"""
Calculations provided by aiida_gromacs.
This calculation configures the ability to use the 'gmx genion' executable.
"""
import os
from aiida.common import CalcInfo, CodeInfo
from aiida.engine import CalcJob
from aiida.orm import SinglefileData, Str
from aiida.plugins import DataFactory
GenionParameters = DataFactory("gromacs.genion")
[docs]
class GenionCalculation(CalcJob):
"""
AiiDA calculation plugin wrapping the 'gmx genion' executable.
AiiDA plugin wrapper for converting PDB files to GRO files.
"""
[docs]
@classmethod
def define(cls, spec):
"""Define inputs and outputs of the calculation."""
# yapf: disable
super().define(spec)
# Define inputs and outputs of the calculation.
spec.input('command',
valid_type=Str, required=False,
help='The command used to execute the job.')
# set default values for AiiDA options
# TODO: something changed about withmpi in aiida-2.4.0, needs investigation.
spec.inputs['metadata']['options']['withmpi'].default = False
spec.inputs['metadata']['options']['resources'].default = {
'num_machines': 1,
'num_mpiprocs_per_machine': 1,
}
# Required inputs.
spec.inputs['metadata']['options']['parser_name'].default = 'gromacs.genion'
spec.input('metadata.options.output_filename', valid_type=str, default='genion.out')
spec.input('tprfile', valid_type=SinglefileData, help='Input tpr file.')
spec.input('topfile', valid_type=SinglefileData, help='Input topology file.')
spec.input('parameters', valid_type=GenionParameters, help='Command line parameters for gmx genion')
spec.input('metadata.options.output_dir', valid_type=str, default=os.getcwd(),
help='Directory where output files will be saved when parsed.')
# Optional inputs.
spec.input(
'metadata.options.filename_stdin',
valid_type=str,
required=False,
help='Filename that should be redirected to the shell command using the stdin file descriptor.',
)
spec.input('instructions_file', valid_type=SinglefileData, required=False, help='Instructions for generating index file')
spec.input('metadata.options.stdin_filename', valid_type=str, required=False, help='name of file used in stdin.')
spec.input('n_file', required=False, valid_type=SinglefileData, help='Index file.')
# Default outputs.
spec.output('stdout', valid_type=SinglefileData, help='stdout')
spec.output('grofile', valid_type=SinglefileData, help='Output gro file with ions added.')
spec.output('topfile', valid_type=SinglefileData, help='Output topology with ions added.')
spec.exit_code(300, 'ERROR_MISSING_OUTPUT_FILES', message='Calculation did not produce all expected output files.')
[docs]
def prepare_for_submission(self, folder):
"""
Create input files.
:param folder: an `aiida.common.folders.Folder` where the plugin should temporarily place all files
needed by the calculation.
:return: `aiida.common.datastructures.CalcInfo` instance
"""
codeinfo = CodeInfo()
# Setup data structures for files.
input_options = ["tprfile", "topfile", "n_file", "instructions_file"]
cmdline_input_files = {}
input_files = []
# Map input files to AiiDA plugin data types.
for item in input_options:
if item in self.inputs:
cmdline_input_files[item] = self.inputs[item].filename
input_files.append((
self.inputs[item].uuid,
self.inputs[item].filename,
self.inputs[item].filename,
))
# Form the commandline.
codeinfo.cmdline_params = self.inputs.parameters.cmdline_params(cmdline_input_files)
# Form stdin file for index instructions
codeinfo.stdin_name = self.inputs['metadata']['options'].get('stdin_filename', None)
codeinfo.code_uuid = self.inputs.code.uuid
codeinfo.stdout_name = self.metadata.options.output_filename
codeinfo.withmpi = self.inputs.metadata.options.withmpi
# Prepare a `CalcInfo` to be returned to the engine
calcinfo = CalcInfo()
calcinfo.codes_info = [codeinfo]
calcinfo.local_copy_list = input_files
calcinfo.retrieve_list = [
self.metadata.options.output_filename,
self.inputs.parameters["o"],
self.inputs.topfile.filename,
]
return calcinfo