version 4.3....................................9 6 Installation 10 7 Running CPMD 11 8 Files 12 II Reference Manual 15 9 Input File Reference 15 9.1 Basic rules........................................ -
TURBOMOLE: Modular Program Suite for Ab Initio Quantum-Chemical and Condensed- Matter Simulations
TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed- matter simulations Cite as: J. Chem. Phys. 152, 184107 (2020); https://doi.org/10.1063/5.0004635 Submitted: 12 February 2020 . Accepted: 07 April 2020 . Published Online: 13 May 2020 Sree Ganesh Balasubramani, Guo P. Chen, Sonia Coriani, Michael Diedenhofen, Marius S. Frank, Yannick J. Franzke, Filipp Furche, Robin Grotjahn, Michael E. Harding, Christof Hättig, Arnim Hellweg, Benjamin Helmich-Paris, Christof Holzer, Uwe Huniar, Martin Kaupp, Alireza Marefat Khah, Sarah Karbalaei Khani, Thomas Müller, Fabian Mack, Brian D. Nguyen, Shane M. Parker, Eva Perlt, Dmitrij Rappoport, Kevin Reiter, Saswata Roy, Matthias Rückert, Gunnar Schmitz, Marek Sierka, Enrico Tapavicza, David P. Tew, Christoph van Wüllen, Vamsee K. Voora, Florian Weigend, Artur Wodyński, and Jason M. Yu COLLECTIONS Paper published as part of the special topic on Electronic Structure SoftwareESS2020 ARTICLES YOU MAY BE INTERESTED IN PSI4 1.4: Open-source software for high-throughput quantum chemistry The Journal of Chemical Physics 152, 184108 (2020); https://doi.org/10.1063/5.0006002 NWChem: Past, present, and future The Journal of Chemical Physics 152, 184102 (2020); https://doi.org/10.1063/5.0004997 CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations The Journal of Chemical Physics 152, 194103 (2020); https://doi.org/10.1063/5.0007045 J. Chem. Phys. 152, 184107 (2020); https://doi.org/10.1063/5.0004635 152, 184107 © 2020 Author(s). The Journal ARTICLE of Chemical Physics scitation.org/journal/jcp TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations Cite as: J. -
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.