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Welcome to nanoSCULPT

Welcome to nanoSCULPT, a tool/methodology to generate complex and realistic structures for atomistic simulations. This wiki provides you with detailed installation instructions, along with examples on running and using nanoSCULPT.

Please note that both the code and this wiki are work in progress. Feel free to add stuff to this wiki to make it more understandable. If you do not have write access to the wiki, please send your additions/suggestions to the developers of nanoSCULPT.

Also, please do not hesitate to send the developers your wishlist for including new features into nanoSCULPT.

Brief background/history

Atomistic simulations have now established themselves as a valuable tool in advancing our understanding on the fundamental mechanisms of deformation in materials. Although increase in computing power has made large-scale simulations with billions, or even trillions, of atoms a reality, majority of atomistic studies are performed with rather simplistic setups involving quasi-2D or 3D planar geometries. Notwithstanding the importance of controlled studies with such well-defined structures, we feel that the scientific community would greatly benefit from a methodology and tool that would help generate more realistic configurations for atomistic simulations. Ideally, such a tool would enable a one-to-one reconstruction of experimental data.

With this in mind, we set out developing nanoSCULPT. The idea was to have a lightweight program that would run on all machines with basic system requirements. Created through concerted efforts between two groups at the FAU Erlangen-Nürnberg and the University of Stuttgart, the program was originally hosted separately by the individual groups. This repository now brings the code into one place, making development easier.

The figure below illustrates the principle of working of nanoSCULPT

GraphicalAbstractV2.jpg

Principal developers

A. Prakash, Materials Science and Engineering, Institute I, Friedrich-Alexander-Universität Erlangen-Nürnberg

Martin Hummel, IMWF, Universität Stuttgart

Siegfried Schmauder, IMWF, Universität Stuttgart

Erik Bitzek, Materials Science and Engineering, Institute I, Friedrich-Alexander-Universität Erlangen-Nürnberg

License

NanoSCULPT is licensed under the GNU public license version 3 and is available free of cost for academic and scientific usage. Please remember to cite nanoSCULPT (see below) when publishing results obtained with the software.

Version

The current stable version of nanoSCULPT is v1.2.

The latest development version is from 25-Jul-2016 and contains a patch for a bug that hindered certain regions from being filled when the cuboidal box had aspect ratios above 15.

How to obtain nanoSCULPT

nanoSCULPT is public repository. You can clone the repository as follows:

git clone https://arunpksh@bitbucket.org/arunpksh/nanosculpt.git

The subfolder v1.2 contains the latest stable build

This, however, requires you to have git installed on your machine. If not you can find instructions here.

Please take some time to familiarize yourself with bitbucket and git, if you already do not know them. You might perhaps find the Bitbucket documentation pages as useful resource/starting point.

This additional page can also help you kick off especially if you are starting from scratch.

Citing nanoSCULPT

If you use nanoSCULPT for your research, please cite nanoSCULPT in your publications as follows:

A. Prakash, J. Guénolé, J. Wang, J. Müller, E. Spiecker, M.J. Mills, I. Povstugar, P. Choi, D. Raabe and E. Bitzek [2015], Atom probe informed simulations of dislocation–precipitate interactions reveal the importance of local interface curvature, Acta Materialia, 92, 33-45

A. Prakash, M. Hummel, S. Schmauder and E. Bitzek [2015], NanoSCULPT: A methodology for generating complex realistic configurations for atomistic simulations, MethodsX, 3, 219-230

System requirements

  • Gnu C compiler gcc
  • Gnu make tool gmake/make
  • Git version control system git

Please note that although we try to write code that is platform independent, we are unable to test it on all platforms. The current version of the code has been tested on a x64 linux system with a gcc compiler.

Compiling nanoSCULPT

To compile nanoSCULPT, just change to the source directory and execute $> make clean $> make

The above commands should create an executable nanoSCULPT in your source directory. Copy it to your bin directory to have it accessible everywhere.

Running nanoSCULPT

Running nanoSCULPT requires a parameter file. Please refer to this page for more details.

Once you have generated your parameter file, you can call nanoSCULPT as follows: $> nanoSCULPT <ParameterFile>

A convention is to provide the extension .nsparam to the nanosculpt parameter file. This is, however, not mandatory.

Examples

To help new users, a few examples are provided along with the source code. These can be found in the examples directory of each build. A detailed description of the examples is provided in the Examples page.

We hope you find nanoSCULPT useful for your research. If you have any questions, please do not hesitate to contact the nanoSCULPT team.

Have fun!

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