if __name__ == "__main__":
IS_QUEUE = True
USERNAME = "******"
#PASSWORD = getpass.getpass()
PASSWORD = "******"
if IS_QUEUE:
logging.basicConfig(format='%(name)s:%(levelname)s:%(message)s', level=logging.INFO)
else:
logdir = str(pathlib.Path(".").resolve())
logging.basicConfig(filename = logdir + "/singlesites_workflow.log", level=logging.INFO)
# set up the LaunchPad and reset it
#launchpad = mylaunchpad.create_launchpad(USERNAME, PASSWORD, server = "atlas")
launchpad = mylaunchpad.create_launchpad(USERNAME, PASSWORD, server = "serenity")
#launchpad = mylaunchpad.create_launchpad(USERNAME, PASSWORD, server = "serenity", lpadname = "mjfireworkstriton")
#launchpad.reset('', require_password=False)
wf = get_singlesites_workflow(username = "******",
password = PASSWORD,
template_path = str(pathlib.Path("../templates/cp2k_mm_energy.inp").resolve()),
worker_target_path = "/wrk/jagermar/DONOTREMOVE/workflow_runs/singlesites/testruns/ptcu_db",
extdb_ids = [1921,1922],
reference_energy = -1.16195386047558 * 0.5,
adsorbate_name = "H",
chunk_size = 10,
max_calculations = 50,
adsite_types = ["top", "bridge"], #, "hollow"],
n_max_restarts = 1,
skip_dft = False,
from critcatworks.workflows import generate_nanoclusters_workflow
from critcatworks.database import mylaunchpad
if __name__ == "__main__":
IS_QUEUE = True
USERNAME = "******"
#PASSWORD = getpass.getpass()
PASSWORD = "******"
if IS_QUEUE:
logging.basicConfig(format='%(name)s:%(levelname)s:%(message)s', level=logging.INFO)
else:
logdir = str(pathlib.Path(".").resolve())
logging.basicConfig(filename = logdir + "/nanocluster_workflow.log", level=logging.INFO)
# set up the LaunchPad and reset it
launchpad = mylaunchpad.create_launchpad(USERNAME, PASSWORD,)
#launchpad.reset('', require_password=False)
bondlength_dct = {
"Fe" : 2.3,
"Co" : 2.3,
"Ni" : 2.4,
"Cu" : 2.5,
"Ti" : 2.7,
"Pt" : 2.6,}
wf = generate_nanoclusters_workflow(username = USERNAME, password = PASSWORD,
worker_target_path = "/wrk/jagermar/DONOTREMOVE/workflow_runs/generator/testruns", extdb_connect = {},
shape = "ico", nanocluster_size = 3, compositions = [6, 13, 28, 42, 49], elements = ["Fe","Co", "Ni","Cu","Ti", "Pt"], generate_pure_nanoclusters = True,
n_configurations = 10, n_initial_configurations = 100, bondlength_dct = bondlength_dct ,
)
# store workflow
IS_QUEUE = True
USERNAME = "******"
#PASSWORD = getpass.getpass()
PASSWORD = "******"
if IS_QUEUE:
logging.basicConfig(format='%(name)s:%(levelname)s:%(message)s',
level=logging.INFO)
else:
logdir = str(pathlib.Path(".").resolve())
logging.basicConfig(filename=logdir + "/uniquemolsites_workflow.log",
level=logging.INFO)
# set up the LaunchPad and reset it
launchpad = mylaunchpad.create_launchpad(USERNAME,
PASSWORD,
server="atlas")
#launchpad.reset('', require_password=False)
structures = read_structures_locally("../nc_structures")
# setup nh3 molecule with anchor x
pos = np.array([[0.00000000e+00, 0.00000000e+00, 1.16489000e-01],
[0.00000000e+00, 9.39731000e-01, -2.71808000e-01],
[8.13831000e-01, -4.69865000e-01, -2.71808000e-01],
