BioBB CP2K Command Line Help

Generic usage:

biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>

Cp2k_prep

Helper bb to prepare inputs for the CP2K QM tool module.

Get help

Command:

cp2k_prep -h

usage: cp2k_prep [-h] [-c CONFIG] [--input_inp_path INPUT_INP_PATH] [--input_pdb_path INPUT_PDB_PATH] [--input_rst_path INPUT_RST_PATH] -o OUTPUT_INP_PATH

Prepares input files for the CP2K QM tool.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  -o OUTPUT_INP_PATH, --output_inp_path OUTPUT_INP_PATH
                        Output CP2K input configuration file. Accepted formats: inp, in, txt.

optional arguments:
  --input_inp_path INPUT_INP_PATH
                        Input configuration file (CP2K run options). Accepted formats: inp, in, txt, wfn.
  --input_pdb_path INPUT_PDB_PATH
                        Input PDB file. Accepted formats: pdb.
  --input_rst_path INPUT_RST_PATH
                        Input restart file (WFN). Accepted formats: wfn.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • input_inp_path (string): Input configuration file (CP2K run options). File type: input. Sample file. Accepted formats: INP, IN, TXT, WFN

  • input_pdb_path (string): Input PDB file. File type: input. Sample file. Accepted formats: PDB

  • input_rst_path (string): Input restart file (WFN). File type: input. Sample file. Accepted formats: WFN

  • output_inp_path (string): Output CP2K input configuration file. File type: output. Sample file. Accepted formats: INP, IN, TXT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • simulation_type (string): (energy) Default options for the cp2k_in file. Each creates a different inp file.

  • cp2k_in (object): ({}) CP2K run options specification.

  • cell_cutoff (number): (5.0) CP2K cell cutoff, to build the cell around the system (only used if input_pdb_path is defined).

  • remove_tmp (boolean): (True) Remove temporal files.

  • restart (boolean): (False) Do not execute if output files exist.

  • sandbox_path (string): (./) Parent path to the sandbox directory.

YAML

Common config file

properties:
  simulation_type: energy

Command line

cp2k_prep --config config_cp2k_prep.yml --input_inp_path cp2k_energy.inp --input_pdb_path H2O_box.pdb --input_rst_path cp2k.wfn --output_inp_path cp2k_prep_out.inp

JSON

Common config file

{
  "properties": {
    "simulation_type": "energy"
  }
}

Command line

cp2k_prep --config config_cp2k_prep.json --input_inp_path cp2k_energy.inp --input_pdb_path H2O_box.pdb --input_rst_path cp2k.wfn --output_inp_path cp2k_prep_out.inp

Cp2k_run

Wrapper of the CP2K QM tool module.

Get help

Command:

cp2k_run -h

usage: cp2k_run [-h] [-c CONFIG] -i INPUT_INP_PATH --output_log_path OUTPUT_LOG_PATH --output_outzip_path OUTPUT_OUTZIP_PATH --output_rst_path OUTPUT_RST_PATH

Running atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems using CP2K QM tool.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  -i INPUT_INP_PATH, --input_inp_path INPUT_INP_PATH
                        Input configuration file (CP2K run options). Accepted formats: inp, in, txt, wfn.
  --output_log_path OUTPUT_LOG_PATH
                        Output log file. Accepted formats: log, out, txt, o.
  --output_outzip_path OUTPUT_OUTZIP_PATH
                        Output files. Accepted formats: zip, gzip, gz.
  --output_rst_path OUTPUT_RST_PATH
                        Output restart file. Accepted formats: wfn.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

  • input_inp_path (string): Input configuration file (CP2K run options). File type: input. Sample file. Accepted formats: INP, IN, TXT, WFN

  • output_log_path (string): Output log file. File type: output. Sample file. Accepted formats: LOG, OUT, TXT, O

  • output_outzip_path (string): Output files. File type: output. Sample file. Accepted formats: ZIP, GZIP, GZ

  • output_rst_path (string): Output restart file. File type: output. Sample file. Accepted formats: WFN

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

  • binary_path (string): (cp2k.sopt) CP2K binary path to be used.

  • param_path (string): (None) Path to the CP2K parameter data files (BASIS_SET, POTENTIALS, etc.). If not provided, the parameter data files included in the package will be used.

  • mpi_bin (string): (None) Path to the MPI runner. Usually “mpirun” or “srun”.

  • mpi_np (integer): (0) Number of MPI processes. Usually an integer bigger than 1.

  • mpi_flags (string): (None) Path to the MPI hostlist file.

  • remove_tmp (boolean): (True) Remove temporal files.

  • restart (boolean): (False) Do not execute if output files exist.

  • sandbox_path (string): (./) Parent path to the sandbox directory.

YAML

Common config file

properties:
  remove_tmp: true

Command line

cp2k_run --config config_cp2k_run.yml --input_inp_path cp2k_energy.inp --output_log_path cp2k_run_out.log --output_outzip_path cp2k_run_out.zip --output_rst_path cp2k_run_out.wfn

JSON

Common config file

{
  "properties": {
    "remove_tmp": true
  }
}

Command line

cp2k_run --config config_cp2k_run.json --input_inp_path cp2k_energy.inp --output_log_path cp2k_run_out.log --output_outzip_path cp2k_run_out.zip --output_rst_path cp2k_run_out.wfn