def main():
parser = argparse.ArgumentParser(description="print information about the database")
parser.add_argument("database", type=str, help="Database file name")
parser.add_argument("--write-disconnect",
dest="writeDPS", action="store_true",
help="generate min.dat and ts.dat to use with disconnectDPS")
parser.add_argument("-m",
dest="writeMinima", action="store_true",
help="dump minima to screen")
parser.add_argument("-t",
dest="writeTS", action="store_true",
help="dump transition states to screen")
parser.add_argument("-p",
dest="properties", action="store_true",
help="print system properties")
parser.add_argument("-s",
dest="summary", action="store_true",
help="print summary")
parser.add_argument("-S",
dest="summary_long", action="store_true",
help="print long summary")
args = parser.parse_args()
if args.summary_long:
args.summary = True
db = Database(db=args.database, createdb=False)
if args.properties or args.summary:
print_system_properties(db)
if args.summary:
print "number of minima:", db.number_of_minima()
print "number of transition states:", db.number_of_transition_states()
if args.summary_long:
long_summary(db)
if args.writeMinima:
print "List of minima: energy id fvib pgorder"
print "---------------"
for m in db.minima():
print "%f\t\tid %d %s %s" % (m.energy, m._id, str(m.fvib), str(m.pgorder))
print "END\n"
if args.writeTS:
print "List of transition states:"
print "--------------------------"
for ts in db.transition_states():
print "%d\t<->\t%d\tid %d\tenergies %f %f %f" % \
(ts.minimum1._id, ts.minimum2._id, ts._id, ts.minimum1.energy, ts.energy, ts.minimum2.energy)
print "END\n"
if args.writeDPS:
writeDPS(db)
def main():
parser = argparse.ArgumentParser(description="print information about the database")
parser.add_argument("database", type=str, help="Database file name")
parser.add_argument("--write-pathsample-db",
dest="write_pathsample", action="store_true",
help="generate a pathsample database by writing files min.data, ts.data, points.min, and points.ts")
parser.add_argument("-m",
dest="writeMinima", action="store_true",
help="dump minima to screen")
parser.add_argument("-t",
dest="writeTS", action="store_true",
help="dump transition states to screen")
parser.add_argument("-p",
dest="properties", action="store_true",
help="print system properties")
parser.add_argument("-s",
dest="summary", action="store_true",
help="print summary")
parser.add_argument("-S",
dest="summary_long", action="store_true",
help="print long summary")
args = parser.parse_args()
if args.summary_long:
args.summary = True
db = Database(db=args.database, createdb=False)
if args.properties or args.summary:
print_system_properties(db)
if args.summary:
print "number of minima:", db.number_of_minima()
print "number of transition states:", db.number_of_transition_states()
if args.summary_long:
long_summary(db)
if args.writeMinima:
print "List of minima: energy id fvib pgorder"
print "---------------"
for m in db.minima():
print "%f\t\tid %d %s %s" % (m.energy, m._id, str(m.fvib), str(m.pgorder))
print "END\n"
if args.writeTS:
print "List of transition states:"
print "--------------------------"
for ts in db.transition_states():
print "%d\t<->\t%d\tid %d\tenergies %f %f %f" % \
(ts.minimum1._id, ts.minimum2._id, ts._id, ts.minimum1.energy, ts.energy, ts.minimum2.energy)
print "END\n"
if args.write_pathsample:
write_pathsample_db(db)
def main():
parser = argparse.ArgumentParser(description="print information about the database")
parser.add_argument("database", type=str, help="Database file name")
parser.add_argument("--write-pathsample-db",
dest="write_pathsample", action="store_true",
help="generate a pathsample database by writing files min.data, ts.data, points.min, and points.ts")
parser.add_argument("--write-dummy-db",
dest="write_pathsample_dummy", action="store_true",
help="generate a pathsample database without the points files - min.data and ts.data only")
parser.add_argument("-m",
dest="writeMinima", action="store_true",
help="dump minima to screen")
parser.add_argument("--minimum", type=int, default=0, help="print the coordinates of a particular minimum to the screen")
parser.add_argument("-t",
dest="writeTS", action="store_true",
help="dump transition states to screen")
parser.add_argument("-p",
dest="properties", action="store_true",
help="print system properties")
parser.add_argument("-s",
dest="summary", action="store_true",
help="print summary")
parser.add_argument("-S",
dest="summary_long", action="store_true",
help="print long summary")
parser.add_argument("-l",
dest="long_output", action="store_true",
help="Allow long output to be printed")
args = parser.parse_args()
if args.summary_long:
args.summary = True
suppress = not args.long_output
db = Database(db=args.database, createdb=False)
if args.properties or args.summary:
print_system_properties(db,suppress_long=suppress)
if args.summary:
print "number of minima:", db.number_of_minima()
print "number of transition states:", db.number_of_transition_states()
if args.summary_long:
long_summary(db)
if args.minimum > 0:
m = db.getMinimum(args.minimum)
print m.energy, m._id
x = m.coords.reshape(-1,3)
print x
if args.writeMinima:
print "List of minima: energy id fvib pgorder"
print "---------------"
for m in db.minima():
print "%f\t\tid %d %s %s" % (m.energy, m._id, str(m.fvib), str(m.pgorder))
print "END\n"
if args.writeTS:
print "List of transition states:"
print "--------------------------"
for ts in db.transition_states():
print "%d\t<->\t%d\tid %d\tenergies %f %f %f" % \
(ts.minimum1._id, ts.minimum2._id, ts._id, ts.minimum1.energy, ts.energy, ts.minimum2.energy)
print "END\n"
if args.write_pathsample:
write_pathsample_db(db)
elif args.write_pathsample_dummy:
write_pathsample_db(db, False)
