def main_init(args):
"""Initialize a FlowProject from a template.
The available templates are defined in the template module.
"""
if not args.alias.isidentifier():
raise ValueError(
"The alias '{}' is not a valid Python identifier and can therefore "
"not be used as a FlowProject alias.".format(args.alias)
)
try:
get_project()
except LookupError:
init_project(name=args.alias)
print(
"Initialized signac project with name '{}' in "
"current directory.".format(args.alias),
file=sys.stderr,
)
try:
return template.init(alias=args.alias, template=args.template)
except OSError as error:
raise RuntimeError(
f"Error occurred while trying to initialize a flow project: {error}"
)
def main():
project = signac.init_project("rpa", workspace="workspace")
for N in range(76, 96 + 2, 2):
for T in (0.0, 0.5, 1.0, 2.0):
statepoint = dict(
# atomic number Z
proton_number=50, # fixed atomic number
# neutron number N
neutron_number=N,
# nucleus angular momentum
angular_momentum=1, #
# nucleus parity
parity="-", #
# system temperature in MeV
temperature=T,
# transition energy in MeV
transition_energy=0.42, # 0.42 is random
)
project.open_job(statepoint).init()
for job in project:
nprot = job.sp.proton_number
nneutr = job.sp.neutron_number
nucleus = util.get_nucleus(proton_number=nprot, neutron_number=nneutr)
job.doc.setdefault("nucleus", nucleus)
def test_sync_merge(self):
project_b = signac.init_project("ProjectB",
os.path.join(self.tmpdir.name, "b"))
self.call("python -m signac init ProjectA".split())
project_a = signac.Project()
for i in range(4):
project_a.open_job({"a": i}).init()
project_b.open_job({"a": i}).init()
project_a.open_job({"c": 1}).init()
project_b.open_job({"b": 1}).init()
project_b.open_job({"a": 4}).init()
assert len(project_a) == 5
assert len(project_b) == 6
# sync with projects having diffent schema
with pytest.raises(ExitCodeError):
self.call("python -m signac sync {} {}".format(
os.path.join(self.tmpdir.name, "b"), self.tmpdir.name).split())
assert len(project_a) == 5
assert len(project_b) == 6
self.call("python -m signac sync {} {} --merge".format(
os.path.join(self.tmpdir.name, "b"), self.tmpdir.name).split())
assert len(project_a) == 7
assert len(project_b) == 6
def main(args, random_seed):
project = signac.init_project('MyProject')
statepoints_init = []
for replication_index in range(args.num_replicas):
for p in np.linspace(0.5, 5.0, 10):
statepoint = dict(
# system size
N=512,
# Lennard-Jones potential parameters
sigma=1.0,
epsilon=1.0,
r_cut=2.5,
# random seed
seed=random_seed * (replication_index + 1),
# thermal energy
kT=1.0,
# presure
p=p,
# thermostat coupling constant
tau=1.0,
# barostat coupling constant
tauP=1.0)
project.open_job(statepoint).init()
statepoints_init.append(statepoint)
# Writing statepoints to hash table as backup
project.write_statepoints(statepoints_init)
def model_experiments_finished(job: signac.Project.Job, key="succeeded"):
if not model_experiments_needed(job):
return False
for featureJob, splitJob, feature_graph_name, feature_graph_files in feature_split_iter(job):
if re.search(get_exp_regex(job), feature_graph_name) is None:
continue
elif splitJob not in utils.signac_tools.getSplitProject(featureJob).find_jobs(
task_args.split_filter, task_args.split_doc_filter):
continue
md5_str = "_".join(map(lambda x: calculate_md5(
splitJob.fn(x)), feature_graph_files))
exp_args_list = task_args.model_args or splitJob.doc.get(
expCode, default=[])
if exp_args_list == [] and is_tuning():
exp_args_list = [""]
for args in exp_args_list:
if task_args.arg_regex is not None and re.search(task_args.arg_regex, args) is None:
continue
dataset_dir = splitJob.workspace()
datasetDirObj = Path(dataset_dir)
# Workspace path
workspaceDirObj = datasetDirObj / workspaceRoot # type:Path
if not (workspaceDirObj.exists() and workspaceDirObj.is_dir()):
return False
modelProject = signac.init_project(
name=expProjectName, root=str(workspaceDirObj))
run_id = "{}@{}".format(args, md5_str)
if is_tuning():
run_id += "[tuning]"
if not any(map(lambda job_i: job_i.doc.get(key, False), modelProject.find_jobs(filter={"run_id": run_id}))):
return False
return True
def main():
project = signac.init_project("Ideal-Gas-Example-Project")
