Modules of the Month

  Description This module sets up the European Environment for Scientific Software Installations (EESSI) for use in GitHub Workflows. The European Environment for Scientific Software Installations (EESSI) is a collaboration […]Read More »

  This work relates to the implementation of a performance portable version of DL_MESO (DPD) using the Kokkos library. It focuses on porting to DL_MESO (DPD) the first and second loops […]Read More »

  This module improves the connection of n2p2 to HPC software, in particular to LAMMPS, by creating a pull request to the official LAMMPS repository. Furthermore, the build process for […]Read More »

  This module describes the work done in E-CAM in cooperation with the HemeLB code from the CompBioMed Centre of Excellence. HemeLB is a high performance lattice-Boltzmann solver optimised for […]Read More »

  Description The program performs Orbital-Free Density Functional Theory Molecular Dynamics (OF-DFT-MD) using the Mass-Zero (MaZe) constrained molecular dynamics approach described in [1]. This method enforces, at each time step, the […]Read More »

  Description This module concerns the implementation of the E-CAM Load Balancing Library (ALL) in the multi-GPU version of DL_MESO_DPD code. The intention is to allow for better performance when […]Read More »

  Description The module PerGauss (Per iodic Gauss ians) consists on an implementation of periodic boundary conditions for gaussian bases for the Quantics program package. In quantum dynamics, the choice of coordinates is crucial to […]Read More »

  For analysis of molecular dynamics (MD) simulations MDTraj is a fast and commonly used analysis. However MDTraj has some restrictions such as (1) the whole trajectory needs to fit into memory, […]Read More »

  Description CLstunfti is an extendable Python toolbox to compute scattering of electrons with a given kinetic energy in liquids and amorphous solids. It uses a continuum trajectory model with […]Read More »

  Description The module minDist2segments_KKT returns the minimal distance between two line segments. It uses the Karush-Kuhn-Tucker conditions (KKT) for the minimization under constraints. Practical application We use the present module to avoid […]Read More »

This module is the first in a sequence that will form the overall capabilities of the E-CAM High Throughout Computing (HTC) library. In particular this module deals with creating a […]Read More »

Maximally-localised Wannier functions (MLWFs) are routinely used to compute from first- principles advanced materials properties that require very dense Brillouin zone (BZ) integration and to build accurate tight-binding models for […]Read More »

Quantum Monte Carlo (QMC) methods are a class of ab initio, stochastic techniques for the study of quantum systems. While QMC simulations are computationally expensive, they have the advantage of […]Read More »

PANNA is a package for training and validating neural networks to represent atomic potentials. It implements configurable all-to-all connected deep neural network architectures which allow for the exploration of training […]Read More »

Description pyscal is a python module for the calculation of local atomic structural environments including Steinhardt’s bond orientational order parameters[1] during post-processing of atomistic simulation data. The core functionality of pyscal is […]Read More »

This module implements the first version of the DL_MESO_DPD Mesoscale Simulation Package, with multiple NVidia Graphical Processing Units (GPUs). In this module the main framework of a multi-GPU version of […]Read More »

This module shows how LAMMPS can be used as Molecular Dynamic (MD) engine in OpenPathSampling (OPS) and it also provide a benchmark for the impact of OPS overhead over the […]Read More »

FFTXlib is mainly a rewrite and optimisation of earlier versions of FFT related routines inside Quantum ESPRESSO (QE) pre-v6; and finally their replacement. Despite many similarities, current version of FFTXlib […]Read More »

Here present two featured software modules of the month: ParaDiS with precipitates ParaDiS with precipitates optimized to HPC environment that provide extensions to the ParaDIS Discrete dislocation dynamics (DDD) code […]Read More »

MatrixSwitch is a module which acts as an intermediary interface layer between high-level and low-level routines dealing with matrix storage and manipulation. It allows a seamlessly switch between different software implementations […]Read More »

The Grand Canonical Adaptive resolution scheme (GC-AdResS) gives a methodological description to partition a simulation box into different regions with different degrees of accuracy. For more details on the theory […]Read More »

The porting of DL_MESO_DPD [1,2] to graphic cards (GPUs) was reported in deliverable D4.2 of E-CAM[3] (for a single GPU) and deliverable D4.3 [4] (for multiple GPUs) (Figure 1), and […]Read More »

  CTMQC is a module for excited-state nonadiabatic dynamics. It is used to simulate the coupled dynamics of electrons and nuclei (ideally in gas phase molecular systems) in response to, […]Read More »

  Module SCDM_WFs implements the selected columns of the density matrix (SCDM) method [1] for building localized Wannier Functions (WFs). Wannier90 [2] is a post-processing tool for the computation of the Maximally Localised Wannier […]Read More »

  The QQ-Interface module connects the full quantum nonadiabatic wavefunction propagation code Quantics to the time-dependent density functional theory (TDDFT) module of the electronic structure program Q-Chem. Q-Chem provides analytic gradients, Hessians and […]Read More »

  PLUMED is a widely used and versatile rare-event sampling and analysis code that can be used with various Molecular Dynamics (MD) engines. It has a very intuitive and versatile […]Read More »

  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 […]Read More »

  PaPIM code is a package to study the (quantum) properties of materials, and in particular time correlation functions, via the so-called mixed quantum-classical methods. In these schemes, quantum evolution […]Read More »

  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, […]Read More »

  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 […]Read More »

  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 […]Read More »

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 […]Read More »

  Contacts can be an important tool for defining (meta)stable states in processes involving biomolecules. For example, an analysis of contacts can be particularly useful when defining bound states during […]Read More »

  The LocConQubit module implements the Local Control Theory[1,2], an algorithm for on-the-fly construction of a time-dependent potential that drives the evolution of a Hamiltonian towards one of its eigenstates. […]Read More »

GRASP_sampling performs a stratified sampling of the configurations, described by vectors, of a system to build a representative training set in a fitting procedure. Given a list of candidate configurations, […]Read More »

Geomoltools is a set of eight pre- and post-treatment Fortran codes that can be used to easily manipulate molecular geometries, allowing to minimize the average energy obtained for a range […]Read More »

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 […]Read More »

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, […]Read More »

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 […]Read More »

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 […]Read More »

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 […]Read More »

SQARE (solvers for quantum atomic radial equations) is a library of utilities intended for dealing with functions discretized on radial meshes, wave-equations with spherical symmetry and their corresponding quantum states. […]Read More »

Module ClassMC samples the system phase space using the classical Boltzmann distribution function and calculates the time correlation functions from the sampled initial conditions. For more information check the module […]Read More »

This module, based on OpenPathSampling, calculates the flux out of a state and through an interface, or the rate of the transition between two states, while running a trajectory. For […]Read More »