"""
Calculations provided by aiida_gromacs.
This calculation configures the ability to use the 'gmx mdrun' executable.
"""
import os
from aiida.common import CalcInfo, CodeInfo
from aiida.engine import CalcJob
from aiida.orm import SinglefileData, Dict, Str, FolderData, List
from aiida.plugins import DataFactory
MdrunParameters = DataFactory("gromacs.mdrun")
[docs]
class MdrunCalculation(CalcJob):
"""
AiiDA calculation plugin wrapping the 'gmx mdrun' 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
# TODO: remove this for production release.
spec.inputs['metadata']['options']['max_wallclock_seconds'].default = 86400
spec.inputs['metadata']['options']['resources'].default = {
'num_machines': 1,
'num_mpiprocs_per_machine': 1,
'num_cores_per_mpiproc': 5,
}
# Required inputs.
spec.inputs['metadata']['options']['parser_name'].default = 'gromacs.mdrun'
spec.input('metadata.options.output_filename', valid_type=str, default='mdrun.out')
spec.input('tprfile', valid_type=SinglefileData, help='Input structure.')
spec.input('parameters', valid_type=MdrunParameters, help='Command line parameters for gmx mdrun')
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('cpi_file', valid_type=SinglefileData, required=False, help='Checkpoint file')
spec.input('table_file', valid_type=SinglefileData, required=False, help='xvgr/xmgr file')
spec.input('tableb_file', valid_type=SinglefileData, required=False, help='xvgr/xmgr file')
spec.input('tablep_file', valid_type=SinglefileData, required=False, help='xvgr/xmgr file')
spec.input('rerun_file', valid_type=SinglefileData, required=False, help='Trajectory: xtc trr cpt gro g96 pdb tng')
spec.input('ei_file', valid_type=SinglefileData, required=False, help='ED sampling input')
spec.input('multidir_file', valid_type=SinglefileData, required=False, help='Run directory')
spec.input('awh_file', valid_type=SinglefileData, required=False, help='xvgr/xmgr file')
spec.input('membed_file', valid_type=SinglefileData, required=False, help='Generic data file')
spec.input('mp_file', valid_type=SinglefileData, required=False, help='Topology file')
spec.input('mn_file', valid_type=SinglefileData, required=False, help='Index file')
spec.input('plumed_file', valid_type=SinglefileData, required=False, help='Plumed file')
spec.input_namespace("plumed_inpfiles", valid_type=SinglefileData,
required=False, dynamic=True, help="inputs referenced in plumed input file")
spec.input_namespace("plumed_dirs", valid_type=FolderData, required=False, dynamic=True,
help="path to directory where inputs referenced in plumed input file are")
# Required outputs.
spec.output('stdout', valid_type=SinglefileData, help='stdout')
spec.output('trrfile', valid_type=SinglefileData, help='Output trajectory.')
spec.output('grofile', valid_type=SinglefileData, help='Output structure file.')
spec.output('logfile', valid_type=SinglefileData, help='Output log file.')
spec.output('enfile', valid_type=SinglefileData, help='Output energy file.')
# Optional outputs.
spec.output('x_file', required=False, valid_type=SinglefileData, help='Compressed trajectory (tng format or portable xdr format)')
spec.output('cpo_file', required=False, valid_type=SinglefileData, help='Checkpoint file.')
spec.output('dhdl_file', required=False, valid_type=SinglefileData, help='xvgr/xmgr file')
spec.output('field_file', required=False, valid_type=SinglefileData, help='xvgr/xmgr file')
spec.output('tpi_file', required=False, valid_type=SinglefileData, help='xvgr/xmgr file')
spec.output('tpid_file', required=False, valid_type=SinglefileData, help='xvgr/xmgr file')
spec.output('eo_file', required=False, valid_type=SinglefileData, help='xvgr/xmgr file')
spec.output('px_file', required=False, valid_type=SinglefileData, help='xvgr/xmgr file')
spec.output('pf_file', required=False, valid_type=SinglefileData, help='xvgr/xmgr file')
spec.output('ro_file', required=False, valid_type=SinglefileData, help='xvgr/xmgr file')
spec.output('ra_file', required=False, valid_type=SinglefileData, help='Log file')
spec.output('rs_file', required=False, valid_type=SinglefileData, help='Log file')
spec.output('rt_file', required=False, valid_type=SinglefileData, help='Log file')
spec.output('mtx_file', required=False, valid_type=SinglefileData, help='Hessian Matrix')
spec.output('if_file', required=False, valid_type=SinglefileData, help='xvgr/xmgr file')
spec.output('swap_file', required=False, valid_type=SinglefileData, help='xvgr/xmgr file')
# set the list of output file names from plumed as an input so that it can be
# iterated over in the parser later.
spec.input('plumed_outfiles', valid_type=List, required=False,
help='List of plumed output file names.')
# Outputs outside of gromacs
spec.output('logfile_metadata', valid_type=Dict, help='metadata extracted from gromacs logfile')
#spec.output('test', valid_type=Dict)
# 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['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 = CodeInfo()
# Setup data structures for files.
input_options = ["tprfile", "cpi_file", "table_file", "tableb_file", "tablep_file", "rerun_file", "ei_file", "multidir_file", "awh_file", "membed_file", "mp_file", "mn_file", "plumed_file", "plumed_inpfiles", "plumed_dirs"]
output_options = ["c", "e", "g", "o", "x", "cpo", "dhdl", "field", "tpi", "tpid", "eo", "px", "pf", "ro", "ra", "rs", "rt", "mtx", "if", "swap", "logfile_metadata"]
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:
# If we have a dynamics data type then iterate the dict.
if item == "plumed_dirs":
for directory, obj in self.inputs[item].items():
input_files.append(
(
obj.uuid,
".",
directory,
)
)
elif item == "plumed_inpfiles":
for _, obj in self.inputs[item].items():
input_files.append(
(
obj.uuid,
obj.filename,
obj.filename,
)
)
else:
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])
if "plumed_outfiles" in self.inputs: # check there are plumed output files.
for name in self.inputs.plumed_outfiles:
output_files.append(str(name)) # save plumed output filename to list
# 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