def test_dojo_report_base_api(self):
"""Testing dojo report low-level API."""
report = DojoReport.from_hints(10, "Si")
#print(report)
assert report.symbol == "Si"
assert report.element.symbol == "Si"
assert report.ecuts
assert not report.trials
for trial in report.ALL_TRIALS:
assert not report.has_trial(trial)
assert report.check()
#prev_ecuts = copy(report.ecuts)
#report.add_ecuts(10000)
#assert np.all(report.ecuts == prev_ecuts + [10000])
report.add_hints([10, 20, 30])
assert report.has_hints
#assert report.hints.low.ecut == 10
#assert report.hints.high.ecut == 30
#assert not report.md5
# Test add_entry
with self.assertRaises(ValueError):
report.add_entry("foobar", ecut=10, entry={})
assert not report.has_trial("deltafactor", ecut=10)
report.add_entry("deltafactor", ecut=10, entry={})
print(report)
def copy_hints(from_djrepo, to_djrepo, verbose):
from_report = DojoReport.from_file(from_djrepo)
if "hints" not in from_report:
print("hints are not present in source", to_djrepo)
return 1
to_report = DojoReport.from_file(to_djrepo)
if "hints" in to_report:
print("hints are already available in destination", to_djrepo)
return 2
if verbose:
print("Copying hints %s --> %s" % (from_djrepo, to_djrepo))
# Add hints, and tags. Write new json file.
to_report["hints"] = from_report["hints"]
to_report["tags"] = from_report.get("tags", [])
to_report.json_write()
return 0
def copy_hints(from_djrepo, to_djrepo, verbose):
from_report = DojoReport.from_file(from_djrepo)
if "hints" not in from_report:
print("hints are not present in source", to_djrepo)
return 1
to_report = DojoReport.from_file(to_djrepo)
if "hints" in to_report:
print("hints are already available in destination", to_djrepo)
return 2
if verbose:
print("Copying hints %s --> %s" % (from_djrepo, to_djrepo))
# Add hints, and tags. Write new json file.
to_report["hints"] = from_report["hints"]
to_report["tags"] = from_report.get("tags", [])
to_report.json_write()
return 0
def djrepo_convert(options):
raise NotImplementedError()
# Version 1.0 to 2.0
new_version = "2.0"
for path in options.paths:
report = DojoReport.from_file(path)
old_version = report["version"]
if old_version == new_version: continue
report = report.to_version(new_version)
report.json_write()
return 0
def djrepo_convert(options):
raise NotImplementedError()
# Version 1.0 to 2.0
new_version = "2.0"
for path in options.paths:
report = DojoReport.from_file(path)
old_version = report["version"]
if old_version == new_version: continue
report = report.to_version(new_version)
report.json_write()
return 0
def dojopseudo_from_file(filepath):
"""
Factory function used to construct a :class:`Pseudo` object from file.
A DojoPseudo has a DojoReport section and this function adds the report
to the object.
Args:
filepath: Path of the pseudopotential file or djrepo file.
.. note::
We cannot subclass Pseudo because it's actually the abstract base class
and Pseudo.from_file is the factory function that returns the concreate subclass.
"""
filepath = os.path.abspath(filepath)
dojo_report = None
if filepath.endswith(".djrepo"):
dojo_report = DojoReport.from_file(filepath)
pp_basename = dojo_report["basename"]
filepath = os.path.join(os.path.dirname(filepath), pp_basename)
# Init pseudo from file. Return None if parser error.
pseudo = Pseudo.from_file(filepath)
if pseudo is None: return pseudo
#pseudo.__class__.dojo_report = property(lambda self: self.a + 1)
if dojo_report is not None:
# We've already read the report.
pseudo.dojo_report = dojo_report
return pseudo
# Read DojoReport and add it to pseudos
root, ext = os.path.splitext(filepath)
djrepo = root + ".djrepo"
if not os.path.exists(djrepo):
raise RuntimeError("Cannot find djrepo file at %s" % djrepo)
pseudo.dojo_report = DojoReport.from_file(djrepo)
return pseudo
def dojopseudo_from_file(filepath):
"""
Factory function used to construct a :class:`Pseudo` object from file.
