added option for periodic averaging
This commit is contained in:
parent
0b4e75c201
commit
2daad7542e
|
@ -4,9 +4,18 @@
|
|||
import os,sys
|
||||
import math # noqa
|
||||
import numpy as np
|
||||
from optparse import OptionParser
|
||||
from optparse import OptionParser, OptionGroup
|
||||
import damask
|
||||
|
||||
#"https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions"
|
||||
def periodicAverage(Points, Box):
|
||||
theta = (Points/Box[1]) * (2.0*np.pi)
|
||||
xi = np.cos(theta)
|
||||
zeta = np.sin(theta)
|
||||
theta_avg = np.arctan2(-1.0*zeta.mean(), -1.0*xi.mean()) + np.pi
|
||||
Pmean = Box[1] * theta_avg/(2.0*np.pi)
|
||||
return Pmean
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
|
@ -35,7 +44,23 @@ parser.add_option('-a','--all',
|
|||
action = 'store_true',
|
||||
help = 'apply mapping function also to grouping column')
|
||||
|
||||
parser.set_defaults(function = 'np.average')
|
||||
group = OptionGroup(parser, "periodic averaging", "")
|
||||
|
||||
group.add_option('-p','--periodic',
|
||||
dest = 'periodic',
|
||||
action = 'store_true',
|
||||
help = 'calculate average in periodic space defined by periodic length [%default]')
|
||||
group.add_option('--boundary',
|
||||
dest = 'boundary', metavar = 'MIN MAX',
|
||||
type = 'float', nargs = 2,
|
||||
help = 'define periodic box end points %default')
|
||||
|
||||
parser.add_option_group(group)
|
||||
|
||||
parser.set_defaults(function = 'np.average',
|
||||
all = False,
|
||||
periodic = False,
|
||||
boundary = [0.0, 1.0])
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
||||
|
@ -92,6 +117,9 @@ for name in filenames:
|
|||
grpTable = np.empty((len(values), cols)) # initialize output
|
||||
|
||||
for i in xrange(len(values)): # iterate over groups (unique values in grpColumn)
|
||||
if options.periodic :
|
||||
grpTable[i] = periodicAverage(table.data[index[i]:index[i+1]],options.boundary) # apply periodicAverage mapping function
|
||||
else :
|
||||
grpTable[i] = np.apply_along_axis(mapFunction,0,table.data[index[i]:index[i+1]]) # apply mapping function
|
||||
if not options.all: grpTable[i,grpColumn] = table.data[index[i],grpColumn] # restore grouping column value
|
||||
|
||||
|
|
Loading…
Reference in New Issue