E-CAM related work labeled as “Excellent Science” by the EC Innovation Radar Initiative

The Innovation Radar aims to identify high-potential innovations and innovators. It is an important source of actionable intelligence on innovations emerging from research and innovation projects funded through European Union programmes.

E-CAM is associated to the following Innovations (Innovation topic: excellence science):

    1. Improved Simulation Software Packages for Molecular Dynamics (see link)
    2. Improved software modules for Meso– and multi–scale modelling (see link)

Related to the work of our E-CAM funded Postdoctoral researchers supervised by scientists in the team, working on:

  • Development of the OpenPathSampling package to study rare events  (Universiteit van Amsterdam). Link1
  • Implementation of GPU version of DL_MESO_DPD (Hartree Centre (STFC)). Link
  • Development of polarizable mesoscale model for DL_MESO_DPD (Hartree Centre (STFC)). Link
  • Development of the GC-AdResS scheme (Freie Universitaet Berlin). Link

  • Implementation of hierarchical strategy on ESPResSO++ (Max Plank Institute for Polymer Research, Mainz). Link
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9 software modules recently delivered in the area of Meso and Multi-scale Modelling

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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E-CAM Case Study: Mesoscale models for polarisable solvents: application to oil-water interfaces

Dr. Silvia Chiacchiera, Science and Technology Facilities Council, United Kingdom

Abstract

Water is a polar liquid and has a dielectric permittivity much higher than typical apolar liquids, such as light oils. This strong dielectric contrast at water-oil interfaces affects electrostatics and is important, for example, to include these effects to describe biomolecular processes and water-oil mixtures involving surfactants, as detergents. In this pilot project, developed in collaboration with Unilever and Manchester University, we have proposed and analysed a class of polarisable solvent models to be used in Dissipative Particle Dynamics (DPD), a coarse-grained particle-based simulation method commonly used in various industrial sectors. Related software modules for the DL_MESO package have also been developed.

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Improving I/O of DL_MESO_DPD files using SIONlib

 

This module implements the SIONlib library to optimize the I/O (writing/reading) of the trajectory files generated by DL_MESO_DPD, the Dissipative Particle Dynamics (DPD) code from the DL_MESO package. SIONlib is a library for writing and reading binary data to/from several thousands of processors into one or a small number of physical files. For parallel access to files, only the open and close functions are collective, while the writing and reading of files can be done asynchronously. [1] In DL_MESO_DPD’s last release (version 2.6), the MPI version of DL_MESO_DPD generates multiple trajectory files, one for each MPI task. The interface with SIONlib optimizes the data writing so that just one physical file is produced from several MPI tasks. This drastic reduction in the number of output files is a benefit for the I/O of the code, and simplifies the maintenance of the output, especially for a large number of MPI tasks.

This module is part of the newly developed utilities for the DL_MESO_DPD code within the pilot project on Polarizable Mesoscale Models.

Practical application and exploitation of the code

The implementation of this module generates a single trajectory file (history.sion) in a parallel run of DL_MESO_DPD, instead of multiple (HISTORY) ones. Accordingly, analogous modifications have to be implemented in the post-processing utilities that read the HISTORY files. As an example, the changes were implemented in a formatting utility. Besides showing how to adapt the reading, this allows a robust check of the implementation, since the output is human readable, contains the full trajectories, and can be readily compared with outputs obtained using the standard version of DL_MESO_DPD.

The next released version of DL_MESO_DPD (in development) will tackle the writing of files differently, producing a single trajectory file from the start. However, the interface proposed here provides this feature to the users of version 2.6, and represents an alternative solution for the handling of the trajectories.

It should be noted that this implementation is meant to show the feasibility of the interfacing, not to deal with all the possible cases. Thus, the module’s functionality is restricted to the relevant case in which: i) the simulation is run in parallel using MPI, ii) a single SIONlib-type physical file is produced, and iii) the post-processing is done by a single process.

While SIONlib is optimized for a large number of MPI tasks, even the reduction from several output files to just one represents a benefit, for example when it comes to the maintenance of the simulation output.

 

[1] http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html

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New E-CAM modules based on DL_MESO_DPD

 

The software

DL_MESO_DPD, is the Dissipative Particle Dynamics (DPD) code from the mesoscopic simulation package DL_MESO[1], developed by Dr. Michael Seaton at Daresbury Laboratory (UK). This open source code is available from Science and Technology Facilities Council (STFC) under both academic (free) and commercial (paid) licenses.

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Analysis of charge dipole moments in DL_MESO_DPD

The present module, gen_dipole.f90, is a generalization of the dipole.f90 post-processing utility of DL_MESO_DPD, the Dissipative Particle Dynamics (DPD) code from the DL_MESO package. It processes the trajectory (HISTORY) files to obtain the charge dipole moments of all the (neutral) molecules in the system. It produces files dipole_* containing the time evolution of relevant quantities (see module documentation for more information). In the case of a single molecular species, it also prints to the standard output the Kirkwood number g_k and the relative electric permittivity \epsilon_r for this species, together with an estimate for their errors (standard error).

The module can be applied to systems including molecules with a generic charge structure, as long as each molecule is neutral (otherwise the charge dipole moment would be frame-dependent).

gen_dipole.f9 is available under BSD license, and is a post-processing utilities to be used with DL_MESO in its last released version, version 2.6 (dating November 2015). They have been developed in the context of the pilot project 1 of WP 4, which concerns the derivation of a realistic polarizable model of water to be used in DPD simulations. This project involves a collaboration between computational scientists (STFC Daresbury), academia (University of Manchester), and industry (Unilever). This and other modules based on DL_MESO_DPD have recently been reported in deliverable D4.2: Meso- and multi-scale modelling E-CAM modules I, available for consultation here.

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