DOCSLIB.ORG

August 2019 LAMMPS Users' Workshop and Symposium Program

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
August 2019 LAMMPS Users' Workshop and Symposium Program August 2019 LAMMPS Users’ Workshop and Symposium Program The sixth LAMMPS Workshop and Symposium will be held in Albuquerque, NM, at the University of New Mexico (UNM) Continuing Education Building (1634 University Blvd NE, map). Thanks to our funders We thank the DOE/NNSA ASC program for support in hosting this workshop. We also thank these partners for graciously providing additional financial support: • Materials Design Inc., Tues lunch and coffee/snacks • JSOL Corp., Wed and Thurs lunches • Center for Non-Linear Studies (CNLS) at Los Alamos National Laboratory, travel expenses for several presenters Day 1: Tuesday August 13th, 2019 8:30 AM – 12:00 PM Beginners Tutorial Part I Coffee and bagels will be available 8:30 AM Welcome and Tutorial Overview, Axel Kohlmeyer (Temple U) 8:45 AM A Brief Overview of Molecular Dynamics, Statistical Mechanics, Atomic Potentials, Stan Moore (Sandia) 9:30 AM A Quick Tour of LAMMPS, Steve Plimpton (Sandia) Input scripts and output, classes of commands, basic & more advanced features, parallelism 10:15 AM Break 10:30 AM Self-Study Tutorial with Provided Exercises 12:00 PM - 1:00 PM Lunch in lobby (pizza, salad, lemonade and water) 1 PM - 5:30 PM Beginners Tutorial Part II, with 3 optional Intermediate Sessions 1:00 Continued Self-Study Tutorial with Provided Exercises or LAMMPS Examples 2:00 Advanced System building using VMD/TopoTools and LAMMPS, Axel Kohlmeyer (Temple U) 3:15 PM Break: Coffee and cookies will be available. 3:30 Compiling LAMMPS from Source, Richard Berger, Axel Kohlmeyer (Temple U) 4:00 OpenKIM Tutorial, Ryan Elliot and Ellad Tadmor (U Minnesota) 5:00 PM Dinner We will provide info and coordinate at the end of the tutorial on 2-3 nearby restaurants where we can gather and socialize for dinner. Car pooling is encouraged. • Matanza, 3225 Central Ave NE • Range Cafe, 2200 Menaul Blvd NE • Los Cuates, 4901 Lomas Blvd NE Day 2: Wednesday August 14th, 2019 8:30 AM – 12:00 PM General session of technical talks Session chair: Aidan Thompson (Sandia) Coffee and bagels will be available 8:30 Steve Plimpton, (Sandia National Labs) "Welcome and what's new in LAMMPS" 9:00 (keynote) Vasily Bulatov (Lawrence Livermore National Lab) Crossing Materials Scales with LAMMPS 9:45 (invited) Alex Stukowski (Darmstadt University of Technology) OVITO 3.0: A powerful data analysis and visualization solution for LAMMPS users 10:15 AM Break 10:30 Mitch Wood, Sandia National Labs Top-Down versus Bottom-Up Multiscale Modeling of Energetic Materials 10:45 Remi Dingreville, Sandia National Labs Insights into modeling radiation damage using atomistic simulations 10:30 Robert Elder, U.S. Army Research Laboratory Simulation studies of shock wave propagation and reflection in semi-crystalline polyethylene 11:00 Julien Tranchida, Sandia National Labs SPIN, a package for coupled spin and lattice simulations in LAMMPS 11:15 Javier Rojas, Universidad de Santiago de Chile Modulated strength on FeNi nanowires 11:30 Sungkwang Mun, Mississippi State University Modified Embedded Atom Method with Bond Order Implementation in LAMMPS 11:45 Andrew Rohskopf, MIT Vibrationally Accurate Interatomic Potentials 12:00 PM - 1:00 PM: Box lunches from UNM catering (lobby) 1:00 PM - 5:30 PM General Session of technical talks Session chair: Mitch