A DojoPseudo has a DojoReport section and this function adds the report
to the object.
Args:
filepath: Path of the pseudopotential file or djrepo file.
.. note::
We cannot subclass Pseudo because it's actually the abstract base class
and Pseudo.from_file is the factory function that returns the concreate subclass.
"""
filepath = os.path.abspath(filepath)
dojo_report = None
if filepath.endswith(".djrepo"):
dojo_report = DojoReport.from_file(filepath)
pp_basename = dojo_report["basename"]
filepath = os.path.join(os.path.dirname(filepath), pp_basename)
# Init pseudo from file. Return None if parser error.
pseudo = Pseudo.from_file(filepath)
if pseudo is None: return pseudo
#pseudo.__class__.dojo_report = property(lambda self: self.a + 1)
if dojo_report is not None:
# We've already read the report.
pseudo.dojo_report = dojo_report
return pseudo
# Read DojoReport and add it to pseudos
root, ext = os.path.splitext(filepath)
djrepo = root + ".djrepo"
if not os.path.exists(djrepo):
raise RuntimeError("Cannot find djrepo file at %s" % djrepo)
pseudo.dojo_report = DojoReport.from_file(djrepo)
return pseudo
def add_entry_to_dojoreport(self,
entry,
overwrite_data=False,
pop_trial=False):
"""
Write/update the DOJO_REPORT section of the pseudopotential.
Important paramenters such as the name of the dojo_trial and the energy cutoff
are provided by the sub-class.
Client code is responsible for preparing the dictionary with the data.
Args:
entry: Dictionary with results.
overwrite_data: If False, the routine raises an exception if this entry is
already filled.
pop_trial: True if the trial should be removed before adding the new entry.
"""
root, ext = os.path.splitext(self.dojo_pseudo.filepath)
djrepo = root + ".djrepo"
self.history.info("Writing dojreport data to %s" % djrepo)
# Update file content with Filelock.
with FileLock(djrepo):
# Read report from file.
file_report = DojoReport.from_file(djrepo)
# Create new entry if not already there
dojo_trial = self.dojo_trial
if pop_trial:
file_report.pop(dojo_trial, None)
if dojo_trial not in file_report:
file_report[dojo_trial] = {}
# Convert float to string with 1 decimal digit.
dojo_ecut = "%.1f" % self.ecut
# Check that we are not going to overwrite data.
if dojo_ecut in file_report[dojo_trial]:
if not overwrite_data:
raise RuntimeError(
"dojo_ecut %s already exists in %s. Cannot overwrite data"
% (dojo_ecut, dojo_trial))
else:
file_report[dojo_trial].pop(dojo_ecut)
# Update file_report by adding the new entry and write new file
file_report[dojo_trial][dojo_ecut] = entry
# Write new dojo report and update the pseudo attribute
file_report.json_write()
self._pseudo.dojo_report = file_report
def test_dojo_report_base_api(self):
"""Testing dojo report low-level API."""
#report = DojoReport.from_hints(10, "Si")
pseudo = pdj_data.pseudo("Si.psp8")
ppgen_hints = {
"low": {
"ecut": 8.0,
"pawecutdg": 8.0
},
"normal": {
"ecut": 10.0,
"pawecutdg": 10.0
},
"high": {
"ecut": 16.0,
"pawecutdg": 16.0
},
}
report = DojoReport.empty_from_pseudo(pseudo, ppgen_hints, devel=False)
repr(repr)
str(report)
assert report.symbol == "Si"
assert report.element.symbol == "Si"
assert report.ecuts
assert not report.trials
for trial in report.ALL_TRIALS:
assert not report.has_trial(trial)
assert not report.has_hints
assert report.check()
#prev_ecuts = copy(report.ecuts)
#report.add_ecuts(10000)
#assert np.all(report.ecuts == prev_ecuts + [10000])
report.add_hints([10, 20, 30])
assert report.has_hints
assert report["hints"]["low"]["ecut"] == 10
assert report["hints"]["high"]["ecut"] == 30
assert not report.isvalidated
#assert not report.md5
# Test add_entry
with self.assertRaises(ValueError):
report.add_entry("foobar", ecut=10, entry={})
assert not report.has_trial("deltafactor", ecut=10)
report.add_entry("deltafactor", ecut=10, entry={})
repr(report)
str(report)
assert report.has_trial("deltafactor", ecut=10)
def add_entry_to_dojoreport(self, entry, overwrite_data=False, pop_trial=False):
"""
Write/update the DOJO_REPORT section of the pseudopotential.