# sweep over 10 pressures evenly spaced between 0.5 and 5.0
for p in np.linspace(0.5, 5.0, 10):
statepoint = dict(
# system size
N=512,
# Lennard-Jones potential parameters
sigma=1.0,
epsilon=1.0,
r_cut=2.5,
# thermal energy
kT=1.0,
# pressure
p=float(p),
# thermostat coupling constant
tau=1.0,
# barostat coupling constant
tauP=1.0,
)
# open the job and initialize
job = project.open_job(statepoint)
# define run steps in the job document so that run_steps
# can be changed without modifying the statepoint
job.doc["run_steps"] = 5000
print(f"initializing state point with id {job.id} and p = {job.sp.p}")
job.init()
def init_project():
# Initialize project
project = signac.init_project("nvt-1x1x1nm_1-layer")
# Define temperature
temperature = 298.0 * u.K
# Define number of waters in the pore
nwater = 24
# Run for 500 M steps
nsteps_eq = 5000000
nsteps_prod = 505000000
# For reproducibility
np.random.seed(1)
for run in range(3):
# Define the state point
state_point = {
"T": float(temperature.in_units(u.K).value),
"nsteps": {
"equil" : nsteps_eq,
"prod" : nsteps_prod,
},
"run": run,
"nwater" : nwater,
"seed1" : np.random.randint(10**8),
"seed2" : np.random.randint(10**8),
}
job = project.open_job(state_point)
job.init()
def main(args, random_seed):
project = signac.init_project('Lennard-Jones-Fluid-Example-Project')
for replication_index in range(args.num_replicas):
for p in np.linspace(0.5, 5.0, 10):
statepoint = dict(
# system size
N=512,
# Lennard-Jones potential parameters
sigma=1.0,
epsilon=1.0,
r_cut=2.5,
# random seed
seed=random_seed * (replication_index + 1),
# thermal energy
kT=1.0,
# presure
p=p,
# thermostat coupling constant
tau=1.0,
# barostat coupling constant
tauP=1.0)
project.open_job(statepoint).init()
def test_sync_file(self):
self.call("python -m signac init ProjectA".split())
project_a = signac.Project()
project_b = signac.init_project("ProjectB", os.path.join(self.tmpdir.name, "b"))
job_src = project_a.open_job({"a": 0}).init()
job_dst = project_b.open_job({"a": 0}).init()
for i, job in enumerate([job_src, job_dst]):
with open(job.fn("test"), "w") as file:
file.write("x" * (i + 1))
# FileSyncConflict
with pytest.raises(ExitCodeError):
self.call(
"python -m signac sync {} {}".format(
os.path.join(self.tmpdir.name, "b"), self.tmpdir.name
).split()
)
self.call(
"python -m signac sync {} {} --strategy never".format(
os.path.join(self.tmpdir.name, "b"), self.tmpdir.name
).split()
)
with open(job_dst.fn("test")) as file:
assert file.read() == "xx"
with pytest.raises(ExitCodeError):
self.call(
"python -m signac sync {} {}".format(
os.path.join(self.tmpdir.name, "b"), self.tmpdir.name
).split()
)
self.call(
"python -m signac sync {} {} --update".format(
os.path.join(self.tmpdir.name, "b"), self.tmpdir.name
).split()
)
def test_clone(self):
self.call('python -m signac init ProjectA'.split())
project_a = signac.Project()
project_b = signac.init_project('ProjectB',
os.path.join(self.tmpdir.name, 'b'))
job = project_a.open_job({'a': 0})
job.init()
assert len(project_a) == 1
assert len(project_b) == 0
self.call("python -m signac clone {} {}".format(
os.path.join(self.tmpdir.name, 'b'), job.id).split())
assert len(project_a) == 1
assert job in project_a
assert len(project_b) == 1
assert job in project_b
# cloning a job that exist at both source and destination
err = self.call("python -m signac clone {} {}".format(
os.path.join(self.tmpdir.name, 'b'), job.id).split(),
error=True)
assert 'Destination already exists' in err
assert len(project_a) == 1
assert job in project_a
assert len(project_b) == 1
assert job in project_b
# checking for id that does not exit at source
with pytest.raises(ExitCodeError):
self.call("python -m signac clone {} 9bfd29df07674bc5".format(
os.path.join(self.tmpdir.name, 'b')).split())
assert len(project_a) == 1
assert len(project_b) == 1
def main(args, random_seed):
project = signac.init_project("TerminalGroupScreeningNewWithOld")
logging.info("Init begin: {}".format(datetime.datetime.today()))
logging.info("Initialized project name")
statepoints = list()
# generate the new top and bottom monolayers
for replication_index in range(args.num_replicas):
for terminal_group_a in terminal_groups_A:
