Source code for cp2k.cp2k_run

#!/usr/bin/env python3

"""Module containing the Cp2kRun class and the command line interface."""
import argparse
import shutil
import os
from pathlib import Path, PurePath
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from import file_utils as fu
from import launchlogger
from biobb_cp2k.cp2k.common import check_input_path, check_output_path

[docs]class Cp2kRun(BiobbObject): """ | biobb_cp2k Cp2kRun | Wrapper of the `CP2K QM tool <>`_ module. | Runs atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems using CP2K QM tool. Args: input_inp_path (str): Input configuration file (CP2K run options). File type: input. `Sample file <>`_. Accepted formats: inp (edam:format_2330), in (edam:format_2330), txt (edam:format_2330), wfn (edam:format_2333). output_log_path (str): Output log file. File type: output. `Sample file <>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330). output_outzip_path (str): Output files. File type: output. `Sample file <>`_. Accepted formats: zip (edam:format_3987), gzip (edam:format_3987), gz (edam:format_3987). output_rst_path (str): Output restart file. File type: output. `Sample file <>`_. Accepted formats: wfn (edam:format_2333). properties (dict - Python dictionary object containing the tool parameters, not input/output files): * **binary_path** (*str*) - ("cp2k.sopt") CP2K binary path to be used. * **param_path** (*str*) - (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** (*str*) - (None) Path to the MPI runner. Usually "mpirun" or "srun". * **mpi_np** (*int*) - (0) [0~1000|1] Number of MPI processes. Usually an integer bigger than 1. * **mpi_flags** (*str*) - (None) Path to the MPI hostlist file. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. Examples: This is a use example of how to use the building block from Python:: from biobb_cp2k.cp2k.cp2k_run import cp2k_run prop = { 'binary_path': 'cp2k.sopt' } cp2k_run(input_inp_path='/path/to/cp2k_input.inp', output_log_path='/path/to/cp2k_log.log', output_outzip_path='/path/to/', output_rst_path='/path/to/cp2k_rst.wfn', properties=prop) Info: * wrapped_software: * name: CP2K * version: >=7.1.0 * license: GPL-2.0 * multinode: mpi * ontology: * name: EDAM * schema: """ def __init__(self, input_inp_path: str, output_log_path: str, output_outzip_path: str, output_rst_path: str, properties: dict = None, **kwargs) -> None: properties = properties or {} # Call parent class constructor super().__init__(properties) self.locals_var_dict = locals().copy() # Input/Output files self.io_dict = { 'in': {'input_inp_path': input_inp_path}, 'out': {'output_log_path': output_log_path, 'output_outzip_path': output_outzip_path, 'output_rst_path': output_rst_path} } # Properties specific for BB = properties self.binary_path = properties.get('binary_path', 'cp2k.sopt') self.param_path = properties.get('param_path', None) # Properties for MPI self.mpi_bin = properties.get('mpi_bin') self.mpi_np = properties.get('mpi_np') self.mpi_flags = properties.get('mpi_flags') # Check the properties self.check_properties(properties) self.check_arguments()
[docs] def check_data_params(self, out_log, out_err): """ Checks input/output paths correctness """ # Check input(s) self.io_dict["in"]["input_inp_path"] = check_input_path(self.io_dict["in"]["input_inp_path"], "input_inp_path", False, out_log, self.__class__.__name__) # Check output(s) self.io_dict["out"]["output_log_path"] = check_output_path(self.io_dict["out"]["output_log_path"], "output_log_path", False, out_log, self.__class__.__name__) self.io_dict["out"]["output_outzip_path"] = check_output_path(self.io_dict["out"]["output_outzip_path"], "output_outzip_path", False, out_log, self.__class__.__name__) self.io_dict["out"]["output_rst_path"] = check_output_path(self.io_dict["out"]["output_rst_path"], "output_rst_path", False, out_log, self.__class__.__name__)