Important paramenters such as the name of the dojo_trial and the energy cutoff
are provided by the sub-class.
Client code is responsible for preparing the dictionary with the data.
Args:
entry: Dictionary with results.
overwrite_data: If False, the routine raises an exception if this entry is
already filled.
pop_trial: True if the trial should be removed before adding the new entry.
"""
#root, ext = os.path.splitext(self.dojo_pseudo.filepath)
#djrepo = root + ".djrepo"
djrepo = self.djrepo_path
self.history.info("Writing dojreport data to %s" % djrepo)
# Update file content with Filelock.
with FileLock(djrepo):
# Read report from file.
file_report = DojoReport.from_file(djrepo)
# Create new entry if not already there
dojo_trial = self.dojo_trial
if pop_trial:
file_report.pop(dojo_trial, None)
if dojo_trial not in file_report:
file_report[dojo_trial] = {}
# Convert float to string with 1 decimal digit.
dojo_ecut = "%.1f" % self.ecut
# Check that we are not going to overwrite data.
if dojo_ecut in file_report[dojo_trial]:
if not overwrite_data:
raise RuntimeError("dojo_ecut %s already exists in %s. Cannot overwrite data" %
(dojo_ecut, dojo_trial))
else:
file_report[dojo_trial].pop(dojo_ecut)
# Update file_report by adding the new entry and write new file
file_report[dojo_trial][dojo_ecut] = entry
# Write new dojo report and update the pseudo attribute
file_report.json_write()
self._pseudo.dojo_report = file_report
def test_dojo_report_base_api(self):
"""Testing dojo report low-level API."""
#report = DojoReport.from_hints(10, "Si")
pseudo = pdj_data.pseudo("Si.psp8")
ppgen_hints = {
"low": {"ecut": 8.0, "pawecutdg": 8.0},
"normal": {"ecut": 10.0, "pawecutdg": 10.0},
"high": { "ecut": 16.0, "pawecutdg": 16.0},
}
report = DojoReport.empty_from_pseudo(pseudo, ppgen_hints, devel=False)
repr(repr); str(report)
assert report.symbol == "Si"
assert report.element.symbol == "Si"
assert report.ecuts
assert not report.trials
for trial in report.ALL_TRIALS:
assert not report.has_trial(trial)
assert not report.has_hints
assert report.check()
#prev_ecuts = copy(report.ecuts)
#report.add_ecuts(10000)
#assert np.all(report.ecuts == prev_ecuts + [10000])
report.add_hints([10, 20, 30])
assert report.has_hints
assert report["hints"]["low"]["ecut"] == 10
assert report["hints"]["high"]["ecut"] == 30
assert not report.isvalidated
#assert not report.md5
# Test add_entry
with self.assertRaises(ValueError):
report.add_entry("foobar", ecut=10, entry={})
assert not report.has_trial("deltafactor", ecut=10)
report.add_entry("deltafactor", ecut=10, entry={})
repr(report); str(report)
assert report.has_trial("deltafactor", ecut=10)
def main():
website = 'website'
usage = "Usage: " \
"create_dojosite_tar.py path\n" \
"creates the tar for the pseudo dojo website. To change the pseudos included change the list\n" \
"PSEUDOS_TO_INCLUDE in create_dojosite_tar.py"
if "--help" in sys.argv or "-h" in sys.argv:
print(usage)
return 1
mock = False
# create the main directory for the website file-system
if os.path.isdir(website):
print(
'directory website already exists first move it away then rerun.')
