def fix_filepath(pp_filepath):
pseudo = dojopseudo_from_file(pp_filepath)
if pseudo is None:
print("Error while parsing %s" % pp_filepath)
return 1
# Change md5
pseudo.dojo_report["md5"] = pseudo.compute_md5()
if pseudo.dojo_report["pseudo_type"] == "norm-conserving":
pseudo.dojo_report["pseudo_type"] = "NC"
# Add basename
if "basename" not in pseudo.dojo_report:
pseudo.dojo_report["basename"] = pseudo.basename
if pseudo.dojo_report["basename"] != pseudo.basename:
print("Inconsistent basename in %s" % pp_filepath)
return 1
# Remove ebands
#pseudo.dojo_report.pop("ebands", None)
#if pseudo.dojo_report.pop("phonon", None) is None: return 0
# Rename entries in FR pseudos.
#oldnew = [("deltafactor", "deltafactor_soc"),
# ("gbrv_fcc", "gbrv_fcc_soc"),
# ("gbrv_bcc", "gbrv_bcc_soc")]
#for old, new in oldnew:
# if old in pseudo.dojo_report:
# pseudo.dojo_report[new] = pseudo.dojo_report.pop(old)
#pseudo.dojo_report.reorder()
pseudo.dojo_report.json_write()
return 0
def fix_filepath(pp_filepath):
pseudo = dojopseudo_from_file(pp_filepath)
if pseudo is None:
print("Error while parsing %s" % pp_filepath)
return 1
# Change md5
pseudo.dojo_report["md5"] = pseudo.compute_md5()
if pseudo.dojo_report["pseudo_type"] == "norm-conserving":
pseudo.dojo_report["pseudo_type"] = "NC"
# Add basename
if "basename" not in pseudo.dojo_report:
pseudo.dojo_report["basename"] = pseudo.basename
if pseudo.dojo_report["basename"] != pseudo.basename:
print("Inconsistent basename in %s" % pp_filepath)
return 1
# Remove ebands
#pseudo.dojo_report.pop("ebands", None)
#if pseudo.dojo_report.pop("phonon", None) is None: return 0
# Rename entries in FR pseudos.
#oldnew = [("deltafactor", "deltafactor_soc"),
# ("gbrv_fcc", "gbrv_fcc_soc"),
# ("gbrv_bcc", "gbrv_bcc_soc")]
#for old, new in oldnew:
# if old in pseudo.dojo_report:
# pseudo.dojo_report[new] = pseudo.dojo_report.pop(old)
#pseudo.dojo_report.reorder()
pseudo.dojo_report.json_write()
return 0
def check_pseudo_path(path, verbose=0):
"""
Check a pseudopotential given the filepath. Warnings are printed to stdout.
Return 0 if success.
"""
pseudo = dojopseudo_from_file(path)
if pseudo is None:
cprint("[%s] Pseudo.from_file returned None. Something wrong in file!" % path, "red")
return 1
return check_pseudo(pseudo, verbose=verbose)
def check_pseudo_path(path, verbose=0):
"""
Check a pseudopotential given the filepath. Warnings are printed to stdout.
Return 0 if success.
"""
pseudo = dojopseudo_from_file(path)
if pseudo is None:
cprint("[%s] Pseudo.from_file returned None. Something wrong in file!" % path, "red")
return 1
return check_pseudo(pseudo, verbose=verbose)
def djrepo_pop(options):
"""Remove trials from djrepo files."""
for path in options.paths:
pseudo = dojopseudo_from_file(path)
report = pseudo.dojo_report
count = 0
for trial in options.trials:
if report.pop(trial, None) is not None:
cprint("[%s] removed from %s" % (trial, path), "yellow")
count += 1
if count != 0:
pseudo.dojo_report.json_write()
def djrepo_pop(options):
"""Remove trials from djrepo files."""
for path in options.paths:
pseudo = dojopseudo_from_file(path)
report = pseudo.dojo_report
count = 0
for trial in options.trials:
if report.pop(trial, None) is not None:
cprint("[%s] removed from %s" % (trial, path), "yellow")
count += 1
if count != 0:
pseudo.dojo_report.json_write()
def get_pseudos(options):
"""
Find pseudos in paths, return :class:`DojoTable` object sorted by atomic number Z.
Accepts filepaths or directory.
