def test_abinit_utils():
"""
Tests (pychemia.code.abinit) [utils] :
"""
if pychemia.HAS_SCIPY and pychemia.HAS_SCIENTIFIC:
from pychemia.code.abinit import xyz2input, netcdf2dict, psp_name
filename = "pychemia/test/data/abinit_05/abinit-o_OUT.nc"
print(len(netcdf2dict(filename)))
assert len(netcdf2dict(filename)) == 310
assert psp_name(1, 'LDA', 'FHI') == '01-H.LDA.fhi'
filename = "pychemia/test/data/abinit_05/abinit_DS11.xyz"
assert xyz2input(filename).variables['natom'] == 2
def test_abinit_utils():
"""
Tests (pychemia.code.abinit) [utils] :
"""
if pychemia.HAS_SCIPY and pychemia.HAS_SCIENTIFIC:
from pychemia.code.abinit import xyz2input, netcdf2dict, psp_name
filename = "pychemia/test/data/abinit_01/abinit-o_OUT.nc"
print(len(netcdf2dict(filename)))
assert len(netcdf2dict(filename)) == 310
assert psp_name(1, 'LDA', 'FHI') == '01-H.LDA.fhi'
filename = "pychemia/test/data/abinit_01/abinit_DS11.xyz"
assert xyz2input(filename).variables['natom'] == 2
def test_abinit_utils():
"""
Test (pychemia.code.abinit) [utils] :
"""
from pychemia.utils.netcdf import netcdf2dict
from pychemia.code.abinit import xyz2input, psp_name
filename = "tests/data/abinit_05/abinit-o_OUT.nc"
print(len(netcdf2dict(filename)))
assert len(netcdf2dict(filename)) == 45
assert psp_name(1, 'LDA', 'FHI') == '01-H.LDA.fhi'
filename = "tests/data/abinit_01/abinit_DS11.xyz"
assert xyz2input(filename).variables['natom'] == 2
def test_abinit_utils():
"""
Tests (pychemia.code.abinit) [utils] :
"""
from pychemia.utils.netcdf import netcdf2dict
from pychemia.code.abinit import xyz2input, psp_name
filename = "tests/data/abinit_05/abinit-o_OUT.nc"
print(len(netcdf2dict(filename)))
assert len(netcdf2dict(filename)) == 45
assert psp_name(1, 'LDA', 'FHI') == '01-H.LDA.fhi'
filename = "tests/data/abinit_01/abinit_DS11.xyz"
assert xyz2input(filename).variables['natom'] == 2
def get_all_psps(basedir, exchange, kind):
directory = basedir + os.sep + exchange + '_' + kind
if not os.path.isdir(directory):
os.mkdir(directory)
if kind == 'PAW':
rpath = get_rpath_psp(kind, exchange)
filename = rpath.split('/')[-1]
if not os.path.isfile(directory + '/' + filename):
u = urlopen(rpath)
f = open(directory + os.sep + filename, 'wb')
meta = u.info()
file_size = int(meta.getheaders("Content-Length")[0])
print("Downloading: %s Bytes: %s" % (filename, file_size))
file_size_dl = 0
block_sz = 8192
while True:
readed_buffer = u.read(block_sz)
if not readed_buffer:
break
file_size_dl += len(readed_buffer)
f.write(readed_buffer)
status = r"%10d [%3.2f%%]" % (file_size_dl, file_size_dl * 100. / file_size)
status += chr(8) * (len(status) + 1)
print(status, end='')
f.close()
print('\n')
try:
tar = tarfile.open(directory + '/' + filename, 'r:gz')
for item in tar:
if not os.path.exists(item.name):
tar.extract(item, path=directory)
except tarfile.ReadError:
name = os.path.basename(filename)
print(name[:name.rfind('.')], '<filename>')
elif kind == 'HGH':
while True:
succeed = True
ftp = ftplib.FTP('ftp.abinit.org') # connect to host, default port
ftp.login() # user anonymous, passwd anonymous@
ftp.cwd('pub/abinitio/Psps/LDA_HGH/')
for filename in ftp.nlst():
if not os.path.exists(directory + '/' + filename) or os.path.getsize(directory + '/' + filename) == 0:
print('Getting %s' % filename)
try:
ftp.retrbinary('RETR ' + filename, open(directory + '/' + filename, 'wb').write)
except ftplib.error_perm:
print('Failed to get ', filename)
succeed = False
ftp.close()
if succeed:
break
else:
ftp = ftplib.FTP('ftp.abinit.org') # connect to host, default port
ftp.login() # user anonymous, passwd anonymous@
missing_psps = []
for i in range(1, 113):
if kind == 'GTH' and i > 17:
continue
if kind == 'CORE' and i not in [6, 7]:
continue