return
else:
os.makedirs(website)
# walk the current tree, create the directory structure and copy the .in, .psp8, and .djrepo files
print('copying selected pseudos:\n%s' % PSEUDOS_TO_INCLUDE)
for pseudo_set in PSEUDOS_TO_INCLUDE:
xc = pseudo_set.split('-')[1].lower()
for acc in ACCURACIES:
with open(os.path.join(pseudo_set, rnACC[acc] + '.txt')) as f:
pseudos = f.readlines()
print(pseudos)
name = "nc-fr-04_%s_%s" % (xc, rnACC[acc])
os.makedirs(os.path.join(website, name))
pseudo_data = {}
for pseudo in pseudos:
p = pseudo.strip()
if not os.path.isfile(os.path.join(pseudo_set, p)):
continue
try:
for extension in ['in', 'psp8', 'djrepo', 'out']:
copyfile(
os.path.join(pseudo_set,
p).replace('psp8', extension),
os.path.join(
website, name,
os.path.split(p)[1].replace('psp8',
extension)))
try:
write_notebook_html(os.path.join(
website, name,
os.path.split(p)[1]),
tmpfile=False,
mock=False)
except:
print('write notebook failed for {}'.format(pseudo))
try:
nv = make_upf(os.path.join(website, name,
os.path.split(p)[1]),
mock=mock,
calctype="fully-relativistic")
except RuntimeError:
nv = 'NA'
p_name = os.path.split(p)[1]
# todo see if this works
el.replace('_r', '')
el = p_name.split('-')[0].split('.')[0]
el.replace('3+_f', '')
for extension in ['psp8', 'upf', 'djrepo', 'html', 'psml']:
os.rename(
os.path.join(website, name,
p_name.replace('psp8', extension)),
os.path.join(website, name, el + '.' + extension))
# os.remove(os.path.join(website, name, os.path.split(p)[1].replace('psp8', 'out')))
print('%s %s %s %s ' %
('mocked' if mock else 'done', xc, acc, p))
dojoreport = DojoReport.from_file(
os.path.join(website, name, el + '.djrepo'))
try:
low_hint = dojoreport["hints"]["low"]["ecut"]
normal_hint = dojoreport["hints"]["normal"]["ecut"]
high_hint = dojoreport["hints"]["high"]["ecut"]
except KeyError:
high_hint = 'na'
normal_hint = 'na'
low_hint = 'na'
try:
delta_ecuts = list(dojoreport["deltafactor"].keys())
print(delta_ecuts)
delta_ecut = delta_ecuts[-1]
delta = dojoreport["deltafactor"][delta_ecut][
"dfact_meV"]
delta_s = "%1.1f" % round(delta, 1)
deltap = dojoreport["deltafactor"][delta_ecut][
"dfactprime_meV"]
deltap_s = "%1.1f" % round(deltap, 1)
except (KeyError, TypeError):
delta_s = 'na'
deltap_s = 'na'
try:
gb_ecuts = dojoreport["gbrv_bcc"].keys()
gb_ecut = gb_ecuts[-1]
gb = dojoreport["gbrv_bcc"][gb_ecut]["a0_rel_err"]
gf_ecuts = dojoreport["gbrv_fcc"].keys()
gf_ecut = gf_ecuts[-1]
gf = dojoreport["gbrv_fcc"][gf_ecut]["a0_rel_err"]
gb_s = "%0.2f" % round((gb + gf) / 2, 1)
except KeyError:
gb_s = 'na'
print("%s %s %s %s %s %s %s" %
(nv, low_hint, normal_hint, high_hint, delta_s,
deltap_s, gb_s))
pseudo_data[el] = {
'nv': nv,
'hh': high_hint,
'hl': low_hint,
'hn': normal_hint,
'd': delta_s,
'dp': deltap_s,
'gb': gb_s
}
except RuntimeError: # (IOError, ValueError, CellExecutionError, OSError):
print('missing %s %s ' % (pseudo_set, p))
pass
with open(os.path.join(website, name + '.json'), 'w') as fp:
json.dump(pseudo_data, fp=fp, indent=2)
return
def oncv_run(options):
"""
Run oncvpsp, generate djrepo file, plot results. Requires input file.
