SeqQuest Input Reference Manual
Table of Contents
- Global structure of input file
- Tutorials and examples
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)
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 band structure post-processing step is selected in the
the specification is required in an input section for the
band structure section,
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
- ... 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
- bandstructure - specifies band structure to compute
- ... bands structure input
- end bandstructure - end of b.s. input section
- 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
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.
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.
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.
This Example discusses the computation of the band structure for a bulk CdS crystal.
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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Last updated: February 22, 2014