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Index
Contents
About CPMD
Introduction
Capabilities
Citation
Contributions
Mailing list
Important constants and conversion factors
About this manual
Recommendations for further reading
Original Literature
CPMD Development History
CPMD License
Installing and Running CPMD
Installation
Prerequisites
Compiling CPMD
Running CPMD
CPMD on Parallel Computers
Tutorial
Introduction
Prerequisites
Pseudopotential Files
The Basics: Running CPMD, Input and Outputs
Wavefunction Optimization
Choosing the Plane Wave Cutoff
Geometry Optimization
Car-Parrinello Molecular Dynamics
Some Commented CPMD Job Examples
Electron Structure and Wavefunction Properties
Vibrational Spectra
Path-Integral MD
Further Job Types
Theory
Molecular Dynamics and ab initio Molecular dynamics
Equations of Motion
Microcanonical Ensemble
Numerical Integration
Extended System Approach
Ab initio Molecular Dynamics
Born-Oppenheimer Molecular Dynamics
Car-Parrinello Molecular Dynamics
Comparing BOMD and CPMD
Calculating the Electronic Structure from Pseudopotentials and Plane Waves
Unit Cell and Plane Wave Basis
Kinetic Energy and Local Potentials
Electrostatic Energy
Exchange and Correlation Energy
Car-Parrinello Equations
Metals; Free Energy Functional
Charged Systems
Position Operator in Periodic Systems
Dipole Moments and IR Spectra
Localized Orbitals, Wannier Functions
Pseudopotentials
Why Pseudopotentials ?
Norm-Conserving Pseudopotentials
Pseudopotentials in the Plane Wave Basis
Dual-Space Gaussian (Goedecker-Teter-Hutter) Pseudopotentials
Example: Pseudopotentials for Oxygen
Non-linear Core Correction
Implementation
Total Energy and Gradients
Fast Fourier Transforms
Density and Force Calculations in Practice
Saving Computer Time
Exchange and Correlation Functionals
User's Guide
Hints and Tricks for setting up CPMD calculations
Pseudopotentials and Plane Wave Cutoff
Wavefunction Initialization
Wavefunction Convergence
Cell Size Requirements for Isolated Systems
Controlling adiabaticity for CP-dynamics in practice
Geometry Optimization
Molecular Dynamics
Restarts
TDDFT
Perturbation Theory / Linear Response
Metadynamics
Restricted Open-Shell Calculations
Hints on using the Free Energy Functional (FEMD)
The Davidson analysis and the shared electron number
Mean Free Energy Path Minimization
CPMD/Gromos QM/MM Calculations
Gromacs/CPMD QM/MM Calculations
Post-Processing Tools and File Formats
General Tools
cpmd2cube
Fourier
Vreco_CPMD
xyz-Files
DCD Files
The TRAJECTORY File
The MOVIE File
Reference Manual
Input File Reference
Basic rules
Input Sections
List of Keywords by Sections
Alphabetic List of Keywords
Further details of the input
List of keywords for Gromos/AmberFF QM/MM
Output File Reference
F.A.Q.
Questions and Answers
How to Report Problems
Explanation of Warnings and Error Messages
Pseudopotentials
File Formats and Interpretation of Data
Input Parameter Values
Bibliography
Index
Costas Bekas 2008-09-04