[docs] @launchlogger def launch(self): """Launches the execution of the Cp2kRun module.""" # check input/output paths and parameters self.check_data_params(self.out_log, self.err_log) # Setup Biobb if self.check_restart(): return 0 self.stage_files() # Creating temporary folder self.tmp_folder = fu.create_unique_dir() fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log) shutil.copy2(self.io_dict["in"]["input_inp_path"], self.tmp_folder) # set path to the CP2K parameter data files if not self.param_path: # os.environ["CP2K_DATA_DIR"] = str(PurePath(myself.__file__).parent.joinpath('cp2k_data')) os.environ["CP2K_DATA_DIR"] = str(Path(os.getenv("CONDA_PREFIX")).joinpath('cp2k_aux').joinpath('cp2k_data')) else: if not Path(PurePath(self.param_path)).exists(): fu.log(self.__class__.__name__ + ': Unexisting %s folder, exiting' % self.param_path, self.out_log) raise SystemExit(self.__class__.__name__ + ': Unexisting %s folder' % self.param_path) os.environ["CP2K_DATA_DIR"] = self.param_path # Command line # cp2k.sopt -i benzene_dimer.inp -o mp2_test.out self.cmd = ['cd', self.tmp_folder, ';', self.binary_path, '-i', PurePath(self.io_dict["in"]["input_inp_path"]).name, '-o', PurePath(self.io_dict["out"]["output_log_path"]).name] # general mpi properties if self.mpi_bin: mpi_cmd = [self.mpi_bin] if self.mpi_np: mpi_cmd.append('-n') mpi_cmd.append(str(self.mpi_np)) if self.mpi_flags: mpi_cmd.extend(self.mpi_flags) self.cmd = mpi_cmd + self.cmd # Run Biobb block self.run_biobb() # Gather output files in a single zip file self.output = PurePath(self.tmp_folder).joinpath("") out_files = [] restart = '' for root, dirs, files in os.walk(self.tmp_folder): for file in files: # fu.log('FILE %s ' % file, self.out_log) # if file.endswith('.out'): # out_files.append(file) # elif file.endswith('.wfn'): # restart = file if file.endswith('.wfn'): restart = self.tmp_folder + '/' + file else: out_files.append(self.tmp_folder + '/' + file) fu.zip_list(self.output, out_files, self.out_log) # Copy outputs from temporary folder to output path shutil.copy2(self.output, PurePath(self.io_dict["out"]["output_outzip_path"])) shutil.copy2(PurePath(self.tmp_folder).joinpath(PurePath(self.io_dict["out"]["output_log_path"]).name), PurePath(self.io_dict["out"]["output_log_path"])) if restart: shutil.copy2(restart, PurePath(self.io_dict["out"]["output_rst_path"])) # Copy files to host self.copy_to_host() # remove temporary folder(s) self.tmp_files.extend([ self.stage_io_dict.get("unique_dir"), self.tmp_folder ]) self.remove_tmp_files() self.check_arguments(output_files_created=True, raise_exception=False) return self.return_code
[docs]def cp2k_run(input_inp_path: str, output_log_path: str, output_outzip_path: str, output_rst_path: str, properties: dict = None, **kwargs) -> int: """Create :class:`Cp2kRun <cp2k.cp2k_run.Cp2kRun>`cp2k.cp2k_run.Cp2kRun class and execute :meth:`launch() <cp2k.cp2k_run.Cp2kRun.launch>` method""" return Cp2kRun(input_inp_path=input_inp_path, output_log_path=output_log_path, output_outzip_path=output_outzip_path, output_rst_path=output_rst_path, properties=properties).launch()
[docs]def main(): parser = argparse.ArgumentParser(description='Running atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems using CP2K QM tool.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) parser.add_argument('--config', required=False, help='Configuration file') # Specific args required_args = parser.add_argument_group('required arguments') required_args.add_argument('--input_inp_path', required=True, help='Input configuration file (QM run options). Accepted formats: inp, in, txt.') required_args.add_argument('--output_log_path', required=True, help='Output log file. Accepted formats: log, out, txt.') required_args.add_argument('--output_outzip_path', required=True, help='Output trajectory file. Accepted formats: zip, gz, gzip.') required_args.add_argument('--output_rst_path', required=True, help='Output restart file. Accepted formats: wfn.') args = parser.parse_args() # config = args.config if args.config else None args.config = args.config or "{}" # properties = settings.ConfReader(config=config).get_prop_dic() properties = settings.ConfReader(config=args.config).get_prop_dic() # Specific call cp2k_run(input_inp_path=args.input_inp_path, output_log_path=args.output_log_path, output_outzip_path=args.output_outzip_path, output_rst_path=args.output_rst_path, properties=properties)
if __name__ == '__main__': main()