def loadInput(self,argv):
print argv,type(argv)
cl = GetPot(argv)
if cl.search('-i'):
self.unc_inp_file=cl.next('')
print 'Selected uncertainty input',self.unc_inp_file,'...'
#check desired file exists
if not os.path.isfile(self.unc_inp_file):
raise IOError('Uncertainty input not found: '+self.unc_inp_file)
print ' ...found uncertainty input file.'
else:
raise IOError('Requires and input file using -i.')
self.input_file = GetPot(Filename=self.unc_inp_file)
def loadInput(self, argv):
print argv, type(argv)
cl = GetPot(argv)
if cl.search('-i'):
self.unc_inp_file = cl.next('')
print 'Selected uncertainty input', self.unc_inp_file, '...'
#check desired file exists
if not os.path.isfile(self.unc_inp_file):
raise IOError('Uncertainty input not found: ' +
self.unc_inp_file)
print ' ...found uncertainty input file.'
else:
raise IOError('Requires and input file using -i.')
self.input_file = GetPot(Filename=self.unc_inp_file)
def readInputFile(file_name):
ifpot = GetPot(Filename=file_name)
print ifpot.comments
root_node = GPNode('root', None)
buildSectionTree(ifpot, root_node)
populateParams(ifpot, root_node)
# root_node.Print()
return root_node
def createROMLevel(self, lvl, ie):
ROMs = {}
runs = self.getRunSet(lvl)
for run, vrs in runs.iteritems():
print '\nStarting run:', run
chlist, ident = self.makeCase(run)
runfile = ie.writeInput(self.unc_inp_file, chlist, ident)
inp_file = GetPot(Filename=runfile)
exdict = {}
for i in range(len(run)):
exdict[run[i]] = vrs[i]
ex = Executor.ExecutorFactory('SC', exdict, inp_file)
ex.run()
os.system('rm ' + runfile)
ROMs[ident] = ex.ROM
return ROMs
def createROMs(self):
self.ROMs = {}
ident = self.todo.keys()[0]
print '\nStarting run:', ident
inp_file = GetPot(Filename=self.unc_inp_file)
ex_type = inp_file('Problem/executor', '')
print 'ex type:', ex_type
ex = Executor.ExecutorFactory(ex_type, self.varDict, inp_file)
ex.run(verbose=self.verbose)
try:
self.ROMs[ident] = ex.ROM
print 'sampled mean:', ex.ROM.moment(1)
except AttributeError:
pass #MC doesn't store a rom at this point
self.ex = ex
#xs={}
#for key,value in self.varDict.iteritems():
# xs[key]=1
#print 'sampled:',ex.ROM.sample(xs,verbose=False)
return ex
import sys
import time
def g(xa=0.75,loc=2.0,D=0.5,S=1.0):
#S = 1.0 #source strength
#D = 0.5 #diffusion coefficient
#loc = 2.0 #depth in cm
cof = S/xa
#print '...in source.py...'
#print 'D,xa:',D,xa
L = np.sqrt(D/xa)
flux = cof*(1.0-np.exp(-loc/L))
return flux
if __name__=='__main__':
cl = GetPot(sys.argv)
if cl.search('-i'):
inpFileName = ''
inpFileName = cl.next(inpFileName)
input_file=GetPot(Filename=inpFileName)
else: raise IOError('Requires an input file using -i.')
xa = input_file('Problem/xa' ,1.0)
D = input_file('Problem/D' ,1.0)
loc= input_file('Problem/loc',1.0)
S = input_file('Problem/S' ,1.0)
outFileName = input_file('Output/file','test.out')
print 'outFileName:',outFileName
result = g(xa,D,loc,S)
prefix_less_token_name = token_name[len(TokenPrefix):]
# NOTE: The line number might be wrong, because of the comment deletion
lexer_mode.token_id_db[prefix_less_token_name] = \
TokenInfo(prefix_less_token_name, None, None, fh.name, line_n)
# find "#include" statements
include_file_list = include_re_obj.findall(content)
include_file_list = filter(lambda file: file not in done_list, include_file_list)
include_file_list = filter(lambda file: os.access(file, os.F_OK), include_file_list)
work_list.extend(include_file_list)
if __name__ == "__main__":
if len(sys.argv) < 2:
print "error: missing command line parameter: input 'token file'"
sys.exit(-1)
cl = GetPot(sys.argv)
input_file = cl.follow("", "-i")
token_class_file = cl.follow("", "-t")
token_class = cl.follow("token", "--token-class-name")
token_counter_offset = cl.follow(1000, "--offset")
output_file = cl.follow("", "-o")
token_prefix = cl.follow("TKN_", "--tp")
if "" in [input_file, output_file]:
print "error: please specify input (option '-i') and output file (option '-o')"
sys.exit(-1)
do(Setup(input_file, output_file, token_class_file, token_class, token_prefix, token_counter_offset))
import numpy as np
import scipy.stats as stt
import time
import os
from GetPot import GetPot
from sys import *
import InputEditor
import Variables
import Samplers as spr
import Backends as be
import matplotlib.pyplot as plt
starttime = time.time()
#load uncertainty input
cl = GetPot(argv)
if cl.search('-i'):
inpFileName = ''
inpFileName = cl.next(inpFileName)
input_file = GetPot(Filename=inpFileName)
else:
raise IOError('Requires an input file using -i.')
