def run(args):
if not Kdb().check_version():
sys.exit()
if len(args) < 1:
print "first parameter sohuld be either: inert or query"
sys.exit()
if args[0] == 'insert':
if len(args) < 4:
print "parameters for insert should include reactant, saddle, and product files."
sys.exit()
try:
reactant = read_any(args[1])
saddle = read_any(args[2])
product = read_any(args[3])
except IOError:
print "One or more files could not be read."
sys.exit()
try:
mode = Kdb().load_mode(args[3])
except:
mode = None
server_insert(reactant, saddle, product, mode)
elif args[0] == 'query':
if len(args) < 2:
print "parameters for query should include a reactant file."
sys.exit()
try:
reactant = read_any(args[1])
except IOError:
print "could not read reactant file."
sys.exit()
server_query(reactant)
def run(args):
if not Kdb().check_version():
sys.exit()
if len(args) < 1:
print "first parameter sohuld be either: inert or query"
sys.exit()
if args[0] == 'insert':
if len(args) < 4:
print "parameters for insert should include reactant, saddle, and product files."
sys.exit()
try:
reactant = read_any(args[1])
saddle = read_any(args[2])
product = read_any(args[3])
except IOError:
print "One or more files could not be read."
sys.exit()
try:
mode = Kdb().load_mode(args[3])
except:
mode = None
server_insert(reactant, saddle, product, mode)
elif args[0] == 'query':
if len(args) < 2:
print "parameters for query should include a reactant file."
sys.exit()
try:
reactant = read_any(args[1])
except IOError:
print "could not read reactant file."
sys.exit()
server_query(reactant)
name = db.get_name(args['reactant'].get_chemical_symbols())
entries = db.get_process(name)
return entries, name
if __name__ == "__main__":
# Parse command line options.
parser = OptionParser(usage = "%prog [options] reactant.con")
parser.add_option("-a", "--alias", dest = "alias",
help = "the name of the SQL kdb",
default = KDB_NAME)
parser.add_option("--nodupes", dest = "nodupes", action="store_true",
help = "detect and remove duplicate suggestions (can be expensive)")
options, args = parser.parse_args()
# Make sure we get the reactant file name.
if len(args) < 1:
parser.print_help()
sys.exit()
# Load the reactant con file.
reactant = read_any(args[0])
# get database params
db = LocalDB(options.alias)
params = db.get_params()
#create isntance of LocalQuery and run query()
query_sub_class = LocalQuery()
query_sub_class.query(reactant, "./kdbmatches", dc=params['dc'], nf=params['nf'], nodupes=options.nodupes, kdbname=options.alias)
#!/usr/bin/env python
import aselite
from sys import argv, exit
if len(argv) < 3:
print 'usage: center.py FILE STDDEV'
print ' randomly displaces the atoms in FILE by a gaussian with'
print ' a standard deviation of STDDEV'
print
exit(0)
filename = argv[1]
stddev = float(argv[2])
atoms = aselite.read_any(filename)
atoms.rattle(stddev)
atoms.write(filename)
dest="alias",
help="the name of the SQL kdb",
default=KDB_NAME)
parser.add_option(
"--nodupes",
dest="nodupes",
action="store_true",
help="detect and remove duplicate suggestions (can be expensive)")
options, args = parser.parse_args()
# Make sure we get the reactant file name.
if len(args) < 1:
parser.print_help()
sys.exit()
# Load the reactant con file.
reactant = read_any(args[0])
# get database params
db = LocalDB(options.alias)
params = db.get_params()
#create isntance of LocalQuery and run query()
query_sub_class = LocalQuery()
query_sub_class.query(reactant,
"./kdbmatches",
dc=params['dc'],
nf=params['nf'],
nodupes=options.nodupes,
kdbname=options.alias)
#!/usr/bin/env python
import aselite
from sys import argv, exit
if len(argv) < 2 or len(argv) > 3 or '-h' in argv:
print('usage: center.py FILE [DISTANCE]')
print(' centers the structure in the current box and')
print(' optionally adds DISTANCE amount of vacuum to FILE')
print()
exit(0)
filename = argv[1]
if len(argv) == 3:
distance = float(argv[2])
else:
distance = None
atoms = aselite.read_any(filename)
if distance:
atoms.center(distance)
else:
atoms.center()
atoms.write(filename)
parser.add_option("-m",
"--mac",
dest="mac",
action="store",
type="float",
help="mobile atom cutoff parameter",
default=None)
options, args = parser.parse_args()
# Make sure we get the reactant, saddle, product, and mode files.
if len(args) < 3:
parser.print_help()
sys.exit()
# Load the reactant, saddle, product, and mode files.
reactant = read_any(args[0])
saddle = read_any(args[1])
product = read_any(args[2])
mode = None
if options.mode is not None:
mode = insert_sub_class.load_mode(options.mode)
# load previous params
db = LocalDB(KDB_NAME)
params = db.get_params()
if options.nf is None:
options.nf = params['nf']
if options.dc is None:
options.dc = params['dc']
if options.mac is None:
options.mac = params['mac']
if __name__ == "__main__":
insert_sub_class = RemoteInsert()
# Parse command line options.
parser = OptionParser(usage = "%prog [options] reactant saddle product mode")
parser.add_option("-o", "--mode", dest = "mode",
help = "optional mode file",
default = None)
options, args = parser.parse_args()
# Make sure we get the reactant, saddle, product, and mode files.
if len(args) < 3:
parser.print_help()
sys.exit()
# Load the reactant, saddle, product, and mode files.
reactant = read_any(args[0])
saddle = read_any(args[1])
product = read_any(args[2])
mode = None
if options.mode is not None:
mode = insert_sub_class.load_mode(options.mode)
# load previous params
db = RemoteDB()
params = db.get_params()
nf = params['nf']
dc = params['dc']
mac = params['mac']
insert_sub_class.insert(reactant, saddle, product, mode, nf=nf, dc=dc, mac=mac)
#!/usr/bin/env python
import sys
import aselite
if len(sys.argv) < 3:
print 'usage: 2con.py IN OUT'
print ' converts file IN of type POSCAR or xyz to con and saves it to OUT'
print
sys.exit(0)
traj = aselite.read_any(sys.argv[1])
aselite.write_con(sys.argv[2], traj)