arc_parser

arc_parser is a small program written in Rust that parses .arc files produced by the LASP program.

Completed Functions

• Print the minimum energy structures in the .arc file
• Count the structures in an .arc file
• Identify duplicate minimum structures
• Export the global minimum structure or the structure at the speficied position
• List all energies of structures
• Rearrange atoms in a structure along the X, Y, or Z axis
• Scale the crystal along the X, Y, or Z axis
• Calculate interplanar spacing of a given surface (specified by 3 atoms)
• Check if the result of the LASP program is valid
• Extract unconverged LASP structures
• compare the structure of two files and find the substructure in file1 that is similar to the structure in file2. This function uses multithreading to accelerate the process.

Functions in Progress

• Automatically analyze exposure of crystal surface
• Analyze symmetry of structure
• Find substructure that is similar to a reference structure in a given .arc file

Usage

From version 0.2.0, the usage has changed. Users can now use subcommands to specify the type of task. For example:

./arc_parser parse -f myfile.arc

or

./arc_parser check -p .

The following subcommands are supported:

parse

The parse subcommand provides basic analytics for the target .arc file.

Arguments

• Use -f or --file to specify the file you want to parse.
• Use -m or --minimum to print the minimum energy structures in the .arc file.
• Use -c or --count to count the structures in the .arc file.
• Use -C or --consistency to check if the structures in the .arc file have consistent atom composition and view the atom composition.
• Use -l or --list to list all energies present in the .arc file.
  • Note that energy differences less than 0.001 eV will be considered the same.
• Use --extract to extract the structure to extracted.arc. An argument is needed to specify the structure you want to extract. The first structure is numbered 1 and so on. If you use 0 as an argument, the program will automatically extract the minumum structure.
• Use --coord to specify the structure that you want to analyze for coordination number.
  • Note that the first structure in the .arc file is number 0.
  • If no number is specified, the structure with the minimum energy will be automatically analyzed.

check

The check subcommand helps you verify whether the result of the LASP program is valid.

Arguments

• Use -p or --path to specify the path to the directory of the result.

modify

The modify subcommand performs modifications to the structure and outputs the structure to another .arc file.

Arguments

• Use -f or --file to specify the file that you want to modify.
• Use -n or --number to specify the structure that you want to modify.
  • Note that the first structure in the .arc file is number 0.
  • If no number is specified, the structure with the minimum energy is automatically selected.
• Use -r or --rearrange to rearrange atoms of the structure.
  • You should specify x, y, or z after this argument.
• Use -s or --scale to scale the cell of the structure.
  • You should specify one or three number(s) after this argument.
  • If one number is specified, the whole cell will be scaled by that proportion.
  • If three numbers are specified, the a, b, and c values will be scaled by the three proportions respectively.
  • Note that if you shrink the cell by specifying a proportion less than 1, it is possible that the cell can't hold all the atoms.

compare

Arguments

• Use -f or --file1 to specify the first input file.
  • this input file can have multiple structures.
• Use -F or --file2 to speficy the second input file.
  • this input file is regarded as the reference file. Only the first structure is used as the reference
• Use -t or --threads to specify the number of threads you want to create.
  • this program uses multithreading to accelerate the compare process
  • by default, the progeram parallel over different structures, i.e. each thread handles a structure.

More subcommand arguments are still in progress.