for terminal_group_b in terminal_groups_new_B:
if terminal_group_a != terminal_group_b:
the_statepoint = dict(
# Carbon backbone length
chainlength=17,
# Number of monolayer chains
n=100,
# Random seed
seed=random_seed * (replication_index + 1),
# Terminal group chemistries
terminal_groups=tuple(
sorted((terminal_group_a, terminal_group_b))))
project.open_job(statepoint=the_statepoint).init()
statepoints.append(the_statepoint)
logging.info(
msg="At the statepoint: {}".format(the_statepoint))
# write statepoints to signac statepoint file
project.write_statepoints(statepoints=statepoints)
def test_import_sync(self):
project_b = signac.init_project("ProjectB",
os.path.join(self.tmpdir.name, "b"))
self.call("python -m signac init ProjectA".split())
prefix_data = os.path.join(self.tmpdir.name, "data")
project_a = signac.Project()
for i in range(4):
project_a.open_job({"a": i}).init()
project_b.open_job({"a": i}).init()
job_dst = project_a.open_job({"a": 0})
job_src = project_b.open_job({"a": 0})
job_src.document["a"] = 0
project_b.export_to(prefix_data)
err = self.call(f"python -m signac import {prefix_data}".split(),
error=True)
assert "Import failed" in err
self.call(f"python -m signac import {prefix_data} --sync".split(),
error=True)
assert len(project_a) == 4
assert "a" in job_dst.document
assert job_dst.document["a"] == 0
out = self.call(
f"python -m signac import {prefix_data} --sync-interactive",
"print(str(tmp_project), len(tmp_project)); exit()",
shell=True,
)
assert "ProjectA" in out
assert "4" in out
def main(args):
project = signac.init_project('oak_ridge_ray')
statepoints_init = []
temperatures = [283, 288, 293, 298, 303, 308, 313, 318, 323, 328, 333]
cations = ['EMIM', 'BMIM', 'HMIM']
for cation in cations:
for temp in temperatures:
if cation == 'EMIM':
for conc in ES_conc:
statepoint = dict(cation=cation,
T=temp,
concIL=float(conc[0]),
concACN=float(conc[1]))
project.open_job(statepoint).init()
statepoints_init.append(statepoint)
if cation == 'BMIM':
for conc in BS_conc:
statepoint = dict(cation=cation,
T=temp,
concIL=float(conc[0]),
concACN=float(conc[1]))
project.open_job(statepoint).init()
statepoints_init.append(statepoint)
if cation == 'HMIM':
for conc in HS_conc:
statepoint = dict(cation=cation,
T=temp,
concIL=float(conc[0]),
concACN=float(conc[1]))
project.open_job(statepoint).init()
statepoints_init.append(statepoint)
# Writing statepoints to hash table as a backup
project.write_statepoints(statepoints_init)
def test_import_sync(self):
project_b = signac.init_project('ProjectB',
os.path.join(self.tmpdir.name, 'b'))
self.call('python -m signac init ProjectA'.split())
prefix_data = os.path.join(self.tmpdir.name, 'data')
project_a = signac.Project()
for i in range(4):
project_a.open_job({'a': i}).init()
project_b.open_job({'a': i}).init()
job_dst = project_a.open_job({'a': 0})
job_src = project_b.open_job({'a': 0})
job_src.document['a'] = 0
project_b.export_to(prefix_data)
err = self.call(
"python -m signac import {}".format(prefix_data).split(),
error=True)
assert "Import failed" in err
self.call(
"python -m signac import {} --sync".format(prefix_data).split(),
error=True)
assert len(project_a) == 4
assert 'a' in job_dst.document
assert job_dst.document['a'] == 0
out = self.call('python -m signac import {} --sync-interactive'.format(
prefix_data),
'print(str(tmp_project), len(tmp_project)); exit()',
shell=True)
assert 'ProjectA' in out
assert '4' in out
def main():
project = signac.init_project("project")
param_names, param_combinations = get_parameters()
# Create the generate jobs
for params in param_combinations:
parent_statepoint = dict(zip(param_names, params))
parent_job = project.open_job(parent_statepoint)
parent_job.init()
try:
parent_job.doc.setdefault("steps", parent_statepoint["n_steps"])
except:
parent_job.doc.setdefault(
"steps", np.sum(parent_statepoint["anneal_sequence"]))
parent_job.doc.setdefault("step_sequence",
parent_statepoint["anneal_sequence"])
if parent_job.sp['signac_args'] is not [None]:
parent_job.doc.setdefault("use_signac", True)
parent_job.doc.setdefault("slab_files",
parent_job.sp['signac_args'])
elif parent_job.sp['slab_file'] is not [None]:
