def main():
parser = argparse.ArgumentParser(description="""
convert an OPTIM database to a pele sqlite database. Four files are needed. Normally they are called:
points.min : the coordinates of the minima in binary format
min.data : additional information about the minima (like the energy)
points.ts : the coordinates of the transition states
min.ts : additional information about transition states (like which minima they connect)
Other file names can optionally be passed. Some fortran compilers use non-standard endianness to save the
binary data. If your coordinates are garbage, try changing the endianness.
""", formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('--ndof', help='Number of total degrees of freedom (e.g. 3*number of atoms). This is simply the length of a coordinates vector.',
type=int, default=None)
parser.add_argument('--Database','-d', help = 'Name of database to write into', type = str, default="optimdb.sqlite")
parser.add_argument('--Mindata','-m', help = 'Name of min.data file', type = str, default="min.data")
parser.add_argument('--Tsdata','-t', help = 'Name of ts.data file', type = str, default="ts.data")
parser.add_argument('--Pointsmin','-p', help = 'Name of points.min file', type = str, default="points.min")
parser.add_argument('--Pointsts','-q', help = 'Name of points.ts file', type = str, default="points.ts")
parser.add_argument('--endianness', help = 'set the endianness of the binary data. Can be "<" for little-endian or ">" for big-endian', type = str, default="=")
args = parser.parse_args()
db = Database(args.Database)
cv = OptimDBConverter(database=db, ndof=args.ndof, mindata=args.Mindata,
tsdata=args.Tsdata, pointsmin=args.Pointsmin, pointsts=args.Pointsts,
endianness=args.endianness)
cv.setAccuracy()
cv.convert()
cv.db.session.commit()
def main():
parser = argparse.ArgumentParser(description="""
convert an OPTIM database to a pele sqlite database. Four files are needed. Normally they are called:
points.min : the coordinates of the minima in binary format
min.data : additional information about the minima (like the energy)
points.ts : the coordinates of the transition states
min.ts : additional information about transition states (like which minima they connect)
Other file names can optionally be passed. Some fortran compilers use non-standard endianness to save the
binary data. If your coordinates are garbage, try changing the endianness.
""", formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('--ndof', help='Number of total degrees of freedom (e.g. 3*number of atoms). This is simply the length of a coordinates vector.',
type=int, default=None)
parser.add_argument('--parentDB', help = 'Name of parent pinned database from which the system properties will be copied. Choose a small one!')
parser.add_argument('--Database','-d', help = 'Name of database to write into', type = str, default="optimdb.sqlite")
parser.add_argument('--Mindata','-m', help = 'Name of min.data file', type = str, default="min.data")
parser.add_argument('--Tsdata','-t', help = 'Name of ts.data file', type = str, default="ts.data")
parser.add_argument('--Pointsmin','-p', help = 'Name of points.min file', type = str, default="points.min")
parser.add_argument('--Pointsts','-q', help = 'Name of points.ts file', type = str, default="points.ts")
parser.add_argument('--endianness', help = 'set the endianness of the binary data. Can be "<" for little-endian or ">" for big-endian', type = str, default="=")
parser.add_argument('--nopoints', help = 'Load the metadata for minima and transition states without reading the coordinates (usually to save storage space)', action = 'store_true')
args = parser.parse_args()
system, basedb, x0 = create_frozenblj_system_from_db(args.parentDB)
db = Database(args.Database)
props = basedb.properties(as_dict=True)
for key, prop in props.iteritems():
db.add_property(key, prop)
cv = OptimDBConverter(database=db, ndof=args.ndof, mindata=args.Mindata,
tsdata=args.Tsdata, pointsmin=args.Pointsmin, pointsts=args.Pointsts,
endianness=args.endianness, coords_converter=system.coords_converter.get_reduced_coords)
cv.setAccuracy()
if args.nopoints:
cv.convert_no_coords()
else:
cv.convert()
cv.db.session.commit()
def main():
parser = argparse.ArgumentParser(
description="""
convert an OPTIM database to a pele sqlite database. Four files are needed. Normally they are called:
points.min : the coordinates of the minima in binary format
min.data : additional information about the minima (like the energy)
points.ts : the coordinates of the transition states
min.ts : additional information about transition states (like which minima they connect)
Other file names can optionally be passed. Some fortran compilers use non-standard endianness to save the
binary data. If your coordinates are garbage, try changing the endianness.
""",
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
'--ndof',
help=
'Number of total degrees of freedom (e.g. 3*number of atoms). This is simply the length of a coordinates vector.',
type=int,
default=None)
parser.add_argument('--Database',
'-d',
help='Name of database to write into',
type=str,
default="optimdb.sqlite")
parser.add_argument('--Mindata',
'-m',
help='Name of min.data file',
type=str,
default="min.data")
parser.add_argument('--Tsdata',
'-t',
help='Name of ts.data file',
type=str,
default="ts.data")
parser.add_argument('--Pointsmin',
'-p',
help='Name of points.min file',
type=str,
default="points.min")
parser.add_argument('--Pointsts',
'-q',
help='Name of points.ts file',
type=str,
default="points.ts")
parser.add_argument(
'--endianness',
help=
'set the endianness of the binary data. Can be "<" for little-endian or ">" for big-endian',
type=str,
default="=")
args = parser.parse_args()
db = Database(args.Database)
cv = OptimDBConverter(database=db,
ndof=args.ndof,
mindata=args.Mindata,
tsdata=args.Tsdata,
pointsmin=args.Pointsmin,
pointsts=args.Pointsts,
endianness=args.endianness)
cv.setAccuracy()
cv.convert()
cv.db.session.commit()