Wood (Sandia) 1:00 (invited) Niels Gronbech-Jensen (UC Davis) Acquisition of Precise Statistics in Stochastic Langevin Molecular Dynamics 1:30 Kipton Barros, Los Alamos National Lab Building better datasets: active learning and transfer learning 1:45 Andrew Garmon, Clemson University Parallel Trajectory Splicing 2:00 Yidong Xia, Idaho National Laboratory Adaptive MPI for LAMMPS 2:15 Stan Moore, Sandia National Labs LAMMPS KOKKOS Package: The quest for performance portable MD 2:30 Lucas Hale, NIST Interatomic Potentials Repository and iprPy 2:45 Ellad Tadmor, University of Minnesota OpenKIM: A Repository of Tested Interatomic Potentials for use with LAMMPS 3:00 Ryan Elliott, University of Minnesota A How-To Tutorial on Using OpenKIM with LAMMPS 3:15 PM Break: Coffee and cookies will be available. 3:30 Dan Bolintineanu, Sandia National Labs Granular simulations with LAMMPS: enhanced contact models and applications to powder rheology 3:45 Huilin Ye, University of Connecticut A highly efficient and portable fluid-structure simulation package implemented in LAMMPS 4:00 Adrian Diaz, University of Florida CAC simulation with LAMMPS 4:15 Ketan Khare, NIST Quantitative Integration of Atomistic Simulation and Experiment for Cross-linked Epoxy Network 4:30 Allan Avila, University of California, Santa Barbara Modeling Hydrogen-Oxygen Combustion via Programmable Potentials 4:45 Jacob Gissinger, University of Colorado DisARMMD: Distance-Actuated Reaction Mechanisms in Molecular Dynamics 5:00 (invited) Susan Rempe (Sandia National Labs) Assessing Biomolecular Hydration Mimicry for Ion Permeation through Membrane Channels 6:00 No-host dinner and tram ride to top of Sandia Mountains We have a group reservation at the County Line Barbecue, 9600 Tramway Blvd NE, which is 13 miles from the UNM conf center, at the foot of the Sandia mountains. Car pooling encouraged. We've ordered the Cadillac family style menu (see page 2), which includes all-you-can-eat ribs, several other BBQ meats, sides, and homemade ice cream. Vegetarian options (e.g. kabobs) are also available. With tax and tip it comes to $38 per person. Pricey, but lunches are provided, and it's our one big workshop social event! After dinner, those who wish can join us to ride the ABQ Tram ($25) to the top of the mountain (6000 up to 10000 ft elevation) and see the city views and lights. Even in the summer it can be cool and windy on top, so it's a good idea to bring a light jacket or sweater. This is also a good test of whether you're scared of heights (1000 ft drop across the final canyon). Day 3: Thursday August 15th, 2019 8:30 AM - 10:30 AM General Session of technical talks Session chair: Stan Moore (Sandia) Coffee and bagels will be available 8:30 (invited) Ray Shan (Materials Design Inc.) High Value from High Throughput: Harness the Power of LAMMPS with MedeA 9:00 Christoph Kloss, DCS Computing Marketplace - towards an online gateway to materials modelling 9:15 Kosuke Ohata, JSOL Corporation Integrated simulation system for soft materials, J-OCTA 9:30 Andrew Jewett, The Scripps Research Institute General Agent Based Modeling in LAMMPS 9:45 Godehard Sutmann, Juelich Supercomputing Centre, Forschungszentrum Juelich A Load Balancing Library for Particle Simulation Codes 10:00 (invited) Xiang-Guo Li (UC San Diego) Quantum-accurate Force Fields from Machine Learning of Large Materials Data 10:30 AM Group photo (Matt Lane) 10:35 AM - 12:00 PM Poster Session Session chair: Julien Tranchida (Sandia) For the first time this year, we will have an award for the best poster, judged by a sophisticated machine learning algorithm (with possible human intervention). 