PIM_wd: Module for sampling of the quantum Wigner distribution

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The PIM_wd module implements the exact quantum Wigner probability distribution function sampling algorithm of the Phase Integration Method [1], and is the main subroutine for the quantum correlation function calculations in the PaPIM code. The module samples the thermal Wigner density using a generalised Monte Carlo scheme for sampling phase space points. The scheme combines the Penalty [2] and Kennedy [3] algorithms to sample noisy probability densities. This is necessary because the estimator of the quantum thermal density is not known analytically but must be computed via a statistical average affected by uncertainty. The sampled points are the basis for the calculation of time-independent and time-dependent system observables.

The module was developed as the main component of the PaPIM code, but also as a standalone subroutine that can be easily implemented in other methods (e.g. the whole family of so-called linearised approximations of quantum dynamics) for which phase space sampling of the exact quantum Wigner probability distribution is required. Because the Phase Integration Method samples a set of independent phase space points, independent instances of the PIM_wd module can be run in parallel in order to parallelise the phase space sampling. In the PaPIM package, the parallelisation is accomplished using MPI, which has proved to provide good scalability of the PaPIM code. The module will also be adapted for HTC capabilities.

Practical application and exploitation of the code

The code has been extensively used for the calculation of the infrared absorption spectrum of CH5+ in the gas phase. [4] This highly flexible molecule is considered a standard benchmark of approximate quantum methods, and has experimental interest, for example, in the context of green chemistry.

This module is part of the modules in deliverable D3.3 which were developed during the E-CAM ESDW7.

 

[1] M. Monteferrante, S. Bonella, G. Ciccotti Quantum dynamical structure factor of liquid neon via a quasiclassical symmetrized method J. Chem. Phys. 138 (2013) 054118

[2] D. M. Ceperley, M. Dewing The penalty method for random walks with uncertain energies J. Chem. Phys. 110 (1999) 9812

[3] A. D. Kennedy, J. Kuti Noise without Noise: A New Monte Carlo Method Phys. Rev. Lett. 54 (1985) 2473

[4] O. Asvany, P. K. P, B. Redlich, I. Hegemann, S. Schlemmer, D. Marx Understanding the infrared spectrum of bare CH5+ Science 309 (2005) 1219

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PRACE Workshop on HPC in Molecular and Atomistic Simulations @ICHEC

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ICHEC, in a collaboration with E-CAM, is organizing a funded PRACE course at the University College Dublin from 13th to 15th June 2018 for all interested in the use of HPC in their molecular and atomistic simulations. This course aims to provide a general overview of HPC and relevant applications for researchers involved in molecular and atomistic simulations, encompassing areas such as computational and physical chemistry. It is targeted mainly at researchers who may have little to no prior experience in using parallel applications on HPC systems. For more information click here.

 

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HPC-in-a-day Workshop

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A one day hands-on HPC workshop organized by CECAM, E-CAM and ICHEC was held at the University College Dublin on May 29, 2018. Continue reading…

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Issue 8 – May 2018

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E-CAM Newsletter of May 2018

 

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High Throughput Computing Workshop

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E-CAM is organising a one week (16-20 July 2018) Extended Software Development Workshop in Turin, Italy that will focus on intelligent high throughput computing (HTC) as a technique that crosses many domains within the molecular simulation community in general and the E-CAM community in particular. The workshop will be a hybrid learning/coding event targeted at scientists with particular problems to solve. There will be 3 days of tutorial content presenting 3 different task management frameworks and 2 days code development time with the framework developers to help you integrate them into your application. Continue reading…

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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.

Continue reading…

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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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New report published: Identification / Selection of E-CAM Electronic Structure Codes for Development

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Read our latest report on the state of the art codes and methods in Quantum Monte Carlo, Density Functional Theory (DFT) and beyond DFT methods. This report contains a review of the software available in these areas and on the basic features that the majority of these codes have in common with a view to modularisation. Based on that, a list of software development projects to be developed by E-CAM is discussed.

Full report available here.

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