parent_job.doc.setdefault("use_signac", False)
parent_job.doc.setdefault("slab_files", parent_job.sp['slab_file'])
if custom_job_doc:
for key in custom_job_doc:
parent_job.doc.setdefault(key, custom_job_doc[key])
project.write_statepoints()
def init_project():
# Initialize project
project = signac.init_project("a1x1x1nm_1-layer")
# Define temperature
temperature = 298.0 * u.K
# Define chemical potentials
mus = [
-43.0 * u.kJ / u.mol,
-42.0 * u.kJ / u.mol,
]
# Run for 300 M steps
nsteps_gcmc = 300000000
# For reproducibility
np.random.seed(9597)
for mu in mus:
for run in range(3):
# Define the state point
state_point = {
"T": float(temperature.in_units(u.K).value),
"mu": float(mu.in_units(u.kJ / u.mol).value),
"nsteps_gcmc": nsteps_gcmc,
"seed1": np.random.randint(10**8),
"seed2": np.random.randint(10**8),
"run": run,
}
job = project.open_job(state_point)
job.init()
def main(args, random_seed):
project = signac.init_project('TerminalGroupScreeningMixed')
statepoints = []
for replication_index in range(args.num_replicas):
for terminal_group_a in terminal_groups_a:
for terminal_group_b in terminal_groups_b:
if terminal_group_a != terminal_group_b:
statepoint = dict(
# Carbon backbone length
chainlength=17,
# Number of monolayer chains
n=100,
# Random seed
seed=random_seed * (replication_index + 1),
# Terminal group chemistries
terminal_groups=tuple(
sorted((terminal_group_a, terminal_group_b))))
project.open_job(statepoint).init()
statepoints.append(statepoint)
'''
------------------------------------------
Writing statpoints to hash table as backup
------------------------------------------
'''
project.write_statepoints(statepoints)
def make_project(alias="project", root=None, **kwargs):
r"""Initialize a project for testing.
The initialized project has a few operations and a few jobs that are in
various points in the workflow defined by the project.
Parameters
----------
alias : str
Python identifier used as a file name for the template output.
(Default value = ``"project"``)
root : str
Directory where the output file is placed. Uses the current working
directory if None. (Default value = None)
\*\*kwargs
Keyword arguments forwarded to :meth:`signac.testing.init_jobs`.
Returns
-------
:class:`signac.Project`
Project with initialized jobs.
"""
init(alias=alias, root=root, template="testing")
project = signac.init_project(name=alias, root=root)
signac.testing.init_jobs(project, **kwargs)
return project
def test_sync_merge(self):
project_b = signac.init_project('ProjectB',
os.path.join(self.tmpdir.name, 'b'))
self.call('python -m signac init ProjectA'.split())
project_a = signac.Project()
for i in range(4):
project_a.open_job({'a': i}).init()
project_b.open_job({'a': i}).init()
project_a.open_job({'c': 1}).init()
project_b.open_job({'b': 1}).init()
project_b.open_job({'a': 4}).init()
assert len(project_a) == 5
assert len(project_b) == 6
# sync with projects having diffent schema
with pytest.raises(ExitCodeError):
self.call('python -m signac sync {} {}'.format(
os.path.join(self.tmpdir.name, 'b'), self.tmpdir.name).split())
assert len(project_a) == 5
assert len(project_b) == 6
self.call('python -m signac sync {} {} --merge'.format(
os.path.join(self.tmpdir.name, 'b'), self.tmpdir.name).split())
assert len(project_a) == 7
assert len(project_b) == 6
def init_project():
# Initialize project
project = signac.init_project("gromacs_nvt1x1x1-1nm_1-layer")
# Define temperature
temperature = 298.0 * u.K
# Start with a few different number of waters in the pore
nwaters = [1, 23, 24]
for nwater in nwaters:
if nwater == 1:
nsteps = 100000000
else:
nsteps = 50000000
# Define the state point
state_point = {
"T": float(temperature.in_units(u.K).value),
"nwater": nwater,
"nsteps": nsteps,
}
job = project.open_job(state_point)
job.init()
def test_move(self):
self.call('python -m signac init ProjectA'.split())
project_a = signac.Project()
project_b = signac.init_project('ProjectB',
os.path.join(self.tmpdir.name, 'b'))
job = project_a.open_job({'a': 0})
job.init()
assert len(project_a) == 1
assert len(project_b) == 0
self.call("python -m signac move {} {}".format(
os.path.join(self.tmpdir.name, 'b'), job.id).split())
assert len(project_a) == 0
