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Introduction

Introduction of the CPMD Tutorial

Introduction

 

The aim of this webpage is to help you getting started using the CPMD program. CPMD is an ab initio electronic structure and molecular dynamics (MD) program using a plane wave/pseudopotential implementation of density functional theory (DFT). It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimizations, Born-Oppenheimer MD, path integral MD, response functions, QM/MM, excited states and calculation of some electronic properties. For further information you may want to take a look at the CPMD consortium homepage.

 

The first part of this tutorial shall introduce you to the format of CPMD input files for some typical calculations and the relevant parts of the resulting output file. The remainder will provide you with some exercises, grouped into several consecutive sections, to practice running CPMD calculations successfully for some exemplary scenarios and at the same time explore the strengths and limitations of the Car-Parrinello MD approach for single molecules and small (bulk) systems.

 

Explanation of the theoretical background is limited to the absolute minimum, so to take full advantage of the examples presented here, you are referred to the CPMD manual and the appropriate introductory literature.

The examples can run effectively on an Intel Core i5 (2.53 GHz, OS/X) with 4 GB of available memory (most of tests require ca. 1GB, few more). Nonetheless, references have been generated on an IBM Blade power7 (with 8 mpi tasks and 1 OMP task per CPMD run) with 64 GB of available memory. Estimates of the execution time and memory requirements will be given based on this more performant setup.

 

For visualization of the results you may want to take a look at the tutorial on visualizing results from CPMD (and other electron structure or molecular dynamics programs) with the VMD program.

 

 

History and Credits

 

This tutorial was initially put together by Carme Rovira, Roger Rousseau, Axel Kohlmeyer  and first presented in its initial form at the Centre for Research in Theoretical Chemistry of the Parc Cientific de Barcelona in 2004.

Some of the examples were inspired by the 2002 CECAM tutorial on Car-Parrinello Molecular Dynamics. Originally this tutorial was available at Axel's webpage and since 2009 removed from the Internet. Upon completion of the new CPMD website, I decided to bring back the original files and most of what you can find here is a revival of what was available in Axel's original version. The content has been updated and the exercises tested/modified to be always compliant with the most recent version of CPMD.

 

 

Development Notice

 

Please note, that these webpages are continuously under occasional development and some parts have not been fully checked for errors. So you have to be careful. There may be many typos, dangling links, or other errors. Sections that are known to be problematic have been clearly marked with a red exclamation mark (Big Red Exclamation Mark). If you have any comments, contributions, or corrections please send them to me.

 
 

Notes

 

All of the examples presented here were tested with CPMD version 3.17.1 on different available architectures: OS/X (GNU compilers), Power7 (IBM compilers). Since they cover mostly rather basic issues, many of the examples are likely to work with older (or newer) versions of the code. Occasionally some features will not work with certain CPMD versions.


Please contact me if there are compatibility problems with newer or older versions of CPMD or on other platforms. Any other form of feedback, e.g. corrections, enhancements, or new example inputs, is also highly welcome. When reporting problems, please use the "Send This" button at end of the document, and insert in the right field your comment.



Citation/Bookmark

 

If you want to cite or bookmark these pages please use the URL http://www.cpmd.org/cpmd-tutorial .

 

 

Basic Infos and Useful Literature

 

Car-Parrinello molecular dynamics (CP-MD) simulations bring together methods from classical molecular dynamics (MD), solid state physics and quantum chemistry, so some background knowledge in all of these areas is needed to perform meaningful CPMD simulations. There is a lot of introductory literature about those topics available. Here follows a list of some suggestions:

 

 

Recommended review articles: 

  1. "Molecular Dynamics without effective potentials via the Car-Parrinello approach", D. K.Remler and P. A. Madden

  2. "Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients" M.C. Payne, M.P. Teter, D.C. Allen, T.A. Arias and J.D. Joannopoulos

  3. "Ab initio molecular dynamics: Theory and Implementation", D. Marx and J. Hutter

  4. "Ab initio molecular dynamics: Basic Theory and Advanced Methods", D. Marx and J. Hutter
  5. "Density Functional Theory: Basics, New Trends and Applications ", J. Kohanoff and N. Gidopoulos, Handbook of Molecular Physics and Quantum Chemistry, ed. Stephen Wilson. Volume 2, Part 5, Chapter 26, pp 532-568 (Wiley, Chichester, 2003)

 

Webpages with introductory material or links to it:

  1. On the CPMD homepage.

  2. NIC Series [Vol 3]: Modern Methods and Algorithms of Quantum Chemistry Proceedings, Second Edition 

  3. NIC Series [Vol 10]: Quantum Simulations of Complex Many-Body Systems: From Theory to Algorithms - Lecture Notes
  4. NIC Series [Vol 23]: Computational Soft Matter: From Synthetic Polymers to Proteins, Lecture Notes

 

How to use this Tutorial

 

The next three pages (up to Geometry Optimization and MD) are a short introduction into the 'mechanics' of running a CPMD job, usually something that would be explained to you in person by an advisor during the course of your first steps with CPMD. Since we don't have this way of communication here, it is suggested, you start the tutorial pages from this point and then go back and forth in whatever way you need it.


To further help you, you can also browse not only the full directory tree with the collected input files, but also a similar directory with collected reference outputs and a directory with collected additional material

See the Downloads Section for downloadable archives with the complete inputs, outputs, RESTARTs and all generated files (all split into different archives in order to make easier the download of appropriate parts).

 

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