"""
calphy: a Python library and command line interface for automated free
energy calculations.
Copyright 2021 (c) Sarath Menon^1, Yury Lysogorskiy^2, Ralf Drautz^2
^1: Max Planck Institut für Eisenforschung, Dusseldorf, Germany
^2: Ruhr-University Bochum, Bochum, Germany
calphy is published and distributed under the Academic Software License v1.0 (ASL).
calphy is distributed in the hope that it will be useful for non-commercial academic research,
but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
calphy API is published and distributed under the BSD 3-Clause "New" or "Revised" License
See the LICENSE FILE for more details.
More information about the program can be found in:
Menon, Sarath, Yury Lysogorskiy, Jutta Rogal, and Ralf Drautz.
“Automated Free Energy Calculation from Atomistic Simulations.” Physical Review Materials 5(10), 2021
DOI: 10.1103/PhysRevMaterials.5.103801
For more information contact:
sarath.menon@ruhr-uni-bochum.de/yury.lysogorskiy@icams.rub.de
"""
import os
import numpy as np
import time
import yaml
import warnings
from calphy.input import read_inputfile #, create_identifier
import calphy.scheduler as pq
import argparse as ap
from calphy import __version__ as version
[docs]def run_jobs(inputfile):
"""
Spawn jobs which are submitted to cluster
Parameters
----------
options : dict
dict containing input options
Returns
-------
None
"""
#the jobs are well set up in calculations dict now
#Step 1 - loop over calcs dict
#Step 2 - check input structure of calc and create lattice if needed
#Step 3 - Submit job
#read the input file
calculations = read_inputfile(inputfile)
print("Total number of %d calculations found" % len(calculations))
for count, calc in enumerate(calculations):
identistring = calc.create_identifier()
scriptpath = os.path.join(os.getcwd(), ".".join([identistring, "sub"]))
errfile = os.path.join(os.getcwd(), ".".join([identistring, "err"]))
#the below part assigns the schedulers
#now we have to write the submission scripts for the job
#parse Queue and import module
if calc.queue.scheduler == "local":
scheduler = pq.Local(calc.queue.__dict__, cores=calc.queue.cores)
elif calc.queue.scheduler == "slurm":
scheduler = pq.SLURM(calc.queue.__dict__, cores=calc.queue.cores)
elif calc.queue.scheduler == "sge":
scheduler = pq.SGE(calc.queue.__dict__, cores=calc.queue.cores)
else:
raise ValueError("Unknown scheduler")
#for lattice just provide the number of position
scheduler.maincommand = "calphy_kernel -i %s -k %d"%(inputfile,
count)
scheduler.write_script(scriptpath)
_ = scheduler.submit()
[docs]def main():
"""
Main method to parse arguments and run jobs
Paramaters
----------
None
Returns
-------
None
"""
arg = ap.ArgumentParser()
#argument name of input file
arg.add_argument("-i", "--input", required=False, type=str,
help="name of the input file")
arg.add_argument("-v", "--version", action='store_true',
help="name of the input file")
#parse args
args = vars(arg.parse_args())
if args["version"]:
print(version)
else:
#spawn job
if args["input"]:
run_jobs(args["input"])