10:35 AM One-minute poster advertisements 11:00 AM Posters in lobby See the list of posters at the end of this document 12:00 PM Box lunches from UNM catering (lobby) 12:55 PM Presentation of best poster award. This is being given in honor of Ahmed Ismail, a former collaborator of many of us at Sandia, and a LAMMPS contributor and user, who passed away this year. 1:00-5:30 PM Breakout Sessions (two parallel tracks A and B) Session chair: Aidan Thompson (Sandia) 1:00-1:15: one-minute breakout advertisements Track A 1:15-2:15 PM Pre- and post-processing tools & visualization (tutorial) Chaired by Mitch Wood (Sandia) Alex Stukowski (Darmstadt University of Technology) This presentation will demonstrate how to use OVITO with LAMMPS. Andrew Jewett (The Scripps Research Institute) "Creating molecular assemblies and force fields with Moltemplate" This presentation will demonstrate how to use Moltemplate, PACKMOL, and VIPSTER (time permitting). 2:15-3:15 PM Adding features to LAMMPS (tutorial) Presented by Richard Berger and Axel Kohlmeyer (Temple U) Topics: code structure, git, Github, best practices 3:15 PM Break: Coffee and cookies will be available. 3:30-4:30 PM Machine-learned interatomic potentials (contributed) Chaired by Thomas O'Connor (Sandia) 3:30 PM Ying Li, University of Connecticut Machine learning force field for polymer modeling 3:45 PM Chun-Wei Pao, Research Center for Applied Sciences, Academia Sinica Neural Network Potential of Complex Perovskite Materials and Their Implementation to LAMMPS 4:00 PM James Hickman, NIST Development of physically informed neural network (PINN) interatomic potentials 4:15 PM Mary Alice Cusentino, Sandia National Labs Machine Learned Interatomic Potentials for Modeling Plasma Material Interactions 4:30-5:30 PM Solid-state and soft materials (contributed) Chaired by Amalie Frischknecht (Sandia) 4:30 PM Tuan Ho, Sandia National Labs Molecular Simulation of the Multicomponent Interaction in Shale Nanopores 4:45 PM Rafael Gonzalez, Center for Applied Nanotechnology, Universidad Mayor Molecular simulations of carbon allotropes in processes with creation and destruction of chemical bonds 5:00 PM Omar Almahmoud, University of North Texas Water vapor diffusion in polyurethane silica nano-composite 5:15 PM Samuel Baltazar, Universidad de Santiago de Chile Nanostructurated systems for water remediation process Track B 1:15-2:15 PM VOTCA and LAMMPS for electronic spectroscopy and transport: Part I (tutorial) Chaired by Christoph Junghans (LANL) In this breakout (and the following one) you will learn how to use VOTCA to simulate electron/hole/exciton transport and compute optical spectra for organic molecules using LAMMPS trajectories. The 2 hours will start with a 25 min introduction and explanation of the theory and the implementation in VOTCA. This is followed by a hands-on session. If you want to participate in the hands-on session, please have docker installed on your laptop: • Windows: https://docs.docker.com/docker-for-windows/install/ • MacOs: https://docs.docker.com/docker-for-mac/ • Ubuntu: https://docs.docker.com/install/linux/docker-ce/ubuntu/ 2:15-3:15 PM VOTCA and LAMMPS for electronic spectroscopy and transport: Part II (tutorial) Chaired by Christoph Junghans (LANL) See description in previous breakout.
