def __init__(self, file):
if not isinstance(file, str):
file_name = file.name
file.close()
else:
file_name = file
if not CRYSTOUT.acceptable(file_name):
raise FileNotFoundError(
"{} is not a valid CRYSTAL output file".format(file_name))
result = CRYSTOUT(file_name)
self.info = result.info
def test_failed_elastic():
"""Failed elastic constants calculation"""
test_file = os.path.join(DATA_DIR, 'failed_elastic.out')
with pytest.raises(CRYSTOUT_Error) as ex:
CRYSTOUT(test_file)
assert 'Inadequate elastic calculation' in ex.msg
def test_elastic():
"""Elastic constants calculation"""
test_file = os.path.join(DATA_DIR, '1674.out')
parser = CRYSTOUT(test_file)
info = parser.info
assert info['prog'] == '17 1.0.2' # CRYSTAL version
assert info['finished'] == 2 # finished without errors
assert info['energy'] == -6.2238169993737E+02 * Ha # energy in eV
assert info['k'] == '8x8x8' # Monkhorst-Pack net
assert info['elastic']['K_V'] == 33.87
test_file = os.path.join(DATA_DIR, '2324.out')
parser = CRYSTOUT(test_file)
info = parser.info
assert info['elastic']['elastic_moduli'][0] == [
659.2238, -404.2543, -249.8055, 0.0, 0.0, 0.0
]
def test_freqcalc():
"""Phonon dispersion"""
test_file = os.path.join(DATA_DIR, 'qua_hf_2d_f.out')
parser = CRYSTOUT(test_file)
info = parser.info
assert info['prog'] == '06 1.0' # CRYSTAL version
assert info['finished'] == 2 # finished without errors
assert info['energy'] == -1.3167028008915E+03 * Ha # energy in eV
assert info['k'] == '3x3x3' # Monkhorst-Pack net
assert info['phonons']['td']['et'] == [0.144398520226] # Et in eV/cell
test_file = os.path.join(DATA_DIR, 'raman.out')
parser = CRYSTOUT(test_file)
info = parser.info
assert info['prog'] == '14 1.0.1' # CRYSTAL version
assert info['energy'] == -7473.993352557831
assert info['phonons']['zpe'] == 0.09020363263183974
assert info['phonons']['td']['t'][0] == 298.15
def test_incomplete():
"""Incomplete OUT file, single-point calculation"""
test_file = os.path.join(DATA_DIR, 'incomplete.out')
parser = CRYSTOUT(test_file)
info = parser.info
assert info['finished'] == 1 # not finished
assert info['energy'] is None # energy in eV
assert info['k'] == '12x12x12' # Monkhorst-Pack net
assert not info['ncycles']
def test_spin():
"""Spin calculation"""
test_file = os.path.join(DATA_DIR, 'test37.out')
parser = CRYSTOUT(test_file)
info = parser.info
assert info['prog'] == '17 1.0.1' # CRYSTAL version
assert info['finished'] == 2 # finished without errors
assert info['energy'] == -3.0283685769288E+03 * Ha # energy in eV
assert info['k'] == '4x4x1' # Monkhorst-Pack net
assert info['spin']
def test_elastic_bug_2():
"""Elastic constants calculation (one more)"""
test_file = os.path.join(DATA_DIR, '2324.out')
parser = CRYSTOUT(test_file)
info = parser.info
assert info['prog'] == '17 1.0.2' # CRYSTAL version
assert info['finished'] == 2 # finished without errors
assert info['energy'] == -6.3910338752478E+03 * Ha # energy in eV
assert info['k'] == '8x8x8' # Monkhorst-Pack net
assert info['elastic']['K_V'] == -122.44
def test_optgeom():
"""Geometry optimization"""
test_file = os.path.join(DATA_DIR, 'optgeom.out')
parser = CRYSTOUT(test_file)
info = parser.info
assert info['prog'] == '14 1.0.2' # CRYSTAL version