"""
# Select calc_type
calc_type = dict(nor="non-relativistic",
sr="scalar-relativistic",
fr="fully-relativistic")[options.rel]
# Build names of psp8 and djson files from input and relativistic mode.
in_path = options.filename
root, _ = os.path.splitext(in_path)
# Enforce convention on output files.
if options.rel == "nor":
if not root.endswith("_nor"): root += "_nor"
elif options.rel == "fr":
if not root.endswith("_r"):
root += "_r"
cprint(
"FR calculation with input file without `_r` suffix. Will add `_r` to output files",
"yellow")
# Build names of output files.
psp8_path = root + ".psp8"
djrepo_path = root + ".djrepo"
out_path = root + ".out"
if os.path.exists(psp8_path):
cprint(
"%s already exists and will be overwritten" %
os.path.relpath(psp8_path), "yellow")
if os.path.exists(djrepo_path):
cprint(
"%s already exists and will be overwritten" %
os.path.relpath(djrepo_path), "yellow")
if os.path.exists(out_path):
cprint(
"%s already exists and will be overwritten" %
os.path.relpath(out_path), "yellow")
# Build Generator and start generation.
oncv_ppgen = OncvGenerator.from_file(in_path, calc_type, workdir=None)
print(oncv_ppgen)
print(oncv_ppgen.input_str)
oncv_ppgen.start()
retcode = oncv_ppgen.wait()
if oncv_ppgen.status != oncv_ppgen.S_OK:
cprint("oncvpsp returned %s. Exiting" % retcode, "red")
return 1
# Tranfer final output file.
shutil.copy(oncv_ppgen.stdout_path, out_path)
# Parse the output file
onc_parser = OncvOutputParser(out_path)
onc_parser.scan()
if not onc_parser.run_completed:
cprint("oncvpsp output is not complete. Exiting", "red")
return 1
# Extract psp8 files from the oncvpsp output and write it to file.
s = onc_parser.get_psp8_str()
with open(psp8_path, "wt") as fh:
fh.write(s)
# Write upf if available.
upf_str = onc_parser.get_upf_str()
if upf_str is not None:
with open(psp8_path.replace(".psp8", ".upf"), "wt") as fh:
fh.write(upf_str)
pseudo = Pseudo.from_file(psp8_path)
if pseudo is None:
cprint("Cannot parse psp8 file: %s" % psp8_path, "red")
return 1
# Initialize and write djson file.
report = DojoReport.empty_from_pseudo(pseudo,
onc_parser.hints,
devel=False)
report.json_write()
return 0
def on_all_ok(self):
"""
Results are written to the dojoreport.
"""
def vol2a(vol):
"""Function to compute cubic a0 from primitive v0 (depends on struct_type)"""
return (4 * vol) ** (1/3.)
entries = {}
for task in self:
ecut = task.input["ecut"]
#final_structure = task.get_final_structure()
with task.open_hist() as hist:
final_structure = hist.final_structure
initial_energy = hist.etotals[0]
# Convert float to string with 1 decimal digit.
dojo_ecut = "%.1f" % ecut
entries[dojo_ecut] = {
"relaxed_a": vol2a(final_structure.volume),
"initial_energy_ev_per_atom": float(initial_energy) / len(final_structure),
}
#print(entries)