Load more

Recommended publications
  • Release 0.11 Todd Gamblin
    Spack Documentation Release 0.11 Todd Gamblin Feb 07, 2018 Basics 1 Feature Overview 3 1.1 Simple package installation.......................................3 1.2 Custom versions & configurations....................................3 1.3 Customize dependencies.........................................4 1.4 Non-destructive installs.........................................4 1.5 Packages can peacefully coexist.....................................4 1.6 Creating packages is easy........................................4 2 Getting Started 7 2.1 Prerequisites...............................................7 2.2 Installation................................................7 2.3 Compiler configuration..........................................9 2.4 Vendor-Specific Compiler Configuration................................ 13 2.5 System Packages............................................. 16 2.6 Utilities Configuration.......................................... 18 2.7 GPG Signing............................................... 20 2.8 Spack on Cray.............................................. 21 3 Basic Usage 25 3.1 Listing available packages........................................ 25 3.2 Installing and uninstalling........................................ 42 3.3 Seeing installed packages........................................ 44 3.4 Specs & dependencies.......................................... 46 3.5 Virtual dependencies........................................... 50 3.6 Extensions & Python support...................................... 53 3.7 Filesystem requirements........................................
    [Show full text]
  • VOTCA Manual
    VOTCA USER MANUAL December 5, 2020 Version: 1.6.2 (gitid: 23edb9f) Programs version: 1.6.2 gitid: 23edb9f © VOTCA development team www.votca.org ii Disclamer This manual is not complete. The best way to start using the software is to look at provided tutorials. The reference section is generated automatically from the source code, so please make sure that your software and manual versions match. Citations Development of this software depends on academic research grants. If you are using the package, please cite the following papers [1] Relative entropy and optimization-driven coarse-graining methods in VOTCA, S.Y. Mashayak, Mara Jochum, Konstantin Koschke, N.R. Aluru, Victor Rühle, and Christoph Junghans, PLoS one 10, e131754 (2015) [2] Hybrid approaches to coarse-graining using the VOTCA package: liquid hexane, Victor Rühle and Christoph Junghans, Macromol. Theory Simul. 20, 472 (2011) [3] Versatile Object-oriented Toolkit for Coarse-graining Applications Victor Rühle, Christoph Junghans, Alexander Lukyanov, Kurt Kremer, and Denis Andrienko J. Chem. Theor. Comp. 5, 3211, 2009 Development The core development is currently taking place at the Los Alamos National Laboratory and Max Planck Institute for Polymer Research, Mainz, Germany. Copyright votca is free software. The entire package is available under the Apache License. For details, check the LICENSE file in the source code. The votca source code is available on our homepage, www.votca.org. Contents 1 Introduction 1 2 Theoretical background 3 2.1 Mapping .......................................... 3 2.2 Boltzmann inversion ................................... 4 2.2.1 Separation of bonded and non-bonded degrees of freedom .......... 5 2.3 Iterative methods ....................................
    [Show full text]
  • Manual-5.0.7.Pdf
    GROMACS Groningen Machine for Chemical Simulations USER MANUAL Version 5.0.7 GROMACS USER MANUAL Version 5.0.7 Contributions from Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Par¨ Bjelkmar, Rudi van Drunen, Anton Feenstra, Sebastian Fritsch, Gerrit Groenhof, Christoph Junghans, Jochen Hub, Peter Kasson, Carsten Kutzner, Brad Lambeth, Per Larsson, Justin A. Lemkul, Erik Marklund, Peiter Meulenhoff, Teemu Murtola, Szilard´ Pall,´ Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Christian Wennberg and Maarten Wolf. Mark Abraham, Berk Hess, David van der Spoel, and Erik Lindahl. c 1991–2000: Department of Biophysical Chemistry, University of Groningen. Nijenborgh 4, 9747 AG Groningen, The Netherlands. c 2001–2015: The GROMACS development teams at the Royal Institute of Technology and Uppsala University, Sweden. More information can be found on our website: www.gromacs.org. iv Preface & Disclaimer This manual is not complete and has no pretention to be so due to lack of time of the contributors – our first priority is to improve the software. It is worked on continuously, which in some cases might mean the information is not entirely correct. Comments on form and content are welcome, please send them to one of the mailing lists (see www.gromacs.org), or open an issue at redmine.gromacs.org. Corrections can also be made in the GROMACS git source repository and uploaded to gerrit.gromacs.org. We release an updated version of the manual whenever we release a new version of the software, so in general it is a good idea to use a manual with the same major and minor release number as your GROMACS installation.
