Comics & Science ? The E-CAM issue: an experiment in dissemination
The E-CAM issue of Comics & Science has just been released on-line…and it’s just the beginning of the adventure! Identifying exciting and original tools to engage the general public […]Read More »E-CAM Final Report
E-CAM started in October 2015 and received funding from the European Union’s Horizon 2020 R&I program for a period of 66-months. Built around the scientific community of the Centre […]Read More »Issue 16 – April 2021
E-CAM Newsletter of April 2021 Get the latest news from E-CAM, sign up for our newsletter.Read More »Challenges to Industry of drug substance development
Computation based methods play a growing role in all stages of accelerated medicine pipelines responding to industry challenges of drug substance development. Abstract APC was created In 2011 by […]Read More »Development of an HTC-based, scalable committor analysis tool in OpenPathSampling opens avenues to investigate enzymatic mechanisms linked to Covid-19
The E-CAM HPC Centre of Excellence and a PRACE team in Wroclaw have teamed up to develop High Throughput Computing (HTC) based tools to enable the computational investigation of reaction […]Read More »Proof of concept : recognition as a disruptive technology
Abstract The transformation of a beautiful idea born via simulation into a commercial opportunity is recognised as a disruptive technology. At the heart of this ongoing story is advanced […]Read More »New publication is out: “Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook”
Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook Peter G. Bolhuis and David W. H. Swenson Adv. Theory Simul. 2021, […]Read More »EESSI-based GitHub Action for Continuous Integration
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 »March Module of the Month: DL_MESO (DPD) on Kokkos for enhanced performance portability
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 »March Module of the Month: n2p2 – Improved link to HPC MD software
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 »Implementation of High-Dimensional Neural Network Potentials
Abstract In this conversation with Andreas Singraber, post-doc in E-CAM until last month, we will discover the ensemble of his work to expand the Neural Network Potential (NNP) Package […]Read More »February Module of the Month: ALL library implementation in HemeLB, a CoE collaboration
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 »Industry training at the MESOSCALE
To further expand the portfolio of activities targeted at industrialists, E-CAM has established a series of new events targeted at training interested industrial researchers on the simulation and modelling […]Read More »Another successful online training event !
Our last Extended Software Development Workshop (ESDW) took place on the 18th-22nd January[1], and given its length (5 days) and it’s nature (theory and hands-on training sessions) it was […]Read More »January Module of the Month: MaZe, Mass-Zero Constrained Dynamics for Orbital Free Density Functional Theory
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 »Issue 15 – December 2020
E-CAM Newsletter of December 2020 Get the latest news from E-CAM, sign up for our newsletter.Read More »The ALL Load Balancing Library
Abstract Scalability of parallel applications depends on a number of characteristics, among which is efficient communication, equal distribution of work or efficient data lay-out. Especially for methods based on […]Read More »December Module of the Month: Load balancing for multi-GPU DL_MESO
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 »Proof of concept : Metamorphosis
Abstract The transformation of a beautiful idea born via simulation into a commercial opportunity is described as it progresses from proof of concept towards a product. At the heart […]Read More »New article: Quantum Monte Carlo determination of the principal Hugoniot of deuterium
A new article from E-CAM partners at the Maison de la Simulation (CEA, CNRS, Univ. Paris-Sud), have published a new article: Quantum Monte Carlo determination of the principal Hugoniot […]Read More »Conversation with the authors of the E-CAM Comics “Ekham the Wise”
During the making-of of the E-CAM Comics the collaboration with the founders and directors of the Comics&Science magazine, Roberto Natalini and Andrea Plazzi, and with the authors of the comics, Giovanni […]Read More »LearnHPC: dynamic creation of HPC infrastructure for educational purposes
Abstract In a newly successful PRACE-ICEI proposal, E-CAM, FocusCoE, HPC Carpentry and EESSI join forces to bring HPC resources to the classroom in a simple, secure and scalable way. […]Read More »November Module of the Month: PerGauss, Periodic Boundary Conditions for gaussian bases