#load problem-specific information
templateFile = input_file('Problem/templateFile', '')
#maxSamples = input_file('Problem/totalSamples',0)
storeFlux = input_file('Problem/storeFlux', 0)
execDir = input_file('Problem/execDir', '')
inputDir = input_file('Problem/inputDir', '')
input_editor = input_file('Problem/input_editor', '')
# find "#include" statements
include_file_list = include_re_obj.findall(content)
include_file_list = filter(lambda file: file not in done_list,
include_file_list)
include_file_list = filter(lambda file: os.access(file, os.F_OK),
include_file_list)
work_list.extend(include_file_list)
if __name__ == "__main__":
if len(sys.argv) < 2:
print "error: missing command line parameter: input 'token file'"
sys.exit(-1)
cl = GetPot(sys.argv)
input_file = cl.follow("", "-i")
token_class_file = cl.follow("", "-t")
token_class = cl.follow("token", "--token-class-name")
token_counter_offset = cl.follow(1000, "--offset")
output_file = cl.follow("", "-o")
token_prefix = cl.follow("TKN_", "--tp")
if "" in [input_file, output_file]:
print "error: please specify input (option '-i') and output file (option '-o')"
sys.exit(-1)
do(
Setup(input_file, output_file, token_class_file, token_class,
token_prefix, token_counter_offset))
def createROMs(self):
print ''
print 'Beginning HDMR term calculations...'
self.ROMs = {}
ie = InputEditor.HDMR_IO()
#reference run
chlist, ident = self.makeCase({})
runfile = ie.writeInput(self.unc_inp_file, chlist, ident)
inp_file = GetPot(Filename=runfile)
ex = Executor.ExecutorFactory('SC', {}, inp_file)
ex.run(verbose=False)
os.system('rm ' + runfile)
self.ROMs[ident] = ex.ROM
# rest of runs
numruns = {}
for i in range(1, self.hdmr_level + 1):
nr = 0
print '\n===================================='
print ' STARTING %i-INPUT INTERACTIONS' % i
print '====================================\n'
new = self.createROMLevel(i, ie)
for key, value in new.iteritems():
nr += 1
self.ROMs[key] = value
print '\nnumber of order %i runs: %i' % (i, nr)
numruns[i] = nr
xs = {}
for key, value in self.varDict.iteritems():
xs[key] = 1
#for key,value in self.ROMs.iteritems():
# print 'mean',key,':',value.moment(1)
print '\nROMs per level:'
for key, value in numruns.iteritems():
print ' ', key, value
#for rom in self.ROMs.values():
# pk.dump(rom.serializable(),file('hdmr_'+rom.case()+'.pk','w'))
self.HDMR_ROM = ROM.HDMR_ROM(self.ROMs, self.varDict)
print 'Total Det. Runs:', self.HDMR_ROM.numRunsToCreate()
print 'HDMR sampled', self.HDMR_ROM.sample(xs, self.hdmr_level)[1]
#store output
case = 'hdmr'
case += '_' + self.input_file('Sampler/SC/indexSet', '')
case += '_N' + str(len(self.varDict))
case += '_H' + str(self.hdmr_level)
#case+= '_L'+self.input_file('Sampler/SC/expOrd','')
mean = self.HDMR_ROM.moment(self.hdmr_level, r=1, verbose=False)
if self.input_file('HDMR/anova', 0) > 0:
secm, contribs = self.HDMR_ROM.moment(self.hdmr_level,
r=2,
anova=True)
anovaFileName = case + '.anova'
anovaFile = file(anovaFileName, 'w')
anovaFile.writelines('Variables,Contribution,Percent\n')
for i, j in contribs.iteritems():
name = '-'.join(i.split('_')[1:])
value = str(j**2 / secm)
anovaFile.writelines(name + ',' + str(j**2) + ',' + value +
'\n')
anovaFile.close()
print 'ANOVA analysis written to', anovaFileName
else:
secm = self.HDMR_ROM.moment(self.hdmr_level, r=2, verbose=False)
outFile = file(case + '.out', 'a')
outFile.writelines('\nRuns,SC Level,Mean\n')
outFile.writelines(str(self.HDMR_ROM.numRunsToCreate()) + ',')
outFile.writelines(self.input_file('Sampler/SC/expOrd', '') + ',')
outFile.writelines('%1.15e,%1.15e \n' % (mean, secm - mean * mean))
outFile.close()