def dojo_make_hints(options):
from pymatgen.util.io_utils import ask_yesno, prompt
import numpy as np
for pseudo in options.pseudos:
try:
report = pseudo.dojo_report
hints = report.compute_hints()
print("hints for %s computed from deltafactor prime: %s" % (pseudo.basename, hints))
report.plot_deltafactor_convergence()
ans = ask_yesno("Do you accept the hints? [Y]")
if ans:
report.add_hints(hints)
print(report.has_hints)
pseudo.write_dojo_report(report)
else:
print("The dojoreport contains ecuts :\n%s" % report.ecuts)
new_ecuts = prompt("Enter new ecuts to compute (comma-separated values or empty string to abort)")
if len(new_ecuts) == 0:
print("Exit requested by user")
return
new_ecuts = np.array([float(k) for k in new_ecuts.strip().split(",")])
print(new_ecuts)
report.add_ecuts(new_ecuts)
pseudo.write_dojo_report(report)
except None: # Exception as exc:
print(pseudo.basename, "raised: ", str(exc))
def start(self):
"""
Starts the scheduler in a new thread. Returns 0 if success.
In standalone mode, this method will block until there are no more scheduled jobs.
"""
self.history.append("Started on %s" % time.asctime())
self.start_time = time.time()
if not has_apscheduler:
raise RuntimeError("Install apscheduler with pip")
if has_sched_v3:
self.sched.add_job(self.callback, "interval", **self.sched_options)
else:
self.sched.add_interval_job(self.callback, **self.sched_options)
errors = self.flow.look_before_you_leap()
if errors:
self.exceptions.append(errors)
return 1
# Try to run the job immediately. If something goes wrong return without initializing the scheduler.
self._runem_all()
if self.exceptions:
self.cleanup()
self.send_email(
msg=
"Error while trying to run the flow for the first time!\n %s" %
self.exceptions)
return 1
try:
self.sched.start()
return 0
except KeyboardInterrupt:
self.shutdown(msg="KeyboardInterrupt from user")
if ask_yesno(
"Do you want to cancel all the jobs in the queue? [Y/n]"):
print("Number of jobs cancelled:", self.flow.cancel())
self.flow.pickle_dump()
return -1
def start(self):
"""
Starts the scheduler in a new thread. Returns 0 if success.
In standalone mode, this method will block until there are no more scheduled jobs.
"""
self.history.append("Started on %s" % time.asctime())
self.start_time = time.time()
if not has_apscheduler:
raise RuntimeError("Install apscheduler with pip")
if has_sched_v3:
self.sched.add_job(self.callback, "interval", **self.sched_options)
else:
self.sched.add_interval_job(self.callback, **self.sched_options)
errors = self.flow.look_before_you_leap()
if errors:
self.exceptions.append(errors)
return 1
# Try to run the job immediately. If something goes wrong return without initializing the scheduler.
self._runem_all()
if self.exceptions:
self.cleanup()
self.send_email(msg="Error while trying to run the flow for the first time!\n %s" % self.exceptions)
return 1
try:
self.sched.start()
return 0
except KeyboardInterrupt:
self.shutdown(msg="KeyboardInterrupt from user")
if ask_yesno("Do you want to cancel all the jobs in the queue? [Y/n]"):
print("Number of jobs cancelled:", self.flow.cancel())
self.flow.pickle_dump()
return -1
def dojo_make_hints(options):
"""Add hints for energy cutoffs"""
for pseudo in options.pseudos:
if not pseudo.has_dojo_report:
cprint("[%s] No DojoReport. Ignoring pseudo" % p.basename, "red")
continue
report = pseudo.dojo_report
try:
hints = report.compute_hints()
print("hints for %s computed from deltafactor prime: %s" % (pseudo.basename, hints))
report.plot_deltafactor_convergence(xc=pseudo.xc)
ans = ask_yesno("Do you accept the hints? [Y]")
if ans:
report.add_hints(hints)
print(report.has_hints)
report.json_write()
else:
print("The dojoreport contains ecuts :\n%s" % report.ecuts)
new_ecuts = prompt("Enter new ecuts to compute (comma-separated values or empty string to abort)")
if not new_ecuts:
print("Exit requested by user")
return
new_ecuts = np.array([float(k) for k in new_ecuts.strip().split(",")])
print("new_ecuts", new_ecuts)
report.add_ecuts(new_ecuts)
report.json_write()
except Exception as exc:
cprint("[%s]: python exception: %s" % (pseudo.basename, type(exc)), "red")
if options.verbose: print(straceback())
return 0
def dojo_validate(options):
"""Validate the pseudo."""
pseudos = options.pseudos
data, errors = pseudos.get_dojo_dataframe()
for p in pseudos:
try:
# test if report is present
if not p.has_dojo_report:
cprint("[%s] No DojoReport. Ignoring pseudo" % p.basename, "red")
continue
report = p.dojo_report
# test if already validated
if 'validation' in report:
cprint('this pseudo was validated by %s on %s.' % (
report['validation']['validated_by'], report['validation']['validated_on']), "red")
if not ask_yesno('Would you like to validate it again? [Y/n]'):
continue
# test for ghosts
print('\n= GHOSTS TEST ===========================================\n')
if report.has_trial('ghosts'):
for ecut in report['ghosts']:
if "ghost_free_upto_eV" in report["ghosts"][ecut]:
print('%s: Pseudo is reported to be ghost free up to %s eV' % (
ecut, report["ghosts"][ecut]["ghost_free_upto_eV"]))
else:
report.plot_ebands(ecut=ecut)
ans = float(prompt('Please enter the energy (eV) up until there is no sign of ghosts:\n'))
if ans > 0:
report["ghosts"][ecut]["ghost_free_upto_eV"] = ans
report.json_write()
else:
cprint('no ghosts trial present, pseudo cannot be validated', "red")
continue
# test trials
print('\n= TRIALS TEST ===========================================\n')
try:
error = report.check(check_trials=None)
if error:
cprint("[%s] Validation problem" % p.basename, "red")
if options.verbose:
print(error)
print()
except Exception as exc:
cprint("[%s] Python exception: %s" % (p.basename, type(exc)), "red")
if options.verbose:
print(exc)
print("")
accuracies = ["low", "normal", "high"]
keys = ['hint', 'deltafactor', 'gbrv_bcc', 'gbrv_fcc', 'phonon']
tablefmt = "grid"
floatfmt=".2f"
print('\n= ECUTS TEST ===========================================\n')
for acc in accuracies:
columns = ["symbol"]
headers = ["symbol"]
for k in keys:
entry = acc + "_ecut_" + k
if entry in data:
columns.append(entry)
headers.append(k)
print('ECUTS for accuracy %s:' % acc)
print(tabulate(data[columns], headers=headers, tablefmt=tablefmt, floatfmt=floatfmt))
# TODO
# test hash
# plot the model core charge
except Exception as exc:
cprint("[%s] python exception" % p.basename, "red")
if options.verbose: print(straceback())
# ask the final question
if ask_yesno('Will you validate this pseudo? [n]'):
name = prompt("Please enter your name for later reference: ")
report['validation'] = {'validated_by': name, 'validated_on': strftime("%Y-%m-%d %H:%M:%S", gmtime())}
report.json_write()
return 0
