"""
Data types provided by plugin
Register data types via the "aiida.data" entry point in setup.json.
"""
# You can directly use or subclass aiida.orm.data.Data
# or any other data type listed under 'verdi data'
from voluptuous import Optional, Required, Schema
from aiida.orm import Dict
# A subset of mdrun command line options
cmdline_options = {
Required("c", default="confout.gro"): str,
Required("e", default="energy.edr"): str,
Required("g", default="md.log"): str,
Required("o", default="trajectory.trr"): str,
Optional("x"): str,
Optional("cpo"): str,
Optional("dhdl"): str,
Optional("field"): str,
Optional("tpi"): str,
Optional("tpid"): str,
Optional("eo"): str,
Optional("px"): str,
Optional("pf"): str,
Optional("ro"): str,
Optional("ra"): str,
Optional("rs"): str,
Optional("rt"): str,
Optional("mtx"): str,
Optional("if"): str,
Optional("swap"): str,
Optional("xvg"): str,
Optional("dd"): str,
Optional("ddorder"): str,
Optional("npme"): str,
Optional("nt"): str,
Optional("ntmpi"): str,
Optional("ntomp"): str,
Optional("ntomp_pme"): str,
Optional("pin"): str,
Optional("pinoffset"): str,
Optional("pinstride"): str,
Optional("gpu_id"): str,
Optional("gputasks"): str,
Optional("ddcheck"): str,
Optional("rdd"): str,
Optional("rcon"): str,
Optional("dlb"): str,
Optional("dds"): str,
Optional("nb"): str,
Optional("nstlist"): str,
Optional("tunepme"): str,
Optional("pme"): str,
Optional("pmefft"): str,
Optional("bonded"): str,
Optional("update"): str,
Optional("v"): str,
Optional("pforce"): str,
Optional("reprod"): str,
Optional("cpt"): str,
Optional("cpnum"): str,
Optional("append"): str,
Optional("nsteps"): str,
Optional("maxh"): str,
Optional("replex"): str,
Optional("nex"): str,
Optional("reseed"): str,
}
[docs]
class MdrunParameters(Dict): # pylint: disable=too-many-ancestors
"""
Command line options for diff.
This class represents a python dictionary used to
pass command line options to the executable.
"""
# "voluptuous" schema to add automatic validation
schema = Schema(cmdline_options)
# pylint: disable=redefined-builtin
[docs]
def __init__(self, dict=None, **kwargs):
"""
Constructor for the data class
Usage: ``MdrunParameters(dict{'ignore-case': True})``
:param parameters_dict: dictionary with commandline parameters
:param type parameters_dict: dict
"""
dict = self.validate(dict)
super().__init__(dict=dict, **kwargs)
[docs]
def validate(self, parameters_dict):
"""Validate command line options.
Uses the voluptuous package for validation. Find out about allowed keys using::
print(MdrunParameters).schema.schema
:param parameters_dict: dictionary with commandline parameters
:param type parameters_dict: dict
:returns: validated dictionary
"""
return MdrunParameters.schema(parameters_dict)
[docs]
def cmdline_params(self, input_files):
"""Synthesize command line parameters.
e.g. [ '--ignore-case', 'filename1', 'filename2']
:param pdbfile: Name of input pdb file
:param type pdbfile: str
"""
parameters = []
parameters.append("mdrun")
parameters.extend(["-s", input_files["tprfile"]])
if "cpi_file" in input_files: parameters.extend(["-cpi", input_files["cpi_file"]])
if "table_file" in input_files: parameters.extend(["-table", input_files["cpi_file"]])
if "tableb_file" in input_files: parameters.extend(["-tableb", input_files["tableb_file"]])
if "tablep_file" in input_files: parameters.extend(["-tablep", input_files["tablep_file"]])
if "rerun_file" in input_files: parameters.extend(["-rerun", input_files["rerun_file"]])
if "ei_file" in input_files: parameters.extend(["-ei", input_files["ei_file"]])
if "multidir_file" in input_files: parameters.extend(["-multidir", input_files["multidir_file"]])
if "awh_file" in input_files: parameters.extend(["-awh", input_files["awh_file"]])
if "membed_file" in input_files: parameters.extend(["-membed", input_files["membed_file"]])
if "mp_file" in input_files: parameters.extend(["-mp", input_files["mp_file"]])
if "mn_file" in input_files: parameters.extend(["-mn", input_files["mn_file"]])
parm_dict = self.get_dict()
for key, value in parm_dict.items():
parameters.extend(["-" + key, value])
return [str(p) for p in parameters]
[docs]
def __str__(self):
"""String representation of node.
Append values of dictionary to usual representation. E.g.::
uuid: b416cbee-24e8-47a8-8c11-6d668770158b (pk: 590)
{'ignore-case': True}
"""
string = super().__str__()
string += "\n" + str(self.get_dict())
return string