def getDOS(
Data = "test_cases/ni_0300/sqe.pkl",
MT = "test_cases/ni_0300/mqe.pkl",
C_ms = numpy.arange(0.0,2.0,0.1),
backgroundFrac = 0.90,
constantFrac = 0.00,
cutoff = 8.5,
elasticCutAvg = 3,
longE = 40.0,
cutRange = (1e-20,1e20),
eStop = 60.0 ,
T = 300.0,
M = 58.6934,
N = 10,
Tol = 1.0e-7,
maxIter = 50,
interactive = True,
viewDirectory = 'tmp',
outputDir = 'tmp',
):
"""
This is the `main` function for finding a DOS and a multiphonon/
multiple scattering correction from experimental scattering.
user.py contains the user modifiable parameters.
"""
# *** LJ ***
# check output dirs
_checkOutdir( viewDirectory )
_checkOutdir( outputDir )
# copy the magic html file
shutil.copy( os.path.join(paths.data, magic_html ), viewDirectory )
#shutil.copy(magic_html, viewDirectory)
if interactive:
# open a browser
viewhtml = os.path.abspath( os.path.join( viewDirectory, magic_html ) )
bthread = BrowserThread( 'file://' + viewhtml )
bthread.start()
# record time
import time
time1 = time.time()
# **********
# --- Prep S(Q,E)for calculation -----------------------------------------------
sqe = expSqe(Data,T,M,cutRange=cutRange)
# *** LJ ***
if not MT: mqe = None
else: mqe = expSqe( MT,T,M,cutRange=cutRange)
# **********
if mqe: sqe.removeBackground(mqe,backgroundFrac,constantFrac)
sqe.cropForCalc(cutoff,longE,eStop,elasticCutAvg)
sqe.norm2one()
sqe.expand(2.0)
sqe0 = expSqe(sqe)
sqe.plotSE(viewDirectory)
sqe.plotSQE(viewDirectory,lower=1e-30,upper=2.5e-4)
sqe.plotMask(viewDirectory)
# --- Fitting ------------------------------------------------------------------
C_ms += 1.0 # This is a hack, until the internal rep of C_ms is changed.
# ------------------------------------------------------------------------------
res = getCorrectedScatter(sqe,C_ms,N,Tol,maxIter,interactive,vd=viewDirectory)
sqeCalc,dosCalc,cmsCalc,res,C_ms,lsqSc,lsqMu,lsqSl,LSQ \
= getBestSol(sqe0,res,C_ms)
dosCalc.plotDOS(viewDirectory)
# --- Output to file and pickle ------------------------------------------------
cp.dump((sqe0,C_ms,res,lsqSc,lsqMu,lsqSl,LSQ),\
open( os.path.join( outputDir,"all.pkl") ,'wb'),-1)
cp.dump((sqe0,sqeCalc,dosCalc,cmsCalc),\
open( os.path.join( outputDir,"sol.pkl") ,'wb'),-1)
# *** LJ ***
saveDOSasHistogram( dosCalc, os.path.join( outputDir, "doshist.pkl") )
# **********
f = open( os.path.join( outputDir,"C_ms" ),'w')
f.write( "C_ms = %lf\n" % (C_ms[numpy.argmin( numpy.array(LSQ)**2 )]-1.0) )
f.close()
io.write(dosCalc.e,dosCalc.g, os.path.join( outputDir,"Dos" ) )
io.write(dosCalc.e,dosCalc.gz, os.path.join( outputDir,"Dos.z" ) )
io.write(sqe0.e,sqe0.se, os.path.join( outputDir,"Se.exp" ) )
io.write(sqe0.e,nar(nar(sqeCalc)), os.path.join( outputDir,"Se.clc" ) )
io.write(sqe0.e,nar(nar(sqeCalc[1:])),os.path.join( outputDir,"Multi.clc") )
io.write(sqe0.e,nar(nar(sqeCalc[1:]))/(cmsCalc),\
os.path.join( outputDir,"Mph.clc" ) )
io.write(sqe0.e,(cmsCalc-1.0)*nar(nar(sqeCalc[1:]))/cmsCalc\
,os.path.join( outputDir,"Msc.clc" ) )
# --- `Interactive` Output -----------------------------------------------------
SQE = expSqe(sqe0.q,sqe0.e,nar(sqeCalc),sqe0.sqerr,sqe0.T,sqe0.M,cutRange=cutRange)
plotComp(sqe0,sqeCalc,viewDirectory)
plotLSQ(C_ms,lsqSc,lsqMu,lsqSl,LSQ,viewDirectory)
plotSQE(SQE,viewDirectory,'sqeCalc.png',title='S(Q,E) Calculated',\
lower=1e-30,upper=2.5e-4)
return
G = Gnuplot.Gnuplot()
Gd = Gnuplot.Data
G('set grid')
#------------------------------------------------------------------------------
#---- Setup objects -----------------------------------------------------------