# Convert to JSON and add results to the dojo report.
#entry = dict(ecut=self.ecut, pawecutdg=self.dojo_pawecutdg, kppa=self.dojo_kppa)
#self.add_entry_to_dojoreport(entry)
#return results
djrepo = self.djrepo_path
# Update file content with Filelock.
with FileLock(djrepo):
# Read report from file.
file_report = DojoReport.from_file(djrepo)
# Create new entry if not already there
dojo_trial = self.dojo_trial
#if pop_trial:
# file_report.pop(dojo_trial, None)
if dojo_trial not in file_report:
file_report[dojo_trial] = {}
# Convert float to string with 1 decimal digit.
#dojo_ecut = "%.1f" % self.ecut
# Check that we are not going to overwrite data.
#if dojo_ecut in file_report[dojo_trial]:
# if not overwrite_data:
# raise RuntimeError("dojo_ecut %s already exists in %s. Cannot overwrite data" %
# (dojo_ecut, dojo_trial))
# else:
# file_report[dojo_trial].pop(dojo_ecut)
# Update file_report by adding the new entry and write new file
for dojo_ecut, entry in entries.items():
file_report[dojo_trial][dojo_ecut] = entry
# Write new dojo report and update the pseudo attribute
file_report.json_write()
self._pseudo.dojo_report = file_report
return dict(returncode=0, message="Lattice paramenters computed and stored in djrepo file")
def main():
website = 'website'
usage = "Usage: " \
"create_dojosite_tar.py path\n" \
"creates the tar for the pseudo dojo website. To change the pseudos included change the list\n" \
"PSEUDOS_TO_INCLUDE in create_dojosite_tar.py"
if "--help" in sys.argv or "-h" in sys.argv:
print(usage)
return 1
mock = False
# create the main directory for the website file-system
if os.path.isdir(website):
print('directory website already exists first move it away then rerun.')
return
else:
os.makedirs(website)
# walk the current tree, create the directory structure and copy the .in, .psp8, and .djrepo files
print('copying selected pseudos:\n%s' % PSEUDOS_TO_INCLUDE)
for pseudo_set in PSEUDOS_TO_INCLUDE:
xc = pseudo_set.split('-')[1].lower()
for acc in ACCURACIES:
with open(os.path.join(pseudo_set, rnACC[acc]+'.txt')) as f:
pseudos = f.readlines()
print(pseudos)
name = "nc-fr-04_%s_%s" % (xc, rnACC[acc])
os.makedirs(os.path.join(website, name))
pseudo_data = {}
for pseudo in pseudos:
p = pseudo.strip()
if not os.path.isfile(os.path.join(pseudo_set, p)):
continue
try:
for extension in ['in', 'psp8', 'djrepo', 'out']:
copyfile(os.path.join(pseudo_set, p).replace('psp8', extension),
os.path.join(website, name, os.path.split(p)[1].replace('psp8', extension)))
try:
write_notebook_html(os.path.join(website, name, os.path.split(p)[1]), tmpfile=False, mock=False)
except:
print('write notebook failed for {}'.format(pseudo))
try:
nv = make_upf(os.path.join(website, name, os.path.split(p)[1]), mock=mock,
calctype="fully-relativistic")
except RuntimeError:
nv = 'NA'
p_name = os.path.split(p)[1]
# todo see if this works
el.replace('_r', '')
el = p_name.split('-')[0].split('.')[0]
el.replace('3+_f', '')
for extension in ['psp8', 'upf', 'djrepo', 'html', 'psml']:
os.rename(os.path.join(website, name, p_name.replace('psp8', extension)),
os.path.join(website, name, el + '.' + extension))
# os.remove(os.path.join(website, name, os.path.split(p)[1].replace('psp8', 'out')))
print('%s %s %s %s ' % ('mocked' if mock else 'done', xc, acc, p))
dojoreport = DojoReport.from_file(os.path.join(website, name, el + '.djrepo'))
try:
low_hint = dojoreport["hints"]["low"]["ecut"]
normal_hint = dojoreport["hints"]["normal"]["ecut"]
high_hint = dojoreport["hints"]["high"]["ecut"]
except KeyError:
