Path density for OpenPathSampling

Module path density implements path density calculations for the OpenPathSampling (OPS) package, including a generic multidimensional sparse histogram, and plotting functions for the two-dimensional case. Path density plots provide a way to visualize kinetic information obtained from path sampling, such as the mechanism of a rare event. In addition, the code in this module can also be used to visualize thermodynamic information such as free energy landscapes.

This module has been incorporated into the core of OPS, an open-source Python package for path sampling that wraps around other classical Molecular Dynamics (MD) codes [1]. An easy-to-read article on the use of path sampling methods to study rare events, and the role of the OPS package to performing these simulations can be found here.

At first glance, a typical path density plot may appear similar to a two-dimensional free energy landscape plot. They are both “heatmap”-type plots, plotting a two-dimensional histogram in some pair of collective variables. However, path density differs from free energy in several important respects:

  • A path density plot is histogrammed according to the number of paths, not the number of configurations. So if a cell is visited more than once during a path, it still only gets counted once.
  • A path density plot may interpolate across cells that the path jumps over. This is because it is assumed that the input must actually be continuous.

These differences can prevent metastable regions from overwhelming the transition regions in the plot. When looking at mechanisms, the path density is a more useful tool than the raw configurational probability.

Module documentation can be found here, including a link to the source code. This and other software modules for studying the thermodynamics and kinetics of rare events where recently documented in deliverable D1.2.: Classical MD E-CAM modules I, available here.

Motivation and exploitation

The path density is one of the most important tools for visualizing mechanisms, and is often one of the first things to analyze in order to draw scientific conclusions about the mechanism from transition path sampling simulations. This module was used to illustrate the differences between dynamics of the wild-type and oncogenic mutant forms of KRas, as part of one student’s master’s thesis and another student’s bachelor’s thesis at the University of Amsterdam. Results from those projects are currently in preparation for publication [2].

 

[1] Jan-Hendrik Prinz, David W.H. Swenson, Peter G. Bolhuis, and John D. Chodera. OpenPathSampling: A Python framework for path sampling simulations. I. Introduction and usage. In prep.
[2] Sander Roet, Ferry Hooft, Peter G. Bolhuis, David W.H. Swenson, and Jocelyne Vreede. Simulating the dynamics of oncogenic and wild-type KRas. In prep.

Share

Second-Order Differencing Scheme

This module, SodLib, provides exact wavefunction propagation using the second-order differencing (SOD) integrator scheme to solve the time-dependent Schrödinger equation as described by Leforestier et al, J. Comp Phys, 94, 59-80, 1991. Within this scheme the time interval is determined through dividing hbar by the eigenvalue of the Hamiltonian operator with the largest absolute value. This routine has been implemented and tested as an added functionality within the Quantics software package available through CCPForge.

Quantics is a package to study chemical reactions of molecules whose main developer (G. Worth, University College London) is a member of E-CAM’s WP3 – Quantum Dynamics. It incorporates a variety of quantum dynamical methods joined by the fact that the state system is usually described via wavefunctions (containing the quantum analogue of the information given by positions and velocities for classical atoms). It is increasingly used by the computational chemistry community for scientific applications. Work is on-going in E-CAM to improve its scalability (see E-CAM deliverable D7.2 ) and add new functionalities in view of applications to study materials and light harvesting complexes.

Module documentation can be found here, including a link to the source code.

Practical application and exploitation of the code

The module is currently being used in a Phd thesis and the results of this application will provide benchmarks for a model describing proton-transfer in a condensed phase system.

 

Share

A Conversation on Neural Networks, from Polymorph Recognition to Acceleration of Quantum Simulations

 

With Prof. Christoph Dellago (CD), University of Vienna, and Dr. Donal Mackernan (DM), University College Dublin.

 

Abstract

Recently there has been a dramatic increase in the use of machine learning in physics and chemistry, including its use to accelerate simulations of systems at an ab-initio level of accuracy, as well as for pattern recognition. It is now clear that these developments will significantly increase the impact of simulations on large scale systems requiring a quantum level of treatment, both for ground and excited states. These developments also lend themselves to simulations on massively parallel computing platforms, in many cases using classical simulation engines for quantum systems.