"""
exts = ("psp8", "xml")
paths = options.pseudos
if len(paths) == 1:
# Handle directory argument
if os.path.isdir(paths[0]):
top = os.path.abspath(paths[0])
paths = find_exts(top, exts, exclude_dirs="_*")
# Handle glob syntax e.g. "./*.psp8"
elif "*" in paths[0]:
paths = glob.glob(paths[0])
if options.verbose > 1: print("Will read pseudo from: %s" % paths)
pseudos = []
for p in paths:
try:
pseudo = dojopseudo_from_file(p)
if pseudo is None:
cprint("[%s] Pseudo.from_file returned None. Something wrong in file!" % p, "red")
continue
pseudos.append(pseudo)
except Exception as exc:
cprint("[%s] Python exception. This pseudo will be ignored" % p, "red")
if options.verbose: print(exc)
table = DojoTable(pseudos)
# Here we select a subset of pseudos according to family or rows
if options.rows:
table = table.select_rows(options.rows)
elif options.family:
table = table.select_families(options.family)
# here we select chemical symbols.
if options.symbols:
table = table.select_symbols(options.symbols)
return table.sort_by_z()
def get_pseudos(options):
"""
Find pseudos in paths, return :class:`DojoTable` object sorted by atomic number Z.
Accepts filepaths or directory.
"""
exts = ("psp8", "xml")
paths = options.pseudos
if len(paths) == 1:
# Handle directory argument
if os.path.isdir(paths[0]):
top = os.path.abspath(paths[0])
paths = find_exts(top, exts, exclude_dirs="_*")
# Handle glob syntax e.g. "./*.psp8"
elif "*" in paths[0]:
paths = glob.glob(paths[0])
if options.verbose > 1: print("Will read pseudo from: %s" % paths)
pseudos = []
for p in paths:
try:
pseudo = dojopseudo_from_file(p)
if pseudo is None:
cprint("[%s] Pseudo.from_file returned None. Something wrong in file!" % p, "red")
continue
pseudos.append(pseudo)
except Exception as exc:
cprint("[%s] Python exception. This pseudo will be ignored" % p, "red")
if options.verbose: print(exc)
table = DojoTable(pseudos)
# Here we select a subset of pseudos according to family or rows
if options.rows:
table = table.select_rows(options.rows)
elif options.family:
table = table.select_families(options.family)
# here we select chemical symbols.
if options.symbols:
table = table.select_symbols(options.symbols)
return table.sort_by_z()
def djrepo_recalc(options):
"""
Recompute the deltafactor from the data stored in the dojoreport.
This function is used when the deltafactor reference results have been changed.
"""
for path in options.paths:
pseudo = dojopseudo_from_file(path)
data = pseudo.dojo_report["deltafactor"]
# Recompute delfactor for the different ecut.
for ecut, entry in data.items():
new_entry, eos_fit = dojo_dfact_results(pseudo, entry["num_sites"], entry["volumes"], entry["etotals"])
print("ecut: ", ecut, "(new - old) df:", new_entry["dfact_meV"] - entry["dfact_meV"])
data[ecut] = new_entry
# Write new djson file.
pseudo.dojo_report.json_write()
return 0
def djrepo_recalc(options):
"""
Recompute the deltafactor from the data stored in the dojoreport.
This function is used when the deltafactor reference results have been changed.
"""
for path in options.paths:
pseudo = dojopseudo_from_file(path)
data = pseudo.dojo_report["deltafactor"]
# Recompute delfactor for the different ecut.
for ecut, entry in data.items():
new_entry, eos_fit = dojo_dfact_results(pseudo, entry["num_sites"],
entry["volumes"],
entry["etotals"])
print("ecut: ", ecut, "(new - old) df:",
new_entry["dfact_meV"] - entry["dfact_meV"])
data[ecut] = new_entry
# Write new djson file.
pseudo.dojo_report.json_write()
return 0
def djrepo_check(options):
"""Check djrepo files."""
retcode = 0
for path in options.paths:
#print(path)
pseudo = dojopseudo_from_file(path)
report = pseudo.dojo_report
validation = report.get("validation", None)
if validation is None:
retcode += 1
cprint("[%s]: no validation entry" % path)
continue
hints = report.get("hints", None)
if hints is None:
retcode += 1
cprint("[%s]: no hints entry" % path)
continue
for k in ("low", "normal", "high"):
if k not in hints:
retcode += 1
cprint("[hint=%s]: not present" % k)
continue
return retcode
def djrepo_check(options):
"""Check djrepo files."""
retcode = 0
for path in options.paths:
#print(path)
pseudo = dojopseudo_from_file(path)
report = pseudo.dojo_report
validation = report.get("validation", None)
if validation is None:
retcode += 1
cprint("[%s]: no validation entry" % path)
continue
hints = report.get("hints", None)
if hints is None:
retcode += 1
cprint("[%s]: no hints entry" % path)
continue
for k in ("low", "normal", "high"):
if k not in hints:
retcode += 1
cprint("[hint=%s]: not present" % k)
continue
return retcode
def main():
def str_examples():
return """\
Usage Example:
ppdojo_run.py Si.psp8 => Build pseudo_dojo flow for Si.fhi
"""
def show_examples_and_exit(error_code=1):
"""Display the usage of the script."""
