Topics in Classical MD – Extended Software Development Workshop

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E-CAM is organising an Extended Software Development Workshop in Topics in Classical MD from 3 to 12 April 2019, which is a major coding initiative that will combine lectures; coding sessions and hands-on training.

Topics at this workshop will include using and extending modern MD software in the domains of:

  • advanced path sampling methods (and the software package OpenPathSampling)
  • metadynamics and the calculation of collective variables (and the software package PLUMED)
  • machine learning for molecular dynamics simulatons (including local structure recognition and representation of potential energy surfaces).

In addition, this workshop will feature an emphasis on performance testing and benchmarking software, with particular focus on high performance computing.

This is a great opportunity to bring your software development project in all specialist domains of Classical MD and spend two weeks in the beautiful city of Lyon with other peers and with experienced coders. More information and apply through the CECAM website at: https://www.cecam.org/workshop-1802.html.

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Two papers introducing OpenPathSampling, a software package to study rare events

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Two papers introducing to OpenPathSampling (OPS) were recently published : 

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9 software modules recently delivered in the area of Meso and Multi-scale Modelling

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In this report for Deliverable 4.4 [1]  of E-CAM, nine software modules in meso– and multi–scale modelling are presented. Four of the modules have been implemented in DL_MESO_DPD:

• Ewald method for the GPU version of DL_MESO_DPD

• Smooth Particle Mesh Ewald (SPME) method for the GPU version of DL_MESO_DPD

• Analysis of local tetrahedral ordering for DL_MESO_DPD[2]

• Consistency check of input files in DL_MESO_DPD[2]

Five of the modules concern the Grand Canonical Adaptive Resolution Scheme (GC-AdResS) and have been developed, implemented and tested in/with GROMACS 5.1.0 and GROMACS 5.1.5 [3]. The patches provided are for GROMACS 5.1.5. The modules provide a recipe to simplify the implementation and to allow to look into a microcanonical (i.e., NVE-like) environment. They are based on the same principles as the Abrupt AdResS modules reported in a previous deliverable D4.3[4].

Furthermore, we provide all the tools necessary to run and check the AdResS simulations. The modules are:

• Local Thermostat Abrupt AdResS

• Thermodynamic Force Calculator for Abrupt AdResS

• Energy (AT)/Energy(interface) ratio: Necessary condition for AdResS simulations

• Velocity-Velocity autocorrelation function for AdResS

• AdResS-Radial Distribution Function (RDF).

A short description is written for each module, followed by a link to the respective Merge-Request on the GitLab service of E-CAM. These merge requests contain detailed information about the code development, testing and documentation of the modules.

Full report available here.

[1] S. Chiacchiera, J. Castagna, and C. Krekeler, “Meso– and multi–scale modelling E-CAM modules III,” Jan. 2019. [Online]. Available: https://doi.org/10.5281/zenodo.2555012

[2] This work is part of an E-CAM pilot project focused on the development of Polarizable Mesoscale Models

[3] This work is part of an E-CAM pilot project focused on the development of the GC-AdResS scheme

[4] B. Duenweg, J. Castagna, S. Chiacchiera, H. Kobayashi, and C. Krekeler, “Meso– and multi–scale modelling E-CAM modules II,” Mar. 2018. [Online]. Available: https://doi.org/10.5281/zenodo.1210075

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Issue 9 – October 2018

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E-CAM Newsletter of October 2018

 

Get the latest news from E-CAM, sign up for our quarterly newsletter.

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E-CAM program of events 2019 is out

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Check out our program of events for this year, running from April 2019 to February 2020:

E-CAM Events 2019

See the details of each event to learn how to apply. E-CAM events are part of the annual CECAM flagship program, and are hosted at the different CECAM Nodes locations.

E-CAM runs three types of events every year:

  • Scoping workshops (SCOWs)
  • State-of-the-art workshop (SAWs)
  • Extended Software Development Workshops (ESDWs)

For their definition see here. If you require any further information contact us at info@e-cam2020.eu.

Apply now!

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Meet us at the PASC18 conference in Basel on 2-4 July 2018

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E-CAM will have an exhibition stand at the PASC18 Conference, that will be held from July 2 to 4, 2018 at the Congress Center Basel, Switzerland. PASC18

PASC18 is the fifth edition of the PASC Conference series, an international platform for the exchange of competences in scientific computing and computational science, with a strong focus on methods, tools, algorithms, application challenges, and novel techniques and usage of high performance computing. PASC18 is co-sponsored by the Association for Computing Machinery (ACM) and the Swiss National Supercomputing Centre (CSCS).

Meet us there!

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The launch of the E-CAM Online Training Portal

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We are pleased to announce that our E-CAM training portal is now online. Access instructions here.