 

Continue reading…

Share

First GPU version of the DL_MESO_DPD code

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. E-CAM’s Work-package 4 (WP4), Meso and Multi-scale Modelling, makes use of the DL_MESO_DPD code. See this article on our news feed, for more information on how it is used within E-CAM.

In order to accelerate the DL_MESO_DPD code on the latest and future exascale hardware, a first version for NVidia GPUs has been developed. This is only a starting point, it does not yet cover all the possible cases and it does not yet support multiple GPUs. However, it represents an HPC milestone for the application, complementing the already present parallel versions developed for shared and distributed memory (MPI/OpenMP).

Module documentation including purpose, testing and background information, can be found here. The GPU-version to CPU-version performance analysis can be found in the module documentation and in deliverable D7.2.: E-CAM software porting and benchmarking data I, recently submitted to the EU.

[1] Michael A. Seaton, Richard L. Anderson, SebastianMetz, andWilliamSmith. DL_meso: highly scalable mesoscale simulations. Molecular Simulation, 39(10):796–821, September 2013.

Share

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.

Continue reading…

Share

Rare events, path sampling and the OpenPathSampling package

 

In the last few years, modelling of rare events has made tremendous progress and several computational methods have been put forward to study these events. Despite this effort, new approaches have not yet been included, with adequate efficiency and scalability, in common simulation packages. One objective of the Classical Dynamics Work Package of the project E-CAM is to close this gap. The present text is an easy-to-read article on the use of path sampling methods to study rare events, and the role of the OpenPathSampling package to performing these simulations. Practical applications of rare events sampling and scalabilities opportunities in OpenPathSampling are also discussed.

Continue reading…

Share

LibOMM : Orbital Minimization Method Library

Purpose

The library LibOMM solves the Kohn-Sham equation as a generalized eigenvalue problem for a fixed Hamiltonian. It implements the orbital minimization method (OMM), which works within a density matrix formalism. The basic strategy of the OMM is to find the set of Wannier functions (WFs) describing the occupied subspace by direct unconstrained minimization of an appropriately-constructed functional. The density matrix can then be calculated from the WFs. The solver is usually employed within an outer self-consistency (SCF) cycle. Therefore, the WFs resulting from one SCF iteration can be saved and then re-used as the initial guess for the next iteration.

More information on the module’s documentation can be found here, and the source code is available from the E-CAM Gitlab here. The algorithms and implementation of the library are described in https://arxiv.org/abs/1312.1549v1.

This module is an effort from the Electronic Structure Library Project (ESL), and it was initiated during an E-CAM Extended Software Development Workshop in Zaragoza in June 2016. This and other codes revolved around the broad theme of solvers, were recently reported in Deliverable D2.1.: Electronic structure E-CAM modules I, available for download and consultation here.

Practical application and exploitation of the module

libOMM is one of the libraries supported and enhanced by the Electronic Structure Infrastructure ELSI [1], which in turn is interfaced with the DGDFT, FHI-aims, NWChem, and SIESTA codes.

[1] The electronic structure infrastructure ELSI  provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, molecular biochemistry, and many other fields [https://arxiv.org/abs/1705.11191v1].

Share

AI Quantum Breakthrough: ANAKIN-ME Webinar

The development of a new methodology, known as Accurate NeurAl networK engINe for Molecular Energies (ANAKIN-ME, or ANI for short), is able, it is claimed,  to describe the forces in molecules as accurately as density functional theory (DFT), but hundreds of thousands of times faster. This combination of speed and accuracy could allow researchers to tackle problems that were previously impossible, leading to breakthroughs in the arenas of drug discovery and materials science.  Details of the method by J. S. Smith  O. Isayev   and  A. E. Roitberg built on earlier work of Michele Parrinello are available in a 2017 publication entitled “ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost” arXiv:1610.08935v4 .

The methodology  has been ported to NVIDIA, and will be the subject of a  webinar hosted by NVIDIA, University of Florida, University of North Carolina, on 20 September 2017 from 10am-11am PST . Sign up for the webinar here.

Share

Webinars series: Best Practices for HPC Software Developers

E-CAM strongly recommends software developers interested in HPC to attend the webinar series on Best Practices for HPC organized by the IDEAS project in collaboration with the DOE/ASCR computing facilities (ALCF, NERSC, and OLCF), and the Exascale Computing Project (ECP).

Information on the webinars programme available here.

Share

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.

Share