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 »Registration open for Extended Software Development Workshop in HPC for Mesoscale Simulation
Few software, like DL_MESO, userMESO and LAMMPS, can currently simulate large Dissipative Particle Dynamics (DPD) simulations. In particular, DL_MESO [1, 2] has recently been ported to multi-GPU architectures and runs […]Read More »|QBN 〉 Webinar on “Quantum Computing for Material Science and Pharma”
Quantum Business Network |QBN 〉 manages the collaborative processes within the quantum technology ecosystem. The vision of |QBN〉 is to transform the German and the European quantum community to […]Read More »The E-CAM Issue of Comics&Science presented at the international comics festival of Lucca 2020
Following the recent publication of the E-CAM issue of Comics&Science, our Comics will have its first official “outing” this Friday 30 October at the Lucca Comics&Games Festival. The presentation […]Read More »Dask-traj
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 »E-CAM article on the EU Research Magazine
An article about E-CAM has just been released with the Autumn edition of the EU Research Magazine. The EU research magazine is Europe’s leader in research dissemination. The piece […]Read More »Issue 14 – September 2020
E-CAM Newsletter of September 2020 Get the latest news from E-CAM, sign up for our newsletter.Read More »A possible roadmap for the coarse graining and multiscale simulation community
A community-driven review with contributions from E-CAM “Unfolding the prospects of computational (bio)materials modeling” has just been published in the Journal of Chemical Physics on the history, developments, and […]Read More »E-CAM Industrial Case Study: Calculations for Applications in Photovoltaic Devices
Dr. David Lopez, Universidad de Córdoba, Spain Abstract The need to find easily renewable and environmentally friendly energy sources alternative to the traditional fossil fuels is nowadays a global quest. […]Read More »CLstunfti: An extendable Python toolbox to compute scattering of electrons with a given kinetic energy in liquids and amorphous solids
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 »Addressing interactive HTC workloads with HPC characteristics: introduction to E-CAM’s HTC library
Abstract Traditionally high-throughput computing (HTC) workloads are looked down upon in the HPC space, however the scientific use case for extreme-scale resources required by coordinated HTC workflows exists. For […]Read More »Minimal distance segment to segment with Karush-Kuhn-Tucker conditions
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 »Accelerating the design and discovery of materials with tailored properties using first principles high-throughput calculations and automated generation of Wannier functions
A successful collaboration between the EU H2020 E-CAM and MaX Centres of Excellence, and the Swiss NCCR MARVEL Abstract In a recent paper[1], researchers from the Centres of Excellence […]Read More »E-CAM is helping to organise a session on HPC Carpentry at CarpentryCon @ Home
HPC Carpentry – a way forward E-CAM is helping to organise a session on HPC Carpentry during CarpentryCon @ Home that aims to foster a scalable HPC training model. Join […]Read More »New CECAM webinar series: “The importance of being H.P.C. Earnest”
The new CECAM webinar series entitled “The importance of being H.P.C. Earnest”, will focus on of HPC as an enabler of leading-edge simulation and modelling, and on the science made possible by combining state-of-the-art methods with optimal exploitation of supercomputing resourcesRead More »The CoE PoP and how it can support E-CAM users
About POP HPC facilities are a major capital investment and often run close to capacity. Improving the efficiency of application software running on these facilities either speeds up time to […]Read More »E-CAM High Throughput Computing Library
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 »The CECAM Electronic Structure Library and the modular software development paradigm
E-CAM is working closely with the Electronic Structure Library (ESL) initiative since some years now. A review of the CECAM ESL is now out and can be accessed at https://arxiv.org/abs/2005.05756. […]Read More »Issue 13 – April 2020
E-CAM Newsletter of April 2020 Get the latest news from E-CAM, sign up for our newsletter.Read More »E-CAM interview with Massimo Noro, Director of Business Development at STFC
In 2019, Massimo Noro was invited by the CECAM Headquarters at EPFL (E-CAM coordinator) to give a lecture in the framework of the CECAM/MARVEL Mary Ann Mansigh Conversation Series, entitled […]Read More »Some useful tips to help moving to online training
