"""
Calculations provided by aiida_amber.
Register calculations via the "aiida.calculations" entry point in setup.json.
"""
import os
from aiida.common import CalcInfo, datastructures
from aiida.engine import CalcJob
from aiida.orm import List, SinglefileData
from aiida.plugins import DataFactory
AntechamberParameters = DataFactory("amber.antechamber")
[docs]
class AntechamberCalculation(CalcJob):
"""
AiiDA calculation plugin wrapping the antechamber executable.
AiiDA plugin wrapper for the amber 'antechamber' command.
"""
[docs]
@classmethod
def define(cls, spec):
"""Define inputs and outputs of the calculation."""
# yapf: disable
super().define(spec)
# set default values for AiiDA options
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 = "amber.antechamber"
spec.input('metadata.options.output_filename', valid_type=str,
default='antechamber.out', help='name of file produced by default.')
spec.input('metadata.options.output_dir', valid_type=str, default=os.getcwd(),
help='Directory where output files will be saved when parsed.')
spec.input('parameters', valid_type=AntechamberParameters,
help='Command line parameters for antechamber')
spec.input("input_file", valid_type=SinglefileData,
help="input structure file for antechamber")
# optional inputs
spec.input('charge_file', valid_type=SinglefileData, required=False, help='charge file')
spec.input('additional_file', valid_type=SinglefileData, required=False, help='additional file')
spec.input('res_top_file', valid_type=SinglefileData, required=False, help='residue toplogy file')
spec.input('check_file', valid_type=SinglefileData, required=False, help='check file for gaussian')
spec.input('esp_file', valid_type=SinglefileData, required=False, help='gaussian esp file')
# required outputs
spec.output('stdout', valid_type=SinglefileData, help='stdout')
spec.output('output_file', valid_type=SinglefileData, help='output file')
# optional outputs
# set the list of output file names as an input so that it can be
# iterated over in the parser later.
spec.input('antechamber_outfiles', valid_type=List, required=False,
help='List of antechamber output file names.')
# IMPORTANT:
# Use spec.outputs.dynamic = True to make the entire output namespace
# fully dynamic. This means any number of output files
# can be linked to a node.
spec.outputs.dynamic = True
spec.inputs.dynamic = True
spec.inputs['metadata']['options'].dynamic = True
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 = datastructures.CodeInfo()
# Setup data structures for files.
# Any input files used
input_options = [
"input_file",
"charge_file",
"additional_file",
"res_top_file",
"check_file",
"esp_file",
]
# Any output files produced
output_options = ["o"]
cmdline_input_files = {}
input_files = []
output_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,
)
)
# Add output files to retrieve list.
output_files.append(self.metadata.options.output_filename)
for item in output_options:
if item in self.inputs.parameters:
output_files.append(self.inputs.parameters[item])
# Form the commandline.
codeinfo.cmdline_params = self.inputs.parameters.cmdline_params(
cmdline_input_files
)
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 = output_files
return calcinfo