def __str__(self):
"""String representation."""
table = [list(self.fields.keys())]
for it in range(self.num_iterations):
row = map(str, (self[k][it] for k in self.keys()))
table.append(row)
stream = StringIO()
pprint_table(table, out=stream)
stream.seek(0)
return "".join(stream)
def __str__(self):
"""String representation."""
table = [list(self.fields.keys())]
for it in range(self.num_iterations):
row = map(str, (self[k][it] for k in self.keys()))
table.append(row)
stream = StringIO()
pprint_table(table, out=stream)
stream.seek(0)
return "".join(stream)
def compute_hints(ecut_list, etotal, atols_mev, pseudo, min_numpts=1, stream=sys.stdout):
de_low, de_normal, de_high = [a / (1000 * Ha_eV) for a in atols_mev]
num_ene = len(etotal)
etotal_inf = etotal[-1]
ihigh = check_conv(etotal, de_high, min_numpts=min_numpts)
inormal = check_conv(etotal, de_normal)
ilow = check_conv(etotal, de_low)
accidx = {"H": ihigh, "N": inormal, "L": ilow}
table = []
app = table.append
app(["iter", "ecut", "etotal", "et-e_inf [meV]", "accuracy",])
for idx, (ec, et) in enumerate(zip(ecut_list, etotal)):
line = "%d %.1f %.7f %.3f" % (idx, ec, et, (et-etotal_inf)* Ha_eV * 1.e+3)
row = line.split() + ["".join(c for c,v in accidx.items() if v == idx)]
app(row)
if stream is not None:
from pymatgen.util.string_utils import pprint_table
stream.write("pseudo: %s\n" % pseudo.name)
pprint_table(table, out=stream)
ecut_high, ecut_normal, ecut_low = 3 * (None,)
exit = (ihigh != -1)
if exit:
ecut_low = ecut_list[ilow]
ecut_normal = ecut_list[inormal]
ecut_high = ecut_list[ihigh]
aug_ratios = [1,]
aug_ratio_low, aug_ratio_normal, aug_ratio_high = 3 * (1,)
data = {
"exit" : ihigh != -1,
"etotal" : list(etotal),
"ecut_list" : ecut_list,
"aug_ratios" : aug_ratios,
"low" : {"ecut": ecut_low, "aug_ratio": aug_ratio_low},
"normal" : {"ecut": ecut_normal, "aug_ratio": aug_ratio_normal},
"high" : {"ecut": ecut_high, "aug_ratio": aug_ratio_high},
"pseudo_name": pseudo.name,
"pseudo_path": pseudo.path,
"atols_mev" : atols_mev,
"dojo_level" : 0,
}
return data
def show_intrawork_deps(self):
"""Show the dependencies within the `Workflow`."""
table = [["Task #"] + [str(i) for i in range(len(self))]]
for ii, task1 in enumerate(self):
line = (1 + len(self)) * [""]
line[0] = str(ii)
for jj, task2 in enumerate(self):
if task1.depends_on(task2):
line[jj+1] = "^"
table.append(line)
pprint_table(table)
def show_status(self, stream=sys.stdout):
"""
Report the status of the workflows and the status
of the different tasks on the specified stream.
"""
for i, work in enumerate(self):
print(80 * "=")
print("Workflow #%d: %s, Finalized=%s\n" %
(i, work, work.finalized))
table = [[
"Task", "Status", "Queue_id", "Errors", "Warnings", "Comments",
"MPI", "OMP", "num_restarts", "max_restarts", "Task Class"
]]
for task in work:
task_name = os.path.basename(task.name)
# Parse the events in the main output.
report = task.get_event_report()
events = map(str, 3 * ["N/A"])
if report is not None:
events = map(str, [
report.num_errors, report.num_warnings,
report.num_comments
])
cpu_info = map(str, [task.mpi_ncpus, task.omp_ncpus])
task_info = map(str, [
task.num_restarts, task.max_num_restarts,
task.__class__.__name__
])
table.append([task_name,
str(task.status),
str(task.queue_id)] + events + cpu_info +
task_info)
pprint_table(table, out=stream)
def show_status(self, stream=sys.stdout):
"""
Report the status of the workflows and the status
of the different tasks on the specified stream.
"""
for i, work in enumerate(self):
print(80*"=")
print("Workflow #%d: %s, Finalized=%s\n" % (i, work, work.finalized) )
table = [[
"Task", "Status", "Queue_id",
"Errors", "Warnings", "Comments",
"MPI", "OMP",
"num_restarts", "max_restarts", "Task Class"
]]
for task in work:
task_name = os.path.basename(task.name)
# Parse the events in the main output.
report = task.get_event_report()
events = map(str, 3*["N/A"])
if report is not None:
events = map(str, [report.num_errors, report.num_warnings, report.num_comments])
cpu_info = map(str, [task.mpi_ncpus, task.omp_ncpus])
task_info = map(str, [task.num_restarts, task.max_num_restarts, task.__class__.__name__])
table.append(
[task_name, str(task.status), str(task.queue_id)] +
events +
cpu_info +
task_info
)
pprint_table(table, out=stream)
def print_table(self, stream=sys.stdout):
pprint_table(self.to_table(), out=stream)
def compute_hints(ecut_list,
etotal,
atols_mev,
pseudo,
min_numpts=1,
stream=sys.stdout):
de_low, de_normal, de_high = [a / (1000 * Ha_eV) for a in atols_mev]
num_ene = len(etotal)
etotal_inf = etotal[-1]
ihigh = check_conv(etotal, de_high, min_numpts=min_numpts)
inormal = check_conv(etotal, de_normal)
ilow = check_conv(etotal, de_low)
accidx = {"H": ihigh, "N": inormal, "L": ilow}
table = []
app = table.append
app([
"iter",
"ecut",
"etotal",
"et-e_inf [meV]",
"accuracy",
])
for idx, (ec, et) in enumerate(zip(ecut_list, etotal)):
line = "%d %.1f %.7f %.3f" % (idx, ec, et,
(et - etotal_inf) * Ha_eV * 1.e+3)
row = line.split() + [
"".join(c for c, v in accidx.items() if v == idx)
]
app(row)
if stream is not None:
from pymatgen.util.string_utils import pprint_table
stream.write("pseudo: %s\n" % pseudo.name)
pprint_table(table, out=stream)
ecut_high, ecut_normal, ecut_low = 3 * (None, )
exit = (ihigh != -1)
if exit:
ecut_low = ecut_list[ilow]
ecut_normal = ecut_list[inormal]
ecut_high = ecut_list[ihigh]
aug_ratios = [
1,
]
aug_ratio_low, aug_ratio_normal, aug_ratio_high = 3 * (1, )
data = {
"exit": ihigh != -1,
"etotal": list(etotal),
"ecut_list": ecut_list,
"aug_ratios": aug_ratios,
"low": {
"ecut": ecut_low,
"aug_ratio": aug_ratio_low
},
"normal": {
"ecut": ecut_normal,
"aug_ratio": aug_ratio_normal
},
"high": {
"ecut": ecut_high,
"aug_ratio": aug_ratio_high
},
"pseudo_name": pseudo.name,
"pseudo_path": pseudo.path,
"atols_mev": atols_mev,
"dojo_level": 0,
}
return data