print(str_examples())
sys.exit(error_code)
parser = argparse.ArgumentParser(epilog=str_examples())
parser.add_argument('-m', '--manager', type=str, default=None, help="Manager file")
parser.add_argument('-w', '--workdir', type=str, default=None,
help="Working directory. Default: Automatically generated from pseudo name.")
parser.add_argument('-d', '--dry-run', default=False, action="store_true",
help="Dry run, build the flow without submitting it")
parser.add_argument('--paral-kgb', type=int, default=0, help="Paral_kgb input variable.")
parser.add_argument('--soc', default=False, action="store_true", help=(
"Perform non-collinear run (nspinor==2, kptopt=3). Pseudo must have spin-orbit characteristic"))
#parser.add_argument('-n', '--new-ecut', type=int, default=None, action="store",
# help="Extend the ecut grid with the new-ecut point")
def parse_trials(s):
if s == "all": return ["df", "gbrv"]
return s.split(",")
parser.add_argument('--trials', default="all", type=parse_trials,
help=("List of tests e.g --trials=ghosts,df,gbrv\n"
" ghosts: tests ghost states in the conduction region.\n"
" df: test delta factor against all electron reference.\n"
" gbrv: test fcc and bcc lattice parameters against AE reference.\n"
" phgamma: test violation of the acoustic sum rule\n"))
parser.add_argument('--loglevel', default="ERROR", type=str,
help="set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG")
parser.add_argument('-v', '--verbose', default=0, action='count', # -vv --> verbose=2
help='Verbose, can be supplied multiple times to increase verbosity')
parser.add_argument('path', help='pseudopotential file.')
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
options.manager = abilab.TaskManager.as_manager(options.manager)
from pseudo_dojo import logo1
cprint(logo1(), "red")
pseudo = dojopseudo_from_file(options.path)
if pseudo is None:
cprint("Error while parsing: %s" % options.path)
cprint("Check your file. Returning 1")
return 1
flow = build_flow(pseudo, options)
if flow is None:
cprint("DOJO_REPORT is already computed for pseudo %s." % options.path, "magenta")
return 1
if options.dry_run:
flow.build_and_pickle_dump(abivalidate=False)
return 0
else:
# Run the flow with the scheduler.
return flow.make_scheduler().start()
def main():
def str_examples():
return """\
Usage example:
dojogbrv.py info => Print all entries in the GBRV database.
"""
def show_examples_and_exit(err_msg=None, error_code=1):
"""Display the usage of the script."""
sys.stderr.write(str_examples())
if err_msg: sys.stderr.write("Fatal Error\n" + err_msg + "\n")
sys.exit(error_code)
# Parent parser for common options.
copts_parser = argparse.ArgumentParser(add_help=False)
copts_parser.add_argument(
'--loglevel',
default="ERROR",
type=str,
help=
"set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG"
)
copts_parser.add_argument(
'-v',
'--verbose',
default=0,
action='count', # -vv --> verbose=2
help='Verbose, can be supplied multiple times to increase verbosity')
copts_parser.add_argument(
'-d',
'--dry-run',
default=False,
action="store_true",
help=
("Dry run, build the flow and check validity of input files without submitting"
))
# Build the main parser.
parser = argparse.ArgumentParser(
epilog=str_examples(),
parents=[copts_parser],
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('pseudo', help='Pseudopotential file.')
# Create the parsers for the sub-commands
#subparsers = parser.add_subparsers(dest='command', help='sub-command help', description="Valid subcommands")
# Subparser for the gendb command.
#p_gendb = subparsers.add_parser('gendb', parents=[copts_parser], help=gbrv_gendb.__doc__)
#p_gendb.add_argument('djson_path', help='Path of the djson file.')
