Spring shooting – A module for improving efficiency of transition path sampling

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Transition path sampling is most efficient when paths are generated from the top of the free energy barrier. However, complex (biomolecular) activated processes, such as nucleation or protein binding/unbinding, can have asymmetric and peaked barriers. Using uniform selection on these type of processes will not be efficient, as it, on average, results in selected points that are not on the top of the barrier. Paths generated from these points have a low acceptance probability and accepted transition paths decorrelate slowly, resulting in a low overall efficiency. The Spring shooting module was developed to increase the efficiency of path sampling of these types of barriers, without any prior knowledge of the barrier shape. The spring shooting algorithm uses a shooting point selector that is biased with a spring potential. This bias pulls the selection of points towards the transition state at the top of the barrier. The paths that are generated from points selected by this biased selector therefore have an increased acceptance probability and the decorrelation between accepted transition paths is also increased. This results in a higher overall efficiency. The spring shooting algorithm is described in more detail in a paper by Brotzakis and Bolhuis. [1]  This module was developed during the ESDW on classical molecular dynamics held in Amsterdam.

 

[1] Z. F. Brotzakis, P. G. Bolhuis A one-way shooting algorithm for transition path sampling of asymmetric barriers J. Chem. Phys. 145 (2016) 164112

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New publication is out: “Adaptive Resolution Molecular Dynamics Technique: Down to the Essential”

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A new publication by the Theoretical and Mathematical Physics in Molecular Simulation group of the Freie Universität Berlin, lead by Prof. Luigi Delle Site, E-CAM partner, was published in the Journal of Chemical Physics. In it, the authors study the application of the thermodynamic force in the coupling region of an adaptive resolution molecular dynamics simulation (AdResS) approach which assures thermodynamic equilibrium and proper exchange of molecules between atomistically resolved and coarse-grained regions.

The publication post-print version is open access and can be downloaded directly from the Zenodo repository here. The publisher AIP version can be found at https://doi.org/10.1063/1.5031206.

This work was performed in the context of the E-CAM pilot project on the development of the GC-AdResS scheme, which is a collaboration with MODAL AG. One of its goals is to develop a library or recipe with which GC-AdResS can be implemented in any MD Code. The current focus is to adjust the implemented version of GC-AdResS in GROMACS. The long-term goal of this project is to promote and stimulate the community to use it as a tool for multiscale simulations and analysis. More information about this pilot project can be found here.

Article

Title: Adaptive Resolution Molecular Dynamics Technique: Down to the Essential

Authors: Christian Krekeler, Animesh Agarwal, Christoph Junghans, Matej Praprotnik, Luigi Delle Site

Abstract: We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution Molecular Dynamics (MD) set-up, assures thermodynamic equilibrium between atomistically resolved and coarse-grained regions, allowing the proper exchange of molecules. We numerically prove that indeed for systems as relevant as liquid water and 1,3-dimethylimidazolium chloride ionic liquid, the combined action of the TD force and thermostat allows for computationally efficient and numerically accurate simulations, beyond the current capabilities of adaptive resolution set-ups, which employ switching functions in the coupling region.

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Symmetry Adapted Wannier Functions – a Component of the Wannier90

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Symmetry Adapted Wannier Functions is a module within Wannier90 which is devoted to the construction of Wannier function (WF) with a given symmetry. The procedure implemented in this module enables one to control the symmetry and center of the WFs and also simplifies the minimisation of the spread functional under these symmetry constraints.

This module is part of the nine modules reported in Deliverable D2.3 which together deal with the implementation of symmetry adapted WFs, to improve the symmetery of the WFs and related electronic-structure quantities, such as band structure and density of states; improvements in the interpolation of band structures, developments in the selection of the k-point mesh to increase accuracy, ability of performing non-collinear spin calculations as well as interface layer modules to tight-binding codes.

Starting from an E-CAM ESDW3 in San Sebastian organised by the Wannier90 developers, a set of nine modules were produced to meet the desire of the electronic-structure community to extend the use of WFs, and in particular of Maximally Localised Wannier Functions (MLWFs), to a broader class of physical and chemical problems by adding new functionality to the Wannier90 code.

All modules are accessible through the Wannier90 code, which in turn is interfaced with the all the most popular DFT codes. Wannier90 is used as a postprocessing tool. Therefore, the end users of electronic-structure codes, such as DFT, Tight Binding and Quantum Monte Carlo codes, that are interfaced with these modules via Wannier90, will benefit from the functionalities they provide, e.g. WFs with improved symmetry, spin-orbit calculations etc., and they can focus on developing new ideas, and new science without needing to rewrite functionalities that are already established.

Practical application and exploitation of the code

Wannier functions are an important class of functions which enable one to obtain a real-space picture of the electronic structure of a system. They provide an insightful chemical analysis of the nature of bonding, and chemical reaction in condensed-matter physics, similar to the role played by localised molecular orbitals in chemistry. They are also a powerful tool in the study of dielectric properties via the modern theory of polarisation. In the condensed-matter community WFs are employed in the construction of model Hamiltonians for, e.g., correlated-electron and magnetic systems (to study new quantum phases of matter) and are used as building blocks in first-principles Tight Binding Hamiltonians, where chemically accurate Hamiltonians are constructed directly on the Wannier basis, rather than fitted or inferred from macroscopic considerations. [1]

Wannier90 [2] is a program that, for a given system, generates the Wannier functions with minimum spatial spreads, known as MLWFs, among the class of all possible WFs. The locality of MLWFs can be exploited to compute, among other things, band-structure, density of states and Fermi surfaces at modest computational cost.

The developed modules have been used to study the properties of strongly correlated materials and to assess the quality of high-level quantum methods. [3]

 

[1] A. A. Mostofi, J. R. Yates, Y.-S. Lee, I. Souza, D. Vanderbilt, N. Marzari wannier90: A tool for obtaining maximally-localised wannier functions Comput. Phys. Commun 178 (2008) 685

[2] N. Marzari, A. A. Mostofi, J. R. Yates, I. Souza, D. Vanderbilt Maximally localized wannier functions: Theory and applications Rev. Mod. Phys. 84 (2012) 1419

[3] L. Boehnke, F. Nilsson, F. Aryasetiawan, P. Werner When strong correlations become weak: Consistent merging of GW and DMFT Phys. Rev. B 94 (2016) 201106

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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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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

 

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

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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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