Careful these pages are outdated unsupported archival copies

1. 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. It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimizations, Born-Oppenheimer MD, path integral MD, response functions, excited states and calculation of some electronic properties. For further information you may want to take a look at the CPMD consortium homepage at http://www.cpmd.org/.

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. As far as possible the examples were designed to be doable on a single processor desktop Linux PC with a fair amount of Memory (ca. 512MB, most need less, few more) and estimates of the execution time and memory requirements will be given where available.

This tutorial was initially put together by Carme Rovira, Roger Rousseau, and Axel Kohlmeyer and first presented in its initial form at 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.

For visualization of the results you may want to take a look at the tutorial on vizualizing results from CPMD (and other electron structure or molecular dynamics programs) with the VMD program by the same author available under http://www.theochem.ruhr-uni-bochum.de/go/cpmd-vmd.html.

Part 1

Contents

1.1. Development Notice

still under development Please note, that this webpage is still under (occasional) active development and some parts have not been fully checked for errors. So you have to be careful. There may be many typos, thinkos, dangling links, or other errors. Sections that are known to be problematic have been marked with the image on the left. If you have any comments, contributions, or corrections please send them to axel.kohlmeyer@theochem.ruhr-uni-bochum.de.

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1.2. Notes

All of the examples presented here were tested with CPMD version 3.9.2 on a Linux machine. 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 axel.kohlmeyer@theochem.ruhr-uni-bochum.de 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 state the revision id of the tutorial, which is available (in small print) at end of the document.

1.3. Recent Changes

2005/01/13: More broken links fixed.

Data for the H2O Spectra calculation and some inputs provided.

The single H2O MD is now using rotation/translation removal.
2005/01/06: Several errors from the first public version fixed.

The generic warning on the top of each page has been turned into individual warnings in the sections that have not been revised or are still being developed.

Directory names for the inputs and outputs are now prepended with numbers to force a specific ordering when browsing the input/output directories.
2005/01/03: Webpage made publically available.

1.4. Citation / Bookmark

If you want to cite or bookmark these pages please use the URL
http://www.theochem.ruhr-uni-bochum.de/go/cpmd-tutor.html
as the underlying link might change in the future.

The whole tutorial webpage is also available as a single file PDF document for easy printing (182 kByte).

See the Downloads Section for archives with the complete inputs or outputs.

Top of Page

Part 1

2. Table of Contents

1. Introduction
     1.1. Development Notice
     1.2. Notes
     1.3. Recent Changes
     1.4. Citation / Bookmark
2. Table of Contents
3. Preparation and Installation Issues
     3.1. Compiling CPMD
     3.2. Running CPMD
     3.3. Running cpmd2cube
4. The Theory: Some Fundamental Infos and Useful Literature
5. The Basics: Running CPMD, Input and Output Formats
     5.1. Wavefunction Optimization: a) Input File Format
     5.2. Wavefunction Optimization: b) Output File Format
     5.3. Geometry Optimization
     5.4. Car-Parrinello Molecular Dynamics
     5.5. Further Job Types
     5.6. How to Use the Tutorial
6. Exercise: Electron Structure and Geometry Optimization
     6.1. Hydrogen Molecule
     6.2. Water Molecule
     6.3. Ammonia Molecule
7. Exercise: Car-Parrinello Molecular Dynamics
     7.1. Hydrogen Molecule
     7.2. Ammonia Molecule in Gas Phase
     7.3. Glycine Molecule in Gas Phase
     7.4. Glycine with Thermostats
8. Exercise: Bulk Systems
     8.1. Bulk Silicon
     8.2. Hydronium Ion in Bulk Water
9. Exercise: Determination of Dynamic Properties
     9.1. Calculation of Vibrational Spectra
     9.2. The 'Dragging Effect'
10. Proton Transfer in a Catalytic Triade Model
     10.1. Preparing a Model from a Large System
     10.2. Equilibration with a Blocked Reaction Path
     10.3. Modelling Part of the Reaction Path
     10.4. Calculating Electron Structure Properties and Visualizations
11. Credits
12. Downloads
13. File distribution policy

Theoretische Chemie, Ruhr-Universität Bochum,Germany http://www.theochem.ruhr-uni-bochum.de/go/cpmd-tutor.html

Homepage Axel Kohlmeyer

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