    [Show full text]
  • Simulating Soft Matter with Espresso, Espresso++ and VOTCA
    ESPResSo Summer School 2013 October 7 to October 11, University of Stuttgart Simulating Soft Matter with ESPResSo, ESPResSo++ and VOTCA Max Planck Institute http://www.espresso-pp.de for Polymer Research ESPResSo++ Key Features • ESPResSo++ is an open-source simulation package designed to perform molecular dynamics and monte carlo simulations of condensed matter systems using traditional and state-of-the-art techniques. • Flexibility due to Python/C++ integration Analysis Visualization • Extensibility due to object oriented design • Easy script-guided creation of complex NumPy SciPy PyMol VMD topologies • Quick incorporation of new interactions and analysis methods Python scripting • Use of standard short- and long range language interactions: e.G. Lennard-Jones, Stillinger- Weber, FENE, OPLS, Dihedrals, Ewald Advanced C++ Kernel Coulomb, etc. • Parallelization • Efficient implementation of advanced • Time-critical algorithms: e.G. (H-)AdResS, Parallel algorithms Tempering, dynamic bonds, etc. • Data storage • On-the-fly analysis and visualization • Extensible modular • Applicable to large systems and large numbers design of CPUs due to efficient parallelisation Outline of the talk • Simulating a dense polymer melt (general workflow) • Some things to know about python • Typical ESPResSo++ python script and ESPResSo++ modules hierarchy • System setup and basic classes - Some information about PMI in between • Inside ESPReSo++ an overview of the C++ class structure • Integrator, Interactions, Storage Outline of the afternoon tutorial session • Installation of ESPResSo++ • Basic System Setup • Simple Lennard Jones System • Advanced Lennard Jones System with graphical output • Polymer Melt Example: simulating a dense polymer melt System setup Create random polymer chains Warmup the system Equilibrate the system Snapshot of an equilibrated dense ring polymer melt, Output equilibrated number of chains Nc=200, chain length lc=200 particles, density ρ=0.85 [N/V3] configuration You will have time in the afternoon tutorial session to work with this example in more detail.
    [Show full text]
  • Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA
    RESEARCH ARTICLE Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA S. Y. Mashayak1, Mara N. Jochum2, Konstantin Koschke2, N. R. Aluru1, Victor Rühle3, Christoph Junghans4* 1 Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, United States of America, 2 Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany, 3 Department of Chemistry, University of Cambridge, Cambridge, United Kingdom, 4 Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of a11111 America * [email protected] Abstract OPEN ACCESS We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative Citation: Mashayak SY, Jochum MN, Koschke K, Aluru NR, Rühle V, Junghans C (2015) Relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water Entropy and Optimization-Driven Coarse-Graining and more complex water-methanol mixture systems. The CG potentials obtained from both Methods in VOTCA. PLoS ONE 10(7): e0131754. methods are then evaluated by comparing the pair distributions from the coarse-grained to doi:10.1371/journal.pone.0131754 the reference atomistic simulations. In addition to the newly implemented methods, we Editor: Xuhui Huang, Hong Kong University of have also added a parallel analysis framework to improve the computational efficiency of Science and Technology, HONG KONG the coarse-graining process. Received: November 12, 2014 Accepted: June 5, 2015 Published: July 20, 2015 Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, 1 Introduction transmitted, modified, built upon, or otherwise used In recent years, coarse-grained simulations have become an important tool for investigating by anyone for any lawful purpose.