high_hint = 'na'
normal_hint = 'na'
low_hint = 'na'
try:
delta_ecuts = list(dojoreport["deltafactor"].keys())
print(delta_ecuts)
delta_ecut = delta_ecuts[-1]
delta = dojoreport["deltafactor"][delta_ecut]["dfact_meV"]
delta_s = "%1.1f" % round(delta, 1)
deltap = dojoreport["deltafactor"][delta_ecut]["dfactprime_meV"]
deltap_s = "%1.1f" % round(deltap, 1)
except (KeyError, TypeError):
delta_s = 'na'
deltap_s = 'na'
try:
gb_ecuts = dojoreport["gbrv_bcc"].keys()
gb_ecut = gb_ecuts[-1]
gb = dojoreport["gbrv_bcc"][gb_ecut]["a0_rel_err"]
gf_ecuts = dojoreport["gbrv_fcc"].keys()
gf_ecut = gf_ecuts[-1]
gf = dojoreport["gbrv_fcc"][gf_ecut]["a0_rel_err"]
gb_s = "%0.2f" % round((gb + gf)/2, 1)
except KeyError:
gb_s = 'na'
print("%s %s %s %s %s %s %s" % (nv, low_hint, normal_hint, high_hint, delta_s, deltap_s, gb_s))
pseudo_data[el] = {'nv': nv, 'hh': high_hint, 'hl': low_hint, 'hn': normal_hint, 'd': delta_s,
'dp': deltap_s, 'gb': gb_s}
except RuntimeError: # (IOError, ValueError, CellExecutionError, OSError):
print('missing %s %s ' % (pseudo_set, p))
pass
with open(os.path.join(website, name + '.json'), 'w') as fp:
json.dump(pseudo_data, fp=fp, indent=2)
return
def add_dojoreport_to_pseudo(pseudo):
"""Add the dojoreport to a pseudo."""
if not hasattr(pseudo, "dojo_report"):
pseudo.dojo_report = DojoReport.from_file(pseudo.djrepo_path)
return pseudo
def oncv_run(options):
"""
Run oncvpsp, generate djrepo file, plot results. Requires input file.
"""
# Select calc_type
calc_type = dict(nor="non-relativistic",
sr="scalar-relativistic",
fr="fully-relativistic")[options.rel]
# Build names of psp8 and djson files from input and relativistic mode.
in_path = options.filename
root, _ = os.path.splitext(in_path)
# Enforce convention on output files.
if options.rel == "nor":
if not root.endswith("_nor"): root += "_nor"
elif options.rel == "fr":
if not root.endswith("_r"):
root += "_r"
cprint("FR calculation with input file without `_r` suffix. Will add `_r` to output files", "yellow")
# Build names of output files.
psp8_path = root + ".psp8"
djrepo_path = root + ".djrepo"
out_path = root + ".out"
if os.path.exists(psp8_path):
cprint("%s already exists and will be overwritten" % os.path.relpath(psp8_path), "yellow")
if os.path.exists(djrepo_path):
cprint("%s already exists and will be overwritten" % os.path.relpath(djrepo_path), "yellow")
if os.path.exists(out_path):
cprint("%s already exists and will be overwritten" % os.path.relpath(out_path), "yellow")
# Build Generator and start generation.
oncv_ppgen = OncvGenerator.from_file(in_path, calc_type, workdir=None)
print(oncv_ppgen)
print(oncv_ppgen.input_str)
oncv_ppgen.start()
retcode = oncv_ppgen.wait()
if oncv_ppgen.status != oncv_ppgen.S_OK:
cprint("oncvpsp returned %s. Exiting" % retcode, "red")
return 1
# Tranfer final output file.
shutil.copy(oncv_ppgen.stdout_path, out_path)
# Parse the output file
onc_parser = OncvOutputParser(out_path)
onc_parser.scan()
if not onc_parser.run_completed:
cprint("oncvpsp output is not complete. Exiting", "red")
return 1
# Extract psp8 files from the oncvpsp output and write it to file.
s = onc_parser.get_pseudo_str()
with open(psp8_path, "wt") as fh:
fh.write(s)
pseudo = Pseudo.from_file(psp8_path)
if pseudo is None:
cprint("Cannot parse psp8 file: %s" % psp8_path, "red")
return 1
# Initialize and write djson file.
report = DojoReport.empty_from_pseudo(pseudo, onc_parser.hints, devel=False)
report.json_write()
return 0
def add_dojoreport_to_pseudo(pseudo):
"""Add the dojoreport to a pseudo."""