[-8.13831000e-01, -4.69865000e-01, -2.71808000e-01],
[0.00000000e+00, -1.54520895e-06, 1.91648900e+00]])
adsorbate_x = ase.Atoms('NH3X', positions=pos)
wf = get_uniquemolsites_workflow(
if __name__ == "__main__":
import logging
IS_QUEUE = True
USERNAME = "******"
PASSWORD = getpass.getpass()
if IS_QUEUE:
logging.basicConfig(format='%(name)s:%(levelname)s:%(message)s',
level=logging.INFO)
else:
logdir = str(pathlib.Path(".").resolve())
logging.basicConfig(filename=logdir + "/coverage_workflow.log",
level=logging.INFO)
# set up the LaunchPad and reset it
launchpad = mylaunchpad.create_launchpad(USERNAME,
PASSWORD,
lpadname="mjfireworkstriton")
#launchpad.reset('', require_password=False)
wf = get_coverage_workflow(
username="******",
password=PASSWORD,
template_path=str(
pathlib.Path("./templates/triton_gopt.inp").resolve()),
worker_target_path=
"/scratch/work/jagerm1/workflow_runs/coverage/production/selected_ptni_clusters_topbridgehollow_nremaining80",
extdb_ids=[245, 251],
reference_energy=-1.16195386047558 * 0.5,
adsorbate_name="H",
max_iterations=4,
adsite_types=[
logpath = "fw_logs"
try:
os.makedirs(logpath)
except OSError as e:
if e.errno != errno.EEXIST:
raise
abspath = str(pathlib.Path(logpath).resolve())
if IS_QUEUE:
logging.basicConfig(format='%(name)s:%(levelname)s:%(message)s', level=logging.INFO)
else:
logging.basicConfig(filename = abspath + "/logfile_ranked_adsites.log", level=logging.INFO)
USERNAME = "******"
PASSWORD = "******"
launchpad = mylaunchpad.create_launchpad(USERNAME, PASSWORD, server = "serenity", lpadname = "mjfireworks")
with open('autogenerated_launchpad.yaml', 'w') as outfile:
yaml.dump(launchpad.to_dict(), outfile, default_flow_style=False)
# run the jobs found in the launchpad
# (added previously by other routine)
if IS_OFFLINE:
rlaunch_command = "rlaunch singleshot --offline"
else:
lpad_abspath = str(pathlib.Path("autogenerated_launchpad.yaml").resolve())
rlaunch_command = "rlaunch -l " + lpad_abspath + " singleshot"
print(rlaunch_command)
if IS_QUEUE:
dummy fireworks Workflow
"""
# create the Firework consisting of multiple tasks
firetask1 = TemplateWriterTask({'context': {'opt1': 5.0, 'opt2': 'fast method'}, 'template_file': 'simple_template.txt', 'output_file': 'inputs.txt'})
firetask2 = ScriptTask.from_str('wc -w < inputs.txt > words.txt')
firetask3 = FileTransferTask({'files': [{'src': 'words.txt', 'dest': '~/words.txt'}], 'mode': 'copy'})
wf = Firework([firetask1, firetask2, firetask3])
return wf
if __name__ == "__main__":
import logging
IS_QUEUE = False
print("dummy workflow")
if IS_QUEUE:
logging.basicConfig(format='%(name)s:%(levelname)s:%(message)s', level=logging.INFO)
else:
logdir = str(pathlib.Path(".").resolve())
logging.basicConfig(filename = logdir + "/logfile_dummy_workflow.log", level=logging.INFO)
# set up the LaunchPad and reset it
launchpad = mylaunchpad.create_launchpad()
launchpad.reset('', require_password=False)
wf = dummy_workflow()
# store workflow and launch it locally, single shot
launchpad.add_wf(wf)
#launch_rocket(launchpad, FWorker())
rapidfire(launchpad, FWorker())