if kind == 'FHI' and exchange == 'LDA' and i in [57, 59, 63, 65, 66, 67, 90, 94, 102, 110, 111, 112]:
continue
if kind == 'TM' and exchange == 'LDA' and i in [104, 105, 106, 107, 108, 109, 110, 111, 112]:
continue
if kind == 'FHI' and exchange == 'GGA' and i in [57, 59, 63, 65, 66, 67, 90, 94, 102, 110, 111, 112]:
continue
if kind == 'AE' and exchange == 'DEN' and i in [57, 59, 63, 65, 66, 67, 90, 94, 102, 110, 111, 112]:
continue
if kind == 'GTH' and exchange == 'LDA' and i in [2, 10]:
continue
if kind == 'FC' and exchange == 'DEN' and i in [63, 65, 66, 67, 110, 111, 112]:
continue
filename = psp_name(i, exchange, kind)
if not os.path.isfile(directory + '/' + filename) or os.path.getsize(directory + '/' + filename) == 0:
print('Getting...' + filename)
nofile = True
while nofile:
retr = 'RETR ' + get_rpath_psp(kind, exchange, i) + filename
try:
ftp.retrbinary(retr, open(directory + '/' + filename, 'wb').write)
nofile = False
if os.path.getsize(directory + '/' + filename) == 0:
os.remove(directory + '/' + filename)
except ftplib.error_perm:
print('Could not download ' + retr)
missing_psps.append(i)
ftp.close()
time.sleep(5)
print('Reconnecting...')
if os.path.isfile(directory + '/' + filename):
os.remove(directory + '/' + filename)
ftp = ftplib.FTP('ftp.abinit.org') # connect to host, default port
ftp.login() # user anonymous, passwd anonymous@
nofile = False
ftp.close()
if len(missing_psps) > 0:
print("kind == '%s' and exchange == '%s' and i in %s" % (kind, exchange, missing_psps))
def get_all_psps(basedir, exchange, kind):
directory = basedir + os.sep + exchange + '_' + kind
if not os.path.isdir(directory):
os.mkdir(directory)
if kind in ['PAW', 'ONC']:
rpath = get_rpath_psp(kind, exchange)
filename = rpath.split('/')[-1]
if not os.path.isfile(directory + '/' + filename):
u = urlopen(rpath)
f = open(directory + os.sep + filename, 'wb')
meta = u.info()
file_size = int(meta.get("Content-Length"))
print("Downloading: %s Bytes: %s" % (filename, file_size))
file_size_dl = 0
block_sz = 8192
while True:
readed_buffer = u.read(block_sz)
if not readed_buffer:
break
file_size_dl += len(readed_buffer)
f.write(readed_buffer)
status = r"%10d [%3.2f%%]" % (file_size_dl, file_size_dl * 100. / file_size)
status += chr(8) * (len(status) + 1)
print(status, end='')
f.close()
print('\n')
else:
print('All files are downloaded')
try:
tar = tarfile.open(directory + '/' + filename, 'r:gz')
for item in tar:
if not os.path.exists(item.name):
tar.extract(item, path=directory)
except tarfile.ReadError:
name = os.path.basename(filename)
print(name[:name.rfind('.')], '<filename>')
elif kind == 'HGH':
while True:
succeed = True
ftp = ftplib.FTP('ftp.abinit.org') # connect to host, default port
ftp.login() # user anonymous, passwd anonymous@
ftp.cwd('pub/abinitio/Psps/LDA_HGH/')
for filename in ftp.nlst():
if not os.path.exists(directory + '/' + filename) or os.path.getsize(directory + '/' + filename) == 0:
print('Getting %s' % filename)
try:
ftp.retrbinary('RETR ' + filename, open(directory + '/' + filename, 'wb').write)
except ftplib.error_perm:
print('Failed to get ', filename)
succeed = False
ftp.close()
if succeed:
print('All files are downloaded')
break
else:
files = []
for i in range(1, 113):
if kind == 'GTH' and i > 17:
continue
if kind == 'CORE' and i not in [6, 7]:
continue
if kind == 'FHI' and exchange == 'LDA' and i in [57, 59, 63, 65, 66, 67, 90, 94, 102, 110, 111, 112]:
continue
if kind == 'TM' and exchange == 'LDA' and i in [104, 105, 106, 107, 108, 109, 110, 111, 112]:
continue
if kind == 'FHI' and exchange == 'GGA' and i in [57, 59, 63, 65, 66, 67, 90, 94, 102, 110, 111, 112]:
continue
if kind == 'AE' and exchange == 'DEN' and i in [57, 59, 63, 65, 66, 67, 90, 94, 102, 110, 111, 112]:
continue
if kind == 'GTH' and exchange == 'LDA' and i in [2, 10]:
continue
if kind == 'FC' and exchange == 'DEN' and i in [63, 65, 66, 67, 110, 111, 112]:
continue
filename = psp_name(i, exchange, kind)
filepath = get_rpath_psp(kind, exchange, i)
if not os.path.isfile(directory + '/' + filename) or os.path.getsize(directory + '/' + filename) == 0:
files.append((filename, directory, filepath))
if len(files) == 0:
print("All files are downloaded")
else:
print("Downloading %d PSP files" % len(files))
nth = 12
pool = ThreadPoolExecutor(nth)
index = 0
p = nth * [None]
while index < len(files):
for i in range(nth):
if index < len(files):
p[i] = pool.submit(worker, *(files[index]))
index += 1
for i in range(nth):
try:
p[i].result()
except AttributeError:
print("Complete")
if len(files) > 0:
print("kind == '%s' and exchange == '%s'" % (kind, exchange))
for i in files:
print(" %s" % str(i))
def get_all_psps(basedir, exchange, kind):
directory = basedir + os.sep + exchange + '_' + kind
if not os.path.isdir(directory):
os.mkdir(directory)
if kind == 'PAW':
rpath = get_rpath_psp(kind, exchange)
filename = rpath.split('/')[-1]
if not os.path.isfile(directory + '/' + filename):
u = urlopen(rpath)
f = open(directory + os.sep + filename, 'wb')
meta = u.info()
file_size = int(meta.get("Content-Length")[0])
print("Downloading: %s Bytes: %s" % (filename, file_size))
file_size_dl = 0
block_sz = 8192
while True:
readed_buffer = u.read(block_sz)
if not readed_buffer:
break
file_size_dl += len(readed_buffer)
f.write(readed_buffer)
status = r"%10d [%3.2f%%]" % (file_size_dl,
file_size_dl * 100. / file_size)
status += chr(8) * (len(status) + 1)
print(status, end='')
f.close()
print('\n')
else:
print('All files are downloaded')
try:
tar = tarfile.open(directory + '/' + filename, 'r:gz')
for item in tar:
if not os.path.exists(item.name):
tar.extract(item, path=directory)
except tarfile.ReadError:
name = os.path.basename(filename)
print(name[:name.rfind('.')], '<filename>')
elif kind == 'HGH':
while True:
succeed = True
ftp = ftplib.FTP('ftp.abinit.org') # connect to host, default port
ftp.login() # user anonymous, passwd anonymous@
ftp.cwd('pub/abinitio/Psps/LDA_HGH/')
for filename in ftp.nlst():
if not os.path.exists(directory + '/' +
filename) or os.path.getsize(
directory + '/' + filename) == 0:
print('Getting %s' % filename)
try:
ftp.retrbinary(
'RETR ' + filename,
open(directory + '/' + filename, 'wb').write)
except ftplib.error_perm:
print('Failed to get ', filename)
succeed = False
ftp.close()
if succeed:
print('All files are downloaded')
break
else:
files = []
for i in range(1, 113):
if kind == 'GTH' and i > 17:
continue
if kind == 'CORE' and i not in [6, 7]:
continue
if kind == 'FHI' and exchange == 'LDA' and i in [
57, 59, 63, 65, 66, 67, 90, 94, 102, 110, 111, 112
]:
continue
if kind == 'TM' and exchange == 'LDA' and i in [
104, 105, 106, 107, 108, 109, 110, 111, 112
]:
continue
if kind == 'FHI' and exchange == 'GGA' and i in [
57, 59, 63, 65, 66, 67, 90, 94, 102, 110, 111, 112
]:
continue
if kind == 'AE' and exchange == 'DEN' and i in [
57, 59, 63, 65, 66, 67, 90, 94, 102, 110, 111, 112
]:
continue
if kind == 'GTH' and exchange == 'LDA' and i in [2, 10]:
continue
if kind == 'FC' and exchange == 'DEN' and i in [
63, 65, 66, 67, 110, 111, 112
]:
continue
filename = psp_name(i, exchange, kind)
filepath = get_rpath_psp(kind, exchange, i)
if not os.path.isfile(directory + '/' +
filename) or os.path.getsize(directory +
'/' +
filename) == 0:
files.append((filename, directory, filepath))
if len(files) == 0:
print("All files are downloaded")
else:
print("Downloading %d PSP files" % len(files))
nth = 12
pool = ThreadPoolExecutor(nth)