    [Show full text]
  • Spack Documentation Release
    Spack Documentation Release Todd Gamblin May 18, 2017 Basics 1 Feature Overview 3 1.1 Simple package installation.......................................3 1.2 Custom versions & configurations....................................3 1.3 Customize dependencies.........................................4 1.4 Non-destructive installs.........................................4 1.5 Packages can peacefully coexist.....................................4 1.6 Creating packages is easy........................................4 2 Getting Started 7 2.1 Prerequisites...............................................7 2.2 Installation................................................7 2.3 Compiler configuration..........................................9 2.4 Vendor-Specific Compiler Configuration................................ 13 2.5 System Packages............................................. 16 2.6 Utilities Configuration.......................................... 18 2.7 Spack on Cray.............................................. 21 3 Basic Usage 23 3.1 Listing available packages........................................ 23 3.2 Installing and uninstalling........................................ 34 3.3 Seeing installed packages........................................ 36 3.4 Specs & dependencies.......................................... 38 3.5 Virtual dependencies........................................... 42 3.6 Extensions & Python support...................................... 44 3.7 Filesystem requirements......................................... 47 3.8 Getting Help..............................................
    [Show full text]
  • Manual-2016.Pdf
    GROMACS Groningen Machine for Chemical Simulations Reference Manual Version 2016 GROMACS Reference Manual Version 2016 Contributions from Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Sebastian Fritsch, Gerrit Groenhof, Christoph Junghans, Jochen Hub, Peter Kasson, Carsten Kutzner, Brad Lambeth, Per Larsson, Justin A. Lemkul, Erik Marklund, Peiter Meulenhoff, Teemu Murtola, Szilárd Páll, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Christian Wennberg and Maarten Wolf. Mark Abraham, Berk Hess, David van der Spoel, and Erik Lindahl. c 1991–2000: Department of Biophysical Chemistry, University of Groningen. Nijenborgh 4, 9747 AG Groningen, The Netherlands. c 2001–2018: The GROMACS development teams at the Royal Institute of Technology and Uppsala University, Sweden. More information can be found on our website: www.gromacs.org. iv Preface & Disclaimer This manual is not complete and has no pretention to be so due to lack of time of the contributors – our first priority is to improve the software. It is worked on continuously, which in some cases might mean the information is not entirely correct. Comments on form and content are welcome, please send them to one of the mailing lists (see www.gromacs.org), or open an issue at redmine.gromacs.org. Corrections can also be made in the GROMACS git source repository and uploaded to gerrit.gromacs.org. We release an updated version of the manual whenever we release a new version of the software, so in general it is a good idea to use a manual with the same major and minor release number as your GROMACS installation.
    [Show full text]
  • Meso– and Multi–Scale Modelling E-CAM Modules II E-CAM Deliverable 4.3 Deliverable Type: Other Delivered in March, 2018
    Meso– and multi–scale modelling E-CAM modules II E-CAM Deliverable 4.3 Deliverable Type: Other Delivered in March, 2018 E-CAM The European Centre of Excellence for Software, Training and Consultancy in Simulation and Modelling Funded by the European Union under grant agreement 676531 E-CAM Deliverable 4.3 Page ii Project and Deliverable Information Project Title E-CAM: An e-infrastructure for software, training and discussion in simulation and modelling Project Ref. Grant Agreement 676531 Project Website https://www.e-cam2020.eu EC Project Officer Juan PELEGRIN Deliverable ID D4.3 Deliverable Nature Other Dissemination Level Public Contractual Date of Delivery Project Month 28(January, 2018) Actual Delivery Date 30th March, 2018 Deliverable Description 9 software modules delivered to the E-CAM repository in the area of meso– and multi–scale modelling, based on user requests and their documenta- tion. Document Control Information Title: Meso– and multi–scale modelling E-CAM modules II ID: D4.3 Version: As of 30th March, 2018 Document Status: Accepted by WP leader Available at: https://www.e-cam2020.eu/deliverables Document history: Internal Project Management Link Review Review Status: Reviewed Written by: Burkhard Dünweg (DE-SMSM, Max Planck Institute for Polymer Research) Contributors: Jony Castagna and Silvia Chiacchiera (Science and Technology Facilities Authorship Council); Hideki Kobayashi (Max Planck Institute for Polymer Research); Christian Krekeler (Free University of Berlin) Reviewed by: Ana Catarina Mendonça (EPFL) Approved by: Burkhard Dünweg (Max Planck Institute for Polymer Research) Document Keywords Keywords: E-CAM, CECAM, Module, DL_MESO_DPD, ESPResSo++, GC-AdResS, GPU, DPD, dipole moments, polymer melts, equilibration, coarse–graining 30th March, 2018 Disclaimer:This deliverable has been prepared by the responsible Work Package of the Project in accordance with the Consortium Agreement and the Grant Agreement.
