def __init__(self):
my_parser = Results()
my_parser.multi()
my_parser.parser.add_argument('-E','--beads',help='beads for structure analysis',default=['62'],
type = str, nargs = '+')
my_parser.parser.add_argument('-abc','--vectors', help='unit cell vectors. For folding coordinates into a unit cell',
type = float, nargs = '+', default = [20.022,19.899,13.383])
args = vars(my_parser.parse_args())
self.args = args
self.checks()
def __init__(self, regionMap):
my_parser = Results()
my_parser.parser.add_argument(
'-ID',
'--name',
help='Name of db for molecule number counting',
type=str)
my_parser.parser.add_argument('-B',
'--bead',
help='bead for structure analysis',
default=['COM'],
type=str,
nargs='+')
my_parser.parser.add_argument(
'-abc',
'--vectors',
help='unit cell vectors. For folding coordinates into a unit cell',
type=float,
nargs='+',
default=[20.022, 19.899, 13.383])
my_parser.parser.add_argument(
'-g',
'--gridName',
help='energy grid file name',
default='/Users/dejacor/Documents/butanol-water'
'/323K/MFI/energy_grid_114_O.out',
type=str)
my_parser.parser.add_argument(
'-M',
'--mergedGridName',
help='energy grid merged file name',
default='/Users/dejacor/Documents/butanol-water/323K/MFI/'
'energy-grids-merged/new_channels.xyz',
type=str)
my_args = vars(my_parser.parse_args())
self.args = my_args
self.defaultLabel = 'other'
self.boxLengths = self.args['vectors']
self.mergedGridName = self.args['mergedGridName']
self.numIndep = self.args['indep']
self.gridName = self.args['gridName']
self.channelMap = regionMap
self.checks()
self.initGrids()
self.count = {
name: [0 for i in self.numIndep]
for name in self.regionNames
}
self.data = {region: [] for region in self.regionNames}
self.averages = {region: {} for region in self.regionNames}
self.N = dict()
def __init__(self):
my_parser = Results()
my_parser.parser.add_argument('-ID',
'--name',
help='Name of output db',
type=str)
my_parser.parser.add_argument(
'-abc',
'--vectors',
help='unit cell vectors.' +
'For folding coordinates into a unit cell',
type=float,
nargs='+',
default=[20.022, 19.899, 13.383])
my_args = vars(my_parser.parse_args())
self.args = my_args
self.checks()
def __init__(self):
my_parser = Results()
my_parser.parser.add_argument(
'-ID',
'--name',
help='Name of db for molecule number counting',
type=str)
my_parser.parser.add_argument('-B',
'--bead',
help='bead for structure analysis',
default=['COM'],
type=str,
nargs='+')
my_parser.parser.add_argument(
'-abc',
'--vectors',
help='unit cell vectors. For folding coordinates into a unit cell',
type=float,
nargs='+',
default=[20.022, 19.899, 13.383])
my_parser.parser.add_argument(
'-lmn',
'--replications',
help='unit cell vectors. For folding coordinates into a unit cell',
type=int,
nargs='+')
my_args = vars(my_parser.parse_args())
if my_args['verbosity'] > 0:
print(my_args)
self.args = my_args
assert len(self.args['replications']
) == 3, 'No replications provided: {}'.format(
self.args['replications'])
FindRegion.__init__(self, self.args['vectors'],
self.args['replications'])
self.numIndep = self.args['indep']
self.checks()
self.init_grids()
self.count = {
name: [0 for i in self.numIndep]
for name in self.regionNames
}
self.data = {region: [] for region in self.regionNames}
self.averages = {region: {} for region in self.regionNames}
def __init__(self):
my_parser = Results()
my_parser.multi()
my_parser.parser.add_argument('-B1','--bead1',help='bead from for rdf',
type = str,nargs='+')
my_parser.parser.add_argument('-M1','--mol1',help='mol from for rdf',
type = str,nargs='+')
my_parser.parser.add_argument('-B2','--bead2',help='bead to for rdf',
type = str,nargs='+')
my_parser.parser.add_argument('-M2','--mol2',help='mol to for rdf',
type = str,nargs='+')
my_parser.parser.add_argument('-bins','--bins',help='radial bin size for rdf',
type = float,default=0.2)
my_parser.parser.add_argument('-r','--rmax',help='max radius for rdf',
type = float, default=14.0)
my_parser.parser.add_argument('-d','--dimensions',help='Dimensions for RDF',
type = str,nargs='+',default=['x','y','z'])
args = vars(my_parser.parse_args())
self.args = args
self.checks()