SeqQuest Input Reference Manual

SeqQuest
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Table of Contents

  1. Overview
  2. Global structure of input file
  3. Tutorials and examples

Overview

Quest uses a structured input file divided into sections of related data. The input is designed to be self-documenting. The input is keyword-driven (left-justified) followed by lines with (mostly) free-format data. Only the first few characters of a keyword line are significant; the remainder of a line can be used as documentation, aiding understanding and modification of an input file.

Global structure of input file

The SeqQuest input file begins with a command options section that controls the global operations of the code. Unless instructed otherwise in the command section, the code will stop after an SCF calculation, before a force evaluation. The first required "keyword" is the "setup data" which begins the setup data input section that defines the structural characteristics of the problem. After the setup section ends, the optional run phase input data section begins processing the file. The run phase section has embedding within it an optional geometry relaxation input section and cell optimization input section for minimization, and a section for defining a molecular dynamics simulation. If the NEB transition state finder is invoked (in the command options), the NEB data input section is required and sets up a multi-image "chain-of-states" calculation to find a transition barrier.
... command options
...
setup data - begin setup phase input
...
... setup structure data
...
end setup phase data - end of setup phase input section
run phase data - begin run phase data input section
...
... run phase input data
...
dynamics - invokes molecular dynamics (MD) input section
...
... dynamics control input
...
end dynamics - end of MD input section
...
geometry relaxation - invokes geometry relaxation input section
...
... geometry relaxation input
...
end geometry relaxation - end of geometry relaxation input section
...
cell optimization - invokes cell input section
...
... cell optimization input
...
end cell optimization - end of cell optimization input section
...
end run phase data - end of run phase input section
neb data - begin data controlling NEB transition state finder
...
... NEB control input
...
end neb data - end NEB data

Tutorials and examples

Molecule Tutorial

This Tutorial discusses the construction of input file for molecules. Using a variety of molecules, it describes the special considerations that go into constructing true finite boundary conditions in a supercell code, and illustrates the use of successively more sophisticated input to aid ease of use and to trigger additional functionality in the code.

Slab: CO/Ru(0001)

This Tutorial discusses the construction of the adsorption of CO in the hexagonal (0001) surface of Ru. It starts with a very simple input file to look at the clean bulk-terminated surface, illustrates the use of successively more sophisticated input options to aid ease of use and trigger additional functionality in the code, and deals with some of the special issues that arise in designing slab calculations to examine chemistry at surfaces.

Bulk: wurtzite GaN

This Tutorial discusses the construction of an input file for a bulk wurtzite gallium-nitride crystal. It begins with a very simple (and flawed) input file, and illustrates the use of successively more sophisticated input to aid ease of use and to trigger additional functionality in the code.

NEB: reaction of hydrogen and ethlylene

This Tutorial discusses the construction of an input file for finding the reaction mechanism and transition state for the reaction of hydrogen and ethylene:
H2 + C2H4 &rarr C2H6
using the nudged elastic band method (NEB). The example shown is for a molecular calculation, but the NEB input is applicable to slab or bulk calculations as well.

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Send questions and comments to: Peter Schultz at paschul@sandia.gov
Last updated: July 8, 2010