E-CAM has built up a collection of (hopefully) useful information to help our community, other Centres of Excellence, and interested groups, transition to online training. The information originates from community-contributed […]Read More »Automated high-throughput Wannierisation, a successful collaboration between E-CAM and the MaX Centre of Excellence
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 »Protein based biosensors: application in detecting influenza
Donal MacKernan, University College Dublin & E-CAM An E-CAM transverse action is the development of a protein based sensor (pending patent filled in by UCD[1,2]) with applications in medical diagnostics, […]Read More »QMCPack Interfaces for Electronic Structure Computations
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 »New publication is out: “Towards extreme scale dissipative particle dynamics simulations using multiple GPGPUs”
E-CAM researchers working at the Hartree Centre – Daresbury Laboratory have co-designed the DL_MESO Mesoscale Simulation package to run on multiple GPUs, and ran for the first time a Dissipative […]Read More »6 software modules delivered in the area of Quantum Dynamics
In this report for Deliverable 3.5 of E-CAM [1], 6 software modules in quantum dynamics are presented. All modules stem from the activities initiated during the State-of-the-Art Workshop held […]Read More »Issue 12 – December 2019
E-CAM Newsletter of December 2019 Get the latest news from E-CAM, sign up for our newsletter.Read More »PANNA: Properties from Artificial Neural Network Architectures
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 »New publication is out: “Atomistic insight into the kinetic pathways for Watson–Crick to Hoogsteen transitions in DNA”
Title: Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA Authors: Vreede J, Pérez de Alba Ortíz A, Bolhuis PG, and Swenson DWH Nucleic Acids Research 2019, Vol. 47, No. 21, […]Read More »Pyscal- A python module for structural analysis of atomic environments
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 »E-CAM Case Study: The development of the GC-AdResS scheme:
from smooth coupling to a direct interface (abrupt) Dr. Christian Krekeler, Freie Universität Berlin Abstract GC-AdResS is a technique that speeds up computations without loss of accuracy for key system […]Read More »PRACE/E-CAM successful collaboration produces task scheduling library for optimising time-scale molecular dynamics simulations
Challenge E-CAM is interested in the challenge of bridging up timescales. To study molecular dynamics with atomistic detail, timesteps must be used on the order of a femto-second. Many problems […]Read More »A Conversation on The Fourth Industrial Revolution: Opportunities & Trends for Particle Based Simulation
Abstract In the margins of a recent multiscale simulation workshop a discussion began between a prominent pharmaceutical industry scientist, and E-CAM and EMMC regarding the unfolding Fourth Industrial Revolution […]Read More »Multi-GPU version of DL_MESO_DPD
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 »E-CAM State of the Art Workshop: CHALLENGES IN MULTIPHASE FLOWS
We would like to draw your attention to a school cum workshop on CHALLENGES IN MULTIPHASE FLOWS that will run on Dec 9-12, 2019, at the Monash University Prato Center,see http://monash.it/, […]Read More »Integrating LAMMPS with OpenPathSampling
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, a rewrite and optimisation of earlier versions of FFT related routines inside QE pre-v6
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 »Issue 11 – June 2019
E-CAM Newsletter of June 2019 Get the latest news from E-CAM, sign up for our quarterly newsletter.Read More »Extension of the ParaDiS code to include precipitate interactions, and code optimisation to run on HPC environment
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 »Upcoming event: Extended Software Development Workshop in Mesoscopic simulation models and HPC
E-CAM partners at Aalto University (CECAM Finish Node) in collaboration with the HPC training experts from the CSC Supercomputing Centre, are organizing a joint Extended Software Development Workshop from 15-19 October 2019 , aimed […]Read More »Mesoscale simulation of billion atom complex systems using thousands of GPGPU’s, an industry success story
Dr. Jony Castagna, Science and Technology Facilities Council, United Kingdom Abstract Jony Castagna recounts his transition from industry scientist to research software developer at the STFC, his E-CAM rewrite of […]Read More »Open call for CECAM flagship programme 2020
The CECAM CALL for workshops and schools that will run from April 2020 to March 2021 is now open! This is also the opportunity to submit an E-CAM proposal. The text of the call […]Read More »DBCSR@MatrixSwitch, an optimised library to deal with sparse matrices