assert info['finished'] == 2 # finished without errors
assert info['energy'] == -1.400469343370E+03 * Ha # energy in eV
assert info['k'] == '3x3x3' # Monkhorst-Pack net
assert len(info['ncycles']) == 11 # number of optimization steps
assert len(
info['structures']) == 12 # structures before and after each opt step
def test_single_dft():
"""Single-point calculation; DFT; ECP basis"""
test_file = os.path.join(DATA_DIR, 'test39_dft.out')
parser = CRYSTOUT(test_file)
info = parser.info
assert info['finished'] == 2 # finished without errors
assert info['energy'] == -4.8538264773648E+02 * Ha # energy in eV
assert info['k'] == '6x6x6' # Monkhorst-Pack net
assert info['H'] == "LDA/PZ_LDA"
assert info['ncycles'][0] == 9
assert info['electrons']['basis_set']['ecp']['Ge'][0][1] == (0.82751,
-1.26859, -1)
assert info['electrons']['basis_set']['bs']['Ge'][0][1] == (1.834, 0.4939,
0.006414)
def test_single_hf():
"""Single-point calculation; HF; standard AE basis"""
test_file = os.path.join(DATA_DIR, 'test08.out')
parser = CRYSTOUT(test_file)
info = parser.info
pprint(info)
assert info['prog'] == '17 1.0.1' # CRYSTAL version
assert info['finished'] == 2 # finished without errors
assert info['energy'] == -5.7132081224317E+02 * Ha # energy in eV
assert info['k'] == '8x8x8' # Monkhorst-Pack mesh
assert info['H'] == 'Hartree-Fock'
assert info['ncycles'][0] == 6
assert not info['electrons']['basis_set']['ecp']
assert info['electrons']['basis_set']['bs']['Si']
def test_band_gap():
"""Elastic constants calculation"""
test_file = os.path.join(DATA_DIR, '1674.out')
parser = CRYSTOUT(test_file)
info = parser.info
assert info['prog'] == '17 1.0.2' # CRYSTAL version
assert info['conduction'][0] == {
'state': 'INSULATING',
'top_valence': 14,
'bottom_virtual': 15,
'band_gap': 6.2079,
'band_gap_type': 'INDIRECT'
}
test_file = os.path.join(DATA_DIR, 'mgo_sto3g.out')
parser = CRYSTOUT(test_file)
info = parser.info
assert info['prog'] == '14 1.0.1' # CRYSTAL version
assert info['conduction'][0] == {
'state': 'INSULATING',
'top_valence': 10,
'bottom_virtual': 11,
'band_gap': 19.72174073396588,
'band_gap_type': 'DIRECT'
}
def download_basis_library():
library = {}
while True:
if not known_page_names:
break
page = known_page_names.pop(0)
r = requests.get('http://www.crystal.unito.it/Basis_Sets/%s.html' %
page)
if r.status_code != 200:
logging.warning("NO PAGE FOR %s" % page)
continue
soup = BeautifulSoup(r.content, 'html.parser')
for a in soup.find_all('a'):
anchor = a.get('href', '')
if anchor.startswith('http') and anchor.endswith(
'.html') and '#' not in anchor:
logging.warning("PAGE %s HAS AN EXTERNAL LINK: %s" %
(page, anchor))
known_page_names.append(anchor.split('/')[-1][:-5])
for basis in soup.find_all('pre'):
title = basis.findPrevious('p').text.strip()
if not title:
title = basis.findPrevious('font').text.strip()
parts = [
item for item in linebreak.split(basis.text) if len(item) > 2
]
page = page.split(
'_'
)[0] # PS such as http://www.crystal.unito.it/Basis_Sets/oxygen_baranek.html
# Correct mis-formats in the BS library at the CRYSTAL website
if page == 'sulphur' and '10.1002/jcc.23153' in parts[1]:
# "1 0" -> "1.0"
parts[0] = parts[0].replace(
