ArcaNN XYZ Frame Extractor

The ArcaNN XYZ Frame Extractor is a command-line tool that processes trajectory files in the XYZ format. It allows you to extract frames from a trajectory file based on specified options and write them to a new trajectory file.

Features

• Extract frames from an XYZ trajectory file
• Specify frame extraction interval (--stride)
• Skip initial frames (--skip)
• Mode options for comment lines (--mode): nothing, copy, extended
• Can use a CP2K cell file using the --cell_file option
• Can write extended xyz as output

Requirements

• Python >= 3.6
• Additional Python dependencies can be installed using the requirements.txt file

Installation

1. Download the ArcaNN XYZ Frame Extractor

   Option a. Clone the ArcaNN XYZ Frame Extractor repository:

   git clone https://github.com/arcann-chem/xyz_frame_extractor.git

   Option b. Download the archive by clicking on the green Code button and then download zip

   unzip xyz_frame_extractor-main.zip -d xyz_frame_extractor

2. Navigate to the project directory:

   cd xyz_frame_extractor

3. Install the dependencies and the module (please do not forget the dot at the end):

   pip install -r requirements.txt .

Usage

Go to the directory where the trajectory is located or otherwise specify the absolute path of the file of the trajectory, then

python -m xyz_frame_extractor input.xyz output.xyz --stride 2 --skip 10 --mode extended --cell_file input.cell

• input.xyz is the name of the input XYZ trajectory file (if not in the directory specify the absolute path)
• output.xyz is the name of the output XYZ trajectory file (if needed, specify the absolute path where you want to locate your file)
• --stride (optional) specifies the frame extraction interval (default: 1).
• --skip (optional) specifies the number of frames to skip from the beginning of the trajectory (default: 0).
• --mode (optional) specifies the comment line (default: frame): frame, cp2k or cell.
  • nothing write the comment line as Frame: {step_number}
  • copy copy the comment line from the input to the output
  • extended write the comment as extended xyz. If no other argument is provided, it will assume your input xyz is in extended format and copy the comment line (but it will not copy the auxiliaries properties !)
    • use --cell_file to provide a CP2K cell file to write extended xyz format (CP2K format is Frame Time xx xy xz yx yy yz zx zy zz)
    • use --lattice and provide a string either in the format A B C or xx xy xz yx yy yz zx zy zz to write extended xyz format (but constant cell)

Note: The input and output file paths are required parameters, while --stride, --skip, --mode, --cell_file and --lattice are optional.

Examples

1. Extract frames from input.xyz with a stride of 2, skipping the first 10 frames:

   python -m xyz_frame_extractor input.xyz output.xyz --stride 2 --skip 10

2. Extract frames from input.xyz with a stride of 50 without skipping any frames:

   python -m xyz_frame_extractor $HOME/inputs/input.xyz  $HOME/outputs/output.xyz --stride 50

License

Distributed under the GNU Affero General Public License v3.0. See LICENSE for more information.

Contact

For any questions or inquiries, please contact the ArcaNN developers group at https://github.com/arcann-chem.