    [Show full text]
  • VOTCA Manual
    VOTCA USER MANUAL August 31, 2014 Version: 1.2.4 (867f09edac05) Programs version: 44f48249bf70 c VOTCA development team www.votca.org Contents 1 Introduction 1 2 Theoretical background 3 2.1 Mapping .......................................... 3 2.2 Boltzmann inversion ................................... 4 2.2.1 Separation of bonded and non-bonded degrees of freedom .......... 5 2.3 Iterative methods ..................................... 6 2.4 Iterative Boltzmann Inversion .............................. 6 2.5 Inverse Monte Carlo ................................... 6 2.6 Force Matching ...................................... 7 3 Input files 9 3.1 Mapping files ....................................... 9 3.2 Verification of a mapping ................................ 10 3.3 Advanced topology handling ............................... 10 3.4 Trajectories ........................................ 12 3.5 Setting files ........................................ 12 3.6 Table formats ....................................... 13 4 Preparing coarse-grained runs 15 4.1 Generating a topology file for a coarse-grained run .................. 15 4.2 Post-processing of the potential ............................. 15 4.2.1 Clipping of poorly sampled regions ....................... 16 4.2.2 Resampling .................................... 16 4.2.3 Extrapolation ................................... 16 4.2.4 Exporting the table ............................... 16 4.2.5 An example on non-bonded interactions .................... 17 4.3 Alternatives .......................................
    [Show full text]
  • Simulating Soft Matter with Espresso, Espresso++ and VOTCA
    http://www.icp.uni-stuttgart.de Institut für Computerphysik, Universität Stuttgart, Institut Universität Germany für Computerphysik, Stuttgart, ESPResSo, ESPResSo++ and VOTCA” and ESPResSo++ ESPResSo, Welcome to the Summer School Summer tothe Welcome “ http://www.icp.uni-stuttgart.de Matter with Soft Simulating http://www.icp.uni-stuttgart.de 2013 October 7-11 Olaf Lenz Olaf http://www.icp.uni-stuttgart.de Institut für Computerphysik, Universität Stuttgart, Institut Universität Germany für Computerphysik, Stuttgart, Simulating ESPResSo Institut für Computerphysik, Universität Stuttgart, Institut Universität Germany für Computerphysik, Stuttgart, ESPResSo, ESPResSo++ and VOTCA” and ESPResSo++ ESPResSo, Welcome to the Summer School Summer tothe Welcome ESPResSo, ESPResSo++ and VOTCA” and ESPResSo++ ESPResSo, Welcome to the Summer School Summer tothe Welcome Institut für Computerphysik, Universität Stuttgart, Institut Universität Germany für Computerphysik, Stuttgart, ESPResSo, ESPResSo++ and VOTCA” and ESPResSo++ ESPResSo, Welcome to the Summer School Summer tothe Welcome “ “ Simulating Soft Matter with Matter with Soft Simulating Simulating Soft Matter with Matter with Soft Simulating “ Simulating Soft Matter with Matter with Soft Simulating 6 7-11 October 2013 October 7-11 th SummerICP Schoolthe at 7-11 October 2013 October 7-11 Olaf Lenz Olaf 7-11 October 2013 October 7-11 Soft Matter ++ Olaf Lenz Olaf Olaf Lenz Olaf and MPI for Polymer Research, Mainz Research, Polymer for MPI VOTCA with ESPResSo 1 , Generic Program • Mornings (9:00-12:30)
    [Show full text]
  • Between the Scales: Water from Different Perspectives