"\r\n0 3 1 0.0 1 0\r\n 0.5207010100 1.00000000000000",
"\r\n0 3 1 0.0 1.0\r\n 0.5207010100 1.00000000000000")
elif page == 'sulphur' and '10.1002/jcc.26013' in parts[1]:
# "1 0" -> "1.0"
parts[0] = parts[0].replace(
"\r\n0 3 1 0.0 1 0\r\n 0.4107010100 1.0000000000000",
"\r\n0 3 1 0.0 1.0\r\n 0.4107010100 1.0000000000000")
elif page == 'titanium' and 'Mahmoud' in parts[1]:
# remove "Ti"
parts[0] = parts[0].replace("Ti\r\n22 9\r\n", "22 9\r\n")
elif page == 'bismuth' and 'weihrich' in title:
# remove comment
parts[0] = parts[0].replace(
"ECP modified from Hay and Wadt, JCP 82, 284 (1985)", "")
elif page == 'mercury' and 'weihrich' in title:
# remove comments
parts[0] = parts[0].replace(
"ECP modified from Hay and Wadt, JCP 82, 1985", "")
elif page == 'thallium' and 'Bachhuber' in title:
# fix INPUT
parts[0] = parts[0].replace("13. 6 5 6 6 6 0 0",
"13. 6 5 6 6 6 0")
elif page == 'oxygen' and 'corno' in title:
# remove comments
parts[0] = parts[0].replace("same as gatti_1994", "").replace(
"gatti_1994 modified", "")
elif page == 'plutonium' and '_NO_G_' in title:
# fix Pu ECP format
parts[0] = parts[0].replace("294 11", "294 9")
elif page == 'polonium' and 'TZVP_rev2' in title:
# fix Po
parts[0] = parts[0].replace("282 12", "284 12")
# NB. sometimes the comments get included afterwards
expected_element = chemical_symbols[ref_page_names.index(page)]
parsed = CRYSTOUT.parse_bs_input(parts[0], as_d12=False)
gbasis = dict(data=parts[0].strip(),
meta=" ".join(parts[1:]).replace("\n", " ").replace(
"\r", "").strip(),
title=title)
element = list(parsed['bs'].keys())[0]
assert expected_element == element, "%s is on the page of %s" % (
element, expected_element)
library.setdefault(element, []).append(gbasis)
return library
def check_status():
parser = argparse.ArgumentParser(
description="Submit task to yascheduler daemon")
parser.add_argument('-j',
'--jobs',
required=False,
default=None,
nargs='*')
parser.add_argument('-v',
'--view',
required=False,
default=None,
nargs='?',
type=bool,
const=True)
parser.add_argument('-o',
'--convergence',
required=False,
default=None,
nargs='?',
type=bool,
const=True,
help='needs -v option')
parser.add_argument('-i',
'--info',
required=False,
default=None,
nargs='?',
type=bool,
const=True)
parser.add_argument('-k',
'--kill',
required=False,
default=None,
nargs='?',
type=bool,
const=True)
args = parser.parse_args()
config = ConfigParser()
config.read(CONFIG_FILE)
yac = Yascheduler(config)
statuses = {
yac.STATUS_TO_DO: "QUEUED",
yac.STATUS_RUNNING: "RUNNING",
yac.STATUS_DONE: "FINISHED"
}
local_parsing_ready, local_calc_snippet = False, False
if args.jobs:
tasks = yac.queue_get_tasks(jobs=args.jobs)
else:
tasks = yac.queue_get_tasks(status=(yac.STATUS_RUNNING,
yac.STATUS_TO_DO))
if args.view or args.kill:
if not tasks:
print('NO MATCHING TASKS FOUND')
return
ssh_custom_key = {}
for filename in os.listdir(config.get('local', 'data_dir')):
if not filename.startswith('yakey') or not os.path.isfile(
os.path.join(config.get('local', 'data_dir'), filename)):
continue
key_path = os.path.join(config.get('local', 'data_dir'), filename)
pmk_key = RSAKey.from_private_key_file(key_path)
print('LOADED KEY %s' % key_path)