assert job not in project_a
assert len(project_b) == 1
assert job in project_b
# moving a job that already exists at destination
project_a.open_job({'a': 0}).init()
err = self.call("python -m signac move {} {}".format(
os.path.join(self.tmpdir.name, 'b'), job.id).split(),
error=True)
assert 'Destination already exists' in err
assert len(project_a) == 1
assert job in project_a
assert len(project_b) == 1
assert job in project_b
# moving a job that does not exits
with pytest.raises(ExitCodeError):
self.call("python -m signac move {} 9bfd29df07674bc5".format(
os.path.join(self.tmpdir.name, 'b')).split())
assert len(project_a) == 1
assert len(project_b) == 1
def main():
talys_proj = signac.init_project("talys", workspace="workspace")
logger.info("talys project: %s" % talys_proj.workspace())
rpa_proj = signac.get_project(root="../rpa/")
logger.info("rpa project: %s" % rpa_proj.workspace())
for psf, jobs in rpa_proj.find_jobs({
"proton_number": 50
}).groupbydoc("photon_strength_function"):
for rpa_job in jobs:
logger.info(f"Processing %s.." % rpa_job.workspace())
sp = rpa_proj.open_job(id=rpa_job.id).statepoint()
for yn in "y", "n":
sp.update(
dict(
# flag for calculation of astrophysics reaction rate
astro=yn))
talys_job = talys_proj.open_job(sp).init()
util.copy_file(source=rpa_job.fn(psf),
destination=talys_job.fn(psf))
talys_job.doc.setdefault("photon_strength_function", psf)
talys_api.energy_file(talys_job)
talys_api.input_file(talys_job)
def getSplitProject(featureJob: signac.Project.Job):
try:
splitProject = signac.get_project(root=featureJob.workspace(),
search=False)
except LookupError:
splitProject = signac.init_project("SyntheticExperimentSplits",
root=featureJob.workspace(),
workspace="splits")
return splitProject
def getFeatureProject(graphJob: signac.Project.Job):
try:
featureProject = signac.get_project(root=graphJob.workspace(),
search=False)
except LookupError:
featureProject = signac.init_project("SyntheticExperimentFeatures",
root=graphJob.workspace(),
workspace="features")
return featureProject
def setup_random_project(N, num_keys=1, num_doc_keys=0,
data_size=0, data_std=0, seed=0, root=None):
random.seed(seed)
if not isinstance(N, int):
raise TypeError("N must be an integer!")
with TemporaryDirectory(dir=root) as tmp:
project = signac.init_project('benchmark-N={}'.format(N), root=tmp)
generate_random_data(project, N, num_keys, num_doc_keys, data_size, data_std)
yield project
def main(args):
project = signac.init_project('Alkanes')
for seed in range(args.num_replicas):
for C_n in [6, 8, 10]:
statepoint = dict(
# length of alkane
C_n=C_n,
# random seed
seed=seed)
project.open_job(statepoint).init()
def make_project(alias='project', root=None, **kwargs):
"""Initialize a project for testing.
The initialized project has a few operations and a few jobs that are in
various points in the workflow defined by the project.
"""
init(alias=alias, root=root, template='testing')
project = signac.init_project(name=alias, root=root)
signac.testing.init_jobs(project, **kwargs)
return project
def main(parameters):
project = signac.init_project(project_name)
param_names, param_combinations = get_parameters(parameters)
# Create the generate jobs
for params in param_combinations:
parent_statepoint = dict(zip(param_names, params))
parent_job = project.open_job(parent_statepoint)
parent_job.init()
parent_job.doc.setdefault("steps", sum(parent_statepoint["n_steps"]))
project.write_statepoints()
print(f"Initialized. ({len(param_combinations)} total jobs)")
def main(args):
"""For the particles synthesized by Zhe at the Secanna group"""
project = signac.init_project('SecannaAssembly')
pfs = round_wrap(np.linspace(0.55, 0.60, 5, endpoint=True))
truncations = round_wrap(np.arange(0.47, 0.84, 0.02))
structures = ['cubicdiamond', 'hexagonaldiamond']
sps = cartesian(pf=pfs, truncation=truncations, structure=structures)
for sp in sps:
project.open_job(sp).init()
def main(args):
if not os.path.exists(PROJECT_DIR):
os.makedirs(PROJECT_DIR)
elif args.force:
import shutil
shutil.rmtree(PROJECT_DIR)
os.makedirs(PROJECT_DIR)
else:
return
p = signac.init_project(name=gen.PROJECT_NAME, root=PROJECT_DIR)
p.import_from(origin=gen.ARCHIVE_DIR)