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 »Software vendor SMEs as a boost for technology transfer in industrial simulative pipelines
The E-CAM Scoping Workshop “Building the bridge between theories and software: SME as a boost for technology transfer in industrial simulative pipelines”, organised in May 2018 at the Fondazione Istituto […]Read More »Abrupt GC-AdResS: A new and more general implementation of the Grand Canonical Adaptive Resolution Scheme (GC-AdResS)
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 »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 […]Read More »New E-CAM publication is out: “Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir”
New publication from E-CAM partners working at the Institute of Mathematics of the Freie Universität Berlin: Molecular Dynamics of Open Systems: Construction of a Mean‐Field Particle Reservoir Authors: Luigi Delle […]Read More »Open Postdoctoral Position in Mesoscale Modeling in Nanostructured Materials
In the context of the EU H2020 project E-CAM we are seeking a highly qualified post-doctoral researcher for an exciting collaborative project on the fundamental challenges of driven transport in […]Read More »Issue 10 – March 2019
E-CAM Newsletter of March 2019 Get the latest news from E-CAM, sign up for our quarterly newsletter.Read More »Scientific Report from State-of-the-Art Workshop “Improving the accuracy of ab-initio predictions for materials” is available on our website
The workshop scientific report from the E-CAM State-of-the-Art Workshop Improving the accuracy of ab-initio predictions for materials, that took place on the 17-20 September 2018 at the CECAM-FR-MOSER Node (France), […]Read More »Scientific Report from State-of-the-Art Workshop “Large Scale activated event simulations” is available on our website
The workshop scientific report from the E-CAM State-of-the-Art Workshop Large scale activated event simulations that took place on the 1-3 October 2018 in the CECAM-AT Node (Austria), is now available […]Read More »Porting of electrostatics to the GPU version of DL_MESO_DPD
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 »Topics in Classical MD – Extended Software Development Workshop
E-CAM is organising an Extended Software Development Workshop in Topics in Classical MD from 3 to 12 April 2019, which is a major coding initiative that will combine lectures; coding […]Read More »Two papers introducing OpenPathSampling, a software package to study rare events
Two papers introducing to OpenPathSampling (OPS) were recently published : OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics [1] OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building […]Read More »CTMQC, a module for excited-state nonadiabatic dynamics
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 »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 […]Read More »Issue 9 – October 2018
E-CAM Newsletter of October 2018 Get the latest news from E-CAM, sign up for our quarterly newsletter.Read More »E-CAM program of events 2019 is out
Check out our program of events for this year, running from April 2019 to February 2020: E-CAM Events 2019 See the details of each event to learn how to apply. […]Read More »SCDM_WFs
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 »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 […]Read More »QQ-Interface (Quantics-QChem-Interface)
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 »New publication is out: “Unimolecular FRET Sensors: Simple Linker Designs and Properties”
A new publication by researchers at University College Dublin and Boston University including E-CAM funded corresponding author Dr. Donal MacKernan was published in Nano Communication Networks. The measurement of […]Read More »PLUMED wrapper for OpenPathSampling
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 »The Curse of Dimensionality in Data-Intensive Modeling in Medicine, Biology, and Diagnostics
With Prof. Tim Conrad (TC), Free University of Berlin, and Dr. Donal Mackernan (DM), University College Dublin. Abstract Until recently the idea that methods rooted in statistical physics could be […]Read More »Scientific reports from the 2018 E-CAM workshops are now available on our website
The scientific reports* from the following workshops conducted in year 3 of the project E-CAM (2018): E-CAM Scoping Workshop: “Solubility prediction”, 14 – 15 May 2018, Ecole Normale Supérieure […]Read More »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 […]Read More »PaPIM: A code for Quantum Time Correlation Functions
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 »E-CAM Case Study: Designing control pulses for superconducting qubit systems with local control theory
