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] [--config CONFIG] --output_inp_path OUTPUT_INP_PATH [--input_inp_path INPUT_INP_PATH] [--input_pdb_path INPUT_PDB_PATH] [--input_rst_path INPUT_RST_PATH]
Prepares input files for the CP2K QM tool.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
--input_inp_path INPUT_INP_PATH
Input configuration file (QM options) (CP2K inp). Accepted formats: inp, in, txt.
--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.
required arguments:
--output_inp_path OUTPUT_INP_PATH
Output CP2K input inp file. Accepted formats: inp, in, txt.
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: PDB
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..
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] [--config CONFIG] --input_inp_path 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.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_inp_path INPUT_INP_PATH
Input configuration file (QM run options). Accepted formats: inp, in, txt.
--output_log_path OUTPUT_LOG_PATH
Output log file. Accepted formats: log, out, txt.
--output_outzip_path OUTPUT_OUTZIP_PATH
Output trajectory file. Accepted formats: zip, gz, gzip.
--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..
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