e,g = io.load(dosFile)
dE = e[1] - e[0]
E = numpy.arange(floor(-maxE/dE)*dE, (ceil(maxE/dE)+1)*dE, dE)
#if e[0]==0.0: #dos contains 0 point
# E = numpy.concatenate((-1*e[::-1],e[1:]))
#else: #dos does not contain 0 point
# E = numpy.concatenate((numpy.append(-1*e[::-1],0.0),e))
Q = numpy.arange(minQ, maxQ, dQ)
fakeSqe = numpy.outer(Q,E)
sqe = expSqe.expSqe(Q,E,fakeSqe,fakeSqe,T,M,cutRange=cutRange)
e = numpy.arange(0.0, maxE+dE, dE)
dos = numpy.zeros(len(e))
if len(g) <= len(dos):
dos[:len(g)] += g
else:
dos += g[:len(dos)]
dos = densityOfStates.densityOfStates(e,dos,cutRange=cutRange)
#------------------------------------------------------------------------------
#---- Get multiphonon scattering ----------------------------------------------
ANE = multiphonon.AthroughN(sqe,dos,N)
#for i in range(len(ANE)):
# print 'ane',ANE[i]
SNQ = multiphonon.SthroughN(sqe,dos,N)
def getCorrectedScatter(sqe, Ei, C_ms, N, Tol, maxIter, interactive, vd=False):
"""
sqe = experimental S(Q,E) in instance of class expSqe
C_ms = list of multipliers
C_ms[i]*S_2+(Q,E) = S_2+(Q,E) + multiple scattering
N = number of terms to evaluate in multiphonon expansion
Tol = convergence at iteration N+1 when (g_{N+1}(E) - g_N(E))^2 < Tol
interactive = if True, print information while iterating
Returns a list `res` of self consistent solutions for the DOS from the
scattering, one for each value in C_ms.
res[i] = [ S(Q,E), dos, C_ms[i] ]
where S(Q,E) = numpy.array{ S_1(Q,E), S_2(Q,E), ..., S_N(Q,E) }
"""
sqe0 = expSqe(sqe)
res = []
i = 0
tot = len(C_ms)
cmsStrLen = 0
#----For outputting named files---------
for x in C_ms:
if len(str(x)) > cmsStrLen:
cmsStrLen = len(str(x))
#-----------------------------------------------------------------
for x in C_ms:
i += 1
if interactive:
print " "
print "--- Multiple scattering Factor "+str(i)+" of "+str(tot)\
+" -------------------------------"
print "Dos converged to ... "
sys.stdout.flush()
dos = sqe2dos(sqe0, Ei)
dos0 = Dos(dos.e,dos.g,cutRange=sqe.cutRange)
another = True
iter = 0
while another == True:
SQE = getSQE(sqe0,dos,N,x)
sqeSears = getSQE(sqe0,dos,N,x)
sqe.sqe = sqe0.sqe - sqeSearsGeometryEffects(sqe0,dos,N)[1:] - doubleScatteringSqe()
#sqe.sqe = sqe0.sqe - (nar(SQE[1:]) # [1:] is for subtracting multiple contributions;
dos = sqe2dos(sqe, Ei)
if nar( (dos.gz-dos0.gz)**2.0 ) > Tol and iter < maxIter:
print "Penalty = %le" %nar( (dos.gz-dos0.gz)**2 )
sys.stdout.flush()
dos0 = Dos(dos.e,dos.g,cutRange=sqe.cutRange)
iter += 1
else:
if iter == maxIter:
print "NOT CONVERGED AFTER %d ITERATIONS" % iter
print "Final penalty: %le" % nar( (dos.gz-dos0.gz)**2 )
sys.stdout.flush()
another = False
res.append( [SQE, dos , x] )
if interactive:
plotSQE(expSqe(sqe0.q,sqe0.e,nar(res[-1][0]),sqe0.sqerr,sqe0.T,sqe0.M),\
vd,'sqeCalc.png',title='S(Q,E) Calculated at '+str(x),lower=1e-30,\
upper=2.5e-4)
plotComp(sqe0,res[-1][0],vd)
res[-1][1].plotDOS(vd)
#----For outputting named files---------
#------ This probably doesn't work in windows, b/c "cp" ---------
cmsStr = str(x)
while len(cmsStr) < cmsStrLen:
cmsStr += '0'
os.system("cp " + os.path.join(vd,"dos.png") + " " + \
os.path.join(vd,"dos-" + cmsStr + ".png") )
os.system("cp " + os.path.join(vd,"sqeCalc.png") + " " + \
os.path.join(vd,"sqeCalc-" + cmsStr + ".png") )
os.system("cp " + os.path.join(vd,"seComp.png") + " " + \
os.path.join(vd,"seComp-" + cmsStr + ".png") )
#-----------------------------------------------------------------
print " --- "
print " "
return res
