Standard Cluster Tool - v1.6 (14 December 2024)

Authors: Oliver Warschkow, Steven R. Schofield, University College London

Usage

sct <template> [<options> ...] <cluster-descriptor>

Templates

• Si
  Si(001) surface template generated using
  VASP GGA_DFT (Warschkow et al. Surf.Sci. 2007).

• Si2024
  Si(001) surface template generated using
  CASTEP v19, PBE, USP, (8x4x1) MP, 800 eV, 20 layers (Schofield 2024).

• Ge2024
  Ge(001) surface template generated using
  CASTEP v19, PBE, USP, (8x4x1) MP, 800 eV, 20 layers (Schofield 2024).

• DSi
  Si(001) surface template generated using
  DMol3 PBE/DZP (Tracey et al. JCP 2012).

Options

• -p2x1
  Selects a p(2x1) flat-dimer pattern.
  Default dimer-buckling pattern.

• -c4x2
  Selects a c(4x2) buckled dimer pattern.

• -c4x2inv
  Selects a c(4x2) buckled dimer pattern with opposite orientation to the -c4x2 option.

• -p2x2
  Selects a p(2x2) buckled dimer pattern.

• -p2x2inv
  Selects a p(2x2) buckled dimer pattern with opposite orientation to the -p2x2 option.

• -xyz
  Prints cluster in XYZ file format.
  Default output format.

• -gaussian
  Prints cluster as a Gaussian input structure with opt=ModRedunant constraint flags.

• -ascending
  Prints structure ordered by atomic layer starting with the deepest layer.
  Default ordering of atoms.

• -descending
  Prints structure ordered by atomic layer surface (dimer) layer.

• -hfirst
  Reorders atoms so that the terminating hydrogen atoms come before any of the cluster atoms.
  Default output order.

• -hlast
  Reorders atoms so that the terminating hydrogen atoms come after the cluster atoms.

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Example Usage

Single-Dimer Cluster

sct Si2024 -gaussian "4'" > my_cluster.gjf

Creates a single-dimer, single-row Si9H12 cluster in Gaussian input format.
Note: The third argument is written as <four><prime>, where "four" refers to the number of silicon layers below the dimer, and "prime" indicates that this is not a "wide" cluster.

Two-Dimer Cluster

sct Si2024 -gaussian "4'4'" > my_cluster.gjf

Creates a two-dimer cluster Si15H16.

Four-Dimer-in-Two-Rows Cluster

sct Si2024 -gaussian "4'4'|4'4'" > my_cluster.gjf

Creates a four-dimer-in-two-rows cluster Si35H32.
Note: Each "four" has a prime, and rows are separated by a vertical bar.

Cluster with Varying Depth

sct Si2024 -gaussian "2'4'2'" > my_cluster.gjf

Creates a cluster with varying depth, combining numbers for different depths.

Installation

Prerequisites

Ensure you have the following installed on your system:

• Git
• A compatible C++ compiler (e.g., GCC or Clang)
• make (build tool)

Steps

1. Clone the Repository
   Clone the repository to your local machine:

git clone https://github.com/srschofield/standard-cluster-tool.git
cd standard-cluster-tool

2. Build the Project
   Compile the source code using the provided Makefile:

make

This will generate the required binaries in the project directory.

3. Install the Tool
   To make the binary accessible system-wide, run:

make install

This will copy the binary to /usr/local/bin.

4. Run the Tool
   If installed into your path, you can run the tool system-wide using:

sct

Alternatively, if not installed, run it directly from the project directory:

./sct