    Between the Scales: Water from different Perspectives Dissertation zur Erlangung des Grades “Doktor der Naturwissenschaften” am Fachbereich Physik der Johannes Gutenberg-Universit¨at Mainz Christoph Junghans geb. in Merseburg Max-Planck-Institut f¨ur Polymerforschung Mainz, 9. August 2010 Tag der m¨undlichen Pr¨ufung: 29. Okt. 2010 Abstract Water is one of the most frequently studied fluids on earth. In this thesis, water was investigated at two resolutions using multi-scale computer simu- lation techniques. First, the atomistic and coarse-grained resolutions were studied separately. In the atomistic resolution, a water molecule is described chemically by three atoms, while in the coarse-grained case, a molecule is modeled by a sphere. In this work, various coarse-grained models have been developed using different coarse-graining techniques, mainly iterative Boltzmann inversion and iterative inverse Monte Carlo, which are structure-based approaches that aim to reproduce distributions, such as the pair distribution functions, of the atomistic model. In this context the Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) was developed. It was studied to which extent the coarse-grained models can simultane- ously reproduce several properties of the underlying atomistic model, such as thermodynamic properties like pressure and compressibility or structural properties, which have not been used in the coarse-graining process, e. g. the tetrahedral packing behavior, which is responsible for many special properties of water. Subsequently, these two resolutions were combined using the adaptive res- olution scheme, which combines the advantage of atomistic details in a small cavity of high resolution with the computational efficiency of the coarse- grained model in order to access larger time and length scales.
    [Show full text]
  • CADES Software List
    CADES Software list Software Type* Current versions Versions to Versions to disable Notes list on (C/L keep cades /A) open abaqus A 2019 (default) 2019 N/A aflow A 1.0 (default) 1.0 N/A amber A 16 (default); 18 16; 18 N/A Move default version from 16 to 18 AMS L 2018 2018 N/A anaconda2 A 5.1.0 (default) 5.1.0 N/A anaconda3 A 5.1.0 (default) 5.1.0 N/A ArmForge A 18.0 (default) 18.0 N/A ATLAS L 3.10.3 (default) 3.10.3 N/A autoconf A 2.69 (default) 2.69 N/A automake A 1.15 (default) 1.15 N/A bioconda A 09-18 09-18 N/A special build upon user request blas L 3.8.0 (default) 3.8.0 N/A blast L 2.10 2.10 N/A boost L 1.61.0; 1.64.0; 1.67.0 (default); 1.67.0-pe3; 1.67.0; 1.67.0-pe3; 1.61.0; 1.64.0 move default version to 1.69.0; 1.70.0 1.69.0; 1.70.0 1.70.0 bzip2 L 1.0.6 (default) 1.0.6 N/A caffe L 1.0 1.0 N/A cctools A 6.2.7 (default) 6.2.7 N/A cdo A 1.8.2 (default) 1.8.2 N/A cmake C 3.8.2; 3.11.0 (default); 3.11.4; 3.12.0 3.11.0; 3.11.4; 3.8.2 move default version to 3.12.0 3.12.0 conda-forge A 09-18 09-18 N/A special build upon user request cp2k A 5.1 (default); 6.1; 6.1-parallel; 7.0-cuda 6.1; 6.1- 5.1 move default version to parallel; 7.0-cuda 6.1 cuda A 8.0(default); 9.0; 9.2; 10.1; 11.0 9.2; 10.1; 11.0 8.0; 9.0 move default version to 11.0 cudnn L 7.1.4 7.1.4 N/A curl A 7.61.1 7.61.1 N/A darshan A 3.1.4 3.1.4 N/A dftbplus A 19.1; 19.1-mpi 19.1; 19.1-mpi N/A dgal L 3.0.1 (default) 3.0.1 N/A dl_poly A 4.09; 4.09_hpc 4.09; 4.09_hpc 4.09 special build upon user request DOCK A 6.9 6.9 N/A eden A clm clm N/A eigen3 L 3.3.7 3.3.7 N/A exodus L 5.14
    [Show full text]