ssh_custom_key = {'pkey': pmk_key}
break
if args.convergence:
try:
from pycrystal import CRYSTOUT
from numpy import nan
local_parsing_ready = True
except:
pass
if args.view:
yac.cursor.execute(
'SELECT task_id, label, metadata, ip FROM yascheduler_tasks WHERE status=%s AND task_id IN (%s);'
% (yac.STATUS_RUNNING, ', '.join(
[str(task['task_id']) for task in tasks])))
for row in yac.cursor.fetchall():
print("." * 50 + "ID%s %s at %s@%s:%s" %
(row[0], row[1], config.get('remote', 'user'), row[3],
row[2]['remote_folder']))
ssh_conn = SSH_Connection(host=row[3],
user=config.get('remote', 'user'),
connect_kwargs=ssh_custom_key)
try:
result = ssh_conn.run('tail -n15 %s/OUTPUT' %
row[2]['remote_folder'],
hide=True)
except UnexpectedExit:
print('OUTDATED TASK, SKIPPING')
else:
print(result.stdout)
if local_parsing_ready:
local_calc_snippet = os.path.join(
config.get('local', 'data_dir'), 'local_calc_snippet.tmp')
try:
ssh_conn.get(row[2]['remote_folder'] + '/OUTPUT',
local_calc_snippet)
except IOError as err:
continue
calc = CRYSTOUT(local_calc_snippet)
output_lines = ''
if calc.info['convergence']:
output_lines += str(calc.info['convergence']) + "\n"
if calc.info['optgeom']:
for n in range(len(calc.info['optgeom'])):
try:
ncycles = calc.info['ncycles'][n]
except IndexError:
ncycles = "^"
output_lines += "{:8f}".format(calc.info['optgeom'][n][0] or nan) + " " + \
"{:8f}".format(calc.info['optgeom'][n][1] or nan) + " " + \
"{:8f}".format(calc.info['optgeom'][n][2] or nan) + " " + \
"{:8f}".format(calc.info['optgeom'][n][3] or nan) + " " + \
"E={:12f}".format(calc.info['optgeom'][n][4] or nan) + " eV" + " " + \
"(%s)" % ncycles + "\n"
print(output_lines)
elif args.kill:
if not args.jobs:
print('NO JOBS GIVEN')
return
yac.cursor.execute(
'SELECT ip FROM yascheduler_tasks WHERE status=%s AND task_id IN (%s);'
% (yac.STATUS_RUNNING, ', '.join(
[str(task['task_id']) for task in tasks])))
for row in yac.cursor.fetchall():
ssh_conn = SSH_Connection(host=row[0],
user=config.get('remote', 'user'),
connect_kwargs=ssh_custom_key)
try:
result = ssh_conn.run('pkill %s' % yac.RUNNING_MARKER,
hide=True)
except:
pass
elif args.info:
for task in tasks:
print('task_id={}\tstatus={}\tlabel={}\tip={}'.format(
task['task_id'], statuses[task['status']], task['label'],
task['ip'] or '-'))
else:
for task in tasks:
print('{} {}'.format(task['task_id'], statuses[task['status']]))
yac.connection.close()
if local_calc_snippet and os.path.exists(local_calc_snippet):
os.unlink(local_calc_snippet)
class Mock(Calculator):
def __init__(self, *args, **kwargs):
Calculator.__init__(self)
def get_property(self, *args, **kwargs):
return 42
for root, dirs, files in os.walk(sys.argv[1]):
# NB beware of the broken links (clean e.g. find . -type l -exec rm -f {} \;)
for filename in files:
target = root + os.sep + filename
if not CRYSTOUT.acceptable(target):
continue
logging.info("*"*25 + root + os.sep + filename + "*"*25)
skipped = False
# Parsing with ejp
tic = time.time()
with open(target) as fp:
try:
ejp_result = Ejpcry.read_file(fp, log_warnings=False)
except Exception as err:
logging.error("EJP FAILED TO PARSE: %s" % str(err))
skipped = True
ejp_perf = round(time.time() - tic, 3)