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(error_code=1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
pseudo = options.pseudo = dojopseudo_from_file(options.pseudo)
ecut = ecut_from_pseudo(pseudo)
workdir = pseudo.basename + "_DOJO_RELAX"
if os.path.exists(workdir):
cprint("Directory %s already exists" % workdir, "red")
return 1
flow = abilab.Flow(workdir=workdir)
pawecutdg = 2 * ecut if pseudo.ispaw else None
jth_afcc = dict(
La=5.272,
Ce=4.769,
Pr=4.608,
Nd=4.531,
Pm=4.499,
Sm=4.516,
Eu=4.630,
Gd=4.723,
Tb=4.835,
Dy=4.918,
Ho=5.012,
Er=5.073,
Tm=5.120,
Yb=5.163,
Lu=5.589,
)
a_guess = jth_afcc[pseudo.symbol]
from pseudo_dojo.dojo.works import RelaxWithGbrvParamsWork
ecut_list = [ecut, ecut + 10, ecut + 20]
work = RelaxWithGbrvParamsWork(a_guess,
"fcc",
pseudo,
ecut_list=ecut_list,
pawecutdg=None,
ngkpt=(8, 8, 8))
#ngkpt=(12, 12, 12))
#spin_mode="unpolarized", include_soc=False, tolvrs=1.e-10, smearing="fermi_dirac:0.001 Ha",
#ecutsm=0.05, chksymbreak=0)
flow.register_work(work)
#flow.build_and_pickle_dump(abivalidate=True)
#return 0
return flow.make_scheduler().start()
def pseudo(filename):
"""Returns a `Pseudo` object."""
return dojopseudo_from_file(os.path.join(dirpath, filename))
def pseudos(*filenames):
"""Returns a PseudoTable constructed from the input filenames located in tests/data/pseudos."""
return DojoTable(
[dojopseudo_from_file(os.path.join(dirpath, f)) for f in filenames])
def pseudo(filename):
"""Returns a `Pseudo` object."""
return dojopseudo_from_file(os.path.join(dirpath, filename))
def pseudos(*filenames):
"""Returns a PseudoTable constructed from the input filenames located in tests/data/pseudos."""
return DojoTable([dojopseudo_from_file(os.path.join(dirpath, f)) for f in filenames])
def main():
def str_examples():
return """\
Usage Example:
dojo_run.py Si.psp8 => Build pseudo_dojo flow for Si.psp8 pseudo
"""
def show_examples_and_exit(error_code=1):
"""Display the usage of the script."""
print(str_examples())
sys.exit(error_code)
parser = argparse.ArgumentParser(epilog=str_examples())
parser.add_argument('-m',
'--manager',
type=str,
default=None,
help="Manager file")
parser.add_argument(
'-w',
'--workdir',
type=str,
default=None,
help=
"Working directory. Default: Automatically generated from pseudo name."
)
parser.add_argument('-d',
'--dry-run',
default=False,
action="store_true",
help="Dry run, build the flow without submitting it")
parser.add_argument('--paral-kgb',
type=int,
default=0,
help="Paral_kgb input variable.")
parser.add_argument(
'--soc',
default=False,
action="store_true",
help=
("Perform non-collinear run (nspinor==2, kptopt=3). Pseudo must have spin-orbit characteristic"
))
#parser.add_argument('-n', '--new-ecut', type=int, default=None, action="store",
# help="Extend the ecut grid with the new-ecut point")
def parse_trials(s):
if s == "all": return ["df", "gbrv"]
return s.split(",")
parser.add_argument('--trials',
default="all",
type=parse_trials,
help="""\
List of tests e.g --trials=ghosts,df,gbrv.
ghosts: tests ghost states in the conduction region.
df: test delta factor against all electron reference.
gbrv: test fcc and bcc lattice parameters against AE reference.
phgamma: test violation of the acoustic sum rule
raren_relax: Structural relaxation for lantanide + nitrogen in rocksalt structure"""
)
parser.add_argument(
'--loglevel',
default="ERROR",
type=str,
help=
"set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG"
)
parser.add_argument(
'-v',
'--verbose',
default=0,
action='count', # -vv --> verbose=2
help='Verbose, can be supplied multiple times to increase verbosity')
parser.add_argument('path', help='pseudopotential file.')
try:
options = parser.parse_args()
except Exception as exc:
show_examples_and_exit(1)
# loglevel is bound to the string value obtained from the command line argument.
# Convert to upper case to allow the user to specify --loglevel=DEBUG or --loglevel=debug
import logging
numeric_level = getattr(logging, options.loglevel.upper(), None)
if not isinstance(numeric_level, int):
raise ValueError('Invalid log level: %s' % options.loglevel)
logging.basicConfig(level=numeric_level)
options.manager = abilab.TaskManager.as_manager(options.manager)
from pseudo_dojo import logo1
cprint(logo1(), "red")
pseudo = dojopseudo_from_file(options.path)
if pseudo is None:
cprint("Error while parsing: %s" % options.path)
cprint("Check your file. Returning 1")
return 1
flow = build_flow(pseudo, options)
if flow is None:
cprint("DOJO_REPORT is already computed for pseudo %s." % options.path,
"magenta")
return 1
if options.dry_run:
flow.build_and_pickle_dump(abivalidate=False)
return 0
else:
# Run the flow with the scheduler.
return flow.make_scheduler().start()