if not hasattr(pseudo, "dojo_report"):
pseudo.dojo_report = DojoReport.from_file(pseudo.djrepo_path)
return pseudo
def main():
website = 'website'
usage = "Usage: " \
"create_dojosite_tar.py path\n" \
"creates the tar for the pseudo dojo website. To change the pseudos included change the list\n" \
"PSEUDOS_TO_INCLUDE in create_dojosite_tar.py"
if "--help" in sys.argv or "-h" in sys.argv:
print(usage)
return 1
try:
path = sys.argv[1]
except:
print(usage)
return 1
mock = False
# create the main directory for the website file-system
if os.path.isdir(website):
print(
'directory website already exists first move it away then rerun.')
return
else:
os.makedirs(website)
# walk the current tree, create the directory structure and copy the .in, .psp8, and .djrepo files
print('copying selected pseudos:\n%s' % PSEUDOS_TO_INCLUDE)
a = 0
for pseudo_set in PSEUDOS_TO_INCLUDE:
xc = pseudo_set.split('-')[1].lower()
for acc in ACCURACIES:
with open(os.path.join(pseudo_set, acc)) as f:
pseudos = f.readlines()
name = "%s_%s_sr" % (xc, acc[0])
#for fmt in ['psp8', 'upf', 'html', 'djrepo']:
# os.makedirs(os.path.join(website, '%s_%s' % (name, fmt)))
os.makedirs(os.path.join(website, name))
for pseudo in pseudos:
p = pseudo.strip()
try:
for extension in ['in', 'psp8', 'djrepo', 'out']:
copyfile(
os.path.join(pseudo_set,
p).replace('psp8', extension),
os.path.join(
website, name,
os.path.split(p)[1].replace('psp8',
extension)))
try:
write_notebook_html(os.path.join(
website, name,
os.path.split(p)[1]),
tmpfile=False,
mock=mock)
except:
pass
try:
nv = make_upf(os.path.join(website, name,
os.path.split(p)[1]),
mock=mock,
calctype="scalar-relativistic")
except None:
nv = 'NA'
p_name = os.path.split(p)[1]
el = p_name.split('-')[0].split('.')[0]
for extension in ['psp8', 'upf', 'djrepo', 'html']:
os.rename(
os.path.join(website, name,
p_name.replace('psp8', extension)),
os.path.join(website, name, el + '.' + extension))
os.remove(
os.path.join(
website, name,
os.path.split(p)[1].replace('psp8', 'out')))
print('%s %s %s %s ' %
('mocked' if mock else 'done', xc, acc, p))
dojoreport = DojoReport.from_file(
os.path.join(website, name, el + '.djrepo'))
try:
normal_hint = dojoreport["hints"]["normal"]["ecut"]
except KeyError:
normal_hint = 'NA'
try:
delta_ecuts = dojoreport["deltafactor"].keys()
delta_ecut = delta_ecuts[-1]
delta = dojoreport["deltafactor"][delta_ecut][
"dfact_meV"]
delta_s = "%1.1f" % round(delta, 1)
except KeyError:
delta_s = 'NA'
print("%s %s %s" % (nv, normal_hint, delta_s))
with open(os.path.join(website, name, el + '.txt'),
'w') as f:
f.write("%s %s %s" % (nv, normal_hint, delta_s))
except (IOError, ValueError, CellExecutionError, OSError):
print('missing %s %s ' % (pseudo_set, p))
pass
#a += 1
#if a > 0:
# mock = True
return