index = 0
p = nth * [None]
while index < len(files):
for i in range(nth):
if index < len(files):
p[i] = pool.submit(worker, *(files[index]))
index += 1
for i in range(nth):
try:
p[i].result()
except AttributeError:
print("Complete")
if len(files) > 0:
print("kind == '%s' and exchange == '%s' and i in %s" %
(kind, exchange, files))
def get_all_psps(basedir, exchange, kind):
directory = basedir + os.sep + exchange + '_' + kind
if not os.path.isdir(directory):
os.mkdir(directory)
if kind == 'PAW':
rpath = get_rpath_psp(kind, exchange)
filename = rpath.split('/')[-1]
if not os.path.isfile(directory + '/' + filename):
u = urlopen(rpath)
f = open(directory + os.sep + filename, 'wb')
meta = u.info()
file_size = int(meta.getheaders("Content-Length")[0])
print("Downloading: %s Bytes: %s" % (filename, file_size))
file_size_dl = 0
block_sz = 8192
while True:
readed_buffer = u.read(block_sz)
if not readed_buffer:
break
file_size_dl += len(readed_buffer)
f.write(readed_buffer)
status = r"%10d [%3.2f%%]" % (file_size_dl,
file_size_dl * 100. / file_size)
status += chr(8) * (len(status) + 1)
print(status, end='')
f.close()
print('\n')
try:
tar = tarfile.open(directory + '/' + filename, 'r:gz')
for item in tar:
if not os.path.exists(item.name):
tar.extract(item, path=directory)
except tarfile.ReadError:
name = os.path.basename(filename)
print(name[:name.rfind('.')], '<filename>')
elif kind == 'HGH':
while True:
succeed = True
ftp = ftplib.FTP('ftp.abinit.org') # connect to host, default port
ftp.login() # user anonymous, passwd anonymous@
ftp.cwd('pub/abinitio/Psps/LDA_HGH/')
for filename in ftp.nlst():
if not os.path.exists(directory + '/' +
filename) or os.path.getsize(
directory + '/' + filename) == 0:
print('Getting %s' % filename)
try:
ftp.retrbinary(
'RETR ' + filename,
open(directory + '/' + filename, 'wb').write)
except ftplib.error_perm:
print('Failed to get ', filename)
succeed = False
ftp.close()
if succeed:
break
else:
ftp = ftplib.FTP('ftp.abinit.org') # connect to host, default port
ftp.login() # user anonymous, passwd anonymous@
missing_psps = []
for i in range(1, 113):
if kind == 'GTH' and i > 17:
continue
if kind == 'CORE' and i not in [6, 7]:
continue
if kind == 'FHI' and exchange == 'LDA' and i in [
57, 59, 63, 65, 66, 67, 90, 94, 102, 110, 111, 112
]:
continue
if kind == 'TM' and exchange == 'LDA' and i in [
104, 105, 106, 107, 108, 109, 110, 111, 112
]:
continue
if kind == 'FHI' and exchange == 'GGA' and i in [
57, 59, 63, 65, 66, 67, 90, 94, 102, 110, 111, 112
]:
continue
if kind == 'AE' and exchange == 'DEN' and i in [
57, 59, 63, 65, 66, 67, 90, 94, 102, 110, 111, 112
]:
continue
if kind == 'GTH' and exchange == 'LDA' and i in [2, 10]:
continue
if kind == 'FC' and exchange == 'DEN' and i in [
63, 65, 66, 67, 110, 111, 112
]:
continue
filename = psp_name(i, exchange, kind)
if not os.path.isfile(directory + '/' +
filename) or os.path.getsize(directory +
'/' +
filename) == 0:
print('Getting...' + filename)
nofile = True
while nofile:
retr = 'RETR ' + get_rpath_psp(kind, exchange,
i) + filename
try:
ftp.retrbinary(
retr,
open(directory + '/' + filename, 'wb').write)
nofile = False
if os.path.getsize(directory + '/' + filename) == 0:
os.remove(directory + '/' + filename)
except ftplib.error_perm:
print('Could not download ' + retr)
missing_psps.append(i)
ftp.close()
time.sleep(5)
print('Reconnecting...')
if os.path.isfile(directory + '/' + filename):
os.remove(directory + '/' + filename)
ftp = ftplib.FTP(
'ftp.abinit.org') # connect to host, default port
ftp.login() # user anonymous, passwd anonymous@
nofile = False
ftp.close()
if len(missing_psps) > 0:
print("kind == '%s' and exchange == '%s' and i in %s" %
(kind, exchange, missing_psps))