Dr. Momir Mališ, École Polytechnique Fédérale de Lausanne, Switzerland Abstract A quantum logic gate is one of the key components of the quantum computer, and designing an effective quantum […]Read More »Spring shooting – A module for improving efficiency of transition path sampling
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 »New publication is out: “Adaptive Resolution Molecular Dynamics Technique: Down to the Essential”
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 […]Read More »Symmetry Adapted Wannier Functions – a Component of the Wannier90
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 »Meet us at the PASC18 conference in Basel on 2-4 July 2018
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 […]Read More »PIM_wd: Module for sampling of the quantum Wigner distribution
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 »PRACE Workshop on HPC in Molecular and Atomistic Simulations @ICHEC
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 […]Read More »HPC-in-a-day Workshop
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.Read More »Issue 8 – May 2018
E-CAM Newsletter of May 2018 Get the latest news from E-CAM, sign up for our quarterly newsletter.Read More »High Throughput Computing Workshop
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 […]Read More »The launch of the E-CAM Online Training Portal
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: […]Read More »E-CAM Case Study: The implementation of a hierarchical equilibration strategy for polymer melts, to help studying the rheological properties of new composite materials
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 […]Read More »Coarse-Graining module, a Component of the Hierarchical Equilibration Strategy for Polymer Melts
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 »6 software modules recently delivered in the area of Quantum Dynamics
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 […]Read More »New report published: Identification / Selection of E-CAM Electronic Structure Codes for Development
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 […]Read More »Open call for CECAM flagship event proposals 2019
The CECAM CALL for workshops and schools that will run from April 2019 to March 2020 is now open! The text for the call and information on how […]Read More »Contact Map – a package for analyzing and exploring contacts, from a trajectory generated by MD
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 »Scientific reports from the 2017 E-CAM workshops, are now available on our website
The scientific reports* from the following workshops conducted in year 2 of the project E-CAM (2017): E-CAM Scoping Workshop: “From the Atom to the Material” , 18- 20 September […]Read More »New report published: Identification / Selection of E-CAM Quantum Dynamics Codes for Development
As technologies reach atomic length and energy scales, the simulation of quantum effects acquires practical interest beyond basic science in areas ranging from sustainable energy, to medicine, to quantum […]Read More »Metal-ion force field developed by E-CAM using novel Machine Learning procedure is now available for download
The database of the force fields developed by the SNS SMART group (SNS, Pisa, Italy), including the metal-ions force fields optimized within E-CAM using novel Machine Learning procedure (reported […]Read More »LocConQubit, a module for the construction of controlled pulses on isolated qubit systems using the Local Control Theory
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 »E-CAM flyer with 2018 workshop program
[pdf-embedder url="https://www.e-cam2020.eu/wp-content/uploads/2018/02/E-CAM-Flyer18.pdf"]Read More »Issue 7 – January 2018
E-CAM Newsletter of January 2018 Get the latest news from E-CAM, sign up for our quarterly newsletter.Read More »The simulation of metal ions in protein-water systems using machine learning: An E-CAM case study and conversation
With Dr. Francesco Fracchia, Scuola Normale Superiore di Pisa Interviewer: Dr. Donal Mackernan, University College Dublin Abstract One quarter to one third of all proteins require metals to […]Read More »GRASP Sampling – a module to build a representative data set for a fitting procedure
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 »From Rational Design of Molecular Biosensors to Patent and potential Start-up
Dr. Donal Mackernan, University College Dublin Abstract The power of advanced simulation combined with statistical theory , experimental know-how and high performance computing is used to design a protein […]Read More »New publication using the GC-AdResS molecular dynamics technique
The publication “Probing spatial locality in ionic liquids with the grand canonical adaptive resolution molecular dynamics technique (GC-AdResS)“ by the Theoretical and Mathematical Physics in Molecular Simulation group of […]Read More »E-CAM program of events 2018 is out
