# Resources

## Online discussion forum for readers of the *Modeling Materials* (MM) book

*Modeling Materials*(MM) book

A discussion forum for readers of the MM book has been set up here. This is a place where readers can discuss topics related to the book and ask each other questions. The authors will monitor the forum and provide input when appropriate.

## Programs used with the *Modeling Materials* (MM) book

*Modeling Materials*(MM) book

**MiniMol**is a minimal molecular dynamics (MD) and molecular statics (MS) program provided with the book*Modeling Materials: Continuum, Atomistic and Multiscale Techniques*by Ellad B. Tadmor and Ronald E. Miller, Cambridge University Press, 2011. The program is based on "md3.f90", a Fortran 90 program written by Furio Ercolessi as an MD tutorial, which the authors have adapted and extended with his gracious permission. A number of homework problems in the MM book use MiniMol to help teach the reader about the implementation and use of MD. Input files for these assignments are given here.

MiniMol has the following capabilities/features:

MS simulations, which involve energy minimization of static configurations using a conjugate gradient (CG) minimizer.

Constant energy MD.

Constant temperature MD with one of the following:

velocity rescaling

Nosé-Hoover thermostat

Langevin thermostat

Periodic boundary conditions (PBCs) for an orthogonal periodic box using the minimum image convention.

Some versions of MiniMol are "KIM-compliant" which means that they are compatible with the Knowledgebase of Interatomic Models (KIM) application programming interface (API) (for details see https://openkim.org and the explanation below). KIM-compliant versions of MiniMol will work with any interatomic model conforming to the KIM API.

Four versions of MiniMol are available for download (see table below):

A stand-alone Fortran 90 version that is driven by a simple text input file and writes text output. This version should work with any Fortran 90 compiler. The source code is provided so that Fortran programmers can understand the implementation and make changes in order to do the exercises in the MM book. Initial atomic configurations can be generated on nanoHUB (see below) or with the Fortran 90 utility "BuildBox" provided on this site. To download, see table below.

A stand-alone C version that is driven by a simple text input file and writes text output. This version should work with any C compiler. The source code is provided so that C programmers can understand the implementation and make changes in order to do the exercises in the MM book. Initial atomic configurations can be generated on nanoHUB (see below) or with the Fortran 90 utility "BuildBox" provided on this site. To download, see table below.

A KIM-compliant Fortran 90 version with the same characteristics as version 1 above. To download, see table below.

A GUI-driven version on www.nanoHUB.org. Anyone can register for a free account on nanoHUB and use their resources to run the MiniMol application (called a "tool" on nanoHUB). This version is KIM-compliant and also includes a crystal generating utility (based on BuildBox) that can be used to produce initial atomic configurations for the simulation of single crystals. These configuration files can be downloaded from nanoHUB and used as input for the stand-alone versions listed above.

**BuildBox**is a Fortran 90 utility that can be used to generate single crystals in .XYZ file format. BuildBox allows the generation of a complex (multilattice) crystal by defining a set of three Bravais lattice vectors and a basis (motif) of an arbitrary number of atoms associated with each lattice site. The crystal can then be arbitrarily scaled and rotated. Finally, the rotated crystal can be built to span an orthogonal simulation box with the periodic boundary conditions calculated to generate a perfect infinite crystal. To download, see table below.**Quasicontinuum (QC)**is a multiscale method which couples an atomistic region modeled using standard MS (or MD) with a continuum region modeled using a nonlinear finite element method (FEM). More information on the QC method along with downloadable freely-available code is available at http://qcmethod.org. The method is also discussed in the MM book where some of the homework problems use the QC code.

Note: To unpack a tgz file on a unix/linux machine, type `tar zxvf file.tgz`. To unpack a zip file, type `unzip file.zip'.

## Freely-available* atomistic and multiscale software

*free access may be limited to academic institutions

**MultiBench***Modell. Simul. Mater. Sci. Eng.*,**17**:053001, 2009) and in Chapter 12 of the MM book. The MultiBench program is based on the QC code mentioned above and is written in Fortran 90. It can be downloaded from the QC website.

**Knowledgebase of Interatomic Models (KIM)**Development of an online open resource for standardized testing and long-term warehousing of interatomic models (potentials and force fields) and data.

Development of an application programming interface (API) standard for atomistic simulations, which will allow any interatomic model to work seamlessly with any atomistic simulation code.

Development of a quantitative theory of transferability of interatomic models to provide guidance for selecting application-appropriate models based on rigorous criteria, and error bounds on results.

The KIM project is open to all researchers interested in atomistic simulations. More information is available at the KIM project website: https://openkim.org

**Atomistic visualization programs**AtomEye – Atomistic configuration viewer (MIT)

AViz – Atomistic Vizualization software (Technion)

Avogadro – Advanced molecule editor and visualizer

iMol – Molecular visualizer for Mac OS X

Jmol – An open-source Java viewer for chemical structures in 3D.

OVITO – Open VIsualization TOol (TU Darmstadt)

PyMOL – PYthon-based MOLecular visualization system (DeLano Scientific LLC)

RasM0l – Molecular graphics visualization tool (ARCiB Laboratory, Downling College)

VMD – Visual Molecular Dynamics (U. Illinois)

**Atomistic simulation framworks**ASE – Python-based Atomistic Simulation Environment (TU Denmark)

CP2K – Fortran 95 package for classical and quantum calculations

QUIP/libAtoms – QUantum and Interatomic Potentials MD framework (University of Cambridge)

**Classical molecular dynamics (MD) programs**ASAP – As Soon As Possible MD program (TU Denmark)

DL_POLY – Daresbury Laboratory POLY (=many) tools MD program (STFC/Daresbury Lab, UK)

GROMACS – GROningen MAchine for Chemical Simulation (CBR, Stockholm)

HALMD – (GPU based) Highly Accelerated Large-scale Molecular Dynamics (University of Munich, Germany)

HOOMD-blue – (GPU based) Highly Optimized Object-oriented Many-particle Dynamics (U. Michigan)

IMD – The ITAP Molecular Dynamics program (ITAP, U. Stuttgart/MPI)

LAMMPS – Large-scale Atomic/Molecular Massively Parallel Simulator (Sandia)

MiniMol – MINImal MOLecular simulation code (Modeling Materials)

MOLDY – MOLecular DYnamics (U. Oxford)

NAMD – Not (just) Another Molecular Dynamics program (U. Illinois)

OpenMM – OPEN source library for Molecular Modeling simulations (Stanford University)

**Density functional theory (DFT) programs**ABINIT – AB INITio (Université Catholique de Louvain, Corning Inc., et al.)

BigDFT – massively parallel electronic structure code with GPU support

ESPRESSO – opEn Source Package for Research in Electronic Structure, Simulation and Optimization

GPAW – Grid-based Projector-Augmented Wave method (TU Denmark)

NWChem – NorthWest computational Chemistry (PNNL)

Qbox – scalable parallel first principles MD code written in C++/MPI (UC Davis)

Quickstep – DFT using mixed Gaussian and plane waves approach (part of CP2K package, see above)

SeqQuest – QUantum Electronic STructure (Sandia)

SIESTA – Spanish Initiative for Electronic Simulations with Thousands of Atoms

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