Author Archives: Dan Gezelter

DAMASK the Dsseldorf Advanced Material Simulation Kit

DAMASK is a flexible and hierarchically structured model of material point behavior for the solution of (thermo-) elastoplastic boundary value problems. Its main purpose is the simulation of crystal plasticity within a finite-strain continuum mechanical framework. DAMASK is currently coupled … Continue reading

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rOpenSci

At rOpenSci we are creating packages that allow access to data repositories through the R statistical programming environment that is already a familiar part of the workflow of many scientists. Our tools not only facilitate drawing data into an environment … Continue reading

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GitHub Science Showcase

Scientists around the world are working together to solve some of the biggest questions in research. Take a look at some of the examples featured here to find out more. Find GitHub Science Showcase at: https://github.com/showcases/science

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A modest proposal

Dear Professor X, Thank you for the invitation to review for the Journal of X.  I appreciate the work you do and have done for the X community. That said, I have decided not to review for Elsevier journals unless the … Continue reading

Posted in Open Access, open science | 1 Comment

Open Science Codefest

The National Center for Ecological Analysis and Synthesis (NCEAS) at UCSB is co-sponsoring the Open Science Codefest 2014, which aims to bring together researchers from ecology, biodiversity science, and other earth and environmental sciences with computer scientists, software engineers, and developers to collaborate … Continue reading

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Energy system modelling with ASCEND

This a major release of the program. It introduces major modifications on the usage of Tonatiuh from previous versions of the program. In this new release, the user must decide what ray tracing results to save and how to save … Continue reading

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compute_fep

Free energy perturbation for LAMMPS, with soft-core pair potentials. Uses FEP, Thermodynamic Integration (TI), Mezei FDTI, and Bennet Acceptance Ratio methods. It can be used for alchemical transformations of pair potentials or charges in selected atoms. Find compute_fep at: https://github.com/agiliopadua/compute_fep

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SciDraw

SciDraw is a system for preparing publication-quality scientific figures with Mathematica. SciDraw provides both a framework for structuring figures and tools for generating their content. SciDraw helps with generating figures involving mathematical plots, data plots, and diagrams. The package allows … Continue reading

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MUSCLE

MUSCLE 2 – The Multiscale Coupling Library and Environment is a portable framework to do multiscale modeling and simulation on distributed computing resources. The generic coupling mechanism of MUSCLE is suitable for many types of multiscale applications, notably for multiscale … Continue reading

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Dendrimer Builder Toolkit (DBT)

DBT can be used to build polymers (linear or hyperbranched) for use in AMBER depending upon multiplicity of joining residues. DBT sequences and calculates the number of residues required for building dendrimer (or polymer), which further depends on core multiplicity … Continue reading

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