Check out our program of events for this year, running from April 2018 to February 2019: E-CAM Events 2018 See the workshop details to learn how to apply. E-CAM events […]Read More »New article is out: “Force Field Parametrization of Metal Ions from Statistical Learning Techniques”
This paper from E-CAM partners working in Scuola Normale Superiore (Pisa, Italy) describes a novel statistical procedure, developed to optimize the parameters of non-bonded force fields of metal ions […]Read More »Geomoltools: A set of software modules to easily manipulate molecular geometries
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 »Issue 6 – October 2017
E-CAM Newsletter of October 2017Read More »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 […]Read More »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, […]Read More »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 […]Read More »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 […]Read More »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 […]Read More »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 […]Read More »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 […]Read More »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 […]Read More »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 […]Read More »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 […]Read More »Solvers for quantum atomic radial equations
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 »E-CAM in the organizing committee of CECAM workshop on Quantum Computing and HPC
An event to bring together the quantum information and HPC communities to discuss their specific expertise and outline the bridges that will eventually identify: (1) the future role of quantum […]Read More »Workshop for Industrial EsD users @ ISC17
The ETP4HPC initiative is inviting the industrial HPC users to a attend a workshop in June 22, Frankfurt, to discuss their needs and expectations regarding the potential use of Extreme […]Read More »E-CAM has a new front page
Take a look at our new front page: check out our upcoming events; latest news; stories; learn more about some of our software developments; among many others interesting topics. We […]Read More »ClassMC
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 »Direct MD (on-the-fly) flux/rate in OpenPathSampling
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 »Does our simulation community need EXASCALE ?
By Prof. David Ceperley, University of Illinois Urbana-Champaign The computer simulation of electrons, atoms, molecules, and their assemblies in soft and hard matter is foundational for many scientific disciplines and […]Read More »Technology transfer from the academic world to industry is a difficult process in all scientific fields
By Prof. Mike Payne, University of Cambridge In many countries there is increasing demand for measurable socio-economic impact from academic research. Perhaps the UK is furthest down this path with […]Read More »High Performance Computing, Computer Simulation, and Theoretical Physics: Evolution or Revolution?
By Prof. Giovanni Ciccotti, University of Rome La Sapienza Numerical physics, i.e. numerical calculations serving the needs of traditional theoretical physics, exists at least since the times of Galileo, and […]Read More »New newsletter is out
In our fifth newsletter, we highlight the programme of events 2017, and present the profiles of the new Project Technical Manager, Ignacio Pagonabarraga, and the Project Coordinator, Ana Catarina Mendonça. […]Read More »E-CAM article on the Psi-k Newsletter
The Psi-k Newsletter of December 2016 presents articles on the European Centers of Excellence NOMAD, E-CAM and MaX, highlighting what they are developing and can offer to the community. View […]Read More »Issue 5 – January 2017
In our fifth newsletter, we highlight the programme of events 2017, and present the profiles of the new Project Technical Manager, Ignacio Pagonabarraga, and the Project Coordinator, Ana Catarina Mendonça. […]Read More »Issue 4 – September 2016
In our fourth newsletter read about the outcomes of some of our first workshops. Download NewsletterRead More »Issue 3 – June 2016
In our third edition of the E-CAM quarterly find the full programme of our training events for the rest of 2016 as well as profiles of all of our postdocs […]Read More »Issue 2 – March 2016
In our second edition of the E-CAM Quarterly find the full list of all of our training events and employment opportunities. The Editorial features Professor Giovanni Ciccotti who asks whether […]Read More »Issue 1 – January 2016
Abstract Issue 1 – January 2016 The first E-CAM newsletter highlighting our kick-off meeting in Dublin in October 2015, our first management team appointments, and the E-CAM “Science View”. Download […]Read More »