The goals and expected impacts for our online training infrastructure are to:

  •   Collect the content captured at our Extended Software Development Workshops (ESDWs), allowing participants to re-visit lectures or demonstrations in their own time, both during and after the meeting. Such material can also be used by people who did not have the opportunity to attend the ESDW in person (particularly interested industries);
  •   Generate online training modules for each ESDW, which will be a set of preparatory materials shared with the participants of the event and that will allow everyone to acquire the same basic knowledge before the meeting;
  •   Be a repository for the data associated to our events, such as captured lectures, lecture materials, reading materials, tutorial content and software requirements;
  •   Build tutorials on programming best practices to develop software for extreme-scale hardware, that we can propose to the extended E-CAM community;
  •   Associate with other groups and projects with similar training scope, to cover for different and broader training material.

 

Information on the access to the portal, terminology and instructions for ESDW participants is at this link. The content of the training portal  is freely available upon registration, but we also keep a selection of publicly available lectures accessible directly from the E-CAM website.

 

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E-CAM Case Study: The implementation of a hierarchical equilibration strategy for polymer melts, to help studying the rheological properties of new composite materials

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Dr. Hideki Kobayashi, Max-Planck-Institut für Polymerforschung, Germany

Abstract

The ability to accurately determine and predict properties of newly developed polymer materials is highly important to researchers and industry, but at the same time represents a significant theoretical and computational challenge. We have developed a novel multiscale simulation method based on the hierarchical equilibration strategy, which significantly decreases the equilibrium properties calculation time while satisfying the thermodynamic consistency. A number of E-CAM modules was developed and implemented in he ESPResSo++ software package.

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Coarse-Graining module, a Component of the Hierarchical Equilibration Strategy for Polymer Melts

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To study the properties of polymer melts by numerical simulations, equilibrated configurations must be prepared. However, the relaxation time for high molecular weight polymer melts is huge and increases, according to reptation theory, with the third power of the molecular weight. Hence, an effective method for decreasing the equilibration time is required. The hierarchical strategy pioneered in Ref. [1] is a particularly suitable way to do this. The present module provides a part of that method.

To decrease the relaxation time, microscopic monomers are coarse-grained (CG) by mapping each subchain with N_{b} monomers onto a soft blob. The CG system is then characterized by a much lower molecular weight and thus is equilibrated quickly. The present module provides a python script which performs this coarse-graining procedure. The implementation details can be seen in the module’s documentation on our software Library here. This module is part of a set of codes that together implement the Hierarchical Equilibration strategy of Ref. [1], in the ESPResSO++ [2] (for the complete list of modules, see here under ESPResSO++).

 

Practical application and exploitation of the code

The development of a multiscale method for polymer blends and block copolymers is fundamentally new and needs to be based on first-principles theory. This is therefore an intellectual challenge in its own right. Furthermore, this paves the way to analyze the physical properties of novel composite materials that attract the attention of industrial companies. Such materials may be promising ingredients of new products like e.g. efficient and environment-friendly car tires. The implementation of the Hierarchical Equilibration strategy in the ESPResSO++ package is a step towards achieving this goal. In particular,  the practical application of this strategy is the E-CAM pilot project in collaboration with Michelin aimed at studying the Rheological Properties of New Composite Materials.

E-CAM deliverables D4.2 and D4.3 contain more information on the suite of programs developed under this pilot project.

 

[1] Zhang, G., Moreira, L. A., Stuehn, T., Daoulas, K. C., and Kremer, K., Equilibration of High Molecular Weight Polymer Melts: A Hierarchical Strategy, ACS Macro Lett., 3, 198-203 (2014)

[2] ESPResSo++ is the “Extensible Software Package for Research in Soft Matter based upon C++”, a general-purpose simulation package for soft-matter research, mainly developed at the Max Planck Institute for Polymer Research Mainz. It is freely available under the GNU Public License. http://www.espresso-pp.de/

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6 software modules recently delivered in the area of Quantum Dynamics

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In this report for Deliverable 3.3 of E-CAM [1], 6 software modules in quantum dynamics are presented. Four modules stem from some of the activities performed during the Extended Software Development Workshop (ESDW) held by E-CAM at University College Dublin in July 2017 and originate from input of E-CAM’s academic user base. The other two modules were developed following discussions with our industrial partner IBM, in the framework of E-CAM’s pilot project on Quantum Computing.

Following the order of presentation, the 6 modules are named: LocConQubit, OpenQubit, PaPIM, PIM_wd, PIM_qcf, Openmpbeads. They include code for generation of controlled pulses for qubits and for calculation of quantum time correlation functions and their documentation.

In this report, a short description is written for each module, followed by a link to the respective Merge-Request on theGitLab service of E-CAM. These merge requests contain detailed information about the code development, testing and documentation of the modules. A performance analysis for PaPIM, a package merging the functionality of several modules for quantum dynamics developed in E-CAM and structured to act as a high-performance container for future modules, is also presented. This analysis was performed by the E-CAM software group, in collaboration with the POP Center of Excellence for Computing Applications.

[1] S. Bonella, M. Mališ, A. O’Cais, and L. Liang, “D3.3.: Quantum dynamics e-cam modules ii,” Mar. 2018. [Online]. Available: https://doi.org/10.5281/zenodo.1210077.

Full report available here.

 

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